Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002869.1 Hibiscus syriacus cultivar Beakdansim tig00005916_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: 91248
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:7120 original size:19 final size:20
Alignment explanation
Indices: 7098--7141 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
7088 AGAAAAAAAT
7098 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
7117 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
7137 AAAAG
1 AAAAG
7142 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:22943 original size:45 final size:45
Alignment explanation
Indices: 22876--22970 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
22866 AGAGTTATCA
* *
22876 ATGCA-CCCCTTAAAATGGAAACATCGAATGCAATTGGTGCATCG
1 ATGCATCCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCG
* * *
22920 ATGCATCCCCTTAAAATGAAAACATCGAAGGTAATTTGTGTATCG
1 ATGCATCCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCG
22965 ATGCAT
1 ATGCAT
22971 GGGTAGTGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 5 0.11
45 40 0.89
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (45 bp):
ATGCATCCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCG
Found at i:23022 original size:20 final size:20
Alignment explanation
Indices: 22997--23034 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
22987 CACATGTTAA
*
22997 AGAATGCATTGATGCACTGT
1 AGAATGCATTGATACACTGT
23017 AGAATGCATTGATACACT
1 AGAATGCATTGATACACT
23035 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (20 bp):
AGAATGCATTGATACACTGT
Found at i:28084 original size:64 final size:63
Alignment explanation
Indices: 27963--28104 Score: 178
Period size: 64 Copynumber: 2.2 Consensus size: 63
27953 ATGCACAGAA
* * * *
27963 AGTGCATCGATGCACCCCTTAAAATGGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-
1 AGTGCATCGATGCACCCCTTAAAATGAAAACATCAAAGGCAATTGGTGCATCAATGCAT-AGGT
* * * *
28026 AGTGCATCGATGCATCCCCTTAAAATGAAAACATCAAAGGTAATTTGTGTATCAATGCATGGGT
1 AGTGCATCGATGCA-CCCCTTAAAATGAAAACATCAAAGGCAATTGGTGCATCAATGCATAGGT
*
28090 AGTGTATCGATGCAC
1 AGTGCATCGATGCAC
28105 ATGTTAAAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 17 0.25
64 51 0.75
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (63 bp):
AGTGCATCGATGCACCCCTTAAAATGAAAACATCAAAGGCAATTGGTGCATCAATGCATAGGT
Found at i:29337 original size:435 final size:435
Alignment explanation
Indices: 28527--29397 Score: 1715
Period size: 435 Copynumber: 2.0 Consensus size: 435
28517 AAACACTATT
28527 AAGTGTTAATGAGAGAATATAAAATAAGTTATGAAATTATAGGAATATAGAAGATAAGTCAAGAG
1 AAGTGTTAATGAGAGAATATAAAATAAGTTATGAAATTATAGGAATATAGAAGATAAGTCAAGAG
28592 ATGTATGGAAATGGAAATAGATGTTTATGAAGAGTCATAGGAGAACAAATATAAGTCATATGATA
66 ATGTATGGAAATGGAAATAGATGTTTATGAAGAGTCATAGGAGAACAAATATAAGTCATATGATA
28657 ATGAAATATAAGACTATATGAATACATGGTTATGAGATAAAATATGTAATAATAGGGAAAATATG
131 ATGAAATATAAGACTATATGAATACATGGTTATGAGATAAAATATGTAATAATAGGGAAAATATG
*
28722 ATGAAAGTGAGTTCATGAAAAGTGATAGGAACTAGGTAAACATGGGTAACAGTACATGCATAATG
196 ATGAAAGTGAGTTCATGAAAAGTGATAGGAACTAGGTAAACATGGGTAACAATACATGCATAATG
*
28787 GAAACATGAGTTGGACAAGTACATAGTGGTATGATCCATTATGAGAATTAATATAATAGAGTTTT
261 GAAACATGAGTTGGACAAGTACATAGTGGTATGATCCATTATGAGAATTAATATAATAGAGCTTT
28852 TTGATTTAATGAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGGGAATAATATA
326 TTGATTTAATGAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGGGAATAATATA
28917 TCAATTAGGAAACTTGAATATAAAGGGATGATACGAATATGTAAG
391 TCAATTAGGAAACTTGAATATAAAGGGATGATACGAATATGTAAG
28962 AAGTGTTAATGAGAGAATATAAAATAAGTTATGAAATTATAGGAATATAGAAGATAAGTCAAGAG
1 AAGTGTTAATGAGAGAATATAAAATAAGTTATGAAATTATAGGAATATAGAAGATAAGTCAAGAG
29027 ATGTATGGAAATGGAAATAGATGTTTATGAAGAGTCATAGGAGAACAAATATAAGTCATATGATA
66 ATGTATGGAAATGGAAATAGATGTTTATGAAGAGTCATAGGAGAACAAATATAAGTCATATGATA
*
29092 ATGAAATATAAGACTATGTGAATACATGGTTATGAGATAAAATATGTAATAATAGGGAAAATATG
131 ATGAAATATAAGACTATATGAATACATGGTTATGAGATAAAATATGTAATAATAGGGAAAATATG
29157 ATGAAAGTGAGTTCATGAAAAGTGATAGGAACTAGGTAAACATGGGTAACAATACATGCATAATG
196 ATGAAAGTGAGTTCATGAAAAGTGATAGGAACTAGGTAAACATGGGTAACAATACATGCATAATG
29222 GAAACATGAGTTGGACAAGTACATAGTGGTATGATCCATTATGAGAATTAATATAATAGAGCTTT
261 GAAACATGAGTTGGACAAGTACATAGTGGTATGATCCATTATGAGAATTAATATAATAGAGCTTT
29287 TTGATTTAATGAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGGGAATAATATA
326 TTGATTTAATGAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGGGAATAATATA
29352 TCAATTAGGAAACTTGAATATAAAGGGATGATACGAATATGTAAG
391 TCAATTAGGAAACTTGAATATAAAGGGATGATACGAATATGTAAG
29397 A
1 A
29398 TAAGTTATAT
Statistics
