Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024107.1 Corchorus olitorius cultivar O-4 contig24140, whole genome shotgun sequence
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: 55523
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:478 original size:49 final size:48
Alignment explanation
Indices: 416--545 Score: 140
Period size: 49 Copynumber: 2.7 Consensus size: 48
406 TTACTTTTCC
* ** *
416 TGCACCTTTTCTCAATTTTTACTACAAAACTGA-ACTTTT-ATTTTTACT
1 TGCACTTTTTCTCAATTTTTAAGACAAAACTGATA-TTTTAATTTTCA-T
*
464 TGCATCTTTTTCTCAATTTTTAAGACAAAATTGATATTTTAATTTTCAT
1 TGCA-CTTTTTCTCAATTTTTAAGACAAAACTGATATTTTAATTTTCAT
* * *
513 TGCACTTTTTATCAATTTTT-TGACAAAATTGAT
1 TGCACTTTTTCTCAATTTTTAAGACAAAACTGAT
546 TGGCACGCTC
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
47 12 0.17
48 19 0.26
49 34 0.47
50 7 0.10
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.49
Consensus pattern (48 bp):
TGCACTTTTTCTCAATTTTTAAGACAAAACTGATATTTTAATTTTCAT
Found at i:786 original size:37 final size:38
Alignment explanation
Indices: 722--799 Score: 113
Period size: 37 Copynumber: 2.0 Consensus size: 38
712 GGGATCGGCT
722 ATTTATGATAGTTATTAGGTGTGGGAATCCATACGATCCC
1 ATTTATGATAG-T-TTAGGTGTGGGAATCCATACGATCCC
* *
762 ATTTATGATAG-TTAGGTGTGGGAATCCTTATGATCCC
1 ATTTATGATAGTTTAGGTGTGGGAATCCATACGATCCC
799 A
1 A
800 ACTCTTCTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 25 0.69
40 11 0.31
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (38 bp):
ATTTATGATAGTTTAGGTGTGGGAATCCATACGATCCC
Found at i:6380 original size:17 final size:16
Alignment explanation
Indices: 6340--6390 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
6330 CATGTAATCT
*
6340 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
6356 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
6373 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
6390 T
1 T
6391 GGGGGTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:15034 original size:21 final size:21
Alignment explanation
Indices: 14986--15034 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
14976 TAAAAATAAC
* *
14986 AATTAAAAAGAAAGCAATTAA
1 AATTAAAAACAAAGCAAGTAA
*
15007 AACTAAAAACAAAGCAAAGT-A
1 AATTAAAAACAAAGC-AAGTAA
15028 AATTAAA
1 AATTAAA
15035 TCTAATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAGTAA
Found at i:16390 original size:19 final size:18
Alignment explanation
Indices: 16353--16392 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
16343 CTCTTGAGAT
16353 AATTCTTCATTAGTCTTC
1 AATTCTTCATTAGTCTTC
16371 AATTCTTCAAATTA-TCTTC
1 AATTCTTC--ATTAGTCTTC
16390 AAT
1 AAT
16393 AAATCTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTCTTCATTAGTCTTC
Found at i:21099 original size:27 final size:27
Alignment explanation
Indices: 21069--21198 Score: 179
Period size: 27 Copynumber: 4.8 Consensus size: 27
21059 ATTAGGGTAG
* *
21069 TCCAGGGGCATTTCAGTCATTTGAACA
1 TCCAGGGGCATTTTAGTCATTTGCACA
*
21096 TCCAGGGGCATTTTGGTCATTTGCACA
1 TCCAGGGGCATTTTAGTCATTTGCACA
*
21123 TTCAGGGGCATTTTAGTCATTTGCACA
1 TCCAGGGGCATTTTAGTCATTTGCACA
* *
21150 TCCAGGAGCATTTTAGTCATTCGCACA
1 TCCAGGGGCATTTTAGTCATTTGCACA
** *
21177 TTTAGGGGCATTTTGGTCATTT
