Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 20 of 22
Found at i:3372777 original size:33 final size:32
Alignment explanation
Indices: 3372731--3372816 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 32
3372721 GATTTTATAT
*
3372731 TTATATA-AATTTTATTATAT-AAATTATTCATA
1 TTATATATATTTTTATTAT-TCAAA-TATTCATA
* *
3372763 TTATATATATTTTTAATTATTCAAATATTTATT
1 TTATATATATTTTT-ATTATTCAAATATTCATA
*
3372796 TTATATCATATTTTAATTATT
1 TTATAT-ATATTTTTATTATT
3372817 TTTTATATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
32 7 0.15
33 24 0.52
34 15 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (32 bp):
TTATATATATTTTTATTATTCAAATATTCATA
Found at i:3372807 original size:12 final size:12
Alignment explanation
Indices: 3372787--3372853 Score: 75
Period size: 12 Copynumber: 5.6 Consensus size: 12
3372777 AATTATTCAA
3372787 ATATT-TATTTT
1 ATATTATATTTT
*
3372798 ATATCATATTTT
1 ATATTATATTTT
*
3372810 A-ATTATTTTTT
1 ATATTATATTTT
3372821 ATATTATATTTAT
1 ATATTATATTT-T
*
3372834 ATAATTATATTTA
1 AT-ATTATATTTT
3372847 ATATTAT
1 ATATTAT
3372854 TAATTCTACA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
11 13 0.28
12 20 0.43
13 5 0.11
14 9 0.19
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:3373690 original size:2 final size:2
Alignment explanation
Indices: 3373685--3373720 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3373675 ACACGCACGT
3373685 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3373721 GCTTGGAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3374856 original size:19 final size:19
Alignment explanation
Indices: 3374824--3374871 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
3374814 TCACAATATC
* *
3374824 AATAATAAAAAGTG-TTAA
1 AATATTAAATAGTGATTAA
*
3374842 AATTATTAAATAGTGATTAT
1 AA-TATTAAATAGTGATTAA
3374862 AATATTAAAT
1 AATATTAAAT
3374872 TACGACTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 18 0.72
20 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (19 bp):
AATATTAAATAGTGATTAA
Found at i:3375350 original size:2 final size:2
Alignment explanation
Indices: 3375343--3375378 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3375333 GAGTGTTTAA
3375343 AT AT 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 AT AT
3375379 TGTTGTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3376517 original size:25 final size:25
Alignment explanation
Indices: 3376489--3376538 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3376479 AGATAAATCA
*
3376489 TAAATCATTAATTATAATAAAATTT
1 TAAATCATTAATTACAATAAAATTT
3376514 TAAATCATTAATTACAATAAAATTT
1 TAAATCATTAATTACAATAAAATTT
3376539 ATTCTTTTGG
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:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (25 bp):
TAAATCATTAATTACAATAAAATTT
Found at i:3376936 original size:16 final size:16
Alignment explanation
Indices: 3376914--3376948 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3376904 TTGTCGATTG
*
3376914 ATTTTTTTT-TTTATA
1 ATTTTTTTTGTTTTTA
3376929 ATTTTTTTTGTTTTTA
1 ATTTTTTTTGTTTTTA
3376945 ATTT
1 ATTT
3376949 ATAGATCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (16 bp):
ATTTTTTTTGTTTTTA
Found at i:3377696 original size:6 final size:7
Alignment explanation
Indices: 3377661--3377695 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
3377651 AGAAAAGTTA
*
3377661 TAAATGT
1 TAAATTT
*
3377668 TAAAATT
1 TAAATTT
3377675 TAAATTT
1 TAAATTT
3377682 TAAATTT
1 TAAATTT
3377689 TAAATTT
1 TAAATTT
3377696 ATTGGGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (7 bp):
TAAATTT
Found at i:3380216 original size:2 final size:2
Alignment explanation
Indices: 3380211--3380249 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3380201 TAAACGAATT
* * *
3380211 TA TA TA TA TA AA TA TA TA TA TA TA TT TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3380250 TGTGGATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:3380551 original size:9 final size:8
Alignment explanation
Indices: 3380517--3380554 Score: 67
Period size: 8 Copynumber: 4.6 Consensus size: 8
3380507 AAATCAAAGA
3380517 TGGGCACT
1 TGGGCACT
3380525 TGGGCACT
1 TGGGCACT
3380533 TGGGCACT
1 TGGGCACT
3380541 TGGGCCACT
1 TGGG-CACT
3380550 TGGGC
1 TGGGC
3380555 TTAAATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.11, C:0.26, G:0.39, T:0.24
Consensus pattern (8 bp):
TGGGCACT
Found at i:3380593 original size:18 final size:18
Alignment explanation
Indices: 3380570--3380604 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3380560 TTAAAGATGC
*
3380570 AATTATATTTTTTATTTT
1 AATTATATTATTTATTTT
3380588 AATTATATTATTTATTT
1 AATTATATTATTTATTT
3380605 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:3380617 original size:18 final size:21
Alignment explanation
Indices: 3380573--3380619 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3380563 AAGATGCAAT
3380573 TATATTT-TTTATTTTAATTA
1 TATATTTATTTATTTTAATTA
3380593 TATTATTTATTTA-TTT-ATTA
1 TA-TATTTATTTATTTTAATTA
3380613 -ATATTTA
1 TATATTTA
3380620 ATTCGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.24
19 1 0.04
20 6 0.24
21 8 0.32
22 4 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATATTTATTTATTTTAATTA
Found at i:3382631 original size:2 final size:2
Alignment explanation
Indices: 3382614--3382663 Score: 84
Period size: 2 Copynumber: 25.0 Consensus size: 2
3382604 ACACATATGA
3382614 AT AT A- AT AT CAT 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 AT AT AT AT AT
3382656 AT AT AT AT
1 AT AT AT AT
3382664 GAGCAATACT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.93
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3384334 original size:26 final size:25
Alignment explanation
Indices: 3384300--3384394 Score: 77
Period size: 29 Copynumber: 3.7 Consensus size: 25
3384290 TTTATTTTTT
*
3384300 TATTATAATTA-TAAATATAA-AAA
1 TATTATAATAATTAAATATAATAAA
*
3384323 TATTATAATAATTAATTATAATAAA
1 TATTATAATAATTAAATATAATAAA
* * *
3384348 TATTAATTATAAATATTAATAATAATAAT
1 TATT-ATAAT-AAT-TAAAT-ATAATAAA
* *
3384377 TATTAAAATTATTAAATA
1 TATTATAATAATTAAATA
3384395 ATAACTGTCT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
23 10 0.18
24 8 0.14
25 8 0.14
26 8 0.14
27 5 0.09
28 6 0.11
29 11 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TATTATAATAATTAAATATAATAAA
Found at i:3384342 original size:13 final size:13
Alignment explanation
Indices: 3384324--3384391 Score: 59
Period size: 13 Copynumber: 5.1 Consensus size: 13
3384314 ATATAAAAAT
3384324 ATTATAATAATTA
1 ATTATAATAATTA
3384337 ATTATAATAAATATTA
1 ATTATAAT--A-ATTA
3384353 ATTATAA-ATATTA
1 ATTATAATA-ATTA
*
3384366 ATAATAATAATT-
1 ATTATAATAATTA
* *
3384378 ATTAAAATTATTA
1 ATTATAATAATTA
3384391 A
1 A
3384392 ATAATAACTG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
12 9 0.20
13 24 0.52
14 1 0.02
15 1 0.02
