Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 13 of 32
Found at i:7162849 original size:17 final size:17
Alignment explanation
Indices: 7162804--7162845 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
7162794 ACATCTATAC
7162804 ATTAATA-TTTAA-TAA
1 ATTAATATTTTAATTAA
7162819 ATTAATATTTTAATTAA
1 ATTAATATTTTAATTAA
7162836 A-TAATATTTT
1 ATTAATATTTT
7162846 TAATCAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.28
16 14 0.56
17 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTAATATTTTAATTAA
Found at i:7181217 original size:21 final size:21
Alignment explanation
Indices: 7181171--7181218 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
7181161 TAAACCTAAT
*
7181171 GGCAAAGATAAGAAAAATAAA
1 GGCACAGATAAGAAAAATAAA
*
7181192 GGCACAGATAAGAAATATAAA
1 GGCACAGATAAGAAAAATAAA
7181213 GGCACA
1 GGCACA
7181219 AATTTATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.58, C:0.10, G:0.21, T:0.10
Consensus pattern (21 bp):
GGCACAGATAAGAAAAATAAA
Found at i:7189337 original size:15 final size:15
Alignment explanation
Indices: 7189317--7189350 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7189307 CTTAATGTGC
*
7189317 GCTGCTGCAGTTGCT
1 GCTGCTGCAGTGGCT
*
7189332 GCTGCTGCTGTGGCT
1 GCTGCTGCAGTGGCT
7189347 GCTG
1 GCTG
7189351 AGCAGCTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.26, G:0.38, T:0.32
Consensus pattern (15 bp):
GCTGCTGCAGTGGCT
Found at i:7196750 original size:29 final size:29
Alignment explanation
Indices: 7196709--7196780 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
7196699 CAAATAAATT
* * *
7196709 TTTAAATTATTATATAAATTT-TTTAAAAA
1 TTTATATTTTTAT-TAAATTTAATTAAAAA
* **
7196738 TTTATATTTTTATTATATTTAATTAAATT
1 TTTATATTTTTATTAAATTTAATTAAAAA
7196767 TTTATATTTTTATT
1 TTTATATTTTTATT
7196781 TTAAATNNNN
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 6 0.17
29 30 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTATATTTTTATTAAATTTAATTAAAAA
Found at i:7196784 original size:21 final size:21
Alignment explanation
Indices: 7196737--7196786 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
7196727 TTTTTTAAAA
*
7196737 ATTTATATTTTTATTATATTT
1 ATTTAAATTTTTATTATATTT
* *
7196758 AATTAAATTTTTA-TATTTTT
1 ATTTAAATTTTTATTATATTT
7196778 ATTTTAAAT
1 A-TTTAAAT
7196787 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTAAATTTTTATTATATTT
Found at i:7197252 original size:17 final size:17
Alignment explanation
Indices: 7197212--7197258 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
7197202 AATTTTTAAT
*
7197212 TTTTTAAAATAATAATTA
1 TTTTTAAAAT-ATAAATA
*
7197230 TATTTAAAATATAAATA
1 TTTTTAAAATATAAATA
7197247 TTTTTAAAATAT
1 TTTTTAAAATAT
7197259 GATATTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTTAAAATATAAATA
Found at i:7198589 original size:26 final size:25
Alignment explanation
Indices: 7198544--7198598 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
7198534 CTTTTCATTG
*
7198544 AAAATTCGTCGAAAATTTTCAACGA
1 AAAATTCGTCGAAAAATTTCAACGA
* **
7198569 AAAATTCTGTCTAAAAATTTCGTCGA
1 AAAATTC-GTCGAAAAATTTCAACGA
7198595 AAAA
1 AAAA
7198599 AGTGCATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (25 bp):
AAAATTCGTCGAAAAATTTCAACGA
Found at i:7198884 original size:23 final size:23
Alignment explanation
Indices: 7198853--7198897 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
7198843 ACTTGCCATC
*
7198853 ATAAGCAAAGACTATCAATTGTT
1 ATAAACAAAGACTATCAATTGTT
7198876 ATAAACAAAGACTATCAATTGT
1 ATAAACAAAGACTATCAATTGT
7198898 AAACTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (23 bp):
ATAAACAAAGACTATCAATTGTT
Found at i:7199012 original size:28 final size:28
Alignment explanation
Indices: 7198969--7199025 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
7198959 TCTCCACATG
*
7198969 CCAGAGCCCACTGTTCAGAATACTCATT
1 CCAGAGCCCACGGTTCAGAATACTCATT
7198997 CCAGAGCCCACGGTTCAGAATACTCATT
1 CCAGAGCCCACGGTTCAGAATACTCATT
7199025 C
1 C
7199026 GACAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (28 bp):
CCAGAGCCCACGGTTCAGAATACTCATT
Found at i:7199340 original size:28 final size:28
Alignment explanation
Indices: 7199308--7199395 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
7199298 TTGCCGGTGA
7199308 GAGGAAAGGGAGAGACGCCAGTAATAGG
1 GAGGAAAGGGAGAGACGCCAGTAATAGG
* * * * * *
7199336 GAGGAAA--AAGA-AGGGCTGTCAGT-GA
1 GAGGAAAGGGAGAGACGCCAGT-AATAGG
*
7199361 GAGGAAAGGGAGAGACGCCAATAATAGG
1 GAGGAAAGGGAGAGACGCCAGTAATAGG
7199389 GAGGAAA
1 GAGGAAA
7199396 AAGAAGGGTT
Statistics
Matches: 42, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
25 13 0.31
26 5 0.12
27 5 0.12
28 19 0.45
ACGTcount: A:0.42, C:0.09, G:0.41, T:0.08
Consensus pattern (28 bp):
GAGGAAAGGGAGAGACGCCAGTAATAGG
Found at i:7199386 original size:53 final size:53
Alignment explanation
Indices: 7199304--7199459 Score: 249
Period size: 53 Copynumber: 2.9 Consensus size: 53
7199294 GTTGTTGCCG
7199304 GTGAGAGGAAAGGGAGAGACGCCAGTAATAGGGAGGAAAAAGAAGGGCTGTCA
1 GTGAGAGGAAAGGGAGAGACGCCAGTAATAGGGAGGAAAAAGAAGGGCTGTCA
* * * *
7199357 GTGAGAGGAAAGGGAGAGACGCCAATAATAGGGAGGAAAAAGAAGGGTTATCG
1 GTGAGAGGAAAGGGAGAGACGCCAGTAATAGGGAGGAAAAAGAAGGGCTGTCA
* * *
7199410 GTGAAAGGAGAGGGAGAGACGCCGGTAATAGGGAGGAAAAAGAAGGGCTG
1 GTGAGAGGAAAGGGAGAGACGCCAGTAATAGGGAGGAAAAAGAAGGGCTG
7199460 CCAACGTAGG
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 93 1.00
ACGTcount: A:0.40, C:0.08, G:0.42, T:0.10
Consensus pattern (53 bp):
GTGAGAGGAAAGGGAGAGACGCCAGTAATAGGGAGGAAAAAGAAGGGCTGTCA
Found at i:7200471 original size:23 final size:24
Alignment explanation
Indices: 7200445--7200489 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
7200435 TTGTCCGTTG
7200445 GAAAATTCCATTAAAAA-TCTGTC
1 GAAAATTCCATTAAAAAGTCTGTC
**
7200468 GAAAATTCTGTTAAAAAGTCTG
1 GAAAATTCCATTAAAAAGTCTG
7200490 ATGGGAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (24 bp):
GAAAATTCCATTAAAAAGTCTGTC
Found at i:7200571 original size:110 final size:109
Alignment explanation
Indices: 7200388--7200585 Score: 247
Period size: 110 Copynumber: 1.8 Consensus size: 109
7200378 TAGCGAGTTT
* * *
7200388 TAAATTTTTTTAGCTCCTAAACTTTCCGACGGATTTTCAACGGATTATTGTCCGTTGGAAAATTC
1 TAAATTTTTTTAGCTCCTAAACTTTCCGACGGATTTCCAAAGAATTATTGTCCGTTGGAAAATTC
**
7200453 CATTAAAAA-TCTGTCGAAAATTCTGTTAAAAAGTCTGATGGGAG
66 CAACAAAAATTC-GTCGAAAATTCTGTTAAAAAGTCTGATGGGAG
* * * * **
7200497 TAAATTTTTTTGAAG-TCTTAAATTTTCCGATGGATTTCCAAAGAATTATTTTTTGTTGGAAAAT
1 TAAATTTTTTT--AGCTCCTAAACTTTCCGACGGATTTCCAAAGAATTATTGTCCGTTGGAAAAT
*
7200561 TCCAACAAAAATTCGTTGAAAATTC
64 TCCAACAAAAATTCGTCGAAAATTC
7200586 CATTGGAAAG
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
109 11 0.15
110 59 0.80
111 4 0.05
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (109 bp):
TAAATTTTTTTAGCTCCTAAACTTTCCGACGGATTTCCAAAGAATTATTGTCCGTTGGAAAATTC
CAACAAAAATTCGTCGAAAATTCTGTTAAAAAGTCTGATGGGAG
Found at i:7200596 original size:110 final size:109
Alignment explanation
Indices: 7200388--7200617 Score: 239
Period size: 110 Copynumber: 2.1 Consensus size: 109
7200378 TAGCGAGTTT
* * *
7200388 TAAATTTTTTTAGCTCCTAAACTTTCCGACGGATTTTCAACGGATTATTGTCCGTTGGAAAATTC
1 TAAATTTTTTTAGCTCCTAAACTTTCCGACGGATTTCCAAAGAATTATTGTCCGTTGGAAAATTC
** ** **
7200453 CATTAAAAATCTGTCGAAAATTCTGTTAAAAAGTCTGATGGGAG
66 CAACAAAAATCTGTCGAAAATTCCATTAAAAAGTCTGACCGGAG
* * * * **
7200497 TAAATTTTTTTGAAG-TCTTAAATTTTCCGATGGATTTCCAAAGAATTATTTTTTGTTGGAAAAT
1 TAAATTTTTTT--AGCTCCTAAACTTTCCGACGGATTTCCAAAGAATTATTGTCCGTTGGAAAAT
* ** *
7200561 TCCAACAAAAAT-TCGTTGAAAATTCCATTGGAAAGTTTGACCGGAG
64 TCCAACAAAAATCT-GTCGAAAATTCCATTAAAAAGTCTGACCGGAG
*
7200607 TAATTTTTTTT
1 TAAATTTTTTT
7200618 TTGCATCAAA
Statistics
Matches: 98, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
109 12 0.12
110 84 0.86
111 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (109 bp):
TAAATTTTTTTAGCTCCTAAACTTTCCGACGGATTTCCAAAGAATTATTGTCCGTTGGAAAATTC
CAACAAAAATCTGTCGAAAATTCCATTAAAAAGTCTGACCGGAG
