Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2113
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: 61744
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3486 original size:79 final size:78
Alignment explanation
Indices: 3384--3607 Score: 274
Period size: 79 Copynumber: 2.8 Consensus size: 78
3374 GCTCCTCGTT
* *
3384 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
3449 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
3464 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
3527 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * *
3542 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
3606 GA
63 GA
3608 CATCATTCAA
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
78 38 0.30
79 53 0.42
80 34 0.27
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:3501 original size:39 final size:40
Alignment explanation
Indices: 3384--3607 Score: 275
Period size: 40 Copynumber: 5.7 Consensus size: 40
3374 GCTCCTCGTT
* *
3384 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
3424 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
3464 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
3503 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
3542 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
3583 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3608 CATCATTCAA
Statistics
Matches: 167, Mismatches: 9, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
38 2 0.01
39 73 0.44
40 75 0.45
41 17 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:9614 original size:29 final size:29
Alignment explanation
Indices: 9579--9652 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
9569 GTTGTGAGAT
* *
9579 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
9608 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
9637 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
9653 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:11969 original size:27 final size:27
Alignment explanation
Indices: 11868--11974 Score: 130
Period size: 27 Copynumber: 3.9 Consensus size: 27
11858 AGGAAGCGTC
*
11868 CTGGTGGC-CATGCCACAAATATCTG-AT
1 CTGGTGGCTC-TGCCAC-ATTATCTGTAT
11895 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACAT-TATCTGTAT
11922 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
11950 CTGGTGACTCTGTCACATTATCTGT
1 CTGGTGGCTCTGCCACATTATCTGT
11975 TCGGCAGCCA
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
26 1 0.01
27 53 0.74
28 18 0.25
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:11972 original size:54 final size:54
Alignment explanation
Indices: 11868--11976 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 54
11858 AGGAAGCGTC
*
11868 CTGGTGGCCATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCCATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
11922 CTGGTGGCTC-TGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGC-CATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
11976 C
1 C
11977 GGCAGCCATA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
54 30 0.61
55 19 0.39
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (54 bp):
CTGGTGGCCATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:18871 original size:27 final size:27
Alignment explanation
Indices: 18839--18950 Score: 118
Period size: 27 Copynumber: 4.1 Consensus size: 27
18829 AGGAAGCGTC
*
18839 CTGGTGGCTATGCCACAAATATCTGAT
1 CTGGTGGCTCTGCCACAAATATCTGAT
* *
18866 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAAATATCTGAT
* * *
18893 CTGGTGGCTCTGCAACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAAATATCTG-AT
* * * *
