Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003318.1 Hibiscus syriacus cultivar Beakdansim tig00006989_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: 62314
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:1106 original size:20 final size:20
Alignment explanation
Indices: 1083--1120 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1073 GTCAATATTT
1083 TTTA-TCTACTTTTAAAGGGA
1 TTTATTCTA-TTTTAAAGGGA
*
1103 TTTATTGTATTTTAAAGG
1 TTTATTCTATTTTAAAGG
1121 AAATAAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTATTCTATTTTAAAGGGA
Found at i:1490 original size:29 final size:28
Alignment explanation
Indices: 1448--1511 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
1438 GAATTTTAAA
* * *
1448 ATTATAAAATAGATATTAACTTTGAATTTT
1 ATTA-AAAATAGATATCAAC-GTGAAATTT
1478 ATTAAAAATAGATATCAACGTGAAATTT
1 ATTAAAAATAGATATCAACGTGAAATTT
1506 ATTAAA
1 ATTAAA
1512 GAGGTGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 13 0.42
29 14 0.45
30 4 0.13
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (28 bp):
ATTAAAAATAGATATCAACGTGAAATTT
Found at i:5042 original size:12 final size:12
Alignment explanation
Indices: 5025--5566 Score: 96
Period size: 12 Copynumber: 44.2 Consensus size: 12
5015 AATAAATCGA
5025 AGCTTATAAACG
1 AGCTTATAAACG
*
5037 AGCTTATAAAGG
1 AGCTTATAAACG
* * *
5049 GGTTTATAAATG
1 AGCTTATAAACG
*
5061 AGCTTATAAACA
1 AGCTTATAAACG
*
5073 AGCTTATAAA-T
1 AGCTTATAAACG
*
5084 AGGCTTGTAAACG
1 A-GCTTATAAACG
* *
5097 AACTTATAAACA
1 AGCTTATAAACG
***
5109 AG----TCCCCG
1 AGCTTATAAACG
5117 AGCTTATAAACG
1 AGCTTATAAACG
*
5129 AGCTTATAAACAA
1 AGCTTATAAAC-G
* * *
5142 ATTCGTGATTGAACG
1 A-GC-TTA-TAAACG
*
5157 AACTTATAAACG
1 AGCTTATAAACG
5169 AG-TTCATAATCGAACG
1 AGCTT-AT-A---AACG
*
5185 AGCTTATAAAAG
1 AGCTTATAAACG
*
5197 AG-TCCATAAAACG
1 AGCT-TAT-AAACG
*
5210 AGCTTATAAATG
1 AGCTTATAAACG
* * * *
5222 A-CTCCACAACCA
1 AGCT-TATAAACG
* *
5234 AGCGTATAAAAG
1 AGCTTATAAACG
*
5246 AG-TCTATAAATG
1 AGCT-TATAAACG
*
5258 AGCTTATAAAGG
1 AGCTTATAAACG
* * *
5270 GGTTTATAAATG
1 AGCTTATAAACG
*
5282 AGCTTATAAACA
1 AGCTTATAAACG
*
5294 AGCTTATAAA-T
1 AGCTTATAAACG
*
5305 AGGCTTGTAAACG
1 A-GCTTATAAACG
* *
5318 AACTTATAAATG
1 AGCTTATAAACG
* *
5330 AACTTATAAACA
1 AGCTTATAAACG
***
5342 AG-TCCCCAAACG
1 AGCT-TATAAACG
*
5354 AGCTTATAAACA
1 AGCTTATAAACG
***
5366 AG-TCCCCAAACG
1 AGCT-TATAAACG
* *
5378 AGCTTGTAAACA
1 AGCTTATAAACG
* *
5390 AGTCCGTGATTGAACG
1 AG--C-TTA-TAAACG
*
5406 AACTTATAAACG
1 AGCTTATAAACG
*
5418 A-ATTCATAATCGAACG
1 AGCTT-AT-A---AACG
5434 AGCTTATAAACG
1 AGCTTATAAACG
*
5446 AG-TCCATAAACG
1 AGCT-TATAAACG
*
5458 TGCTTATAAACG
1 AGCTTATAAACG
* *
5470 A-CTCCACAAACG
1 AGCT-TATAAACG
*
5482 AGCTTATAAAAG
1 AGCTTATAAACG
5494 AG-TCTATAAA-G
1 AGCT-TATAAACG
* *
5505 GGCTTATGAACG
1 AGCTTATAAACG
*
5517 AG-TCAATAAACG
1 AGCT-TATAAACG
* *
5529 GGCTTATGAACG
1 AGCTTATAAACG
*
5541 AG-TCGATAAACG
1 AGCT-TATAAACG
* *
5553 GGCTTATGAACG
1 AGCTTATAAACG
5565 AG
1 AG
5567 TCGATAAACA
Statistics
Matches: 365, Mismatches: 115, Indels: 100
0.63 0.20 0.17
Matches are distributed among these distances:
8 4 0.01
11 24 0.07
12 272 0.75
13 26 0.07
14 5 0.01
15 6 0.02
16 24 0.07
17 4 0.01
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (12 bp):
AGCTTATAAACG
Found at i:5103 original size:36 final size:36
Alignment explanation
Indices: 5016--5110 Score: 109
Period size: 36 Copynumber: 2.6 Consensus size: 36
5006 AAACTTATAA
* * *
5016 ATAAATCGAAGCTTATAAACGAGCTTATAAAGGGGTTT
1 ATAAA-CGAA-CTTATAAACAAGCTTATAAAGAGGCTT
* * *
5054 ATAAATGAGCTTATAAACAAGCTTATAAATAGGCTT
1 ATAAACGAACTTATAAACAAGCTTATAAAGAGGCTT
*
5090 GTAAACGAACTTATAAACAAG
1 ATAAACGAACTTATAAACAAG
5111 TCCCCGAGCT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
36 41 0.85
37 2 0.04
38 5 0.10
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (36 bp):
ATAAACGAACTTATAAACAAGCTTATAAAGAGGCTT
Found at i:5199 original size:28 final size:27
Alignment explanation
Indices: 5125--5219 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 27
5115 CGAGCTTATA
* * *
5125 AACGAGCTTATAAACA-AATTCGTGATTG
1 AACGAGCTTATAAA-AGAGTTCAT-AATG
* *
5153 AACGAACTTATAAACGAGTTCATAATCG
1 AACGAGCTTATAAAAGAGTTCATAAT-G
*
5181 AACGAGCTTATAAAAGAGTCCATAA--
