Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2232
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: 32443
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Found at i:5552 original size:30 final size:30
Alignment explanation
Indices: 5518--5578 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
5508 TTTTCCGAGC
5518 TTGGGGACAAAAGTGT-AATTATGCAAAAGT
1 TTGGGGACAAAAGTGTAAATT-TGCAAAAGT
* * *
5548 TTGGGGGCAAAATTGTAAATTTTCAAAAGT
1 TTGGGGACAAAAGTGTAAATTTGCAAAAGT
5578 T
1 T
5579 GGGTGGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGGGGACAAAAGTGTAAATTTGCAAAAGT
Found at i:6019 original size:25 final size:25
Alignment explanation
Indices: 5986--6034 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5976 ATGTGAAAGG
*
5986 GGGTTGCTATGTGCTGATTCCCCGA
1 GGGTTGCTAAGTGCTGATTCCCCGA
6011 GGGTTGCTAAGTGCTGATTCCCCG
1 GGGTTGCTAAGTGCTGATTCCCCG
6035 GTTCATTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (25 bp):
GGGTTGCTAAGTGCTGATTCCCCGA
Found at i:6085 original size:102 final size:102
Alignment explanation
Indices: 5920--6167 Score: 384
Period size: 102 Copynumber: 2.5 Consensus size: 102
5910 GGGTTACTGT
*
5920 GTGCTGATTCCCCGATTCATTGG-GGTGCTATGTGCG-TGATCCACCATATCTTTGAAATGTGAA
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCTTTGAAATGTGAA
5983 AGGGGGTTGCTATGTGCTGATT-CCCCGA-GGGTTGCTAA
65 A--GGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
*
6021 GTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAA
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAA
6086 GGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
66 GGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
*
6123 GTGCTGATT-CCCGATTCA--GCGTGGTGCTAAGTGCGAGATCCACCA
1 GTGCTGATTCCCCGATTCATTG-GTGGTGCTAAGTGCGATATCCACCA
6168 ATAACGGTTA
Statistics
Matches: 138, Mismatches: 4, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
99 1 0.01
100 43 0.31
101 36 0.26
102 57 0.41
103 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.30
Consensus pattern (102 bp):
GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAA
GGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
Found at i:11928 original size:13 final size:13
Alignment explanation
Indices: 11910--11934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11900 ACATATTTGA
11910 GTAAGTAAATATG
1 GTAAGTAAATATG
11923 GTAAGTAAATAT
1 GTAAGTAAATAT
11935 ACACAAATAG
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:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
GTAAGTAAATATG
Found at i:12374 original size:50 final size:50
Alignment explanation
Indices: 12305--12636 Score: 441
Period size: 50 Copynumber: 6.6 Consensus size: 50
12295 TGTGAGCCAG
* *
12305 TGTAAGACCATGTCAGGGACATGGCGCTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* * *
12355 TGTAAGACCTTGTCTGGGACATTGCGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* * * *
12405 TGTAAGACCATGTTTGGGACATGGCGTTGGCGCCGAGATAAGAAGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* *
12455 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCACA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* * *
12505 TGTAAGACCATGTCTAGGACATAGCGTTGGCACCGAGATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* * * * **
12555 CGTAAGACTATGTCTGGGACATGGC-ATGGACACCGATATGAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGG-CACCGAGATGAGAGGTCCCA
* * *
12605 TGTAAGACCATATCTGGGATATGGCATTGGCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCA
12637 ATATAGAAAA
Statistics
Matches: 243, Mismatches: 37, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
49 3 0.01
50 237 0.98
51 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
Found at i:12684 original size:49 final size:47
Alignment explanation
Indices: 12305--12685 Score: 183
Period size: 50 Copynumber: 7.7 Consensus size: 47
12295 TGTGAGCCAG
* * * * * **
12305 TGTAAGACCATGTCAGGGACATGGCGCTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACTATGTCTGGGACATGGC-TTGGCA-C-ATATGAAAACTCCCA
* * * **
12355 TGTAAGACCT-TGTCTGGGACATTGCGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGA-CTATGTCTGGGACATGGC-TTGGCAC--ATATGAAAACTCCCA
* * * * *
12405 TGTAAGACCATGTTTGGGACATGGCGTTGGCGCCGAGAT-AAGAAGTCCCA
1 TGTAAGACTATGTCTGGGACATGGC-TTGGC-AC-ATATGAA-AACTCCCA
* * * ** *
12455 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCACA
1 TGTAAGACTATGTCTGGGACATGGC-TTGGCA-C-ATATGAAAACTCCCA
* * * * * ** *
