Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold713
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 18965
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4636 original size:20 final size:20
Alignment explanation
Indices: 4607--4683 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
4597 GTAAAAGGAC
4607 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
4627 AGAATATATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
4647 TA-CATGTATCGATATATTGA
1 -AGAATGTATCGATACATTGA
*
4667 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
4684 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:5324 original size:99 final size:97
Alignment explanation
Indices: 5072--5317 Score: 264
Period size: 98 Copynumber: 2.5 Consensus size: 97
5062 TGAAAAATAA
* * * * * * *
5072 GGCTGGAGTATCCCCTCAGAGGAATGGGGTTAGAATGTCCCCAATG-ATGACAATTTAGGTAATG
1 GGCTGGAGTAT-CCCTCGGAGGAAT-GGGTTGGAGTATCCCCGATGAATGACAATTTAAGTAATA
* *
5136 ATAAGATTTAAATCTTGACAAGTTTTAAAAGTGG
64 ATAAGATTTAAATCTTCACAAGTTTTAAAAATGG
* * ** * *
5170 GGTTGGAGTATCCCTTAGGAGGAATGGGATTGGAGTATCCTTGA-CAATGATAATTTAAGTGAA-
1 GGCTGGAGTATCCC-TCGGAGGAATGGG-TTGGAGTATCCCCGATGAATGACAATTTAAGT-AAT
5233 AATAAGATTTAAATCTTCACAAGTTTTAAAAAATGG
63 AATAAGATTTAAATCTTCACAAGTTTT-AAAAATGG
5269 GGCTGGAGTATCTCCTCGGAGGAATAGGGTTGGAGTATCCCCGATGAAT
1 GGCTGGAGTATC-CCTCGGAGGAAT-GGGTTGGAGTATCCCCGATGAAT
5318 AGAATTTTGA
Statistics
Matches: 120, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
97 6 0.05
98 64 0.53
99 42 0.35
100 8 0.07
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (97 bp):
GGCTGGAGTATCCCTCGGAGGAATGGGTTGGAGTATCCCCGATGAATGACAATTTAAGTAATAAT
AAGATTTAAATCTTCACAAGTTTTAAAAATGG
Found at i:6587 original size:20 final size:21
Alignment explanation
Indices: 6551--6589 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6541 TTGGACATGT
*
6551 TAAAATGTATGGAACATGGCA
1 TAAAATGCATGGAACATGGCA
6572 TAAAATGCAT-GAACATGG
1 TAAAATGCATGGAACATGG
6590 GTTGTTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (21 bp):
TAAAATGCATGGAACATGGCA
Found at i:8269 original size:13 final size:13
Alignment explanation
Indices: 8251--8277 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8241 TACATTAATA
8251 AATGTATCGATAC
1 AATGTATCGATAC
8264 AATGTATCGATAC
1 AATGTATCGATAC
8277 A
1 A
8278 TTTATCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:8274 original size:33 final size:33
Alignment explanation
Indices: 8231--8297 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
8221 CCGCCAAGGA
*
8231 AATGTGTCGATACATTAATAAATGTATCGATAC
1 AATGTATCGATACATTAATAAATGTATCGATAC
* * *
8264 AATGTATCGATACATTTATCATTGTATCGATAC
1 AATGTATCGATACATTAATAAATGTATCGATAC
8297 A
1 A
8298 TTTGGATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (33 bp):
AATGTATCGATACATTAATAAATGTATCGATAC
Found at i:9239 original size:20 final size:22
Alignment explanation
Indices: 9199--9239 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
9189 CAGCCCTTAA
*
9199 TCATGCATTTTTTTACTATGTT
1 TCATGCATTTTTTAACTATGTT
9221 TCATGCA-TTTTTAAC-ATGT
1 TCATGCATTTTTTAACTATGT
9240 CTAACACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.54
Consensus pattern (22 bp):
TCATGCATTTTTTAACTATGTT
Found at i:11633 original size:13 final size:13
Alignment explanation
Indices: 11606--11651 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
11596 GCACCCCATC
11606 TTTTAATTTTAATT
1 TTTTAATTTT-ATT
11620 TTTTAATTTTATT
1 TTTTAATTTTATT
