Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010627.1 Corchorus capsularis cultivar CVL-1 contig10648, 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: 118036
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:5386 original size:45 final size:45
Alignment explanation
Indices: 5335--5424 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
5325 TAATAGAGTA
5335 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
*
5380 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
5425 AGAAGTAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
Found at i:6627 original size:158 final size:164
Alignment explanation
Indices: 6252--6674 Score: 554
Period size: 158 Copynumber: 2.6 Consensus size: 164
6242 AGAGTAAGTA
* * * *
6252 ATTTTTTTCGTCTTTTCCCACTTGACAGATTACTTAAATGTCCCAACTTTTGATTCTTGAGGGGA
1 ATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGACGGGA
* * * *
6317 TTAAATAACTATACTTTTTGTTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAG
66 TT--ATAAC-ATACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAG
* * * ** *
6382 ATCCCTATCAAGGCTTGCTTTTGGAGTTAGAGAACTT
128 ATCCCCATCAAGGATTGATGATGGAGTTAGAAAACTT
6419 ATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGACGGGA
1 ATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGACGGGA
* *
6484 -T-T-A-AT-CTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTGGTGGAATTAATAGAAGATC
66 TTATAACATACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATC
6544 CCCATCAAGGATTGATGAT-GAGTTAGAAAACTT
131 CCCATCAAGGATTGATGATGGAGTTAGAAAACTT
* * *
6577 ATTTTTTTCGTCTTTACCTACTTGGCAGATTACTCAAATGTCCTAACTTTTGATTCTTGA-GTTG
1 ATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGACG-GG
*
6641 ATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
65 ATT--ATAAC-ATACTTTTTGGTCATTTCTCAAT
6675 TGACAAATGA
Statistics
Matches: 227, Mismatches: 20, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
157 1 0.00
158 73 0.32
159 64 0.28
160 2 0.01
162 2 0.01
163 2 0.01
165 1 0.00
166 21 0.09
167 61 0.27
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (164 bp):
ATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGACGGGA
TTATAACATACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATC
CCCATCAAGGATTGATGATGGAGTTAGAAAACTT
Found at i:9178 original size:30 final size:30
Alignment explanation
Indices: 9142--9205 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
9132 CATCACATGC
*
9142 GCCATCGCATGGGACAACCGGCCACAACTG
1 GCCATCGCATGGGACAACCGGCCACAACCG
*
9172 GCCATCGCATGGGGCAACCGGCCACAACCG
1 GCCATCGCATGGGACAACCGGCCACAACCG
9202 GCCA
1 GCCA
9206 ATGGATCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.25, C:0.39, G:0.28, T:0.08
Consensus pattern (30 bp):
GCCATCGCATGGGACAACCGGCCACAACCG
Found at i:15760 original size:30 final size:30
Alignment explanation
Indices: 15726--15786 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
15716 CATCGCATGA
15726 GCCATCGCATGGGACAACCGGCCACAACCG
1 GCCATCGCATGGGACAACCGGCCACAACCG
* *
15756 GCCATCGCATGGGGCAACCGGCGACAACCG
1 GCCATCGCATGGGACAACCGGCCACAACCG
15786 G
1 G
15787 TGAATGGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.38, G:0.31, T:0.07
Consensus pattern (30 bp):
GCCATCGCATGGGACAACCGGCCACAACCG
Found at i:18415 original size:21 final size:22
Alignment explanation
Indices: 18391--18438 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
18381 CTGCTGCTGC
*
18391 AAATTAAGAG-TGAATTTAACA
1 AAATTAAGAGTTGAATTGAACA
* *
18412 AAATCAAGAGTTGAATTGAAGA
1 AAATTAAGAGTTGAATTGAACA
18434 AAATT
1 AAATT
18439 CAGTTTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.27
Consensus pattern (22 bp):
AAATTAAGAGTTGAATTGAACA
Found at i:18482 original size:20 final size:21
Alignment explanation
Indices: 18443--18482 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18433 AAAATTCAGT
18443 TTGGAACTCATTGAAATCAAG
1 TTGGAACTCATTGAAATCAAG
* *
18464 TTGGAATTCA-TGGAATCAA
1 TTGGAACTCATTGAAATCAA
18483 ATTAGGGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (21 bp):
TTGGAACTCATTGAAATCAAG
Found at i:21277 original size:10 final size:10
Alignment explanation
Indices: 21262--21295 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
21252 GAGGACTCTA
21262 GAATTTTCTG
1 GAATTTTCTG
21272 GAATTTTCTG
1 GAATTTTCTG
21282 GAATTTTCTG
1 GAATTTTCTG
