Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold58
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: 1582273
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 125418 characters in sequence are not A, C, G, or T
File 5 of 10
Found at i:601177 original size:79 final size:79
Alignment explanation
Indices: 601092--601245 Score: 186
Period size: 79 Copynumber: 1.9 Consensus size: 79
601082 TTTCACAATC
* * * * *
601092 GGGGATACGCCAACTCC-GATTTTATTTCC-AAAACACCAATTTCTCATAATTGGGGATACTCTA
1 GGGGATACGCCAACCCCAG-CTTTA-TTCCTAAAACACCAATTTCTCACAATCGGGGATACTCCA
601155 ACCCCGTTATTTCCGA
64 ACCCCGTTATTTCCGA
* * ***
601171 GGGGATACTCCAACCCCAGCTTTATTCCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
1 GGGGATACGCCAACCCCAGCTTTATTCCTAAAACACCAATTTCTCACAATCGGGGATACTCCAAC
601236 CCCGTTATTT
66 CCCGTTATTT
601246 TTGCGAGAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
78 4 0.06
79 58 0.92
80 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GGGGATACGCCAACCCCAGCTTTATTCCTAAAACACCAATTTCTCACAATCGGGGATACTCCAAC
CCCGTTATTTCCGA
Found at i:601285 original size:28 final size:27
Alignment explanation
Indices: 601223--601295 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
601213 CTCACAATCG
*
601223 GGGATACTCCAACCCCGTTATTTTTGC
1 GGGATACTCCAACCCCGTTATTTTTGA
* *
601250 GAGAATACTCCAACTCCGTTATTTTTGAA
1 G-GGATACTCCAACCCCGTTATTTTTG-A
601279 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
601296 ATTTTAGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.03
28 37 0.95
29 1 0.03
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (27 bp):
GGGATACTCCAACCCCGTTATTTTTGA
Found at i:601339 original size:79 final size:79
Alignment explanation
Indices: 601254--601419 Score: 214
Period size: 79 Copynumber: 2.1 Consensus size: 79
601244 TTTTGCGAGA
**
601254 ATACTCCAACTCC-GTTATTTTTGAA-GGGATACTCCAACCCCGATTTTAGTTT-CAAAACATC-
1 ATACTCCAAC-CCTGTTA-TTTCCAAGGGGATACTCCAACCCCGATTTTA-TTTCCAAAACA-CA
* *
601315 AATTTTCTATAATTAGGG
62 AATTTTCCATAATCAGGG
*
601333 ATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAGAACACAAATT
1 ATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACAAATT
601398 TTCCATAATCAGGG
66 TTCCATAATCAGGG
*
601412 ATCCTCCA
1 ATACTCCA
601420 GCCCCGTTGT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
78 11 0.14
79 66 0.86
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (79 bp):
ATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACAAATT
TTCCATAATCAGGG
Found at i:601427 original size:186 final size:186
Alignment explanation
Indices: 601093--601427 Score: 437
Period size: 186 Copynumber: 1.8 Consensus size: 186
601083 TTCACAATCG
* * *
601093 GGGATACGCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCATAATTGGGGATACTCTAACC
1 GGGATACGCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCATAATTAGGGATACTCCAACC
* * *** *
601158 CCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTCCTAAAATATTGATTTCTCACAATCG
66 CCGTTATTTCCAAGGGGATACTCCAACCCCAGCTTTATTCCTAAAACACAAATTTCTCACAATCA
601223 GGGATACTCCAACCCCGTTATTTTTGCGAGAATACTCCAACTCCGTTATTTTTGAA
131 GGGATACTCCAACCCCGTTATTTTTGCGAGAATACTCCAACTCCGTTATTTTTGAA
* *
601279 GGGATACTCCAACCCCGATTTTAGTTT-CAAAACATCAATTT-TCTATAATTAGGGATACTCCAA
1 GGGATACGCCAACCCCGATTTTA-TTTCCAAAACACCAATTTCTC-ATAATTAGGGATACTCCAA
* * * *
601342 CCCTGTTATTTCCAAGGGGATACTCCAACCCC-GATTTTATTTCC-AGAACACAAATTT-TCCAT
64 CCCCGTTATTTCCAAGGGGATACTCCAACCCCAG-CTTTA-TTCCTAAAACACAAATTTCT-CAC
* *
601404 AATCAGGGATCCTCCAGCCCCGTT
126 AATCAGGGATACTCCAACCCCGTT
601428 GTTATCACCC
Statistics
Matches: 127, Mismatches: 17, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
185 4 0.03
186 116 0.91
187 7 0.06
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (186 bp):
GGGATACGCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCATAATTAGGGATACTCCAACC
CCGTTATTTCCAAGGGGATACTCCAACCCCAGCTTTATTCCTAAAACACAAATTTCTCACAATCA
GGGATACTCCAACCCCGTTATTTTTGCGAGAATACTCCAACTCCGTTATTTTTGAA
Found at i:602675 original size:32 final size:32
Alignment explanation
Indices: 602639--602723 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
602629 CATAAATGTA
* * *
602639 GCCTATGCTAACTATTGTAGCTTATTAGCTTG
1 GCCTATGCTAACTATTGTAACTCATTAGCTAG
* *
602671 GCCTATAG-TAACTATTATAACTCGTTAGCTAG
1 GCCTAT-GCTAACTATTGTAACTCATTAGCTAG
* *
602703 GTCTATACTAACTATTGTAAC
1 GCCTATGCTAACTATTGTAAC
602724 CTATTGGCAG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
32 42 0.98
33 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (32 bp):
GCCTATGCTAACTATTGTAACTCATTAGCTAG
Found at i:603173 original size:23 final size:23
Alignment explanation
Indices: 603147--603199 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
603137 TATACTTACC
*
603147 TCTTCCTATTCCAAAAACTTAAA
1 TCTTCCTACTCCAAAAACTTAAA
* *
603170 TCTTCCTCCTCTAAAAACTTAAA
1 TCTTCCTACTCCAAAAACTTAAA
603193 TCTTCCT
1 TCTTCCT
603200 CCAAAACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.30, G:0.00, T:0.38
Consensus pattern (23 bp):
TCTTCCTACTCCAAAAACTTAAA
Found at i:603205 original size:20 final size:20
Alignment explanation
Indices: 603156--603205 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 20
603146 CTCTTCCTAT
603156 TCCAAAAACTTAAATCTTCC
1 TCCAAAAACTTAAATCTTCC
603176 TCCTCTAAAAACTTAAATCTTCC
1 T-C-C-AAAAACTTAAATCTTCC
603199 TCCAAAA
1 TCCAAAA
603206 CAATCAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.19
21 2 0.07
22 2 0.07
23 18 0.67
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (20 bp):
TCCAAAAACTTAAATCTTCC
Found at i:606193 original size:38 final size:38
Alignment explanation
Indices: 606092--606229 Score: 138
Period size: 38 Copynumber: 3.6 Consensus size: 38
606082 GGTTCAAAAT
* *
606092 AAAAATCACTATTATAAACCGGT-G-ACATGATTTAATAC
1 AAAAATCACTATTATTATCCGGTGGCACA-G-TTTAATAC
* * * *
606130 AAAAATCACTATTCTTATTCAGTGGCACAGTTTATTAC
1 AAAAATCACTATTATTATCCGGTGGCACAGTTTAATAC
* * *
606168 AAAAATCACTATTATTATCTGGTGGCACAATTCAATAC
1 AAAAATCACTATTATTATCCGGTGGCACAGTTTAATAC
*
606206 AAAAA-CTACTATTTTTATCCGGTG
1 AAAAATC-ACTATTATTATCCGGTG
606230 CATGGTTCGA
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
37 1 0.01
38 76 0.93
39 2 0.02
40 3 0.04
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.33
Consensus pattern (38 bp):
AAAAATCACTATTATTATCCGGTGGCACAGTTTAATAC
Found at i:607139 original size:19 final size:20
Alignment explanation
Indices: 607115--607153 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
607105 AACTGAAATT
607115 TATATTAT-TTTTAACTAAA
1 TATATTATATTTTAACTAAA
* *
607134 TATATTGTATTTTAGCTAAA
1 TATATTATATTTTAACTAAA
607154 AATAATATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
TATATTATATTTTAACTAAA
Found at i:613516 original size:18 final size:19
Alignment explanation
Indices: 613493--613529 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
613483 AGGTAAGTTT
613493 ATTTATTTAA-ATTTAAAA
1 ATTTATTTAATATTTAAAA
613511 ATTTATTTAATATTTAAAA
1 ATTTATTTAATATTTAAAA
613530 GAGTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTATTTAATATTTAAAA
Found at i:620177 original size:17 final size:18
Alignment explanation
Indices: 620157--620194 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
620147 CTACTTGTAA
*
620157 AAATCAGCTTTTAA-TAT
1 AAATCAGCTTCTAAGTAT
*
620174 AAATCAGGTTCTAAGTAT
1 AAATCAGCTTCTAAGTAT
620192 AAA
1 AAA
620195 AATTCAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
AAATCAGCTTCTAAGTAT
Found at i:620430 original size:57 final size:55
Alignment explanation
Indices: 620253--620434 Score: 162
Period size: 57 Copynumber: 3.3 Consensus size: 55
620243 CTAATTGCTC
* ** * *
620253 TTGATCGCCACCATGACATTATCCTTATCAGTGACTCCAAGTCACC-TA--AACT
1 TTGATCGCCACCATGGCATTATTATTATCAGTGACACCAAGTCACCTTACCAAAT
* * * * *
620305 TTGA-CTGCCACAATGGTATAACTATTA--AGTGACTA-CAAGTCACCTTGCCAAAT
1 TTGATC-GCCACCATGGCATTATTATTATCAGTGAC-ACCAAGTCACCTTACCAAAT
* *
620358 CCTGATTGCCACCATGGCATTATTATTATCAGTGACACCAAGTCACCCTTACCAAAT
1 -TTGATCGCCACCATGGCATTATTATTATCAGTGACACCAAGTCA-CCTTACCAAAT
620415 TATGATCGCCACCATGGCAT
1 T-TGATCGCCACCATGGCAT
620435 CATCAATGAC
Statistics
Matches: 99, Mismatches: 19, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
50 15 0.15
51 2 0.02
52 18 0.18
53 3 0.03
54 20 0.20
55 1 0.01
56 13 0.13
57 27 0.27
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (55 bp):
TTGATCGCCACCATGGCATTATTATTATCAGTGACACCAAGTCACCTTACCAAAT
Found at i:620454 original size:51 final size:51
Alignment explanation
Indices: 620385--620487 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 51
620375 CATTATTATT
* * * *
620385 ATCAGTGACACCAAGTCACCCTTACCAAATTATGATCGCCACCATGGCATC
1 ATCAATGACACCAAGTCACCCTTACCAAAATATAATCGCCACCAAGGCATC
* * *
620436 ATCAATGACGCCAAGTCACGCTTACCAAAATCTAATCGCCACCAAGGCATC
1 ATCAATGACACCAAGTCACCCTTACCAAAATATAATCGCCACCAAGGCATC
620487 A
1 A
620488 CTATTAGTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.34, C:0.33, G:0.14, T:0.19
Consensus pattern (51 bp):
ATCAATGACACCAAGTCACCCTTACCAAAATATAATCGCCACCAAGGCATC
Found at i:627140 original size:33 final size:33
Alignment explanation
Indices: 627103--627169 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
627093 TTCAACGATT
627103 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
627136 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
627169 T
1 T
627170 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:627141 original size:13 final size:13
Alignment explanation
Indices: 627123--627147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
627113 CATAAAATGT
627123 TGTATCGATACAA
1 TGTATCGATACAA
627136 TGTATCGATACA
1 TGTATCGATACA
627148 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:627228 original size:13 final size:13
Alignment explanation
Indices: 627210--627234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
627200 ATTACTCAAA
627210 TGTATCGATACAT
1 TGTATCGATACAT
627223 TGTATCGATACA
1 TGTATCGATACA
627235 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:627299 original size:52 final size:52
Alignment explanation
Indices: 627243--627362 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
627233 CACTGATCTT
* *
627243 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
*
627295 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
627347 TGTATCGATACATGCA
1 TGTATCGATACATGCA
627363 AGTAACTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
Found at i:636635 original size:43 final size:43
Alignment explanation
Indices: 636585--636709 Score: 160
Period size: 43 Copynumber: 2.9 Consensus size: 43
636575 TTTAGGGATA
* * * * *
636585 TTTGCAATTTTTCCATAATAATTTCATACATATTAGGGATCGT
1 TTTGCAATTTTTTCATAATGATTTCATACATATTAAGGAACAT
* *
636628 TTTGCAATTTTTTCATAATGATTTCATAAATATCAAGGAACAT
1 TTTGCAATTTTTTCATAATGATTTCATACATATTAAGGAACAT
* * *
636671 TTTGTAATTTTTTCATAATGATTTAATGCATATTAAGGA
1 TTTGCAATTTTTTCATAATGATTTCATACATATTAAGGA
636710 CTTTAATATA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (43 bp):
TTTGCAATTTTTTCATAATGATTTCATACATATTAAGGAACAT
