Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 26
Found at i:4538016 original size:50 final size:48
Alignment explanation
Indices: 4537953--4538051 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 48
4537943 TGCACATGAA
* *
4537953 GACTTTGGCGCCAAGATGAACAAGCATATCACCATTCGGCCAAGGGAGAT
1 GACTTTGGCGCCAAGATGAACAA-CAGATCACCATTCGACCAAGGG-GAT
*
4538003 GACTTTGGTGCCAAGATGAACAACAGATCACCATTCGACCAAGGGGAT
1 GACTTTGGCGCCAAGATGAACAACAGATCACCATTCGACCAAGGGGAT
4538051 G
1 G
4538052 TTGATTCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 4 0.09
49 20 0.43
50 22 0.48
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.18
Consensus pattern (48 bp):
GACTTTGGCGCCAAGATGAACAACAGATCACCATTCGACCAAGGGGAT
Found at i:4538662 original size:13 final size:13
Alignment explanation
Indices: 4538640--4538675 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
4538630 ATCCATTCAT
4538640 TTAT-ATCTTTAC
1 TTATCATCTTTAC
4538652 TTATCATCTTTAC
1 TTATCATCTTTAC
*
4538665 TTATCTTCTTT
1 TTATCATCTTT
4538676 GTTTGAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATCATCTTTAC
Found at i:4538811 original size:195 final size:195
Alignment explanation
Indices: 4538479--4538873 Score: 718
Period size: 195 Copynumber: 2.0 Consensus size: 195
4538469 CTTATTTGGC
* *
4538479 TTGTTTGAGATACATTTTCATCACCATCATCCATTAAACTTCAACACCATTATCCATCTTTCATT
1 TTGTTTGAGATACATTTTCATCACCATCATCCATTAAACTTCAACACCATCATCCATCTTCCATT
*
4538544 GACAACCACCGACATCATCATCTTCAACATAATTTCGTAGCCAACTCTTTTATTCCTTTATTTCT
66 GACAACCACCAACATCATCATCTTCAACATAATTTCGTAGCCAACTCTTTTATTCCTTTATTTCT
*
4538609 TTTTATATCATTTATTTACTTATCCATTCATTTATATCTTTACTTATCATCTTTACTTATCTTCT
131 TTTTATATCATTTATTTACTTATCCATTCATTTATATCTTTACTTATCACCTTTACTTATCTTCT
*
4538674 TTGTTTGAGATACATTTTCATCACCATCATCCATTCAACTTCAACACCATCATCCATCTTCCATT
1 TTGTTTGAGATACATTTTCATCACCATCATCCATTAAACTTCAACACCATCATCCATCTTCCATT
* *
4538739 GACGACCACCAACATCATCATCTTCAACATAATTTCGTAGCCAACTCTTTTATTCTTTTATTTCT
66 GACAACCACCAACATCATCATCTTCAACATAATTTCGTAGCCAACTCTTTTATTCCTTTATTTCT
*
4538804 TTTTATATCATTTATTTACTTATCCATTCCTTTATATCTTTACTTATCACCTTTACTTATCTTCT
131 TTTTATATCATTTATTTACTTATCCATTCATTTATATCTTTACTTATCACCTTTACTTATCTTCT
4538869 TTGTT
1 TTGTT
4538874 GCAACTATAC
Statistics
Matches: 192, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
195 192 1.00
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.45
Consensus pattern (195 bp):
TTGTTTGAGATACATTTTCATCACCATCATCCATTAAACTTCAACACCATCATCCATCTTCCATT
GACAACCACCAACATCATCATCTTCAACATAATTTCGTAGCCAACTCTTTTATTCCTTTATTTCT
TTTTATATCATTTATTTACTTATCCATTCATTTATATCTTTACTTATCACCTTTACTTATCTTCT
Found at i:4542852 original size:96 final size:96
Alignment explanation
Indices: 4542696--4542887 Score: 235
Period size: 96 Copynumber: 2.0 Consensus size: 96
4542686 GAAGGCGGGT
* * *
4542696 CAAAGTCCTAATTACCACCCCTTAGAATGGATTTGCAAGGCTGGGTCTTTGCTCTCTATAGCACT
1 CAAAGTCCGAATTACCACCCCTTAGAATGGATTTGCAAGACTGAGTCTTTGCTCTCTATAGCACT
*
4542761 GGTTCTTCCTTGGTCAATTCTAGGATACTATC
66 GGTTCTTCCTTGGT-AATTCTAAGATACTATC
* ** * * *
4542793 CAAAGTTCGAATTACCGTCCCTTAGAAT-GATTTGTAAGATTGAGTCTTTGCTCGT-TATAGCAT
1 CAAAGTCCGAATTACCACCCCTTAGAATGGATTTGCAAGACTGAGTCTTTGCTC-TCTATAGCAC
* * *
4542856 TGGTTCTTTCTTGGTTATTCTAAGATATTATC
65 TGGTTCTTCCTTGGTAATTCTAAGATACTATC
4542888 ATTTTCACCA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
95 14 0.17
96 42 0.52
97 25 0.31
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.38
Consensus pattern (96 bp):
CAAAGTCCGAATTACCACCCCTTAGAATGGATTTGCAAGACTGAGTCTTTGCTCTCTATAGCACT
GGTTCTTCCTTGGTAATTCTAAGATACTATC
Found at i:4549392 original size:20 final size:20
Alignment explanation
Indices: 4549367--4549404 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4549357 TAAAACCCCT
*
4549367 TTGAAAACACATGATTTTTA
1 TTGAAAACACATAATTTTTA
*
4549387 TTGAAAATACATAATTTT
1 TTGAAAACACATAATTTT
4549405 AATGAAGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (20 bp):
TTGAAAACACATAATTTTTA
Found at i:4549410 original size:19 final size:20
Alignment explanation
Indices: 4549368--4549410 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
4549358 AAAACCCCTT
* *
4549368 TGAAAACACATGATTTTTAT
1 TGAAAACACATGAATTTTAA
*
4549388 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
4549407 TGAA
1 TGAA
4549411 GATAAATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:4558214 original size:16 final size:16
Alignment explanation
Indices: 4558180--4558213 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4558170 TTCAACTTTC
*
4558180 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTCTCT
4558196 TTTCTTTTTCTTC-CT
1 TTTCTTTTTCTTCTCT
4558211 TTT
1 TTT
4558214 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTCTCT
Found at i:4558241 original size:23 final size:25
Alignment explanation
Indices: 4558202--4558255 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
4558192 TTCTTTTCTT
4558202 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
4558227 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
4558250 TTTCTT
1 TTTCTT
4558256 TGCTCGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:4562170 original size:16 final size:16
Alignment explanation
Indices: 4562136--4562169 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4562126 TTCAACTTTC
*
4562136 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTCTCT
4562152 TTTCTTTTTCTTC-CT
1 TTTCTTTTTCTTCTCT
4562167 TTT
1 TTT
4562170 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTCTCT
Found at i:4565616 original size:18 final size:18
Alignment explanation
Indices: 4565590--4565632 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4565580 ATTGGAGTAT
*
4565590 AAAAA-AAGAAAGAAAAG
1 AAAAAGAAGAAACAAAAG
*
4565607 AAAAAGAAGAATCAAAAG
1 AAAAAGAAGAAACAAAAG
*
4565625 CAAAAGAA
1 AAAAAGAA
4565633 AAGTGAAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAAGAAGAAACAAAAG
Found at i:4569719 original size:24 final size:23
Alignment explanation
Indices: 4569670--4569720 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
4569660 AAATAAAATA
**
4569670 AAAGCACTCAAAAGAAGAAAGTG
1 AAAGCACTCAAAAGAAGAAAAAG
4569693 AAAGCACTCGAAAAGAAGAAAAAG
1 AAAGCACTC-AAAAGAAGAAAAAG
4569717 AAAG
1 AAAG
4569721 AAAGAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.61, C:0.12, G:0.22, T:0.06
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAAAAG
Found at i:4573994 original size:24 final size:23
Alignment explanation
Indices: 4573945--4573995 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
4573935 AAATAAAATA
**
4573945 AAAGCACTCAAAAGAAGAAAGTG
1 AAAGCACTCAAAAGAAGAAAAAG
4573968 AAAGCACTCGAAAAGAAGAAAAAG
1 AAAGCACTC-AAAAGAAGAAAAAG
4573992 AAAG
1 AAAG
4573996 AAAGAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.61, C:0.12, G:0.22, T:0.06
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAAAAG
Found at i:4578877 original size:16 final size:16
Alignment explanation
Indices: 4578858--4578906 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
4578848 GTGTTGTAAC
*
4578858 AAAAGCAACAAGAAGA
1 AAAAGCAAAAAGAAGA
4578874 AAAAG-AAAGAAGAA-A
1 AAAAGCAAA-AAGAAGA
4578889 AAAA-CAAAAAGAAGA
1 AAAAGCAAAAAGAAGA
4578904 AAA
1 AAA
4578907 GACTCCTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 5 0.17
15 14 0.48
16 10 0.34
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGCAAAAAGAAGA
Found at i:4586964 original size:23 final size:24
Alignment explanation
Indices: 4586936--4586995 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
4586926 AAAATCAGCA
4586936 AAGAAAAT-AAATGCACTC-AAAAG
1 AAGAAAATGAAA-GCACTCGAAAAG
* *
4586959 AAGAAATTGAAAGCACTCGGAAAG
1 AAGAAAATGAAAGCACTCGAAAAG
*
4586983 AAGAAAAAGAAAG
1 AAGAAAATGAAAG
4586996 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.60, C:0.10, G:0.20, T:0.10
Consensus pattern (24 bp):
AAGAAAATGAAAGCACTCGAAAAG
Found at i:4588113 original size:24 final size:24
Alignment explanation
Indices: 4588065--4588115 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4588055 TCACTTCAAG
* *
4588065 TTGAAGATTCAATAAACATGTCTT
1 TTGAAGAATCAATAAACATGACTT
* *
4588089 TTGAAGAATCAATAGACGTGACTT
1 TTGAAGAATCAATAAACATGACTT
4588113 TTG
1 TTG
4588116 GTGATGAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (24 bp):
TTGAAGAATCAATAAACATGACTT
Found at i:4592394 original size:21 final size:20
Alignment explanation
Indices: 4592368--4592410 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
4592358 TTTGATAATT
4592368 AAAGAAATT-AAATGGAAATGA
1 AAAG-AATTGAAATGGAAA-GA
4592389 AAAGAATTGAAATGGAAAGA
1 AAAGAATTGAAATGGAAAGA
4592409 AA
1 AA
4592411 TGTTATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (20 bp):
AAAGAATTGAAATGGAAAGA
Found at i:4603410 original size:5 final size:6
Alignment explanation
Indices: 4603395--4603425 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
4603385 CAACTTTGTT
4603395 TTTTTC TTTTTC TTTTTC -TTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
4603426 CCTTTTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:4603416 original size:11 final size:11
Alignment explanation
Indices: 4603395--4603425 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
4603385 CAACTTTGTT
4603395 TTTTTCTTTTTC
