Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4233.1
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: 73316
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 1754 characters in sequence are not A, C, G, or T
Found at i:5756 original size:39 final size:40
Alignment explanation
Indices: 5599--5816 Score: 273
Period size: 40 Copynumber: 5.5 Consensus size: 40
5589 GCTACTCGTT
* *
5599 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
5639 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAGTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
5679 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
5719 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
5758 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
5799 CAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGACTTA
5817 GCCTGGACAT
Statistics
Matches: 159, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.01
39 33 0.21
40 111 0.70
41 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:5783 original size:119 final size:120
Alignment explanation
Indices: 5599--5816 Score: 291
Period size: 119 Copynumber: 1.8 Consensus size: 120
5589 GCTACTCGTT
*
5599 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
5664 ATTTAGT-AAGTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTCAAGTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
5719 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* **
5781 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 GGATATAGTCAAGTAGCACAAAGCCTTCGGGACTTA
5817 GCCTGGACAT
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.05
119 58 0.68
120 23 0.27
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTCAAGTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:12228 original size:40 final size:40
Alignment explanation
Indices: 12149--12325 Score: 198
Period size: 40 Copynumber: 4.5 Consensus size: 40
12139 CGGATGATAA
* *
12149 CCGGACTAAGATCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGATCCGAAGGCATTTATGCGAGTTGCTATAT
* * * *
12189 CCGGGCTATGTTCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGATCCGAAGGCATTTATGCGAGTTG-CTATAT
* * *
12229 CCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCTATAT
1 CCGGGCTAAGATCCGAAGGCATTTATGCGAGTTGCTATAT
* * * *
12269 CCGGGCTAAGACCCGAGGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGATCCGAAGGCATTTATGCGAGTTGCTATAT
12309 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGAT-CCGAAG
12326 ATAGTTGGGT
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 100 0.86
41 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGATCCGAAGGCATTTATGCGAGTTGCTATAT
Found at i:12290 original size:80 final size:80
Alignment explanation
Indices: 12149--12325 Score: 234
Period size: 80 Copynumber: 2.2 Consensus size: 80
12139 CGGATGATAA
* * * * **
12149 CCGGACTAAGATCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTTCCGAAGGCATTTA
1 CCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
*
12214 TGCTAG-TGATTATAT
66 TGCGAGTTG-TTATAT
* *
12229 CCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCTATATCCGGGCTAAGACCCGAGGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
12294 TGCGAGTTGTTATAT
66 TGCGAGTTGTTATAT
12309 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
12326 ATAGTTGGGT
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 1 0.01
79 13 0.15
80 70 0.81
81 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
TGCGAGTTGTTATAT
Found at i:20348 original size:40 final size:40
Alignment explanation
Indices: 20269--20445 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
20259 CGGATGATAA
* *
20269 CCGGACTAAGATCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * * * *
20309 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT
20349 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* *
20389 CCGGGCTAAGACCCGAGGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
20429 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
20446 ATACTTGGGT
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 14 0.12
40 102 0.86
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:22930 original size:34 final size:34
Alignment explanation
