Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006888.1 Corchorus capsularis cultivar CVL-1 contig06909, 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: 27157
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:7528 original size:22 final size:22
Alignment explanation
Indices: 7387--7604 Score: 137
Period size: 22 Copynumber: 10.0 Consensus size: 22
7377 ATCACTTTGT
*
7387 AGATTATCAAAATTTCTTAGTG
1 AGATTATCAAAATTTCATAGTG
* * *
7409 TGACTATCAAAATTTCATAATG
1 AGATTATCAAAATTTCATAGTG
* *
7431 TA-ATTATCCAAATTTCATAATG
1 -AGATTATCAAAATTTCATAGTG
* * *
7453 TGGTTA-CAAAAATTTCATAG-A
1 AGATTATC-AAAATTTCATAGTG
* * *
7474 AGGTAATCAAAATTTGAT-GTTG
1 AGATTATCAAAATTTCATAG-TG
* *
7496 TGCTTATCAAAATTTCATAGTG
1 AGATTATCAAAATTTCATAGTG
* *
7518 AGATTAACAAAA-TTCTATAGGG
1 AGATTATCAAAATTTC-ATAGTG
* *
7540 A-AGTTATCAAAA-TTCCTAGGG
1 AGA-TTATCAAAATTTCATAGTG
*
7561 AGGTTATCAAAATTTCATAGT-
1 AGATTATCAAAATTTCATAGTG
* *
7582 ATGGTTATCCAAATTTCATAGTG
1 A-GATTATCAAAATTTCATAGTG
7605 TACCAAATCA
Statistics
Matches: 153, Mismatches: 30, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.01
21 34 0.22
22 117 0.76
23 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
AGATTATCAAAATTTCATAGTG
Found at i:7727 original size:22 final size:22
Alignment explanation
Indices: 7702--7781 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
7692 TTTTATAGTA
7702 TGGTTATCAAAGTTTCATAATG
1 TGGTTATCAAAGTTTCATAATG
* *
7724 TGGTAATCAAAATTTCAT-A-G
1 TGGTTATCAAAGTTTCATAATG
* * *
7744 -GATTAACGAAA-TTTCATAGTG
1 TGGTTATC-AAAGTTTCATAATG
*
7765 TGGGTATCAAAGTTTCA
1 TGGTTATCAAAGTTTCA
7782 CAGGGATTAG
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
19 10 0.23
20 4 0.09
21 5 0.11
22 25 0.57
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAGTTTCATAATG
Found at i:10897 original size:41 final size:41
Alignment explanation
Indices: 10850--10952 Score: 188
Period size: 41 Copynumber: 2.5 Consensus size: 41
10840 CAAGAGTCGA
**
10850 ATGACTTAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCG
10891 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCG
10932 ATGACTTGTTCTTGAATTGAT
1 ATGACTTGTTCTTGAATTGAT
10953 GATAATTTGA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (41 bp):
ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCG
Found at i:11293 original size:16 final size:16
Alignment explanation
Indices: 11268--11302 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
11258 ATCTAAAATA
*
11268 CTTCAGAGCTTTTCTG
1 CTTCAAAGCTTTTCTG
11284 CTTCAAAGCTTTTCTG
1 CTTCAAAGCTTTTCTG
11300 CTT
1 CTT
11303 TCTGAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.46
Consensus pattern (16 bp):
CTTCAAAGCTTTTCTG
Found at i:12373 original size:21 final size:24
Alignment explanation
Indices: 12325--12389 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 24
12315 CTCATAGAGT
12325 GATTATCGAAATTTCATAGAGATCA
1 GATTATCGAAATTTCATAGAGA-CA
12350 GATTATCGAAATTT-ATAG-GA-A
1 GATTATCGAAATTTCATAGAGACA
*
12371 GATTATCAAAATTTCATAG
1 GATTATCGAAATTTCATAG
12390 TGTTGTTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 14 0.37
22 4 0.11
23 2 0.05
24 4 0.11
25 14 0.37
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (24 bp):
GATTATCGAAATTTCATAGAGACA
Found at i:12515 original size:21 final size:22
Alignment explanation
Indices: 12272--12518 Score: 123
Period size: 22 Copynumber: 11.3 Consensus size: 22
12262 TAAAAGTCTC
*
12272 AATTTCATAAAGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* *
12292 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* * * * *
12312 AATCTCATAGAGTGATTATCGA
