Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008868.1 Hibiscus syriacus cultivar Beakdansim tig00112102_pilon, 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: 66495
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4672 original size:15 final size:15
Alignment explanation
Indices: 4652--4682 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4642 ATATGTCCAC
4652 GTCCTGAGCAAATAA
1 GTCCTGAGCAAATAA
4667 GTCCTGAGCAAATAA
1 GTCCTGAGCAAATAA
4682 G
1 G
4683 AAAGAAGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (15 bp):
GTCCTGAGCAAATAA
Found at i:14308 original size:4 final size:4
Alignment explanation
Indices: 14195--14288 Score: 84
Period size: 4 Copynumber: 23.5 Consensus size: 4
14185 GGCAGTAATG
* * * *
14195 TTTA TTTA TTTA TTTA TTTA TTTGAA TTTA TGTA TTCA TTTA TTT- CTAA
1 TTTA TTTA TTTA TTTA TTTA TTT--A TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
14244 TTTA TTTG TTTT TTTA TTTG TTTG TTT- TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
14289 CCACTCAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
3 4 0.05
4 66 0.89
6 4 0.05
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:20401 original size:83 final size:82
Alignment explanation
Indices: 20302--20515 Score: 259
Period size: 83 Copynumber: 2.6 Consensus size: 82
20292 GTGTTTCTTA
*
20302 AACAAACGCCGCGATAGAGTAGTACTTTAGCTGCGTTTTTATACAAA-TGCCAAAATAGGGATCG
1 AACAAACGCCGCGATAGAGTAGTACTTTA-CTGCGTTTTTATACAAACT-CCAAAATAGGGATCA
* * *
20366 TTTATGGTGGTATTTTTCT
64 TTTATAGTGGCATTTTTCC
* * * **
20385 AATAAACGCCGTGATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTCCTCAATAGGGATCAT
1 AACAAACGCCGCGATAGAGTAGTACTTTA-CTGCGTTTTTATACAAACTCCAAAATAGGGATCAT
*
20450 TTATATTGGCATTTTTCC
65 TTATAGTGGCATTTTTCC
* * * *
20468 AACAAATGTCGCGATAGAGTAGTACTTTAATGGCGTTTTTATATAAAC
1 AACAAACGCCGCGATAGAGTAGTACTTTACT-GCGTTTTTATACAAAC
20516 ACCGTAATAG
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
83 110 0.99
84 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (82 bp):
AACAAACGCCGCGATAGAGTAGTACTTTACTGCGTTTTTATACAAACTCCAAAATAGGGATCATT
TATAGTGGCATTTTTCC
Found at i:20858 original size:38 final size:40
Alignment explanation
Indices: 20767--20872 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 40
20757 CTTGTCTTTT
*
20767 GTGGCGCTTTTAAACAAACGCCGCAATAAATCAGTGCAGTA
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG-A
* *
20808 GTGGCGTTTTTAAACAAACGCCGCAATAAGTTAGTG-A-A
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
*
20846 GTGGTGTTTTTAAATACAAACGCCGCA
1 GTGGCGTTTTT-AA-ACAAACGCCGCA
20873 TGTTTTGGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
38 11 0.19
39 2 0.03
40 13 0.22
41 33 0.56
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (40 bp):
GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
Found at i:22318 original size:22 final size:22
Alignment explanation
Indices: 22293--22347 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
22283 TTTGTAAAGC
22293 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
22315 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
22337 CTTCTTGATCC
1 CTTCTTGATCC
22348 GTCTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Found at i:25127 original size:62 final size:62
Alignment explanation
Indices: 25030--25155 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
25020 ACCCGTTTTT
25030 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
25092 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
25154 AT
1 AT
25156 GATACGTAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (62 bp):
ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
Found at i:37495 original size:60 final size:60
Alignment explanation
Indices: 37368--37504 Score: 134
Period size: 60 Copynumber: 2.3 Consensus size: 60
37358 ATAATTGGGT
* * * * * *
37368 GACCATTTTGTAACTTTTAATATTCAAGGGACTCAACAAAGCAATTTACTATAGTTAAAG
1 GACCATTTTGTAACTTTTAATAGTAAAAGGACTCAACAAAGCAAGTAACTATAGTCAAAG
* * * * * *
37428 GATCATTTTGTAACTTTTAATAGTAAAAGGACTTAATAAAG-TAGTAACATATAGTCGAGG
1 GACCATTTTGTAACTTTTAATAGTAAAAGGACTCAACAAAGCAAGTAAC-TATAGTCAAAG
37488 GACCATTTATGT-ACTTT
1 GACCATTT-TGTAACTTT
37505 ACCCTAAATA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
59 4 0.06
60 55 0.89
61 3 0.05
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTAAAAGGACTCAACAAAGCAAGTAACTATAGTCAAAG
Found at i:39551 original size:4 final size:4
Alignment explanation
Indices: 39542--39728 Score: 80
Period size: 4 Copynumber: 46.8 Consensus size: 4
39532 GGCAGTAGTG
** * *
39542 TTTA TTTA TTTA TTTA TTTA TTT- TGAA TTTA TGTA TTCA TTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
39588 CTAA TTTA TTTG TTT- TTTA TTTG TTTG TTT- TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* ** ** ** **
39634 TTCCA CTCAAA TTTA TTTA TTT- TAAA TTTA TTTA TTTA GGTA TTT- TGAA
1 TT-TA -T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
39683 TTTA TTTG TTTG TTTA TTTG TTTA TTTCAAA ATTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT---A TTTA TTTA TTTA TTT
39729 GAAGGGATAT
Statistics
Matches: 134, Mismatches: 37, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
3 10 0.07
4 117 0.87
5 2 0.01
6 2 0.01
7 3 0.02
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:39606 original size:11 final size:12
Alignment explanation
