Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 13 of 22
Found at i:6635058 original size:29 final size:28
Alignment explanation
Indices: 6635026--6635094 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
6635016 AATATTAAAT
* *
6635026 AATATTCTTTATAATATTTATTAA-AGTTA
1 AATATT-TTTAT-ATATTAAATAATAGTTA
* *
6635055 AATATTATTAATATATTAAATAATATTTA
1 AATATT-TTTATATATTAAATAATAGTTA
6635084 AATATTTTTAT
1 AATATTTTTAT
6635095 TTTCCTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (28 bp):
AATATTTTTATATATTAAATAATAGTTA
Found at i:6635058 original size:45 final size:49
Alignment explanation
Indices: 6634976--6635081 Score: 132
Period size: 45 Copynumber: 2.2 Consensus size: 49
6634966 TAAATCATAC
* **
6634976 TAAATAATATTCTTTATTATATTTATTGTATTCAAATA-A-T-A-ATAT
1 TAAATAATATTCTTTATAATATTTATTAAATTCAAATATATTAATATAT
6635021 TAAATAATATTCTTTATAATATTTATTAAAGTT-AAATATTATTAATATAT
1 TAAATAATATTCTTTATAATATTTATTAAA-TTCAAATA-TATTAATATAT
6635071 TAAATAATATT
1 TAAATAATATT
6635082 TAAATATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
45 32 0.62
46 2 0.04
47 1 0.02
48 1 0.02
49 1 0.02
50 15 0.29
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (49 bp):
TAAATAATATTCTTTATAATATTTATTAAATTCAAATATATTAATATAT
Found at i:6635065 original size:42 final size:42
Alignment explanation
Indices: 6634958--6635065 Score: 112
Period size: 45 Copynumber: 2.5 Consensus size: 42
6634948 TATATTCTTC
* * *
6634958 ATTAAATTTAAATCA-TACTAAATAATATTCTTTATTATATTT
1 ATTAAA-TTAAATAATTATTAAATAATATTCTTTATAATATTT
**
6635000 ATTGTATTCAAATAATAATATTAAATAATATTCTTTATAATATTT
1 ATTAAATT-AAATAAT--TATTAAATAATATTCTTTATAATATTT
6635045 ATTAAAGTTAAAT-ATTATTAA
1 ATTAAA-TTAAATAATTATTAA
6635066 TATATTAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
41 2 0.04
42 15 0.28
44 2 0.04
45 33 0.61
46 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (42 bp):
ATTAAATTAAATAATTATTAAATAATATTCTTTATAATATTT
Found at i:6636536 original size:25 final size:25
Alignment explanation
Indices: 6636500--6636635 Score: 175
Period size: 25 Copynumber: 5.4 Consensus size: 25
6636490 AGAAGTGGAT
6636500 GGATAATTTTACCATCAGAATCTAA
1 GGATAATTTTACCATCAGAATCTAA
* *
6636525 GAATAATTTTACCATCAGAATTTAA
1 GGATAATTTTACCATCAGAATCTAA
* * *
6636550 GAATAATTTTACCACCAGAAGT-AAA
1 GGATAATTTTACCATCAGAA-TCTAA
* *
6636575 TGGATAATTTAACTATCAGAATCTAA
1 -GGATAATTTTACCATCAGAATCTAA
*
6636601 GGATAATTTTACCATCAAAATCTAA
1 GGATAATTTTACCATCAGAATCTAA
6636626 GGATAATTTT
1 GGATAATTTT
6636636 GTCACTAAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
25 77 0.80
26 19 0.20
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (25 bp):
GGATAATTTTACCATCAGAATCTAA
Found at i:6636536 original size:51 final size:50
Alignment explanation
Indices: 6636476--6636635 Score: 162
Period size: 51 Copynumber: 3.2 Consensus size: 50
6636466 TTTTTTAATT
* *
6636476 ATAATTTTACCA-CTAGAAGTGGATGGATAATTTTACCATCAGAATCTAAGA
1 ATAATTTTACCATC-AGAA-TGGAAGGATAATTTTACCATCAGAATCTAAGG
** * * *
6636527 ATAATTTTACCATCAGAATTTAAGAATAATTTTACCACCAGAAGT-AAATGG
1 ATAATTTTACCATCAGAATGGAAGGATAATTTTACCATCAGAA-TCTAA-GG
* * ** *
6636578 ATAATTTAACTATCAGAATCTAAGGATAATTTTACCATCAAAATCTAAGG
1 ATAATTTTACCATCAGAATGGAAGGATAATTTTACCATCAGAATCTAAGG
6636628 ATAATTTT
1 ATAATTTT
6636636 GTCACTAAAA
Statistics
Matches: 90, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
50 32 0.36
51 57 0.63
52 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (50 bp):
ATAATTTTACCATCAGAATGGAAGGATAATTTTACCATCAGAATCTAAGG
Found at i:6636654 original size:76 final size:76
Alignment explanation
Indices: 6636476--6636661 Score: 264
Period size: 76 Copynumber: 2.4 Consensus size: 76
6636466 TTTTTTAATT
*
6636476 ATAATTTTACCACTAGAAGTGGATGGATAATTTTACCATCAGAATCTAAGAATAATTTTACCATC
1 ATAATTTTACCACTAGAAGTGGATGGATAATTTAACCATCAGAATCTAAGAATAATTTTACCATC
* *
6636541 AGAATTTAAGA
66 AAAATCTAAGA
* ** * *
6636552 ATAATTTTACCACCAGAAGTAAATGGATAATTTAACTATCAGAATCTAAGGATAATTTTACCATC
1 ATAATTTTACCACTAGAAGTGGATGGATAATTTAACCATCAGAATCTAAGAATAATTTTACCATC
*
6636617 AAAATCTAAGG
66 AAAATCTAAGA
** *
6636628 ATAATTTTGTCACTAAAAGTGGATGGATAATTTA
1 ATAATTTTACCACTAGAAGTGGATGGATAATTTA
6636662 CCACCAAAAG
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 95 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (76 bp):
ATAATTTTACCACTAGAAGTGGATGGATAATTTAACCATCAGAATCTAAGAATAATTTTACCATC
AAAATCTAAGA
Found at i:6642234 original size:23 final size:24
Alignment explanation
Indices: 6642187--6642234 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
6642177 AAATATTAAA
*
6642187 ATTTAAAAATTATATTTAAATAAT
1 ATTTAAAAATTATAATTAAATAAT
* *
6642211 ATTTAAACATT-TAATTCAATAAT
1 ATTTAAAAATTATAATTAAATAAT
6642234 A
1 A
6642235 GGTGTACGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAAAAATTATAATTAAATAAT
Found at i:6648107 original size:2 final size:2
Alignment explanation
Indices: 6648102--6648134 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6648092 TATGTGTGTG
*
6648102 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6648135 TTTAATAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:6653914 original size:26 final size:26
Alignment explanation
Indices: 6653861--6653915 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
6653851 TTGTTTCAGA
* *
6653861 TATGATTTAAGTTTTAATTTATTTTT
1 TATGAGTTAAGTTTTAATTTATTATT
6653887 TATGAGTTAA-TTTTAATTTATTAATT
1 TATGAGTTAAGTTTTAATTTATT-ATT
6653913 TAT
1 TAT
6653916 TTTTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (26 bp):
TATGAGTTAAGTTTTAATTTATTATT
Found at i:6657995 original size:33 final size:32
Alignment explanation
Indices: 6657943--6658011 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
6657933 ACTAACGTAG
* * *
6657943 CATGTTATATATCATAATTGATAATGATGTGA
1 CATGTTACATATCATAATTGATAATAATATGA
* *
6657975 CATGTTAACATATTATAATTGATGATAATATGA
1 CATGTT-ACATATCATAATTGATAATAATATGA
6658008 CATG
1 CATG
6658012 CTAATTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (32 bp):
CATGTTACATATCATAATTGATAATAATATGA
Found at i:6663048 original size:27 final size:27
Alignment explanation
Indices: 6663007--6663069 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
6662997 GCGAGAGGAA
6663007 GAGAA-AGGATAGGGAAGAAGGGGGAG
1 GAGAAGAGGATAGGGAAGAAGGGGGAG
* * * *
6663033 GAGGAGAGGATGGGGAAGGAGGTGGAG
1 GAGAAGAGGATAGGGAAGAAGGGGGAG
6663060 GAGAAGAGGA
1 GAGAAGAGGA
6663070 GTTGAGTGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.38, C:0.00, G:0.57, T:0.05
Consensus pattern (27 bp):
GAGAAGAGGATAGGGAAGAAGGGGGAG
Found at i:6664555 original size:2 final size:2
Alignment explanation
Indices: 6664548--6664574 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6664538 CATCTGCACT
6664548 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
6664575 TTTGACTTTG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:6665153 original size:2 final size:2
Alignment explanation
Indices: 6665146--6665177 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6665136 TGTTTAGAAC
6665146 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
6665178 ATTTAGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6667144 original size:30 final size:29
Alignment explanation
Indices: 6667105--6667204 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
6667095 CATTAGTAAT
* *
6667105 AAAGACTTATTTAACTCAAAATAAAAGTA
1 AAAGGCTTATTTAAATCAAAATAAAAGTA
* *
6667134 AAATGGCTTATTTGATTCAAAAT-AAAGTA
1 AAA-GGCTTATTTAAATCAAAATAAAAGTA
* *
6667163 TAAGGACTTAATTAAATGC--AATAAAAGTA
1 AAAGG-CTTATTTAAAT-CAAAATAAAAGTA
6667192 TAAAGGCTTATTT
1 -AAAGGCTTATTT
6667205 GAATTTTCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
28 5 0.09
29 31 0.54
30 21 0.37
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (29 bp):
AAAGGCTTATTTAAATCAAAATAAAAGTA
Found at i:6667172 original size:29 final size:28
