Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: C7679
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 5527
ACGTcount: A:0.20, C:0.27, G:0.33, T:0.20
Found at i:1341 original size:12 final size:12
Alignment explanation
Indices: 1321--1363 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
1311 AGAATGTGAA
*
1321 GAGAATGGTGGG
1 GAGAGTGGTGGG
1333 GAGAGTGGTGGG
1 GAGAGTGGTGGG
1345 GAGAGTGGTGGG
1 GAGAGTGGTGGG
1357 GAGAGTG
1 GAGAGTG
1364 TTCTATGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.21, C:0.00, G:0.63, T:0.16
Consensus pattern (12 bp):
GAGAGTGGTGGG
Left flanking sequence: Indices 821 -- 1320
GAGCCTGCTGAGGGCCGCCAGTTGACCCTGGCGTTGACCATTGGGTTGTCGTACTTTTTCGGTGG
TTTTGTGCCGTTGGTGCCCTACTTTTTCGCCAACCACGTTGGCACCGGGTTGATGATCTCGGTGC
TTGTGATGTTGATCACGTTGTTCATTTTCGGGTACGTCAAGACCCTGATTGCCCTTGGCGACGAC
TGTGGACGGGCCAAGAAATTCAGCGAAGGAATACAGATGGTGGCAATCGGATCGATTGCCGCCGG
TTCAGCATGGACGCTTGTGTACCTCATCGATAACTAGCCGATAAACCCCCGTGGCTAGCATTTGC
CGTGTACTGGACCCGGCGGCCTGGTTGGAAACTCAGGCGCGGGCCAGTGGCTCCTACGTGCGTTG
AGCGCATTTAATACCATAGAAATACATGATAATAGGATAGAGGGTGAGTGATGACGGGGACAATG
CGTTTGAGTGTAGAGATAGAGTGTGAGTGCTGGGGAGAATGTGAA
Right flanking sequence: Indices 1364 -- 1863
TTCTATGGGTTAGCAAGGGCAAGTGAATTTTTACACGTCAGACACTTCTTGCTGGGGCGTAGGTG
CAGTGTGGTAAAATATTTCGGCTGGTTGCCTGCATCTTTAGGTTATGGCTTTAGGCAGTTGACGT
ATGCAACCTTATGCGAGATGAGCCGTTGGCGTGGGGGCAACGGAAGCGATTAATGAGGCAATTGT
GACTCTGAGGGAGCAGAAAATGGGCTTTGAATAGTGGCTTGCATTTGTATCAGTCACACGGATCT
GTGGGCCAATTTGTGGACCCGTTTGTGGCCCCACTGGTGTCTGTTACGGTGAGGGATTCAATCGA
AATTAGCTCCTAGCCGGAGAAAAGCTCGTAGCTCCAGAATTGTTGTCCACGTTTCATACCAGCAA
CGTCTACACAGAAGAACACTATCCAGAGTCAGTATTGGCTACGCAACACCTATTAGTTCGTGTCA
TGCGTGGGTCACCATTGCCACACTCATTTAAGAATTTCTTGATCA
Found at i:2793 original size:19 final size:19
Alignment explanation
Indices: 2769--2835 Score: 100
Period size: 19 Copynumber: 3.5 Consensus size: 19
2759 TTCTACAAAT
2769 AATCGTACCTTCTTCCACA
1 AATCGTACCTTCTTCCACA
*
2788 ATTCGTACCTTCTTCCACA
1 AATCGTACCTTCTTCCACA
*
2807 AATC-TCACCTTCTCCCACA
