Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold314
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: 29722
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Found at i:2188 original size:38 final size:39
Alignment explanation
Indices: 2070--2249 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 39
2060 AGCACTCGTT
** *
2070 CAAATGCCTTCGGGACAAAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAG-CCGGAAT-TAGTAACTCGCA
* * *
2110 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTT-AGCCGGAATTAGTAACTCGCA
*
2150 CCAATGCCTTCGGG-CTTAGCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCGGAATTAGTAACTCGCA
* *
2188 CAAATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAG-CCGGAAT-TAGTAAC-TCGCA
2229 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
2250 CGAACATCAT
Statistics
Matches: 121, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
37 2 0.02
38 28 0.23
39 12 0.10
40 65 0.54
41 14 0.12
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCGGAATTAGTAACTCGCA
Found at i:2237 original size:78 final size:79
Alignment explanation
Indices: 2098--2249 Score: 202
Period size: 78 Copynumber: 1.9 Consensus size: 79
2088 AGCCCGGTTA
* * *
2098 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACCAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGATATAGTAACTAGCACCAAAGCCTTCGG
2163 G-CTTAGCCGGAAT
66 GACTTAGCCGGAAT
** * *
2176 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA-CAAAGCCTTC
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCAGATATAGTAAC-TAGCACCAAAGCCTTC
2239 GGGACTTAGCC
64 GGGACTTAGCC
2250 CGAACATCAT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
77 3 0.05
78 50 0.78
79 11 0.17
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (79 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGATATAGTAACTAGCACCAAAGCCTTCGG
GACTTAGCCGGAAT
Found at i:5677 original size:218 final size:219
Alignment explanation
Indices: 5387--5802 Score: 613
Period size: 218 Copynumber: 1.9 Consensus size: 219
5377 AATGCTTTGA
* * * * *
5387 TAATGCATCAATTGTATATTTGCGACTATGACTGTGTACGACGACAAGTCTACTATGTTTGTCAC
1 TAATGCATAAATTGTATATTTGCAACTACGACTGTGTACAACGACAAGTCTACTATGTTTGGCAC
* * *
5452 TTAGTGTGCATTTTGAGATAGCTTCAGG-TATAAA-ATGCACTTAGTGTGTGAATTGGAATAGCT
66 TTAGTGTGCATTTCGAGATAGCTTC-GGCTATAAATA-GCACTTAGTGCGCGAATTGGAATAGCT
** * *
5515 TCGGCTATATGAGGCACTAAGAGTACGATACCGAGATAGCTTTGGTTTAAATGTGATGGCACGAA
129 TCGGCTATATGAGGCACTAAGAGTACGATACCGAGATAGCTTCAGTTTAAATGTAATGACACGAA
5580 GTGTGCGAAATTGTTATAGCTTCGGC
194 GTGTGCGAAATTGTTATAGCTTCGGC
* *
5606 TAATGCATAAATTGT-TATTTGCAATTACGACTGTGTACAACGACAAGTCTACTGTGTTTGGCAC
1 TAATGCATAAATTGTATATTTGCAACTACGACTGTGTACAACGACAAGTCTACTATGTTTGGCAC
* *
5670 TTAGTGTGCGTTTCGAGATAGCTTCGGCTATAAATAGCATTTAGTGCGCGAATTGGAATAGCTTC
66 TTAGTGTGCATTTCGAGATAGCTTCGGCTATAAATAGCACTTAGTGCGCGAATTGGAATAGCTTC
* * * *
5735 GGCTATATGAGGCACTAAGTGTGCGATACGGAGATAGCTTCAGTTTAAATGTAATGACACTAAGT
131 GGCTATATGAGGCACTAAGAGTACGATACCGAGATAGCTTCAGTTTAAATGTAATGACACGAAGT
5800 GTG
196 GTG
5803 TGAGTTCTTG
Statistics
Matches: 175, Mismatches: 20, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
217 2 0.01
218 158 0.90
219 15 0.09
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (219 bp):
TAATGCATAAATTGTATATTTGCAACTACGACTGTGTACAACGACAAGTCTACTATGTTTGGCAC
TTAGTGTGCATTTCGAGATAGCTTCGGCTATAAATAGCACTTAGTGCGCGAATTGGAATAGCTTC
GGCTATATGAGGCACTAAGAGTACGATACCGAGATAGCTTCAGTTTAAATGTAATGACACGAAGT
GTGCGAAATTGTTATAGCTTCGGC
Found at i:13793 original size:28 final size:28
Alignment explanation
Indices: 13751--13815 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
13741 CCCATCACGA
* * *
13751 AACAGTATCAGGTGGGCCTTAGCCCAAT
1 AACAGAATCAAGTGGGCCTAAGCCCAAT
13779 AACAGAATCAAGTGGGCCTAAGCCCAAT
1 AACAGAATCAAGTGGGCCTAAGCCCAAT
13807 -ACAGAATCA
1 AACAGAATCA
13816 GTATCAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (28 bp):
AACAGAATCAAGTGGGCCTAAGCCCAAT
Found at i:14262 original size:27 final size:27
Alignment explanation
Indices: 14232--14296 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
14222 GGGCATAATC
*
14232 GTCATTCTACCA-TACAGGGGTATTACG
1 GTCATTCTA-CATTACAAGGGTATTACG
* *
14259 GTCATTTTACATTACAAGGGTATTTCG
1 GTCATTCTACATTACAAGGGTATTACG
* *
14286 GTGATTTTACA
1 GTCATTCTACA
14297 AACTAGGGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (27 bp):
GTCATTCTACATTACAAGGGTATTACG
Found at i:19844 original size:30 final size:30
Alignment explanation
Indices: 19808--19864 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
19798 CTGAAACTAG
*
19808 TTAAATCGCACACTTAGTGCCAAAGCTACT
1 TTAAATCCCACACTTAGTGCCAAAGCTACT
19838 TTAAATCCCACACTTAGTGCCAAAGCT
1 TTAAATCCCACACTTAGTGCCAAAGCT
19865 TCCGATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (30 bp):
TTAAATCCCACACTTAGTGCCAAAGCTACT
Found at i:23659 original size:27 final size:27
Alignment explanation
Indices: 23629--23806 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
23619 ATATTGAGCC
* *
23629 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
23656 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
23683 CGCACACTTAGTGCTACATAGTCAACCT
1 CGCACACTTAGTGCTACATAATCAA-CT
** ** *
23711 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
23738 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
23765 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
*
23792 CGTACACTTAGTGCT
1 CGCACACTTAGTGCT
23807 GTACAATTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 103 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:23768 original size:82 final size:81
Alignment explanation
Indices: 23650--23805 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 81
23640 TGCTATATAA
* *
23650 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTC-AACCTCGC
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCGAA--TCGC
23714 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * ** *
23732 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGTA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
23796 CACTTAGTGC
65 CACTTAGTGC
23806 TGTACAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
81 15 0.23
82 48 0.74
83 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Done.