Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008795.1 Corchorus capsularis cultivar CVL-1 contig08816, 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: 23600
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:165 original size:22 final size:21
Alignment explanation
Indices: 135--175 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
125 GAGAACTTTT
**
135 TTATAAATTTTTTTAACCTTC
1 TTATAAATTTAATTAACCTTC
156 TTATGAAATTTAATTAACCT
1 TTAT-AAATTTAATTAACCT
176 CGAAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.51
Consensus pattern (21 bp):
TTATAAATTTAATTAACCTTC
Found at i:345 original size:22 final size:22
Alignment explanation
Indices: 307--411 Score: 79
Period size: 22 Copynumber: 4.7 Consensus size: 22
297 AAAACCTCCA
* *
307 TATG-AATTGTCAGTAATCACAT
1 TATGAAATTGTGA-TAATCACAC
* *
329 TCTGAAATTTTGATAATCACAC
1 TATGAAATTGTGATAATCACAC
* * *
351 TATGAAATTGTGATAACCTCGC
1 TATGAAATTGTGATAATCACAC
* *
373 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTGTGAT-AATC-ACAC
*
396 TATGAAATTTTGATAA
1 TATGAAATTGTGATAA
412 ACCTCCCTAT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
22 43 0.62
23 24 0.35
24 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:453 original size:22 final size:22
Alignment explanation
Indices: 331--625 Score: 146
Period size: 22 Copynumber: 13.6 Consensus size: 22
321 AATCACATTC
**
331 TGAAATTTTGATAA-TCACACTA
1 TGAAATTTTGATAACTTTC-CTA
* *
353 TGAAATTGTGATAAC-CTCGCTA
1 TGAAATTTTGATAACTTTC-CTA
*
375 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAACT-TTCCTA
* *
398 TGAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACTTTCCTA
* *
421 TAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAACTTTCCTA
*
443 TGAAATCTTGATAA-----CTA
1 TGAAATTTTGATAACTTTCCTA
* * *
460 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACTTTCCTA
** * *
481 TGATTTTTTGATAAC-CTCATTA
1 TGAAATTTTGATAACTTTC-CTA
* *
503 TGAAATTTTGTTAA-TCTCCCTA
1 TGAAATTTTGATAACT-TTCCTA
* * *
525 TGAAATTTTGATCTAC-ATACTA
1 TGAAATTTTGAT-AACTTTCCTA
* ** * *
547 TAAAATTTTGATAACCCTCTTG
1 TGAAATTTTGATAACTTTCCTA
* ***
569 TGAAATTTTGAAAACTAAACTA
1 TGAAATTTTGATAACTTTCCTA
*
591 TGAAATTTTGATAACCTTCAC-A
1 TGAAATTTTGATAACTTTC-CTA
613 TGAAATTTTGATA
1 TGAAATTTTGATA
626 TCCTCCCTGA
Statistics
Matches: 202, Mismatches: 54, Indels: 34
0.70 0.19 0.12
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
21 6 0.03
22 145 0.72
23 34 0.17
24 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACTTTCCTA
Found at i:553 original size:44 final size:44
Alignment explanation
Indices: 177--625 Score: 219
Period size: 44 Copynumber: 10.3 Consensus size: 44
167 AATTAACCTC
* * * * *
177 GAAATTTTGA-AGACCTCAATATGAAATTTTGATAACTTCCCAAT
1 GAAATTTTGATA-ACATCACTATAAAATTTTGATAACCTCCCTAT
* * * * *
221 GAAATTTTGATAACCAACACTATGAGATGTTGATAACCTCCATAT
1 GAAATTTTGATAA-CATCACTATAAAATTTTGATAACCTCCCTAT
** * * * *
266 GGTATATTGATAAC--CACGTTATGAAAA-TTTAAAAACCTCCATAT
1 GAAATTTTGATAACATCAC--TAT-AAAATTTTGATAACCTCCCTAT
* * * * * * * *
310 G-AATTGTCAGTAATCA-CATTCTGAAATTTTGATAATCACACTAT
1 GAAATTTTGA-TAA-CATCACTATAAAATTTTGATAACCTCCCTAT
* * * * * *
354 GAAATTGTGATAACCTCGCTATGAAATTTTGATAAATCTTCCTAT
1 GAAATTTTGATAACATCACTATAAAATTTTGAT-AACCTCCCTAT
* * * * *
399 GAAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTAT
1 GAAATTTTGAT-AACATCACTATAAAATTTTGATAACCTCCCTAT
*
444 GAAATCTTGATAAC-T-AC----AAATTTTGATAACCTCCCTAT
1 GAAATTTTGATAACATCACTATAAAATTTTGATAACCTCCCTAT
** * * * * *
482 GATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTAT
1 GAAATTTTGATAACATCACTATAAAATTTTGATAACCTCCCTAT
* * *
526 GAAATTTTGATCTACAT-ACTATAAAATTTTGATAACC-CTCTTGT
1 GAAATTTTGAT-AACATCACTATAAAATTTTGATAACCTC-CCTAT
* * * *
570 GAAATTTTGAAAAC-TAAACTATGAAATTTTGATAACCTTCAC-AT
1 GAAATTTTGATAACAT-CACTATAAAATTTTGATAACC-TCCCTAT
614 GAAATTTTGATA
1 GAAATTTTGATA
626 TCCTCCCTGA
Statistics
Matches: 309, Mismatches: 71, Indels: 50
0.72 0.17 0.12
Matches are distributed among these distances:
38 29 0.09
39 1 0.00
40 1 0.00
42 5 0.02
43 12 0.04
44 155 0.50
45 83 0.27
46 23 0.07
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (44 bp):
GAAATTTTGATAACATCACTATAAAATTTTGATAACCTCCCTAT
Found at i:619 original size:66 final size:65
Alignment explanation
Indices: 331--630 Score: 240
Period size: 66 Copynumber: 4.6 Consensus size: 65
321 AATCACATTC
* * * ** **
331 TGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAATCTTCC
1 TGAAATTTTGATAACCTCACTATGAAATTTTGATAACCTCATTATGAAATTTTGA-AAA-CTAAC
396 TA
64 TA
* * * *
398 TGAAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTC-TTATGAAATCTTG---A-TAAC
1 TGAAATTTTGAT-AACCTCACTATGAAATTTTGATAAC-CTCATTATGAAATTTTGAAAACTAAC
458 TA
64 TA
* * ** * * **
460 -CAAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCT
1 TGAAATTTTGATAACCTCACTATGAAATTTTGATAACCTCATTATGAAATTTTG-AAAACTAACT
524 A
65 A
* * * *
525 TGAAATTTTGATCTACAT-ACTATAAAATTTTGATAACCCTC-TTGTGAAATTTTGAAAACTAAA
1 TGAAATTTTGAT-AACCTCACTATGAAATTTTGATAA-CCTCATTATGAAATTTTGAAAACT-AA
588 CTA
63 CTA
*
591 TGAAATTTTGATAACCTTCAC-ATGAAATTTTGATATCCTC
1 TGAAATTTTGATAACC-TCACTATGAAATTTTGATAACCTC
631 CCTGAATTTT
Statistics
Matches: 184, Mismatches: 35, Indels: 30
0.74 0.14 0.12
Matches are distributed among these distances:
59 2 0.01
60 34 0.18
61 10 0.05
62 4 0.02
64 1 0.01
65 14 0.08
66 65 0.35
67 21 0.11
68 31 0.17
69 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (65 bp):
TGAAATTTTGATAACCTCACTATGAAATTTTGATAACCTCATTATGAAATTTTGAAAACTAACTA
Found at i:669 original size:19 final size:20
Alignment explanation
Indices: 591--663 Score: 94
Period size: 19 Copynumber: 3.6 Consensus size: 20
581 AACTAAACTA
* *
591 TGAAATTTTGATAACCTTCACA
1 TGAAATTTTGATATCC-TC-CC
613 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
633 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
652 TGAAATTTTGAT
1 TGAAATTTTGAT
664 TACTCCATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
19 18 0.38
20 12 0.26
21 2 0.04
22 15 0.32
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:708 original size:19 final size:20
Alignment explanation
Indices: 591--709 Score: 82
Period size: 19 Copynumber: 5.8 Consensus size: 20
581 AACTAAACTA
591 TGAAATTTTGATAACCTTCAC
1 TGAAATTTTGATAACCTTC-C
* *
612 ATGAAATTTTGATATCCTCCC
1 -TGAAATTTTGATAACCTTCC
*
633 TG-AATTTTGATATCC-TCC
1 TGAAATTTTGATAACCTTCC
* * **
651 TTGAAATTTTGATTACTCCATAA
1 -TGAAATTTTGA-TA-ACCTTCC
* * *
674 TAAAAGTTTAATAACCTTCC
1 TGAAATTTTGATAACCTTCC
694 T-AAATTTTGATAACCT
1 TGAAATTTTGATAACCT
710 CCCCAGAAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
18 2 0.03
19 28 0.36
20 14 0.18
21 5 0.06
22 28 0.36
23 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (20 bp):
TGAAATTTTGATAACCTTCC
Found at i:775 original size:44 final size:43
Alignment explanation
Indices: 725--867 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 43
715 GAAATACCAC
725 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTTGTAATCACATTTT-AAAATTTGATAACCTCTT
* * * * *
769 TATGAAA-TTTTGATAACCTC-TTTATAAAATTTTGTTGACCCCTT
1 TATGAAATTTTTG-TAATCACATTT-TAAAA-TTTGATAACCTCTT
