Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: C7533
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: 1330
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.35
Found at i:950 original size:29 final size:29
Alignment explanation
Indices: 918--975 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
908 TATAAGTTAG
*
918 TATACTTAT-TATATAAGTATATATATATA
1 TATACTTATAT-TATAAATATATATATATA
*
947 TATATTTATATTATAAATATATATATATA
1 TATACTTATATTATAAATATATATATATA
976 AATATATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
TATACTTATATTATAAATATATATATATA
Left flanking sequence: Indices 418 -- 917
AATTCATAAAGTTAAACTTAATGAAACAATAGCAATTAATTGTGCTGAAATAGCAAATGAATAAG
GAATCATAGAAATTAAGTTAGCAACTAAAATAAAGTTAAATAATGAGAAAATTAAAGGGAAATAA
TATCCTCCTTTAGCTCCAATTTGGCTTTTAACCATATTTAAAACTGTATCATAAATAGCTAATAC
TGCTACTCCTCATCTTGTTCATCCTAAATAACTTTTATTTAATAAAATTGAAATACCATAAATTA
ATGATACTACAATAATTAAATAAATTACATAATTTGTTAAACTTAATGTTAAAATATTATTTATT
GTAAATAATGGTTTGATCTCAAATTGATCTAATGGTGAAAAAATCATTTTGTTTATATTTATTTA
TTTTTATTTACTTATATATATATTTTTTCCTTTTATTTTATATGGAAATATTTATATATTAGTTT
ATAATTTATAATTCTAACTTATTTATATATAATTTTATAAGTTAG
Right flanking sequence: Indices 976 -- 1330
AATATATTTCTTTTAGATATATATTTATAATTTAACAATAATAGTTCTAGCTAATAATAATCTTA
AAATATTTGGTAATAAAATTGTTGAAACAAAGTAAATTAAGAAACCTAAAGCTAAAATACCAAAA
GTTAATAAATTTAAAAAGTAAAAAGGTACTAATTGAGGCATTATAATTATAATAATTATTTGATA
AAAATATATATATAAATTATATATATATATTAAAATATATAAAATATATCAGATCGGGAGGACTC
GAACCCCCAGTACCCTACACCCAATGCAGATGCGTTACCAATTACGCTACAATCTGTTTAAGAAT
ATAAAGATCTAATCCTTCATATATATATAT
Found at i:999 original size:2 final size:2
Alignment explanation
Indices: 935--982 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
925 ATTATATAAG
* *
935 TA TA TA TA TA TA TA TA TT TA TA T- TA TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
976 AA TA TA T
1 TA TA TA T
983 TTCTTTTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 435 -- 934
TTAATGAAACAATAGCAATTAATTGTGCTGAAATAGCAAATGAATAAGGAATCATAGAAATTAAG
TTAGCAACTAAAATAAAGTTAAATAATGAGAAAATTAAAGGGAAATAATATCCTCCTTTAGCTCC
AATTTGGCTTTTAACCATATTTAAAACTGTATCATAAATAGCTAATACTGCTACTCCTCATCTTG
TTCATCCTAAATAACTTTTATTTAATAAAATTGAAATACCATAAATTAATGATACTACAATAATT
AAATAAATTACATAATTTGTTAAACTTAATGTTAAAATATTATTTATTGTAAATAATGGTTTGAT
CTCAAATTGATCTAATGGTGAAAAAATCATTTTGTTTATATTTATTTATTTTTATTTACTTATAT
ATATATTTTTTCCTTTTATTTTATATGGAAATATTTATATATTAGTTTATAATTTATAATTCTAA
CTTATTTATATATAATTTTATAAGTTAGTATACTTATTATATAAG
Right flanking sequence: Indices 983 -- 1330
TTCTTTTAGATATATATTTATAATTTAACAATAATAGTTCTAGCTAATAATAATCTTAAAATATT
TGGTAATAAAATTGTTGAAACAAAGTAAATTAAGAAACCTAAAGCTAAAATACCAAAAGTTAATA