16 11 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTATAATAATTA
Found at i:3384346 original size:16 final size:16
Alignment explanation
Indices: 3384327--3384382 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
3384317 TAAAAATATT
3384327 ATAATAATTAATTATA
1 ATAATAATTAATTATA
3384343 ATAA-ATATTAATTAT-
1 ATAATA-ATTAATTATA
*
3384358 A-AAT-ATTAATAATA
1 ATAATAATTAATTATA
*
3384372 ATAATTATTAA
1 ATAATAATTAA
3384383 AATTATTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 8 0.24
14 3 0.09
15 5 0.15
16 18 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAATAATTAATTATA
Found at i:3384357 original size:29 final size:29
Alignment explanation
Indices: 3384324--3384382 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
3384314 ATATAAAAAT
*
3384324 ATTAT-AATAATTAATTATAATAAATATTA
1 ATTATAAAT-ATTAATAATAATAAATATTA
*
3384353 ATTATAAATATTAATAATAATAATTATTA
1 ATTATAAATATTAATAATAATAAATATTA
3384382 A
1 A
3384383 AATTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATTATAAATATTAATAATAATAAATATTA
Found at i:3384586 original size:2 final size:2
Alignment explanation
Indices: 3384579--3384612 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3384569 GCTTTCCTTT
3384579 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3384613 GAGTTACTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3387889 original size:3 final size:3
Alignment explanation
Indices: 3387876--3387916 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3387866 GAGTTTGGAG
*
3387876 TCA TTA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
3387917 TTACTTCTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:3389711 original size:2 final size:2
Alignment explanation
Indices: 3389706--3389734 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3389696 TACACACATT
3389706 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3389735 TATTTATGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3389782 original size:43 final size:44
Alignment explanation
Indices: 3389721--3389806 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 44
3389711 ATATATATAT
3389721 ATATATATATATATTATTTATGGTATCTTAACTGCC-TTCCTAC
1 ATATATATATATATTATTTATGGTATCTTAACTGCCTTTCCTAC
*
3389764 ATATATATATATATTATTTATGGTATCTTAATTGCCTTTCCTA
1 ATATATATATATATTATTTATGGTATCTTAACTGCCTTTCCTA
3389807 ACCTAACTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 35 0.85
44 6 0.15
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (44 bp):
ATATATATATATATTATTTATGGTATCTTAACTGCCTTTCCTAC
Found at i:3390341 original size:2 final size:2
Alignment explanation
Indices: 3390334--3390368 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3390324 CCAAATCTTA
3390334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3390369 CCCAAAGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3393162 original size:14 final size:14
Alignment explanation
Indices: 3393143--3393169 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3393133 CTATGCAATG
3393143 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
3393157 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
3393170 AATCAATTTT
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:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:3393435 original size:22 final size:23
Alignment explanation
Indices: 3393405--3393448 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
3393395 ATTACTGAAG
*
3393405 TTAATAATTCATTATTTTATAAA
1 TTAATAATTCAGTATTTTATAAA
3393428 TTAA-AATTCAGTATTTTATAA
1 TTAATAATTCAGTATTTTATAA
3393449 TTCTAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAATAATTCAGTATTTTATAAA
Found at i:3402389 original size:2 final size:2
Alignment explanation
Indices: 3402382--3402412 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3402372 AATGGTCTTA
3402382 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3402413 AAAAAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3402931 original size:2 final size:2
Alignment explanation
Indices: 3402924--3402956 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3402914 GAATCACATT
*
3402924 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3402957 CATTATATCA
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:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3403589 original size:12 final size:12
Alignment explanation
Indices: 3403572--3403606 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3403562 ACAAAGGGGA
3403572 GAGCCTGTGCCT
1 GAGCCTGTGCCT
*
3403584 GAGCCTGAGCCT
1 GAGCCTGTGCCT
*
3403596 GAGCTTGTGCC
1 GAGCCTGTGCC
3403607 CCTGAGGAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.11, C:0.31, G:0.34, T:0.23
Consensus pattern (12 bp):
GAGCCTGTGCCT
Found at i:3405008 original size:10 final size:10
Alignment explanation
Indices: 3404993--3405111 Score: 54
Period size: 10 Copynumber: 11.7 Consensus size: 10
3404983 ATTTTATTAC
3404993 TTAAATTATA
1 TTAAATTATA
*
3405003 TTAAATTATT
1 TTAAATTATA
3405013 TTAAATTCATA
1 TTAAATT-ATA
*
3405024 TT-TA-TATA
1 TTAAATTATA
3405032 TT---TTATAA
1 TTAAATTAT-A
*
3405040 TTAAATTTTA
1 TTAAATTATA
*
3405050 ATAATTTATTATCA
1 TTAA---ATTAT-A
*
3405064 TTAAATAATAA
1 TTAAATTAT-A
3405075 TTAAAATTATA
1 TT-AAATTATA
*
3405086 TTATATTA-A
1 TTAAATTATA
3405095 TTCAAATTA-A
1 TT-AAATTATA
3405105 TTAAATT
1 TTAAATT
3405112 TAAAATTTAT
Statistics
Matches: 85, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.04
8 8 0.09
9 9 0.11
10 34 0.40
11 17 0.20
12 6 0.07
13 4 0.05
14 4 0.05
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (10 bp):
TTAAATTATA
Found at i:3405033 original size:21 final size:20
Alignment explanation
Indices: 3404993--3405111 Score: 59
Period size: 21 Copynumber: 5.8 Consensus size: 20
3404983 ATTTTATTAC
3404993 TTAAATTATATTAAATTATT
1 TTAAATTATATTAAATTATT
*
3405013 TTAAATTCATATT-TATATATT
1 TTAAATT-ATATTAAAT-TATT
* * *
3405034 TTATAATTAAATTTTAA-TAAT
1 TTA-AATTATA-TTAAATTATT
*
3405055 TT--ATTATCATTAAATAATAAT
1 TTAAATTAT-ATTAAAT--TATT
* * *
3405076 TAAAATTATATTATATTAAT
1 TTAAATTATATTAAATTATT
*
3405096 TCAAATTA-ATTAAATT
1 TTAAATTATATTAAATT
3405112 TAAAATTTAT
Statistics
Matches: 78, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
18 8 0.10
19 8 0.10
20 20 0.26
21 24 0.31
22 12 0.15
23 6 0.08
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAATTATATTAAATTATT
Found at i:3405123 original size:30 final size:31
Alignment explanation
Indices: 3405035--3405125 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 31
3405025 TTATATATTT
3405035 TATAATTAAATTTTAATAATTTATTATCATTAAA
1 TATAATTAAA-TTTAA-AATTTATTA-CATTAAA
* *
3405069 TAATAATTAAAATT-ATATTATATTA-ATTCAAA
1 T-ATAATTAAATTTAAAATT-TATTACATT-AAA
3405101 T-TAATTAAATTTAAAATTTATTACA
1 TATAATTAAATTTAAAATTTATTACA
3405126 AACAGGTGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
30 15 0.31
31 8 0.17
32 7 0.15
33 6 0.12
34 3 0.06
35 9 0.19