Indices: 39591--39632 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
39581 TTTATTTCTA
39591 ATTTATTTGTTT
1 ATTTATTTGTTT
39603 -TTTATTTGTTT
1 ATTTATTTGTTT
* *
39614 GTTT-TTTATTT
1 ATTTATTTGTTT
39625 ATTTATTT
1 ATTTATTT
39633 ATTCCACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 20 0.77
12 6 0.23
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
ATTTATTTGTTT
Found at i:39609 original size:15 final size:15
Alignment explanation
Indices: 39591--39628 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
39581 TTTATTTCTA
39591 ATTTATTTGTTTTTT
1 ATTTATTTGTTTTTT
*
39606 ATTTGTTTGTTTTTT
1 ATTTATTTGTTTTTT
39621 ATTTATTT
1 ATTTATTT
39629 ATTTATTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (15 bp):
ATTTATTTGTTTTTT
Found at i:39660 original size:15 final size:15
Alignment explanation
Indices: 39642--39670 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39632 TATTCCACTC
39642 AAATTTATTTATTTT
1 AAATTTATTTATTTT
39657 AAATTTATTTATTT
1 AAATTTATTTATTT
39671 AGGTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AAATTTATTTATTTT
Found at i:39670 original size:23 final size:22
Alignment explanation
Indices: 39545--39701 Score: 97
Period size: 23 Copynumber: 6.9 Consensus size: 22
39535 AGTAGTGTTT
39545 ATTTATTTATTTATTTATTTTGA
1 ATTTATTTATTTATTTATTTT-A
* *
39568 ATTTATGTATTCATTTATTTCTA
1 ATTTATTTATTTATTTATTT-TA
*
39591 ATTTATTTGTTT-TTTATTTGT-
1 ATTTATTTATTTATTTATTT-TA
* *
39612 TTGTTTTTTATTTATTTA-TTT-
1 AT-TTATTTATTTATTTATTTTA
* **
39633 ATTCCACTCAAATTTATTTATTTTAA
1 ATT-TA-T-TTATTTATTTATTTT-A
**
39659 ATTTATTTATTTAGGTATTTTGA
1 ATTTATTTATTTATTTATTTT-A
* *
39682 ATTTATTTGTTTGTTTATTT
1 ATTTATTTATTTATTTATTT
39702 GTTTATTTCA
Statistics
Matches: 101, Mismatches: 24, Indels: 18
0.71 0.17 0.13
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 19 0.19
23 69 0.68
24 5 0.05
25 1 0.01
26 3 0.03
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (22 bp):
ATTTATTTATTTATTTATTTTA
Found at i:41891 original size:18 final size:18
Alignment explanation
Indices: 41870--41914 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
41860 CTCATTTTTT
41870 TTAATTTTTTTTAAATTA
1 TTAATTTTTTTTAAATTA
****
41888 TTAATCAACTTTAAATTA
1 TTAATTTTTTTTAAATTA
41906 TTAATTTTT
1 TTAATTTTT
41915 AAATTATCCA
Statistics
Matches: 19, Mismatches: 8, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATTTTTTTTAAATTA
Found at i:41915 original size:15 final size:15
Alignment explanation
Indices: 41877--41921 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 15
41867 TTTTTAATTT
41877 TTTTTAAATTATTAA
1 TTTTTAAATTATTAA
*
41892 TCAACTTTAAATTATTAA
1 T---TTTTAAATTATTAA
41910 TTTTTAAATTAT
1 TTTTTAAATTAT
41922 CCATGAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 11 0.44
18 14 0.56
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTTAAATTATTAA
Found at i:44841 original size:5 final size:5
Alignment explanation
Indices: 44831--44859 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
44821 TGTTTGGCTC
44831 TGATT TGATT TGATT TGATT TGATT TGAT
1 TGATT TGATT TGATT TGATT TGATT TGAT
44860 CTTTTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (5 bp):
TGATT
Found at i:47000 original size:16 final size:16
Alignment explanation
Indices: 46963--47002 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
46953 TTTTCTTTTT
*
46963 ATCGAATTGTAACAAA
1 ATCGATTTGTAACAAA
46979 ATCGATTTGTAACAAA
1 ATCGATTTGTAACAAA
46995 ATCGATTT
1 ATCGATTT
47003 TTTACTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (16 bp):
ATCGATTTGTAACAAA
Found at i:51385 original size:78 final size:78
Alignment explanation
Indices: 51303--51448 Score: 220
Period size: 78 Copynumber: 1.9 Consensus size: 78
51293 AGAAAAAAAT
* * * *
51303 AACATTTTAGGTAGCGTCCAATATTAACATTTTCGGTAAAAAAATAATATTTTAGGTAGCGTTTT
1 AACATTTTAGGTAGCGCCCAATATCAACATTTTCAGTAAAAAAATAATATTTTAAGTAGCGTTTT
51368 ACCCAAAATGATA
66 ACCCAAAATGATA
* * **
51381 AACATTTTAGGTAGCGCCCAATATCAACATTTTCAGTAGAAAAATAATGTTTTAAGTATTGTTTT
1 AACATTTTAGGTAGCGCCCAATATCAACATTTTCAGTAAAAAAATAATATTTTAAGTAGCGTTTT
51446 ACC
66 ACC
51449 AGAAATATTA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 60 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (78 bp):
AACATTTTAGGTAGCGCCCAATATCAACATTTTCAGTAAAAAAATAATATTTTAAGTAGCGTTTT
ACCCAAAATGATA
Found at i:53123 original size:21 final size:21
Alignment explanation
Indices: 53006--53123 Score: 71
Period size: 21 Copynumber: 5.7 Consensus size: 21
52996 ACGCGAAATA
**
53006 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
53026 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
53046 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
** ** *
53067 AAAATCGCATTGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
53088 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
53109 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
53124 ATATGAAAAT
Statistics
Matches: 72, Mismatches: 22, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.33
21 45 0.62
22 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:53134 original size:20 final size:19
Alignment explanation
Indices: 53108--53162 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
53098 TGCGATTTTC
*
53108 CAAAATCGCAACGCGAATA
1 CAAAATCGCAACGCGAACA
* *
53127 TGAAAATCGCAAAGCGAACA
1 -CAAAATCGCAACGCGAACA
