Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 12 of 29
Found at i:4263480 original size:17 final size:18
Alignment explanation
Indices: 4263460--4263499 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
4263450 AATAAAATTT
4263460 TAATTATAA-ATTAAAAA
1 TAATTATAACATTAAAAA
* *
4263477 TAATTTTAACTTTAAAAA
1 TAATTATAACATTAAAAA
4263495 TAATT
1 TAATT
4263500 TTAAGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATTATAACATTAAAAA
Found at i:4263510 original size:18 final size:18
Alignment explanation
Indices: 4263471--4263511 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
4263461 AATTATAAAT
*
4263471 TAAAAATAATTTTAACTT
1 TAAAAATAATTTTAACTA
*
4263489 TAAAAATAATTTTAAGTA
1 TAAAAATAATTTTAACTA
4263507 TAAAA
1 TAAAA
4263512 TTTTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAAAATAATTTTAACTA
Found at i:4263767 original size:14 final size:14
Alignment explanation
Indices: 4263748--4263774 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4263738 TGGTAATTTA
4263748 TTTTTTATAAGTTC
1 TTTTTTATAAGTTC
4263762 TTTTTTATAAGTT
1 TTTTTTATAAGTT
4263775 ATAATTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTTATAAGTTC
Found at i:4263952 original size:16 final size:16
Alignment explanation
Indices: 4263933--4263969 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4263923 CTAAAACTCT
**
4263933 TTTTTAAAAAATTTTA
1 TTTTTAAAAAAAATTA
4263949 TTTTTAAAAAAAATTA
1 TTTTTAAAAAAAATTA
4263965 TTTTT
1 TTTTT
4263970 TTTAAAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTTAAAAAAAATTA
Found at i:4263959 original size:18 final size:19
Alignment explanation
Indices: 4263938--4263976 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4263928 ACTCTTTTTT
4263938 AAAAAATT-TTATTTTTAA
1 AAAAAATTATTATTTTTAA
*
4263956 AAAAAATTATTTTTTTTAA
1 AAAAAATTATTATTTTTAA
4263975 AA
1 AA
4263977 GCTTTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAAAATTATTATTTTTAA
Found at i:4265430 original size:2 final size:2
Alignment explanation
Indices: 4265423--4265447 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4265413 AAGGTTCCAT
4265423 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
4265448 TTGTATATTT
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:4270325 original size:2 final size:2
Alignment explanation
Indices: 4270318--4270346 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4270308 ACAAACAAAA
4270318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4270347 GGGAAGGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4272529 original size:14 final size:14
Alignment explanation
Indices: 4272510--4272538 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4272500 CTTTTATGAA
4272510 AAATAATAACTTTT
1 AAATAATAACTTTT
4272524 AAATAATAACTTTT
1 AAATAATAACTTTT
4272538 A
1 A
4272539 GAGTTAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATAATAACTTTT
Found at i:4272767 original size:19 final size:19
Alignment explanation
Indices: 4272740--4272793 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
4272730 CTGAAGCTCA
*
4272740 TTTTTAAAAAATTTTA-TT
1 TTTTTAAAAAAATTTACTT
*
4272758 TTTTTAAAAAAAGTTACTT
1 TTTTTAAAAAAATTTACTT
4272777 TTTTTAAAAAAAATTTA
1 TTTTT-AAAAAAATTTA
4272794 AAATTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 14 0.45
19 7 0.23
20 10 0.32
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTTAAAAAAATTTACTT
Found at i:4284629 original size:19 final size:19
Alignment explanation
Indices: 4284607--4284646 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
4284597 TTTTACCCTT
*
4284607 TTAATTAA-AAGATTATATA
1 TTAATTAATAA-ATTAAATA
4284626 TTAATTAATAAATTAAATA
1 TTAATTAATAAATTAAATA
4284645 TT
1 TT
4284647 TATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TTAATTAATAAATTAAATA
Found at i:4284639 original size:27 final size:28
Alignment explanation
Indices: 4284609--4284664 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
4284599 TTACCCTTTT
*
4284609 AATTAAA-AGATTATATAT-TAATTAATA
1 AATTAAATA-ATTATATATAAAATTAATA
*
4284636 AATTAAATATTTATATATAAAATTAATA
1 AATTAAATAATTATATATAAAATTAATA
4284664 A
1 A
4284665 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (28 bp):
AATTAAATAATTATATATAAAATTAATA
Found at i:4288609 original size:68 final size:67
Alignment explanation
Indices: 4288475--4288631 Score: 183
Period size: 68 Copynumber: 2.3 Consensus size: 67
4288465 GCCCGGTACA
* * * * *
4288475 GGGGTAATAATACTACAGGGGTCAAGATTGGTGAACATGCCATATTTTTCCCTTAGAATCTTGGT
1 GGGGTAAGAATACCACA-AGGTCAAGATTAGTGAACATGCCATACTTTTCCCTTAGAATCTTGGT
4288540 GTG
65 GTG
* * *
4288543 GGGGTAAGAATACCATAAGGTCAAGATTAGTGAACGTGCCCT-CTTTTCCTCTTATGAAT-TTCG
1 GGGGTAAGAATACCACAAGGTCAAGATTAGTGAACATGCCATACTTTTCC-CTTA-GAATCTT-G
4288606 GTGTG
63 GTGTG
*
4288611 GGGGTAAGAATATCACAAGGT
1 GGGGTAAGAATACCACAAGGT
4288632 TAAATTGGGC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
66 6 0.08
67 27 0.36
68 43 0.57
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (67 bp):
GGGGTAAGAATACCACAAGGTCAAGATTAGTGAACATGCCATACTTTTCCCTTAGAATCTTGGTG
TG
Found at i:4288658 original size:68 final size:66
Alignment explanation
Indices: 4288475--4288662 Score: 159
Period size: 68 Copynumber: 2.8 Consensus size: 66
4288465 GCCCGGTACA
* * * * *
4288475 GGGGTAATAATACTACAGGGGTCAAGATT-GGTGAACATGCCATATTTTTCCCTTAGAATCTTGG
1 GGGGTAAGAATACCACA-AGGTCAAGATTAGG-GAACGTACCAT-TTTTTCCCTTAGAATCTTGG
4288539 TGTG
63 TGTG
* * * * *
4288543 GGGGTAAGAATACCATAAGGTCAAGATTAGTGAACGTGCCCTCTTTTCCTCTTATGAAT-TTCGG
1 GGGGTAAGAATACCACAAGGTCAAGATTAGGGAACGTACCATTTTTTCC-CTTA-GAATCTT-GG
4288607 TGTG
63 TGTG
* * *
4288611 GGGGTAAGAATATCACAAGGTTAA-ATT-GGGCAAATGTACCATTTTTTCCCTT
1 GGGGTAAGAATACCACAAGGTCAAGATTAGGG--AACGTACCATTTTTTCCCTT
4288663 TTTAAGCTCA
Statistics
Matches: 98, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
66 8 0.08
67 31 0.32
68 59 0.60
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (66 bp):
GGGGTAAGAATACCACAAGGTCAAGATTAGGGAACGTACCATTTTTTCCCTTAGAATCTTGGTGT
G
Found at i:4293856 original size:22 final size:23
Alignment explanation
Indices: 4293802--4293857 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
4293792 TTTGGACTTA
*
4293802 AATATTTTTTTAGTATTTCATAT
1 AATATTTGTTTAGTATTTCATAT
4293825 AATATCTTGTTTAGT-TTT-ATATT
1 AATAT-TTGTTTAGTATTTCATA-T
*
4293848 TATATTTGTT
1 AATATTTGTT
4293858 CGACATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 8 0.28
23 13 0.45
24 8 0.28
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (23 bp):
AATATTTGTTTAGTATTTCATAT
Found at i:4301060 original size:61 final size:62
Alignment explanation
Indices: 4300964--4301120 Score: 203
Period size: 61 Copynumber: 2.6 Consensus size: 62
4300954 TCCATTGACC
* * * **
4300964 CAAATCTATTGATATATTTGGACAATGTATCGATAGAAATTATATAAAATG-TTCCTTTCTT
1 CAAATCTATTGATACATTTGGACAATGTATCGATAGAAATTATACAAAATGTTTCCCTAATT
** *
4301025 CAAATCTATCAATACATTTGGACAATGTATTGATAGAAATTATACAAAATGTTTCCCTAATT
1 CAAATCTATTGATACATTTGGACAATGTATCGATAGAAATTATACAAAATGTTTCCCTAATT
*
4301087 CAAATCTATTGATACATTCTTG--AATGTATCGATA
1 CAAATCTATTGATACATT-TGGACAATGTATCGATA
4301121 AAAAATTCAT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
61 57 0.70
62 23 0.28
63 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (62 bp):
CAAATCTATTGATACATTTGGACAATGTATCGATAGAAATTATACAAAATGTTTCCCTAATT
Found at i:4311858 original size:10 final size:10
Alignment explanation
Indices: 4311843--4311872 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
4311833 CTGTATCTGC
4311843 AGAATACAGT
1 AGAATACAGT
4311853 AGAATACAGT
1 AGAATACAGT
4311863 AGAATACAGT
1 AGAATACAGT
4311873 GGATCAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (10 bp):
AGAATACAGT
Found at i:4315594 original size:28 final size:28
Alignment explanation
Indices: 4315560--4315614 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
4315550 GTTTAAAATT
* *
4315560 TTATTTATGTTTGGTGTAATGTATTTGC
1 TTATTTATATATGGTGTAATGTATTTGC
*
4315588 TTATTTATATATGGTGTAATTTATTTG
1 TTATTTATATATGGTGTAATGTATTTG
4315615 TTTGTAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.18, T:0.58
Consensus pattern (28 bp):
TTATTTATATATGGTGTAATGTATTTGC
Found at i:4322099 original size:16 final size:16
Alignment explanation
Indices: 4322078--4322108 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4322068 TTGATAAAAA
4322078 AATAAAATAAATTACT
1 AATAAAATAAATTACT
*
4322094 AATAAAATAACTTAC
1 AATAAAATAAATTAC
4322109 ACATTATCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAAATAAATTACT
Found at i:4336171 original size:13 final size:13
Alignment explanation
Indices: 4336153--4336184 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4336143 GACTTGTGCA
4336153 TAGGTTTGAATTC
1 TAGGTTTGAATTC
*
4336166 TAGGTTTGGATTC
1 TAGGTTTGAATTC
4336179 TAGGTT
1 TAGGTT
4336185 AGTAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.06, G:0.28, T:0.47
Consensus pattern (13 bp):
TAGGTTTGAATTC
Found at i:4338776 original size:20 final size:19
Alignment explanation
Indices: 4338753--4338802 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
4338743 ATTGAATTGG
4338753 TTAATTTAAATTAAATAAGA
1 TTAATTTAAATTAAATAA-A
*
4338773 TTAATTTAAATT-AATTAA
1 TTAATTTAAATTAAATAAA
4338791 TTAA-TTAAATTA
1 TTAATTTAAATTA
4338803 TAATTCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 7 0.25
18 5 0.18
19 4 0.14
20 12 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTAATTTAAATTAAATAAA
Found at i:4343214 original size:18 final size:18
Alignment explanation
Indices: 4343169--4343214 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
4343159 TGACTACTTC
4343169 TTGATGCTCTACTATTTT
1 TTGATGCTCTACTATTTT
*
4343187 TTTATGCTCTACTATTTT
