Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3390
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: 45480
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:354 original size:40 final size:40
Alignment explanation
Indices: 233--423 Score: 227
Period size: 39 Copynumber: 5.0 Consensus size: 40
223 TCGATCCTTT
* * *
233 GTGCGAGATACTAAATCC-GGTTAAGTCCCGAAGGCTTTC
1 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
272 GTGCGAGTTATTAAATCCGGGTTAAGT-CCGAAGGCATTC
1 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
*
311 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGTC
1 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
351 GTGCGAGTTGTTAAATCC----TATGT-CCGAAGGCATT-
1 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
* * * * *
385 GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
424 TGAACGAGGA
Statistics
Matches: 134, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
34 14 0.10
35 10 0.07
36 4 0.03
38 5 0.04
39 65 0.49
40 36 0.27
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
Found at i:365 original size:79 final size:74
Alignment explanation
Indices: 231--421 Score: 240
Period size: 79 Copynumber: 2.5 Consensus size: 74
221 GATCGATCCT
* **
231 TTGTGCGAGATACTAAATCC-GGTTAAGTCCCGAAGGCTTTCGTGCGAGTTATTAAATCCGGGTT
1 TTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTATTAAATCC----T
295 AAGTCCGAAGGCA
62 AAGTCCGAAGGCA
* * *
308 TTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAATCCTATG
1 TT-GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTATTAAATCCTAAG
373 TCCGAAGGCA
65 TCCGAAGGCA
* * * *
383 TTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCA
1 TTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCA
422 TTTGAACGAG
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
74 32 0.32
75 15 0.15
77 2 0.02
78 16 0.16
79 36 0.36
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (74 bp):
TTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTATTAAATCCTAAGT
CCGAAGGCA
Found at i:7523 original size:40 final size:40
Alignment explanation
Indices: 7440--7702 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
7430 TTGAATGCTG
* * * * * *
7440 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
7480 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
7520 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
7560 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
7600 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
7640 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
7679 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
7703 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:7722 original size:79 final size:80
Alignment explanation
Indices: 7479--7737 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
7469 AAGTGAATAT
* * * * * * *
7479 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
7543 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
7559 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
7624 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
7639 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
7703 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
7718 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
7738 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:15092 original size:13 final size:13
Alignment explanation
Indices: 15074--15102 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
15064 GGTTATTTAT
15074 TAAACTAATTAAC
1 TAAACTAATTAAC
15087 TAAACTAATTAAC
1 TAAACTAATTAAC
15100 TAA
1 TAA
15103 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:18130 original size:46 final size:44
Alignment explanation
Indices: 18079--18254 Score: 194
Period size: 46 Copynumber: 3.9 Consensus size: 44
18069 ATGTTTGGGC
18079 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
* * * *
18123 ATGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GC
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGA
*
18171 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-A
* * *
18216 CACCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18255 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 97 0.89
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (44 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
Found at i:18233 original size:92 final size:92
Alignment explanation
Indices: 18076--18246 Score: 288
Period size: 92 Copynumber: 1.9 Consensus size: 92
18066 AGGATGTTTG
* ***
18076 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAACACCCGAACTCGTTGAG
*
18141 TTGAGTCCGAGTTCGTGAATGTAACTA
66 TTGAGTCCAAGTTCGTGAATGTAACTA
*
18168 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAACACCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAACACCCGAACTCGTTGAG
18233 TTGAGTCCAAGTTC
66 TTGAGTCCAAGTTC
18247 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (92 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAACACCCGAACTCGTTGAG
TTGAGTCCAAGTTCGTGAATGTAACTA
Found at i:21192 original size:15 final size:15
Alignment explanation
Indices: 21172--21240 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
21162 GTATCTTGGG
21172 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
21187 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
21202 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
21217 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
21232 TTTCTTTAT
1 TTTCTTTAT
21241 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:21241 original size:30 final size:30
Alignment explanation
Indices: 21163--21250 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
21153 CATAGTATCG
* * * *
21163 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
21193 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
21223 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
21251 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:23641 original size:46 final size:46
Alignment explanation
Indices: 23591--23766 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
23581 TGTTTGGGCA
23591 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
23637 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-AAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
23682 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
23730 -CCTGAGCTCATTGAGTTGAATCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
23767 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 5 0.05
46 60 0.56
47 29 0.27
48 3 0.03
50 2 0.02
51 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:23746 original size:93 final size:93
Alignment explanation
Indices: 23587--23758 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
23577 AGGATGTTTG
* * *
23587 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGTCCGAACTCATTGAG
*
23652 TTGAGTCCGAGTTCGTGAAATGAAACTA
66 TTGAATCCGAGTTCGTGAAATGAAACTA
*
23680 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG-CCTGAGCTCATTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGTCC-GAACTCATTGA
23744 GTTGAATCCGAGTTC
65 GTTGAATCCGAGTTC
23759 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGTCCGAACTCATTGAG
TTGAATCCGAGTTCGTGAAATGAAACTA
Found at i:28069 original size:40 final size:40
Alignment explanation
Indices: 28025--28249 Score: 272
Period size: 40 Copynumber: 5.6 Consensus size: 40
28015 CTTGCGCAAG
* * *
28025 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
28065 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
28105 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
28145 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGTACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * * *
28185 GCCTTCGGATCTTAGTCCGGTTGTAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
28226 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
28250 CATTCGAATA
Statistics
Matches: 155, Mismatches: 27, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.01
40 127 0.82
41 27 0.17
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:37969 original size:19 final size:20
Alignment explanation
Indices: 37932--37969 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
37922 ATAAGGTGGT
37932 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
37952 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
37970 TGTGGTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:44969 original size:89 final size:91
Alignment explanation
Indices: 44823--44987 Score: 253
Period size: 89 Copynumber: 1.8 Consensus size: 91
44813 GCCCCTAAGT
* * * *
44823 GAACTTGGACTCAACTCAAGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAAG
1 GAACTCGGACGCAACTCAAGAGCTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCAAG
44888 AGTTCGGATGCCTAGTTACATCTCAC
66 AGTTCGGATGCCTAGTTACATCTCAC
* * *
44914 GAACTCGGACGCAACTCAAG-GTTCGGACGCTCGCATCCAT-AGTGAACTCGGACTCAACTCACG
1 GAACTCGGACGCAACTCAAGAGCTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCAAG
44977 AGTTCGGATGC
66 AGTTCGGATGC
44988 TCACCACCCT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
89 32 0.48
90 17 0.25
91 18 0.27
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.21
Consensus pattern (91 bp):
GAACTCGGACGCAACTCAAGAGCTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCAAG
AGTTCGGATGCCTAGTTACATCTCAC
Found at i:45001 original size:44 final size:43
Alignment explanation
Indices: 44914--45002 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 43
44904 TACATCTCAC
*
44914 GAACTCGGACGCAACTCAAGGTTCGGACGCTCGCATCCATAGT
1 GAACTCGGACGCAACTCAAGGTTCGGACGCTCCCATCCATAGT
* * * *
44957 GAACTCGGACTCAACTCACGAGTTCGGATGCTCACCA-CCCTAGT
1 GAACTCGGACGCAACTCAAG-GTTCGGACGCTC-CCATCCATAGT
45001 GA
1 GA
45003 CATGTCACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 18 0.46
44 19 0.49
45 2 0.05
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (43 bp):
GAACTCGGACGCAACTCAAGGTTCGGACGCTCCCATCCATAGT
Done.