Matches: 433, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
435 433 1.00
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (435 bp):
AAGTGTTAATGAGAGAATATAAAATAAGTTATGAAATTATAGGAATATAGAAGATAAGTCAAGAG
ATGTATGGAAATGGAAATAGATGTTTATGAAGAGTCATAGGAGAACAAATATAAGTCATATGATA
ATGAAATATAAGACTATATGAATACATGGTTATGAGATAAAATATGTAATAATAGGGAAAATATG
ATGAAAGTGAGTTCATGAAAAGTGATAGGAACTAGGTAAACATGGGTAACAATACATGCATAATG
GAAACATGAGTTGGACAAGTACATAGTGGTATGATCCATTATGAGAATTAATATAATAGAGCTTT
TTGATTTAATGAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGGGAATAATATA
TCAATTAGGAAACTTGAATATAAAGGGATGATACGAATATGTAAG
Found at i:30172 original size:23 final size:23
Alignment explanation
Indices: 30142--30201 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
30132 CATTTTATAT
30142 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
30165 GGCACTTCGGTGCAATTCTATGT
1 GGCACTTCGGTGCAATTCTACGC
30188 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
30202 TTTATACGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:39218 original size:5 final size:5
Alignment explanation
Indices: 39208--39242 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
39198 GCTTGGCATG
39208 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC
39243 AATGAAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTTTC
Found at i:40690 original size:60 final size:60
Alignment explanation
Indices: 40583--40764 Score: 154
Period size: 60 Copynumber: 3.0 Consensus size: 60
40573 GTATATATGT
* * *
40583 ATAGTTTGGGATGAAATTGGAATGTTCAAAAAGTTCAGGGACCAATTTAGAATGAAGGTC
1 ATAGTTTGGGATGAAATTGAAATATTCAAAAAGTTCAGGGACCAATTTAAAATGAAGGTC
*** * *
40643 ATAGTTTGGGGATGAAATTGAAATATTC-AAAAGTTTTTGGACTAATTTAAAATGATA-GTA
1 ATAGTTT-GGGATGAAATTGAAATATTCAAAAAGTTCAGGGACCAATTTAAAATGA-AGGTC
* * * * * * * * * *
40703 ATAAATTAGAGATAAAATTAAAATATTTAAAAA-TTTAGGGACTAATTTAAAATAAATGTC
1 AT-AGTTTGGGATGAAATTGAAATATTCAAAAAGTTCAGGGACCAATTTAAAATGAAGGTC
40763 AT
1 AT
40765 GCTTTTAAGG
Statistics
Matches: 99, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
59 1 0.01
60 72 0.73
61 26 0.26
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAATATTCAAAAAGTTCAGGGACCAATTTAAAATGAAGGTC
Found at i:40753 original size:29 final size:29
Alignment explanation
Indices: 40663--40756 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
40653 GATGAAATTG
* * **
40663 AAATATTCAAAAGTTTTTGGACTAATTTA
1 AAATATTTAAAAATTTAGGGACTAATTTA
* * *
40692 AAATGATAGTAATAAA-TTAGAGA-TAAAATTA
1 AAAT-AT-TTAA-AAATTTAGGGACT-AATTTA
40723 AAATATTTAAAAATTTAGGGACTAATTTA
1 AAATATTTAAAAATTTAGGGACTAATTTA
40752 AAATA
1 AAATA
40757 AATGTCATGC
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 3 0.06
29 23 0.47
30 6 0.12
31 15 0.31
32 2 0.04
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (29 bp):
AAATATTTAAAAATTTAGGGACTAATTTA
Found at i:46127 original size:43 final size:42
Alignment explanation
Indices: 46070--46198 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 42
46060 TATTTAAACT
* * *
46070 CCAAAGTAATAATCCACAAATATACCAAAATAACATATTATAA
1 CCAAAGTAACAATCCACAAATACA-CAAAATAACATATTACAA
* * *
46113 CCAAAGTAACAATCCACAAATGCATTAAAATAACATATTACAG
1 CCAAAGTAACAATCCACAAATACA-CAAAATAACATATTACAA
*
46156 CCAAAGTAACAATCCACAAGTACACAAAACTAACATATTACAA
1 CCAAAGTAACAATCCACAAATACACAAAA-TAACATATTACAA
46199 TCATTCTTGA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 4 0.05
43 70 0.95
ACGTcount: A:0.53, C:0.22, G:0.05, T:0.20
Consensus pattern (42 bp):
CCAAAGTAACAATCCACAAATACACAAAATAACATATTACAA
Found at i:48652 original size:31 final size:31
Alignment explanation
Indices: 48594--48652 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
48584 GTGGAGGGAT
* *
48594 TTAAATTGGACGGACTAATAATATTAGATAC
1 TTAAATCGGACGGACTAATAACATTAGATAC
*
48625 TTAAATCGGACGGA-TAGATAACGTTAGA
1 TTAAATCGGACGGACTA-ATAACATTAGA
48653 GACTATTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 22 0.92
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (31 bp):
TTAAATCGGACGGACTAATAACATTAGATAC
Found at i:50729 original size:20 final size:21
Alignment explanation
Indices: 50678--50785 Score: 114
Period size: 21 Copynumber: 5.2 Consensus size: 21
50668 ATTCTGACTA
* *
50678 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTACCTAAT
* * *
50699 TCACGTTGCGATTTACGTAA-
1 TCGCATTGCGATTTACCTAAT
*
50719 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
*
50740 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
*
50761 TCGCACTT-CGATTTACGTAA-
1 TCGCA-TTGCGATTTACCTAAT
50781 TCGCA
1 TCGCA
50786 ACGAGATTCT
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