Found at i:7203478 original size:2 final size:2
Alignment explanation
Indices: 7203471--7203496 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7203461 ACTACTCTAT
7203471 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
7203497 GCGGGAATTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:7209365 original size:2 final size:2
Alignment explanation
Indices: 7209358--7209382 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7209348 GATAATTGAC
7209358 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 T
7209383 TCCAAACTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7211253 original size:22 final size:21
Alignment explanation
Indices: 7211234--7211278 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
7211224 TGCAATATTA
7211234 TATT-ATAATAAGTT-GTATAT
1 TATTAATAATAA-TTAGTATAT
7211254 TATTAATAATAATTAGTATTAT
1 TATTAATAATAATTAGTA-TAT
7211276 TAT
1 TAT
7211279 GATGATGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.27
21 10 0.45
22 6 0.27
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
TATTAATAATAATTAGTATAT
Found at i:7224164 original size:10 final size:10
Alignment explanation
Indices: 7224135--7224167 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
7224125 CTCTCTCTCT
*
7224135 ATATATATAT
1 ATATATATAA
7224145 ATATATATAA
1 ATATATATAA
7224155 ATATATATAA
1 ATATATATAA
7224165 ATA
1 ATA
7224168 AAAGAACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATAA
Found at i:7224181 original size:2 final size:2
Alignment explanation
Indices: 7224134--7224163 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
7224124 TCTCTCTCTC
*
7224134 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7224164 AATAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7226894 original size:2 final size:2
Alignment explanation
Indices: 7226889--7226927 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
7226879 CATGTGTGTG
7226889 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7226928 TGACAAGACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7233973 original size:42 final size:42
Alignment explanation
Indices: 7233914--7233994 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
7233904 GTAAACTCTA
7233914 AACTTTTCCGATTCACATTAGATCAGTCCTTGATTGTTTCTT
1 AACTTTTCCGATTCACATTAGATCAGTCCTTGATTGTTTCTT
*
7233956 AACTTTTCCTATTCACATTAGATCAGTCCTTGATTGTTT
1 AACTTTTCCGATTCACATTAGATCAGTCCTTGATTGTTT
7233995 ACTTTATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (42 bp):
AACTTTTCCGATTCACATTAGATCAGTCCTTGATTGTTTCTT
Found at i:7240504 original size:54 final size:55
Alignment explanation
Indices: 7240321--7240548 Score: 164
Period size: 54 Copynumber: 4.2 Consensus size: 55
7240311 TCGGGACTAG
* * * ** ** * *
7240321 CCCTCTCT-TTCCTATAAGGACTTCGACTGGAGCCACGAGCATGGTCAGCACCAG
1 CCCTCTCTCTTCCTATAAGGACTACGACTAGAGCCACGACCATAATCAGGGCTAC
** * * * * *
7240375 CCCTCTCTCTT-CGGTAAGGACTACGGCTAGTGCCCCGGCCATATTCAGGGCTAGC
1 CCCTCTCTCTTCCTATAAGGACTACGACTAGAGCCACGACCATAATCAGGGCTA-C
* * ** * * *
7240430 TCCATCTCTC-T--TATAGGGACTTGGACT-GCGGCCCCGACCATAATCAGGGCTCC
1 -CCCTCTCTCTTCCTATAAGGACTACGACTAG-AGCCACGACCATAATCAGGGCTAC
*
7240483 CCCTCTC-CTTCCTATAAGGACTACGACTAGAGCCACGGCCATAATCAGGGCTAC
1 CCCTCTCTCTTCCTATAAGGACTACGACTAGAGCCACGACCATAATCAGGGCTAC
7240537 CCCTCTCTCTTC
1 CCCTCTCTCTTC
7240549 GGTAGGGACT
Statistics
Matches: 131, Mismatches: 34, Indels: 17
0.72 0.19 0.09
Matches are distributed among these distances:
51 1 0.01
52 7 0.05
53 2 0.02
54 105 0.80
55 8 0.06
56 8 0.06
ACGTcount: A:0.20, C:0.36, G:0.21, T:0.24
Consensus pattern (55 bp):
CCCTCTCTCTTCCTATAAGGACTACGACTAGAGCCACGACCATAATCAGGGCTAC
Found at i:7240558 original size:54 final size:54
Alignment explanation
Indices: 7240375--7240558 Score: 169
Period size: 54 Copynumber: 3.4 Consensus size: 54
7240365 TCAGCACCAG
* * * *
7240375 CCCTCTCTCTTCGGTAAGGACTACGGCTAGTGCCCCGGCCATATTCAGGGCTAGC
1 CCCTCTCTCTTCGATAAGGACTACGACTAGAGCCCCGGCCATAATCAGGGCTA-C
* * ** * * *
7240430 TCCATCTCTCTT--ATAGGGACTTGGACT-GCGGCCCCGACCATAATCAGGGCTCC
1 -CCCTCTCTCTTCGATAAGGACTACGACTAG-AGCCCCGGCCATAATCAGGGCTAC
* *
7240483 CCCTCTC-CTTCCTATAAGGACTACGACTAGAGCCACGGCCATAATCAGGGCTAC
1 CCCTCTCTCTT-CGATAAGGACTACGACTAGAGCCCCGGCCATAATCAGGGCTAC
* *
7240537 CCCTCTCTCTTCGGTAGGGACT
1 CCCTCTCTCTTCGATAAGGACT
7240559 TGGAGATCGC
Statistics
Matches: 101, Mismatches: 21, Indels: 14
0.74 0.15 0.10
Matches are distributed among these distances:
51 3 0.03
52 6 0.06
53 2 0.02
54 76 0.75
55 4 0.04
56 10 0.10
ACGTcount: A:0.19, C:0.35, G:0.22, T:0.24
Consensus pattern (54 bp):
CCCTCTCTCTTCGATAAGGACTACGACTAGAGCCCCGGCCATAATCAGGGCTAC
Found at i:7247307 original size:24 final size:25
Alignment explanation
Indices: 7247248--7247299 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
7247238 AAGAGTCTTA
7247248 ATTAAATTTTAATTGGTTATAGTAT
1 ATTAAATTTTAATTGGTTATAGTAT
7247273 ATTAAATTTTAATTGGTTATA-TAT
1 ATTAAATTTTAATTGGTTATAGTAT
7247297 ATT
1 ATT
7247300 GTGTTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (25 bp):
ATTAAATTTTAATTGGTTATAGTAT
Found at i:7265825 original size:2 final size:2
Alignment explanation
Indices: 7265818--7265853 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7265808 TAATGTACAT
7265818 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
7265854 AAGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7268464 original size:25 final size:23
Alignment explanation
Indices: 7268419--7268465 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
7268409 ATCTTTGGAA
*
7268419 TATAGAAATAATAAAAGACATAT
1 TATAGAAATAATAAAACACATAT
*
7268442 TATAGAAATATGATAATACACATA
1 TATAGAAATA--ATAAAACACATA
7268466 CTAGGAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
25 10 0.50
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (23 bp):
TATAGAAATAATAAAACACATAT
Found at i:7269345 original size:21 final size:21
Alignment explanation
Indices: 7269319--7269398 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
7269309 TACAGAAACA
7269319 TGTTACACGCCATGATTAGAT
1 TGTTACACGCCATGATTAGAT
* * * *
7269340 TGTTACATGCCATGTATAAAAACG
1 TGTTACACGCCATG-AT-TAGA-T
* * * *
7269364 TGTGACACGGCATGGTTAGGT
1 TGTTACACGCCATGATTAGAT
7269385 TGTTACACGCCATG
1 TGTTACACGCCATG
7269399 TACAAAAATA
Statistics
Matches: 42, Mismatches: 14, Indels: 6
0.68 0.23 0.10
Matches are distributed among these distances:
21 25 0.60
22 3 0.07
23 3 0.07
24 11 0.26
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (21 bp):
TGTTACACGCCATGATTAGAT
Found at i:7269372 original size:45 final size:45
Alignment explanation
Indices: 7269295--7269411 Score: 135
Period size: 45 Copynumber: 2.6 Consensus size: 45
7269285 TACACCATGA
* * * *
7269295 TGTTACACACTATGTACAGAAACATGTTACACGCCATGATTAGAT
1 TGTTACACGCCATGTACAAAAACATGTGACACGCCATGATTAGAT
* * * * * *
7269340 TGTTACATGCCATGTATAAAAACGTGTGACACGGCATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTGACACGCCATGATTAGAT
*
7269385 TGTTACACGCCATGTACAAAAATATGT
1 TGTTACACGCCATGTACAAAAACATGT
7269412 TCATGTCATG
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (45 bp):
TGTTACACGCCATGTACAAAAACATGTGACACGCCATGATTAGAT
Found at i:7269512 original size:26 final size:25
Alignment explanation
Indices: 7269459--7269588 Score: 102
Period size: 26 Copynumber: 5.0 Consensus size: 25
7269449 AAAATACTAT
* *
7269459 TGTTACACGCCATG-TACAAAAACA
1 TGTTACACGCCATGTTAAAAAAAAA
7269483 TGTTACACGCCATGTTAAAAAAAAA
1 TGTTACACGCCATGTTAAAAAAAAA
* *
7269508 CTGTTGTTACACGCTATG-TAAAAAAACA
1 ----TGTTACACGCCATGTTAAAAAAAAA
* * ***
7269536 TGTTACATGTCATGGTTAAAAAAGGT
1 TGTTACACGCCAT-GTTAAAAAAAAA
*
7269562 TGTTACACGTCATGTTGAAAAAAAAA
1 TGTTACACGCCATGTT-AAAAAAAAA
7269588 T
1 T
7269589 ACTATTATTA
Statistics
Matches: 84, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
24 24 0.29
25 12 0.14
26 26 0.31
28 9 0.11
29 13 0.15
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (25 bp):
TGTTACACGCCATGTTAAAAAAAAA
Found at i:7269518 original size:53 final size:54
