Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 20 of 190
Found at i:3038159 original size:23 final size:23
Alignment explanation
Indices: 3038126--3038195 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
3038116 TTCTGTTCAA
* *
3038126 GCTACTACAAACGTCGAATGGGT
1 GCTACTGCAAACGTTGAATGGGT
3038149 GCTACTGCAAACGTTGAATGGGT
1 GCTACTGCAAACGTTGAATGGGT
* *
3038172 GCAACTGCAAACATTGAATGGGT
1 GCTACTGCAAACGTTGAATGGGT
3038195 G
1 G
3038196 GAACGAGCAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.23
Consensus pattern (23 bp):
GCTACTGCAAACGTTGAATGGGT
Found at i:3038299 original size:87 final size:87
Alignment explanation
Indices: 3038153--3038319 Score: 280
Period size: 87 Copynumber: 1.9 Consensus size: 87
3038143 ATGGGTGCTA
* * *
3038153 CTGCAAACGTTGAATGGGTGCAACTGCAAACATTGAATGGGTGGAACGAGCAGAGCTTCGTTGAG
1 CTGCAAACGTCGAATGGGTGCAACTGCAAACATCGAATGGGTGGAACGAGCAGAGCTTCGTTGAA
3038218 GGATCGGGTTCTGTTGAAGCTG
66 GGATCGGGTTCTGTTGAAGCTG
* * *
3038240 CTGCAAACGTCGAATGGGTGCTACTGCAAACGTCGAATGGGTGGAACGAGCAGGGCTTCGTTGAA
1 CTGCAAACGTCGAATGGGTGCAACTGCAAACATCGAATGGGTGGAACGAGCAGAGCTTCGTTGAA
3038305 GGATCGGGTTCTGTT
66 GGATCGGGTTCTGTT
3038320 CAAGATCGGG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (87 bp):
CTGCAAACGTCGAATGGGTGCAACTGCAAACATCGAATGGGTGGAACGAGCAGAGCTTCGTTGAA
GGATCGGGTTCTGTTGAAGCTG
Found at i:3038382 original size:49 final size:49
Alignment explanation
Indices: 3038310--3038461 Score: 224
Period size: 49 Copynumber: 3.2 Consensus size: 49
3038300 TTGAAGGATC
*
3038310 GGGTTCTGTTCAAGATCGGGTTCTGTTGAAGCTGCTGCAAACGTCGAAT
1 GGGTTCTGTTCAAGATCAGGTTCTGTTGAAGCTGCTGCAAACGTCGAAT
*
3038359 GGGTTCTGTTCAAGATCAGGTTCTGTTGAAGCTGCTGCAAATGTCGAAT
1 GGGTTCTGTTCAAGATCAGGTTCTGTTGAAGCTGCTGCAAACGTCGAAT
* * *
3038408 GGGTTCTGTT---GA--AGCTGCTGCTGAAGCTGCTGCAAACGTCGAAT
1 GGGTTCTGTTCAAGATCAGGTTCTGTTGAAGCTGCTGCAAACGTCGAAT
3038452 GGGTTCTGTT
1 GGGTTCTGTT
3038462 GAAGCTGCTG
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
44 38 0.39
46 2 0.02
49 57 0.59
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.32
Consensus pattern (49 bp):
GGGTTCTGTTCAAGATCAGGTTCTGTTGAAGCTGCTGCAAACGTCGAAT
Found at i:3038435 original size:44 final size:44
Alignment explanation
Indices: 3038336--3038472 Score: 193
Period size: 44 Copynumber: 3.0 Consensus size: 44
3038326 CGGGTTCTGT
* * *
3038336 TGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAGGTTCTGT
1 TGAAGCTGCTGCAAACGTCGAATGGGTTCTGTT---GA--AGCTGCTGC
*
3038385 TGAAGCTGCTGCAAATGTCGAATGGGTTCTGTTGAAGCTGCTGC
1 TGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGC
3038429 TGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGC
1 TGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGC
3038473 AATCGTCGAA
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
44 49 0.59
46 2 0.02
49 32 0.39
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (44 bp):
TGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGC
Found at i:3038470 original size:32 final size:32
Alignment explanation
Indices: 3038429--3038525 Score: 176
Period size: 32 Copynumber: 3.0 Consensus size: 32
3038419 AAGCTGCTGC
3038429 TGAAGCTGCTGCAAACGTCGAATGGGTTCTGT
1 TGAAGCTGCTGCAAACGTCGAATGGGTTCTGT
*
3038461 TGAAGCTGCTGCAATCGTCGAATGGGTTCTGT
1 TGAAGCTGCTGCAAACGTCGAATGGGTTCTGT
*
3038493 TGAAGCTACTGCAAACGTCGAATGGGTTCTGT
1 TGAAGCTGCTGCAAACGTCGAATGGGTTCTGT
3038525 T
1 T
3038526 CAAGATCAGG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (32 bp):
TGAAGCTGCTGCAAACGTCGAATGGGTTCTGT
Found at i:3038576 original size:32 final size:32
Alignment explanation
Indices: 3038535--3038606 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
3038525 TCAAGATCAG
*
3038535 GTTCTGTTGAAGCTACTGCAATCATCGAATGA
1 GTTCTGTTGAAGCTACTGCAAACATCGAATGA
* *
3038567 GTTCTGTTGAAGCTACTGCAAACGTCGAATGG
1 GTTCTGTTGAAGCTACTGCAAACATCGAATGA
3038599 GTTCTGTT
1 GTTCTGTT
3038607 CAAGATCAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (32 bp):
GTTCTGTTGAAGCTACTGCAAACATCGAATGA
Found at i:3038586 original size:113 final size:108
Alignment explanation
Indices: 3038377--3038606 Score: 316
Period size: 113 Copynumber: 2.1 Consensus size: 108
3038367 TTCAAGATCA
* * *
3038377 GGTTCTGTTGAAGCTGCTGCAAATGTCGAATGGGTTCTGTTGAAGCTGCTGCTGAAGCTGCTGCA
1 GGTTCTGTTGAAGCTACTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGCTGAAGCTACTGCA
* * * *
3038442 AACGTCGAATGGGTTCTGTTGAAGCTGCTGCAATCGTCGAATG
66 AACATCGAATGAGTTCTGTTGAAGCTACTGCAAACGTCGAATG
* * *
3038485 GGTTCTGTTGAAGCTACTGCAAACGTCGAATGGGTTCTGTTCAAGATCAGGTTCTGTTGAAGCTA
1 GGTTCTGTTGAAGCTACTGCAAACGTCGAATGGGTTCTGTT---GA--AGCTGCTGCTGAAGCTA
*
3038550 CTGCAATCATCGAATGAGTTCTGTTGAAGCTACTGCAAACGTCGAATG
61 CTGCAAACATCGAATGAGTTCTGTTGAAGCTACTGCAAACGTCGAATG
3038598 GGTTCTGTT
1 GGTTCTGTT
3038607 CAAGATCAAG
Statistics
Matches: 106, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
108 39 0.37
111 2 0.02
113 65 0.61
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (108 bp):
GGTTCTGTTGAAGCTACTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGCTGAAGCTACTGCA
AACATCGAATGAGTTCTGTTGAAGCTACTGCAAACGTCGAATG
Found at i:3038657 original size:32 final size:32
Alignment explanation
Indices: 3038616--3038687 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
3038606 TCAAGATCAA
3038616 GTTCTGTTGAAACTGCTGCAAACGTCGAATGG
1 GTTCTGTTGAAACTGCTGCAAACGTCGAATGG
*
3038648 GTTCTGTTGAAGCTGCTGCAAACGTCGAATGG
1 GTTCTGTTGAAACTGCTGCAAACGTCGAATGG
3038680 GTTCTGTT
1 GTTCTGTT
3038688 CAAGATCAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (32 bp):
GTTCTGTTGAAACTGCTGCAAACGTCGAATGG
Found at i:3038700 original size:49 final size:48
Alignment explanation
Indices: 3038647--3038833 Score: 247
Period size: 49 Copynumber: 3.9 Consensus size: 48
3038637 ACGTCGAATG
3038647 GGTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATC
1 GGTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATC
* *
3038695 AGGTTCTGTTGAAGCTGCTGCAAACGTTGAATGGATTCTGTTCAAGATC
1 -GGTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATC
* * *
3038744 GGATTCTGTTCAAGCTACTGCAAACGTCGAATGGGTTCTGTTGAA-A-C
1 GG-TTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATC
* * * *
3038791 --TACTGCTGAAGCTGCAGCAAACATCGAATGGGTTCTGTTCAAG
1 GGTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAG
3038834 CTTTTTAAAG
Statistics
Matches: 122, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
44 35 0.29
47 1 0.01
48 3 0.02
49 83 0.68
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (48 bp):
GGTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATC
Found at i:3039198 original size:22 final size:22
Alignment explanation
Indices: 3039173--3039226 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
3039163 TCGATAATAA
3039173 TCGAATCGAATTCGAGTTTTCT
1 TCGAATCGAATTCGAGTTTTCT
3039195 TCGAATCGAATTCGAGTTTTCT
1 TCGAATCGAATTCGAGTTTTCT
3039217 TCGAATCGAA
1 TCGAATCGAA
3039227 CCCGAATAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (22 bp):
TCGAATCGAATTCGAGTTTTCT
Found at i:3045714 original size:22 final size:22
Alignment explanation
Indices: 3045667--3045725 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
3045657 ATTAATTAAT
**
3045667 TAATTTTATATTTATATATATT
1 TAATTTTATATTTATATATAAA
3045689 TAATTTTATATTTATAT-TAAAA
1 TAATTTTATATTTATATAT-AAA
3045711 TAATATTTTATATTT
1 T-A-ATTTTATATTT
3045726 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 1 0.03
22 19 0.59
23 1 0.03
24 11 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TAATTTTATATTTATATATAAA
Found at i:3045723 original size:24 final size:23
Alignment explanation
Indices: 3045669--3045744 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
3045659 TAATTAATTA
* * *
3045669 ATTTTATATTTATATATATTTA-
1 ATTTTATATTTATATAAAATAAT
3045691 ATTTTATATTTATATTAAAATAAT
1 ATTTTATATTTATA-TAAAATAAT
* *
3045715 ATTTTATATTTTTAAAAAATAAT
1 ATTTTATATTTATATAAAATAAT
3045738 ATTTTAT
1 ATTTTAT
3045745 TAATTTCGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
22 14 0.30
23 20 0.43
24 13 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTTATATTTATATAAAATAAT
Found at i:3046524 original size:8 final size:8
Alignment explanation
Indices: 3046513--3046537 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3046503 TTTTTTTAAA
3046513 TTAAAAGT
1 TTAAAAGT
3046521 TTAAAAGT
1 TTAAAAGT
