Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003813.1 Hibiscus syriacus cultivar Beakdansim tig00008174_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: 94031
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:606 original size:21 final size:20
Alignment explanation
Indices: 582--622 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
572 TAAATCATTA
582 TCTTAGCTCCTTAATA-TTAGT
1 TCTTAGCT--TTAATACTTAGT
603 TCTTAGCTTTAATACTTAGT
1 TCTTAGCTTTAATACTTAGT
623 AGGATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 5 0.26
21 8 0.42
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (20 bp):
TCTTAGCTTTAATACTTAGT
Found at i:3084 original size:2 final size:2
Alignment explanation
Indices: 3077--3113 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3067 GTTAATTCTT
3077 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3114 TGAGAACCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5460 original size:60 final size:60
Alignment explanation
Indices: 5366--5480 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
5356 TAATTGGATG
*
5366 AATTTGGGGATGAAATTGAAAGATCTAAATGTTTAGGGACTAATTTAGAATGAGATTTAT
1 AATTTGGGGATGAAATTGAAAGATCTAAATGTTTAAGGACTAATTTAGAATGAGATTTAT
* * *
5426 AATTTGGGGATGAAATTTGAATGTTC-ACAA-GTTTAAGGACTAATTTAGACTGAGA
1 AATTTGGGGATGAAA-TTGAAAGATCTA-AATGTTTAAGGACTAATTTAGAATGAGA
5481 GTCATAGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 39 0.80
61 10 0.20
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.34
Consensus pattern (60 bp):
AATTTGGGGATGAAATTGAAAGATCTAAATGTTTAAGGACTAATTTAGAATGAGATTTAT
Found at i:5746 original size:31 final size:31
Alignment explanation
Indices: 5711--5787 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
5701 TCAAAATGCA
5711 TAAGATATGGTCACCTTCGTTTTTATTTAAT
1 TAAGATATGGTCACCTTCGTTTTTATTTAAT
** * **
5742 TAAGATATGGTCATTTTTGTTTTTATTTCTT
1 TAAGATATGGTCACCTTCGTTTTTATTTAAT
* *
5773 TAAGATGTGATCACC
1 TAAGATATGGTCACC
5788 ACGGGTTAAC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (31 bp):
TAAGATATGGTCACCTTCGTTTTTATTTAAT
Found at i:7273 original size:23 final size:24
Alignment explanation
Indices: 7229--7273 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
7219 ATAAATTTAA
* *
7229 TGTATAATAATAAATAATATATAT
1 TGTATAATAATAAACAACATATAT
*
7253 TGTA-AATAATATACAACATAT
1 TGTATAATAATAAACAACATAT
7274 TTATTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (24 bp):
TGTATAATAATAAACAACATATAT
Found at i:7921 original size:25 final size:25
Alignment explanation
Indices: 7885--7935 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
7875 AAGCTTAAAA
* *
7885 TATTTTTTTCATATCATATTTTTAT
1 TATTTTTATCATATAATATTTTTAT
7910 TATTTTTATCATATAATATTTTTAT
1 TATTTTTATCATATAATATTTTTAT
7935 T
1 T
7936 TAAAAATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTTTTATCATATAATATTTTTAT
Found at i:8125 original size:23 final size:20
Alignment explanation
Indices: 8085--8132 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
8075 AAATATGATG
*
8085 TATATTATTTACAGTATAATGT
1 TATATCATTTACAGTAT-AT-T
*
8107 TATATCATTATACATTATATT
1 TATATCATT-TACAGTATATT
8128 TATAT
1 TATAT
8133 GTTGAGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.26
22 10 0.43
23 7 0.30
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (20 bp):
TATATCATTTACAGTATATT
Found at i:14247 original size:30 final size:29
Alignment explanation
Indices: 14186--14395 Score: 231
Period size: 30 Copynumber: 7.1 Consensus size: 29
14176 GATGCATTGT
* *
14186 TGACATCTGCATGGGATAAACTCCCGCTC
1 TGACATCTGCATGGGATAAATTCCCGTTC
*
14215 TGACATCTGTATGGGATAAATTTCCCGTTC
1 TGACATCTGCATGGGATAAA-TTCCCGTTC
* *
14245 TGACATATGCATGGGATAAACTTCTCGTTC
1 TGACATCTGCATGGGATAAA-TTCCCGTTC
* *
14275 TTACATCTGTATGGGATAAACTTCCCGTTC
1 TGACATCTGCATGGGATAAA-TTCCCGTTC
* *
14305 TGACATCTGTAGGGGATAAATTCCTCGTTC
1 TGACATCTGCATGGGATAAATTCC-CGTTC
* * *
14335 TGACATATACATGGGATAAACTCCCTGTTC
1 TGACATCTGCATGGGATAAATTCCC-GTTC
* * * *
14365 TGACATATGCATGGGATTATTTCCCATTC
1 TGACATCTGCATGGGATAAATTCCCGTTC
14394 TG
1 TG
14396 TTTCACTTGG
Statistics
Matches: 155, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
29 29 0.19
30 126 0.81
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (29 bp):
