Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015621.1 Corchorus capsularis cultivar CVL-1 contig15642, 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: 44302
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:369 original size:2 final size:2
Alignment explanation
Indices: 362--395 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
352 TCGTATACCC
362 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
396 AAACAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3956 original size:33 final size:33
Alignment explanation
Indices: 3895--4004 Score: 107
Period size: 33 Copynumber: 3.3 Consensus size: 33
3885 GCCTGGGCCG
* * *
3895 GGTCGCGACCTCACCATGGCATAGTCGCGTGCT
1 GGTCGCGACCGCACCATGGCAGAGTCGCGAGCT
3928 GGTCGCGACCGCACCATGGCACGA-TCGCGAGCT
1 GGTCGCGACCGCACCATGGCA-GAGTCGCGAGCT
* * * * * *
3961 GGGCGCGACAGCGCCATGCCATG-GTCGCGAACA
1 GGTCGCGACCGCACCATGGCA-GAGTCGCGAGCT
3994 GGTCGCGACCG
1 GGTCGCGACCG
4005 TGCCATTATC
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
33 62 0.98
34 1 0.02
ACGTcount: A:0.17, C:0.35, G:0.35, T:0.14
Consensus pattern (33 bp):
GGTCGCGACCGCACCATGGCAGAGTCGCGAGCT
Found at i:4423 original size:22 final size:23
Alignment explanation
Indices: 4376--4435 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
4366 TCTGTTTCTT
4376 CTCTCTCCACCAGTGAGAGCTCTC
1 CTCT-TCCACCAGTGAGAGCTCTC
*
4400 CTCTTCCAGCAGTGA-AGGCT-TC
1 CTCTTCCACCAGTGAGA-GCTCTC
*
4422 CTCTTGCCATCAGT
1 CTCTT-CCACCAGT
4436 ACAAGCTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 8 0.25
23 20 0.62
24 4 0.12
ACGTcount: A:0.17, C:0.37, G:0.18, T:0.28
Consensus pattern (23 bp):
CTCTTCCACCAGTGAGAGCTCTC
Found at i:11188 original size:22 final size:22
Alignment explanation
Indices: 11163--11468 Score: 141
Period size: 22 Copynumber: 14.1 Consensus size: 22
11153 GAATTGTTAG
*
11163 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
11185 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
11207 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
11229 TAAATCTTC-CTATAAAATTTTGA
1 T-AATC-ACACTATGAAATTTTGA
* * *
11252 TTAATCTCCCTATAAAATTTTGA
1 -TAATCACACTATGAAATTTTGA
** * *
11275 TAACTTTC-TTATGAAATCTTG-
1 TAA-TCACACTATGAAATTTTGA
*
11296 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
11313 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
11335 TAATCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
** *
11357 TAATTTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
11379 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
11401 TAA-CCCTCTTGTGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* *
11423 -AAACTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
11445 TAACCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
11467 TA
1 TA
11469 TCCTCCCTGA
Statistics
Matches: 217, Mismatches: 49, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
16 7 0.03
17 2 0.01
18 1 0.00
19 2 0.01
21 8 0.04
22 151 0.70
23 43 0.20
24 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:11246 original size:23 final size:23
Alignment explanation
Indices: 11215--11299 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
11205 GATAACCTCG
*
11215 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
11238 CTATAAAATTTTGATTAATCTCC
1 CTATAAAATTTTGATAAATCTTC
*
11261 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
11283 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
