Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2996
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: 28278
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2748 original size:27 final size:27
Alignment explanation
Indices: 2707--2807 Score: 114
Period size: 27 Copynumber: 3.7 Consensus size: 27
2697 GAGGAAGCGT
*
2707 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
2734 TCTGGTGGCTCTGCCACATATATCT-A
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
2760 TTCTGGTGGCTTCTGCCACGACTATCTGTA
1 -TCTGGTGGC-TCTGCCACAAATATCTG-A
* *
2790 TCTGGTGACTCTGTCACA
1 TCTGGTGGCTCTGCCACA
2808 TTACTGTTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
26 1 0.02
27 32 0.52
28 20 0.32
29 8 0.13
30 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:2818 original size:54 final size:54
Alignment explanation
Indices: 2705--2819 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
2695 TGGAGGAAGC
*
2705 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * * *
2759 ATTCTGGTGGCTTCTGCCACGACTATCTGTATCTGGTGACTCTGTCACAT-TA-CT
1 GTTCTGGTGGC-TATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
2813 GTTCTGG
1 GTTCTGG
2820 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 18 0.35
55 16 0.31
56 18 0.35
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:8395 original size:25 final size:25
Alignment explanation
Indices: 8367--8421 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
8357 GGTTTAAAGA
8367 ATTCGCACACACAGTGCCTCA-ATTC
1 ATTCGCACACACAGTGCCT-ATATTC
*
8392 ATTCGCACACATAGTGCCTATATTC
1 ATTCGCACACACAGTGCCTATATTC
8417 ATTCG
1 ATTCG
8422 TTATTACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (25 bp):
ATTCGCACACACAGTGCCTATATTC
Found at i:8639 original size:40 final size:40
Alignment explanation
Indices: 8585--8785 Score: 312
Period size: 40 Copynumber: 5.0 Consensus size: 40
8575 GATTACACAT
* * *
8585 CACCGGCACGAATGCCCTTCAGGACTTAGCCCGGATGTAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATGTAA
* * *
8625 CATCAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATGTAA
* *
8665 CACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATGTAA
* *
8705 CACCAGCACGATTGCTCTTCGGGACTTAGCCCAGATGTAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATGTAA
8745 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATGTAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATGTAA
8785 C
1 C
8786 TCTCAATTCT
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 146 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATGTAA
Found at i:24049 original size:203 final size:202
Alignment explanation
Indices: 23654--24432 Score: 1248
Period size: 203 Copynumber: 3.8 Consensus size: 202
23644 TAGGCCGCAG
* *
23654 CATAACAGATCTGGCCTTCAGATGTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGT
1 CATAGCAGATCTCGCCTTCAGATGTT-TACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGT
*
23719 TTACAA-GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCTA
65 TTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGA-GAAGCAAATCTA
23783 AGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGA
129 AGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGA
23848 GAGCAGACA
194 GAGCAGACA
23857 CATAGCAGATCTCGCCTTCAGATGATTTCACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG
1 CATAGCAGATCTCGCCTTCAGATG-TTT-ACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG
*
23922 TTTACAAGGAACAAATTGAAGACATAGCTGATTTGGCTTTCACGTGATTACGAGAAGCAAATCTA
64 TTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGAGAAGCAAATCTA
23987 AGATGATTTGTCGTCTCTGTAT-GTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGA
129 AGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGA
24051 GAGCAGACA
