Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010806.1 Corchorus capsularis cultivar CVL-1 contig10827, 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: 61468
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:2450 original size:10 final size:10
Alignment explanation
Indices: 2435--2496 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
2425 TAAAGGATCA
2435 TGTGGCCGGT
1 TGTGGCCGGT
2445 TGTGGCCGGT
1 TGTGGCCGGT
*
2455 TGTGGCCGGG
1 TGTGGCCGGT
** *
2465 CATGGCCGAAT
1 TGTGGCCG-GT
2476 CATGTGGCCGGT
1 --TGTGGCCGGT
2488 TGTGGCCGG
1 TGTGGCCGG
2497 GCATGTCCTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 34 0.83
12 1 0.02
13 6 0.15
ACGTcount: A:0.06, C:0.23, G:0.47, T:0.24
Consensus pattern (10 bp):
TGTGGCCGGT
Found at i:7040 original size:2 final size:2
Alignment explanation
Indices: 7028--7063 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
7018 CATTAAAATC
* *
7028 AT AT GT AT AT AT AA 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 AT AT AT AT
7064 TGTGTATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10509 original size:30 final size:30
Alignment explanation
Indices: 10469--10527 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
10459 TGTCTTCAAG
10469 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCGCATCATTCCT
*
10499 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATCATTCC
10528 CTCCCCCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCT
Found at i:10912 original size:33 final size:33
Alignment explanation
Indices: 10870--10988 Score: 175
Period size: 33 Copynumber: 3.6 Consensus size: 33
10860 TTCTTTTCAC
* * *
10870 CCAAAACAGAATTTTTTTTAATGCTATAATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
*
10903 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
*
10936 CCAAAACAGAATTATTTACAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
10969 CCAAAACAGATTTGTTTTCA
1 CCAAAACAGAATTATTTTCA
10989 TCACAATTAG
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATGATCAA
Found at i:11006 original size:66 final size:66
Alignment explanation
Indices: 10870--11011 Score: 160
Period size: 66 Copynumber: 2.2 Consensus size: 66
10860 TTCTTTTCAC
* ** * * *
10870 CCAAAACAGAATTTTTTTTAATGCTATAATCAACCAAAACAGAATTATTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTACAATGCTATAATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
10935 A
66 A
* * * * *
10936 CCAAAACAGAATTATTTACAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGC
1 CCAAAACAGAATTATTTACAATGCTATAATCAACCAAAACAGAATTATTTGCAAT-ACAATGAGC
*
11000 AT
65 AA
11002 CCAAAACAGA
1 CCAAAACAGA
11012 TTTAGTATCA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
65 2 0.03
66 61 0.97
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (66 bp):
CCAAAACAGAATTATTTACAATGCTATAATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
A
Found at i:11041 original size:33 final size:33
Alignment explanation
Indices: 11004--11108 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
10994 ATTAGCATCC
11004 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCACAAACAACACTT
* * *
11037 AAAACAGATTTAGTGTCAAT-GCAAACAACACTC
1 AAAACAGATTTAGTATC-ATCACAAACAACACTT
** *
11070 AAATTAGGTTTAGTATCATCACAAACAACA-TCT
1 AAAACAGATTTAGTATCATCACAAACAACACT-T
11103 AAAACA
1 AAAACA
11109 CTCTTTGCAA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
32 3 0.05
33 53 0.91
34 2 0.03
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.24
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACTT
Found at i:15289 original size:2 final size:2
Alignment explanation
Indices: 15282--15307 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15272 CTCTTATAGA