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (31 bp):
TATAATTAAATTTAAAATTTATTACATTAAA
Found at i:3405938 original size:41 final size:40
Alignment explanation
Indices: 3405893--3405969 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
3405883 TTAAATTAAA
*
3405893 TTAAA-TTAATTAATTAATTATATAATA-AAAAATATTTTTAT
1 TTAAATTTAATT-A-TAAATAT-TAATATAAAAATATTTTTAT
3405934 TTAAATTTAATTATAAATATTAATATAAAAATATTT
1 TTAAATTTAATTATAAATATTAATATAAAAATATTT
3405970 ATAAATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
39 5 0.15
40 16 0.48
41 6 0.18
42 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (40 bp):
TTAAATTTAATTATAAATATTAATATAAAAATATTTTTAT
Found at i:3406472 original size:15 final size:15
Alignment explanation
Indices: 3406429--3406478 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
3406419 TTATTTTAAA
*
3406429 AATATTTATTAAATTT
1 AATATTTA-TAATTTT
*
3406445 AA-ATTTAT-TTTTT
1 AATATTTATAATTTT
3406458 AATATTTATAATTTT
1 AATATTTATAATTTT
*
3406473 TATATT
1 AATATT
3406479 AAAATATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 14 0.50
16 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATATTTATAATTTT
Found at i:3407212 original size:18 final size:18
Alignment explanation
Indices: 3407178--3407215 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3407168 TTATTTATAT
*
3407178 TTTAAATTATTAATTTAA
1 TTTAAATTATAAATTTAA
*
3407196 TTTAAATT-TAAATTTTA
1 TTTAAATTATAAATTTAA
3407213 TTT
1 TTT
3407216 TTGTTAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATTATAAATTTAA
Found at i:3407483 original size:20 final size:19
Alignment explanation
Indices: 3407458--3407510 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
3407448 TAATTATATT
3407458 TAAAATATATTATATTTATA
1 TAAAATATATTATATTTA-A
* *
3407478 TAAAATTTAATATA-TTAA
1 TAAAATATATTATATTTAA
**
3407496 TAATTTATATTATAT
1 TAAAATATATTATAT
3407511 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 11 0.42
19 3 0.12
20 12 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAATATATTATATTTAA
Found at i:3407505 original size:33 final size:34
Alignment explanation
Indices: 3407461--3407543 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 34
3407451 TTATATTTAA
3407461 AATATA-TTATATTTATATAAAA-TTTAATATATT
1 AATATATTTATATTTATATAAAATTTTAA-ATATT
3407494 AATA-ATTTATA-TTATATAAAATTTTAAATATT
1 AATATATTTATATTTATATAAAATTTTAAATATT
*
3407526 TATATATTTAT-TTTATAT
1 AATATATTTATATTTATAT
3407544 TCGTATAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
32 19 0.42
33 26 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
AATATATTTATATTTATATAAAATTTTAAATATT
Found at i:3407511 original size:20 final size:17
Alignment explanation
Indices: 3407450--3407510 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 17
3407440 ATAATTTATA
3407450 ATTATATTTAA-AATAT
1 ATTATATTTAATAATAT
*
3407466 ATTATATTTATATAAAAT
1 ATTATATTTA-ATAATAT
3407484 -TTAATATATTAATAATTTAT
1 ATT-ATAT-TTAATAA--TAT
3407504 ATTATAT
1 ATTATAT
3407511 AAAATTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
16 10 0.28
17 3 0.08
18 12 0.33
19 3 0.08
20 6 0.17
21 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTATATTTAATAATAT
Found at i:3407511 original size:32 final size:33
Alignment explanation
Indices: 3407425--3407543 Score: 109
Period size: 33 Copynumber: 3.5 Consensus size: 33
3407415 TTGTGTTTGA
* *
3407425 ATATTT-TATTATAATATAATTTATAATTATATTTAAA
1 ATATTTATATTAT-ATAAAATTT-TAA--ATA-TTAAT
3407462 ATATATTATATTTATATAAAA-TTTAATATATTAAT
1 ATAT-TTATA-TTATATAAAATTTTAA-ATATTAAT
*
3407497 A-ATTTATATTATATAAAATTTTAAATATTTAT
1 ATATTTATATTATATAAAATTTTAAATATTAAT
*
3407529 ATATTTATTTTATAT
1 ATATTTATATTATAT
3407544 TCGTATAACA
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
32 18 0.25
33 22 0.30
34 2 0.03
35 5 0.07
36 4 0.05
37 7 0.10
38 4 0.05
39 7 0.10
40 4 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
ATATTTATATTATATAAAATTTTAAATATTAAT
Found at i:3407516 original size:16 final size:16
Alignment explanation
Indices: 3407427--3407517 Score: 62
Period size: 16 Copynumber: 5.2 Consensus size: 16
3407417 GTGTTTGAAT
*
3407427 ATTT-TATTATAATATA
1 ATTTATATTAT-ATAAA
3407443 ATTTATAATTATATTTAAAA
1 ATTTAT-ATTATA--T-AAA
3407463 TATATTATATTTATATAAA
1 -AT-TTATA-TTATATAAA
3407482 ATTTA-A-TATATTAATA
1 ATTTATATTATA-TAA-A
3407498 ATTTATATTATATAAA
1 ATTTATATTATATAAA
3407514 ATTT
1 ATTT
3407518 TAAATATTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 24
0.71 0.01 0.28
Matches are distributed among these distances:
14 4 0.06
15 3 0.05
16 16 0.26
17 9 0.15
18 11 0.18
19 4 0.06
20 3 0.05
21 3 0.05
22 9 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATATTATATAAA
Found at i:3407715 original size:17 final size:15
Alignment explanation
Indices: 3407673--3407715 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3407663 AAACATATCA
*
3407673 TAATTTTAATTATTT
1 TAATTTTATTTATTT
*
3407688 TAATATTATTTATCTT
1 TAATTTTATTTAT-TT
3407704 TACATTTTATTT
1 TA-ATTTTATTT
3407716 TATTATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 11 0.48
16 4 0.17
17 8 0.35
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (15 bp):
TAATTTTATTTATTT
Found at i:3408434 original size:20 final size:21
Alignment explanation
Indices: 3408398--3408436 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3408388 AAATATATAT
3408398 AATAAATGAAAAAATTTTAAA
1 AATAAATGAAAAAATTTTAAA
*
3408419 AATAAAT-AATAAATTTTA
1 AATAAATGAAAAAATTTTA
3408437 TGATTGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AATAAATGAAAAAATTTTAAA
Found at i:3408762 original size:18 final size:18
Alignment explanation
Indices: 3408739--3408773 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3408729 ATTATGTATC
*
3408739 AAATAATATTAATTTAAT
1 AAATAAAATTAATTTAAT
*
3408757 AAATAAAATTATTTTAA
1 AAATAAAATTAATTTAA
3408774 AATTTAAAAT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAAAATTAATTTAAT
Found at i:3409672 original size:19 final size:18
Alignment explanation
Indices: 3409638--3409673 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3409628 ATTTAAAAAT
*
3409638 AAATTATAATTAATATAA
1 AAATTATAAATAATATAA
3409656 AAATTATGAAATAATATA
1 AAATTAT-AAATAATATA
3409674 TATTATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAATTATAAATAATATAA
Found at i:3410966 original size:12 final size:12
Alignment explanation
Indices: 3410950--3411020 Score: 97
Period size: 12 Copynumber: 5.7 Consensus size: 12
3410940 GACGATGATT
3410950 ATGATGAGTTTG
1 ATGATGAGTTTG
*
3410962 GTGATGAGTTTG
1 ATGATGAGTTTG
*
3410974 ATGATGAATTTG
1 ATGATGAGTTTG
3410986 ATGATGAGTTTGAAG
1 ATGATGAGTTT---G
3411001 ATGATGAGTTTG
1 ATGATGAGTTTG
3411013 ATGATGAG
1 ATGATGAG
3411021 GAGGAATTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
12 40 0.77
15 12 0.23
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (12 bp):
ATGATGAGTTTG
Found at i:3410992 original size:15 final size:14