3046529 TTAAAAGT
1 TTAAAAGT
3046537 T
1 T
3046538 CAAATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (8 bp):
TTAAAAGT
Found at i:3055702 original size:15 final size:14
Alignment explanation
Indices: 3055682--3055733 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
3055672 GATAAAAAAT
3055682 AATTTTAATTATTGA
1 AATTTTAATTATT-A
3055697 AATTTTAATT-TTA
1 AATTTTAATTATTA
3055710 AATTTATTAATTATT-
1 AA-TT-TTAATTATTA
3055725 AATTTTAAT
1 AATTTTAAT
3055734 AACAATTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 8 0.24
14 6 0.18
15 18 0.53
16 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
AATTTTAATTATTA
Found at i:3055726 original size:22 final size:21
Alignment explanation
Indices: 3055681--3055732 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
3055671 AGATAAAAAA
3055681 TAATTTT-AATTATTGAAATTT
1 TAATTTTAAATTATT-AAATTT
3055702 TAATTTTAAATTTATT-AATTAT
1 TAATTTTAAA-TTATTAAATT-T
3055724 TAATTTTAA
1 TAATTTTAA
3055733 TAACAATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.39
22 12 0.43
23 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATTTTAAATTATTAAATTT
Found at i:3056308 original size:17 final size:16
Alignment explanation
Indices: 3056259--3056309 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 16
3056249 AAGAATGCAA
3056259 AGAATTAGTCACGAAT
1 AGAATTAGTCACGAAT
* * * *
3056275 A-AATTCGTGAAGTAT
1 AGAATTAGTCACGAAT
3056290 AGCAATTAGTCACGAAT
1 AG-AATTAGTCACGAAT
3056307 AGA
1 AGA
3056310 CTAATCGTGA
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 12 0.48
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (16 bp):
AGAATTAGTCACGAAT
Found at i:3062841 original size:20 final size:21
Alignment explanation
Indices: 3062805--3062856 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3062795 ATCGAAATTA
3062805 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
3062827 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
3062848 AT-AAATATT
1 ATAAAATATT
3062857 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:3062847 original size:21 final size:22
Alignment explanation
Indices: 3062805--3062856 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
3062795 ATCGAAATTA
3062805 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
3062827 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
3062848 AT-AAATATT
1 ATAAAATATT
3062857 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:3063469 original size:29 final size:28
Alignment explanation
Indices: 3063424--3063517 Score: 77
Period size: 28 Copynumber: 3.3 Consensus size: 28
3063414 TCTCAAAAAA
* *
3063424 AATTATTTTATAAAAAAATTAAAATTATC
1 AATTTTTTTA-AAAAAAATTAAAAATATC
*
3063453 AATTTTTTTAAATAAAAATTTTAAAAAGAT-
1 AATTTTTTTAAA-AAAAA--TTAAAAATATC
* * *
3063483 -A-TTTTTGAAAAAAAGTTAAAAGTATC
1 AATTTTTTTAAAAAAAATTAAAAATATC
3063509 AATTTTTTT
1 AATTTTTTT
3063518 TAAATAAAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
25 8 0.16
27 5 0.10
28 15 0.29
29 15 0.29
31 8 0.16
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (28 bp):
AATTTTTTTAAAAAAAATTAAAAATATC
Found at i:3063598 original size:60 final size:61
Alignment explanation
Indices: 3063419--3063816 Score: 365
Period size: 60 Copynumber: 6.7 Consensus size: 61
3063409 TAAAATCTCA
* *
3063419 AAAAAAAT-TATTTTATA-AAAAAA-TTAAAATTATCAATTTTT-TT---AAATAAAAATTTT
1 AAAAAAATAT-TTTTA-AGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAATAAAAATTTT
* * * * * *
3063475 AAAAAGATATTTTTGA-AAAAAAGTTAAAAGTATCAATTTTT-TT--TAAATAAAGATTCT
1 AAAAAAATATTTTTAAGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAATAAAAATTTT
*
3063532 AAAAAAATATTTTTGAGAAAAAA-TTGAGAA-TA-CTAATTTTTCTTAAAAAAT-AAAATTTT
1 AAAAAAATATTTTTAAGAAAAAAGTTGA-AAGTATC-AATTTTTCTTAAAAAATAAAAATTTT
* *
3063591 CAAAAAAAATATTTTTAA-AAAAAAGTTGAAAGTATCAA-TTTTCTTCAAAAATAAAAATTTC
1 --AAAAAAATATTTTTAAGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAATAAAAATTTT
* *
3063652 AGAAAAAATA-TTTTAAGGAAAAA-TT-AAGAGTATCAATTTTTCTTAAAAGATAAAAATTTT
1 A-AAAAAATATTTTTAAGAAAAAAGTTGAA-AGTATCAATTTTTCTTAAAAAATAAAAATTTT
* * **
3063712 AAAAAAATATTTTTCA-AAAAAAGTTGAAAGTATCAATTTTTTTTTTTAAAATAAAAATTTTT
1 AAAAAAATATTTTTAAGAAAAAAGTTGAAAGTATCAA-TTTTTCTTAAAAAATAAAAA-TTTT
* * *
3063774 AAAAAAA-AATTTTAAG-AAAAATTTGAAAGTATCACTTTTTCTT
1 AAAAAAATATTTTTAAGAAAAAAGTTGAAAGTATCAATTTTTCTT
3063817 GTATACATGC
Statistics
Matches: 289, Mismatches: 28, Indels: 46
0.80 0.08 0.13
Matches are distributed among these distances:
55 7 0.02
56 31 0.11
57 39 0.13
58 12 0.04
59 36 0.12
60 81 0.28
61 71 0.25
62 12 0.04
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (61 bp):
AAAAAAATATTTTTAAGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAATAAAAATTTT
Found at i:3063604 original size:15 final size:15
Alignment explanation
Indices: 3063576--3063614 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3063566 AATTTTTCTT
3063576 AAAAAATAAAATTTTC
1 AAAAAA-AAAATTTTC
* *
3063592 AAAAAAAATATTTTT
1 AAAAAAAAAATTTTC
3063607 AAAAAAAA
1 AAAAAAAA
3063615 GTTGAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAAAAAAATTTTC
Found at i:3063781 original size:14 final size:15
Alignment explanation
Indices: 3063754--3063786 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3063744 TCAATTTTTT
3063754 TTTTTAAAATAAAAA
1 TTTTTAAAATAAAAA
3063769 TTTTTAAAA-AAAAA
1 TTTTTAAAATAAAAA
3063783 TTTT
1 TTTT
3063787 AAGAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTTTAAAATAAAAA
Found at i:3063797 original size:12 final size:13
Alignment explanation
Indices: 3063755--3063794 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
3063745 CAATTTTTTT
3063755 TTTTAAAATAAAAA
1 TTTTAAAA-AAAAA
3063769 TTTTTAAAAAAAAA
1 -TTTTAAAAAAAAA
3063783 TTTTAAGAAAAA
1 TTTTAA-AAAAA
3063795 TTTGAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
TTTTAAAAAAAAA
Found at i:3069024 original size:21 final size:21
Alignment explanation
Indices: 3069000--3069044 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3068990 TTGTGAACCA
*
3069000 AAATCCTAGAAA-TTTTGGATG
1 AAATCCTA-AAATTTTTGAATG
*
3069021 AAATTCTAAAATTTTTGAATG
1 AAATCCTAAAATTTTTGAATG
3069042 AAA
1 AAA
3069045 ACCTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (21 bp):
AAATCCTAAAATTTTTGAATG
Found at i:3069218 original size:17 final size:17
Alignment explanation
Indices: 3069132--3069221 Score: 74
Period size: 17 Copynumber: 5.3 Consensus size: 17
3069122 AAGTCTTATA
* *
3069132 AATCTCTAATTTTTGCG
1 AATCTTTAATTCTTGCG
* *
3069149 AAT-TTGAAAATCTTGCG
1 AATCTT-TAATTCTTGCG
* * *
3069166 AATCTTCAATTTTTGTG
1 AATCTTTAATTCTTGCG
* *
3069183 AATCTTTAACTATTGCG
1 AATCTTTAATTCTTGCG
*
3069200 AATCTTTAATTCTTACG
1 AATCTTTAATTCTTGCG
3069217 AATCT
1 AATCT
3069222 ATTTTCCTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
16 1 0.02
17 53 0.95
18 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (17 bp):
AATCTTTAATTCTTGCG
Found at i:3069584 original size:85 final size:85
Alignment explanation
Indices: 3069444--3069697 Score: 382
Period size: 85 Copynumber: 3.0 Consensus size: 85
3069434 CATTTTATTC
* *
3069444 TTTGGCTTAGTCCAAGTTATTCTTTTCAGACTTCGGTTCAATCCAAGACATTTTGTTTTGGATTT
1 TTTGGCTTAGTCCAAGTTATTCTTTTCATACTTCGGTTCAATCCAAGTCATTTTGTTTTGGATTT
3069509 CGGCCTATGCTAGATCCTTA
66 CGGCCTATGCTAGATCCTTA
* *
3069529 TTTGGCTTAGTCCAAGTTATTATTTTCATACTTCGGTTCAATCTAAGTCATTTTGTTTTGGATTT
1 TTTGGCTTAGTCCAAGTTATTCTTTTCATACTTCGGTTCAATCCAAGTCATTTTGTTTTGGATTT
* * * *
3069594 CGACTTATGCTATATCCTTT
66 CGGCCTATGCTAGATCCTTA
** * *
3069614 TTTGGCTTAGTCCAAGTTATTCTTTTCATACTTCAATTTAATCCAGGTCATTTTGTTTTGGATTT
1 TTTGGCTTAGTCCAAGTTATTCTTTTCATACTTCGGTTCAATCCAAGTCATTTTGTTTTGGATTT
* *
3069679 CAGCCTATGCCAGATCCTT
66 CGGCCTATGCTAGATCCTT
3069698 TTTCAATTCA
Statistics
Matches: 150, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 150 1.00
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (85 bp):
TTTGGCTTAGTCCAAGTTATTCTTTTCATACTTCGGTTCAATCCAAGTCATTTTGTTTTGGATTT
CGGCCTATGCTAGATCCTTA
Found at i:3071294 original size:17 final size:17
Alignment explanation
Indices: 3071272--3071306 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3071262 CAGCTAGAAT
3071272 ACGTGAAAGAAAAGGCC
1 ACGTGAAAGAAAAGGCC
3071289 ACGTGAAAGAAAAGGCC
1 ACGTGAAAGAAAAGGCC
3071306 A
1 A
3071307 AGGCTAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.29, T:0.06