1 TTGATGCTCTACTATTTT
*
4343205 TTGATTCTCT
1 TTGATGCTCT
4343215 TCAATTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.15, C:0.17, G:0.09, T:0.59
Consensus pattern (18 bp):
TTGATGCTCTACTATTTT
Found at i:4361242 original size:22 final size:22
Alignment explanation
Indices: 4361206--4361256 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
4361196 GATTGTCTTT
*
4361206 TTTTTAAATTAATTTTTCA-TTA
1 TTTTTAAATTAATTTAT-AGTTA
4361228 TTTTTAAA-TATATTTATAGTTA
1 TTTTTAAATTA-ATTTATAGTTA
4361250 TTTTTAA
1 TTTTTAA
4361257 CACAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTTAAATTAATTTATAGTTA
Found at i:4371440 original size:60 final size:60
Alignment explanation
Indices: 4371346--4371477 Score: 205
Period size: 60 Copynumber: 2.2 Consensus size: 60
4371336 TAATGATCAC
* *
4371346 ATACATTCTCTTATTTAAGAAAGAGAAATTTAAATTAAATTTATTGAATAAAAGTATATT
1 ATACATTCACTTATTTAAGAAAGAGAAATTTAAATTAAATTTATTGAACAAAAGTATATT
* * *
4371406 CTACATTCACTTATTTAAGAAAGAGACATTTAAATTAAATTTATTGAGCAAAAGTATATT
1 ATACATTCACTTATTTAAGAAAGAGAAATTTAAATTAAATTTATTGAACAAAAGTATATT
4371466 ATACA--CACTTAT
1 ATACATTCACTTAT
4371478 CATTGAAACA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 7 0.11
60 59 0.89
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (60 bp):
ATACATTCACTTATTTAAGAAAGAGAAATTTAAATTAAATTTATTGAACAAAAGTATATT
Found at i:4371450 original size:30 final size:30
Alignment explanation
Indices: 4371356--4371450 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
4371346 ATACATTCTC
4371356 TTATTTAAGAAAGAGAAATTTAAATTAAAT
1 TTATTTAAGAAAGAGAAATTTAAATTAAAT
* * * * * *
4371386 TTATTGAATAAA-AGTATATTCTACATT-CAC
1 TTATTTAAGAAAGAG-AAATT-TAAATTAAAT
*
4371416 TTATTTAAGAAAGAGACATTTAAATTAAAT
1 TTATTTAAGAAAGAGAAATTTAAATTAAAT
4371446 TTATT
1 TTATT
4371451 GAGCAAAAGT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
29 7 0.14
30 35 0.71
31 7 0.14
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (30 bp):
TTATTTAAGAAAGAGAAATTTAAATTAAAT
Found at i:4372137 original size:15 final size:17
Alignment explanation
Indices: 4372113--4372149 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
4372103 GGCACATTTA
4372113 ATTTTATGTTTA-GAT-
1 ATTTTATGTTTATGATG
*
4372128 ATTTTGTGTTTATGATG
1 ATTTTATGTTTATGATG
4372145 ATTTT
1 ATTTT
4372150 TAATTACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (17 bp):
ATTTTATGTTTATGATG
Found at i:4372453 original size:57 final size:57
Alignment explanation
Indices: 4372348--4372666 Score: 295
Period size: 57 Copynumber: 5.6 Consensus size: 57
4372338 ATTCATAGGT
* * * * ** *
4372348 AATGACTAAATCACTAATAAAAATTCCATTGATAATTGTC-AACAGAATTCCGTCT-AA
1 AATGACTAAATTACCAACAAAAATTCCATTGGTAATT-TCTAATGGAATTCCGT-TGGA
* * * * *
4372405 AATGACTAGATTACAAATAAAAATTCCATTAGTAATTTCTAATGGAATTCTGTTGGA
1 AATGACTAAATTACCAACAAAAATTCCATTGGTAATTTCTAATGGAATTCCGTTGGA
** * * * *
4372462 AGCGACTAAAGTACCAACAAAAATTTCATTGGTAATTT-TCAATGGAATTCCGTCGGG
1 AATGACTAAATTACCAACAAAAATTCCATTGGTAATTTCT-AATGGAATTCCGTTGGA
* ** *** *
4372519 AATGACCAAATTACCAACAAAAATTCTGTTGGTAATTTCTAACAAAATTCAGTTGGA
1 AATGACTAAATTACCAACAAAAATTCCATTGGTAATTTCTAATGGAATTCCGTTGGA
* * * *
4372576 AGTGACTAAATTACCAACAAAAATTTCATTGGTAATTTC-AATGGAATTCCATTGGG
1 AATGACTAAATTACCAACAAAAATTCCATTGGTAATTTCTAATGGAATTCCGTTGGA
** *
4372632 AATGACTAAATTAGTAACAAAAATTCTATTGGTAA
1 AATGACTAAATTACCAACAAAAATTCCATTGGTAA
4372667 CAAAAATTCT
Statistics
Matches: 209, Mismatches: 49, Indels: 9
0.78 0.18 0.03
Matches are distributed among these distances:
56 45 0.22
57 163 0.78
58 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (57 bp):
AATGACTAAATTACCAACAAAAATTCCATTGGTAATTTCTAATGGAATTCCGTTGGA
Found at i:4372668 original size:18 final size:18
Alignment explanation
Indices: 4372645--4372684 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
4372635 GACTAAATTA
4372645 GTAACAAAAATTCTATTG
1 GTAACAAAAATTCTATTG
4372663 GTAACAAAAATTCTATTG
1 GTAACAAAAATTCTATTG
4372681 GTAA
1 GTAA
4372685 TTTCCAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
GTAACAAAAATTCTATTG
Found at i:4373620 original size:14 final size:14
Alignment explanation
Indices: 4373597--4373628 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4373587 CTTTAAGCTC
4373597 TTCAAACTCTAATT
1 TTCAAACTCTAATT
*
4373611 TTCAAGCTCTAATT
1 TTCAAACTCTAATT
4373625 TTCA
1 TTCA
4373629 GTTTTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (14 bp):
TTCAAACTCTAATT
Found at i:4374361 original size:38 final size:38
Alignment explanation
Indices: 4374276--4374366 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 38
4374266 CTTTATGCCA
* * * *
4374276 ATGTGAATATGGATGAATGAATGCCCGCTTTTATGATG
1 ATGTGAGTGTGGATGAATAAATGCCCACTTTTATGATG
* *
4374314 ATGTGAGTGTGGATGAATAAATTCCCATTTTTATGAT-
1 ATGTGAGTGTGGATGAATAAATGCCCACTTTTATGATG
4374351 AT-TGCAAGTGTGGATG
1 ATGTG--AGTGTGGATG
4374367 CATGAATACC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 2 0.04
37 2 0.04
38 41 0.91
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.36
Consensus pattern (38 bp):
ATGTGAGTGTGGATGAATAAATGCCCACTTTTATGATG
Found at i:4375774 original size:24 final size:25
Alignment explanation
Indices: 4375747--4375795 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
4375737 TATGTTTACA
4375747 TGAAAT-GATATATGA-AACTATATG
1 TGAAATGGAT-TATGACAACTATATG
*
4375771 TGAAATGGATTATGACAATTATATG
1 TGAAATGGATTATGACAACTATATG
4375796 AAATGCTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.35
Consensus pattern (25 bp):
TGAAATGGATTATGACAACTATATG
Found at i:4382215 original size:50 final size:50
Alignment explanation
Indices: 4382140--4382239 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
4382130 ACAGACTTTG
* *
4382140 TACTTATAGGATAATGATCACTAGAGTGCTCATCACTATAATAATCATAA
1 TACTTATAGGACAATGATCACTAGAGTGCCCATCACTATAATAATCATAA
4382190 TACTTATAGGACAATGATCACTAGAGTGCCCATCACTATAATAATCATAA
1 TACTTATAGGACAATGATCACTAGAGTGCCCATCACTATAATAATCATAA
4382240 GTAATAAAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (50 bp):
TACTTATAGGACAATGATCACTAGAGTGCCCATCACTATAATAATCATAA
Found at i:4388377 original size:44 final size:44
Alignment explanation
Indices: 4388314--4388399 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
4388304 AGGTACCTAG
* * *
4388314 AACTTTACTTAGGGTGGAATATAACATATCATGTTATAGTGCAA
1 AACTTTACTTAAGATGGAATATAACATATCATATTATAGTGCAA
*
4388358 AACTTTACTTAAGATGGAATATAATATATCATATTATAGTGC
1 AACTTTACTTAAGATGGAATATAACATATCATATTATAGTGC
4388400 TAGCAGCCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (44 bp):
AACTTTACTTAAGATGGAATATAACATATCATATTATAGTGCAA
Found at i:4390736 original size:34 final size:34
Alignment explanation
Indices: 4390673--4390772 Score: 173
Period size: 34 Copynumber: 2.9 Consensus size: 34
4390663 TAAATTATCA
* *
4390673 AAAACAAATATCTCAAATATCAACTTAAATAACTC
1 AAAACAAATAT-TCAAGTAACAACTTAAATAACTC
4390708 AAAACAAATATTCAAGTAACAACTTAAATAACTC
1 AAAACAAATATTCAAGTAACAACTTAAATAACTC
4390742 AAAACAAATATTCAAGTAACAACTTAAATAA
1 AAAACAAATATTCAAGTAACAACTTAAATAA
4390773 AATTACAAGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
34 52 0.83
35 11 0.17
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (34 bp):
AAAACAAATATTCAAGTAACAACTTAAATAACTC
Found at i:4394630 original size:35 final size:36
Alignment explanation
Indices: 4394555--4394631 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 36
4394545 AGGGTCATGC
* *
4394555 GTAACCTTTACAACATGCCTTTTGCAAGATTAGGCT
1 GTAACCTTTACAACATGCCTTTTGCAAGATCAAGCT
* *
4394591 -TAACCTTTACAACATGCCTTTTGTAGGATCAAG-T
1 GTAACCTTTACAACATGCCTTTTGCAAGATCAAGCT
4394625 GTAACCT
1 GTAACCT
4394632 CTACCAAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 1 0.03
35 35 0.97
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (36 bp):
GTAACCTTTACAACATGCCTTTTGCAAGATCAAGCT
Found at i:4397096 original size:18 final size:19
Alignment explanation
Indices: 4397056--4397098 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
4397046 ATTGTCGAAT
4397056 CCAAAGGCTAAATCCAAAGA
1 CCAAAGGCTAAA-CCAAAGA
* *
4397076 CCAAAGTCTAAA-CAAATA
1 CCAAAGGCTAAACCAAAGA
4397094 CCAAA
1 CCAAA
4397099 TCCAAACTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.53, C:0.26, G:0.09, T:0.12
Consensus pattern (19 bp):
CCAAAGGCTAAACCAAAGA
Found at i:4401532 original size:20 final size:20
Alignment explanation
Indices: 4401507--4401548 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4401497 TCATTAGTGT
4401507 AAGGTATGCATGAGTTTAGC
1 AAGGTATGCATGAGTTTAGC
4401527 AAGGTATGCATGAGTTTAGC
1 AAGGTATGCATGAGTTTAGC
4401547 AA
1 AA
4401549 TATGGGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (20 bp):
AAGGTATGCATGAGTTTAGC
Found at i:4403648 original size:21 final size:21
Alignment explanation
Indices: 4403620--4403697 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
4403610 TGCACTCTGT
4403620 TTCA-AATGTATCGATACATG
1 TTCATAATGTATCGATACATG
* *
4403640 TTCATAATGTATCAATGCAT-
1 TTCATAATGTATCGATACATG
* ** * *
4403660 ATGGTCATGTATTGATACATG
1 TTCATAATGTATCGATACATG
* *
4403681 TTCCTAATGCATCGATA
1 TTCATAATGTATCGATA
4403698 TAATTTTTCC
Statistics
Matches: 41, Mismatches: 15, Indels: 3
0.69 0.25 0.05
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (21 bp):
TTCATAATGTATCGATACATG
Found at i:4406572 original size:30 final size:30
Alignment explanation
Indices: 4406538--4406596 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
4406528 CTGCACGAGG
* *
4406538 GGGTGTCATGACAATTATTTCATGACTTGA
1 GGGTGTCATGACAATGATTTCATAACTTGA
*
4406568 GGGTGTCATGATAATGATTTCATAACTTG
1 GGGTGTCATGACAATGATTTCATAACTTG
4406597 GCTCAACGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (30 bp):
GGGTGTCATGACAATGATTTCATAACTTGA