TGACATCTGCATGGGATAAATTCCCGTTC
Found at i:14340 original size:90 final size:89
Alignment explanation
Indices: 14188--14381 Score: 284
Period size: 90 Copynumber: 2.2 Consensus size: 89
14178 TGCATTGTTG
*
14188 ACATCTGCATGGGATAAACTCCCGCTCTGACATCTGTATGGGATAAATTTCCCGTTCTGACATAT
1 ACATCTGCATGGGATAAACTCCCGCTCTGACATCTGTAGGGGATAAATTTCCCGTTCTGACATAT
*
14253 GCATGGGATAAACTTCTCGTTCTT
66 ACATGGGATAAACTTCTCGTTCTT
* *
14277 ACATCTGTATGGGATAAACTTCCCGTTCTGACATCTGTAGGGGATAAA-TTCCTCGTTCTGACAT
1 ACATCTGCATGGGATAAAC-TCCCGCTCTGACATCTGTAGGGGATAAATTTCC-CGTTCTGACAT
* *
14341 ATACATGGGATAAAC-TCCCTGTTCTG
64 ATACATGGGATAAACTTCTC-GTTCTT
*
14367 ACATATGCATGGGAT
1 ACATCTGCATGGGAT
14382 TATTTCCCAT
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
89 25 0.27
90 69 0.73
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (89 bp):
ACATCTGCATGGGATAAACTCCCGCTCTGACATCTGTAGGGGATAAATTTCCCGTTCTGACATAT
ACATGGGATAAACTTCTCGTTCTT
Found at i:18128 original size:30 final size:30
Alignment explanation
Indices: 18087--18183 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
18077 ATTGATGCAT
*
18087 TTCTGACATATGCATGGGATAAACTCCCCG
1 TTCTAACATATGCATGGGATAAACTCCCCG
18117 TTCTAACATATGCATGGGATAAACTCCCCG
1 TTCTAACATATGCATGGGATAAACTCCCCG
* * *
18147 TTCTGACATCTGCATGGGATAAACTCCCAG
1 TTCTAACATATGCATGGGATAAACTCCCCG
18177 TTCTAAC
1 TTCTAAC
18184 TTCTACATGG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (30 bp):
TTCTAACATATGCATGGGATAAACTCCCCG
Found at i:18193 original size:30 final size:30
Alignment explanation
Indices: 18087--18196 Score: 157
Period size: 30 Copynumber: 3.7 Consensus size: 30
18077 ATTGATGCAT
* *
18087 TTCTGACATATGCATGGGATAAACTCCCCG
1 TTCTAACATCTGCATGGGATAAACTCCCCG
*
18117 TTCTAACATATGCATGGGATAAACTCCCCG
1 TTCTAACATCTGCATGGGATAAACTCCCCG
* *
18147 TTCTGACATCTGCATGGGATAAACTCCCAG
1 TTCTAACATCTGCATGGGATAAACTCCCCG
* *
18177 TTCTAACTTCTACATGGGAT
1 TTCTAACATCTGCATGGGAT
18197 TATATCCCCG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 73 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (30 bp):
TTCTAACATCTGCATGGGATAAACTCCCCG
Found at i:18278 original size:49 final size:48
Alignment explanation
Indices: 18208--18341 Score: 189
Period size: 49 Copynumber: 2.8 Consensus size: 48
18198 ATATCCCCGT
* *
18208 TTTATTTT-TGTTAGGATCCTCTATGGAGGGCTAAATTACCATTTTAA
1 TTTATTTTATGTTGGGATCCTCTATGGAGGGCTAAATTACCATTCTAA
18255 TTTATGTTTATGTTGGGATCCTCTATGGAGGGCTAAATTACCATTCTAA
1 TTTAT-TTTATGTTGGGATCCTCTATGGAGGGCTAAATTACCATTCTAA
* * * *
18304 TTTACATTTATGTTGGGATCCTTTACGAAGGGCTAAAT
1 TTTA-TTTTATGTTGGGATCCTCTATGGAGGGCTAAAT
18342 CCCCAGTATG
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
47 5 0.06
48 3 0.04
49 70 0.90
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (48 bp):
TTTATTTTATGTTGGGATCCTCTATGGAGGGCTAAATTACCATTCTAA
Found at i:22376 original size:30 final size:30
Alignment explanation
Indices: 22334--22674 Score: 441
Period size: 30 Copynumber: 11.4 Consensus size: 30
22324 ATGTATTTTA
*
22334 GACATCTGCATGGGATAAACTCCTCGTTCT
1 GACATCTGCATGGGATAAACTCCCCGTTCT
* * * **
22364 AACATTTGCATGGGATAAATTCCCTATTCT
1 GACATCTGCATGGGATAAACTCCCCGTTCT
* * * *
22394 GACTTCTACATGGGATAAACTCCCTGTTGT
1 GACATCTGCATGGGATAAACTCCCCGTTCT
* * *
22424 GACAGCTGCATGGGATAAACTCTCTGTTCT
1 GACATCTGCATGGGATAAACTCCCCGTTCT
22454 GACATCTGCATGGGATAAACTCCCCGTTCT
1 GACATCTGCATGGGATAAACTCCCCGTTCT
* *
22484 GACATATGCATGGGATAAACTCCCTGTTCT
1 GACATCTGCATGGGATAAACTCCCCGTTCT
* *
22514 GACATCTGTATAGGATAAACTCCCCGTTCT
1 GACATCTGCATGGGATAAACTCCCCGTTCT
*
22544 GACATCTGCATAGGATAAACTCCCCGTTCT
1 GACATCTGCATGGGATAAACTCCCCGTTCT
* *
22574 GACATCTGCTTGGGATAAACTCCCCTTTCT
1 GACATCTGCATGGGATAAACTCCCCGTTCT
*
22604 GACATCTGCATGGGATAAATTCCCTC-TTCT
1 GACATCTGCATGGGATAAACTCCC-CGTTCT
* * *
22634 GACATCTGCATGGGATAAACTACTCTTTCT
1 GACATCTGCATGGGATAAACTCCCCGTTCT
*
22664 GATATCTGCAT
1 GACATCTGCAT
22675 AAGATTATAT
Statistics
Matches: 272, Mismatches: 37, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
29 1 0.00
30 270 0.99
31 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (30 bp):
GACATCTGCATGGGATAAACTCCCCGTTCT
Found at i:24097 original size:19 final size:20
Alignment explanation