1 AACGAGCTTATAAAAGAGTTCATAATG
5206 AACGAGCTTATAAA
1 AACGAGCTTATAAA
5220 TGACTCCACA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
25 14 0.25
27 2 0.04
28 41 0.72
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (27 bp):
AACGAGCTTATAAAAGAGTTCATAATG
Found at i:5265 original size:24 final size:24
Alignment explanation
Indices: 5121--5622 Score: 233
Period size: 24 Copynumber: 20.2 Consensus size: 24
5111 TCCCCGAGCT
* *
5121 TATAAACGAGCTTATAAACAAATTC
1 TATAAACGAGCTTATAAAC-GAGTC
* *
5146 GTGATTGAACGAACTTATAAACGAGTTC
1 -T-A-TAAACGAGCTTATAAACGAG-TC
* *
5174 ATAATCGAACGAGCTTATAAAAGAGTC
1 -T-AT-AAACGAGCTTATAAACGAGTC
* * *
5201 CATAAAACGAGCTTATAAATGACTC
1 TAT-AAACGAGCTTATAAACGAGTC
* * * * * *
5226 CACAACCAAGCGTATAAAAGAGTC
1 TATAAACGAGCTTATAAACGAGTC
* * * *
5250 TATAAATGAGCTTATAAAGGGGTT
1 TATAAACGAGCTTATAAACGAGTC
* *
5274 TATAAATGAGCTTATAAACAAG-C
1 TATAAACGAGCTTATAAACGAGTC
* * *
5297 TTATAAA-TAGGCTTGTAAACGA-AC
1 -TATAAACGA-GCTTATAAACGAGTC
* * *
5321 TTATAAATGAACTTATAAACAAGTC
1 -TATAAACGAGCTTATAAACGAGTC
*** *
5346 CCCAAACGAGCTTATAAACAAGTC
1 TATAAACGAGCTTATAAACGAGTC
*** * *
5370 CCCAAACGAGCTTGTAAACAAGTCC
1 TATAAACGAGCTTATAAACGAGT-C
* * *
5395 GTGATTGAACGAACTTATAAACGAATTC
1 -T-A-TAAACGAGCTTATAAACG-AGTC
*
5423 ATAATCGAACGAGCTTATAAACGAGTC
1 -T-AT-AAACGAGCTTATAAACGAGTC
* * *
5450 CATAAACGTGCTTATAAACGACTC
1 TATAAACGAGCTTATAAACGAGTC
* * *
5474 CACAAACGAGCTTATAAAAGAGTC
1 TATAAACGAGCTTATAAACGAGTC
* *
5498 TATAAA-GGGCTTATGAACGAGTC
1 TATAAACGAGCTTATAAACGAGTC
* * *
5521 AATAAACGGGCTTATGAACGAGTC
1 TATAAACGAGCTTATAAACGAGTC
* * *
5545 GATAAACGGGCTTATGAACGAGTC
1 TATAAACGAGCTTATAAACGAGTC
* * *
5569 GATAAAC-AGGCTTATGAGCGAGTC
1 TATAAACGA-GCTTATAAACGAGTC
*
5593 GAT-AACTGAGCTTATAAACGAGTC
1 TATAAAC-GAGCTTATAAACGAGTC
*
5617 GATAAA
1 TATAAA
5623 TGAGTCAATA
Statistics
Matches: 379, Mismatches: 77, Indels: 41
0.76 0.15 0.08
Matches are distributed among these distances:
23 23 0.06
24 246 0.65
25 30 0.08
26 1 0.00
27 9 0.02
28 68 0.18
29 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (24 bp):
TATAAACGAGCTTATAAACGAGTC
Found at i:5453 original size:28 final size:28
Alignment explanation
Indices: 5374--5454 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
5364 CAAGTCCCCA
* * * * *
5374 AACGAGCTTGTAAACAAGTCCGTGATTG
1 AACGAGCTTATAAACGAGTCCATAATCG
* * *
5402 AACGAACTTATAAACGAATTCATAATCG
1 AACGAGCTTATAAACGAGTCCATAATCG
5430 AACGAGCTTATAAACGAGTCCATAA
1 AACGAGCTTATAAACGAGTCCATAA
5455 ACGTGCTTAT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (28 bp):
AACGAGCTTATAAACGAGTCCATAATCG
Found at i:9663 original size:27 final size:29
Alignment explanation
Indices: 9611--9670 Score: 97
Period size: 27 Copynumber: 2.1 Consensus size: 29
9601 AGTGTCACAC
9611 TATCTTTGAAAAATAATAATAATAATAAAT
1 TATCTTT-AAAAATAATAATAATAATAAAT
9641 TATCTTT-AAAA-AATAATAATAATAAAT
1 TATCTTTAAAAATAATAATAATAATAAAT
9668 TAT
1 TAT
9671 AATATCATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 19 0.63
28 4 0.13
30 7 0.23
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (29 bp):
TATCTTTAAAAATAATAATAATAATAAAT
Found at i:10662 original size:11 final size:11
Alignment explanation
Indices: 10641--10708 Score: 70
Period size: 11 Copynumber: 6.2 Consensus size: 11
10631 AAAAAACCGT
10641 TATAC-AATTA
1 TATACTAATTA
10651 TATACTAA-T-
1 TATACTAATTA
*
10660 TATACTAATGA
1 TATACTAATTA
*
10671 TTATAGTAATTA
1 -TATACTAATTA
10683 TATACTATAATTA
1 TATAC--TAATTA
10696 TATACTAATTA
1 TATACTAATTA
10707 TA
1 TA
10709 GTAATGAAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
9 8 0.17
10 6 0.12
11 14 0.29
12 9 0.19
13 11 0.23
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (11 bp):
TATACTAATTA
Found at i:10695 original size:13 final size:13
Alignment explanation
Indices: 10677--10702 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10667 ATGATTATAG
10677 TAATTATATACTA
1 TAATTATATACTA
10690 TAATTATATACTA
1 TAATTATATACTA
10703 ATTATAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATTATATACTA
Found at i:11417 original size:21 final size:21
Alignment explanation
Indices: 11302--11417 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
11292 GCGAAATAAA
**
11302 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
