Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 23 of 29
Found at i:9535770 original size:263 final size:266
Alignment explanation
Indices: 9535270--9535796 Score: 810
Period size: 263 Copynumber: 2.0 Consensus size: 266
9535260 TTATGTGAGT
*
9535270 CACCATCTAAAGAGAAGCTTGCAAAACAATTACATTTGGGCTCAAGGAGAAGAAAGCTCATGTAT
1 CACCATCTAAAGAGAAGCTTGCAAAACAATTACATTTGGGCACAAGGAGAAGAAAGCTCATGTAT
* * * *
9535335 GGCATAGTTCAGCAGAATCATAACTAATTTCAAAGAGACAAACAGTTGAAAATCATATAGAAATG
66 GGCATAGTTCACCACAATC--AACTAATTTCAAAGAGACAAACAGTTGAAAAGCAAATAGAAATG
* * **
9535400 AACAAAAAATGATTATACATGGAAAATGACAACATTACTCTCTCATTGCTGTCATGAGTCATGAC
129 AACAAAAAATGATTATACAGGGAAAATGACAACATTACTCTCTCATTGCTGTCATAAGTCACAAC
* * * *
9535465 CTTCCATTTCTATCCAAAAAGTTTCCTAGTTTAAATCTACCAAAGGAAATATGATCTCCAGA-AC
194 CTTCCATTTCTATCCAAAAAGTTTACTAATTGAAACCTACCAAAGGAAATATGATCTCCA-ACAC
9535529 CCCCCTAGA
258 CCCCCTAGA
*
9535538 CACCATCTAAAGAG-AGCTTGCAAAATAATTACATTTGGGCACAAGGAGAAGAAAGCTCATGTAT
1 CACCATCTAAAGAGAAGCTTGCAAAACAATTACATTTGGGCACAAGGAGAAGAAAGCTCATGTAT
* * *
9535602 GGCATAGTTCACCACAATC-A-TAGTTTCAAAGAGATAAACAGTTGAAAAGCAAATAGAACTGAA
66 GGCATAGTTCACCACAATCAACTAATTTCAAAGAGACAAACAGTTGAAAAGCAAATAGAAATGAA
* * *
9535665 CAAAAAATGATTATACAGGGAAGATGACAGCATTAGTCTCTCATTGCTGTCATAAGTCACAACCT
131 CAAAAAATGATTATACAGGGAAAATGACAACATTACTCTCTCATTGCTGTCATAAGTCACAACCT
*
9535730 TCCATTTCTATCCAAAAAGTTTACTAATTGAAGCCTACCAAAGGAAATATGATCTCCAACACCCC
196 TCCATTTCTATCCAAAAAGTTTACTAATTGAAACCTACCAAAGGAAATATGATCTCCAACACCCC
9535795 CC
261 CC
9535797 ATAACACATC
Statistics
Matches: 237, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
262 1 0.00
263 156 0.66
264 1 0.00
267 65 0.27
268 14 0.06
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.24
Consensus pattern (266 bp):
CACCATCTAAAGAGAAGCTTGCAAAACAATTACATTTGGGCACAAGGAGAAGAAAGCTCATGTAT
GGCATAGTTCACCACAATCAACTAATTTCAAAGAGACAAACAGTTGAAAAGCAAATAGAAATGAA
CAAAAAATGATTATACAGGGAAAATGACAACATTACTCTCTCATTGCTGTCATAAGTCACAACCT
TCCATTTCTATCCAAAAAGTTTACTAATTGAAACCTACCAAAGGAAATATGATCTCCAACACCCC
CCTAGA
Found at i:9539991 original size:23 final size:23
Alignment explanation
Indices: 9539965--9540009 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
9539955 TGTTATTCTA
9539965 CTTTTTAAATAATTGAACTAAAC
1 CTTTTTAAATAATTGAACTAAAC
9539988 CTTTTTAAATAATTGAACTAAA
1 CTTTTTAAATAATTGAACTAAA
9540010 TTTTGGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (23 bp):
CTTTTTAAATAATTGAACTAAAC
Found at i:9542451 original size:9 final size:9
Alignment explanation
Indices: 9542437--9542462 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9542427 CTATAGATGA
9542437 AAAAATTTT
1 AAAAATTTT
9542446 AAAAATTTT
1 AAAAATTTT
9542455 AAAAATTT
1 AAAAATTT
9542463 AAGAATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAAATTTT
Found at i:9542592 original size:27 final size:25
Alignment explanation
Indices: 9542537--9542593 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
9542527 TATTTAATAA
* *
9542537 AAAAATTATATATTTAAAAATTATT
1 AAAAATTATATATTAAAAAATTATC
9542562 AAAAATATATAATATATAAAAAATT-TC
1 AAAAAT-TAT-ATAT-TAAAAAATTATC
9542589 AAAAA
1 AAAAA
9542594 CTTTGAAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.22
26 3 0.11
27 10 0.37
28 8 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAAATTATATATTAAAAAATTATC
Found at i:9560344 original size:23 final size:23
Alignment explanation
Indices: 9560318--9560363 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
9560308 TAAAATAAAA
*
9560318 TTTAAATTTAGAAGTA-ATATTTT
1 TTTAAATTTA-AAATATATATTTT
*
9560341 TTTAATTTTAAAATATATATTTT
1 TTTAAATTTAAAATATATATTTT
9560364 AAATCAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTAAATTTAAAATATATATTTT
Found at i:9561318 original size:28 final size:29
Alignment explanation
Indices: 9561254--9561319 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