1 TCCAGGGGCATTTTAGTCATTT
21199 TAAGTTCACT
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (27 bp):
TCCAGGGGCATTTTAGTCATTTGCACA
Found at i:22412 original size:27 final size:27
Alignment explanation
Indices: 22340--22429 Score: 153
Period size: 27 Copynumber: 3.3 Consensus size: 27
22330 GGGATTTTGG
*
22340 GGTCATTTGCACATCCAGGGGCATTTT
1 GGTCATTTGCACATTCAGGGGCATTTT
22367 GGTCATATTGCACATTCAGGGGCATTTT
1 GGTCAT-TTGCACATTCAGGGGCATTTT
*
22395 GGTCATTTGCATATTCAGGGGCATTTT
1 GGTCATTTGCACATTCAGGGGCATTTT
22422 GGTCATTT
1 GGTCATTT
22430 TAAATTCACT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
27 34 0.57
28 26 0.43
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (27 bp):
GGTCATTTGCACATTCAGGGGCATTTT
Found at i:22820 original size:12 final size:12
Alignment explanation
Indices: 22803--22827 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22793 TGCATATCCC
22803 ATCATTTTAGTT
1 ATCATTTTAGTT
22815 ATCATTTTAGTT
1 ATCATTTTAGTT
22827 A
1 A
22828 GCAGTCTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (12 bp):
ATCATTTTAGTT
Found at i:29882 original size:8 final size:8
Alignment explanation
Indices: 29863--29923 Score: 61
Period size: 8 Copynumber: 7.4 Consensus size: 8
29853 AAATTCCCAT
*
29863 AAAAATAA
1 AAAAATGA
29871 AAAAGATGA
1 AAAA-ATGA
29880 AAAAATGA
1 AAAAATGA
29888 AGAAAA-GA
1 A-AAAATGA
**
29896 ATGAATGA
1 AAAAATGA
29904 AACAAATGA
1 AA-AAATGA
29913 AAAAATGA
1 AAAAATGA
29921 AAA
1 AAA
29924 TAAAGGCACT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
7 2 0.05
8 24 0.55
9 18 0.41
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (8 bp):
AAAAATGA
Found at i:29921 original size:17 final size:16
Alignment explanation
Indices: 29863--29923 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
29853 AAATTCCCAT
*
29863 AAAAATAAAAAAGATGA
1 AAAAATGAAAAA-ATGA
29880 AAAAATGAAGAAAA-GA
1 AAAAATGAA-AAAATGA
**
29896 ATGAATGAAACAAATGA
1 AAAAATGAAA-AAATGA
29913 AAAAATGAAAA
1 AAAAATGAAAA
29924 TAAAGGCACT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 1 0.03
16 13 0.36
17 19 0.53
18 3 0.08
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (16 bp):
AAAAATGAAAAAATGA
Found at i:30328 original size:19 final size:19
Alignment explanation
Indices: 30304--30349 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
30294 AAGAAATTCC
30304 AAAAAAAAAAATCAAAAAT
1 AAAAAAAAAAATCAAAAAT
**
30323 AAAAAAATCAATCAAAAAT
1 AAAAAAAAAAATCAAAAAT
30342 AAAAAAAA
1 AAAAAAAA
30350 TAAAAAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAAAAAAAATCAAAAAT
Found at i:30376 original size:28 final size:26
Alignment explanation
Indices: 30310--30377 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
30300 TTCCAAAAAA
30310 AAAAATCAAAAATAAAAAAATCAATC
1 AAAAATCAAAAATAAAAAAATCAATC
*
30336 AAAAATAAAAAAAATAAAAAAATCATAATC
1 AAAAAT--CAAAAATAAAAAAATC--AATC
30366 -AAAATCGAAAAA
1 AAAAATC-AAAAA
30378 GAATTGATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
26 6 0.17
28 20 0.57
29 5 0.14
30 4 0.11
ACGTcount: A:0.75, C:0.09, G:0.01, T:0.15
Consensus pattern (26 bp):
AAAAATCAAAAATAAAAAAATCAATC
Found at i:30688 original size:9 final size:9
Alignment explanation