1 TTTTTC-TTTTC
4603407 TTTTTCTTTTC
1 TTTTTCTTTTC
4603418 TTTTTCTT
1 TTTTTCTT
4603426 CCTTTTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:4605849 original size:19 final size:19
Alignment explanation
Indices: 4605827--4605873 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
4605817 TTTTAGAATA
*
4605827 CAAAGTGTCTTCTCAACGC
1 CAAAGTGTCTTCTCAAAGC
4605846 CAAAGTGTCTTCTCAAAGC
1 CAAAGTGTCTTCTCAAAGC
4605865 CAAAGTGTC
1 CAAAGTGTC
4605874 CCATAAGTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (19 bp):
CAAAGTGTCTTCTCAAAGC
Found at i:4606363 original size:24 final size:24
Alignment explanation
Indices: 4606336--4606386 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4606326 TGTGGATCAC
* *
4606336 CAAAAGTCACGTTTATTGATTCTT
1 CAAAAGACACGTTTATTGAATCTT
* *
4606360 CAAAAGACATGTTTCTTGAATCTT
1 CAAAAGACACGTTTATTGAATCTT
4606384 CAA
1 CAA
4606387 CTTGAATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (24 bp):
CAAAAGACACGTTTATTGAATCTT
Found at i:4608814 original size:474 final size:473
Alignment explanation
Indices: 4607963--4609260 Score: 1992
Period size: 474 Copynumber: 2.7 Consensus size: 473
4607953 AATGATTCGA
* * * ** *
4607963 CTAGGAAGCTTATTCACAAACAACCCCATGCTTGTTAGGTAGCTCCACACTCAAGCTAACTTGG-
1 CTAGGAAGCTTGTTCACAAAC-AGCCCATGCTTGCTAACTAGCTCCACACTCAAGCTAGCTTGGA
* * * * *
4608027 AGGAGACACATGCATGTCCAAGATGGAGCACATGACCAGCCATCATCCCTTACACAAGGATGCAC
65 AGGAGACACATGCATGCCCAAGATGGAGCACATGACCAGCTATCATCCCATGCACAAGGCTGCAC
*
4608092 CACATGGCTTCCTAGAACACCCATGTGCGTGCCATATGACCAGCCCCATGTGCCTTGCATGTGGT
130 CACATGGCTCCCTAGAACACCCATGTGCGTGCCATATGACCAGCCCCATGTGCCTTGCATGTGGT
* * *
4608157 ATCATTTAAGAGCCAGGATGAAGAGCCCTCCCACTATTCGGCCAAACATCATTTCCCATCCAATT
195 ATCATTT-AGAGCCAAGATGAAGAGCCCTCTCACTATTCGGCCAAGCATCATTTCCCATCCAATT
* *
4608222 TGGCACCAACTTGAAGGGACACAAGAGCTATTCGGCCAAGGGATATTACCCAGCATTTAAACTGA
259 TGGCGCCAACTTGAAGGGACACAAGAGCTATTCGGCCAAGGGATATTACCTAGCATTTAAACTGA
* * * * *
4608287 ACCATTATCTCTATTTAGCATTAAATTATTTTATTTTAAAATGTGACAAGGCCTGGCCGAAACCC
324 ACCATTATCTCTATTTAGTATTAAATTATATCATTTTAAAAGGTCACAAGGCCTGGCCGAAACCC
* *
4608352 ATGTGCATGCCATATGACCAGCCCTAATGTAGTTATAGAGCTGAATATAGTTGAACAAATAGTTA
389 ATGTGCATGCCATATGACCAGCCCTAATATAGTTATAGAGCTGAATATAGCTGAACAAATAGTTA
4608417 TGGAGCTCACAAGGACTCGG
454 TGGAGCTCACAAGGACTCGG
* **
4608437 CTAGGAAGCTTGTTCATAAACAGCCCATGCTTGCTAACTAGCTCCACACAAAAGCTAGCTTGGAA
1 CTAGGAAGCTTGTTCACAAACAGCCCATGCTTGCTAACTAGCTCCACACTCAAGCTAGCTTGGAA
4608502 GGAGACACATGCATGCCCAAGATGGAGCACATGACCAGCTATCATCCCATGCACAAGGCTGCACC
66 GGAGACACATGCATGCCCAAGATGGAGCACATGACCAGCTATCATCCCATGCACAAGGCTGCACC
*
4608567 ACATGGCTCCCTAGAACACCCATGTGCGTGCCATATGACCAGCCCCATGTGCCTTGCATATGGTA
131 ACATGGCTCCCTAGAACACCCATGTGCGTGCCATATGACCAGCCCCATGTGCCTTGCATGTGGTA
*
4608632 TCGTTTAGGAGCCAAGATGAAGAGCCCTCTCACTATTCGGCCAAGCATCATTTCCCATCCAATTT
196 TCATTTA-GAGCCAAGATGAAGAGCCCTCTCACTATTCGGCCAAGCATCATTTCCCATCCAATTT
* *
4608697 GGCGCCAACTTGAAGGGACACAAGAGCTATTCGGCCAAGGGATATCACCTAGCTTTTAAACTGAA
260 GGCGCCAACTTGAAGGGACACAAGAGCTATTCGGCCAAGGGATATTACCTAGCATTTAAACTGAA
*
4608762 CCATTATCTCTATTTAGTATTAAATTATATCATTTTAAAAGGTCATAAGGCCTGGCCGAAACCCA
325 CCATTATCTCTATTTAGTATTAAATTATATCATTTTAAAAGGTCACAAGGCCTGGCCGAAACCCA
** * * * *
4608827 TGTGTGTGCCATATGACCAGCCCTCATATAGTTATGGAGCTGAATGTAGCTGAACATATAGTTAT
390 TGTGCATGCCATATGACCAGCCCTAATATAGTTATAGAGCTGAATATAGCTGAACAAATAGTTAT
4608892 GGAGCTCACAAGGACTCGG
455 GGAGCTCACAAGGACTCGG
4608911 CTAGGAAGCTTGTTCACAAACAGCCCATGCTTGCTAACTAGCTCCACACTCAAGCTAGCTTGGAA
1 CTAGGAAGCTTGTTCACAAACAGCCCATGCTTGCTAACTAGCTCCACACTCAAGCTAGCTTGGAA
* * *
4608976 TGAGACACAAGCATGCCCAAGATGGAGCACATGACCAGCTATCATACCATGCACAAGGCTGCACC
66 GGAGACACATGCATGCCCAAGATGGAGCACATGACCAGCTATCATCCCATGCACAAGGCTGCACC
* * *
4609041 ACAAGGCTCCCTAGAACACCCATGTGCGTGCCATATGATCAGTCCTCATGTGCCTTGCATGTGGT
131 ACATGGCTCCCTAGAACACCCATGTGCGTGCCATATGACCAG-CCCCATGTGCCTTGCATGTGGT
* ** * * *
4609106 ATCATTTAGACGCCAAGATGAAGAGCCCTTTTC-CTATTCGATCAAGCATAATCTCCAATCCAAT
195 ATCATTTAGA-GCCAAGATGAAGAGCCC-TCTCACTATTCGGCCAAGCATCATTTCCCATCCAAT
* * * * *
4609170 TTAGCGCCAACTTGAAGGGACAAAAGAGCTATTCGGCCAAGGGTTATTACCCT-CCATTTAAATT
258 TTGGCGCCAACTTGAAGGGACACAAGAGCTATTCGGCCAAGGGATATTA-CCTAGCATTTAAACT
*
4609234 GAACCATCATCTCTATTT-GTAATTAAA
322 GAACCATTATCTCTATTTAGT-ATTAAA
4609261 ATATGACTTT
Statistics
Matches: 754, Mismatches: 63, Indels: 13
0.91 0.08 0.02
Matches are distributed among these distances:
473 36 0.05
474 566 0.75
475 146 0.19
476 6 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (473 bp):
CTAGGAAGCTTGTTCACAAACAGCCCATGCTTGCTAACTAGCTCCACACTCAAGCTAGCTTGGAA
GGAGACACATGCATGCCCAAGATGGAGCACATGACCAGCTATCATCCCATGCACAAGGCTGCACC
ACATGGCTCCCTAGAACACCCATGTGCGTGCCATATGACCAGCCCCATGTGCCTTGCATGTGGTA
TCATTTAGAGCCAAGATGAAGAGCCCTCTCACTATTCGGCCAAGCATCATTTCCCATCCAATTTG
GCGCCAACTTGAAGGGACACAAGAGCTATTCGGCCAAGGGATATTACCTAGCATTTAAACTGAAC
CATTATCTCTATTTAGTATTAAATTATATCATTTTAAAAGGTCACAAGGCCTGGCCGAAACCCAT
GTGCATGCCATATGACCAGCCCTAATATAGTTATAGAGCTGAATATAGCTGAACAAATAGTTATG
GAGCTCACAAGGACTCGG
Found at i:4611177 original size:24 final size:25
Alignment explanation
Indices: 4611148--4611202 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
4611138 AAATCCAGCA
*
4611148 AAGAAAACAT-AAAGCACTC-AAAAG
1 AAGAAAA-ATGAAAGCACCCAAAAAG
*
4611172 AAG-AAATTGAAAGCACCCAAAAAG
1 AAGAAAAATGAAAGCACCCAAAAAG
4611196 AAGAAAA
1 AAGAAAA
4611203 GTAAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.04
23 11 0.42
24 11 0.42
25 3 0.12
ACGTcount: A:0.64, C:0.15, G:0.15, T:0.07
Consensus pattern (25 bp):
AAGAAAAATGAAAGCACCCAAAAAG
Found at i:4611208 original size:24 final size:23
Alignment explanation
Indices: 4611148--4611208 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
4611138 AAATCCAGCA
*
4611148 AAGAAAACATAAAGCACTCAAAAG
1 AAGAAAA-ATAAAGCACCCAAAAG
*
4611172 AAG-AAATTGAAAGCACCCAAAAAG
1 AAGAAAAAT-AAAGCACCC-AAAAG
*
4611196 AAGAAAAGTAAAG
1 AAGAAAAATAAAG
4611209 AAAAGAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.03
23 11 0.35
24 15 0.48
25 4 0.13
ACGTcount: A:0.62, C:0.13, G:0.16, T:0.08
Consensus pattern (23 bp):
AAGAAAAATAAAGCACCCAAAAG
Found at i:4621999 original size:35 final size:37
Alignment explanation
Indices: 4621930--4622009 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
4621920 ATACTATCTC
*
4621930 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
4621967 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
4622002 CATCACCA
1 CATCACCA
4622010 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:4622443 original size:15 final size:16
Alignment explanation
Indices: 4622423--4622496 Score: 66
Period size: 15 Copynumber: 4.8 Consensus size: 16
4622413 AGTTATCATC
4622423 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
*
4622438 ATAATATA-TGTAGATG
1 ATAATA-ACTATAGATG
*
4622454 AAAATAACTATAGAT-
1 ATAATAACTATAGATG
*
4622469 ATAATATA-TGTAGATG
1 ATAATA-ACTATAGATG
*
4622485 AAAATAACTATA
1 ATAATAACTATA
4622497 TTAAAATATT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
15 25 0.54
16 21 0.46
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:4622460 original size:31 final size:31
Alignment explanation
Indices: 4622425--4622496 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
4622415 TTATCATCAT
4622425 AATAACTATAGATATAATATATGTAGATGAA
1 AATAACTATAGATATAATATATGTAGATGAA
4622456 AATAACTATAGATATAATATATGTAGATGAA
1 AATAACTATAGATATAATATATGTAGATGAA
4622487 AATAACTATA
1 AATAACTATA
4622497 TTAAAATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (31 bp):
AATAACTATAGATATAATATATGTAGATGAA
Found at i:4627271 original size:23 final size:25
Alignment explanation
Indices: 4627231--4627284 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
4627221 TCTTTTTCTT
4627231 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
4627256 TTTCTT-CTTTTT-AGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
4627279 TTTCTT
1 TTTCTT
4627285 TGCTTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 15 0.56
24 6 0.22
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.63
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:4632381 original size:13 final size:13
Alignment explanation
Indices: 4632365--4632389 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4632355 AACAAGTAGG
4632365 GTTTTAAGGGTTT
1 GTTTTAAGGGTTT
4632378 GTTTTAAGGGTT
1 GTTTTAAGGGTT
4632390 GGAAACAAGG
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:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (13 bp):
GTTTTAAGGGTTT
Found at i:4636454 original size:24 final size:25
Alignment explanation
Indices: 4636427--4636474 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
4636417 GCCTATTTTT
* * *
4636427 GATGAGGAACCTGAA-ACAATGCAA
1 GATGAAGAAACTGAAGAAAATGCAA
4636451 GATGAAGAAACTGAAGAAAATGCA
1 GATGAAGAAACTGAAGAAAATGCA
4636475 GATCATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (25 bp):
GATGAAGAAACTGAAGAAAATGCAA
Found at i:4645083 original size:18 final size:18
Alignment explanation
Indices: 4645062--4645099 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4645052 CCTTACACAC
4645062 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
*
4645080 TTTGCCACAACAACGCCA
1 TTTGCCACAACAACACCA
4645098 TT