9561244 TCAAGCAATT
* *
9561254 TTAAACAATTCTAACAATTTAATATTTTTG
1 TTAAA-AATTCTAAAAATTTAATATTTTTC
* *
9561284 TTTAAAATTTTAAAAATTT-ATATTTTTC
1 TTAAAAATTCTAAAAATTTAATATTTTTC
9561312 TTAAAAAT
1 TTAAAAAT
9561320 AATATGATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 15 0.48
29 12 0.39
30 4 0.13
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (29 bp):
TTAAAAATTCTAAAAATTTAATATTTTTC
Found at i:9561335 original size:21 final size:19
Alignment explanation
Indices: 9561293--9561335 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
9561283 GTTTAAAATT
* *
9561293 TTAAAAATTTATATTTTTC
1 TTAAAAATATATATTATTC
9561312 TTAAAAATAATATGATTATTC
1 TTAAAAAT-ATAT-ATTATTC
9561333 TTA
1 TTA
9561336 CCCACAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAAAAATATATATTATTC
Found at i:9581050 original size:19 final size:19
Alignment explanation
Indices: 9581026--9581062 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
9581016 AATTCTAAAA
9581026 CTTAGAGATTTCAAAGCAG
1 CTTAGAGATTTCAAAGCAG
9581045 CTTAGAGATTTCAAAGCA
1 CTTAGAGATTTCAAAGCA
9581063 CTATTTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (19 bp):
CTTAGAGATTTCAAAGCAG
Found at i:9581436 original size:16 final size:16
Alignment explanation
Indices: 9581398--9581441 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
9581388 ATTAAAAGAT
* *
9581398 AATTTTATAAAATTTTG
1 AATTTTAT-ATATTTTA
9581415 AA-TTTATATATTTTA
1 AATTTTATATATTTTA
9581430 AATTTTATATAT
1 AATTTTATATAT
9581442 AAAAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 14 0.58
17 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
AATTTTATATATTTTA
Found at i:9593035 original size:30 final size:30
Alignment explanation
Indices: 9593001--9593071 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
9592991 TTTTATATTA
* *
9593001 AAAATTGAACAAAACTAAGAA-TATACTAAC
1 AAAATTCAACAAAACTAA-AAGTATAATAAC
*
9593031 AAAATTCAACAAAATTAAAAGTATAATAAC
1 AAAATTCAACAAAACTAAAAGTATAATAAC
9593061 AAAATTCAACA
1 AAAATTCAACA
9593072 TCAACCCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.21
Consensus pattern (30 bp):
AAAATTCAACAAAACTAAAAGTATAATAAC
Found at i:9610428 original size:54 final size:53
Alignment explanation
Indices: 9610367--9610489 Score: 162
Period size: 54 Copynumber: 2.3 Consensus size: 53
9610357 AGGAACAAAA
* * *
9610367 TTATAAAATTATTATAGAGATAAAATTATAAAATTTTTCAAAAATAAGA-ATATG
1 TTATAAAATTATTATAAAGATAAAATTATAAAACTTTTAAAAAATAA-ATAT-TG
* *
9610421 TTATAAAATTATTGTAAAGATAAAGTTATAAAACTTTTAAAAAATAAATATTG
1 TTATAAAATTATTATAAAGATAAAATTATAAAACTTTTAAAAAATAAATATTG
9610474 TTATAAAA--ATTATAAA
1 TTATAAAATTATTATAAA
9610490 AATTTTGAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 7 0.11
53 11 0.18
54 44 0.71
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (53 bp):
TTATAAAATTATTATAAAGATAAAATTATAAAACTTTTAAAAAATAAATATTG
Found at i:9610448 original size:25 final size:24
Alignment explanation
Indices: 9610367--9610461 Score: 68
Period size: 25 Copynumber: 3.7 Consensus size: 24
9610357 AGGAACAAAA
* *
9610367 TTATAAAATTATTATAGAGATAAAA
1 TTATAAAATTATT-TAAAGATAAAG
*
9610392 TTATAAAATT-TTTCAAAAATAAGAATATG
1 TTATAAAATTATTT-AAAGAT---AA-A-G
9610421 TTATAAAATTATTGTAAAGATAAAG
1 TTATAAAATTATT-TAAAGATAAAG
*
9610446 TTATAAAACT-TTTAAA
1 TTATAAAATTATTTAAA
9610462 AAATAAATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
23 5 0.09
24 8 0.14
25 20 0.35
26 1 0.02
27 4 0.07
28 1 0.02
29 10 0.18
30 7 0.12
31 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (24 bp):
TTATAAAATTATTTAAAGATAAAG
Found at i:9611168 original size:2 final size:2
Alignment explanation
Indices: 9611161--9611186 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9611151 CTCTTAACCT
9611161 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
