Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1885
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: 39308
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1101 original size:43 final size:41
Alignment explanation
Indices: 1024--1211 Score: 224
Period size: 43 Copynumber: 4.8 Consensus size: 41
1014 ACCGGCTCTT
*
1024 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1065 AGCCTGCCTAGACTTATAAGTCTGAAATGTGTCACCGGC--T-
1 AGCCTG-CTAGACTTAT-AGTCTGAAATGTGTCACCGGCATTA
1105 AG-CT--TAG--TT-TAG-CTGAAATGTGTCCACCGG-ATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGT-CACCGGCATTA
1139 AGCCTGCTAGACTTATAGTCTGAAATGGTGTCCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAAT-GTGT-CACCGGCATTA
1182 AGCCTGCTAGAC-TATAGTCTG-AAT-TGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
1212 TAACGCTCAT
Statistics
Matches: 131, Mismatches: 1, Indels: 33
0.79 0.01 0.20
Matches are distributed among these distances:
31 11 0.08
32 8 0.06
33 2 0.02
34 4 0.03
35 2 0.02
36 3 0.02
37 3 0.02
38 3 0.02
39 7 0.05
40 5 0.04
41 17 0.13
42 30 0.23
43 36 0.27
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:1171 original size:42 final size:41
Alignment explanation
Indices: 1117--1204 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 41
1107 CTTAGTTTAG
1117 CTGAAATGTGTCCACCGG-ATTAAGCCTGCTAGACTTATAGT
1 CTGAAATGTGTCCACCGGCATTAAGCCTGCTAGAC-TATAGT
1158 CTGAAATGGTGTCCACCGGCATTAAGCCTGCTAGACTATAGT
1 CTGAAAT-GTGTCCACCGGCATTAAGCCTGCTAGACTATAGT
1200 CTGAA
1 CTGAA
1205 TTGTCACTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
41 7 0.16
42 22 0.49
43 16 0.36
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (41 bp):
CTGAAATGTGTCCACCGGCATTAAGCCTGCTAGACTATAGT
Found at i:8401 original size:33 final size:33
Alignment explanation
Indices: 8332--8429 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
8322 CTATACCCAT
* * *
8332 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
8369 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
8402 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
8430 ATATACATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:8691 original size:41 final size:40
Alignment explanation
Indices: 8646--8838 Score: 309
Period size: 39 Copynumber: 4.8 Consensus size: 40
8636 ACCGGCTCTT
*
8646 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAAT-TGTCACCGGCATTA
8687 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAAT-TGTCACCGGCATTA
8728 AGCCTGCTAGACTTATAGTCTGAAA-TGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATTGTCACCGGCATTA
8767 AGCCTGCTAGACTTATAGTCTGAAATT-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATTGTCACCGGCATTA
* * *
8806 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAAT-TGTCAC
8839 TAACGATAAA
Statistics
Matches: 145, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
39 74 0.51
40 2 0.01
41 69 0.48
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (40 bp):
AGCCTGCTAGACTTATAGTCTGAAATTGTCACCGGCATTA
Found at i:8786 original size:80 final size:78
Alignment explanation
Indices: 8646--8838 Score: 305
Period size: 80 Copynumber: 2.4 Consensus size: 78
8636 ACCGGCTCTT
*
8646 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTAAGCCTGCTAGACTTATAGTCTGAA
1 AGCCTGCTAGACTTATAGTCTGAAA--TGTCACCGGCATTAAGCCTGCTAGACTTATAGTCTGAA
8711 ATGTGTCACCGGCATTA
64 AT-T-TCACCGGCATTA
8728 AGCCTGCTAGACTTATAGTCTGAAATGTCACCGGCATTAAGCCTGCTAGACTTATAGTCTGAAAT
1 AGCCTGCTAGACTTATAGTCTGAAATGTCACCGGCATTAAGCCTGCTAGACTTATAGTCTGAAAT
8793 TTCACCGGCATTA
66 TTCACCGGCATTA
* *
8806 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAA--ATGTCAC
8839 TAACGATAAA
Statistics
Matches: 106, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
78 34 0.32
79 1 0.01
80 47 0.44
82 24 0.23
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (78 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTCACCGGCATTAAGCCTGCTAGACTTATAGTCTGAAAT
TTCACCGGCATTA
Found at i:16053 original size:30 final size:32
Alignment explanation
Indices: 15993--16056 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
15983 CACTTATTTT
15993 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
16026 CACCTATGCCGAATGCAACATATATATATAT
1 CACCTATGCCGAATGCAACACATAAATATAT
16057 ACATATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:16314 original size:41 final size:41
Alignment explanation
Indices: 16269--16442 Score: 332
Period size: 41 Copynumber: 4.3 Consensus size: 41
16259 ACCGGCTCTT
*
16269 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
16310 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
16351 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
16392 AGCCTGCTAGACTTATAGTCTGAAATGT-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
16432 AGCCTGCTAGA
1 AGCCTGCTAGA
16443 TTAGTCTGAA
Statistics
Matches: 132, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
40 23 0.17
41 109 0.83
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:28316 original size:30 final size:30
