Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold429
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: 32625
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:99 original size:47 final size:47
Alignment explanation
Indices: 5--316 Score: 481
Period size: 47 Copynumber: 6.5 Consensus size: 47
1 TCCA
5 ATTCATCACATCGGCCATTAGGCCCTATCACAATATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGG-CCTATCACAATATATACACTTTCAC
53 ATTCATCACATCGGCCATTAGGCCTATCACATATATATACAC-TTCAC
1 ATTCATCACATCGGCCATTAGGCCTATCACA-ATATATACACTTTCAC
*
100 ATTCATCACATCGGCCATTAGGCCTATCTC-ATATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGGCCTATCACAATATATACACTTTCAC
*
146 ATTCATCACATCGGCCATTAGGCCTTATCAC-GTATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGGCC-TATCACAATATATACACTTTCAC
193 ATTCATCACATCGGCCATTAGGCCTTATTCACCATATATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGGCC-TA-TCA-CA-ATATATACACTTTCAC
244 ATTCATCACATCGGCCATTAGGCCTTATCACATATATATTACACTTT-AC
1 ATTCATCACATCGGCCATTAGGCC-TATCACA-ATATA-TACACTTTCAC
293 A-TCATCACATCGGCCATTAGGCCT
1 ATTCATCACATCGGCCATTAGGCCT
317 TACTATCATT
Statistics
Matches: 252, Mismatches: 4, Indels: 17
0.92 0.01 0.06
Matches are distributed among these distances:
45 10 0.04
46 29 0.12
47 91 0.36
48 57 0.23
49 12 0.05
50 11 0.04
51 42 0.17
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.31
Consensus pattern (47 bp):
ATTCATCACATCGGCCATTAGGCCTATCACAATATATACACTTTCAC
Found at i:166 original size:93 final size:95
Alignment explanation
Indices: 5--316 Score: 499
Period size: 93 Copynumber: 3.3 Consensus size: 95
1 TCCA
5 ATTCATCACATCGGCCATTAGGCCCTATCACAATATATACACTTTCACATTCATCACATCGGCCA
1 ATTCATCACATCGGCCATTAGG-CCTATCACAATATATACACTTTCACATTCATCACATCGGCCA
70 TTAGGCC-TATCACATATATATACACTTCAC
65 TTAGGCCTTATCACATATATATACACTTCAC
*
100 ATTCATCACATCGGCCATTAGGCCTATCTC-ATATATACACTTTCACATTCATCACATCGGCCAT
1 ATTCATCACATCGGCCATTAGGCCTATCACAATATATACACTTTCACATTCATCACATCGGCCAT
*
164 TAGGCCTTATCAC--GTATATACACTTTCAC
66 TAGGCCTTATCACATATATATACAC-TTCAC
193 ATTCATCACATCGGCCATTAGGCCTTATTCACCATATATATACACTTTCACATTCATCACATCGG
1 ATTCATCACATCGGCCATTAGGCC-TA-TCA-CA-ATATATACACTTTCACATTCATCACATCGG
*
258 CCATTAGGCCTTATCACATATATATTACACTTTAC
62 CCATTAGGCCTTATCACATATATA-TACACTTCAC
293 A-TCATCACATCGGCCATTAGGCCT
1 ATTCATCACATCGGCCATTAGGCCT
317 TACTATCATT
Statistics
Matches: 202, Mismatches: 5, Indels: 17
0.90 0.02 0.08
Matches are distributed among these distances:
92 9 0.04
93 69 0.34
94 15 0.07
95 24 0.12
96 1 0.00
98 48 0.24
99 22 0.11
100 9 0.04
101 5 0.02
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.31
Consensus pattern (95 bp):
ATTCATCACATCGGCCATTAGGCCTATCACAATATATACACTTTCACATTCATCACATCGGCCAT
TAGGCCTTATCACATATATATACACTTCAC
Found at i:3987 original size:81 final size:78
Alignment explanation
Indices: 3886--4038 Score: 225
Period size: 81 Copynumber: 1.9 Consensus size: 78
3876 CGAATACACG
* *
3886 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATTATAACACCAGCACGAATGCTCTTCGGA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGA-TACAACA-CAGCACGAATGCTCTTCGG-
3951 ACTTAGCCCGGATACA
63 ACTTAGCCCGGATACA
* * * *
3967 TCACTAGCATGAATGCTCTTCGGGACCTAGCCCGGATACATCATAGCATGAATGCTCTTCGGACT
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATACAACACAGCACGAATGCTCTTCGGACT
4032 TAGCCCG
66 TAGCCCG
4039 ATTTAGTAAC
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
78 10 0.15
79 17 0.26
80 5 0.08
81 34 0.52
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (78 bp):
TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATACAACACAGCACGAATGCTCTTCGGACT
TAGCCCGGATACA
Found at i:3998 original size:40 final size:40
Alignment explanation
Indices: 3886--4038 Score: 202
Period size: 40 Copynumber: 3.9 Consensus size: 40
3876 CGAATACACG