194 GAGCAGACA
24060 CATAGCAGATCTCGCCTTCAGATGATTTCACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG
1 CATAGCAGATCTCGCCTTCAGATG-TTT-ACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG
*
24125 TTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGAAAAGCAAATCTA
64 TTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGAGAAGCAAATCTA
24190 AGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGA
129 AGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGA
*
24255 GAGCAGATA
194 GAGCAGACA
* * *
24264 CATAGCAGATCTCACCTTC-GATGTTTATGCTGAAG-GGATCCAAGATGGTTTGGCATCCTTATG
1 CATAGCAGATCTCGCCTTCAGATGTTTA--CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG
* * * * *
24327 CTTACAAGGAGCAAATCGAA-TCATAGTTGATTTGGCTTTCACGTGCTTACGTTA-AAGCAAATC
64 TTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACG--AGAAGCAAATC
* * * * *
24390 TAAGATGATTTGGCAT-TCTGTATTGTCAGGGAACAAATCGAAG
127 TAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAG
24433 AAATAGATTT
Statistics
Matches: 548, Mismatches: 20, Indels: 18
0.94 0.03 0.03
Matches are distributed among these distances:
201 53 0.10
202 70 0.13
203 235 0.43
204 147 0.27
205 43 0.08
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (202 bp):
CATAGCAGATCTCGCCTTCAGATGTTTACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGTT
TACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGAGAAGCAAATCTAAG
ATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGA
GCAGACA
Found at i:24582 original size:44 final size:44
Alignment explanation
Indices: 24466--25047 Score: 423
Period size: 44 Copynumber: 13.4 Consensus size: 44
24456 TAGACGGGGG
* * * * * * * *
24466 CAGATCAAAGATAGCAGATATCGCCTTCCTGAG-TTACAGTGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
**
24509 GCAGATCGAAGATTTCAGA--TGGCATCCCTGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* *
24552 CA-AGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGAAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * * *
24596 CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTAGAGCGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* **
24640 GAAGATCGAAGATTTC-GCA--TGGCATCCCTGTGCTTATAGGG--
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
*
24681 -A-A-C-AAG-TAGCAGATTTGGCATCCTTGTGCTTATAGGGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * * * **
24720 CAGATCGAAGATAGCATATCTGACATTCCTGTGCTTACAGTAAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* ** *
24764 GCAGATCGACGATTTCAGCA--TGGCATCCTTGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* * *
24808 CA-AGTTGAAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
1 CAGA-TCG-AAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * * * * **
24853 CAGATCAAAGATAGCAGATCTGACATTCCTATGCTTACAGTAAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * ** *
24897 GTAGATGGAAGATTTCAGCA--TGGCATCCCTATGCTTATAGGGAA
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* * * *
24941 CA-AGTTGAAAAACAGCAGATTTGGCATCCCTATGCTTATAGGGAA
1 CAGA-TCG-AAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* *
24986 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGTTTATATGGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
25030 CAGATCGAAGA-AGCAGAT
1 CAGATCGAAGATAGCAGAT
25048 CGAAGAACTC
Statistics
Matches: 419, Mismatches: 88, Indels: 63
0.74 0.15 0.11
Matches are distributed among these distances:
35 3 0.01
36 4 0.01
37 22 0.05
38 1 0.00
39 1 0.00
40 1 0.00
41 2 0.00
42 25 0.06
43 45 0.11
44 218 0.52
45 93 0.22
46 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (44 bp):
CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
Found at i:24888 original size:133 final size:132
Alignment explanation
Indices: 24466--25004 Score: 760
