Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019745.1 Corchorus olitorius cultivar O-4 contig19778, 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: 116630
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:373 original size:27 final size:24
Alignment explanation
Indices: 338--398 Score: 63
Period size: 27 Copynumber: 2.5 Consensus size: 24
328 CTAATTCATG
*
338 AAAATTAATTATAAATTATTTCAAATT
1 AAAACTAATTATAAA-TA-TT-AAATT
365 AAAACTAATTA-AAATATTAAATT
1 AAAACTAATTATAAATATTAAATT
*
388 -AAACAAATTAT
1 AAAACTAATTAT
399 GAAAATGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 9 0.29
23 5 0.16
24 2 0.06
25 2 0.06
26 3 0.10
27 10 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAACTAATTATAAATATTAAATT
Found at i:991 original size:17 final size:16
Alignment explanation
Indices: 947--1022 Score: 91
Period size: 16 Copynumber: 4.8 Consensus size: 16
937 GTCGGGTTGA
947 TTGGGTTCGGGTCATT
1 TTGGGTTCGGGTCATT
*
963 TTGGGTTTGGGTCATT
1 TTGGGTTCGGGTCATT
979 TTCGGGTTCGGGTCA-T
1 TT-GGGTTCGGGTCATT
* * *
995 TTGGATTCGGATAATT
1 TTGGGTTCGGGTCATT
*
1011 TCGGGTTCGGGT
1 TTGGGTTCGGGT
1023 ACCCAAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
15 9 0.18
16 30 0.60
17 11 0.22
ACGTcount: A:0.09, C:0.12, G:0.37, T:0.42
Consensus pattern (16 bp):
TTGGGTTCGGGTCATT
Found at i:1071 original size:17 final size:17
Alignment explanation
Indices: 1031--1071 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1021 GTACCCAAAA
1031 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
1048 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
1064 TTTCGGGT
1 TTTCGGGT
1072 TGGGCGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:4555 original size:29 final size:29
Alignment explanation
Indices: 4500--4555 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
4490 ATATATTTTA
* *
4500 TATAGTATATATAATATGTATTGTGATGT
1 TATAGTATATATAATATATATTATGATGT
*
4529 TATATTATATAT-ATATATATATATGAT
1 TATAGTATATATAATATATAT-TATGAT
4556 AAAAAACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (29 bp):
TATAGTATATATAATATATATTATGATGT
Found at i:4807 original size:2 final size:2
Alignment explanation
Indices: 4796--4824 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4786 CTCATACTTT
4796 TA TA -A 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
4825 ACTGATAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5228 original size:12 final size:10
Alignment explanation
Indices: 5200--5230 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
5190 CAAAATTTTC
5200 AATTCTCTCA
1 AATTCTCTCA
5210 AATTCTCTCA
1 AATTCTCTCA
5220 AATTCTCTCA
1 AATTCTCTCA
5230 A
1 A
5231 CCTTCAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
AATTCTCTCA
Found at i:5585 original size:108 final size:108
Alignment explanation
Indices: 5396--5612 Score: 425
Period size: 108 Copynumber: 2.0 Consensus size: 108
5386 TGACATATCC
5396 ATACCCATTTAAGCTAAATGAATTGTCAAATACTTATTAAAGAATAAAAGGAAATTAAAGGAAAA
1 ATACCCATTTAAGCTAAATGAATTGTCAAATACTTATTAAAGAATAAAAGGAAATTAAAGGAAAA
5461 TCTATAAGGATTAAAAAAAAACACAAGAAAATGGCGGGTCGCG
66 TCTATAAGGATTAAAAAAAAACACAAGAAAATGGCGGGTCGCG
*
5504 ATACCCATTTAATCTAAATGAATTGTCAAATACTTATTAAAGAATAAAAGGAAATTAAAGGAAAA
1 ATACCCATTTAAGCTAAATGAATTGTCAAATACTTATTAAAGAATAAAAGGAAATTAAAGGAAAA
5569 TCTATAAGGATTAAAAAAAAACACAAGAAAATGGCGGGTCGCG
66 TCTATAAGGATTAAAAAAAAACACAAGAAAATGGCGGGTCGCG
5612 A
1 A
5613 CACGGATCGC
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (108 bp):
ATACCCATTTAAGCTAAATGAATTGTCAAATACTTATTAAAGAATAAAAGGAAATTAAAGGAAAA