Found at i:636771 original size:58 final size:57
Alignment explanation
Indices: 636705--636829 Score: 133
Period size: 58 Copynumber: 2.2 Consensus size: 57
636695 AATGCATATT
* **
636705 AAGGACTTTAATATAATTTTATAAATTTTGATGTCATTTAAGTAATTTTCTATGATA
1 AAGGACTTTAATACAATTTTATAAATTTTGATACCATTTAAGTAATTTTCTATGATA
* * * * * * * *
636762 AAGGAACTTTGATGCCATTTTGTGAATTTTGATACCATTTAGGTCATTTTCTATGATCT
1 AAGG-ACTTTAATACAATTTTATAAATTTTGATACCATTTAAGTAATTTTCTATGAT-A
636821 AAGGACTTT
1 AAGGACTTT
636830 TGTGCAAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
57 4 0.07
58 47 0.85
59 4 0.07
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (57 bp):
AAGGACTTTAATACAATTTTATAAATTTTGATACCATTTAAGTAATTTTCTATGATA
Found at i:639089 original size:86 final size:75
Alignment explanation
Indices: 638966--639204 Score: 352
Period size: 75 Copynumber: 3.0 Consensus size: 75
638956 CGTACATTGG
* *
638966 GCACAATGGAGCAAACTATGCCAACCAAAATCCCAAGAAAGACTAGGTTTTAGACATTTACATTT
1 GCACAACGGAGCAAACTATGCCAACCAAAATCTCAAGAAAGACTAGGTTTTAGACATTTACATTT
639031 CTTTAATCTA
66 CTTTAATCTA
639041 GCACAACGGAGCAAACTATGGTTGAACTATGCCAACCAAAATCTCAAGAAAGACTAGGTTTTAGA
1 GCACAACGGAG----C-A------AACTATGCCAACCAAAATCTCAAGAAAGACTAGGTTTTAGA
639106 CATTTACATTTCTTTAATCTA
55 CATTTACATTTCTTTAATCTA
*
639127 GCACAATGGAGCAAACTATGCCAACCAAAATCTCAAGAAAGACTAGGTTTTAGACATTTACATTT
1 GCACAACGGAGCAAACTATGCCAACCAAAATCTCAAGAAAGACTAGGTTTTAGACATTTACATTT
639192 CTTTAATCTA
66 CTTTAATCTA
639202 GCA
1 GCA
639205 TTACTTGCTA
Statistics
Matches: 150, Mismatches: 3, Indels: 22
0.86 0.02 0.13
Matches are distributed among these distances:
75 75 0.50
79 1 0.01
80 1 0.01
81 1 0.01
82 1 0.01
86 71 0.47
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (75 bp):
GCACAACGGAGCAAACTATGCCAACCAAAATCTCAAGAAAGACTAGGTTTTAGACATTTACATTT
CTTTAATCTA
Found at i:641580 original size:21 final size:22
Alignment explanation
Indices: 641542--641587 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
641532 ATCTGTTGAA
* **
641542 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
641563 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
641585 ACT
1 ACT
641588 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:644058 original size:20 final size:20
Alignment explanation
Indices: 644033--644078 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
644023 AAGAATTGAA
*
644033 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
644053 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
644073 GAGGGA
1 GAGGGA
644079 GCCTTTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:646335 original size:2 final size:2
Alignment explanation
Indices: 646328--646364 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
646318 TTAAAAAGTA
646328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
646365 AGTTGCTCAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:646932 original size:16 final size:15
Alignment explanation
Indices: 646911--646941 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
646901 TCGATACATC
646911 ACTGTTCATCACTGTT
1 ACTGTTCAT-ACTGTT
646927 ACTGTTCATACTGTT
1 ACTGTTCATACTGTT
646942 CACGTATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (15 bp):
ACTGTTCATACTGTT
Found at i:647012 original size:18 final size:19
Alignment explanation
Indices: 646986--647023 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
646976 TGTTCATAAC
646986 TATTCA-TGTATCGATACA
1 TATTCAGTGTATCGATACA
*
647004 TATTTATGTGTATCGATACA
1 TATTCA-GTGTATCGATACA
647024 GTGTATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (19 bp):
TATTCAGTGTATCGATACA
Found at i:647029 original size:13 final size:13
Alignment explanation
Indices: 647011--647036 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
647001 ACATATTTAT
647011 GTGTATCGATACA
1 GTGTATCGATACA
647024 GTGTATCGATACA
1 GTGTATCGATACA
647037 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:650822 original size:13 final size:13
Alignment explanation
Indices: 650804--650828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
650794 TTTTCCAGAT
650804 TGTATCGATACAA
1 TGTATCGATACAA
650817 TGTATCGATACA
1 TGTATCGATACA
650829 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:651688 original size:21 final size:21
Alignment explanation
Indices: 651663--651714 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
651653 TTGTATAAAT
651663 TTTGTATTAAAGGGAAGAACA
1 TTTGTATTAAAGGGAAGAACA
*
651684 TTTGTATTAAAGGGAAGAACG
1 TTTGTATTAAAGGGAAGAACA
651705 TTTGTATTAA
1 TTTGTATTAA
651715 GGGGGAGAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (21 bp):
TTTGTATTAAAGGGAAGAACA
Found at i:656201 original size:20 final size:20
Alignment explanation
Indices: 656176--656213 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
656166 AAAACACTTG
*
656176 GAAAATTTTTTTTTAGCTTA
1 GAAAATATTTTTTTAGCTTA
656196 GAAAATATTTTTTTAGCT
1 GAAAATATTTTTTTAGCT
656214 CTAAATAAAC
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:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (20 bp):
GAAAATATTTTTTTAGCTTA
Found at i:658264 original size:20 final size:20
Alignment explanation
Indices: 658221--658272 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
658211 CTTAACTGTT
*
658221 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
658240 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
658260 TGTATCGATACAT
1 TGTATCGATACAT
658273 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:665411 original size:20 final size:20
Alignment explanation
Indices: 665364--665410 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
665354 CAACTTGAGC
* *
665364 TTTTCTTTCTTTGTTTTCCT
1 TTTTTTTTCTTTGTTATCCT
665384 TTTTTTTTCTTT-TTAT-CT
1 TTTTTTTTCTTTGTTATCCT
665402 TTTTATTTT
1 TTTT-TTTT
665411 TAGATGTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.25
19 7 0.29
20 11 0.46
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTTTTTCTTTGTTATCCT
Found at i:665423 original size:19 final size:18
Alignment explanation
Indices: 665399--665442 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
665389 TTTCTTTTTA
665399 TCTTTTTATTTTTAGATG
1 TCTTTTTATTTTTAGATG
665417 TCTTTTTATTTTTAGATG
1 TCTTTTTATTTTTAGATG
665435 TCTTTTTA
1 TCTTTTTA
665443 CATTTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.68
Consensus pattern (18 bp):
TCTTTTTATTTTTAGATG
Found at i:668338 original size:20 final size:20
Alignment explanation
Indices: 668285--668343 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
668275 GATACATTGG
* *
668285 TGTATCGATACATGTATGAA
1 TGTATCGATACATTTATCAA
* *
668305 TGTATCAATACATTTTTCAA
1 TGTATCGATACATTTATCAA
668325 TGTATCGATACATTCTATC
1 TGTATCGATACATT-TATC
668344 TCTTTACCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 29 0.91
21 3 0.09
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTATCAA
Found at i:672267 original size:51 final size:50
Alignment explanation
Indices: 672191--672309 Score: 161
Period size: 51 Copynumber: 2.3 Consensus size: 50
672181 TATTTCTGAG
*
672191 GGGATACTCCAACCCCGATTTTA-TTTCTAAAACA-CTAGTTTTTCACAATC
1 GGGATACTCCAACCCCGATTTTATTTTC-AAAACATC-AATTTTTCACAATC
* *
672241 AGGGATACTCCAACTCTGATTTTATTTTCAAAACATCAATTTTTCACAATC
1 -GGGATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTCACAATC
672292 GAGGATACTCCAACCCCG
1 G-GGATACTCCAACCCCG
672310 TTATTTTCGA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
50 1 0.02
51 54 0.90
52 5 0.08
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (50 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTCACAATC
Found at i:672324 original size:79 final size:79
Alignment explanation
Indices: 672241--672388 Score: 224
Period size: 79 Copynumber: 1.9 Consensus size: 79
672231 TTTCACAATC
* * *
672241 AGGGATACTCCAACTCTGATTTTATTTTCAAAACATCAATTTTTCACAATCGAGGATACTCCAAC
1 AGGGATACTCCAACTCCGACTTTATTTTCAAAACATCAATTTCTCACAATCGAGGATACTCCAAC
672306 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* * ** *
672320 AGGGATACTCCAACTCCGGCTTTATTTTCAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
1 AGGGATACTCCAACTCCGACTTTATTTTCAAAACATCAATTTCTCACAATCGAGGATACTCCAAC
672385 CCCG
66 CCCG
672389 ACCTTATTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
AGGGATACTCCAACTCCGACTTTATTTTCAAAACATCAATTTCTCACAATCGAGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:672397 original size:51 final size:51
Alignment explanation
Indices: 672321--672439 Score: 168
Period size: 51 Copynumber: 2.3 Consensus size: 51
672311 TATTTTCGAA
* * * * *
672321 GGGATACTCCAACTCCGGCTTTATTT-TCAAAATATTGATTTCTCACAATCG
1 GGGATACTCCAACCCCGACCTTATTTCT-AAAACATCGATTTCTCACAATCG
*
672372 GGGATACTCCAACCCCGACCTTATTTCTAAAACATCGATTTTTCACAATCG
1 GGGATACTCCAACCCCGACCTTATTTCTAAAACATCGATTTCTCACAATCG
672423 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
672440 TTATTTTCGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 60 0.98
52 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (51 bp):
GGGATACTCCAACCCCGACCTTATTTCTAAAACATCGATTTCTCACAATCG
Found at i:672455 original size:79 final size:78
Alignment explanation
Indices: 672371--672599 Score: 262
Period size: 79 Copynumber: 2.9 Consensus size: 78
672361 TCTCACAATC
* **
672371 GGGGATACTCCAACCCCGACCTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCTGATTTTATTT-TAAAACATCGATTTTTCACAATCGGGGATACTCCAAC
672436 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * * * * *
672450 GGGGATACTCCAACTCTAATTTTATTTTCAAAATATCGA-TTTTCTAGAATCAGGGATACTCTAA
1 GGGGATACTCCAACCCTGATTTTATTTT-AAAACATCGATTTTTC-ACAATCGGGGATACTCCAA
* *
672514 CCCTGTTATTTTTGA
64 CCCCGTTATTTTCGA
* * * * * *
672529 GGGGATATTCTAACCTTGATTTTATTTTTAGAACATCGATTTTTCATAATCGGGGATACTCCAGC
1 GGGGATACTCCAACCCTGATTTTA-TTTTAAAACATCGATTTTTCACAATCGGGGATACTCCAAC
672594 CCCGTT
65 CCCGTT
672600 GTTATCTCCA
Statistics
Matches: 123, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
78 6 0.05
79 108 0.88
80 9 0.07
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (78 bp):
GGGGATACTCCAACCCTGATTTTATTTTAAAACATCGATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:672516 original size:130 final size:130
Alignment explanation
Indices: 672132--672516 Score: 476
Period size: 130 Copynumber: 3.0 Consensus size: 130
672122 AACCTTGGTT
* * *
672132 TTATTTCCAAAACATCAAATTTTT-ATAATCGGGGATACTCCAATCCCGTTA-TTTCTGAGGGGA
1 TTATTTCTAAAACATC-AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGA
* * * * *
672195 TACTCCAACCCCGATTTTA-TTTCTAAAACACTAGTTTTTC-ACAATCAGGGATACTCCAACTCT
64 TACTCCAACTCCGATTTTATTTTC-AAAATA-TAGATTTTCTACAATCAGGGATACTCCAACCCC
**
672258 GATT
127 GACC
* *
672262 TTATTT-TCAAAACATCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTCGAAGGGAT
1 TTATTTCT-AAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
** * *
672326 ACTCCAACTCCGGCTTTATTTTCAAAATATTGA-TTTCTCACAATCGGGGATACTCCAACCCCGA
65 ACTCCAACTCCGATTTTATTTTCAAAATATAGATTTTCT-ACAATCAGGGATACTCCAACCCCGA
672390 CC
129 CC
*