Alignment explanation
Indices: 6667110--6667209 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 28
6667100 GTAATAAAGA
* *
6667110 CTTATTTAACTCAAAATAAAAGTAAAATGG
1 CTTATTTAATTCAAAAT-AAAGTATAA-GG
*
6667140 CTTATTTGATTCAAAATAAAGTATAAGG
1 CTTATTTAATTCAAAATAAAGTATAAGG
* * *
6667168 ACTTAATTAAATGCAATA-AAAGTATAAAGG
1 -CTT-ATTTAATTCAAAATAAAGTAT-AAGG
6667198 CTTATTTGAATT
1 CTTATTT-AATT
6667210 TTCTAAAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
28 5 0.09
29 24 0.42
30 28 0.49
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (28 bp):
CTTATTTAATTCAAAATAAAGTATAAGG
Found at i:6670201 original size:22 final size:20
Alignment explanation
Indices: 6670166--6670235 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
6670156 GAATAATTTG
6670166 AATATTAATATTTTAAATTA
1 AATATTAATATTTTAAATTA
6670186 AATATTAATATATTT---TTA
1 AATATTAATAT-TTTAAATTA
* *
6670204 ATTTTTAATATTTTAAATTA
1 AATATTAATATTTTAAATTA
6670224 AATATTAATATT
1 AATATTAATATT
6670236 CATCAAACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.07
18 12 0.29
20 24 0.57
21 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATTAATATTTTAAATTA
Found at i:6671216 original size:25 final size:24
Alignment explanation
Indices: 6671179--6671251 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 24
6671169 GTTAATATTC
* * *
6671179 TAAAAATTAAAATAAATAATTATAT
1 TAAAATTTTAAATAAA-AATTATAA
*
6671204 TAAAATTTTAAATAACAATTTATAA
1 TAAAATTTTAAATAA-AAATTATAA
6671229 TAAATATTTTAAATTAAAAATTA
1 TAAA-ATTTTAAA-TAAAAATTA
6671252 CATATTATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 23 0.57
26 14 0.35
27 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAAATTTTAAATAAAAATTATAA
Found at i:6679801 original size:2 final size:2
Alignment explanation
Indices: 6679794--6679818 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6679784 CTCATTCTGC
6679794 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
6679819 AATTCGGACT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:6681129 original size:20 final size:20
Alignment explanation
Indices: 6681062--6681129 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
6681052 AAGAATATGT
** *
6681062 TTTCTAACTGCGTAATTTAA
1 TTTCTAACTATGTAATTTTA
* *
6681082 TTTCTAACTGATTTACATATT-
1 TTTCTAACT-ATGTA-ATTTTA
6681103 TTT-TAACTATGTAATTTTA
1 TTTCTAACTATGTAATTTTA
6681122 TTTCTAAC
1 TTTCTAAC
6681130 AGATGTCAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 4 0.11
19 7 0.19
20 18 0.49
21 5 0.14
22 3 0.08
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.51
Consensus pattern (20 bp):
TTTCTAACTATGTAATTTTA
Found at i:6690410 original size:2 final size:2
Alignment explanation
Indices: 6690360--6690397 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6690350 TTACAGAAGT
*
6690360 GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6690398 CATAGATAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6692377 original size:19 final size:20
Alignment explanation
Indices: 6692340--6692377 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6692330 ACAATATATT
**
6692340 AAATAAAAATATTTTTTAAA
1 AAATAAAAATATTAATTAAA
6692360 AAATAAAAAT-TTAATTAA
1 AAATAAAAATATTAATTAA
6692378 TTTTAACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAAAAATATTAATTAAA
Found at i:6696836 original size:119 final size:119
Alignment explanation
Indices: 6696683--6696919 Score: 413
Period size: 119 Copynumber: 2.0 Consensus size: 119
6696673 ATATTTATAT
* *
6696683 ATATTTTTTAACATAATAAATCTTTTCCATTTAAATATTT-GACTTATTAATAAGTATATATATC
1 ATATTTTTTAACACAATAAATCTTTTCCACTTAAATATTTAG-CTTATTAATAAGTATATATATC
*
6696747 ATTTACTTAAAATTTTATATTTTTCAAATATTTTTTCAATTTAATTCCTCAATAA
65 ATTTACTTAAAATTTTATATTTTTCAAATATTTATTCAATTTAATTCCTCAATAA
*
6696802 ATATTTTTTAACACAATAAATCTTTTTCACTTAAATATTTAGCTTATTAATAAGTATATATATCA
1 ATATTTTTTAACACAATAAATCTTTTCCACTTAAATATTTAGCTTATTAATAAGTATATATATCA
*
6696867 TTTACTTAAAATTTTATATTTTTTAAATATTTATTCAATTTAATTCCTCAATA
66 TTTACTTAAAATTTTATATTTTTCAAATATTTATTCAATTTAATTCCTCAATA
6696920 CCTCAATTTT
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
119 111 0.99
120 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (119 bp):
ATATTTTTTAACACAATAAATCTTTTCCACTTAAATATTTAGCTTATTAATAAGTATATATATCA
TTTACTTAAAATTTTATATTTTTCAAATATTTATTCAATTTAATTCCTCAATAA
Found at i:6698723 original size:30 final size:29
Alignment explanation
Indices: 6698663--6698739 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
6698653 TTAAATTACT
* * *
6698663 TTTTTAAACTTTTATTATATTTAATCAAA
1 TTTTTATACTTTTATTTTATTAAATCAAA
6698692 TTTTTATACTTTTATTTTAAGTTAAAT-AAA
1 TTTTTATACTTTTATTTT-A-TTAAATCAAA
* *
6698722 TTTTAATATTTTTATTTT
1 TTTTTATACTTTTATTTT
6698740 TGATAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.39
30 20 0.49
31 5 0.12
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (29 bp):
TTTTTATACTTTTATTTTATTAAATCAAA
Found at i:6698746 original size:29 final size:30
Alignment explanation
Indices: 6698689--6698747 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
6698679 ATATTTAATC
* *
6698689 AAATTTTTATACTTTTATTTTAAGTTAAAT
1 AAATTTTAATACTTTTATTTTAAGATAAAT
* *
6698719 AAATTTTAATATTTTTATTTT-TGATAAAT
1 AAATTTTAATACTTTTATTTTAAGATAAAT
6698748 TTTTTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (30 bp):
AAATTTTAATACTTTTATTTTAAGATAAAT
Found at i:6698856 original size:26 final size:29
Alignment explanation
Indices: 6698793--6698858 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
6698783 ATTATTTATT
* *
6698793 AACATATCATAATTAATGACAGATATATT
1 AACAGATCATAATTAATGACAGATATATA
* *
6698822 AACATATCATAATTAATGATA-ATATA-A
1 AACAGATCATAATTAATGACAGATATATA
6698849 AAC-GATCATA
1 AACAGATCATA
6698859 TGATCATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.18
27 3 0.09
28 5 0.15
29 20 0.59
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.32
Consensus pattern (29 bp):
AACAGATCATAATTAATGACAGATATATA
Found at i:6700390 original size:21 final size:21
Alignment explanation
Indices: 6700366--6700406 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6700356 ATCTTCCTCA
* *
6700366 TCATCGGATTCGCTCTCACTC
1 TCATCAGATTCGCTATCACTC
*
6700387 TCATTAGATTCGCTATCACT
1 TCATCAGATTCGCTATCACT
6700407 ATAAGACGAT
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:0.20, C:0.32, G:0.12, T:0.37
Consensus pattern (21 bp):
TCATCAGATTCGCTATCACTC
Found at i:6701819 original size:19 final size:20
Alignment explanation
Indices: 6701783--6701820 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
6701773 AAAAAAATAT
* *
6701783 TTAAAAAAGTTTTTAAATTA
1 TTAAAAAAGATTTAAAATTA
6701803 TTAAAAAA-ATTTAAAATT
1 TTAAAAAAGATTTAAAATT
6701821 TTTTTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TTAAAAAAGATTTAAAATTA
Found at i:6726802 original size:22 final size:22
Alignment explanation
Indices: 6726750--6726807 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
6726740 GTTGTTCTTA
*
6726750 GCATTGCGTGACTTATTGATAG
1 GCATTGCATGACTTATTGATAG
*
6726772 GTCATTGCATGACTTCTT-ATAAG
1 G-CATTGCATGACTTATTGAT-AG
6726795 GCATTGCATGACT
1 GCATTGCATGACT
6726808 GTTATCTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (22 bp):
GCATTGCATGACTTATTGATAG
Found at i:6729714 original size:20 final size:19
Alignment explanation
Indices: 6729686--6729749 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
6729676 TAGTAAATCT
6729686 ATATATATATAATTTAAAAA
1 ATATATATA-AATTTAAAAA
* *
6729706 ATATTTATAAATAATAAAAA
1 ATATATATAAAT-TTAAAAA
* *
6729726 TTATATAAAAATTTTAAAAA
1 ATATATATAAA-TTTAAAAA
6729746 ATAT
1 ATAT
6729750 CTTTTATAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.09
20 31 0.89
21 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATATATAAATTTAAAAA
Found at i:6730352 original size:52 final size:52
Alignment explanation