11322 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
11342 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
11363 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
11383 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
11405 AATCGCAACGCGA
1 AATCGCAACGCGA
11418 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:11430 original size:20 final size:20
Alignment explanation
Indices: 11405--11517 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
11395 GATTTTCCAG
* *
11405 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
11425 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
11445 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
11465 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
11485 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
11505 AATCGCAACGCGA
1 AATCGCAACGCGA
11518 TTTTTAAAGC
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
19 2 0.02
20 79 0.95
21 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:11468 original size:40 final size:39
Alignment explanation
Indices: 11405--11517 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 39
11395 GATTTTCCAG
* ** *
11405 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
11445 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
*
11485 TATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
11518 TTTTTAAAGC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.02
40 60 0.95
41 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.18
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:11934 original size:33 final size:33
Alignment explanation
Indices: 11895--11962 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
11885 TTCACTTAGA
11895 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
11928 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
11961 TT
1 TT
11963 CAAGTTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.10, C:0.24, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:12070 original size:21 final size:20
Alignment explanation
Indices: 12044--12152 Score: 88
Period size: 21 Copynumber: 5.7 Consensus size: 20
12034 TGCAGAAGAG
12044 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
12065 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
12085 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
*
12107 TCGCAATGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
12121 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
*
12140 TCGCAACGCGAAA
1 TCGCAACGAGAAA
12153 CCAAATCGCA
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
14 10 0.14
16 2 0.03
17 2 0.03
19 12 0.17
20 11 0.15
21 24 0.34
22 10 0.14
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:12160 original size:18 final size:19
Alignment explanation
Indices: 12119--12162 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
12109 GCAATGAGAG
*
12119 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATCAA
*
12138 AATCGCAACGCGAAA-CCA
1 AATCGCAACGCGAAATCAA
12156 AATCGCA
1 AATCGCA
12163 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAATCAA
Found at i:12188 original size:19 final size:19
Alignment explanation
Indices: 12158--12285 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
12148 CGAAACCAAA
*
12158 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
12177 TCGCGTTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
12191 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
12210 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
12224 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
12244 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
12264 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
12284 TC
1 TC
12286 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
14 19 0.22
16 6 0.07
17 6 0.07
19 21 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:12202 original size:14 final size:14
Alignment explanation
Indices: 12180--12236 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
12170 TTTCATTTCG
*
12180 CGTTACGATTCTCT
1 CGTTGCGATTCTCT
*
12194 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
12213 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
