Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1000
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: 81131
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:43375 original size:24 final size:24
Alignment explanation
Indices: 43340--43405 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
43330 CGCCACACGA
* * *
43340 TCGTGTGCCAGGTCATGTGGTAGG
1 TCGTGTGACAGGCCATGTGATAGG
*
43364 -CTGTGTGACAGGCCGTGTGATAGG
1 TC-GTGTGACAGGCCATGTGATAGG
43388 TCGTGTGACAGGCCATGT
1 TCGTGTGACAGGCCATGT
43406 AATTCATTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 33 0.94
25 1 0.03
ACGTcount: A:0.15, C:0.18, G:0.39, T:0.27
Consensus pattern (24 bp):
TCGTGTGACAGGCCATGTGATAGG
Found at i:44202 original size:22 final size:22
Alignment explanation
Indices: 44174--44218 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44164 GGTAGGAAAT
*
44174 TGCATCTGTATTTAATATGTTC
1 TGCATCTATATTTAATATGTTC
**
44196 TGCATCTATATTTGTTATGTTC
1 TGCATCTATATTTAATATGTTC
44218 T
1 T
44219 ATAACTGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (22 bp):
TGCATCTATATTTAATATGTTC
Found at i:47222 original size:28 final size:28
Alignment explanation
Indices: 47187--47248 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
47177 CATTTACTTC
* *
47187 TATTTATCAATAATTTATTTTTTTAT-AT
1 TATTTATC-ATAATTTACTATTTTATAAT
* *
47215 TATTTATCCTATTTTACTATTTTATAAT
1 TATTTATCATAATTTACTATTTTATAAT
47243 TATTTA
1 TATTTA
47249 ATTTTAGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (28 bp):
TATTTATCATAATTTACTATTTTATAAT
Found at i:48487 original size:25 final size:25
Alignment explanation
Indices: 48459--48508 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
48449 CAGGTAAGGC
48459 TCCTTCTCCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
* *
48484 TCCTTTTTCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
48509 CTTCTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.04, C:0.36, G:0.04, T:0.56
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCGTTCTTCAT
Found at i:50804 original size:12 final size:12
Alignment explanation
Indices: 50774--50806 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
50764 TTGTAACAGG
50774 AAACCAGCA-GC
1 AAACCAGCATGC
50785 AAACCAGCATGC
1 AAACCAGCATGC
*
50797 AGACCAGCAT
1 AAACCAGCAT
50807 CCTAGCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.06
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:51432 original size:21 final size:21
Alignment explanation
Indices: 51406--51456 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
51396 CGCTGTTTCT
*
51406 AATCTCACTGCTACAGTACCC
1 AATCTCACTGCTACAGTAACC
*
51427 AATCTCA--GCTACAGTAACT
1 AATCTCACTGCTACAGTAACC
51446 AATCTCACTGC
1 AATCTCACTGC
51457 CACCGCTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 17 0.65
21 9 0.35
ACGTcount: A:0.31, C:0.33, G:0.10, T:0.25
Consensus pattern (21 bp):
AATCTCACTGCTACAGTAACC
Found at i:54520 original size:13 final size:13
Alignment explanation
Indices: 54502--54526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54492 ATCTGTTTGG
54502 ATATGAAATTGAT
1 ATATGAAATTGAT
54515 ATATGAAATTGA
1 ATATGAAATTGA
54527 CATTGAATTT
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:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
ATATGAAATTGAT
Found at i:57404 original size:35 final size:35
Alignment explanation
Indices: 57356--57426 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
57346 GTGACCAAAC
*
57356 AACCGAAATTTAAGACTAATTTTGACATTATGCCT
1 AACCGAAAATTAAGACTAATTTTGACATTATGCCT
*
57391 AACCGAAAATTAAGATTAATTTTGACATTATGCCT
1 AACCGAAAATTAAGACTAATTTTGACATTATGCCT
57426 A
1 A
57427 GAAACTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (35 bp):
AACCGAAAATTAAGACTAATTTTGACATTATGCCT
Found at i:58141 original size:2 final size:2
Alignment explanation
Indices: 58134--58165 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
58124 AGAAGTAAAT
58134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58166 ACCACTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61457 original size:24 final size:24
Alignment explanation
Indices: 61430--61477 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