20 21 0.28
21 51 0.69
22 2 0.03
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTACCTAAT
Found at i:50745 original size:21 final size:21
Alignment explanation
Indices: 50678--50774 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
50668 ATTCTGACTA
* *
50678 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTTCCTAAT
* * * *
50699 TCACGTTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
50719 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
50740 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
50761 TCGCACTT-CGATTT
1 TCGCA-TTGCGATTT
50775 ACGTAATCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
20 16 0.25
21 47 0.72
22 2 0.03
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:51680 original size:24 final size:24
Alignment explanation
Indices: 51648--51701 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
51638 GTATTCGAAA
51648 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
51672 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
51696 TTTGAT
1 TTTGAT
51702 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:54255 original size:19 final size:20
Alignment explanation
Indices: 54173--54266 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
54163 GGCATTCATT
*
54173 TGACTATCGCAACACGAAAA
1 TGACTATCGCAACGCGAAAA
* **
54193 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-C-GCGAAAA
*
54214 TGTCTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
*
54234 TGACTATCGCAATGCG-AAA
1 TGACTATCGCAACGCGAAAA
**
54253 TGAAAATCGCAACG
1 TGACTATCGCAACG
54267 AGGGAATCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 15 0.26
20 28 0.49
21 13 0.23
22 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGAAAA
Found at i:54295 original size:19 final size:19
Alignment explanation
Indices: 54219--54303 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 19
54209 CTTAATGTCT
* **
54219 ATCGCAACGCGAAAATGACT
1 ATCGCAAAGCG-AAATGAAA
*
54239 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
**
54258 ATCGC-AA-CG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
54272 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
54291 ATCGCAACGCGAA
1 ATCGCAAAGCGAA
54304 TTTAGTTTCG
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
14 7 0.14
15 3 0.06
16 2 0.04
17 2 0.04
18 2 0.04
19 25 0.49
20 10 0.20
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:54329 original size:20 final size:20
Alignment explanation
Indices: 54304--54394 Score: 99
Period size: 19 Copynumber: 5.0 Consensus size: 20
54294 GCAACGCGAA
54304 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCGTTGCGATT
54324 TTTAGTTTCGCGTTGCGA-T
1 TTTAGTTTCGCGTTGCGATT
54343 TTT-G--T--CGTTGCGATT
1 TTTAGTTTCGCGTTGCGATT
*
54358 TTCA-TTTCGCGTTGCGATT
1 TTTAGTTTCGCGTTGCGATT
* *
54377 TTCA-TTTCGCATTGCGAT
1 TTTAGTTTCGCGTTGCGAT
54395 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
14 8 0.13
15 3 0.05
16 1 0.02
17 1 0.02
18 1 0.02
19 31 0.49
20 18 0.29
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (20 bp):
TTTAGTTTCGCGTTGCGATT
Found at i:54371 original size:33 final size:34
Alignment explanation
Indices: 54314--54378 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
54304 TTTAGTTTCG
*
54314 CGTTGCGATTTTTAGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCAGTTTCGCGTTGCGATTTTGT
54348 CGTTGCGATTTTCA-TTTCGCGTTGCGATTTT
1 CGTTGCGATTTTCAGTTTCGCGTTGCGATTTT
54379 CATTTCGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.09, C:0.17, G:0.25, T:0.49
Consensus pattern (34 bp):
CGTTGCGATTTTCAGTTTCGCGTTGCGATTTTGT
Found at i:54400 original size:19 final size:19
Alignment explanation
Indices: 54359--54402 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
54349 GTTGCGATTT
* **
54359 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATAG
54378 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
54397 TCATTT
1 TCATTT
54403 TTTCCTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:54521 original size:14 final size:14
Alignment explanation
Indices: 54502--54537 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
54492 ATCAATTAAG
54502 CAAATCAACTTTTA
1 CAAATCAACTTTTA
*
54516 CAAATCATCTTTTA
1 CAAATCAACTTTTA
54530 CAAATCAA
1 CAAATCAA
54538 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
CAAATCAACTTTTA
Found at i:56389 original size:19 final size:19
Alignment explanation
Indices: 56349--56439 Score: 101
Period size: 19 Copynumber: 4.6 Consensus size: 19
56339 TCTGGAACTT
*
56349 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
56370 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