12227 CGTTGCGATT
1 CGTTGCGATT
12237 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:12205 original size:33 final size:33
Alignment explanation
Indices: 12163--12285 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
12153 CCAAATCGCA
12163 TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
*
12196 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
*
12229 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT---AC-G--ATTCTCTCG
12270 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
12286 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.56
34 2 0.03
35 6 0.08
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.27
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
Found at i:12247 original size:21 final size:21
Alignment explanation
Indices: 12221--12285 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
12211 CGCGTTGCGA
12221 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
12242 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
12262 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
12283 TTC
1 TTC
12286 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:14308 original size:92 final size:93
Alignment explanation
Indices: 13959--14734 Score: 1483
Period size: 92 Copynumber: 8.4 Consensus size: 93
13949 TAGATTGCTT
*
13959 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
14024 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
14051 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAACACTGTGAAATAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-AACACTGTGAAATAGT
14116 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
14145 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
14210 TTTGTCTTTGTTTTGTCTTTTGATTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
14238 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
14302 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
14330 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-ACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
14394 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
14422 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
14486 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
14513 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
14577 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
14605 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
14670 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
14698 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
14735 AATACCCTGA
Statistics
Matches: 674, Mismatches: 3, Indels: 13
0.98 0.00 0.02
Matches are distributed among these distances:
91 96 0.14
92 308 0.46
93 201 0.30
94 69 0.10
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:14888 original size:14 final size:14
Alignment explanation
Indices: 14867--14925 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
14857 ACGCGAAATG
14867 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
14881 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
14900 AAAATCGCAACGAC
1 AAAATCGCAACGAC
14914 AAAATCGCAACG
1 AAAATCGCAACG
14926 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:14892 original size:33 final size:33
Alignment explanation
Indices: 14848--14941 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
14838 CACGAAACTT
**
14848 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
*
14881 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
14914 AAAATCGCAACGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
14942 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:14937 original size:19 final size:19
Alignment explanation
Indices: 14832--14941 Score: 96
Period size: 19 Copynumber: 6.3 Consensus size: 19
14822 TAGTTTACTT
* *
14832 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
**
14852 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
14871 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
14885 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
14904 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
14918 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
14937 TCGCA
1 TCGCA