1 TT
4645100 CATACTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.37, G:0.08, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:4656820 original size:35 final size:36
Alignment explanation
Indices: 4656774--4656876 Score: 172
Period size: 36 Copynumber: 2.9 Consensus size: 36
4656764 ATGAAATTTA
*
4656774 GTGATGATATAGGCGTGAT-ATGGTGATGGACTATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACGATG
*
4656809 GTGATGATATAGGCGTGATAATGGTGATGGAAGATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACGATG
*
4656845 GTGATGATATAGGCATGATAATGGTGATGGAC
1 GTGATGATATAGGCGTGATAATGGTGATGGAC
4656877 AGATTGTATC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.29
Consensus pattern (36 bp):
GTGATGATATAGGCGTGATAATGGTGATGGACGATG
Found at i:4657262 original size:19 final size:20
Alignment explanation
Indices: 4657215--4657264 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
4657205 GAAACCCCTT
**
4657215 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
4657235 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
4657254 TGAAGATACAT
1 TGAAAATACAT
4657265 TCTCTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:4660018 original size:35 final size:36
Alignment explanation
Indices: 4659979--4660083 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
4659969 AAATGGAATT
*
4659979 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
* * *
4660014 TGGTGATGATATAGGCATGATAATGGTGATAGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
4660050 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
4660084 AGATTGTATC
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 20 0.32
36 42 0.68
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
Found at i:4664040 original size:8 final size:8
Alignment explanation
Indices: 4664027--4664092 Score: 60
Period size: 8 Copynumber: 7.6 Consensus size: 8
4664017 TGGCTTGTAT
4664027 TTTTTTTC
1 TTTTTTTC
4664035 TTTTTTTC
1 TTTTTTTC
*
4664043 TTTTTCTC
1 TTTTTTTC
4664051 TTTTTTTC
1 TTTTTTTC
*
4664059 TGAATTTTTC
1 T--TTTTTTC
*
4664069 TTCTTTGTC
1 TT-TTTTTC
4664078 TTTTCTTTTC
1 -TTT-TTTTC
4664088 TTTTT
1 TTTTT
4664093 GTACTCCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
8 25 0.53
9 9 0.19
10 13 0.28
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (8 bp):
TTTTTTTC
Found at i:4675855 original size:21 final size:19
Alignment explanation
Indices: 4675816--4675865 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 19
4675806 CGGTCAAGAG
*
4675816 CATGTATCTTCATAAAAAT
1 CATGTATTTTCATAAAAAT
4675835 CATGTATTTTCATCAAAAAAT
1 CATGTATTTTCAT--AAAAAT
4675856 CATGTATTTT
1 CATGTATTTT
4675866 AAAAGGGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:4691554 original size:20 final size:20
Alignment explanation
Indices: 4691529--4691597 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
4691519 GCCTCATATC
4691529 ATACATCGAGCTGAGCCGTA
1 ATACATCGAGCTGAGCCGTA
*
4691549 ATACATCAAG-TG-GCCGTAGA
1 ATACATCGAGCTGAGCCGT--A
* *
4691569 GCATACATCGAGCCGAGCTGTA
1 --ATACATCGAGCTGAGCCGTA
4691591 ATACATC
1 ATACATC
4691598 AAGCGGTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 17 0.44
22 10 0.26
23 1 0.03
24 4 0.10
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (20 bp):
ATACATCGAGCTGAGCCGTA
Found at i:4691574 original size:42 final size:42
Alignment explanation
Indices: 4691508--4691600 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
4691498 AGAAATGCCT
* * *
4691508 TACATCAAGTGGCCTCATATCATACATCGAGCTGAGCCGTAA
1 TACATCAAGTGGCCTCAGAGCATACATCGAGCCGAGCCGTAA
*
4691550 TACATCAAGTGGCCGT-AGAGCATACATCGAGCCGAGCTGTAA
1 TACATCAAGTGGCC-TCAGAGCATACATCGAGCCGAGCCGTAA
4691592 TACATCAAG
1 TACATCAAG
4691601 CGGTAATTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (42 bp):
TACATCAAGTGGCCTCAGAGCATACATCGAGCCGAGCCGTAA
Found at i:4695800 original size:15 final size:16
Alignment explanation
Indices: 4695780--4695809 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4695770 TGAGAGCAGA
4695780 GAAAAAGAA-ATTTTT
1 GAAAAAGAACATTTTT
4695795 GAAAAAGAACATTTT
1 GAAAAAGAACATTTT
4695810 GAGGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.30
Consensus pattern (16 bp):
GAAAAAGAACATTTTT
Found at i:4703153 original size:19 final size:19
Alignment explanation
Indices: 4703122--4703163 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
4703112 AGGGAATAAT
4703122 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
4703141 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
4703160 AATA
1 AATA
4703164 AAGAAAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:4704491 original size:2 final size:2
Alignment explanation
Indices: 4704480--4704509 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4704470 TAACTATAGG
4704480 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4704510 GAAAATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4707774 original size:19 final size:19
Alignment explanation
Indices: 4707743--4707784 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
4707733 AGGGAATAAT
4707743 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
4707762 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
4707781 AATA
1 AATA
4707785 AAGAAAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:4711473 original size:24 final size:24
Alignment explanation
Indices: 4711435--4711483 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
4711425 TTCTTCCACC
4711435 AAGGCTCTGATTACCACTTGATGT
1 AAGGCTCTGATTACCACTTGATGT
4711459 AAGGCTTCTGA-TACCACTTGATGT
1 AAGGC-TCTGATTACCACTTGATGT
4711483 A
1 A
4711484 TGAAACTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (24 bp):
AAGGCTCTGATTACCACTTGATGT
Found at i:4715812 original size:42 final size:42
Alignment explanation
Indices: 4715745--4715875 Score: 190
Period size: 42 Copynumber: 3.1 Consensus size: 42
4715735 AGAAACACCT
*
4715745 TACATCAAGTGGCCTCAGAGCATACATCGAGCCGAGCCGTCA
1 TACATCAAGTGGCCTCAGAGCATACATCGAGCCGAGCCGTAA
* * * * *
4715787 TATATCAAATGGCCTCAGAGAATACATAGAGCTGAGCCGTAA
1 TACATCAAGTGGCCTCAGAGCATACATCGAGCCGAGCCGTAA
* *
4715829 TACATCAAGTGGCCTCATAGCATACATCGAGTCGAGCCGTAA
1 TACATCAAGTGGCCTCAGAGCATACATCGAGCCGAGCCGTAA
4715871 TACAT
1 TACAT
4715876 GAAGCGGTAA
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (42 bp):
TACATCAAGTGGCCTCAGAGCATACATCGAGCCGAGCCGTAA
Found at i:4720660 original size:17 final size:17
Alignment explanation
Indices: 4720634--4720672 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
4720624 CCTTGCTGCC
4720634 ATGT-AAGAATATAGTA
1 ATGTGAAGAATATAGTA
4720650 ATGTGAAGAATATAGTA
1 ATGTGAAGAATATAGTA
4720667 ATGTGA
1 ATGTGA
4720673 GCTATGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (17 bp):
ATGTGAAGAATATAGTA
Found at i:4723554 original size:15 final size:15
Alignment explanation
Indices: 4723519--4723547 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4723509 GTGCTTCAAC
4723519 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
4723533 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
4723548 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:4730977 original size:17 final size:17
Alignment explanation
Indices: 4730957--4730998 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4730947 ACTACTTCCC
4730957 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
4730974 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
4730991 TTAATGAA
1 TAAATGAA
4730999 CAATATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:4737582 original size:17 final size:17
Alignment explanation
Indices: 4737562--4737603 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4737552 ACTACTTCCC
4737562 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
4737579 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
4737596 TTAATGAA
1 TAAATGAA
4737604 CAATATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:4744949 original size:14 final size:14
Alignment explanation
Indices: 4744930--4744956 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4744920 TTTTTTCACG
4744930 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
4744944 ATTTTTATTTTTT
1 ATTTTTATTTTTT
4744957 GCTTTTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:4744962 original size:14 final size:14
Alignment explanation
Indices: 4744929--4744963 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4744919 TTTTTTTCAC
4744929 GATTTTTATTTTTT
1 GATTTTTATTTTTT
*
4744943 TATTTTTATTTTTT
1 GATTTTTATTTTTT
*
4744957 GCTTTTT
1 GATTTTT
4744964 TCACTAACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.80
Consensus pattern (14 bp):
GATTTTTATTTTTT
Found at i:4746389 original size:17 final size:17
Alignment explanation
Indices: 4746369--4746410 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4746359 ACTACTTCCC
4746369 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
4746386 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
4746403 TTAATGAA
1 TAAATGAA
4746411 CAATATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:4751036 original size:18 final size:19
Alignment explanation
Indices: 4751006--4751041 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4750996 CTTTTTCTCC
*
4751006 ACTCTTAATGTCTTTTTCA