61420 TCCTCGAGGG
61430 GGCAATTTGTTGCCACGTCAGCAA
1 GGCAATTTGTTGCCACGTCAGCAA
61454 GGCAATTTGTTGCCACGTCAGCAA
1 GGCAATTTGTTGCCACGTCAGCAA
61478 AGCACGCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (24 bp):
GGCAATTTGTTGCCACGTCAGCAA
Found at i:62621 original size:26 final size:26
Alignment explanation
Indices: 62550--62622 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 26
62540 TTTTTTTATA
62550 TTTTAAATAAAAACATAAAAATTTATATT
1 TTTTAAAT--AAA-ATAAAAATTTATATT
* *
62579 TTTT-AA-AAATTCAAAAAATTATAATT
1 TTTTAAATAAAAT-AAAAATTTAT-ATT
62605 TTTTAAATAAAATAAAAA
1 TTTTAAATAAAATAAAAA
62623 ACATGAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
24 1 0.03
25 12 0.32
26 7 0.19
27 7 0.19
28 6 0.16
29 4 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTTAAATAAAATAAAAATTTATATT
Found at i:62641 original size:18 final size:17
Alignment explanation
Indices: 62618--62658 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
62608 TAAATAAAAT
*
62618 AAAAAACATGAAAAATTA
1 AAAAAAC-TCAAAAATTA
*
62636 AAAAAACTCTAAAATTA
1 AAAAAACTCAAAAATTA
62653 AAAAAA
1 AAAAAA
62659 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAAAACTCAAAAATTA
Found at i:62667 original size:18 final size:18
Alignment explanation
Indices: 62618--62669 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
62608 TAAATAAAAT
*
62618 AAAAAACATGAAAAATTAA
1 AAAAAAAAT-AAAAATTAA
***
62637 AAAAACTCT-AAAATTAA
1 AAAAAAAATAAAAATTAA
62654 AAAAAAAATAAAAATT
1 AAAAAAAATAAAAATT
62670 TCCAAAAACT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 14 0.54
18 6 0.23
19 6 0.23
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAAAAATAAAAATTAA
Found at i:63148 original size:24 final size:23
Alignment explanation
Indices: 63113--63173 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
63103 CTTTTTTAAA
*
63113 TAAAACAT-AAAAATTTATATTT
1 TAAAAAATAAAAAATTTATATTT
* *
63135 TAAAAAAATCAAAATTTTATATTT
1 T-AAAAAATAAAAAATTTATATTT
*
63159 TTAAAAATAAAAAAT
1 TAAAAAATAAAAAAT
63174 ACATAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 17 0.53
24 14 0.44
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAAAATAAAAAATTTATATTT
Found at i:63166 original size:23 final size:23
Alignment explanation
Indices: 63112--63171 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
63102 TCTTTTTTAA
63112 ATAAAACATAAAAATTTATATTTT
1 ATAAAA-ATAAAAATTTATATTTT
* *
63136 AAAAAAATCAAAATTTTATATTTT
1 ATAAAAAT-AAAAATTTATATTTT
63160 -TAAAAATAAAAA
1 ATAAAAATAAAAA
63172 ATACATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 4 0.13
23 8 0.26
24 19 0.61
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAAAAATAAAAATTTATATTTT
Found at i:63186 original size:23 final size:22
Alignment explanation
Indices: 63160--63244 Score: 91
Period size: 24 Copynumber: 3.7 Consensus size: 22
63150 TTTATATTTT
*
63160 TAAAAATAAAAAATACATAAAAA
1 TAAAAATAAAAAA-ACTTAAAAA
*
63183 TAAAAATAAAAAAAATCTTTAAAAT
1 TAAAAAT-AAAAAAA-C-TTAAAAA
*
63208 TCAAAATAAAAAAACTTAAAAA
1 TAAAAATAAAAAAACTTAAAAA
*
63230 TATAAA-AAAAAAACT
1 TAAAAATAAAAAAACT
63245 CCAAAGTTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.17
22 10 0.19
23 9 0.17
24 14 0.26
25 11 0.21
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAAAATAAAAAAACTTAAAAA
Found at i:63720 original size:21 final size:20
Alignment explanation
Indices: 63694--63733 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
63684 TTTCTAAAAA
63694 TAAAAAATATATGAAAAATTT
1 TAAAAAATATAT-AAAAATTT
63715 TAAAAAATATATAAAAATT
1 TAAAAAATATATAAAAATT
63734 CAATATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAAAAATATATAAAAATTT
Found at i:72771 original size:31 final size:31
Alignment explanation
Indices: 72688--72755 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
72678 TTGAACGGTT
72688 GGTGACCAAAAATGAAAATTT--TGAATAGTTG
1 GGTGACCAAAAATG-AAATTTACT-AATAGTTG
72719 GGTGACCAAAAATGAAATTTACTAATAGTTG
1 GGTGACCAAAAATGAAATTTACTAATAGTTG
72750 GGTGAC
1 GGTGAC
72756 TACCAGTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
30 6 0.17
31 28 0.80
32 1 0.03
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.28
Consensus pattern (31 bp):
GGTGACCAAAAATGAAATTTACTAATAGTTG
Done.