14942 TTGCGATTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.27
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 30 0.41
20 12 0.16
ACGTcount: A:0.46, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:14959 original size:19 final size:19
Alignment explanation
Indices: 14937--15077 Score: 139
Period size: 19 Copynumber: 7.6 Consensus size: 19
14927 GAAACCAAAA
*
14937 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
14956 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
14972 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
14989 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
15008 TCGCGTTGCGATTTTTGGTT
1 TCGCGTTGCGA-TTTTCATT
* *
15028 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
15047 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
15067 TCGTGTTGCGA
1 TCGCGTTGCGA
15078 AAGTAAACTA
Statistics
Matches: 102, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 5 0.05
19 54 0.53
20 30 0.29
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:15020 original size:52 final size:55
Alignment explanation
Indices: 14937--15077 Score: 164
Period size: 58 Copynumber: 2.5 Consensus size: 55
14927 GAAACCAAAA
* *
14937 TCGCATTGCGATTTTCA-TTTCGCGTTGCGA-TTCT-G-TCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTT-AGTTTCGCGTTGCGATTTCTGGTTCGTTGCGATTCTCATT
* *
14989 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTAGTTTCGCGTTGCGATTTCTGG--T-TCGTTGCGATTCTCATT
*
15047 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTT-AGTTTCGCGTTGCGA
15078 AAGTAAACTA
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
52 27 0.36
53 3 0.04
54 1 0.01
58 31 0.41
59 13 0.17
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (55 bp):
TCGCGTTGCGATTTTAGTTTCGCGTTGCGATTTCTGGTTCGTTGCGATTCTCATT
Found at i:15049 original size:39 final size:39
Alignment explanation
Indices: 14937--15061 Score: 129
Period size: 39 Copynumber: 3.4 Consensus size: 39
14927 GAAACCAAAA
* *
14937 TCGCATTGCGA-TTTTCATTTCGCGTTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATTCTCATT
* **
14972 T--CGTTGCGA-TTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATTCTCATT
** *
15008 TCGCGTTGCGATTTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATTCTCATT
15047 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
15062 AAGTTTCGTG
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
33 26 0.35
34 1 0.01
35 2 0.03
36 2 0.03
38 8 0.11
39 36 0.48
ACGTcount: A:0.09, C:0.20, G:0.24, T:0.47
Consensus pattern (39 bp):
TCGCGTTGCGATTTTTCATTTCGCGTTGCGATTCTCATT
Found at i:15068 original size:39 final size:39
Alignment explanation
Indices: 14973--15077 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 39
14963 GCGATTCTGT
* * * **
14973 CGTTGCGATTTTCA-TTTCGCGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAAGTTTCTCGTTGCGATTCTCATTTCG
**
15011 CGTTGCGATTTTTGGTTTCTCGTTGCGATTCTCATTTCG
1 CGTTGCGATTTTAAGTTTCTCGTTGCGATTCTCATTTCG
15050 CGTTGCGATTTTAAGTTTCGT-GTTGCGA
1 CGTTGCGATTTTAAGTTTC-TCGTTGCGA
15078 AAGTAAACTA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
38 12 0.21
39 44 0.77
40 1 0.02
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.47
Consensus pattern (39 bp):
CGTTGCGATTTTAAGTTTCTCGTTGCGATTCTCATTTCG
Found at i:17010 original size:14 final size:14
Alignment explanation
Indices: 16991--17029 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
16981 ATTGTTTAAT
16991 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
17005 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
17019 TGATTGTGTAA
1 TGATT-TGTAA
17030 TTGATGCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:17140 original size:19 final size:19
Alignment explanation
Indices: 17116--17203 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
17106 GCATTATGTT
17116 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
17135 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
17152 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
17168 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
17187 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
17204 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:17235 original size:53 final size:53
Alignment explanation