Alignment explanation
Indices: 7269438--7269558 Score: 181
Period size: 53 Copynumber: 2.2 Consensus size: 54
7269428 TTATTATACA
*
7269438 CCATGTTAAAAAAAATACTATTGTTACACGCCATGTACAAAAACATGTTACACG
1 CCATGTTAAAAAAAATACTATTGTTACACGCCATGTAAAAAAACATGTTACACG
* * *
7269492 CCATGTTAAAAAAAA-ACTGTTGTTACACGCTATGTAAAAAAACATGTTACATG
1 CCATGTTAAAAAAAATACTATTGTTACACGCCATGTAAAAAAACATGTTACACG
*
7269545 TCATGGTTAAAAAA
1 CCAT-GTTAAAAAA
7269559 GGTTGTTACA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 37 0.61
54 24 0.39
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (54 bp):
CCATGTTAAAAAAAATACTATTGTTACACGCCATGTAAAAAAACATGTTACACG
Found at i:7269520 original size:29 final size:28
Alignment explanation
Indices: 7269438--7269629 Score: 100
Period size: 24 Copynumber: 6.9 Consensus size: 28
7269428 TTATTATACA
*
7269438 CCATGTTAAAAAAAATACTATTGTTACACG
1 CCATGTT-AAAAAAA-ACTGTTGTTACACG
* *
7269468 CCATG-T-ACAAAAAC--ATGTTACACG
1 CCATGTTAAAAAAAACTGTTGTTACACG
7269492 CCATGTTAAAAAAAAACTGTTGTTACACG
1 CCATGTT-AAAAAAAACTGTTGTTACACG
* * *
7269521 CTATG-T-AAAAAAAC--ATGTTACATG
1 CCATGTTAAAAAAAACTGTTGTTACACG
* *
7269545 TCATGGTT--AAAAAA-GGTTGTTACACG
1 CCAT-GTTAAAAAAAACTGTTGTTACACG
* * *
7269571 TCATGTTGAAAAAAAAATACTATTATTACACG
1 CCATGTT---AAAAAAA-ACTGTTGTTACACG
* * *
7269603 TCATGTTGAAAAAATATTGTTGTTACA
1 CCATGTT-AAAAAAAACTGTTGTTACA
7269630 TGGCATATTC
Statistics
Matches: 127, Mismatches: 19, Indels: 33
0.71 0.11 0.18
Matches are distributed among these distances:
24 24 0.19
25 11 0.09
26 23 0.18
27 12 0.09
28 1 0.01
29 23 0.18
30 16 0.13
31 1 0.01
32 16 0.13
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (28 bp):
CCATGTTAAAAAAAACTGTTGTTACACG
Found at i:7269851 original size:17 final size:17
Alignment explanation
Indices: 7269825--7269865 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
7269815 TTGATTAAAA
7269825 ATTG-AAAAAAAAATTT
1 ATTGAAAAAAAAAATTT
7269841 ATTGAAAAAAAAAATTT
1 ATTGAAAAAAAAAATTT
7269858 ATTGAAAA
1 ATTGAAAA
7269866 CTTAGGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (17 bp):
ATTGAAAAAAAAAATTT
Found at i:7270374 original size:27 final size:27
Alignment explanation
Indices: 7270336--7270479 Score: 182
Period size: 27 Copynumber: 5.3 Consensus size: 27
7270326 CACAATTTTC
7270336 TTTAATTATTACACGTCATGTTGAAAA
1 TTTAATTATTACACGTCATGTTGAAAA
7270363 TTTAATTATTACACG-CTATGTTGAAAA
1 TTTAATTATTACACGTC-ATGTTGAAAA
*
7270390 TTAAATTATTACACGTCATGTTGAAAAA
1 TTTAATTATTACACGTCATGTTG-AAAA
* * *
7270418 TATAATTATTACATGTTATGTTGAAAA
1 TTTAATTATTACACGTCATGTTGAAAA
* * * *
7270445 TTTAATTATTCCACATTATGTTAAAAA
1 TTTAATTATTACACGTCATGTTGAAAA
7270472 TTTTAATT
1 -TTTAATT
7270480 GTAACATACC
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.01
27 71 0.69
28 31 0.30
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (27 bp):
TTTAATTATTACACGTCATGTTGAAAA
Found at i:7270479 original size:55 final size:54
Alignment explanation
Indices: 7270336--7270479 Score: 198
Period size: 55 Copynumber: 2.6 Consensus size: 54
7270326 CACAATTTTC
*
7270336 TTTAATTATTACACGTCATGTTGAAAATTTAATTATTACACGCTATGTTGAAAA
1 TTTAATTATTACACGTCATGTTAAAAATTTAATTATTACACGCTATGTTGAAAA
* * * *
7270390 TTAAATTATTACACGTCATGTTGAAAAATATAATTATTACATGTTATGTTGAAAA
1 TTTAATTATTACACGTCATGTT-AAAAATTTAATTATTACACGCTATGTTGAAAA
* * *
7270445 TTTAATTATTCCACATTATGTTAAAAATTTTAATT
1 TTTAATTATTACACGTCATGTTAAAAA-TTTAATT
7270480 GTAACATACC
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
54 26 0.33
55 52 0.67
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (54 bp):
TTTAATTATTACACGTCATGTTAAAAATTTAATTATTACACGCTATGTTGAAAA
Found at i:7270508 original size:82 final size:82
Alignment explanation
Indices: 7270338--7270500 Score: 200
Period size: 82 Copynumber: 2.0 Consensus size: 82
7270328 CAATTTTCTT
* * *
7270338 TAATTATTACACGTCATGTTGAAAATTTAATTATTACACGCTATGTTGAAAATTAAATTATTACA
1 TAATTATTACACGTCATGTTGAAAATTTAATTATTACACACTATGTTAAAAATTAAATTATAACA
** *
7270403 CGTCATGTTGAAAAATA
66 CACCATGATGAAAAATA
* * * * * *
7270420 TAATTATTACATGTTATGTTGAAAATTTAATTATTCCACATTATGTTAAAAATTTTAATTGTAAC
1 TAATTATTACACGTCATGTTGAAAATTTAATTATTACACACTATGTTAAAAA-TTAAATTATAAC
*
7270485 ATACCATGATGAAAAA
65 ACACCATGATGAAAAA
7270501 GTTATTATCC
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
82 46 0.69
83 21 0.31
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (82 bp):
TAATTATTACACGTCATGTTGAAAATTTAATTATTACACACTATGTTAAAAATTAAATTATAACA
CACCATGATGAAAAATA
Found at i:7281293 original size:6 final size:6
Alignment explanation
Indices: 7281282--7281307 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7281272 GCCACGCCCG
7281282 CAAGCT CAAGCT CAAGCT CAAGCT CA
1 CAAGCT CAAGCT CAAGCT CAAGCT CA
7281308 GTCTTTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (6 bp):
CAAGCT
Found at i:7292500 original size:17 final size:17
Alignment explanation
Indices: 7292475--7292508 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
7292465 TTTGATTCAG
*
7292475 TTTAATTATGTTTATTT
1 TTTAATTATGTTAATTT
*
7292492 TTTACTTATGTTAATTT
1 TTTAATTATGTTAATTT
7292509 GTGTCAAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (17 bp):
TTTAATTATGTTAATTT
Found at i:7313669 original size:13 final size:14
Alignment explanation
Indices: 7313634--7313671 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
7313624 AAATCTAATT
*
7313634 AATATTTATAATAA
1 AATATTTAAAATAA
*
7313648 AATATTTAAAATGA
1 AATATTTAAAATAA
7313662 AA-ATTTAAAA
1 AATATTTAAAA
7313672 AAGTAAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
AATATTTAAAATAA
Found at i:7314106 original size:17 final size:16
Alignment explanation
Indices: 7314086--7314117 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
7314076 GATATAACTG
7314086 AAAGACAATTATATATA
1 AAAGACAATTA-ATATA
7314103 AAAGACAATTAATAT
1 AAAGACAATTAATAT
7314118 TTCAATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAGACAATTAATATA
Found at i:7315229 original size:15 final size:14
Alignment explanation
Indices: 7315204--7315237 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
7315194 TTTCTAATTT
7315204 TATAATAATTATAA
1 TATAATAATTATAA
*
7315218 TATAATTAATTATAT
1 TATAA-TAATTATAA
7315233 TATAA
1 TATAA
7315238 ATATATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATAATAATTATAA
Found at i:7315464 original size:9 final size:9
Alignment explanation
Indices: 7315452--7315476 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
7315442 CCAATTCCAA
7315452 TAATTCTAT
1 TAATTCTAT
7315461 TAATTCTAT
1 TAATTCTAT
7315470 TAATTCT
1 TAATTCT
7315477 TAATTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (9 bp):
TAATTCTAT
Found at i:7321630 original size:19 final size:18
Alignment explanation
Indices: 7321599--7321634 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7321589 TATTATAACC
7321599 TTTGAATAAATATAATTG
1 TTTGAATAAATATAATTG
*
7321617 TTTGAAATAGATATAATT
1 TTTG-AATAAATATAATT
7321635 ATTTAAGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (18 bp):
TTTGAATAAATATAATTG
Found at i:7324552 original size:12 final size:13
Alignment explanation
Indices: 7324537--7324566 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
7324527 GATTTTGCTT
7324537 TTCAAATTTGAA-
1 TTCAAATTTGAAC
7324549 TTCAAATTTGAAC
1 TTCAAATTTGAAC
7324562 TTCAA
1 TTCAA
7324567 CATATAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (13 bp):
TTCAAATTTGAAC
Found at i:7326038 original size:112 final size:112
Alignment explanation
Indices: 7325841--7326066 Score: 301
Period size: 112 Copynumber: 2.0 Consensus size: 112
7325831 TAATTGTTGC
* * * * *
7325841 ATCTCAAGGGTATACATACAGCATTAAGCAAAATTTAATGGACAACTTAATTAAGTAGGTATTAG
1 ATCTCAAGGGTATACAAACAACATTAAGAAAAATTTAATGGACAACTTAATTAAGAAAGTATTAG
*
7325906 AATAATTTAAGAGTTTATGTTTGATACATGGGTTATGGTATATAAAA
66 AATAATTTAAGAGTTTATGTTTGATACATGCGTTATGGTATATAAAA
* **
7325953 ATCTCAAGGGTATACAAATAATGTTAAGAAAAATTTAATGGACAACTTAATTAAGAAAGTATTAG