1 AATTTCATAAAGAGGTTATCAA
* * *
12334 AATTTCATAGAGATCAGATTATCGA
1 AATTTCATA-A-A-GAGGTTATCAA
12359 AATTT-ATAGGAAGA--TTATCAA
1 AATTTCATA--AAGAGGTTATCAA
** **
12380 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
* *
12402 AATTTCA-AAGCGAGGTTCTCAA
1 AATTTCATAA-AGAGGTTATCAA
* * * * * *
12424 AATTACATAATGTGATTATTAG
1 AATTTCATAAAGAGGTTATCAA
* * * *
12446 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGAGGTTATCAA
*
12468 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
12490 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
12512 ATTTTCA
1 AATTTCA
12519 AAATGTTATT
Statistics
Matches: 170, Mismatches: 44, Indels: 24
0.71 0.18 0.10
Matches are distributed among these distances:
19 1 0.01
20 21 0.12
21 21 0.12
22 103 0.61
23 3 0.02
24 5 0.03
25 16 0.09
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:12745 original size:22 final size:22
Alignment explanation
Indices: 12676--12746 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
12666 TTTAAATTAT
* *
12676 CAAAATTTCATAGT-ATGTAGAA
1 CAAAATTTCATAGTGAGGT-TAA
* *
12698 CAAAATTTCATAGGGAGATTAA
1 CAAAATTTCATAGTGAGGTTAA
* *
12720 CAAAATTTCATAATGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
12742 CAAAA
1 CAAAA
12747 AATCAGAAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 38 0.95
23 2 0.05
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:12833 original size:25 final size:23
Alignment explanation
Indices: 12776--12862 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
12766 AAATTTTTAG
* * * *
12776 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAATAT
12798 TTATCAAAATTTTATAAGGAAGT-T
1 TTATCAAAATTTTAT-AGGAA-TAT
*
12822 TATATCAAAATTTTATTGGAATAT
1 T-TATCAAAATTTTATAGGAATAT
*
12846 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
12863 CGAGTACTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
22 13 0.25
23 19 0.36
24 7 0.13
25 14 0.26
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAATAT
Found at i:12854 original size:23 final size:24
Alignment explanation
Indices: 12776--12857 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 24
12766 AAATTTTTAG
* * *
12776 TTATCAAGATTTCATAAGAAAG--
1 TTATCAAAATTTTATAAGGAAGTT
12798 TTATCAAAATTTTATAAGGAAGTT
1 TTATCAAAATTTTATAAGGAAGTT
*
12822 TATATCAAAATTTTAT-TGGAA-TAT
1 T-TATCAAAATTTTATAAGGAAGT-T
12846 TTATCAAAATTT
1 TTATCAAAATTT
12858 CATAGCGAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
22 19 0.37
23 12 0.23
24 7 0.13
25 14 0.27
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (24 bp):
TTATCAAAATTTTATAAGGAAGTT
Found at i:17018 original size:30 final size:31
Alignment explanation
Indices: 16960--17024 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
16950 AACTTTATGT
* *
16960 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTCTAAAACATA
*
16991 TTTCCAATTTTACCCTT-TTTCTAAAACATA
1 TTTCCAATTGTACCCTTATTTCTAAAACATA
17021 TTTC
1 TTTC
17025 TAAATTGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTCTAAAACATA
Found at i:17224 original size:38 final size:37
Alignment explanation
Indices: 17150--17231 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
17140 TCAATTTGCC
*
17150 TTTTTATTTCCAACGTCCTATTTAATTTTACCTTTTG
1 TTTTTGTTTCCAACGTCCTATTTAATTTTACCTTTTG
** *
17187 TTTTTGTTTCCAATCGTTGTATTTAACTTTT-CTTTTTG
1 TTTTTGTTTCCAA-CGTCCTATTTAA-TTTTACCTTTTG
*
17225 TCTTTGT
1 TTTTTGT
17232 CACCGATTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 12 0.32
38 22 0.58
39 4 0.11
ACGTcount: A:0.15, C:0.16, G:0.09, T:0.61
Consensus pattern (37 bp):
TTTTTGTTTCCAACGTCCTATTTAATTTTACCTTTTG
Found at i:17623 original size:6 final size:6
