Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1587
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: 44005
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:386 original size:21 final size:22
Alignment explanation
Indices: 355--398 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
345 AACATACCTT
355 AGCCTAGTTACATGCATGGCCG
1 AGCCTAGTTACATGCATGGCCG
377 AGCCT-GTTACATGCATGGCCG
1 AGCCTAGTTACATGCATGGCCG
398 A
1 A
399 ACCTCTCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (22 bp):
AGCCTAGTTACATGCATGGCCG
Found at i:7193 original size:39 final size:39
Alignment explanation
Indices: 7096--7205 Score: 150
Period size: 39 Copynumber: 2.8 Consensus size: 39
7086 AGCCCGGTTA
* *
7096 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTC-GGACTTAACCCAGAAT
* *
7136 TAGTAACTCGCACCAATGCCTTCGG-CTTTAGCCCAGAAT
1 TAGTAACTCGCACAAATGCCTTCGGAC-TTAACCCAGAAT
7175 TAGTAACTCGCACAAATGCCTTCGGATCTTA
1 TAGTAACTCGCACAAATGCCTTCGGA-CTTA
7206 GTCCGGATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
38 1 0.02
39 35 0.56
40 25 0.40
41 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (39 bp):
TAGTAACTCGCACAAATGCCTTCGGACTTAACCCAGAAT
Found at i:7252 original size:40 final size:40
Alignment explanation
Indices: 7049--7252 Score: 222
Period size: 40 Copynumber: 5.1 Consensus size: 40
7039 CGGAATTTAA
** *
7049 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7089 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7129 CCGGATTTAGTAACTCGCACCAATGCCTTC-GG-CTTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGAC-TTAGC
* *
7168 CCAGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
7208 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
7248 CCGGA
1 CCGGA
7253 CATCATTCGA
Statistics
Matches: 139, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
39 35 0.25
40 90 0.65
41 13 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:9357 original size:42 final size:43
Alignment explanation
Indices: 9292--9408 Score: 132
Period size: 44 Copynumber: 2.7 Consensus size: 43
9282 ATGTAATTAA
* * *
9292 ATAT-CGAAGCCACTGTCCTAGACA-GGATCTTAAACG-AAATC
1 ATATACGATGCCAATGTCCCAGACATGG-TCTTAAACGTAAATC
*
9333 ATATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATC
1 ATATACGATGCCAATGTCCCAGACATGGTCTTAAACGTAAATC
* * *
9376 ACAAATCGATGCCAACGTCCCAGACATGGTCTT
1 ATATA-CGATGCCAATGTCCCAGACATGGTCTT
9409 CCATGATAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
41 4 0.06
42 25 0.38
43 10 0.15
44 26 0.40
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (43 bp):
ATATACGATGCCAATGTCCCAGACATGGTCTTAAACGTAAATC
Found at i:9396 original size:44 final size:43
Alignment explanation
Indices: 9258--9408 Score: 141
Period size: 42 Copynumber: 3.5 Consensus size: 43
9248 TAGTACAACA
* * * * *
9258 CCAACGTCTCAGACGTGGTCTTACATGT-AATTAAATATCGAAG
1 CCAACGTCCCAGACATGGTCTTACACGTAAATCAAA-ATCGATG
* * *
9301 CC-ACTGTCCTAGACA-GGATCTTAAACG-AAATC-ATATACGATG
1 CCAAC-GTCCCAGACATGG-TCTTACACGTAAATCAAAAT-CGATG
*
9343 CCAATGTCCCAGACATGGTCTTACACGTAAATCACAAATCGATG
1 CCAACGTCCCAGACATGGTCTTACACGTAAATCA-AAATCGATG
9387 CCAACGTCCCAGACATGGTCTT
1 CCAACGTCCCAGACATGGTCTT
9409 CCATGATAAC
Statistics
Matches: 86, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
41 2 0.02
42 28 0.33
43 27 0.31
44 26 0.30
45 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
CCAACGTCCCAGACATGGTCTTACACGTAAATCAAAATCGATG