Found at i:4406885 original size:2 final size:2
Alignment explanation
Indices: 4406878--4406905 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4406868 TCTTGCAAGC
4406878 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
4406906 TTAAAGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4415241 original size:15 final size:15
Alignment explanation
Indices: 4415221--4415257 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
4415211 ACTTGGCAGC
4415221 ATCTCAACACGGATA
1 ATCTCAACACGGATA
4415236 ATCTCAACACGGATA
1 ATCTCAACACGGATA
4415251 ATCTCAA
1 ATCTCAA
4415258 AAACAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.22
Consensus pattern (15 bp):
ATCTCAACACGGATA
Found at i:4421058 original size:25 final size:25
Alignment explanation
Indices: 4421030--4421079 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4421020 AGAAACAAGT
*
4421030 TTTTGAGATTTAAAAAATCAGTATG
1 TTTTAAGATTTAAAAAATCAGTATG
4421055 TTTTAAGATTTAAAAAATCAGTATG
1 TTTTAAGATTTAAAAAATCAGTATG
4421080 CAAAGAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (25 bp):
TTTTAAGATTTAAAAAATCAGTATG
Found at i:4421085 original size:23 final size:24
Alignment explanation
Indices: 4421035--4421085 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
4421025 CAAGTTTTTG
**
4421035 AGATTTAAAAAATCAGTATGTTTTA
1 AGATTTAAAAAATCAGTATG-TCAA
4421060 AGATTTAAAAAATCAGTATG-CAA
1 AGATTTAAAAAATCAGTATGTCAA
4421083 AGA
1 AGA
4421086 AGTACTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
25 20 0.83
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (24 bp):
AGATTTAAAAAATCAGTATGTCAA
Found at i:4424570 original size:19 final size:19
Alignment explanation
Indices: 4424546--4424587 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4424536 AAGTTTTCTC
* *
4424546 AATTAGTATCTAGCTTTAA
1 AATTAGCATCAAGCTTTAA
*
4424565 AATTAGCATCAAGCTTTAG
1 AATTAGCATCAAGCTTTAA
4424584 AATT
1 AATT
4424588 GTCTCTTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (19 bp):
AATTAGCATCAAGCTTTAA
Found at i:4430066 original size:80 final size:80
Alignment explanation
Indices: 4429933--4430240 Score: 311
Period size: 80 Copynumber: 3.9 Consensus size: 80
4429923 TAACATTTCC
* * * * *
4429933 ATAAATCA-TCATCATGCTTAGCTCATAATGTATATGACTATCTCAACACATACATCTTATGGCA
1 ATAAATCACTCA-CATGCTTAGCCCATAGTATATATGACTATCCCAACACATACATCTCATGGCA
*
4429997 TGCATTTTAAAACCTT
65 TGCATTTTATAACCTT
* * * ***
4430013 ATAAATCACTCTCATGCTTAACCCATTGTATATATGACTATTTAAACACATACATCTCATGAG-A
1 ATAAATCACTCACATGCTTAGCCCATAGTATATATGACTATCCCAACACATACATCTCATG-GCA
* * * *
4430077 TACATTTCATAATCTC
65 TGCATTTTATAACCTT
* * * * *
4430093 ATAAATTACTCACATGCTTAGCCTACAG-AGTATATGACTATCCCAACACATACA-CTTATGGTA
1 ATAAATCACTCACATGCTTAGCCCATAGTA-TATATGACTATCCCAACACATACATCTCATGGCA
*
4430156 TGTATTTTATAACCTCT
65 TGCATTTTATAACCT-T
* * * *
4430173 -TAAATCACTCACATGCTTAGCCCATAATGTATATGACTATTCCAACACATACACCTCATGGCAT
1 ATAAATCACTCACATGCTTAGCCCATAGTATATATGACTATCCCAACACATACATCTCATGGCAT
4430237 GCAT
66 GCAT
4430241 GTTACAATCT
Statistics
Matches: 183, Mismatches: 38, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
78 1 0.01
79 64 0.35
80 115 0.63
81 3 0.02
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (80 bp):
ATAAATCACTCACATGCTTAGCCCATAGTATATATGACTATCCCAACACATACATCTCATGGCAT
GCATTTTATAACCTT
Found at i:4430222 original size:159 final size:160
Alignment explanation
Indices: 4429962--4430257 Score: 411
Period size: 159 Copynumber: 1.9 Consensus size: 160
4429952 AGCTCATAAT
* *
4429962 GTATATGACTATCTCAACACATACATCTTATGGCATGCATTTTAAAACCTTATAAATCACTCTCA
1 GTATATGACTATCCCAACACATACATCTTATGGCATGCATTTTAAAACCTTATAAATCACTCACA
** * * *
4430027 TGCTTAACCCATTGTATATATGACTATTTAAACACATACATCTCATGAG-ATACAT-TTCATAAT
66 TGCTTAACCCATAATATATATGACTATTCAAACACATACACCTCATG-GCATACATGTT-ACAAT
4430090 CTCATAAATTACTCACATGCTTAGCCTACAGA
129 CTCATAAATTACTCACATGCTTAGCCTACAGA
* * *
4430122 GTATATGACTATCCCAACACATACA-CTTATGGTATGTATTTTATAACCTCT-TAAATCACTCAC
1 GTATATGACTATCCCAACACATACATCTTATGGCATGCATTTTAAAACCT-TATAAATCACTCAC
* * * *
4430185 ATGCTTAGCCCATAATGTATATGACTATTCCAACACATACACCTCATGGCATGCATGTTACAATC
65 ATGCTTAACCCATAATATATATGACTATTCAAACACATACACCTCATGGCATACATGTTACAATC
4430250 TCATAAAT
130 TCATAAAT
4430258 GGAGCTCATG
Statistics
Matches: 119, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
158 1 0.01
159 91 0.76
160 27 0.23
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (160 bp):
GTATATGACTATCCCAACACATACATCTTATGGCATGCATTTTAAAACCTTATAAATCACTCACA
TGCTTAACCCATAATATATATGACTATTCAAACACATACACCTCATGGCATACATGTTACAATCT
CATAAATTACTCACATGCTTAGCCTACAGA
Found at i:4434762 original size:25 final size:25
Alignment explanation
Indices: 4434725--4434774 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
4434715 TTTCAATATA
4434725 AGAAAAGAAAATAAAAACAATATTT
1 AGAAAAGAAAATAAAAACAATATTT
* *
4434750 AGAAGAGAGAATAAAAACAATATTT
1 AGAAAAGAAAATAAAAACAATATTT
4434775 GTAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (25 bp):
AGAAAAGAAAATAAAAACAATATTT
Found at i:4438960 original size:340 final size:343
Alignment explanation
Indices: 4438403--4439083 Score: 818
Period size: 340 Copynumber: 2.0 Consensus size: 343
4438393 TAATTATTAT
* * * *
4438403 TATATATATACTTTTAATATAAATATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATG
1 TATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTATTAACATTACAAAAATTATA
* *
4438468 ACTTATAAAATTATTAATTATAATATACATAATTGTTTATATAATCTTATAATATATATACTTAA
66 ACTTATAAAATTATTAATTATAATATACATAATTGTTTATATAAACTTATAATATATATACCTAA
* * * * *
4438533 AAAAAGGTTTTTAAGAGTAGAATAGTTTTGGAATCTAAGTGATTTTTTCAATTTCTTGAAATTAA
131 AAAAAGGTTTGTAAGAGTAGAATAGCTCTGAAAACTAAGTGATTTTTTCAATTTCTTGAAATTAA
* * *
4438598 GAACAAATCCATATAATTAATTAAATTAATTCATAAAACTATTATTATTAATTAACTTGTAATTT
196 GAACAAATCCATATAATTAATTAAATTAATTCATAAAACTATAATTATTAATTAACTTATAATAT
*
4438663 CTTTTAATAAATATAGTTTATATAT-T-GT-G-TTAATTTATAAGAAATATAATTACTATTATAT
261 CTTTTAATAAATATACTTTATATATATAGTAGATTAATTTATAAGAAATATAATTACTATTATAT
4438724 ATATACTAAAATATTTTTAG
326 ATAT--TAAAATATTTTTAG
*
4438744 TATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTATTAGCATTAC-AAAATTATA
1 TATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTATTAACATTACAAAAATTATA
*
4438808 ACTTATAAAATTATTAATTATAATATATATATATAACTTTGTTTATATAAAC-T-T-ATATA-A-
66 ACTTATAAAATTATTAA-T-T-ATA-ATATACATAA--TTGTTTATATAAACTTATAATATATAT
* * * * ** *
4438868 ACCTAAAGAGAA-G-TTGTGAGATTAGAATAGCTCT-AAAACTTAGTTTTTTATTTTAATTT-TA
125 ACCTAAA-AAAAGGTTTGTAAGAGTAGAATAGCTCTGAAAACTAAGTGATTT-TTTCAATTTCT-
* * ** *
4438929 T-ATAATTAAGGACAAA-CCTGTATGGTTAATTAAATTAATTTATAAAACTATAATTATTAATTA
187 TGA-AATTAAGAACAAATCC-ATATAATTAATTAAATTAATTCATAAAACTATAATTATTAATTA
* * * * * *
4438992 ATTTATAATATCTTTTAATATATATACTTTATATATATATTAGATTTATTTATTAGGAATATAAT
250 ACTTATAATATCTTTTAATAAATATACTTTATATATATAGTAGATTAATTTATAAGAAATATAAT
4439057 TACTATTATATATATTAAAATATTTTT
315 TACTATTATATATATTAAAATATTTTT
4439084 TATGTGTGCG
Statistics
Matches: 290, Mismatches: 35, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
339 14 0.05
340 132 0.46
341 60 0.21
342 18 0.06
343 9 0.03
344 43 0.15
345 1 0.00
346 13 0.04
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (343 bp):
TATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTATTAACATTACAAAAATTATA
ACTTATAAAATTATTAATTATAATATACATAATTGTTTATATAAACTTATAATATATATACCTAA
AAAAAGGTTTGTAAGAGTAGAATAGCTCTGAAAACTAAGTGATTTTTTCAATTTCTTGAAATTAA
GAACAAATCCATATAATTAATTAAATTAATTCATAAAACTATAATTATTAATTAACTTATAATAT
CTTTTAATAAATATACTTTATATATATAGTAGATTAATTTATAAGAAATATAATTACTATTATAT
ATATTAAAATATTTTTAG
Found at i:4444152 original size:114 final size:115
Alignment explanation
Indices: 4443986--4444252 Score: 283
Period size: 114 Copynumber: 2.3 Consensus size: 115
4443976 TCCATGTCGA
* * *
4443986 GTCACATATTCTCACCATGGCGTGTCACATATGCTCACCCGAGGGTGTCACATATTCTCACCATG
1 GTCACATATTCTCACCATGGCGTGTCACATATGCTCACCCGAGGGTGCCACATATTCCCACAATG
* *
4444051 TCATCTCACATATT-TCCTCCATGGCGTGTCA-ATATTCTCACCCTCTCAT
66 TCATCTCACAGATTCT-CACCATGGCGTGTCACATATTCTCACCCTCTCAT
* * * * *
4444100 GTCACGTATTTTCACCATGGCGTGTCACATATTCTCA-CC-ATGTTGTGCCACATATTCCCTCAA
1 GTCACATATTCTCACCATGGCGTGTCACATATGCTCACCCGA-G-GGTGCCACATATTCCCACAA
* * * * ** *
4444163 TGTCGTCTCACAGATTCTCACCATGGCGTGTCACATATTCCCTCCATGGCTT
64 TGTCATCTCACAGATTCTCACCATGGCGTGTCACATATTCTCACCCTCTCAT
* * *
4444215 GTCACATATTC-CTTCCATGGCGTCTCACATATTCTCAC
1 GTCACATATTCTC-ACCATGGCGTGTCACATATGCTCAC
4444253 ATGTGGTGTC
Statistics
Matches: 126, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
112 1 0.01
113 3 0.02
114 78 0.62
115 44 0.35
ACGTcount: A:0.21, C:0.32, G:0.14, T:0.33
Consensus pattern (115 bp):
GTCACATATTCTCACCATGGCGTGTCACATATGCTCACCCGAGGGTGCCACATATTCCCACAATG
TCATCTCACAGATTCTCACCATGGCGTGTCACATATTCTCACCCTCTCAT
Found at i:4444201 original size:160 final size:158
Alignment explanation
Indices: 4443937--4444365 Score: 396
Period size: 160 Copynumber: 2.7 Consensus size: 158
4443927 CCATCCATAG
** * * * * * * * * *
4443937 CATGTCACATATTCCTTCCATGGCATGTCACATACTCCCTCCATGTCGAGTCACATATTCTCACC
1 CATGTCACATATTCCCACCATGACGTGTCACATATTCTCACCATGT--TGTCACATATTCCCTCA
* * * ** ** *
4444002 ATGGCGTGTCACATATGCTCACCCGAGGGTGTCACATATTCTCACCATGTCATCTCACATATTTC
64 ATGGCGTATCACAGATTCTCACATGAACGTGTCACATATTCTCACCATGGCATCTCACATA-TTC
* *
4444067 C-TCCATGGCGTGTCA-ATATTCTCACCCTCT
128 CTTCCATGGCGTCTCACATATTCTCA-CATCT
* ** *
4444097 CATGTCACGTATTTTCACCATGGCGTGTCACATATTCTCACCATGTTGTGCCACATATTCCCTCA
1 CATGTCACATATTCCCACCATGACGTGTCACATATTCTCACCATGTTGT--CACATATTCCCTCA
* * * * * * *
4444162 ATGTCGTCTCACAGATTCTCACCATG-GCGTGTCACATATTCCCTCCATGGCTTGTCACATATTC