21292 GAAT
1 GAAT
21296 CTGGCAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.47
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:22853 original size:23 final size:24
Alignment explanation
Indices: 22822--22866 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
22812 AACATTCTTA
*
22822 AAAATTCAAAGCAATCA-TCAATC
1 AAAACTCAAAGCAATCACTCAATC
*
22845 AAAACTCAAATCAATCACTCAA
1 AAAACTCAAAGCAATCACTCAA
22867 AATATGCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.53, C:0.24, G:0.02, T:0.20
Consensus pattern (24 bp):
AAAACTCAAAGCAATCACTCAATC
Found at i:23252 original size:15 final size:16
Alignment explanation
Indices: 23228--23258 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
23218 AAAATCCTAA
23228 AAAACAAAAGAAAAAT
1 AAAACAAAAGAAAAAT
23244 AAAAC-AAAGAAAAAT
1 AAAACAAAAGAAAAAT
23259 TATGGGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAACAAAAGAAAAAT
Found at i:23542 original size:10 final size:10
Alignment explanation
Indices: 23521--23572 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
23511 CGGATGGCAC
23521 GGCATAGGCCG
1 GGCAT-GGCCG
23532 GGCATGGCCG
1 GGCATGGCCG
23542 GGCATGGTGCGCG
1 GGCAT-G-GC-CG
* *
23555 GACAAGGCCG
1 GGCATGGCCG
23565 GGCATGGC
1 GGCATGGC
23573 ACGGTGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
10 18 0.53
11 8 0.24
12 3 0.09
13 5 0.15
ACGTcount: A:0.15, C:0.27, G:0.48, T:0.10
Consensus pattern (10 bp):
GGCATGGCCG
Found at i:36738 original size:17 final size:17
Alignment explanation
Indices: 36716--36752 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
36706 ACCGCTGGAT
*
36716 AAAGACTTTTGCCGGAC
1 AAAGACTTTTGCCAGAC
36733 AAAGACTTTTGCCAGAC
1 AAAGACTTTTGCCAGAC
36750 AAA
1 AAA
36753 AGGGTAGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (17 bp):
AAAGACTTTTGCCAGAC
Found at i:41112 original size:31 final size:31
Alignment explanation
Indices: 41077--41142 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
41067 AACTTTATGT
* * *
41077 TTTCCGATTGTACCCTTATTT-TTAAAACATA
1 TTTCCAATTGTACCCTT-TTTCTCAAAACAAA
41108 TTTCCAATTGTACCCTTTTTCTCAAAACAAA
1 TTTCCAATTGTACCCTTTTTCTCAAAACAAA
41139 TTTC
1 TTTC
41143 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.44
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTTCTCAAAACAAA
Found at i:41330 original size:38 final size:37
Alignment explanation
Indices: 41264--41361 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 37
41254 TCAATTTGTC
41264 TTTTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTG
1 TTTTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTG
* ** * *
41301 TTTTTGTTTCCCATCGTTGTATTTAATTTTTCTTTTTG
1 TTTTTGTTT-CCAACGTCCTATTTAATTTTGCCTTTTG
* *
41339 TCTTTGTCTCCAACGTCCTATTT
1 TTTTTGTTTCCAACGTCCTATTT
41362 GGACTTATAT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 20 0.40
38 30 0.60
ACGTcount: A:0.12, C:0.19, G:0.10, T:0.58
Consensus pattern (37 bp):
TTTTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTG
Found at i:42568 original size:22 final size:22
Alignment explanation
Indices: 42540--42743 Score: 107
Period size: 22 Copynumber: 9.3 Consensus size: 22
42530 TGTCTCTATG
42540 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
42562 TGGTTATTATAATTTCATGATGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
42585 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
42606 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* *
42629 -AGTTATCAAAA-TTC--AAGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
42648 TGGTTACCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
42670 TGGTTACCAAAATTTCATAATA
1 TGGTTATCAAAATTTCATAAGA
* * * *
42692 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
42716 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
42738 TGGTTA
1 TGGTTA
42744 ATTATCACAA
Statistics
Matches: 140, Mismatches: 29, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 10 0.07
21 6 0.04
22 101 0.72
23 4 0.03
24 17 0.12
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:42610 original size:44 final size:43
Alignment explanation
Indices: 42536--42688 Score: 168
Period size: 44 Copynumber: 3.5 Consensus size: 43
42526 TTCTTGTCTC
* * ** *
42536 TATGTGGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCA
1 TATGAGGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCA
