Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1696
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: 35861
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:2427 original size:24 final size:24
Alignment explanation
Indices: 2400--2450 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
2390 GCCTAGCCTC
2400 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACT-GGGCAAAGCCCT
*
2424 TTTTAGTAAACTGGGCAAAGCCCT
1 TTTTAATAAACTGGGCAAAGCCCT
2448 TTT
1 TTT
2451 CGCACTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (24 bp):
TTTTAATAAACTGGGCAAAGCCCT
Found at i:2525 original size:21 final size:21
Alignment explanation
Indices: 2498--2558 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
2488 TATAATGAGT
2498 ATATCATAGCATATCATGTGC
1 ATATCATAGCATATCATGTGC
* *
2519 ATCTCATAACATATCATGTGC
1 ATATCATAGCATATCATGTGC
*
2540 ATATTAT-GTCATATCATGT
1 ATATCATAG-CATATCATGT
2559 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (21 bp):
ATATCATAGCATATCATGTGC
Found at i:2552 original size:10 final size:11
Alignment explanation
Indices: 2484--2558 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 11
2474 ACCCAAACCA
*
2484 TGCATATAATG
1 TGCATATCATG
* *
2495 AGTATATCAT-
1 TGCATATCATG
*
2505 AGCATATCATG
1 TGCATATCATG
*
2516 TGCATCTCAT-
1 TGCATATCATG
**
2526 AACATATCATG
1 TGCATATCATG
*
2537 TGCATATTATG
1 TGCATATCATG
2548 T-CATATCATG
1 TGCATATCATG
2558 T
1 T
2559 ATAAAAATAT
Statistics
Matches: 49, Mismatches: 13, Indels: 5
0.73 0.19 0.07
Matches are distributed among these distances:
10 25 0.51
11 24 0.49
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (11 bp):
TGCATATCATG
Found at i:4949 original size:47 final size:46
Alignment explanation
Indices: 4883--5038 Score: 172
Period size: 47 Copynumber: 3.3 Consensus size: 46
4873 ATTGTGGGCT
4883 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-TATGAGAGCC
* * * * *
4929 AGTGTAAGACTATGTCTGGGACATGGCATCAG-CATCGAAACGAGTGCT
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCCA-CGATATGAGAGCC
* * * *
4977 AGTGTAAGACATGTCTGGTACATGCATCGGCTACGATATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATATGAGAGCC
5023 AGTGTAAGACCATGTC
1 AGTGTAAGA-CATGTC
5039 CTGGATATGG
Statistics
Matches: 90, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
46 32 0.36
47 34 0.38
48 23 0.26
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATATGAGAGCC
Found at i:5049 original size:94 final size:94
Alignment explanation
Indices: 4880--5052 Score: 260
Period size: 94 Copynumber: 1.8 Consensus size: 94
4870 GTTATTGTGG
*
4880 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACTATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTC
4945 TGGGACATGGCATCAGCATCGAAACGAGT
66 TGGGACATGGCATCAGCATCGAAACGAGT
* * * *
4974 GCTAGTGTAAGACATGTCTGGTACATGCATCGGCTACGA-TATGATAGTCAGTGTAAGACCATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCCAGTGTAAGACCATGT
*
5038 CCT-GGATATGGCATC
65 -CTGGGACATGGCATC
5053 GACTTGAGAT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 68 0.96
95 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTC
TGGGACATGGCATCAGCATCGAAACGAGT
Found at i:5086 original size:94 final size:93
Alignment explanation
Indices: 4883--5100 Score: 239
Period size: 94 Copynumber: 2.3 Consensus size: 93
4873 ATTGTGGGCT
*
4883 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACTATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
*
4948 GACATGGCATCAGCATCGAAACGAGTGCT
66 GACATGGCATCAGCATCGAAACGAG-GCA
* * * *
4977 AGTGTAAGACATGTCTGGTACATGCATCGGCTACGA-TATGATAGTCAGTGTAAGACCATGTCCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCCAGTGTAAGACCATGT-CT
