Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2914
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: 41067
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:431 original size:21 final size:22
Alignment explanation
Indices: 386--451 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 22
376 AAAGATATAT
386 AGATATATAAGATATAATATTAATA
1 AGATATA-AAGATAT-ATA-TAATA
411 AGATATAAAGATATATA-AAT-
1 AGATATAAAGATATATATAATA
431 AG-TATAATA-ATATATATAATA
1 AGATATAA-AGATATATATAATA
452 GGACAAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
19 12 0.32
20 6 0.16
21 3 0.08
23 3 0.08
24 7 0.18
25 7 0.18
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (22 bp):
AGATATAAAGATATATATAATA
Found at i:2137 original size:87 final size:87
Alignment explanation
Indices: 2010--2482 Score: 729
Period size: 87 Copynumber: 5.5 Consensus size: 87
2000 CTTCCACCTA
* *
2010 CTCCACTACAACCGATGAAGGCAAGGCCTT-GTTTTCGATCTGTTTCGCTGTTAACGCAGGAAGG
1 CTCCACTACAACCGATGGAGGCAAGG-CTTCGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
* *
2074 CCAGATCTGCTATCTTTAACCAA
65 CAAGATCTGCTATCTTTAACCAG
* * * * *
2097 CTCCGCTGCAACCGATGGAGGTAAGGCTTCGTTTTTGATCTGCTTCACTGTTAACGCAGGAAGGC
1 CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
2162 AAGATCTGCTATCTTTAACCAG
66 AAGATCTGCTATCTTTAACCAG
* *
2184 CTCCACTACAACCGATGGAGGCAAGGCTTCATTTTC-ATCTGCTTCGCTGTTAA--TAGGAAGGC
1 CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
2246 AAGATCTGCTATCTTTAACCAG
66 AAGATCTGCTATCTTTAACCAG
* * * *
2268 CTCCGCTGCAACCGATGGAGGCAAGGCTTCGTTTCCGATCTGCTTCACTGTTAACGCAGGAAGGC
1 CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
2333 AAGATCTGCTATCTTTAACCAG
66 AAGATCTGCTATCTTTAACCAG
* *
2355 CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAATGCAAGAAGGC
1 CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
* * *
2420 AAAATTTACTATCTTTAACCAG
66 AAGATCTGCTATCTTTAACCAG
2442 CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCT
1 CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCT
2483 TCACTGATCT
Statistics
Matches: 351, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
84 62 0.18
85 16 0.05
86 19 0.05
87 254 0.72
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (87 bp):
CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
AAGATCTGCTATCTTTAACCAG
Found at i:2487 original size:171 final size:173
Alignment explanation
Indices: 2010--2488 Score: 754
Period size: 171 Copynumber: 2.8 Consensus size: 173
2000 CTTCCACCTA
* * *
2010 CTCCACTACAACCGATGAAGGCAAGGCCTT-GTTTTCGATCTGTTTCGCTGTTAACGCAGGAAGG
1 CTCCACTACAACCGATGGAGGCAAGG-CTTCGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGG
* * * *
2074 CCAGATCTGCTATCTTTAACCAACTCCGCTGCAACCGATGGAGGTAAGGCTTCGTTTTTGATCTG
65 CAAGATCTGCTATCTTTAACCAGCTCCGCTGCAACCGATGGAGGCAAGGCTTCGTTTTCGA-CTG
2139 CTTCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAG
129 CTTCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAG
*
2184 CTCCACTACAACCGATGGAGGCAAGGCTTCATTTTC-ATCTGCTTCGCTGTTAAT--AGGAAGGC
1 CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGC
*
2246 AAGATCTGCTATCTTTAACCAGCTCCGCTGCAACCGATGGAGGCAAGGCTTCGTTTCCGATCTGC
66 AAGATCTGCTATCTTTAACCAGCTCCGCTGCAACCGATGGAGGCAAGGCTTCGTTTTCGA-CTGC
2311 TTCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAG
130 TTCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAG
*
2355 CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAATGCAAGAAGGC
1 CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGC
* * * * *
2420 AAAATTTACTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGA-T-CT
66 AAGATCTGCTATCTTTAACCAGCTCCGCTGCAACCGATGGAGGCAAGGCTTCGTTTTCGACTGCT
2483 TCACTG
131 TCACTG
2489 ATCTGTTCTC
Statistics
Matches: 284, Mismatches: 17, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
171 155 0.55
172 19 0.07
173 19 0.07
174 91 0.32
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (173 bp):
CTCCACTACAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGC
AAGATCTGCTATCTTTAACCAGCTCCGCTGCAACCGATGGAGGCAAGGCTTCGTTTTCGACTGCT
TCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAG
Found at i:3558 original size:21 final size:21
Alignment explanation
Indices: 3532--3578 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3522 GGTATAGCAG
3532 GATCACCACATGCCCCAATCT
1 GATCACCACATGCCCCAATCT
** *
3553 GATCACTTCATGCCCCATTCT
1 GATCACCACATGCCCCAATCT
3574 GATCA
1 GATCA