* * * * *
813 TATGAAATTCTTATAATCACATTATATAATTTTGATAACCTCGCT
1 TATGAAATTTTTGTAATCACATTTTA-AAATTTGATAACCTC-TT
858 T-TGAAATTTT
1 TATGAAATTTT
868 AACAATGCTA
Statistics
Matches: 76, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
43 12 0.16
44 55 0.72
45 9 0.12
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.45
Consensus pattern (43 bp):
TATGAAATTTTTGTAATCACATTTTAAAATTTGATAACCTCTT
Found at i:820 original size:22 final size:22
Alignment explanation
Indices: 749--852 Score: 95
Period size: 22 Copynumber: 4.7 Consensus size: 22
739 AATCACATTT
* *
749 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTTTA
*
771 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTTTA
* * *
793 TAAAATTTTGTTGACCCCTTTA
1 TGAAATTTTGATAACCCCTTTA
* * *
815 TGAAATTCTT-ATAATCACATTA
1 TGAAATT-TTGATAACCCCTTTA
837 T-ATAATTTTGATAACC
1 TGA-AATTTTGATAACC
853 TCGCTTTGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.04
22 62 0.93
23 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTTTA
Found at i:929 original size:25 final size:23
Alignment explanation
Indices: 875--939 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 23
865 TTTAACAATG
* *
875 CTATGAAATTTTGACAAT-CTTC
1 CTATGAAATTTTGATAATCCATC
897 CTAT-AAATTTTGATAATCCGATC
1 CTATGAAATTTTGATAATCC-ATC
*
920 TCTATGAAATTTCGATAATC
1 -CTATGAAATTTTGATAATC
940 ACTCTATGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.33
22 5 0.14
23 2 0.06
24 4 0.11
25 13 0.36
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCCATC
Found at i:947 original size:22 final size:22
Alignment explanation
Indices: 724--948 Score: 85
Period size: 22 Copynumber: 10.3 Consensus size: 22
714 AGAAATACCA
724 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
747 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * *
768 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * * *
790 TTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
*
812 TTATGAAATTCTT-ATAATCACAT
1 CTATGAAATT-TTGATAATCAC-T
* * *
835 -TAT-ATAATTTTGATAACCTCG
1 CTATGA-AATTTTGATAATCACT
* *
856 CTTTGAAA-TTT--TAA-CAAT
1 CTATGAAATTTTGATAATCACT
* *
874 GCTATGAAATTTTGACAATC-TT
1 -CTATGAAATTTTGATAATCACT
896 CCTAT-AAATTTTGATAATCCGATCT
1 -CTATGAAATTTTGATAAT-C-A-CT
*
921 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
943 CTATGA
1 CTATGA
949 GATTGGATAA
Statistics
Matches: 155, Mismatches: 29, Indels: 37
0.70 0.13 0.17
Matches are distributed among these distances:
18 1 0.01
19 10 0.06
20 3 0.02
21 23 0.15
22 94 0.61
23 6 0.04
24 5 0.03
25 13 0.08
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:1027 original size:22 final size:23
Alignment explanation
Indices: 998--1052 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
988 AAATTGAGAC
* *
998 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
1019 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
1041 TTTTGATAACCT
1 TTTTGATAACCT
1053 CCCCATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:1063 original size:22 final size:22
Alignment explanation
Indices: 1013--1063 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1003 TAACCTTCAT
*
1013 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
1035 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
1057 ATGAAAT
1 ATGAAAT
1064 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:1195 original size:22 final size:24
Alignment explanation
Indices: 1170--1227 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
1160 AATTAACCAC
1170 CCTATGAAATTTCAATAACC-GA-