11300 CTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:11483 original size:19 final size:20
Alignment explanation
Indices: 11456--11506 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
11446 AACCTTCATA
11456 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
11476 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
11495 TGAAATTTTGAT
1 TGAAATTTTGAT
11507 TACTCTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:11648 original size:22 final size:22
Alignment explanation
Indices: 11587--11841 Score: 146
Period size: 22 Copynumber: 11.6 Consensus size: 22
11577 AGAAATAACA
* *
11587 TTATGAAATTTTTG-TAAACACAT
1 TTATGAAA-TTTTGATAACCTC-T
*
11610 TT-TGAAAATTTGATAACCTCT
1 TTATGAAATTTTGATAACCTCT
11631 TTATGAAATTTTGATAACCTCT
1 TTATGAAATTTTGATAACCTCT
* * * *
11653 TTATAAAATTTTGTTGACCCCT
1 TTATGAAATTTTGATAACCTCT
* * * *
11675 CTATGAAATTTTGATAATCACA
1 TTATGAAATTTTGATAACCTCT
* * *
11697 TTACGTAATTTTGATAACCTCGC
1 TTATGAAATTTTGATAACCTC-T
****
11720 TT-TGAAATTTTGATAACAAAA
1 TTATGAAATTTTGATAACCTCT
* *
11741 CTATGAAATTTTGATAATCT-T
1 TTATGAAATTTTGATAACCTCT
11762 TCTAT-AAATTTTGATAATCCGATCT
1 T-TATGAAATTTTGATAA-CC--TCT
* * * *
11787 CTATGAAATTTCGATAATCACT
1 TTATGAAATTTTGATAACCTCT
* *
11809 CTATGAGA-TTTGATAACCT-T
1 TTATGAAATTTTGATAACCTCT
* *
11829 CTATCAAATTTTG
1 TTATGAAATTTTG
11842 GTACTCCCCA
Statistics
Matches: 177, Mismatches: 44, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
20 7 0.04
21 32 0.18
22 117 0.66
23 4 0.02
24 5 0.03
25 12 0.07
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCTCT
Found at i:11688 original size:66 final size:66
Alignment explanation
Indices: 11612--11778 Score: 169
Period size: 66 Copynumber: 2.5 Consensus size: 66
11602 AAACACATTT
* * * * * ****
11612 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC-TTTATAAAATTTTGTTGACCCCTC
1 TGAAATTTTGATAATCTCTTTATGAAATTTTGATAACCTCGCTT-TAAAATTTTGATAACAAAAC
11676 TA
65 TA
* * * * *
11678 TGAAATTTTGATAATCACATTACGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAAAACT
1 TGAAATTTTGATAATCTCTTTATGAAATTTTGATAACCTCGCTTTAAAATTTTGATAACAAAACT
11743 A
66 A
11744 TGAAATTTTGATAATCT-TTCTAT-AAATTTTGATAA
1 TGAAATTTTGATAATCTCTT-TATGAAATTTTGATAA
11779 TCCGATCTCT
Statistics
Matches: 81, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
65 12 0.15
66 67 0.83
67 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (66 bp):
TGAAATTTTGATAATCTCTTTATGAAATTTTGATAACCTCGCTTTAAAATTTTGATAACAAAACT
A
Found at i:11893 original size:22 final size:23
Alignment explanation
Indices: 11864--11918 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
11854 AAATTGAGAC
* *
11864 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
11885 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
*
11907 TTTTGACAACCT
1 TTTTGATAACCT
11919 CCCCATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:11963 original size:22 final size:23
Alignment explanation
Indices: 11938--11995 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 23
11928 ATATTTAATC
11938 AAATTTTGT-TAACCACACTATG
1 AAATTTTGTATAACCACACTATG
* * *
11960 AAATTCTTATATAACCTCGCTATG
1 AAATT-TTGTATAACCACACTATG
*
11984 ACATTTTG-ATAA
1 AAATTTTGTATAA
11996 TCTCTTTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
22 9 0.31
23 5 0.17
24 15 0.52
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (23 bp):
AAATTTTGTATAACCACACTATG
Found at i:12095 original size:24 final size:22
Alignment explanation