Alignment explanation
Indices: 3410928--3411019 Score: 64
Period size: 12 Copynumber: 7.4 Consensus size: 14
3410918 AGATGGAAGC
3410928 GATGATGA-TT-AT
1 GATGATGATTTGAT
*
3410940 GACGATGA-TT-AT
1 GATGATGATTTGAT
*
3410952 GATGA-G-TTTGGT
1 GATGATGATTTGAT
3410964 GATGA-G-TTTGAT
1 GATGATGATTTGAT
3410976 GATGA--ATTTGAT
1 GATGATGATTTGAT
*
3410988 GATGA-G-TTTGAA
1 GATGATGATTTGAT
3411000 GATGATGAGTTTGAT
1 GATGATGA-TTTGAT
3411015 GATGA
1 GATGA
3411020 GGAGGAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
11 3 0.04
12 53 0.79
13 1 0.01
15 10 0.15
ACGTcount: A:0.29, C:0.01, G:0.32, T:0.38
Consensus pattern (14 bp):
GATGATGATTTGAT
Found at i:3415563 original size:2 final size:2
Alignment explanation
Indices: 3415556--3415596 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3415546 ATGTGATTCT
3415556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3415597 TCCTGTATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3428565 original size:61 final size:61
Alignment explanation
Indices: 3428499--3428620 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
3428489 GTAACTATAG
*
3428499 CATGCAATCACGATAAAAGAAAATAGAAAAGTTTTTACACATAATTTTTTGGTTTACCCAA
1 CATGCAATCACGATAAAAGAAAATAGAAAAGTTTGTACACATAATTTTTTGGTTTACCCAA
* *
3428560 CATGCAATCATGATAAAAGAAAATAGAAAAGTTTGTACATATAATTTTTTGGTTTACCCAA
1 CATGCAATCACGATAAAAGAAAATAGAAAAGTTTGTACACATAATTTTTTGGTTTACCCAA
3428621 GTTTCCAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (61 bp):
CATGCAATCACGATAAAAGAAAATAGAAAAGTTTGTACACATAATTTTTTGGTTTACCCAA
Found at i:3429881 original size:117 final size:118
Alignment explanation
Indices: 3429675--3429914 Score: 410
Period size: 117 Copynumber: 2.0 Consensus size: 118
3429665 TTCTGTCTCT
*
3429675 GTTTCTATCCATGAAAGTTAGAATTCTTAATCGTTTTGGTGAATTCATGCTTAAATTTTCATTTA
1 GTTTCTATCCATGAAAGTTAGAATTCTTAATCGTTTTGGTGAATTCATGCTCAAATTTTCATTTA
* *
3429740 GGTTTTTCTCTTTCTGCTTTTTTATGAGTGCTGAATGAT-AAGTTGTGGTTTG
66 GGTTTTTCTCTTTCTGCTTTTTTATGAGTGCTGAATGATAAAGATGTGGTTTC
* *
3429792 GTTTCTATCCATGAAAGTTAGAATTCTTGATCGTTTTGGTGAATTCATGCTCCAATTTTCATTTA
1 GTTTCTATCCATGAAAGTTAGAATTCTTAATCGTTTTGGTGAATTCATGCTCAAATTTTCATTTA
* *
3429857 GGTTTTTCTTTTTCTGCTTTTTTATGATTGCTGAATGATAAAGATGTGGTTTC
66 GGTTTTTCTCTTTCTGCTTTTTTATGAGTGCTGAATGATAAAGATGTGGTTTC
3429910 GTTTC
1 GTTTC
3429915 AGTTTTATAA
Statistics
Matches: 115, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
117 99 0.86
118 16 0.14
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (118 bp):
GTTTCTATCCATGAAAGTTAGAATTCTTAATCGTTTTGGTGAATTCATGCTCAAATTTTCATTTA
GGTTTTTCTCTTTCTGCTTTTTTATGAGTGCTGAATGATAAAGATGTGGTTTC
Found at i:3436023 original size:2 final size:2
Alignment explanation
Indices: 3436016--3436076 Score: 61
Period size: 2 Copynumber: 31.0 Consensus size: 2
3436006 AGCTATTTTC
* ** *
3436016 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT -T AT CC GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3436057 AT AT AT AT GT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3436077 TTTCTGTTGG
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3441665 original size:17 final size:17
Alignment explanation
Indices: 3441643--3441682 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
3441633 TCTCTATAAT
3441643 TACATGATTAGCGTCCG
1 TACATGATTAGCGTCCG
3441660 TACATGATTAGCGTCCG
1 TACATGATTAGCGTCCG
3441677 TACATG
1 TACATG
3441683 CTATCAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (17 bp):
TACATGATTAGCGTCCG
Found at i:3447303 original size:35 final size:35
Alignment explanation
Indices: 3447259--3447326 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
3447249 GAAAAAATGT
*
3447259 AAATTTTTTTATATT-TTATAA-TTAAATTTAAATAA
1 AAATATTTTTA-ATTATTA-AATTTAAATTTAAATAA
*
3447294 AAATATTTTTAATTATTAAATTTAATTTTAAAT
1 AAATATTTTTAATTATTAAATTTAAATTTAAAT
3447327 TAATTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 5 0.17
35 24 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
AAATATTTTTAATTATTAAATTTAAATTTAAATAA
Found at i:3447319 original size:13 final size:12
Alignment explanation
Indices: 3447301--3447337 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
3447291 TAAAAATATT
3447301 TTTAATTATTAAA
1 TTTAATT-TTAAA
3447314 TTTAATTTTAAA
1 TTTAATTTTAAA
3447326 -TTAA-TTTAAA
1 TTTAATTTTAAA
3447336 TT
1 TT
3447338 GATAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 6 0.26
11 5 0.22
12 5 0.22
13 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:3448084 original size:7 final size:7
Alignment explanation
Indices: 3448074--3448099 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3448064 AATTATATTA
3448074 AAATTTT
1 AAATTTT
3448081 AAATTTT
1 AAATTTT
3448088 AAATTTT
1 AAATTTT
3448095 AAATT
1 AAATT
3448100 CAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:3453034 original size:2 final size:2
Alignment explanation
Indices: 3453029--3453062 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3453019 AAAGAAAAGG
*
3453029 GA GA GA GA GT GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3453063 AGCTATTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:3461288 original size:6 final size:6
Alignment explanation
Indices: 3461259--3461297 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
3461249 AATATTAAAA
* *
3461259 AAATTT -AATTT AAATTT AAATTT AATTTT AAATAT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
3461298 AATCGAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:3461290 original size:18 final size:17
Alignment explanation
Indices: 3461243--3461297 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
3461233 TTTTTTATTT
3461243 TAAA-TTAATATTAAA-A
1 TAAATTTAAT-TTAAATA
*
3461259 -AAATTTAATTTAAATT
1 TAAATTTAATTTAAATA
3461275 TAAATTTAATTTTAAATA
1 TAAATTTAA-TTTAAATA
3461293 TAAAT
1 TAAAT
3461298 AATCGAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 8 0.24
16 5 0.15
17 8 0.24
18 12 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAATTTAAATA
Found at i:3461672 original size:4 final size:4
Alignment explanation
Indices: 3461653--3461689 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
3461643 AAATTTTATA
*
3461653 ATTT ATATT GTTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
3461690 TATTGGCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:3471658 original size:22 final size:22
Alignment explanation
Indices: 3471616--3471659 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3471606 AATATTAAAA
*
3471616 AATATATTATAATATATTTTGT
1 AATATATTATAATATAATTTGT
3471638 AATAT-TTATAATATTAATTTGT
1 AATATATTATAATA-TAATTTGT
3471660 TATTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
AATATATTATAATATAATTTGT
Found at i:3472267 original size:27 final size:28
Alignment explanation
Indices: 3472214--3472275 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
3472204 TATAAAATTT
* ** *