672392 TTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATA
1 TTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATA
** * * *
672457 CTCCAACTCTAATTTTATTTTCAAAATATCGATTTTCTAGAATCAGGGATACTCTAACCC
66 CTCCAACTCCGATTTTATTTTCAAAATATAGATTTTCTACAATCAGGGATACTCCAACCC
672517 TGTTATTTTT
Statistics
Matches: 220, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
128 4 0.02
129 9 0.04
130 193 0.88
131 14 0.06
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (130 bp):
TTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATA
CTCCAACTCCGATTTTATTTTCAAAATATAGATTTTCTACAATCAGGGATACTCCAACCCCGACC
Found at i:676447 original size:52 final size:52
Alignment explanation
Indices: 676369--676518 Score: 232
Period size: 52 Copynumber: 2.9 Consensus size: 52
676359 CGAAATATGA
*
676369 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* *
676421 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
676473 AAATTTGCCTGCATGTATCGATACA--AAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTTA-AT-AGTGTATCGATACAT
676519 TTGAGTATTG
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.98
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:677374 original size:52 final size:52
Alignment explanation
Indices: 677272--677781 Score: 203
Period size: 43 Copynumber: 9.8 Consensus size: 52
677262 GATATTGGGT
* * * *
677272 TTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCATA-GTCAGCGACATTAGAC
1 TTAAAGATGAG-AAAA--ATGCCAATGTGCTGATTCA-AGGCCAGCAACATTGGAC
* * **
677327 TTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTT
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATT-GGAC
** * *
677380 TTAAAGATGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGAC
1 TTAAAGATGA-GA--AAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * ** ** *
677435 TTAAAGATGAAGATAAGAAAAGTGATAAAGATGCCAAT-ATGTTGATTCACGGCCAACGATATTG
1 TTAAAGATG-AG---A-AAAA-TGCCAATG-TG-C--TGAT-TCAAGGC-CAG-CAAC---ATTG
*
677499 GGC
50 GAC
* * * *
677502 TTAAAGATGAGAAAAAGGATGTCAATGTGCTAATTCAAGGCCAGCTACATTGAAC
1 TTAAAGATGAG-AAAA--ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * * *
677557 TTAAAGATG-GAAAAGGTGCCAATATACTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAA-ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
*
677609 TT-AA-A-G-G-----TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * *
677652 TTAAAGA--AG-AAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* *
677701 TT-AA-A-G-G-----TGCCAATGTGCTAATTCAAGGCCAGCTACATTGGA-
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* ** *
677743 TTTAAGAT--G-AAGGTGCCAATATGCTGATTCAAGGCCAGC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGC
677782 TATATTGGGC
Statistics
Matches: 360, Mismatches: 57, Indels: 83
0.72 0.11 0.17
Matches are distributed among these distances:
42 2 0.01
43 69 0.19
44 4 0.01
45 2 0.01
47 2 0.01
48 26 0.07
49 38 0.11
50 1 0.00
51 3 0.01
52 60 0.17
53 14 0.04
54 7 0.02
55 36 0.10
56 32 0.09
57 3 0.01
58 8 0.02
59 4 0.01
60 5 0.01
61 4 0.01
62 5 0.01
63 7 0.02
64 10 0.03
65 1 0.00
66 2 0.01
67 15 0.04
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (52 bp):
TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
Found at i:677436 original size:108 final size:107
Alignment explanation
Indices: 677247--677444 Score: 238
Period size: 108 Copynumber: 1.8 Consensus size: 107
677237 ACCAATACGT
* * * * *
677247 TGATTCACGACCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCATAG
1 TGATTCAAGACCAACAACATTGGGTTTAAAGATGAGAAAAAGGATGCCAATATGCTGATTCATAG
* * *
677312 TCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGC
66 CCAGCAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGC
* **
677354 TGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATGATGAAGG-TGCCAATATGCTGATTCA-
1 TGATTCAAGACCAACAACATTGGG-TTTAAAGATGA-GAAAAAGGATGCCAATATGCTGATTCAT
* *
677417 AGGCCAGCAATATTGGACTTAAAGATGA
64 A-GCCAGCAACATTAGACTTAAAGATGA
677445 AGATAAGAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
107 21 0.28
108 48 0.64
109 6 0.08
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (107 bp):
TGATTCAAGACCAACAACATTGGGTTTAAAGATGAGAAAAAGGATGCCAATATGCTGATTCATAG
CCAGCAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGC
Found at i:677559 original size:122 final size:123
Alignment explanation
Indices: 677342--677565 Score: 299
Period size: 122 Copynumber: 1.8 Consensus size: 123
677332 GATGAGAAAA
* * **
677342 ATGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATGATGAAGGTGCCAATA
1 ATGCCAATATGCTGATTCAAGGCCAACAACATTGGGTCTTAAAGATGATGAAAAAGGTGCCAATA
* * *
677407 TGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATAAGAAAAGTGATAAAG
66 TGCTAATTCAAGGCCAGCAACATTGAACTTAAAGATGAAGATAAGAAAAGTGATAAAG
* * * * *
677465 ATGCCAATATGTTGATTCACGGCCAACGATATTGGG-CTTAAAGATGA-GAAAAAGGATGTCAAT
1 ATGCCAATATGCTGATTCAAGGCCAACAACATTGGGTCTTAAAGATGATGAAAAAGG-TGCCAAT
* *
677528 GTGCTAATTCAAGGCCAGCTACATTGAACTTAAAGATG
65 ATGCTAATTCAAGGCCAGCAACATTGAACTTAAAGATG
677566 GAAAAGGTGC
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
121 6 0.07
122 49 0.57
123 31 0.36
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (123 bp):
ATGCCAATATGCTGATTCAAGGCCAACAACATTGGGTCTTAAAGATGATGAAAAAGGTGCCAATA
TGCTAATTCAAGGCCAGCAACATTGAACTTAAAGATGAAGATAAGAAAAGTGATAAAG
Found at i:677589 original size:230 final size:231
Alignment explanation
Indices: 677167--677596 Score: 591
Period size: 230 Copynumber: 1.9 Consensus size: 231
677157 GTCTCGTAGT
* * * * * *
677167 GTGCCACTATGCAGATTCAAGGCCTGCCACACTGGACTTAAAGATGATGAGGATGAAGAGCGATA
1 GTGCCAATATGCAGATTCAAGGCCAGCAACACTGGACTTAAAGATGAAGAGGAAGAAAAGCGATA
*
677232 AAAGGACCAATACGTTGATTCACGACCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAA
66 AAAGGACCAATACGTTGATTCACGACCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAA
* * * * *
677297 TGTGCTGATTCATAGTCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCTGATTCAA
131 TGTGCTAATTCATAGCCAGCGACATTAGACTTAAAGATGAGAAAAATGCCAATATACTGATTCAA
677362 GGCCAACAACATTGGGTTTTAAAGATGATGATGAAG
196 GGCCAACAACATTGGGTTTTAAAGATGATGATGAAG
* * * * *
677398 GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGA-TAAGAAAAGTGATA
1 GTGCCAATATGCAGATTCAAGGCCAGCAACACTGGACTTAAAGATGAAGAGGAAGAAAAGCGATA
* * *
677462 AAGATG-CCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
66 AA-AGGACCAATACGTTGATTCACGACCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
* *
677526 ATGTGCTAATTCA-AGGCCAGCTACATT-GAACTTAAAGATG-GAAAAGGTGCCAATATACTGAT
130 ATGTGCTAATTCATA-GCCAGCGACATTAG-ACTTAAAGATGAGAAAA-ATGCCAATATACTGAT
677588 TCAAGGCCA
192 TCAAGGCCA
677597 GCTATATTGG
Statistics
Matches: 173, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
229 7 0.04
230 121 0.70
231 45 0.26
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.23
Consensus pattern (231 bp):
GTGCCAATATGCAGATTCAAGGCCAGCAACACTGGACTTAAAGATGAAGAGGAAGAAAAGCGATA
AAAGGACCAATACGTTGATTCACGACCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAA
TGTGCTAATTCATAGCCAGCGACATTAGACTTAAAGATGAGAAAAATGCCAATATACTGATTCAA
GGCCAACAACATTGGGTTTTAAAGATGATGATGAAG
Found at i:677630 original size:43 final size:44
Alignment explanation
Indices: 677569--677799 Score: 295
Period size: 43 Copynumber: 5.1 Consensus size: 44
677559 AAAGATGGAA
*
677569 AAGGTGCCAATATACTGATTCAAGGCCAGCTATATTGGACTTA-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
* *
677612 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--AG
677658 AAGAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-
1 AAG---GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
* * * *
677704 AAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGATTTAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT---A-G
*
677752 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
677796 AAGG
1 AAGG
677800 GTTGCCATCG
Statistics
Matches: 163, Mismatches: 14, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
43 74 0.45
44 5 0.03
45 2 0.01
46 7 0.04
47 1 0.01
48 37 0.23
49 37 0.23
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (44 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
Found at i:677687 original size:49 final size:48
Alignment explanation
Indices: 677524--677794 Score: 285
Period size: 43 Copynumber: 5.8 Consensus size: 48
677514 AAAAGGATGT
* * * *
677524 CAATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAA-GTGC
* *
677576 CAATATACTGATTCAAGGCCAGCTATATTGGACTT--A-AAG--GTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGC
*
677619 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAAGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG-AAGTGC
*
677668 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AAG--GTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGC
* * * *
677711 CAATGTGCTAATTCAAGGCCAGCTACATTGGA-TTTAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAA-GTGC
* *
677759 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
677795 GAAGGGTTGC
Statistics
Matches: 186, Mismatches: 20, Indels: 29
0.79 0.09 0.12
Matches are distributed among these distances:
42 2 0.01
43 69 0.37
44 1 0.01
45 3 0.02
46 7 0.04
47 1 0.01
48 32 0.17
49 40 0.22
50 1 0.01
52 30 0.16
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGC
Found at i:677702 original size:92 final size:92
Alignment explanation
Indices: 677515--677799 Score: 437
Period size: 92 Copynumber: 3.1 Consensus size: 92
677505 AAGATGAGAA
* * *
677515 AAAGGATGTCAATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGA-AG-AAA-GTGCCAAT
*
677580 ATACTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
*
677611 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAAGTGCCAATATGC
1 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAAGTGCCAATATGC
677676 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * *
677703 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGA-TTTAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAAGTGCCAATATGC
*
677767 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGACTT
677794 AGAAGG
1 A-AAGG
677800 GTTGCCATCG
Statistics
Matches: 178, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
91 48 0.27
92 81 0.46
93 3 0.02
94 1 0.01
95 40 0.22
96 5 0.03
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAAGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:677835 original size:32 final size:31
Alignment explanation
Indices: 677787--677921 Score: 209
Period size: 32 Copynumber: 4.3 Consensus size: 31
677777 CCAGCTATAT
* *
677787 TGGGCTTAGA-AGGGTTGCCATCGACTTGTG
1 TGGGCTTTGAGAGGGTTGCCACCGACTTGTG
677817 TGGGCTTTCGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTT-GAGAGGGTTGCCACCGACTTGTG
*
677849 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTA
1 TGGGCTTT-GAGAGGGTTGCCACCGACTTGTG
677881 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAG-AGGGTTGCCACCGACTTGTG
677913 TGGGCTTTG
1 TGGGCTTTG
677922 GAGAAGGTGA
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
30 7 0.07
31 5 0.05
32 85 0.88