Indices: 12031--12170 Score: 86
Period size: 22 Copynumber: 6.3 Consensus size: 22
12021 TTGTGATAAT
* *
12031 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
12053 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
* * **
12075 TAACTTGATCCTATGAAATTTTGG
1 TAAC--CAACCTATGAAATTTTAA
* *
12099 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
12121 TAACC-TCGTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
12143 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
12165 TAACCA
1 TAACCA
12171 CTTAGAGACA
Statistics
Matches: 91, Mismatches: 22, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
21 2 0.02
22 70 0.77
23 3 0.03
24 16 0.18
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:12358 original size:19 final size:20
Alignment explanation
Indices: 12327--12369 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
12317 TATTGACATT
12327 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTAAAAAG
12346 TAAAATATT-AAATTCAAAAAG
1 TAAAA-ATTGAAATT-AAAAAG
12367 TAA
1 TAA
12370 TAGTAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (20 bp):
TAAAAATTGAAATTAAAAAG
Found at i:12746 original size:31 final size:31
Alignment explanation
Indices: 12681--12746 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
12671 TGGCAATTTA
* *
12681 GAAATATGTTTTAAAGAAAAGGGTACAATTG
1 GAAATATGTTTTAAAGAAAAGGATACAATCG
*
12712 GAAATATGTTTTAAA-AATAAGGATACTATCG
1 GAAATATGTTTTAAAGAA-AAGGATACAATCG
12743 GAAA
1 GAAA
12747 ATATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAGAAAAGGATACAATCG
Found at i:13288 original size:23 final size:22
Alignment explanation
Indices: 13262--13313 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
13252 TGAAATTTTA
*
13262 ATAACCAACACTATGAGATGTTG
1 ATAACCAACA-TATGAGATATTG
** *
13285 ATAACCTCCATATGATATATTG
1 ATAACCAACATATGAGATATTG
13307 ATAACCA
1 ATAACCA
13314 CGTTATGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (22 bp):
ATAACCAACATATGAGATATTG
Found at i:13444 original size:22 final size:23
Alignment explanation
Indices: 13386--13662 Score: 118
Period size: 22 Copynumber: 12.9 Consensus size: 23
13376 GATTATCACA
*
13386 CTATGAAATTTTGATAAATCTTC
1 CTATGAAATTTTGATAACTCTTC
*
13409 CTATAAAATTTTGATAACT-TTC
1 CTATGAAATTTTGATAACTCTTC
* *
13431 TTATGAAATCTTGATAA------
1 CTATGAAATTTTGATAACTCTTC
*
13448 CTA-CAAATTTTGATAACCTC--C
1 CTATGAAATTTTGATAA-CTCTTC
** *
13469 CTATGATTTTTTTGATAAATC-TC
1 CTATGA-AATTTTGATAACTCTTC
* *
13492 ATTATGAAATTTTGTTAA-T-TTCC
1 -CTATGAAATTTTGATAACTCTT-C
* *
13515 CTATGAAATTTTGAT--CTACATA
1 CTATGAAATTTTGATAACT-CTTC
*
13537 CTATGAAATTTTGATAAC-CCTC
1 CTATGAAATTTTGATAACTCTTC
* * * ***
13559 TTATGACATTTTGAAAACT-AAA
1 CTATGAAATTTTGATAACTCTTC
13581 CTATGAAATTTTGATAAAC-CTTC
1 CTATGAAATTTTGAT-AACTCTTC
* *
13604 ATATGAAATTTTGATATC-CTTC
1 CTATGAAATTTTGATAACTCTTC
*
13626 C--TG-AATTTTGAT-A-TCCTC
1 CTATGAAATTTTGATAACTCTTC
*
13644 CT-TGAAATTTTGATTACTC
1 CTATGAAATTTTGATAACTC
13663 CATAATAAAA
Statistics
Matches: 191, Mismatches: 39, Indels: 49
0.68 0.14 0.18
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
18 4 0.02
19 11 0.06
20 11 0.06
21 5 0.03
22 87 0.46
23 54 0.28
24 6 0.03
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (23 bp):
CTATGAAATTTTGATAACTCTTC
Found at i:13654 original size:20 final size:21
Alignment explanation
Indices: 13584--13657 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 21
13574 AACTAAACTA
* *