Indices: 17116--17222 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
17106 GCATTATGTT
17116 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
17168 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
17221 GA
1 GA
17223 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:17240 original size:19 final size:19
Alignment explanation
Indices: 17212--17398 Score: 185
Period size: 19 Copynumber: 10.7 Consensus size: 19
17202 AACGAGAGAA
*
17212 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
17231 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
17250 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
17267 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
17283 TTGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
17301 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
17317 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
17334 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
17352 TCCGCATTGCGATTTTC--T
1 T-CGCATTGCGATTTTCATT
*
17370 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
17386 TCGCATTGCGATT
1 TCGCATTGCGATT
17399 CTCTCGTTGC
Statistics
Matches: 142, Mismatches: 9, Indels: 34
0.77 0.05 0.18
Matches are distributed among these distances:
14 22 0.15
15 3 0.02
16 15 0.11
17 10 0.07
18 36 0.25
19 42 0.30
20 14 0.10
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:17380 original size:52 final size:52
Alignment explanation
Indices: 17218--17398 Score: 303
Period size: 52 Copynumber: 3.5 Consensus size: 52
17208 AGAATCGCAA
17218 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGA-TTTCATTTCCGCATTGCGATTCTCTCGT
*
17271 TGCGA-TTTCATTTTGCATTGCGATTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTCATTTCCGCATTGCGATTCTCTCGT
* *
17321 TGCGATTTTCATTTCGCATTGCGATTTCATTTCCGCATTGCGATTTTCTTGT
1 TGCGATTTTCATTTCGCATTGCGATTTCATTTCCGCATTGCGATTCTCTCGT
*
17373 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
17399 CTCTCGTTGC
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
50 24 0.20
51 33 0.27
52 59 0.49
53 5 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:17399 original size:85 final size:82
Alignment explanation
Indices: 17236--17431 Score: 236
Period size: 85 Copynumber: 2.3 Consensus size: 82
17226 TCATTTCGCA
*
17236 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTCATTTTGCATTGCGATTTCATT
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTT-ATCTTG-ATTGCGATTTCATT
17301 TCGCATTGCGATTCTCTCG
64 TCGCATTGCGATTCTCTCG
* *
17320 TTGCGATTTTCATTT-CGCATTGCGATTTCATTTCCGCATTGCGATTT-TCTTG-TTGGGATTTT
1 TTGCGATTTTCATTTCCGCATTGCGA-TTC-TCT-CG--TTGCGATTTATCTTGATTGCGA-TTT
17382 CATTTCGCATTGCGATTCTCTCG
60 CATTTCGCATTGCGATTCTCTCG
* * **
17405 TTGCGATTGTAATTTCCGTGTTGCGAT
1 TTGCGATTTTCATTTCCGCATTGCGAT
17432 AGTCAAATGC
Statistics
Matches: 98, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
83 10 0.10
84 23 0.23
85 42 0.43
86 14 0.14
88 9 0.09
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (82 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTATCTTGATTGCGATTTCATTTC
GCATTGCGATTCTCTCG
Found at i:17420 original size:33 final size:32
Alignment explanation
Indices: 17236--17412 Score: 146
Period size: 33 Copynumber: 5.2 Consensus size: 32
17226 TCATTTCGCA
17236 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGA-TTTCATTT-CGCATTGCGATTCTCTCG
* *
17270 TTGCGATTTCATTTTGCATTGCGATTTCATTTCG
1 TTGCGATTTCATTTCGCATTGCGA-TTC-TCTCG
* *
17304 CATTGCGA-TTC-TCTCG--TTGCGATTTTCATTTCG
1 --TTGCGATTTCATTTCGCATTGCGA--TTC-TCTCG
* *
17337 CATTGCGATTTCATTTCCGCATTGCGATTTTCTTG
1 --TTGCGATTTCATTT-CGCATTGCGATTCTCTCG
*
17372 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGA-TTTCATTTCGCATTGCGATTCTCTCG
17405 TTGCGATT
1 TTGCGATT
17413 GTAATTTCCG
Statistics
Matches: 120, Mismatches: 12, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
32 17 0.14
33 55 0.46
34 24 0.20
35 8 0.07
36 10 0.08
38 6 0.05
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCATTGCGATTCTCTCG
Found at i:20649 original size:20 final size:20
Alignment explanation
Indices: 20621--20829 Score: 208
Period size: 20 Copynumber: 10.4 Consensus size: 20
20611 AAATTTCAGT
* * * *
20621 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