TCTATAAGGATTAAAAAAAAACACAAGAAAATGGCGGGTCGCG
Found at i:5674 original size:22 final size:23
Alignment explanation
Indices: 5644--5686 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5634 GCTTCTTGCG
*
5644 TTTTTCTTT-ATATCCTTTTAGA
1 TTTTCCTTTAATATCCTTTTAGA
*
5666 TTTTCCTTTAATTTCCTTTTA
1 TTTTCCTTTAATATCCTTTTA
5687 TCCTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.16, C:0.16, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTCCTTTAATATCCTTTTAGA
Found at i:22887 original size:22 final size:22
Alignment explanation
Indices: 22814--23036 Score: 143
Period size: 22 Copynumber: 10.0 Consensus size: 22
22804 TCTTGTCTCT
* *
22814 GTGTGATTATCAAAATTTCAAAA
1 GTGTGGTTATCAAAATTTC-ATA
* * *
22837 G-ATGGTTATTATAATTTCATGA
1 GTGTGGTTATCAAAATTTCAT-A
* **
22859 G-GAGGTTATCAAAATACCATA
1 GTGTGGTTATCAAAATTTCATA
*
22880 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
22902 -TG-GAAGTTATCAAAATTTCATT
1 GTGTG--GTTATCAAAATTTCATA
*
22924 G-GAAGGTTATCAAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
*
22946 GTGTGGTTACCAAAATTTCATAA
1 GTGTGGTTATCAAAATTTCAT-A
** * *
22969 GATCAGGTTATTAAAATTTCTTA
1 G-TGTGGTTATCAAAATTTCATA
* **
22992 G-GAAGGTTATTGAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
* *
23014 GTGTGGTTATCACAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
23036 G
1 G
23037 AAAGGTTATC
Statistics
Matches: 155, Mismatches: 33, Indels: 25
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 5 0.03
22 126 0.81
23 7 0.05
24 16 0.10
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:23108 original size:22 final size:22
Alignment explanation
Indices: 23083--23176 Score: 79
Period size: 22 Copynumber: 4.4 Consensus size: 22
23073 AGGTTATAAG
*
23083 AATTTCATAGTGTGGTCAACAA
1 AATTTCATAGTGTGGTTAACAA
*
23105 AATTTC--A-TGAGGTT-ACTAA
1 AATTTCATAGTGTGGTTAAC-AA
* * * * *
23124 TATTTCATGGAGAGGTTATCAA
1 AATTTCATAGTGTGGTTAACAA
*
23146 AATTTCATAGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTAACAA
23168 AATTTCATA
1 AATTTCATA
23177 TGAAGGTTAT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.04
19 12 0.21
20 1 0.02
22 41 0.72
23 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTAACAA
Found at i:23172 original size:141 final size:143
Alignment explanation
Indices: 22927--23191 Score: 351
Period size: 141 Copynumber: 1.8 Consensus size: 143
22917 TTTCATTGGA
* * * *
22927 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAAGATCAGGTTATTAAAATTTCTTA
1 AGGTTATCAAAATTTCATAGTGTGGTCAACAAAATTTCAT-AGA--AGGTTACTAAAATTTCATA
** * * *
22992 GGAAGGTTATTGAAATTTCATAGTGTGGTTATCACAATTTTATA-GAAAGGTTATCAAAGAGATT
63 GGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATATG-AAGGTTATAAAAGAGATT
23056 ATCAAAATGCCATAACG
127 ATCAAAATGCCATAACG
*
23073 AGGTTAT-AAGAATTTCATAGTGTGGTCAACAAAATTTCAT-G-AGGTTACTAATATTTCAT-GG
1 AGGTTATCAA-AATTTCATAGTGTGGTCAACAAAATTTCATAGAAGGTTACTAAAATTTCATAGG
23134 AGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATATGAAGGTTATAAAAG
65 A-AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATATGAAGGTTATAAAAG
23192 TCTCAATTTC
Statistics
Matches: 106, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
140 3 0.03
141 64 0.60
142 1 0.01
144 1 0.01
145 2 0.02
146 35 0.33
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.35
Consensus pattern (143 bp):
AGGTTATCAAAATTTCATAGTGTGGTCAACAAAATTTCATAGAAGGTTACTAAAATTTCATAGGA
AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATATGAAGGTTATAAAAGAGATTATCA
AAATGCCATAACG
Found at i:23174 original size:44 final size:43
Alignment explanation
Indices: 23049--23984 Score: 198