13584 TGAAATTTTGATAAACCTTCAT
1 TGAAATTTTGAT-ATCCTTCCT
13606 ATGAAATTTTGATATCCTTCC-
1 -TGAAATTTTGATATCCTTCCT
13627 TG-AATTTTGATATCC-TCCT
1 TGAAATTTTGATATCCTTCCT
13646 TGAAATTTTGAT
1 TGAAATTTTGAT
13658 TACTCCATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.06
19 15 0.32
20 11 0.23
22 6 0.13
23 12 0.26
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.45
Consensus pattern (21 bp):
TGAAATTTTGATATCCTTCCT
Found at i:13885 original size:44 final size:43
Alignment explanation
Indices: 13741--13903 Score: 127
Period size: 44 Copynumber: 3.7 Consensus size: 43
13731 AATACCACTA
* * *
13741 TGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTT
1 TGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCTCCTT
* *** * * *
13784 ATGAAATTTTGATAACCTTTTTATAAAATTTTGTTGACC-CCTCT
1 -TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCCT-T
*
13828 ATG-AATTTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT
1 -TGAAATTT-TGATAATCACATTATGAAATTTTGATAACCTC-CTT
*
13873 TGAAATTTTGATAA-CAACACTATGAAATTTT
1 TGAAATTTTGATAATC-ACATTATGAAATTTT
13904 AATCTTTCTA
Statistics
Matches: 92, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
43 13 0.14
44 70 0.76
45 7 0.08
46 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (43 bp):
TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCCTT
Found at i:13901 original size:88 final size:88
Alignment explanation
Indices: 13738--13903 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 88
13728 AGAAATACCA
* * * ***
13738 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTT
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
13803 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
13826 CTATG-AATTTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
13889 ACACTATGAAATTTT
64 ACACTATAAAATTTT
13904 AATCTTTCTA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 7 0.11
88 56 0.86
89 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:13961 original size:22 final size:22
Alignment explanation
Indices: 13738--13989 Score: 114
Period size: 22 Copynumber: 11.6 Consensus size: 22
13728 AGAAATACCA
13738 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
13761 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * **
13782 TTATGAAATTTTGATAACCTTT
1 CTATGAAATTTTGATAATCACT
* * * * * *
13804 TTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
13826 CTATG-AATTTCTGATAATCACAT
1 CTATGAAATTT-TGATAATCAC-T
* * * *
13849 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* *
13870 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
**
13892 CTATGAAA-TTT--TAATCTTT
1 CTATGAAATTTTGATAATCACT
13911 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAAT-C-A-CT
*
13935 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
13957 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
*
13977 CTATCAAATTTTG
1 CTATGAAATTTTG
13990 GTACTCCTTA
Statistics
Matches: 176, Mismatches: 36, Indels: 36
0.71 0.15 0.15
Matches are distributed among these distances:
18 3 0.02
19 11 0.06
20 9 0.05
21 29 0.16
22 99 0.56
23 7 0.04
24 6 0.03
25 12 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:14041 original size:22 final size:21
Alignment explanation
Indices: 14012--14361 Score: 95
Period size: 22 Copynumber: 15.8 Consensus size: 21
14002 AAAATGAGAC
14012 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* * *
14033 TTTTGATAATCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