* * *
5041 -GGATATGGCATC-G-ACTTGAGATATGA-GCA
64 GGGACATGGCATCAGCA-TCGA-A-ACGAGGCA
*
5070 AGTGTAAGACTGTGTCTGGGACATGGCATCG
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCG
5101 ACATCCTACC
Statistics
Matches: 106, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
92 1 0.01
93 16 0.15
94 77 0.73
95 12 0.11
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (93 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCAGCATCGAAACGAGGCA
Found at i:6809 original size:43 final size:42
Alignment explanation
Indices: 6733--6903 Score: 150
Period size: 43 Copynumber: 4.0 Consensus size: 42
6723 ATAGGATTTC
* * *
6733 CGATATGTGATCTCTGTAAGACCAGGT-TCGGGACATTGGCAT
1 CGATATGTGATTTCAGTAAGACCATGTCT-GGGACATTGGCAT
* *
6775 CGATATGTGATTTCGAGTAAGACCATGTCTGGGACATCGACAT
1 CGATATGTGATTTC-AGTAAGACCATGTCTGGGACATTGGCAT
* * * *
6818 CG-TAATTGTGA-TTCGTGTAAGACCCTGTCTGGGATAGTGGCAT
1 CGAT-A-TGTGATTTC-AGTAAGACCATGTCTGGGACATTGGCAT
* * * *
6861 CGACATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGATTTCA-GTAAGACCATGTCTGGGACATTGGCAT
6904 TGTACGATAT
Statistics
Matches: 103, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
42 19 0.18
43 78 0.76
44 6 0.06
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
CGATATGTGATTTCAGTAAGACCATGTCTGGGACATTGGCAT
Found at i:12591 original size:14 final size:14
Alignment explanation
Indices: 12572--12601 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12562 GTGTTTATTT
*
12572 TGTGTGAATTTTCA
1 TGTGTGAAATTTCA
12586 TGTGTGAAATTTCA
1 TGTGTGAAATTTCA
12600 TG
1 TG
12602 AATTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (14 bp):
TGTGTGAAATTTCA
Found at i:17805 original size:30 final size:30
Alignment explanation
Indices: 17771--17831 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
17761 TCCTTAACTC
17771 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
17801 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
17831 A
1 A
17832 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:19811 original size:19 final size:19
Alignment explanation
Indices: 19765--19813 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
19755 GGCGACGGTC
*
19765 TCGGGTACAGGGCGTTACA
1 TCGGGTACGGGGCGTTACA
19784 TCGGGTACGGGGCGTTACA
1 TCGGGTACGGGGCGTTACA
19803 TCGGGTACGGG
1 TCGGGTACGGG
19814 TAAGGGGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.16, C:0.20, G:0.43, T:0.20
Consensus pattern (19 bp):
TCGGGTACGGGGCGTTACA
Found at i:19971 original size:17 final size:15
Alignment explanation
Indices: 19947--19983 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
19937 TAGGCCATGT
*
19947 GTCACACATAACTGA
1 GTCACACACAACTGA
19962 GTCACACACAACTGA
1 GTCACACACAACTGA
19977 GTCACAC
1 GTCACAC
19984 GCCCGTGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (15 bp):
GTCACACACAACTGA
Found at i:22180 original size:25 final size:25
Alignment explanation
Indices: 22152--22201 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
22142 ACCATTCAAG
22152 AACATTCATGGAAAGTCCCTAAACA
1 AACATTCATGGAAAGTCCCTAAACA
*
22177 AACATTCATGGCAAGTCCCTAAACA
1 AACATTCATGGAAAGTCCCTAAACA
22202 TTTAACACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (25 bp):
AACATTCATGGAAAGTCCCTAAACA
Found at i:24901 original size:24 final size:25
Alignment explanation
Indices: 24874--24925 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
24864 GCCTAGCCTC
*
24874 TTTTAAT-AACTGGGGTAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
*
24898 TTTTAGTAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
24923 TTT
1 TTT
24926 CGCACTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:25000 original size:21 final size:21