1 CCTATGAAATTTCAATAACCTGAT
* * *
1192 CCTAAGAGATTTTAATAACCTGAT
1 CCTATGAAATTTCAATAACCTGAT
1216 CCTATGAAATTT
1 CCTATGAAATTT
1228 TGGTAATCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 17 0.59
23 2 0.07
24 10 0.34
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (24 bp):
CCTATGAAATTTCAATAACCTGAT
Found at i:1270 original size:22 final size:21
Alignment explanation
Indices: 1170--1301 Score: 66
Period size: 22 Copynumber: 6.0 Consensus size: 21
1160 AATTAACCAC
** *
1170 CCTATGAAATTTCAATAACCGA
1 CCTATGAAATTTTGATAACC-T
* * *
1192 CCTAAGAGATTTTAATAACCTGAT
1 CCTATGAAATTTTGATAACC---T
* *
1216 CCTATGAAATTTTGGTAATCAT
1 CCTATGAAATTTTGATAA-CCT
* *
1238 ACTATGGAATTTTGATAACCT
1 CCTATGAAATTTTGATAACCT
* *
1259 CCTCATGAAATTGTAATAACCAT
1 CCT-ATGAAATTTTGATAACC-T
* * *
1282 CTTATAAAATTTTGTTAACC
1 CCTATGAAATTTTGATAACC
1302 ACATAGAGAA
Statistics
Matches: 82, Mismatches: 23, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
21 4 0.05
22 60 0.73
23 3 0.04
24 14 0.17
25 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (21 bp):
CCTATGAAATTTTGATAACCT
Found at i:1864 original size:31 final size:31
Alignment explanation
Indices: 1799--1857 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1789 TGGCAATTTA
1799 GAAATATGTTTTAAAGAAAAGGGTACAACTG
1 GAAATATGTTTTAAAGAAAAGGGTACAACTG
1830 GAAATATGTTTTAAA-AATAAGGGTACAA
1 GAAATATGTTTTAAAGAA-AAGGGTACAA
1858 TCGGAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTTAAAGAAAAGGGTACAACTG
Found at i:2461 original size:2 final size:2
Alignment explanation
Indices: 2449--2493 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
2439 TGAAATAAAT
2449 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2492 TA
1 TA
2494 AACAAAGCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:9935 original size:25 final size:25
Alignment explanation
Indices: 9901--9950 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
9891 AGGAGATGAG
9901 GAATATAATAGGAGGCATGAAATCT
1 GAATATAATAGGAGGCATGAAATCT
*
9926 GAATATAATAGGATGCATGAAATCT
1 GAATATAATAGGAGGCATGAAATCT
9951 CTCTGCAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (25 bp):
GAATATAATAGGAGGCATGAAATCT
Found at i:10296 original size:9 final size:9
Alignment explanation
Indices: 10282--10316 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
10272 ACATAGGGAG
10282 AAATTAATA
1 AAATTAATA
10291 AAATTAATA
1 AAATTAATA
10300 AAATTTTAATA
1 AAA--TTAATA
10311 AAATTA
1 AAATTA
10317 TGCTGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 15 0.62
11 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AAATTAATA
Found at i:18597 original size:5 final size:5
Alignment explanation
Indices: 18578--18617 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
18568 CAAGGAAAAC
* *
18578 GAAAA GAAAG AGAAAG GAAAG GAAAG GAAAA GAAAG GAAA
1 GAAAG GAAAG -GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
18618 TTGAGTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:18607 original size:15 final size:16
Alignment explanation
Indices: 18572--18617 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
18562 TCCAAACAAG
*
18572 GAAAACGAAAAGAAAGA
1 GAAAA-GAAAGGAAAGA
*
18589 GAAAGGAAAGGAAAG-
1 GAAAAGAAAGGAAAGA
18604 GAAAAGAAAGGAAA
1 GAAAAGAAAGGAAA
18618 TTGAGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 9 0.35
17 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00
Consensus pattern (16 bp):
GAAAAGAAAGGAAAGA
Found at i:20334 original size:40 final size:40
Alignment explanation
Indices: 20289--20371 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