Alignment explanation
Indices: 17612--17643 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
17602 AAAAGATTAA
17612 ACTAAC ACTAAC ACTAAC ACTAAC ACTAAC AC
1 ACTAAC ACTAAC ACTAAC ACTAAC ACTAAC AC
17644 ATACAATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
ACTAAC
Found at i:17831 original size:22 final size:21
Alignment explanation
Indices: 17806--17905 Score: 110
Period size: 22 Copynumber: 4.6 Consensus size: 21
17796 TAGTTATTAT
*
17806 AATTTCATGAGGAGGTTATCAA
1 AATTTCAT-AGGAGGTTACCAA
* *
17828 AATTCCATAGTGTGGTTACCAA
1 AATTTCATAG-GAGGTTACCAA
* *
17850 AATTTCATATGGAAGTTATCAA
1 AATTTCATA-GGAGGTTACCAA
*
17872 AATTTCATAGTGTGGTTACCAA
1 AATTTCATAG-GAGGTTACCAA
17894 AATTTCATAGGA
1 AATTTCATAGGA
17906 TCAAGTTATT
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
21 4 0.06
22 59 0.92
23 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (21 bp):
AATTTCATAGGAGGTTACCAA
Found at i:17854 original size:44 final size:43
Alignment explanation
Indices: 17806--17905 Score: 164
Period size: 44 Copynumber: 2.3 Consensus size: 43
17796 TAGTTATTAT
*
17806 AATTTCATGAGGAGGTTATCAAAATTCCATAGTGTGGTTACCAA
1 AATTTCAT-AGGAAGTTATCAAAATTCCATAGTGTGGTTACCAA
*
17850 AATTTCATATGGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
1 AATTTCATA-GGAAGTTATCAAAATTCCATAGTGTGGTTACCAA
17894 AATTTCATAGGA
1 AATTTCATAGGA
17906 TCAAGTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
43 4 0.08
44 49 0.92
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (43 bp):
AATTTCATAGGAAGTTATCAAAATTCCATAGTGTGGTTACCAA
Found at i:17878 original size:66 final size:66
Alignment explanation
Indices: 17772--17903 Score: 160
Period size: 66 Copynumber: 2.0 Consensus size: 66
17762 CTTGTCTCTA
* * *
17772 TGTGGTTAACAAAATTTCACAAGATAGTTATTATAATTTCATGAG-GAGGTTATCAAAATTCCAT
1 TGTGGTTAACAAAATTTCACAAGATAGTTATCAAAATTTCAT-AGTGAGGTTACCAAAATTCCAT
17836 AG
65 AG
* * * * *
17838 TGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCAT
1 TGTGGTTAACAAAATTTCACA-AGATAGTTATCAAAATTTCATAGTGAGGTTACCAAAATTCCAT
17902 AG
65 AG
17904 GATCAAGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 2 0.04
66 52 0.93
67 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (66 bp):
TGTGGTTAACAAAATTTCACAAGATAGTTATCAAAATTTCATAGTGAGGTTACCAAAATTCCATA
G
Found at i:17942 original size:22 final size:22
Alignment explanation
Indices: 17910--17957 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
17900 ATAGGATCAA
17910 GTTATTAAAATTTCT-TAAGTTG
1 GTTATTAAAATTT-TATAAGTTG
* *
17932 GTTATTGAAATTTTATAGGTTG
1 GTTATTAAAATTTTATAAGTTG
17954 GTTA
1 GTTA
17958 ATTATCACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (22 bp):
GTTATTAAAATTTTATAAGTTG
Found at i:17950 original size:46 final size:46
Alignment explanation
Indices: 17820--17923 Score: 160
Period size: 44 Copynumber: 2.3 Consensus size: 46
17810 TCATGAGGAG
*
17820 GTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGG---AA
1 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA-GGATCAA
17864 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCAA
1 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCAA
*
17910 GTTATTAAAATTTC
1 GTTATCAAAATTTC
17924 TTAAGTTGGT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
43 2 0.04
44 38 0.69
46 15 0.27
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (46 bp):
GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCAA
Found at i:18046 original size:22 final size:23
Alignment explanation
Indices: 17991--18050 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
17981 TTATCAAAGA
*
17991 TATATCAAAATGTCATAGCGAGGT
