Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5071.1
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: 34206
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:950 original size:21 final size:21
Alignment explanation
Indices: 926--969 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
916 TTTAAATCAC
926 TTTTCTCACTTT-TTTCTCTTTT
1 TTTTC-CACTTTCTTT-TCTTTT
948 TTTTCCACTTTCTTTTCTTTT
1 TTTTCCACTTTCTTTTCTTTT
969 T
1 T
970 CTTTTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTCCACTTTCTTTTCTTTT
Found at i:984 original size:21 final size:22
Alignment explanation
Indices: 925--988 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
915 TTTTAAATCA
*
925 CTTTTCTCACTTTTTTCTCTTTT
1 CTTTT-TCATTTTTTTCTCTTTT
*
948 -TTTTCCACTTTCTTTTCT-TTTT
1 CTTTTTCA-TTT-TTTTCTCTTTT
970 CTTTTTCATTTTTTT-TCTT
1 CTTTTTCATTTTTTTCTCTT
989 GCTTTTTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
20 1 0.03
21 8 0.24
22 13 0.38
23 12 0.35
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (22 bp):
CTTTTTCATTTTTTTCTCTTTT
Found at i:12432 original size:15 final size:15
Alignment explanation
Indices: 12412--12466 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
12402 ACTCTCCTCA
*
12412 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
12427 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
12442 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
12456 TTCTTTT-TCTC
1 TTCTTTTCTCTC
12467 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:15595 original size:30 final size:30
Alignment explanation
Indices: 15561--15657 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
15551 TAAACTAAAA
*
15561 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
15591 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
15621 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
15650 ATGAGCTA
1 -TGAGCTA
15658 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:18096 original size:18 final size:18
Alignment explanation
Indices: 18068--18116 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
18058 AAGAGAATGA
*
18068 GAAAAAGGAAAGCGAAATT
1 GAAAAA-GAAAGCGAAAGT
* *
18087 GAAAAAGAAAGTGAGAGT
1 GAAAAAGAAAGCGAAAGT
18105 GAAGAAAGAAAG
1 GAA-AAAGAAAG
18117 AAAAATGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.59, C:0.02, G:0.31, T:0.08
Consensus pattern (18 bp):
GAAAAAGAAAGCGAAAGT
Found at i:24025 original size:11 final size:12
Alignment explanation
Indices: 23993--24025 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
23983 GAGCTACAGC
23993 AAACTTAATTAT
1 AAACTTAATTAT
*
24005 AAACTGAATTA-
1 AAACTTAATTAT
24016 AAACTTAATT
1 AAACTTAATT
24026 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:24093 original size:20 final size:21
Alignment explanation
Indices: 24057--24095 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
24047 AGCTGAATCA
*
24057 AGCTGAATTCTAGCTCAAACG
1 AGCTGAATTCGAGCTCAAACG
24078 AGCTGAA-TCGAGCTCAAA
1 AGCTGAATTCGAGCTCAAA
24096 TGAACTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
AGCTGAATTCGAGCTCAAACG
Found at i:27376 original size:52 final size:52
Alignment explanation
Indices: 26394--27349 Score: 1858
Period size: 52 Copynumber: 18.4 Consensus size: 52
26384 AAAATTACTA
* *
26394 AAATACCCCTATAGGGTAAATTATCGAAATACCCTTATAGGGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
* *
26446 AAATACCCCTATAGGGTAAATTATCGAAATACCCTTATAGGGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
*
26498 AAATACCCCTATAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
26550 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
26602 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
26654 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
26706 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
26758 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
26810 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
26862 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
26914 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
26966 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
27018 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
27070 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
27122 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
27174 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
27226 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
27278 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
*
27330 AAATACCCCTATAGGGTAAA
1 AAATACCCCTACAGGGTAAA
27350 ATGACTGTTT
Statistics
Matches: 901, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 901 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (52 bp):
AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
Found at i:30238 original size:29 final size:29
Alignment explanation
Indices: 30206--30262 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
30196 TGCGCGGGAT
30206 TAAATTGTACAGCACTAAGTGTACGATTC
1 TAAATTGTACAGCACTAAGTGTACGATTC
*
30235 TAAATTGTACAGCACTAAGTGTGCGATT
1 TAAATTGTACAGCACTAAGTGTACGATT
30263 TGACTATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (29 bp):
TAAATTGTACAGCACTAAGTGTACGATTC
Found at i:30284 original size:27 final size:27
Alignment explanation
Indices: 30245--30422 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
30235 TAAATTGTAC
30245 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
30272 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
30298 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* **
30326 GGCACTAAGTGTGCGAGTCCGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
30354 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
30381 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
30408 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
30423 GGCTCAATAT
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 102 0.83
28 21 0.17
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:30361 original size:82 final size:81
Alignment explanation
Indices: 30246--30401 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
30236 AAATTGTACA
** * *
30246 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGATCCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
30310 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
30327 GCACTAAGTGTGCGAGTCCGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGA-TCCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
30392 TGCGAGTTGA
65 TGCGAATTGA
30402 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 16 0.25
82 49 0.75
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGATCCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:30413 original size:82 final size:81
Alignment explanation
Indices: 30242--30422 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
30232 TTCTAAATTG
** * *
30242 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
30307 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
30323 TGCGGCACTAAGTGTGCGAGTCCGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TCCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
30387 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
30405 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
30423 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:31045 original size:32 final size:32
Alignment explanation
Indices: 31009--31069 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
30999 ATCATTTTGG
31009 CATGTATAAGCTAGTACGTTGTGTTTGAATTA
1 CATGTATAAGCTAGTACGTTGTGTTTGAATTA
*
31041 CATGTATAAGCTATTACGTTGTGTTTGAA
1 CATGTATAAGCTAGTACGTTGTGTTTGAA
31070 CTTTGGCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (32 bp):
CATGTATAAGCTAGTACGTTGTGTTTGAATTA
Found at i:32586 original size:30 final size:30
Alignment explanation
Indices: 32539--32632 Score: 172
Period size: 30 Copynumber: 3.2 Consensus size: 30
32529 CAAGTAGCCG
32539 AAGCTAG-TTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
*
32568 AAGCTAGTTTAGATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
32598 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
32628 AAGCT
1 AAGCT
32633 TCCGATTCAT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
29 7 0.11
30 55 0.89
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (30 bp):
AAGCTAGTTTAAATCGCACACTTAGTGCCA
Done.