Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011640.1 Corchorus capsularis cultivar CVL-1 contig11661, 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: 33087
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:520 original size:266 final size:266
Alignment explanation
Indices: 3--1196 Score: 1861
Period size: 266 Copynumber: 4.5 Consensus size: 266
1 GC
3 CATCACCAATTTGAATGGCATCTGTGCCATCAGTAATCATAGGAATGAGAAAGATCCTTTATGTC
1 CATCACCAATTTGAATGGCATCTGTGCCATCA-TAATCATAGGAATGAGAAAGATCCTTTATGTC
* * * *
68 AGATACAACATGATGAGAAGCCCCACAATCCATACACCAAGTTTTGCCATGGTTTGACTTGTTAT
65 AGATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGTCATGGTTTGAGTTGTCAT
* * * * * * * * *
133 CATTTATATT-TAAACATTGCTGTGTAAATTATATCAAATACAACAGAATTATGGTATCTTTCTC
130 CCTTTAT-TTCAAAACATTGATGTGTATATTATACCAAATACAACAGAAGTAAGTTATCTTTCCC
* * * **
197 AATCAATTCATATATATGGTATCAGTGCAAGTAATTTCATTGTTACCGACACGAGTGATAAGCAA
194 AATCAATTCTTATATATGGTATCAATGCAAGTAATTTCATTGTTACCAATGCGAGTGATAAGCAA
*
262 ACTTAAGT
259 ACGTAAGT
* * * * *
270 CATCACCAATTTGAATGACATTTGTGCCATCATAATAATAGGAAAGAGAAACATCCTTTATGTCA
1 CATCACCAATTTGAATGGCATCTGTGCCATCATAATCATAGGAATGAGAAAGATCCTTTATGTCA
*
335 GATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGTTATGGTTTGAGTTGTCATC
66 GATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGTCATGGTTTGAGTTGTCATC
400 CTTTATTTCAAAACATTGATGTGTATATTATACCAAATACAACAGAAGTAAGTTATCTTTCCCAA
131 CTTTATTTCAAAACATTGATGTGTATATTATACCAAATACAACAGAAGTAAGTTATCTTTCCCAA
* * *
465 TCAATTTTTATATATTGTATCAATGCAAGTAATTTCATTGTTATCAATGCGAGTGATAAGCAAAC
196 TCAATTCTTATATATGGTATCAATGCAAGTAATTTCATTGTTACCAATGCGAGTGATAAGCAAAC
*
530 GTAAGC
261 GTAAGT
* *
536 CATCACCAATTTGAATGGCATCTGTGCGATCATAATCATAGGAATGAGAAAGATCATTTATGTCA
1 CATCACCAATTTGAATGGCATCTGTGCCATCATAATCATAGGAATGAGAAAGATCCTTTATGTCA
*
601 GATACATCATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGTCATGGTTTGAGTTGTCATC
66 GATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGTCATGGTTTGAGTTGTCATC
* * *
666 CTTTATTTCAAAACATTGATGTGTATATTATACCAAATACAACAGATGTAAGCTATCTTTTCCAA
131 CTTTATTTCAAAACATTGATGTGTATATTATACCAAATACAACAGAAGTAAGTTATCTTTCCCAA
* * *
731 TCAATTATTATATATTGTATCAATGCAAGTAATTTCATTGTTATCAATGCGAGTGATAAGCAAAC
196 TCAATTCTTATATATGGTATCAATGCAAGTAATTTCATTGTTACCAATGCGAGTGATAAGCAAAC
796 GTAAGT
261 GTAAGT
* ** *
802 CATCACCAATTTAAATGGCATCTGTGTGATCATAATCATAGGAATGAGAAAGATCATTTATGTCA
1 CATCACCAATTTGAATGGCATCTGTGCCATCATAATCATAGGAATGAGAAAGATCCTTTATGTCA
* *
867 GATACAACATGATGAGAAGCCCTATAATCCATACACCAAGTTTTGTTATGGTTTGAGTTGTCATC
66 GATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGTCATGGTTTGAGTTGTCATC
932 CTTTATTTCAAAACATTGATGTGTATATTATACCAAATACAACAGAAGTAAGTTATCTTTCCCAA
131 CTTTATTTCAAAACATTGATGTGTATATTATACCAAATACAACAGAAGTAAGTTATCTTTCCCAA
* * * * *
997 TCAATTCTTATATATGGTATCAGTGTATGTAATTTCATTATTACCTATGCGAGTGATAAGCAAAC