20641 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* ***
20661 GTTGCGATTTACAGATTTTC
1 GTTGCGATTTACGGATACGC
*
20681 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
*
20701 GTTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATACGC
*
20721 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
20741 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
20761 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
20781 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
20801 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
20821 GTTGCGATT
1 GTTGCGATT
20830 CTTGAAAATC
Statistics
Matches: 162, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.02
20 156 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:22371 original size:75 final size:75
Alignment explanation
Indices: 22280--22434 Score: 265
Period size: 75 Copynumber: 2.1 Consensus size: 75
22270 AAAATTATGA
* * * *
22280 TGAAGCTTATGAAGGTGAAGACCAGATCATTGAGGAAGTACAAACTGCTCATATGAAAGAAAATT
1 TGAAGCTCATGAAGGTGAAGACCAGATCAATGAGGAAGTACAAACTACTCATAGGAAAGAAAATT
22345 CAGGTGAAAT
66 CAGGTGAAAT
*
22355 TGAAGCTCATGTAGGTGAAGACCAGATCAATGAGGAAGTACAAACTACTCATAGGAAAGAAAATT
1 TGAAGCTCATGAAGGTGAAGACCAGATCAATGAGGAAGTACAAACTACTCATAGGAAAGAAAATT
22420 CAGGTGAAAT
66 CAGGTGAAAT
22430 TGAAG
1 TGAAG
22435 AACTTTCACT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (75 bp):
TGAAGCTCATGAAGGTGAAGACCAGATCAATGAGGAAGTACAAACTACTCATAGGAAAGAAAATT
CAGGTGAAAT
Found at i:23378 original size:88 final size:85
Alignment explanation
Indices: 23165--23366 Score: 266
Period size: 84 Copynumber: 2.4 Consensus size: 85
23155 AGTCTAGGAC
* * *
23165 TTTC-TTCTTGGCAGAGTGATTGTTAATTGTATATTTTACT-AAATTCCATAATTGTATGAAAGA
1 TTTCATTCTTGGTAGAGTGATTGTTAATTGTATATTTTACTAAAATACCATAATCGTATGAAAGA
*
23228 GTATAGGACAACATACATGT
66 ATATAGGACAACATACATGT
* *
23248 TTTCATTCTTGCTAGAGTCATTGTTAATTGTATATTTTACTAAAATACCATAATCGTATGAAAGA
1 TTTCATTCTTGGTAGAGTGATTGTTAATTGTATATTTTACTAAAATACCATAATCGTATGAAAGA
* *
23313 ATCTATGACTTATACATACATGT
66 ATATAGGAC--A-ACATACATGT
*
23336 TTTCATTCTTGGTGGAGTTGATT-TTAATTGT
1 TTTCATTCTTGGTAGAG-TGATTGTTAATTGT
23367 CTTTTTAACT
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
83 4 0.04
84 33 0.32
85 27 0.26
87 1 0.01
88 33 0.32
89 4 0.04
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (85 bp):
TTTCATTCTTGGTAGAGTGATTGTTAATTGTATATTTTACTAAAATACCATAATCGTATGAAAGA
ATATAGGACAACATACATGT
Found at i:35926 original size:464 final size:458
Alignment explanation
Indices: 35034--35934 Score: 1124
Period size: 464 Copynumber: 1.9 Consensus size: 458
35024 GTGTTTGTAC
* * **
35034 TCATAAATGCAAATTTTTGGTTATTCAGTTATGGAAATCAAAATGCTTAGGATATGGGTTGTTGT
1 TCATAAATGCAAATTTGTGGTTATTCAATTATGGAAATCAAAATGCTTAGGATATGAATTGTTGT
* * *
35099 AAGTTGGAAAGAATGTAGGTGATTTGGTCAGTTTATAAATGCTTTCTGCCCTATGTTATGACTGG
66 AAGTTGGAAAGAATGTAGGTGATTTGGCCAGTTTATAAATGCTGTCTGCCCTATGTTATGACTGA
*** ** * * * *
35164 TATCATCTTCCAAATATATAAAAAATATAGGGGGGGAATACCTTTAGAAGAAATTAGCATATCCT
131 TATCATCTTCCAAATATATAAAAAATATAGAAAGAAAAAACCTTTAGAAGAAATGAGCATAGCCG
* * *
35229 AGTTAAACACACACTCATCATATGATACATGTCTAATACTCAATTGTCCAGTTGTCGTTCAATTT
196 AGATAAACACACACTCA-C--A-GATAC---TCCAACACTCAATTGTCCAGTTGTCGTTCAATTT
* * * *
35294 TCCTTTAGGTGCCTGTTGTGCAGATTCTTTGGTGACTTGAGATATTTTGGCTTAATTTAATATAG
254 TCCTTCAGATGCCTGTTGTGCAGATTCTTTGGTGACTAGAGATATTTTGGCTTAATTTAATATAA
35359 GACTAAATTTTGATTTGTGATGTAAACATTCGATATGAATTCCATGTTTTATATTAGTCCATCAT
319 GACTAAATTTTGATTTGTGATGTAAACATTCGATATGAATTCCATGTTTTATATTAGTCCATCAT
* **
35424 GATTGAATTTGAATGATATTCATCCCTTCTAGATATGAGCTCGATCAGACACTCTTTTAGACAAA
384 GATCGAATTTGAATGATACCCATCCCTTCTAGATATGAGCTCGATCAGACACTCTTTTAGACAAA
35489 CCACTTACAT
449 CCACTTACAT
*
35499 TCATAAATGCAAATTTGTGGCTTA-TCAATTATGGAAATCAGAATGCTTAGGATATGAATTGTTG
1 TCATAAATGCAAATTTGTGG-TTATTCAATTATGGAAATCAAAATGCTTAGGATATGAATTGTTG
* *
35563 TAAGTTGGAAAGAATGT-GGATGATTTGGCCAGTTTATAAATTCTGTCTGTCCTATGTTATACCG
65 TAAGTTGGAAAGAATGTAGG-TGATTTGGCCAGTTTATAAATGCTGTCTGCCCTATGTTAT---G
* *
35627 ACTGATATCATCTTCGAAATAT-TAGAAAAATTTAGAAAAGAAAAAACCTTT-GAAAGAAATGAG
126 ACTGATATCATCTTCCAAATATATA-AAAAATATAG-AAAGAAAAAACCTTTAG-AAGAAATGAG
* ** * *
35690 CATAGCCGAGATAAACACATAC-C-C-G-TAC-CCAACACTCGCTTGTCC-GCTTGTCTTTCGAT