1 AATCGT-ACCTTCTTCCACA
2826 AATCGTACCT
1 AATCGTACCT
2836 ACCTTTCATC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 1 0.02
19 41 0.95
20 1 0.02
ACGTcount: A:0.25, C:0.39, G:0.04, T:0.31
Consensus pattern (19 bp):
AATCGTACCTTCTTCCACA
Left flanking sequence: Indices 2269 -- 2768
CTTAGGTGGTTACTCAATAAAAACCTGAAGATACTGATTTAAGCCTTGCCTTTACATCAATTGTT
CACTCAAAACATACAATATTGCCTCAACCACAAATCCTTCAGACCTGACAACCTCACATTCCTTT
CAAACCCTTCACCATAGTTTATTAAACTTATTCCACCATTTTTATCTTCCCCCTTTCACCCACTA
CACCCCACCACCGTTTACCCTTCAACCTGTCAACCCTGCAGCGAGCTGCATAAATAGGTAGCATC
ACAGACCTGTAGTGCCTCATTTCTATTAGCTTGATGCCGGTAATTCCTTTAAGATACGCCACTAG
CAAAGCTAGCACGCCTAGTCAACAGATAAGATTCGTTCGTTATCGCAATTATGTAGACAAATCAC
TCCACGAACGAAGAACGCCACACCCACAAAATCAAGAAAGAGCTCTCAATCTGTCAATCCTTATT
GTGCCTGGACCTGAATACCACAAACTTAGCCTCCTTTCTACAAAT
Right flanking sequence: Indices 2836 -- 3335
ACCTTTCATCTACAAATCGTACCATCCTTTCCTCTTCCTTCATTCCTATAAATAATACATCTTCT
TCTTCTACTCTACTGCTTCAAAAGATCGCCAAACTCCATCAACTCAAAGATCAACGACATGTTCG
GACAAATGCGGTCGCACGCGTCAATCACGTTGCCCTTGTCGGTGACGTTGGCCACCACCACGTCG
GAACTGGCACCGGCGGTGCCCAGCTTCAAGAGCTCGTACGCCTGGTTGACGCCAAGGCCAAACTT
GGCCATGAAGAACGCGACAATCACACACGCCAGACGGGACACCCCGCACTGGCAGTGCACCAAGA
TGCGCTGGCCGCGGTCCAAGTACTGTTGCATGGTGTCGGTGATGTGTCCGAGGTCCTTGGAGATG
GCCAGCGTGTGCTGCCACGGGACATACATGTAGAGGGGCGTGAGTGGAGCCAGCGGGTTAGGAGC
ACTGGAGGGAGCTCCAGAGGCAGAACCAGAACCAGAACCAGAACC
Found at i:3320 original size:6 final size:6
Alignment explanation
Indices: 3311--3349 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
3301 GCTCCAGAGG
3311 CAGAAC CAGAAC CAGAAC CAGAAC CAGAAC CAGAAC CAG
1 CAGAAC CAGAAC CAGAAC CAGAAC CAGAAC CAGAAC CAG
3350 TAGAACCAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.33, G:0.18, T:0.00
Consensus pattern (6 bp):
CAGAAC
Left flanking sequence: Indices 2811 -- 3310
TCACCTTCTCCCACAAATCGTACCTACCTTTCATCTACAAATCGTACCATCCTTTCCTCTTCCTT
CATTCCTATAAATAATACATCTTCTTCTTCTACTCTACTGCTTCAAAAGATCGCCAAACTCCATC
AACTCAAAGATCAACGACATGTTCGGACAAATGCGGTCGCACGCGTCAATCACGTTGCCCTTGTC