3579 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.38, G:0.11, T:0.26
Consensus pattern (21 bp):
GATCACCACATGCCCCAATCT
Found at i:3809 original size:9 final size:8
Alignment explanation
Indices: 3773--3808 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
3763 CTATTTTGAC
3773 TTTGATTTT
1 TTTGA-TTT
3782 TTTGATTT
1 TTTGATTT
3790 TTTGATTT
1 TTTGATTT
3798 TTTGATTT
1 TTTGATTT
3806 TTT
1 TTT
3809 TTGAATTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 22 0.81
9 5 0.19
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (8 bp):
TTTGATTT
Found at i:10141 original size:30 final size:29
Alignment explanation
Indices: 10107--10178 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
10097 ATATATTACA
10107 TAAAAATAAAAGATATAAGTATGTATATCG
1 TAAAAATAAAAGATATAAGTATGTATAT-G
* *
10137 T-AAAATAAAACAATGTAAGTATGTATATG
1 TAAAAATAAAA-GATATAAGTATGTATATG
* *
10166 TATATATAAAAGA
1 TAAAAATAAAAGA
10179 AAATAGACGT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.31
Consensus pattern (29 bp):
TAAAAATAAAAGATATAAGTATGTATATG
Found at i:10307 original size:18 final size:18
Alignment explanation
Indices: 10286--10345 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
10276 AAAATATGTT
*
10286 TATAAAAAGATATATAGA
1 TATAAAAAGATATAAAGA
*
10304 TATATAATAAGATATAAATA
1 TATA-AA-AAGATATAAAGA
*
10324 TATAATAAGATATAAAGA
1 TATAAAAAGATATAAAGA
10342 TATA
1 TATA
10346 TATAAATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 19 0.53
19 3 0.08
20 14 0.39
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
TATAAAAAGATATAAAGA
Found at i:18652 original size:31 final size:31
Alignment explanation
Indices: 18617--18683 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
18607 TTTAACAGCT
*
18617 GGTGACCAGAAAAGAAAATTTCGAATAATTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
*
18648 GGTGACCAGAAAAGAAAATCTCGAATAGTTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
18679 GGTGA
1 GGTGA
18684 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (31 bp):
GGTGACCAGAAAAGAAAATCTCGAATAATTG
Found at i:22660 original size:31 final size:31
Alignment explanation
Indices: 22625--22691 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
22615 TTTAACAGCT
*
22625 GGTGACCAGAAAAGAAAATTTCGAATAATTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
*
22656 GGTGACCAGAAAAGAAAATCTCGAATAGTTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
22687 GGTGA
1 GGTGA
22692 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (31 bp):
GGTGACCAGAAAAGAAAATCTCGAATAATTG
Found at i:26668 original size:31 final size:31
Alignment explanation
Indices: 26633--26699 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
26623 TTTAACAGCT
*
26633 GGTGACCAGAAAAGAAAATTTCGAATAATTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
*
26664 GGTGACCAGAAAAGAAAATCTCGAATAGTTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
26695 GGTGA
1 GGTGA
26700 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (31 bp):
GGTGACCAGAAAAGAAAATCTCGAATAATTG
Found at i:30675 original size:31 final size:31
Alignment explanation
Indices: 30640--30706 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
30630 TTTAACAGCT
*
30640 GGTGACCAGAAAAGAAAATTTCGAATAATTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
*
30671 GGTGACCAGAAAAGAAAATCTCGAATAGTTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
30702 GGTGA
1 GGTGA
30707 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (31 bp):
GGTGACCAGAAAAGAAAATCTCGAATAATTG
Found at i:34686 original size:31 final size:31
Alignment explanation
Indices: 34651--34717 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
34641 TTTAACAGCT
*
34651 GGTGACCAGAAAAGAAAATTTCGAATAATTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
*
34682 GGTGACCAGAAAAGAAAATCTCGAATAGTTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
34713 GGTGA
1 GGTGA
34718 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (31 bp):
GGTGACCAGAAAAGAAAATCTCGAATAATTG
Found at i:38689 original size:30 final size:31
Alignment explanation
Indices: 38655--38720 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
38645 TTTAACAGCT
*
38655 GGTGACCAGAAAA-AAAATTTCGAATAATTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
*
38685 GGTGACCAGAAAAGAAAATCTCGAATAGTTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
38716 GGTGA
1 GGTGA
38721 TCATTTTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (31 bp):
GGTGACCAGAAAAGAAAATCTCGAATAATTG
Done.