12505 TGTAAGACCATGTCTAGGACATAGCGTTGGCACCGAGATGAGAGGTCCCC
1 TGTAAGACTATGTCTGGGACATGGC-TTGGCA-C-ATATGAAAACTCCCA
* * *
12555 CGTAAGACTATGTCTGGGACATGGCATGGACACCGATATGAGAACTCCCA
1 TGTAAGACTATGTCTGGGACATGGCTTGG-CA-C-ATATGAAAACTCCCA
* * *
12605 TGTAAGACCATATCTGGGATATGGCATTGGCA-ATATAGAAAACATCCCA
1 TGTAAGACTATGTCTGGGACATGGC-TTGGCACATAT-GAAAAC-TCCCA
*
12654 TGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 TGTAAGACTATGTCTGGGACATGGC-TTGGCA
12686 TGTTATTATC
Statistics
Matches: 279, Mismatches: 41, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
47 4 0.01
48 5 0.02
49 38 0.14
50 226 0.81
51 6 0.02
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (47 bp):
TGTAAGACTATGTCTGGGACATGGCTTGGCACATATGAAAACTCCCA
Found at i:14382 original size:30 final size:31
Alignment explanation
Indices: 14348--14415 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
14338 TTGCCCAAGA
** * **
14348 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATACAAAAAATTTGAAGGACCAATAGT
14378 GTAAATACAAAAAATTTGAAGGACCAATAGT
1 GTAAATACAAAAAATTTGAAGGACCAATAGT
14409 GTAAATA
1 GTAAATA
14416 TTTTAAGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (31 bp):
GTAAATACAAAAAATTTGAAGGACCAATAGT
Found at i:21791 original size:130 final size:130
Alignment explanation
Indices: 21558--21813 Score: 381
Period size: 130 Copynumber: 2.0 Consensus size: 130
21548 AATCATCGAG
* * *
21558 AATCACTTGACCGGCTAAACCTAAAAAACTTCTAACCTCAAATACATTTCTCGGAGGCTTCTAAT
1 AATCACTTGACCGGCTAAACCCAAAAAACTTCTAACCTCAAATACATTTCTCAGAGGCTTCCAAT
* * ** *
21623 CAACAATAGCTAAAATTTTTCTTGGATCAACTCTAATGCCTTC-AGCTGATACAACATGTCCAAT
66 CAACAACAGCTAAAATATTTCTAAGATCAACTCTAATGCCTTCGA-CCGATACAACATGTCCAAT
21687 A
130 A
* * *
21688 AATCACTTGACCGGCTAAACCCAGAAAACTTCTAACCTCTAATACATTTCTCAGATGCTTCCAAT
1 AATCACTTGACCGGCTAAACCCAAAAAACTTCTAACCTCAAATACATTTCTCAGAGGCTTCCAAT
21753 CAACAACAGCTAAAATATTTCTCAAG-TCAACTCTAATGCCTTCGACCGATACAACATGTCC
66 CAACAACAGCTAAAATATTTCT-AAGATCAACTCTAATGCCTTCGACCGATACAACATGTCC
21814 TAGAAATCTG
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
130 111 0.98
131 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (130 bp):
AATCACTTGACCGGCTAAACCCAAAAAACTTCTAACCTCAAATACATTTCTCAGAGGCTTCCAAT
CAACAACAGCTAAAATATTTCTAAGATCAACTCTAATGCCTTCGACCGATACAACATGTCCAATA
Found at i:23952 original size:21 final size:20
Alignment explanation
Indices: 23915--23957 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
23905 CGTGAGGGTT
*
23915 TTTTTAATTTGAATATTATAA
1 TTTTTAAATTGAATATT-TAA
23936 TTTTTAAATT-AATTATTTAA
1 TTTTTAAATTGAA-TATTTAA
23956 TT
1 TT
23958 AGGCTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTAAATTGAATATTTAA
Found at i:25095 original size:19 final size:19
Alignment explanation
Indices: 25073--25115 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
25063 TATTTTTCAA
25073 AAATTAATTTGTTTT-TTT
1 AAATTAATTTGTTTTGTTT
25091 CAAA-TAATTTGTTTTGTTT
1 -AAATTAATTTGTTTTGTTT
25110 AAATTA
1 AAATTA
25116 TTTTATTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (19 bp):
AAATTAATTTGTTTTGTTT
Found at i:27177 original size:79 final size:81
Alignment explanation
Indices: 27034--27217 Score: 234
Period size: 79 Copynumber: 2.3 Consensus size: 81
27024 GCTACTCGTT
* * *
27034 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGG
* *
27098 ATTTAGTAAC-TCGCA
66 ATATAGTAACTTAGCA
* **
27113 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCG
* *
27176 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
27193 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27218 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
78 33 0.36
79 39 0.43
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGG
ATATAGTAACTTAGCA
Found at i:27217 original size:40 final size:40
Alignment explanation
Indices: 27015--27217 Score: 220
Period size: 39 Copynumber: 5.1 Consensus size: 40
27005 CGGAATTTAA
** *
27015 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
27055 CCGGTTATAGTAACTCGCACAATTGCCTTC-GGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
27094 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
27133 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
27173 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
27213 CCGGA
1 CCGGA
27218 CATCATTCAA
Statistics
Matches: 137, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.01
39 67 0.49
40 56 0.41
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.