* **
14055 TTTTGACAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
*
14077 TATTTG-TAACCTCCTGATGAAA
1 T-TTTGATAACCTCAT-ATGAAA
*
14099 TTTTGTTAACCAT-ACTATGAAA
1 TTTTGATAACC-TCA-TATGAAA
* * *
14121 TTTTTAGT-ACCTCGCTATGACA
1 TTTTGA-TAACCTC-ATATGAAA
*
14143 TTTTGATAACCTTTC-TATAAAA
1 TTTTGATAACC--TCATATGAAA
* * *
14165 TTGTGATAATTAACCACCCTATGAAA
1 TT-T--TGA-TAACC-TCATATGAAA
** * * *
14191 TTTCAATAACCAACCTAAGAAA
1 TTTTGATAACC-TCATATGAAA
* *
14213 TTTT-ATAACCTGATCCTAAGAAA
1 TTTTGATAACC---TCATATGAAA
* *
14236 TTTTGGTAACCACAGTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
14258 TTTTGGTAACTTCCATATGAGAA
1 TTTTGATAACCT-CATATGA-AA
* *
14281 -TTTGGTAACCACACTATTG-AA
1 TTTTGATAACCTCA-TA-TGAAA
*
14302 TTTTGATAACCTCCTCATGAAA
1 TTTTGATAACCTCAT-ATGAAA
** * *
14324 TCATAATAACCATCTTATGAAA
1 TTTTGATAACC-TCATATGAAA
*
14346 TTTTGATAACCACATA
1 TTTTGATAACCTCATA
14362 GAGATAAAAA
Statistics
Matches: 250, Mismatches: 48, Indels: 62
0.69 0.13 0.17
Matches are distributed among these distances:
21 31 0.12
22 161 0.64
23 34 0.14
24 7 0.03
25 4 0.02
26 13 0.05
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:14801 original size:31 final size:30
Alignment explanation
Indices: 14736--14801 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
14726 ATGGCAATTT
* *
14736 AGAAATATATATTTAAAAAAAGGTATAATC
1 AGAAATATATATTTAAAAAAAGGTACAATA
14766 AGAAATATAT-TTTAAAAAAATGGGTACAATA
1 AGAAATATATATTTAAAAAAA--GGTACAATA
14797 AGAAA
1 AGAAA
14802 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 10 0.31
30 10 0.31
31 12 0.38
ACGTcount: A:0.58, C:0.03, G:0.12, T:0.27
Consensus pattern (30 bp):
AGAAATATATATTTAAAAAAAGGTACAATA
Found at i:15634 original size:22 final size:21
Alignment explanation
Indices: 15584--15635 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
15574 TAAAATAATT
15584 ATAAAATATTGAATTTAATTAA
1 ATAAAATA-TGAATTTAATTAA
*
15606 ATGAAAATA-GAATTTTTATTAGA
1 AT-AAAATATGAA-TTTAATTA-A
15629 ATAAAAT
1 ATAAAAT
15636 TGTATATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.12
22 14 0.54
23 9 0.35
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (21 bp):
ATAAAATATGAATTTAATTAA
Found at i:21593 original size:22 final size:22
Alignment explanation
Indices: 21567--21612 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
21557 TGCACATCAA
*
21567 AACCACTATAAAGTTTCAAACC
1 AACCACTATAAAATTTCAAACC
*
21589 AACCACTATAAAATTTCAGACC
1 AACCACTATAAAATTTCAAACC
21611 AA
1 AA
21613 TCCAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.26, G:0.04, T:0.22
Consensus pattern (22 bp):
AACCACTATAAAATTTCAAACC
Found at i:21621 original size:22 final size:22
Alignment explanation
Indices: 21567--21623 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
21557 TGCACATCAA
* *
21567 AACCACTATAAAGTTTCAAACC
1 AACCACAATAAAATTTCAAACC
* *
21589 AACCACTATAAAATTTCAGACC
1 AACCACAATAAAATTTCAAACC
21611 AATCCA-AATAAAA
1 AA-CCACAATAAAA
21624 GATAATCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.51, C:0.25, G:0.04, T:0.21
Consensus pattern (22 bp):
AACCACAATAAAATTTCAAACC
Found at i:25800 original size:9 final size:9
Alignment explanation
Indices: 25788--25818 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
25778 CAAAGCCAAT
25788 TTTTTTTTA
1 TTTTTTTTA
25797 TTTTTTTTA
1 TTTTTTTTA
25806 TTTTTTTT-
1 TTTTTTTTA
25814 TTTTT
1 TTTTT
25819 ATAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.06, C:0.00, G:0.00, T:0.94