Period size: 44 Copynumber: 21.5 Consensus size: 43
23039 AGGTTATCAA
* ** *
23049 AGAGATTATCAAAATGCCATAACGAGGTTAT-AAGAATTTCATAG
1 AGAGGTTATCAAAATTTCAT-AGGAGGTTATCAA-AATTTCATAG
* * * * * *
23093 TGTGGTCAACAAAATTTCAT--GAGGTTA-CTAATATTTCATGG
1 AGAGGTTATCAAAATTTCATAGGAGGTTATC-AAAATTTCATAG
*
23134 AGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATATG
1 AGAGGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATA-G
* * *
23179 A-AGGTTATAAAAGTCTCAATTTCATAAGGA-G-TACCAAAATTTAATAG
1 AGAGGTTAT-CAA-----AATTTCAT-AGGAGGTTATCAAAATTTCATAG
* * *
23226 A-AGATTATC-AAATATCATA-GAGTGATTATCGAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAGGAG-G-TTATCAAAATTTCATAG
*
23268 AGATCGGATTATCAAAATTT-ATAGGAAGGTTATCAAAATTTTATAG
1 AGA--GG-TTATCAAAATTTCATAGG-AGGTTATCAAAATTTCATAG
* *** * * *
23314 TGTTCTTATCAAAATTACAAAGCGAGGTTATCAAAATTACATA-
1 AGAGGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAG
* * * * * *
23357 ATGTGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAG
1 A-GAGGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAG
* * * *
23402 AGAGGTTATCAAATTTTCA-A-AATGTAATCACCAAAATTTCAT--
1 AGAGGTTATCAAAATTTCATAGGAGGT--T-ATCAAAATTTCATAG
* * *
23444 AGTGG---T----ATTTC-TGGGGAGCTTATCAAAATTTCATAG
1 AGAGGTTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAG
* * * * *
23480 TA-TGGTTA-CTAAA--T--TAGGAAGGTTATTATAACTTTTATTATG
1 -AGAGGTTATCAAAATTTCATAGG-AGGTTATCA-AAATTTCA-TA-G
* * *
23522 -GA-GATATCAAAATTTCA-GGGAGGATATCAAAATTTCATATG
1 AGAGGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATA-G
* *
23563 AAGATTAGTTTAGTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAG
1 -AG---AG----GTTATCAAAATTTCATAGGA-GGTTATCAAAATTTCATAG
* * * * **
23615 GGAGATTAACAAAATTTCATAATGAGGTTATCAAAAAATCATAG
1 AGAGGTTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAG
* * * *
23659 GGAGGCTATCAAAA-TT--T-GTA-GTTATCAAGATTTCATA-
1 AGAGGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAG
* * * *
23696 AGGAGGTTATCAAAATTTTATAGGGAGGTTTATCAGAATTTTACAG
1 A-GAGGTTATCAAAATTTCATA-GGAGG-TTATCAAAATTTCATAG
** *
23742 -GAAGGTTTATCAAAATTTCATAACAAGGTTATCACAATTTCATAG
1 AG-AGG-TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAG
* * * * * * * *
23787 TGTGATTATCAAAATTTTAGAGTGTGATTA-CTAACAA-TTCATAT
1 AGAGGTTATCAAAATTTCATAG-GAGGTTATC-AA-AATTTCATAG
* * * * * * *
23831 AGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATATCATATG
1 AGAGGTTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATA-G
* * * * * *
23876 A-AGGTAATCAACATCTCATAGTGTTGGTTATCGAAATTTCATTG
1 AGAGGTTATCAAAATTTCATAG-G-AGGTTATCAAAATTTCATAG
* ** * * *
23920 GGAAATAAACAAAATTTCATAGTGAGGTCT-TCAAAA-TTCTTAAG
1 AGAGGTTATCAAAATTTCATAG-GAGGT-TATCAAAATTTCAT-AG
* *
23964 GGAGGTTAACAAAATTTCATA
1 AGAGGTTATCAAAATTTCATA
23985 ATAACAAGGT
Statistics
Matches: 641, Mismatches: 158, Indels: 186
0.65 0.16 0.19
Matches are distributed among these distances:
34 12 0.02
35 5 0.01
36 3 0.00
37 3 0.00
38 30 0.05
39 13 0.02
40 18 0.03
41 45 0.07
42 28 0.04
43 34 0.05
44 248 0.39
45 80 0.12
46 43 0.07
47 16 0.02
48 17 0.03
49 1 0.00
50 9 0.01
51 16 0.02
52 3 0.00
53 17 0.03
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (43 bp):
AGAGGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAG
Found at i:23184 original size:22 final size:21
Alignment explanation
Indices: 23102--23420 Score: 134
Period size: 22 Copynumber: 14.5 Consensus size: 21
23092 GTGTGGTCAA
23102 CAAAATTTCAT-G-AGGTTA-
1 CAAAATTTCATAGAAGGTTAT
* *
23120 CTAATATTTCATGGAGAGGTTAT
1 C-AAAATTTCATAGA-AGGTTAT