Alignment explanation
Indices: 28282--28341 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28272 TGGCTTTGTA
28282 ATGGTTCTTATATTTATATATGTATGTGGC
1 ATGGTTCTTATATTTATATATGTATGTGGC
* * *
28312 ATGGTTGTTATGTTTGTATATGTATGTGGC
1 ATGGTTCTTATATTTATATATGTATGTGGC
28342 CTTAAGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.50
Consensus pattern (30 bp):
ATGGTTCTTATATTTATATATGTATGTGGC
Found at i:31420 original size:47 final size:47
Alignment explanation
Indices: 31368--31918 Score: 886
Period size: 47 Copynumber: 11.6 Consensus size: 47
31358 GATAATTGTG
* *
31368 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
31415 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
31462 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
31511 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
31560 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
31607 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
31654 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
31703 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
31752 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
31799 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
31846 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
31893 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
31919 TCCCGAAGGG
Statistics
Matches: 476, Mismatches: 24, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
47 288 0.61
49 188 0.39
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:31475 original size:96 final size:94
Alignment explanation
Indices: 31368--31918 Score: 886
Period size: 96 Copynumber: 5.8 Consensus size: 94
31358 GATAATTGTG
* *
31368 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* *
31433 GTGATAAGGCCGAATGGCCAATGTGATGA
66 GTGATAAGGCCTAATGGCCGATGTGATGA
31462 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
31527 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
62 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
31560 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* *
31625 GTGATAAGGCCGAATGGCCAATGTGATGA
66 GTGATAAGGCCTAATGGCCGATGTGATGA
31654 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
31719 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
62 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
31752 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
*
31817 GTGATGAGGCCTAATGGCCGATGTGATGA
66 GTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * * *
31846 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
31911 GTGATAAG
66 GTGATAAG
31919 TCCCGAAGGG
Statistics
Matches: 429, Mismatches: 20, Indels: 16
0.92 0.04 0.03
Matches are distributed among these distances:
94 152 0.35
96 187 0.44
98 90 0.21
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (94 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:34201 original size:40 final size:40
Alignment explanation
Indices: 34142--34499 Score: 528
Period size: 40 Copynumber: 9.1 Consensus size: 40
34132 AGGTCTCGAC
34142 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
34181 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
34221 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
34261 GATGTA-CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
34300 GATGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
34339 GATGTATCCGGACTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
34379 GATGTATCCGGGCTAAGT-TCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * * * *
34418 AATATATCCGTGCTAA-ACCTCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCC-CGAAGAGCATTCATGCTAGT
* * * * *
34458 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
34498 GA
1 GA
34500 CGTGTATTCG
Statistics
Matches: 291, Mismatches: 22, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
39 111 0.38
40 178 0.61
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:34306 original size:79 final size:80
Alignment explanation
Indices: 34142--34486 Score: 538
Period size: 79 Copynumber: 4.4 Consensus size: 80
34132 AGGTCTCGAC
*
34142 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
34206 AGCATTCATGCTAGT
66 AGCATTCATGCTAGT
34221 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA-CCGGGCTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
34285 AGCATTCATGCTAGT
66 AGCATTCATGCTAGT
*
34300 GATGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
34364 AGCATTCATGCTAGT
66 AGCATTCATGCTAGT
* * * * *
34379 GATGTATCCGGGCTAAGT-TCGAAGAGCATTCGTGCTAGTAATATATCCGTGCTAA-ACCTCGAA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC-CGAA
* *
34442 GAGCATTCGTGCTGGT
65 GAGCATTCATGCTAGT
* * *
34458 GTTATATCCGGGCTAGGTCCCGAAGAGCA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCA
34487 ATCATGCTGG
Statistics
Matches: 248, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
78 29 0.12
79 170 0.69
80 49 0.20
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
AGCATTCATGCTAGT
Done.