3472214 TATATAATATATAATATTTTAATTGTGA
1 TATATAATATAAAATATTACAAATGTGA
3472242 T-TATAATATAAAATATTACAAATGTGA
1 TATATAATATAAAATATTACAAATGTGA
3472269 TATATAA
1 TATATAA
3472276 ACGTGAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (28 bp):
TATATAATATAAAATATTACAAATGTGA
Found at i:3473525 original size:27 final size:27
Alignment explanation
Indices: 3473491--3473556 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
3473481 ATTTAAAGTT
3473491 ATTAAAAAATTAA-ATCTTAATT-ATAAA
1 ATTAAAAAATTAATAT-TTAATTAAT-AA
* *
3473518 ATTAAAAATTTAATATTTTATTAATAA
1 ATTAAAAAATTAATATTTAATTAATAA
*
3473545 ATTAAATAATTA
1 ATTAAAAAATTA
3473557 TCGAGGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
ATTAAAAAATTAATATTTAATTAATAA
Found at i:3477467 original size:10 final size:10
Alignment explanation
Indices: 3477452--3477476 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3477442 TGATATGTGA
3477452 TATAGTTATT
1 TATAGTTATT
3477462 TATAGTTATT
1 TATAGTTATT
3477472 TATAG
1 TATAG
3477477 CATATTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (10 bp):
TATAGTTATT
Found at i:3482572 original size:2 final size:2
Alignment explanation
Indices: 3482565--3482607 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3482555 AAATAAAACG
*
3482565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3482607 T
1 T
3482608 GCCAACGGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3482790 original size:19 final size:21
Alignment explanation
Indices: 3482756--3482795 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3482746 ATATTAATTT
*
3482756 AAAATTATTTTATTATTTTAA
1 AAAATTATTTTATTATATTAA
3482777 AAAATTA-TTT-TTATATTAA
1 AAAATTATTTTATTATATTAA
3482796 TATTTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAAATTATTTTATTATATTAA
Found at i:3484392 original size:8 final size:8
Alignment explanation
Indices: 3484379--3484406 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3484369 CAAGAATTTG
3484379 ACTTCGTA
1 ACTTCGTA
3484387 ACTTCGTA
1 ACTTCGTA
3484395 ACTTCGTA
1 ACTTCGTA
3484403 ACTT
1 ACTT
3484407 AATGTCATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (8 bp):
ACTTCGTA
Found at i:3489923 original size:8 final size:8
Alignment explanation
Indices: 3489903--3489959 Score: 51
Period size: 8 Copynumber: 6.5 Consensus size: 8
3489893 ATTAATAATT
3489903 TATTTTATA
1 TATTTT-TA
3489912 TATTTTTA
1 TATTTTTA
*
3489920 TATTTATA
1 TATTTTTA
3489928 TATTCATATTA
1 TATT--T-TTA
*
3489939 TATTTATTT
1 TATTT-TTA
3489948 TATTTTTA
1 TATTTTTA
3489956 TATT
1 TATT
3489960 ATTTTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 19 0.46
9 15 0.37
10 1 0.02
11 6 0.15
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (8 bp):
TATTTTTA
Found at i:3489927 original size:6 final size:6
Alignment explanation
Indices: 3489890--3489959 Score: 51
Period size: 6 Copynumber: 12.0 Consensus size: 6
3489880 TAAAATTTTA
* *
3489890 TATATT AATAATT TAT-TT TATA-- TATTTT TATATT TATATAT TCATA-T
1 TATATT TAT-ATT TATATT TATATT TATATT TATATT TATAT-T T-ATATT
*
3489937 TATATT TAT-TT TATTTT TATATT
1 TATATT TATATT TATATT TATATT
3489960 ATTTTTAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
4 3 0.06
5 13 0.25
6 25 0.49
7 7 0.14
8 3 0.06
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:3489931 original size:36 final size:36
Alignment explanation
Indices: 3489886--3489959 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
3489876 TATATAAAAT
3489886 TTTATATATTAATAATT-TATTT-TATATATTTTTATA
1 TTTATATATTAAT-ATTATATTTAT-TATATTTTTATA
* *
3489922 TTTATATATTCATATTATATTTATTTTATTTTTATA
1 TTTATATATTAATATTATATTTATTATATTTTTATA
3489958 TT
1 TT
3489960 ATTTTTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 3 0.09
36 30 0.88
37 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (36 bp):
TTTATATATTAATATTATATTTATTATATTTTTATA
Found at i:3489966 original size:22 final size:22
Alignment explanation
Indices: 3489901--3489976 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 22
3489891 ATATTAATAA
3489901 TTTA-TTTTATA-TATTTTTAT
1 TTTATTTTTATATTATTTTTAT
* *
3489921 ATTTATATATTCATATTATATTTAT
1 -TTTAT-T-TTTATATTATTTTTAT
*
3489946 TTTATTTTTATATTATTTTTAA
1 TTTATTTTTATATTATTTTTAT
*
3489968 TTAATTTTT
1 TTTATTTTT
3489977 TGTATTGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 4 0.09
22 21 0.47
23 2 0.04
24 10 0.22
25 8 0.18
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTATTTTTATATTATTTTTAT
Found at i:3489975 original size:11 final size:11
Alignment explanation
Indices: 3489905--3489976 Score: 67
Period size: 11 Copynumber: 6.4 Consensus size: 11
3489895 TAATAATTTA
3489905 TTTTATA-TAT
1 TTTTATATTAT
3489915 TTTTATATTTAT
1 TTTTATA-TTAT
*
3489927 ATATTCATATTAT
1 -T-TTTATATTAT
* *
3489940 ATTTATTTTAT
1 TTTTATATTAT
3489951 TTTTATATTAT
1 TTTTATATTAT
3489962 TTTTA-ATTAAT
1 TTTTATATT-AT
3489973 TTTT
1 TTTT
3489977 TGTATTGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
10 10 0.20
11 28 0.55
12 3 0.06
13 5 0.10
14 5 0.10
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:3491210 original size:15 final size:15
Alignment explanation
Indices: 3491190--3491219 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3491180 GATTTGAATG
3491190 CAATTCTCGCTCTTA
1 CAATTCTCGCTCTTA
3491205 CAATTCTCGCTCTTA
1 CAATTCTCGCTCTTA
3491220 TTTCTATGCT
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:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (15 bp):
CAATTCTCGCTCTTA
Found at i:3495945 original size:52 final size:52
Alignment explanation
Indices: 3495883--3495991 Score: 191
Period size: 52 Copynumber: 2.1 Consensus size: 52
3495873 AAGTATCAAA
* * *
3495883 AAGAACAAATTGGCAATCCAAATTGTTGAAATCCTGTTGTTTTTGTAATTAT
1 AAGAACAAATTGGCAACCCAAATCGTTGAAACCCTGTTGTTTTTGTAATTAT
3495935 AAGAACAAATTGGCAACCCAAATCGTTGAAACCCTGTTGTTTTTGTAATTAT
1 AAGAACAAATTGGCAACCCAAATCGTTGAAACCCTGTTGTTTTTGTAATTAT
3495987 AAGAA
1 AAGAA
3495992 TATTAAATGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (52 bp):
AAGAACAAATTGGCAACCCAAATCGTTGAAACCCTGTTGTTTTTGTAATTAT
Found at i:3496835 original size:14 final size:15
Alignment explanation
Indices: 3496816--3496844 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3496806 TATTATTATT
3496816 TTATTTA-TTAAATA
1 TTATTTATTTAAATA
3496830 TTATTTATTTAAATA
1 TTATTTATTTAAATA
3496845 AATTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTTATTTAAATA
Found at i:3496846 original size:19 final size:19
Alignment explanation
Indices: 3496809--3496847 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3496799 ATATTTATAT
*
3496809 TATTATTTTATTTATTAAA
1 TATTATTTTATTTAATAAA
3496828 TATTA-TTTATTTAAATAAA
1 TATTATTTTATTT-AATAAA
3496847 T
1 T
3496848 TTTAATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATTTTATTTAATAAA
Found at i:3496870 original size:11 final size:10
Alignment explanation
Indices: 3496863--3496894 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