196 TCAATTCTTATATATGGTATCAATGCAAGTAATTTCATTGTTACCAATGCGAGTGATAAGCAAAC
*
1062 TTAAGT
261 GTAAGT
* *
1068 CATCACCAATTTGAATGGCATCTGTGCCATCATAATCATAAGAATGAGAAAGATCCTTCATGTCA
1 CATCACCAATTTGAATGGCATCTGTGCCATCATAATCATAGGAATGAGAAAGATCCTTTATGTCA
* *
1133 GATACAACATGATGAGAATCCCCATAATCCATACACCAAGTTTT-TCCATGGTTAGAGTTGTCAT
66 GATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGT-CATGGTTTGAGTTGTCAT
1197 GATTGGCTAT
Statistics
Matches: 855, Mismatches: 70, Indels: 5
0.92 0.08 0.01
Matches are distributed among these distances:
265 3 0.00
266 822 0.96
267 30 0.04
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (266 bp):
CATCACCAATTTGAATGGCATCTGTGCCATCATAATCATAGGAATGAGAAAGATCCTTTATGTCA
GATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGTCATGGTTTGAGTTGTCATC
CTTTATTTCAAAACATTGATGTGTATATTATACCAAATACAACAGAAGTAAGTTATCTTTCCCAA
TCAATTCTTATATATGGTATCAATGCAAGTAATTTCATTGTTACCAATGCGAGTGATAAGCAAAC
GTAAGT
Found at i:5532 original size:2 final size:2
Alignment explanation
Indices: 5525--5549 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5515 TAACTTGTAA
5525 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5550 AAGATATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6004 original size:101 final size:97
Alignment explanation
Indices: 5857--6047 Score: 274
Period size: 101 Copynumber: 1.9 Consensus size: 97
5847 CCCAATAATT
* * * *
5857 AAAGTCCTCAAGGACAAGGGCATTTATAAGTCCCTAAACACAGAGGCATCTATATCAAAGTCCCC
1 AAAGTCCTCAAGCACAAGGGCATTTATAAATCCCTAAACACAGAGGCACCTATACCAAAGTCCCC
* *
5922 AGACACATATAACACAGGGGCAATTCTCTCTC
66 AAACACATATAACACAAGGGCAATTCTCTCTC
*
5954 AAAGTCCTCAAGCACAAGGGCATCTATACTAAAATCCCTAAACACAGAGGCACCTTTACCAAAGT
1 AAAGTCCTCAAGCACAAGGGCAT-T-TA-T-AAATCCCTAAACACAGAGGCACCTATACCAAAGT
*
6019 CCCTAAACACATATAACACAAGGGCAATT
62 CCCCAAACACATATAACACAAGGGCAATT
6048 TTCCTCTCTA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
97 22 0.27
98 1 0.01
99 2 0.02
100 1 0.01
101 56 0.68
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.19
Consensus pattern (97 bp):
AAAGTCCTCAAGCACAAGGGCATTTATAAATCCCTAAACACAGAGGCACCTATACCAAAGTCCCC
AAACACATATAACACAAGGGCAATTCTCTCTC
Found at i:7593 original size:20 final size:20
Alignment explanation
Indices: 7568--7608 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
7558 CAAGTTTCAA
7568 ATTAATTGAAAATCGATGTG
1 ATTAATTGAAAATCGATGTG
7588 ATTAATTGAAAATCGATGTG
1 ATTAATTGAAAATCGATGTG
7608 A
1 A
7609 GTATTGGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (20 bp):
ATTAATTGAAAATCGATGTG
Found at i:7930 original size:20 final size:20
Alignment explanation
Indices: 7905--7945 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
7895 CAAGTTTCAA
7905 ATTAATTGAAAATCGATGTG
1 ATTAATTGAAAATCGATGTG
7925 ATTAATTGAAAATCGATGTG
1 ATTAATTGAAAATCGATGTG
7945 A
1 A