53147 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
53163 TATCCGTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.11
Consensus pattern (19 bp):
CAAAATCGCAACGCGAACA
Found at i:53172 original size:20 final size:20
Alignment explanation
Indices: 53149--53263 Score: 160
Period size: 20 Copynumber: 5.7 Consensus size: 20
53139 AGCGAACACA
53149 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
53169 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
*
53189 TTAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* * *
53209 TAAATCGCAACG-ATAATACA
1 TAAATCGCAACGCGT-ATCCG
53229 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
53250 TAAATCGCAACGCG
1 TAAATCGCAACGCG
53264 ATATTTAAAG
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 65 0.79
21 15 0.18
22 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:53174 original size:40 final size:40
Alignment explanation
Indices: 53110--53264 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
53100 CGATTTTCCA
* ** * *
53110 AAATCGCAACGCGAATATGAAAATCGCAAAGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
53150 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
53190 TAATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
53230 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
53265 TATTTAAAGC
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.01
40 61 0.64
41 33 0.35
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:53685 original size:33 final size:33
Alignment explanation
Indices: 53646--53716 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
53636 TTCACTTAGA
*
53646 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
53679 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
53712 TTTCA
1 TTTCA
53717 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:53839 original size:20 final size:20
Alignment explanation
Indices: 53796--53905 Score: 117
Period size: 21 Copynumber: 5.8 Consensus size: 20
53786 TGCAGAAGAG
*
53796 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
**
53817 TCGCAACGAGAGAATGACTA
1 TCGCAACGAGAGAATGAAAA
53837 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
53858 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
53872 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
53891 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
53906 CGCAACGCGA
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.20
20 21 0.28
21 24 0.32
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:53853 original size:41 final size:39
Alignment explanation
Indices: 53796--53905 Score: 142
Period size: 41 Copynumber: 2.9 Consensus size: 39
53786 TGCAGAAGAG
*
53796 TCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACTA
1 TCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGA--A
53837 TCGCAACGAGAGAAATGAAAATCGCAAC--GAG-A-GAA
1 TCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGAA
*
53872 TCGCAAC--GCGAAATGAAAATCGCAACGAGAGAAT
1 TCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
53906 CGCAACGCGA
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
33 18 0.29
35 11 0.17
36 1 0.02
37 2 0.03
38 1 0.02
39 3 0.05
41 27 0.43
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (39 bp):
TCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGAA
Found at i:53875 original size:14 final size:14
Alignment explanation
Indices: 53856--53912 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
53846 GAGAAATGAA
53856 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
53870 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
53889 AATCGCAACGAGAG
1 AATCGCAACGAGAG
53903 AATCGCAACG
1 AATCGCAACG
53913 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:53889 original size:33 final size:33
Alignment explanation
Indices: 53848--53928 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
53838 CGCAACGAGA
53848 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
53881 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
53914 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
53929 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:53946 original size:19 final size:19
Alignment explanation
Indices: 53924--54021 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
53914 GAAACCAAAA
*
53924 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
53943 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
53957 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
53976 TCGCGTTGCGA--TT-A--
1 TCGCGTTGCGATTTTCATT
* *
53990 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
54009 TCGCGTTGCGATT
1 TCGCGTTGCGATT
54022 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:53965 original size:14 final size:14
Alignment explanation
Indices: 53946--54035 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
53936 TTTCATTTCG
53946 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
53960 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
53979 CGTTGCGATTATCT
1 CGTTGCGATTCTCT
*
53993 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
54012 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
54026 CGTTGCGATT
1 CGTTGCGATT
54036 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 1 0.02
16 4 0.07
17 4 0.07
18 1 0.02
19 20 0.33
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:53971 original size:33 final size:33