15282 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
15308 CTTTATACTC
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:22648 original size:19 final size:19
Alignment explanation
Indices: 22621--22669 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
22611 TAATTAATTG
22621 TTTAAATATTAAATTTTTA
1 TTTAAATATTAAATTTTTA
* *
22640 TTTATATATTATATTTTTA
1 TTTAAATATTAAATTTTTA
* *
22659 CTTAAAAATTA
1 TTTAAATATTA
22670 CTCATAATCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAAATATTAAATTTTTA
Found at i:24367 original size:30 final size:30
Alignment explanation
Indices: 24306--24813 Score: 647
Period size: 30 Copynumber: 16.7 Consensus size: 30
24296 AGAAATCTCC
*
24306 ATTGACACCAGAAGTTGTCAATGGTCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* *
24337 ATTGATACCAGAAGTTGTCATGAGCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
24367 ATTGACACCAGAAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* *
24397 ATTGACACCAGAAGTTGTCAATGGTCTTAAA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
*
24428 ATTGACACTAGAAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
24458 ATTGACACCAGAAGTTGTCAATGATCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* *
24489 AATGACACCAGAAGTTGTCAATGGTCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* * *
24520 AATGACATCAAAAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
*
24550 AATGACACCAGAAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* * *
24580 AATGACACTAGGAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* * *
24610 AATGACACCAGAAGTTGTCATGATAAATTTCCA
1 ATTGACACCAGAAGTTGTCATGAT---CTTACA
* * * *
24643 AATGACACTAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* * * *
24673 ATTGACAACAGAAGTTGTCATCATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* *
24703 ATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* * *
24733 ATTGACACCAGAAGTTGTCATCATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* * *
24763 ATTGACACCAGAAGTTGTCATCATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
24793 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
24814 AACTAATTTC
Statistics
Matches: 439, Mismatches: 33, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
30 310 0.71
31 102 0.23
33 27 0.06
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGATCTTACA
Found at i:24842 original size:183 final size:183
Alignment explanation
Indices: 24306--24846 Score: 685
Period size: 183 Copynumber: 3.0 Consensus size: 183
24296 AGAAATCTCC
* *
24306 ATTGACACCAGAAGTTGTCAATGGTCTTACAATTGATACCAGAAGTTGTCATGAGCTTACAATTG
1 ATTGACACCAGAAGTTGTCAATGGTCTTACAATTGACACCAGAAGTTGTCATGATCTTACAATTG
* *
24371 ACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCAATGGTCTTAAAATTGACAC
66 ACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTC-ATGATCTTACAATTGACAC
* * * *
24436 TAGAAGTTGTCATGAT--CTTACAATTGACACCAGAAGTTGTCAATGATCTTACA
130 CAGAAGTTGTCATGATAATTTCCAATTGACACTAGAAGTTGTC-ATGATCTTACA
* * * * *
24489 AATGACACCAGAAGTTGTCAATGGTCTTACAAATGACATCAAAAGTTGTCATGATCTTACAAATG
1 ATTGACACCAGAAGTTGTCAATGGTCTTACAATTGACACCAGAAGTTGTCATGATCTTACAATTG
* * * *
24554 ACACCAGAAGTTGTCATGATCTTACAAATGACACTAGGAGTTGTCATGATCTTACAAATGACACC
66 ACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTACAATTGACACC
* * *
24619 AGAAGTTGTCATGATAAATTTCCAAATGACACTAGAAGTTGTCATGATTTTGCA
131 AGAAGTTGTCATGAT-AATTTCCAATTGACACTAGAAGTTGTCATGATCTTACA
* ** * * * *
24673 ATTGACAACAGAAGTTGTC-ATCATTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAATTG
1 ATTGACACCAGAAGTTGTCAATGGTCTTACAATTGACACCAGAAGTTGTCATGATCTTACAATTG
* * * * * *