* *
3886 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATTATA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGA-TACA
* * * *
3927 ACACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATACA
*
3967 TCACTAGCATGAATGCTCTTCGGGACCTAGCCCGGATACA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATACA
* *
4007 TCA-TAGCATGAATGCTCTTC-GGACTTAGCCCG
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCG
4039 ATTTAGTAAC
Statistics
Matches: 100, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
38 11 0.11
39 17 0.17
40 41 0.41
41 31 0.31
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATACA
Found at i:4059 original size:38 final size:40
Alignment explanation
Indices: 4017--4111 Score: 117
Period size: 38 Copynumber: 2.5 Consensus size: 40
4007 TCATAGCATG
* *
4017 AATGCTCTTCGGACTTAGCCC-GATTTAGTAACTCG-ACC
1 AATGCTCTTCGGACTTAGCCCGGAATTAGTAACTCGCACA
* *
4055 AATGCT-TTCGGGCTTAGCCCGGAATTAGTATCTCGCACA
1 AATGCTCTTCGGACTTAGCCCGGAATTAGTAACTCGCACA
4094 AATGC-CTTCGGATCTTAG
1 AATGCTCTTCGGA-CTTAG
4112 TCTGGATATG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
37 13 0.27
38 18 0.38
39 12 0.25
40 5 0.10
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (40 bp):
AATGCTCTTCGGACTTAGCCCGGAATTAGTAACTCGCACA
Found at i:4464 original size:47 final size:47
Alignment explanation
Indices: 4410--4530 Score: 138
Period size: 47 Copynumber: 2.6 Consensus size: 47
4400 ATTCTCTCTT
* ** *
4410 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCTGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAACGTGATG
* * *
4457 AATGTGAAAGTATATATATATGTGA-CAGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAG--TGTATATATGTGATAAGGCCGAATGGCCAACGTGATG
*
4505 -ATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
4531 TCCCGAAGGG
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
45 11 0.18
46 2 0.03
47 19 0.31
48 17 0.28
49 12 0.20
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAACGTGATG
Found at i:4701 original size:35 final size:36
Alignment explanation
Indices: 4647--4722 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 36
4637 CCGAGCTCTA
* * *
4647 AAGACTCGATGACTACGTGTGGGATT-TGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAATTATGTCCGGGT
*
4682 AAGACCCGATAACTTCGTGTGGAATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAATTATGTCCGGGT
4718 AAGAC
1 AAGAC
4723 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 22 0.61
36 14 0.39
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (36 bp):
AAGACCCGATAACTACGTGTGGAATTATGTCCGGGT
Found at i:4942 original size:37 final size:38
Alignment explanation
Indices: 4886--4965 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 38
4876 CCGAGCTCTA
* * *
4886 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGG-T
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGTT
*
4923 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGTT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGTT
4961 AAGAC
1 AAGAC
4966 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 32 0.84
38 6 0.16
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (38 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGTT
Found at i:7136 original size:29 final size:28
Alignment explanation
Indices: 7093--7147 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
7083 AAGTTATACC
*
7093 GATTTGACTTTGGGCCATGTATATCAGCT
1 GATTTGACTTCGGGCCATG-ATATCAGCT
*
7122 GATTTGGCTTCGGGCCATGATATCAG
1 GATTTGACTTCGGGCCATGATATCAG
7148 TACTTCGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (28 bp):
GATTTGACTTCGGGCCATGATATCAGCT
Found at i:10513 original size:21 final size:21
Alignment explanation
Indices: 10489--10532 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
10479 ACTCAAATTC
10489 ATCCTAAATTTAAAATTTTGA