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.30
Consensus pattern (31 bp):
TGGGCTTTGAGAGGGTTGCCACCGACTTGTG
Found at i:678009 original size:33 final size:30
Alignment explanation
Indices: 677930--678411 Score: 198
Period size: 35 Copynumber: 14.7 Consensus size: 30
677920 TGGAGAAGGT
677930 GAAAGA-TGCCACGAAGTTGT-GACTTAAA-
1 GAAAGAGTGCCACG-AGTTGTGGACTTAAAG
*
677958 GAAAG-GTGCCACGAGTTGTGAACTTAAAGG
1 GAAAGAGTGCCACGAGTTGTGGACTTAAA-G
* *
677988 GAAAAGAGTGCCACTGAGTTGTGGGCTTGAAAA
1 G-AAAGAGTGCCAC-GAGTTGTGGACTT-AAAG
678021 GACAAGA-TGCCACGGAGTTGTGGACTTTAAAAG
1 GA-AAGAGTGCCAC-GAGTTGTGGAC-TT-AAAG
*
678054 GAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 GAAAGAGTGCCAC-GAGTTGTGGAC-TT--AAAG
* * *
678088 GAAAAAGGTGCCACGGAATTGTGGGCTTTAAAAAG
1 GAAAGA-GTGCCAC-GAGTTGTGGAC-TT--AAAG
* *
678123 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAG
1 GAAAGA-GTGCCAC-GAGTTGTGGAC-TT-AAAG
*
678157 G-AAG-GTGCCACAGAGTTGTGGGCTTTAAAAAG
1 GAAAGAGTGCCAC-GAGTTGTGGAC-TT--AAAG
* * *
678189 GAAA-AGGTGCCACGGAGTTATGGGCTTTAAAAA
1 GAAAGA-GTGCCAC-GAGTTGTGGAC-TT-AAAG
* *
678222 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAG
1 GAAAGA-GTGCCAC-GAGTTGTGGAC-TT-AAAG
* *
678256 GAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 GAAAGA-GTGCCAC-GAGTTGTGGAC-TT--AAAG
*
678291 GAACA-AGGTGCCACGGAGTTGTGGGCTTTGAAAG
1 GAA-AGA-GTGCCAC-GAGTTGTGGAC-TT-AAAG
*
678325 G-AAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
1 GAAAGAGTGCCAC-GAGTTGTGGAC-TT--AAAG
* * *
678357 GAAAAAGGTGCCATGGAGTTGTGGGCTTTGAAAG
1 GAAAGA-GTGCCA-CGAGTTGTGGAC-TT-AAAG
678391 G-AAG-GTGCCACGGAGTTGTGG
1 GAAAGAGTGCCAC-GAGTTGTGG
678412 GCTTTATAAA
Statistics
Matches: 397, Mismatches: 30, Indels: 51
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.02
28 19 0.05
30 1 0.00
31 62 0.16
32 39 0.10
33 60 0.15
34 103 0.26
35 106 0.27
36 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (30 bp):
GAAAGAGTGCCACGAGTTGTGGACTTAAAG
Found at i:678183 original size:66 final size:65
Alignment explanation
Indices: 677955--678489 Score: 593
Period size: 66 Copynumber: 8.0 Consensus size: 65
677945 GTTGTGACTT
* ** * * *
677955 AAAGAAAGGTGCCAC-GAGTTGTGAAC-TTAAAGGGAAAAGAGTGCCACTGAGTTGTGGGC-TTG
1 AAAGGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAG-GTGCCACGGAGTTGTGGGCTTTA
678017 A
65 A
* * *
678018 AAAGACAAGATGCCACGGAGTTGTGGACTTTAAAAGG-AAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAG-GAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAG-GTGCCACGGAGTTGTGGGCTTT
678082 AA
64 AA
*
678084 AAAGGAAAAAGGTGCCACGGAATTGTGGGCTTTAAAAAGGAAAAAGGTGCCACGGAGTTGTGGGC
1 AAAGG---AAGGTGCCACGGAGTTGTGGGCTTT-AAAAGG-AAAAGGTGCCACGGAGTTGTGGGC
*
678149 TTT-G
61 TTTAA
* *
678153 AAAGGAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAAGGTGCCACGGAGTTATGGGCTTTA
1 AAAGGAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTA
678218 A
65 A
* *
678219 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTT
1 AAAG--GAAGGTGCCACGGAGTTGTGGGCTTTAAAAGG-AAAAGGTGCCACGGAGTTGTGGGCTT
678284 TAA
63 TAA
*
678287 AAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTGAAAGG--AAGGTGCCACGGAGTTGTGGGCTT
1 AAAGG---AAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTT
678350 TAA
63 TAA
* *
678353 AAAGGAAAAAGGTGCCATGGAGTTGTGGGCTTTGAAAGG--AAGGTGCCACGGAGTTGTGGGCTT
1 AAAGG---AAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAGGTGCCACGGAGTTGTGGGC-T
678416 TATAAA
62 T-T-AA
* *
678422 AAAGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGTAAAAGAGTGCCACGGAGTTGTGGGC
1 AAAG--GAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GG-AAAAG-GTGCCACGGAGTTGTGGGC
678487 TTT
61 TTT
678490 GAGCAGAGAT
Statistics
Matches: 419, Mismatches: 26, Indels: 46
0.85 0.05 0.09
Matches are distributed among these distances:
63 4 0.01
64 9 0.02
65 59 0.14
66 134 0.32
67 7 0.02
68 105 0.25
69 50 0.12
70 22 0.05
71 5 0.01
72 5 0.01
73 19 0.05
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (65 bp):
AAAGGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAA
Found at i:678207 original size:168 final size:168
Alignment explanation
Indices: 677995--678491 Score: 743
Period size: 168 Copynumber: 3.0 Consensus size: 168
677985 AGGGAAAAGA
* * * * *
677995 GTGCCACTGAGTTGTGGGC-TTGAAAA-GACAAGATGCCACGGAGTTGTGGACTTTAAAAGGAAA
1 GTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAA
*
678058 GAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGGTGCCACGGAATTGTGGGCTTTAAAAAG
66 GAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
678123 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAG
131 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAG
* *
678161 GTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAAGGTGCCACGGAGTTATGGGCTTTAAAAAGAAA
1 GTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAA
* *
678226 AAGGTGCCACGGAGTTGTGGGCTTT-GAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
66 GA-GTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
*
678290 GGAACAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAG
130 GGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAG
* * *
678329 GTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGGTGCCATGGAGTTGTGGGCTTTGAAAGG-A
1 GTGCCACAGAGTTGTGGGCTTTAAAAAGG-AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * *
678393 AG-GTGCCACGGAGTTGTGGGCTTTATAAAAAAGAACAAGGTGCCACGGAGTTGTGGACTTTAAA
65 AGAGTGCCACGGAGTTGTGGGC-TT-TAAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
* *
678457 AGGGTAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
128 AAGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGA
678492 GCAGAGATTG
Statistics
Matches: 299, Mismatches: 24, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
166 37 0.12
167 8 0.03
168 139 0.46
169 91 0.30
170 24 0.08
ACGTcount: A:0.31, C:0.12, G:0.35, T:0.22
Consensus pattern (168 bp):
GTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAA
GAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAG
Found at i:678250 original size:134 final size:135
Alignment explanation
Indices: 677959--678489 Score: 710
Period size: 134 Copynumber: 3.9 Consensus size: 135
677949 TGACTTAAAG
** * * *
677959 AAAGGTGCCAC-GAGTTGTGAAC-TT-AAAGGGAAAAGAGTGCCACTGAGTTGTGGGC-TTGAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAA
*
678020 AGACAAGATGCCACGGAGTTGTGGACTTTAAAAGGAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
65 AGACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
678085 AAGGAA
130 AAGGAA
* * *
678091 AAAGGTGCCACGGAATTGTGGGCTTTAAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-GAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-GAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
* * * *
678155 AG-GAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGGAAA-AGGTGCCACGGAGTTATGGGCTTTA
65 AGACAAGGTGCCACGGAGTTGTGGACTTT-AAAAGGAAAGA-GTGCCACGGAGTTGTGGGCTTTA
678218 AAAA-GAA
128 AAAAGGAA
678225 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
* *
678290 GGAACAAGGTGCCACGGAGTTGTGGGCTTTGAAAGG-AAG-GTGCCACGGAGTTGTGGGCTTTAA
66 -G-ACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAGAGTGCCACGGAGTTGTGGGCTTTAA
678353 AAAGGAA
129 AAAGGAA
*
678360 AAAGGTGCCATGGAGTTGTGGGCTTTGAAAGG---AAGGTGCCACGGAGTTGTGGGCTTTATAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAAAGGTGCCACGGAGTTGTGGGC-TT-T-AA
678422 AAAGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGTAAAAGAGTGCCACGGAGTTGTGGGC
63 AAAG-ACAAGGTGCCACGGAGTTGTGGACTTTAAAA-GG--AAAGAGTGCCACGGAGTTGTGGGC
678487 TTT
124 TTT
678490 GAGCAGAGAT
Statistics
Matches: 357, Mismatches: 21, Indels: 35
0.86 0.05 0.08
Matches are distributed among these distances:
132 33 0.09
133 43 0.12
134 114 0.32
135 101 0.28
136 17 0.05
137 24 0.07
138 3 0.01
139 22 0.06
ACGTcount: A:0.31, C:0.12, G:0.35, T:0.21
Consensus pattern (135 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
GACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
AGGAA
Found at i:678504 original size:31 final size:31
Alignment explanation
Indices: 678469--678619 Score: 155
Period size: 31 Copynumber: 4.9 Consensus size: 31
678459 GGTAAAAGAG
* * * *
678469 TGCCACGGAGTTGTGGGCTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
* * *
678500 TGCCACTGAGTCATGGACTTTGAAAAAAAGGA-
1 TGCCACTGAGTCGTGGACTTTG-AGAAGA-GAT
*
678532 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGAT
* *
678562 TGCCACTGAGTCGTGGGCTTTGCGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
*
678593 TGCCACTGAGTCGTGGACTTTAAGAAG
1 TGCCACTGAGTCGTGGACTTTGAGAAG
678620 GTATTTGAAG
Statistics
Matches: 99, Mismatches: 15, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
29 2 0.02
30 24 0.24
31 46 0.46
32 25 0.25
33 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:679582 original size:16 final size:16
Alignment explanation
Indices: 679563--679599 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
679553 TTCCTTCTTT
679563 TTTTTTTTTGTTATTG
1 TTTTTTTTTGTTATTG
*
679579 TTTTTTTTTGTTTTTG
1 TTTTTTTTTGTTATTG
679595 TTTTT
1 TTTTT
679600 GTGAAGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (16 bp):
TTTTTTTTTGTTATTG
Found at i:679592 original size:22 final size:21
Alignment explanation
Indices: 679560--679601 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
679550 GTTTTCCTTC
679560 TTTTTTTTTTTTGTTATTGTT
1 TTTTTTTTTTTTGTTATTGTT
*
679581 TTTTTTTGTTTTTGTTTTTGT
1 TTTTTTT-TTTTTGTTATTGT
679602 GAAGATTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (21 bp):
TTTTTTTTTTTTGTTATTGTT
Found at i:679600 original size:6 final size:6
Alignment explanation
Indices: 679561--679601 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
679551 TTTTCCTTCT
* *
679561 TTTTTT TTTTTG TTATTG -TTTT- TTTTTG TTTTTG TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
679602 GAAGATTAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
5 7 0.23
6 23 0.77
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:679662 original size:16 final size:17
Alignment explanation
Indices: 679641--679683 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
679631 CTCACTGAGA
*
679641 TTTTCTGTTT-TGTTTT
1 TTTTCTGTTTCTCTTTT
*
679657 TTTTCTTTTTCTCTTTT
1 TTTTCTGTTTCTCTTTT
*
679674 TTTTGTGTTT
1 TTTTCTGTTT
679684 GGAAAAGAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.81
Consensus pattern (17 bp):
TTTTCTGTTTCTCTTTT
Found at i:686945 original size:52 final size:52
Alignment explanation
Indices: 686867--687016 Score: 214
Period size: 52 Copynumber: 2.9 Consensus size: 52
686857 CAAAATATGA
* *
686867 AAATTTACTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* * *
686919 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
686971 AAATTTGCCTGCATGTATCGATACA--AAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTTA-AT-AGTGTATCGATACAT
687017 TTGAGTAATG
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:687093 original size:33 final size:33
Alignment explanation
Indices: 687056--687122 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