56389 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
*
56409 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAATG
*
56428 AAAATCTCAACG
1 AAAATCGCAACG
56440 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
19 31 0.52
20 18 0.30
21 11 0.18
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:56418 original size:39 final size:39
Alignment explanation
Indices: 56349--56446 Score: 133
Period size: 39 Copynumber: 2.5 Consensus size: 39
56339 TCTGGAACTT
* * ** *
56349 AAAATCGCAACGTGAAAAATGACTATCGCAACGCGAAATG
1 AAAATCGCAACGAG-AGAATGAAAATCGCAACGCGAAACG
56389 AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACG
1 AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACG
*
56428 AAAATCTCAACGAGAGAAT
1 AAAATCGCAACGAGAGAAT
56447 CGCAACAAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 39 0.75
40 13 0.25
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.12
Consensus pattern (39 bp):
AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACG
Found at i:56487 original size:20 final size:19
Alignment explanation
Indices: 56462--56571 Score: 131
Period size: 19 Copynumber: 5.9 Consensus size: 19
56452 CAAGATTATA
*
56462 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGA-TTTTC
56482 GTTTCGCGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTC
56500 G--T--CGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
*
56515 ATTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
56534 GTTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
* *
56553 ATTCTCTCGTTGCGATTTT
1 GTT-TCGCGTTGCGATTTT
56572 TATTTCAACC
Statistics
Matches: 80, Mismatches: 4, Indels: 12
0.83 0.04 0.12
Matches are distributed among these distances:
14 12 0.15
16 1 0.01
17 1 0.01
18 1 0.01
19 37 0.46
20 28 0.35
ACGTcount: A:0.07, C:0.19, G:0.25, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTC
Found at i:56783 original size:94 final size:94
Alignment explanation
Indices: 56668--57043 Score: 584
Period size: 94 Copynumber: 4.1 Consensus size: 94
56658 ATGGATTGCA
* *
56668 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
56732 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAACAACCGAACAAAT
* *
56761 TTACTTTCAACCAAAAGTCAAAACAAAGACAAATACTAACTTCTCAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
56826 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAACAACCGAACAAAT
56855 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
56920 TTAGCAGAATTGGCAATAACCGAATAAAT
66 TTAGCAGAATTGGCAACAACCGAACAAAT
* *
56949 TTAC-TTCAACCAAAAGATAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
57009 TTTAGCAGTATTGGCAACAACCGAATAAAT
65 TTTAGCAGAATTGGCAACAACCGAACAAAT
57039 TTACT
1 TTACT
57044 AAGCAATCTA
Statistics
Matches: 266, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
90 40 0.15
93 22 0.08
94 204 0.77
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAACAACCGAACAAAT
Found at i:58757 original size:20 final size:20
Alignment explanation
Indices: 58732--58837 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
58722 TTTTGGTTGA
58732 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
58752 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
58771 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
*
58792 AAT-----T-GCAACGCGA-
1 AATGAAAATCGCAACGAGAG
58805 AATGAAAATCGCAACGAGA-
1 AATGAAAATCGCAACGAGAG
58824 AATGAAAATCGCAA
1 AATGAAAATCGCAA
58838 TGCGATTTTG
Statistics
Matches: 72, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.04
14 8 0.11
15 1 0.01
18 1 0.01
19 23 0.32
20 35 0.49
21 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:58774 original size:40 final size:39
Alignment explanation
Indices: 58730--58842 Score: 141
Period size: 40 Copynumber: 3.1 Consensus size: 39
58720 TCTTTTGGTT
58730 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
**
58769 GGAAATGACTATCGCAACGAGAGAAT-----T-GCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
*
58803 GAAATGAAAATCGCAACGAGA-AATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
58841 GA
1 GA
58843 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
32 3 0.05
33 19 0.31
34 7 0.11
35 1 0.02
37 1 0.02
38 8 0.13
40 23 0.37
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (39 bp):
GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
Found at i:58820 original size:19 final size:19
Alignment explanation
Indices: 58730--58842 Score: 110
Period size: 19 Copynumber: 6.1 Consensus size: 19
58720 TCTTTTGGTT
*
58730 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
58749 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