1 TATA-CAAAATTTCATAGCGAGGT
* *
18015 TATA-AGAATTTCATAGCGTGGT
1 TATACAAAATTTCATAGCGAGGT
18037 TA-ACAAAATTTCAT
1 TATACAAAATTTCAT
18051 TTGGAGGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 26 0.84
24 4 0.13
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
TATACAAAATTTCATAGCGAGGT
Found at i:18059 original size:22 final size:22
Alignment explanation
Indices: 18034--18088 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
18024 TTCATAGCGT
**
18034 GGTTAACAAAATTTCATTTGGA
1 GGTTAACAAAATTTCATGGGGA
*
18056 GGTT-ACTAATATTTCATGGGGA
1 GGTTAAC-AAAATTTCATGGGGA
*
18078 GGTTATCAAAA
1 GGTTAACAAAA
18089 GTTTATAGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
21 2 0.08
22 23 0.88
23 1 0.04
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (22 bp):
GGTTAACAAAATTTCATGGGGA
Found at i:18193 original size:22 final size:23
Alignment explanation
Indices: 18141--18395 Score: 137
Period size: 22 Copynumber: 11.6 Consensus size: 23
18131 TAAGGAGTAC
* *
18141 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
18162 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
18183 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
**
18208 CAAAATTT-ATAG-GAAAATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
18229 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
18251 CAAAATTTCAAAGCGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
18273 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * * *
18295 CAGAATTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* * *
18317 CAAAATTTTATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
18339 CAAAATTTCATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
18361 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
18382 CAAAAATTTCATAG
1 C-AAAATTTCATAG
18396 TGGTATTTCT
Statistics
Matches: 184, Mismatches: 33, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
20 10 0.05
21 25 0.14
22 126 0.68
23 6 0.03
24 4 0.02
25 13 0.07
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:18295 original size:44 final size:44
Alignment explanation
Indices: 18225--18392 Score: 162
Period size: 44 Copynumber: 3.8 Consensus size: 44
18215 TATAGGAAAA
* *
18225 TTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAATG-TGATTATCAAAATTTCAAAGAGAGG
* * * *
18269 TTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAGG
* * * * * *
18313 TCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAA-AGAGG
1 TTATCAAAATTTCATAATGTGATTATCAAAATTTCA-AAGAGAGG
* *
18357 TTATCAAATTTTCAAAATGTGATTA-CAAAAATTTCA
1 TTATCAAAATTTCATAATGTGATTATC-AAAATTTCA
18393 TAGTGGTATT
Statistics
Matches: 97, Mismatches: 24, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
43 3 0.03
44 93 0.96
45 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAGG
Found at i:18321 original size:66 final size:66
Alignment explanation
Indices: 18224--18370 Score: 161
Period size: 66 Copynumber: 2.2 Consensus size: 66
18214 TTATAGGAAA
* ** * * *
18224 ATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATG
1 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAATG
18288 TG
65 TG
* * * * *
18290 ATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGA
1 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATGT
18355 G
66 G
* *
18356 GTTATCAAATTTTCA
1 ATTATCAAAATTTCA
18371 AAATGTGATT
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
66 64 0.97
67 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (66 bp):
ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATGT
G
Found at i:18594 original size:22 final size:22
Alignment explanation