Indices: 24065--24102 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
24055 TCAAAGTTGA
*
24065 AAATGATTTTATTTTGAAAG
1 AAATGATTTGATTTTGAAAG
24085 AAAT-ATTTGATTTTGAAA
1 AAATGATTTGATTTTGAAA
24103 AACAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (20 bp):
AAATGATTTGATTTTGAAAG
Found at i:28687 original size:68 final size:68
Alignment explanation
Indices: 28578--28715 Score: 258
Period size: 68 Copynumber: 2.0 Consensus size: 68
28568 TTAAGGTGCG
28578 ATTGGGACACCATAAAAACGGGTGATTTTAATAAATATAAATTAAATTGATAAAAGCCTTCCAAT
1 ATTGGGACACCATAAAAACGGGTGATTTTAATAAATATAAATTAAATTGATAAAAGCCTTCCAAT
28643 GAT
66 GAT
* *
28646 ATTGGGACACCATAAAAACGGGTTATTTTAATAAATATAAATTAATTTGATAAAAGCCTTCCAAT
1 ATTGGGACACCATAAAAACGGGTGATTTTAATAAATATAAATTAAATTGATAAAAGCCTTCCAAT
28711 GAT
66 GAT
28714 AT
1 AT
28716 CGCGACACGT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (68 bp):
ATTGGGACACCATAAAAACGGGTGATTTTAATAAATATAAATTAAATTGATAAAAGCCTTCCAAT
GAT
Found at i:30971 original size:16 final size:16
Alignment explanation
Indices: 30893--30973 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
30883 TAGGTTAAAC
30893 TAATATTAAATTAT-T
1 TAATATTAAATTATAT
* *
30908 T-ATATTTAATATATTT
1 TAATATTAAAT-TATAT
**
30924 TAA-AACAAATTA-AT
1 TAATATTAAATTATAT
* *
30938 ATATTCTTAAATTAATAT
1 -TAATATTAAATT-ATAT
30956 TAATATTAAATTATAT
1 TAATATTAAATTATAT
30972 TA
1 TA
30974 GTATATTTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 13
0.67 0.15 0.18
Matches are distributed among these distances:
14 9 0.19
15 8 0.17
16 17 0.35
17 12 0.25
18 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATATTAAATTATAT
Found at i:30992 original size:59 final size:57
Alignment explanation
Indices: 30887--31011 Score: 162
Period size: 59 Copynumber: 2.2 Consensus size: 57
30877 AATATTTAGG
* *
30887 TTAAACTAATATTAAATTATTTATATTTAATATATTTTAAAACAAATTAATATATTC
1 TTAAATTAATATTAAATTAATTATATTTAATATATTTTAAAACAAATTAATATATTC
* **
30944 TTAAATTAATATTAATATTAAATTATA-TTAGTATATTTTTAATTCAAATTAATATATTC
1 TTAAATTAATATTAA-ATT-AATTATATTTAATATA-TTTTAAAACAAATTAATATATTC
*
31003 TCAAATTAA
1 TTAAATTAA
31012 ACTAGTTTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
57 14 0.24
58 10 0.17
59 35 0.59
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (57 bp):
TTAAATTAATATTAAATTAATTATATTTAATATATTTTAAAACAAATTAATATATTC
Found at i:31077 original size:17 final size:18
Alignment explanation
Indices: 31054--31093 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
31044 AAAATAAAAT
31054 TATTTAATTGAAATTTTA
1 TATTTAATTGAAATTTTA
* *
31072 -ATTTAATTTAATTTTTA
1 TATTTAATTGAAATTTTA
31089 TATTT
1 TATTT
31094 TTACACGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTTAATTGAAATTTTA
Found at i:33466 original size:30 final size:30
Alignment explanation
Indices: 33431--33493 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
33421 CCGTTAATAA
* *
33431 ATTGGCATAATTATATATTTGATCTTTAAT
1 ATTGGCATAATTATACATTTGATCATTAAT
*
33461 ATTGGCATAATTATACATTTGGTCATTAAT
1 ATTGGCATAATTATACATTTGATCATTAAT
33491 ATT
1 ATT
33494 TACATATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (30 bp):
ATTGGCATAATTATACATTTGATCATTAAT
Found at i:34076 original size:94 final size:94
Alignment explanation
Indices: 33966--34272 Score: 533
Period size: 94 Copynumber: 3.3 Consensus size: 94
33956 TTATTCGGTT
* * *
33966 AATAAATTTCGATTCGATTAACGGTCAAATAATTTCGATTCGATTAATGGTTAAAGAAAAAAATC
1 AATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGTTTCGATTAATGGTTAAAGAAAAAAATC
* *
34031 GGTTGATTTGGTTTGGTTAATAATTTTCA
66 GGTTAATTTGGTTCGGTTAATAATTTTCA
**
34060 AATAAATTTCGGTTCGATTAATTGTCAAATAATTTTGTTTCGATTAATGGTTAAAGAAAAAAATC
1 AATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGTTTCGATTAATGGTTAAAGAAAAAAATC
34125 GGTTAATTTGGTTCGGTTAATAATTTTCA
66 GGTTAATTTGGTTCGGTTAATAATTTTCA
**
34154 AATAAATTTCGGTTCGATTAATTGTCAAATAATTTTGTTTCGATTAATGGTTAAAGAAAAAAATC
1 AATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGTTTCGATTAATGGTTAAAGAAAAAAATC
34219 GGTTAATTTGGTTCGGTTAATAATTTTCA
66 GGTTAATTTGGTTCGGTTAATAATTTTCA
34248 AATAAATTTCGGTTCGATTAACGGT
1 AATAAATTTCGGTTCGATTAACGGT
34273 TAAAAAAATA
Statistics