7946 GTATTGGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (20 bp):
ATTAATTGAAAATCGATGTG
Found at i:8011 original size:28 final size:28
Alignment explanation
Indices: 7958--8014 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
7948 ATTGGTACCT
* *
7958 AAAATGGAATGACTCTGATGCCAAAAAA
1 AAAATGAAATGACTCTGATGACAAAAAA
*
7986 AAAATGAAATGACTCT-ATCGATAAAAAA
1 AAAATGAAATGACTCTGAT-GACAAAAAA
8014 A
1 A
8015 TTAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.54, C:0.12, G:0.14, T:0.19
Consensus pattern (28 bp):
AAAATGAAATGACTCTGATGACAAAAAA
Found at i:8256 original size:22 final size:22
Alignment explanation
Indices: 8228--8274 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
8218 AATAATTATG
8228 ATTTTACTATAAAAGAAAAGAA
1 ATTTTACTATAAAAGAAAAGAA
8250 ATTTTACTATAAAAGAAAAGAA
1 ATTTTACTATAAAAGAAAAGAA
8272 ATT
1 ATT
8275 CAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (22 bp):
ATTTTACTATAAAAGAAAAGAA
Found at i:12916 original size:18 final size:18
Alignment explanation
Indices: 12880--12923 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12870 TCAGACTATT
* *
12880 AAAAAAAACTGACTAAAC
1 AAAACAAACTAACTAAAC
* *
12898 AACACAAACTAACTCAAC
1 AAAACAAACTAACTAAAC
12916 AAAACAAA
1 AAAACAAA
12924 TTGACGAAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.66, C:0.23, G:0.02, T:0.09
Consensus pattern (18 bp):
AAAACAAACTAACTAAAC
Found at i:22464 original size:17 final size:17
Alignment explanation
Indices: 22442--22477 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
22432 GTTCAAAACT
22442 ATTTCCTAAAAAGACAC
1 ATTTCCTAAAAAGACAC
22459 ATTTCCTAAAAAGACAC
1 ATTTCCTAAAAAGACAC
22476 AT
1 AT
22478 ATCAACCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (17 bp):
ATTTCCTAAAAAGACAC
Found at i:24777 original size:4 final size:4
Alignment explanation
Indices: 24768--24826 Score: 55
Period size: 4 Copynumber: 14.8 Consensus size: 4
24758 ATAGTTTCCT
* * * * * * *
24768 TATA TATA TATA TATA CATA CATA CATA AATA CATA CATA CATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
24816 TATA TATA TAT
1 TATA TATA TAT
24827 TTGATACATC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (4 bp):
TATA
Found at i:24826 original size:8 final size:8
Alignment explanation
Indices: 24769--24823 Score: 65
Period size: 8 Copynumber: 6.9 Consensus size: 8
24759 TAGTTTCCTT
*
24769 ATATATAT
1 ATATATAC
24777 ATATATAC
1 ATATATAC
*
24785 ATACATAC
1 ATATATAC
*
24793 ATAAATAC
1 ATATATAC
*
24801 ATACATAC
1 ATATATAC
*
24809 ATATATAT
1 ATATATAC
24817 ATATATA
1 ATATATA
24824 TATTTGATAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAC
Found at i:29589 original size:15 final size:15
Alignment explanation
Indices: 29555--29595 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
29545 GGTGAGTGTG
29555 GGTGAGTATCTCACCA
1 GGTGAGTAT-TCACCA