1 ACTCTTAATGTCTCTTTCA
4751025 ACTCTT-ATGTCTCTTTC
1 ACTCTTAATGTCTCTTTC
4751042 TTTGTTGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.17, C:0.25, G:0.06, T:0.53
Consensus pattern (19 bp):
ACTCTTAATGTCTCTTTCA
Found at i:4751924 original size:6 final size:7
Alignment explanation
Indices: 4751908--4751933 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4751898 TTCACGATTG
4751908 TTTTTAT
1 TTTTTAT
4751915 TTTTTAT
1 TTTTTAT
4751922 TTTTTAT
1 TTTTTAT
4751929 TTTTT
1 TTTTT
4751934 CACAAACCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:4756975 original size:36 final size:36
Alignment explanation
Indices: 4756889--4756964 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
4756879 ACCTAAACAT
* * * *
4756889 CACCATCTTCCATCACCATTTTCACGCCTATATCAC
1 CACCATCCTCTATCACCATTTTCACGCCTAAATAAC
* *
4756925 TACCATCTTCTATCACCA-TTTCACGCCTAAATAAC
1 CACCATCCTCTATCACCATTTTCACGCCTAAATAAC
4756960 CACCA
1 CACCA
4756965 CTCCCTTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.29, C:0.39, G:0.03, T:0.29
Consensus pattern (36 bp):
CACCATCCTCTATCACCATTTTCACGCCTAAATAAC
Found at i:4759808 original size:17 final size:17
Alignment explanation
Indices: 4759788--4759829 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4759778 ACTACTTCCC
4759788 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
4759805 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
4759822 TTAATGAA
1 TAAATGAA
4759830 CAATATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:4761875 original size:30 final size:29
Alignment explanation
Indices: 4761832--4761889 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
4761822 CACTCTTTAA
* *
4761832 ATTTTTTCTTTTTTTTTCTTTATTTCACG
1 ATTTTTTATTTTTTTTGCTTTATTTCACG
*
4761861 ATTTTTTATATTTTTTTGCTTTTTTTCAC
1 ATTTTTTAT-TTTTTTTGCTTTATTTCAC
4761890 TAACCCGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (29 bp):
ATTTTTTATTTTTTTTGCTTTATTTCACG
Found at i:4763310 original size:17 final size:17
Alignment explanation
Indices: 4763290--4763331 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4763280 ACTACTTCCC
4763290 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
4763307 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
4763324 TTAATGAA
1 TAAATGAA
4763332 CAATATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:4765115 original size:15 final size:16
Alignment explanation
Indices: 4765066--4765118 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
4765056 TTGATGTTCA
4765066 CTCTTGCCTTTTACCG
1 CTCTTGCCTTTTACCG
4765082 CTCTTGCCTTTTACCG
1 CTCTTGCCTTTTACCG
*
4765098 CTCTTGCC-TTTACTG
1 CTCTTGCCTTTTACCG
4765113 CTCTTG
1 CTCTTG
4765119 TTTTCCATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
15 12 0.33
16 24 0.67
ACGTcount: A:0.06, C:0.36, G:0.13, T:0.45
Consensus pattern (16 bp):
CTCTTGCCTTTTACCG
Found at i:4766838 original size:17 final size:17
Alignment explanation
Indices: 4766818--4766859 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4766808 ACTACTTCCC
4766818 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
4766835 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
4766852 TTAATGAA
1 TAAATGAA
4766860 CAATATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:4768541 original size:16 final size:16
Alignment explanation
Indices: 4768503--4768534 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4768493 CCTTGATGGT
4768503 CACTCTTGCCTTTTAC
1 CACTCTTGCCTTTTAC
*
4768519 CACTCTTTCCTTTTAC
1 CACTCTTGCCTTTTAC
4768535 TGCTCTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.38, G:0.03, T:0.47
Consensus pattern (16 bp):
CACTCTTGCCTTTTAC
Found at i:4768830 original size:31 final size:30
Alignment explanation
Indices: 4768785--4768844 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
4768775 GCACTCTTTA
* *
4768785 AATTTTTTCTTTTTTTTTCTTTTTTTCACG
1 AATTTTTTATTTTTTTTGCTTTTTTTCACG
4768815 AATTTTTTATATTTTTTTGCTTTTTTTCAC
1 AATTTTTTAT-TTTTTTTGCTTTTTTTCAC
4768845 TAACCCGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.13, C:0.12, G:0.03, T:0.72
Consensus pattern (30 bp):
AATTTTTTATTTTTTTTGCTTTTTTTCACG
Found at i:4775383 original size:15 final size:15
Alignment explanation
Indices: 4775372--4775400 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4775362 ACTCAAAAAG
4775372 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
4775387 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
4775401 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:4782107 original size:15 final size:14
Alignment explanation
Indices: 4782089--4782152 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 14
4782079 ATCTGTACAA
4782089 AAGAAAGAAATGATT
1 AAGAAAGAAATGA-T
*
4782104 AAGATAGAAAT-AT
1 AAGAAAGAAATGAT
*
4782117 AA-ATAAGAAATGGAAG
1 AAGA-AAGAAAT-G-AT
4782133 AAGAAAGGAAATGAT
1 AAGAAA-GAAATGAT
4782148 AAGAA
1 AAGAA
4782153 TTGAAATGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
12 1 0.03
13 9 0.23
14 1 0.03
15 16 0.41
16 6 0.15
17 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (14 bp):
AAGAAAGAAATGAT
Found at i:4787795 original size:22 final size:22
Alignment explanation
Indices: 4787755--4787796 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4787745 AAATATGTGG
*
4787755 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
4787777 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
4787797 ACTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:4794388 original size:17 final size:16
Alignment explanation
Indices: 4794366--4794405 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
4794356 CATGGTTTTC
4794366 AGAACCAGACCGGTCAA
1 AGAACC-GACCGGTCAA
*
4794383 AGAACCGGCCGGTCAA
1 AGAACCGACCGGTCAA
4794399 AGAACCG
1 AGAACCG
4794406 GCCGTGCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.38, C:0.30, G:0.28, T:0.05
Consensus pattern (16 bp):
AGAACCGACCGGTCAA
Found at i:4794396 original size:16 final size:16
Alignment explanation
Indices: 4794375--4794409 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
4794365 CAGAACCAGA
4794375 CCGGTCAAAGAACCGG
1 CCGGTCAAAGAACCGG
4794391 CCGGTCAAAGAACCGG
1 CCGGTCAAAGAACCGG
4794407 CCG
1 CCG
4794410 TGCTACCGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.31, T:0.06
Consensus pattern (16 bp):
CCGGTCAAAGAACCGG
Found at i:4794437 original size:18 final size:18
Alignment explanation
Indices: 4794414--4794448 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4794404 CGGCCGTGCT
4794414 ACCGGTTCA-ACCGGTCGA
1 ACCGG-TCAGACCGGTCGA
4794432 ACCGGTCAGACCGGTCG
1 ACCGGTCAGACCGGTCG
4794449 TAAGAACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.20, C:0.34, G:0.31, T:0.14
Consensus pattern (18 bp):
ACCGGTCAGACCGGTCGA
Found at i:4795153 original size:16 final size:16
Alignment explanation
Indices: 4795132--4795170 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
4795122 ATATGAAAAC
4795132 AAGTGCTTATTCTTTA
1 AAGTGCTTATTCTTTA
4795148 AAGTGCTTATTCTTTA
1 AAGTGCTTATTCTTTA
4795164 AAGTGCT
1 AAGTGCT
4795171 CGATACATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (16 bp):
AAGTGCTTATTCTTTA
Found at i:4796763 original size:13 final size:13
Alignment explanation
Indices: 4796745--4796776 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
4796735 ATTTAACCAA
4796745 CACCATCTTCCAT
1 CACCATCTTCCAT
4796758 CACCATCTTCCAT
1 CACCATCTTCCAT
4796771 CACCAT
1 CACCAT
4796777 TCACGCATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.25, C:0.47, G:0.00, T:0.28
Consensus pattern (13 bp):
CACCATCTTCCAT
Found at i:4802622 original size:24 final size:21
Alignment explanation
Indices: 4802587--4802629 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
4802577 GGCTCATTCT
*
4802587 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
4802610 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
4802630 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:4803877 original size:24 final size:23
Alignment explanation
Indices: 4803850--4803909 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
4803840 ACTTTTCTTT
*
4803850 CTTTCTTTTTCTTATTTTTGAGTG
1 CTTTCTTTTTCTT-CTTTTGAGTG
**
4803874 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTCTTTTGAGTG
4803897 CTTT-TATTTTCTT
1 CTTTCT-TTTTCTT
4803910 TGCTGATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.10, C:0.15, G:0.10, T:0.65
Consensus pattern (23 bp):
CTTTCTTTTTCTTCTTTTGAGTG
Found at i:4803895 original size:23 final size:23
Alignment explanation
Indices: 4803865--4803909 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4803855 TTTTTCTTAT
4803865 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAGTGCTTTCAATTTCTTC
* *
4803888 TTTTGAGTGCTTTTATTTTCTT
1 TTTTGAGTGCTTTCAATTTCTT
4803910 TGCTGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.62
Consensus pattern (23 bp):
TTTTGAGTGCTTTCAATTTCTTC
Found at i:4808956 original size:10 final size:10
Alignment explanation
Indices: 4808941--4808970 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
4808931 GATGTCAAAG
4808941 GTAGCTGAAT
1 GTAGCTGAAT
4808951 GTAGCTGAAT
1 GTAGCTGAAT
4808961 GTAGCTGAAT
1 GTAGCTGAAT
4808971 ATGCTGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (10 bp):
GTAGCTGAAT
