Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold535
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: 82589
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 2278 characters in sequence are not A, C, G, or T
Found at i:1118 original size:13 final size:13
Alignment explanation
Indices: 1100--1125 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1090 AAATTAAGCA
1100 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
1113 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
1126 AGGTTAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TCTTCTTCTTCTT
Found at i:2249 original size:193 final size:193
Alignment explanation
Indices: 1920--2314 Score: 736
Period size: 193 Copynumber: 2.0 Consensus size: 193
1910 TGTTAATATT
1920 TTTCATCAATTATACATATTTTTATTGGTAACATATCAAATTTAGCCCTCTAAGTTTAAACATTT
1 TTTCATCAATTATACATATTTTTATTGGTAACATATCAAATTTAGCCCTCTAAGTTTAAACATTT
*
1985 TGTCAATTTCATCTCAACATTTACATATTATGTCAATTTTATTCTAATTTAAAAATTTAGTCCAC
66 TATCAATTTCATCTCAACATTTACATATTATGTCAATTTTATTCTAATTTAAAAATTTAGTCCAC
* * *
2050 AACTTTTATACATTCTATCAATTTGATCTTGATTTAACAAATTTAGTCTGTAAAATTTACATA
131 AACTTTTATACATTCTATCAATTTGATCTTGATTTAACAAACTTAATCTGCAAAATTTACATA
*
2113 TTTCATCAATTATACATATTTTTATTGGTAACATATCAAATTTAGCCTTCTAAGTTTAAACATTT
1 TTTCATCAATTATACATATTTTTATTGGTAACATATCAAATTTAGCCCTCTAAGTTTAAACATTT
*
2178 TATCAATTTCATCTCAACATTTACATATTATGTCAGTTTTATTCTAATTTAAAAATTTAGTCCAC
66 TATCAATTTCATCTCAACATTTACATATTATGTCAATTTTATTCTAATTTAAAAATTTAGTCCAC
2243 AACTTTTATACATTCTATCAATTTGATCTTGATTTAACAAACTTAATCTGCAAAATTTACATA
131 AACTTTTATACATTCTATCAATTTGATCTTGATTTAACAAACTTAATCTGCAAAATTTACATA
2306 TTTCATCAA
1 TTTCATCAA
2315 CATTTACGCA
Statistics
Matches: 196, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
193 196 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.44
Consensus pattern (193 bp):
TTTCATCAATTATACATATTTTTATTGGTAACATATCAAATTTAGCCCTCTAAGTTTAAACATTT
TATCAATTTCATCTCAACATTTACATATTATGTCAATTTTATTCTAATTTAAAAATTTAGTCCAC
AACTTTTATACATTCTATCAATTTGATCTTGATTTAACAAACTTAATCTGCAAAATTTACATA
Found at i:3772 original size:30 final size:30
Alignment explanation
Indices: 3738--3805 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
3728 CTTAAGGGAA
3738 AAAAGTTACAATTCAA-TCATTGAACTATTC
1 AAAAGTTAC-ATTCAAGTCATTGAACTATTC
* *
3768 AAAAGTTTTCATTTAAGTCATTGAACTATTC
1 AAAAG-TTACATTCAAGTCATTGAACTATTC
3799 AAAAGTT
1 AAAAGTT
3806 TTTATTTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (30 bp):
AAAAGTTACATTCAAGTCATTGAACTATTC
Found at i:3791 original size:31 final size:31
Alignment explanation
Indices: 3754--3818 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
3744 TACAATTCAA
3754 TCATTGAACTATTCAAAAGTTTTCATTTAAG
1 TCATTGAACTATTCAAAAGTTTTCATTTAAG
*
3785 TCATTGAACTATTCAAAAGTTTTTATTTAAG
1 TCATTGAACTATTCAAAAGTTTTCATTTAAG
3816 TCA
1 TCA
3819 CTGAGCTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (31 bp):
TCATTGAACTATTCAAAAGTTTTCATTTAAG
Found at i:9279 original size:1 final size:1
Alignment explanation
Indices: 9275--9299 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
9265 TTCTTTTTCC
9275 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