*
42579 TGATGAGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCA
1 T-ATGAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCA
*
42623 TATGGAAGTTATCAAAA-TTCA-AGTGTGGTTACCAAAATTTCA
1 TAT-GAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCA
* *
42665 TAGTGTGGTTACCAAAATTTCATA
1 TA-TGAGGTTATCAAAATTTCATA
42689 ATATCAGGTT
Statistics
Matches: 93, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
42 33 0.35
43 13 0.14
44 47 0.51
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (43 bp):
TATGAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCA
Found at i:42661 original size:42 final size:43
Alignment explanation
Indices: 42572--42666 Score: 149
Period size: 42 Copynumber: 2.2 Consensus size: 43
42562 TGGTTATTAT
*
42572 AATTTCATGATGAGGTTATCAAAATTCCATAGTGTGGTTACCAA
1 AATTTCAT-ATGAAGTTATCAAAATTCCATAGTGTGGTTACCAA
42616 AATTTCATATGGAAGTTATCAAAATT-CA-AGTGTGGTTACCAA
1 AATTTCATAT-GAAGTTATCAAAATTCCATAGTGTGGTTACCAA
42658 AATTTCATA
1 AATTTCATA
42667 GTGTGGTTAC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
42 23 0.47
43 4 0.08
44 22 0.45
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (43 bp):
AATTTCATATGAAGTTATCAAAATTCCATAGTGTGGTTACCAA
Found at i:42804 original size:22 final size:22
Alignment explanation
Indices: 42779--43176 Score: 145
Period size: 22 Copynumber: 17.9 Consensus size: 22
42769 ATCAAAGAGA
* *
42779 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
42801 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
42823 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* *
42845 TTA-CTAATATTTCATAGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* * * *
42867 TTGTCAAAATTTTATAGTGTGC
1 TTATCAAAATTTCATAGTGAGG
42889 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
42911 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
42936 AGTACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * *
42958 TTATC-AAATCTCATAGAGTA-C
1 TTATCAAAATTTCATAGTG-AGG
* * **
42979 TTATCGAAATTTCATAGAAATCAAA
1 TTATCAAAATTTCATAG---TGAGG
*
43004 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGTG-AGG
* **
43025 TTATCAAAAATTTCATGGTGTTG
1 TTATC-AAAATTTCATAGTGAGG
* *
43048 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
43070 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
43092 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * **
43114 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
43136 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
43158 TTA-CAAAAATTTCATAGTG
1 TTATC-AAAATTTCATAGTG
43177 GTATTTCTGG
Statistics
Matches: 276, Mismatches: 73, Indels: 54
0.68 0.18 0.13
Matches are distributed among these distances:
20 9 0.03
21 28 0.10
22 191 0.69
23 16 0.06
24 6 0.02
25 16 0.06
26 6 0.02
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:42912 original size:66 final size:66
Alignment explanation
Indices: 42790--42913 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
42780 TATCAAAATG
* *
42790 TCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATTAGGAGGTTACTAATAT
1 TCATAGCGAGGTTATAAGAATTTCATAGTGTGCTTAACAAAATTTCATTAGAAGGTTACTAATAT
42855 T
66 T
* * * *
42856 TCATAGGGAGGTTGTCAA-AATTTTATAGTGTGCTTATCAAAATTTCA-TATGAAGGTTA
1 TCATAGCGAGGTTAT-AAGAATTTCATAGTGTGCTTAACAAAATTTCATTA-GAAGGTTA
42914 TAAAAGTCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
65 2 0.04
66 46 0.92
67 2 0.04
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (66 bp):
TCATAGCGAGGTTATAAGAATTTCATAGTGTGCTTAACAAAATTTCATTAGAAGGTTACTAATAT
T
Found at i:43301 original size:22 final size:22
Alignment explanation
Indices: 43273--43744 Score: 179
Period size: 22 Copynumber: 21.6 Consensus size: 22
43263 CAAGGGAGGA
*
43273 TATCAAAATTTCATTTGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
43295 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
43317 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* * *
43339 TATTAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
43360 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
43383 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
43405 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
43427 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
43443 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * * *
43465 TGTCAAAATTTTATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * * *
43487 CTATTAAAATTTTATAGGAAGATT
1 -TATCAAAATTTCATATGAAG-GT
* *
43511 TATCAAAACTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
43533 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
43555 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
43577 TA-CTAACAA-TTCATATGAAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
43599 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
43621 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
43643 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
*
43666 TATCAAAATTTCATTGTGAA-GT
1 TATCAAAATTTCA-TATGAAGGT
43688 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
43710 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
*
43732 TAACAAAATTTCA
1 TATCAAAATTTCA
43745 CAAGAATGTT
Statistics
Matches: 336, Mismatches: 83, Indels: 62
0.70 0.17 0.13
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 2 0.01
21 17 0.05
22 240 0.71
23 61 0.18
24 3 0.01
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:43518 original size:23 final size:23
Alignment explanation
Indices: 43467--43518 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
43457 AAGAAAGTTG
* *
43467 TCAAAATTTTATAGGGAGGTCTA
1 TCAAAATTTTATAGGAAGATCTA
* *
43490 TTAAAATTTTATAGGAAGATTTA
1 TCAAAATTTTATAGGAAGATCTA
43513 TCAAAA
1 TCAAAA
43519 CTTCATAGCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (23 bp):
TCAAAATTTTATAGGAAGATCTA
Found at i:43690 original size:45 final size:45
Alignment explanation
Indices: 43617--43702 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
43607 TTTCATAACG
* * *
43617 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
43662 TGGTTATCAAAATTTCAT-TGTGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATATG-GAAGTTATCAAAATCTCATA
43703 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 2 0.06
45 33 0.94
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:44926 original size:36 final size:36
Alignment explanation
Indices: 44877--44959 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
44867 TCTTTTCTAG
*
44877 ATTAAGTCCTTTATTGACTCCACTTAATTACCATGA
1 ATTAAGTCTTTTATTGACTCCACTTAATTACCATGA
*
44913 ATTAAGTCTTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGTCTTTTATTGACTCCACTTAATTACCATGA
*
44949 ATTAAGCCTTT
1 ATTAAGTCTTT
44960 ATTCTACTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (36 bp):
ATTAAGTCTTTTATTGACTCCACTTAATTACCATGA
Found at i:44970 original size:31 final size:34
Alignment explanation
Indices: 44877--44971 Score: 115
Period size: 36 Copynumber: 2.8 Consensus size: 34
44867 TCTTTTCTAG
44877 ATTAAGTCCTTTATTGACTCCACTTAATTACCATGA
1 ATTAAGTCCTTTATT-ACT-CACTTAATTACCATGA
* *
44913 ATTAAGTCTTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGTCCTTTATT-ACT-CACTTAATTACCATGA
44949 ATTAAG-CCTTTATT-CT-ACTTAAT
1 ATTAAGTCCTTTATTACTCACTTAAT
44972 ATCCCTTCCT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
31 7 0.12
33 2 0.04
35 7 0.12
36 40 0.71
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.42
Consensus pattern (34 bp):
ATTAAGTCCTTTATTACTCACTTAATTACCATGA
Found at i:45052 original size:36 final size:36
Alignment explanation
Indices: 45008--45281 Score: 378
Period size: 36 Copynumber: 7.7 Consensus size: 36
44998 CTTTTTACTA
* *
45008 AATTTCCTTGAAATTAAGTCAGTC-TTTCATTTACCT
1 AATTTCCTTGAAACTAAGCCAGTCTTTTC-TTTACCT
* *
45044 AGTCTCCTTGAAACTAAGCCAGTC----CTTTACCT
1 AATTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCT
* *
45076 AGTTTCCTTGACACTAAGCCAGTCTTTTCTTTACCT
1 AATTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCT
*
45112 AATTTCCTCGAAACTAAGCCAGTCTTTTCTTTACCT
1 AATTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCT
* *
45148 AATTTCCTTGAAATTAAGTCAGTCTTTTCTTTACCT
1 AATTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCT
* *
45184 AGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACTT
1 AATTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCT
* *
45220 AATTTCTTTGAAATTAAGCCAGTCTTTTCTTTACCT
1 AATTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCT
*
45256 AATTTCCTTGAAACTAAGCCGGTCTT
1 AATTTCCTTGAAACTAAGCCAGTCTT
45282 CTTTCAGTCT
Statistics
Matches: 211, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