Found at i:4811630 original size:17 final size:18
Alignment explanation
Indices: 4811596--4811630 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4811586 GATGAGCTAG
*
4811596 TTGTTGATTCTCTTTGAT
1 TTGTTGATTCTATTTGAT
4811614 TTGTTGATTC-ATTTGAT
1 TTGTTGATTCTATTTGAT
4811631 AGCTCCTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.09, G:0.17, T:0.60
Consensus pattern (18 bp):
TTGTTGATTCTATTTGAT
Found at i:4816518 original size:13 final size:14
Alignment explanation
Indices: 4816486--4816523 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
4816476 AGATATTATT
* *
4816486 TCCATAACCATCTT
1 TCCATCACCATCTC
4816500 TCCATCACCATC-C
1 TCCATCACCATCTC
4816513 TCCATCACCAT
1 TCCATCACCAT
4816524 TAACGCCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (14 bp):
TCCATCACCATCTC
Found at i:4827401 original size:18 final size:18
Alignment explanation
Indices: 4827378--4827448 Score: 65
Period size: 18 Copynumber: 3.7 Consensus size: 18
4827368 CAAGTGAAAT
*
4827378 ATTTTTTTTTTCATTTTTC
1 ATTTTCTTTTTC-TTTTTC
4827397 ATTTT-TTTTCTCTTTTT-
1 ATTTTCTTTT-TCTTTTTC
4827414 ATTTTCTTTCTTCTTCGTTTTC
1 ATTTTCTTT-TTC-T--TTTTC
4827436 ATTTTCTTTTTCT
1 ATTTTCTTTTTCT
4827449 ATATTTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
17 5 0.11
18 14 0.31
19 9 0.20
20 1 0.02
21 7 0.16
22 9 0.20
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.76
Consensus pattern (18 bp):
ATTTTCTTTTTCTTTTTC
Found at i:4827403 original size:17 final size:16
Alignment explanation
Indices: 4827381--4827461 Score: 72
Period size: 17 Copynumber: 4.7 Consensus size: 16
4827371 GTGAAATATT
4827381 TTTTTTTTCATTTTTCA
1 TTTTTTTTC-TTTTTCA
*
4827398 TTTTTTTTCTCTTTTTA
1 TTTTTTTTCT-TTTTCA
* * *
4827415 TTTTCTTTCTTCTTCG
1 TTTTTTTTCTTTTTCA
4827431 TTTTCATTTTCTTTTTCTA
1 TTTT--TTTTCTTTTTC-A
4827450 TATTTTTTTCTT
1 T-TTTTTTTCTT
4827462 CTGTTTTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
16 8 0.16
17 23 0.45
18 16 0.31
19 1 0.02
20 3 0.06
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTTTTTCTTTTTCA
Found at i:4827405 original size:11 final size:10
Alignment explanation
Indices: 4827391--4827483 Score: 60
Period size: 11 Copynumber: 8.5 Consensus size: 10
4827381 TTTTTTTTCA
4827391 TTTTTCATTTT
1 TTTTTC-TTTT
4827402 TTTTCTCTTTT
1 TTTT-TCTTTT
*
4827413 TATTTTCTTTC
1 T-TTTTCTTTT
*
4827424 TTCTTCGTTTT
1 TTTTTC-TTTT
*
4827435 CATTTTCTTTT
1 -TTTTTCTTTT
* * *
4827446 TCTATATTTT
1 TTTTTCTTTT
4827456 TTTCTTCTGTTT
1 TTT-TTCT-TTT
4827468 TTTTTCTTTT
1 TTTTTCTTTT
4827478 GTTTTT
1 -TTTTT
4827484 TCTTCTTCTT
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 15 0.24
11 33 0.52
12 15 0.24
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.77
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:4827458 original size:18 final size:17
Alignment explanation
Indices: 4827381--4827477 Score: 71
Period size: 17 Copynumber: 5.8 Consensus size: 17
4827371 GTGAAATATT
4827381 TTTTTTTTCATTTTTC-A
1 TTTTTTTTC-TTTTTCTA
4827398 TTTTTTTTCTCTTTT-TA
1 TTTTTTTTCT-TTTTCTA
* *
4827415 TTTTCTTTCTTCTTCGT-
1 TTTTTTTTCTTTTTC-TA
*
4827432 TTTCATTTTCTTTTTCTA
1 TTT-TTTTTCTTTTTCTA
*
4827450 TATTTTTTTC---TTCTG
1 T-TTTTTTTCTTTTTCTA
4827465 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
4827478 GTTTTTTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 8 0.13
15 5 0.08
16 4 0.06
17 28 0.44
18 16 0.25
19 2 0.03
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTTTTCTTTTTCTA
Found at i:4827471 original size:14 final size:14
Alignment explanation
Indices: 4827452--4827492 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
4827442 TTTTTCTATA
4827452 TTTTTTTCTTCTGT
1 TTTTTTTCTTCTGT
*
4827466 TTTTTTTCTTTTGT
1 TTTTTTTCTTCTGT
4827480 TTTTTCTTCTTCT
1 TTTTT-TTCTTCT
4827493 TATAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (14 bp):
TTTTTTTCTTCTGT
Found at i:4827483 original size:15 final size:15
Alignment explanation
Indices: 4827380--4827490 Score: 57
Period size: 17 Copynumber: 6.8 Consensus size: 15
4827370 AGTGAAATAT
4827380 TTTTTTTTTCATTTT-
1 TTTTTTTTTC-TTTTG
4827395 TCATTTTTTTTCTCTTT-
1 T--TTTTTTTTCT-TTTG
4827412 TTATTTTCTTTCTTCTTCG
1 TT-TTTT-TTTCTT-TT-G
* *
4827431 TTTTCATTTTCTTTTTC
1 TTTT-TTTTTC-TTTTG
*
4827448 TATATTTTTTTCTTCTG
1 T-T-TTTTTTTCTTTTG
4827465 -TTTTTTTTCTTTTG
1 TTTTTTTTTCTTTTG
*
4827479 TTTTTTCTTCTT
1 TTTTTTTTTCTT
4827491 CTTATAATAT
Statistics
Matches: 76, Mismatches: 7, Indels: 26
0.70 0.06 0.24
Matches are distributed among these distances:
14 12 0.16
15 13 0.17
16 6 0.08
17 24 0.32
18 14 0.18
19 7 0.09
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTTTTTTCTTTTG
Found at i:4830385 original size:45 final size:46
Alignment explanation
Indices: 4830336--4830436 Score: 141
Period size: 47 Copynumber: 2.2 Consensus size: 46
4830326 TATAAAATCT
4830336 CTTACCATTT-ATCCCATAACCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATCCCATAACCTCGTAAGCTTATTTTACCAAAATA
* * * *
4830381 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT-AATCCCATAACCTCGTAAGCTTATTTTACCAAAATA
*
4830428 CTTGCCATT
1 CTTACCATT
4830437 ATACTGTAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
45 10 0.20
47 39 0.80
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.39
Consensus pattern (46 bp):
CTTACCATTTAATCCCATAACCTCGTAAGCTTATTTTACCAAAATA
Found at i:4841911 original size:72 final size:72
Alignment explanation
Indices: 4841788--4841930 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
4841778 ATTGATAATA
* ** * * * *
4841788 AATAGCAAACACATGTATATTATGCATATAATCATCAATAGCAAGAGCATATATATCATTCATAT
1 AATAACAAACACATGTATACCATGCATATAATCATCAATAGCAAGAACATATACATCATGCAAAT
4841853 AATCATC
66 AATCATC
*
4841860 AATAACAAACACATGTATACCATGCATATAATCATTAATAGCAAGAACATATACATCATGCAAAT
1 AATAACAAACACATGTATACCATGCATATAATCATCAATAGCAAGAACATATACATCATGCAAAT
4841925 AATCAT
66 AATCAT
4841931 TAGTAGAAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (72 bp):
AATAACAAACACATGTATACCATGCATATAATCATCAATAGCAAGAACATATACATCATGCAAAT
AATCATC
Found at i:4841932 original size:36 final size:36
Alignment explanation
Indices: 4841788--4841930 Score: 164
Period size: 36 Copynumber: 4.0 Consensus size: 36
4841778 ATTGATAATA
* *
4841788 AATAGCAA-ACACATGTATATTATGCATATAATCATC
1 AATAGCAAGA-ACATATATATCATGCATATAATCATC
* *
4841824 AATAGCAAGAGCATATATATCATTCATATAATCATC
1 AATAGCAAGAACATATATATCATGCATATAATCATC
* * * *
4841860 AATAACAA-ACACATGTATACCATGCATATAATCATT
1 AATAGCAAGA-ACATATATATCATGCATATAATCATC
* *
4841896 AATAGCAAGAACATATACATCATGCAAATAATCAT
1 AATAGCAAGAACATATATATCATGCATATAATCAT
4841931 TAGTAGAAAG
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
35 1 0.01
36 86 0.97
37 2 0.02
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (36 bp):
AATAGCAAGAACATATATATCATGCATATAATCATC
Found at i:4843897 original size:2 final size:2
Alignment explanation
Indices: 4843890--4843915 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4843880 GAAGTTCTTC
4843890 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4843916 TGATATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4846244 original size:51 final size:51
Alignment explanation
Indices: 4846182--4846355 Score: 163
Period size: 51 Copynumber: 3.4 Consensus size: 51
4846172 ACTAAACATG
* * *
4846182 AACA-ACTTACACAAGTGAAATTTAACACATAATTCCAGCATTAATCTCAT
1 AACAGACTTACACCAGTCAAATTTAACACACAATTCCAGCATTAATCTCAT
* * * * * ** *
4846232 AACAGACTTACACCGGTCATATTTAGCATACAATTTCAATATTGAA-CTCAC
1 AACAGACTTACACCAGTCAAATTTAACACACAATTCCAGCATT-AATCTCAT
* ** * *
4846283 AAAAGACTTACATGAGTCAATTTTATCACACAATTCCAGCATTAATCTCAT
1 AACAGACTTACACCAGTCAAATTTAACACACAATTCCAGCATTAATCTCAT
* *
4846334 CACAAACTTACACCAGTCAAAT
1 AACAGACTTACACCAGTCAAAT
4846356 CTGACATATA
Statistics
Matches: 92, Mismatches: 29, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
50 6 0.07
51 84 0.91
52 2 0.02
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (51 bp):
AACAGACTTACACCAGTCAAATTTAACACACAATTCCAGCATTAATCTCAT
Found at i:4848478 original size:80 final size:80
Alignment explanation
Indices: 4848345--4848503 Score: 300
Period size: 80 Copynumber: 2.0 Consensus size: 80
4848335 TAATTCGATC
4848345 ATCGAACTTTATCCAAAAATGAATAAGGAATATCATTTTGAAAATAGGTGAAAGAGTTTATCAAA
1 ATCGAACTTTATCCAAAAATGAATAAGGAATATCATTTTGAAAATAGGTGAAAGAGTTTATCAAA
4848410 CAACATAAGATCAAT
66 CAACATAAGATCAAT
* *
4848425 ATCGAACTTTATCCAAAAATGATTAAGGGATATCATTTTGAAAATAGGTGAAAGAGTTTATCAAA
1 ATCGAACTTTATCCAAAAATGAATAAGGAATATCATTTTGAAAATAGGTGAAAGAGTTTATCAAA
4848490 CAACATAAGATCAA
66 CAACATAAGATCAA
4848504 CATTCGACTG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (80 bp):
ATCGAACTTTATCCAAAAATGAATAAGGAATATCATTTTGAAAATAGGTGAAAGAGTTTATCAAA
CAACATAAGATCAAT
Found at i:4850405 original size:36 final size:35
Alignment explanation
Indices: 4850357--4850732 Score: 349
Period size: 36 Copynumber: 10.5 Consensus size: 35
4850347 GTAACTAGTG
* * *
4850357 CATGTATCTCATGCATATACTCATCAATAGCAAGA
1 CATGTATATCATGCATATAATCATCAGTAGCAAGA
* * *
4850392 GCATGTATATCATGCATATAATCATCAATGGAAAGAA
1 -CATGTATATCATGCATATAATCATCAGTAGCAAG-A
* * * *
4850429 TATGTATACCATGCATATAATCATCAATTGCAAGCA
1 CATGTATATCATGCATATAATCATCAGTAGCAAG-A
* * * * *