188 CATAGCCGAGATAAACACACACTCACAGATACTCCAACACTCAATTGTCCAG-TTGTCGTTCAAT
35749 TTTCCTTCAGATGCCTGTTGTGCAGATTCTTTGGTGA-TGAGAGATA-TTTGGCTTATGTTAATA
252 TTTCCTTCAGATGCCTGTTGTGCAGATTCTTTGGTGACT-AGAGATATTTTGGC-----TTAAT-
*
35812 ACTTAATATAAGACTAAATTTTGATTTGTGATGTGAACATTCGATATGAATTCCATGTTTTATAT
310 --TTAATATAAGACTAAATTTTGATTTGTGATGTAAACATTCGATATGAATTCCATGTTTTATAT
* * * *
35877 TGGTCTATCATGATCGCATTTGAATGATACCCATCTCTTCTAGATATGAGCTCGATCA
373 TAGTCCATCATGATCGAATTTGAATGATACCCATCCCTTCTAGATATGAGCTCGATCA
35935 TAGTTACTTA
Statistics
Matches: 377, Mismatches: 41, Indels: 37
0.83 0.09 0.08
Matches are distributed among these distances:
456 8 0.02
457 64 0.17
461 8 0.02
462 1 0.00
464 114 0.30
465 108 0.29
466 4 0.01
467 2 0.01
468 32 0.08
469 36 0.10
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (458 bp):
TCATAAATGCAAATTTGTGGTTATTCAATTATGGAAATCAAAATGCTTAGGATATGAATTGTTGT
AAGTTGGAAAGAATGTAGGTGATTTGGCCAGTTTATAAATGCTGTCTGCCCTATGTTATGACTGA
TATCATCTTCCAAATATATAAAAAATATAGAAAGAAAAAACCTTTAGAAGAAATGAGCATAGCCG
AGATAAACACACACTCACAGATACTCCAACACTCAATTGTCCAGTTGTCGTTCAATTTTCCTTCA
GATGCCTGTTGTGCAGATTCTTTGGTGACTAGAGATATTTTGGCTTAATTTAATATAAGACTAAA
TTTTGATTTGTGATGTAAACATTCGATATGAATTCCATGTTTTATATTAGTCCATCATGATCGAA
TTTGAATGATACCCATCCCTTCTAGATATGAGCTCGATCAGACACTCTTTTAGACAAACCACTTA
CAT
Found at i:42407 original size:21 final size:23
Alignment explanation
Indices: 42368--42422 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
42358 ATCAACCCAA
* *
42368 AATAAAAAAAATTATTTT-ATTC
1 AATAAAAATAATGATTTTAATTC
*
42390 AATAAAAATAATGA-TTTAATTG
1 AATAAAAATAATGATTTTAATTC
42412 AA-AAAAATAAT
1 AATAAAAATAAT
42423 ATATAGAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
AATAAAAATAATGATTTTAATTC
Found at i:42418 original size:22 final size:21
Alignment explanation
Indices: 42371--42422 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
42361 AACCCAAAAT
* *
42371 AAAAAA-AATTATTTTATTCA
1 AAAAAATAATGATTTAATTCA
*
42391 ATAAAAATAATGATTTAATTGA
1 A-AAAAATAATGATTTAATTCA
42413 AAAAAATAAT
1 AAAAAATAAT
42423 ATATAGAGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 14 0.52
22 12 0.44
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (21 bp):
AAAAAATAATGATTTAATTCA
Found at i:51856 original size:38 final size:37
Alignment explanation
Indices: 51814--51895 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
51804 ATAAAAATAT
* **
51814 ATTTAAATTATATAAAAGTTCAA-AAAATTATATTAAAA
1 ATTTAAATGATATAAAAAAT-AATAAAATTATA-TAAAA
* *
51852 ATTTAAGTGATTTAAAAAATAATAAAATTATATAAAA
1 ATTTAAATGATATAAAAAATAATAAAATTATATAAAA
51889 ATTTAAA
1 ATTTAAA
51896 ACTTTTAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
37 13 0.35
38 24 0.65
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.37
Consensus pattern (37 bp):
ATTTAAATGATATAAAAAATAATAAAATTATATAAAA
Found at i:57561 original size:18 final size:19
Alignment explanation
Indices: 57534--57576 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
57524 TTTGGATAAG
* *
57534 ATTATGGATAAGAAA-ATT
1 ATTATTGATAACAAATATT
57552 ATTATTGATAACAAATATT
1 ATTATTGATAACAAATATT
*
57571 TTTATT
1 ATTATT
57577 ATTAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (19 bp):
ATTATTGATAACAAATATT
Found at i:57637 original size:91 final size:86
Alignment explanation
Indices: 57443--57645 Score: 307
Period size: 91 Copynumber: 2.3 Consensus size: 86
57433 TGAAATAAGC
*
57443 ATAAGATTATGGATAAGAAAATTATTCTTGATAACAAATTTTTTTTATTAAATATTTATATTATT
1 ATAAGATTATGGATAAGAAAATTATTATTGATAACAAATTTTTTTTATTAAATATTTATATTATT
*
57508 AAATTTATAATTGATCTTTGG
66 AAATTTATAATTGATCTGTGG
* *
57529 ATAAGATTATGGATAAGAAAATTATTATTGATAACAAATATTTTTATTATTAATTATTTTTTATG
1 ATAAGATTATGGATAAGAAAATTATTATTGATAACAAAT-TTTTT-TTATTAA--A-TATTTATA
57594 TTATTAAATTTATAATTGATCTGTGG
61 TTATTAAATTTATAATTGATCTGTGG
* *
57620 ATAAAATTATGGTTAAGAAAATTATT
1 ATAAGATTATGGATAAGAAAATTATT
57646 TTAAATTTAC
Statistics
Matches: 106, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
86 38 0.36
87 5 0.05
88 7 0.07
90 1 0.01
91 55 0.52
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.47
Consensus pattern (86 bp):
ATAAGATTATGGATAAGAAAATTATTATTGATAACAAATTTTTTTTATTAAATATTTATATTATT
AAATTTATAATTGATCTGTGG
Done.