29571 GGTGAGTATT-ACACA
1 GGTGAGTATTCAC-CA
29586 GGTGAGTATT
1 GGTGAGTATT
29596 GTACTGGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.08
15 13 0.54
16 9 0.38
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (15 bp):
GGTGAGTATTCACCA
Found at i:29607 original size:16 final size:16
Alignment explanation
Indices: 29586--29713 Score: 128
Period size: 16 Copynumber: 8.4 Consensus size: 16
29576 GTATTACACA
29586 GGTGAGTATTGTACTG
1 GGTGAGTATTGTACTG
29602 GGTGAGTATTGTACTG
1 GGTGAGTATTGTACTG
29618 GGTGAG---TG---TG
1 GGTGAGTATTGTACTG
* **
29628 GGTGAGTATCT-CACCA
1 GGTGAGTAT-TGTACTG
** *
29644 GGTGAGTATTACAC-A
1 GGTGAGTATTGTACTG
29659 GGTGAGTATTGTACTG
1 GGTGAGTATTGTACTG
29675 GGTGAGTATTGTACTG
1 GGTGAGTATTGTACTG
*
29691 AGTGAGTATTGTACTG
1 GGTGAGTATTGTACTG
29707 GGTGAGT
1 GGTGAGT
29714 GTGGGTGAGT
Statistics
Matches: 96, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.08
13 2 0.02
14 1 0.01
15 14 0.15
16 71 0.74
ACGTcount: A:0.21, C:0.09, G:0.37, T:0.34
Consensus pattern (16 bp):
GGTGAGTATTGTACTG
Found at i:29614 original size:73 final size:73
Alignment explanation
Indices: 29529--29697 Score: 329
Period size: 73 Copynumber: 2.3 Consensus size: 73
29519 GGCCTCACCA
29529 GGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAGGTGAGTATTACACAGGTGAGTA
1 GGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAGGTGAGTATTACACAGGTGAGTA
29594 TTGTACTG
66 TTGTACTG
29602 GGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAGGTGAGTATTACACAGGTGAGTA
1 GGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAGGTGAGTATTACACAGGTGAGTA
29667 TTGTACTG
66 TTGTACTG
*
29675 GGTGAGTATTGTACTGAGTGAGT
1 GGTGAGTATTGTACTGGGTGAGT
29698 ATTGTACTGG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 95 1.00
ACGTcount: A:0.22, C:0.10, G:0.36, T:0.32
Consensus pattern (73 bp):
GGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAGGTGAGTATTACACAGGTGAGTA
TTGTACTG
Found at i:29632 original size:57 final size:57
Alignment explanation
Indices: 29571--29681 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 57
29561 TATCTCACCA
** *
29571 GGTGAGTAT-T-ACACAGGTGAGTATTGTACTGGGTGAGTATTGTACTGGGTGAGTGTG
1 GGTGAGTATCTCAC-CAGGTGAGTATTACAC-AGGTGAGTATTGTACTGGGTGAGTGTG
29628 GGTGAGTATCTCACCAGGTGAGTATTACACAGGTGAGTATTGTACTGGGTGAGT
1 GGTGAGTATCTCACCAGGTGAGTATTACACAGGTGAGTATTGTACTGGGTGAGT
29682 ATTGTACTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
57 32 0.65
58 15 0.31
59 2 0.04
ACGTcount: A:0.23, C:0.10, G:0.36, T:0.32
Consensus pattern (57 bp):
GGTGAGTATCTCACCAGGTGAGTATTACACAGGTGAGTATTGTACTGGGTGAGTGTG
Found at i:29662 original size:15 final size:15
Alignment explanation
Indices: 29628--29668 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
29618 GGTGAGTGTG
29628 GGTGAGTATCTCACCA
1 GGTGAGTAT-TCACCA
29644 GGTGAGTATT-ACACA