Consensus pattern (17 bp):
ACGTGAAAGAAAAGGCC
Found at i:3071958 original size:61 final size:59
Alignment explanation
Indices: 3071798--3072277 Score: 457
Period size: 61 Copynumber: 8.0 Consensus size: 59
3071788 AAATAAAAAA
* * * *
3071798 TAAAAAGATAAAATTTCAAATAAAA-ATTTACTTTATGAAAAAGTTAAAATTATCAATTTTT-T
1 TAAAAATA-AAAATTTCAAA-AAAATA-TT--TTTAAGAAAAAATTAAAAGTATCAATTTTTCT
* * *
3071860 T-AAAATAAAAATTT-GAAAAAGTATTTTTGAGAAAAAATTAAAAGTATCAATTTTTCT
1 TAAAAATAAAAATTTCAAAAAAATATTTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
*
3071917 TAAAAATAAAGATTTCAAAAAAATATATTTTTAAGAAAAAATTAAGAA-TA-CTAATTTTTCT
1 TAAAAATAAAAATTTC-AAAAAA-ATATTTTTAAGAAAAAATTAA-AAGTATC-AATTTTTCT
* * * *
3071978 TAAAAAGTAAAAATTTCAAGAAAATA-TTTTATGAAAAAGTTGAAAGTATCAATTTTTCT
1 TAAAAA-TAAAAATTTCAAAAAAATATTTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
* * *
3072037 TAAAAAATAAAAATTTTAAAAAAGGTATTTTTAAGAAAAAATTGAAAGTATCAA-TTTTCT
1 T-AAAAATAAAAATTTCAAAAAA-ATATTTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
* * * *
3072097 TCGAAAATAAAAATTTTCTTAAAAAA-A--TTTAAG-AAAAATTGATAGTATCAATTTTTCT
1 T-AAAAATAAAAA-TTTC-AAAAAAATATTTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
* * * *
3072155 TAAAGGATAAAAATTTCAAAAATATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTTCT
1 TAAA-AATAAAAATTTCAAAAAAATATTTTT-AAGAAAAAATTAAAAGTATCAATTTTTCT
* *
3072215 TGAAAATAAAAAGTTTTAAAGAAAA-ATATTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
1 TAAAAATAAAAA-TTTCAAA-AAAATAT-TTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
3072276 TA
1 TA
3072278 TATAAATGTA
Statistics
Matches: 352, Mismatches: 40, Indels: 53
0.79 0.09 0.12
Matches are distributed among these distances:
56 31 0.09
57 26 0.07
58 39 0.11
59 53 0.15
60 82 0.23
61 104 0.30
62 17 0.05
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (59 bp):
TAAAAATAAAAATTTCAAAAAAATATTTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
Found at i:3072024 original size:120 final size:118
Alignment explanation
Indices: 3071798--3072277 Score: 491
Period size: 120 Copynumber: 4.0 Consensus size: 118
3071788 AAATAAAAAA
* * * * * *
3071798 TAAAAAGATAAAATTTCAAATAAAAAT-TTACTTTATGAAAAAGTTAAAATTATCAATTTTT-TT
1 TAAAAATA-AAAATTTCAAA-AAATATATT--TTTAAGAAAAAATTGAAAGTATCAATTTTTCTT
* * *
3071861 -AAAATAAAAA-TTTGAAAAAGTATTTTTGAGAAAAAATTAAAAGTATCAATTTTTCT
62 GAAAATAAAAATTTTCAAAAAATA-TTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
* * *
3071917 TAAAAATAAAGATTTCAAAAAAATATATTTTTAAGAAAAAATT--AAGAATACTAATTTTTCTTA
1 TAAAAATAAAAATTTC-AAAAAATATATTTTTAAGAAAAAATTGAAAGTAT-C-AATTTTTCTTG
* * *
3071980 AAAAGTAAAAA-TTTCAAGAAAATATTTTATGAAAAAGTTGAAAGTATCAATTTTTCT
63 AAAA-TAAAAATTTTCAA-AAAATATTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
* **
3072037 TAAAAAATAAAAATTTTAAAAAAGGTATTTTTAAGAAAAAATTGAAAGTATCAA-TTTTCTTCGA
1 T-AAAAATAAAAATTTCAAAAAATATATTTTTAAGAAAAAATTGAAAGTATCAATTTTTCTT-GA
* *
3072101 AAATAAAAATTTTCTTAAAAAA-A-TTTAAG-AAAAATTGATAGTATCAATTTTTCT
64 AAATAAAAATTTTC--AAAAAATATTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
* *
3072155 TAAAGGATAAAAATTTC-AAAAATATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTTCTTGA
1 TAAA-AATAAAAATTTCAAAAAATATATTTTT-AAGAAAAAATTGAAAGTATCAATTTTTCTTGA
*
3072218 AAATAAAAAGTTTTAAAGAAAAATATTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
64 AAATAAAAA-TTTT-CA-AAAAATATTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
3072276 TA
1 TA
3072278 TATAAATGTA
Statistics
Matches: 307, Mismatches: 30, Indels: 46
0.80 0.08 0.12
Matches are distributed among these distances:
115 4 0.01
116 1 0.00
117 63 0.21
118 67 0.22
119 35 0.11
120 82 0.27
121 48 0.16
122 7 0.02
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (118 bp):
TAAAAATAAAAATTTCAAAAAATATATTTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTGAAA
ATAAAAATTTTCAAAAAATATTTTAAGAAAAAATTAAAAGTATCAATTTTTCT
Found at i:3079507 original size:24 final size:24
Alignment explanation
Indices: 3079480--3079555 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 24
3079470 AAATTATTTC
3079480 TTTAATTAATTAATTAATTTTATA
1 TTTAATTAATTAATTAATTTTATA
*
3079504 TTT-A-TATATATATTTAATTTTATA
1 TTTAATTA-AT-TAATTAATTTTATA
* *
3079528 TTTATATTAA-AAATAATATTTTATA
1 TTTA-ATTAATTAATTA-ATTTTATA
3079553 TTT
1 TTT
3079556 TTAAAAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
22 2 0.05
23 3 0.07
24 22 0.52
25 11 0.26
26 2 0.05
27 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTAATTAATTAATTAATTTTATA
Found at i:3079509 original size:6 final size:6
Alignment explanation
Indices: 3079498--3079535 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
3079488 ATTAATTAAT
*
3079498 TTTATA TTTATA TATATA TTTA-A TTTTATA TTTATA TT
1 TTTATA TTTATA TTTATA TTTATA -TTTATA TTTATA TT
3079536 AAAAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 1 0.04
6 26 0.93
7 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTATA
Found at i:3079554 original size:25 final size:23
Alignment explanation
Indices: 3079520--3079574 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
3079510 TATATATTTA
*
3079520 ATTTTATATTTATATTAAAAATAAT
1 ATTTTATATTT-T-TAAAAAATAAT
3079545 ATTTTATATTTTTAAAAAATAAT
1 ATTTTATATTTTTAAAAAATAAT
3079568 ATTTTAT
1 ATTTTAT
3079575 TAATTTCGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 17 0.59
24 1 0.03
25 11 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTTATATTTTTAAAAAATAAT
Found at i:3079562 original size:23 final size:25
Alignment explanation
Indices: 3079496--3079574 Score: 92
Period size: 24 Copynumber: 3.3 Consensus size: 25
3079486 TAATTAATTA
* * * *
3079496 ATTTTATATTTATATATATATTTA-
1 ATTTTATATTTATATAAAAAATAAT
*
3079520 ATTTTATATTTATATTAAAAATAAT
1 ATTTTATATTTATATAAAAAATAAT
3079545 ATTTTATATTT-T-TAAAAAATAAT
1 ATTTTATATTTATATAAAAAATAAT
3079568 ATTTTAT
1 ATTTTAT
3079575 TAATTTCGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 17 0.35
24 20 0.42
25 11 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTTATATTTATATAAAAAATAAT
Found at i:3080355 original size:8 final size:8
Alignment explanation
Indices: 3080344--3080368 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3080334 TTTTTTTAAA
3080344 TTAAAAGT
1 TTAAAAGT
3080352 TTAAAAGT
1 TTAAAAGT
3080360 TTAAAAGT
1 TTAAAAGT
3080368 T
1 T
3080369 CAAATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (8 bp):
TTAAAAGT
Found at i:3089557 original size:15 final size:14
Alignment explanation
Indices: 3089537--3089588 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
3089527 GATAAAAAAT
3089537 AATTTTAATTATTGA
1 AATTTTAATTATT-A
3089552 AATTTTAATT-TTA
1 AATTTTAATTATTA
3089565 AATTTATTAATTATT-
1 AA-TT-TTAATTATTA
3089580 AATTTTAAT
1 AATTTTAAT
3089589 AACAATTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 8 0.24
14 6 0.18
15 18 0.53
16 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
AATTTTAATTATTA
Found at i:3089581 original size:22 final size:21
Alignment explanation
Indices: 3089536--3089587 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
3089526 AGATAAAAAA
3089536 TAATTTT-AATTATTGAAATTT
1 TAATTTTAAATTATT-AAATTT
3089557 TAATTTTAAATTTATT-AATTAT
1 TAATTTTAAA-TTATTAAATT-T
3089579 TAATTTTAA
1 TAATTTTAA
3089588 TAACAATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.39
22 12 0.43
23 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATTTTAAATTATTAAATTT
Found at i:3090165 original size:17 final size:16
Alignment explanation
Indices: 3090116--3090166 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 16
3090106 AAGAATGCAA
3090116 AGAATTAGTCACGAAT
1 AGAATTAGTCACGAAT
* * * *
3090132 A-AATTCGTGAAGTAT
1 AGAATTAGTCACGAAT
3090147 AGCAATTAGTCACGAAT
1 AG-AATTAGTCACGAAT
3090164 AGA
1 AGA
3090167 CTAATCGTGA
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 12 0.48
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (16 bp):
AGAATTAGTCACGAAT
Found at i:3090689 original size:21 final size:21
Alignment explanation
Indices: 3090665--3090704 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3090655 TGAGATTCGA
* *
3090665 ATATCAAACTTATTAGATATT
1 ATATCAAAATAATTAGATATT
3090686 ATATCAAAATAATTAGATA
1 ATATCAAAATAATTAGATA
3090705 AACCAATTGA
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:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (21 bp):