3496853 TACATTTATA
3496863 TATTATTTTT
1 TATTATTTTT
3496873 TATTATATTTT
1 TATTAT-TTTT
3496884 TATTATTTTT
1 TATTATTTTT
3496894 T
1 T
3496895 CATTCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TATTATTTTT
Found at i:3498187 original size:2 final size:2
Alignment explanation
Indices: 3498180--3498212 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3498170 GTTAAAGGGA
3498180 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3498213 TGGACAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3513460 original size:3 final size:3
Alignment explanation
Indices: 3513452--3513480 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3513442 TTATGCACAC
3513452 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3513481 CATATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3515680 original size:15 final size:15
Alignment explanation
Indices: 3515656--3515711 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 15
3515646 TTATTTGACG
3515656 TTAA-ATATAATTTT
1 TTAATATATAATTTT
3515670 TTAATATATAAAATTGTT
1 TTAATATAT--AATT-TT
*
3515688 TGAAT-T-TAATTTT
1 TTAATATATAATTTT
3515701 TTAATATATAA
1 TTAATATATAA
3515712 AATTATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
13 6 0.18
14 9 0.26
15 7 0.21
16 1 0.03
17 5 0.15
18 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (15 bp):
TTAATATATAATTTT
Found at i:3515701 original size:31 final size:31
Alignment explanation
Indices: 3515663--3515724 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
3515653 ACGTTAAATA
*
3515663 TAATTTTTTAATATATAAAATTGTTTGAATT
1 TAATTTTTTAATATATAAAATTATTTGAATT
*
3515694 TAATTTTTTAATATATAAAATTATTTTAATT
1 TAATTTTTTAATATATAAAATTATTTGAATT
3515725 CAAACGGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (31 bp):
TAATTTTTTAATATATAAAATTATTTGAATT
Found at i:3515838 original size:20 final size:18
Alignment explanation
Indices: 3515815--3515862 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
3515805 TTAAAATATT
3515815 ATATATTTTTATAAATTTTA
1 ATATATTTTTAT--ATTTTA
*
3515835 ATATATTATTATATTTTA
1 ATATATTTTTATATTTTA
3515853 ATTATATTTT
1 A-TATATTTT
3515863 ATAGACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 7 0.28
20 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATATTTTTATATTTTA
Found at i:3515850 original size:18 final size:17
Alignment explanation
Indices: 3515815--3515865 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 17
3515805 TTAAAATATT
3515815 ATATATTTTTATAAATTTTA
1 ATATA-TTTTAT--ATTTTA
3515835 ATATATTATTATATTTTA
1 ATATATT-TTATATTTTA
3515853 ATTATATTTTATA
1 A-TATATTTTATA
3515866 GACATATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 12 0.41
19 8 0.28
20 9 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATATTTTATATTTTA
Found at i:3517635 original size:13 final size:12
Alignment explanation
Indices: 3517614--3517658 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
3517604 TTTCAATTTT
3517614 TTTTGTTTCTGA
1 TTTTGTTTCTGA
*
3517626 TTTTGTTTTCTAGG
1 TTTTG-TTTCT-GA
3517640 TTTTGTTTCTGA
1 TTTTGTTTCTGA
3517652 TTTTGTT
1 TTTTGTT
3517659 GTTTTCCTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 13 0.45
13 10 0.34
14 6 0.21
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.69
Consensus pattern (12 bp):
TTTTGTTTCTGA
Found at i:3517859 original size:12 final size:12
Alignment explanation
Indices: 3517844--3517889 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
3517834 TTCAATGTTT
3517844 TTTTGTTTCTGA
1 TTTTGTTTCTGA
*
3517856 TTTTGTTTTCTAGGG
1 TTTTG-TTTCT--GA
3517871 TTTTGTTTCTGA
1 TTTTGTTTCTGA
3517883 TTTTGTT
1 TTTTGTT
3517890 GTTTTCCTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 13 0.45
13 5 0.17
14 5 0.17
15 6 0.21
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.67
Consensus pattern (12 bp):
TTTTGTTTCTGA
Found at i:3517952 original size:231 final size:229
Alignment explanation
Indices: 3517551--3518011 Score: 904
Period size: 231 Copynumber: 2.0 Consensus size: 229
3517541 TGCTGAGACT
3517551 ATAGTAATTGTTACTTATGCCAAAGATGGGGAATGGCTGAGAAAATCATATGTTTTCAATTTTTT
1 ATAGTAATTGTTACTTATGCCAAAGATGGGGAATGGCTGAGAAAATCATATGTTTTCAATTTTTT
3517616 TTGTTTCTGATTTTGTTTTCTAGGTTTTGTTTCTGATTTTGTTGTTTTCCTGCCATAGCTGTTTT
66 TTGTTTCTGATTTTGTTTTCTAGGTTTTGTTTCTGATTTTGTTGTTTTCCTGCCATAGCTGTTTT
3517681 AATTGTTCGTTTGGTATGTTGTTTACTGACTTTTTTCTCTGCCTTTTCTCTGGTAATTTGTTTCC
131 AATTGTTCGTTTGGTATGTTGTTTACTGACTTTTTTCTCTGCCTTTTCTCTGGTAATTTGTTTCC
3517746 TCTATAGCCATCTGCTTCTTTGGATGAACTAATA
196 TCTATAGCCATCTGCTTCTTTGGATGAACTAATA
3517780 ATAGTAATTGTTACTTATGCCAAAGATGGGGAATGGCTGAGAAAATCATATGTTTTCAATGTTTT
1 ATAGTAATTGTTACTTATGCCAAAGATGGGGAATGGCTGAGAAAATCATATGTTTTCAAT-TTTT
3517845 TTTGTTTCTGATTTTGTTTTCTAGGGTTTTGTTTCTGATTTTGTTGTTTTCCTGCCATAGCTGTT
65 TTTGTTTCTGATTTTGTTTTCTA-GGTTTTGTTTCTGATTTTGTTGTTTTCCTGCCATAGCTGTT
3517910 TTAATTGTTCGTTTGGTATGTTGTTTACTGACTTTTTTCTCTGCCTTTTCTCTGGTAATTTGTTT
129 TTAATTGTTCGTTTGGTATGTTGTTTACTGACTTTTTTCTCTGCCTTTTCTCTGGTAATTTGTTT
3517975 CCTCTATAGCCATCTGCTTCTTTGGATGAACTAATA
194 CCTCTATAGCCATCTGCTTCTTTGGATGAACTAATA
3518011 A
1 A
3518012 ACTCAGTTAT
Statistics
Matches: 230, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
229 60 0.26
230 27 0.12
231 143 0.62
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.49
Consensus pattern (229 bp):
ATAGTAATTGTTACTTATGCCAAAGATGGGGAATGGCTGAGAAAATCATATGTTTTCAATTTTTT
TTGTTTCTGATTTTGTTTTCTAGGTTTTGTTTCTGATTTTGTTGTTTTCCTGCCATAGCTGTTTT
AATTGTTCGTTTGGTATGTTGTTTACTGACTTTTTTCTCTGCCTTTTCTCTGGTAATTTGTTTCC
TCTATAGCCATCTGCTTCTTTGGATGAACTAATA
Found at i:3518384 original size:3 final size:3
Alignment explanation
Indices: 3518370--3518402 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3518360 TGTTTTTTCT
*
3518370 TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3518403 AAAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:3522198 original size:13 final size:13
Alignment explanation
Indices: 3522180--3522204 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3522170 TGTCTCTGAT
3522180 GATTTTTTTTTTG
1 GATTTTTTTTTTG
3522193 GATTTTTTTTTT
1 GATTTTTTTTTT
3522205 CAAATGTCTG
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:0.08, C:0.00, G:0.12, T:0.80
Consensus pattern (13 bp):
GATTTTTTTTTTG
Found at i:3531691 original size:6 final size:6
Alignment explanation
Indices: 3531682--3531706 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3531672 GATGATGATA
3531682 ATCCAG ATCCAG ATCCAG ATCCAG A
1 ATCCAG ATCCAG ATCCAG ATCCAG A
3531707 AGAAAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
ATCCAG
Found at i:3536276 original size:15 final size:15
Alignment explanation
Indices: 3536258--3536317 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 15
3536248 AAATTTAATT
3536258 TTTAATTATTTTTAA
1 TTTAATTATTTTTAA
3536273 TTTAATT-TTTTATATA
1 TTTAATTATTTT-TA-A