Indices: 18567--18640 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
18557 ATATATGTAG
*
18567 ATCAAAATATCATAGGGAGATT
1 ATCAAAATATCATAAGGAGATT
* * * *
18589 AACAAAATTTCATAATGAGGTT
1 ATCAAAATATCATAAGGAGATT
* *
18611 ATCAAAAAATCATACGGAGATT
1 ATCAAAATATCATAAGGAGATT
18633 ATCAAAAT
1 ATCAAAAT
18641 TTGTAGTTAT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (22 bp):
ATCAAAATATCATAAGGAGATT
Found at i:18697 original size:23 final size:23
Alignment explanation
Indices: 18669--18771 Score: 93
Period size: 23 Copynumber: 4.5 Consensus size: 23
18659 CATTAGAAAA
*
18669 TTATCAATATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
18692 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
18715 TTATCAAAATTTACATAGCGAGG-
1 TTATCAAAATTT-TATAGGGAGGT
* * * * *
18738 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
18760 TTATCAAAATTT
1 TTATCAAAATTT
18772 CAGAATGTAA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.01
22 17 0.25
23 43 0.64
24 6 0.09
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:18763 original size:22 final size:22
Alignment explanation
Indices: 18715--18773 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
18705 ATAGGAAGAT
*
18715 TTATCAAAATTTACATAGCGAGG
1 TTATCAAAATTT-CATAGCGAGA
* * *
18738 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGCGAGA
18760 TTATCAAAATTTCA
1 TTATCAAAATTTCA
18774 GAATGTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGA
Found at i:18931 original size:22 final size:21
Alignment explanation
Indices: 18875--19003 Score: 123
Period size: 22 Copynumber: 5.9 Consensus size: 21
18865 GTCTCTATGT
*
18875 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
18896 TAGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
18919 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
18941 GGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
18963 AGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
18985 GGTTACCAAAATTTCATAG
1 GGTTATCAAAATTTCATAG
19004 TATCATGTTA
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
21 3 0.03
22 79 0.92
23 4 0.05
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:18978 original size:66 final size:66
Alignment explanation
Indices: 18872--19004 Score: 171
Period size: 66 Copynumber: 2.0 Consensus size: 66
18862 CTTGTCTCTA
* * * *
18872 TGTGGTTATCAAAATTTCATAAGATAGTTATTATAATTTCATGAG-GAGGTTATCAAAATTCCAT
1 TGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCAT-AGTGAGGTTACCAAAATTCCAT
18936 AG
65 AG
* * *
18938 TGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCAT
1 TGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATAGTGAGGTTACCAAAATTCCAT
19002 AG
65 AG
19004 T
1 T
19005 ATCATGTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 2 0.03
66 54 0.93
67 2 0.03
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (66 bp):
TGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATAGTGAGGTTACCAAAATTCCATA
G
Found at i:19035 original size:46 final size:43
Alignment explanation
Indices: 18906--19003 Score: 160
Period size: 44 Copynumber: 2.2 Consensus size: 43
18896 TAGTTATTAT
* *
18906 AATTTCATGAGGAGGTTATCAAAATTCCATAGTGTGGTTACCAA
1 AATTTCAT-AGGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
18950 AATTTCATATGGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
1 AATTTCATA-GGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
18994 AATTTCATAG
1 AATTTCATAG
19004 TATCATGTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
43 2 0.04
44 49 0.96
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (43 bp):
AATTTCATAGGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