ATATCAAAATAATTAGATATT
Found at i:3091650 original size:2 final size:2
Alignment explanation
Indices: 3091645--3091675 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3091635 TGTGTGTGTG
3091645 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3091676 TGAATGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3095332 original size:22 final size:22
Alignment explanation
Indices: 3095307--3095348 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3095297 TTCATAAATT
* *
3095307 ATTTGAATTCGATTCGAATAAA
1 ATTTAAATTCGACTCGAATAAA
*
3095329 ATTTAAATTTGACTCGAATA
1 ATTTAAATTCGACTCGAATA
3095349 TTATTGAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
ATTTAAATTCGACTCGAATAAA
Found at i:3101759 original size:24 final size:24
Alignment explanation
Indices: 3101724--3101775 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3101714 TCCCTCTAAT
3101724 CTCACCTCCTTCCAGCTAAGACAA
1 CTCACCTCCTTCCAGCTAAGACAA
* * *
3101748 CTCACCTTCTTCTAGGTAAGACAA
1 CTCACCTCCTTCCAGCTAAGACAA
3101772 CTCA
1 CTCA
3101776 AAAACACCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.37, G:0.10, T:0.25
Consensus pattern (24 bp):
CTCACCTCCTTCCAGCTAAGACAA
Found at i:3101820 original size:16 final size:15
Alignment explanation
Indices: 3101799--3101828 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3101789 CAATTATACA
3101799 TATATTTATATATTAG
1 TATATTTATA-ATTAG
3101815 TATATTTATAATTA
1 TATATTTATAATTA
3101829 TAATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TATATTTATAATTAG
Found at i:3101889 original size:28 final size:27
Alignment explanation
Indices: 3101826--3101891 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
3101816 ATATTTATAA
* *
3101826 TTATAATTTTTTATTTAATATTAGATAT
1 TTAT-ATTTTTTAATTAATAATAGATAT
* * *
3101854 TTAAATTTTTTAATTATTAATAGATTT
1 TTATATTTTTTAATTAATAATAGATAT
3101881 GTTATATTTTT
1 -TTATATTTTT
3101892 AAAAAATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 19 0.61
28 12 0.39
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (27 bp):
TTATATTTTTTAATTAATAATAGATAT
Found at i:3104792 original size:5 final size:5
Alignment explanation
Indices: 3104777--3104809 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3104767 TAAACGGCAA
*
3104777 GGTTG GTTTG GGTTG GGTTG GGTTG GGTTG GGT
1 GGTTG GGTTG GGTTG GGTTG GGTTG GGTTG GGT
3104810 GAGGGAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.58, T:0.42
Consensus pattern (5 bp):
GGTTG
Found at i:3106401 original size:24 final size:24
Alignment explanation
Indices: 3106374--3106428 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
3106364 TTTTTATTAA
* *
3106374 AATTTTTTTAATCATAATTATAAT
1 AATTTTTTAAATCATAAGTATAAT
*
3106398 AATTTTTTAAATTATAAGTATAAT
1 AATTTTTTAAATCATAAGTATAAT
*
3106422 AACTTTT
1 AATTTTT
3106429 ATTATTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (24 bp):
AATTTTTTAAATCATAAGTATAAT
Found at i:3106435 original size:24 final size:23
Alignment explanation
Indices: 3106377--3106436 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
3106367 TTATTAAAAT
* *
3106377 TTTTTTAATCATAATTATAATAA
1 TTTTTTAATTATAAGTATAATAA
3106400 TTTTTTAAATTATAAGTATAATAA
1 TTTTTT-AATTATAAGTATAATAA
3106424 CTTTTATT-ATTAT
1 -TTTT-TTAATTAT
3106437 TTTTAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 6 0.19
24 20 0.62
25 4 0.12
26 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTTTAATTATAAGTATAATAA
Found at i:3106949 original size:19 final size:19
Alignment explanation
Indices: 3106925--3106961 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3106915 TAATTTAATT
3106925 TTATATTAAATTTATTTAA
1 TTATATTAAATTTATTTAA
**
3106944 TTATATTTTATTTATTTA
1 TTATATTAAATTTATTTA
3106962 TTAATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATATTAAATTTATTTAA
Found at i:3107638 original size:33 final size:33
Alignment explanation
Indices: 3107596--3107659 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
3107586 TCATCCCTAT
3107596 CCATCTCTTCATTTCTTGCCATTCTTTTTTTAC
1 CCATCTCTTCATTTCTTGCCATTCTTTTTTTAC
3107629 CCATCTCTTCATTTCTTGCCATTCTTTTTTT
1 CCATCTCTTCATTTCTTGCCATTCTTTTTTT
3107660 TTTTTCAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.11, C:0.30, G:0.03, T:0.56
Consensus pattern (33 bp):
CCATCTCTTCATTTCTTGCCATTCTTTTTTTAC
Found at i:3107963 original size:11 final size:11
Alignment explanation
Indices: 3107943--3107980 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3107933 AATATATCAA
3107943 TAAATAATAAT
1 TAAATAATAAT
*
3107954 TAAATTATAAT
1 TAAATAATAAT
*
3107965 TAAATAA-ATT
1 TAAATAATAAT
3107975 TAAATA
1 TAAATA
3107981 GAAAACTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATAATAAT
Found at i:3108058 original size:4 final size:4
Alignment explanation
Indices: 3108049--3108106 Score: 52
Period size: 4 Copynumber: 15.5 Consensus size: 4
3108039 TATTATTATT
* * * *
3108049 ATAA ATAA AT-A AGAA ATAA AT-A ATAA ATAT AT-A ATAA ATGA ATGA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
3108094 AT-A ATAA ATAA AT
1 ATAA ATAA ATAA AT
3108107 TATAAATGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
3 10 0.22
4 35 0.78
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:3108096 original size:26 final size:26
Alignment explanation
Indices: 3108067--3108117 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
3108057 ATAAGAAATA
*
3108067 AATAATAAATATATAATAAATGAATG
1 AATAATAAATAAATAATAAATGAATG
*
3108093 AATAATAAATAAATTATAAATGAAT
1 AATAATAAATAAATAATAAATGAAT
3108118 TTATTTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (26 bp):
AATAATAAATAAATAATAAATGAATG
Found at i:3108113 original size:11 final size:11
Alignment explanation
Indices: 3108049--3108104 Score: 69
Period size: 11 Copynumber: 5.1 Consensus size: 11
3108039 TATTATTATT
3108049 ATAAATAAATA
1 ATAAATAAATA
*
3108060 AGAAATAAATA
1 ATAAATAAATA
*
3108071 ATAAATATATA
1 ATAAATAAATA
*
3108082 ATAAATGAATGA
1 ATAAATAAAT-A
3108094 AT-AATAAATA
1 ATAAATAAATA
3108104 A
1 A
3108105 ATTATAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
10 2 0.05
11 33 0.87
12 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (11 bp):
ATAAATAAATA
Found at i:3109198 original size:23 final size:23
Alignment explanation
Indices: 3109172--3109216 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3109162 TAAAAATTAT
3109172 ATTCATAATTAAATATTATATTC
1 ATTCATAATTAAATATTATATTC
*
3109195 ATTCATAATTAATTATTATATT
1 ATTCATAATTAAATATTATATT
3109217 ATTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTCATAATTAAATATTATATTC
Found at i:3109225 original size:23 final size:23
Alignment explanation
Indices: 3109176--3109232 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
3109166 AATTATATTC
* *
3109176 ATAATTAAATATTATATTCATTC
1 ATAATTAATTATTATATTCATTA
3109199 ATAATTAATTATTATATT-ATTAA
1 ATAATTAATTATTATATTCATT-A
*
3109222 ATAATCAATTA
1 ATAATTAATTA
3109233 ATAAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATTAATTATTATATTCATTA
Found at i:3109748 original size:24 final size:24
Alignment explanation
Indices: 3109721--3109767 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
3109711 TATGAACGAT
3109721 TTATAAATATAATATAA-ATTAAAC
1 TTAT-AATATAATATAATATTAAAC
**
3109745 TTATAATATGTTATAATATTAAA
1 TTATAATATAATATAATATTAAA
3109768 ATGAGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TTATAATATAATATAATATTAAAC
Found at i:3114064 original size:43 final size:43
Alignment explanation
Indices: 3114016--3114104 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
3114006 CTTCAGTTGC
* ** * *
3114016 AATGAACTTTCCATGTTTTCCTGATAGATTATTTTAATTTCGA
1 AATGAACTTTCCACGTAATCCTGATAGACTATTTTAATTTCCA
*
3114059 AATGAACTTTCCACGTAATCCTGATGGACTATTTTAATTTCCA
1 AATGAACTTTCCACGTAATCCTGATAGACTATTTTAATTTCCA
3114102 AAT
1 AAT
3114105 TAGACTTGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (43 bp):
AATGAACTTTCCACGTAATCCTGATAGACTATTTTAATTTCCA
Found at i:3118508 original size:14 final size:14
Alignment explanation
Indices: 3118461--3118508 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3118451 TTCAATTCAC
*
3118461 ATATATAAAAATAAT
1 ATATATAATAA-AAT
3118476 ATA-ATAATAAAA-
1 ATATATAATAAAAT
3118488 AT-T-TAATAAAAT
1 ATATATAATAAAAT
3118500 ATATATAAT
1 ATATATAAT
3118509 TTTTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
11 8 0.29
12 4 0.14
13 3 0.11