1 ATCCTAAATTTAAAATTTTGA
10510 ATCCTAAATTTAAAATTTTGA
1 ATCCTAAATTTAAAATTTTGA
10531 AT
1 AT
10533 TATAAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (21 bp):
ATCCTAAATTTAAAATTTTGA
Found at i:10538 original size:21 final size:21
Alignment explanation
Indices: 10493--10538 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
10483 AAATTCATCC
*
10493 TAAATTTAAAATTTTGAATCC
1 TAAATTTAAAATTTTGAATCA
*
10514 TAAATTTAAAATTTTGAATTA
1 TAAATTTAAAATTTTGAATCA
10535 TAAA
1 TAAA
10539 CATTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (21 bp):
TAAATTTAAAATTTTGAATCA
Found at i:20921 original size:29 final size:29
Alignment explanation
Indices: 20850--20957 Score: 137
Period size: 29 Copynumber: 3.8 Consensus size: 29
20840 CTCACATACT
* * *
20850 TGTATCTGGCCCATTAAGCCC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* * *
20878 TGCATATGGCCCATTAGGCCCAAATTACC
1 TGTATATGGCCCATTAGGCCCAAATCACA
20907 TGTATATGGCCCATTAGGCCCAAATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
20936 TTTATATGGCCCGTTAGGCCCA
1 TGTATATGGCCCATTAGGCCCA
20958 GTCACATTCA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 18 0.26
29 50 0.74
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:21223 original size:16 final size:16
Alignment explanation
Indices: 21186--21217 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21176 AAACTTTCAG
21186 CTTTTCGGCATTTCGA
1 CTTTTCGGCATTTCGA
21202 CTTTTCGGCATTTCGA
1 CTTTTCGGCATTTCGA
21218 TATTTCAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (16 bp):
CTTTTCGGCATTTCGA
Found at i:21908 original size:52 final size:52
Alignment explanation
Indices: 21808--21911 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 52
21798 AGTGAAACAA
* * *
21808 AGAAATCGGCACAAAGAAAATAAAAAGAAGAACAAGGATTTTCAGCTTTTAG
1 AGAAATCGGCACAAAGAAAAGAAAAAGAACAAAAAGGATTTTCAGCTTTTAG
* * * **
21860 AGAAATCGGCAGAAAGAAAAGGAAGAA-AACAAAAAGGGTTTTTGGCTTTTAG
1 AGAAATCGGCACAAAGAAAA-GAAAAAGAACAAAAAGGATTTTCAGCTTTTAG
21912 GGAAGAGGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
52 39 0.91
53 4 0.09
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.19
Consensus pattern (52 bp):
AGAAATCGGCACAAAGAAAAGAAAAAGAACAAAAAGGATTTTCAGCTTTTAG
Found at i:23912 original size:40 final size:40
Alignment explanation
Indices: 23727--23912 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
23717 GCTCCTCGTT
* *
23727 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
23767 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
23807 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
23847 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
23888 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
23913 CATCATTCAA
Statistics
Matches: 128, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
39 3 0.02
40 113 0.88
41 12 0.09
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:31672 original size:41 final size:41
Alignment explanation
Indices: 31627--31810 Score: 134
Period size: 40 Copynumber: 4.6 Consensus size: 41
31617 TCCTCATGTT
*
31627 CAAATGCCTGTCGGACATAGCGCC-GG-TTATAGTAACTC-GCA
1 CAAATGCCT-TCGGACTTAGC-CCGGGATT-TAGTAACTCGGCA
*
31668 CAAATGCCTTC-GACTTAACCCGGGATTTAGTAACTCGGCA
1 CAAATGCCTTCGGACTTAGCCCGGGATTTAGTAACTCGGCA
* * * *
31708 CAAATG-CTTCGGACTTAGCCCGCGAATTAGTATCTC-GTA
1 CAAATGCCTTCGGACTTAGCCCGGGATTTAGTAACTCGGCA
* * * * **
31747 AAAATGCCGTT-GGATCTTAGTCC-GGATAT-GTCACTTAGCA
1 CAAATGCC-TTCGGA-CTTAGCCCGGGATTTAGTAACTCGGCA
**
31787 CAAAAACCTTCGGACTTAGCCCGG
1 CAAATGCCTTCGGACTTAGCCCGG
31811 ACACATTCAA
Statistics
Matches: 113, Mismatches: 20, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
38 2 0.02
39 41 0.36
40 52 0.46
41 18 0.16
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (41 bp):
CAAATGCCTTCGGACTTAGCCCGGGATTTAGTAACTCGGCA
Done.