18921 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAAATATCTGAT
18947 CTGG
1 CTGG
18951 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.74
28 14 0.19
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAAATATCTGAT
Found at i:18943 original size:54 final size:54
Alignment explanation
Indices: 18839--18950 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
18829 AGGAAGCGTC
* *
18839 CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCAACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * *
18893 CTGGTGGCTCTGCAACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCAACAAATATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
18947 CTGG
1 CTGG
18951 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCAACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:22593 original size:15 final size:13
Alignment explanation
Indices: 22562--22586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22552 TACAGGGGAT
22562 ACATGGTCGTGTC
1 ACATGGTCGTGTC
22575 ACATGGTCGTGT
1 ACATGGTCGTGT
22587 GTGACATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (13 bp):
ACATGGTCGTGTC
Found at i:24081 original size:42 final size:42
Alignment explanation
Indices: 23976--24130 Score: 143
Period size: 42 Copynumber: 3.7 Consensus size: 42
23966 TACCATACCA
* * * * * *
23976 ATGCCATATCCCAGATATGATCTTACATGAAATCTA-GTATTG
1 ATGCCATATCCTAGATATGGTCTTACACGAAGTC-ACATATAG
* * **
24018 ATGGCAATAGCCTAGATATGGTCTTACACGAAGTTTCATATCA-
1 AT-GCCATATCCTAGATATGGTCTTACACGAAGTCACATAT-AG
* * *
24061 ATGCCATATCCTAAATATGGTCTTACATGAGGTCACATATAG
1 ATGCCATATCCTAGATATGGTCTTACACGAAGTCACATATAG
*
24103 ATGCCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCTAGATATGGTCTTACAC
24131 ATAGTCTTAG
Statistics
Matches: 89, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
41 1 0.01
42 58 0.65
43 30 0.34
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCTAGATATGGTCTTACACGAAGTCACATATAG
Found at i:25981 original size:41 final size:40
Alignment explanation
Indices: 25936--26086 Score: 149
Period size: 41 Copynumber: 3.7 Consensus size: 40
25926 ACCAGAGTGT
** * *
25936 AAACAGGGGCATGTGTGTGCAATTCAAAGGTATCGAAGTAC
1 AAACAGGGGCACATATGTGAAATTCAAAGGTA-CGAAGTAC
* * * * *
25977 AAACAGGGGCACGTACGTGAAATTTAAGGGTACCGTAGTAC
1 AAACAGGGGCACATATGTGAAATTCAAAGGTA-CGAAGTAC
* * * * *
26018 AAACAGGGGCACATATGTGTAATTTAAGGGTACTAAATAC
1 AAACAGGGGCACATATGTGAAATTCAAAGGTACGAAGTAC
*
26058 AAACAGGGGCATATATGTGAAATTCAAAG
1 AAACAGGGGCACATATGTGAAATTCAAAG
26087 AATAATTAAG
Statistics
Matches: 92, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 30 0.33
41 62 0.67
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (40 bp):
AAACAGGGGCACATATGTGAAATTCAAAGGTACGAAGTAC
Found at i:26074 original size:40 final size:41
Alignment explanation
Indices: 25971--26081 Score: 154
Period size: 41 Copynumber: 2.7 Consensus size: 41
25961 AAAGGTATCG
* *
25971 AAGTACAAACAGGGGCACGTACGTGAAATTTAAGGGTACCGT
1 AAGTACAAACAGGGGCACATATGTGAAATTTAAGGGTACC-T
*
26013 -AGTACAAACAGGGGCACATATGTGTAATTTAAGGGTA-CT
1 AAGTACAAACAGGGGCACATATGTGAAATTTAAGGGTACCT
* *
26052 AAATACAAACAGGGGCATATATGTGAAATT
1 AAGTACAAACAGGGGCACATATGTGAAATT
26082 CAAAGAATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 1 0.02
40 27 0.44
41 34 0.55
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (41 bp):
AAGTACAAACAGGGGCACATATGTGAAATTTAAGGGTACCT
Found at i:27177 original size:17 final size:17
Alignment explanation
Indices: 27155--27190 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
27145 CCACTGTTCC
27155 CCTAAAGGAATTTTCGT
1 CCTAAAGGAATTTTCGT
27172 CCTAAAGGAATTTTCGT
1 CCTAAAGGAATTTTCGT
27189 CC
1 CC