Alignment explanation
Indices: 53929--54043 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
53919 CAAAATCGCA
53929 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
53962 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
53995 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
54028 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
54044 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:55893 original size:93 final size:93
Alignment explanation
Indices: 55734--56109 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
55724 TAGATTGCTT
*
55734 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55799 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
55827 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55892 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
55920 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55985 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
56013 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
56078 TTTGTCTTTGTTTTGTCTATTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
56105 AGTAA
1 AGTAA
56110 TGCAATCCAT
Statistics
Matches: 281, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 275 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:56197 original size:19 final size:19
Alignment explanation
Indices: 56157--56285 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
56147 TAGTTTACTT
* *
56157 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
56177 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
56196 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
56215 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
56229 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
56248 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
56262 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
56281 TCGCA
1 TCGCA
56286 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:56236 original size:33 final size:32
Alignment explanation
Indices: 56193--56285 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
56183 CGCGAAACCA
**
56193 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
56225 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
56258 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
56286 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:56283 original size:52 final size:52
Alignment explanation
Indices: 56157--56285 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
56147 TAGTTTACTT
**
56157 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
56209 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
56262 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
56286 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:56303 original size:19 final size:19
Alignment explanation
Indices: 56281--56415 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
56271 GAAACCAAAA
*
56281 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
56300 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
56316 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
56333 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
56349 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
56366 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
56385 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
56405 TCGTGTTGCGA
1 TCGCGTTGCGA
56416 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:56322 original size:14 final size:14
Alignment explanation
Indices: 56303--56359 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
56293 TTTCATTTCG
56303 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
56317 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
56334 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
56350 CGTTGCGATT
1 CGTTGCGATT
56360 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:56328 original size:33 final size:33
Alignment explanation
Indices: 56286--56378 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
56276 CAAAATCGCA
*
56286 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
56319 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
56352 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
56379 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:58352 original size:14 final size:14
Alignment explanation
Indices: 58333--58368 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
58323 ATTGTTTAAT
58333 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
58347 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
58361 TGATTTGT
1 TGATTTGT
58369 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:58498 original size:19 final size:19
Alignment explanation
Indices: 58474--58590 Score: 181
Period size: 19 Copynumber: 6.4 Consensus size: 19
58464 AAAATTGACT
58474 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
58493 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
58512 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
58531 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
58545 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
58564 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
58584 ATCGCAA
1 ATCGCAA
58591 CGGGAGAATC
Statistics
Matches: 90, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 58 0.64