4850465 CATGTACATTATTCATATAATCATTAGTAGCATACA
1 CATGTATATCATGCATATAATCATCAGTAGCA-AGA
* *
4850501 CATGTATATCATGCATAAAATCATCAGTCGCAAGTA
1 CATGTATATCATGCATATAATCATCAGTAGCAAG-A
* * * *
4850537 CATGTATATGATGCATAAAATCATCTGTAGCAAGCG
1 CATGTATATCATGCATATAATCATCAGTAGCAAG-A
* **
4850573 CATGTATATCATGCATATAAT-ATTTAGTATTAAGCA
1 CATGTATATCATGCATATAATCA-TCAGTAGCAAG-A
*
4850609 CATGAATATCATGCATATAATCATCAGTAGCAAGCA
1 CATGTATATCATGCATATAATCATCAGTAGCAAG-A
* * * * *
4850645 CATGTGTATCAGGCACATAATCATTAGTAGCAAGCG
1 CATGTATATCATGCATATAATCATCAGTAGCAAG-A
* * *
4850681 CATGCATATCATGCACATAATCATCAGTAGCAAAA
1 CATGTATATCATGCATATAATCATCAGTAGCAAGA
4850716 GCATGTATATCATGCAT
1 -CATGTATATCATGCAT
4850733 GGGGACATCA
Statistics
Matches: 279, Mismatches: 55, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
35 2 0.01
36 274 0.98
37 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (35 bp):
CATGTATATCATGCATATAATCATCAGTAGCAAGA
Found at i:4850542 original size:108 final size:107
Alignment explanation
Indices: 4850338--4850732 Score: 396
Period size: 108 Copynumber: 3.7 Consensus size: 107
4850328 TCATCAACAT
* * * * * * * * *
4850338 TAATCATAAGTAACTAGTGCATGTATCTCATGCATATACTCATCAATAGCAAGAGCATGTATATC
1 TAATCATCAGTAGCAAGCGCATGTATATCATGCATATAATCATTAGTAGCAACA-CATGTATATC
* * * * *
4850403 ATGCATATAATCATCAATGGAAAGAATATGTATACCATGCATA
65 ATGCATATAATCATCAGTAGCAAGAACATGTATATCATGCATA
* * * * * *
4850446 TAATCATCAATTGCAAGCACATGTACATTATTCATATAATCATTAGTAGCATACACATGTATATC
1 TAATCATCAGTAGCAAGCGCATGTATATCATGCATATAATCATTAGTAGCA-ACACATGTATATC
* * * *
4850511 ATGCATAAAATCATCAGTCGCAAGTACATGTATATGATGCATA
65 ATGCATATAATCATCAGTAGCAAGAACATGTATATCATGCATA
* * ** *
4850554 AAATCATCTGTAGCAAGCGCATGTATATCATGCATATAAT-ATTTAGTATTAAGCACATGAATAT
1 TAATCATCAGTAGCAAGCGCATGTATATCATGCATATAATCA-TTAGTAGCAA-CACATGTATAT
* * * *
4850618 CATGCATATAATCATCAGTAGCAAGCACATGTGTATCAGGCACA
64 CATGCATATAATCATCAGTAGCAAGAACATGTATATCATGCATA
* * * * *
4850662 TAATCATTAGTAGCAAGCGCATGCATATCATGCACATAATCATCAGTAGCAAAAGCATGTATATC
1 TAATCATCAGTAGCAAGCGCATGTATATCATGCATATAATCATTAGTAGCAACA-CATGTATATC
4850727 ATGCAT
65 ATGCAT
4850733 GGGGACATCA
Statistics
Matches: 231, Mismatches: 51, Indels: 10
0.79 0.17 0.03
Matches are distributed among these distances:
107 3 0.01
108 225 0.97
109 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (107 bp):
TAATCATCAGTAGCAAGCGCATGTATATCATGCATATAATCATTAGTAGCAACACATGTATATCA
TGCATATAATCATCAGTAGCAAGAACATGTATATCATGCATA
Found at i:4855858 original size:21 final size:20
Alignment explanation
Indices: 4855830--4855868 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4855820 CATTGCAGGA
*
4855830 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
4855850 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
4855869 GACCCTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:4865429 original size:2 final size:2
Alignment explanation
Indices: 4865422--4865524 Score: 206
Period size: 2 Copynumber: 51.5 Consensus size: 2
4865412 TAGTTGCTAC
4865422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4865464 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4865506 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
4865525 TCATTTATGG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 101 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4865843 original size:81 final size:81
Alignment explanation
Indices: 4865677--4865845 Score: 196
Period size: 81 Copynumber: 2.1 Consensus size: 81
4865667 AGACATTTAT
* * *
4865677 TCTTTTACCCAATGGTATTTAACCTTTCATGTAACTGGCATGATTGACACCTTTCTACCAAAGGC
1 TCTTTTACCCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTACCAAAGAC
* ** *
4865742 ACAATTATAGTTTTAG
66 ACAACTATAGCATTAA
* * ** *
4865758 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATGATTGACACCTTTCTGTCAAATAC
1 TCTTTTACCCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTACCAAAGAC
* *
4865823 ACAGCTA-GGCCATTAA
66 ACAACTATAG-CATTAA
4865839 TCTTTTA
1 TCTTTTA
4865846 TTTTAGAAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 1 0.01
81 72 0.99
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (81 bp):
TCTTTTACCCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTACCAAAGAC
ACAACTATAGCATTAA
Found at i:4866245 original size:26 final size:26
Alignment explanation
Indices: 4866209--4866259 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
4866199 TGCCTTAATG
4866209 CATCATTTCATGCATTTCATTTATGA
1 CATCATTTCATGCATTTCATTTATGA
*
4866235 CATCCTTTCATGCATTTCATTTATG
1 CATCATTTCATGCATTTCATTTATG
4866260 GATTCATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.47
Consensus pattern (26 bp):
CATCATTTCATGCATTTCATTTATGA
Found at i:4871409 original size:26 final size:26
Alignment explanation
Indices: 4871341--4871423 Score: 97
Period size: 26 Copynumber: 3.4 Consensus size: 26
4871331 TTATTACTTA
4871341 ATTTCATTTATGGCATCCTTT-A---
1 ATTTCATTTATGGCATCCTTTCATGC
* * *
4871363 A-TTCCTTAAT-GCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
4871387 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
4871413 ATTTCATTTAT
1 ATTTCATTTAT
4871424 AGATTCATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
20 8 0.16
21 8 0.16
22 1 0.02
24 1 0.02
25 7 0.14
26 24 0.49
ACGTcount: A:0.23, C:0.20, G:0.08, T:0.48
Consensus pattern (26 bp):
ATTTCATTTATGGCATCCTTTCATGC
Found at i:4871781 original size:22 final size:22
Alignment explanation
Indices: 4871749--4871826 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
4871739 ATACCCTACC
*
4871749 ATGGTATCGATACTTCTACATT
1 ATGGTACCGATACTTCTACATT
*
4871771 ATGGTACCGATACCTTTCT-C-TC
1 ATGGTACCGATA-C-TTCTACATT
* * *
4871793 A--GTATCGATACTACTACACT
1 ATGGTACCGATACTTCTACATT
4871813 ATGGTACCGATACT
1 ATGGTACCGATACT
4871827 CCCTTTCAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
18 3 0.07
19 2 0.05
20 9 0.21
22 23 0.53
23 2 0.05
24 4 0.09
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (22 bp):
ATGGTACCGATACTTCTACATT
Found at i:4871800 original size:42 final size:41
Alignment explanation
Indices: 4871752--4871885 Score: 180
Period size: 41 Copynumber: 3.2 Consensus size: 41
4871742 CCCTACCATG
* ** *
4871752 GTATCGATACTTCTACATTATGGTACCGATACCTTTCTCTCA
1 GTATCGATACTTCTACACTATGGTACCGATA-CTCCCTTTCA
*
4871794 GTATCGATACTACTACACTATGGTACCGATACTCCCTTTCA
1 GTATCGATACTTCTACACTATGGTACCGATACTCCCTTTCA
**
4871835 GTATCGATA-TTACTACACTATGGTATTGATACTCCCTTTCA
1 GTATCGATACTT-CTACACTATGGTACCGATACTCCCTTTCA
4871876 GTATCGATAC
1 GTATCGATAC
4871886 CATTTTGACA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
40 1 0.01
41 52 0.63
42 29 0.35
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (41 bp):
GTATCGATACTTCTACACTATGGTACCGATACTCCCTTTCA
Found at i:4871842 original size:19 final size:19
Alignment explanation
Indices: 4871820--4871885 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
4871810 ACTATGGTAC
4871820 CGATACTCCCTTTCAGTAT
1 CGATACTCCCTTTCAGTAT
* * *
4871839 CGATATTACTACACTAT-GGTAT
1 CG--A-TACT-CCCTTTCAGTAT
*
4871861 TGATACTCCCTTTCAGTAT
1 CGATACTCCCTTTCAGTAT
4871880 CGATAC
1 CGATAC
4871886 CATTTTGACA
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
18 4 0.12
19 15 0.44
20 1 0.03
21 1 0.03
22 9 0.26
23 4 0.12
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (19 bp):
CGATACTCCCTTTCAGTAT
Found at i:4871860 original size:22 final size:21
Alignment explanation
Indices: 4871794--4871865 Score: 51
Period size: 22 Copynumber: 3.4 Consensus size: 21
4871784 CTTTCTCTCA
4871794 GTATCGATACTACTACACTATG
1 GTATCGATA-TACTACACTATG
* * * *
4871816 GTACCG--ATACT-CCCTTTCA
1 GTATCGATATACTACACTAT-G
4871835 GTATCGATATTACTACACTATG
1 GTATCGATA-TACTACACTATG
*
4871857 GTATTGATA
1 GTATCGATA
4871866 CTCCCTTTCA
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
18 4 0.11
19 9 0.25
20 1 0.03
21 1 0.03
22 17 0.47
23 4 0.11
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (21 bp):
GTATCGATATACTACACTATG
Found at i:4875217 original size:16 final size:16
Alignment explanation
Indices: 4875198--4875284 Score: 57
Period size: 17 Copynumber: 5.1 Consensus size: 16
4875188 TACGCCTAAG
4875198 AAGGAAAAAAAGGAAA
1 AAGGAAAAAAAGGAAA
* *
4875214 AAGGTAAAAAAGACAAA
1 AAGGAAAAAAAG-GAAA
* *
4875231 AAGACAAAAAGAAAGAAA
1 AAG-GAAAAA-AAGGAAA
* *
4875249 AAAGAAAATAAAGAAAA
1 AAGGAAAA-AAAGGAAA
* *
4875266 AAAGAAAAATAAAGAAA
1 AAGGAAAAA-AAGGAAA
4875283 AA
1 AA
4875285 ATAAAAAGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
16 12 0.22
17 30 0.56
18 10 0.19
19 2 0.04
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.03
Consensus pattern (16 bp):
AAGGAAAAAAAGGAAA
Found at i:4875239 original size:17 final size:16
Alignment explanation
Indices: 4875237--4875356 Score: 86
Period size: 17 Copynumber: 7.3 Consensus size: 16
4875227 CAAAAAGACA
*
4875237 AAAAGAAAGAAAAAAG
1 AAAATAAAGAAAAAAG
4875253 AAAATAAAGAAAAAAAG
1 AAAATAAAG-AAAAAAG
*
4875270 AAAAATAAAGAAAAAATA
1 -AAAATAAAGAAAAAA-G
* *
4875288 AAAAGAAAAAATAAAAG
1 AAAATAAAGAA-AAAAG
*
4875305 AAAA-AATA-AAAAATAA
1 AAAATAA-AGAAAAA-AG
*
4875321 AAAATAAA-AAATAA-
1 AAAATAAAGAAAAAAG
*
4875335 AAAATAAAAAATAAAAG
1 AAAATAAAGAA-AAAAG
4875352 AAAAT
1 AAAAT
4875357 GAGAGGCTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