**
23143 CAAAATTTCATAGTGTGGTTAT
1 CAAAATTTCATAG-AAGGTTAT
23165 CAAAATTTCATATGAAGGTTAT
1 CAAAATTTCATA-GAAGGTTAT
* * * *
23187 -AAAAGTCTCAATTTCATAAGGAGTAC
1 CAAAA-TTTC-A--T-AGAAGG-TTAT
* *
23213 CAAAATTTAATAGAAGATTAT
1 CAAAATTTCATAGAAGGTTAT
*
23234 C-AAATATCATAG-AGTGATTAT
1 CAAAATTTCATAGAAG-G-TTAT
*
23255 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGA-A--GG-TTAT
23280 CAAAATTT-ATAGGAAGGTTAT
1 CAAAATTTCATA-GAAGGTTAT
* * *
23301 CAAAATTTTATAG-TGTTCTTAT
1 CAAAATTTCATAGAAG--GTTAT
* * *
23323 CAAAATTACAAAGCGAGGTTAT
1 CAAAATTTCATAG-AAGGTTAT
* *
23345 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGAAG-G-TTAT
* * *
23367 CAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAGA-AGGTTAT
*
23389 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTCATAGA-AGGTTAT
*
23411 CAAATTTTCA
1 CAAAATTTCA
23421 AAATGTAATC
Statistics
Matches: 228, Mismatches: 42, Indels: 58
0.70 0.13 0.18
Matches are distributed among these distances:
18 1 0.00
19 11 0.05
20 12 0.05
21 26 0.11
22 134 0.59
23 6 0.03
24 7 0.03
25 21 0.09
26 6 0.03
27 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
CAAAATTTCATAGAAGGTTAT
Found at i:23735 original size:23 final size:23
Alignment explanation
Indices: 23680--23759 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
23670 AAATTTGTAG
* * *
23680 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTTATAGGGAGGT
23702 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
23725 TTATCAGAATTTTACAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
23748 TTATCAAAATTT
1 TTATCAAAATTT
23760 CATAACAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 19 0.38
23 31 0.62
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:23769 original size:23 final size:22
Alignment explanation
Indices: 23579--23785 Score: 140
Period size: 22 Copynumber: 9.6 Consensus size: 22
23569 AGTTTAGTTT
*
23579 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * *
23601 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATAAGAAGGTTA
*
23623 ACAAAATTTCATAATG-AGGTTA
1 TCAAAATTTCATAA-GAAGGTTA
** * * *
23645 TCAAAAAATCATAGGGAGGCTA
1 TCAAAATTTCATAAGAAGGTTA
*
23667 TCAAAA-TT--T--GTA-GTTA
1 TCAAAATTTCATAAGAAGGTTA
* *
23683 TCAAGATTTCATAAGGAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * *
23705 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATAAGAAGG-TTA
* * * *
23728 TCAGAATTTTACAGGAAGGTTTA
1 TCAAAATTTCATAAGAAGG-TTA
*
23751 TCAAAATTTCATAACAAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
*
23773 TCACAATTTCATA
1 TCAAAATTTCATA
23786 GTGTGATTAT
Statistics
Matches: 147, Mismatches: 29, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
16 8 0.05
17 4 0.03
19 2 0.01
21 4 0.03
22 91 0.62
23 38 0.26
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (22 bp):
TCAAAATTTCATAAGAAGGTTA
Found at i:23810 original size:22 final size:22
Alignment explanation
Indices: 23770--23816 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
23760 CATAACAAGG
* *
23770 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
*
23792 TTATCAAAATTTTAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
23814 TTA
1 TTA
23817 CTAACAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:24090 original size:22 final size:22
Alignment explanation
Indices: 24043--24090 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
24033 TTTTGTTATT
* *
24043 AAAATTTCATAGGAAGGTTATT
1 AAAATTTCATAGGAAGGTCATC
24065 AAAATTTCATAAGG-AGGTCATC
1 AAAATTTCAT-AGGAAGGTCATC
24087 AAAA
1 AAAA
24091 ATAGTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATC
Found at i:25077 original size:25 final size:25
Alignment explanation
Indices: 25047--25094 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
25037 ATAATTGGAC
25047 TTTTTTATGATTTGGGCATTAATAT
1 TTTTTTATGATTTGGGCATTAATAT
*
25072 TTTTTTATGATTTGGGCTTTAAT
1 TTTTTTATGATTTGGGCATTAAT
25095 CTTAATTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.21, C:0.04, G:0.17, T:0.58
Consensus pattern (25 bp):
TTTTTTATGATTTGGGCATTAATAT
Found at i:27089 original size:6 final size:6
Alignment explanation
Indices: 27078--27103 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27068 AGTGATCATA
27078 TGATTT TGATTT TGATTT TGATTT TG
1 TGATTT TGATTT TGATTT TGATTT TG
27104 TTGTCTGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.19, T:0.65
Consensus pattern (6 bp):
TGATTT
Found at i:27174 original size:22 final size:22
Alignment explanation
Indices: 27115--27192 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
27105 TGTCTGTGTG
27115 GTTATCAAAATTCCATAAGGATA
1 GTTATCAAAATT-CATAAGGATA
* *
27138 -TTATTATAATTTCATAAGGA-A
1 GTTATCA-AAATTCATAAGGATA
***
27159 GTTATCAAAATCTCATATCAAT-
1 GTTATCAAAAT-TCATAAGGATA
27181 GTTATCAAAATT
1 GTTATCAAAATT
27193 TCATTGTGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
21 5 0.11
22 35 0.80
23 4 0.09
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTCATAAGGATA
Found at i:27278 original size:44 final size:42
Alignment explanation
Indices: 27166--27293 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 42
27156 GAAGTTATCA
* * * *
27166 AAATCTCATATCAATGTTATCAAAATTTCATTGTGTGTGGTTACCC
1 AAAT-TCATATGAAAGTTATCAAAATTTCA-T-AGTGTGG-TAACC
*
27212 AAATTCATATGGAAGTTATCAAAATTTCATAGTGTGGTAACC
1 AAATTCATATGAAAGTTATCAAAATTTCATAGTGTGGTAACC
*
27254 AAACCTTCATA-GAAAGGTTATCAAAATTTCATAGAGTGGT
1 AAA--TTCATATGAAA-GTTATCAAAATTTCATAGTGTGGT
27294 TATTAAAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
42 7 0.10
43 9 0.12
44 30 0.42
45 22 0.31
46 4 0.06
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (42 bp):
AAATTCATATGAAAGTTATCAAAATTTCATAGTGTGGTAACC
Found at i:27294 original size:22 final size:22
Alignment explanation
Indices: 27226--27377 Score: 112
Period size: 22 Copynumber: 6.8 Consensus size: 22
27216 TCATATGGAA
*
27226 GTTATCAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGAGTG
* * ** **
27248 GTAACCAAACCTTCATAGAAAG
1 GTTATCAAAATTTCATAGAGTG
27270 GTTATCAAAATTTCATAGAGTG
1 GTTATCAAAATTTCATAGAGTG
* *
27292 GTTATTAAAATTTTATAG-GATCAG
1 GTTATCAAAATTTCATAGAG-T--G
* * *
27316 ATTATTAAAATTTCATAG-GAAG
1 GTTATCAAAATTTCATAGAG-TG
27338 GTTATCAAAATTTCATA-ATGTG
1 GTTATCAAAATTTCATAGA-GTG
* *
27360 TTTAACAAAATTTCATAG
1 GTTATCAAAATTTCATAG
27378 CAAGTTTACA
Statistics
Matches: 101, Mismatches: 23, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
21 1 0.01
22 80 0.79
23 1 0.01
24 19 0.19
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGAGTG
Found at i:27384 original size:22 final size:22
Alignment explanation
Indices: 27322--27385 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
27312 TCAGATTATT
* * *
27322 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAGCAAGTTTAAC
****
27344 AAAATTTCATAATGTGTTTAAC
1 AAAATTTCATAGCAAGTTTAAC
27366 AAAATTTCATAGCAAGTTTA
1 AAAATTTCATAGCAAGTTTA
27386 CATTGTGTGG
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGCAAGTTTAAC
Found at i:27451 original size:22 final size:22
Alignment explanation
Indices: 27395--27502 Score: 73
Period size: 22 Copynumber: 5.0 Consensus size: 22
27385 ACATTGTGTG
*
27395 GTTATCAAAATTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAA
* * **
27417 GTTATTAAGATTTCATTGGGAA
1 GTTATCAAAATTTCATAAGGAA
* *
27439 GTTATCAAAATTT--T-AGTATG
1 GTTATCAAAATTTCATAAGGA-A
* *
27459 GTTATTC-AAATTTCATAAAGTA
1 GTTA-TCAAAATTTCATAAGGAA
*
27481 GTTACCAAAATTTCAT-AGGAA
1 GTTATCAAAATTTCATAAGGAA
27502 G
1 G
27503 GTTTAAAAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
19 2 0.03
20 11 0.17
21 7 0.11
22 42 0.67
23 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAA
Found at i:27556 original size:22 final size:22
Alignment explanation
Indices: 27531--27649 Score: 72
Period size: 22 Copynumber: 5.5 Consensus size: 22
27521 CATAAGGCGC
27531 TTATCAAAATTTAATAGGGAGG
1 TTATCAAAATTTAATAGGGAGG
* * * *
27553 TTATCGAGAATTTTATAGTGTGG
1 TTATC-AAAATTTAATAGGGAGG
* *
27576 TTATAAAAATTTCAT---GAGG
1 TTATCAAAATTTAATAGGGAGG
* *
27595 TT-TCAAAATCTT-ATA-GAATGT
1 TTATCAAAAT-TTAATAGGGA-GG
*
27616 TTATCAAAATTTCAA-AGCGAGG
1 TTATCAAAATTT-AATAGGGAGG
27638 TTATCAAAATTT
1 TTATCAAAATTT
27650 CAAAGCGATG
Statistics
Matches: 74, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
18 8 0.11
19 7 0.09
20 1 0.01
21 5 0.07
22 34 0.46
23 19 0.26
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTAATAGGGAGG
Found at i:27650 original size:22 final size:22
Alignment explanation
Indices: 27616--27657 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
27606 TATAGAATGT
27616 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCAAAGCGAGG
27638 TTATCAAAATTTCAAAGCGA
1 TTATCAAAATTTCAAAGCGA
27658 TGTTGGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (22 bp):
TTATCAAAATTTCAAAGCGAGG
Found at i:27755 original size:30 final size:31
Alignment explanation
Indices: 27679--27755 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
27669 ATACCATACA
* *
27679 GGTCCCTCTACTTACAAAAAGGGATCAATTT
1 GGTCCCTTTACTTACAAAAACGGATCAATTT
* * *
27710 GGTCCCCTAAC-TACAAAAACTG-TCAATTT
1 GGTCCCTTTACTTACAAAAACGGATCAATTT
27739 GGTCCCTTTACTTACAA
1 GGTCCCTTTACTTACAA
27756 TTTGGTGTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 16 0.42
30 14 0.37
31 8 0.21
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (31 bp):
GGTCCCTTTACTTACAAAAACGGATCAATTT
Found at i:30093 original size:2 final size:2
Alignment explanation
Indices: 30086--30114 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30076 ATAATATGTA
30086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30115 ATTGGCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32970 original size:31 final size:29
Alignment explanation
Indices: 32935--33006 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
32925 GCTTATTACC
32935 CAAATTAATCCCTTAATTATCCATTTTGGGA
1 CAAATTAATCCCTTAATT-T-CATTTTGGGA
*** **
32966 CAAATTGGCCCCTTAATTTTTTTTTGGGA
1 CAAATTAATCCCTTAATTTCATTTTGGGA
*
32995 CAAATAAATCCC
1 CAAATTAATCCC
33007 ATAACTTTTA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
29 16 0.50
30 1 0.03
31 15 0.47
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (29 bp):
CAAATTAATCCCTTAATTTCATTTTGGGA
Found at i:36233 original size:12 final size:12
Alignment explanation
Indices: 36216--36240 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36206 TCCTGCCAAA
36216 TGCTATGAGATT
1 TGCTATGAGATT
36228 TGCTATGAGATT
1 TGCTATGAGATT
36240 T
1 T
36241 ACATTAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (12 bp):
TGCTATGAGATT
Found at i:55593 original size:10 final size:10
Alignment explanation
Indices: 55578--55602 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55568 CTATCCACGG
55578 TTAGTGGAGT
1 TTAGTGGAGT
55588 TTAGTGGAGT
1 TTAGTGGAGT