1 ATCTCAAGGGTATACAAACAACATTAAGAAAAATTTAATGGACAACTTAATTAAGAAAGTATTAG
** * * * *
7326018 TCTTATTGT-AGAGTTTATGTTTGATAGATGCGTTATGGTTTGTAAAA
66 AATAATT-TAAGAGTTTATGTTTGATACATGCGTTATGGTATATAAAA
7326065 AT
1 AT
7326067 TTAATGTGCA
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
112 97 0.99
113 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (112 bp):
ATCTCAAGGGTATACAAACAACATTAAGAAAAATTTAATGGACAACTTAATTAAGAAAGTATTAG
AATAATTTAAGAGTTTATGTTTGATACATGCGTTATGGTATATAAAA
Found at i:7331240 original size:11 final size:11
Alignment explanation
Indices: 7331219--7331250 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
7331209 TTTATATATT
7331219 ATATATTTTTAA
1 ATAT-TTTTTAA
7331231 ATATTTTTTAA
1 ATATTTTTTAA
7331242 ATATTTTTT
1 ATATTTTTT
7331251 TATTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
ATATTTTTTAA
Found at i:7332840 original size:18 final size:20
Alignment explanation
Indices: 7332817--7332857 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
7332807 ATTTAAGTTA
7332817 TTTATTTATA-TTA-TTATT
1 TTTATTTATATTTATTTATT
7332835 TTTATTTATATTTATTTATT
1 TTTATTTATATTTATTTATT
7332855 TTT
1 TTT
7332858 TTCAATTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
19 3 0.14
20 8 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTATATTTATTTATT
Found at i:7334684 original size:21 final size:17
Alignment explanation
Indices: 7334672--7334712 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
7334662 TTTAAGTTAT
7334672 TTATTTATATATTATTA
1 TTATTTATATATTATTA
7334689 TTATTTATAT-TTATTTA
1 TTATTTATATATTA-TTA
7334706 TT-TTTAT
1 TTATTTAT
7334713 CAATTCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTATATATTATTA
Found at i:7334722 original size:23 final size:23
Alignment explanation
Indices: 7334673--7334728 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
7334663 TTAAGTTATT
* * *
7334673 TATTTATATATTATTATTATTTA
1 TATTTATTTATTATTATCAATTA
* *
7334696 TATTTATTTATTTTTATCAATTC
1 TATTTATTTATTATTATCAATTA
7334719 TATTCTATTT
1 TATT-TATTT
7334729 GCTCATATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTATTTATTATTATCAATTA
Found at i:7337204 original size:15 final size:15
Alignment explanation
Indices: 7337184--7337213 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7337174 AAAATTAAAC
7337184 TTTACGTTTTGAATA
1 TTTACGTTTTGAATA
7337199 TTTACGTTTTGAATA
1 TTTACGTTTTGAATA
7337214 ACCTTCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (15 bp):
TTTACGTTTTGAATA
Found at i:7345950 original size:3 final size:3
Alignment explanation
Indices: 7345942--7345967 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7345932 TTAACTGTTT
7345942 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
7345968 CAAGCGGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:7359961 original size:22 final size:24
Alignment explanation
Indices: 7359935--7359994 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
7359925 AACTTTCAAT
7359935 TTAAA-TAAAA-AATATTAAAAAA
1 TTAAATTAAAATAATATTAAAAAA
*
7359957 TTAAATTAAAATAATTTTAAAAGTAA
1 TTAAATTAAAATAATATTAAAA--AA
7359983 -TAAATTAAAATA
1 TTAAATTAAAATA
7359995 TTATGATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 5 0.15
23 5 0.15
24 9 0.27
25 12 0.36
26 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
TTAAATTAAAATAATATTAAAAAA
Found at i:7359990 original size:30 final size:27
Alignment explanation
Indices: 7359952--7360025 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 27
7359942 AAAAATATTA
7359952 AAAAATTAAATTAAAATAATTTTAAAAGT
1 AAAAATTAAATTAAAATAATTTT-AAA-T
* ** *
7359981 AATAAATTAAAATATTATGATTTTAAAT
1 AA-AAATTAAATTAAAATAATTTTAAAT
7360009 AAAAACTTAAATTAAAA
1 AAAAA-TTAAATTAAAA
7360026 AATATCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
27 3 0.08
28 11 0.31
29 5 0.14
30 17 0.47
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAAATTAAATTAAAATAATTTTAAAT
Found at i:7388288 original size:5 final size:5
Alignment explanation
Indices: 7388278--7388302 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
7388268 GTTCATTTAA
7388278 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
7388303 GATAAGAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:7413012 original size:38 final size:38
Alignment explanation
Indices: 7412970--7413056 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 38
7412960 AAAGCAGTAC
**
7412970 AGTAAAACTAAGAATAAGTAAAGAATAAGGGAGCATAG
1 AGTAAAACTAAGAATAAGTAAAGAATAAGCCAGCATAG
** * * * *
7413008 AGTAAAGTTGAGAATAGGTAGAGAATAATCCAGCATAG
1 AGTAAAACTAAGAATAAGTAAAGAATAAGCCAGCATAG
*
7413046 AGTAAGACTAA
1 AGTAAAACTAA
7413057 AAATGGGATG
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (38 bp):
AGTAAAACTAAGAATAAGTAAAGAATAAGCCAGCATAG
Found at i:7413496 original size:27 final size:26
Alignment explanation
Indices: 7413459--7413515 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
7413449 TTTTTATTTT
* *
7413459 ATTT-TTTAAATAGTAATAATTTATA
1 ATTTATTTAAATAATAATAATTGATA
7413484 ATTTATTTAAAATAATAATAATTGATA
1 ATTTATTT-AAATAATAATAATTGATA
7413511 ATTTA
1 ATTTA
7413516 AATTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 3 0.11
27 21 0.75
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
ATTTATTTAAATAATAATAATTGATA
Found at i:7413547 original size:41 final size:41
Alignment explanation
Indices: 7413486--7413583 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
7413476 AATTTATAAT
* * * *
7413486 TTATTTAAAATAATAATAATTGATAATTTAAATTTTAATATT
1 TTATTTAAAAT-TTAATAATTAATAATTTAAATATTAATATA
* *
7413528 TTGTTTAAAATTTAATAATTAATATTTTAAATATTAATATA
1 TTATTTAAAATTTAATAATTAATAATTTAAATATTAATATA
*
7413569 TTATTTATAATTTAA
1 TTATTTAAAATTTAA
7413584 ATATTATTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 38 0.79
42 10 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (41 bp):
TTATTTAAAATTTAATAATTAATAATTTAAATATTAATATA
Found at i:7413595 original size:17 final size:17
Alignment explanation
Indices: 7413548--7413644 Score: 65
Period size: 17 Copynumber: 5.5 Consensus size: 17
7413538 TTTAATAATT
7413548 AATATT-TTA-AATATTA
1 AATATTATTATAAT-TTA
7413564 ATATATTATTTATAATTTA
1 A-ATATTA-TTATAATTTA
*
7413583 AATATTATTATAATTAA
1 AATATTATTATAATTTA
* * * *
7413600 AATAGTGTAATAATTTT
1 AATATTATTATAATTTA
*
7413617 AAT-TTATTTTTAAATTTAA
1 AATATTA-TTAT-AATTT-A
7413636 AATATTATT
1 AATATTATT
7413645 TTTTATAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
16 2 0.03
17 31 0.50
18 11 0.18
19 12 0.19
20 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATATTATTATAATTTA
Found at i:7415453 original size:31 final size:31
Alignment explanation
Indices: 7415417--7415475 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
7415407 AACTTCATAC
* *
7415417 TTTTATTTTGAATCAAATAAATTCTTATATT
1 TTTTATTTTCAATCAAATAAACTCTTATATT
* *
7415448 TTTTATTTTCAGTGAAATAAACTCTTAT
1 TTTTATTTTCAATCAAATAAACTCTTAT
7415476 GATTAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (31 bp):
TTTTATTTTCAATCAAATAAACTCTTATATT
Found at i:7419405 original size:3 final size:3
Alignment explanation
Indices: 7419397--7419421 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7419387 GAGAGGAAAA
7419397 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
7419422 TTAATAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:7426236 original size:13 final size:14
Alignment explanation
Indices: 7426218--7426251 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
7426208 AAAATTATGT
7426218 TAAATTTA-TTTGA
1 TAAATTTATTTTGA
*
7426231 TAAATTTATTTTTA
1 TAAATTTATTTTGA
7426245 TAAATTT
1 TAAATTT
7426252 TATATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
TAAATTTATTTTGA
Found at i:7426277 original size:17 final size:18
Alignment explanation
Indices: 7426257--7426290 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
7426247 AATTTTATAT
7426257 AAATAAGTTAT-TTAATA
1 AAATAAGTTATATTAATA
*
7426274 AAATAATTTATATTAAT
1 AAATAAGTTATATTAAT
7426291 TTAATTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AAATAAGTTATATTAATA