64 ATGGCGTATCACAGATTCTCA-CATGAACGTGTCACATATTCTCACCATGGCATCTCACATATTC
*
4444226 CTTCCATGGCGTCTCACATATTCTCACATGT
128 CTTCCATGGCGTCTCACATATTCTCACATCT
** * * *
4444257 GGTGTCACATGTTCCCTCCATGACGTGTCACATATTCTCACCATGTTGTCACATATTCCCTCCAT
1 CATGTCACATATTCCCACCATGACGTGTCACATATTCTCACCATGTTGTCACATATTCCCTCAAT
* * * *
4444322 GGCGTATCATATATTCTCACTTGAACGTGTCACATACTCTCACC
66 GGCGTATCACAGATTCTCACATGAACGTGTCACATATTCTCACC
4444366 CTACCGTGTC
Statistics
Matches: 217, Mismatches: 46, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
157 3 0.01
158 48 0.22
159 4 0.02
160 151 0.70
161 11 0.05
ACGTcount: A:0.21, C:0.32, G:0.14, T:0.33
Consensus pattern (158 bp):
CATGTCACATATTCCCACCATGACGTGTCACATATTCTCACCATGTTGTCACATATTCCCTCAAT
GGCGTATCACAGATTCTCACATGAACGTGTCACATATTCTCACCATGGCATCTCACATATTCCTT
CCATGGCGTCTCACATATTCTCACATCT
Found at i:4444452 original size:23 final size:23
Alignment explanation
Indices: 4443910--4444552 Score: 364
Period size: 23 Copynumber: 27.8 Consensus size: 23
4443900 TATTCCTTTG
* *
4443910 ATGGCATGTCTCATATTC-CATCC
1 ATGGCGTGTCACATATTCTCA-CC
* * *
4443933 ATAGCATGTCACATATTC-CTTCC
1 ATGGCGTGTCACATATTCTC-ACC
* * * *
4443956 ATGGCATGTCACATACTCCCTCC
1 ATGGCGTGTCACATATTCTCACC
* *
4443979 ATGTCGAGTCACATATTCTCACC
1 ATGGCGTGTCACATATTCTCACC
*
4444002 ATGGCGTGTCACATATGCTCACCC
1 ATGGCGTGTCACATATTCTCA-CC
4444026 GA-GG-GTGTCACATATTCTCACC
1 -ATGGCGTGTCACATATTCTCACC
* * * *
4444048 ATGTCATCTCACATATT-TCCTCC
1 ATGGCGTGTCACATATTCT-CACC
4444071 ATGGCGTGTCA-ATATTCTCACC
1 ATGGCGTGTCACATATTCTCACC
* ** * * *
4444093 CTCTCATGTCACGTATTTTCACC
1 ATGGCGTGTCACATATTCTCACC
4444116 ATGGCGTGTCACATATTCTCACC
1 ATGGCGTGTCACATATTCTCACC
** * * * *
4444139 ATGTTGTGCCACATATTCCCTCA
1 ATGGCGTGTCACATATTCTCACC
* * *
4444162 ATGTCGTCTCACAGATTCTCACC
1 ATGGCGTGTCACATATTCTCACC
* *
4444185 ATGGCGTGTCACATATTCCCTCC
1 ATGGCGTGTCACATATTCTCACC
* *
4444208 ATGGCTTGTCACATATTC-CTTCC
1 ATGGCGTGTCACATATTCTC-ACC
*
4444231 ATGGCGTCTCACATATTCTCA-C
1 ATGGCGTGTCACATATTCTCACC
* * *
4444253 ATGTG-GTGTCACATGTTCCCTCC
1 ATG-GCGTGTCACATATTCTCACC
*
4444276 ATGACGTGTCACATATTCTCACC
1 ATGGCGTGTCACATATTCTCACC
* * *
4444299 AT-G-TTGTCACATATTCCCTCC
1 ATGGCGTGTCACATATTCTCACC
* *
4444320 ATGGCGTATCATATATTCTCA-C
1 ATGGCGTGTCACATATTCTCACC
* * *
4444342 TTGAACGTGTCACATACTCTCACC
1 ATG-GCGTGTCACATATTCTCACC
* ** *
4444366 CTACCGTGTCACATATTCTCAAC
1 ATGGCGTGTCACATATTCTCACC
*
4444389 AT-GC-TGCATCATATATTCCCTC-CC
1 ATGGCGTG--TCACATATT--CTCACC
* *
4444413 ACT-CCATGTCGTCTCACATATTCTCATC
1 A-TGGC--GT-G--TCACATATTCTCACC
4444441 ATGGCGTGTCACATATTCTCTCACC
1 ATGGCGTGTCACATA-T-TCTCACC
* * * * *
4444466 ATGACATGTCACTTATTCCCTCC
1 ATGGCGTGTCACATATTCTCACC
* * * *
4444489 ATGGCATCTCACATATTATCACA
1 ATGGCGTGTCACATATTCTCACC
* * * *
4444512 ATGGCATGTCACATGTTCTTAAC
1 ATGGCGTGTCACATATTCTCACC
* *
4444535 ATGTCGTGTCATATATTC
1 ATGGCGTGTCACATATTC
4444553 CTTTGTGGTC
Statistics
Matches: 472, Mismatches: 117, Indels: 62
0.73 0.18 0.10
Matches are distributed among these distances:
21 20 0.04
22 41 0.09
23 355 0.75
24 12 0.03
25 25 0.05
26 2 0.00
27 4 0.01
28 4 0.01
29 9 0.02
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.33
Consensus pattern (23 bp):
ATGGCGTGTCACATATTCTCACC
Found at i:4450280 original size:47 final size:46
Alignment explanation
Indices: 4450211--4450474 Score: 192
Period size: 47 Copynumber: 5.6 Consensus size: 46
4450201 CCAAGTGAAA
* * * *
4450211 AAAAACTCCTTACCTTTAAATGAGGCTGTGCAACTTTAAATGATTGG
1 AAAAACTCCTCATCTCTAAATGAGGCTATGCAACTTTAAATGATT-G
* * * *
4450258 GAAAACTCCTCATTTCTAAATGAGGCTATGAAACTTAAAATGATTAG
1 AAAAACTCCTCATCTCTAAATGAGGCTATGCAACTTTAAATGATT-G
* * * ** * ** *
4450305 GAAAGCTCCTCA-CTTCAAAACCAAGCTACACAACTTTAAAATGATTT
1 AAAAACTCCTCATC-TCTAAATGAGGCTATGCAACTTT-AAATGATTG
* * *
4450352 AAACA-T-CTCATCTCTAAATGAGGTTATGTAACTTTAAAATGATTG
1 AAAAACTCCTCATCTCTAAATGAGGCTATGCAACTTT-AAATGATTG
* * * *
4450397 AAAAAAGCTCCTTATCTCTAAACGAGGCTATGTAACTTCAAAATGATTG
1 -AAAAA-CTCCTCATCTCTAAATGAGGCTATGCAACTT-TAAATGATTG
* *
4450446 AAAAAGTTCTTCATCTCTAAATGAGGCTA
1 AAAAA-CTCCTCATCTCTAAATGAGGCTA
4450475 CATAAGTTTA
Statistics
Matches: 168, Mismatches: 41, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
45 28 0.17
46 6 0.04
47 66 0.39
48 34 0.20
49 34 0.20
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (46 bp):
AAAAACTCCTCATCTCTAAATGAGGCTATGCAACTTTAAATGATTG
Found at i:4450472 original size:48 final size:49
Alignment explanation
Indices: 4450210--4450497 Score: 208
Period size: 48 Copynumber: 6.1 Consensus size: 49
4450200 ACCAAGTGAA
* * * * *
4450210 AAAAAACTCCTT-ACCTTTAAATGAGGCTGTGCAACTTT-AAATGATTGG
1 AAAAAGCTCCTTCATCTCTAAATGAGGCTATGTAACTTTAAAATGATT-G
* * *
4450258 GAAAA-CTCC-TCATTTCTAAATGAGGCTATGAAAC-TTAAAATGATT-
1 AAAAAGCTCCTTCATCTCTAAATGAGGCTATGTAACTTTAAAATGATTG
* * ** * *** *
4450303 AGGAAAGCTCC-TCA-CTTCAAAACCAAGCTACACAACTTTAAAATGATTT
1 A-AAAAGCTCCTTCATC-TCTAAATGAGGCTATGTAACTTTAAAATGATTG
* *
4450352 AAACA--T-C-TCATCTCTAAATGAGGTTATGTAACTTTAAAATGATTG
1 AAAAAGCTCCTTCATCTCTAAATGAGGCTATGTAACTTTAAAATGATTG
* *
4450397 AAAAAAGCTCCTT-ATCTCTAAACGAGGCTATGTAACTTCAAAATGATTG
1 -AAAAAGCTCCTTCATCTCTAAATGAGGCTATGTAACTTTAAAATGATTG
* ** * *
4450446 AAAAAG-TTCTTCATCTCTAAATGAGGCTACATAAGTTTAAAAAGATTG
1 AAAAAGCTCCTTCATCTCTAAATGAGGCTATGTAACTTTAAAATGATTG
4450494 AAAA
1 AAAA
4450498 TTTTTCTTTT
Statistics
Matches: 188, Mismatches: 38, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
45 28 0.15
46 12 0.06
47 54 0.29
48 58 0.31
49 35 0.19
50 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.30
Consensus pattern (49 bp):
AAAAAGCTCCTTCATCTCTAAATGAGGCTATGTAACTTTAAAATGATTG
Found at i:4451359 original size:108 final size:108
Alignment explanation
Indices: 4451170--4451377 Score: 335
Period size: 108 Copynumber: 1.9 Consensus size: 108
4451160 CCATGTTATA
* * * *
4451170 AATCTTTGTACATAAGTCACCTTTTCAGGTTTTCAACTTGATTGCCTTCCTTGGATTCAAATTGT
1 AATCTTTGTACATAAGTCACCTTTTCAGGTTTTCAACTTAATTACCTCCCTTAGATTCAAATTGT
*
4451235 CCTTTTAGGTTTTCACCTTGAACCTTTTTTTTTCTATGCTATC
66 CCTTTTAGGCTTTCACCTTGAACCTTTTTTTTTCTATGCTATC
**
4451278 AATCTTTGTACATAAGTCACCTTTTTGGGTTTTCAACTTAATTACCTCCCTTAGATTCAAATTGT
1 AATCTTTGTACATAAGTCACCTTTTCAGGTTTTCAACTTAATTACCTCCCTTAGATTCAAATTGT
* *
4451343 CTTTTTGGGCTTTCACCTTGAACCTTTTTTTTTCT
66 CCTTTTAGGCTTTCACCTTGAACCTTTTTTTTTCT
4451378 TTTTCTTCTT
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 91 1.00
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.48
Consensus pattern (108 bp):
AATCTTTGTACATAAGTCACCTTTTCAGGTTTTCAACTTAATTACCTCCCTTAGATTCAAATTGT
CCTTTTAGGCTTTCACCTTGAACCTTTTTTTTTCTATGCTATC
Found at i:4456004 original size:14 final size:13
Alignment explanation
Indices: 4455978--4456012 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
4455968 CAAATTCAAA
4455978 TAATTAAATTAAT
1 TAATTAAATTAAT
4455991 TAATTAAATCTAAT
1 TAATTAAAT-TAAT
*
4456005 TAACTAAA
1 TAATTAAA
4456013 ATTTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:4457086 original size:27 final size:26
Alignment explanation
Indices: 4457056--4457113 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
4457046 TTAAATTAAA
*
4457056 ATAAACTCACTTAAAAATAAACT-AATT
1 ATAAACTAAC-TAAAAAT-AACTAAATT
*
4457083 ATAAAAGTAACTAAAAATAACTAAATT
1 AT-AAACTAACTAAAAATAACTAAATT
4457110 ATAA
1 ATAA
4457114 TTTAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 6 0.22
27 15 0.56
28 6 0.22
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (26 bp):
ATAAACTAACTAAAAATAACTAAATT
Found at i:4457088 original size:16 final size:17
Alignment explanation
Indices: 4457052--4457088 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
4457042 AATATTAAAT
*
4457052 TAAAATAAACTCACTTA
1 TAAAATAAACTCAATTA
4457069 -AAAATAAACT-AATTA
1 TAAAATAAACTCAATTA
4457084 TAAAA
1 TAAAA
4457089 GTAACTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAATAAACTCAATTA
Found at i:4460060 original size:14 final size:14
Alignment explanation
Indices: 4460043--4460069 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4460033 ATAATTAAAT
4460043 TAATTAACTAAAAC
1 TAATTAACTAAAAC
4460057 TAATTAACTAAAA
1 TAATTAACTAAAA
4460070 TTTAAACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:4463912 original size:18 final size:18
Alignment explanation
Indices: 4463889--4463926 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4463879 GTATCACTAA
4463889 TCCATGAAATCCTTTGCC
1 TCCATGAAATCCTTTGCC
*
4463907 TCCATGCAATCCTTTGCC
1 TCCATGAAATCCTTTGCC
4463925 TC
1 TC
4463927 TATTTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.37, G:0.11, T:0.34
Consensus pattern (18 bp):
TCCATGAAATCCTTTGCC
Found at i:4464708 original size:50 final size:48
Alignment explanation
Indices: 4464622--4464804 Score: 161
Period size: 44 Copynumber: 3.9 Consensus size: 48
4464612 TTGAGACAAA
* * *
4464622 GTATATAGTTTG-TATCTAGTTGAACTCAACTT-GACTCATTTAGGTATT
1 GTATATATTTTGTTATCTAATTGATCTCAA-TTAGACTCATTTAGGTA-T
4464670 GGTATATATTTTGTTATCTAATTGATCTCAATTAGACTCATTTA---A-
1 -GTATATATTTTGTTATCTAATTGATCTCAATTAGACTCATTTAGGTAT
* *
4464715 GTATATATTTTGTTATCTATAGTTCATCTCAACTAGACTCATTTA-G---
1 GTATATATTTTGTTATCTA-A-TTGATCTCAATTAGACTCATTTAGGTAT
* * * * *
4464761 GTATATATTTCGTTATCTAGTTTATTTCAACTAGACTCATTTAG
1 GTATATATTTTGTTATCTAATTGATCTCAATTAGACTCATTTAG
4464805 ATTTTATGTA
Statistics
Matches: 119, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
44 40 0.34
45 1 0.01
46 39 0.33
47 1 0.01
49 13 0.11
50 25 0.21
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (48 bp):
GTATATATTTTGTTATCTAATTGATCTCAATTAGACTCATTTAGGTAT
Found at i:4464752 original size:46 final size:46
Alignment explanation
Indices: 4464671--4464803 Score: 184