Matches: 204, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 204 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (94 bp):
AATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGTTTCGATTAATGGTTAAAGAAAAAAATC
GGTTAATTTGGTTCGGTTAATAATTTTCA
Found at i:34101 original size:26 final size:27
Alignment explanation
Indices: 34051--34107 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
34041 GTTTGGTTAA
*
34051 TAATTTTCAAATAAATTTCGGTTCGAT
1 TAATTGTCAAATAAATTTCGGTTCGAT
* *
34078 TAATTGTCAAAT-AATTTTGTTTCGAT
1 TAATTGTCAAATAAATTTCGGTTCGAT
34104 TAAT
1 TAAT
34108 GGTTAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (27 bp):
TAATTGTCAAATAAATTTCGGTTCGAT
Found at i:34195 original size:26 final size:27
Alignment explanation
Indices: 34145--34201 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
34135 GTTCGGTTAA
*
34145 TAATTTTCAAATAAATTTCGGTTCGAT
1 TAATTGTCAAATAAATTTCGGTTCGAT
* *
34172 TAATTGTCAAAT-AATTTTGTTTCGAT
1 TAATTGTCAAATAAATTTCGGTTCGAT
34198 TAAT
1 TAAT
34202 GGTTAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (27 bp):
TAATTGTCAAATAAATTTCGGTTCGAT
Found at i:34336 original size:166 final size:167
Alignment explanation
Indices: 34140--34439 Score: 521
Period size: 166 Copynumber: 1.8 Consensus size: 167
34130 ATTTGGTTCG
** * *
34140 GTTAATAATTTTCAAATAAATTTCGGTTCGATTAATTGTCAAATAATTTTGTTTCGATTAATGGT
1 GTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATAGT
*
34205 TAAAGAAAAAA-ATCGGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
66 TAAAGAAAAAATATCGGTTAATTTGGTTAGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
34269 CGGTTAAAAAAATAACTTATTTTATTCAGTTAATTCT
131 CGGTTAAAAAAATAACTTATTTTATTCAGTTAATTCT
*
34306 GTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATAGT
1 GTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATAGT
* *
34371 TAAAGAAAAAATTTCGGTTAATTTGGTTAGGTTAATAATTTTCAAATAAATTTCGGTTCGATTTA
66 TAAAGAAAAAATATCGGTTAATTTGGTTAGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
34436 CGGT
131 CGGT
34440 CAAATAATTT
Statistics
Matches: 125, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
166 71 0.57
167 54 0.43
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (167 bp):
GTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATAGT
TAAAGAAAAAATATCGGTTAATTTGGTTAGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
CGGTTAAAAAAATAACTTATTTTATTCAGTTAATTCT
Found at i:34349 original size:260 final size:260
Alignment explanation
Indices: 34046--34540 Score: 823
Period size: 260 Copynumber: 1.9 Consensus size: 260
34036 ATTTGGTTTG
** * *
34046 GTTAATAATTTTCAAATAAATTTCGGTTCGATTAATTGTCAAATAATTTTGTTTCGATTAATGGT
1 GTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATAGT
*
34111 TAAAGAAAAAA-ATCGGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
66 TAAAGAAAAAATATCGGTTAATTTGGTTAGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
** * * * *
34175 TTGTCAAATAATTTTGTTTCGATTAATGGTTAAAGAAAAAAATCGGTTAATTTGGTTCGGTTAAT
131 CGGTCAAATAATTTCGGTTCGATTAAT-GTTAAAG-AAAAAATCGATTAATTTGGTTCGATTAAT
34240 AATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAA-AAAATAACTTATTTTATTCAGTTAATT
194 AATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAATAACTTATTTTATTCAGTTAATT
34304 CT
259 CT
*
34306 GTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATAGT
1 GTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATAGT
* *
34371 TAAAGAAAAAATTTCGGTTAATTTGGTTAGGTTAATAATTTTCAAATAAATTTCGGTTCGATTTA
66 TAAAGAAAAAATATCGGTTAATTTGGTTAGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
*
34436 CGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAATCGATTGATTTGGTTCGATTAATAA
131 CGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAATCGATTAATTTGGTTCGATTAATAA
34501 TTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAA
196 TTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAA
34541 ATTAATTTAT
Statistics
Matches: 218, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
259 63 0.29
260 82 0.38
261 73 0.33
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (260 bp):
GTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATAGT
TAAAGAAAAAATATCGGTTAATTTGGTTAGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
CGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAATCGATTAATTTGGTTCGATTAATAA
TTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAATAACTTATTTTATTCAGTTAATTCT
Found at i:34531 original size:92 final size:94
Alignment explanation
Indices: 34307--34531 Score: 364
Period size: 95 Copynumber: 2.4 Consensus size: 94
34297 GTTAATTCTG
* *
34307 TTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATAGTT
1 TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATAGTT
* *
34372 AAAGAAAAAATTTCGGTTAATTTGGTTAGG
66 AAAGAAAAAA-TTCGATTAATTTGGTTAGA
*
34402 TTAATAATTTTCAAATAAATTTCGGTTCGATTTACGGTCAAATAATTTCGGTTCGATTAAT-GTT
1 TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATAGTT
* *
34466 AAAGAAAAAA-TCGATTGATTTGGTTCGA
66 AAAGAAAAAATTCGATTAATTTGGTTAGA
34494 TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
1 TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
34532 TAAAGAAAAA
Statistics
Matches: 122, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
92 51 0.42
94 13 0.11
95 58 0.48
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.40
Consensus pattern (94 bp):
TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATAGTT
AAAGAAAAAATTCGATTAATTTGGTTAGA
Found at i:36602 original size:5 final size:5
Alignment explanation
Indices: 36592--36696 Score: 210
Period size: 5 Copynumber: 21.0 Consensus size: 5
36582 AAAACGAAGA
36592 TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG
1 TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG
36642 TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG
1 TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG TGATG
36692 TGATG
1 TGATG
36697 ATTAGGTCAC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 100 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
TGATG
Found at i:38291 original size:2 final size:2
Alignment explanation
Indices: 38284--38318 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
38274 TATAAACATC
* *
38284 AG AG AG AG AG GG AG GG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
38319 AAATAATACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41459 original size:31 final size:32
Alignment explanation
Indices: 41413--41473 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
41403 TTTAAAATTT
41413 ATTTCATAATAATTTAATAAA-TTTTAATGACC
1 ATTTCATAATAATTTAA-AAAGTTTTAATGACC
*
41445 ATTTTATAAT-ATTTAAAAAGTTTTAATGA
1 ATTTCATAATAATTTAAAAAGTTTTAATGA
41474 ATGTTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.11
31 15 0.56
32 9 0.33
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (32 bp):
ATTTCATAATAATTTAAAAAGTTTTAATGACC
Found at i:41498 original size:29 final size:30
Alignment explanation
Indices: 41413--41503 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 30
41403 TTTAAAATTT
* *
41413 ATTTCATAATAATTTAATAAATTTTAATGACC
1 ATTTTATAAT-ATTTAA-AAATTTTAATGAAC
*
41445 ATTTTATAATATTTAAAAAGTTTTAATGAAT
1 ATTTTATAATATTTAAAAA-TTTTAATGAAC
* *
41476 GTTTTATAAT-TTCT-AAAATTTTAGTGAA
1 ATTTTATAATATT-TAAAAATTTTAATGAA
41504 AAATATTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.17
30 9 0.17
31 25 0.48
32 9 0.17
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (30 bp):
ATTTTATAATATTTAAAAATTTTAATGAAC
Found at i:41785 original size:13 final size:13
Alignment explanation
Indices: 41767--41803 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
41757 CAGAAGTTAA
41767 AATTATAAAATTT
1 AATTATAAAATTT
41780 AATTATAAAA-TT
1 AATTATAAAATTT
41792 AATTTATAAAAT
1 AA-TTATAAAAT
41804 ATATCACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTATAAAATTT
Found at i:42037 original size:27 final size:27
Alignment explanation
Indices: 41999--42083 Score: 161
Period size: 27 Copynumber: 3.1 Consensus size: 27
41989 CAACGCGAAC
41999 TTCGACTATCGCAATGCGATTTACATA
1 TTCGACTATCGCAATGCGATTTACATA
42026 TTCGACTATCGCAATGCGATTTACATA
1 TTCGACTATCGCAATGCGATTTACATA
*
42053 TTCGACTATCGCATTGCGATTTACATA
1 TTCGACTATCGCAATGCGATTTACATA
42080 TTCG
1 TTCG
42084 CATTGCGATA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.35
Consensus pattern (27 bp):
TTCGACTATCGCAATGCGATTTACATA
Found at i:42590 original size:39 final size:39
Alignment explanation
Indices: 42536--42636 Score: 193
Period size: 39 Copynumber: 2.6 Consensus size: 39