58769 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
* *
58787 G--A-GAGAATTGCAACGC
1 GAAATGAAAATCGCAACGC
*
58803 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
58822 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
58841 GA
1 GA
58843 TTTTGGTTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
14 8 0.11
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 32 0.42
20 28 0.37
21 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:58871 original size:19 final size:19
Alignment explanation
Indices: 58838--58882 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
58828 AAAATCGCAA
**
58838 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
58857 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
58876 TGCGATT
1 TGCGATT
58883 CTCTTGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:59527 original size:21 final size:20
Alignment explanation
Indices: 59481--59551 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
59471 TGATAGTCAG
59481 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
59501 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
59521 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
59542 ATTCGCATTG
1 ATTCGCATTG
59552 GGAATTATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 28 0.61
21 18 0.39
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:59569 original size:41 final size:41
Alignment explanation
Indices: 59483--59569 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
59473 ATAGTCAGAT
* * *
59483 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAA
* *
59524 TCGCATTGCGATTTACGTATTCGCATTGGGAATTAT-GAAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAA
59565 TCGCA
1 TCGCA
59570 ACGCGAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 36 0.90
42 4 0.10
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAA
Found at i:60512 original size:20 final size:20
Alignment explanation
Indices: 60487--60578 Score: 80
Period size: 20 Copynumber: 4.6 Consensus size: 20
60477 GACCAACAAA
* *
60487 ATCGCAATGCGATCTCCAGT
1 ATCGCAATGCGATTTCCACT
* *
60507 ATCGCAAAT-CAATTTCCA-G
1 ATCGC-AATGCGATTTCCACT
**
60526 ATTCGCAATGCGATTTTGACT
1 A-TCGCAATGCGATTTCCACT
**
60547 ATCGCAATGCGATTTTGACT
1 ATCGCAATGCGATTTCCACT
60567 ATCGCAATGCGA
1 ATCGCAATGCGA
60579 ATATGTAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
19 4 0.07
20 53 0.87
21 4 0.07
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
ATCGCAATGCGATTTCCACT
Found at i:60572 original size:40 final size:40
Alignment explanation
Indices: 60528--60654 Score: 123
Period size: 40 Copynumber: 3.1 Consensus size: 40
60518 ATTTCCAGAT
*
60528 TCGCAATGCGATTTTGACTATCGCAATGCGATTTTGACTA
1 TCGCAATGCGATTATGACTATCGCAATGCGATTTTGACTA
* * * *
60568 TCGCAATGCGAATATGTA-AATCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATG-ACTATCGCAATGCGATTTTGACTA
* * * * *
60608 TCGCAACGCGATAAT-ACATAATCACAATGCCATTTTGACTG
1 TCGCAATGCGATTATGAC-T-ATCGCAATGCGATTTTGACTA
60649 TCGCAA
1 TCGCAA
60655 CGCTGAATTT
Statistics
Matches: 69, Mismatches: 14, Indels: 7
0.77 0.16 0.08
Matches are distributed among these distances:
38 1 0.01
40 45 0.65
41 23 0.33
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (40 bp):
TCGCAATGCGATTATGACTATCGCAATGCGATTTTGACTA
Found at i:60610 original size:20 final size:20
Alignment explanation
Indices: 60528--60619 Score: 114
Period size: 20 Copynumber: 4.6 Consensus size: 20
60518 ATTTCCAGAT
60528 TCGCAATGCGATTTTGACTA
1 TCGCAATGCGATTTTGACTA
60548 TCGCAATGCGATTTTGACTA
1 TCGCAATGCGATTTTGACTA
* * *
60568 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTTTG-ACTA
* *
60588 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTTTGACTA
*
60608 TCGCAACGCGAT
1 TCGCAATGCGAT
60620 AATACATAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
19 1 0.02
20 61 0.97
21 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTTTGACTA
Found at i:63784 original size:18 final size:18
Alignment explanation
Indices: 63752--63786 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
63742 AGAAAAAGGC
**
63752 AATCAAAATTGCAATCAA
1 AATCAAAATCCCAATCAA
63770 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
63787 CAACCGGCTT
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:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:64132 original size:250 final size:250
Alignment explanation
Indices: 63679--64175 Score: 951
Period size: 250 Copynumber: 2.0 Consensus size: 250
63669 AGTGCAATCA
63679 CAATCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCAAAGCTCATATGGTGTCAAG
1 CAATCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCAAAGCTCATATGGTGTCAAG
*
63744 AAAAAGGCAATCAAAATTGCAATCAAAATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGA
66 AAAAAGGCAATCAAAATCGCAATCAAAATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGA
63809 CTATTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATTTTATGTGTAAACTTTTA
131 CTATTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATTTTATGTGTAAACTTTTA
63874 CTATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATCTG
196 CTATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATCTG
*
63929 CAATTATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCAAAGCTCATATGGTGTCAAG
1 CAATCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCAAAGCTCATATGGTGTCAAG
*
63994 AAAAAGGCAATCAAAATCGCAATTAAAATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGA
66 AAAAAGGCAATCAAAATCGCAATCAAAATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGA
64059 CTATTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATTTTATGTGTAAACTTTTA
131 CTATTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATTTTATGTGTAAACTTTT-
64124 AC-ATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGAT
195 ACTATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGAT
64176 TTGTTCAGTT
Statistics
Matches: 243, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
250 241 0.99
251 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (250 bp):
CAATCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCAAAGCTCATATGGTGTCAAG
AAAAAGGCAATCAAAATCGCAATCAAAATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGA
CTATTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATTTTATGTGTAAACTTTTA
CTATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATCTG
Found at i:64346 original size:140 final size:140
Alignment explanation
Indices: 64094--64376 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
64084 GCAAACGTTG
64094 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
64159 TTGAACATTGCTATGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
64224 CGAATTTGAC
131 CGAATTTGAC
64234 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
**
64299 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGGTTATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
64364 CGAATTTGAC
131 CGAATTTGAC
64374 TAT
1 TAT
64377 CGCAACGCAA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.44
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:64377 original size:20 final size:20
Alignment explanation
Indices: 64354--64507 Score: 109
Period size: 20 Copynumber: 8.3 Consensus size: 20
64344 TTCATTTGGT
64354 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTTGAC
64374 TATCGCAACGC-AA----A-
1 TATCGCAACGCGAATTTGAC
*
64388 AATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTTGAC
* *
64408 TATCGCAACGTGAATTTGAT
1 TATCGCAACGCGAATTTGAC
* * * *
64428 TATCGCAATGGGAATTTAAA
1 TATCGCAACGCGAATTTGAC
*
64448 TATCGCAACGAGAA----A-
1 TATCGCAACGCGAATTTGAC
* * *
64463 -ATCGCAAAGCGTATTAGAC
1 TATCGCAACGCGAATTTGAC
64482 TATCGCAACGCGAA-TTGAC
1 TATCGCAACGCGAATTTGAC
*
64501 TTTCGCA
1 TATCGCA
64508 TTGCGATTTT
Statistics
Matches: 105, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
14 20 0.19
15 3 0.03
16 1 0.01
18 1 0.01
19 13 0.12
20 67 0.64
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (20 bp):
TATCGCAACGCGAATTTGAC
Found at i:64468 original size:74 final size:74
Alignment explanation
Indices: 64347--64497 Score: 205
Period size: 74 Copynumber: 2.0 Consensus size: 74
64337 TTACACATTC
* * * * *
64347 ATTTGGTTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGAATTTGACTATC
1 ATTTGATTATCGCAACGCGAATTTAAATATCGCAACGCAAAAATCGCAAAGCGAATTAGACTATC
*
64412 GCAACGTGA
66 GCAACGCGA
* * *
64421 ATTTGATTATCGCAATGGGAATTTAAATATCGCAACG-AGAAAATCGCAAAGCGTATTAGACTAT
1 ATTTGATTATCGCAACGCGAATTTAAATATCGCAACGCA-AAAATCGCAAAGCGAATTAGACTAT
64485 CGCAACGCGA
65 CGCAACGCGA
64495 ATT
1 ATT
64498 GACTTTCGCA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
73 1 0.01
74 66 0.99
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (74 bp):
ATTTGATTATCGCAACGCGAATTTAAATATCGCAACGCAAAAATCGCAAAGCGAATTAGACTATC
GCAACGCGA
Found at i:64486 original size:34 final size:34
Alignment explanation
Indices: 64355--64491 Score: 116
Period size: 34 Copynumber: 3.9 Consensus size: 34
64345 TCATTTGGTT
*
64355 ATCGCAACGCGAATTTGACTATCGCAACGCA-AAA
1 ATCGCAACGCGAATTAGACTATCGCAACG-AGAAA
* *
64389 ATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGA
1 ATCGCAACGCGAATTAGACTATCGCAACGAGAA----A
* * *
64427 TTATCGCAATGGGAATTTA-AATATCGCAACGAGAAA
1 --ATCGCAACGCGAA-TTAGACTATCGCAACGAGAAA