20 16 0.18
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:58553 original size:33 final size:36
Alignment explanation
Indices: 58474--58590 Score: 159
Period size: 33 Copynumber: 3.2 Consensus size: 36
58464 AAAATTGACT
58474 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
*
58512 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
58545 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GC-G-AATGAAA
58584 ATCGCAA
1 ATCGCAA
58591 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
33 29 0.41
34 1 0.01
35 1 0.01
36 3 0.04
38 27 0.38
39 10 0.14
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:58622 original size:53 final size:53
Alignment explanation
Indices: 58492--58609 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
58482 GCGAAATGAA
58492 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
*
58544 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
58597 AATCGCAATGCGA
1 AATCGCAATGCGA
58610 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:58627 original size:19 final size:19
Alignment explanation
Indices: 58599--58801 Score: 194
Period size: 19 Copynumber: 11.7 Consensus size: 19
58589 AACGGGAGAA
* *
58599 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
58618 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
58634 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
58651 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
58670 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
58689 TCGCATTTCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
58705 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
58722 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
58738 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
58755 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
58773 T-G--TTGAGATTTTCATT
1 TCGCATTGCGATTTTCATT
58789 TCGCATTGCGATT
1 TCGCATTGCGATT
58802 CTCTCGTTGC
Statistics
Matches: 151, Mismatches: 12, Indels: 42
0.74 0.06 0.20
Matches are distributed among these distances:
14 28 0.19
16 23 0.15
17 19 0.13
18 3 0.02
19 66 0.44
20 12 0.08
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:58680 original size:71 final size:70
Alignment explanation
Indices: 58599--58806 Score: 291
Period size: 71 Copynumber: 3.0 Consensus size: 70
58589 AACGGGAGAA
* *
58599 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
*
58664 TTCATT
66 TTC-TC
*
58670 TCGCATTGCGATTTTCATTTCGCATTTCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
58733 TTCTC
66 TTCTC
* *
58738 TCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGAGATTTTCATTTCGCATTGCGA
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGA
*
58800 TTCTCTC
64 TTTTCTC
58807 GTTGCGATTG
Statistics
Matches: 125, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
66 15 0.12
67 38 0.30
68 5 0.04
69 7 0.06
71 60 0.48
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (70 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
TTCTC
Found at i:58746 original size:14 final size:14
Alignment explanation
Indices: 58697--58748 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
58687 TTTCGCATTT
58697 CGATTCTCTCGTTG
1 CGATTCTCTCGTTG
*
58711 CGATTTTCATTTCGCATTG
1 CGA--TTC-TCTCG--TTG
58730 CGATTCTCTCGTTG
1 CGATTCTCTCGTTG
58744 CGATT
1 CGATT
58749 TTCATTTCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 11 0.35
16 7 0.23
17 7 0.23
19 6 0.19
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (14 bp):
CGATTCTCTCGTTG
Found at i:58823 original size:33 final size:33
Alignment explanation
Indices: 58605--58815 Score: 307
Period size: 33 Copynumber: 6.2 Consensus size: 33
58595 AGAATCGCAA
*
58605 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
58638 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
*
58676 TGCGATTTTCATTTCGCATTTCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
58709 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
58742 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
58776 TGAGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
58809 TGCGATT
1 TGCGATT
58816 GTAATTTCCG
Statistics
Matches: 161, Mismatches: 9, Indels: 16
0.87 0.05 0.09
Matches are distributed among these distances:
32 1 0.01
33 92 0.57
34 29 0.18
35 8 0.05
36 7 0.04
38 24 0.15
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:58825 original size:67 final size:66
Alignment explanation
Indices: 58605--58823 Score: 305
Period size: 67 Copynumber: 3.2 Consensus size: 66
58595 AGAATCGCAA
*
58605 TGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TC
58670 TCGCAT
63 TCG--T
* *
58676 TGCGATTTTCATTTCGCATTTCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCG
58741 T
66 T
* * *
58742 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGAGATTTTCATTTCGCATTGCGATTCTCT
1 TGCGATTTTAATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
58806 CGT
64 CGT
*
58809 TGCGATTGTAATTTC
1 TGCGATTTTAATTTC
58824 CGTGTTGCGA
Statistics
Matches: 138, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
66 16 0.12
67 59 0.43
68 5 0.04
69 3 0.02
71 55 0.40
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (66 bp):
TGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCG
T
Found at i:62041 original size:20 final size:20
Alignment explanation