24737 ACACCAGAAGTTGTCATCATTTTGCAATTGACACCAGAAGTTGTCATCATTTTGCAATTGACACC
66 ACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTACAATTGACACC
* * *
24802 AGAAGTTGTCATAACTAATTTCCATTTGGCA-TATGAAGTTGTCAT
131 AGAAGTTGTCATGA-TAATTTCCAATTGACACTA-GAAGTTGTCAT
24847 TGTGCTTTAA
Statistics
Matches: 307, Mismatches: 46, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
182 33 0.11
183 226 0.74
184 27 0.09
185 21 0.07
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (183 bp):
ATTGACACCAGAAGTTGTCAATGGTCTTACAATTGACACCAGAAGTTGTCATGATCTTACAATTG
ACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTACAATTGACACC
AGAAGTTGTCATGATAATTTCCAATTGACACTAGAAGTTGTCATGATCTTACA
Found at i:24846 original size:153 final size:149
Alignment explanation
Indices: 24306--24815 Score: 597
Period size: 153 Copynumber: 3.4 Consensus size: 149
24296 AGAAATCTCC
* * * * * **
24306 ATTGACACCAGAAGTTGTCAATGGTCTTACAATTGATACCAGAAGTTGTCATGAGCTTACAATTG
1 ATTGACACCAGAAGTTGTC-ATGATTTTACAAATGACACCAGAAGTTGTCATAATTTTACAATTG
* * *
24371 ACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCAATGGTCTTAAAATTGACAC
65 ACA-TAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTC-ATGATCTTACAATTGACAC
24436 TAGAAGTTGTCATGATCTTACA
128 TAGAAGTTGTCATGATCTTACA
* ** * *
24458 ATTGACACCAGAAGTTGTCAATGATCTTACAAATGACACCAGAAGTTGTCAATGGTCTTACAAAT
1 ATTGACACCAGAAGTTGTC-ATGATTTTACAAATGACACCAGAAGTTGTC-ATAATTTTACAATT
* * *
24523 GACATCAAAAGTTGTCATGATCTTACAAATGACACCAGAAGTTGTCATGATCTTACAAATGACAC
64 GACAT-AGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTACAATTGACAC
*
24588 TAGGAGTTGTCATGATCTTACA
128 TAGAAGTTGTCATGATCTTACA
* * * * *
24610 AATGACACCAGAAGTTGTCATGATAAATTTCCAAATGACACTAGAAGTTGTCATGATTTTGCAAT
1 ATTGACACCAGAAGTTGTCATGAT---TTTACAAATGACACCAGAAGTTGTCATAATTTTACAAT
* * * * * *
24675 TGACAACAGAAGTTGTCATCATTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACA
63 TGAC-ATAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTACAATTGACA
* * * *
24740 CCAGAAGTTGTCATCATTTTGCA
127 CTAGAAGTTGTCATGATCTTACA
* * *
24763 ATTGACACCAGAAGTTGTCATCATTTTGCAATTGACACCAGAAGTTGTCATAA
1 ATTGACACCAGAAGTTGTCATGATTTTACAAATGACACCAGAAGTTGTCATAA
24816 CTAATTTCCA
Statistics
Matches: 311, Mismatches: 41, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
150 25 0.08
151 5 0.02
152 102 0.33
153 156 0.50
154 23 0.07
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (149 bp):
ATTGACACCAGAAGTTGTCATGATTTTACAAATGACACCAGAAGTTGTCATAATTTTACAATTGA
CATAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTACAATTGACACTAG
AAGTTGTCATGATCTTACA
Found at i:29424 original size:33 final size:33
Alignment explanation
Indices: 29387--29505 Score: 193
Period size: 33 Copynumber: 3.6 Consensus size: 33
29377 TTCTTTTCAC
* *
29387 CCAAAACAAAATTATTTTCAATGTTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
*
29420 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
29453 CCAAAACAGAATTATTTTCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
29486 CCAAAACAGATTTGTTTTCA
1 CCAAAACAGAATTATTTTCA
29506 TCACAATTAG
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATGATCAA
Found at i:29556 original size:33 final size:32
Alignment explanation
Indices: 29519--29592 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 32
29509 CAATTAGCAT
*
29519 TCAAAACAGATTTAGTGTC-ATCGCAAACAACA
1 TCAAAACAGATTTAGT-ACAATCGCAAACAACA
** *
29551 CTCAAATTAGGTTTAGTACAATCGCAAACAACA
1 -TCAAAACAGATTTAGTACAATCGCAAACAACA
29584 TCTAAAACA
1 TC-AAAACA
29593 CTCTTTACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.23
Consensus pattern (32 bp):
TCAAAACAGATTTAGTACAATCGCAAACAACA
Found at i:33592 original size:32 final size:31