14 10 0.36
15 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATATAATAAAAT
Found at i:3118546 original size:15 final size:15
Alignment explanation
Indices: 3118518--3118559 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
3118508 TTTTTAATTT
3118518 TTTATATATAAATTAA
1 TTTATATAT-AATTAA
3118534 TTTATATATAATTAA
1 TTTATATATAATTAA
**
3118549 CATATATATAA
1 TTTATATATAA
3118560 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTATATATAATTAA
Found at i:3119107 original size:18 final size:18
Alignment explanation
Indices: 3119084--3119148 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
3119074 TTTTAAAATT
3119084 TTTTATATAAAATATATA
1 TTTTATATAAAATATATA
*
3119102 TTTTATATAACATATA-A
1 TTTTATATAAAATATATA
**
3119119 TATAAATATAAAATAATATAA
1 T-TTTATATAAAAT-ATAT-A
3119140 TTTGTATAT
1 TTT-TATAT
3119149 TTTTAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
17 2 0.06
18 24 0.67
19 3 0.08
20 1 0.03
21 6 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TTTTATATAAAATATATA
Found at i:3119457 original size:26 final size:25
Alignment explanation
Indices: 3119400--3119499 Score: 91
Period size: 28 Copynumber: 3.9 Consensus size: 25
3119390 TCTATTTTTT
3119400 TATTTTTTTTAA-ACGTTTCAAAATTATA
1 TATTTTTTTTAATA--TTT-AAAATT-TA
*
3119428 TATTTTTTTTGAATATTTAAAATTTT
1 TATTTTTTTT-AATATTTAAAATTTA
*
3119454 TATTTTTTAT-AT-TTTAAAA-TTA
1 TATTTTTTTTAATATTTAAAATTTA
*
3119476 TATTTATTTTTAATATTAAAAATT
1 TATTT-TTTTTAATATTTAAAATT
3119500 ATAAAATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
22 7 0.11
23 11 0.18
24 4 0.07
25 6 0.10
26 11 0.18
27 6 0.10
28 13 0.21
29 2 0.03
30 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTTTTTTTAATATTTAAAATTTA
Found at i:3119510 original size:48 final size:49
Alignment explanation
Indices: 3119419--3119544 Score: 123
Period size: 49 Copynumber: 2.6 Consensus size: 49
3119409 TAAACGTTTC
* * * * **
3119419 AAAATTATATATTTTTTTTGAATATTTAAAATTTTTATTTTTTATAT-TT-T
1 AAAATTATAT-TTATTTTT-AATATTAAAAATTATAAAATTTTA-ATCTTAT
3119469 AAAATTATATTTATTTTTAATATTAAAAATTATAAAATTTTAATCTTAT
1 AAAATTATATTTATTTTTAATATTAAAAATTATAAAATTTTAATCTTAT
* *
3119518 AAATATT-TTTTTAATTTTAATATTAAA
1 AAA-ATTATATTTATTTTTAATATTAAA
3119545 TATATTAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
47 2 0.03
48 21 0.32
49 29 0.45
50 13 0.20
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (49 bp):
AAAATTATATTTATTTTTAATATTAAAAATTATAAAATTTTAATCTTAT
Found at i:3135861 original size:16 final size:17
Alignment explanation
Indices: 3135840--3135872 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3135830 TTTTATTATT
*
3135840 ATATTTTAT-TTTTTTA
1 ATATTTAATATTTTTTA
3135856 ATATTTAATATTTTTTA
1 ATATTTAATATTTTTTA
3135873 TTTTAGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATATTTAATATTTTTTA
Found at i:3137178 original size:32 final size:32
Alignment explanation
Indices: 3137137--3137201 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3137127 ACACTCTCTT
3137137 TAATCTTAAGAGCTTAGTTTCACGTAACAAAC
1 TAATCTTAAGAGCTTAGTTTCACGTAACAAAC
3137169 TAATCTTAAGAGCTTAGTTTCACGTAACAAAC
1 TAATCTTAAGAGCTTAGTTTCACGTAACAAAC
3137201 T
1 T
3137202 TCGAAACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.32
Consensus pattern (32 bp):
TAATCTTAAGAGCTTAGTTTCACGTAACAAAC
Found at i:3138901 original size:6 final size:6
Alignment explanation
Indices: 3138890--3138914 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3138880 GGTAGTTAAT
3138890 AATACA AATACA AATACA AATACA A
1 AATACA AATACA AATACA AATACA A
3138915 TCTATAATCT
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:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AATACA
Found at i:3144096 original size:53 final size:56
Alignment explanation
Indices: 3143991--3144120 Score: 149
Period size: 56 Copynumber: 2.3 Consensus size: 56
3143981 TTGACTTGAT
*
3143991 GATCTTATATATATA-TATGCTAAGTACTTGATGATCTTATATATTATATATATAA
1 GATCTTATATATATATTAAGCTAAGTACTTGATGATCTTATATATTATATATATAA
* *
3144046 GATCTTATATATATATGTAAGAC-AAG-ACTTGATGATCTTCTATATTTATATTATATTA
1 GATCTTATATATATAT-TAAG-CTAAGTACTTGATGATCTTATATA-TTATA-TATATAA
* *
3144104 TATATATATATATATAT
1 GATCT-TATATATATAT
3144121 ATATACATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
55 15 0.23
56 17 0.27
57 11 0.17
58 10 0.16
59 11 0.17
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.46
Consensus pattern (56 bp):
GATCTTATATATATATTAAGCTAAGTACTTGATGATCTTATATATTATATATATAA
Found at i:3144109 original size:2 final size:2
Alignment explanation
Indices: 3144086--3144130 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
3144076 GATGATCTTC
*
3144086 TA TA TT TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3144126 CA TA T
1 TA TA T
3144131 TCCCAACCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3146650 original size:11 final size:11
Alignment explanation
Indices: 3146634--3146673 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
3146624 TAATTTTCTT
3146634 ATTTTTATTAA
1 ATTTTTATTAA
3146645 ATTTTTATATAA
1 ATTTTTAT-TAA
3146657 A-TTTTATTAA
1 ATTTTTATTAA
*
3146667 AATTTTA
1 ATTTTTA
3146674 GATCGTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 19 0.70
12 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTTTATTAA
Found at i:3147510 original size:20 final size:20
Alignment explanation
Indices: 3147485--3147523 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3147475 ATTTCATATT
*
3147485 AAAAATAATATATAAAAATA
1 AAAAATAAAATATAAAAATA
*
3147505 AAAAATAAAATTTAAAAAT
1 AAAAATAAAATATAAAAAT
3147524 CGATGAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATAAAATATAAAAATA
Found at i:3148830 original size:13 final size:13
Alignment explanation
Indices: 3148812--3148837 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3148802 TATCAATATC
3148812 TTTTTACTAGAAA
1 TTTTTACTAGAAA
3148825 TTTTTACTAGAAA
1 TTTTTACTAGAAA
3148838 AAAGATATGT
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:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTTTACTAGAAA
Found at i:3154688 original size:28 final size:28
Alignment explanation
Indices: 3154635--3154688 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3154625 AATTAACATA
* *
3154635 TCTAATTTTATTATTTACTTTTAATACG
1 TCTAATTTTATCATTTACTTTAAATACG
3154663 TCTAATTTTATCATTTA-TTTCAAATA
1 TCTAATTTTATCATTTACTTT-AAATA
3154689 AACAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.56
Consensus pattern (28 bp):
TCTAATTTTATCATTTACTTTAAATACG
Found at i:3155297 original size:18 final size:17
Alignment explanation
Indices: 3155272--3155309 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3155262 TAGATACCAT
3155272 TTTATTATTATTA-TTTA
1 TTTATTATT-TTATTTTA
3155289 TTTATTTATTTTATTTTA
1 TTTA-TTATTTTATTTTA
3155307 TTT
1 TTT
3155310 TCTCTTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTATTTTATTTTA
Found at i:3155306 original size:14 final size:14
Alignment explanation
Indices: 3155270--3155309 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
3155260 TGTAGATACC
3155270 ATTTTATTATTA-TT
1 ATTTTATT-TTATTT
3155284 A-TTTA-TTTATTT
1 ATTTTATTTTATTT
3155296 ATTTTATTTTATTT
1 ATTTTATTTTATTT
3155310 TCTCTTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.13
12 4 0.17
13 8 0.35
14 8 0.35
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
ATTTTATTTTATTT
Found at i:3156141 original size:20 final size:19
Alignment explanation
Indices: 3156090--3156145 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 19
3156080 AATTGAATCA
3156090 GATTAGATCAAACTAAACCATT
1 GATTAGATC--AC-AAACCATT
*
3156112 GACT-GAATCATCAAACCATT
1 GATTAG-ATCA-CAAACCATT
3156132 GATTAGATCACAAA
1 GATTAGATCACAAA
3156146 ACTGCTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 4 0.14
20 16 0.55
21 3 0.10
22 6 0.21
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.25
Consensus pattern (19 bp):
GATTAGATCACAAACCATT
Found at i:3156265 original size:14 final size:15
Alignment explanation
Indices: 3156246--3156278 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
3156236 TTTTATATGT
3156246 TATTTTTATT-TTAA
1 TATTTTTATTATTAA
3156260 -ATTTTTATTATTAA
1 TATTTTTATTATTAA
3156274 TATTT
1 TATTT
3156279 ATGCATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTTATTATTAA
Found at i:3160688 original size:20 final size:21
Alignment explanation