Indices: 22882--22954 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
22872 ATGTGACATA
*
22882 CTTATAACAGATCAA-ACCAGTAGCATTTAATATG
1 CTTATAACAGATCAATA-CAGTAGCAATTAATATG
* * **
22916 CTTATATCATATCAATATGGTAGCAATTAATATG
1 CTTATAACAGATCAATACAGTAGCAATTAATATG
22950 CTTAT
1 CTTAT
22955 CTAAAATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 32 0.97
35 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (34 bp):
CTTATAACAGATCAATACAGTAGCAATTAATATG
Found at i:22964 original size:34 final size:34
Alignment explanation
Indices: 22901--22965 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
22891 GATCAAACCA
* * *
22901 GTAGCATTTAATATGCTTATATCATATCAATATG
1 GTAGCAATTAATATGCTTATATAAAATCAATATG
*
22935 GTAGCAATTAATATGCTTATCTAAAATCAAT
1 GTAGCAATTAATATGCTTATATAAAATCAAT
22966 TCGATAGCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Consensus pattern (34 bp):
GTAGCAATTAATATGCTTATATAAAATCAATATG
Found at i:22974 original size:34 final size:34
Alignment explanation
Indices: 22902--22975 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
22892 ATCAAACCAG
* * * *
22902 TAGCATTTAATATGCTTATATCATATCAATATGG
1 TAGCAATTAATATGCTTATATAAAATCAATATGA
*
22936 TAGCAATTAATATGCTTATCTAAAATCAAT-TCGA
1 TAGCAATTAATATGCTTATATAAAATCAATAT-GA
22970 TAGCAA
1 TAGCAA
22976 AGTACATGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 1 0.03
34 33 0.97
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (34 bp):
TAGCAATTAATATGCTTATATAAAATCAATATGA
Found at i:24676 original size:23 final size:21
Alignment explanation
Indices: 24649--24693 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
24639 CGTCATTCAT
24649 TCATCTCTCAATTCACATTCTTC
1 TCATCTCTC-ATTCACATT-TTC
* *
24672 TCATCTTTCTTTCACATTTTC
1 TCATCTCTCATTCACATTTTC
24693 T
1 T
24694 TCCCTCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.18, C:0.31, G:0.00, T:0.51
Consensus pattern (21 bp):
TCATCTCTCATTCACATTTTC
Found at i:30037 original size:24 final size:24
Alignment explanation
Indices: 30005--30055 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
29995 AAGTCTGTCA
* **
30005 GGATAGGATTTAGGAGTTGATAAG
1 GGATAGGATTTAAGAGCAGATAAG
30029 GGATAGGATTTAAGAGCAGATAAG
1 GGATAGGATTTAAGAGCAGATAAG
30053 GGA
1 GGA
30056 GGAAATCTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.24
Consensus pattern (24 bp):
GGATAGGATTTAAGAGCAGATAAG
Found at i:31515 original size:27 final size:27
Alignment explanation
Indices: 31477--31579 Score: 122
Period size: 27 Copynumber: 3.8 Consensus size: 27
31467 AAGCGTCCTA
*
31477 GTGGCTATGCCACAATTATCTGATCTG
1 GTGGCTCTGCCACAATTATCTGATCTG
31504 GTGGCTCTGCCACATATT-TCT-ATTCTG
1 GTGGCTCTGCCACA-ATTATCTGA-TCTG
*
31531 GTGGCTCTGCCACGATTATCTGTATCTG
1 GTGGCTCTGCCACAATTATCTG-ATCTG
* *
31559 GTGACTCTGTCAC-ATTATCTG
1 GTGGCTCTGCCACAATTATCTG
31580 TTTTGGCAGC
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
26 4 0.06
27 44 0.66
28 18 0.27
29 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.37
Consensus pattern (27 bp):
GTGGCTCTGCCACAATTATCTGATCTG
Found at i:37921 original size:62 final size:62
Alignment explanation
Indices: 37822--37946 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
37812 TACGAGGCAT
37822 TACCAGACTTAACCATACACATAGTCGAAAATCGGGCCATAAAATTTCATTTAATTCAAAAC
1 TACCAGACTTAACCATACACATAGTCGAAAATCGGGCCATAAAATTTCATTTAATTCAAAAC
*
37884 TACCAGACTTAACCATACACATAGTCGAAAATTGGGCCATAAAATTTCATTTAATTCAAAAC
1 TACCAGACTTAACCATACACATAGTCGAAAATCGGGCCATAAAATTTCATTTAATTCAAAAC
37946 T
1 T
37947 TTTTGAACAC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.27
Consensus pattern (62 bp):
TACCAGACTTAACCATACACATAGTCGAAAATCGGGCCATAAAATTTCATTTAATTCAAAAC
Found at i:39336 original size:49 final size:50
Alignment explanation
Indices: 39246--39465 Score: 230
Period size: 49 Copynumber: 4.4 Consensus size: 50
39236 ATATCCCGCG
* * * * *
39246 CTTAGTACTACACATGCGACC-AATTATCCGGTACACATAGTATCCTGCA
1 CTTAGTACTACACACGTGACCTAATTATCTGATACACATAGTAGCCTGCA
* ** * * *
39295 CTT-GTACTACACATGTGACCTAACCATTTGATACACGTAGTAGCTTGCA
1 CTTAGTACTACACACGTGACCTAATTATCTGATACACATAGTAGCCTGCA
* * * * * *
39344 CTTAGTACGACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCA
1 CTTAGTACTACACACGTGACCTAA-TTATCTGATACACATAGTAGCCTGCA