* *
64463 ATCGCAAAGCGTATTAGACTATCGCAACG
1 ATCGCAACGCGAATTAGACTATCGCAACG
64492 CGAATTGACT
Statistics
Matches: 84, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
33 3 0.04
34 52 0.62
36 1 0.01
38 1 0.01
40 25 0.30
41 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (34 bp):
ATCGCAACGCGAATTAGACTATCGCAACGAGAAA
Found at i:66122 original size:21 final size:21
Alignment explanation
Indices: 66062--66179 Score: 119
Period size: 21 Copynumber: 5.6 Consensus size: 21
66052 GTGAATCGGG
* * * *
66062 CTCTTGAATGGTGGTAGGGAC
1 CTCTTGAACGATGGGAGGGGC
* **
66083 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
66104 CTCTTGAACGATGGGAGGGGA
1 CTCTTGAACGATGGGAGGGGC
** *
66125 CTCTTGAGGGATGGTAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
66146 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGGGAGGGGC
66167 CTCTTGAACGATG
1 CTCTTGAACGATG
66180 ACAGGTGAGT
Statistics
Matches: 77, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:66129 original size:42 final size:42
Alignment explanation
Indices: 66078--66184 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
66068 AATGGTGGTA
* *
66078 GGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGATGGGAG
1 GGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAG
** **
66121 GGGACTCTTGAGGGATGGTAGGGGCCTCTTGAACGATAGGAG
1 GGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAG
* *
66163 AGGCCTCTTGAACGATGACAGG
1 GGGACTCTTGAACGATGACAGG
66185 TGAGTCGGGC
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
42 48 0.92
43 4 0.08
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.20
Consensus pattern (42 bp):
GGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAG
Found at i:66806 original size:19 final size:18
Alignment explanation
Indices: 66778--66828 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
66768 TACGTGAAAA
*
66778 TCGCAATGCGAATTTAGTT
1 TCGCATTGCGAATTTA-TT
* *
66797 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGA-ATTTATT
66816 TCGCATTGC-AATT
1 TCGCATTGCGAATT
66829 ATCCCGTTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 2 0.08
18 1 0.04
19 19 0.73
20 4 0.15
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (18 bp):
TCGCATTGCGAATTTATT
Found at i:66877 original size:20 final size:20
Alignment explanation
Indices: 66833--66901 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
66823 GCAATTATCC
*
66833 CGTTGCGATAGTCAAATT-CG
1 CGTTGCGATAGTC-ACTTCCG
* *
66853 TGTTGTGATAGTCACTTCCG
1 CGTTGCGATAGTCACTTCCG
* * *
66873 CGTTGCGTTAGTCATTTTCG
1 CGTTGCGATAGTCACTTCCG
66893 CGTTGCGAT
1 CGTTGCGAT
66902 TTTTAAGTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCACTTCCG
Found at i:68862 original size:20 final size:20
Alignment explanation
Indices: 68817--68884 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
68807 GAAAGTTAAA
**
68817 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
68837 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * **
68857 AGCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
68877 ATCGCAAC
1 ATCGCAAC
68885 GAGATAATCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.15
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:69361 original size:22 final size:22
Alignment explanation
Indices: 69304--69354 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
69294 GATGGAGATA
*
69304 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
69326 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
69348 GACGGAT
1 GACGGAT
69355 GTTGTCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:69551 original size:20 final size:20
Alignment explanation
Indices: 69528--69612 Score: 93
Period size: 20 Copynumber: 4.2 Consensus size: 20
69518 TTATCGCAAC
*
69528 GCGATAGTCAGAATCGTGTT
1 GCGATAGTCAGAATCGCGTT
*
69548 GCGATAGTAAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
*
69568 GCGATTATGT--GTTATCGCGTT
1 GCGA-TA-GTCAG-AATCGCGTT
*
69589 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
69609 GCGA
1 GCGA
69613 ATCTGGAAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.04
20 37 0.67
21 14 0.25
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:73104 original size:21 final size:21
Alignment explanation
Indices: 73078--73130 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
73068 CCGACTAAGT
73078 TCGGGTCGGGTTTGAATAATA
1 TCGGGTCGGGTTTGAATAATA
73099 TCGGGTCGGGTTTGAATAATA
1 TCGGGTCGGGTTTGAATAATA
73120 TCGGGTCGGGT
1 TCGGGTCGGGT
73131 ATCGGGGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.11, G:0.38, T:0.32
Consensus pattern (21 bp):
TCGGGTCGGGTTTGAATAATA