Indices: 30676--30705 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
30666 AAAATTGAAA
30676 AAAAAAAAG
1 AAAAAAAAG
30685 AAAAAAAAG
1 AAAAAAAAG
*
30694 AAAAAAAGG
1 AAAAAAAAG
30703 AAA
1 AAA
30706 GAATAGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:32337 original size:169 final size:169
Alignment explanation
Indices: 32052--32383 Score: 547
Period size: 169 Copynumber: 2.0 Consensus size: 169
32042 ATACGAGTAT
*
32052 CATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAAGTTTAAAATCCTTGTTCAAGGTC
1 CATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGGTTAAGTTTAAAATCCTTGTTCAAGGTC
*
32117 TCAATTCAAAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTC
66 TCAATTCAAAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATCAATTC
32182 TGATAAGTCCTCCGAGCAATTGATAAAACCTCCGGGTAC
131 TGATAAGTCCTCCGAGCAATTGATAAAACCTCCGGGTAC
* * * *
32221 CATTTGATTTCATCAAGTTTTTCATCAAAAGTTCATGGTTAAGTTTAAGATCCTTGTTTAAGGTC
1 CATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGGTTAAGTTTAAAATCCTTGTTCAAGGTC
* * * *
32286 TCAATTCAAGGTTTGCGTTGGTAAGTCCTCCGGGCACAAGTTCAGAAACCTCTGGGTATCAATTC
66 TCAATTCAAAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATCAATTC
* * *
32351 TGATAAGTCCTCCGGGCATTTGATAAGACCTCC
131 TGATAAGTCCTCCGAGCAATTGATAAAACCTCC
32384 AGGCATTTCA
Statistics
Matches: 150, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
169 150 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (169 bp):
CATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGGTTAAGTTTAAAATCCTTGTTCAAGGTC
TCAATTCAAAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATCAATTC
TGATAAGTCCTCCGAGCAATTGATAAAACCTCCGGGTAC
Found at i:32376 original size:20 final size:20
Alignment explanation
Indices: 32351--32391 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
32341 GTATCAATTC
* *
32351 TGATAAGTCCTCCGGGCATT
1 TGATAAGACCTCCAGGCATT
32371 TGATAAGACCTCCAGGCATT
1 TGATAAGACCTCCAGGCATT
32391 T
1 T
32392 CATATTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (20 bp):
TGATAAGACCTCCAGGCATT
Found at i:32493 original size:39 final size:39
Alignment explanation
Indices: 32417--32569 Score: 198
Period size: 39 Copynumber: 4.2 Consensus size: 39
32407 AACTATTATA
* * * *
32417 CTTTGTCAATTTATTTTCGATCCTGGTTTAGGATCATTG
1 CTTTATCAGTTTACTTTCAATCCTGGTTTAGGATCATTG
*
32456 CTTTATCAGTTTACTTTCAATTCTGGTTTAGGATCATTG
1 CTTTATCAGTTTACTTTCAATCCTGGTTTAGGATCATTG
32495 C-TT-T-A---T--TTT-AATCCTGGTTTAGGATCATTG
1 CTTTATCAGTTTACTTTCAATCCTGGTTTAGGATCATTG
32525 CTTTATCAGTTTACTTTCAATCCTGGTTTAGGATCATTG
1 CTTTATCAGTTTACTTTCAATCCTGGTTTAGGATCATTG
32564 CTTTAT
1 CTTTAT
32570 TTTAATCCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
30 21 0.21
31 5 0.05
32 1 0.01
33 2 0.02
36 2 0.02
37 1 0.01
38 5 0.05
39 62 0.63
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.49
Consensus pattern (39 bp):
CTTTATCAGTTTACTTTCAATCCTGGTTTAGGATCATTG
Found at i:32512 original size:30 final size:30
Alignment explanation
Indices: 32478--33144 Score: 774
Period size: 30 Copynumber: 21.7 Consensus size: 30
32468 ACTTTCAATT
32478 CTGGTTTAGGATCATTGCTTTATTTTAATC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
32508 CTGGTTTAGGATCATTGCTTTATCAGTTTACTTTCAATC