1 GGTGAGTATTCAC-CA
29659 GGTGAGTATT
1 GGTGAGTATT
29669 GTACTGGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.08
15 13 0.54
16 9 0.38
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (15 bp):
GGTGAGTATTCACCA
Found at i:29680 original size:89 final size:88
Alignment explanation
Indices: 29555--29742 Score: 306
Period size: 89 Copynumber: 2.1 Consensus size: 88
29545 GGTGAGTGTG
*
29555 GGTGAGTATCTCACCAGGTGAGTATTACACAGGTGAGTATTGTACTGGGTGAGTATTGTACTGGG
1 GGTGAGTAT-TCACCAGGTGAGTATTACACAGGTGAGTATTGTACTGAGTGAGTATTGTACTGGG
29620 TGAGTGTGGGTGAGTATCTCACCA
65 TGAGTGTGGGTGAGTATCTCACCA
** *
29644 GGTGAGTATT-ACACAGGTGAGTATTGTACTGGGTGAGTATTGTACTGAGTGAGTATTGTACTGG
1 GGTGAGTATTCAC-CAGGTGAGTATTACAC-AGGTGAGTATTGTACTGAGTGAGTATTGTACTGG
29708 GTGAGTGTGGGTGAGTATCTCACCA
64 GTGAGTGTGGGTGAGTATCTCACCA
29733 GGTGAGTATT
1 GGTGAGTATT
29743 TGTATTGGGT
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
87 2 0.02
88 15 0.16
89 76 0.82
ACGTcount: A:0.22, C:0.11, G:0.35, T:0.32
Consensus pattern (88 bp):
GGTGAGTATTCACCAGGTGAGTATTACACAGGTGAGTATTGTACTGAGTGAGTATTGTACTGGGT
GAGTGTGGGTGAGTATCTCACCA
Found at i:32440 original size:30 final size:29
Alignment explanation
Indices: 32372--32441 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
32362 ATTGGTTCTC
*
32372 CCCTGGTGCGTGGCACTAGGGGAATCCCT
1 CCCTGGTGCGCGGCACTAGGGGAATCCCT
* * *
32401 CCCTGGTGCGCGGCGCTGGGGGAGTCCCT
1 CCCTGGTGCGCGGCACTAGGGGAATCCCT
32430 CCCTTGGTGCGC
1 CCC-TGGTGCGC
32442 ACTGGGGGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 28 0.78
30 8 0.22
ACGTcount: A:0.07, C:0.34, G:0.39, T:0.20
Consensus pattern (29 bp):
CCCTGGTGCGCGGCACTAGGGGAATCCCT
Found at i:32452 original size:27 final size:27
Alignment explanation
Indices: 32384--32507 Score: 97
Period size: 27 Copynumber: 4.4 Consensus size: 27
32374 CTGGTGCGTG
* *
32384 GCACTAGGGGAATCCCTCCC-TGGTGCGC
1 GCACTGGGGGAGTCCCTCCCTTGGT--GC
*
32412 GGCGCTGGGGGAGTCCCTCCCTTGGTGC
1 -GCACTGGGGGAGTCCCTCCCTTGGTGC
**
32440 GCACTGGGGGAGTATCTCCCCTGGTGGTGC
1 GCACTGGGGGAGTCCCT-CCCT--TGGTGC
* ** *
32470 GCACTTGGGGAGTGTCTCCCCTGGTGC
1 GCACTGGGGGAGTCCCTCCCTTGGTGC
*
32497 GCGCTGGGGGA
1 GCACTGGGGGA
32508 TTGACTTCCC
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
27 29 0.36
28 6 0.08
29 20 0.25
30 25 0.31
ACGTcount: A:0.09, C:0.30, G:0.40, T:0.21
Consensus pattern (27 bp):
GCACTGGGGGAGTCCCTCCCTTGGTGC
Found at i:32468 original size:30 final size:30
Alignment explanation
Indices: 32368--32495 Score: 108
Period size: 30 Copynumber: 4.4 Consensus size: 30
32358 GGGAATTGGT
*
32368 TCTCCCCTGGTGCGTG-GCACTAGGGGA--A
1 TCTCCCCTGGTG-GTGCGCACTGGGGGAGTA
* * * *
32396 TCCCTCCCTGGT-GCGCGGCGCTGGGGGAGTC
1 TCTC-CCCTGGTGGTGC-GCACTGGGGGAGTA
*
32427 CCT-CCCT--TGGTGCGCACTGGGGGAGTA
1 TCTCCCCTGGTGGTGCGCACTGGGGGAGTA
* *
32454 TCTCCCCTGGTGGTGCGCACTTGGGGAGTG