9611187 GGTTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9616640 original size:18 final size:20
Alignment explanation
Indices: 9616603--9616643 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
9616593 ACATATTTAC
*
9616603 CACATTTCATATACTATATT
1 CACATTTCATAGACTATATT
9616623 CACATTT-ATAGA-TATATT
1 CACATTTCATAGACTATATT
9616641 CAC
1 CAC
9616644 CATGTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 4 0.20
20 7 0.35
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (20 bp):
CACATTTCATAGACTATATT
Found at i:9620309 original size:46 final size:46
Alignment explanation
Indices: 9620235--9620324 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
9620225 ACATTGGGAG
* * *
9620235 CTATGAGAAAGTCTTGTTAAGGATCAGTGTAGAAATATATTTCATA
1 CTATGAGAAAGTCTTGCTAAGGAACAGTGCAGAAATATATTTCATA
* *
9620281 CTATGAGAACGTCTTGCTCAGGAACAGTGCAGAAATATATTTCA
1 CTATGAGAAAGTCTTGCTAAGGAACAGTGCAGAAATATATTTCA
9620325 ACAATATGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (46 bp):
CTATGAGAAAGTCTTGCTAAGGAACAGTGCAGAAATATATTTCATA
Found at i:9631972 original size:23 final size:22
Alignment explanation
Indices: 9631923--9631980 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
9631913 AATATCATAT
9631923 TAATA-TTTTAATAATAAATAA
1 TAATATTTTTAATAATAAATAA
* *
9631944 TAATATTTTTATTATTAAATCAA
1 TAATATTTTTAATAATAAAT-AA
*
9631967 TAATA-TGTTAATAA
1 TAATATTTTTAATAA
9631981 AATTTTAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 5 0.17
22 18 0.60
23 7 0.23
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TAATATTTTTAATAATAAATAA
Found at i:9632380 original size:21 final size:21
Alignment explanation
Indices: 9632354--9632416 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
9632344 TTTTAATAGG
9632354 AAATTATTAATAGTTATTAAT
1 AAATTATTAATAGTTATTAAT
9632375 AAATTATTAATAGTTATTAAT
1 AAATTATTAATAGTTATTAAT
9632396 AAATTATTAATA-TT-TTAAT
1 AAATTATTAATAGTTATTAAT
9632415 AA
1 AA
9632417 TGACAGATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.17
20 2 0.05
21 33 0.79
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
AAATTATTAATAGTTATTAAT
Found at i:9634620 original size:15 final size:15
Alignment explanation
Indices: 9634602--9634730 Score: 74
Period size: 15 Copynumber: 8.5 Consensus size: 15
9634592 TATTCTATTT
9634602 TTTAAATATTAATAA
1 TTTAAATATTAATAA
9634617 TTTATAAT-TTAAGTAAA
1 TTTA-AATATTAA-T-AA
9634634 CTATT-AATAATTAATAA
1 -T-TTAAAT-ATTAATAA
*
9634651 TTTAAATATTAATATT
1 TTTAAATATTAATA-A
*
9634667 TTTAAATACTAAT-A
1 TTTAAATATTAATAA
*
9634681 TTT---TATTTATAA
1 TTTAAATATTAATAA
*
9634693 TTT-AATATTATTATGA
1 TTTAAATATTA--ATAA
*
9634709 TTAAAATATTAATAA
1 TTTAAATATTAATAA
*
9634724 TTCAAAT
1 TTTAAAT
9634731 TAATTTCAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
11 5 0.06
12 4 0.04
14 7 0.08
15 26 0.29
16 25 0.28
17 14 0.16
18 2 0.02
19 6 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:9634638 original size:27 final size:26
Alignment explanation
Indices: 9634604--9634655 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
9634594 TTCTATTTTT
*
9634604 TAAATATTAATAATTTATAATTTAAG
1 TAAATATTAATAATTAATAATTTAAG
9634630 TAAACTATTAATAATTAATAATTTAA
1 TAAA-TATTAATAATTAATAATTTAA
9634656 ATATTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAATATTAATAATTAATAATTTAAG
Found at i:9634670 original size:16 final size:16
Alignment explanation
Indices: 9634651--9634684 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
9634641 TAATTAATAA
*
9634651 TTTAAATATTAATATT
1 TTTAAATACTAATATT
9634667 TTTAAATACTAATATT
1 TTTAAATACTAATATT
9634683 TT
1 TT
9634685 ATTTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAATACTAATATT
Found at i:9634924 original size:8 final size:8
Alignment explanation
Indices: 9634911--9634943 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
9634901 TTTGTTTTCA
9634911 TTAAAATT
1 TTAAAATT
9634919 TTAAAATT