32 29 0.14
33 1 0.00
36 181 0.86
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (36 bp):
AATTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCT
Found at i:45293 original size:11 final size:11
Alignment explanation
Indices: 45277--45383 Score: 169
Period size: 11 Copynumber: 9.7 Consensus size: 11
45267 AACTAAGCCG
45277 GTCTTCTTTCA
1 GTCTTCTTTCA
45288 GTCTTCTTTCA
1 GTCTTCTTTCA
* *
45299 GTCTCCTTTCT
1 GTCTTCTTTCA
45310 GTCTTCTTTCA
1 GTCTTCTTTCA
45321 GTCTTCTTTCA
1 GTCTTCTTTCA
*
45332 GTCTCCTTTCA
1 GTCTTCTTTCA
45343 GTCTTCTTTCA
1 GTCTTCTTTCA
* *
45354 GTCTTTTTTCT
1 GTCTTCTTTCA
45365 GTCTTCTTTCA
1 GTCTTCTTTCA
45376 GTCTTCTT
1 GTCTTCTT
45384 CCGCCTAATT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 86 1.00
ACGTcount: A:0.07, C:0.28, G:0.09, T:0.56
Consensus pattern (11 bp):
GTCTTCTTTCA
Found at i:45487 original size:36 final size:36
Alignment explanation
Indices: 45437--45529 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
45427 GGATTAAAAC
* * *
45437 CTTTGCTGACTTTACTTAATTCTTGTCAAATTAAGT
1 CTTTGCTAATTTTACTTAATTCTTGTCAAATCAAGT
*
45473 CTTTGCTAATTTTACTTAATTCTTGTGAAATCAAGT
1 CTTTGCTAATTTTACTTAATTCTTGTCAAATCAAGT
*
45509 CCTTGCTAATTTTACTTAATT
1 CTTTGCTAATTTTACTTAATT
45530 TGTTTCCTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (36 bp):
CTTTGCTAATTTTACTTAATTCTTGTCAAATCAAGT
Found at i:45630 original size:36 final size:36
Alignment explanation
Indices: 45532--45740 Score: 240
Period size: 36 Copynumber: 5.7 Consensus size: 36
45522 ACTTAATTTG
* * *
45532 TTTCCTTGAAA-TCAAGTCTGTGCTTATCCTTACCTAA
1 TTTCCTTGAAACT-AAGTCAGT-CTTTTCTTTACCTAA
* * * *
45569 TTTCCTTTCTTAAAACTGAGCCAGTCTTTTCTCTACCTAA
1 TTT-C---CTTGAAACTAAGTCAGTCTTTTCTTTACCTAA
*
45609 TTTCCTTGAAACTAAGTCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGTCAGTCTTTTCTTTACCTAA
* *
45645 TTTCCTTGAAACTAAGTTAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGTCAGTCTTTTCTTTACCTAA
* *
45681 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACTTAA
1 TTTCCTTGAAACTAAGTCAGTCTTTTCTTTACCTAA
*
45717 TTTCCTTGAAATTAAGTCAGTCTT
1 TTTCCTTGAAACTAAGTCAGTCTT
45741 CTAATGTTCT
Statistics
Matches: 148, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
36 116 0.78
37 3 0.02
38 1 0.01
39 1 0.01
40 15 0.10
41 11 0.07
42 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.44
Consensus pattern (36 bp):
TTTCCTTGAAACTAAGTCAGTCTTTTCTTTACCTAA
Found at i:45775 original size:108 final size:107
Alignment explanation
Indices: 45581--45794 Score: 234
Period size: 108 Copynumber: 2.0 Consensus size: 107
45571 TCCTTTCTTA
* ** *
45581 AAACTGAGCCAGTCTTTTCTCTACCTAATTTCCTTGAAACTAAGTCAGTCTTTTCTTTACCTAGT
1 AAACTAAGCCAGTCTTTTCTCTACCTAATTTCCTTGAAACTAAGTCAGTCTTTAATTTACCTAGC
** * * *
45646 TTCCTTGAAACTAAGTTAGTCTTTTCTTTACCTAGTTTCCTTG
66 TTAATTGAAACTAAGTCAGTCTATT-TTTACCTAATTTCCTTG
* * * *
45689 AAACTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGTCAGTCTTCTAATGTT-CTTA
1 AAACTAAGCCAGTCTTTTCTCTACCTAATTTCCTTGAAACTAAGTCAGTCTT-TAAT-TTACCTA
** * *
45753 -CTTAATTGCCATTAAGTCAGTCTATTTTTACTTAATTTCCTT
64 GCTTAATTGAAACTAAGTCAGTCTATTTTTACCTAATTTCCTT
45795 TAATTTAACT
Statistics
Matches: 87, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
107 14 0.16
108 66 0.76
109 5 0.06
110 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (107 bp):
AAACTAAGCCAGTCTTTTCTCTACCTAATTTCCTTGAAACTAAGTCAGTCTTTAATTTACCTAGC
TTAATTGAAACTAAGTCAGTCTATTTTTACCTAATTTCCTTG
Found at i:55159 original size:33 final size:33
Alignment explanation
Indices: 55122--55188 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
55112 ATTTGTGTAG
* *
55122 TTTTTGAGGAGGTGATACAATATTATTCAAATC
1 TTTTTGAGGAGATGATACAATATTATTAAAATC
55155 TTTTTGAGGAGATGATACAATATTATTAAAATC
1 TTTTTGAGGAGATGATACAATATTATTAAAATC
55188 T
1 T
55189 CATTACATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40
Consensus pattern (33 bp):
TTTTTGAGGAGATGATACAATATTATTAAAATC
Found at i:62983 original size:18 final size:18
Alignment explanation
Indices: 62962--62997 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
62952 GAAGTATCAT
62962 GTGCAACTTCACCAGAAG
1 GTGCAACTTCACCAGAAG
*
62980 GTGCAGCTTCACCAGAAG
1 GTGCAACTTCACCAGAAG
62998 TTTCTCCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.17
Consensus pattern (18 bp):
GTGCAACTTCACCAGAAG