Indices: 3160643--3160691 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
3160633 ACCGAAATTA
3160643 ATAAAATA-T-TTTTTAAAAT
1 ATAAAATATTATTTTTAAAAT
3160662 ATAAAATATTATTTTTAAAAT
1 ATAAAATATTATTTTTAAAAT
3160683 AT-AAATATT
1 ATAAAATATT
3160692 TAAATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.29
20 8 0.29
21 12 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:3160697 original size:8 final size:8
Alignment explanation
Indices: 3160677--3160717 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3160667 ATATTATTTT
3160677 TAAA-ATA
1 TAAATATA
*
3160684 TAAATATT
1 TAAATATA
3160692 TAAATATA
1 TAAATATA
*
3160700 TAATTATA
1 TAAATATA
3160708 TAAATATA
1 TAAATATA
3160716 TA
1 TA
3160718 TAAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAATATA
Found at i:3160730 original size:26 final size:24
Alignment explanation
Indices: 3160681--3160731 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
3160671 TATTTTTAAA
* *
3160681 ATATAAATATTTAAATATATAATT
1 ATATAAATATTTAAATAAAAAATT
3160705 ATATAAATATATATAAATAAAAAATT
1 ATATAAATAT-T-TAAATAAAAAATT
3160731 A
1 A
3160732 ATTAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 1 0.04
26 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATAAATATTTAAATAAAAAATT
Found at i:3165380 original size:25 final size:27
Alignment explanation
Indices: 3165352--3165410 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
3165342 TTCAAAATTA
3165352 ATAAAATAATA-TTTTTTAA-A-AATAT
1 ATAAAATAATATTTTTTTAATATAA-AT
*
3165377 ATAAAATATTATTTTTTTAATATAAAT
1 ATAAAATAATATTTTTTTAATATAAAT
3165404 ATAAAAT
1 ATAAAAT
3165411 TAAATAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 10 0.33
26 8 0.27
27 10 0.33
28 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAAAATAATATTTTTTTAATATAAAT
Found at i:3165412 original size:25 final size:25
Alignment explanation
Indices: 3165352--3165412 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
3165342 TTCAAAATTA
*
3165352 ATAAAATAATATTTTTTAAAAATAT
1 ATAAAATTATATTTTTTAAAAATAT
3165377 ATAAAA-TATTATTTTTTTAATATAA-AT
1 ATAAAATTA-TA-TTTTTTAA-A-AATAT
3165404 ATAAAATTA
1 ATAAAATTA
3165413 AATAAATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 1 0.03
25 8 0.27
26 8 0.27
27 9 0.30
28 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATAAAATTATATTTTTTAAAAATAT
Found at i:3166035 original size:42 final size:42
Alignment explanation
Indices: 3165967--3166073 Score: 162
Period size: 42 Copynumber: 2.5 Consensus size: 42
3165957 TTAGCTATCA
* * *
3165967 CATAAGATTACTTTCTCCTTAACCACCCTTCCACTAATATGG
1 CATATGATTATTTTCTCCTTAGCCACCCTTCCACTAATATGG
3166009 CATATGATTATTTTCTCCTTAGCCACCCTTCCACTAATATGG
1 CATATGATTATTTTCTCCTTAGCCACCCTTCCACTAATATGG
*
3166051 CATCTGATTACTTTT-TCCTTAGC
1 CATATGATTA-TTTTCTCCTTAGC
3166074 TAAAGCAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 56 0.93
43 4 0.07
ACGTcount: A:0.24, C:0.29, G:0.08, T:0.38
Consensus pattern (42 bp):
CATATGATTATTTTCTCCTTAGCCACCCTTCCACTAATATGG
Found at i:3167818 original size:13 final size:13
Alignment explanation
Indices: 3167800--3167825 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3167790 ATCATGGACA
3167800 CTAATTAATGTAT
1 CTAATTAATGTAT
3167813 CTAATTAATGTAT
1 CTAATTAATGTAT
3167826 GTTAAGTTAT
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:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
CTAATTAATGTAT
Found at i:3169368 original size:25 final size:24
Alignment explanation
Indices: 3169330--3169382 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
3169320 TTATTTTTTC
*
3169330 ATTTTTTTTGT-TTTTGCTAT-TT
1 ATTTTTTTTTTATTTTGCTATCTT
*
3169352 ATTTTTTTTATTATTTTGTTATCTT
1 ATTTTTTTT-TTATTTTGCTATCTT
3169377 ATTTTT
1 ATTTTT
3169383 AATGTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 1 0.04
24 8 0.31
25 8 0.31
ACGTcount: A:0.13, C:0.04, G:0.06, T:0.77
Consensus pattern (24 bp):
ATTTTTTTTTTATTTTGCTATCTT
Found at i:3169517 original size:19 final size:19
Alignment explanation
Indices: 3169493--3169532 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3169483 AAATTGGAAA
3169493 AAATAAAAAAATGAAAAAT
1 AAATAAAAAAATGAAAAAT
* * *
3169512 AAATAAATATATTAAAAAT
1 AAATAAAAAAATGAAAAAT
3169531 AA
1 AA
3169533 GAAAAGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (19 bp):
AAATAAAAAAATGAAAAAT
Found at i:3171805 original size:51 final size:52
Alignment explanation
Indices: 3171729--3171852 Score: 171
Period size: 52 Copynumber: 2.4 Consensus size: 52
3171719 TATAACCATA
*
3171729 CAAACTTGTCC-ATTAAGAATCCCTTT-CATCTAGAATTCTTCTCCTGTAAAT
1 CAAACTTG-CCTATTAAGAATCCCTTTCCATCTAGAATTCTTCTCCTGCAAAT
* * * *
3171780 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCATCTAGAATTCTTCTCCTGCAAAT
*
3171832 CAAACTTACCTATTAAGAATC
1 CAAACTTGCCTATTAAGAATC
3171853 ATTTTTCTCT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
50 2 0.03
51 23 0.35
52 40 0.62
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCATCTAGAATTCTTCTCCTGCAAAT
Found at i:3171837 original size:52 final size:51
Alignment explanation
Indices: 3171729--3171884 Score: 170
Period size: 52 Copynumber: 3.0 Consensus size: 51
3171719 TATAACCATA
* * * * *
3171729 CAAACTTGTCC-ATTAAGAATCCCTTTCATCTAGAATTCTTCTCCTGTAAAT
1 CAAACTTG-CCTATTAAGAATCCCTTTCTTTTAGAATTCTTCTCTTGCAAGT
3171780 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTT-CTTTTAGAATTCTTCTCTTGCAAGT
* ** * * * *
3171832 CAAACTTACCTATTAAGAATCATTTTTCTCTTAGAATTTTTTTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC-CCTTTCTTTTAGAATTCTTCTCTTGCAAGT
3171884 C
1 C
3171885 TTCTTATCCA
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
50 2 0.02
51 23 0.26
52 62 0.69
53 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCCTTTCTTTTAGAATTCTTCTCTTGCAAGT
Found at i:3171927 original size:11 final size:11
Alignment explanation
Indices: 3171911--3171935 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3171901 AATATCTGAT
3171911 AAATCTCAAAC
1 AAATCTCAAAC
3171922 AAATCTCAAAC
1 AAATCTCAAAC
3171933 AAA
1 AAA
3171936 CCTCTTATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATCTCAAAC
Found at i:3172454 original size:16 final size:17
Alignment explanation
Indices: 3172424--3172456 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3172414 ATAAACTTAA
3172424 TTTTTAAAAATTTAAAT
1 TTTTTAAAAATTTAAAT
*
3172441 TTTTTTAAAA-TTAAAT
1 TTTTTAAAAATTTAAAT
3172457 AATTAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTAAAAATTTAAAT
Found at i:3175546 original size:13 final size:13
Alignment explanation
Indices: 3175528--3175553 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3175518 TAATTTATCG
3175528 ATTTTAATTTTTA
1 ATTTTAATTTTTA
3175541 ATTTTAATTTTTA
1 ATTTTAATTTTTA
3175554 TTTAATCATT
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):
ATTTTAATTTTTA
Found at i:3176746 original size:17 final size:17
Alignment explanation
Indices: 3176712--3176759 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
3176702 TTATTTAAAG
*
3176712 ATAAATATTCTTAATAA
1 ATAAAAATTCTTAATAA
* *
3176729 ATAAAAATTTTTAGTAA
1 ATAAAAATTCTTAATAA
*
3176746 ATTAAAATTCTTAA
1 ATAAAAATTCTTAA
3176760 CGATCAAGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (17 bp):
ATAAAAATTCTTAATAA
Found at i:3176833 original size:27 final size:27
Alignment explanation
Indices: 3176773--3176833 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
3176763 TCAAGTAATA
* *
3176773 AAATTTTATAAATATAAAATAATTATT
1 AAATTTTATAAATATAAAATAAATATG
*
3176800 AACTTTTA-AAATTATGAAAA-AAATATG
1 AAATTTTATAAA-TAT-AAAATAAATATG
3176827 AAATTTT
1 AAATTTT
3176834 TATATGAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.11
27 21 0.75
28 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (27 bp):
AAATTTTATAAATATAAAATAAATATG
Found at i:3179978 original size:18 final size:18
Alignment explanation
Indices: 3179955--3179991 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3179945 TGAGATGAGG
*
3179955 TGATATACAGGAGAAACT
1 TGATATACAAGAGAAACT
3179973 TGATATACAAGAGAAACT
1 TGATATACAAGAGAAACT
3179991 T
1 T
3179992 TCTTTAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (18 bp):
TGATATACAAGAGAAACT
Found at i:3180721 original size:20 final size:20
Alignment explanation
Indices: 3180681--3180736 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
3180671 GTAAGTTGTA
*