1 TTAAAATT
9634927 TTAAAATT
1 TTAAAATT
9634935 TTAAAATT
1 TTAAAATT
9634943 T
1 T
9634944 AATAGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTAAAATT
Found at i:9640923 original size:2 final size:2
Alignment explanation
Indices: 9640918--9640950 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9640908 CTCCTATATA
9640918 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
9640951 TTTAACAAGG
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:9645963 original size:21 final size:22
Alignment explanation
Indices: 9645939--9645989 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
9645929 TCATATACTC
*
9645939 TTATTATTAA-CATATAAA-TAT
1 TTATTATTAATCA-AAAAATTAT
* *
9645960 TTATGACTAATCAAAAAATTAT
1 TTATTATTAATCAAAAAATTAT
9645982 TTATTATT
1 TTATTATT
9645990 TTTATATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (22 bp):
TTATTATTAATCAAAAAATTAT
Found at i:9646207 original size:26 final size:24
Alignment explanation
Indices: 9646148--9646208 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
9646138 AATTAATTAT
* * *
9646148 AAAAATTTATTTGATTGAAAATAA
1 AAAAAATTATTTAATAGAAAATAA
9646172 AAATATAATTATTTAATAGAAAATAA
1 AAA-A-AATTATTTAATAGAAAATAA
9646198 TGAAAAAATTA
1 --AAAAAATTA
9646209 AAATTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 3 0.10
25 1 0.03
26 22 0.73
27 1 0.03
28 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (24 bp):
AAAAAATTATTTAATAGAAAATAA
Found at i:9646264 original size:23 final size:25
Alignment explanation
Indices: 9646221--9646273 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
9646211 ATTTATTTGA
9646221 ATTTTTTATATTTGTTCAAAATATT
1 ATTTTTTATATTTGTTCAAAATATT
*
9646246 ATTTTTT-TATTT-TTTAAAATATT
1 ATTTTTTATATTTGTTCAAAATATT
9646269 -TTTTT
1 ATTTTT
9646274 ATCTTAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 10 0.37
24 5 0.19
25 7 0.26
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (25 bp):
ATTTTTTATATTTGTTCAAAATATT
Found at i:9647527 original size:23 final size:22
Alignment explanation
Indices: 9647501--9647556 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
9647491 CCTTAAAGTT
*
9647501 TTGTGTAATTATTTTGCTATTTA
1 TTGTGTAATTATTTTG-TAATTA
* **
9647524 TTGTTTTCTTATTTTGTAATTA
1 TTGTGTAATTATTTTGTAATTA
9647546 TTG-GTAATTAT
1 TTGTGTAATTAT
9647557 GCATAAATCC
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
21 5 0.19
22 8 0.31
23 13 0.50
ACGTcount: A:0.21, C:0.04, G:0.12, T:0.62
Consensus pattern (22 bp):
TTGTGTAATTATTTTGTAATTA
Found at i:9662557 original size:13 final size:13
Alignment explanation
Indices: 9662536--9662570 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
9662526 TTATTATATT
9662536 TATATTATACTAA
1 TATATTATACTAA
* *
9662549 TATAATATATTAA
1 TATATTATACTAA
9662562 TATATTATA
1 TATATTATA
9662571 ATAGCATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
TATATTATACTAA
Found at i:9662557 original size:18 final size:18
Alignment explanation
Indices: 9662536--9662573 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9662526 TTATTATATT
9662536 TATATT-ATACTAATATAA
1 TATATTAATA-TAATATAA
*
9662554 TATATTAATATATTATAA
1 TATATTAATATAATATAA
9662572 TA
1 TA
9662574 GCATTATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATTAATATAATATAA
Found at i:9666336 original size:22 final size:22
Alignment explanation
Indices: 9666308--9666357 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
9666298 TGAACACCAT
9666308 GGACAATCCAGTTGAGCAGCCG
1 GGACAATCCAGTTGAGCAGCCG
9666330 GGACAATCCAGTTGAGCAGCCG
1 GGACAATCCAGTTGAGCAGCCG
*
9666352 GCACAA
1 GGACAA
9666358 CCAAATCCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.12
Consensus pattern (22 bp):
GGACAATCCAGTTGAGCAGCCG
Found at i:9668697 original size:2 final size:2
Alignment explanation
Indices: 9668690--9668727 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