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:28132 original size:68 final size:68
Alignment explanation
Indices: 27996--28125 Score: 224
Period size: 68 Copynumber: 1.9 Consensus size: 68
27986 GCTTAAATTT
* **
27996 GTGCAATATTAGATTATTAGAATTTCATACTATTTGATTCAACAAGATGTCAATGGTGTTGCTGT
1 GTGCAATATTAGATTATTAGAATCTCATACTATTTGATTCAACAAGACATCAATGGTGTTGCTGT
28061 TCG
66 TCG
*
28064 GTGCAATATTAGATTATTAGAATCTCATACTATTTGATTGAACAAGACATCAATGGTGTTGC
1 GTGCAATATTAGATTATTAGAATCTCATACTATTTGATTCAACAAGACATCAATGGTGTTGC
28126 ATTTCGGAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (68 bp):
GTGCAATATTAGATTATTAGAATCTCATACTATTTGATTCAACAAGACATCAATGGTGTTGCTGT
TCG
Found at i:28156 original size:25 final size:25
Alignment explanation
Indices: 28108--28160 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
28098 TGATTGAACA
*
28108 AGACATCAATGGTGTTGCATTTCGG
1 AGACATCAATGGTGTTACATTTCGG
*
28133 AGACGTCAATGGTGTTAC-TGTTCGG
1 AGACATCAATGGTGTTACAT-TTCGG
28158 AGA
1 AGA
28161 ACTTAACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (25 bp):
AGACATCAATGGTGTTACATTTCGG
Found at i:40651 original size:12 final size:12
Alignment explanation
Indices: 40621--40662 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
40611 CTGCTGCTGC
*
40621 CTTCTTCTCCTT
1 CTTCTTTTCCTT
40633 -TTCCTTTTCCTT
1 CTT-CTTTTCCTT
*
40645 CTTCTTTTTCTT
1 CTTCTTTTCCTT
40657 CTTCTT
1 CTTCTT
40663 CGCTGCAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
CTTCTTTTCCTT
Found at i:41403 original size:147 final size:148
Alignment explanation
Indices: 41252--41669 Score: 610
Period size: 149 Copynumber: 2.8 Consensus size: 148
41242 ATCCTCCTTG
* * *
41252 TCACCTGCCTCATCATCAAGCTCATCAAGTGCAACTGCCGCAAACAAGTTTCCACCCTTCTTTCC
1 TCACCTGCTTCATCATCAAGCTCATCAAGTGCAACTGCTGCAAACGAGTTTCCACCCTTCTTTCC
* * *
41317 ACCCTTTGACTTCTTCTTTTTCCCCGTCAAAGCTTTGACAACCATATCATCATCGTCT-A-TATT
66 ACCCTTGGACTTCTT-TTTTTCCCTGTCAAAGCTTTGACAACCATATCATCATCGTCTAATTACT
41380 CTCTTCCTCAACCACCTCT
130 CTCTTCCTCAACCACCTCT
*
41399 TCACCTG-TTCCATCATCAAGCTCATCAAGTGAAACTGCTGCAAACGAGTTTCCACCCTTCTTTC
1 TCACCTGCTT-CATCATCAAGCTCATCAAGTGCAACTGCTGCAAACGAGTTTCCACCCTTCTTTC
* * * *
41463 CTCCCTTGGACTTCTTTTTTTACCTGTCAAAGCTTTGGCAACCATATCATCATCCTCTAATTTAC
65 CACCCTTGGACTTCTTTTTTTCCCTGTCAAAGCTTTGACAACCATATCATCATCGTCTAA-TTAC
41528 TCTCTTCCTCAACCACCTCT
129 TCTCTTCCTCAACCACCTCT
** *
41548 TCACCTGCTTCATCATCAAGCTCATCAAGTGCAACTGCTGCAAACGAGTTTCCTGCTTTCTTTCC
1 TCACCTGCTTCATCATCAAGCTCATCAAGTGCAACTGCTGCAAACGAGTTTCCACCCTTCTTTCC
* * *
41613 CCCCTTGGACTTCTTTTTTTTCCCTTTCAAAGCTTT-AGCGACCATATCATCATCGTC
66 ACCCTTGGACTTC-TTTTTTTCCCTGTCAAAGCTTTGA-CAACCATATCATCATCGTC
41670 GTCATCATCC
Statistics
Matches: 243, Mismatches: 21, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
146 39 0.16
147 73 0.30
149 92 0.38
150 39 0.16
ACGTcount: A:0.22, C:0.34, G:0.10, T:0.34
Consensus pattern (148 bp):
TCACCTGCTTCATCATCAAGCTCATCAAGTGCAACTGCTGCAAACGAGTTTCCACCCTTCTTTCC
ACCCTTGGACTTCTTTTTTTCCCTGTCAAAGCTTTGACAACCATATCATCATCGTCTAATTACTC
TCTTCCTCAACCACCTCT
Found at i:44045 original size:21 final size:21
Alignment explanation
Indices: 44021--44064 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
44011 TATATCTGAA
*
44021 TTGCTAAAT-ACCGCCCTATTT
1 TTGCT-AATCACCGCCCCATTT
*
44042 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
44063 TT
1 TT
44065 TACGCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Done.