Indices: 62013--62303 Score: 314
Period size: 20 Copynumber: 14.5 Consensus size: 20
62003 AAATTTCAGT
* *
62013 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
62033 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
62053 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
* *
62073 GTTGTGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
62093 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
62113 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
62133 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
62153 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
62173 GTTGCGATTTTATGTATTATC
1 GTTGCGA-TTTACGGATTCTC
* *
62194 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
62214 GTTGCGATTAACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
62234 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
62254 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
62274 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
62294 GTTGCGATTT
1 GTTGCGATTT
62304 TGAAAAATCG
Statistics
Matches: 232, Mismatches: 36, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
20 216 0.93
21 16 0.07
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:62320 original size:21 final size:21
Alignment explanation
Indices: 62290--62368 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 21
62280 ATTTTCATAT
*
62290 TCGCGTTGCGATTTTGAAAAA
1 TCGCATTGCGATTTTGAAAAA
* * * **
62311 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGAAAAA
* *
62332 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAAAAA
*
62353 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
62369 GAAACTGATT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGAAAAA
Found at i:62363 original size:42 final size:43
Alignment explanation
Indices: 62270--62368 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
62260 ATTTATGTGT
* *
62270 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGAAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTCAAAAA
** *
62311 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTCAAAAA
*
62353 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
62369 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 8 0.17
42 36 0.77
43 3 0.06
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTCAAAAA
Found at i:63008 original size:45 final size:46
Alignment explanation
Indices: 62942--63060 Score: 145
Period size: 45 Copynumber: 2.7 Consensus size: 46
62932 GTTAAGCACG
* * **
62942 ACCTAAAATATTATTTGTTCTACCAGAAATATTAATATTAAACTTT
1 ACCTAAAATATTATTTTTTCTACCAAAAATATTAATATTAAACTCA
* * * *
62988 ACCT-AAATATCATTTTTTCTATCAAAAATGTTAATATTAGACTCA
1 ACCTAAAATATTATTTTTTCTACCAAAAATATTAATATTAAACTCA
63033 ACCTAAAATATTA-TTTTT-TACCAAAAAT
1 ACCTAAAATATTATTTTTTCTACCAAAAAT
63061 TAACTAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 9 0.15
45 42 0.68
46 11 0.18
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.40
Consensus pattern (46 bp):
ACCTAAAATATTATTTTTTCTACCAAAAATATTAATATTAAACTCA
Found at i:63102 original size:21 final size:21
Alignment explanation
Indices: 63060--63109 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
63050 TTACCAAAAA
*
63060 TTAACTAAAAAAATTAACATT
1 TTAAATAAAAAAATTAACATT
* *
63081 TTCAATAAAACAAA-TAATATT
1 TTAAATAAAA-AAATTAACATT
63102 TTAAATAA
1 TTAAATAA
63110 CATTTTATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (21 bp):
TTAAATAAAAAAATTAACATT
Found at i:63346 original size:23 final size:23
Alignment explanation
Indices: 63320--63367 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
63310 ATAAAGTACA
*
63320 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
63343 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
63366 AT
1 AT
63368 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:63822 original size:23 final size:23
Alignment explanation
Indices: 63796--63854 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
63786 AACCACTACT
63796 TATTACATTATATAAACGATACC
1 TATTACATTATATAAACGATACC
* *
63819 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACC
*
63842 TATTACATCATAT
1 TATTACATTATAT
63855 TTTTACCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACC
Found at i:64328 original size:39 final size:39
Alignment explanation
Indices: 64274--64359 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
64264 CAAGTTGTAG
*
64274 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
64313 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
64352 ATTTTGAT
1 ATTTTGAT
64360 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:64637 original size:18 final size:18
Alignment explanation
Indices: 64616--64652 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
64606 CGAAATATAT
64616 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
64634 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
64652 A
1 A
64653 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:65115 original size:23 final size:23
Alignment explanation
Indices: 65088--65146 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
65078 ATATAAACGA
* *
65088 ATTACATTATATAAGCGCTACCT
1 ATTACATTATATAAACGATACCT
65111 ATTACATTATATAAACGATACCT
1 ATTACATTATATAAACGATACCT
65134 ATTACATTATATA
1 ATTACATTATATA
65147 CTTGTAGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
ATTACATTATATAAACGATACCT
Done.