9668680 CATTATCCTC
9668690 CT CT 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 CT CT
9668728 TACACAGACA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9680139 original size:15 final size:16
Alignment explanation
Indices: 9680119--9680163 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
9680109 TGCACCAGCA
9680119 AAAGAAATAAAG-AAG
1 AAAGAAATAAAGAAAG
9680134 AAAG-AATAAAGAAAG
1 AAAGAAATAAAGAAAG
9680149 AAAGGAAAT-AAGAAA
1 AAA-GAAATAAAGAAA
9680164 ATCACAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.26
15 10 0.37
16 7 0.26
17 3 0.11
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (16 bp):
AAAGAAATAAAGAAAG
Found at i:9691359 original size:48 final size:48
Alignment explanation
Indices: 9691285--9691478 Score: 313
Period size: 48 Copynumber: 4.1 Consensus size: 48
9691275 GGCCGGCTAA
* * *
9691285 CCCTGCCCCCCCTCTTCCGGCT-CCACGAGTCCCGGTTCTCCCCTGCGG
1 CCCTG-CCCCCCTCCTCCGGCTCCCACGAGTCCCGGTTCCCCCCCGCGG
9691333 CCCTGCCCCGCC-CCTCCGGCTCCCACGAGTCCCGGTTCCCCCCCGCGG
1 CCCTGCCCC-CCTCCTCCGGCTCCCACGAGTCCCGGTTCCCCCCCGCGG
*
9691381 CCCTGCCCCCCTCCTCCGGCTCCCACGAGTCCCGATTCCCCCCCGCGG
1 CCCTGCCCCCCTCCTCCGGCTCCCACGAGTCCCGGTTCCCCCCCGCGG
9691429 CCCTGCCCCCCTCCTCCGGCTCCCACGAGTCCC-GTTCCCCCCCGCGG
1 CCCTGCCCCCCTCCTCCGGCTCCCACGAGTCCCGGTTCCCCCCCGCGG
9691476 CCC
1 CCC
9691479 GCCGGGCTGG
Statistics
Matches: 138, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
47 30 0.22
48 108 0.78
ACGTcount: A:0.05, C:0.60, G:0.20, T:0.15
Consensus pattern (48 bp):
CCCTGCCCCCCTCCTCCGGCTCCCACGAGTCCCGGTTCCCCCCCGCGG
Found at i:9696051 original size:19 final size:18
Alignment explanation
Indices: 9696027--9696069 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
9696017 ATATATAAAA
9696027 ATAAAATATATGATATAGT
1 ATAAAATATATGA-ATAGT
*
9696046 ATAAAAT-TATGAATATT
1 ATAAAATATATGAATAGT
9696063 A-AAAATA
1 ATAAAATA
9696070 AAATGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.23
17 5 0.23
18 5 0.23
19 7 0.32
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (18 bp):
ATAAAATATATGAATAGT
Found at i:9730093 original size:2 final size:2
Alignment explanation
Indices: 9730086--9730121 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
9730076 TAAGCTTGTA
9730086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
9730122 AGATTCTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9751741 original size:39 final size:39
Alignment explanation
Indices: 9751687--9751761 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
9751677 AGGTTAGGAC
9751687 AGGAGTGACTTGTGATCATAAACACTGTATTTGGTTTGG
1 AGGAGTGACTTGTGATCATAAACACTGTATTTGGTTTGG
*
9751726 AGGAGTTACTTGTGATCATAAACACTGTATTTGGTT
1 AGGAGTGACTTGTGATCATAAACACTGTATTTGGTT
9751762 GGACGGAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.37
Consensus pattern (39 bp):
AGGAGTGACTTGTGATCATAAACACTGTATTTGGTTTGG
Found at i:9761723 original size:2 final size:2
Alignment explanation
Indices: 9761716--9761754 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
9761706 TATTTCAGGG
9761716 TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9761755 CCTCCACCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:9767722 original size:82 final size:82
Alignment explanation
Indices: 9767583--9767749 Score: 307
Period size: 82 Copynumber: 2.0 Consensus size: 82
9767573 ATTTGCTGGA
* *
9767583 GGAACTGCTGTGCTTTTTACTTATCCACTTGATTTGATTCGGACTAAATTAGCTTATCAGGTAAA
1 GGAACTGCTGTGCTCTTTACTTATCCACTTGATTTGATTCGCACTAAATTAGCTTATCAGGTAAA
9767648 TAGTTGAATATAAAGCT
66 TAGTTGAATATAAAGCT
*
9767665 GGAACTGCTGTGCTCTTTACTTATCCACTTGATTTGATTCGCACTAAATTAGGTTATCAGGTAAA
1 GGAACTGCTGTGCTCTTTACTTATCCACTTGATTTGATTCGCACTAAATTAGCTTATCAGGTAAA
9767730 TAGTTGAATATAAAGCT
66 TAGTTGAATATAAAGCT
9767747 GGA
1 GGA
9767750 GGCTCTTCAG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (82 bp):
