Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_421
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: 76315
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:5799 original size:45 final size:46
Alignment explanation
Indices: 5714--5801 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 46
5704 TGAACCATGT
**
5714 ATCAGGAAGCTTATTCGGACTAAACAGGAAACTCATAAGAGTTTTA
1 ATCAGGAAGCTTATTAAGACTAAACAGGAAACTCATAAGAGTTTTA
* *
5760 ATCAGGAAGCTTATTAAG-CTTAACAGGTAACTC-TGAAGAGTT
1 ATCAGGAAGCTTATTAAGACTAAACAGGAAACTCAT-AAGAGTT
5802 ATTATTAGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 1 0.03
45 20 0.54
46 16 0.43
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (46 bp):
ATCAGGAAGCTTATTAAGACTAAACAGGAAACTCATAAGAGTTTTA
Found at i:10983 original size:40 final size:40
Alignment explanation
Indices: 10742--10969 Score: 361
Period size: 40 Copynumber: 5.7 Consensus size: 40
10732 TATTCGGATG
* *
10742 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
10782 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
10821 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
**
10861 ATAACCGGGCTAAGTCCCGAAGGCATTTGTATGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
10901 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
10941 ATAACCGAGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
10970 GGAAAGTAGC
Statistics
Matches: 174, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
39 35 0.20
40 139 0.80
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:18774 original size:40 final size:40
Alignment explanation
Indices: 18665--18892 Score: 370
Period size: 40 Copynumber: 5.7 Consensus size: 40
18655 TATTCGGATG
* *
18665 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTAACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
**
18705 A-ATTTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
18744 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
18784 ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
18824 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
18864 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
18893 GGAAGTAGCT
Statistics
Matches: 175, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
39 35 0.20
40 140 0.80
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:22643 original size:40 final size:40
Alignment explanation
Indices: 22551--22773 Score: 220
Period size: 40 Copynumber: 5.6 Consensus size: 40
22541 GCTCCTCGTT
* * * *
22551 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
22591 C-AATGCCTTCGGGAGTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
22630 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
22670 CAAAGGCCTTCGGGGCTTAAGCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
22710 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
22751 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAACCCG
22774 TATAGCATTC
Statistics
Matches: 154, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
39 38 0.25
40 101 0.66
41 15 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:22784 original size:41 final size:41
Alignment explanation
Indices: 22707--22784 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
22697 TTTGTATCTC
* *
22707 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGATACATTCACTTA
*
22748 GCACAAA-GCCTTCGGGA-CTTAGCCCGTATAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGATA-CATTCA
22785 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGATACATTCACTTA
Found at i:30453 original size:39 final size:40
Alignment explanation
Indices: 30408--30579 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
30398 GCTCCTCGTT
* * * *
30408 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
30448 C-AATGCCTTCGGGACTTAACTCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
30487 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
30527 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GCATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
30567 CAAATGCCTTCGG
1 CAAATGCCTTCGG
30580 ATCTTAGTCC
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 33 0.28
40 79 0.68
41 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:35621 original size:30 final size:30
Alignment explanation
Indices: 35587--35647 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
35577 TTCCCGAGCC
35587 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * *
35617 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
35647 T
1 T
35648 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Found at i:44101 original size:15 final size:15
Alignment explanation
Indices: 44081--44110 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44071 ACATGGTATC
44081 CTATCTCGGATTTCT
1 CTATCTCGGATTTCT
*
44096 CTATCTTGGATTTCT
1 CTATCTCGGATTTCT
44111 TTACTTGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (15 bp):
CTATCTCGGATTTCT
Found at i:47194 original size:28 final size:27
Alignment explanation
Indices: 47131--47282 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
47121 ATATTAAGTC
* *
47131 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
47158 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
47186 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
47213 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
47241 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
47268 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
47283 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:47215 original size:55 final size:55
Alignment explanation
Indices: 47131--47307 Score: 264
Period size: 55 Copynumber: 3.2 Consensus size: 55
47121 ATATTAAGTC
* * *
47131 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
47186 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * *
47241 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAA-TCAAACT
47297 CGCACACTTAG
1 CGCACACTTAG
47308 AGCCAATCTC
Statistics
Matches: 111, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
55 95 0.86
56 16 0.14
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:59091 original size:20 final size:20
Alignment explanation
Indices: 59054--59093 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
59044 ACTAAATTTA
*
59054 ATAAATTCTTAAACTTGAGT
1 ATAAATTCTGAAACTTGAGT
* *
59074 ATAAATTGTGAAATTTGAGT
1 ATAAATTCTGAAACTTGAGT
59094 TCTAGAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (20 bp):
ATAAATTCTGAAACTTGAGT
Found at i:63815 original size:30 final size:29
Alignment explanation
Indices: 63781--63875 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 29
63771 TAGTAAAGGT
63781 AAAATTGCACTTTG-TCATCCAAAAATAATA
1 AAAATTG-A-TTTGATCATCCAAAAATAATA
* *
63811 AAAATTTGATTTGATCATTCAAAAATTATA
1 AAAA-TTGATTTGATCATCCAAAAATAATA
** *
63841 AAAATTTGATTTGATCATTTAAAAATTATA
1 AAAA-TTGATTTGATCATCCAAAAATAATA
63871 AAAAT
1 AAAAT
63876 ATAGACTATT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
29 5 0.08
30 52 0.87
31 3 0.05
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.37
Consensus pattern (29 bp):
AAAATTGATTTGATCATCCAAAAATAATA
Found at i:69034 original size:80 final size:79
Alignment explanation
Indices: 68897--69117 Score: 228
Period size: 80 Copynumber: 2.8 Consensus size: 79
68887 TTGAATGCTG
* * * ** * * * * *
68897 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGCGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
*
68961 TGTGCGAGATACTAAA
64 CGTGCGAGATACTAAA
* * *
68977 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* **
69042 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * *
69057 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCA
69118 CTTGAACGAG
Statistics
Matches: 119, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
79 33 0.28
80 82 0.69
81 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAA
Found at i:69101 original size:39 final size:40
Alignment explanation
Indices: 68950--69117 Score: 230
Period size: 40 Copynumber: 4.2 Consensus size: 40
68940 GGACTAAGAT
* * *
68950 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
*
68990 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
** *
69030 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * *
69070 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
69109 CCGAAGGCA
1 CCGAAGGCA
69118 CTTGAACGAG
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
39 32 0.27
40 85 0.73
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:69139 original size:79 final size:80
Alignment explanation
Indices: 68972--69144 Score: 208
Period size: 79 Copynumber: 2.2 Consensus size: 80
68962 GTGCGAGATA
* * *
68972 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
69037 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
69052 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
69116 CACTT-GAACGAGGAG
66 CA-TTCGAACGAGGAG
*
69131 CTATATCC-GGTTAA
1 CTAAATCCGGGTTAA
69145 ATTCCGGAGG
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
78 5 0.06
79 44 0.56
80 29 0.37
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Done.