3180681 ATAT-AATATATACATAT-AT
1 ATATAAATATATA-ATTTAAT
*
3180700 ATATAAATATATTATTTAAT
1 ATATAAATATATAATTTAAT
* *
3180720 ATTTTAATATATAATTT
1 ATATAAATATATAATTT
3180737 TTTATAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATAAATATATAATTTAAT
Found at i:3182803 original size:15 final size:15
Alignment explanation
Indices: 3182780--3182809 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3182770 ATTTTTCTGT
*
3182780 TTTTTTTTTACTTTC
1 TTTTATTTTACTTTC
3182795 TTTTATTTTACTTTC
1 TTTTATTTTACTTTC
3182810 ATTTCCTTCA
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:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTTTACTTTC
Found at i:3183082 original size:26 final size:25
Alignment explanation
Indices: 3183041--3183092 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
3183031 TCATTAATAA
3183041 ATATTAAATGAATATGTTCACAAAT
1 ATATTAAATGAATATGTTCACAAAT
* *
3183066 ATATATAAATGATTATGTTCATAAAT
1 ATAT-TAAATGAATATGTTCACAAAT
3183092 A
1 A
3183093 ATAAACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (25 bp):
ATATTAAATGAATATGTTCACAAAT
Found at i:3183127 original size:10 final size:10
Alignment explanation
Indices: 3183123--3183182 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
3183113 CAAATTTAAA
3183123 TAAATAAATAT
1 TAAATAAAT-T
*
3183134 TAAATAAATA
1 TAAATAAATT
*
3183144 TAAATAAACT
1 TAAATAAATT
*
3183154 TAAATAAATA
1 TAAATAAATT
*
3183164 TAAATGAACTT
1 TAAAT-AAATT
*
3183175 AAAATAAA
1 TAAATAAA
3183183 AAATTAAAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
10 23 0.59
11 16 0.41
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (10 bp):
TAAATAAATT
Found at i:3183158 original size:20 final size:20
Alignment explanation
Indices: 3183122--3183182 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
3183112 TCAAATTTAA
*
3183122 ATAAATAAATATTAAATAAAT
1 ATAAATAAA-CTTAAATAAAT
3183143 ATAAATAAACTTAAATAAAT
1 ATAAATAAACTTAAATAAAT
*
3183163 ATAAATGAACTTAAAATAAA
1 ATAAATAAACTT-AAATAAA
3183183 AAATTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (20 bp):
ATAAATAAACTTAAATAAAT
Found at i:3186557 original size:12 final size:12
Alignment explanation
Indices: 3186540--3186566 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3186530 CTTTTAAAAT
3186540 TTAAATATTATA
1 TTAAATATTATA
3186552 TTAAATATTATA
1 TTAAATATTATA
3186564 TTA
1 TTA
3186567 TAATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATATTATA
Found at i:3187410 original size:2 final size:2
Alignment explanation
Indices: 3187403--3187430 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3187393 ATATTTTAAT
3187403 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
3187431 AATGTGCGAG
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:3190854 original size:3 final size:3
Alignment explanation
Indices: 3190839--3190872 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3190829 AAGACGTACA
*
3190839 ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3190873 AAGGCGAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:3193584 original size:19 final size:19
Alignment explanation
Indices: 3193542--3193585 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3193532 AAATTAAAAT
*
3193542 TAAAATTTTTAATTTATAA
1 TAAAAATTTTAATTTATAA
*
3193561 AAAAAATTTTAATTTA-AGA
1 TAAAAATTTTAATTTATA-A
3193580 TAAAAA
1 TAAAAA
3193586 AGGGATTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAAAATTTTAATTTATAA
Found at i:3195521 original size:19 final size:21
Alignment explanation
Indices: 3195472--3195521 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
3195462 GGGGCACGTG
*
3195472 GGTGGATGGGGGATTGGGTGA
1 GGTGGGTGGGGGATTGGGTGA
3195493 GGTGGG-GGGGGA-TGGAGTG-
1 GGTGGGTGGGGGATTGG-GTGA
3195512 GG-GGGTGGGG
1 GGTGGGTGGGG
3195522 TCATGAGGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.12
19 9 0.35
20 9 0.35
21 5 0.19
ACGTcount: A:0.10, C:0.00, G:0.72, T:0.18
Consensus pattern (21 bp):
GGTGGGTGGGGGATTGGGTGA
Found at i:3195757 original size:16 final size:16
Alignment explanation
Indices: 3195738--3195768 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3195728 TAAAATTAAA
*
3195738 ATTATATTTTAATTTT
1 ATTATATATTAATTTT
3195754 ATTATATATTAATTT
1 ATTATATATTAATTT
3195769 ATGATTTTAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTATATATTAATTTT
Found at i:3196050 original size:25 final size:26
Alignment explanation
Indices: 3196022--3196070 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
3196012 TAAAAACTAA
3196022 AAAATATAAGTTTG-AAAATTTTATT
1 AAAATATAAGTTTGAAAAATTTTATT
3196047 AAAATATAAGTTTGAAAAATTTTA
1 AAAATATAAGTTTGAAAAATTTTA
3196071 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAAATTTTATT
Found at i:3196172 original size:495 final size:492
Alignment explanation
Indices: 3195572--3196515 Score: 1502
Period size: 495 Copynumber: 1.9 Consensus size: 492
3195562 AATTTTGTAA
* * * **
3195572 TTAATTTTTAAAAATTTTTTGGATAAAATTTAATTAAAGGTTTTGAAAATTTATAATTAAAAAAA
1 TTAATTTTTAAAAACTTTTTAGATAAAATCTAATTAAAGGGATTGAAAATTTATAATTAAAAAAA
*
3195637 TTAAGGGATTAATAATTTAATATAATATATATAGAGATTTTAGATGAAAAATTTTGAT-AATTTT
66 TTAAGGGATTAATAATTCAATATAATATATATAGAGATTTTAGATG-AAAATTTTGATAAATTTT
* *
3195701 TTTTGAATAAGTTAGATGAAAAATAATTAAAATTAAA-ATTATATTTTAATTTTATTATATATTA
130 TTTTGAATAAGTTAAATGAAAAATAATTAAAATTAAATATTATATTTTAATTGTATTATATATTA
* * * *
3195765 ATTTATGATTTTATATTTGAAATTTAATAATTTTTTTGTTGTTTTGATATTTATATTGTTGTCAA
195 ATTTATAATTTTATATCT-AAAATTAATAATTTTTTTGTTATTTTGATATTTATATTGTTGTCAA
* * * *
3195830 TTTTTTTTATATTAGATTAATTTTTACTATTTTTGTA-TAATTATTGAAGATTCTATTTATTATA
259 TTCTTTTGATATTAGATTAATTCTTACTATTTTTG-AGTAATTATTGAAAATTCTATTTATTATA
*
3195894 TAATTATTGAAAG-TAATTTGTGATAAAAAAAATTTATATCAATTAGTGTATCAAAAATATTAAG
323 TAATTATTGAAAGCT-ATTTGTGAT-AAAAAAATTTATATCAATTAGTGTATCAAAAAGATTAAG
3195958 TTACTTAATAAATTTAGCATTTTATGATCTATTACTCTTATTAAGATTAAAAACTAAAAACTAAA
386 TTACTTAATAAATTTAGCATTTTATGATCTATTACTCTTA--AA-ATTAAAAACTAAAAACTAAA
3196023 AAATATAAGTTTGAAAATTTTATTAAAATATAAGTTTGAAAAATT
448 AAATATAAGTTTGAAAATTTTATTAAAATATAAGTTTGAAAAATT
* *
3196068 TTAATTTTT-AAAACTTTTTAGATAAAATCTAATTAGAGGGATTGAAGATTTATAATTAAAAAAA
1 TTAATTTTTAAAAACTTTTTAGATAAAATCTAATTAAAGGGATTGAAAATTTATAATTAAAAAAA
3196132 TTAAGGGATTAATAATTCAATATAATATATATAGAGATTTTAGATGAAAATTTTGATAAATTTTT
66 TTAAGGGATTAATAATTCAATATAATATATATAGAGATTTTAGATGAAAATTTTGATAAATTTTT
* * * *
3196197 TTTGTATAAGTTAAATGAAAATTAATTAAAATTAAATATTATATTTTGATTGTGTTATATATTAA
131 TTTGAATAAGTTAAATGAAAAATAATTAAAATTAAATATTATATTTTAATTGTATTATATATTAA
* *
3196262 TTTATAATTTTGTATCTAAAATTAATAATTTTTTTGTTATTTTGGTATTTATATTGTTGTCAATT
196 TTTATAATTTTATATCTAAAATTAATAATTTTTTTGTTATTTTGATATTTATATTGTTGTCAATT
* *
3196327 CTTTTGATATTAGATTAATTCTTATTATTTTTGAGTAATTATTGAAAATTGTATTTATTATATAA
261 CTTTTGATATTAGATTAATTCTTACTATTTTTGAGTAATTATTGAAAATTCTATTTATTATATAA
3196392 TTATTGAAAGCTATTTGTGATAAAAAAATTTATATCAATTAGTGTATCAAAAAGATTAAGTTACT
326 TTATTGAAAGCTATTTGTGATAAAAAAATTTATATCAATTAGTGTATCAAAAAGATTAAGTTACT
** * *
3196457 TAATAAATTTAGTGTTTTATGATCTATTACTCTTAAAATTAAAAATTAAAAATTAAAAA
391 TAATAAATTTAGCATTTTATGATCTATTACTCTTAAAATTAAAAACTAAAAACTAAAAA
3196516 TTAAAAAATT
Statistics
Matches: 413, Mismatches: 31, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
491 20 0.05
492 2 0.00
494 88 0.21
495 254 0.62
496 49 0.12
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.47
Consensus pattern (492 bp):
TTAATTTTTAAAAACTTTTTAGATAAAATCTAATTAAAGGGATTGAAAATTTATAATTAAAAAAA
TTAAGGGATTAATAATTCAATATAATATATATAGAGATTTTAGATGAAAATTTTGATAAATTTTT
TTTGAATAAGTTAAATGAAAAATAATTAAAATTAAATATTATATTTTAATTGTATTATATATTAA
TTTATAATTTTATATCTAAAATTAATAATTTTTTTGTTATTTTGATATTTATATTGTTGTCAATT
CTTTTGATATTAGATTAATTCTTACTATTTTTGAGTAATTATTGAAAATTCTATTTATTATATAA
TTATTGAAAGCTATTTGTGATAAAAAAATTTATATCAATTAGTGTATCAAAAAGATTAAGTTACT
TAATAAATTTAGCATTTTATGATCTATTACTCTTAAAATTAAAAACTAAAAACTAAAAAATATAA
GTTTGAAAATTTTATTAAAATATAAGTTTGAAAAATT
Found at i:3196503 original size:7 final size:7
Alignment explanation
Indices: 3196491--3196522 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
3196481 TATTACTCTT
3196491 AAAATTA
1 AAAATTA
3196498 AAAATTA
1 AAAATTA
3196505 AAAATTA
1 AAAATTA
3196512 AAAATTA
1 AAAATTA
3196519 AAAA
1 AAAA
3196523 ATTTAGCGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATTA
Found at i:3199356 original size:25 final size:25