Indices: 6730270--6730377 Score: 189
Period size: 52 Copynumber: 2.1 Consensus size: 52
6730260 TATTCAACTA
6730270 TATTCATTTATATTATCTTCGAAATAGCTTGCAGTTTACTATGAGCTACTGT
1 TATTCATTTATATTATCTTCGAAATAGCTTGCAGTTTACTATGAGCTACTGT
* * *
6730322 TATTCATTTATATTATCTTGGAAATGGCTTGCAGTTTACTATGGGCTACTGT
1 TATTCATTTATATTATCTTCGAAATAGCTTGCAGTTTACTATGAGCTACTGT
6730374 TATT
1 TATT
6730378 ATGGGATAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (52 bp):
TATTCATTTATATTATCTTCGAAATAGCTTGCAGTTTACTATGAGCTACTGT
Found at i:6738909 original size:3 final size:3
Alignment explanation
Indices: 6738891--6738926 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
6738881 ATCGTTCACC
6738891 AGA AGAA AGA AGGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AG-A AGA A-GA AGA AGA AGA AGA AGA AGA AGA A
6738927 ACTCTCACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6740547 original size:42 final size:42
Alignment explanation
Indices: 6740501--6740584 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
6740491 CATGAAATTG
6740501 CACAGATAACTGCCTTCTTATCTCTTGGACTTAAAGGAAACT
1 CACAGATAACTGCCTTCTTATCTCTTGGACTTAAAGGAAACT
6740543 CACAGATAACTGCCTTCTTATCTCTTGGACTTAAAGGAAACT
1 CACAGATAACTGCCTTCTTATCTCTTGGACTTAAAGGAAACT
6740585 ATGTACTTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (42 bp):
CACAGATAACTGCCTTCTTATCTCTTGGACTTAAAGGAAACT
Found at i:6741501 original size:15 final size:15
Alignment explanation
Indices: 6741481--6741510 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6741471 TGAAGCATTA
6741481 GCTTTGTAGTTTTGG
1 GCTTTGTAGTTTTGG
6741496 GCTTTGTAGTTTTGG
1 GCTTTGTAGTTTTGG
6741511 ACTGTGTTTT
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:0.07, C:0.07, G:0.33, T:0.53
Consensus pattern (15 bp):
GCTTTGTAGTTTTGG
Found at i:6742350 original size:22 final size:20
Alignment explanation
Indices: 6742316--6742364 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
6742306 TATGAAATGA
* *
6742316 TTAAAATATTTTTTATTA-AT
1 TTAAAAAATTATTT-TTATAT
6742336 TTAAAAAATTATTTTTATAT
1 TTAAAAAATTATTTTTATAT
6742356 TTAAAAAAT
1 TTAAAAAAT
6742365 AAAAAAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAAAAATTATTTTTATAT
Found at i:6744024 original size:31 final size:30
Alignment explanation
Indices: 6743960--6744031 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 30
6743950 TATTTTAATT
6743960 TTTTATATAAAAAATAAATTAAATTTATTTGA
1 TTTTA-ATAAAAAATAAATTAAATTTA-TTGA
6743992 TTTTAATAAAATAATAATATTATAA-TTA-TGA
1 TTTTAATAAAA-AATAA-ATTA-AATTTATTGA
6744023 -TTTAATAAA
1 TTTTAATAAA
6744032 GTATATTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
30 9 0.24
31 9 0.24
32 10 0.27
33 7 0.19
34 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (30 bp):
TTTTAATAAAAAATAAATTAAATTTATTGA
Found at i:6750802 original size:26 final size:25
Alignment explanation
Indices: 6750732--6750803 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
6750722 AAGTGGATGG
* * *
6750732 ATAATTTTATCATCAAAATTTAAAA
1 ATAATTTTACCATCAAAAGTGAAAA
* *
6750757 ATAATTTTACCATTAGAAGTGAATAA
1 ATAATTTTACCATCAAAAGTGAA-AA
*
6750783 GTAATTTTACCATCAAAAGTG
1 ATAATTTTACCATCAAAAGTG
6750804 GATGAATGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 18 0.47
26 20 0.53
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (25 bp):
ATAATTTTACCATCAAAAGTGAAAA
Found at i:6754688 original size:19 final size:18
Alignment explanation
Indices: 6754644--6754690 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
6754634 TTCTTACTTT
6754644 CTCTAAATACTTTGTTTC
1 CTCTAAATACTTTGTTTC
*
6754662 CTTTTAAATACTTTGTTTTC
1 C-TCTAAATACTTTG-TTTC
6754682 CTCTAAATA
1 CTCTAAATA
6754691 TTTTCTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.76
20 5 0.20
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.51
Consensus pattern (18 bp):
CTCTAAATACTTTGTTTC
Found at i:6770200 original size:15 final size:15
Alignment explanation
Indices: 6770180--6770211 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6770170 TCTTTTCTTC
6770180 ATTTTTTTATTTATT
1 ATTTTTTTATTTATT
*
6770195 ATTTTTTTATTTTTT
1 ATTTTTTTATTTATT
6770210 AT
1 AT
6770212 ACTATTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
ATTTTTTTATTTATT
Found at i:6772807 original size:2 final size:2
Alignment explanation
Indices: 6772800--6772824 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6772790 ATTATTATGT
6772800 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
6772825 TTCTTAAAAA
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:6773408 original size:25 final size:25
Alignment explanation
Indices: 6773380--6773500 Score: 106
Period size: 25 Copynumber: 4.9 Consensus size: 25
6773370 TATATATATG
**
6773380 ATTTATTATTTTTTAAATATTAATA
1 ATTTATTATAATTTAAATATTAATA
* *
6773405 ATTTATAATTTAATTAAAATATTAATA
1 ATTTAT--TATAATTTAAATATTAATA
6773432 A-TTA--ATAATTTAAATATTAATA
1 ATTTATTATAATTTAAATATTAATA
* * **
6773454 TTTTAGTATAATTTATTTATTAATA
1 ATTTATTATAATTTAAATATTAATA
*
6773479 TTTTATTCATAATTT-AATATTA
1 ATTTATT-ATAATTTAAATATTA
6773501 TTATGATTAC
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
22 16 0.21
23 3 0.04
25 33 0.42
26 10 0.13
27 16 0.21
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (25 bp):
ATTTATTATAATTTAAATATTAATA
Found at i:6773416 original size:22 final size:22
Alignment explanation
Indices: 6773391--6773529 Score: 74
Period size: 22 Copynumber: 6.1 Consensus size: 22
6773381 TTTATTATTT
6773391 TTTAAATATTAATAATTTATAA
1 TTTAAATATTAATAATTTATAA
*
6773413 TTTAATTAAAATATTAATAATTAATAA
1 --T--TT-AAATATTAATAATTTATAA
*
6773440 TTTAAATATTAATATTTTAGTATAA
1 TTTAAATATTAATA-ATT--TATAA
**
6773465 TTTATTTATTAAT-ATTT-T-A
1 TTTAAATATTAATAATTTATAA
* * *
6773484 TTCATAAT-TTAATATTATTATGA
1 TTTA-AATATTAATAAT-TTATAA
6773507 -TTACAATATTAATAATTT-TAA
1 TTTA-AATATTAATAATTTATAA
6773528 TT
1 TT
6773530 AATTTCTAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 28
0.68 0.11 0.22
Matches are distributed among these distances:
19 9 0.10
20 3 0.03
21 5 0.06
22 20 0.23
23 14 0.16
24 1 0.01
25 16 0.18
26 2 0.02
27 18 0.20
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (22 bp):
TTTAAATATTAATAATTTATAA
Found at i:6775133 original size:47 final size:47
Alignment explanation
Indices: 6774925--6775209 Score: 404
Period size: 47 Copynumber: 6.1 Consensus size: 47
6774915 CCAGCCCGGC
* *
6774925 GGGCCGCAGGGGGAATCGGAACTCGT-GGAGCCGGAGGGGGCGGGCA
1 GGGCCGCAGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGCGGGCA
* * *
6774971 GGGCCGCAGGGGGAACCGGGACCCGTGGGAGCCGGAGGGGGGCGAGTA
1 GGGCCGCAGGGGGAACCGGGACTCGTGGGAGCCGGA-GGGGGCGGGCA
6775019 GGGCCGCAGGGGGGAACCGGGACTC-TGGGAGCCGGAGGAGGG-GGGCA
1 GGGCCGCA-GGGGGAACCGGGACTCGTGGGAGCCGGAGG-GGGCGGGCA
*
6775066 GGGCCACA-GGGGAACCGGGACTCGTGGGAGCCGGAGGGGGCGGGCA
1 GGGCCGCAGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGCGGGCA
*
6775112 GGGCCGCAGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGTA
1 GGGCCGCAGGGGGAACCGGGACTCGTGGGAGCCGGA-GGGGGCGGGCA
6775160 GGG-CGC-GAGGGGAACCGGGACTCGTGGGAGCCGGAGGAGGG-GGGCA
1 GGGCCGCAG-GGGGAACCGGGACTCGTGGGAGCCGGAGG-GGGCGGGCA
6775206 GGGC
1 GGGC
6775210 TAGCCCGGCC
Statistics
Matches: 216, Mismatches: 12, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
45 18 0.08
46 58 0.27
47 81 0.38
48 44 0.20
49 15 0.07
ACGTcount: A:0.16, C:0.22, G:0.57, T:0.05
Consensus pattern (47 bp):
GGGCCGCAGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGCGGGCA
Found at i:6775203 original size:141 final size:141
Alignment explanation
Indices: 6774925--6775209 Score: 477
Period size: 141 Copynumber: 2.0 Consensus size: 141
6774915 CCAGCCCGGC
* *
6774925 GGGCCGCAGGGGGAATCGGAACTCGTGGAGCCGGAGGGGGCGGGCAGGGCCGCAGGGGGAACCGG
1 GGGCCACAGGGGGAACCGGAACTCGTGGAGCCGGAGGGGGCGGGCAGGGCCGCAGGGGGAACCGG
*