GGAACTGCTGTGCTCTTTACTTATCCACTTGATTTGATTCGCACTAAATTAGCTTATCAGGTAAA
TAGTTGAATATAAAGCT
Found at i:9777554 original size:3 final size:3
Alignment explanation
Indices: 9777546--9777578 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
9777536 GTGCTAAAAT
*
9777546 TAC TAC TAC TAA TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
9777579 CATAGTTCGA
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:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:9789039 original size:25 final size:25
Alignment explanation
Indices: 9789009--9789067 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
9788999 GCGGCTGAAA
9789009 GTTGAAAAAACGAAAACGTTAAAAG
1 GTTGAAAAAACGAAAACGTTAAAAG
9789034 GTTGAAAAAACGAAAACGTTAAAAG
1 GTTGAAAAAACGAAAACGTTAAAAG
9789059 GTTGAAAAA
1 GTTGAAAAA
9789068 GATCCGCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.17
Consensus pattern (25 bp):
GTTGAAAAAACGAAAACGTTAAAAG
Found at i:9791996 original size:2 final size:2
Alignment explanation
Indices: 9791991--9792034 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
9791981 CTCTCTCTCT
* *
9791991 CA CA CA CA CA CA CA CA CA CA CA CG CG CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
9792033 CA
1 CA
9792035 TTACAGACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.45, C:0.50, G:0.05, T:0.00
Consensus pattern (2 bp):
CA
Found at i:9792717 original size:13 final size:13
Alignment explanation
Indices: 9792699--9792723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9792689 ACGATCTCTG
9792699 TTACTTTCTTTCC
1 TTACTTTCTTTCC
9792712 TTACTTTCTTTC
1 TTACTTTCTTTC
9792724 AGTTTGTGGA
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:0.28, G:0.00, T:0.64
Consensus pattern (13 bp):
TTACTTTCTTTCC
Found at i:9794938 original size:100 final size:98
Alignment explanation
Indices: 9794797--9795101 Score: 434
Period size: 100 Copynumber: 3.1 Consensus size: 98
9794787 GATAATAAAA
*
9794797 AAAAATTATGCAAAGTCAAATAACGTTTAAGAGAATCATAAATCATTAAGACTGTTTCAATTAAG
1 AAAAATTATGCAAAGTCAAATAACGTTTAAGAGAATCATAAATCATTAAGACTGTTTCAACTAAG
*
9794862 CATAAAATCAGTGAAAAATCAGAGGGAATCAAG
66 CATAAAATCAATGAAAAATCAGAGGGAATCAAG
*
9794895 AAAAATTATGCAGAGAGTCAAATAACGTTTAAGGGAATCATAAATCATTAAGACTGTTTCAACTA
1 AAAAATTATGCA-A-AGTCAAATAACGTTTAAGAGAATCATAAATCATTAAGACTGTTTCAACTA
* ** * *
9794960 ATCATATCATTAA--AACAAATCAGAGAGAATCAAG
64 AGCATAAAATCAATGAA-AAATCAGAGGGAATCAAG
* * * * *
9794994 AAAAATTATACAAAGTCATATAACGCTTAAGAGAATTATAAATCATTAAGATTGTTTCAACTAAG
1 AAAAATTATGCAAAGTCAAATAACGTTTAAGAGAATCATAAATCATTAAGACTGTTTCAACTAAG
* *
9795059 CATAAAATCAATGGAAAATTAGAGGGAATCAAG
66 CATAAAATCAATGAAAAATCAGAGGGAATCAAG
9795092 AAAAATTATG
1 AAAAATTATG
9795102 TGGAGTCAAA
Statistics
Matches: 180, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
97 54 0.30
98 40 0.22
99 30 0.17
100 56 0.31
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (98 bp):
AAAAATTATGCAAAGTCAAATAACGTTTAAGAGAATCATAAATCATTAAGACTGTTTCAACTAAG
CATAAAATCAATGAAAAATCAGAGGGAATCAAG
Found at i:9795042 original size:97 final size:95
Alignment explanation
Indices: 9794768--9795101 Score: 380
Period size: 98 Copynumber: 3.4 Consensus size: 95
9794758 ACGTTACAAA
* * * * * *
9794768 ATATCAATATAAAATCAAAGATAATAAAAAAAAATTATGCAAAGTCAAATAACGTTTAAGAGAAT
1 ATATCAGTAAAAAATCAGAGAGAATCAAGAAAAATTATGCAAAGTCAAATAACGTTTAAGAGAAT
*
9794833 CATAAATCATTAAGACTGTTTCAATTAAGC
66 CATAAATCATTAAGACTGTTTCAACTAAGC
* *
9794863 ATAAAATCAGTGAAAAATCAGAGGGAATCAAGAAAAATTATGCAGAGAGTCAAATAACGTTTAAG
1 AT---ATCAGTAAAAAATCAGAGAGAATCAAGAAAAATTATGCA-A-AGTCAAATAACGTTTAAG
* *
9794928 GGAATCATAAATCATTAAGACTGTTTCAACTAATC
61 AGAATCATAAATCATTAAGACTGTTTCAACTAAGC
* * * *
9794963 ATATCATTAAAACAAATCAGAGAGAATCAAGAAAAATTATACAAAGTCATATAACGCTTAAGAGA
1 ATATCAGT-AAA-AAATCAGAGAGAATCAAGAAAAATTATGCAAAGTCAAATAACGTTTAAGAGA
* *
