Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3586
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: 22644
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Found at i:1208 original size:40 final size:40
Alignment explanation
Indices: 1126--1346 Score: 233
Period size: 40 Copynumber: 5.6 Consensus size: 40
1116 GAAATGATGT
* * * *
1126 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATC
* * *
1166 CGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTC
1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATC
*
1206 CGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAAT-
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC
*
1244 CGGGTTAAGTTCCCGAAGGCATTTGTGC-AGTTAC-AAATC
1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATC
* *
1283 CGGGTTAAGTCCCGAAGGGCATTT-TGGCGAGTTACTATA-C
1 CGGGCTAAGTCCCGAA-GGCATTTGT-GCGAGTTACTAAATC
*
1323 CGGGCTATGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
1347 AACGAGGAGC
Statistics
Matches: 154, Mismatches: 16, Indels: 22
0.80 0.08 0.11
Matches are distributed among these distances:
38 20 0.13
39 56 0.36
40 68 0.44
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC
Found at i:1265 original size:79 final size:78
Alignment explanation
Indices: 1126--1346 Score: 211
Period size: 79 Copynumber: 2.8 Consensus size: 78
1116 GAAATGATGT
* * * * * *
1126 CGGGCTAAGTCCCGAA-GGCTTTGT-GCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CGGGCTAAGTCCCGAAGGGCATTGTGGC-GAGTTACTA-AACCGGGCTAAG-TCCCGAAGGCATT
*
1188 TGTGCGAGATACTAATTC
63 TGTGC-AGATAC-AAATC
* *
1206 CGGGCTAAG-CCCGAA-GGCATTG-GTGCGAGTTACTAAATCGGGTTAAGTTCCCGAAGGCATTT
1 CGGGCTAAGTCCCGAAGGGCATTGTG-GCGAGTTACTAAACCGGGCTAAG-TCCCGAAGGCATTT
*
1268 GTGCAGTTACAAATC
64 GTGCAGATACAAATC
* * * *
1283 CGGGTTAAGTCCCGAAGGGCATTTTGGCGAGTTACTATACCGGGCTATGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGGCATTGTGGCGAGTTACTAAACCGGGCTAAGTCCCGAAGGCATTTG
1347 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
77 12 0.10
78 35 0.30
79 59 0.50
80 12 0.10
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (78 bp):
CGGGCTAAGTCCCGAAGGGCATTGTGGCGAGTTACTAAACCGGGCTAAGTCCCGAAGGCATTTGT
GCAGATACAAATC
Found at i:5587 original size:27 final size:27
Alignment explanation
Indices: 5553--5730 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5543 TAAATTGTAC
5553 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
5580 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5606 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
5634 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
5662 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5689 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
5716 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5731 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:5667 original size:82 final size:81
Alignment explanation
Indices: 5554--5709 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
5544 AAATTGTACA
* *
5554 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
5618 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
5635 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
5700 TGCGAGTTGA
65 TGCGAATTGA
5710 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:5721 original size:82 final size:81
Alignment explanation
Indices: 5550--5730 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
5540 GAGTAAATTG
* *
5550 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
5615 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
5631 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
5695 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
5713 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
5731 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:13634 original size:27 final size:27
Alignment explanation
Indices: 13597--13774 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
13587 TAAATTGTAC
13597 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
** *
13624 AGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13650 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
13678 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
13706 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13733 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
13760 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
13775 GACTCAATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 107 0.82
28 23 0.18
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:13710 original size:82 final size:81
Alignment explanation
Indices: 13598--13753 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
13588 AAATTGTACA
*
13598 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
13662 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
13679 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
13744 TGCGAGTTGA
65 TGCGAATTGA
13754 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:13765 original size:82 final size:81
Alignment explanation
Indices: 13594--13774 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
13584 GAGTAAATTG
*
13594 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
13659 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
13675 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
13739 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
13757 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
13775 GACTCAATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:15189 original size:28 final size:28
Alignment explanation
Indices: 15128--15226 Score: 128
Period size: 28 Copynumber: 3.5 Consensus size: 28
15118 TGTTACATTG
* *
15128 GCACTAAGTGTGCGGGTTCAAATTATATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
15157 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
15185 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
15213 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
15227 GGCTTATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
27 1 0.02
28 46 0.72
29 17 0.27
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:22253 original size:28 final size:29
Alignment explanation
Indices: 22188--22286 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
22178 CATGAGATTG
* *
22188 GCACTAAGTGTGCG-GGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGGTTC-GATTATATA
22217 GCACTAAGTGTGCGAGGTT-GATTATATA
1 GCACTAAGTGTGCGAGGTTCGATTATATA
*
22245 GCACTAAGTGTGCGA-GTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGGTTCGATTATAT-A
22273 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
22287 GGCTTATTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
27 4 0.06
28 42 0.66
29 14 0.22
30 4 0.06
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGGTTCGATTATATA
Done.