GGTGACGTTGGCCACCACCACGTCGGAACTGGCACCGGCGGTGCCCAGCTTCAAGAGCTCGTACG
CCTGGTTGACGCCAAGGCCAAACTTGGCCATGAAGAACGCGACAATCACACACGCCAGACGGGAC
ACCCCGCACTGGCAGTGCACCAAGATGCGCTGGCCGCGGTCCAAGTACTGTTGCATGGTGTCGGT
GATGTGTCCGAGGTCCTTGGAGATGGCCAGCGTGTGCTGCCACGGGACATACATGTAGAGGGGCG
TGAGTGGAGCCAGCGGGTTAGGAGCACTGGAGGGAGCTCCAGAGG
Right flanking sequence: Indices 3350 -- 3849
TAGAACCAGTAAAACTAGTACCAAAACCAGCACCAGTAGAACCAGAACCAGCACTCCCAGCACTC
CCACCACTCGCTCTAGGACCACTGTACGCCCCAGAGAGATCGGGACACTCCTTGGCCACGTTGAT
CACCAAGTCGTACTCGTTGATGTCCACCGCCACCGGCAGCAACTGCGGGTCCAGGTACAAGAAGA
TCCGGTCGTTGAGCACGTTGCGCGGCCCCGCCGGGTACGCGTTGAGCAGGTTCTGCTCCTGGAGC
TCCTCGGGCACCTTCTGGTACGGCACGGTGTAGGTGACGGTGGCCAGCAGCGCTCCGGGGGCCGC
CGCGGGTTTGTAGTGCGACGACGGCGCCAGGGTGGGTGTCAAGAGCGTGGTGGTGATGGTGCCCG
TCAGCTGGAGCTCCGGGGTGGTCACCAGCAGCAGCGGGCGGAGCGGGGCCGCCAGGGGGGCCGCC
AGCAGCGCCAGCGACGGCTGGGACGGCTGGGACGCCGCGGGCGCC
Found at i:4049 original size:13 final size:12
Alignment explanation
Indices: 4020--4047 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4010 GGGACGGGTC
4020 GGGGCCGTGGTG
1 GGGGCCGTGGTG
4032 GGGGCCGTGGTG
1 GGGGCCGTGGTG
4044 GGGG
1 GGGG
4048 GCGGGAGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.71, T:0.14
Consensus pattern (12 bp):
GGGGCCGTGGTG
Left flanking sequence: Indices 3520 -- 4019
AACTGCGGGTCCAGGTACAAGAAGATCCGGTCGTTGAGCACGTTGCGCGGCCCCGCCGGGTACGC
GTTGAGCAGGTTCTGCTCCTGGAGCTCCTCGGGCACCTTCTGGTACGGCACGGTGTAGGTGACGG
TGGCCAGCAGCGCTCCGGGGGCCGCCGCGGGTTTGTAGTGCGACGACGGCGCCAGGGTGGGTGTC
AAGAGCGTGGTGGTGATGGTGCCCGTCAGCTGGAGCTCCGGGGTGGTCACCAGCAGCAGCGGGCG
GAGCGGGGCCGCCAGGGGGGCCGCCAGCAGCGCCAGCGACGGCTGGGACGGCTGGGACGCCGCGG
GCGCCACCAGCGACGCCTGGGCTATAGCCTGGGGCTGGGAGGACGTGGCCAGCGATGCCAGCACC
GCCAGGCGGGCCAGCGACGGGCCCAGGCCCTGCGACTGCACCGACGCCGCCAGGGTCGCCGAGGT
GTTGGGAGGGGCCACGGTGCCCGCTGGGGCGGCCAGGGACGGGTC
Right flanking sequence: Indices 4048 -- 4547
GCGGGAGGCGGGGGAGGCGGGGCAGGGTTCAAGACACCCCCCGAGGGCCCCCCACCGCCCATGGC
ATTGCCCAGTTTGTCCCCACGGGTACCACCCAGTTTGTCGTCCACTTTGTCGTCTTTGTCGTCTT
TGTCGTCCACTCTGTCGTCCACCTCCATGGGCAACGGCGGCAACGCCTTCGCATTAAGCTCCAGC