Found at i:14010 original size:24 final size:24
Alignment explanation
Indices: 13983--14084 Score: 132
Period size: 24 Copynumber: 4.2 Consensus size: 24
13973 AAGGCTGTCA
13983 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
*
14007 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* * *
14031 GAAGAGGATGTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
** * *
14055 GGAGATCATATAGGAGCTGATTAG
1 GGAGAAGATTTAGGAGCTGATAAG
14079 GGAGAA
1 GGAGAA
14085 CGGAGTTCAC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.36, C:0.05, G:0.39, T:0.20
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:15394 original size:26 final size:27
Alignment explanation
Indices: 15339--15412 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
15329 AAGAATAGTT
* * *
15339 AAATTACTTA-ATACCCCTATGTATGG
1 AAATTACTCATATACCCCTAGGTATGA
* *
15365 AAATTACTGATATACCCCTAGGTGT-A
1 AAATTACTCATATACCCCTAGGTATGA
15391 AAATTAC-CATTATACCCCTAGG
1 AAATTACTCA-TATACCCCTAGG
15413 GTTACTGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 1 0.02
26 28 0.68
27 12 0.29
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATTACTCATATACCCCTAGGTATGA
Found at i:15549 original size:27 final size:26
Alignment explanation
Indices: 15509--15619 Score: 82
Period size: 27 Copynumber: 4.2 Consensus size: 26
15499 AGGAAGCTTC
15509 CTGGTGGCTA-TGCCACAATTATCTGAT
1 CTGGTGGC-ACTGCCAC-ATTATCTGAT
15536 CTGGTGGCACTGCCACATATATCT-ATT
1 CTGGTGGCACTGCCACAT-TATCTGA-T
* * * *
15563 CTGATGGCTCTGCTACAATTATCTGTT
1 CTGGTGGCACTGCCAC-ATTATCTGAT
** * * *
15590 CTAATGACACTGTCACATTATCTGTT
1 CTGGTGGCACTGCCACATTATCTGAT
15616 CTGG
1 CTGG
15620 CAGCCACGCT
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
26 16 0.24
27 50 0.74
28 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (26 bp):
CTGGTGGCACTGCCACATTATCTGAT
Found at i:15601 original size:54 final size:53
Alignment explanation
Indices: 15513--15618 Score: 131
Period size: 54 Copynumber: 2.0 Consensus size: 53
15503 AGCTTCCTGG
** *
15513 TGGCTATGCCACAATTATCTGATCTGGTGGCACTGCCACATATATCTATTCTGA
1 TGGCTATGCCACAATTATCTGATCTAATGACACTGCCACAT-TATCTATTCTGA
* * * * *
15567 TGGCTCTGCTACAATTATCTGTTCTAATGACACTGTCACATTATCTGTTCTG
1 TGGCTATGCCACAATTATCTGATCTAATGACACTGCCACATTATCTATTCTG
15619 GCAGCCACGC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
53 10 0.23
54 34 0.77
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.37
Consensus pattern (53 bp):
TGGCTATGCCACAATTATCTGATCTAATGACACTGCCACATTATCTATTCTGA
Found at i:21913 original size:24 final size:24
Alignment explanation
Indices: 21886--21986 Score: 148
Period size: 24 Copynumber: 4.2 Consensus size: 24
21876 AAGGCTGTCA
*
21886 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
21910 GGAGAGGATTTAGGAGCTCATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
21934 GGAGAGGATGTAGGAGCTAATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
21958 GGAGAGGATTTAGGATCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
21982 GGAGA
1 GGAGA
21987 ACGGTGTTGG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.35, C:0.05, G:0.40, T:0.21
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:23458 original size:27 final size:26
Alignment explanation
Indices: 23418--23528 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
23408 AGGAAGCGTC
*
23418 CTGGTGGCTA-TGCCACAATTATCTGAT
1 CTGGTGGC-ACTGCCAC-ATTATCTGTT