1 TCTCCCCTGGTGGTGCGCACTGGGGGAGTA
32484 TCTCCCCTGGTG
1 TCTCCCCTGGTG
32496 CGCGCTGGGG
Statistics
Matches: 78, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
27 17 0.22
28 10 0.13
29 20 0.26
30 30 0.38
31 1 0.01
ACGTcount: A:0.08, C:0.31, G:0.38, T:0.23
Consensus pattern (30 bp):
TCTCCCCTGGTGGTGCGCACTGGGGGAGTA
Found at i:32518 original size:27 final size:27
Alignment explanation
Indices: 32416--32525 Score: 96
Period size: 27 Copynumber: 4.0 Consensus size: 27
32406 GTGCGCGGCG
** *
32416 CTGGGGGAGTCCCTCCCTTGGTGCGCA
1 CTGGGGGAGTGACTCCCCTGGTGCGCA
32443 CTGGGGGAGT-ATCTCCCCTGGTGGTGCGCA
1 CTGGGGGAGTGA-CTCCCC---TGGTGCGCA
* * *
32473 CTTGGGGAGTGTCTCCCCTGGTGCGCG
1 CTGGGGGAGTGACTCCCCTGGTGCGCA
* * *
32500 CTGGGGGATTGACTTCCCTGGCGCGC
1 CTGGGGGAGTGACTCCCCTGGTGCGC
32526 CTCTCCCCTT
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
27 44 0.65
30 24 0.35
ACGTcount: A:0.07, C:0.30, G:0.39, T:0.24
Consensus pattern (27 bp):
CTGGGGGAGTGACTCCCCTGGTGCGCA
Found at i:32662 original size:27 final size:29
Alignment explanation
Indices: 32624--32695 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
32614 TTTTTTAGTT
*
32624 GGGATTCT-TCCCTTGGT-ACAG-CACTA
1 GGGAGTCTCTCCCTTGGTCACAGACACTA
*
32650 GGGAGTCTCTCCCCTGGTGCACAGACACTA
1 GGGAGTCTCTCCCTTGGT-CACAGACACTA
32680 GGGAG--TCTCCCTTGGT
1 GGGAGTCTCTCCCTTGGT
32696 GCGCGGACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 7 0.18
27 8 0.21
28 10 0.26
29 4 0.10
30 10 0.26
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (29 bp):
GGGAGTCTCTCCCTTGGTCACAGACACTA
Found at i:32664 original size:28 final size:29
Alignment explanation
Indices: 32624--32688 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
32614 TTTTTTAGTT
* *
32624 GGGATTCT-TCCCTTGGT-ACAG-CACTA
1 GGGAGTCTCTCCCCTGGTCACAGACACTA
32650 GGGAGTCTCTCCCCTGGTGCACAGACACTA
1 GGGAGTCTCTCCCCTGGT-CACAGACACTA
32680 GGGAGTCTC
1 GGGAGTCTC
32689 CCTTGGTGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 7 0.21
27 8 0.24
29 4 0.12
30 14 0.42
ACGTcount: A:0.18, C:0.29, G:0.28, T:0.25
Consensus pattern (29 bp):
GGGAGTCTCTCCCCTGGTCACAGACACTA
Found at i:32689 original size:28 final size:28
Alignment explanation
Indices: 32641--32719 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
32631 TTCCCTTGGT
32641 ACAG-CACTAGGGAGTCTCTCCCCTGGTGC
1 ACAGACACTAGGGAG--TCTCCCCTGGTGC
*
32670 ACAGACACTAGGGAGTCTCCCTTGGTGC
1 ACAGACACTAGGGAGTCTCCCCTGGTGC
* * *
32698 GCGGACATTAGGGGAGTCTCCC
1 ACAGACACTA-GGGAGTCTCCC
32720 GTAGTGCGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 19 0.43
29 15 0.34
30 10 0.23
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.20
Consensus pattern (28 bp):
ACAGACACTAGGGAGTCTCCCCTGGTGC
Found at i:32761 original size:151 final size:153
Alignment explanation
Indices: 32591--32891 Score: 482