Alignment explanation
Indices: 24976--25033 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
24966 AATGAGTATT
*
24976 TCATAGCATATCATGTGCATC
1 TCATAGCATATCATGTGCATA
*
24997 TCATAACATATCATGTGCATA
1 TCATAGCATATCATGTGCATA
*
25018 TTAT-GTCATATCATGT
1 TCATAG-CATATCATGT
25034 ATAAAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (21 bp):
TCATAGCATATCATGTGCATA
Found at i:25027 original size:10 final size:11
Alignment explanation
Indices: 24981--25033 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
24971 GTATTTCATA
24981 GCATATCATGT
1 GCATATCATGT
* *
24992 GCATCTCAT-A
1 GCATATCATGT
*
25002 ACATATCATGT
1 GCATATCATGT
*
25013 GCATATTATGT
1 GCATATCATGT
25024 -CATATCATGT
1 GCATATCATGT
25034 ATAAAAATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (11 bp):
GCATATCATGT
Found at i:27512 original size:47 final size:44
Alignment explanation
Indices: 27358--27575 Score: 131
Period size: 47 Copynumber: 4.7 Consensus size: 44
27348 ATTGTGGGCT
* **
27358 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGAGAACC
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCACGA-TATGA-AGTC
* * * *
27404 AGTGTAAGACTATGTCTGGGAGATGGAATCGGCATCGAAACG-AGTGC
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCA-CGATATGAAGT-C
*
27451 TAGTGTAAGACATGTCTGGCACATGCATCGGCTACGATATGATAGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGC-ACGATATGA-AGTC
* * *
27498 AGTGTAAGACCATGTCTTGGATATGGCATCGACTTGA-GATATG-AG-C
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC---ACGATATGAAGTC
*
27544 AAGTGTAAGACCATGTTTGGGACATGGCATCG
1 -AGTGTAAGA-CATGTCTGGGACAT-GCATCG
27576 ACATCCTACC
Statistics
Matches: 138, Mismatches: 20, Indels: 27
0.75 0.11 0.15
Matches are distributed among these distances:
46 33 0.24
47 70 0.51
48 27 0.20
49 7 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCACGATATGAAGTC
Found at i:28418 original size:31 final size:31
Alignment explanation
Indices: 28380--28441 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
28370 AAATAAAAAG
28380 AAAGAAAAAGAGTTTGAGACATTCGGCTATT
1 AAAGAAAAAGAGTTTGAGACATTCGGCTATT
28411 AAAGAAAAAGAGTTTGAGACATTCGGCTATT
1 AAAGAAAAAGAGTTTGAGACATTCGGCTATT
28442 TGAAAGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.26
Consensus pattern (31 bp):
AAAGAAAAAGAGTTTGAGACATTCGGCTATT
Found at i:28609 original size:15 final size:15
Alignment explanation
Indices: 28589--28627 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
28579 TTATTGAAGA
28589 TATGTTTTGGGTTAG
1 TATGTTTTGGGTTAG
28604 TATGTTTTGGGTTAG
1 TATGTTTTGGGTTAG
28619 TATGTTTTG
1 TATGTTTTG
28628 ATGAATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.31, T:0.56
Consensus pattern (15 bp):
TATGTTTTGGGTTAG
Found at i:29242 original size:42 final size:42
Alignment explanation
Indices: 29194--29362 Score: 166
Period size: 43 Copynumber: 4.0 Consensus size: 42
29184 ATAGGATTTC
* *
29194 CGATATGTGATCTC-TGTAAGATCAGGTCTGGGACATTGGCAT
1 CGATATGTGAT-TCGTGTAAGACCATGTCTGGGACATTGGCAT
* * *
29236 CGATATGTGATTTCGAGTAAGATCATGT-TGGGACA-TCGCAT
1 CGATATGTGA-TTCGTGTAAGACCATGTCTGGGACATTGGCAT
* *
29277 CG-TAATTGTGATTCGTGTAAGACCCTGTCTGGGACAGTGGCAT
1 CGAT-A-TGTGATTCGTGTAAGACCATGTCTGGGACATTGGCAT
* * * *
29320 CGACATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGATT-CGTGTAAGACCATGTCTGGGACATTGGCAT
29363 TGTATGATAT
Statistics
Matches: 106, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
40 1 0.01
41 22 0.21
42 38 0.36
43 45 0.42
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (42 bp):
CGATATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCAT
Done.