687046 AGTAGCTTAA
687056 ATTGTATCGATAAAAAAATATATGTATCGATAC
1 ATTGTATCGATAAAAAAATATATGTATCGATAC
* * * *
687089 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATAAAAAAATATATGTATCGATAC
687122 A
1 A
687123 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATAAAAAAATATATGTATCGATAC
Found at i:687096 original size:13 final size:13
Alignment explanation
Indices: 687078--687102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
687068 AAAAAATATA
687078 TGTATCGATACAT
1 TGTATCGATACAT
687091 TGTATCGATACA
1 TGTATCGATACA
687103 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:692014 original size:52 final size:52
Alignment explanation
Indices: 691936--692064 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
691926 CGAAATATGA
*
691936 AAATTTGCCTGCATGTATCGATACATTTTGTAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
691988 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
692040 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
692065 AACATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:692075 original size:52 final size:51
Alignment explanation
Indices: 691936--692084 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
691926 CGAAATATGA
* *
691936 AAATTTGCCTGCATGTATCGATACATTTTGTAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-ATTATAGTGTATCGATACATCTGGGC
* *
691988 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-ATTATAGTGTATCGATACATCTGGGC
**
692040 AAATTTGCCTGCATGTATCGATACAAACATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAATTAT-AGTGTATCGATACA
692085 ATGTATCGAT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 2 0.02
52 88 0.98
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACAATTATAGTGTATCGATACATCTGGGC
Found at i:692110 original size:33 final size:33
Alignment explanation
Indices: 692073--692184 Score: 122
Period size: 33 Copynumber: 3.4 Consensus size: 33
692063 CAAACATCAG
692073 TGTATCGATACAATGTATCGATAATTTGAGTAA
1 TGTATCGATACAATGTATCGATAATTTGAGTAA
* * * **
692106 TGTATCGATACATTTTTTCGCAGTAGCTT-A--AA
1 TGTATCGATACAATGTATCG-A-TAATTTGAGTAA
692138 TTGTATCGATACAATGTATCGATACATTTGAGTAA
1 -TGTATCGATACAATGTATCGATA-ATTTGAGTAA
692173 TGTATCGATACA
1 TGTATCGATACA
692185 TTTTTTCGCA
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
31 2 0.03
32 5 0.08
33 35 0.56
34 14 0.23
35 6 0.10
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATAATTTGAGTAA
Found at i:692157 original size:13 final size:13
Alignment explanation
Indices: 692139--692163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
692129 TAGCTTAAAT
692139 TGTATCGATACAA
1 TGTATCGATACAA
692152 TGTATCGATACA
1 TGTATCGATACA
692164 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:692189 original size:66 final size:66
Alignment explanation
Indices: 692073--692218 Score: 283
Period size: 67 Copynumber: 2.2 Consensus size: 66
692063 CAAACATCAG
692073 TGTATCGATACAATGTATCGATAATTTGAGTAATGTATCGATACATTTTTTCGCAGTAGCTTAAA
1 TGTATCGATACAATGTATCGATAATTTGAGTAATGTATCGATACATTTTTTCGCAGTAGCTTAAA
692138 T
66 T
692139 TGTATCGATACAATGTATCGATACATTTGAGTAATGTATCGATACATTTTTTCGCAGTAGCTTAA
1 TGTATCGATACAATGTATCGATA-ATTTGAGTAATGTATCGATACATTTTTTCGCAGTAGCTTAA
692204 AT
65 AT
692206 TGTATCGATACAA
1 TGTATCGATACAA
692219 AACTTATGTA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 23 0.29
67 56 0.71
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (66 bp):
TGTATCGATACAATGTATCGATAATTTGAGTAATGTATCGATACATTTTTTCGCAGTAGCTTAAA
T
Found at i:692215 original size:33 final size:33
Alignment explanation
Indices: 692106--692217 Score: 124
Period size: 33 Copynumber: 3.4 Consensus size: 33
692096 ATTTGAGTAA
692106 TGTATCGATACATTTTTTCGCAGTAGCTTAAAT
1 TGTATCGATACATTTTTTCGCAGTAGCTTAAAT
* * *
692139 TGTATCGATACAATGTATCG-A-TA-CATTTGAGTAA-
1 TGTATCGATACATTTTTTCGCAGTAGC--TT-A--AAT
692173 TGTATCGATACATTTTTTCGCAGTAGCTTAAAT
1 TGTATCGATACATTTTTTCGCAGTAGCTTAAAT
692206 TGTATCGATACA
1 TGTATCGATACA
692218 AAACTTATGT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
30 1 0.02
31 2 0.03
32 5 0.08
33 30 0.47
34 18 0.28
35 5 0.08
36 2 0.03
37 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATTTTTTCGCAGTAGCTTAAAT
Found at i:692230 original size:19 final size:18
Alignment explanation
Indices: 692206--692303 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
692196 TAGCTTAAAT
692206 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
692225 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
692238 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
692257 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
692270 TGTATCAATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
692290 TGTATCGATACAAA
1 TGTATCGATACAAA
692304 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.38
20 12 0.19
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:692243 original size:13 final size:13
Alignment explanation
Indices: 692225--692281 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
692215 ACAAAACTTA
692225 TGTATCGATACAT
1 TGTATCGATACAT
692238 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
692256 ATGTATCGATACAT
1 -TGTATCGATACAT
*
692270 TGTATCAATACA
1 TGTATCGATACA
692282 ACACTTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:692245 original size:32 final size:32
Alignment explanation
Indices: 692204--692301 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
692194 AGTAGCTTAA
*
692204 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
692236 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
692268 ATTGTATCAATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
692301 A
1 A
692302 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 48 0.76
33 15 0.24
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:693217 original size:92 final size:89
Alignment explanation
Indices: 693031--693418 Score: 467
Period size: 92 Copynumber: 4.2 Consensus size: 89
693021 GGCTAGCGAT
* * * * *
693031 ATTGGACTTAAAGATAAAGGTGCTAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG
1 ATTGGACTTAAAGA-GAA--TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--
693096 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
57 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
*
693129 ATTGGACTTAAAGAAGAAATTGCCAATATGCTGATTCACGGCCAGCGATATTGGACTTAAAGGTG
1 ATTGGACTTAAAG-AG-AA-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
693194 CCAATGTGCTGATTCAAGGCCAGCTAC
63 CCAATGTGCTGATTCAAGGCCAGCTAC
*
693221 ATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG
1 ATTGGACTTAAAGA-GAA--TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
*
693286 CCAATGTGCTGATTCAAGGCCAGCTAT
63 CCAATGTGCTGATTCAAGGCCAGCTAC
* *
693313 ATTGGACTTAAAG-G--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAG
1 ATTGGACTTAAAGAGAATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAG
*
693375 GTGCCAATGTGCTGATTCAAGGCCAGCGAC
60 GTGCCAATGTGCTGATTCAAGGCCAGCTAC
693405 ATTGGACTTAAAGA
1 ATTGGACTTAAAGA
693419 TGAAGATGAG
Statistics
Matches: 263, Mismatches: 16, Indels: 27
0.86 0.05 0.09
Matches are distributed among these distances:
86 35 0.13
90 2 0.01
91 3 0.01
92 173 0.66
94 1 0.00
98 46 0.17
99 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (89 bp):
ATTGGACTTAAAGAGAATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCA
ATGTGCTGATTCAAGGCCAGCTAC
Found at i:693283 original size:22 final size:22
Alignment explanation
Indices: 693258--693326 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
693248 ATGCTGATTC
693258 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
693280 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
693301 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
693323 AAGG
1 AAGG
693327 TGCCAATGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:693304 original size:21 final size:21
Alignment explanation
Indices: 693280--693347 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
693270 ATTGGACTTA
693280 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
* * *
693301 AAGGCCAGCTATAT-TG--GACTTA
1 AAGG--TGCCA-ATGTGCTGA-TTC
693323 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
693344 AAGG
1 AAGG
693348 CCAGCGACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATGTGCTGATTC
Found at i:693331 original size:24 final size:24
Alignment explanation
Indices: 693261--693331 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
693251 CTGATTCAAG
693261 GCCAGCTATATTGGACTTAAAGGT
1 GCCAGCTATATTGGACTTAAAGGT
* * ** *
693285 GCCA-ATGTGCT-GA-TTCAA-G-
1 GCCAGCTATATTGGACTTAAAGGT
693304 GCCAGCTATATTGGACTTAAAGGT
1 GCCAGCTATATTGGACTTAAAGGT
693328 GCCA
1 GCCA
693332 ATGTGCTGAT
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.19
22 6 0.19
23 4 0.12
24 8 0.25
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (24 bp):
GCCAGCTATATTGGACTTAAAGGT
Found at i:693420 original size:49 final size:49
Alignment explanation
Indices: 693025--693423 Score: 519
Period size: 49 Copynumber: 8.5 Consensus size: 49
693015 ATATGCGGCT
* * *
693025 AGCGATATTGGACTTAAAGATAAAGGTGCTAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
*
693074 AGCAACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* * ** * *
693123 AGCTACATTGGACTTAAAGAAGAAATTGCCAATATGCTGATTCACGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
*
693172 AGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* *
693215 AGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* *
693264 AGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* *
693307 AGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
693350 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
693399 AGCGACATTGGACTTAAAGATGAAG
1 AGCGACATTGGACTTAAAGATGAAG
693424 ATGAGAAAAG
Statistics
Matches: 315, Mismatches: 23, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
43 118 0.37
45 2 0.01
47 2 0.01
49 193 0.61
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
Found at i:693467 original size:135 final size:135
Alignment explanation
Indices: 693045--693437 Score: 522
Period size: 135 Copynumber: 2.9 Consensus size: 135
693035 GACTTAAAGA
*
693045 TAAAGGTGCTAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGGTGCCAATGTG
1 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGGTGCCAATGTG
* ** *
693110 CTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAATTGCCAATATGCTGATTCACGGCCAGC
66 CTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAA-TGAGAA-A-G-TGATTCAAGGCCA--
*
693175 GATATTGGACT
125 GATATTTGACT
* *
693186 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
1 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGGTGCCAATGTG
* * * * *
693251 CTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTG---CTGATTCAAGGCCAGCTAT
66 CTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AAATGAGAAAGTGATTCAAGGCCAG--AT
*
693313 ATTGGACT
128 ATTTGACT
*
693321 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTG
1 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGGTGCCAATGTG
*
693386 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGAGAAAAGTGAT
66 CTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA-ATGAG-AAAGTGAT
693438 AAAGATGCCA
Statistics
Matches: 225, Mismatches: 19, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
133 1 0.00
134 1 0.00
135 121 0.54
139 4 0.02
141 96 0.43
142 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (135 bp):
TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGGTGCCAATGTG
CTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAATGAGAAAGTGATTCAAGGCCAGATATT
TGACT
Found at i:693554 original size:43 final size:44
Alignment explanation
Indices: 693501--693633 Score: 178
Period size: 49 Copynumber: 2.9 Consensus size: 44
693491 AAAAGGATGT
693501 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGGTGC
* *
693544 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTT----A-GAAGGTGC
* *
693593 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAGAAGG
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGG
693634 GTTGCCACTG
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
43 33 0.42
44 5 0.06
45 1 0.01
47 1 0.01
49 38 0.49
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (44 bp):
CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGGTGC
Found at i:693669 original size:32 final size:29
Alignment explanation
Indices: 693621--693877 Score: 221
Period size: 29 Copynumber: 8.6 Consensus size: 29
693611 CCAGCGATAT
693621 TGGGC-TTAGAAGGGTTGCCACTGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACTGAC-T-TG
*
693651 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACTGAC-T-TG
*
693683 TGGGCTTTGAGAAGGGTTGCCACCGACTTG
1 TGGGCTTT-AGAAGGGTTGCCACTGACTTG
* **
693713 TGTGCGCTTTAGAGGGGATTGCCACCAACTTG
1 TG-G-GCTTTAGAAGGG-TTGCCACTGACTTG
* ** *
693745 TGGGCTTTGGAAAAGATGCCACTGACTTG
1 TGGGCTTTAGAAGGGTTGCCACTGACTTG
* *
693774 TAGGCTTTGGAAAAGGG-TGCCACTGACTTG
1 TGGGCTTT--AGAAGGGTTGCCACTGACTTG
* ** *
693804 TGGGCTTTTGAAAAGATGCCACTGACTTG
1 TGGGCTTTAGAAGGGTTGCCACTGACTTG
* ** *
693833 TGGGCTTTGGAAAAGATGCCACTGACTTG
1 TGGGCTTTAGAAGGGTTGCCACTGACTTG
*
693862 TGGGCTTTTGAAGGGT
1 TGGGCTTTAGAAGGGT
693878 GAGGAATATC
Statistics
Matches: 193, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
28 3 0.02
29 71 0.37
30 37 0.19
31 17 0.09
32 62 0.32
33 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.29
Consensus pattern (29 bp):
TGGGCTTTAGAAGGGTTGCCACTGACTTG
Found at i:693749 original size:62 final size:64
Alignment explanation
Indices: 693621--693753 Score: 195
Period size: 64 Copynumber: 2.1 Consensus size: 64
693611 CCAGCGATAT
* * *
693621 TGGGC-TT-AGAAGGGTTGCCACTGACTTGTGTGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGCGCTTTAGAGAGGGTTGCCACCAACTTGTG
693683 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGCGCTTTAGAG-GGGATTGCCACCAAC-T-TG
1 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGCGCTTTAGAGAGGG-TTGCCACCAACTTGTG
693745 TGGGCTTTG
1 TGGGCTTTG
693754 GAAAAGATGC
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
62 16 0.25
63 6 0.09
64 43 0.66
ACGTcount: A:0.16, C:0.19, G:0.36, T:0.29
Consensus pattern (64 bp):
TGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGCGCTTTAGAGAGGGTTGCCACCAACTTGTG
Found at i:693772 original size:29 final size:29
Alignment explanation
Indices: 693740--693869 Score: 224
Period size: 29 Copynumber: 4.4 Consensus size: 29
693730 ATTGCCACCA
693740 ACTTGTGGGCTTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGGAAAAGATGCCACTG
* *
693769 ACTTGTAGGCTTTGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGGAAAA-GATGCCACTG
*
693799 ACTTGTGGGCTTTTGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGGAAAAGATGCCACTG
693828 ACTTGTGGGCTTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGGAAAAGATGCCACTG
693857 ACTTGTGGGCTTT
1 ACTTGTGGGCTTT
693870 TGAAGGGTGA
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
29 68 0.72
30 26 0.28
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (29 bp):
ACTTGTGGGCTTTGGAAAAGATGCCACTG
Found at i:693803 original size:59 final size:58
Alignment explanation
Indices: 693740--693869 Score: 224
Period size: 59 Copynumber: 2.2 Consensus size: 58
693730 ATTGCCACCA
*
693740 ACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTAGGCTTTGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTAGGCTTTGGAAAA-GATGCCACTG
* *
693799 ACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTAGGCTTTGGAAAAGATGCCACTG
693857 ACTTGTGGGCTTT
1 ACTTGTGGGCTTT
693870 TGAAGGGTGA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
58 22 0.32
59 46 0.68
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (58 bp):
ACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTAGGCTTTGGAAAAGATGCCACTG
Found at i:695325 original size:9 final size:10
Alignment explanation
Indices: 695307--695365 Score: 61
Period size: 9 Copynumber: 6.1 Consensus size: 10
695297 ATCCGGATCC
695307 TTTTTGTTTG
1 TTTTTGTTTG
695317 TTTTT-TTTG
1 TTTTTGTTTG
695326 TTTTTGTTT-
1 TTTTTGTTTG
695335 TTTTTGTTT-
1 TTTTTGTTTG
* *
695344 TATTTATTTGG
1 TTTTTGTTT-G
*
695355 TTTTTTTTTG
1 TTTTTGTTTG
695365 T
1 T
695366 GGAGGACGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
9 25 0.60
10 10 0.24
11 7 0.17
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (10 bp):
TTTTTGTTTG
Found at i:695333 original size:15 final size:15
Alignment explanation
Indices: 695313--695344 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
695303 ATCCTTTTTG
695313 TTTGTTTTTTTTGTT
1 TTTGTTTTTTTTGTT
695328 TTTGTTTTTTTTGTT
1 TTTGTTTTTTTTGTT
695343 TT
1 TT
695345 ATTTATTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTGTTTTTTTTGTT
Found at i:695340 original size:24 final size:23
Alignment explanation
Indices: 695307--695362 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
695297 ATCCGGATCC
* * *
695307 TTTTTGTTTGTTTTTTTTGTTTTTG
1 TTTTT-TTTGTTTTATTT-ATTTGG
695332 TTTTTTTTGTTTTATTTATTTGG
1 TTTTTTTTGTTTTATTTATTTGG
695355 TTTTTTTT
1 TTTTTTTT
695363 TGTGGAGGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 12 0.43
24 11 0.39
25 5 0.18
ACGTcount: A:0.04, C:0.00, G:0.12, T:0.84
Consensus pattern (23 bp):
TTTTTTTTGTTTTATTTATTTGG
Found at i:705957 original size:24 final size:24
Alignment explanation
Indices: 705930--705980 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
705920 CAATCAAACC
705930 TTTGTTTACTCCCATTTTACTAAA
1 TTTGTTTACTCCCATTTTACTAAA
705954 TTTGTTTACTCCCATTTTACTAAA
1 TTTGTTTACTCCCATTTTACTAAA
705978 TTT
1 TTT
705981 ATTAGTCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTGTTTACTCCCATTTTACTAAA
Found at i:707892 original size:52 final size:52
Alignment explanation
Indices: 707814--707942 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
707804 CGAAATATGA
*
707814 AAATTTGCCTGCATGTATCGATACATTTTGTAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
707866 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
707918 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
707943 AACATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:707953 original size:52 final size:51
Alignment explanation
Indices: 707814--707962 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
707804 CGAAATATGA
* *
707814 AAATTTGCCTGCATGTATCGATACATTTTGTAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-ATTATAGTGTATCGATACATCTGGGC
* *
707866 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACA-ATTATAGTGTATCGATACATCTGGGC
**
707918 AAATTTGCCTGCATGTATCGATACAAACATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAATTAT-AGTGTATCGATACA
707963 ATGTATCGAT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
51 2 0.02
52 89 0.98
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACAATTATAGTGTATCGATACATCTGGGC
Found at i:707969 original size:13 final size:13
Alignment explanation
Indices: 707951--707975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
707941 CAAACATCAG
707951 TGTATCGATACAA
1 TGTATCGATACAA
707964 TGTATCGATACA
1 TGTATCGATACA
707976 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:708042 original size:19 final size:18
Alignment explanation
Indices: 708018--708114 Score: 88
Period size: 19 Copynumber: 5.7 Consensus size: 18
708008 TAGCTTAAAT
708018 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
708037 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
708050 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
708069 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
708082 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
708102 TGTATCGATACAA
1 TGTATCGATACAA
708115 CTCGTTGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 25
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.35
20 13 0.20
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:708055 original size:13 final size:13
Alignment explanation
Indices: 708037--708093 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
708027 ACAAAACTTA
708037 TGTATCGATACAT
1 TGTATCGATACAT
708050 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
708068 ATGTATCGATACAT
1 -TGTATCGATACAT
708082 TGTATCGATACA
1 TGTATCGATACA
708094 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:708057 original size:32 final size:32
Alignment explanation
Indices: 708016--708113 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
708006 AGTAGCTTAA
*
708016 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
708048 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
708080 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
708113 A
1 A
708114 ACTCGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 49 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:711341 original size:19 final size:19
Alignment explanation
Indices: 711317--711371 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
711307 AATTCAACAA
711317 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
711336 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
711355 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
711372 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:711448 original size:33 final size:33
Alignment explanation
Indices: 711391--711453 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
711381 GCCAAGGAAA
***
711391 TGTATCGATACATTTTTCTGTGTATCGATAAAT
1 TGTATCGATACATGGATCTGTGTATCGATAAAT
*
711424 TGTATCGATACATGGATCTTTGTATCGATA
1 TGTATCGATACATGGATCTGTGTATCGATA
711454 CATTTGGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATAAAT
Found at i:713982 original size:28 final size:27
Alignment explanation
Indices: 713915--713987 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
713905 CTTCACAATC
* *
713915 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
713942 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
713970 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
713988 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:714032 original size:51 final size:51