GGCAGCAACCGCACCCGGCGCCGGCGCTCGCTGGGCAGGGTGGCGGCCACGAGCTTGGGTTTCTC
AAAGTCGAGCCCGGGGTGGGGTGCCCCCAGCAGCTGGCGCAGGTGCCCCCGCTCGGGGTGGCGCC
GCGGGGCGTCCACGTCGAGCACCGCCACCTTGCCCTCGAGCTTCAGCGGGTCGAGGGTCTTGAGC
AGGCGCGGGTGGCGCGGGGGCGGCAGCAGCAGCGGCAGCAGCAGTGGCAGTGGGGCCTGGCCCGA
CTTGCGCTGGCTCTGCTGCTTTTTGCGCACGGTGCGGCAGCGGAG
Found at i:4163 original size:12 final size:12
Alignment explanation
Indices: 4146--4199 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
4136 TACCACCCAG
4146 TTTGTCGTCCAC
1 TTTGTCGTCCAC
4158 TTTGTCGT---C
1 TTTGTCGTCCAC
4167 TTTGTCGT---C
1 TTTGTCGTCCAC
4176 TTTGTCGTCCAC
1 TTTGTCGTCCAC
*
4188 TCTGTCGTCCAC
1 TTTGTCGTCCAC
4200 CTCCATGGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
9 18 0.47
12 20 0.53
ACGTcount: A:0.06, C:0.31, G:0.19, T:0.44
Consensus pattern (12 bp):
TTTGTCGTCCAC
Left flanking sequence: Indices 3646 -- 4145
ACGGTGGCCAGCAGCGCTCCGGGGGCCGCCGCGGGTTTGTAGTGCGACGACGGCGCCAGGGTGGG
TGTCAAGAGCGTGGTGGTGATGGTGCCCGTCAGCTGGAGCTCCGGGGTGGTCACCAGCAGCAGCG
GGCGGAGCGGGGCCGCCAGGGGGGCCGCCAGCAGCGCCAGCGACGGCTGGGACGGCTGGGACGCC
GCGGGCGCCACCAGCGACGCCTGGGCTATAGCCTGGGGCTGGGAGGACGTGGCCAGCGATGCCAG
CACCGCCAGGCGGGCCAGCGACGGGCCCAGGCCCTGCGACTGCACCGACGCCGCCAGGGTCGCCG
AGGTGTTGGGAGGGGCCACGGTGCCCGCTGGGGCGGCCAGGGACGGGTCGGGGCCGTGGTGGGGG
CCGTGGTGGGGGGCGGGAGGCGGGGGAGGCGGGGCAGGGTTCAAGACACCCCCCGAGGGCCCCCC
ACCGCCCATGGCATTGCCCAGTTTGTCCCCACGGGTACCACCCAG
Right flanking sequence: Indices 4200 -- 4699
CTCCATGGGCAACGGCGGCAACGCCTTCGCATTAAGCTCCAGCGGCAGCAACCGCACCCGGCGCC
GGCGCTCGCTGGGCAGGGTGGCGGCCACGAGCTTGGGTTTCTCAAAGTCGAGCCCGGGGTGGGGT
GCCCCCAGCAGCTGGCGCAGGTGCCCCCGCTCGGGGTGGCGCCGCGGGGCGTCCACGTCGAGCAC
CGCCACCTTGCCCTCGAGCTTCAGCGGGTCGAGGGTCTTGAGCAGGCGCGGGTGGCGCGGGGGCG
GCAGCAGCAGCGGCAGCAGCAGTGGCAGTGGGGCCTGGCCCGACTTGCGCTGGCTCTGCTGCTTT
TTGCGCACGGTGCGGCAGCGGAGGAGCTCCTCGTTGGTCTTCTCCGGGACCTGGGGGGGCACTTC
GTCCACGTCCATGGGCTCGGGCGCCGGGGGCACGGGGGCCGCCGGGGCCACGGGGTAGTGCGCCA
CCTGGGGCGGGGGCGCCGGGAGCCGGGGCATGGCGAACGGGGGCG
Found at i:4171 original size:9 final size:9