14 8 0.09
15 6 0.07
16 25 0.29
17 34 0.40
18 13 0.15
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.09
Consensus pattern (16 bp):
AAAATAAAGAAAAAAG
Found at i:4875240 original size:1 final size:1
Alignment explanation
Indices: 4875236--4875355 Score: 69
Period size: 1 Copynumber: 120.0 Consensus size: 1
4875226 ACAAAAAGAC
* * * * * * * * * * *
4875236 AAAAAGAAAGAAAAAAGAAAATAAAGAAAAAAAGAAAAATAAAGAAAAAATAAAAAGAAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
4875301 AAAGAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4875356 TGAGAGGCTT
Statistics
Matches: 81, Mismatches: 38, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.08
Consensus pattern (1 bp):
A
Found at i:4875240 original size:18 final size:17
Alignment explanation
Indices: 4875222--4875309 Score: 88
Period size: 17 Copynumber: 4.9 Consensus size: 17
4875212 AAAAGGTAAA
4875222 AAAGACAAAAAGACAAAAAG
1 AAAGA-AAAAAG--AAAAAG
*
4875242 AAAGAAAAAAG-AAAAT
1 AAAGAAAAAAGAAAAAG
*
4875258 AAAGAAAAAAAGAAAAAT
1 AAAG-AAAAAAGAAAAAG
*
4875276 AAAGAAAAAATAAAAAG
1 AAAGAAAAAAGAAAAAG
*
4875293 AAAAAATAAAAGAAAAA
1 AAAGAA-AAAAGAAAAA
4875310 ATAAAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.13
17 23 0.38
18 18 0.30
19 6 0.10
20 5 0.08
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAAG
Found at i:4875252 original size:7 final size:7
Alignment explanation
Indices: 4875203--4875350 Score: 83
Period size: 7 Copynumber: 20.6 Consensus size: 7
4875193 CTAAGAAGGA
4875203 AAAAAAGG
1 AAAAAA-G
*
4875211 AAAAAGG
1 AAAAAAG
4875218 TAAAAAAG
1 -AAAAAAG
4875226 ACAAAAAG
1 A-AAAAAG
4875234 ACAAAAAG
1 A-AAAAAG
4875242 ---AAAG
1 AAAAAAG
4875246 AAAAAAG
1 AAAAAAG
4875253 AAAATAAAG
1 -AAA-AAAG
4875262 AAAAAAAG
1 -AAAAAAG
4875270 AAAAATAAAG
1 --AAA-AAAG
4875280 AAAAAA-
1 AAAAAAG
*
4875286 TAAAAAG
1 AAAAAAG
4875293 -AAAAA-
1 AAAAAAG
*
4875298 ATAAAAG
1 AAAAAAG
*
4875305 AAAAAAT
1 AAAAAAG
*
4875312 AAAAAAT
1 AAAAAAG
*
4875319 AAAAAAT
1 AAAAAAG
*
4875326 AAAAAAT
1 AAAAAAG
*
4875333 AAAAAAT
1 AAAAAAG
*
4875340 AAAAAAT
1 AAAAAAG
4875347 AAAA
1 AAAA
4875351 GAAAATGAGA
Statistics
Matches: 122, Mismatches: 6, Indels: 25
0.80 0.04 0.16
Matches are distributed among these distances:
4 4 0.03
6 14 0.11
7 53 0.43
8 35 0.29
9 12 0.10
10 4 0.03
ACGTcount: A:0.82, C:0.01, G:0.09, T:0.07
Consensus pattern (7 bp):
AAAAAAG
Found at i:4875271 original size:8 final size:8
Alignment explanation
Indices: 4875201--4875355 Score: 81
Period size: 8 Copynumber: 18.6 Consensus size: 8
4875191 GCCTAAGAAG
4875201 GAAAAAAA
1 GAAAAAAA
* *
4875209 GGAAAAAG
1 GAAAAAAA
*
4875217 GTAAAAAA
1 GAAAAAAA
*
4875225 GACAAAAA
1 GAAAAAAA
4875233 GACAAAAAGA
1 GA-AAAAA-A
*
4875243 AAGAAAAAA
1 GA-AAAAAA
4875252 GAAAATAAA
1 GAAAA-AAA
4875261 GAAAAAAA
1 GAAAAAAA
4875269 GAAAAATAAA
1 G-AAAA-AAA
4875279 GAAAAAATA
1 GAAAAAA-A
4875288 -AAAAGAAA
1 GAAAA-AAA
4875296 -AAATAAAA
1 GAAA-AAAA
4875304 GAAAAAATA
1 GAAAAAA-A
4875313 -AAAAATAA
1 GAAAAA-AA
4875321 -AAAATAAA
1 GAAAA-AAA
4875329 -AAATAAAA
1 GAAA-AAAA
*
4875337 -AATAAAA
1 GAAAAAAA
*
4875344 -AATAAAA
1 GAAAAAAA
4875351 GAAAA
1 GAAAA
4875356 TGAGAGGCTT
Statistics
Matches: 121, Mismatches: 12, Indels: 28
0.75 0.07 0.17
Matches are distributed among these distances:
7 11 0.09
8 66 0.55
9 33 0.27
10 11 0.09
ACGTcount: A:0.81, C:0.01, G:0.10, T:0.07
Consensus pattern (8 bp):
GAAAAAAA
Found at i:4875331 original size:47 final size:49
Alignment explanation
Indices: 4875201--4875356 Score: 135
Period size: 51 Copynumber: 3.1 Consensus size: 49
4875191 GCCTAAGAAG
* * *
4875201 GAAAA-AAAGGAAAAAGGTAAAAAAGACAAAAAGACAAAAAGAAAGAA-AAAA
1 GAAAATAAA-GAAAAA--TAAAAAATACAAAAA-ATAAAAAGAAAAAATAAAA
* *
4875252 GAAAATAAAGAAAAAAAGAAAAATAAAGAAAAAATAAAAAGAAAAAATAAAA
1 GAAAATAAAGAAAAATA-AAAAAT--ACAAAAAATAAAAAGAAAAAATAAAA
*
4875304 GAAAA-AATA-AAAAATAAAAAAT--AAAAAATAAAAAATAAAAAATAAAA
1 GAAAATAA-AGAAAAATAAAAAATACAAAAAAT-AAAAAGAAAAAATAAAA
4875351 GAAAAT
1 GAAAAT
4875357 GAGAGGCTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
46 7 0.08
47 21 0.23
49 1 0.01
50 11 0.12
51 31 0.34
52 19 0.21
ACGTcount: A:0.81, C:0.01, G:0.10, T:0.08
Consensus pattern (49 bp):
GAAAATAAAGAAAAATAAAAAATACAAAAAATAAAAAGAAAAAATAAAA
Found at i:4875350 original size:13 final size:13
Alignment explanation
Indices: 4875253--4875350 Score: 98
Period size: 12 Copynumber: 7.7 Consensus size: 13
4875243 AAGAAAAAAG
*
4875253 AAAATAAAGA-AA
1 AAAATAAAAATAA
*
4875265 AAAAGAAAAAT-A
1 AAAATAAAAATAA
*
4875277 AAGA-AAAAATAA
1 AAAATAAAAATAA
4875289 AAAGA-AAAAATAA
1 AAA-ATAAAAATAA
*
4875302 AAGA-AAAAATAA
1 AAAATAAAAATAA
4875314 AAAATAAAAAATAA
1 AAAAT-AAAAATAA
4875328 AAAATAAAAAATAA
1 AAAAT-AAAAATAA
4875342 AAAATAAAA
1 AAAATAAAA
4875351 GAAAATGAGA
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.08
12 27 0.36
13 15 0.20
14 27 0.36
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:4878208 original size:136 final size:136
Alignment explanation
Indices: 4877911--4878582 Score: 880
Period size: 136 Copynumber: 4.9 Consensus size: 136
4877901 TCCACATATA
* * * * *
4877911 CAATGGAGAGTTCATAATGAGAAGTGCTCCTCCAACAGATGGAGAAAAATTTCATAATGAGAAGA
1 CAATGGAGAGTTCATAATGAGAAGAGCTCCTCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
** ** *
4877976 ACTTGTTTAACCTATTGCGCGATTCACAAACACTTTGAATCAACAATGCCTCGCTTGAGGGATTG
66 ACTTGTTCGACCTATTGCTAGATTCAC-AACACTTTGAATCAACAACGCCTCGCTTGAGGGATTG
4878041 ACATTTC
130 ACATTTC
* * ** * *
4878048 CAATAGAGAATTCATAATGAGAAGAGCTCCTATGATAGAGGGAGAATAAGTTCATAATGAGAAGA
1 CAATGGAGAGTTCATAATGAGAAGAGCTCCTCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
* * * * * *
4878113 ACTTGTTCGACCTATTGCTTGATTTACAACACTTTGAATCAGCAACACCTTGCCTGAGGGATTGA
66 ACTTGTTCGACCTATTGCTAGATTCACAACACTTTGAATCAACAACGCCTCGCTTGAGGGATTGA
4878178 CATTTC
131 CATTTC
* * ** *
4878184 CAATGGAGAGTTCATAATCAGAAGAACTAATCCGACAGAGGGAGAAGAAGTTCATAATGAGAATA
1 CAATGGAGAGTTCATAATGAGAAGAGCTCCTCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
* * * * *
4878249 ACTTGTTTGACCTATTACTATATTCATAACACTTTGAATCAGCAACGCCTCGCTTGAGGGATTGA
66 ACTTGTTCGACCTATTGCTAGATTCACAACACTTTGAATCAACAACGCCTCGCTTGAGGGATTGA
4878314 CATTTC
131 CATTTC
* * * *
4878320 CAATGGAGAGTTCCTAATGAGAAGAACTCATTCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
1 CAATGGAGAGTTCATAATGAGAAGAGCTCCTCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
* * *
4878385 ACTTGCTCGACCTATTGCTAGATTCACAACACTTCGAATCAACAATGCCTCGCTTGAGGGATTGA
66 ACTTGTTCGACCTATTGCTAGATTCACAACACTTTGAATCAACAACGCCTCGCTTGAGGGATTGA
4878450 CATTTC
131 CATTTC
* * * *
4878456 CAATGAAGAATTCATAATGAGAAGAGCTCCTCCGAAAGAGGGAGAAGAAGTTCATAATGGGAAGA
1 CAATGGAGAGTTCATAATGAGAAGAGCTCCTCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
* * * *
4878521 ACTTGTTCGACCTATTGCTAGATTTACAACA-TTTCAAATCAGA-AACGCCTCGTTTAAGGGAT
66 ACTTGTTCGACCTATTGCTAGATTCACAACACTTT-GAATCA-ACAACGCCTCGCTTGAGGGAT
4878583 CATTATTTCG
Statistics
Matches: 465, Mismatches: 68, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
135 2 0.00
136 385 0.83
137 78 0.17
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (136 bp):
CAATGGAGAGTTCATAATGAGAAGAGCTCCTCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
ACTTGTTCGACCTATTGCTAGATTCACAACACTTTGAATCAACAACGCCTCGCTTGAGGGATTGA
CATTTC
Found at i:4881894 original size:51 final size:52
Alignment explanation
Indices: 4881839--4882039 Score: 171
Period size: 51 Copynumber: 3.9 Consensus size: 52
4881829 TTTCATGATG
* * * *
4881839 GACTTACAACATTCAAATTTAACATATAATT-CATCGGTTGTACTTAACATA
1 GACTTACACCACTCAAATTTAACATATAATTCCACCGGTGGTACTTAACATA
* * *
4881890 GACTTAGACCACTCAAATTTATCATATAATTCCACCGGTGGTACTTAACGTA
1 GACTTACACCACTCAAATTTAACATATAATTCCACCGGTGGTACTTAACATA
* * * * * *
4881942 GACTTACACCAGTCAAA-TTAAC-TCTTAATTCTAGCAGTGGTA-TACAACATA
1 GACTTACACCACTCAAATTTAACAT-ATAATTCCACCGGTGGTACT-TAACATA
* * * * *
4881993 GACTTACACGAGTCAAA-TTAAC-TCTTATTTCCAACGGTGGTACTTAA
1 GACTTACACCACTCAAATTTAACAT-ATAATTCCACCGGTGGTACTTAA
4882040 TCTATGTATC
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
50 2 0.02
51 89 0.72
52 33 0.27
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (52 bp):
GACTTACACCACTCAAATTTAACATATAATTCCACCGGTGGTACTTAACATA
Found at i:4886578 original size:18 final size:18
Alignment explanation
Indices: 4886551--4886599 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
4886541 GAAGCATAGA
* *
4886551 AGAGATAGAGATTGAGGC
1 AGAGACAGAGATAGAGGC
4886569 AGAGACAGAGATAGAGGC
1 AGAGACAGAGATAGAGGC
4886587 AGAGACAGAGATA
1 AGAGACAGAGATA
4886600 AAGACTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.45, C:0.08, G:0.37, T:0.10
Consensus pattern (18 bp):
AGAGACAGAGATAGAGGC
Found at i:4887530 original size:16 final size:16
Alignment explanation
Indices: 4887509--4887569 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
4887499 ATATTGAAAC
4887509 TTGAACTCAAAAAGGA
1 TTGAACTCAAAAAGGA
4887525 TTGAACTCAAAAAGGA
1 TTGAACTCAAAAAGGA
*
4887541 TTGAACTCAAAAAGGC
1 TTGAACTCAAAAAGGA
4887557 TTGAACTCAAAAA
1 TTGAACTCAAAAA
4887570 AAAATTTAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (16 bp):
TTGAACTCAAAAAGGA
Found at i:4889279 original size:31 final size:31
Alignment explanation