Alignment explanation
Indices: 713970--714140 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
713960 TTATTTCTGA
* * *
713970 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
714021 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
714074 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
714126 GAGGATACTCCAACC
1 GGGGATACTCCAACC
714141 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:714159 original size:28 final size:28
Alignment explanation
Indices: 714123--714204 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
714113 ATTTTTCACA
*
714123 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
714151 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
714179 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
714205 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:722502 original size:1 final size:1
Alignment explanation
Indices: 722498--722587 Score: 81
Period size: 1 Copynumber: 90.0 Consensus size: 1
722488 CCTTCTTTTT
* * * * * * * *
722498 AAAAAAAAACAAAAAAATAAAAAAAATAAAAAAAATAAAACAAAAAAAACAAAAACATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
722563 CAAAAACAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
722588 GAGAAAAGAA
Statistics
Matches: 67, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.88, C:0.07, G:0.01, T:0.04
Consensus pattern (1 bp):
A
Found at i:722541 original size:31 final size:29
Alignment explanation
Indices: 722498--722585 Score: 122
Period size: 31 Copynumber: 2.9 Consensus size: 29
722488 CCTTCTTTTT
722498 AAAAAAAAACAAAAAAATAAAAAAAATAAA
1 AAAAAAAAACAAAAAAA-AAAAAAAATAAA
*
722528 AAAAATAAAACAAAAAAAACAAAAACATAAA
1 AAAAA-AAAACAAAAAAAA-AAAAAAATAAA
722559 AAAACAAAAACAAAAAAAGAAAAAAAA
1 AAAA-AAAAACAAAAAAA-AAAAAAAA
722586 AAGAGAAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
30 6 0.12
31 44 0.85
32 2 0.04
ACGTcount: A:0.88, C:0.07, G:0.01, T:0.05
Consensus pattern (29 bp):
AAAAAAAAACAAAAAAAAAAAAAAATAAA
Found at i:722550 original size:40 final size:39
Alignment explanation
Indices: 722499--722585 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 39
722489 CTTCTTTTTA
722499 AAAAAAAACAAAAAAATAAAAAAA-ATAAAAAAAATAAAAC
1 AAAAAAAACAAAAAAATAAAAAAACA-AAAAAAAA-AAAAC
* * *
722539 AAAAAAAACAAAAACATAAAAAAACAAAAACAAAAAAAG
1 AAAAAAAACAAAAAAATAAAAAAACAAAAAAAAAAAAAC
722578 AAAAAAAA
1 AAAAAAAA
722586 AAGAGAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 12 0.28
40 30 0.70
41 1 0.02
ACGTcount: A:0.87, C:0.07, G:0.01, T:0.05
Consensus pattern (39 bp):
AAAAAAAACAAAAAAATAAAAAAACAAAAAAAAAAAAAC
Found at i:722594 original size:12 final size:11
Alignment explanation
Indices: 722498--722602 Score: 74
Period size: 11 Copynumber: 9.1 Consensus size: 11
722488 CCTTCTTTTT
*
722498 AAAAAAAAACA
1 AAAAAAAAAGA
722509 AAAAAATAAA-A
1 AAAAAA-AAAGA
722520 AAAATAAAAA-A
1 AAAA-AAAAAGA
722531 AATAAAACAAA-A
1 AA-AAAA-AAAGA
*
722543 AAAACAAAAACA
1 AAAA-AAAAAGA
722555 TAAAAAAACAA-A
1 -AAAAAAA-AAGA
722567 AACAAAAAAAGA
1 AA-AAAAAAAGA
722579 AAAAAAAAAGA
1 AAAAAAAAAGA
*
722590 GAAAAGAAAAGA
1 -AAAAAAAAAGA
722602 A
1 A
722603 CCTACTTAAG
Statistics
Matches: 82, Mismatches: 1, Indels: 22
0.78 0.01 0.21
Matches are distributed among these distances:
11 38 0.46
12 38 0.46
13 6 0.07
ACGTcount: A:0.86, C:0.06, G:0.05, T:0.04
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:723983 original size:62 final size:60
Alignment explanation
Indices: 723667--724099 Score: 453
Period size: 55 Copynumber: 7.5 Consensus size: 60
723657 CTTTTCACCC
*
723667 TTTAGTCCTCAAAGAGCAGGACGCC-TTTC----AAAGCCCACACAAGTTGATGGCA-TT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTT
* * * * *
723721 TTCCAGTCCTCAAAAAGCAAGATG-C----CTTTTAAAGCCTACACAAGTTGGTGGCACTT
1 TT-TAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTT
* *
723777 TTTAGTCCTCAAGGAGCA-GATCGCC-TTTC----AAAGCCCACACAAGTTGGTGGCATTT
1 TTTAGTCCTCAAAGAGCAGGA-CGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTT
* * * *
723832 TTTAGTCCTCAAAGAGTAGGACGCC-TTTC----AAAGTCCACACAAGCTGGTGGCAC-C
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTT
*
723886 TTTAATCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCA-CTT
* * * * *
723948 TCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAGCCCATAAAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTC-TTTTAAAGCCCACACAAGTTGGTGGCACTT
** * *
724009 TCCAGTCCTCAAAGAGTAGGACGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACTT
724070 TTTAGTCCTCAAAGAGCAGGACGCCTTTTC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTC
724100 CTTCTCTCCT
Statistics
Matches: 318, Mismatches: 39, Indels: 37
0.81 0.10 0.09
Matches are distributed among these distances:
51 1 0.00
54 28 0.09
55 124 0.39
56 8 0.03
59 1 0.00
60 25 0.08
61 80 0.25
62 51 0.16
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (60 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTT
Found at i:724224 original size:86 final size:87
Alignment explanation
Indices: 724067--724329 Score: 284
Period size: 86 Copynumber: 3.0 Consensus size: 87
724057 GTTGGTGGCA
* * * * *
724067 CTTTTTAGTCCTCAAAGAGCAGGACGCC---TTTTCCTTCTCTCCTTTGTCCTCAAAGGGTAGGA
1 CTTTTTAGTCCTCAAAGAGCAAGACGCCTTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAGTAGGA
*
724129 CACATTTCATTTCCTTCTTTTC
66 CGCATTTCATTTCCTTCTTTTC
* * * *
724151 CTTTTTA-TCCTCAAAGAGCATGATGCCTTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGC
1 CTTTTTAGTCCTCAAAGAGCAAGACGCCTTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAGTAGGA
* *
724215 CGCACTTCATTTCTTTCTTTTC
66 CGCATTTCATTTCCTTCTTTTC
* * * * * *
724237 CCTTCTAGT-TTCCAAAGAGCAAGACGCACTTTATTTTCCTTTTTCTTTTGTCCTCAAAGAGTAG
1 CTTTTTAGTCCT-CAAAGAGCAAGACGC-CTTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAGTAG
* *
724301 GACGCATTTCGTTTTCCTTTTTTTC
64 GACGCATTTC-ATTTCCTTCTTTTC
724326 CTTT
1 CTTT
724330 GTCCTCGAAA
Statistics
Matches: 146, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
83 18 0.12
84 7 0.05
86 53 0.36
87 14 0.10
88 40 0.27
89 14 0.10
ACGTcount: A:0.17, C:0.26, G:0.13, T:0.44
Consensus pattern (87 bp):
CTTTTTAGTCCTCAAAGAGCAAGACGCCTTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAGTAGGA
CGCATTTCATTTCCTTCTTTTC
Found at i:724347 original size:44 final size:43
Alignment explanation
Indices: 724074--724348 Score: 196
Period size: 44 Copynumber: 6.4 Consensus size: 43
724064 GCACTTTTTA
* *
724074 GTCCTCAAAGAGCAGGACGC----CTTTTCC-TTCTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTCTTTTCCTTTTTTTCCTTT
* * * * *
724112 GTCCTCAAAGGGTAGGACACATTTCATTTCCTTCTTTTCCTTTTT
1 GTCCTCAAAGAGCAGGACGCATTTCTTTTCCTTTTTTTCC--TTT
* * * * *
724157 ATCCTCAAAGAGCATGATGCCTTT-TTTTTC-TTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTCTTTTCCTTTTTTTCCTTT
* * *
724198 GTCCTCAAAGAGCAGGCCGCACTTCATTT-CTTTCTTTTCCCTTCT
1 GTCCTCAAAGAGCAGGACGCATTTCTTTTCCTTT-TTTT-CCTT-T
* * * *
724243 AGT-TTCCAAAGAGCAAGACGCACTTTATTTTCC--TTTTTCTTTT
1 -GTCCT-CAAAGAGCAGGACGCA-TTTCTTTTCCTTTTTTTCCTTT
*
724286 GTCCTCAAAGAGTAGGACGCATTTCGTTTTCCTTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTC-TTTTCCTTTTTTTCCTTT
724330 GTCCTCGAAA-AGCAGGACG
1 GTCCTC-AAAGAGCAGGACG
724349 TACTCTTTTT
Statistics
Matches: 179, Mismatches: 37, Indels: 36
0.71 0.15 0.14
Matches are distributed among these distances:
38 17 0.09
41 25 0.14
42 33 0.18
43 18 0.10
44 34 0.19
45 29 0.16
46 17 0.09
47 5 0.03
48 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.41
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCATTTCTTTTCCTTTTTTTCCTTT
Found at i:727611 original size:79 final size:77
Alignment explanation
Indices: 727431--727649 Score: 212
Period size: 79 Copynumber: 2.8 Consensus size: 77
727421 TTTCATCTCG
* * * * *
727431 GGGATACTCCAA-CCTCGGTTTTATTTTCAAAACATCAATTTTTCATAATCGGGATACTCCAATC
1 GGGATACTCCAACCCT-AGTTTTATTTCCAAAACACCAATTTTTCACAATAGGGATACTCCAATC
727495 CCGTTATTTCCGA
65 CCGTTATTTCCGA
* * * * *
727508 GGGACACTCCAACCC-CGATTTTATTCCCAAAACACCAATTTTTCACCATTAGGTATACTCCAA-
1 GGGATACTCCAACCCTAG-TTTTATTTCCAAAACACCAATTTTTCA-CAATAGGGATACTCCAAT
*
727571 CCC-TCTCATTTTCGA
64 CCCGT-T-ATTTCCGA
* * * *
727586 GAGGATACTCCAACCCTAGTTTTATTTCTAAAACACTAATTTTCCACAATCGGGGATACTCCAA
1 G-GGATACTCCAACCCTAGTTTTATTTCCAAAACACCAATTTTTCACAAT-AGGGATACTCCAA
727650 CTCTGATTTT
Statistics
Matches: 115, Mismatches: 19, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
76 2 0.02
77 39 0.34
78 26 0.23
79 47 0.41
80 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (77 bp):
GGGATACTCCAACCCTAGTTTTATTTCCAAAACACCAATTTTTCACAATAGGGATACTCCAATCC
CGTTATTTCCGA
Found at i:727649 original size:51 final size:51
Alignment explanation
Indices: 727586--727705 Score: 161
Period size: 51 Copynumber: 2.4 Consensus size: 51
727576 TCATTTTCGA
* *
727586 GAGGATACTCCAACCCT-AGTTTTATTTCTAAAACACTAATTTTCCACAATC
1 GAGGATACTCCAACCCTGA-TTTTATTTCCAAAACACCAATTTTCCACAATC
* * * *
727637 GGGGATACTCCAACTCTGATTTTATTTCCAAAATACCAATTTTTCACAATC
1 GAGGATACTCCAACCCTGATTTTATTTCCAAAACACCAATTTTCCACAATC
*
727688 GAGGATACTCTAACCCTG
1 GAGGATACTCCAACCCTG
727706 TTATTTCATC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 58 0.98
52 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
GAGGATACTCCAACCCTGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:727721 original size:28 final size:28
Alignment explanation
Indices: 727685--727756 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
727675 ATTTTTCACA
* *
727685 ATCGAGGATACTCTAACCCTGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
727713 ATCGAGGATACTCCAACCCCGTTATTT-
1 ATCGAGGATACTCCAACCCCGTTATTTC
727740 -TCGAAGGGATACTCCAA
1 ATCG-A-GGATACTCCAA
727757 TCCTAGCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 3 0.08
27 1 0.03
28 36 0.90
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:727756 original size:158 final size:158
Alignment explanation
Indices: 727562--727891 Score: 375
Period size: 158 Copynumber: 2.1 Consensus size: 158
727552 ACCATTAGGT
*
727562 ATACTCCAACCCTC-TCATTTTCGAGAGGATACTCCAACCCTAGTTTTA-TTTCTAAAACACTAA
1 ATACTCCAACCC-CGTCATTTTCGAGAGGATACTCCAACCCTAGCTTTATTTTC-AAAACACTAA
* * *** *
727625 TTT-TCCACAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAATACCAATTTTTCACAATCG
64 TTTCT-CACAATCGGGGATACTCCAACCCCGACCATATTTCCAAAACACCAATTTTTCACAATCG
*
727689 AGGATACTCTAACCCTGTTA-TTTC-ATCGAGG
128 AGGATACTCCAACCCTGTTATTTTCGAT-GA-G
* * * * *
727720 ATACTCCAACCCCGTTATTTTCGA-AGGGATACTCCAATCCTAGCTTTATTTTCAAAATATTGAT
1 ATACTCCAACCCCGTCATTTTCGAGA-GGATACTCCAACCCTAGCTTTATTTTCAAAACACTAAT
* * * * * * *
727784 TTCTCACAATTGGGGATACTCCAACCCCGGCCATATTTCTAAAGCATCGATTTTTCACAATCGGG
65 TTCTCACAATCGGGGATACTCCAACCCCGACCATATTTCCAAAACACCAATTTTTCACAATCGAG
727849 GATACTCCAACCCTGTTATTTTCGATGAG
130 GATACTCCAACCCTGTTATTTTCGATGAG
*
727878 ATACACCAACCCCG
1 ATACTCCAACCCCG
727892 ATTTTACTTT
Statistics
Matches: 145, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
157 2 0.01
158 130 0.90