1 CTGGTTTAGGATCATTGC-TT-T-A---T--TTT-AATC
32547 CTGGTTTAGGATCATTGCTTTATTTTAATC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
*
32577 CCGGTTTAGGATCATTGCTTTATTTTAATC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
*
32607 CTGGCTTAGGATCATTGCTTTATTTTAATC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
*
32637 CTGGTTTAGGATCATTGCTTTATTTCAATC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
* *
32667 CTGGTTGAGGATCATTGCTTTATTTCAATC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
* * * *
32697 CTGGTTGAGGATCATTGCTTTGTTTCAGTC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
* * * *
32727 ATGGTTGAGGATTATTGCTTTTATTTTAATT
1 CTGGTTTAGGATCATTGC-TTTATTTTAATC
* *
32758 TTGGTTTAGGATCATTGCTTTATTTCAATC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
* ** *
32788 CTGGTTGAGGATCATTGCTTTATTCCAGTC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
*
32818 CTGGTTGAGGATCATTGC-TTATTTTTAATC
1 CTGGTTTAGGATCATTGCTTTA-TTTTAATC
* *
32848 CTGGTTTAGGATCATTGATTTATTTCAATC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
* * *
32878 CTGGTTGAGGATCATTGCTTTATTTCAGTC
1 CTGGTTTAGGATCATTGCTTTATTTTAATC
* * *
32908 CTGGTTGAGGATCATTG-TTTATTCCTCAATA
1 CTGGTTTAGGATCATTGCTTTATT--TTAATC
32939 CTGGTTTAGGATCATTG-TTTATTTCTCAATC
1 CTGGTTTAGGATCATTGCTTTATTT-T-AATC
32970 CTGGTTTAGGATCATTG-TTTATTTCTCAATC
1 CTGGTTTAGGATCATTGCTTTATTT-T-AATC
33001 CTGGTTTAGGATCATTG-TTTATTTCTCAATC
1 CTGGTTTAGGATCATTGCTTTATTT-T-AATC
*
33032 CTGGTTTATGATCATTG-TTTATTTCTCAATC
1 CTGGTTTAGGATCATTGCTTTATTT-T-AATC
33063 CTGGTTTAGGATCATTG-TTTATTTCTCAATC
1 CTGGTTTAGGATCATTGCTTTATTT-T-AATC
* *
33094 CTGGTTTAGGATCGTTG-TTTATCTCTCAATC
1 CTGGTTTAGGATCATTGCTTTAT-T-TTAATC
33125 CTGGTTTAGGATCATTGCTT
1 CTGGTTTAGGATCATTGCTT
33145 CATCAATTAA
Statistics
Matches: 576, Mismatches: 42, Indels: 36
0.88 0.06 0.06
Matches are distributed among these distances:
29 10 0.02
30 306 0.53
31 223 0.39
32 4 0.01
33 3 0.01
36 2 0.00
37 1 0.00
38 5 0.01
39 22 0.04
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.47
Consensus pattern (30 bp):
CTGGTTTAGGATCATTGCTTTATTTTAATC
Found at i:33040 original size:18 final size:18
Alignment explanation
Indices: 33017--33070 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
33007 TAGGATCATT
33017 GTTTATTTCTCAATCCTG
1 GTTTATTTCTCAATCCTG
**
33035 GTTTA-TGATC-AT--T-
1 GTTTATTTCTCAATCCTG
33048 GTTTATTTCTCAATCCTG
1 GTTTATTTCTCAATCCTG
33066 GTTTA
1 GTTTA
33071 GGATCATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
13 5 0.19
14 4 0.15
15 2 0.07
16 2 0.07
17 4 0.15
18 10 0.37
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.52
Consensus pattern (18 bp):
GTTTATTTCTCAATCCTG
Found at i:33272 original size:32 final size:32
Alignment explanation
Indices: 33216--33299 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 32
33206 TTATTACTTT
* * *
33216 AGTT-TATTTGAATCTTGATCATTGCTTCATC
1 AGTTATATTTCAATCATGATTATTGCTTCATC
* **
33247 AGTTATATTTCAGTCATGATTATTGCTTTGTC
1 AGTTATATTTCAATCATGATTATTGCTTCATC
* *
33279 AGTTTTATTTCAATCCTGATT
1 AGTTATATTTCAATCATGATT
33300 TAGGATCATT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 4 0.09
32 39 0.91
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.50