Alignment explanation
Indices: 3199299--3199355 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
3199289 TTTTATCTAA
3199299 AAAATTTTCAAACTTATATTTTAAT
1 AAAATTTTCAAACTTATATTTTAAT
**
3199324 AAAATTTTCAAACTTAT-TTTTTTT
1 AAAATTTTCAAACTTATATTTTAAT
3199348 AAAATTTT
1 AAAATTTT
3199356 TGGCTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (25 bp):
AAAATTTTCAAACTTATATTTTAAT
Found at i:3200354 original size:18 final size:18
Alignment explanation
Indices: 3200333--3200372 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3200323 GAGTTTTATT
* *
3200333 TTTTACTTTTGTTTTTGC
1 TTTTACTTTTATTTTTAC
3200351 TTTTACTTTTATTTTTAC
1 TTTTACTTTTATTTTTAC
3200369 TTTT
1 TTTT
3200373 GCAGGCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTACTTTTATTTTTAC
Found at i:3218828 original size:21 final size:21
Alignment explanation
Indices: 3218798--3218845 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3218788 AAAGTAAAGT
*
3218798 TTTTCTATATTCCTTTAGAGGA
1 TTTT-TATATTCCTTAAGAGGA
* *
3218820 TTTTTATATTTCTTAAGATGA
1 TTTTTATATTCCTTAAGAGGA
3218841 TTTTT
1 TTTTT
3218846 TTGGGGAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.58
Consensus pattern (21 bp):
TTTTTATATTCCTTAAGAGGA
Found at i:3227136 original size:14 final size:14
Alignment explanation
Indices: 3227117--3227149 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3227107 TTCGACAAAG
3227117 AGTTTACTTGTATT
1 AGTTTACTTGTATT
3227131 AGTTTACTTGTATT
1 AGTTTACTTGTATT
*
3227145 GGTTT
1 AGTTT
3227150 TATTAAGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.58
Consensus pattern (14 bp):
AGTTTACTTGTATT
Found at i:3227380 original size:20 final size:21
Alignment explanation
Indices: 3227339--3227381 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3227329 ATTATGTTAA
3227339 TATTTAATTTGTTTACATTTT
1 TATTTAATTTGTTTACATTTT
3227360 TATTTAATTT-TTTA-ATATTT
1 TATTTAATTTGTTTACAT-TTT
3227380 TA
1 TA
3227382 ATATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.10
20 9 0.43
21 10 0.48
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTTAATTTGTTTACATTTT
Found at i:3227441 original size:24 final size:23
Alignment explanation
Indices: 3227392--3227441 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
3227382 ATATTTTAAA
**
3227392 ATTAAAATTAAAATAAATAATTT
1 ATTAAAATTAAAATAAATAAAAT
3227415 ATTATAAA-TAAAATAAAATAAAAT
1 ATTA-AAATTAAAAT-AAATAAAAT
3227439 ATT
1 ATT
3227442 GGTTTTCGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
ATTAAAATTAAAATAAATAAAAT
Found at i:3236707 original size:6 final size:6
Alignment explanation
Indices: 3236696--3236720 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3236686 TGTTTCAGGA
3236696 GAAGAT GAAGAT GAAGAT GAAGAT G
1 GAAGAT GAAGAT GAAGAT GAAGAT G
3236721 TGATGAAATT
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:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GAAGAT
Found at i:3238116 original size:168 final size:168
Alignment explanation
Indices: 3237844--3238185 Score: 578
Period size: 168 Copynumber: 2.0 Consensus size: 168
3237834 TAATGCACTA
*
3237844 AATATCAATTTTAATATCGAAGTTTTGTTAAGAGCTTAAATTCAAATCTCATTGGTGTGTTTTAA
1 AATATCAATTTTAATATCGAAGTTTTGTTAAGAGCTTAAATTCAAATCTCATTGGTGTGATTTAA
3237909 TTAATTAATTAATAATTAATAATTGATTATATAAATATAATATTATAAGTTTGATTATTAGTGTA
66 TTAATTAATTAATAATTAATAATTGATTATATAAATATAATATTATAAGTTTGATTATTAGTGTA
3237974 ATTTTTAAAAATAAAAAATCAAAGTTTTGTTTAACAAT
131 ATTTTTAAAAATAAAAAATCAAAGTTTTGTTTAACAAT
* * *
3238012 AATATCAAATTTTAATGTCGAAGTTTTGTTAAGATCTTAAATTCAAATTTCATT-GTGTGATTTA
1 AATATC-AATTTTAATATCGAAGTTTTGTTAAGAGCTTAAATTCAAATCTCATTGGTGTGATTTA
* * * *
3238076 ATTAATTAATTAGTAATTAATAGTTGATTATATGAATATAATATTATGAGTTTGATTATTAGTGT
65 ATTAATTAATTAATAATTAATAATTGATTATATAAATATAATATTATAAGTTTGATTATTAGTGT
**
3238141 AATTTTTAAAAATAAAAAATCAAAGTTTTGTTTGCCAAT
130 AATTTTTAAAAATAAAAAATCAAAGTTTTGTTTAACAAT
3238180 AATATC
1 AATATC
3238186 TTCACTTTTT
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
168 119 0.73
169 44 0.27
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (168 bp):
AATATCAATTTTAATATCGAAGTTTTGTTAAGAGCTTAAATTCAAATCTCATTGGTGTGATTTAA
TTAATTAATTAATAATTAATAATTGATTATATAAATATAATATTATAAGTTTGATTATTAGTGTA
ATTTTTAAAAATAAAAAATCAAAGTTTTGTTTAACAAT
Found at i:3238445 original size:13 final size:13
Alignment explanation
Indices: 3238427--3238452 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3238417 TTTATTTATT
3238427 TTTTAAAATTTTA
1 TTTTAAAATTTTA
3238440 TTTTAAAATTTTA
1 TTTTAAAATTTTA
3238453 AGTATTTGAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAAAATTTTA
Found at i:3248524 original size:51 final size:51
Alignment explanation
Indices: 3248448--3248550 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
3248438 TTCTGCTCCC
* *
3248448 AATAACCAAAGAAACCATGGTAAAACATCTGATAACAGAAGGGCATATGCA
1 AATAACCAAAGAAACCACGGTAAAACATCTGATAACAGAAGGGCAAATGCA
* *
3248499 AATAACCAAAGAAGCCACGGTAAAACATCTGATAACAGGAGGGCAAATGCA
1 AATAACCAAAGAAACCACGGTAAAACATCTGATAACAGAAGGGCAAATGCA
3248550 A
1 A
3248551 GGAAATAAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.49, C:0.18, G:0.19, T:0.14
Consensus pattern (51 bp):
AATAACCAAAGAAACCACGGTAAAACATCTGATAACAGAAGGGCAAATGCA
Found at i:3250384 original size:30 final size:34
Alignment explanation
Indices: 3250313--3250386 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 34
3250303 ATATACGATG
3250313 TAAAAATTATAAATATAATATAATTTAAAATTTTAA
1 TAAAAATTATAAATATAATATAA-TTAAAA-TTTAA
*
3250349 TAAAAATTATAAATA-AATTTAA-TAAAA-TTAA
1 TAAAAATTATAAATATAATATAATTAAAATTTAA
*
3250380 AAAAAAT
1 TAAAAAT
3250387 CTATTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 10 0.28
33 5 0.14
35 6 0.17
36 15 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (34 bp):
TAAAAATTATAAATATAATATAATTAAAATTTAA
Found at i:3251372 original size:34 final size:35
Alignment explanation
Indices: 3251334--3251410 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
3251324 AATACATCCC
* *
3251334 AAATTTTATAA-TTTTTCAAAAATAAATTTTTAAA
1 AAATTATATAATTTTTTCAAAAATAAACTTTTAAA
* *
3251368 AAATTATATAATTTTTTTAAAATTAAACTTTTAAA
1 AAATTATATAATTTTTTCAAAAATAAACTTTTAAA
3251403 AAATTATA
1 AAATTATA
3251411 AACCTTCTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
34 10 0.26
35 28 0.74
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (35 bp):
AAATTATATAATTTTTTCAAAAATAAACTTTTAAA
Found at i:3251406 original size:16 final size:16
Alignment explanation
Indices: 3251343--3251408 Score: 62
Period size: 16 Copynumber: 4.0 Consensus size: 16
3251333 CAAATTTTAT
*
3251343 AATTTTTCAAAAA-TA
1 AATTTTTAAAAAATTA
3251358 AATTTTTAAAAAATTATA
1 AATTTTTAAAAAA-T-TA
**
3251376 TAATTTTTTTAAAATTA
1 -AATTTTTAAAAAATTA
*
3251393 AACTTTTAAAAAATTA
1 AATTTTTAAAAAATTA
3251409 TAAACCTTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
15 12 0.29
16 13 0.32
17 2 0.05
18 3 0.07
19 11 0.27
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTTTAAAAAATTA
Found at i:3251459 original size:34 final size:33
Alignment explanation
Indices: 3251339--3251486 Score: 102
Period size: 35 Copynumber: 4.3 Consensus size: 33
3251329 ATCCCAAATT
* *
3251339 TTATAATTTTTC-AAAAATAAATTTTTAAAAAA
1 TTATAATCTTTCTAAAAATAAACTTTTAAAAAA
* * *
3251371 TTATATAATTTTTTTAAAATTAAACTTTTAAAAAA
1 -T-TATAATCTTTCTAAAAATAAACTTTTAAAAAA
* * * *
3251406 TTATAAACCTTCTTGAAAATAAA-TTTAAGAAAAA
1 TTATAATCTTTC-TAAAAATAAACTTTTA-AAAAA
* * **
3251440 TTATGAATCTTTCTAAAAATTTAATTTTCTAAAATT
1 TTAT-AATCTTTCTAAAAA-TAAACTTT-TAAAAAA
3251476 TTATAATCTTT
1 TTATAATCTTT
3251487 TGAAAATTTA
Statistics
Matches: 90, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
33 12 0.13
34 33 0.37
35 34 0.38
36 10 0.11
37 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (33 bp):
TTATAATCTTTCTAAAAATAAACTTTTAAAAAA
Found at i:3251470 original size:16 final size:17
Alignment explanation
Indices: 3251435--3251496 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 17
3251425 TAAATTTAAG
3251435 AAAAATTATGAATCTTTCT
1 AAAAATT-T-AATCTTTCT
3251454 AAAAATTTAAT-TTTCT
1 AAAAATTTAATCTTTCT
*
3251470 AAAATTTTATAATCTTT-T
1 AAAA-ATT-TAATCTTTCT
*
3251488 GAAAATTTA
1 AAAAATTTA
3251497 TATAATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 11 0.30
17 7 0.19
18 9 0.24
19 10 0.27
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
AAAAATTTAATCTTTCT
Done.