Alignment explanation
Indices: 33533--33599 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 31
33523 ATTGATGTAT
*
33533 TCTC-TTCTGTCTGGAATAATAGAAATTCTC
1 TCTCTTTCTCTCTGGAATAATAGAAATTCTC
*
33563 TCTCTTTCTCTCTGGAATTAATAGGAATTCTC
1 TCTCTTTCTCTCTGGAA-TAATAGAAATTCTC
33595 TCTCT
1 TCTCT
33600 CTCTTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 4 0.12
31 11 0.33
32 18 0.55
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (31 bp):
TCTCTTTCTCTCTGGAATAATAGAAATTCTC
Found at i:33651 original size:3 final size:3
Alignment explanation
Indices: 33643--33679 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
33633 CATAACATAA
33643 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
33680 TGTATTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:37832 original size:72 final size:72
Alignment explanation
Indices: 37743--37909 Score: 271
Period size: 72 Copynumber: 2.3 Consensus size: 72
37733 AAACAGCCAA
* * * *
37743 TAGCTCTTGAATTATCAAAAATCTTTATTATTCATCATCCAAAACAGAATTTGCACAACTATATT
1 TAGCTCTTGAATTATCAAAAATCTCTATTATTCATAATCCAAAACAAAATTTGCAAAACTATATT
37808 AGAGCCC
66 AGAGCCC
* *
37815 TAGCTCTTGAATTATCAAACATCTCTATTATTCATAATTCAAAACAAAATTTGCAAAACTATATT
1 TAGCTCTTGAATTATCAAAAATCTCTATTATTCATAATCCAAAACAAAATTTGCAAAACTATATT
37880 AGAGCCC
66 AGAGCCC
*
37887 TAGCTCTTGAATAATCAAAAATC
1 TAGCTCTTGAATTATCAAAAATC
37910 GAAGCAAAGT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 87 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.33
Consensus pattern (72 bp):
TAGCTCTTGAATTATCAAAAATCTCTATTATTCATAATCCAAAACAAAATTTGCAAAACTATATT
AGAGCCC
Found at i:41902 original size:64 final size:63
Alignment explanation
Indices: 41791--41919 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 63
41781 CAGTTCAGCC
41791 GGTTGAACCGGTGGTTAAACCGCTTAAAAGATTTTTTAAAGAAAAAAACATTTTTAGTATAAAA
1 GGTTGAACCGGTGGTTAAACCGCTTAAAAGATTTTTTAAAG-AAAAAACATTTTTAGTATAAAA
*
41855 GGTTGAACCGGTGGTTAAACCGTTTAAAAGATTTTTTTTAAAGAAAAAACATTTTTAGTATAAAA
1 GGTTGAACCGGTGGTTAAACCGCTTAAAAGA--TTTTTTAAAGAAAAAACATTTTTAGTATAAAA
41920 TAAATATAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
64 30 0.48
65 22 0.35
66 10 0.16
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (63 bp):
GGTTGAACCGGTGGTTAAACCGCTTAAAAGATTTTTTAAAGAAAAAACATTTTTAGTATAAAA
Found at i:45523 original size:25 final size:25
Alignment explanation
Indices: 45486--45534 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
45476 GGGGACTTTG
*
45486 GGGGCGGTGTCTTTGCTGTGTTCAA
1 GGGGCAGTGTCTTTGCTGTGTTCAA
*
45511 GGGGCAGTTTCTTTGCTGTGTTCA
1 GGGGCAGTGTCTTTGCTGTGTTCA
45535 GTTCTACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.08, C:0.16, G:0.37, T:0.39
Consensus pattern (25 bp):
GGGGCAGTGTCTTTGCTGTGTTCAA
Found at i:50377 original size:54 final size:54
Alignment explanation
Indices: 50305--50514 Score: 219
Period size: 54 Copynumber: 3.9 Consensus size: 54
50295 TTCAACCCCA
** * * * * *
50305 CTTTGAATTTCAAAATTTCTTGGAGCAACTCCATTATTTGATTTAGCCCTTATT
1 CTTTGAATTTCAAAATTTCCAGCACCAACTCCATTAGTTGATTCAGCCCTTACT
** * *
50359 CTTTGAATTTCAGGATTTCCAGCACCAACTCCATTAGTTGGTTCAGCCCTTCCT
1 CTTTGAATTTCAAAATTTCCAGCACCAACTCCATTAGTTGATTCAGCCCTTACT
* * * * *
50413 CTTTGAATTTCAACA-TT-CAGCACCAACTCCATTAGTTGGTTCAACCATTCCT
1 CTTTGAATTTCAAAATTTCCAGCACCAACTCCATTAGTTGATTCAGCCCTTACT
* * * *
50465 CTTTGAATTTC-AAATTCCCAGCAGCAACTCCATGAGTTGATTCAACCCTT
1 CTTTGAATTTCAAAATTTCCAGCACCAACTCCATTAGTTGATTCAGCCCTT
50515 TCTCCATGAT
Statistics
Matches: 133, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
51 2 0.02
52 45 0.34
53 30 0.23
54 56 0.42
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (54 bp):