Found at i:7427161 original size:48 final size:48
Alignment explanation
Indices: 7427078--7427188 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 48
7427068 CTCTCATATA
* *
7427078 AAATAA-ATTATTATACTATAACTTTAATGAAATATTATAGTCTAATT
1 AAATAATACTATTATACTATAACTCTAATGAAATATTATAGTCTAATT
* * * *
7427125 AGATAATACTATTATAGTATAACTCTAACT-AGATATTATAGTTTAATT
1 AAATAATACTATTATACTATAACTCTAA-TGAAATATTATAGTCTAATT
*
7427173 AAATAATAGTATTATA
1 AAATAATACTATTATA
7427189 TAAAAATTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
47 5 0.09
48 48 0.89
49 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.41
Consensus pattern (48 bp):
AAATAATACTATTATACTATAACTCTAATGAAATATTATAGTCTAATT
Found at i:7427185 original size:24 final size:23
Alignment explanation
Indices: 7427110--7427188 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 23
7427100 TTTAATGAAA
* *
7427110 TATTATAGTCTAATTAGATAATAC
1 TATTATAGTATAATTA-ATAATAG
* *
7427134 TATTATAGTATAACT-CTAACTAG
1 TATTATAGTATAATTAATAA-TAG
*
7427157 ATATTATAGTTTAATTAAATAATAG
1 -TATTATAGTATAATT-AATAATAG
7427182 TATTATA
1 TATTATA
7427189 TAAAAATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
22 3 0.07
23 2 0.05
24 33 0.75
25 3 0.07
26 3 0.07
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (23 bp):
TATTATAGTATAATTAATAATAG
Found at i:7427209 original size:48 final size:48
Alignment explanation
Indices: 7427078--7427209 Score: 133
Period size: 48 Copynumber: 2.8 Consensus size: 48
7427068 CTCTCATATA
* * * *
7427078 AAATAA-ATTATTATACTATAACTTTAATGAAATATTATAGTCTAATT
1 AAATAATACTATTATAGTAAAACTTTAATTAAATATTATAGTCTAATT
* * * * * *
7427125 AGATAATACTATTATAGTATAACTCTAACTAGATATTATAGTTTAATT
1 AAATAATACTATTATAGTAAAACTTTAATTAAATATTATAGTCTAATT
* *
7427173 AAATAATAGTATTATA-TAAAAATTTTAATTAAATATT
1 AAATAATACTATTATAGT-AAAACTTTAATTAAATATT
7427210 TTAATATGCA
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
47 6 0.09
48 62 0.91
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (48 bp):
AAATAATACTATTATAGTAAAACTTTAATTAAATATTATAGTCTAATT
Found at i:7428838 original size:39 final size:39
Alignment explanation
Indices: 7428784--7428864 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
7428774 TCAGTGTCGG
7428784 TTCAGCGGCACAGCCGTAGGCTGTAGACCGAAATCGTAA
1 TTCAGCGGCACAGCCGTAGGCTGTAGACCGAAATCGTAA
7428823 TTCAGCGGCACAGCCGTAGGCTGTAGACCGAAATCGTAA
1 TTCAGCGGCACAGCCGTAGGCTGTAGACCGAAATCGTAA
7428862 TTC
1 TTC
7428865 CCATATCCTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (39 bp):
TTCAGCGGCACAGCCGTAGGCTGTAGACCGAAATCGTAA
Found at i:7436561 original size:33 final size:33
Alignment explanation
Indices: 7436524--7436593 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
7436514 CCAGGTTTAA
* *
7436524 GTTTAAGCCGCAACACTACTGCAACAAACCATG
1 GTTTAAGCCACAACACTACTGCAACAAACAATG
*
7436557 GTTTAAGCTACAACACTACTGCAACAAACAATG
1 GTTTAAGCCACAACACTACTGCAACAAACAATG
7436590 GTTT
1 GTTT
7436594 GGATGAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (33 bp):
GTTTAAGCCACAACACTACTGCAACAAACAATG
Found at i:7440097 original size:2 final size:2
Alignment explanation
Indices: 7440092--7440128 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
7440082 ATGTACCACG
*
7440092 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7440129 TGGGCTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:7441580 original size:2 final size:2
Alignment explanation
Indices: 7441575--7441605 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7441565 TTTATAATTT
7441575 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7441606 TGGTGTTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7444473 original size:26 final size:25
Alignment explanation
Indices: 7444429--7444482 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
7444419 CAACTTTTAA
*
7444429 ATTTATTTGTTAACGATATAATA-AT
1 ATTTATTTGTTAACAATAT-ATAGAT
*
7444454 ATTTATTTTGTTAATAATATATAGAT
1 ATTTA-TTTGTTAACAATATATAGAT
7444480 ATT
1 ATT
7444483 ATACATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (25 bp):
ATTTATTTGTTAACAATATATAGAT
Found at i:7444991 original size:20 final size:20
Alignment explanation
Indices: 7444953--7444991 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7444943 TGTTAGATAT
* *
7444953 TTTTATTTTTTATTATTTAC
1 TTTTATTATTCATTATTTAC
*
7444973 TTTTATTATTCATTGTTTA
1 TTTTATTATTCATTATTTA
7444992 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTATTATTCATTATTTAC
Found at i:7445623 original size:17 final size:17
Alignment explanation
Indices: 7445576--7445626 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
7445566 AGTATTTAAT
*
7445576 TAATAATTAATTATAAAA
1 TAATAATTTATT-TAAAA
* *
7445594 -ATTTATTTGATTTAAAA
1 TAATAATTT-ATTTAAAA
7445611 TAATAATTTATTTAAA
1 TAATAATTTATTTAAA
7445627 TTTTTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TAATAATTTATTTAAAA
Found at i:7446932 original size:3 final size:3
Alignment explanation
Indices: 7446924--7446953 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
7446914 TTTAGGTTGC
*
7446924 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
7446954 GGCATTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:7452128 original size:15 final size:15
Alignment explanation
Indices: 7452108--7452143 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
7452098 TTATATGTAT
* *
7452108 GATGATGATGATGAC
1 GATGATGACGACGAC
7452123 GATGATGACGACGAC
1 GATGATGACGACGAC
7452138 GATGAT
1 GATGAT
7452144 AATTACGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (15 bp):
GATGATGACGACGAC
Found at i:7452460 original size:6 final size:6
Alignment explanation
Indices: 7452442--7452474 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
7452432 TCATGGATAC
*
7452442 CCCCGA CCACGA CCCCGA CCCCGA CCCCGA CCC
1 CCCCGA CCCCGA CCCCGA CCCCGA CCCCGA CCC
7452475 GCCCTCCCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.67, G:0.15, T:0.00
Consensus pattern (6 bp):
CCCCGA
Found at i:7454022 original size:2 final size:2
Alignment explanation
Indices: 7453974--7454003 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7453964 GCTTATGTAC
7453974 AT AT 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 AT AT
7454004 GTTCGCTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7462649 original size:30 final size:30
Alignment explanation
Indices: 7462615--7462675 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
7462605 TAATCACCGA
7462615 ATATCTTGTTAAATAATAAACTTAAAGTTC
1 ATATCTTGTTAAATAATAAACTTAAAGTTC
7462645 ATATCTTGTTAAATAATAAACTTAAAGTTC
1 ATATCTTGTTAAATAATAAACTTAAAGTTC
7462675 A
1 A
7462676 GATATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (30 bp):
ATATCTTGTTAAATAATAAACTTAAAGTTC
Found at i:7464923 original size:3 final size:3
Alignment explanation
Indices: 7464915--7464941 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
7464905 GAGAGATTGG
7464915 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
7464942 TAGAATACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7473165 original size:2 final size:2
Alignment explanation
Indices: 7473160--7473186 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7473150 TATTATGTTG
7473160 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 A
7473187 AAATCTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7489197 original size:2 final size:2
Alignment explanation
Indices: 7489190--7489228 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
7489180 TTAGGCATTT
* *
7489190 TA TA TA TA TA TA TA TA TA TA TA AA CA TA T- 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
7489229 CATGTAGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:7501052 original size:2 final size:2
Alignment explanation
Indices: 7501045--7501074 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
7501035 TATGAGCAAG
*
7501045 TA TA TA TA CA 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