9795028 ATTATAAATCATTAAGATTGTTTCAACTAAGC
64 ATCATAAATCATTAAGACTGTTTCAACTAAGC
* ** * *
9795060 ATAAAATCAATGGAAAATTAGAGGGAATCAAGAAAAATTATG
1 AT---ATCAGTAAAAAATCAGAGAGAATCAAGAAAAATTATG
9795102 TGGAGTCAAA
Statistics
Matches: 202, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
95 2 0.01
97 54 0.27
98 59 0.29
99 30 0.15
100 57 0.28
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.25
Consensus pattern (95 bp):
ATATCAGTAAAAAATCAGAGAGAATCAAGAAAAATTATGCAAAGTCAAATAACGTTTAAGAGAAT
CATAAATCATTAAGACTGTTTCAACTAAGC
Found at i:9800443 original size:2 final size:2
Alignment explanation
Indices: 9800436--9800469 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
9800426 CAGTTATTTG
* *
9800436 CT CT CT CT CT CT TT CT CT CT GT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9800470 TTCCTTGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (2 bp):
CT
Found at i:9817848 original size:25 final size:25
Alignment explanation
Indices: 9817820--9817872 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
9817810 CTCAATTTTT
9817820 TATTACTTCCTAATTCTCACACTAC
1 TATTACTTCCTAATTCTCACACTAC
* *
9817845 TATTGCTTCTTAATTCTCACACTAC
1 TATTACTTCCTAATTCTCACACTAC
9817870 TAT
1 TAT
9817873 AATTCTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.43
Consensus pattern (25 bp):
TATTACTTCCTAATTCTCACACTAC
Found at i:9836501 original size:2 final size:2
Alignment explanation
Indices: 9836494--9836519 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9836484 CACTTGGACA
9836494 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
9836520 ATGCACACGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9848542 original size:27 final size:27
Alignment explanation
Indices: 9848488--9848542 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
9848478 ATCAATAACA
* * *
9848488 AAGATTGCAATTCTTAATAGATCTTTG
1 AAGATTGCAATTCTAAATAGACCATTG
9848515 AAGATTGCAATTCCTAAAT-GACCATTG
1 AAGATTGCAATT-CTAAATAGACCATTG
9848542 A
1 A
9848543 TTACAACATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (27 bp):
AAGATTGCAATTCTAAATAGACCATTG
Found at i:9853712 original size:23 final size:23
Alignment explanation
Indices: 9853668--9853713 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
9853658 TCTTACGATT
*
9853668 GAAAGAAAGAAGAGAGAGACTGA
1 GAAAGAAAGAAGAAAGAGACTGA
9853691 GAAAGAAAGAAAGAAAGA-ACTGA
1 GAAAGAAAG-AAGAAAGAGACTGA
9853714 TATGTAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.61, C:0.04, G:0.30, T:0.04
Consensus pattern (23 bp):
GAAAGAAAGAAGAAAGAGACTGA
Found at i:9855631 original size:340 final size:341
Alignment explanation
Indices: 9854987--9855655 Score: 905
Period size: 340 Copynumber: 2.0 Consensus size: 341
9854977 GACTGCACGT
* * * * *
9854987 GAATATACACATGTATTGTACTCAAGTGAATTTTTATATCTTGGTATTACCTGACAAGTTGATCA
1 GAATAAACACATGGATTGTACTCAAGTGAATTTTTATACCTTGGTATTACCTAACAAGCTGATCA
* * * * **
9855052 GGTTTTTTTTCTAATTTCTTGAGTTTTATTCTCAACTTTTGGTTCCCTACGCGCGAATATACATG
66 GGTTTTTTCTCTAACTTCTTGAGTTTTATTCTCAACTCTTGGTTCCCTACGCACGAATATACACA
* * * *
9855117 TGCGTTGTGTTTAAGTGAATTTTTATACCTTGACATTACCTGACAAGCTGATCAGGTTTTTCTCT
131 TGCGCTGTGTTCAAGTGAATTTTTATACCTTGACATTACCTGACAAGCTAATCAAGTTTTTCTCT
* *
9855182 AATTTCTTGAGTCTTTTTATCAACTCTTGGTTCAATGTTCACCTTATTTGGTACAACGCTCACCT
196 AACTTCTTGAGTCTTTTTATCAACTCTTGGTTCAATGTTCACCTTATTTGATACAACGCTCACCT
* * * * *
9855247 CACTCTATGTCTATAAATACAACCTCACACTTTCACTCTCAACACACATCAAAGCTTTTCATCTT
261 CACTCCATATCTATAAATACAACCTCACACCTTCACTCTCAACACACACCAAAGCCTTTCATCTT
9855312 CTAAGTTTTCACCTGC
326 CTAAGTTTTCACCTGC
* * *
9855328 GAATAAACACATGGGTTGTGCTCAAGTGAATTTTTGTACCTTGGTATTACCTAACAAGCTGATCA
1 GAATAAACACATGGATTGTACTCAAGTGAATTTTTATACCTTGGTATTACCTAACAAGCTGATCA
* *
9855393 GG-TTTTTCTCTAACTTCTTGAGTTTGT-TTCTCAACTCTTGGTTCCCTGA-GCATGACTATACA
66 GGTTTTTTCTCTAACTTCTTGAGTTT-TATTCTCAACTCTTGGTTCCCT-ACGCACGAATATACA