9300 GGTTTCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10050 original size:4 final size:4
Alignment explanation
Indices: 10037--10066 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
10027 CTGTTATTAT
10037 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
10067 TCTTTATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:10050 original size:12 final size:13
Alignment explanation
Indices: 10041--10073 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
10031 TATTATTTTA
10041 TTATTTATTTA-T
1 TTATTTATTTATT
10053 TTATTTATTTATT
1 TTATTTATTTATT
*
10066 TTCTTTAT
1 TTATTTAT
10074 CAACTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTATTTATT
Found at i:17493 original size:45 final size:45
Alignment explanation
Indices: 17444--17593 Score: 120
Period size: 45 Copynumber: 3.2 Consensus size: 45
17434 AAATAAGGGT
*
17444 TTAGGGTTTCTTAATTAAATTAATTATAAATTTTTAAAAATTAGA
1 TTAGGGTTTCTTGATTAAATTAATTATAAATTTTTAAAAATTAGA
** * ** ** ** * *
17489 TTAGGGTTTAGTGTTTAGGGTTTTTATATAAAAAATTAAATAAATTAGGGT
1 TTAGGGTTTCTTGATTA-AATTAAT-TAT-AAATTTTTAA-AAATTA--GA
* *
17540 TTAGGGTTGCTTGAGTAAATTAATTATAAATTTTTAAAAATTAGA
1 TTAGGGTTTCTTGATTAAATTAATTATAAATTTTTAAAAATTAGA
17585 TTAGGGTTT
1 TTAGGGTTT
17594 AGTGTTTAGG
Statistics
Matches: 73, Mismatches: 26, Indels: 12
0.66 0.23 0.11
Matches are distributed among these distances:
45 22 0.30
46 3 0.04
47 9 0.12
48 14 0.19
49 9 0.12
50 3 0.04
51 13 0.18
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (45 bp):
TTAGGGTTTCTTGATTAAATTAATTATAAATTTTTAAAAATTAGA
Found at i:17707 original size:97 final size:96
Alignment explanation
Indices: 17423--17724 Score: 480
Period size: 96 Copynumber: 3.1 Consensus size: 96
17413 GGTTTTAAGG
* * * *
17423 AAAAATTAAATAAATAAGGGTTTAGGGTTTCTTAATTAAATTAATTATAAATTTTTAAAAATTAG
1 AAAAATTAAATAAATTAGGGTTTAGGGTTGCTTGAGTAAATTAATTATAAATTTTTAAAAATTAG
17488 ATTAGGGTTTAGTGTTTAGGGTTTTTATATA
66 ATTAGGGTTTAGTGTTTAGGGTTTTTATATA
17519 AAAAATTAAATAAATTAGGGTTTAGGGTTGCTTGAGTAAATTAATTATAAATTTTTAAAAATTAG
1 AAAAATTAAATAAATTAGGGTTTAGGGTTGCTTGAGTAAATTAATTATAAATTTTTAAAAATTAG
17584 ATTAGGGTTTAGTGTTTAGGGTTTTTATATA
66 ATTAGGGTTTAGTGTTTAGGGTTTTTATATA
* *
17615 AAAAATTAAATAAATTAGGGTTTAGGGTTGCTTGAGTAAATTAATTTTAAATTTTAAAAAAATTA
1 AAAAATTAAATAAATTAGGGTTTAGGGTTGCTTGAGTAAATTAATTATAAATTTT-TAAAAATTA
* * * **
17680 GATTGGGGTTTAATATTTAGGGTTTTTA-AGG
65 GATTAGGGTTTAGTGTTTAGGGTTTTTATATA
*
17711 AAAAATCAAATAAA
1 AAAAATTAAATAAA
17725 ACTAGTTGTT
Statistics
Matches: 193, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
96 160 0.83
97 33 0.17
ACGTcount: A:0.40, C:0.01, G:0.17, T:0.41
Consensus pattern (96 bp):
AAAAATTAAATAAATTAGGGTTTAGGGTTGCTTGAGTAAATTAATTATAAATTTTTAAAAATTAG
ATTAGGGTTTAGTGTTTAGGGTTTTTATATA
Found at i:18592 original size:42 final size:40
Alignment explanation
Indices: 18521--18621 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
18511 GGGGAAGTGT
** *
18521 TTCCTCAAGGAAGC-ACTT-TGTCCATGTGGACACAAAGCGC
1 TTCCTCAAGGAAGCGTTTTCTGTCCACGTGG--ACAAAGCGC
18561 -TCTCTCAAGGAAGCGTTTTCTGTCCACGTGGACAAAGCGC
1 TTC-CTCAAGGAAGCGTTTTCTGTCCACGTGGACAAAGCGC
**
18601 TTCCTTGAGGAAGCGTTTTCT
1 TTCCTCAAGGAAGCGTTTTCT
18622 TGCTTTATCC
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