Consensus pattern (32 bp):
AGTTATATTTCAATCATGATTATTGCTTCATC
Found at i:33736 original size:27 final size:27
Alignment explanation
Indices: 33665--33750 Score: 136
Period size: 27 Copynumber: 3.1 Consensus size: 27
33655 GGGATTTTGG
* *
33665 GGTCATTTGCACGTCCAGGGGCATTTT
1 GGTCATTTGCACATTCAGGGGCATTTT
*
33692 GGTCATTTTGCATATTCAGGGGCATTTT
1 GGTCA-TTTGCACATTCAGGGGCATTTT
33720 GGTCATTTGCACATTCAGGGGCATTTT
1 GGTCATTTGCACATTCAGGGGCATTTT
33747 GGTC
1 GGTC
33751 CTTTTAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 30 0.56
28 24 0.44
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (27 bp):
GGTCATTTGCACATTCAGGGGCATTTT
Found at i:43406 original size:19 final size:20
Alignment explanation
Indices: 43370--43408 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
43360 TAAAAACTAG
*
43370 AAGAAAAACTAGAACTAGAA
1 AAGAAAAACGAGAACTAGAA
*
43390 AAGAAAAA-GAGATCTAGAA
1 AAGAAAAACGAGAACTAGAA
43409 TTGTGATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.64, C:0.08, G:0.18, T:0.10
Consensus pattern (20 bp):
AAGAAAAACGAGAACTAGAA
Found at i:45715 original size:2 final size:2
Alignment explanation
Indices: 45708--45733 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45698 CCCCATAATC
45708 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
45734 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45738 original size:4 final size:4
Alignment explanation
Indices: 45731--45821 Score: 155
Period size: 4 Copynumber: 22.8 Consensus size: 4
45721 TATATATATA
* *
45731 TATG TATG TATG TATG TATG TATG TATG CATA TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
45779 TATG TATG TATG TATG TATG TATG TATA TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
45822 AAGAGAATCA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 81 1.00
ACGTcount: A:0.27, C:0.01, G:0.22, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:46036 original size:22 final size:22
Alignment explanation
Indices: 46011--46056 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
46001 TCAAGTCAAA
46011 ATTTTAAATCATATATATATAT
1 ATTTTAAATCATATATATATAT
*
46033 ATTTTAAATTATATATATATAT
1 ATTTTAAATCATATATATATAT
46055 AT
1 AT
46057 AACAAGTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTAAATCATATATATATAT
Found at i:48380 original size:2 final size:2
Alignment explanation
Indices: 48373--48400 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48363 CTAAGAAATC
48373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48401 TGATAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49317 original size:18 final size:18
Alignment explanation
Indices: 49283--49317 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49273 ATCCGGCCAT
* *
49283 GGAAGAAGAGGAGGAGGA
1 GGAAGAAGAAGAAGAGGA
49301 GGAAGAAGAAGAAGAGG
1 GGAAGAAGAAGAAGAGG
49318 GAAAAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (18 bp):
GGAAGAAGAAGAAGAGGA
Found at i:49376 original size:13 final size:13
Alignment explanation
Indices: 49356--49458 Score: 136
Period size: 13 Copynumber: 8.0 Consensus size: 13
49346 GGCCGGCGTG
49356 GCGCGGCCCAGGC
1 GCGCGGCCCAGGC
*
49369 GTGCGGCCCAGGC
1 GCGCGGCCCAGGC
*
49382 GCACGGCCCAGGC
1 GCGCGGCCCAGGC