Found at i:74451 original size:26 final size:26
Alignment explanation
Indices: 74419--74528 Score: 74
Period size: 26 Copynumber: 4.3 Consensus size: 26
74409 TATTAACTTT
74419 TTATAATTAAACTTTATAGATTATAA
1 TTATAATTAAACTTTATAGATTATAA
* * * *
74445 TTATAATT--ATTTTAAACAATTATATT
1 TTATAATTAAACTTTATA-GATTATA-A
*
74471 TTATAAATTATATAC-TTA-A-CTT-T--
1 TTAT-AATTA-A-ACTTTATAGATTATAA
74494 TTATAATTAAACTTTATAGATTATAA
1 TTATAATTAAACTTTATAGATTATAA
74520 TTATAATTA
1 TTATAATTA
74529 TTTTAAACAA
Statistics
Matches: 64, Mismatches: 7, Indels: 26
0.66 0.07 0.27
Matches are distributed among these distances:
20 2 0.03
21 4 0.06
22 6 0.09
23 6 0.09
24 7 0.11
25 6 0.09
26 22 0.34
27 6 0.09
29 1 0.02
30 3 0.05
31 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (26 bp):
TTATAATTAAACTTTATAGATTATAA
Found at i:74466 original size:39 final size:39
Alignment explanation
Indices: 74423--74557 Score: 152
Period size: 39 Copynumber: 3.5 Consensus size: 39
74413 AACTTTTTAT
*
74423 AATTAAACTTTATAGATTATAATTATAATTATTTTAAAC
1 AATTAAACTTTATAAATTATAATTATAATTATTTTAAAC
* * * * *
74462 AATTATATTTTATAAATTATATACT-TAACT-TTTT--AT
1 AATTAAACTTTATAAATTATA-ATTATAATTATTTTAAAC
*
74498 AATTAAACTTTATAGATTATAATTATAATTATTTTAAAC
1 AATTAAACTTTATAAATTATAATTATAATTATTTTAAAC
* *
74537 AATTATATTTTATAAATTATA
1 AATTAAACTTTATAAATTATA
74558 TACTTAAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
35 2 0.03
36 23 0.30
37 4 0.05
38 4 0.05
39 41 0.54
40 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.50
Consensus pattern (39 bp):
AATTAAACTTTATAAATTATAATTATAATTATTTTAAAC
Found at i:74497 original size:75 final size:75
Alignment explanation
Indices: 74411--74564 Score: 308
Period size: 75 Copynumber: 2.1 Consensus size: 75
74401 TTATTTCTTA
74411 TTAACTTTTTATAATTAAACTTTATAGATTATAATTATAATTATTTTAAACAATTATATTTTATA
1 TTAACTTTTTATAATTAAACTTTATAGATTATAATTATAATTATTTTAAACAATTATATTTTATA
74476 AATTATATAC
66 AATTATATAC
74486 TTAACTTTTTATAATTAAACTTTATAGATTATAATTATAATTATTTTAAACAATTATATTTTATA
1 TTAACTTTTTATAATTAAACTTTATAGATTATAATTATAATTATTTTAAACAATTATATTTTATA
74551 AATTATATAC
66 AATTATATAC
74561 TTAA
1 TTAA
74565 AAACTATTTA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (75 bp):
TTAACTTTTTATAATTAAACTTTATAGATTATAATTATAATTATTTTAAACAATTATATTTTATA
AATTATATAC
Found at i:74607 original size:75 final size:75
Alignment explanation
Indices: 74411--74598 Score: 254
Period size: 75 Copynumber: 2.5 Consensus size: 75
74401 TTATTTCTTA
* * *
74411 TTAACTTTTTATAATTAAACTTTATAGATTATAATTATAATTATTTTAAACAATTATATTTTATA
1 TTAACTTATTATAATTAAACTTTATAAAATATAATTATAATTATTTTAAACAATTATATTTTATA
74476 AATTATATAC
66 AATTATATAC
* * *
74486 TTAACTTTTTATAATTAAACTTTATAGATTATAATTATAATTATTTTAAACAATTATATTTTATA
1 TTAACTTATTATAATTAAACTTTATAAAATATAATTATAATTATTTTAAACAATTATATTTTATA
74551 AATTATATAC
66 AATTATATAC
* *
74561 TTAAAAAC-TATT-TAATTAAAGTTGTTTAAAATATAATT
1 TT---AACTTATTATAATTAAACTT-TATAAAATATAATT
74599 TTATATTTTT
Statistics
Matches: 104, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
75 77 0.74
76 10 0.10
77 14 0.13
78 3 0.03
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (75 bp):
TTAACTTATTATAATTAAACTTTATAAAATATAATTATAATTATTTTAAACAATTATATTTTATA
AATTATATAC
Found at i:76802 original size:61 final size:61
Alignment explanation
Indices: 76716--76843 Score: 238
Period size: 61 Copynumber: 2.1 Consensus size: 61
76706 AAATACTAGC
76716 AAATAGATAACCATGTAATATGTCACCTATGCAACTAACGTTTTTCAAATATAATACTTAT
1 AAATAGATAACCATGTAATATGTCACCTATGCAACTAACGTTTTTCAAATATAATACTTAT
* *
76777 AAATAGTTAACCATGTACTATGTCACCTATGCAACTAACGTTTTTCAAATATAATACTTAT
1 AAATAGATAACCATGTAATATGTCACCTATGCAACTAACGTTTTTCAAATATAATACTTAT
76838 AAATAG
1 AAATAG
76844 GGCACTCCTT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (61 bp):
AAATAGATAACCATGTAATATGTCACCTATGCAACTAACGTTTTTCAAATATAATACTTAT
Found at i:77952 original size:17 final size:17
Alignment explanation
Indices: 77930--77968 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
77920 ATTGCTTATA
77930 TCATTTAAGTAAAGATG
1 TCATTTAAGTAAAGATG
*
77947 TCATTTAAGTAATGATG
1 TCATTTAAGTAAAGATG
77964 TCATT
1 TCATT
77969 GCTTACATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (17 bp):
TCATTTAAGTAAAGATG
Found at i:82696 original size:17 final size:17
Alignment explanation
Indices: 82674--82712 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
82664 ATTGCTTATA
82674 TCATTTAAGTAAAGATG
1 TCATTTAAGTAAAGATG
*
82691 TCATTTAAGTAATGATG
1 TCATTTAAGTAAAGATG
82708 TCATT
1 TCATT
82713 GCTTACATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (17 bp):
TCATTTAAGTAAAGATG
Done.