42526 TTTAAGGCTT
42536 AATCCCACATAGTATTGGGAACAAGTGTTGGTAATGCTC
1 AATCCCACATAGTATTGGGAACAAGTGTTGGTAATGCTC
42575 AATCCCACATAGTATTGGGAACAAGTGTTGGTAATGCTC
1 AATCCCACATAGTATTGGGAACAAGTGTTGGTAATGCTC
*
42614 AATCCCACATAGTATTGGAAACA
1 AATCCCACATAGTATTGGGAACA
42637 CTATTGGGAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (39 bp):
AATCCCACATAGTATTGGGAACAAGTGTTGGTAATGCTC
Found at i:42751 original size:6 final size:6
Alignment explanation
Indices: 42735--42766 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
42725 GTCCGTCTTG
42735 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
42767 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:42896 original size:23 final size:20
Alignment explanation
Indices: 42859--42930 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
42849 ATTTTGGACT
42859 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAAT-A
*
42880 ATCGCAACGCGAACTTGGACT-
1 ATCGCAA--CGAACTTGGAATA
*
42901 ATCGCAACGAATTTGGAATA
1 ATCGCAACGAACTTGGAATA
42921 CATCGCAACG
1 -ATCGCAACG
42931 CAAACTTCGA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
19 10 0.23
21 23 0.52
23 11 0.25
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAACTTGGAATA
Found at i:42911 original size:42 final size:42
Alignment explanation
Indices: 42852--42937 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
42842 CGTTGCGATT
*
42852 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCAAAC
* *
42894 TTGGACTATCGCAACGAATTTGGAATACATCGCAACGCAAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCAAAC
42936 TT
1 TT
42938 CGAAGTTCGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCAAAC
Found at i:42916 original size:19 final size:19
Alignment explanation
Indices: 42852--42917 Score: 78
Period size: 19 Copynumber: 3.3 Consensus size: 19
42842 CGTTGCGATT
42852 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
42871 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
42894 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
42913 TTGGA
1 TTGGA
42918 ATACATCGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 15 0.38
21 14 0.35
23 11 0.28
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:52200 original size:3 final size:3
Alignment explanation
Indices: 52192--52222 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
52182 TATTCCGTTG
52192 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
52223 ACTTTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:55933 original size:21 final size:21
Alignment explanation
Indices: 55900--55940 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
55890 TTCTGGGCAA
* *
55900 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
55921 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
55941 ACGAACAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:56864 original size:62 final size:62
Alignment explanation
Indices: 56744--56868 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 62
56734 AGGGTCAAGG
* * * * *
56744 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
56806 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAATC-TATGGACT
1 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAA-CATATGGACT
56868 G
1 G
56869 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 56 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (62 bp):
GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
Found at i:56868 original size:31 final size:31
Alignment explanation
Indices: 56744--56853 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
56734 AGGGTCAAGG
56744 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
56775 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
56806 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
56837 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
56854 AGAATCTATG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:57161 original size:17 final size:17
Alignment explanation
Indices: 57141--57176 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
57131 TATGTGTATG
57141 TATGTATTTACTGTAAT
1 TATGTATTTACTGTAAT
57158 TATGTATTTACTGTAAT
1 TATGTATTTACTGTAAT
57175 TA
1 TA
57177 ATCTGATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (17 bp):