Found at i:65659 original size:2 final size:2
Alignment explanation
Indices: 65652--65676 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65642 CATTATTAAT
65652 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
65677 TGTTTTCTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:69232 original size:27 final size:30
Alignment explanation
Indices: 69190--69250 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
69180 CTCTTTTTTT
69190 AATATATTTCTAAATTA-TCATTATAAAAA
1 AATATATTTCTAAATTATTCATTATAAAAA
*
69219 AATATATTT-T-AATTATTTCATTATTAAAA
1 AATATATTTCTAAATTA-TTCATTATAAAAA
69248 AAT
1 AAT
69251 GAAAATTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 5 0.17
28 1 0.03
29 23 0.79
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (30 bp):
AATATATTTCTAAATTATTCATTATAAAAA
Found at i:70452 original size:31 final size:31
Alignment explanation
Indices: 70381--70452 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
70371 GTCTATCAGC
*
70381 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTAATTT
* *
70412 TAATT-ATTTGTTTAATTTAATGC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAGGCTTTAATTT
70442 GTTTTAATTTG
1 -TTTTAATTTG
70453 CAATAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.24
31 24 0.71
32 2 0.06
ACGTcount: A:0.25, C:0.04, G:0.10, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTTTAATTT
Found at i:70814 original size:34 final size:34
Alignment explanation
Indices: 70776--70844 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
70766 GTTTAAAAAA
70776 ATCTTTAAAAAGAGCTTAAACTTGAACCGGGATG
1 ATCTTTAAAAAGAGCTTAAACTTGAACCGGGATG
70810 ATCTTTAAAAAGAGCTTAAACTTGAACCGGGATG
1 ATCTTTAAAAAGAGCTTAAACTTGAACCGGGATG
70844 A
1 A
70845 GCAGGATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (34 bp):
ATCTTTAAAAAGAGCTTAAACTTGAACCGGGATG
Found at i:70996 original size:32 final size:32
Alignment explanation
Indices: 70919--70997 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
70909 GATCCTACCT
* *
70919 AAAA-CCGAACCCGAAAATACCCGAATCCGAC
1 AAAACCCGAACCTGAAAATACCCGAACCCGAC
* ** *
70950 ATAACTAGAGCCTGAAAATACCCGAACCCGA-
1 AAAACCCGAACCTGAAAATACCCGAACCCGAC
70981 AAAAGCCCGAACCTGAA
1 AAAA-CCCGAACCTGAA
70998 CCCGCCAAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
31 6 0.17
32 30 0.83
ACGTcount: A:0.44, C:0.32, G:0.15, T:0.09
Consensus pattern (32 bp):
AAAACCCGAACCTGAAAATACCCGAACCCGAC
Found at i:71320 original size:27 final size:26
Alignment explanation
Indices: 71211--71397 Score: 86
Period size: 27 Copynumber: 7.3 Consensus size: 26
71201 CCATTTTTTT
* * *
71211 AAATATATATCTAAATTGCCATTATCA
1 AAATATAT-TTTAAATTGTCATTATTA
* * * *
71238 AAATATATTTTAATTATGACACTATCA
1 AAATATATTTTAAAT-TGTCATTATTA
* * * *
71265 AAATATAATTTT---GTGTACCTTTTTC
1 AAATAT-ATTTTAAATTGT-CATTATTA
71290 AAATATATTTCTAAATTGTCATTATTA
1 AAATATATTT-TAAATTGTCATTATTA
* * * *
71317 AAATATAATTT---TT-ACA-AAAT-
1 AAATATATTTTAAATTGTCATTATTA
*
71337 AAATATATTTCTAAATTGTCATTATCA
1 AAATATATTT-TAAATTGTCATTATTA
* *
71364 AAATATATTTTAATTATGCCATTATTA
1 AAATATATTTTAAAT-TGTCATTATTA
71391 AAATATA
1 AAATATA
71398 GTAATTTTTT
Statistics
Matches: 118, Mismatches: 27, Indels: 30
0.67 0.15 0.17
Matches are distributed among these distances:
20 9 0.08
21 3 0.03
22 2 0.02
23 2 0.02
24 8 0.07
25 12 0.10
26 11 0.09
27 63 0.53
28 8 0.07
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (26 bp):
AAATATATTTTAAATTGTCATTATTA
Found at i:71813 original size:22 final size:22
Alignment explanation
Indices: 71746--72010 Score: 168
Period size: 22 Copynumber: 12.0 Consensus size: 22
71736 AGTTTAATTT
*
71746 TCAAAATTTCATAG-GGGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* *
71767 TCAAAATTTCATAATGTA--TAGA
1 TCAAAATTTCATAGTG-AGGT-TA
*
71789 TCAAAATTTCATATTGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
** * * *
71811 TCAAAGAACAATGATAGGGTGGTTA
1 TC-AA-AA-TTTCATAGTGAGGTTA
* * * *
71836 TCAAAATTTCACAATAAGGGTA
1 TCAAAATTTCATAGTGAGGTTA
* *
71858 TCAAAATTTTATAGTGAGGTTT
1 TCAAAATTTCATAGTGAGGTTA
71880 TC-AAATTTCATAGTGTA-GTTA
1 TCAAAATTTCATAGTG-AGGTTA
* *
71901 TCAGAATTTCATAG-GAATGTTA
1 TCAAAATTTCATAGTG-AGGTTA
*
71923 TCAAAATTTCATAG-GAAGATTA
1 TCAAAATTTCATAGTG-AGGTTA
* *
71945 TCAAAATTTCATAGTGTGATTA
1 TCAAAATTTCATAGTGAGGTTA
* * *