55598 TTAGT
1 TTAGT
55603 AGACTGCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (10 bp):
TTAGTGGAGT
Found at i:68036 original size:12 final size:12
Alignment explanation
Indices: 68016--68053 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
68006 CTGGTGAAAC
*
68016 TTGGGGCTAAAT
1 TTGGTGCTAAAT
68028 TTGGTGCTAAAT
1 TTGGTGCTAAAT
68040 TT-GTGCCTAAAT
1 TTGGTG-CTAAAT
68052 TT
1 TT
68054 TGGGTCGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.42
Consensus pattern (12 bp):
TTGGTGCTAAAT
Found at i:74058 original size:23 final size:20
Alignment explanation
Indices: 74002--74066 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 20
73992 TTCTTTCAAC
74002 TTTTATTTTATTTA-TATAT
1 TTTTATTTTATTTATTATAT
*
74021 ATTTA-TTTATATTATTAATGGAT
1 TTTTATTTTAT-TTATT-AT--AT
*
74044 TTTTATTTTATTTATTCTAT
1 TTTTATTTTATTTATTATAT
74064 TTT
1 TTT
74067 CCTTTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
18 5 0.14
19 7 0.19
20 6 0.16
21 2 0.05
22 1 0.03
23 11 0.30
24 5 0.14
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTATTTTATTTATTATAT
Found at i:74195 original size:19 final size:19
Alignment explanation
Indices: 74134--74196 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
74124 CTTTTCTACC
74134 TTTATTTTATTTATATACATAT
1 TTTATTTTATTTAT-T-CAT-T
* * **
74156 ATTTATATTATTAATGGATT
1 -TTTATTTTATTTATTCATT
74176 TTTATTTTATTTATTCATT
1 TTTATTTTATTTATTCATT
74195 TT
1 TT
74197 CTTTTTTCAC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 17 0.53
20 1 0.03
21 2 0.06
23 12 0.38
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTATTTTATTTATTCATT
Found at i:76688 original size:27 final size:27
Alignment explanation
Indices: 76650--76703 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
76640 CTTTGCAATT
*
76650 TGTCACAAGAATTATTCA-AAAAAAAAA
1 TGTCACAAGAATT-CTCAGAAAAAAAAA
76677 TGTCACAAGAATTCTCAGAAAAAAAAA
1 TGTCACAAGAATTCTCAGAAAAAAAAA
76704 AAATTCACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.20
Consensus pattern (27 bp):
TGTCACAAGAATTCTCAGAAAAAAAAA
Found at i:77883 original size:16 final size:16
Alignment explanation
Indices: 77864--77940 Score: 66
Period size: 16 Copynumber: 4.8 Consensus size: 16
77854 CCCGAATCCG
77864 AACCCGAAAAAACTCA
1 AACCCGAAAAAACTCA
*
77880 AACCCGAAAAATC-CAA
1 AACCCGAAAAAACTC-A
* * *
77896 AATCCGAAAAATCTGA
1 AACCCGAAAAAACTCA
* * *
77912 AACCCGATAAAACCCG
1 AACCCGAAAAAACTCA
*
77928 AACCTGAAAAAAC
1 AACCCGAAAAAAC
77941 CCGAATTCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
15 1 0.02
16 47 0.98
ACGTcount: A:0.53, C:0.29, G:0.09, T:0.09
Consensus pattern (16 bp):
AACCCGAAAAAACTCA
Found at i:77937 original size:32 final size:31
Alignment explanation
Indices: 77861--77940 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 31
77851 CCGCCCGAAT
77861 CCGAACCCGAAAAAACTCAAACCCGAAAAATC
1 CCGAA-CCGAAAAAACTCAAACCCGAAAAATC
** * *
77893 CAAAATCCGAAAAATCTGAAACCCGATAAAA-C
1 CCGAA-CCGAAAAAACTCAAACCCGA-AAAATC
77925 CCGAACCTGAAAAAAC
1 CCGAACC-GAAAAAAC
77941 CCGAATTCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
31 2 0.05
32 32 0.84
33 4 0.11
ACGTcount: A:0.51, C:0.30, G:0.10, T:0.09
Consensus pattern (31 bp):
CCGAACCGAAAAAACTCAAACCCGAAAAATC
Found at i:78153 original size:16 final size:16
Alignment explanation
Indices: 78134--78226 Score: 62
Period size: 16 Copynumber: 5.8 Consensus size: 16
78124 CCCGAATCCG
*
78134 AATTAACCTGACCCAA
1 AATTAACCCGACCCAA
* *
78150 AATTGACCCGAACCC-G
1 AATTAACCCG-ACCCAA
* * *
78166 AATTAACCTGATCCGA
1 AATTAACCCGACCCAA
* * *
78182 ATTTAACCCGAACCTA