TATGTATTTACTGTAAT
Found at i:57811 original size:206 final size:206
Alignment explanation
Indices: 57453--57865 Score: 799
Period size: 206 Copynumber: 2.0 Consensus size: 206
57443 AGTTGGCACG
*
57453 TAATTAATGTTTTTGAATTGTATATGCTCTGATCGGTTTTGTCAAAAACATGTAAGCTCTGAATA
1 TAATTAATGTTTTTGAATTGTATATGCTCTGATCAGTTTTGTCAAAAACATGTAAGCTCTGAATA
57518 GTTCTGGAAATATTTTGAATAAGTTACATGTACAAAAGTTTTAAATTACTCACTATTTTATACGA
66 GTTCTGGAAATATTTTGAATAAGTTACATGTACAAAAGTTTTAAATTACTCACTATTTTATACGA
*
57583 GTAAATGTTTGAAAAGTCAATGTGATACTTCGGACTCGTATCCGGGTCGGATACGGGTTGGGGGT
131 GTAAATGTTTGAAAAATCAATGTGATACTTCGGACTCGTATCCGGGTCGGATACGGGTTGGGGGT
57648 GTTACATTTAA
196 GTTACATTTAA
*
57659 TAATTAATGTTTTTGAATTGTATATGCTGTGATCAGTTTTGTCAAAAACATGTAAGCTCTGAATA
1 TAATTAATGTTTTTGAATTGTATATGCTCTGATCAGTTTTGTCAAAAACATGTAAGCTCTGAATA
57724 GTTCTGGAAATATTTTGAATAAGTTACATGTACAAAAGTTTTAAATTACTCACTATTTTATACGA
66 GTTCTGGAAATATTTTGAATAAGTTACATGTACAAAAGTTTTAAATTACTCACTATTTTATACGA
57789 GTAAATGTTTGAAAAATCAATGTGATACTTCGGACTCGTATCCGGGTCGGATACGGGTTGGGGGT
131 GTAAATGTTTGAAAAATCAATGTGATACTTCGGACTCGTATCCGGGTCGGATACGGGTTGGGGGT
57854 GTTACATTTAA
196 GTTACATTTAA
57865 T
1 T
57866 GGTATCAGAG
Statistics
Matches: 204, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
206 204 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (206 bp):
TAATTAATGTTTTTGAATTGTATATGCTCTGATCAGTTTTGTCAAAAACATGTAAGCTCTGAATA
GTTCTGGAAATATTTTGAATAAGTTACATGTACAAAAGTTTTAAATTACTCACTATTTTATACGA
GTAAATGTTTGAAAAATCAATGTGATACTTCGGACTCGTATCCGGGTCGGATACGGGTTGGGGGT
GTTACATTTAA
Found at i:60291 original size:21 final size:21
Alignment explanation
Indices: 60265--60309 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
60255 GATTTCTGGG
* *
60265 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
60286 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
60307 CAA
1 CAA
60310 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:61230 original size:62 final size:62
Alignment explanation
Indices: 61110--61234 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 62
61100 AGGGTCGAGG
* * * * *
61110 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
61172 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAATC-TATGGACT
1 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAA-CATATGGACT
61234 G
1 G
61235 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 56 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (62 bp):
GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
Found at i:61234 original size:31 final size:31
Alignment explanation
Indices: 61110--61219 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
61100 AGGGTCGAGG
61110 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
61141 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
61172 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
61203 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
61220 AGAATCTATG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:61527 original size:17 final size:17
Alignment explanation
Indices: 61507--61542 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
61497 TATGTGTATG
61507 TATGTATTTACTGTAAT
1 TATGTATTTACTGTAAT
61524 TATGTATTTACTGTAAT
1 TATGTATTTACTGTAAT
61541 TA
1 TA
61543 ATCTGATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (17 bp):
TATGTATTTACTGTAAT
Found at i:68609 original size:19 final size:19
Alignment explanation
Indices: 68587--68638 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
68577 AACCTGACTT
**
68587 GTTGACTTTGACTTGACCC
1 GTTGACTTTGACTAAACCC
* *
68606 GTTGATTTTGACCAAACCC
1 GTTGACTTTGACTAAACCC
*
68625 ATTGACTTTGACTA
1 GTTGACTTTGACTA
68639 GAGTTGACAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (19 bp):
GTTGACTTTGACTAAACCC
Found at i:75478 original size:39 final size:39
Alignment explanation
Indices: 75424--75501 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
75414 TAGCAGACTG
75424 GCACGAATTGTGACTTGTTATGCTATCTTTAAGGAACGT
1 GCACGAATTGTGACTTGTTATGCTATCTTTAAGGAACGT
75463 GCACGAATTGTGACTTGTTATGCTATCTTTAAGGAACGT
1 GCACGAATTGTGACTTGTTATGCTATCTTTAAGGAACGT
75502 CGGCATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (39 bp):