6774990 GACCCGTGGGAGCCGGAGGGGGGCGAGTAGGGCCGCAGGGGGGAACCGGGACTCTGGGAGCCGGA
66 GACCCGTGGGAGCCGGAGGGGGGCGAGTAGGGCCGCAGAGGGGAACCGGGACTCTGGGAGCCGGA
6775055 GGAGGGGGGCA
131 GGAGGGGGGCA
*
6775066 GGGCCACA-GGGGAACCGGGACTCGTGGGAGCCGGAGGGGGCGGGCAGGGCCGCAGGGGGAACCG
1 GGGCCACAGGGGGAACCGGAACTCGT-GGAGCCGGAGGGGGCGGGCAGGGCCGCAGGGGGAACCG
* *
6775130 GGACTCGTGGGAGCCGGAGGGGGGCGGGTAGGG-CGC-GAGGGGAACCGGGACTCGTGGGAGCCG
65 GGACCCGTGGGAGCCGGAGGGGGGCGAGTAGGGCCGCAGAGGGGAACCGGGACTC-TGGGAGCCG
6775193 GAGGAGGGGGGCA
129 GAGGAGGGGGGCA
6775206 GGGC
1 GGGC
6775210 TAGCCCGGCC
Statistics
Matches: 136, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
139 16 0.12
140 44 0.32
141 76 0.56
ACGTcount: A:0.16, C:0.22, G:0.57, T:0.05
Consensus pattern (141 bp):
GGGCCACAGGGGGAACCGGAACTCGTGGAGCCGGAGGGGGCGGGCAGGGCCGCAGGGGGAACCGG
GACCCGTGGGAGCCGGAGGGGGGCGAGTAGGGCCGCAGAGGGGAACCGGGACTCTGGGAGCCGGA
GGAGGGGGGCA
Found at i:6778785 original size:14 final size:14
Alignment explanation
Indices: 6778747--6778785 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
6778737 CACTTCTCCC
* *
6778747 AAAATGAAAAACAA
1 AAAAAGAAAAAGAA
6778761 AAAAA-AAAAAGAA
1 AAAAAGAAAAAGAA
6778774 AAAAAGAAAAAG
1 AAAAAGAAAAAG
6778786 GCATTTGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:6787859 original size:105 final size:105
Alignment explanation
Indices: 6787677--6787885 Score: 382
Period size: 105 Copynumber: 2.0 Consensus size: 105
6787667 CAAGACCCTG
*
6787677 AGCTAAAACAATGCAGGCACCAGTGCAGGATCCAGCAACAATACAGCGAGGAACAGAAGGGAGAA
1 AGCTAAAACAATGCAGGCACCAGTGCAGGATCCAGCAACAATACAGCGAGGAACAGAAGGAAGAA
6787742 TGAGAGAGAAAATGTGAAGATTATCACAGAGAGAAGAAGT
66 TGAGAGAGAAAATGTGAAGATTATCACAGAGAGAAGAAGT
* *
6787782 AGCTAAAACAATGCAGGCACCAGTGCAGGGTCCAGCAACAATACAGCGAGGAAGAGAAGGAAGAA
1 AGCTAAAACAATGCAGGCACCAGTGCAGGATCCAGCAACAATACAGCGAGGAACAGAAGGAAGAA
*
6787847 TGTGAGAGAAAATGTGAAGATTATCACAGAGAGAAGAAG
66 TGAGAGAGAAAATGTGAAGATTATCACAGAGAGAAGAAG
6787886 GCGGGAGAGT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 100 1.00
ACGTcount: A:0.44, C:0.15, G:0.29, T:0.11
Consensus pattern (105 bp):
AGCTAAAACAATGCAGGCACCAGTGCAGGATCCAGCAACAATACAGCGAGGAACAGAAGGAAGAA
TGAGAGAGAAAATGTGAAGATTATCACAGAGAGAAGAAGT
Found at i:6789551 original size:34 final size:34
Alignment explanation
Indices: 6789508--6789575 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
6789498 TTCAGATTAA
6789508 TTTGCAAGACAACGTCCGGTACCCTCTCGCAGGT
1 TTTGCAAGACAACGTCCGGTACCCTCTCGCAGGT
6789542 TTTGCAAGACAACGTCCGGTACCCTCTCGCAGGT
1 TTTGCAAGACAACGTCCGGTACCCTCTCGCAGGT
6789576 AAACATACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.24
Consensus pattern (34 bp):
TTTGCAAGACAACGTCCGGTACCCTCTCGCAGGT
Found at i:6791093 original size:48 final size:48
Alignment explanation
Indices: 6791021--6791119 Score: 119
Period size: 48 Copynumber: 2.1 Consensus size: 48
6791011 ATGCATCACC
** * **
6791021 TAATCCACACTGTGCACAGATTCAAAG-AGTAAGGTAAAGCAAAAGTAT
1 TAATCCACACTGCCCACAGATTCAAAGCA-CAAGAAAAAGCAAAAGTAT
* *
6791069 TAATCCACAGTGCCCACAGTTTCAAAGCACAAGAAAAAGCAAAAGTAT
1 TAATCCACACTGCCCACAGATTCAAAGCACAAGAAAAAGCAAAAGTAT
6791117 TAA
1 TAA
6791120 AAAGAATAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 42 0.98
49 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (48 bp):
TAATCCACACTGCCCACAGATTCAAAGCACAAGAAAAAGCAAAAGTAT
Found at i:6799118 original size:15 final size:17
Alignment explanation
Indices: 6799093--6799129 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
6799083 TTTAAAAAAA
6799093 GAAAAATAATA-ACGAT
1 GAAAAATAATATACGAT
*
6799109 GAAAAA-AATATAGGAT
1 GAAAAATAATATACGAT
6799125 GAAAA
1 GAAAA
6799130 GAAAATAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.65, C:0.03, G:0.16, T:0.16
Consensus pattern (17 bp):
GAAAAATAATATACGAT
Found at i:6801050 original size:60 final size:60
Alignment explanation
Indices: 6800974--6801086 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
6800964 AAAAACGTTA
* * * *
6800974 AAGCATTTTAAGCATTTTGGAAT-AGTTTTTTATATATGAA-GAAAACTTTTGAGCGTTTT
1 AAGCATTTTAAACATTTTGGAATGA-TTTTTGATATATAAACAAAAACTTTTGAGCGTTTT
6801033 AAGCATTTTTAAACATTTTGGAATGATTTTTGATATATAAACAAAAACTTTTGA
1 AAGCA-TTTTAAACATTTTGGAATGATTTTTGATATATAAACAAAAACTTTTGA
6801087 ACATTTGGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 5 0.11
60 30 0.64
61 12 0.26
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (60 bp):
AAGCATTTTAAACATTTTGGAATGATTTTTGATATATAAACAAAAACTTTTGAGCGTTTT
Found at i:6801257 original size:21 final size:21
Alignment explanation
Indices: 6801233--6801292 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
6801223 AACTTTTAAG
* *
6801233 CATTACGTGACTTATTTTGTA
1 CATTGCGTGACTTATTTTGGA
* * * *
6801254 CATTGCGTAACTGACTTTGGG
1 CATTGCGTGACTTATTTTGGA
6801275 CATTGCGTGACTTATTTT
1 CATTGCGTGACTTATTTT
6801293 TAGGTATTGC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (21 bp):
CATTGCGTGACTTATTTTGGA
Found at i:6801307 original size:22 final size:23
Alignment explanation
Indices: 6801273--6801369 Score: 85
Period size: 22 Copynumber: 4.3 Consensus size: 23
6801263 ACTGACTTTG
* **
6801273 GGCATTGCGTGACTTA-TTTTTA
1 GGCATTGCATGACTTAGTTGGTA
*
6801295 GGTATTGCATGAC-TAGTTGGTA
1 GGCATTGCATGACTTAGTTGGTA
*
6801317 GGCATTGCATGACTT-GTTAGTAA
1 GGCATTGCATGACTTAGTTGGT-A
* *
6801340 GCCATTGCATGAC-TAGTTAGTAA
1 GGCATTGCATGACTTAGTTGGT-A
6801363 GGCATTG
1 GGCATTG
6801370 TGTGATTTAG
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
21 2 0.03
22 33 0.52
23 28 0.44
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (23 bp):
GGCATTGCATGACTTAGTTGGTA
Found at i:6801349 original size:23 final size:23
Alignment explanation
Indices: 6801298--6801369 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
6801288 ATTTTTAGGT
*
6801298 ATTGCATGACTAGTTGGT-AGGC
1 ATTGCATGACTAGTTAGTAAGGC
* *
6801320 ATTGCATGACTTGTTAGTAAGCC
1 ATTGCATGACTAGTTAGTAAGGC
6801343 ATTGCATGACTAGTTAGTAAGGC
1 ATTGCATGACTAGTTAGTAAGGC
6801366 ATTG
1 ATTG
6801370 TGTGATTTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 16 0.36
23 28 0.64
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (23 bp):
ATTGCATGACTAGTTAGTAAGGC
Found at i:6808071 original size:23 final size:23
Alignment explanation
Indices: 6808026--6808072 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
6808016 TTAAGCGATA
* *
6808026 CCTTACTAACTAGTCACATAATG
1 CCTTACTAACAAGTCACACAATG
*
6808049 CCTTACTAACAAGTCATACAATG
1 CCTTACTAACAAGTCACACAATG
6808072 C
1 C
6808073 TTATCAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.09, T:0.28
Consensus pattern (23 bp):
CCTTACTAACAAGTCACACAATG
Found at i:6808115 original size:23 final size:22
Alignment explanation
Indices: 6808060--6808117 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
6808050 CTTACTAACA
* *
6808060 AGTCATACAATGCTTATCAACT
1 AGTCATGCAATGCATATCAACT
*
6808082 AATCA-GACAATGTCATATCAACT
1 AGTCATG-CAATG-CATATCAACT
6808105 AGTCATGCAATGC
1 AGTCATGCAATGC
6808118 TTTAAAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
22 10 0.34
23 18 0.62
24 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (22 bp):
AGTCATGCAATGCATATCAACT
Found at i:6808146 original size:22 final size:21
Alignment explanation
Indices: 6808111--6808189 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
6808101 AACTAGTCAT
* *
6808111 GCAATGCTTTAAAACTAATTAC
1 GCAATGC-CTAAAAATAATTAC
* * *
6808133 GCAATGCCTAAAAATTAGTAAT
1 GCAATGCCTAAAAA-TAATTAC
* *
6808155 GTAATGCCTAAAAAAAGATTAC
1 GCAATGCCTAAAAATA-ATTAC
6808177 GCAATGCCTAAAA
1 GCAATGCCTAAAA
6808190 CTATCAAAAC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
21 6 0.14
22 38 0.86
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (21 bp):
GCAATGCCTAAAAATAATTAC
Found at i:6809772 original size:18 final size:18
Alignment explanation
Indices: 6809737--6809774 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6809727 CCATTATTTT