159 11 0.08
160 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (158 bp):
ATACTCCAACCCCGTCATTTTCGAGAGGATACTCCAACCCTAGCTTTATTTTCAAAACACTAATT
TCTCACAATCGGGGATACTCCAACCCCGACCATATTTCCAAAACACCAATTTTTCACAATCGAGG
ATACTCCAACCCTGTTATTTTCGATGAG
Found at i:727930 original size:79 final size:79
Alignment explanation
Indices: 727833--728015 Score: 233
Period size: 79 Copynumber: 2.3 Consensus size: 79
727823 TAAAGCATCG
* * * *
727833 ATTTTTCACAATCGGGGATACTCCAACCCTGTTATTTTCGATGAGATACACCAACCCCGATTTTA
1 ATTTTCCATAATCGGGGATACTCCAACCCTATTATTTTCGAGGAGATACACCAACCCCGATTTTA
* *
727898 CTTT-CAGAATATCA
66 -TTTCCAGAACACCA
* * * * * *
727912 ATTTTCTATAATCAGGGATACTTCAACCCTATTATTTTCGAGGGGATACTCCAATCCCGATTTTA
1 ATTTTCCATAATCGGGGATACTCCAACCCTATTATTTTCGAGGAGATACACCAACCCCGATTTTA
*
727977 TTTCCAGAACACCG
66 TTTCCAGAACACCA
727991 ATTTTCCATAATCGGGGATACTCCA
1 ATTTTCCATAATCGGGGATACTCCA
728016 GCCTCGTTGT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 3 0.03
79 84 0.97
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
ATTTTCCATAATCGGGGATACTCCAACCCTATTATTTTCGAGGAGATACACCAACCCCGATTTTA
TTTCCAGAACACCA
Found at i:739269 original size:52 final size:52
Alignment explanation
Indices: 739199--739319 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
739189 GAAAATTTAT
*
739199 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
739251 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
739303 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
739320 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:739332 original size:52 final size:51
Alignment explanation
Indices: 739199--739339 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
739189 GAAAATTTAT
739199 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
739251 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
739303 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
739340 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:739346 original size:13 final size:13
Alignment explanation
Indices: 739328--739352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
739318 CAAAGATCAG
739328 TGTATCGATACAA
1 TGTATCGATACAA
739341 TGTATCGATACA
1 TGTATCGATACA
739353 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:739437 original size:13 final size:13
Alignment explanation
Indices: 739419--739443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
739409 CAAAAAAATA
739419 TGTATCGATACAT
1 TGTATCGATACAT
739432 TGTATCGATACA
1 TGTATCGATACA
739444 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:739439 original size:33 final size:33
Alignment explanation
Indices: 739397--739463 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
739387 AGTAGCTTAA
739397 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
739430 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
739463 A
1 A
739464 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:744085 original size:13 final size:13
Alignment explanation
Indices: 744067--744094 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
744057 ATACAAAGAT
744067 CAATGTATCGATA
1 CAATGTATCGATA
744080 CAATGTATCGATA
1 CAATGTATCGATA
744093 CA
1 CA
744095 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:744186 original size:32 final size:32
Alignment explanation
Indices: 744139--744209 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
744129 AGCTTCGTAG
*
744139 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATATATTGTATCGATACAACACTTATGTAT
*
744171 TGATATATTGTATCGATACAACACTTATGTAT
1 CGATATATTGTATCGATACAACACTTATGTAT
744203 CGATATA
1 CGATATA
744210 GTTACTTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (32 bp):
CGATATATTGTATCGATACAACACTTATGTAT
Found at i:744203 original size:19 final size:19
Alignment explanation
Indices: 744147--744207 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
744137 AGCGATACAT
744147 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
* *
744166 TGTATTGAT---ATA--T-
1 TGTATCGATACAACACTTA
744179 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
744198 TGTATCGATA
1 TGTATCGATA
744208 TAGTTACTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
13 8 0.25
14 1 0.03
16 4 0.12
18 1 0.03
19 18 0.56
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:750415 original size:28 final size:28
Alignment explanation
Indices: 750381--751142 Score: 634
Period size: 28 Copynumber: 27.1 Consensus size: 28
750371 TGTTCATCTC
*
750381 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
750409 TTCAAAGCCCACAAGTTAATGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
750436 CTTCAAAGCCCATAGGTCAGTGGCATCCT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
750465 TTCAAAACCCACAAGTTAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
750492 CTTCAAAGCCCATAGGTCAGTGGCATCTT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
750521 TTCAAAGCCCACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
750548 CTTCAAAGCCCATAGGTCAATGACAACCT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
*
750577 TTCAAAG-CCATAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
750603 CTTCAAAGCCCATAGGTTAGTGGCATCCT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
*
750632 TTCAAAGCCTACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
750659 CTTCAAAGCCCATAGGTCAGTGGCATCCT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
*
750688 TTCAAAGCCCACAAGTTAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
750715 CTTCAAAGCTCACAGGTCAGTGGCATTCT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
750744 TTCAAAGTCTACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
750772 TTCAAAGCCAACAGGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
750800 TTTAAAGTCCACAAGTCAGTGGCA-CCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
** * **
750828 TTTTAATCCCACAAGTTGGTGGCA-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
750855 TTCCAAAACCCACAAGTAAGTGGCACCCAT
1 TT-CAAAGCCCACAAGTCAGTGGCATCC-T
* * *
750885 TT-TAAGCCCACAAGTCGGTGGCA-CTTT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* *
750912 TTCCAAAGCCCACAAGTAAGTGGCACCCT
1 TT-CAAAGCCCACAAGTCAGTGGCATCCT
** * *
750941 TTTTAAGCCCACAAGTC-GATAGCACCCT
1 TTCAAAGCCCACAAGTCAG-TGGCATCCT
* *
750969 TCCAAAGCCCACAAGTAAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
** *
750997 TTTTAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
751025 TCCAAAGCCCATAAGTAAGTGACA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
** * *
751053 TTTTAAGCCCACAAGTCGGTGGCAACCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
751081 TCCAAAGCCCACAGGTTAGTGGCACCTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA--TCCT
* *
751111 TTCAAAGTCCACACAAGTCGGTGGCAACCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
751141 TT
1 TT
751143 TTCAATTCCA
Statistics
Matches: 589, Mismatches: 114, Indels: 60
0.77 0.15 0.08
Matches are distributed among these distances:
26 2 0.00
27 42 0.07
28 476 0.81
29 39 0.07
30 16 0.03
31 2 0.00
32 12 0.02
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:751153 original size:31 final size:33
Alignment explanation
Indices: 751062--751167 Score: 102
Period size: 31 Copynumber: 3.5 Consensus size: 33
751052 TTTTTAAGCC
*
751062 CACAAGTCGGTGGCAA-C-C-TTCCAAAG-CC-
1 CACAAGTCGGTGGCAACCTCTTTTCAAAGTCCA
* **
751090 CACAGGTTAGTGGC-ACCTCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCTCTTTTCAAAGTCCA
*
751122 CACAAGTCGGTGGCAACCT-TTTTC-AATTCCA
1 CACAAGTCGGTGGCAACCTCTTTTCAAAGTCCA
*
751153 CATAAGTCGGTGGCA
1 CACAAGTCGGTGGCA
751168 CTTATTTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.02
28 12 0.19
29 1 0.02
30 7 0.11
31 22 0.35
32 16 0.25
33 4 0.06
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (33 bp):
CACAAGTCGGTGGCAACCTCTTTTCAAAGTCCA
Found at i:752156 original size:20 final size:20
Alignment explanation
Indices: 752131--752255 Score: 81
Period size: 20 Copynumber: 5.8 Consensus size: 20
752121 TTTTACCCAG
752131 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
752151 ATGTATCGATATATTCTGTCTTTTACCCA
1 ATGTATCG--ATA--C-AT-TTTT---CA
752180 GATGTATCGATACA-TTTTCTA
1 -ATGTATCGATACATTTTTC-A
* * * *
752201 ATGTATCGATATATGTATGA
1 ATGTATCGATACATTTTTCA
* *
752221 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
752241 ATGTATCGATACATT
1 ATGTATCGATACATT
752256 CTGTCTCTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
20 50 0.62
21 3 0.04
22 3 0.04
23 4 0.05
24 1 0.01
25 1 0.01
26 5 0.06
28 3 0.04
29 2 0.03
30 8 0.10
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:752196 original size:50 final size:50
Alignment explanation
Indices: 752121--752302 Score: 206
Period size: 50 Copynumber: 3.8 Consensus size: 50
752111 AAAGTCACAT
752121 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATATATTCTGTC
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATATATTCTGTC
752171 TTTTACCCAGATGTATCGATACA-TTTTCTAATGTATCGATATA---TG--
1 TTTTACCCAGATGTATCGATACATTTTTC-AATGTATCGATATATTCTGTC
** * * *
752216 ---TA-TGA-ATGTATTGATACATTCTTCAATGTATCGATACATTCTGTC
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATATATTCTGTC
* *
752261 TCTTTACCCAGATGTATCGATACATTTTTTAATGTATAGATA
1 T-TTTACCCAGATGTATCGATACATTTTTCAATGTATCGATA
752303 AATCTAGTTA
Statistics
Matches: 108, Mismatches: 11, Indels: 25
0.75 0.08 0.17
Matches are distributed among these distances:
40 25 0.23
41 5 0.05
42 2 0.02
43 2 0.02
47 2 0.02
49 7 0.06
50 38 0.35
51 27 0.25
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (50 bp):
TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATATATTCTGTC
Found at i:752257 original size:20 final size:19
Alignment explanation
Indices: 752181--752255 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
752171 TTTTACCCAG
752181 ATGTATCGATACATTTTCTA
1 ATGTATCGATACATTTTC-A
* * *
752201 ATGTATCGATATATGTATGA
1 ATGTATCGATACAT-TTTCA
*
752221 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATT-TTCA
752241 ATGTATCGATACATT
1 ATGTATCGATACATT
752256 CTGTCTCTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.93
21 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:754022 original size:52 final size:52
Alignment explanation
Indices: 753937--754107 Score: 163
Period size: 52 Copynumber: 3.3 Consensus size: 52
753927 TTATTTTCGA
* *
753937 GGGGATACTCCAACCCCGGTTTTA--TCGCTAAAACACTAATTTTTCCTCAATC
1 GGGGATACTCCAA-CCCGGTTTTATTTC-CAAAAACACCAATTTTTCCTCAATC
* * *
753989 GGGGATACTCCAATCCCGGTTTTATTTTC-AAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAA-CCCGGTTTTATTTCCAAAAACACCAATTTTTCC-TCAATC
* * * * *
754041 GGGGATATTCCAACTCCGATTCTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAAC-CCGGTTTTATTTCCAAAAACACCAATTTTTCCTCAATC
*
754093 GAGGATACTCCAACC
1 GGGGATACTCCAACC
754108 TCGTTATTTC
Statistics
Matches: 98, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
51 8 0.08
52 75 0.77
53 10 0.10
54 5 0.05
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCGGTTTTATTTCCAAAAACACCAATTTTTCCTCAATC
Done.