Period size: 133 Copynumber: 4.1 Consensus size: 132
24456 TAGACGGGGG
* * * *
24466 CAGATCAAAGATAGCAGATATCG-CCTTCCTGA-G-TTACAGTGAAGCAGATCGAAGATTTCAG-
1 CAGATCGAAGATAGCAGATCT-GACATTCCT-ATGCTTACAGTAAAGCAGATCGAAGATTTCAGC
* *
24527 ATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTATAG
64 ATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAG
*
24592 GAAA
129 GGAA
* * ** *
24596 CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTAGAGCGAAGAAGATCGAAGATTTC-GCAT
1 CAGATCGAAGATAGCAGATCTGACATTCCTATGCTTACAGTAAAGCAGATCGAAGATTTCAGCAT
*
24660 GGCATCCCTGTGCTTATAGGGAACAAG-T------AGCAGATTTGGCATCCTTGTGCTTATAGGG
66 GGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGG
24718 AA
131 AA
* * *
24720 CAGATCGAAGATAGCATATCTGACATTCCTGTGCTTACAGTAAAGCAGATCGACGATTTCAGCAT
1 CAGATCGAAGATAGCAGATCTGACATTCCTATGCTTACAGTAAAGCAGATCGAAGATTTCAGCAT
*
24785 GGCATCCTTGTGCTTATAGGGAACAAGTTGAAAAACAGCAGATTTGGCATCCCTGTGCTTATAGG
66 GGCATCCCTGTGCTTATAGGGAACAAGTTG-AAAACAGCAGATTTGGCATCCCTGTGCTTATAGG
24850 GAA
130 GAA
* * *
24853 CAGATCAAAGATAGCAGATCTGACATTCCTATGCTTACAGTAAAGTAGATGGAAGATTTCAGCAT
1 CAGATCGAAGATAGCAGATCTGACATTCCTATGCTTACAGTAAAGCAGATCGAAGATTTCAGCAT
* *
24918 GGCATCCCTATGCTTATAGGGAACAAGTTGAAAAACAGCAGATTTGGCATCCCTATGCTTATAGG
66 GGCATCCCTGTGCTTATAGGGAACAAGTTG-AAAACAGCAGATTTGGCATCCCTGTGCTTATAGG
24983 GAA
130 GAA
24986 CAGATCGAAGATAGCAGAT
1 CAGATCGAAGATAGCAGAT
25005 TTGGCATCCC
Statistics
Matches: 369, Mismatches: 27, Indels: 23
0.88 0.06 0.05
Matches are distributed among these distances:
124 84 0.23
125 30 0.08
126 1 0.00
129 1 0.00
130 28 0.08
131 52 0.14
133 173 0.47
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (132 bp):
CAGATCGAAGATAGCAGATCTGACATTCCTATGCTTACAGTAAAGCAGATCGAAGATTTCAGCAT
GGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGG
AA
Found at i:25048 original size:13 final size:13
Alignment explanation
Indices: 25030--25054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25020 TTATATGGAA
25030 CAGATCGAAGAAG
1 CAGATCGAAGAAG
25043 CAGATCGAAGAA
1 CAGATCGAAGAA
25055 CTCAAAACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.28, T:0.08
Consensus pattern (13 bp):
CAGATCGAAGAAG
Found at i:25535 original size:22 final size:23
Alignment explanation
Indices: 25503--25559 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
25493 GTAAAGGGGG
*
25503 ATCGATGGTATTTTGAGGA-AGA
1 ATCGATTGTATTTTGAGGAGAGA
*
25525 ATCGATTGTATTTTGGGGAGAGA
1 ATCGATTGTATTTTGAGGAGAGA
**
25548 AGAGATTGTATT
1 ATCGATTGTATT
25560 AGAGGGGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.35
Consensus pattern (23 bp):
ATCGATTGTATTTTGAGGAGAGA
Found at i:25554 original size:23 final size:22
Alignment explanation
Indices: 25510--25559 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
25500 GGGATCGATG
**
25510 GTATTTTGAGGAAGAATCGATT
1 GTATTTTGAGGAAGAAGAGATT
*
25532 GTATTTTGGGGAGAGAAGAGATT
1 GTATTTTGAGGA-AGAAGAGATT
25555 GTATT
1 GTATT
25560 AGAGGGGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (22 bp):
GTATTTTGAGGAAGAAGAGATT
Found at i:26197 original size:40 final size:39
Alignment explanation
Indices: 26153--26269 Score: 180
Period size: 39 Copynumber: 3.0 Consensus size: 39
26143 AAAATAAAGT
26153 ATGGTTTTAATTAATAATAAAAACAAAATAGTATGGGGGA
1 ATGGTTTTAATTAATAAT-AAAACAAAATAGTATGGGGGA
*
26193 ATGGTTTTAATTAATAATAAAACAAAATAATATGGGGGA
1 ATGGTTTTAATTAATAATAAAACAAAATAGTATGGGGGA
* * * *
26232 GTAGTTTTAATTAATAATAAAACAAAGTAGCATGGGGG
1 ATGGTTTTAATTAATAATAAAACAAAATAGTATGGGGG
26270 GAGTGGAATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 53 0.75
40 18 0.25
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.30
Consensus pattern (39 bp):
ATGGTTTTAATTAATAATAAAACAAAATAGTATGGGGGA
Done.