7501075 CATACATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7501963 original size:2 final size:2
Alignment explanation
Indices: 7501949--7501981 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
7501939 GAGGGAGAGA
*
7501949 AT AT -T AT AC 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 AT AT AT AT
7501982 GGGCTCTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7521288 original size:65 final size:65
Alignment explanation
Indices: 7521179--7521309 Score: 226
Period size: 65 Copynumber: 2.0 Consensus size: 65
7521169 AAAGACAGAA
* * *
7521179 TCTTTAAGTCTTTAGCCTAATCTCTTTCATACTAATTTAGATGCTCAATTGTTAGATAGATTTAG
1 TCTTAAAGTCTTTAGCCTAAGCTCTTTAATACTAATTTAGATGCTCAATTGTTAGATAGATTTAG
*
7521244 TCTTAAAGTCTTTAGCCTAAGCTCTTTAATGCTAATTTAGATGCTCAATTGTTAGATAGATTTAG
1 TCTTAAAGTCTTTAGCCTAAGCTCTTTAATACTAATTTAGATGCTCAATTGTTAGATAGATTTAG
7521309 T
1 T
7521310 TATTTGATTG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (65 bp):
TCTTAAAGTCTTTAGCCTAAGCTCTTTAATACTAATTTAGATGCTCAATTGTTAGATAGATTTAG
Found at i:7526386 original size:20 final size:20
Alignment explanation
Indices: 7526354--7526395 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
7526344 ATTCAGAAAA
7526354 TATTTATTAAATAAAAAAATT
1 TATTTATTAAAT-AAAAAATT
*
7526375 TATTTA-TAAATATAAAATT
1 TATTTATTAAATAAAAAATT
7526394 TA
1 TA
7526396 ATTCATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 5 0.25
21 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTATTAAATAAAAAATT
Found at i:7534836 original size:16 final size:18
Alignment explanation
Indices: 7534817--7534855 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
7534807 TATCAAGTAT
7534817 AATAAAAT-TTAAT-ATC
1 AATAAAATCTTAATCATC
7534833 AAT-AAATCTTAATCATC
1 AATAAAATCTTAATCATC
7534850 -ATAAAA
1 AATAAAA
7534856 ATATTTGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.20
16 10 0.50
17 6 0.30
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAAATCTTAATCATC
Found at i:7545422 original size:16 final size:18
Alignment explanation
Indices: 7545386--7545424 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
7545376 ATATAAATAT
7545386 TTTTA-TGATGATTAAGA
1 TTTTATTGATGATTAAGA
7545403 -TTTATTGAT-ATTAA-A
1 TTTTATTGATGATTAAGA
7545418 TTTTATT
1 TTTTATT
7545425 ATACTTGATN
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.05
16 15 0.75
17 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (18 bp):
TTTTATTGATGATTAAGA
Found at i:7550892 original size:19 final size:19
Alignment explanation
Indices: 7550868--7550906 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
7550858 ATATCTATAC
7550868 TAAAAAATAATCAATATGG
1 TAAAAAATAATCAATATGG
* * *
7550887 TAAAAAGTATTCAATGTGG
1 TAAAAAATAATCAATATGG
7550906 T
1 T
7550907 GCTTGTACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (19 bp):
TAAAAAATAATCAATATGG
Found at i:7566419 original size:15 final size:15
Alignment explanation
Indices: 7566397--7566445 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
7566387 ATATAATGTG
7566397 ATTACAAGTAATATA
1 ATTACAAGTAATATA
* *
7566412 ATTGCAAGTAATATG
1 ATTACAAGTAATATA
* *
7566427 ATTACAAGCAATGTA
1 ATTACAAGTAATATA
7566442 ATTA
1 ATTA
7566446 TAAGGAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (15 bp):
ATTACAAGTAATATA
Found at i:7566999 original size:21 final size:21
Alignment explanation
Indices: 7566975--7567018 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
7566965 AATTTATTTG
7566975 ATTTAAAATAAAAAT-ATAAAA
1 ATTT-AAATAAAAATAATAAAA
* *
7566996 ATTTAATTAAATATAATAAAA
1 ATTTAAATAAAAATAATAAAA
7567017 AT
1 AT
7567019 AAAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTTAAATAAAAATAATAAAA
Found at i:7566999 original size:26 final size:27
Alignment explanation
Indices: 7566952--7567034 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
7566942 TTTAATCAAT
* **
7566952 TAATAATAATAAAAATTTATTTGATTTA
1 TAATAAAAATAAAAATTTATTT-AAATA
* *
7566980 AAATAAAAATATAAAAATTTAATTAAATA
1 TAAT-AAAA-ATAAAAATTTATTTAAATA
7567009 TAATAAAAATAAAAATTTATTTAAAT
1 TAATAAAAATAAAAATTTATTTAAAT
7567035 TTTTTGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 17 0.37
28 7 0.15
29 9 0.20
30 13 0.28
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (27 bp):
TAATAAAAATAAAAATTTATTTAAATA
Found at i:7567199 original size:29 final size:29
Alignment explanation
Indices: 7567165--7567222 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
7567155 TTAAACTTTT
*
7567165 TTTTATCTTTTATATTAAAAAAATT-TATA
1 TTTTAT-TTTTATAATAAAAAAATTATATA
*
7567194 TTTTATTTTTTTAATAAAAAAATTATATA
1 TTTTATTTTTATAATAAAAAAATTATATA
7567223 CTAATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTTATTTTTATAATAAAAAAATTATATA
Found at i:7605443 original size:27 final size:26
Alignment explanation
Indices: 7605390--7605441 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
7605380 TTATTTTATT
7605390 TTTAAAATATTAATAATTGATAATTTA
1 TTTAAAATATTAATAATT-ATAATTTA
7605417 TTTAAAATATTAATAA-TATTAATTT
1 TTTAAAATATTAATAATTA-TAATTT
7605442 TAAAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 1 0.04
26 7 0.29
27 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTAAAATATTAATAATTATAATTTA
Found at i:7605445 original size:23 final size:24
Alignment explanation
Indices: 7605387--7605454 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 24
7605377 ATTTTATTTT
7605387 ATTTTTAAAATATTAATAATTGATA
1 ATTTTTAAAATATTAATAATT-ATA
7605412 ATTTATTTAAAATATTAATAA-TATTA
1 A-TT-TTTAAAATATTAATAATTA-TA
*
7605438 A-TTTTAAAATAATAATA
1 ATTTTTAAAATATTAATA
7605455 TTTTATTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
23 14 0.36
24 1 0.03
25 2 0.05
26 6 0.15
27 16 0.41
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (24 bp):
ATTTTTAAAATATTAATAATTATA
Found at i:7605463 original size:20 final size:22
Alignment explanation
Indices: 7605412--7605463 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
7605402 ATAATTGATA
*
7605412 ATTTATTTAAAATATTAATAAT
1 ATTTATTTAAAATAATAATAAT
*
7605434 ATTAATTTTAAAATAATAAT-AT
1 ATTTA-TTTAAAATAATAATAAT
7605456 -TTTATTTA
1 ATTTATTTA
7605464 TAATTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 4 0.15
21 3 0.12
22 6 0.23
23 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTATTTAAAATAATAATAAT
Found at i:7605479 original size:29 final size:28
Alignment explanation
Indices: 7605447--7605541 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 28
7605437 AATTTTAAAA
7605447 TAATAATATTTTATTTATAATTTAATTAT
1 TAATAAT-TTTTATTTATAATTTAATTAT
*
7605476 TAATATTTTATTTATTTA-AATATT-ATTAT
1 TAATA-ATT-TTTATTTATAAT-TTAATTAT
* * *
7605505 TATTAACTTTTTATTT-TATTTTCAAATAT
1 TAATAA-TTTTTATTTATAATTT-AATTAT
7605534 TAATAATT
1 TAATAATT
7605542 GATAATTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
27 2 0.04
28 11 0.21
29 29 0.55
30 11 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TAATAATTTTTATTTATAATTTAATTAT
Found at i:7605485 original size:26 final size:26
Alignment explanation
Indices: 7605450--7605591 Score: 96
Period size: 26 Copynumber: 5.4 Consensus size: 26
7605440 TTTAAAATAA
7605450 TAATATTTTATTTATAATTTAATTAT
1 TAATATTTTATTTATAATTTAATTAT
*
7605476 TAATATTTTA-TT-T-ATTTAAATAT
1 TAATATTTTATTTATAATTTAATTAT
* * *
7605499 TATTATTATTAACTTT-TTATTTTATT-T
1 TAATATT-TT-A-TTTATAATTTAATTAT
* * *
7605526 TCAAATATTAATAATTGATAATTTAAATAT
1 T--AATATT--TTATTTATAATTTAATTAT
* *
7605556 TATTATTTTATTTATAATTTAATCAT
1 TAATATTTTATTTATAATTTAATTAT
*
7605582 TCATATTTTA
1 TAATATTTTA
7605592 AAATACTAAT
Statistics
Matches: 89, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
23 15 0.17
24 3 0.03
25 3 0.03
26 33 0.37
27 5 0.06
28 13 0.15
29 13 0.15
30 4 0.04
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (26 bp):
TAATATTTTATTTATAATTTAATTAT
Found at i:7605499 original size:17 final size:17
Alignment explanation
Indices: 7605477--7605525 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
7605467 TTTAATTATT
7605477 AATATTTTATTTATTTA
1 AATATTTTATTTATTTA