*
49395 GCACGGCCCAGGC
1 GCGCGGCCCAGGC
49408 GCGCGGCCCAGGC
1 GCGCGGCCCAGGC
*
49421 GCGCCGCCCAGGC
1 GCGCGGCCCAGGC
* * *
49434 GCACGGCCC-TGT
1 GCGCGGCCCAGGC
49446 GCGCGGCCCAGGC
1 GCGCGGCCCAGGC
49459 CAAGCTTGGG
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
12 9 0.12
13 68 0.88
ACGTcount: A:0.10, C:0.46, G:0.42, T:0.03
Consensus pattern (13 bp):
GCGCGGCCCAGGC
Found at i:54954 original size:199 final size:200
Alignment explanation
Indices: 54583--55523 Score: 1289
Period size: 199 Copynumber: 4.7 Consensus size: 200
54573 ATAAGTTTAT
* *
54583 TATAAGAAAAATTATACTACAATACATCGTCAGTGGAGTTTAGCAGACTCCACGTGCGGGGTTTA
1 TATAAGAAAAA-T-TA-TACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTA
* * * **
54648 AGGGTTGACATGTCTCCCCTTAAGAAATATGTATTAATATTAAATATTTAATTCGTTATGAAATG
63 AGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATG
* * * *
54713 GGTTATGTGTCAACTTCTTAATCCACTTATGGAGTCCAAAATTTACACTGACAGTGTATCGTATA
128 GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATA
*
54778 ATAGT-CC
193 ATAATCCC
* * *
54785 TATAAGAAAAATTATACAATACACCGCCATTGGAGTTTAGCAGACTGCACGTACGGGGTTTAAGG
1 TATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
* * * * **
54850 GTTGATATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTGATTAATTATGAAATTGAC
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
* ** * * *
54915 AATGTGTCAACTTCTTAACCCGCTTAAAGAGTTCAAAATTTACACAGCCAGTGTATTGTATAATA
131 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
*
54980 AT-AC
196 ATCCC
* * * * *
54984 TATAAGAAAAATTATATAATACACAGTCAGTGGAATTTAGCAGACTACACGTGCAGGGTTTAAGG
1 TATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
*
55049 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTGATTAATTATGAAATGG
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATT-AA-ATATTTAATTAATTATGAAATGG
* *
55114 GGTATGTAGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTTACAGTGTAATGTAT-
129 GGTATGT-GTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATA
55178 ATAATCCC
193 ATAATCCC
* *
55186 TATAAG-AAAATTATACAATACACCGTCAGTGGAATTTAGCAGACTGCACGTGTGGGGTTTAAGG
1 TATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
*
55250 GTTGACATGTGTCCCCTTAGGGAATATATATTAATATTAAATATTTAATTAATTATGAAAT-GGG
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
* *
55314 TATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTTAGACTGACAGTGTATTGTGTATTG
131 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGAC-----A--GTGTATTG
55379 TATAATAATCCC
189 TATAATAATCCC
* * * * * *
55391 TATAAGAAAAATTATACAATACACCGTTAGTGGAGTTTAGTAGACCGCACCTGTGGGGTCTAAGG
1 TATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
* *
55456 GTTGACATGTGTCCCCTCAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAACGGGG
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
55521 TAT
131 TAT
Statistics
Matches: 657, Mismatches: 68, Indels: 23
0.88 0.09 0.03
Matches are distributed among these distances:
197 41 0.06
198 8 0.01
199 272 0.41
200 6 0.01
201 122 0.19
202 68 0.10
204 10 0.02
205 14 0.02
206 110 0.17
207 6 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (200 bp):
TATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
ATCCC
Done.