23445 CTGGTGGCACTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAT-TATCTGTT
*
23472 CTTGTGGCACTGCCACAATTATCTGTT
1 CTGGTGGCACTGCCAC-ATTATCTGTT
* * *
23499 TTGGTGACACTGTCACATTATCTGTT
1 CTGGTGGCACTGCCACATTATCTGTT
23525 CTGG
1 CTGG
23529 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.22
27 56 0.76
28 2 0.03
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (26 bp):
CTGGTGGCACTGCCACATTATCTGTT
Found at i:27147 original size:27 final size:27
Alignment explanation
Indices: 27105--27324 Score: 305
Period size: 27 Copynumber: 8.1 Consensus size: 27
27095 AGGTTGTTAT
27105 ATGACCGTAATGCCCCTATAGGGTAAA
1 ATGACCGTAATGCCCCTATAGGGTAAA
* *
27132 ATGTCCGTAATGCCCCTATAAGGTAAA
1 ATGACCGTAATGCCCCTATAGGGTAAA
*
27159 ATGACCGTAATGCCCCTGTAGGGTAAA
1 ATGACCGTAATGCCCCTATAGGGTAAA
* * *
27186 ATGACCTTAATGCCCTTGTAGGGTAAA
1 ATGACCGTAATGCCCCTATAGGGTAAA
* *
27213 ATGACAGTAATGCCCCTGTAGGGTAAA
1 ATGACCGTAATGCCCCTATAGGGTAAA
27240 ATGACCGTAATGCCCCTATAGGGTAAA
1 ATGACCGTAATGCCCCTATAGGGTAAA
* * *
27267 ATGACAGTAATGCCCTTTGTAGGGTAAA
1 ATGACCGTAATGCCC-CTATAGGGTAAA
* * *
27295 ATGACCATAATACCCCTATATGGTAAA
1 ATGACCGTAATGCCCCTATAGGGTAAA
27322 ATG
1 ATG
27325 TCGATTATGC
Statistics
Matches: 171, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
27 149 0.87
28 22 0.13
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
ATGACCGTAATGCCCCTATAGGGTAAA
Found at i:27497 original size:27 final size:27
Alignment explanation
Indices: 27467--27519 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
27457 GGAAGTTCTG
27467 TACTAGTGGCTATGCCACAATTACTGA
1 TACTAGTGGCTATGCCACAATTACTGA
* * *
27494 TACTTGTGGCTTTGCCACACTTACTG
1 TACTAGTGGCTATGCCACAATTACTG
27520 TTCTGGTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (27 bp):
TACTAGTGGCTATGCCACAATTACTGA
Found at i:27716 original size:28 final size:28
Alignment explanation
Indices: 27683--27745 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
27673 TGTACTGTAT
*
27683 TGTTACTGCATTGGGCCTA-GGCCCACAC
1 TGTTACTGCATAGGG-CTAGGGCCCACAC
* *
27711 TGTTACTGTATAGGGCTAGGGCCCAGAC
1 TGTTACTGCATAGGGCTAGGGCCCACAC
27739 TG-TACTG
1 TGTTACTG
27746 ATACTGAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (28 bp):
TGTTACTGCATAGGGCTAGGGCCCACAC
Found at i:27751 original size:33 final size:33
Alignment explanation
Indices: 27709--27774 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
27699 CTAGGCCCAC
* *
27709 ACTGTTACTGTATAGGGC-TAGGGCCCAGACTGT
1 ACTGATACTGAATAGGGCTTA-GGCCCAGACTGT
*
27742 ACTGATACTGAATAGGGCTTAGGCCTAGACTGT
1 ACTGATACTGAATAGGGCTTAGGCCCAGACTGT
27775 GTTATTCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (33 bp):
ACTGATACTGAATAGGGCTTAGGCCCAGACTGT
Found at i:35768 original size:19 final size:20
Alignment explanation
Indices: 35733--35770 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
35723 ATAAGGTGGT
35733 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
35753 AAGAT-ATGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
35771 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:42897 original size:18 final size:19
Alignment explanation
Indices: 42862--42899 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
42852 GATAAGGTGG
42862 TAAGATGATGAATGATGTT
1 TAAGATGATGAATGATGTT
42881 TAAGAT-ATGATAT-ATGTT
1 TAAGATGATGA-ATGATGTT
42899 T
1 T
42900 TGGTGATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (19 bp):
TAAGATGATGAATGATGTT
Done.