Period size: 44 Copynumber: 3.0 Consensus size: 46
4464661 TTAGGTATTG
* *
4464671 GTATATATTTTGTTATCTA-A-TTGATCTCAATTAGACTCATTTAA
1 GTATATATTTTGTTATCTATAGTTCATCTCAACTAGACTCATTTAA
*
4464715 GTATATATTTTGTTATCTATAGTTCATCTCAACTAGACTCATTTAG
1 GTATATATTTTGTTATCTATAGTTCATCTCAACTAGACTCATTTAA
* * *
4464761 GTATATATTTCGTTATC--TAGTTTATTTCAACTAGACTCATTTA
1 GTATATATTTTGTTATCTATAGTTCATCTCAACTAGACTCATTTA
4464804 GATTTTATGT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 43 0.53
45 1 0.01
46 37 0.46
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (46 bp):
GTATATATTTTGTTATCTATAGTTCATCTCAACTAGACTCATTTAA
Found at i:4465757 original size:36 final size:35
Alignment explanation
Indices: 4465710--4465792 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 35
4465700 AAGTTTGATG
*
4465710 AATATTAATATTCAA-TTTAAAATATTAAAAAATAAA
1 AATATTAATATTCAACTTTAAAAAATT--AAAATAAA
* * *
4465746 AATATTAATATTTAACTTTAAAAAATTTAAATTAA
1 AATATTAATATTCAACTTTAAAAAATTAAAATAAA
4465781 AATATTAATATT
1 AATATTAATATT
4465793 TAAATTATAC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
35 18 0.43
36 14 0.33
37 10 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (35 bp):
AATATTAATATTCAACTTTAAAAAATTAAAATAAA
Found at i:4468473 original size:28 final size:29
Alignment explanation
Indices: 4468442--4468501 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
4468432 TATAATTATA
*
4468442 ATTTTTAAAATTAATAAA-AAATAAAATT
1 ATTTTTAAAATTAATAAATAAATAAAAAT
* * *
4468470 ATTTTTAATATTATTAAATTAATAAAAAT
1 ATTTTTAAAATTAATAAATAAATAAAAAT
4468499 ATT
1 ATT
4468502 AATAATTAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTTTAAAATTAATAAATAAATAAAAAT
Found at i:4477058 original size:8 final size:8
Alignment explanation
Indices: 4477047--4477072 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4477037 AAAAAAAGTT
4477047 TAAAACTA
1 TAAAACTA
4477055 TAAAACTA
1 TAAAACTA
4477063 TAAAACTA
1 TAAAACTA
4477071 TA
1 TA
4477073 CAATGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (8 bp):
TAAAACTA
Found at i:4486178 original size:79 final size:79
Alignment explanation
Indices: 4486043--4486200 Score: 217
Period size: 79 Copynumber: 2.0 Consensus size: 79
4486033 CTAAGGTTTT
* * * *
4486043 TTGTGTTTGCTGGATGTGGTTACTTGTGCTAACACGGCCTGAGCTTTGGGACCAATTGGCGTGGT
1 TTGTGTTTGCTGAATGTGGTTACCTGTGCTAACACGGCATGAGCATTGGGACCAATTGGCGTGGT
* *
4486108 GGTTCTAGACTGTG
66 GATTCTAAACTGTG
*** * *
4486122 TTGTGTTTGCTGAATGTGGTTACCTGTGCTAATGTGGCATGAGCATTGGGAGCAATTGGTGTGGT
1 TTGTGTTTGCTGAATGTGGTTACCTGTGCTAACACGGCATGAGCATTGGGACCAATTGGCGTGGT
4486187 GATTCTAAACTGTG
66 GATTCTAAACTGTG
4486201 ATGGGTTATT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.16, C:0.14, G:0.34, T:0.36
Consensus pattern (79 bp):
TTGTGTTTGCTGAATGTGGTTACCTGTGCTAACACGGCATGAGCATTGGGACCAATTGGCGTGGT
GATTCTAAACTGTG
Found at i:4486229 original size:2 final size:2
Alignment explanation
Indices: 4486222--4486249 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4486212 TTACATAGAG
4486222 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
4486250 TCTGATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4493139 original size:15 final size:15
Alignment explanation
Indices: 4493119--4493148 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4493109 TAGAAATAGG
*
4493119 ATACTTTTCTTATTT
1 ATACTTTCCTTATTT
4493134 ATACTTTCCTTATTT
1 ATACTTTCCTTATTT
4493149 GTTATTTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (15 bp):
ATACTTTCCTTATTT
Found at i:4493385 original size:16 final size:18
Alignment explanation
Indices: 4493359--4493403 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
4493349 CCATGAAAAT
*
4493359 TTATTAATTAATCAA-AA
1 TTATTATTTAATCAATAA
4493376 -TATTATTTAATCAATAA
1 TTATTATTTAATCAATAA
4493393 TTATTAATTTA
1 TTATT-ATTTA
4493404 TACATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 13 0.54
17 2 0.08
18 4 0.17
19 5 0.21
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATTATTTAATCAATAA
Found at i:4493964 original size:17 final size:17
Alignment explanation
Indices: 4493938--4493985 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
4493928 CGAGATTGAC
*
4493938 CAAAAATATT-ATTTAAT
1 CAAAATTATTAATTT-AT
4493955 CAAAATTATTAATTTAT
1 CAAAATTATTAATTTAT
4493972 C-AAA-TATTAATTTA
1 CAAAATTATTAATTTA
4493986 CAGAGGCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.34
16 3 0.10
17 12 0.41
18 4 0.14
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
CAAAATTATTAATTTAT
Found at i:4493981 original size:15 final size:16
Alignment explanation
Indices: 4493940--4493985 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
4493930 AGATTGACCA
4493940 AAAATATT-ATTTAATC
1 AAAATATTAATTT-ATC
4493956 AAAATTATTAATTTATC
1 AAAA-TATTAATTTATC
4493973 -AAATATTAATTTA
1 AAAATATTAATTTA
4493986 CAGAGGCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.36
16 7 0.25
17 7 0.25
18 4 0.14
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAATATTAATTTATC
Found at i:4495134 original size:342 final size:341
Alignment explanation
Indices: 4494463--4495107 Score: 886
Period size: 342 Copynumber: 1.9 Consensus size: 341
4494453 TTTTATTTTT
* * * *
4494463 TTATAAATAAACCCAATGTATATAAAATATATATATTAAAAGACATTCTAAGTCAATGAATAATT
1 TTATAAATAAACACAATATATATAAAATATATATATTAAAAGACATTATAAGTCAATGAATAATC
* **
4494528 ATAGTTTCATTAATTAATTTAATTAACTACATGGATTTATCCTTAATTATATGAAATTAAAAAAA
66 ATAGTTTCATGAATTAATTTAATTAACTACATAAATTTATCCTTAATTATATGAAATTAAAAAAA
* * * * * * * *
4494593 ATAGCTAGGTTTCAAAACTATTTTAATCCACAACTTCTTTTTAGGTTTATTTATTATAAGTTTAT
131 ATAGCTAGATTCCAAAACTATTCTAATCCAAAACTTCTCTTTAAGTATATATATTATAAGTTTAT
*
4494658 ATAAATAAAAGTATATATATTATAATTAATAATTTTATAAATTATAACTTTTGTAATATTAACAC
196 ATAAACAAAAGTATATATATTATAATTAATAATTTTATAAATTATAACTTTTGTAATATTAACAC
* * * *
4494723 AAAATAAAAAGTAAATATATTTATATTTAAAGTATATATATACTAAAAATATTTTATTATATATA
261 AAAAT-AAAAGTAAATATATTTACAATAAAAGTATATATATAC-AAAAATATTATATTATATATA
4494788 TAATAGTAATTACATTTC
324 TAATAGTAATTACATTTC
* * * *
4494806 TTATAAATTAACACAA-ATATATAAACTATATATATTAAAAGACATTATAAGTTAATTAATAATC
1 TTATAAATAAACACAATATATATAAAATATATATATTAAAAGACATTATAAGTCAATGAATAATC
* * *
4494870 ATAGTTTCATGAATTAATTTAATTAATTATATAAATTTTTCCTTAATT-TGATGAAATTAAAAAA
66 ATAGTTTCATGAATTAATTTAATTAACTACATAAATTTATCCTTAATTAT-ATGAAATTAAAAAA
*
4494934 AA-ATGTTAGATTCCAAAACTATTCTAATCTCAAAAGC-TCTCTTTAAGTATATATATTATAAGT
130 AATA-GCTAGATTCCAAAACTATTCTAATC-CAAAA-CTTCTCTTTAAGTATATATATTATAAGT
** * *
4494997 TTATATAAACAATGGTATATATATATTATAATTAATAATTTTATAAGTTATAATTTTTGTAATAT
192 TTATATAAACAAAAG--TATATATATTATAATTAATAATTTTATAAATTATAACTTTTGTAATAT
*
4495062 TAGCACAAAAT-AAAGTAAATATATTTACAATAAAAGTATATATATA
255 TAACACAAAATAAAAGTAAATATATTTACAATAAAAGTATATATATA
4495108 AAATAGTAAT
Statistics
Matches: 264, Mismatches: 32, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
341 2 0.01
342 121 0.46
343 84 0.32
344 1 0.00
345 56 0.21
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (341 bp):
TTATAAATAAACACAATATATATAAAATATATATATTAAAAGACATTATAAGTCAATGAATAATC
ATAGTTTCATGAATTAATTTAATTAACTACATAAATTTATCCTTAATTATATGAAATTAAAAAAA
ATAGCTAGATTCCAAAACTATTCTAATCCAAAACTTCTCTTTAAGTATATATATTATAAGTTTAT
ATAAACAAAAGTATATATATTATAATTAATAATTTTATAAATTATAACTTTTGTAATATTAACAC
AAAATAAAAGTAAATATATTTACAATAAAAGTATATATATACAAAAATATTATATTATATATATA
ATAGTAATTACATTTC
Found at i:4502006 original size:213 final size:212
Alignment explanation
Indices: 4501606--4502215 Score: 807
Period size: 220 Copynumber: 2.8 Consensus size: 212
4501596 TGTTCATTCC
* *
4501606 TACCTAAATCAATGCCAGCTTCCTCTTCCACTGCTTAGCATTTAAAAAATTATTAAAAATTACAA
1 TACCTAAATCAATGCCAGCTTCCTCATCCACTGCTTAGCATTT-AAAAATTATTAAAACTTACAA
*
4501671 TG-ATCTGCAGCGCCAAAATGCTGGCAAAAGCAATGAACAATGAAAGAAAAAAAATGTAGTTCCA
65 -GCATCTGCAGCGCCGAAATGCTGGCAAAAGCAATGAACAATGAAAG-AAAAAAA-GTAGTTCCA
* * * * **
4501735 AAATGATGAGACTAAGGCTTCATCAATACCTCCTTATATGAATCAAAAAGCC-AAAAA-AAAAAG
127 AAATGAAGAGACTACGGCTTCGTCAATACTTCCTTATATGAAAAAAAAAGCCAAAAAAGAAAAAG
*
4501798 TTACAAAAGACTGACTAACAG
192 TGACAAAAGACTGACTAACAG
*
4501819 TACCTAAATCAATGCCAACTTCCTCATCCACTGCTTAGCATTTAAAATATTATTAAAACTTACAA
1 TACCTAAATCAATGCCAGCTTCCTCATCCACTGCTTAGCATTTAAAA-ATTATTAAAACTTACAA
* ** *
4501884 GCATCAGCAAAGCCGTAATGCTGGCAAAAGCAATGAACAATGAAAGAAAAAAAGTAGTTCCAAAA
65 GCATCTGCAGCGCCGAAATGCTGGCAAAAGCAATGAACAATGAAAGAAAAAAAGTAGTTCCAAAA
4501949 TGAAGAGACTACGGCTTCGTCAATACTTCCTTATATGAAAAAAAAAGCCAAAAAAAAAAAGGGAA
130 TGAAGAGACTACGGCTTCGTCAATACTTCCTTATATGAAAAAAAAAGCC-----AAAAAA--GAA
*
4502014 AAAGTGACAAAAGACTGTCTAACAG
188 AAAGTGACAAAAGACTGACTAACAG
4502039 TACCTAAATCAATGCCAGCTTCCTCATCCACTGCTTAGCATTTCAAAAATTATTAAAACTTACAA
1 TACCTAAATCAATGCCAGCTTCCTCATCCACTGCTTAGCATTT-AAAAATTATTAAAACTTACAA
*
4502104 GCATCTGCAGCGCCGAAATGCTGGCAAAAGCAATGAACAATAAAAGCAAAAAACAGAAAAACAGT
65 GCATCTGCAGCGCCGAAATGCTGGCAAAAGCAATGAACAAT----G-----AA-AGAAAAAAAGT
* *
4502169 AGTTCCAAAATGAAGAGA--ACGGCTTCGTCTACACTTCCTTATATGAA
120 AGTTCCAAAATGAAGAGACTACGGCTTCGTCAATACTTCCTTATATGAA
4502216 TCAAGTTAGC
Statistics
Matches: 351, Mismatches: 24, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
211 55 0.16
212 12 0.03
213 96 0.27
217 5 0.01
220 121 0.34
221 4 0.01
224 1 0.00
228 27 0.08
229 2 0.01
230 28 0.08
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (212 bp):
TACCTAAATCAATGCCAGCTTCCTCATCCACTGCTTAGCATTTAAAAATTATTAAAACTTACAAG
CATCTGCAGCGCCGAAATGCTGGCAAAAGCAATGAACAATGAAAGAAAAAAAGTAGTTCCAAAAT
GAAGAGACTACGGCTTCGTCAATACTTCCTTATATGAAAAAAAAAGCCAAAAAAGAAAAAGTGAC
AAAAGACTGACTAACAG
Found at i:4506294 original size:163 final size:162
Alignment explanation
Indices: 4506009--4506334 Score: 503
Period size: 163 Copynumber: 2.0 Consensus size: 162
4505999 AAGACACTTT