AATTTAAAAAGTAAAAAGGTACTAATTGAGGCATTATAATTATAATAATTATTTGATAAAAATAT
ATATATAAATTATATATATATATTAAAATATATAAAATATATCAGATCGGGAGGACTCGAACCCC
CAGTACCCTACACCCAATGCAGATGCGTTACCAATTACGCTACAATCTGTTTAAGAATATAAAGA
TCTAATCCTTCATATATATATAT
Found at i:1193 original size:9 final size:9
Alignment explanation
Indices: 1178--1219 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1168 ATAAAAATAT
1178 ATATATAAA
1 ATATATAAA
* *
1187 TTATAT-AT
1 ATATATAAA
1195 ATATATTAAA
1 ATATA-TAAA
1205 ATATATAAA
1 ATATATAAA
1214 ATATAT
1 ATATAT
1220 CAGATCGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 5 0.19
9 16 0.59
10 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATATAAA
Left flanking sequence: Indices 678 -- 1177
ATGATACTACAATAATTAAATAAATTACATAATTTGTTAAACTTAATGTTAAAATATTATTTATT
GTAAATAATGGTTTGATCTCAAATTGATCTAATGGTGAAAAAATCATTTTGTTTATATTTATTTA
TTTTTATTTACTTATATATATATTTTTTCCTTTTATTTTATATGGAAATATTTATATATTAGTTT
ATAATTTATAATTCTAACTTATTTATATATAATTTTATAAGTTAGTATACTTATTATATAAGTAT
ATATATATATATATTTATATTATAAATATATATATATAAATATATTTCTTTTAGATATATATTTA
TAATTTAACAATAATAGTTCTAGCTAATAATAATCTTAAAATATTTGGTAATAAAATTGTTGAAA
CAAAGTAAATTAAGAAACCTAAAGCTAAAATACCAAAAGTTAATAAATTTAAAAAGTAAAAAGGT
ACTAATTGAGGCATTATAATTATAATAATTATTTGATAAAAATAT
Right flanking sequence: Indices 1220 -- 1330
CAGATCGGGAGGACTCGAACCCCCAGTACCCTACACCCAATGCAGATGCGTTACCAATTACGCTA
CAATCTGTTTAAGAATATAAAGATCTAATCCTTCATATATATATAT
Found at i:1217 original size:19 final size:20
Alignment explanation
Indices: 1171--1219 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1161 TTATTTGATA
1171 AAAATATATATATAAATTAT
1 AAAATATATATATAAATTAT
*
1191 -ATATATATAT-TAAAATATAT
1 AAAATATATATAT-AAAT-TAT
1211 AAAATATAT
1 AAAATATAT
1220 CAGATCGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 13 0.54
20 3 0.12
21 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATATATATAAATTAT
Left flanking sequence: Indices 671 -- 1170
TAAATTAATGATACTACAATAATTAAATAAATTACATAATTTGTTAAACTTAATGTTAAAATATT
ATTTATTGTAAATAATGGTTTGATCTCAAATTGATCTAATGGTGAAAAAATCATTTTGTTTATAT
TTATTTATTTTTATTTACTTATATATATATTTTTTCCTTTTATTTTATATGGAAATATTTATATA
TTAGTTTATAATTTATAATTCTAACTTATTTATATATAATTTTATAAGTTAGTATACTTATTATA
TAAGTATATATATATATATATTTATATTATAAATATATATATATAAATATATTTCTTTTAGATAT
ATATTTATAATTTAACAATAATAGTTCTAGCTAATAATAATCTTAAAATATTTGGTAATAAAATT
GTTGAAACAAAGTAAATTAAGAAACCTAAAGCTAAAATACCAAAAGTTAATAAATTTAAAAAGTA
AAAAGGTACTAATTGAGGCATTATAATTATAATAATTATTTGATA
Right flanking sequence: Indices 1220 -- 1330
CAGATCGGGAGGACTCGAACCCCCAGTACCCTACACCCAATGCAGATGCGTTACCAATTACGCTA
CAATCTGTTTAAGAATATAAAGATCTAATCCTTCATATATATATAT
Done.