11633 TTATT-ATTTTATT
1 TT-TTAATTTTATT
11646 TTTTAA
1 TTTTAA
11652 CCCCGTTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.07
13 16 0.53
14 12 0.40
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTAATTTTATT
Found at i:14773 original size:209 final size:209
Alignment explanation
Indices: 14413--14830 Score: 746
Period size: 209 Copynumber: 2.0 Consensus size: 209
14403 TTTCTCTCCT
*
14413 ACTCCAAGTATAATTCAGGGTCATTTTTCACTTAAAAGTTAGGGATTTTCATCTTAATAAACCTG
1 ACTCCAAGTATAATTCAAGGTCATTTTTCACTTAAAAGTTAGGGATTTTCATCTTAATAAACCTG
* * * * *
14478 TAGACTCCAAATTTTATCCGTGTAATTTTAAAAATAGTCATTATTTAGAATAATTCAATTAATTA
66 TAGACACCAAATTTTATCCGAGTAATTTTAAAAACACTCACTATTTAGAATAATTCAATTAATTA
* *
14543 GGTCATCTTTAATTTAGGTTTGCTGGATTTTGATTAATTGGGCTTAATTCATTTTAATTTAGGCT
131 GGTCATCTTTAATCTAGGTTTGCTGGATTCTGATTAATTGGGCTTAATTCATTTTAATTTAGGCT
14608 TATTTGAAAAAATA
196 TATTTGAAAAAATA
*
14622 ACTCCAAGTATAATTCAAGGTCATTTTTCACTTGAAAGTTAGGGATTTTCATCTTAATAAACCTG
1 ACTCCAAGTATAATTCAAGGTCATTTTTCACTTAAAAGTTAGGGATTTTCATCTTAATAAACCTG
14687 TAGACACCAAATTTTATCCGAGTAATTTTAAAAACACTCACTATTTAGAATAATTCAATTAATTA
66 TAGACACCAAATTTTATCCGAGTAATTTTAAAAACACTCACTATTTAGAATAATTCAATTAATTA
14752 GGTCATCTTTAATCTAGGTTTGCTGGATTCTGATTAATTGGGCTTAATTCATTTTAATTTAGGCT
131 GGTCATCTTTAATCTAGGTTTGCTGGATTCTGATTAATTGGGCTTAATTCATTTTAATTTAGGCT
*
14817 TGTTTGAAAAAATA
196 TATTTGAAAAAATA
14831 CAAAAAAATA
Statistics
Matches: 199, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 199 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (209 bp):
ACTCCAAGTATAATTCAAGGTCATTTTTCACTTAAAAGTTAGGGATTTTCATCTTAATAAACCTG
TAGACACCAAATTTTATCCGAGTAATTTTAAAAACACTCACTATTTAGAATAATTCAATTAATTA
GGTCATCTTTAATCTAGGTTTGCTGGATTCTGATTAATTGGGCTTAATTCATTTTAATTTAGGCT
TATTTGAAAAAATA
Found at i:15183 original size:127 final size:128
Alignment explanation
Indices: 15011--15324 Score: 318
Period size: 127 Copynumber: 2.5 Consensus size: 128
15001 TCTTTATGGA
* ** ** * * *
15011 AAAGGGTCATTTGTGACGTACATGCCAAAGCTATACTTTAGTCATAAAATAGCAAAAAAATTATC
1 AAAGGGTCACTTGTGACCCACACACCAAAACTAAATTTTAGTCATAAAATAG-AAAAAAATTATC
*
15076 AAAAAGAAAAAAAGAA-GAA-AA-AAAT-AAGTGGCCT-GGGTTCAAAACCTAAGCCACCTTTAT
65 AAAAAGAAAAAAA-AATGAAGAATAAATGAA-TGGCCTAGGGTTC-AAACCTAAGCCACATTTAT
15136 AG
127 AG
* * * *
15138 AAAGGGTCATTTGTGACCCATACACCAAAACTAAATTTT-GATCATAAAATAGTAAAAGAATTGT
1 AAAGGGTCACTTGTGACCCACACACCAAAACTAAATTTTAG-TCATAAAATAG-AAAAAAATTAT
* * * * * *
15202 CAAAAAGAAAAAAAAATGAATGAATGAATGAATGGCCTAGGTTTCAAATCTAGGTCACATTTATG
64 CAAAAAGAAAAAAAAATGAA-GAATAAATGAATGGCCTAGGGTTCAAACCTAAGCCACATTTATA
15267 G
128 G
* * *
15268 AAAGGGTTACTTGTGACCCACACATCAAAGCTAAATTTTAGTCATAAAAT-GAAAAAA
1 AAAGGGTCACTTGTGACCCACACACCAAAACTAAATTTTAGTCATAAAATAGAAAAAA
15325 CAAAAAAAAG
Statistics
Matches: 155, Mismatches: 24, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
126 3 0.02
127 68 0.44
128 5 0.03
129 3 0.02
130 68 0.44
131 8 0.05
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (128 bp):
AAAGGGTCACTTGTGACCCACACACCAAAACTAAATTTTAGTCATAAAATAGAAAAAAATTATCA
AAAAGAAAAAAAAATGAAGAATAAATGAATGGCCTAGGGTTCAAACCTAAGCCACATTTATAG
Found at i:15528 original size:7 final size:8
Alignment explanation
Indices: 15509--15535 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
15499 GCTTTCAAAA
15509 AAAAATTC
1 AAAAATTC
15517 AAAAATTC
1 AAAAATTC
15525 AAAAATTC
1 AAAAATTC
15533 AAA
1 AAA
15536 GTGGGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATTC
Done.