7605494 AATATTATTA-TTA-TTA
1 AATATT-TTATTTATTTA
*
7605510 ACT-TTTTATTTTATTT
1 AATATTTTA-TTTATTT
7605526 TCAAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 3 0.11
15 2 0.07
16 8 0.30
17 11 0.41
18 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
AATATTTTATTTATTTA
Found at i:7605510 original size:32 final size:31
Alignment explanation
Indices: 7605453--7605537 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 31
7605443 AAAATAATAA
7605453 TATTTTATTTATAAT-TTAATTATTAA-TATTT
1 TATTTTATTTA-AATATTAATTATTAACT-TTT
7605484 TA-TTTATTTAAATATTATTATTATTAACTTTT
1 TATTTTATTTAAATATTA--ATTATTAACTTTT
7605516 TATTTTATTTTCAAATATTAAT
1 TATTTTA-TTT-AAATATTAAT
7605538 AATTGATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
29 3 0.06
30 11 0.23
31 2 0.04
32 13 0.28
33 7 0.15
34 3 0.06
35 8 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (31 bp):
TATTTTATTTAAATATTAATTATTAACTTTT
Found at i:7605617 original size:123 final size:123
Alignment explanation
Indices: 7605458--7605774 Score: 366
Period size: 123 Copynumber: 2.6 Consensus size: 123
7605448 AATAATATTT
* * *
7605458 TATTTATAATTTAATTATTAATATTTTATTT-ATTTAAATATTATTATTATTAACTTTTTATTTT
1 TATTTATAA--TAAATACTAATATTTTATTTAATTTAAATATTATTATGATTAA-TTTTTATTTT
*
7605522 ATTTTCAAATATTAATAATT-GATAATTTAAATATT-ATTATTTTATTTATAATTTAATCATTCA
63 ATTTT-AAA-ATTAAT-ATTAGATAATTTAAATATTGA-TATTTTATTTATAATTTAATCATTAA
*
7605585 TATTT-T-A-AAATACTAATATTTTATTTAATTTAAATATTATTATGA-TCATTTTTA--TT-TT
1 TATTTATAATAAATACTAATATTTTATTTAATTTAAATATTATTATGATTAATTTTTATTTTATT
* *
7605643 TTAAAATTACTATTAGATAATTTAAATATTGATATTTTATTTGTAATTTAATCATTAA
66 TTAAAATTAATATTAGATAATTTAAATATTGATATTTTATTTATAATTTAATCATTAA
* *
7605701 TATTTAGATAATTTAAATATTGATATTTTATTTAATTTAAATATTATTATGATTAAATTTTTTAT
1 TATTT--ATAA--TAAATACTAATATTTTATTTAATTTAAATATTATTATGATT-AA-TTTTTAT
7605766 TTTATTTTA
60 TTTATTTTA
7605775 TTTTTTAAAT
Statistics
Matches: 164, Mismatches: 10, Indels: 30
0.80 0.05 0.15
Matches are distributed among these distances:
115 3 0.02
116 49 0.30
117 4 0.02
118 4 0.02
119 3 0.02
120 1 0.01
121 6 0.04
122 19 0.12
123 53 0.32
124 1 0.01
125 2 0.01
126 7 0.04
127 5 0.03
128 2 0.01
129 5 0.03
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (123 bp):
TATTTATAATAAATACTAATATTTTATTTAATTTAAATATTATTATGATTAATTTTTATTTTATT
TTAAAATTAATATTAGATAATTTAAATATTGATATTTTATTTATAATTTAATCATTAA
Found at i:7605736 original size:24 final size:24
Alignment explanation
Indices: 7605660--7605745 Score: 104
Period size: 24 Copynumber: 3.5 Consensus size: 24
7605650 TACTATTAGA
7605660 TAATTTAAATATTGATATTTTATTT
1 TAATTTAAATATTGATATTTTA-TT
* **
7605685 GTAATTT-AATCATTAATA-TTTAGA
1 -TAATTTAAAT-ATTGATATTTTATT
7605709 TAATTTAAATATTGATATTTTATT
1 TAATTTAAATATTGATATTTTATT
7605733 TAATTTAAATATT
1 TAATTTAAATATT
7605746 ATTATGATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
23 12 0.24
24 20 0.39
25 7 0.14
26 12 0.24
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.55
Consensus pattern (24 bp):
TAATTTAAATATTGATATTTTATT
Found at i:7605903 original size:156 final size:154
Alignment explanation
Indices: 7605656--7606280 Score: 694
Period size: 156 Copynumber: 4.0 Consensus size: 154
7605646 AAATTACTAT
* * *
7605656 TAGATAATTTAAATATTGATATTTTATTTGTAATTTAATCATTAATATTTAGATAATTTAAATAT
1 TAGATCATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTT---T-A---AAATAT
*
7605721 TGATATTTTATTTAATTTAAATATTATTATGATTAAATTTTTTATTTTATTTTATTTTTTAAATA
59 TAATATTTTATTT-ATTTAAATATTATTATGATT-AA-TTTTTATTTTATTTTATTTTTTAAATA
* *
7605786 CTAATAATTGATAATTTATTTCAAAA-ATTAATAA
121 TTAATAATTAATAATTTATTT-AAAACATTAATAA
* * *
7605820 TAGATCATTTAAATAATAATATTTTA-TTATTATTTGATCATTAATATTTTAAAATATTAATATT
1 TAGATCATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTTTAAAATATTAATATT
* * *
7605884 TAATTTGATTTAAATATTATTATGATCAA----AATTTTATTTTA-TTTTTAAATATTAATAATT
66 TTATTT-ATTTAAATATTATTATGATTAATTTTTATTTTATTTTATTTTTTAAATATTAATAATT
7605944 AATAATTTATTTAAAACATTAA-ATA
130 AATAATTTATTTAAAACATTAATA-A
* * * * *
7605969 TCGATCATTTAAATATTAATATTTTATTTAAAATTTAATCATCAATATTTTAAAACACTAATATT
1 TAGATCATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTTTAAAATATTAATATT
* * * **
7606034 TTATTTTATTTAATTATTATTATGATTACTTTTTTAGTTTATTTTATTTTGGAAATATTAATAAT
66 TTA-TTTATTTAAATATTATTATGATTA-ATTTTTATTTTATTTTATTTTTTAAATATTAATAAT
* *
7606099 TGATAATTTATTTAAAATATTAATAA
129 TAATAATTTATTTAAAACATTAATAA
* * * **
7606125 TTGATGATTTAATTATTAACCTTTTATTTATAATTTAATCATTAATATTTTAAAATATTAATATT
1 TAGATCATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTTTAAAATATTAATATT
* * * * *
7606190 TTATTTATAATTGATATATTATTATGACT-ATTTAT-TTTTAATTTAATTTTTAAATATTAATAA
66 TTATTTAT--TT-AAATATTATTATGATTAATTTTTATTTTATTTTATTTTTTAAATATTAATAA
* *
7606253 TTAATAATTTATTTTAAATATTAATAA
128 TTAATAATTTATTTAAAACATTAATAA
7606280 T
1 T
7606281 TAATAATTTA
Statistics
Matches: 395, Mismatches: 52, Indels: 37
0.82 0.11 0.08
Matches are distributed among these distances:
148 5 0.01
149 59 0.15
150 64 0.16
151 3 0.01
155 66 0.17
156 137 0.35
157 3 0.01
158 13 0.03
159 1 0.00
160 1 0.00
163 20 0.05
164 23 0.06
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (154 bp):
TAGATCATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTTTAAAATATTAATATT
TTATTTATTTAAATATTATTATGATTAATTTTTATTTTATTTTATTTTTTAAATATTAATAATTA
ATAATTTATTTAAAACATTAATAA
Found at i:7606255 original size:7 final size:7
Alignment explanation
Indices: 7606245--7606315 Score: 51
Period size: 7 Copynumber: 10.4 Consensus size: 7
7606235 ATTTTTAAAT
7606245 ATTAATA
1 ATTAATA
7606252 ATTAATA
1 ATTAATA
*
7606259 ATTTAT-
1 ATTAATA
*
7606265 TTTAA-A
1 ATTAATA
7606271 TATTAATA
1 -ATTAATA
7606279 ATTAATA
1 ATTAATA
*
7606286 ATTTAT-
1 ATTAATA
*
7606292 TTTAA-A
1 ATTAATA
7606298 TATTAATA
1 -ATTAATA
*
7606306 ATTGATA
1 ATTAATA
7606313 ATT
1 ATT
7606316 TAAATAATAA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
6 6 0.12
7 41 0.84
8 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (7 bp):
ATTAATA
Found at i:7606272 original size:27 final size:27
Alignment explanation
Indices: 7606228--7606317 Score: 153
Period size: 27 Copynumber: 3.3 Consensus size: 27
7606218 TATTTATTTT
7606228 TAATTTAATTTTTAAATATTAATAATTAA
1 TAATTT-A-TTTTAAATATTAATAATTAA
7606257 TAATTTATTTTAAATATTAATAATTAA
1 TAATTTATTTTAAATATTAATAATTAA
*
7606284 TAATTTATTTTAAATATTAATAATTGA
1 TAATTTATTTTAAATATTAATAATTAA
7606311 TAATTTA
1 TAATTTA
7606318 AATAATAATA
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
27 53 0.88
28 1 0.02
29 6 0.10
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (27 bp):
TAATTTATTTTAAATATTAATAATTAA
Found at i:7606320 original size:22 final size:20
Alignment explanation
Indices: 7606279--7606336 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 20
7606269 AATATTAATA
*
7606279 ATTAATAATTTATTTTAAAT
1 ATTAATAATTTAATTTAAAT
7606299 ATTAATAATTGATAATTTAAAT
1 ATTAATAATT--TAATTTAAAT
* *
7606321 AATAAT-ATTTTATTTA
1 ATTAATAATTTAATTTA
7606337 TAATTTGATC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 6 0.18
20 10 0.30
21 3 0.09
22 14 0.42
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTAATAATTTAATTTAAAT
Found at i:7606578 original size:16 final size:17
Alignment explanation
Indices: 7606557--7606593 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
7606547 AATTTAAAAA
7606557 ATTTTA-AAGAATAATC
1 ATTTTATAAGAATAATC
*
7606573 ATTTTATAAGAATAATT
1 ATTTTATAAGAATAATC
7606590 ATTT
1 ATTT
7606594 CTTAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (17 bp):
ATTTTATAAGAATAATC
Found at i:7610015 original size:14 final size:16
Alignment explanation
Indices: 7609982--7610018 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
7609972 TGTATATCAC
*
7609982 AAATATAAAATTTAAT
1 AAATATAAAACTTAAT
7609998 AAAT-TAAAACTT-AT
1 AAATATAAAACTTAAT
7610012 AAATATA
1 AAATATA
7610019 CAAAATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 9 0.47
16 4 0.21