71967 TCACAATTTCATAAG-GTGGTTG
1 TCAAAATTTCAT-AGTGAGGTTA
* *
71989 TCACAATTTCATAGTGTGGTTA
1 TCAAAATTTCATAGTGAGGTTA
72011 AAGCTTGGTA
Statistics
Matches: 192, Mismatches: 38, Indels: 27
0.75 0.15 0.11
Matches are distributed among these distances:
21 36 0.19
22 132 0.69
23 8 0.04
24 4 0.02
25 12 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAGTGAGGTTA
Found at i:71861 original size:69 final size:68
Alignment explanation
Indices: 71756--71884 Score: 170
Period size: 69 Copynumber: 1.9 Consensus size: 68
71746 TCAAAATTTC
* * * *
71756 ATAGGGGGTTATCAAAATTTCATAATGTATAGATCAAAATTTCATATTGAGGTTATCAAAGAACA
1 ATAGGGGGTTATCAAAATTTCACAATGAAGAGATCAAAATTTCATAGTGAGGTTATCAAAGAACA
71821 ATG
66 ATG
* * *
71824 ATAGGGTGGTTATCAAAATTTCACAAT-AAGGGTATCAAAATTTTATAGTGAGGTTTTCAAA
1 ATAGGG-GGTTATCAAAATTTCACAATGAAGAG-ATCAAAATTTCATAGTGAGGTTATCAAA
71885 TTTCATAGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
68 8 0.15
69 44 0.85
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (68 bp):
ATAGGGGGTTATCAAAATTTCACAATGAAGAGATCAAAATTTCATAGTGAGGTTATCAAAGAACA
ATG
Found at i:72231 original size:2 final size:2
Alignment explanation
Indices: 72224--72248 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
72214 CTAAAACTAG
72224 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
72249 TAAAGAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72679 original size:20 final size:21
Alignment explanation
Indices: 72643--72681 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
72633 TGGGTGTGTG
*
72643 TGTGTGATTGTTTGGTTTGGT
1 TGTGTGATTGATTGGTTTGGT
72664 TGTGTGA-TGATTGGTTTG
1 TGTGTGATTGATTGGTTTG
72682 TAGAGACCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (21 bp):
TGTGTGATTGATTGGTTTGGT
Found at i:73476 original size:29 final size:29
Alignment explanation
Indices: 73434--73490 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
73424 CTTCTCTATA
73434 GAGTTTTGTATGCTTGGAGAAAAGATATT
1 GAGTTTTGTATGCTTGGAGAAAAGATATT
73463 GAGTTTTGTATGCTTGGAGAAAAGATAT
1 GAGTTTTGTATGCTTGGAGAAAAGATAT
73491 CGTCTAAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.37
Consensus pattern (29 bp):
GAGTTTTGTATGCTTGGAGAAAAGATATT
Found at i:75685 original size:19 final size:19
Alignment explanation
Indices: 75646--75685 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
75636 AGTTGAGTTT
** *
75646 TTTGAGTCAGTTTGTTGAG
1 TTTGAGTCAGTCAGTTCAG
75665 TTTGAGTCAGTCAGTTCAG
1 TTTGAGTCAGTCAGTTCAG
75684 TT
1 TT
75686 AGTCACACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.28, T:0.45
Consensus pattern (19 bp):
TTTGAGTCAGTCAGTTCAG
Found at i:77540 original size:17 final size:18
Alignment explanation
Indices: 77512--77548 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
77502 TCTCCCCATA
77512 GTACCTAGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
77530 GTACC-AGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
77547 GT
1 GT
77549 GATAGGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (18 bp):
GTACCTAGGTAGTATGAG
Found at i:80298 original size:183 final size:183
Alignment explanation
Indices: 79951--80362 Score: 456
Period size: 183 Copynumber: 2.2 Consensus size: 183
79941 GTTTTGTAAT
* * * * *
79951 TTCTTGTAATTTTCGGCCTAATTGGTTAAATTAGCCAAAAATCAGTAGGTAAACCTTCCAAAATT
1 TTCTTGTGA-TTTCAGCCTAATTGATTAAATAAGCCAAAAATCAGTAGGTAAACCTT-CAAAACT
* * * * * *
80016 AGGTCATATCACATGAACATAATCCTAATTTGATGAAATCAAGCAAACCATAATAGGCCGAACCC
64 AGGTCATATCACATAAACATAAGCCCAATTTAATGAAACCAAGCAAACCATAATAAGCCGAACCC
* *
80081 CTTTTTGCAAAAATTGCAACTTGGGCGGCAAATTAACTAGCTTGATAAATTAGGG
129 CTTTTTGCAAAAATTGCAACATAGGCGGCAAATTAACTAGCTTGATAAATTAGGG
* *
80136 TTCTTGTGATTTCAGCCTAATTGATT-AATCAAGCCCAAAATCAGTAGGTTAAACCCTT-TAAAC
1 TTCTTGTGATTTCAGCCTAATTGATTAAAT-AAGCCAAAAATCAGTAGG-TAAA-CCTTCAAAAC
* * * * * *
80199 TAGGTTATATCACATAAATATAAGCCCAATTTAATG-AACCAAGCTACCCCTAATAAGCCGAGCC
63 TAGGTCATATCACATAAACATAAGCCCAATTTAATGAAACCAAGCAAACCATAATAAGCCGAACC
* * * * *
80263 CTTTTTTGCAAAAATTGCAACATAGGCGGCAAATTAGCTTGCTTGGTGAATTAGGG
128 CCTTTTTGCAAAAATTGCAACATAGGCGGCAAATTAACTAGCTTGATAAATTAGGG
* ** *
80319 TTTTTGTGATTT-AGGCAAAATT-AGTTAATTAAGCCAAAAATCAG
1 TTCTTGTGATTTCA-GCCTAATTGA-TTAAATAAGCCAAAAATCAG
80363 GGGGTTTAGT
Statistics
Matches: 190, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
182 2 0.01