Alignment explanation
Indices: 4157--4184 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4147 TTGTCGTCCA
4157 CTTTGTCGT
1 CTTTGTCGT
4166 CTTTGTCGT
1 CTTTGTCGT
4175 CTTTGTCGT
1 CTTTGTCGT
4184 C
1 C
4185 CACTCTGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.25, G:0.21, T:0.54
Consensus pattern (9 bp):
CTTTGTCGT
Left flanking sequence: Indices 3657 -- 4156
CAGCGCTCCGGGGGCCGCCGCGGGTTTGTAGTGCGACGACGGCGCCAGGGTGGGTGTCAAGAGCG
TGGTGGTGATGGTGCCCGTCAGCTGGAGCTCCGGGGTGGTCACCAGCAGCAGCGGGCGGAGCGGG
GCCGCCAGGGGGGCCGCCAGCAGCGCCAGCGACGGCTGGGACGGCTGGGACGCCGCGGGCGCCAC
CAGCGACGCCTGGGCTATAGCCTGGGGCTGGGAGGACGTGGCCAGCGATGCCAGCACCGCCAGGC
GGGCCAGCGACGGGCCCAGGCCCTGCGACTGCACCGACGCCGCCAGGGTCGCCGAGGTGTTGGGA
GGGGCCACGGTGCCCGCTGGGGCGGCCAGGGACGGGTCGGGGCCGTGGTGGGGGCCGTGGTGGGG
GGCGGGAGGCGGGGGAGGCGGGGCAGGGTTCAAGACACCCCCCGAGGGCCCCCCACCGCCCATGG
CATTGCCCAGTTTGTCCCCACGGGTACCACCCAGTTTGTCGTCCA
Right flanking sequence: Indices 4185 -- 4684
CACTCTGTCGTCCACCTCCATGGGCAACGGCGGCAACGCCTTCGCATTAAGCTCCAGCGGCAGCA
ACCGCACCCGGCGCCGGCGCTCGCTGGGCAGGGTGGCGGCCACGAGCTTGGGTTTCTCAAAGTCG
AGCCCGGGGTGGGGTGCCCCCAGCAGCTGGCGCAGGTGCCCCCGCTCGGGGTGGCGCCGCGGGGC
GTCCACGTCGAGCACCGCCACCTTGCCCTCGAGCTTCAGCGGGTCGAGGGTCTTGAGCAGGCGCG
GGTGGCGCGGGGGCGGCAGCAGCAGCGGCAGCAGCAGTGGCAGTGGGGCCTGGCCCGACTTGCGC
TGGCTCTGCTGCTTTTTGCGCACGGTGCGGCAGCGGAGGAGCTCCTCGTTGGTCTTCTCCGGGAC
CTGGGGGGGCACTTCGTCCACGTCCATGGGCTCGGGCGCCGGGGGCACGGGGGCCGCCGGGGCCA
CGGGGTAGTGCGCCACCTGGGGCGGGGGCGCCGGGAGCCGGGGCA
Found at i:4474 original size:12 final size:12
Alignment explanation
Indices: 4457--4487 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4447 TGGCGCGGGG
4457 GCGGCAGCAGCA
1 GCGGCAGCAGCA
4469 GCGGCAGCAGCA
1 GCGGCAGCAGCA
*
4481 GTGGCAG
1 GCGGCAG
4488 TGGGGCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.29, G:0.45, T:0.03
Consensus pattern (12 bp):
GCGGCAGCAGCA
Left flanking sequence: Indices 3957 -- 4456
CGCCAGGGTCGCCGAGGTGTTGGGAGGGGCCACGGTGCCCGCTGGGGCGGCCAGGGACGGGTCGG
GGCCGTGGTGGGGGCCGTGGTGGGGGGCGGGAGGCGGGGGAGGCGGGGCAGGGTTCAAGACACCC