*
6809737 AAAAATAATAAGAACATA
1 AAAAATAATAAAAACATA
6809755 AAAAATAA-AAAAAGCATA
1 AAAAATAATAAAAA-CATA
6809773 AA
1 AA
6809775 GTTTACAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.13
Consensus pattern (18 bp):
AAAAATAATAAAAACATA
Found at i:6815606 original size:55 final size:55
Alignment explanation
Indices: 6815522--6815631 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
6815512 ATTTTGAATG
6815522 GTTTGTTACAACAGTCATGTTTACTTTAATAACTATTTCAATATGCATTTCAATC
1 GTTTGTTACAACAGTCATGTTTACTTTAATAACTATTTCAATATGCATTTCAATC
6815577 GTTTGTTACAACAGTCATGTTTACTTTAATAACTATTTCAATATGCATTTCAATC
1 GTTTGTTACAACAGTCATGTTTACTTTAATAACTATTTCAATATGCATTTCAATC
6815632 ACCATCACAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (55 bp):
GTTTGTTACAACAGTCATGTTTACTTTAATAACTATTTCAATATGCATTTCAATC
Found at i:6818803 original size:2 final size:2
Alignment explanation
Indices: 6818796--6818822 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6818786 CATTTTCTGC
6818796 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
6818823 GTGCAAGCCA
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:6834224 original size:12 final size:12
Alignment explanation
Indices: 6834207--6834231 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6834197 TTCATCATCA
6834207 TCATCTTCTTCT
1 TCATCTTCTTCT
6834219 TCATCTTCTTCT
1 TCATCTTCTTCT
6834231 T
1 T
6834232 TTCCGTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATCTTCTTCT
Found at i:6844293 original size:2 final size:2
Alignment explanation
Indices: 6844286--6844314 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6844276 ACATCAAATG
6844286 GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6844315 TGTGTGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6846040 original size:22 final size:22
Alignment explanation
Indices: 6845990--6846040 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
6845980 TTTTTACGAG
* *
6845990 TATAAAATATTTTATAAATTAA
1 TATAAAAAATTGTATAAATTAA
*
6846012 TGA-AAAAAATTGTATTAATTAA
1 T-ATAAAAAATTGTATAAATTAA
6846034 TATAAAA
1 TATAAAA
6846041 TATCTTAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.04
22 22 0.92
23 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (22 bp):
TATAAAAAATTGTATAAATTAA
Found at i:6855967 original size:25 final size:25
Alignment explanation
Indices: 6855929--6856008 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
6855919 TTAATAAACG
* *
6855929 TAATTATAGGGATTGAAAATCACCA
1 TAATTATAGAGATTGAGAATCACCA
* *
6855954 TAATTATAGAGATTGGGATTCACCA
1 TAATTATAGAGATTGAGAATCACCA
*
6855979 TAATTATAGAGATTGAGAATCAACA
1 TAATTATAGAGATTGAGAATCACCA
6856004 TAATT
1 TAATT
6856009 GTAGGGATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (25 bp):
TAATTATAGAGATTGAGAATCACCA
Found at i:6859539 original size:25 final size:25
Alignment explanation
Indices: 6859487--6859574 Score: 124
Period size: 25 Copynumber: 3.6 Consensus size: 25
6859477 TTAATAAACG
*
6859487 TAATTATAGGGATT-GAAATCACCA
1 TAATTATAGGGATTGGGAATCACCA
* *
6859511 TAATTATAAGGATTGGGATTCACCA
1 TAATTATAGGGATTGGGAATCACCA
*
6859536 TAATTATAGGGATTGGGAATCATCA
1 TAATTATAGGGATTGGGAATCACCA
*
6859561 TAATTGTAGGGATT
1 TAATTATAGGGATT
6859575 TTATTTTCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
24 13 0.23
25 43 0.77
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (25 bp):
TAATTATAGGGATTGGGAATCACCA
Found at i:6874048 original size:222 final size:222
Alignment explanation
Indices: 6873659--6874108 Score: 792
Period size: 222 Copynumber: 2.0 Consensus size: 222
6873649 AGAAAAGGCT
6873659 CGAAGATTTAGAGAAAAGATATCAGGGATTAGAAGAAAAATATGTGGGTCTGGAGAAAGAAAGGG
1 CGAAGATTTAGAGAAAAGATATCAGGGATTAGAAGAAAAATATGTGGGTCTGGAGAAAGAAAGGG
* * *
6873724 AATCAACTCTTTGTGAAGTACAAGAGCTACAAGAGTCACTAGAGGCTGAAAAGCAAGAACATTCT
66 AATCAACACTTCGTGAAGTACAAGAGCTACAAGAGTCACTAGAGGCTGAAAAGCAAGAACATGCT
*
6873789 AGTTTTGTGCAGTTGAATGGAAACCGAGTGACTGCTATGGAATCTCAGATCAGTTTTCTAGAAGA
131 AGTTTTGTGCAGTTGAATGGAAACCGAGTGACTGCTATGGAATCTCAGATCAGTTTTCTACAAGA
6873854 GGAAAGTCTGTGCAGGAAGAAGGAGTA
196 GGAAAGTCTGTGCAGGAAGAAGGAGTA
* *
6873881 CGAAGATTTAGAGAAAAGATATCAGGGATTAGAAGAAAAATATGTGGGTTTGGAGAAAGAGAGGG
1 CGAAGATTTAGAGAAAAGATATCAGGGATTAGAAGAAAAATATGTGGGTCTGGAGAAAGAAAGGG
6873946 AATCAACACTTCGTGAAGTACAAGAGCTACAAGAGTCACTAGAGGCTGAAAAGCAAGAACATGCT
66 AATCAACACTTCGTGAAGTACAAGAGCTACAAGAGTCACTAGAGGCTGAAAAGCAAGAACATGCT
* * * *
6874011 AGTTTTTTGCAGTTGAATGGAACCCGAGTGGCTGCTATGGAATCTCAGATCAGTTTTCTACAAGG
131 AGTTTTGTGCAGTTGAATGGAAACCGAGTGACTGCTATGGAATCTCAGATCAGTTTTCTACAAGA
*
6874076 GGAAAGTCTGTGCAGGAAGGAGGAGTA
196 GGAAAGTCTGTGCAGGAAGAAGGAGTA
*
6874103 TGAAGA
1 CGAAGA
6874109 GGAACTGGAC
Statistics
Matches: 216, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
222 216 1.00
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (222 bp):
CGAAGATTTAGAGAAAAGATATCAGGGATTAGAAGAAAAATATGTGGGTCTGGAGAAAGAAAGGG
AATCAACACTTCGTGAAGTACAAGAGCTACAAGAGTCACTAGAGGCTGAAAAGCAAGAACATGCT
AGTTTTGTGCAGTTGAATGGAAACCGAGTGACTGCTATGGAATCTCAGATCAGTTTTCTACAAGA
GGAAAGTCTGTGCAGGAAGAAGGAGTA
Found at i:6890405 original size:24 final size:24
Alignment explanation
Indices: 6890378--6890433 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
6890368 AAGACATTGT
6890378 AAATTTAAACATAATAT-TTTTAAA
1 AAATTTAAA-ATAATATATTTTAAA
*
6890402 AAATTT-AAATTATATATTTTAAA
1 AAATTTAAAATAATATATTTTAAA
*
6890425 ATATTTAAA
1 AAATTTAAA
6890434 TAAACATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 6 0.21
23 14 0.50
24 8 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATTTAAAATAATATATTTTAAA
Found at i:6890442 original size:22 final size:23
Alignment explanation
Indices: 6890395--6890443 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
6890385 AACATAATAT
* *
6890395 TTTTAAAAAATTTAAATTATATA
1 TTTTAAAAAATTTAAATTAAACA
*
6890418 TTTTAAAATATTTAAA-TAAACA
1 TTTTAAAAAATTTAAATTAAACA
6890440 TTTT
1 TTTT
6890444 CAATATCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTAAAAAATTTAAATTAAACA
Found at i:6902115 original size:2 final size:2
Alignment explanation
Indices: 6902108--6902145 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6902098 ATGCTTGCAC
*
6902108 CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6902146 ATATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:6902150 original size:2 final size:2
Alignment explanation
Indices: 6902145--6902169 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6902135 TCTCTCTCTC
6902145 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
6902170 CCTTCAATTT
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:6923329 original size:28 final size:29
Alignment explanation
Indices: 6923275--6923332 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
6923265 TTTTCAAAAG
*
6923275 TTTTTTTATAAAAAGAGAATTCAAATTTAA
1 TTTTTTTATAAAAAGAAAATT-AAATTTAA
6923305 TTTTTTTA-AAAAAGATAAATT-AATTTAA
1 TTTTTTTATAAAAAGA-AAATTAAATTTAA
6923333 ATATTCTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 7 0.27
29 7 0.27
30 12 0.46
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (29 bp):
TTTTTTTATAAAAAGAAAATTAAATTTAA
Found at i:6925537 original size:18 final size:20
Alignment explanation
Indices: 6925516--6925557 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
6925506 TTTTAAGCTC
6925516 AATTAAAATT-TTTTTT-TT
1 AATTAAAATTATTTTTTGTT
**
6925534 AATTTTAATTATTTTTTGTT
1 AATTAAAATTATTTTTTGTT
6925554 AATT
1 AATT
6925558 TTTAGCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
AATTAAAATTATTTTTTGTT
Found at i:6925541 original size:20 final size:20
Alignment explanation
Indices: 6925522--6925559 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6925512 GCTCAATTAA
6925522 AATT-TTTTTT-TTAATTTT
1 AATTATTTTTTGTTAATTTT
6925540 AATTATTTTTTGTTAATTTT