1 AATTAACCCGACCCAA
* *
78198 AATCAACCCAACCCAA
1 AATTAACCCGACCCAA
*
78214 ATTTAACCCGACC
1 AATTAACCCGACC
78227 TGACTCAAAC
Statistics
Matches: 56, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
15 3 0.05
16 49 0.88
17 4 0.07
ACGTcount: A:0.39, C:0.34, G:0.09, T:0.18
Consensus pattern (16 bp):
AATTAACCCGACCCAA
Found at i:78191 original size:32 final size:32
Alignment explanation
Indices: 78122--78224 Score: 107
Period size: 32 Copynumber: 3.2 Consensus size: 32
78112 GCCAAAACCC
*
78122 AACCCGAATCCGAATTAACCTGACCCAAAATT
1 AACCCGAACCCGAATTAACCTGACCCAAAATT
* * * *
78154 GACCCGAACCCGAATTAACCTGATCCGAATTT
1 AACCCGAACCCGAATTAACCTGACCCAAAATT
** * ** *
78186 AACCCGAACCTAAATCAACCCAACCCAAATTT
1 AACCCGAACCCGAATTAACCTGACCCAAAATT
78218 AACCCGA
1 AACCCGA
78225 CCTGACTCAA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.39, C:0.34, G:0.10, T:0.17
Consensus pattern (32 bp):
AACCCGAACCCGAATTAACCTGACCCAAAATT
Found at i:85155 original size:15 final size:15
Alignment explanation
Indices: 85137--85170 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
85127 TTAAAATTAA
85137 AATTTGGTAAATT-TT
1 AATTTGGT-AATTATT
85152 AATTTGGTAATTATT
1 AATTTGGTAATTATT
85167 AATT
1 AATT
85171 AATTGACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
AATTTGGTAATTATT
Found at i:91865 original size:44 final size:44
Alignment explanation
Indices: 91815--91903 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
91805 AAAATGTTGA
* *
91815 CAAGAATCCCATTCTAAAATTAACAAAAACTTTAATATTTTAAT
1 CAAGAATCCCATTCTAAAATTAACAAAAACTTTAACATTTCAAT
91859 CAAGAATCCCATTCTAAAATTAACAAAAACTTTAACATTTCAAT
1 CAAGAATCCCATTCTAAAATTAACAAAAACTTTAACATTTCAAT
91903 C
1 C
91904 TAGTTCCTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.31
Consensus pattern (44 bp):
CAAGAATCCCATTCTAAAATTAACAAAAACTTTAACATTTCAAT
Found at i:110414 original size:25 final size:25
Alignment explanation
Indices: 110363--110414 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
110353 AATAAATATC
*
110363 AAATTAATTTGTAATATAATATGAA
1 AAATTAATTTGTAAAATAATATGAA
* *
110388 AAATTAATTTTTATAAATCATAT-AA
1 AAATTAATTTGTA-AAATAATATGAA
110413 AA
1 AA
110415 TAAAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATTAATTTGTAAAATAATATGAA
Found at i:111726 original size:2 final size:2
Alignment explanation
Indices: 111721--111749 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
111711 GCTATAGAAC
111721 TA TA 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 TA TA T
111750 CACCCCGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:112280 original size:33 final size:36
Alignment explanation
Indices: 112238--112305 Score: 115
Period size: 33 Copynumber: 2.0 Consensus size: 36
112228 GTAAATAAAA
112238 CAATTATAACGAAA-CAG-ATCA-GTGATATCAAAG
1 CAATTATAACGAAATCAGAATCATGTGATATCAAAG
112271 CAATTATAACGAAATCAGAATCATGTGATATCAAA
1 CAATTATAACGAAATCAGAATCATGTGATATCAAA
112306 ACCATGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 14 0.44
34 3 0.09
35 4 0.12
36 11 0.34
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.24
Consensus pattern (36 bp):
CAATTATAACGAAATCAGAATCATGTGATATCAAAG
Found at i:112785 original size:27 final size:28
Alignment explanation
Indices: 112732--112787 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
112722 TCATGCACCC
* * *
112732 AAAATTATTTAATAAAATCATTTATAAA
1 AAAATAATTTAATAAAATCAGTAATAAA
112760 AAAATAATTTAATAAAA-CAGTAATAAA
1 AAAATAATTTAATAAAATCAGTAATAAA
112787 A
1 A
112788 TAGTTCCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAATAATTTAATAAAATCAGTAATAAA
Done.