27191 CTGAAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (17 bp):
CCTAAAGGAATTTTCGT
Found at i:29744 original size:21 final size:21
Alignment explanation
Indices: 29718--29767 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
29708 TGAGTTACTT
29718 ACACGGGCGTGTGTGTCCTCC
1 ACACGGGCGTGTGTGTCCTCC
* *
29739 ACACGGGTGTGTGTGTCCTTC
1 ACACGGGCGTGTGTGTCCTCC
*
29760 ACATGGGC
1 ACACGGGC
29768 ATGTAGACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.12, C:0.28, G:0.34, T:0.26
Consensus pattern (21 bp):
ACACGGGCGTGTGTGTCCTCC
Found at i:33319 original size:2 final size:2
Alignment explanation
Indices: 33314--33368 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
33304 TGTATATATA
*
33314 TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
33356 TG TA TG TG TG TG T
1 TG TG TG TG TG TG T
33369 TTATGGGCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.04, C:0.00, G:0.45, T:0.51
Consensus pattern (2 bp):
TG
Found at i:38944 original size:41 final size:41
Alignment explanation
Indices: 38853--39044 Score: 158
Period size: 41 Copynumber: 4.7 Consensus size: 41
38843 ACCGAAGCGT
* * * ** *
38853 AAACAGGGGCACGTATGTGTAATTTAATGGCACC-AAGTAC
1 AAACAAGGGCATGTATGTGCAATTTAGGGGTACCGAAGTAC
* * *
38893 AAACAGGGGCATGTATGTGTC-ATTCAGGGGTATCGAAGTAC
1 AAACAAGGGCATGTATGTG-CAATTTAGGGGTACCGAAGTAC
* * * * *
38934 AAACAAGGGCACGTATATGCAATTTAGGGGTACCAAAATAT
1 AAACAAGGGCATGTATGTGCAATTTAGGGGTACCGAAGTAC
* *
38975 AAA-TAGTGGCATGTATGTGCAATTTAAGGGTACCGAAGTAC
1 AAACAAG-GGCATGTATGTGCAATTTAGGGGTACCGAAGTAC
** *
39016 AAAC-AGGAGCACATATGTGCAATTCAGGG
1 AAACAAGG-GCATGTATGTGCAATTTAGGG
39045 AATAATTAAG
Statistics
Matches: 120, Mismatches: 26, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
40 30 0.25
41 90 0.75
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (41 bp):
AAACAAGGGCATGTATGTGCAATTTAGGGGTACCGAAGTAC
Found at i:47429 original size:30 final size:30
Alignment explanation
Indices: 47395--47455 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
47385 TCCTTAACTC
47395 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
47425 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
47455 A
1 A
47456 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:51877 original size:30 final size:30
Alignment explanation
Indices: 51843--51903 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
51833 TCCTTAACTC
51843 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
51873 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
51903 A
1 A
51904 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:60813 original size:139 final size:139
Alignment explanation
Indices: 60563--60833 Score: 542
Period size: 139 Copynumber: 1.9 Consensus size: 139
60553 TGCTACTGTG
60563 TTCTGAAAAGGGCTTCGGTCCACTGTGTACTGTTATCTGAATAGGGCTTTGGCCCAATGGGCTCG
1 TTCTGAAAAGGGCTTCGGTCCACTGTGTACTGTTATCTGAATAGGGCTTTGGCCCAATGGGCTCG
60628 AGCTGATTTGGGCTTTGGATGGGTTTCTGTATACACTGAGTTTTCCCAAACTCACCCCCTTTTCC
66 AGCTGATTTGGGCTTTGGATGGGTTTCTGTATACACTGAGTTTTCCCAAACTCACCCCCTTTTCC
60693 CTTCCATCC
131 CTTCCATCC
60702 TTCTGAAAAGGGCTTCGGTCCACTGTGTACTGTTATCTGAATAGGGCTTTGGCCCAATGGGCTCG
1 TTCTGAAAAGGGCTTCGGTCCACTGTGTACTGTTATCTGAATAGGGCTTTGGCCCAATGGGCTCG
60767 AGCTGATTTGGGCTTTGGATGGGTTTCTGTATACACTGAGTTTTCCCAAACTCACCCCCTTTTCC
66 AGCTGATTTGGGCTTTGGATGGGTTTCTGTATACACTGAGTTTTCCCAAACTCACCCCCTTTTCC
60832 CT
131 CT
60834 AGTTGGTGGA
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 132 1.00
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (139 bp):
TTCTGAAAAGGGCTTCGGTCCACTGTGTACTGTTATCTGAATAGGGCTTTGGCCCAATGGGCTCG
AGCTGATTTGGGCTTTGGATGGGTTTCTGTATACACTGAGTTTTCCCAAACTCACCCCCTTTTCC
CTTCCATCC
Done.