GCACGAATTGTGACTTGTTATGCTATCTTTAAGGAACGT
Found at i:82999 original size:27 final size:29
Alignment explanation
Indices: 82969--83033 Score: 91
Period size: 27 Copynumber: 2.3 Consensus size: 29
82959 CCTAAACCCG
*
82969 AACCCGACCCA-AATATCACACTT-AAAA
1 AACCCGACCCAGAATATCAAACTTAAAAA
*
82996 AACCC-AACCAGAATATCAAACTTAAAAA
1 AACCCGACCCAGAATATCAAACTTAAAAA
83024 AACCCGACCC
1 AACCCGACCC
83034 GACCCGACCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 4 0.12
27 16 0.50
28 9 0.28
29 3 0.09
ACGTcount: A:0.49, C:0.34, G:0.05, T:0.12
Consensus pattern (29 bp):
AACCCGACCCAGAATATCAAACTTAAAAA
Found at i:83071 original size:32 final size:33
Alignment explanation
Indices: 83035--83098 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
83025 ACCCGACCCG
83035 ACCCGACCCCTAA-TTTTTAAAAAAAAAATCCA
1 ACCCGACCCCTAATTTTTTAAAAAAAAAATCCA
* *
83067 ACCCGATCCTTAATTTTTTTAAAAAAAAAATC
1 ACCCGACCCCTAA-TTTTTTAAAAAAAAAATC
83099 TGACCCGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 11 0.39
34 17 0.61
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.28
Consensus pattern (33 bp):
ACCCGACCCCTAATTTTTTAAAAAAAAAATCCA
Found at i:86673 original size:2 final size:2
Alignment explanation
Indices: 86668--86738 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
86658 CCTTATAACT
86668 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
86710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
86739 GTACGAAAGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:87819 original size:143 final size:144
Alignment explanation
Indices: 87515--87820 Score: 436
Period size: 143 Copynumber: 2.1 Consensus size: 144
87505 TTTGAAGTAT
* * * *
87515 TGATCGGAGATCCCGATCGCCGGTAAAAGGCTAAAAACCGTTCGACTTATTTTCTCCGATCTGCC
1 TGATCGGAGATCCCGATCGCAGGCAAAAGACCAAAAACCGTTCGACTTATTTTCTCCGATC-GCC
* **
87580 ATCGTCCACCGTCTGATCGTTCTGAATTTTCAGTATGTTGTTTGTGATGGTCTCGCGCAACTTTT
65 ATCGTCCACCGTCTGATCGTCCTGAATTTTCAGTATGTTGTTCATGATGGTCTCGCGCAACTTTT
* *
87645 GACCGTTCGGAATGT
130 GACCATTCGGAATGG
* * * *
87660 TAATCGGCA-CTCCCGATCGCAGGCAAGAGACCAAAAACCGTTCGGCTTATTTTCTCCGATC-CC
1 TGATCGG-AGATCCCGATCGCAGGCAAAAGACCAAAAACCGTTCGACTTATTTTCTCCGATCGCC
* *
87723 CTCGTCCACCGTCTGATCGTCCTGAATTTTCAGTATGTTGTTCATGATGGTCTTGCGCAACTTTT
65 ATCGTCCACCGTCTGATCGTCCTGAATTTTCAGTATGTTGTTCATGATGGTCTCGCGCAACTTTT
87788 GACCATTCGGAATGG
130 GACCATTCGGAATGG
*
87803 TGATCGGAGATTCCGATC
1 TGATCGGAGATCCCGATC
87821 AACGACAAGA
Statistics
Matches: 141, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
142 1 0.01
143 88 0.62
145 51 0.36
146 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (144 bp):
TGATCGGAGATCCCGATCGCAGGCAAAAGACCAAAAACCGTTCGACTTATTTTCTCCGATCGCCA
TCGTCCACCGTCTGATCGTCCTGAATTTTCAGTATGTTGTTCATGATGGTCTCGCGCAACTTTTG
ACCATTCGGAATGG
Found at i:88922 original size:15 final size:15
Alignment explanation
Indices: 88874--88922 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
88864 TTTGACCGGT
88874 CCTTCTTCAACCCAA
1 CCTTCTTCAACCCAA
* **
88889 TCCCTCCTTCAACTAAA
1 --CCTTCTTCAACCCAA
88906 CCTTCTTCAACCCAA
1 CCTTCTTCAACCCAA
88921 CC
1 CC
88923 CTTTCTTCTC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 14 0.54
17 12 0.46
ACGTcount: A:0.27, C:0.47, G:0.00, T:0.27
Consensus pattern (15 bp):
CCTTCTTCAACCCAA
Found at i:88930 original size:17 final size:16
Alignment explanation
Indices: 88874--88930 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
88864 TTTGACCGGT
88874 CCTTCTTCAACCCAATC
1 CCTTCTTCAACCCAA-C
* * *
88891 CCTCCTTCAA-CTAAA
1 CCTTCTTCAACCCAAC
88906 CCTTCTTCAACCCAAC
1 CCTTCTTCAACCCAAC
88922 CCTTTCTTC
1 CC-TTCTTC
88931 TCCTTTTTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 9 0.28
16 8 0.25
17 15 0.47
ACGTcount: A:0.23, C:0.46, G:0.00, T:0.32
Consensus pattern (16 bp):
CCTTCTTCAACCCAAC
Found at i:91221 original size:20 final size:20
Alignment explanation
Indices: 91193--91242 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
91183 ACATTTTCTA
*
91193 TAATTATTTATACAAGAAAC
1 TAATCATTTATACAAGAAAC
* *
91213 TAATCATTTATACAATAAAT
1 TAATCATTTATACAAGAAAC
*
91233 TAACCATTTA
1 TAATCATTTA
91243 AGATCATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (20 bp):
TAATCATTTATACAAGAAAC
Done.