183 106 0.56
184 66 0.35
185 12 0.06
186 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (183 bp):
TTCTTGTGATTTCAGCCTAATTGATTAAATAAGCCAAAAATCAGTAGGTAAACCTTCAAAACTAG
GTCATATCACATAAACATAAGCCCAATTTAATGAAACCAAGCAAACCATAATAAGCCGAACCCCT
TTTTGCAAAAATTGCAACATAGGCGGCAAATTAACTAGCTTGATAAATTAGGG
Found at i:90893 original size:17 final size:18
Alignment explanation
Indices: 90865--90901 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
90855 TCTCCCCATA
90865 GTACCTAGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
90883 GTACC-AGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
90900 GT
1 GT
90902 GATAGGCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (18 bp):
GTACCTAGGTAGTATGAG
Found at i:91559 original size:156 final size:155
Alignment explanation
Indices: 91253--91615 Score: 346
Period size: 156 Copynumber: 2.3 Consensus size: 155
91243 GAGCTTCTCA
* * *
91253 CCTCAAATTGTCCTTAAATG-AAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTCAACGAGCTG-AA
* * *
91317 TTTTGCCAAGGGTCTTAGAATATCCACATAAGACTATGGAAAAAATTATAAGTAAAACGGAGCTC
65 TTTTGCCAAGGGTCTTAGAATATCCACATAAGACTATGGAAAAAATTAGAAGTAAAACCGAACTC
** * *
91382 CCCTTGATGGTGAACTAGGTTT-CCAC
130 CCCTACATAGAGAACTAGGTTTGCC-C
****
91408 CCTTGTGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTC-CAACGAAGCTG-A
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTCAACG-AGCTGAA
* * * *
91471 TTTTCGACC-AGTGTACTTAGATTAT-CACCATAAGGCTATGGGAAAAAA-TAGAAGTGAAACCG
65 TTTT-G-CCAAGGGT-CTTAGAATATCCA-CATAAGACTAT-GGAAAAAATTAGAAGTAAAACCG
* * * * *
91533 AACT-CTCTAACATAGAGAAGTTGGTTTGTCT
125 AACTCCCCT-ACATAGAGAACTAGGTTTGCCC
* ** *
91564 CCTCAAACTGTCCTTAACCGAAAAACTAGCATAAGTTTTTCATGCTAAGTCT
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCT
91616 GTTTGAGATG
Statistics
Matches: 167, Mismatches: 31, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
154 5 0.03
155 29 0.17
156 124 0.74
157 9 0.05
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (155 bp):
CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTCAACGAGCTGAAT
TTTGCCAAGGGTCTTAGAATATCCACATAAGACTATGGAAAAAATTAGAAGTAAAACCGAACTCC
CCTACATAGAGAACTAGGTTTGCCC
Found at i:92915 original size:24 final size:25
Alignment explanation
Indices: 92885--92937 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
92875 TTATTGAAGG
92885 AAATTAAATAAAAAATTTTGGA-GA
1 AAATTAAATAAAAAATTTTGGAGGA
***
92909 AAATTAAATATTTAATTTTGGAGGA
1 AAATTAAATAAAAAATTTTGGAGGA
92934 AAAT
1 AAAT
92938 AAGTGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (25 bp):
AAATTAAATAAAAAATTTTGGAGGA
Found at i:105360 original size:9 final size:7
Alignment explanation
Indices: 105332--105359 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
105322 ACATATATTA
105332 TATATAT
1 TATATAT
105339 TATATAT
1 TATATAT
105346 TATATAT
1 TATATAT
105353 TATATAT
1 TATATAT
105360 AAGTATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATAT
Found at i:109744 original size:13 final size:12
Alignment explanation
Indices: 109721--109788 Score: 100
Period size: 12 Copynumber: 5.5 Consensus size: 12
109711 TTAATACAAG
109721 TATCGACGGATA
1 TATCGACGGATA
109733 TATCGAACGGATA
1 TATCG-ACGGATA
*
109746 TATCGACGGAAA
1 TATCGACGGATA
109758 TATCGAACGGATA
1 TATCG-ACGGATA
*
109771 TATCGACGGAAA
1 TATCGACGGATA
109783 TATCGA
1 TATCGA
109789 GGTATCGATG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
12 28 0.55
13 23 0.45
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:109755 original size:25 final size:25
Alignment explanation
Indices: 109721--109788 Score: 127
Period size: 25 Copynumber: 2.7 Consensus size: 25
109711 TTAATACAAG
*
109721 TATCGACGGATATATCGAACGGATA
1 TATCGACGGAAATATCGAACGGATA
109746 TATCGACGGAAATATCGAACGGATA
1 TATCGACGGAAATATCGAACGGATA
109771 TATCGACGGAAATATCGA
1 TATCGACGGAAATATCGA
109789 GGTATCGATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (25 bp):
TATCGACGGAAATATCGAACGGATA
Found at i:111090 original size:18 final size:18
Alignment explanation
Indices: 111058--111092 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
111048 ATTTACGGAT
**
111058 ATATCGAGATTTATCGAG
1 ATATCGAGAAATATCGAG
111076 ATATCGAGAAATATCGA
1 ATATCGAGAAATATCGA
111093 CAGATATCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (18 bp):
ATATCGAGAAATATCGAG
Done.