39 2 0.04
40 36 0.69
41 4 0.08
42 10 0.19
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
TTCCTCAAGGAAGCGTTTTCTGTCCACGTGGACAAAGCGC
Found at i:19256 original size:19 final size:19
Alignment explanation
Indices: 19217--19272 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
19207 AGATATTAAA
*
19217 TATTAAAATTGATATAAACT
1 TATTAAAATT-ATAAAAACT
19237 TATTAAAATTATAAAAACT
1 TATTAAAATTATAAAAACT
19256 TA-TAAATATTATAAAAA
1 TATTAAA-ATTATAAAAA
19273 TATATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 4 0.12
19 20 0.59
20 10 0.29
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
TATTAAAATTATAAAAACT
Found at i:19260 original size:10 final size:9
Alignment explanation
Indices: 19161--19281 Score: 67
Period size: 9 Copynumber: 13.6 Consensus size: 9
19151 TGAAAATAAT
19161 TAAAAA-TA
1 TAAAAATTA
19169 T-AAAATATA
1 TAAAAAT-TA
*
19178 TAAAATATCA
1 TAAAA-ATTA
*
19188 GAAAAATTA
1 TAAAAATTA
19197 TAAAAA--A
1 TAAAAATTA
*
19204 TAAAGA-TA
1 TAAAAATTA
*
19212 T-TAAA-TA
1 TAAAAATTA
*
19219 TTAAAATTGA
1 TAAAAATT-A
*
19229 TATAAACTTA
1 TA-AAAATTA
*
19239 TTAAAATTA
1 TAAAAATTA
19248 TAAAAACTTA
1 TAAAAA-TTA
*
19258 TAAATATTA
1 TAAAAATTA
19267 TAAAAATATA
1 TAAAAAT-TA
19277 TAAAA
1 TAAAA
19282 TTGAAAAATA
Statistics
Matches: 87, Mismatches: 15, Indels: 20
0.71 0.12 0.16
Matches are distributed among these distances:
7 15 0.17
8 6 0.07
9 32 0.37
10 27 0.31
11 7 0.08
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:19278 original size:19 final size:19
Alignment explanation
Indices: 19161--19280 Score: 61
Period size: 19 Copynumber: 6.7 Consensus size: 19
19151 TGAAAATAAT
19161 TAAAAATATA-AAATA-TA
1 TAAAAATATATAAATATTA
* *
19178 T-AAAATATCAGAAAAATTA
1 TAAAAATAT-ATAAATATTA
19197 TAAAAA-ATA-AAGATA-T-
1 TAAAAATATATAA-ATATTA
19213 T--AAATAT-TAAA-ATTGA
1 TAAAAATATATAAATATT-A
*
19229 TATAAACT-TATTAAA-ATTA
1 TA-AAAATATA-TAAATATTA
19248 TAAAAACT-TATAAATATTA
1 TAAAAA-TATATAAATATTA
19267 TAAAAATATATAAA
1 TAAAAATATATAAA
19281 ATTGAAAAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 34
0.68 0.03 0.29
Matches are distributed among these distances:
13 1 0.01
14 5 0.06
15 4 0.05
16 9 0.11
17 5 0.06
18 16 0.20
19 30 0.37
20 11 0.14
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAAAATATATAAATATTA
Found at i:19583 original size:17 final size:18
Alignment explanation
Indices: 19556--19590 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
19546 CCAATTTAAT
19556 TAAATAAAATATTAAAAA
1 TAAATAAAATATTAAAAA
19574 TAAA-AAAATATTAAAAA
1 TAAATAAAATATTAAAAA
19591 AATCTGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATAAAATATTAAAAA
Found at i:19692 original size:10 final size:9
Alignment explanation
Indices: 19680--19745 Score: 53
Period size: 10 Copynumber: 7.0 Consensus size: 9
19670 TCAGTTCAAG
19680 TTTTTATAA
1 TTTTTATAA
*
19689 GTTTATATCAA
1 -TTTTTAT-AA
*
19700 TTTTAAT-A
1 TTTTTATAA
19708 TTTTTATAA
1 TTTTTATAA
*
19717 CTTTTATAGA
1 TTTTTATA-A
*
19727 TTTTTAATAT
1 TTTTT-ATAA
19737 TTTTTATAA
1 TTTTTATAA
19746 AATTTTAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
8 7 0.16
9 11 0.25
10 21 0.48
11 5 0.11
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:19741 original size:20 final size:21