1 AATTATTTTTTGTTAATTTT
6925560 TAGCATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (20 bp):
AATTATTTTTTGTTAATTTT
Found at i:6926235 original size:2 final size:2
Alignment explanation
Indices: 6926228--6926259 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6926218 TAGCTTAGCA
6926228 AT 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 AT
6926260 TTATGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6926458 original size:22 final size:22
Alignment explanation
Indices: 6926433--6926474 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
6926423 AGTTTTAGGT
6926433 ATTACGTGACTGATTTTTAAAC
1 ATTACGTGACTGATTTTTAAAC
*
6926455 ATTACGTGATTGATTTTTAA
1 ATTACGTGACTGATTTTTAA
6926475 GCAATGCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (22 bp):
ATTACGTGACTGATTTTTAAAC
Found at i:6936254 original size:33 final size:34
Alignment explanation
Indices: 6936189--6936254 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
6936179 AACACATACT
*
6936189 AACAAAAGAAAAAAATAAATCAATCCAAAAAAAG
1 AACAAAAGAAAAAAATAAATCAATCAAAAAAAAG
* *
6936223 AACAAAAG-AGAAAATAAATTAA-CAAAGAAAAA
1 AACAAAAGAAAAAAATAAATCAATCAAA-AAAAA
6936255 TAGAAAGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 3 0.11
33 17 0.61
34 8 0.29
ACGTcount: A:0.74, C:0.09, G:0.08, T:0.09
Consensus pattern (34 bp):
AACAAAAGAAAAAAATAAATCAATCAAAAAAAAG
Found at i:6936267 original size:18 final size:18
Alignment explanation
Indices: 6936246--6936284 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6936236 ATAAATTAAC
6936246 AAAGAAA-AATAGAAAGGA
1 AAAGAAAGAATAGAAA-GA
*
6936264 AAAGAAAGATTAGAAAGA
1 AAAGAAAGAATAGAAAGA
6936282 AAA
1 AAA
6936285 CGCAAAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (18 bp):
AAAGAAAGAATAGAAAGA
Found at i:6936427 original size:22 final size:22
Alignment explanation
Indices: 6936366--6936427 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 22
6936356 AATGTGGGTA
6936366 AAAATAAATAA-A-TAAGAATC
1 AAAATAAATAAGAGTAAGAATC
* * * * *
6936386 CAAATAAAAATAGAGAAAGAGTT
1 AAAATAAATA-AGAGTAAGAATC
6936409 AAAATAAATAAGAGTAAGA
1 AAAATAAATAAGAGTAAGA
6936428 TAAAACATGT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 8 0.26
21 1 0.03
22 9 0.29
23 13 0.42
ACGTcount: A:0.66, C:0.03, G:0.13, T:0.18
Consensus pattern (22 bp):
AAAATAAATAAGAGTAAGAATC
Found at i:6943943 original size:23 final size:23
Alignment explanation
Indices: 6943913--6943958 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6943903 TGAACTTGTC
6943913 GATTACATGATCGAGCAAAGTTT
1 GATTACATGATCGAGCAAAGTTT
6943936 GATTACATGATCGAGCAAAGTTT
1 GATTACATGATCGAGCAAAGTTT
6943959 AGGGTTCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (23 bp):
GATTACATGATCGAGCAAAGTTT
Found at i:6957834 original size:17 final size:19
Alignment explanation
Indices: 6957812--6957851 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
6957802 AATAATAACT
6957812 TATTT-AATTTTTTTTAA-
1 TATTTAAATTTTTTTTAAG
6957829 TATTTAAATTTTTTTTAAG
1 TATTTAAATTTTTTTTAAG
6957848 TATT
1 TATT
6957852 CTATCATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TATTTAAATTTTTTTTAAG
Found at i:6980639 original size:22 final size:22
Alignment explanation
Indices: 6980614--6980669 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
6980604 ACCACATGAT
6980614 ATCAACATCATCAAAATAACAC
1 ATCAACATCATCAAAATAACAC
*
6980636 ATCAACATCATCAAAATAACAT
1 ATCAACATCATCAAAATAACAC
6980658 ATCAACAT-ATCA
1 ATCAACATCATCA
6980670 CATGAAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.21
Consensus pattern (22 bp):
ATCAACATCATCAAAATAACAC
Found at i:6988792 original size:12 final size:13
Alignment explanation
Indices: 6988742--6988794 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 13
6988732 TTAAGTTAAA
*
6988742 TTTATTATATTTG
1 TTTATTATAATTG
*
6988755 ATGTTATTATTAATTT
1 -T-TTATTA-TAATTG
6988771 TTTATTATAATTG
1 TTTATTATAATTG
6988784 TTT-TTATAATT
1 TTTATTATAATT
6988795 ATAGATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.24
13 8 0.24
14 7 0.21
15 7 0.21
16 4 0.12
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (13 bp):
TTTATTATAATTG
Found at i:6988848 original size:19 final size:18
Alignment explanation
Indices: 6988815--6988850 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6988805 AATTGAAATA
6988815 ATAAAATTATATTTAATT
1 ATAAAATTATATTTAATT
*
6988833 ATAAATATTTTATTTAAT
1 ATAAA-ATTATATTTAAT
6988851 CATGTTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAAAATTATATTTAATT
Found at i:6989879 original size:18 final size:18
Alignment explanation
Indices: 6989853--6989887 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6989843 AATGCAATAT
*
6989853 AAATCCCATCTATTTCGC
1 AAATCCCATCCATTTCGC
*
6989871 AAATTCCATCCATTTCG
1 AAATCCCATCCATTTCG
6989888 TCTCAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (18 bp):
AAATCCCATCCATTTCGC
Found at i:6993319 original size:16 final size:16
Alignment explanation
Indices: 6993295--6993328 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6993285 TATTAAGAAA
*
6993295 AATTGATAATAAACTT
1 AATTAATAATAAACTT
*
6993311 AATTAATAATATACTT
1 AATTAATAATAAACTT
6993327 AA
1 AA
6993329 AATATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
AATTAATAATAAACTT
Found at i:6993597 original size:16 final size:15
Alignment explanation
Indices: 6993568--6993606 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
6993558 TATATAATTG
*
6993568 TATAAATATATTATA
1 TATACATATATTATA
*
6993583 TATACATATATTTATT
1 TATACATATA-TTATA
6993599 TATACATA
1 TATACATA
6993607 AACATTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
TATACATATATTATA
Found at i:6993812 original size:220 final size:220
Alignment explanation
Indices: 6993572--6994216 Score: 966
Period size: 212 Copynumber: 3.0 Consensus size: 220
6993562 TAATTGTATA
* *
6993572 AATATATTATATATACATATATTT-ATTTATACATAAACATTACTATAGTTTATAATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTTTA
** * *
6993636 TTTATATGATTACACACAATAATTTTATTAGTTTATCACCTTAGATTTTATAACATATTATTTAT
66 TTTATATGATTACACTTAATAACTTTATTAG-TTATCACCTTAGATTTTATAACATATTGTTTAT
* * *
6993701 AATTAGTTATTATTTATACAAATTTTAATATCAAACATTATAACATCTAAGTTTTGTCATTAATT
130 AATTAGTTATTATTTATACAAACTTTAATATAAAACATTATAACATATAAGTTTTGTCATTAATT
6993766 TCATATATATATATATATAATAAAGT
195 TCATATATATATATATATAATAAAGT
* * *
6993792 CATATATTATATACACATATATTTAATTTATACATAAGCATTACTATAACTTATAATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTTTA
* *
6993857 TTTATATGATGACACTTAATAACTTTATTAGTTATCACTTTAGATTTTATAACATATTGTTTATA
66 TTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTGTTTATA
* * *
6993922 ATTAGTTATTATTTATACAAACTTTAATATAAAACATTTTAACCTATAA--TTTGT-A-TCA-TT
131 ATTAGTTATTATTTATACAAACTTTAATATAAAACATTATAACATATAAGTTTTGTCATTAATTT
*
6993982 -A-AT-TTTATATATATAATAAAGT
196 CATATATATATATATATAATAAAGT
* *
6994004 AATATATTATATATACATATATTTAATTTATACATAAGCATTACTACAATTTAAAATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTTTA
* ** *
6994069 TTTATATGATTACACTTAATAAGTTTATTAGCAATCACCTTAAATTTTATAACATATTGTTTATA
66 TTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTGTTTATA
* * * *
6994134 ATTGGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAGTTATATCATTAATTT
131 ATTAGTTATTATTTATACAAACTTTAATATAAAACATTATAACATATAAGTTTTGTCATTAATTT
6994199 CATATATATATATATATA
196 CATATATATATATATATA
6994217 TAATTATGGA
Statistics
Matches: 379, Mismatches: 37, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
212 182 0.48
213 2 0.01
214 4 0.01
215 3 0.01
216 4 0.01
217 3 0.01
218 6 0.02
219 2 0.01
220 109 0.29
221 64 0.17
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (220 bp):
AATATATTATATATACATATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTTTA
TTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTGTTTATA
ATTAGTTATTATTTATACAAACTTTAATATAAAACATTATAACATATAAGTTTTGTCATTAATTT
CATATATATATATATATAATAAAGT
Found at i:6995621 original size:13 final size:14
Alignment explanation
Indices: 6995589--6995621 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
6995579 TTATCCAAGC
6995589 TTAA-TTATAATTA
1 TTAATTTATAATTA
6995602 TTAATTTATAA-TA
1 TTAATTTATAATTA
6995615 TTAATTT
1 TTAATTT
6995622 TTTTCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAATTTATAATTA
Found at i:6999294 original size:30 final size:29
Alignment explanation
Indices: 6999213--6999299 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
6999203 TCTTTAAAAA
* *
6999213 AAATTAAATAAATCTTTATATTTTTATTATT
1 AAATTAAAT-AATTTTTATACTTTTATT-TT
*
6999244 CAA-TAGAAT-A-TTTT-TACTTTTATTTT
1 AAATTA-AATAATTTTTATACTTTTATTTT
6999270 AAATTAAATAAGTTTTTATACTTTTATTTT
1 AAATTAAATAA-TTTTTATACTTTTATTTT
6999300 GAGTCAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
26 7 0.15
27 12 0.26
28 3 0.07
29 5 0.11
30 14 0.30
31 5 0.11
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (29 bp):
AAATTAAATAATTTTTATACTTTTATTTT
Found at i:6999309 original size:30 final size:29
Alignment explanation
Indices: 6999254--6999310 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
6999244 CAATAGAATA
*
6999254 TTTTTACTTTTATTTTAAATTAAATAAGT
1 TTTTTACTTTTATTTTAAATCAAATAAGT
* *
6999283 TTTTATACTTTTATTTTGAGTCAAATAA
1 TTTT-TACTTTTATTTTAAATCAAATAA
6999311 AACTTATGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (29 bp):
TTTTTACTTTTATTTTAAATCAAATAAGT
Found at i:7008274 original size:13 final size:13
Alignment explanation
Indices: 7008256--7008281 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7008246 ACTGAAACTT
7008256 TCTCTCTTCTCTC
1 TCTCTCTTCTCTC
7008269 TCTCTCTTCTCTC
1 TCTCTCTTCTCTC
7008282 AGTCTATCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (13 bp):
TCTCTCTTCTCTC
Found at i:7015121 original size:11 final size:11
Alignment explanation
Indices: 7015090--7015128 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
7015080 CTAAAACAAG
*
7015090 AAGAAAAAAAA
1 AAGAAAAAAGA
7015101 AAGAAAAAAGA
1 AAGAAAAAAGA
7015112 AAGAAAAAAGA
1 AAGAAAAAAGA
*
7015123 AGGAAA
1 AAGAAA
7015129 TGAAAGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:7015626 original size:2 final size:2
Alignment explanation
Indices: 7015619--7015657 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
7015609 TATATTCAAC
* *
7015619 GA GA GA GA GA AA AA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
7015658 CCTTGGGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7029140 original size:15 final size:16
Alignment explanation
Indices: 7029113--7029152 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
7029103 CACAATTAAA
7029113 TAAAATATTAATAT-TT
1 TAAAAT-TTAATATATT
7029129 TAAAATTTAATATATT
1 TAAAATTTAATATATT
*
7029145 TTAAATTT
1 TAAAATTT
7029153 TAATGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAAATTTAATATATT
Found at i:7029145 original size:17 final size:17
Alignment explanation
Indices: 7029123--7029156 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7029113 TAAAATATTA
7029123 ATATTTTAAAATTTAAT
1 ATATTTTAAAATTTAAT
*
7029140 ATATTTTAAATTTTAAT
1 ATATTTTAAAATTTAAT
7029157 GTAAAAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTTAAAATTTAAT
Found at i:7031410 original size:25 final size:25
Alignment explanation
Indices: 7031382--7031429 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
7031372 AATTTTTTAA
*
7031382 AGAAAATTTTAAAATTATATTTTGT
1 AGAAAATTTTAAAATTAAATTTTGT
7031407 AGAAAATTTTAAAATTAAATTTT
1 AGAAAATTTTAAAATTAAATTTT
7031430 ACAATACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (25 bp):
AGAAAATTTTAAAATTAAATTTTGT
Found at i:7033708 original size:3 final size:3
Alignment explanation
Indices: 7033700--7033725 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7033690 TTAATTAATT
7033700 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
7033726 CTAAAATATT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:7033869 original size:5 final size:5
Alignment explanation
Indices: 7033859--7033895 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
7033849 ACTATCATCA
*
7033859 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT TTTTT GT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GT
7033896 CCCCTGCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
GTTTT
Found at i:7038126 original size:37 final size:37
Alignment explanation
Indices: 7038072--7038145 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
7038062 CTCCAACTGT
7038072 GAGCGTGTTGACCAATATTAAGAACTTTAATTAATTA
1 GAGCGTGTTGACCAATATTAAGAACTTTAATTAATTA
*
7038109 GAGCGTGTTGACTAATATTAAGAACTTTAATTAATTA
1 GAGCGTGTTGACCAATATTAAGAACTTTAATTAATTA
7038146 CAGGTTAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (37 bp):
GAGCGTGTTGACCAATATTAAGAACTTTAATTAATTA
Found at i:7061557 original size:30 final size:30
Alignment explanation
Indices: 7061521--7061616 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
7061511 TAAAAAAAAA
* * * * *
7061521 TATTATTACATGTTATGTTGAAACAAATGT
1 TATTATTACACGTCATATTGAAAAAAATAT
* *
7061551 TGTTATTATACGTCATATTGAAAAAAATAT
1 TATTATTACACGTCATATTGAAAAAAATAT
* * *
7061581 TATTATTACACG-CTATATTCAAAAAACTTT
1 TATTATTACACGTC-ATATTGAAAAAAATAT
7061611 TATTAT
1 TATTAT
7061617 ACTTTAGTAC
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (30 bp):
TATTATTACACGTCATATTGAAAAAAATAT
Found at i:7064549 original size:12 final size:12
Alignment explanation
Indices: 7064534--7064564 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
7064524 AATTTCTCAC
*
7064534 TCTCTCTCTCTT
1 TCTCTCTCACTT
7064546 TCTCTCTCACTT
1 TCTCTCTCACTT
7064558 TCTCTCT
1 TCTCTCT
7064565 ATATATATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (12 bp):
TCTCTCTCACTT
Found at i:7067892 original size:3 final size:3
Alignment explanation
Indices: 7067884--7067921 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
7067874 GTACTGATAA
7067884 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
7067922 AAATTAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:7071257 original size:12 final size:12
Alignment explanation
Indices: 7071240--7071266 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7071230 ATAATCAGAA
7071240 AAATGTGCTTAC
1 AAATGTGCTTAC
7071252 AAATGTGCTTAC
1 AAATGTGCTTAC
7071264 AAA
1 AAA
7071267 GTAATCTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (12 bp):
AAATGTGCTTAC
Found at i:7071818 original size:20 final size:20
Alignment explanation
Indices: 7071790--7071827 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7071780 CCGTTTAGAC
7071790 AAATATCTTTAAAACTTAAT
1 AAATATCTTTAAAACTTAAT
* *
7071810 AAATTTCTTTGAAACTTA
1 AAATATCTTTAAAACTTA
7071828 GTAGAAAATA
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:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (20 bp):
AAATATCTTTAAAACTTAAT
Found at i:7076359 original size:16 final size:16
Alignment explanation
Indices: 7076331--7076372 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
7076321 TTATAATATT
7076331 AAATTT-TTAATTTAAA
1 AAATTTATT-ATTTAAA
*
7076347 ATATTTATTATTTAAA
1 AAATTTATTATTTAAA
7076363 AAATTTATTA
1 AAATTTATTA
7076373 AAATATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATTTATTATTTAAA
Found at i:7077048 original size:16 final size:17
Alignment explanation
Indices: 7077024--7077056 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7077014 ATTAATGAAG
*
7077024 GATATTTTTA-TCTATT
1 GATAATTTTACTCTATT
7077040 GATAATTTTACTCTATT
1 GATAATTTTACTCTATT
7077057 CCTTGCCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (17 bp):
GATAATTTTACTCTATT
Found at i:7077475 original size:38 final size:38
Alignment explanation
Indices: 7077382--7077493 Score: 145
Period size: 38 Copynumber: 2.9 Consensus size: 38