3536289 TTT-ATTAATTTTTAA
1 TTTAATT-ATTTTTAA
3536304 TTTAGATTTATTTT
1 TTTA-A-TTATTTT
3536318 AAATATAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.11
15 16 0.42
16 6 0.16
17 10 0.26
18 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTAATTATTTTTAA
Found at i:3537781 original size:2 final size:2
Alignment explanation
Indices: 3537774--3537826 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3537764 TTTGCGTAGA
3537774 AT AT AT AT AT 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 AT AT AT AT AT
3537816 AT AT AT AT AT A
1 AT AT AT AT AT A
3537827 CACGCACACC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3537975 original size:2 final size:2
Alignment explanation
Indices: 3537970--3537997 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3537960 ACACACATAC
3537970 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
3537998 CTTTTGGTTG
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:3539074 original size:24 final size:24
Alignment explanation
Indices: 3539032--3539078 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3539022 ACTTGGTCCA
*
3539032 ATATTTGGTATAAAATTAATACAC
1 ATATTTGGTACAAAATTAATACAC
**
3539056 ATATTTGGTACAATGTTAATACA
1 ATATTTGGTACAAAATTAATACA
3539079 AAACTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (24 bp):
ATATTTGGTACAAAATTAATACAC
Found at i:3544743 original size:17 final size:16
Alignment explanation
Indices: 3544712--3544748 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
3544702 ATATAAAAAA
*
3544712 ATAATTTAAATATAAT
1 ATAATTTAAAAATAAT
3544728 ATAATATTAAAAATAAT
1 ATAAT-TTAAAAATAAT
3544745 ATAA
1 ATAA
3544749 ATACGATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATTTAAAAATAAT
Found at i:3544757 original size:28 final size:29
Alignment explanation
Indices: 3544708--3544762 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
3544698 TATTATATAA
* *
3544708 AAAAATAATTTAAATATAATAT-AATATT
1 AAAAATAATATAAATACAATATGAATATT
*
3544736 AAAAATAATATAAATACGATATGAATA
1 AAAAATAATATAAATACAATATGAATA
3544763 AATAAATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATAATATAAATACAATATGAATATT
Found at i:3544769 original size:28 final size:26
Alignment explanation
Indices: 3544707--3544769 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
3544697 ATATTATATA
* *
3544707 AAAAAATAATTTAAATATAATATAAT
1 AAAAAATAATATAAATACAATATAAT
*
3544733 ATTAAAAATAATATAAATACGATATGAAT
1 A--AAAAATAATATAAATACAATAT-AAT
3544762 AAATAAAT
1 AAA-AAAT
3544770 GTTTTCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.03
27 2 0.07
28 23 0.77
29 4 0.13
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (26 bp):
AAAAAATAATATAAATACAATATAAT
Found at i:3546423 original size:6 final size:6
Alignment explanation
Indices: 3546414--3546445 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3546404 GGTTTTATTT
3546414 TTTTTC TTTTTC TTTTTC TTTTT- TTTTT- TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
3546446 GTTGGAGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (6 bp):
TTTTTC
Found at i:3546435 original size:21 final size:21
Alignment explanation
Indices: 3546406--3546445 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3546396 CTTTTTAGGG
3546406 TTTTATTTTTTTTCTTTTTCT
1 TTTTATTTTTTTTCTTTTTCT
* *
3546427 TTTTCTTTTTTTTTTTTTT
1 TTTTATTTTTTTTCTTTTT
3546446 GTTGGAGAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (21 bp):
TTTTATTTTTTTTCTTTTTCT
Found at i:3549439 original size:4 final size:4
Alignment explanation
Indices: 3549430--3549486 Score: 78
Period size: 4 Copynumber: 14.2 Consensus size: 4
3549420 AACTCACGCT
* * * *
3549430 TGTA TGTA TGTA TATA TATA TATA TGTA TGTG TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3549478 TGTA TGTA T
1 TGTA TGTA T
3549487 TCAATCAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:3551215 original size:16 final size:18
Alignment explanation
Indices: 3551194--3551226 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3551184 TATGCCTTTT
3551194 TTTTTTA-A-AAAAAATA
1 TTTTTTAGATAAAAAATA
3551210 TTTTTTAGATAAAAAAT
1 TTTTTTAGATAAAAAAT
3551227 TATGATATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TTTTTTAGATAAAAAATA
Found at i:3552630 original size:2 final size:2
Alignment explanation
Indices: 3552623--3552668 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3552613 TGTCAGATGC
3552623 AT AT AT AT AT 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 AT AT AT AT AT
3552665 AT AT
1 AT AT
3552669 TAAACACTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3570752 original size:2 final size:2
Alignment explanation
Indices: 3570741--3570776 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3570731 AAAATAAAAT
3570741 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3570777 GAGATGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3573064 original size:2 final size:2
Alignment explanation
Indices: 3573057--3573094 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3573047 GAGACAATTC
3573057 AT AT AT 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 AT AT AT
3573095 CACACTATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3573436 original size:14 final size:15
Alignment explanation
Indices: 3573404--3573446 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
3573394 ATTGATTTAA
*
3573404 AATATTTATCAAGTTT
1 AATATTTAT-AATTTT
3573420 AATATTTA-AATTTT
1 AATATTTATAATTTT
3573434 AATATTTATAATT
1 AATATTTATAATT
3573447 ATTTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 13 0.52
15 4 0.16
16 8 0.32
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
AATATTTATAATTTT
Found at i:3574408 original size:2 final size:2
Alignment explanation
Indices: 3574395--3574431 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3574385 TTATCCCTGC
* *
3574395 AT AT AT AC AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3574432 CACCATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3574410 original size:10 final size:10
Alignment explanation
Indices: 3574395--3574433 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
3574385 TTATCCCTGC
3574395 ATATATACAT
1 ATATATACAT
*
3574405 ATATATATAT
1 ATATATACAT
3574415 ATATATACAT
1 ATATATACAT
3574425 ATATATACA
1 ATATATACA
3574434 CCATTAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATACAT
Found at i:3575385 original size:13 final size:13
Alignment explanation
Indices: 3575367--3575392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3575357 TTTAAATTAA
3575367 ATTTAATTATTTT
1 ATTTAATTATTTT
3575380 ATTTAATTATTTT
1 ATTTAATTATTTT
3575393 TAAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTAATTATTTT
Found at i:3575461 original size:20 final size:20
Alignment explanation
Indices: 3575436--3575475 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3575426 CTCTTAATAT
*
3575436 TTATAATATTTTTATTTAAA
1 TTATAATATTTTTATATAAA
