Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2178
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: 78845
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:6566 original size:24 final size:24
Alignment explanation
Indices: 6539--6585 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
6529 AAAAGAAAAC
6539 ATTCAATATTTCAATTTAATTAGA
1 ATTCAATATTTCAATTTAATTAGA
*
6563 ATTCAATATTTCAGTTTAATTAG
1 ATTCAATATTTCAATTTAATTAG
6586 CATTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (24 bp):
ATTCAATATTTCAATTTAATTAGA
Found at i:8676 original size:26 final size:26
Alignment explanation
Indices: 8647--8698 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
8637 AATAAAAGAA
8647 AACATTCAATATTTCAATTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
*
8673 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
8699 CATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTAG
Found at i:9462 original size:32 final size:34
Alignment explanation
Indices: 9426--9490 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
9416 TAACAGTGGT
*
9426 ACTGGGCCAGAG-CCCTT-TTCAGATTACAGTAA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAGTAA
**
9458 ACTGGGCCTTAGCCCCTTATTCAGATAACAGTA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAGTA
9491 TGGCCCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.36
33 5 0.18
34 13 0.46
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (34 bp):
ACTGGGCCAGAGCCCCTTATTCAGATAACAGTAA
Found at i:9834 original size:24 final size:26
Alignment explanation
Indices: 9798--9846 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
9788 TCAAACATGC
9798 ATTTAGGTCAATTTAAC-CCTAGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGT
* *
9823 ATTTCGGT-AATTTATCTCCTAGGG
1 ATTTAGGTCAATTTAACTCCTAGGG
9847 GTAAAACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.39
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACTCCTAGGGT
Found at i:11357 original size:26 final size:26
Alignment explanation
Indices: 11321--11376 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
11311 TGAAATTCCA
11321 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
*
11347 ATCATGGAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
11373 ATCA
1 ATCA
11377 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (26 bp):
ATCATGAAACATTTACCTAACCCATT
Found at i:15869 original size:26 final size:26
Alignment explanation
Indices: 15840--15889 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
15830 AATAAAAGAA
15840 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
15866 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
15890 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:17984 original size:26 final size:26
Alignment explanation
Indices: 17955--18004 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
17945 AATAAAAGAA
17955 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
17981 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
18005 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:20081 original size:26 final size:26
Alignment explanation
Indices: 20052--20101 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
20042 AATAAAAGAA
20052 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
20078 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
20102 AGCATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:29676 original size:46 final size:46
Alignment explanation
Indices: 29626--29847 Score: 275
Period size: 46 Copynumber: 4.8 Consensus size: 46
29616 TGTTTGGGCA
* *
29626 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *** * * * * *
29672 TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-ACG
29719 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
29765 CCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATACGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
29811 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29848 GCGGGTTACA
Statistics
Matches: 149, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
46 115 0.77
47 34 0.23
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:29781 original size:93 final size:94
Alignment explanation
Indices: 29622--29847 Score: 307
Period size: 93 Copynumber: 2.4 Consensus size: 94
29612 AGGATGTTTG
* * *
29622 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
** * * *
29687 TTGAGTCTGAGTTCGAGAGATGTA-AC-TA
66 TTGAGTCCAAGTTC-ACAGATGGATACGAA
*
29715 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
**
29780 TTGAGTCCAAGTTCACTTATGGATACGAA
66 TTGAGTCCAAGTTCACAGATGGATACGAA
*
29809 CGC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29848 GCGGGTTACA
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
92 41 0.34
93 75 0.63
94 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (94 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCAAGTTCACAGATGGATACGAA
Found at i:33312 original size:19 final size:18
Alignment explanation
Indices: 33275--33318 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
33265 AAACATACAG
33275 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
33292 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
33311 TACTAATT
1 TAATAATT
33319 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:36614 original size:26 final size:26
Alignment explanation
Indices: 36585--36634 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
36575 AATAAAAGAA
36585 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
36611 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
36635 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:38732 original size:26 final size:26
Alignment explanation
Indices: 38703--38752 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
38693 AATAAAAGAA
38703 AACATTCAATATTTCAATTTAATTGG
1 AACATTCAATATTTCAATTTAATTGG
*
38729 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
38753 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTGG
Found at i:40827 original size:26 final size:26
Alignment explanation
Indices: 40798--40847 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
40788 AATAAAAGAA
40798 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
40824 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
40848 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:42938 original size:26 final size:26
Alignment explanation
Indices: 42909--42960 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
42899 AATAAAAGAA
42909 AACATTCAATATTTCAATTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
*
42935 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
42961 CATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTAG
Found at i:45034 original size:26 final size:26
Alignment explanation
Indices: 45005--45054 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
44995 AATAAAAGAA
*
45005 AACATTCAATGTTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
45031 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
45055 AGCATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:47747 original size:27 final size:27
Alignment explanation
Indices: 47643--47757 Score: 126
Period size: 28 Copynumber: 4.1 Consensus size: 27
47633 AGGAAACATC
*
47643 CTGGTGGCTATGCCACAAATTATCTG-AT
1 CTGGTGGCTCTGCCAC--ATTATCTGTAT
* *
47671 CTGGTGGCTCTGCCACATATATATCTATT
1 CTGGTGGCTCTGCCACAT-TATCTGTA-T
47700 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
47728 CTGGTGACTCTGTCACATTATCTGT-T
1 CTGGTGGCTCTGCCACATTATCTGTAT
47754 CTGG
1 CTGG
47758 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
26 7 0.09
27 13 0.17
28 31 0.41
29 23 0.30
30 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:52072 original size:26 final size:26
Alignment explanation
Indices: 52043--52092 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
52033 AATAAAAGAA
52043 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
* *
52069 AACATTCAATATTTTAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
52093 AGCATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:58948 original size:26 final size:26
Alignment explanation
Indices: 58919--58968 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
58909 CAATAAAGAA
58919 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
58945 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
58969 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:61062 original size:26 final size:26
Alignment explanation
Indices: 61033--61082 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
61023 AATAAAAGAA
61033 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
61059 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
61083 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:63174 original size:26 final size:26
Alignment explanation
Indices: 63145--63194 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
63135 CAATAAAGAA
63145 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
63171 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
63195 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:65269 original size:26 final size:26
Alignment explanation
Indices: 65240--65291 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
65230 CAATAAAAAA
65240 AACATTCAATATTTCAATTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
*
65266 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
65292 CATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTAG
Found at i:67355 original size:26 final size:26
Alignment explanation
Indices: 67326--67375 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
67316 AATAAAAGAA
67326 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
* *
67352 AACATTCAATATTTTAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
67376 AGCATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:74224 original size:26 final size:26
Alignment explanation
Indices: 74195--74244 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
74185 CAATAAAGAA
74195 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
74221 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
74245 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:76320 original size:25 final size:25
Alignment explanation
Indices: 76292--76340 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
76282 CAATAAAGAA
76292 AACATTCAATATTTCAATTTAATTT
1 AACATTCAATATTTCAATTTAATTT
*
76317 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
76341 AGCATTAATT
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:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (25 bp):
AACATTCAATATTTCAATTTAATTT
Found at i:78428 original size:26 final size:26
Alignment explanation
Indices: 78399--78448 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
78389 AATAAAAGAA
78399 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
78425 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
78449 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Done.