Alignment explanation
Indices: 19718--19760 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
19708 TTTTTATAAC
* *
19718 TTTTAT-AGATTTTTAATATT
1 TTTTATAAAATTTTAAATATT
19738 TTTTATAAAATTTTAAATATT
1 TTTTATAAAATTTTAAATATT
19759 TT
1 TT
19761 AATGATTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTATAAAATTTTAAATATT
Found at i:19760 original size:29 final size:30
Alignment explanation
Indices: 19699--19773 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 30
19689 GTTTATATCA
*
19699 ATTTTAATA-TTTTTATAACTTTTATAGAT
1 ATTTTAATATTTTTTATAAATTTTATAGAT
19728 -TTTTAATATTTTTTATAAAATTTTA-A-AT
1 ATTTTAATATTTTTTAT-AAATTTTATAGAT
19756 ATTTTAATGATTTCTTTA
1 ATTTTAAT-ATTT-TTTA
19774 AGTTCATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 10 0.25
29 15 0.38
30 11 0.28
31 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (30 bp):
ATTTTAATATTTTTTATAAATTTTATAGAT
Found at i:21013 original size:17 final size:18
Alignment explanation
Indices: 20974--21022 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
20964 ATTGGACTTG
20974 AGTTTTCAATTTCAATTTT
1 AGTTTTC-ATTTCAATTTT
20993 -GTTTTCATTT-AATTTT
1 AGTTTTCATTTCAATTTT
21009 AGTTTTCAATTTCA
1 AGTTTTC-ATTTCA
21023 TAAAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.22
17 10 0.37
18 10 0.37
19 1 0.04
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.59
Consensus pattern (18 bp):
AGTTTTCATTTCAATTTT
Found at i:22079 original size:1 final size:1
Alignment explanation
Indices: 22073--22103 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
22063 TTAAGAAAGC
22073 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22104 CTCTTATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:36311 original size:23 final size:25
Alignment explanation
Indices: 36284--36340 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 25
36274 GAAAAAATTG
*
36284 AAAATTAATTTG-A-ATATGTTTTT
1 AAAATTAAATTGCACATATGTTTTT
36307 AAAATTAAATTGCTACTATATGTTTTT
1 AAAATTAAATTGC-AC-ATATGTTTTT
36334 AAAATTA
1 AAAATTA
36341 GTATCAAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.38
25 1 0.03
27 17 0.59
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (25 bp):
AAAATTAAATTGCACATATGTTTTT
Found at i:70639 original size:11 final size:9
Alignment explanation
Indices: 70612--70672 Score: 61
Period size: 9 Copynumber: 6.6 Consensus size: 9
70602 ATGGGTTTGC
70612 AAAAATAAA
1 AAAAATAAA
70621 AAAAATAAA
1 AAAAATAAA
70630 AAAAGGATAAA
1 AAAA--ATAAA
* *
70641 ACAAATGAA
1 AAAAATAAA
*
70650 CAAAATAAA
1 AAAAATAAA
70659 AAAAA-AGAA
1 AAAAATA-AA
70668 AAAAA
1 AAAAA
70673 CAAAGGAACG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 1 0.02
9 34 0.79
11 8 0.19
ACGTcount: A:0.82, C:0.03, G:0.07, T:0.08
Consensus pattern (9 bp):
AAAAATAAA
Found at i:72811 original size:21 final size:19
Alignment explanation
Indices: 72787--72827 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
72777 AAAAATCTGA
72787 AAATAAATAAAACAAACAAAG
1 AAATAAA-AAAA-AAACAAAG
*
72808 AAATAAAAAAAAAACTAAG
1 AAATAAAAAAAAAACAAAG
72827 A
1 A
72828 TGAAATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.10
Consensus pattern (19 bp):
AAATAAAAAAAAAACAAAG
Done.