20279 TCTTCAGTGT
20289 TAAATATAATTTTGAATTCGTATATTATGAATAAAGAAAA
1 TAAATATAATTTTGAATTCGTATATTATGAATAAAGAAAA
*
20329 TAAATATAATTTTGAATTCGTATGTTATGAATAAAGAAAA
1 TAAATATAATTTTGAATTCGTATATTATGAATAAAGAAAA
20369 TAA
1 TAA
20372 GTGTTGTGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.37
Consensus pattern (40 bp):
TAAATATAATTTTGAATTCGTATATTATGAATAAAGAAAA
Found at i:22590 original size:2 final size:2
Alignment explanation
Indices: 22578--22616 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
22568 ATATTATTAC
22578 AT AT A- AT AT AT 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 AT AT AT AT AT AT
22617 CAATATAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23114 original size:78 final size:78
Alignment explanation
Indices: 22961--23277 Score: 499
Period size: 78 Copynumber: 4.2 Consensus size: 78
22951 TTGTTTAGCT
* * * *
22961 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACT
*
23021 AAT-TATTTT---A
65 ATTATATTTTACCA
**
23031 TTTTACTATTTTACTCAACTAAAAACTCTTTTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
23096 TTATATTTTACCA
66 TTATATTTTACCA
23109 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
23174 TTATATTTTACCA
66 TTATATTTTACCA
23187 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
23252 TTATATTTTACCA
66 TTATATTTTACCA
23265 TTTTACTATTTTA
1 TTTTACTATTTTA
23278 ATTAAAAAAA
Statistics
Matches: 231, Mismatches: 7, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
70 47 0.20
71 5 0.02
72 1 0.00
73 1 0.00
74 3 0.01
75 6 0.03
78 168 0.73
ACGTcount: A:0.37, C:0.14, G:0.01, T:0.49
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACCA
Found at i:23434 original size:60 final size:60
Alignment explanation
Indices: 23366--23526 Score: 234
Period size: 60 Copynumber: 2.7 Consensus size: 60
23356 GCTAATTGCT
* * ****
23366 CAAATAAGGGCCTAACATTTGACAAAATGCTCAAATAAGGGTTTGATCTATT-AATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCT-TTGAATTTGGC
*
23426 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
*
23486 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
23527 GCTGTCTCAC
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 2 0.02
60 89 0.98
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
Found at i:23506 original size:29 final size:30
Alignment explanation
Indices: 23418--23507 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
23408 TTGATCTATT
* *
23418 AATTTGGCCAAATAAGGACCTAACGTTTGCC
1 AATTTGGCCAAATAAGGGCCTAATGTTTG-C
** ** *
23449 AAAAT-GCTCAAATAAGGGCCCCATCTTTG-
1 AATTTGGC-CAAATAAGGGCCTAATGTTTGC
23478 AATTTGGCCAAATAAGGGCCTAATGTTTGC
1 AATTTGGCCAAATAAGGGCCTAATGTTTGC
23508 CAAAATGCTC
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
29 21 0.48
30 4 0.09
31 19 0.43
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
AATTTGGCCAAATAAGGGCCTAATGTTTGC
Found at i:23526 original size:31 final size:31
Alignment explanation
Indices: 23426--23526 Score: 109
Period size: 31 Copynumber: 3.3 Consensus size: 31
23416 TTAATTTGGC
* *
23426 CAAATAAGGACCTAACGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
** * **
23457 CAAATAAGGGCCCCATCTTTG--AATTTGGC-
1 CAAATAAGGGCCTAATGTTTGCCAAAAT-GCT
23486 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
23517 CAAATAAGGG
1 CAAATAAGGG
23527 GCTGTCTCAC
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
29 21 0.39
30 4 0.07
31 29 0.54
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (31 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCT
Done.