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATAAAACTTAAT
Found at i:7612013 original size:21 final size:21
Alignment explanation
Indices: 7611989--7612029 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7611979 GGGAAGGGGA
* * *
7611989 TATCCTAATCAGGGTCAGGGT
1 TATCCCAATCAAGGACAGGGT
7612010 TATCCCAATCAAGGACAGGG
1 TATCCCAATCAAGGACAGGG
7612030 CTTTCCACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (21 bp):
TATCCCAATCAAGGACAGGGT
Found at i:7623883 original size:2 final size:2
Alignment explanation
Indices: 7623876--7623913 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
7623866 TAGAAGCAAG
7623876 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
7623914 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7628897 original size:54 final size:55
Alignment explanation
Indices: 7628814--7628917 Score: 167
Period size: 54 Copynumber: 1.9 Consensus size: 55
7628804 TTAACAACTT
*
7628814 AACTCTTATAAAATAAAAGTTACTTACAAGATACTAATTG-AAAAAAAAAGAGTA
1 AACTCTTATAAAATAAAACTTACTTACAAGATACTAATTGCAAAAAAAAAGAGTA
*
7628868 AACTCTTATAAAATAAAACTT-TTTCACAAGATACTAATTGCAAAAAAAAA
1 AACTCTTATAAAATAAAACTTACTT-ACAAGATACTAATTGCAAAAAAAAA
7628918 AAATCTACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
53 2 0.04
54 35 0.76
55 9 0.20
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.27
Consensus pattern (55 bp):
AACTCTTATAAAATAAAACTTACTTACAAGATACTAATTGCAAAAAAAAAGAGTA
Found at i:7644682 original size:59 final size:60
Alignment explanation
Indices: 7644609--7644736 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 60
7644599 TTTGGCCAAT
7644609 GATTTT-CCAATATTTAGTCAAATTTGAACACATTACCTATTCCATTTGACTGTTGAATA
1 GATTTTACCAATATTTAGTCAAATTTGAACACATTACCTATTCCATTTGACTGTTGAATA
* * * * *
7644668 -ATTTTACCAATATTTTGTCAAATTTGAGCACATTGCTTATTCCATTTGGCTGTTGAATA
1 GATTTTACCAATATTTAGTCAAATTTGAACACATTACCTATTCCATTTGACTGTTGAATA
7644727 GTATTTTACC
1 G-ATTTTACC
7644737 TGCTTCACCT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
58 5 0.08
59 48 0.79
61 8 0.13
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (60 bp):
GATTTTACCAATATTTAGTCAAATTTGAACACATTACCTATTCCATTTGACTGTTGAATA
Found at i:7645336 original size:29 final size:30
Alignment explanation
Indices: 7645293--7645358 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
7645283 CTTATAGGAA
*
7645293 TTTTAAATTTTTTTATATAATATATAA-AAT
1 TTTTAAATTTATTTATA-AATATATAATAAT
* *
7645323 TTTTAAA-TTATTTATAAATTTTTAATAAT
1 TTTTAAATTTATTTATAAATATATAATAAT
7645352 TTTTAAA
1 TTTTAAA
7645359 ATAATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.22
29 18 0.56
30 7 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTTAAATTTATTTATAAATATATAATAAT
Found at i:7645353 original size:18 final size:18
Alignment explanation
Indices: 7645302--7645358 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 18
7645292 ATTTTAAATT
*
7645302 TTTTTATATAATATATAAAA
1 TTTTTA-ATAATTTAT-AAA
*
7645322 TTTTTAAATTATTTATAAA
1 TTTTT-AATAATTTATAAA
*
7645341 TTTTTAATAATTTTTAAA
1 TTTTTAATAATTTATAAA
7645359 ATAATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 11 0.34
19 8 0.25
20 12 0.38
21 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTTAATAATTTATAAA
Found at i:7645360 original size:19 final size:19
Alignment explanation
Indices: 7645302--7645360 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
7645292 ATTTTAAATT
* *
7645302 TTTTTATATAATATATAAAA
1 TTTTTA-ATAATTTTTAAAA
7645322 TTTTT-A-AATTATTTATAAA
1 TTTTTAATAATT-TTTA-AAA
7645341 TTTTTAATAATTTTTAAAA
1 TTTTTAATAATTTTTAAAA
7645360 T
1 T
7645361 AATTTTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
17 3 0.09
18 4 0.12
19 12 0.36
20 10 0.30
21 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTAATAATTTTTAAAA
Found at i:7645376 original size:15 final size:15
Alignment explanation
Indices: 7645343--7645379 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 15
7645333 TTTATAAATT
7645343 TTTAATAATTTTTAA
1 TTTAATAATTTTTAA
7645358 ---AATAATTTTTAA
1 TTTAATAATTTTTAA
7645370 TTTAATAATT
1 TTTAATAATT
7645380 AATATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
12 12 0.63
15 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAATAATTTTTAA
Found at i:7645928 original size:19 final size:20
Alignment explanation
Indices: 7645885--7645929 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
7645875 TTTATATGTT
*
7645885 TAAT-ATTTTTTAAATTTAA
1 TAATAATTTTTTAAATTAAA
*
7645904 T-TTAATTTTTTAAA-TAAA
1 TAATAATTTTTTAAATTAAA
7645922 TAATAATT
1 TAATAATT
7645930 AAATTATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATAATTTTTTAAATTAAA
Found at i:7646183 original size:2 final size:2
Alignment explanation
Indices: 7646176--7646221 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
7646166 CAATATTGGA
*
7646176 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
7646218 TC TC
1 TC TC
7646222 CATGTTCATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
TC
Found at i:7655252 original size:31 final size:31
Alignment explanation
Indices: 7655206--7655264 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
7655196 TAAAAATATT
* *
7655206 AAATATATATTATATTTTATATA-AATTTTA
1 AAATATATATAATATTATATATATAATTTTA
7655236 AAATAATATATAATATTATATATATAATT
1 AAAT-ATATATAATATTATATATATAATT
7655265 AATTTGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 17 0.68
32 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
AAATATATATAATATTATATATATAATTTTA
Found at i:7655836 original size:160 final size:160
Alignment explanation
Indices: 7655554--7655873 Score: 435
Period size: 160 Copynumber: 2.0 Consensus size: 160
7655544 CATTGATTGG
* * ** * * * * *
7655554 AGGCCCGTCGACAACCAATAGGTCGTAGACACATCACGCCACTTGGTCTCGTATTAAGACTTTAG
1 AGGCCCATCAACAACCAATAGGTCACAGACACACCACACCACCTAGTCTCCTATTAAGACTTTAG
* ** * * * *
7655619 GCTAATCGTAGAATAGTTATTTACTTTAATCTCTTATTATTTACCTTAGTTGTATTAGACTA-TT
66 GCCAATCGTAGAATAGTTATTTACTTTAATCTCTTATTACCTACCCTAATCGTATTAGACCACTT
7655683 AGAAATAGAGTTGTTTTAAGATTAGAGAAAT
131 -GAAATAGAGTTGTTTTAAGATTAGAGAAAT
*
7655714 AGGCCCATCAACAACCAATGGGTCACAGACACACCACACCACCTAGTCTCCTATTAAGACTTTAG
1 AGGCCCATCAACAACCAATAGGTCACAGACACACCACACCACCTAGTCTCCTATTAAGACTTTAG
* * *
7655779 GCCAATTGTAGAATATTTATTTACTTTAATCTCTTGTTACCTACCCTAATCGTATTAGACCACTT
66 GCCAATCGTAGAATAGTTATTTACTTTAATCTCTTATTACCTACCCTAATCGTATTAGACCACTT
*
7655844 GAAGTAGAGTTGTTTTAAGATTAGAGAAAT
131 GAAATAGAGTTGTTTTAAGATTAGAGAAAT
7655874 CTTATATCAT
Statistics
Matches: 138, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
160 136 0.99
161 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (160 bp):
AGGCCCATCAACAACCAATAGGTCACAGACACACCACACCACCTAGTCTCCTATTAAGACTTTAG
GCCAATCGTAGAATAGTTATTTACTTTAATCTCTTATTACCTACCCTAATCGTATTAGACCACTT
GAAATAGAGTTGTTTTAAGATTAGAGAAAT
Found at i:7656183 original size:30 final size:30
Alignment explanation
Indices: 7656149--7656208 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
7656139 CAAATTTATT
* **
7656149 GAGTTTTTGCTTTTTGCATGTTTGTGCAAA
1 GAGTTTTTGCCTTTTGCACCTTTGTGCAAA
7656179 GAGTTTTTGCCTTTTGCACCTTTGTGCAAA
1 GAGTTTTTGCCTTTTGCACCTTTGTGCAAA
7656209 ATTCTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.15, G:0.22, T:0.47
Consensus pattern (30 bp):
GAGTTTTTGCCTTTTGCACCTTTGTGCAAA
Found at i:7658726 original size:12 final size:12
Alignment explanation
Indices: 7658711--7658741 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
7658701 TAAATTTTAA
7658711 AATAAAAAAATT
1 AATAAAAAAATT
7658723 AAT-AAAAAATT
1 AATAAAAAAATT
7658734 AATAAAAA
1 AATAAAAA
7658742 TTATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:7658749 original size:11 final size:10
Alignment explanation
Indices: 7658716--7658749 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
7658706 TTTAAAATAA
7658716 AAAAATTAAT
1 AAAAATTAAT
7658726 AAAAAATTAAT
1 -AAAAATTAAT
7658737 AAAAATTATAT
1 AAAAATTA-AT
7658748 AA
1 AA
7658750 TAGTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAATTAAT
Done.