* * *
4506009 CAAATGCTTGATATTAGGTTCAAGAAAACATGTGATTTTTGTCAAATCAAAACATGATATAACTC
1 CAAATGCTTGACATTAGGTTCAAGAAAACATATGATTTTTGTCAAATCAAAACATGACATAACTC
* * *
4506074 AACGCTAACAATCTCCCCATTTGTGATATGATAAAAATATGAGTATATTGCATTTAAAATTTCTT
66 AACGCTAACAATCTCCCCATTTGTGATATGACAAAAACATGAGCATATTGCATTTAAAATTTCTT
4506139 GAAA-CCTCCCCGTAACTTAATTAGTCTCTATGC
131 GAAATCC-CCCC-TAACTTAATTAGTCTCTATGC
* *
4506172 CAAATGCTTGACATTAGGTTTAAGAAAATATATGATTTTTGTCAAATCAAAACATGACATAACTC
1 CAAATGCTTGACATTAGGTTCAAGAAAACATATGATTTTTGTCAAATCAAAACATGACATAACTC
* * * *
4506237 AAGGCTAATAATCTCCCTC-TTTTTGATATGACAAAAACATGAGCATATTGTATTTAAAATTTCT
66 AACGCTAACAATCTCCC-CATTTGTGATATGACAAAAACATGAGCATATTGCATTTAAAATTTCT
4506301 TGAAATCCCCCCTAACTTAATTAGTCTCTATGC
130 TGAAATCCCCCCTAACTTAATTAGTCTCTATGC
4506334 C
1 C
4506335 CTTGTTGCAA
Statistics
Matches: 149, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
162 22 0.15
163 124 0.83
164 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (162 bp):
CAAATGCTTGACATTAGGTTCAAGAAAACATATGATTTTTGTCAAATCAAAACATGACATAACTC
AACGCTAACAATCTCCCCATTTGTGATATGACAAAAACATGAGCATATTGCATTTAAAATTTCTT
GAAATCCCCCCTAACTTAATTAGTCTCTATGC
Found at i:4509346 original size:21 final size:21
Alignment explanation
Indices: 4509320--4509392 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
4509310 GGCCTTGACC
4509320 ATTTAATTTACAAACATCATG
1 ATTTAATTTACAAACATCATG
* *** * *
4509341 ATTTAAGTTTGCGGCCTTGACT-
1 ATTTAA-TTTACAAACATCA-TG
*
4509363 ATTTAATTTACAAACATCGTG
1 ATTTAATTTACAAACATCATG
4509384 ATTTAATTT
1 ATTTAATTT
4509393 TTCTTTCCAT
Statistics
Matches: 36, Mismatches: 13, Indels: 6
0.65 0.24 0.11
Matches are distributed among these distances:
20 1 0.03
21 21 0.58
22 13 0.36
23 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (21 bp):
ATTTAATTTACAAACATCATG
Found at i:4509368 original size:43 final size:43
Alignment explanation
Indices: 4509307--4509389 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
4509297 CCAACAAGGC
4509307 TGCGGCCTTGACCATTTAATTTACAAACATCATGATTTAAGTT
1 TGCGGCCTTGACCATTTAATTTACAAACATCATGATTTAAGTT
* *
4509350 TGCGGCCTTGACTATTTAATTTACAAACATCGTGATTTAA
1 TGCGGCCTTGACCATTTAATTTACAAACATCATGATTTAA
4509390 TTTTTCTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (43 bp):
TGCGGCCTTGACCATTTAATTTACAAACATCATGATTTAAGTT
Found at i:4511579 original size:24 final size:23
Alignment explanation
Indices: 4511543--4511591 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
4511533 TTTTCAAAGT
*
4511543 AAAAAAAAGATAGAAAATAAAATG
1 AAAAAAAAGATAG-AAAGAAAATG
4511567 AAAAACAAA-ATAGAAAGAAAATG
1 AAAAA-AAAGATAGAAAGAAAATG
4511590 AA
1 AA
4511592 GAAATAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 9 0.39
25 3 0.13
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (23 bp):
AAAAAAAAGATAGAAAGAAAATG
Found at i:4514454 original size:18 final size:18
Alignment explanation
Indices: 4514420--4514461 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4514410 ACTTATTTGG
*
4514420 AGGCATTCGAATGTTGAA
1 AGGCATTCGAAAGTTGAA
4514438 AGGCATTC-AAAGATTGAA
1 AGGCATTCGAAAG-TTGAA
4514456 A-GCATT
1 AGGCATT
4514462 TCAGAGCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (18 bp):
AGGCATTCGAAAGTTGAA
Found at i:4514681 original size:54 final size:52
Alignment explanation
Indices: 4514544--4514724 Score: 161
Period size: 54 Copynumber: 3.4 Consensus size: 52
4514534 GTAACAGTGA
* * * *
4514544 AGTTCATGGTCAAGATTAAGTCGTGAAGACCTTTAAAGCGAGGATATCAAGTAT
1 AGTTCGTGATCAAGATTAAGT--AGAAGACCTTTAAAGCGAAGATATCAAGTAT
* * * * * * *
4514598 AGTTGGTGATTAAGATCAAGTCATGAAGACCCTTGAAGCAAAGATATCAAATAT
1 AGTTCGTGATCAAGATTAAGT-A-GAAGACCTTTAAAGCGAAGATATCAAGTAT
*
4514652 AGTTCGTGATCAAGATTAAGTAGCCAAGACTTTTAAAGCGAAG--ATCAAGTGA-
1 AGTTCGTGATCAAGATTAAGTAG--AAGACCTTTAAAGCGAAGATATCAAGT-AT
*
4514704 AGTTCGTGATCAAGACTAAGT
1 AGTTCGTGATCAAGATTAAGT
4514725 GCAAACTTGT
Statistics
Matches: 102, Mismatches: 21, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
52 27 0.26
53 2 0.02
54 73 0.72
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (52 bp):
AGTTCGTGATCAAGATTAAGTAGAAGACCTTTAAAGCGAAGATATCAAGTAT
Found at i:4517580 original size:21 final size:22
Alignment explanation
Indices: 4517555--4517598 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
4517545 AAGTGATTAA
4517555 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
4517576 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
4517598 T
1 T
4517599 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:4519910 original size:31 final size:29
Alignment explanation
Indices: 4519817--4519969 Score: 136
Period size: 28 Copynumber: 5.3 Consensus size: 29
4519807 AACATATTTG
**
4519817 TCTTAATTTAGAC-A-AAAAATATGTTTGG
1 TCTTAATTTAGACAAGAAAAATAT-TTTTA
* * * *
4519845 TTTTAATTTAGACACG-AAAATATGTTTG
1 TCTTAATTTAGACAAGAAAAATATTTTTA
*
4519873 TCTTAATTTAAGATAAGAAAAATATTTTTTA
1 TCTTAATTT-AGACAAGAAAAATA-TTTTTA
* *
4519904 TCTTAATCTAGACAAGAAAACATATTTGT-
1 TCTTAATTTAGACAAGAAAA-ATATTTTTA
*
4519933 T-TGAATTTAGACAAGATAAAATATTTTTA
1 TCTTAATTTAGACAAGA-AAAATATTTTTA
4519962 TCTTAATT
1 TCTTAATT
4519970 AAACATAAGA
Statistics
Matches: 100, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
28 43 0.43
29 17 0.17
30 25 0.25
31 15 0.15
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (29 bp):
TCTTAATTTAGACAAGAAAAATATTTTTA
Found at i:4519916 original size:59 final size:57
Alignment explanation
Indices: 4519806--4519968 Score: 179
Period size: 59 Copynumber: 2.8 Consensus size: 57
4519796 TAAAAAAAAC
* * ** * * *
4519806 AAACATATTTGTCTTAATTTAGACA-AAAAATATGTTTGGTTTTAATTTAGACACGA
1 AAACATATTTGTCTTAATTTAGAAAGAAAAATATTTTTTATCTTAATCTAGACAAGA
* *
4519862 AAATATGTTTGTCTTAATTTAAGATAAGAAAAATATTTTTTATCTTAATCTAGACAAGA
1 AAACATATTTGTCTTAATTT-AGA-AAGAAAAATATTTTTTATCTTAATCTAGACAAGA
4519921 AAACATATTTGT-TTGAATTTAGACAAGATAAAATA-TTTTTATCTTAAT
1 AAACATATTTGTCTT-AATTTAGA-AAGA-AAAATATTTTTTATCTTAAT
4519969 TAAACATAAG
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
56 18 0.20
57 3 0.03
58 23 0.26
59 46 0.51
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (57 bp):
AAACATATTTGTCTTAATTTAGAAAGAAAAATATTTTTTATCTTAATCTAGACAAGA
Found at i:4519940 original size:87 final size:88
Alignment explanation
Indices: 4519817--4519979 Score: 213
Period size: 87 Copynumber: 1.9 Consensus size: 88
4519807 AACATATTTG
* * * * * *
4519817 TCTTAATTTAGACAAAAAATATGTTTGGTTTTAATTTAGACACG-AAAATATGTTTGTCTTAATT
1 TCTTAATCTAGACAAAAAACATATTTGGTTTGAATTTAGACAAGAAAAATATGTTTATCTTAATT
* *
4519881 TAAGATAAGAAAAATATTTTTTA
66 AAACATAAGAAAAATATTTTTTA
*
4519904 TCTTAATCTAGACAAGAAAACATATTT-GTTTGAATTTAGACAAGATAAAATATTTTTATCTTAA
1 TCTTAATCTAGACAA-AAAACATATTTGGTTTGAATTTAGACAAGA-AAAATATGTTTATCTTAA
4519968 TTAAACATAAGA
64 TTAAACATAAGA
4519980 GTTATCTTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 29 0.45
88 9 0.14
89 26 0.41
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (88 bp):
TCTTAATCTAGACAAAAAACATATTTGGTTTGAATTTAGACAAGAAAAATATGTTTATCTTAATT
AAACATAAGAAAAATATTTTTTA
Found at i:4520142 original size:17 final size:17
Alignment explanation
Indices: 4520120--4520152 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4520110 ATAATAATAA
4520120 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
4520137 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
4520153 TTATCAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:4526954 original size:40 final size:39
Alignment explanation
Indices: 4526860--4527046 Score: 144
Period size: 36 Copynumber: 4.9 Consensus size: 39
4526850 ATAATGATTC
*
4526860 TAAATTGTGTGCTATTATAAAGAACACCCCACAAGGATCAA
1 TAAATTGTGTGCTATTATAAAGAGCACCCC-CAAGGAT-AA
* * *
4526901 -CAA----CTGCTATTATAAAGAGCACCCTCCAAAGATAA
1 TAAATTGTGTGCTATTATAAAGAGCACCC-CCAAGGATAA
* *
4526936 TAAATTGTGTGCTATTATAAAAAGCATCCCCAAGGAT--
1 TAAATTGTGTGCTATTATAAAGAGCACCCCCAAGGATAA
* *
4526973 TAACA---AGTGCTATTATAAAGAGCACCCTCTAAGGATAAA
1 TAA-ATTGTGTGCTATTATAAAGAGCACCC-CCAAGGAT-AA
* *
4527012 AAAATTGTGTACTATTATAATA-AGCACCCCCAAGG
1 TAAATTGTGTGCTATTATAA-AGAGCACCCCCAAGG
4527047 CTTGACAAGT
Statistics
Matches: 114, Mismatches: 17, Indels: 31
0.70 0.10 0.19
Matches are distributed among these distances:
35 21 0.18
36 34 0.30
37 4 0.04
38 2 0.02
39 9 0.08
40 25 0.22
41 18 0.16
42 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (39 bp):
TAAATTGTGTGCTATTATAAAGAGCACCCCCAAGGATAA
Found at i:4526988 original size:75 final size:76
Alignment explanation
Indices: 4526860--4527081 Score: 304
Period size: 76 Copynumber: 2.9 Consensus size: 76
4526850 ATAATGATTC
* *
4526860 TAAATTGTGTGCTATTATAAAGAA-CACCCCACAAGGATCAACAACTGCTATTATAAAGAGCACC
1 TAAATTGTGTGCTATTATAAA-AAGCACCCC-CAAGGATTAACAAGTGCTATTATAAAGAGCACC
4526924 CTCCAAAGAT-AA
64 CTCCAAAGATAAA
*
4526936 TAAATTGTGTGCTATTATAAAAAGCATCCCCAAGGATTAACAAGTGCTATTATAAAGAGCACCCT
1 TAAATTGTGTGCTATTATAAAAAGCACCCCCAAGGATTAACAAGTGCTATTATAAAGAGCACCCT
* *
4527001 CTAAGGATAAA
66 CCAAAGATAAA
* * * * * *
4527012 AAAATTGTGTACTATTATAATAAGCACCCCCAAGGCTTGACAAGTGCTATTATAAAAAGCACCCT
1 TAAATTGTGTGCTATTATAAAAAGCACCCCCAAGGATTAACAAGTGCTATTATAAAGAGCACCCT
*
4527077 TCAAA
66 CCAAA
4527082 TTGTTATCAA
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 41 0.32
76 88 0.68
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (76 bp):
TAAATTGTGTGCTATTATAAAAAGCACCCCCAAGGATTAACAAGTGCTATTATAAAGAGCACCCT
CCAAAGATAAA
Found at i:4527073 original size:35 final size:35
Alignment explanation
Indices: 4526868--4527075 Score: 159
Period size: 35 Copynumber: 5.6 Consensus size: 35
4526858 TCTAAATTGT
*
4526868 GTGCTATTATAAAGAA-CACCCCACAAGGATCAACAA
1 GTGCTATTATAAA-AAGCACCCC-CAAGGATTAACAA