Period size: 151 Copynumber: 2.0 Consensus size: 153
32581 TTTTTTTAAA
* *
32591 CATTATTATTTTTTGTGTTTTATT-TTTTTAGTTGGGATTCTTCCCTTGGTACAGCACTAGGGAG
1 CATTAATATTTTTTATGTTTTATTGTTTTTAGTTGGGATTC-TCCCTTGGTACAGCACTAGGGAG
* *
32655 TCTCTCCCCTGGTGCACAGACACT-AGGGAGTCTCCCTTGGTGCGCGGACATTAGGGGAGTCTCC
65 TCTCCCCCCTGGTGCACAGACACTGAGGGAGTCTCCCTTGGTGCGCGGACACTAGGGGAGTCTCC
*
32719 CGTAGTGCG-TTTTTTTAATAAGT
130 CCTAGTGCGTTTTTTTTAATAAGT
* *
32742 CATTAATATTTTTTATGTTTTATTGTTTTTAGTTGGGATTCTCCCTTGGTGCAGCATTAGGGAGT
1 CATTAATATTTTTTATGTTTTATTGTTTTTAGTTGGGATTCTCCCTTGGTACAGCACTAGGGAGT
* * *
32807 CTCCCCCCTGGTGCGCAGACACTGGGGGAGTCTCCCTTGGTGCGTGGACACTAGGGGAGTCTCCC
66 CTCCCCCCTGGTGCACAGACACTGAGGGAGTCTCCCTTGGTGCGCGGACACTAGGGGAGTCTCCC
32872 CTAGTGCGTTTTTTTTAATA
131 CTAGTGCGTTTTTTTTAATA
32892 TATAACTTGG
Statistics
Matches: 137, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
151 65 0.47
152 61 0.45
153 11 0.08
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (153 bp):
CATTAATATTTTTTATGTTTTATTGTTTTTAGTTGGGATTCTCCCTTGGTACAGCACTAGGGAGT
CTCCCCCCTGGTGCACAGACACTGAGGGAGTCTCCCTTGGTGCGCGGACACTAGGGGAGTCTCCC
CTAGTGCGTTTTTTTTAATAAGT
Found at i:32880 original size:29 final size:29
Alignment explanation
Indices: 32801--32880 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
32791 TGCAGCATTA
* *
32801 GGGAGTCTCCCCCCTGGTGCGCAGACACTGG
1 GGGAGTCT--CCCCTGGTGCGTAGACACTAG
* *
32832 GGGAGTCTCCCTTGGTGCGTGGACACTAG
1 GGGAGTCTCCCCTGGTGCGTAGACACTAG
*
32861 GGGAGTCTCCCCTAGTGCGT
1 GGGAGTCTCCCCTGGTGCGT
32881 TTTTTTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 35 0.81
31 8 0.19
ACGTcount: A:0.12, C:0.30, G:0.36, T:0.21
Consensus pattern (29 bp):
GGGAGTCTCCCCTGGTGCGTAGACACTAG
Found at i:32971 original size:30 final size:30
Alignment explanation
Indices: 32933--33030 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 30
32923 TTGGGGAGTC
32933 TCTCTCCCTTGGCGTGCGGCACCT-AGGGAG
1 TCTCTCCCTTGGCGTGCGGCA-CTGAGGGAG
* * *
32963 TCTGTCCCTTGGCGTGTGGCACTGGGGGAG
1 TCTCTCCCTTGGCGTGCGGCACTGAGGGAG
** * *
32993 TCTCTCCCTTGGCGCACGGCATTGGGGGAG
1 TCTCTCCCTTGGCGTGCGGCACTGAGGGAG
33023 TCTCTCCC
1 TCTCTCCC
33031 CTGGTGCGCA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 57 0.97
ACGTcount: A:0.08, C:0.32, G:0.35, T:0.26
Consensus pattern (30 bp):
TCTCTCCCTTGGCGTGCGGCACTGAGGGAG
Found at i:33063 original size:26 final size:27
Alignment explanation
Indices: 33029--33085 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
33019 GGAGTCTCTC
33029 CCCTGGTGCGCAGACACT-GGGAGTCT
1 CCCTGGTGCGCAGACACTGGGGAGTCT
*
33055 CCCTGGTGCGCGGACACTGGGGGAGTCT
1 CCCTGGTGCGCAGACACT-GGGGAGTCT
33083 CCC
1 CCC
33086 CT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 17 0.61
28 11 0.39
ACGTcount: A:0.12, C:0.33, G:0.37, T:0.18
Consensus pattern (27 bp):
CCCTGGTGCGCAGACACTGGGGAGTCT
Done.