CCCGAGGGCCCCCCACCGCCCATGGCATTGCCCAGTTTGTCCCCACGGGTACCACCCAGTTTGTC
GTCCACTTTGTCGTCTTTGTCGTCTTTGTCGTCCACTCTGTCGTCCACCTCCATGGGCAACGGCG
GCAACGCCTTCGCATTAAGCTCCAGCGGCAGCAACCGCACCCGGCGCCGGCGCTCGCTGGGCAGG
GTGGCGGCCACGAGCTTGGGTTTCTCAAAGTCGAGCCCGGGGTGGGGTGCCCCCAGCAGCTGGCG
CAGGTGCCCCCGCTCGGGGTGGCGCCGCGGGGCGTCCACGTCGAGCACCGCCACCTTGCCCTCGA
GCTTCAGCGGGTCGAGGGTCTTGAGCAGGCGCGGGTGGCGCGGGG
Right flanking sequence: Indices 4488 -- 4987
TGGGGCCTGGCCCGACTTGCGCTGGCTCTGCTGCTTTTTGCGCACGGTGCGGCAGCGGAGGAGCT
CCTCGTTGGTCTTCTCCGGGACCTGGGGGGGCACTTCGTCCACGTCCATGGGCTCGGGCGCCGGG
GGCACGGGGGCCGCCGGGGCCACGGGGTAGTGCGCCACCTGGGGCGGGGGCGCCGGGAGCCGGGG
CATGGCGAACGGGGGCGGGGCGCGGGGCAGCGGCGGCACCGGGGACGCCTGTTTTGGGGGCCGCG
GCGACCGGCGCGGGTCGTCGAGCGGGGGGAACGCCCCGTCCAGCACCACCGCCTCCGGGGAGTTG
GCGGCGGAGAGCGCGGCCAGCCGGCGCTTGGCGACGTGGTGGCGCAGGCCAAAGTCGCCCTCGAG
GGAGTCGTCGCGCTCGTGGGACTTGACCAGCTTGTCGGAGAACAGCGCGGCGTCGCCGAGGCCGC
GGGGCTTGGTGGGGCGCTCGCCGAGCAGGTCGGAGAAGATCAGCG
Found at i:5486 original size:15 final size:15
Alignment explanation
Indices: 5466--5527 Score: 106
Period size: 15 Copynumber: 4.1 Consensus size: 15
5456 GGGCGGGGGA
*
5466 GGAGGAGAGCCCGTG
1 GGAGGAGGGCCCGTG
5481 GGAGGAGGGCCCGTG
1 GGAGGAGGGCCCGTG
*
5496 GGAGGAGGGCCCGGG
1 GGAGGAGGGCCCGTG
5511 GGAGGAGGGCCCGTG
1 GGAGGAGGGCCCGTG
5526 GG
1 GG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.15, C:0.19, G:0.61, T:0.05
Consensus pattern (15 bp):
GGAGGAGGGCCCGTG
Left flanking sequence: Indices 4966 -- 5465
AGCAGGTCGGAGAAGATCAGCGGGGCCTCCAGCAGCACCTCCAGCGGGCGGTGCGGGGGCGGGGT
CGGGGCGTCGAGCAGGGCCGGGGGCGGGGTGGAGGAGGGGGCGTGGGGCGGCGCCTCCGGGGTGT
GCGGGGGCCGGAACGGCAGCACGTGGATGCTCAGCGCCAGGTCCAACTCCAGCGGCGCCAACACC
AACGGCAGCCGGAGCAGGTCGGGCTGCGCCGGGGGCGCGAGCCCCGGGACCTCGGGGGGGAACCA
GAACGGCTTGGCCCCCGGGGGCGCCGGCGCCGGGGGGCGGCGGTGGAGGGTGAGCAGGTCGTTGG
AGGTGTTGGGGTGGGCCATGAGCGCCGGCGGCGCTATCGGGGTGGCGGTGATCAGCGGCGTCATG
AGCCCGTCGTCGTCGCCGTCGTCGCGGTCGTCCACCACGAGGGTGGTGGTGGCGATGGTGCCCGC
GAGCGAGGCCGGGGGCGGCGGGAGCCGCGGGGACAGGGCGGGGGA
Right flanking sequence: None
Done.