* * * *
4526904 CTGCTATTATAAAGAGCACCCTCCAAAGATAATAA-ATTGT
1 GTGCTATTATAAAAAGCACCC-CCAAGGAT--TAACA---A
*
4526944 GTGCTATTATAAAAAGCATCCCCAAGGATTAACAA
1 GTGCTATTATAAAAAGCACCCCCAAGGATTAACAA
* * * *
4526979 GTGCTATTATAAAGAGCACCCTCTAAGGATAAAAAAA
1 GTGCTATTATAAAAAGCACCC-CCAAGGAT-TAACAA
* * *
4527016 TTGTGTACTATTATAATAAGCACCCCCAAGGCTTGACAA
1 --GTG--CTATTATAAAAAGCACCCCCAAGGATTAACAA
4527055 GTGCTATTATAAAAAGCACCC
1 GTGCTATTATAAAAAGCACCC
4527076 TTCAAATTGT
Statistics
Matches: 135, Mismatches: 23, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
35 37 0.27
36 30 0.22
37 12 0.09
38 3 0.02
39 13 0.10
40 24 0.18
41 16 0.12
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (35 bp):
GTGCTATTATAAAAAGCACCCCCAAGGATTAACAA
Found at i:4527914 original size:33 final size:34
Alignment explanation
Indices: 4527844--4527928 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
4527834 AGCAATACCA
*
4527844 ATTGCAATATACTTCTTCCAGGATTATAAGTCTT
1 ATTGCAATATACTTCTTCCAAGATTATAAGTCTT
*
4527878 ATTGCAATATACTTCTTTCAAGATTAT-AGTCTT
1 ATTGCAATATACTTCTTCCAAGATTATAAGTCTT
4527911 ATTGCAATATACTTCTTC
1 ATTGCAATATACTTCTTC
4527929 TAATGGTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 23 0.48
34 25 0.52
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (34 bp):
ATTGCAATATACTTCTTCCAAGATTATAAGTCTT
Found at i:4528830 original size:25 final size:25
Alignment explanation
Indices: 4528799--4528865 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
4528789 CAAGCAACAG
*
4528799 TGAAGTTCCTGATCAAGTCATCAAA
1 TGAAGTTCATGATCAAGTCATCAAA
* *
4528824 TGAAGTTCATGATCAAGTTATCAAG
1 TGAAGTTCATGATCAAGTCATCAAA
**
4528849 CAAAGTTCATGATCAAG
1 TGAAGTTCATGATCAAG
4528866 AATAAGTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (25 bp):
TGAAGTTCATGATCAAGTCATCAAA
Found at i:4528926 original size:54 final size:54
Alignment explanation
Indices: 4528842--4529004 Score: 168
Period size: 54 Copynumber: 3.0 Consensus size: 54
4528832 ATGATCAAGT
* ** *
4528842 TATCAAGCAAAGTTCATGATCAAGAATAAGTCATGAAGACCCTTGAAGCAGAGA
1 TATCAAGCATAGTTGGTGATCAAGATTAAGTCATGAAGACCCTTGAAGCAGAGA
* * * * *
4528896 TATCAAGCGTAGTTGGTGATTAAGATTAAGTCGTGAAGATCCTTGAAG-TGAAGA
1 TATCAAGCATAGTTGGTGATCAAGATTAAGTCATGAAGACCCTTGAAGCAG-AGA
* * * * *
4528950 TATCAAGCATAGTTTGTGATCAAAATTAAGTCGCT-AAGACTCTTGAAGCAAAGA
1 TATCAAGCATAGTTGGTGATCAAGATTAAGTC-ATGAAGACCCTTGAAGCAGAGA
4529004 T
1 T
4529005 CAAGTGAAGT
Statistics
Matches: 88, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
53 1 0.01
54 86 0.98
55 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.26
Consensus pattern (54 bp):
TATCAAGCATAGTTGGTGATCAAGATTAAGTCATGAAGACCCTTGAAGCAGAGA
Found at i:4529351 original size:2 final size:2
Alignment explanation
Indices: 4529344--4529382 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4529334 TAGTGGAGCT
*
4529344 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG 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
4529383 GCTACTTTTC
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4536565 original size:45 final size:45
Alignment explanation
Indices: 4536501--4536590 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
4536491 CCATCATCGG
*
4536501 GGTAATTGTATGTGGGTAAAAACAATATTTTCATGTACACAAACC
1 GGTAATTATATGTGGGTAAAAACAATATTTTCATGTACACAAACC
4536546 GGTAATTATATGTGGGTAAAAACAATATTTTCATGTACACAAACC
1 GGTAATTATATGTGGGTAAAAACAATATTTTCATGTACACAAACC
4536591 CTAGTATGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (45 bp):
GGTAATTATATGTGGGTAAAAACAATATTTTCATGTACACAAACC
Found at i:4539779 original size:13 final size:14
Alignment explanation
Indices: 4539733--4539777 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
4539723 TTTTTAACAT
4539733 TTTTATTGAAAATG
1 TTTTATTGAAAATG
4539747 TTTTATTAGAAAA-G
1 TTTTATT-GAAAATG
4539761 TTTTATTGAAAATG
1 TTTTATTGAAAATG
4539775 TTT
1 TTT
4539778 ATAAATACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.17
14 19 0.66
15 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (14 bp):
TTTTATTGAAAATG
Found at i:4544009 original size:34 final size:30
Alignment explanation
Indices: 4543935--4544013 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 30
4543925 AAGTTTGATG
* *
4543935 AATATTAATATTTAATTTAAATATTAAAAA
1 AATATTAATATTTAATTAAAAAATTAAAAA
* *
4543965 AATATGAATATTTAACTTCAAAAAATTAATTGAA
1 AATATTAATATTTAA-TT-AAAAAATTAA--AAA
4543999 AATATTAATATTTAA
1 AATATTAATATTTAA
4544014 ATTATACAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 14 0.35
31 2 0.05
32 8 0.20
34 16 0.40
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (30 bp):
AATATTAATATTTAATTAAAAAATTAAAAA
Found at i:4544174 original size:75 final size:75
Alignment explanation
Indices: 4544095--4544236 Score: 230
Period size: 75 Copynumber: 1.9 Consensus size: 75
4544085 ATAAATGGAA
* * *
4544095 TAAATCTTACTAATAATTATAATAAAATATATTTCAATGGTCATCATTTGATGAATACACATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAATACACATTTA
4544160 TATATAAGTT
66 TATATAAGTT
* * *
4544170 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATTATCATTTAATGAATATATATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAATACACATTTA
4544235 TA
66 TA
4544237 AGTATAGGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (75 bp):
TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAATACACATTTA
TATATAAGTT
Found at i:4547352 original size:3 final size:3
Alignment explanation
Indices: 4547346--4547372 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4547336 AAGATCTTCA
4547346 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
4547373 GAACGATGCT
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):
AAT
Found at i:4547806 original size:2 final size:2
Alignment explanation
Indices: 4547799--4547825 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4547789 TGCAAAGATT
4547799 GA 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 G
4547826 GTGATAGTTT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4547927 original size:2 final size:2
Alignment explanation
Indices: 4547920--4547947 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4547910 GAGAGTGTTT
4547920 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
4547948 AATTTTGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4554783 original size:21 final size:20
Alignment explanation
Indices: 4554759--4554798 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4554749 CCAGCAAAGG
4554759 ATAAAAGGAGAACTTCTCAAA
1 ATAAAAGGA-AACTTCTCAAA
**
4554780 ATAAAATTAAACTTCTCAA
1 ATAAAAGGAAACTTCTCAA
4554799 GAGTGGCAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (20 bp):
ATAAAAGGAAACTTCTCAAA
Found at i:4561253 original size:2 final size:2
Alignment explanation
Indices: 4561246--4561270 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4561236 ATATTCTTGA
4561246 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 A
4561271 GGCGCTGACC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4586767 original size:20 final size:20
Alignment explanation
Indices: 4586721--4586767 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
4586711 CACGAATGAT
* *
4586721 ACAACTAATATATGATTGAC
1 ACAATTAATATATGATTAAC
**
4586741 ATGATTAATATATGATTAAC
1 ACAATTAATATATGATTAAC
4586761 ACAATTA
1 ACAATTA
4586768 TAATACATTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.34
Consensus pattern (20 bp):
ACAATTAATATATGATTAAC
Found at i:4589651 original size:28 final size:28
Alignment explanation
Indices: 4589600--4589717 Score: 112
Period size: 28 Copynumber: 4.2 Consensus size: 28
4589590 AAAGGTAGTC
* ** * *
4589600 TTGAAACGCAAAAGGTTACACCTGATCG
1 TTGAAAGGCAAAAGGTTATGCCTAATCT
* * *
4589628 TTGAAAGGCAAAAGTTTATGCCTGATTT
1 TTGAAAGGCAAAAGGTTATGCCTAATCT
* * *
4589656 TTGGAAA-GCCAAAGGTTATGCTTAATCC
1 TT-GAAAGGCAAAAGGTTATGCCTAATCT
*
4589684 TTGAAAGGCAAGAGGTTATGCCTAATCT
1 TTGAAAGGCAAAAGGTTATGCCTAATCT
4589712 TTGAAA
1 TTGAAA
4589718 AGGCCAGGGT
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
27 4 0.06
28 64 0.89
29 4 0.06
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (28 bp):
TTGAAAGGCAAAAGGTTATGCCTAATCT
Found at i:4589703 original size:56 final size:56
Alignment explanation
Indices: 4589628--4589734 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
4589618 CACCTGATCG
* * * *
4589628 TTGAAAGGCAAAAGTTTATGCCTGATTTTTGGAAA-GCCAAAGGTTATGCTTAATCC
1 TTGAAAGGCAAAAGGTTATGCCTAATCTTTGAAAAGGCC-AAGGTTATGCTTAATCC
* *
4589684 TTGAAAGGCAAGAGGTTATGCCTAATCTTTGAAAAGGCCAGGGTTATGCTT
1 TTGAAAGGCAAAAGGTTATGCCTAATCTTTGAAAAGGCCAAGGTTATGCTT
4589735 GCTTTTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 41 0.93
57 3 0.07
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (56 bp):
TTGAAAGGCAAAAGGTTATGCCTAATCTTTGAAAAGGCCAAGGTTATGCTTAATCC
Found at i:4589728 original size:28 final size:27
Alignment explanation
Indices: 4589643--4589732 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
4589633 AGGCAAAAGT
* * *
4589643 TTATGCCTGATTTTTGGAAA-GCCAAAGG
1 TTATGCCTAATCTTT-GAAAGGCC-AGGG
* * *
4589671 TTATGCTTAATCCTTGAAAGGCAAGAGG
1 TTATGCCTAATCTTTGAAAGGCCAG-GG
4589699 TTATGCCTAATCTTTGAAAAGGCCAGGG
1 TTATGCCTAATCTTTG-AAAGGCCAGGG
4589727 TTATGC
1 TTATGC
4589733 TTGCTTTTGT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 5 0.10
28 37 0.74
29 8 0.16
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (27 bp):
TTATGCCTAATCTTTGAAAGGCCAGGG
Found at i:4597453 original size:61 final size:61
Alignment explanation
Indices: 4597358--4597482 Score: 232
Period size: 61 Copynumber: 2.0 Consensus size: 61
4597348 CAAGTTAAGT
4597358 ATTGGGAAAGCCATTCCCTAAAGCCTTTAACCCACCAACAATGTTTATAAATCTCTCAAAC