CTTTGAATTTCAAAATTTCCAGCACCAACTCCATTAGTTGATTCAGCCCTTACT
Found at i:50449 original size:52 final size:52
Alignment explanation
Indices: 50330--50514 Score: 219
Period size: 52 Copynumber: 3.5 Consensus size: 52
50320 TTTCTTGGAG
* * * ** *
50330 CAACTCCATTATTTGATTTAGCCCTTATTCTTTGAATTTCAGGATTTCCAGCAC
1 CAACTCCATTAGTTGATTCAACCCTTCCTCTTTGAATTTCA--AATTCCAGCAC
* *
50384 CAACTCCATTAGTTGGTTCAGCCCTTCCTCTTTGAATTTCAACATT-CAGCAC
1 CAACTCCATTAGTTGATTCAACCCTTCCTCTTTGAATTTCAA-ATTCCAGCAC
* * *
50436 CAACTCCATTAGTTGGTTCAACCATTCCTCTTTGAATTTCAAATTCCCAGCAG
1 CAACTCCATTAGTTGATTCAACCCTTCCTCTTTGAATTTCAAATT-CCAGCAC
*
50489 CAACTCCATGAGTTGATTCAACCCTT
1 CAACTCCATTAGTTGATTCAACCCTT
50515 TCTCCATGAT
Statistics
Matches: 116, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
51 3 0.03
52 47 0.41
53 30 0.26
54 36 0.31
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.36
Consensus pattern (52 bp):
CAACTCCATTAGTTGATTCAACCCTTCCTCTTTGAATTTCAAATTCCAGCAC
Found at i:50624 original size:53 final size:54
Alignment explanation
Indices: 50554--50682 Score: 208
Period size: 53 Copynumber: 2.4 Consensus size: 54
50544 TGAGTCTACC
50554 CTTT-CCTTCTGAATTTCAGAATGTCCAACAGCAACTCGATTAGCTGATGCAACA
1 CTTTCCCTT-TGAATTTCAGAATGTCCAACAGCAACTCGATTAGCTGATGCAACA
* *
50608 C-TTCCCTTTGAATTTCAGAATTTCCAACAGCAACTCGATTAGCTGATGCAACC
1 CTTTCCCTTTGAATTTCAGAATGTCCAACAGCAACTCGATTAGCTGATGCAACA
*
50661 CTTTCCCTATGAATTTCAGAAT
1 CTTTCCCTTTGAATTTCAGAAT
50683 CTACAACTGG
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
53 46 0.66
54 24 0.34
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (54 bp):
CTTTCCCTTTGAATTTCAGAATGTCCAACAGCAACTCGATTAGCTGATGCAACA
Found at i:51996 original size:73 final size:74
Alignment explanation
Indices: 51909--52060 Score: 270
Period size: 74 Copynumber: 2.1 Consensus size: 74
51899 AAAAATTCCT
*
51909 TTTGTTTATGTAACAGATTT-ATGTTCTATTAATTTGGAACTTTTGAAACTACAACTTTCTTGTA
1 TTTGTTTATGTAACAGATTTCATGCTCTATTAATTTGGAACTTTTGAAACTACAACTTTCTTGTA
51973 TGTTTCCCC
66 TGTTTCCCC
*
51982 TTTGTTTATGTAACAGATTTCATGCTCTGTTAATTTGGAACTTTTGAAACTACAACTTTCTTGTA
1 TTTGTTTATGTAACAGATTTCATGCTCTATTAATTTGGAACTTTTGAAACTACAACTTTCTTGTA
*
52047 TGTTTCCTC
66 TGTTTCCCC
52056 TTTGT
1 TTTGT
52061 ATATATGAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 20 0.27
74 55 0.73
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (74 bp):
TTTGTTTATGTAACAGATTTCATGCTCTATTAATTTGGAACTTTTGAAACTACAACTTTCTTGTA
TGTTTCCCC
Found at i:52253 original size:14 final size:14
Alignment explanation
Indices: 52234--52262 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52224 TCCTCCTAGT
52234 ACCTTATTGACTTG
1 ACCTTATTGACTTG
52248 ACCTTATTGACTTG
1 ACCTTATTGACTTG
52262 A
1 A
52263 AAAGGACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (14 bp):
ACCTTATTGACTTG
Found at i:61363 original size:48 final size:48
Alignment explanation
Indices: 61285--61443 Score: 148
Period size: 48 Copynumber: 3.4 Consensus size: 48
61275 ATATTCTTGT
* * *
61285 TTTTCCTAAAGT-GCCTTTCCCGGACAGAAGGTG-CTCGTTTAACTTTGG
1 TTTTCCTAAAATGGCC-TTCCCGAACAGAAGGTGAC-AGTTTAACTTTGG
* * *
61333 TTTTCCTAAAATGGCCTTCTCGAACGGAAGGTGACAGTTTAACTTTGT
1 TTTTCCTAAAATGGCCTTCCCGAACAGAAGGTGACAGTTTAACTTTGG
* * * * * *
61381 TTTTCCTAAAATGCCCTTCCCGGACAGAATGTGTCA-TTT-TC-TTGT
1 TTTTCCTAAAATGGCCTTCCCGAACAGAAGGTGACAGTTTAACTTTGG
*
61426 TTTTCCTAAAGTGGCCTT
1 TTTTCCTAAAATGGCCTT
61444 TTCAGACAGA
Statistics
Matches: 94, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
45 20 0.21
46 1 0.01
47 3 0.03
48 66 0.70
49 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (48 bp):
TTTTCCTAAAATGGCCTTCCCGAACAGAAGGTGACAGTTTAACTTTGG
Done.