3575456 TTATAATATTTTTATATAAA
1 TTATAATATTTTTATATAAA
3575476 ACTATTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATAATATTTTTATATAAA
Found at i:3576930 original size:31 final size:35
Alignment explanation
Indices: 3576869--3576938 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 35
3576859 ATATATATAA
* *
3576869 ATTTTTATACATTTATTATATTTAAATAAGTCTTT
1 ATTTTTATACATTTATTATATTCAAATAAGTCATT
3576904 ATTTTT-TA-ATTTA-T-TATTCAAATAAGTCATT
1 ATTTTTATACATTTATTATATTCAAATAAGTCATT
3576935 ATTT
1 ATTT
3576939 GAAACAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 19 0.58
32 1 0.03
33 5 0.15
34 2 0.06
35 6 0.18
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (35 bp):
ATTTTTATACATTTATTATATTCAAATAAGTCATT
Found at i:3576984 original size:19 final size:21
Alignment explanation
Indices: 3576960--3577004 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
3576950 TTGAGAAATT
3576960 ATTTA-TG-TATAAATTAAAA
1 ATTTACTGATATAAATTAAAA
3576979 ATTTATCTGAATATAAATTAAAA
1 ATTTA-CTG-ATATAAATTAAAA
3577002 ATT
1 ATT
3577005 AAAAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.23
21 2 0.09
23 15 0.68
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (21 bp):
ATTTACTGATATAAATTAAAA
Found at i:3577023 original size:29 final size:30
Alignment explanation
Indices: 3576970--3577040 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 30
3576960 ATTTATGTAT
3576970 AAATTAAAAATTTATCTGAATATAAATTAA
1 AAATTAAAAATTTATCTGAATATAAATTAA
3577000 AAATTAAAAATTTAT-T-AACTATAAATTAA
1 AAATTAAAAATTTATCTGAA-TATAAATTAA
**
3577029 ATTTTAAAAATT
1 AAATTAAAAATT
3577041 ATTTAAGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 2 0.05
29 21 0.55
30 15 0.39
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (30 bp):
AAATTAAAAATTTATCTGAATATAAATTAA
Found at i:3585193 original size:2 final size:2
Alignment explanation
Indices: 3585186--3585219 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3585176 ATTCTCATTC
3585186 CT CT CT CT CT CT 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
3585220 ATTTTATTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3592574 original size:3 final size:3
Alignment explanation
Indices: 3592568--3592597 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3592558 TTTAAAAAAG
3592568 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3592598 AGATGAGTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3593357 original size:14 final size:14
Alignment explanation
Indices: 3593338--3593370 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3593328 TGCTTTTAAA
*
3593338 TATTATTTTTATAT
1 TATTATTTATATAT
3593352 TATTATTTATATAT
1 TATTATTTATATAT
3593366 T-TTAT
1 TATTAT
3593371 AATTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTATTTATATAT
Found at i:3615067 original size:19 final size:19
Alignment explanation
Indices: 3615022--3615070 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
3615012 ATAAATATCA
3615022 AATATAAATA--TATATTT
1 AATATAAATATTTATATTT
** *
3615039 TTTATTAATATTTATATTT
1 AATATAAATATTTATATTT
3615058 AATATAAATATTT
1 AATATAAATATTT
3615071 TAATAAAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 7 0.29
19 17 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATAAATATTTATATTT
Found at i:3615500 original size:3 final size:3
Alignment explanation
Indices: 3615492--3615523 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3615482 GAAAACCTCA
3615492 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3615524 AGGTCTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3615643 original size:16 final size:16
Alignment explanation
Indices: 3615616--3615670 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
3615606 TTTAAACTCG
*
3615616 AAAA-AATTTGAATTT
1 AAAATAATTTGAAATT
* * *
3615631 AAAATAGTTTGAACTG
1 AAAATAATTTGAAATT
3615647 AAAATAATTT-AAATT
1 AAAATAATTTGAAATT
*
3615662 AAAAAAATT
1 AAAATAATT
3615671 AAACCCTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
15 15 0.47
16 17 0.53
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (16 bp):
AAAATAATTTGAAATT
Found at i:3616848 original size:18 final size:19
Alignment explanation
Indices: 3616806--3616856 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
3616796 TTTAAAAATT
*
3616806 ATTTTTATATAACAAATTAA
1 ATTTTTATATAA-ATATTAA
*
3616826 TTTTTTATATAAATA-TAA
1 ATTTTTATATAAATATTAA
3616844 A-TTTTA-ATAAATA
1 ATTTTTATATAAATA
3616857 AATATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 7 0.25
17 5 0.18
18 3 0.11
19 2 0.07
20 11 0.39
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTTATATAAATATTAA
Found at i:3616855 original size:16 final size:16
Alignment explanation
Indices: 3616828--3616878 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
3616818 CAAATTAATT
3616828 TTTTATATAAATATAA-A
1 TTTTA-ATAAATA-AATA
3616845 TTTTAATAAATAAATA
1 TTTTAATAAATAAATA
3616861 TTTTAA-AAATAACATA
1 TTTTAATAAATAA-ATA
3616877 TT
1 TT
3616879 ATAACTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.25
16 19 0.59
17 5 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTTAATAAATAAATA
Found at i:3617019 original size:16 final size:16
Alignment explanation
Indices: 3616998--3617034 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
3616988 CTTGAATCTG
3616998 AAAAAACTCAAA-CTCA
1 AAAAAACTCAAATC-CA
3617014 AAAAAACTCAAATCCA
1 AAAAAACTCAAATCCA
3617030 AAAAA
1 AAAAA
3617035 GTTTAAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.68, C:0.22, G:0.00, T:0.11
Consensus pattern (16 bp):
AAAAAACTCAAATCCA
Found at i:3618408 original size:1 final size:1
Alignment explanation
Indices: 3618402--3618431 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3618392 TACAGCGAAG
3618402 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3618432 CACTTGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3620066 original size:2 final size:2
Alignment explanation
Indices: 3620059--3620084 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3620049 TCCGTACCCT
3620059 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
3620085 ACTCTTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3622117 original size:4 final size:4
Alignment explanation
Indices: 3622110--3622143 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
3622100 AAAATTTATT
*
3622110 TTTA TTTA TTTA TTTA TTTA TTTT TTGTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA T
3622144 CGAAATGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3629935 original size:22 final size:22
Alignment explanation
Indices: 3629889--3629938 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 22
3629879 ATGATTTTCT
3629889 TTTATAAAATAATATTTGATAAA
1 TTTA-AAAATAATATTTGATAAA
3629912 TTTAAAATATAATATTT-ATAAA
1 TTTAAAA-ATAATATTTGATAAA
3629934 TTTAA
1 TTTAA
3629939 TATTTGTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TTTAAAAATAATATTTGATAAA
Done.