Found at i:19042 original size:22 final size:22
Alignment explanation
Indices: 18873--19057 Score: 120
Period size: 22 Copynumber: 8.3 Consensus size: 22
18863 TTGTCTCTAT
* *
18873 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATTAAAATTTCATAGG
* * *
18895 ATAGTTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * * *
18917 GAGGTTATCAAAATTCCATAGT
1 GTGGTTATTAAAATTTCATAGG
** *
18939 GTGGTTACCAAAATTTCATATG
1 GTGGTTATTAAAATTTCATAGG
** * *
18961 GAAGTTATCAAAATTTCATAGT
1 GTGGTTATTAAAATTTCATAGG
** *
18983 GTGGTTACCAAAATTTCATAGT
1 GTGGTTATTAAAATTTCATAGG
* * *
19005 ATCATGTTATTAAAATTTCTTAGG
1 GT--GGTTATTAAAATTTCATAGG
* *
19029 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
19051 GTGGTTA
1 GTGGTTA
19058 ATTATCACAA
Statistics
Matches: 123, Mismatches: 36, Indels: 8
0.74 0.22 0.05
Matches are distributed among these distances:
22 106 0.86
23 1 0.01
24 16 0.13
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:19159 original size:22 final size:22
Alignment explanation
Indices: 19134--19191 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
19124 TTCGTAGTGT
**
19134 GGTTAACAAAATTTCATTTGGA
1 GGTTAACAAAATTTCATGGGGA
*
19156 GGTT-ACTAATATTTCATGGGGA
1 GGTTAAC-AAAATTTCATGGGGA
*
19178 GGTTATCAAAATTT
1 GGTTAACAAAATTT
19192 TATAGTGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 2 0.07
22 26 0.90
23 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (22 bp):
GGTTAACAAAATTTCATGGGGA
Found at i:19293 original size:22 final size:23
Alignment explanation
Indices: 19241--19473 Score: 120
Period size: 22 Copynumber: 10.6 Consensus size: 23
19231 TAAGGAGTAC
* *
19241 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
19262 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
19283 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
**
19308 CAAAATTT-ATAG-GAAAATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
19329 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
*
19351 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * * *
19373 CAGAATTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* *
19395 CAAAATTTTATA-ATGA-GGTTAT
1 CAAAATTTCATAGA-GATGATTAT
* *
19417 CAAAATTTCATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
19439 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
19460 CAAAAATTTCATAG
1 C-AAAATTTCATAG
19474 TGGTATTTCT
Statistics
Matches: 167, Mismatches: 27, Indels: 34
0.73 0.12 0.15
Matches are distributed among these distances:
20 10 0.06
21 27 0.16
22 106 0.63
23 7 0.04
24 4 0.02
25 13 0.08
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:19380 original size:44 final size:44
Alignment explanation
Indices: 19224--19473 Score: 183
Period size: 44 Copynumber: 5.7 Consensus size: 44
19214 TAAAAGTCTC
* * *
19224 AATTTCATAA-G-GAGTACCAAAATTTGATAGA-AGGTTATC-A
1 AATTTCATAATGTGATTATCAAAATTTCATAGAGAGGTTATCAA
* * *
19264 AATCTCATAGA-GTGATTATCGAAATTTCATAGAGATCAGATTATCAA
1 AATTTCATA-ATGTGATTATCAAAATTTCATAGAG---AGGTTATCAA
* ** * **
19311 AATTT-AT-AGGAAAATTATCAAAATTTCATAGTGTTGTTATCAA
1 AATTTCATAATG-TGATTATCAAAATTTCATAGAGAGGTTATCAA
* * * * *
19354 AATTACATAATGTGATTATCAGAATTTCATAGAGGGGTCAACAA
1 AATTTCATAATGTGATTATCAAAATTTCATAGAGAGGTTATCAA
* * * *
19398 AATTTTATAATGAGGTTATCAAAATTTCATAAAGAGGTTATCAA
1 AATTTCATAATGTGATTATCAAAATTTCATAGAGAGGTTATCAA
* *
19442 ATTTTCAAAATGTGATTA-CAAAAATTTCATAG
1 AATTTCATAATGTGATTATC-AAAATTTCATAG
19474 TGGTATTTCT
Statistics
Matches: 159, Mismatches: 39, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
40 8 0.05
41 2 0.01
42 16 0.10
43 12 0.08
44 86 0.54