1 ATTGGGAAAGCCATTCCCTAAAGCCTTTAACCCACCAACAATGTTTATAAATCTCTCAAAC
* *
4597419 ATTGGGAAAGCCATTCCCTAAAGCCTTTAACCCACTAGCAATGTTTATAAATCTCTCAAAC
1 ATTGGGAAAGCCATTCCCTAAAGCCTTTAACCCACCAACAATGTTTATAAATCTCTCAAAC
4597480 ATT
1 ATT
4597483 TCATTTATGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.28
Consensus pattern (61 bp):
ATTGGGAAAGCCATTCCCTAAAGCCTTTAACCCACCAACAATGTTTATAAATCTCTCAAAC
Found at i:4604072 original size:36 final size:36
Alignment explanation
Indices: 4604025--4604120 Score: 122
Period size: 36 Copynumber: 2.7 Consensus size: 36
4604015 GCCAAATGCA
* *
4604025 GGGGTAAGAATACCACATGAATAT-TCTCTAGATATG
1 GGGGTAAGAATACCACATGAATATGGCTC-AAATATG
* **
4604061 GGGGTAAGAATATCACACAAATATGGCTCAAATATG
1 GGGGTAAGAATACCACATGAATATGGCTCAAATATG
*
4604097 GGGGTAAGAATGCCACATGAATAT
1 GGGGTAAGAATACCACATGAATAT
4604121 AGCTTATAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 47 0.94
37 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (36 bp):
GGGGTAAGAATACCACATGAATATGGCTCAAATATG
Found at i:4611444 original size:7 final size:7
Alignment explanation
Indices: 4611432--4611464 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
4611422 ATAACTTATC
4611432 ATTTTAA
1 ATTTTAA
4611439 ATTTTAA
1 ATTTTAA
4611446 ATTTTAA
1 ATTTTAA
4611453 ATTATT-A
1 ATT-TTAA
4611460 ATTTT
1 ATTTT
4611465 TTAATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 2 0.08
7 21 0.84
8 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTTTAA
Found at i:4614729 original size:2 final size:2
Alignment explanation
Indices: 4614716--4614755 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
4614706 CACATAACTG
* *
4614716 TC TC TC TT TC TC TC TT 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 TC TC TC TC TC TC TC
4614756 CATAGGTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:4616462 original size:29 final size:29
Alignment explanation
Indices: 4616427--4616520 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
4616417 TTTTGAAGTG
**
4616427 AAGATCAAGCGGCAATAAAGTTAGTGATC
1 AAGATCAAGCGGCAGCAAAGTTAGTGATC
* * *
4616456 AAGATCAATCGGTAGCAAAGTTGGTGATC
1 AAGATCAAGCGGCAGCAAAGTTAGTGATC
* *
4616485 AAGATATCAAGCGGCAGCGAAGTTTGTGATC
1 AAG--ATCAAGCGGCAGCAAAGTTAGTGATC
4616516 AAGAT
1 AAGAT
4616521 ATCAAGTAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 29 0.54
31 25 0.46
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (29 bp):
AAGATCAAGCGGCAGCAAAGTTAGTGATC
Found at i:4616508 original size:31 final size:31
Alignment explanation
Indices: 4616430--4616526 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
4616420 TGAAGTGAAG
**
4616430 ATCAAGCGGCAATAAAGTTAGTGATCAAG--
1 ATCAAGCGGCAGCAAAGTTAGTGATCAAGAT
* * *
4616459 ATCAATCGGTAGCAAAGTTGGTGATCAAGAT
1 ATCAAGCGGCAGCAAAGTTAGTGATCAAGAT
* *
4616490 ATCAAGCGGCAGCGAAGTTTGTGATCAAGAT
1 ATCAAGCGGCAGCAAAGTTAGTGATCAAGAT
4616521 ATCAAG
1 ATCAAG
4616527 TAGTAGCGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 24 0.42
31 33 0.58
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (31 bp):
ATCAAGCGGCAGCAAAGTTAGTGATCAAGAT
Found at i:4616535 original size:31 final size:31
Alignment explanation
Indices: 4616444--4616536 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 31
4616434 AGCGGCAATA
* * * *
4616444 AAGTTAGTGATCAAG--ATCAATCGGTAGCA
1 AAGTTGGTGATCAAGATATCAAGCAGTAGCG
* *
4616473 AAGTTGGTGATCAAGATATCAAGCGGCAGCG
1 AAGTTGGTGATCAAGATATCAAGCAGTAGCG
* *
4616504 AAGTTTGTGATCAAGATATCAAGTAGTAGCG
1 AAGTTGGTGATCAAGATATCAAGCAGTAGCG
4616535 AA
1 AA
4616537 CTTCATAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
29 14 0.26
31 40 0.74
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.24
Consensus pattern (31 bp):
AAGTTGGTGATCAAGATATCAAGCAGTAGCG
Found at i:4616588 original size:46 final size:46
Alignment explanation
Indices: 4616499--4616588 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
4616489 TATCAAGCGG
* * * *
4616499 CAGCGAAGTTTGTGATCAAGATATCAAGTAGTAGCGAACTTCATAA
1 CAGCAAAGTTTGTGATCAAGATATCAAGGAGCAACGAACTTCATAA
*
4616545 CAGCAAAGTTTGTGATCAAGATATCAAGCGA-CAACGAAGTTCAT
1 CAGCAAAGTTTGTGATCAAGATATCAAG-GAGCAACGAACTTCAT
4616589 GATCAAGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
46 37 0.97
47 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (46 bp):
CAGCAAAGTTTGTGATCAAGATATCAAGGAGCAACGAACTTCATAA
Found at i:4616733 original size:54 final size:54
Alignment explanation
Indices: 4616610--4616716 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 54
4616600 CAAAAGCTCG
** *
4616610 TGAGCAAGATTAAGTCATGAAGACCCTTGAAGCAAATATATCAAGTATAGTTCC
1 TGAGCAAGATTAAGTCACCAAGACCCTTGAAGCAAAGATATCAAGTATAGTTCC
* ** *
4616664 TGAGCAAGATTAAGTCACCAAGACTCTTGAAGTGAAGATATCAAGTTTAGTTC
1 TGAGCAAGATTAAGTCACCAAGACCCTTGAAGCAAAGATATCAAGTATAGTTC
4616717 TTGATTAAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (54 bp):
TGAGCAAGATTAAGTCACCAAGACCCTTGAAGCAAAGATATCAAGTATAGTTCC
Found at i:4635809 original size:19 final size:19
Alignment explanation
Indices: 4635785--4635840 Score: 112
Period size: 19 Copynumber: 2.9 Consensus size: 19
4635775 TTGCCTAACT
4635785 AATTTTTAAGTAAGCTTCC
1 AATTTTTAAGTAAGCTTCC
4635804 AATTTTTAAGTAAGCTTCC
1 AATTTTTAAGTAAGCTTCC
4635823 AATTTTTAAGTAAGCTTC
1 AATTTTTAAGTAAGCTTC
4635841 TAAGAAGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (19 bp):
AATTTTTAAGTAAGCTTCC
Found at i:4641163 original size:139 final size:139
Alignment explanation
Indices: 4640913--4641172 Score: 387
Period size: 139 Copynumber: 1.9 Consensus size: 139
4640903 TATAAGCATG
* * * * *
4640913 ATATTTCAAATCATTTTATTTTCCAACTTTACAAATCGATTAATTTCTATCTATTATTTAGTCAA
1 ATATTTCAAATCATTTAATTTTCCAACTTTACAAATAGATTAATTTCTATCTACTATTCAATCAA
* * *
4640978 ATAGATATAGTACAATCAGTGCAAACAGTAACTAACAATTCAGTAATATTTGGTAAATAAATGCT
66 ACAGATATAGTACAATCAGTGCAAACAGCAACTAACAATTCAGTAATATTTAGTAAATAAATGCT
4641043 ACAACAGAT
131 ACAACAGAT
* *
4641052 ATATTTCAAATCATTTAATTTTCCAACTTTGCAGACTAG-TTAATTTCTATCTACTATTCAATCA
1 ATATTTCAAATCATTTAATTTTCCAACTTTACA-AATAGATTAATTTCTATCTACTATTCAATCA
* * *
4641116 AACAGATATAGTAGAATCAGTGCAGACAGCAAGTAACAATTCAGTAATATTTAGTAA
65 AACAGATATAGTACAATCAGTGCAAACAGCAACTAACAATTCAGTAATATTTAGTAA
4641173 CTACATACTA
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
139 104 0.97
140 3 0.03
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.36
Consensus pattern (139 bp):
ATATTTCAAATCATTTAATTTTCCAACTTTACAAATAGATTAATTTCTATCTACTATTCAATCAA
ACAGATATAGTACAATCAGTGCAAACAGCAACTAACAATTCAGTAATATTTAGTAAATAAATGCT
ACAACAGAT
Found at i:4655911 original size:15 final size:16
Alignment explanation
Indices: 4655883--4655919 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
4655873 ACCCGAGAGG
4655883 AAGAAAAGAGAAAGAA
1 AAGAAAAGAGAAAGAA
4655899 AAGAAAA-AGAAAGAA
1 AAGAAAAGAGAAAGAA
*
4655914 AGGAAA
1 AAGAAA
4655920 TGGAGGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAGAAAGAA
Found at i:4657499 original size:28 final size:27
Alignment explanation
Indices: 4657468--4657523 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 27
4657458 AGGCCACAGT
*
4657468 TTGTGATTATACATGACAAGGCCATGAG
1 TTGTG-TTATACATGACAAGGCCAAGAG
* *
4657496 -T-TGTTATACGTGGCAAGGCCAAGAG
1 TTGTGTTATACATGACAAGGCCAAGAG
4657521 TTG
1 TTG
4657524 ATATATATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
25 19 0.83
26 3 0.13
27 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (27 bp):
TTGTGTTATACATGACAAGGCCAAGAG
Found at i:4657512 original size:25 final size:25
Alignment explanation
Indices: 4657474--4657528 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
4657464 CAGTTTGTGA
*
4657474 TTATACATGACAAGGCCATGAGTTG
1 TTATACATGACAAGGCCAAGAGTTG
* *
4657499 TTATACGTGGCAAGGCCAAGAGTTG
1 TTATACATGACAAGGCCAAGAGTTG
*
4657524 ATATA
1 TTATA
4657529 TATGGTTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (25 bp):
TTATACATGACAAGGCCAAGAGTTG
Found at i:4661275 original size:32 final size:32
Alignment explanation
Indices: 4661198--4661276 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 32
4661188 TTTTCTCGAT
* *
4661198 CTACCAGGTCATCATGCAAGTACCACGTGGCA
1 CTACCACGTCATCATGCAAGTACCACGTGACA
* ** * * *
4661230 TTACCACCCCATCATGCAAGTGCTATGTGACA
1 CTACCACGTCATCATGCAAGTACCACGTGACA
4661262 CTACCACGTCATCAT
1 CTACCACGTCATCAT
4661277 ATCAGAGAGA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (32 bp):
CTACCACGTCATCATGCAAGTACCACGTGACA
Found at i:4673969 original size:12 final size:12
Alignment explanation
Indices: 4673952--4673980 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4673942 CAATTTGGTG
4673952 TTTTTTT-CTTT
1 TTTTTTTCCTTT
4673963 TTTTTTTCCTTT
1 TTTTTTTCCTTT
4673975 TTTTTT
1 TTTTTT
4673981 AAAAAGTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTCCTTT
Found at i:4681020 original size:13 final size:13
Alignment explanation
Indices: 4681002--4681026 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4680992 AACGATGCTT
4681002 AATGATGCTTGAG
1 AATGATGCTTGAG
4681015 AATGATGCTTGA
1 AATGATGCTTGA
4681027 TGACTAATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (13 bp):
AATGATGCTTGAG
Found at i:4682457 original size:21 final size:21
Alignment explanation
Indices: 4682428--4682514 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
4682418 TCAAAATTGC
4682428 TTTAATGATCTTTGAACTTGT
1 TTTAATGATCTTTGAACTTGT
* *
4682449 TTTAGTGATCCTTGAACTTGT
1 TTTAATGATCTTTGAACTTGT
* * *
4682470 TTGAATGATTTTTGAAGTTGT
1 TTTAATGATCTTTGAACTTGT
* * *
4682491 TTAAATAAGTTTTTGAACTTGT
1 TTTAATGA-TCTTTGAACTTGT
4682513 TT
1 TT
4682515 GAATAGTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 41 0.75
22 14 0.25
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (21 bp):
TTTAATGATCTTTGAACTTGT
Done.