* * *
39395 CTTAGTACTACACATGCGACC-AATTATCTGATACACGTAGTAGCCTGCA
1 CTTAGTACTACACACGTGACCTAATTATCTGATACACATAGTAGCCTGCA
39444 CTTAGTACTACACACGTGACCT
1 CTTAGTACTACACACGTGACCT
39466 CACAATAGAT
Statistics
Matches: 136, Mismatches: 31, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
48 16 0.12
49 67 0.49
50 18 0.13
51 35 0.26
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (50 bp):
CTTAGTACTACACACGTGACCTAATTATCTGATACACATAGTAGCCTGCA
Found at i:39393 original size:100 final size:100
Alignment explanation
Indices: 39269--39462 Score: 291
Period size: 100 Copynumber: 1.9 Consensus size: 100
39259 ATGCGACCAA
* * *
39269 TTATCCGGTACACATAGTATCCTGCACTT-GTACTACACATGTGACCTAACCATTTGATACACGT
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACCATCTGATACACGT
*
39333 AGTAGCTTGCACTTAGTACGACACACGTGATCGAAG
65 AGTAGCCTGCACTTAGTACGACACACGTGATCGAAG
* * **
39369 TTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGATACACGTA
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAACCATCTGATACACGTA
*
39434 GTAGCCTGCACTTAGTACTACACACGTGA
66 GTAGCCTGCACTTAGTACGACACACGTGA
39463 CCTCACAATA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
100 68 0.81
101 16 0.19
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (100 bp):
TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAACCATCTGATACACGTA
GTAGCCTGCACTTAGTACGACACACGTGATCGAAG
Found at i:39743 original size:27 final size:27
Alignment explanation
Indices: 39713--39766 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39703 CATACAACCC
* *
39713 ATGTAATAGTAATTTAACATTCAATTT
1 ATGTAACAATAATTTAACATTCAATTT
**
39740 ATGTAACAATAATTTGCCATTCAATTT
1 ATGTAACAATAATTTAACATTCAATTT
39767 CACATGGCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (27 bp):
ATGTAACAATAATTTAACATTCAATTT
Found at i:45068 original size:50 final size:49
Alignment explanation
Indices: 44956--45183 Score: 330
Period size: 50 Copynumber: 4.6 Consensus size: 49
44946 CTAGTATGCA
* * ** *
44956 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCTGATACACG
*
45005 TAGTAGCCTGCACTTATTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACCATCTGATACACG
* * ** *
45055 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCTGATACACG
*
45104 TAGTAGCCTGCACTTATTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACCATCTGATACACG
45154 TAGTAGCCTGCACTTAGTACTACACACGTG
1 TAGTAGCCTGCACTTAGTACTACACACGTG
45184 GCCTCACAAT
Statistics
Matches: 158, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
49 73 0.46
50 85 0.54
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCTGATACACG
Found at i:45127 original size:99 final size:99
Alignment explanation
Indices: 44956--45179 Score: 448
Period size: 99 Copynumber: 2.3 Consensus size: 99
44946 CTAGTATGCA
44956 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACGTAGTAGCCTGCACTTA
45021 TTACTACACACGTGACCTAACCATCTGATACACG
66 TTACTACACACGTGACCTAACCATCTGATACACG
45055 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACGTAGTAGCCTGCACTTA
45120 TTACTACACACGTGACCTAACCATCTGATACACG
66 TTACTACACACGTGACCTAACCATCTGATACACG
45154 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
45180 CGTGGCCTCA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 125 1.00
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACGTAGTAGCCTGCACTTA
TTACTACACACGTGACCTAACCATCTGATACACG
Found at i:47701 original size:40 final size:40
Alignment explanation
Indices: 47624--47841 Score: 309
Period size: 40 Copynumber: 5.5 Consensus size: 40
47614 AAACCAAGTA
* *
47624 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
47663 CCTTCGGGACTTAGCCCCGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
47703 CCTTCGGGACTTAGCTCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
47743 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
47783 CCTTCAGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTC-GGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
47823 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
47842 TTATCATCCG
Statistics
Matches: 162, Mismatches: 12, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
39 18 0.11
40 141 0.87
41 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Done.