7077372 ATTCAAGAAC
*
7077382 AAATATTAATGCACATAATGAGTAATAG-TATTGAAAAG
1 AAAT-TTAATGTACATAATGAGTAATAGTTATTGAAAAG
** * *
7077420 AGTTTTAATGTATATAATGAATAATAGTTATTGAAAAG
1 AAATTTAATGTACATAATGAGTAATAGTTATTGAAAAG
*
7077458 AAATTTATTGTACATAATGAGTAATAGTTACTTGAA
1 AAATTTAATGTACATAATGAGTAATAGTTA-TTGAA
7077494 CCCATTATGT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
37 20 0.32
38 37 0.60
39 5 0.08
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.36
Consensus pattern (38 bp):
AAATTTAATGTACATAATGAGTAATAGTTATTGAAAAG
Found at i:7082116 original size:18 final size:17
Alignment explanation
Indices: 7082081--7082113 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7082071 TTATGAGAAG
7082081 TTTTTTAAAAAAATAAT
1 TTTTTTAAAAAAATAAT
*
7082098 TTTTTTAAAAGAATAA
1 TTTTTTAAAAAAATAA
7082114 ATTAACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTTTTAAAAAAATAAT
Found at i:7082359 original size:5 final size:5
Alignment explanation
Indices: 7082349--7082386 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
7082339 CACTCAATTA
7082349 TTATT TTATT TT-TT TTATT TTATTTT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTA--TT TTATT TTATT TT
7082387 TTACTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.13
5 21 0.70
7 5 0.17
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTATT
Found at i:7082363 original size:8 final size:8
Alignment explanation
Indices: 7082346--7082433 Score: 54
Period size: 8 Copynumber: 10.8 Consensus size: 8
7082336 CTACACTCAA
*
7082346 TTATTATT
1 TTATTTTT
7082354 TTATTTTTT
1 TTA-TTTTT
7082363 TTATTTTAT
1 TTATTTT-T
7082372 TT-TTTATT
1 TTATTT-TT
7082380 TTA-TTTT
1 TTATTTTT
*
7082387 TTACTTTT
1 TTATTTTT
** *
7082395 AAAGTTTT
1 TTATTTTT
*
7082403 TTATTATT
1 TTATTTTT
7082411 TTATATTTT
1 TTAT-TTTT
* *
7082420 TTAATTTA
1 TTATTTTT
7082428 TTATTT
1 TTATTT
7082434 GATATGATAA
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
7 5 0.08
8 40 0.65
9 17 0.27
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (8 bp):
TTATTTTT
Found at i:7082373 original size:19 final size:19
Alignment explanation
Indices: 7082349--7082429 Score: 62
Period size: 19 Copynumber: 4.3 Consensus size: 19
7082339 CACTCAATTA
7082349 TTATTTTATTTTTTTTATT
1 TTATTTTATTTTTTTTATT
7082368 TTATTTT-TTATTTTATT-TT
1 TTATTTTATT-TTTT-TTATT
**
7082387 TTACTTTTAAAGTTTTTTA--
1 TTA-TTTT-ATTTTTTTTATT
* *
7082406 TTATTTTATATTTTTTAAT
1 TTATTTTATTTTTTTTATT
7082425 TTATT
1 TTATT
7082430 ATTTGATATG
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
17 8 0.16
18 6 0.12
19 24 0.48
20 8 0.16
21 4 0.08
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.77
Consensus pattern (19 bp):
TTATTTTATTTTTTTTATT
Found at i:7082376 original size:12 final size:12
Alignment explanation
Indices: 7082349--7082395 Score: 67
Period size: 12 Copynumber: 3.7 Consensus size: 12
7082339 CACTCAATTA
7082349 TTATTTTATTTTTT
1 TTATTTTA--TTTT
7082363 TTATTTTATTTT
1 TTATTTTATTTT
7082375 TTATTTTATTTT
1 TTATTTTATTTT
7082387 TTACTTTTA
1 TTA-TTTTA
7082396 AAGTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.59
13 5 0.16
14 8 0.25
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:7082802 original size:17 final size:16
Alignment explanation
Indices: 7082782--7082826 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
7082772 TTTTTCACAC
7082782 TTAATTTTTTATTTGAT
1 TTAATTTTTTATTT-AT
7082799 TTAATTTTTTTATTTAT
1 TTAA-TTTTTTATTTAT
*
7082816 TAAATATTTTT
1 TTAAT-TTTTT
7082827 TATATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 14 0.56
18 10 0.40
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTAATTTTTTATTTAT
Found at i:7082809 original size:18 final size:17
Alignment explanation
Indices: 7082782--7082829 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
7082772 TTTTTCACAC
7082782 TTAA-TTTTTTATTTGAT
1 TTAATTTTTTTATTT-AT
7082799 TTAATTTTTTTATTTAT
1 TTAATTTTTTTATTTAT
*
7082816 TAAATATTTTTTAT
1 TTAAT-TTTTTTAT
7082830 ATAATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTAATTTTTTTATTTAT
Found at i:7090679 original size:12 final size:11
Alignment explanation
Indices: 7090660--7090685 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7090650 TTTTAATTAA
7090660 AAAATTTTTAT
1 AAAATTTTTAT
7090671 AAAATTTTTAT
1 AAAATTTTTAT
7090682 AAAA
1 AAAA
7090686 ATAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAATTTTTAT
Found at i:7090686 original size:12 final size:12
Alignment explanation
Indices: 7090659--7090687 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
7090649 TTTTTAATTA
7090659 AAAAATTTTTAT
1 AAAAATTTTTAT
7090671 -AAAATTTTTAT
1 AAAAATTTTTAT
7090682 AAAAAT
1 AAAAAT
7090688 AATAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAAAATTTTTAT
Found at i:7091206 original size:33 final size:33
Alignment explanation
Indices: 7091133--7091213 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 33
7091123 TGATCATGTT
* * *
7091133 ATCATATTAAATTAACATGTCACATCATCATCA
1 ATCATAATATATTAACATATCACATCATCATCA
* *
7091166 ATCATAATATATTAACATATCACATCATTATTA
1 ATCATAATATATTAACATATCACATCATCATCA
*
7091199 ATTATAATATATTAA
1 ATCATAATATATTAA
7091214 TATACGACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (33 bp):
ATCATAATATATTAACATATCACATCATCATCA
Found at i:7091572 original size:17 final size:17
Alignment explanation
Indices: 7091550--7091593 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
7091540 AAAAAATATA
* *
7091550 AGAGAACGTATTTAGAG
1 AGAGAAAGTATTCAGAG
7091567 AGAGAAAAAGTATTCAGAG
1 AGAG--AAAGTATTCAGAG
7091586 AGAGAAAG
1 AGAGAAAG
7091594 AATATCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.35
19 15 0.65
ACGTcount: A:0.50, C:0.05, G:0.30, T:0.16
Consensus pattern (17 bp):
AGAGAAAGTATTCAGAG
Found at i:7097086 original size:19 final size:19
Alignment explanation
Indices: 7097054--7097096 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
7097044 CCTCATGTTT
*
7097054 AAATATGAAAATAATTAATA
1 AAATATGAAAATAA-TAAAA
*
7097074 AAATAT-AACATAATAAAA
1 AAATATGAAAATAATAAAA
7097092 AAATA
1 AAATA
7097097 AAATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAATATGAAAATAATAAAA
Found at i:7097097 original size:16 final size:16
Alignment explanation
Indices: 7097061--7097104 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
7097051 TTTAAATATG
7097061 AAAATAATTAATAAAATAT
1 AAAATAA-TAA-AAAA-AT
*
7097080 AACATAATAAAAAAAT
1 AAAATAATAAAAAAAT
7097096 AAAATAATA
1 AAAATAATA
7097105 TTTAATCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 10 0.43
17 4 0.17
18 3 0.13
19 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATAATAAAAAAAT
Found at i:7097788 original size:15 final size:15
Alignment explanation
Indices: 7097698--7097786 Score: 115
Period size: 15 Copynumber: 5.9 Consensus size: 15
7097688 ACTTTACAAT
* *
7097698 GCAATGTGATTACAG
1 GCAATGTGATTGCAA
*
7097713 GTAATGTGATTGCAA
1 GCAATGTGATTGCAA
*
7097728 GTAATGTGATTGCAA
1 GCAATGTGATTGCAA
*
7097743 GCAATGTGATAGCAA
1 GCAATGTGATTGCAA
* *
7097758 GCAATGTGATAGCAG
1 GCAATGTGATTGCAA
7097773 GCAATGTGATTGCA
1 GCAATGTGATTGCA
7097787 GGGAAGATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 67 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (15 bp):
GCAATGTGATTGCAA
Found at i:7097963 original size:6 final size:6
Alignment explanation
Indices: 7097952--7098026 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
7097942 ATGTCATATA
* * * *
7097952 TTTTAT TTTTAT TTATTAT TATAAT ATTTTAT ATTTTAT TTTTA- ATATAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT -TTTTAT -TTTTAT TTTTAT TTTTAT
* *
7098002 TTATAT TTTTAT TATTAAT TTTTAT
1 TTTTAT TTTTAT T-TTTAT TTTTAT
7098027 ATAATACCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 3 0.05
6 31 0.56
7 21 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAT
Done.