Indices: 4889244--4889313 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
4889234 CTTTTAAAAC
*
4889244 TTGTAATACAG-CCCCCTAATATTTAGTCCAT
1 TTGTAATACAGTCCCCC-AACATTTAGTCCAT
** *
4889275 TTGTAATATGGTCCCCCAACATTTAGTCCGT
1 TTGTAATACAGTCCCCCAACATTTAGTCCAT
*
4889306 TTGCAATA
1 TTGTAATA
4889314 TGGTCCCCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (31 bp):
TTGTAATACAGTCCCCCAACATTTAGTCCAT
Found at i:4889314 original size:31 final size:32
Alignment explanation
Indices: 4889255--4889321 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
4889245 TGTAATACAG
* *
4889255 CCCCCTAATATTTAGTCCATTTGTAATATGGT
1 CCCCCTAACATTTAGTCCATTTGCAATATGGT
*
4889287 CCCCC-AACATTTAGTCCGTTTGCAATATGGT
1 CCCCCTAACATTTAGTCCATTTGCAATATGGT
4889318 CCCC
1 CCCC
4889322 GACGTAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.34
Consensus pattern (32 bp):
CCCCCTAACATTTAGTCCATTTGCAATATGGT
Found at i:4890490 original size:140 final size:140
Alignment explanation
Indices: 4890238--4890503 Score: 505
Period size: 140 Copynumber: 1.9 Consensus size: 140
4890228 CAGGACACTC
4890238 GAGTTACTTTAGAAGATGATGATAGTTTCGAGGTATAGAGTATCTGGATATCCTTAAGCAAGTGC
1 GAGTTACTTTAGAAGATGATGATAGTTTCGAGGTATAGAGTATCTGGATATCCTTAAGCAAGTGC
4890303 GTGTGGCACTTTAAGACTAAATAGGGCGCAAGGCCCGAACACTCACAAAGGGTGGGTTAGTCCAG
66 GTGTGGCACTTTAAGACTAAATAGGGCGCAAGGCCCGAACACTCACAAAGGGTGGGTTAGTCCAG
4890368 TGTAGTGTCT
131 TGTAGTGTCT
* *
4890378 GAGTTACTTTAGCAGATGATGATAGTTTCGAGGTATAGAGTATCTGTATATCCTTAAGCAAGTGC
1 GAGTTACTTTAGAAGATGATGATAGTTTCGAGGTATAGAGTATCTGGATATCCTTAAGCAAGTGC
*
4890443 GTGTGGCACTTTAAGACTAAATAGGGCGCAAGGCCCGAACACTCACAAGGGGTGGGTTAGT
66 GTGTGGCACTTTAAGACTAAATAGGGCGCAAGGCCCGAACACTCACAAAGGGTGGGTTAGT
4890504 TGAGATGTAT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 123 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (140 bp):
GAGTTACTTTAGAAGATGATGATAGTTTCGAGGTATAGAGTATCTGGATATCCTTAAGCAAGTGC
GTGTGGCACTTTAAGACTAAATAGGGCGCAAGGCCCGAACACTCACAAAGGGTGGGTTAGTCCAG
TGTAGTGTCT
Found at i:4891279 original size:65 final size:65
Alignment explanation
Indices: 4891210--4891393 Score: 214
Period size: 64 Copynumber: 2.9 Consensus size: 65
4891200 GATTTAATTG
*
4891210 AACATCGAATGCATTTCATGCACCGATGCACTCTACATGCATCGATGCACTC-GGAATATTTTTC
1 AACATCGAATGCATTTCATGCATCGATGCACTCTACATGCATCGATGCACTCAGG-ATATTTTTC
4891274 A
65 A
* * **** *
4891275 AACATCAAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACTCTACATGCATCGATGCACTCAGGATATTTTTCA
* * * *
4891339 AACATCGAATGCACTTCATGCATCGTTGCACTCTTA-GTGCACCGATGCACT-AGGA
1 AACATCGAATGCATTTCATGCATCGATGCACTC-TACATGCATCGATGCACTCAGGA
4891394 GTCCAACGGT
Statistics
Matches: 97, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
64 52 0.54
65 45 0.46
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTACATGCATCGATGCACTCAGGATATTTTTCA
Found at i:4891361 original size:64 final size:65
Alignment explanation
Indices: 4891210--4891369 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
4891200 GATTTAATTG
* ***
4891210 AACATCGAATGCATTTCATGCACCGATGCACTCTACATGCATCGATGCACTCGGAATATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGATGCACTCGGAATATTTTTCA
* * * *
4891275 AACATCAAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGG-CTATTTTTC
1 AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGATGCACTC-GGAATATTTTTC
4891338 A
65 A
* *
4891339 AACATCGAATGCACTTCATGCATCGTTGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
4891370 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 37 0.45
65 45 0.55
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGATGCACTCGGAATATTTTTCA
Found at i:4897834 original size:36 final size:36
Alignment explanation
Indices: 4897792--4897990 Score: 181
Period size: 36 Copynumber: 5.6 Consensus size: 36
4897782 AACAATGATA
*
4897792 ATCAATAACAAGAACATGTATATTATGCATATAATC
1 ATCAATAACAAGAACATGTATATCATGCATATAATC
* *
4897828 ATCAATAACAAGAGCATGTATATCATTCATATAATC
1 ATCAATAACAAGAACATGTATATCATGCATATAATC
**
4897864 ATCAATAACAA-ACACATGTATGCCATGCATATAATC
1 ATCAATAACAAGA-ACATGTATATCATGCATATAATC
* * * * *
4897900 ATTAATAGCAAGCACA--TACATCATGCAAATAATC
1 ATCAATAACAAGAACATGTATATCATGCATATAATC
* * ** *
4897934 ATTAGTAGA-AAGTGCATGTATATCATGCATAAAATC
1 ATCAATA-ACAAGAACATGTATATCATGCATATAATC
* * **
4897970 ACCAGTAACAAGTGCATGTAT
1 ATCAATAACAAGAACATGTAT
4897991 TGTTAGTGTG
Statistics
Matches: 134, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
34 25 0.19
35 2 0.01
36 107 0.80
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (36 bp):
ATCAATAACAAGAACATGTATATCATGCATATAATC
Found at i:4899117 original size:78 final size:78
Alignment explanation
Indices: 4899020--4899174 Score: 183
Period size: 77 Copynumber: 2.0 Consensus size: 78
4899010 ATATAGTAAG
*
4899020 TAAACATTAAAAGAATGTAATTCTGATTACAACTCTTTTAATGAAT-TTTAAAT-TCAGAA-TAA
1 TAAACATTAAAAGAATGTAATTCAGATTACAACTC-TTTAATGAATATTT-AATGT-A-AATTAA
*
4899082 TTAAATAAGAGTTTAAA
62 TTAAATAAGAATTTAAA
* * * * *
4899099 TAAACGTT-AAAGAGTGTAATTCAGATTATAATTCTTTAATGGATATTTAATGTAAATTAATTAA
1 TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTAATGAATATTTAATGTAAATTAATTAA
4899163 ATAAGAATTTAA
66 ATAAGAATTTAA
4899175 TTAATTCGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
76 2 0.03
77 31 0.47
78 26 0.39
79 7 0.11
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTAATGAATATTTAATGTAAATTAATTAA
ATAAGAATTTAAA
Found at i:4899624 original size:36 final size:36
Alignment explanation
Indices: 4899532--4899688 Score: 163
Period size: 36 Copynumber: 4.3 Consensus size: 36
4899522 ACTGTTCCAA
* * *
4899532 CATGTATATCATGCATATAA-ATATCAATAGTAAGCA
1 CATGTATATCATGCATATAATA-ATCAGTAGAAAGCG
4899568 CATGTATATCATGCATATAATAATCAGTAGAAAGCG
1 CATGTATATCATGCATATAATAATCAGTAGAAAGCG
* * * ** *
4899604 CATGTGTATCATGCATATAATCATCACTCTACAAGTG
1 CATGTATATCATGCATATAATAATCAGTAGA-AAGCG
* * * * *
4899641 CAAGCATATCATGCATATAATCATCAGTAGCAAGAG
1 CATGTATATCATGCATATAATAATCAGTAGAAAGCG
4899677 CATGTATATCAT
1 CATGTATATCAT
4899689 ATAGGGGGAC
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
36 71 0.71
37 29 0.29
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (36 bp):
CATGTATATCATGCATATAATAATCAGTAGAAAGCG
Found at i:4903295 original size:51 final size:50
Alignment explanation
Indices: 4903234--4903408 Score: 149
Period size: 51 Copynumber: 3.4 Consensus size: 50
4903224 ACTAAACATG
* *
4903234 AACAGACTTACACAAGTGAAATTTAACACATATTTCCAGCATTAATCTCAT
1 AACAGACTTACACAAGTCAAATTTAACACA-ATTTCCAACATTAATCTCAT
** * * * *
4903285 AACAGACTTACACCGGTCATATTTAACATACAATTT-CAATATTGATCTCAC
1 AACAGACTTACACAAGTCAAATTTAAC--ACAATTTCCAACATTAATCTCAT
* * *
4903336 AAAAGACTTACA-AGAGTTAATTTTATCACACAA-TTCCAACATTAATCTCAT
1 AACAGACTTACACA-AGTCAAATTTA--ACACAATTTCCAACATTAATCTCAT
* * *
4903387 CACAAACTTACACCAGTCAAAT
1 AACAGACTTACACAAGTCAAAT
4903409 CTGACATATA
Statistics
Matches: 94, Mismatches: 23, Indels: 14
0.72 0.18 0.11
Matches are distributed among these distances:
50 2 0.02
51 83 0.88
52 4 0.04
53 5 0.05
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.29
Consensus pattern (50 bp):
AACAGACTTACACAAGTCAAATTTAACACAATTTCCAACATTAATCTCAT
Found at i:4906711 original size:23 final size:23
Alignment explanation
Indices: 4906685--4906728 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4906675 TCACCGGTTG
*
4906685 ACCACCGGCTGGTCACTATTCCA
1 ACCACCGACTGGTCACTATTCCA
*
4906708 ACCACTGACTGGTCACTATTC
1 ACCACCGACTGGTCACTATTC
4906729 ACGGCCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.25
Consensus pattern (23 bp):
ACCACCGACTGGTCACTATTCCA
Found at i:4907582 original size:36 final size:36
Alignment explanation
Indices: 4907535--4907957 Score: 670
Period size: 36 Copynumber: 11.8 Consensus size: 36
4907525 TCTGTTCTTA
*
4907535 CTTCACTACTCTTCCGTGGAGGCTAAGATGGTTTTG
1 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
*
4907571 CTTCACTACTCTTCCGTGGAGGCTAAGATGGATTTG
1 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
4907607 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
1 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
*
4907643 CTTCACTACTCTTCCGTGGAGGCTAAGATTGCTTTAG
1 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTT-G
* *
4907680 -TTCACTACACTTCCGTGGAGGCTAAAATGGCTTTG
1 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
* *
4907715 CTTCACTACTCTTCCGTAGAGACTAAGATGGCTTTG
1 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
*
4907751 CTTCACTACTCTTCTGTGGAGGCTAAGATGGCTTTG
1 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
* **
4907787 CTTTACTACTCTTCCGTGGAGGCTAAGATTTCTTTG
1 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
* *
4907823 CTTCACTACTCTTCCGTGGAGGATAA-AGTTGCTTTG
1 CTTCACTACTCTTCCGTGGAGGCTAAGA-TGGCTTTG
*
4907859 CTTCACTACTCTTCCATGGAGGCTAAGATGGCTTTG
1 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
* *
4907895 CTTCACTACTCTTCTGTGGAGGCTAAGATTGCTTTG
1 CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
4907931 CTTCACTACTCTTCCGTGGAGGCTAAG
1 CTTCACTACTCTTCCGTGGAGGCTAAG
4907958 TTTGAAATAA
Statistics
Matches: 356, Mismatches: 27, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
35 2 0.01
36 352 0.99
37 2 0.01
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (36 bp):
CTTCACTACTCTTCCGTGGAGGCTAAGATGGCTTTG
Done.