45 3 0.02
46 27 0.17
47 5 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (44 bp):
AATTTCATAATGTGATTATCAAAATTTCATAGAGAGGTTATCAA
Found at i:19751 original size:23 final size:23
Alignment explanation
Indices: 19723--19802 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
19713 CATAAGAAAA
19723 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
19746 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
19769 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
19791 TTATCACAATTT
1 TTATCAAAATTT
19803 CATATTGTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 11 0.22
23 39 0.78
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:19752 original size:45 final size:44
Alignment explanation
Indices: 19700--19806 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 44
19690 AAAATTTGTA
* *
19700 GTTATCAAGATTTCATAAGAA-AATTATCAAAATTTTATAGGGAG
1 GTTATCAA-ATTTCATAAGAAGAATTATCAAAATTTCATAGCGAG
* * *
19744 GTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
1 G-TTATC-AAATTTCATAAGAAGAATTATCAAAATTTCATAGCGAG
19790 GTTATCACAATTTCATA
1 GTTATCA-AATTTCATA
19807 TTGTGATTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 2 0.04
45 28 0.53
46 23 0.43
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (44 bp):
GTTATCAAATTTCATAAGAAGAATTATCAAAATTTCATAGCGAG
Found at i:19801 original size:22 final size:21
Alignment explanation
Indices: 19578--19806 Score: 119
Period size: 22 Copynumber: 10.6 Consensus size: 21
19568 AGTTTAGTTT
* *
19578 TCAAAATTTTATAAGAGGGTTA
1 TCAAAATTTCATAGGA-GGTTA
* * *
19600 TCAAAATTTCATAGTATGTAGA
1 TCAAAATTTCATAGGAGGT-TA
* *
19622 TCAAAATATCATAGGGAGATT-
1 TCAAAATTTCATA-GGAGGTTA
* *
19643 TAAAAAATTTCATAATGAGGTTA
1 T-CAAAATTTCAT-AGGAGGTTA
** *
19666 TCAAAAAATCATAGGGAGATTA
1 TCAAAATTTCATA-GGAGGTTA
*
19688 TCAAAA-TT--T-GTA-GTTA
1 TCAAAATTTCATAGGAGGTTA
* * **
19704 TCAAGATTTCATAAGAAAATTA
1 TCAAAATTTCAT-AGGAGGTTA
*
19726 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATA-GGAGG-TTA
* *
19749 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAGG-AG-GTTA
19772 TCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATAG-GAGGTTA
*
19794 TCACAATTTCATA
1 TCAAAATTTCATA
19807 TTGTGATTAT
Statistics
Matches: 156, Mismatches: 34, Indels: 34
0.70 0.15 0.15
Matches are distributed among these distances:
16 8 0.05
17 4 0.03
19 2 0.01
21 8 0.05
22 92 0.59
23 41 0.26
24 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (21 bp):
TCAAAATTTCATAGGAGGTTA
Found at i:21413 original size:27 final size:26
Alignment explanation
Indices: 21329--21418 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 26
21319 CCAAGGGGGT
21329 TATGGAGGGTACGGTGGACGTGGAGG
1 TATGGAGGGTACGGTGGACGTGGAGG
*
21355 TAACGGAGGGTACGGTGGACGTGGAGG
1 T-ATGGAGGGTACGGTGGACGTGGAGG
* *
21382 TTATGGAGGGTACGGTGGCCGTGGCGG
1 -TATGGAGGGTACGGTGGACGTGGAGG
21409 CTATGGAGGG
1 -TATGGAGGG
21419 CGCGGTGGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
26 1 0.02
27 55 0.96
28 1 0.02
ACGTcount: A:0.18, C:0.11, G:0.52, T:0.19
Consensus pattern (26 bp):
TATGGAGGGTACGGTGGACGTGGAGG
Found at i:21452 original size:18 final size:18
Alignment explanation
Indices: 21385--21454 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 18
21375 GTGGAGGTTA
*
21385 TGGAGGGTACGGTGGCCG
1 TGGAGGGTACGGTGGACG
* * * * *
21403 TGGCGGCTATGGAGGGCG
1 TGGAGGGTACGGTGGACG
* *
21421 CGGTGGGTACGGTGGACG
1 TGGAGGGTACGGTGGACG
*
21439 TGGAGGGTATGGTGGA
1 TGGAGGGTACGGTGGA
21455 GGCTGCGCCT
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.13, C:0.13, G:0.56, T:0.19
Consensus pattern (18 bp):
TGGAGGGTACGGTGGACG
Done.