* * * * *
9855455 CAT-CGACTGTGTTCAAGTGAATTTTTGTACTTTGGCATTACCTGATAAGCTAATTAAGTTTTTC
129 CATGCG-CTGTGTTCAAGTGAATTTTTATACCTTGACATTACCTGACAAGCTAATCAAGTTTTTC
* * * ** * *
9855519 TCTAACTTCTTGAGTCTTTTTCTCAACTCTTGGTTCAATGTTTACTTTATTTGATGTAGCGCTTA
193 TCTAACTTCTTGAGTCTTTTTATCAACTCTTGGTTCAATGTTCACCTTATTTGATACAACGCTCA
* * *
9855584 CCTCAGTCCATATCTATAAATACAACCTCATACCTTCACTTTCAACACACACCAAAGCCTTTCAT
258 CCTCACTCCATATCTATAAATACAACCTCACACCTTCACTCTCAACACACACCAAAGCCTTTCAT
9855649 CTTCTAA
323 CTTCTAA
9855656 ACATTTTTTG
Statistics
Matches: 283, Mismatches: 42, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
339 2 0.01
340 220 0.78
341 61 0.22
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (341 bp):
GAATAAACACATGGATTGTACTCAAGTGAATTTTTATACCTTGGTATTACCTAACAAGCTGATCA
GGTTTTTTCTCTAACTTCTTGAGTTTTATTCTCAACTCTTGGTTCCCTACGCACGAATATACACA
TGCGCTGTGTTCAAGTGAATTTTTATACCTTGACATTACCTGACAAGCTAATCAAGTTTTTCTCT
AACTTCTTGAGTCTTTTTATCAACTCTTGGTTCAATGTTCACCTTATTTGATACAACGCTCACCT
CACTCCATATCTATAAATACAACCTCACACCTTCACTCTCAACACACACCAAAGCCTTTCATCTT
CTAAGTTTTCACCTGC
Found at i:9855878 original size:30 final size:30
Alignment explanation
Indices: 9855837--9855896 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
9855827 TGGTATTACC
* *
9855837 TGACAAGCTGATCAGGTTTTTCTCTAACTT
1 TGACAAACTGATCAGGTTTTTCTCAAACTT
*
9855867 TGACAAACTGATTAGGTTTTTCTCAAACTT
1 TGACAAACTGATCAGGTTTTTCTCAAACTT
9855897 CTTGAGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (30 bp):
TGACAAACTGATCAGGTTTTTCTCAAACTT
Found at i:9877436 original size:12 final size:12
Alignment explanation
Indices: 9877419--9877443 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9877409 AAGTCTTCCA
9877419 CCTATATCTAGG
1 CCTATATCTAGG
9877431 CCTATATCTAGG
1 CCTATATCTAGG
9877443 C
1 C
9877444 GAGAGATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (12 bp):
CCTATATCTAGG
Found at i:9881509 original size:21 final size:21
Alignment explanation
Indices: 9881485--9881524 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
9881475 CTATGAATAG
9881485 TACAAAGTAAAATTGTTGTTT
1 TACAAAGTAAAATTGTTGTTT
9881506 TACAAAGTAAAATTGTTGT
1 TACAAAGTAAAATTGTTGT
9881525 CTCACTGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (21 bp):
TACAAAGTAAAATTGTTGTTT
Found at i:9882321 original size:5 final size:5
Alignment explanation
Indices: 9882311--9882344 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
9882301 AAAATCAAGG
* *
9882311 TCCCA TCCCA TCCTA TCCCA TCTCA TCCCA TCCC
1 TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCCC
9882345 CTCTCTTCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.18, C:0.56, G:0.00, T:0.26
Consensus pattern (5 bp):
TCCCA
Found at i:9882349 original size:15 final size:15
Alignment explanation
Indices: 9882311--9882349 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
9882301 AAAATCAAGG
* *
9882311 TCCCATCCCATCCTA
1 TCCCATCTCATCCCA
9882326 TCCCATCTCATCCCA
1 TCCCATCTCATCCCA
*
9882341 TCCCCTCTC
1 TCCCATCTC
9882350 TTCCTCCCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.15, C:0.56, G:0.00, T:0.28
Consensus pattern (15 bp):
TCCCATCTCATCCCA
Found at i:9882523 original size:2 final size:2
Alignment explanation
Indices: 9882516--9882541 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9882506 TACTTGATCA
9882516 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
9882542 GGTTCAATCC
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):
AT
Found at i:9891569 original size:2 final size:2
Alignment explanation
Indices: 9891564--9891590 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9891554 CAAATCCATT
9891564 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
9891591 TTTCGCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9892146 original size:21 final size:24
Alignment explanation
Indices: 9892122--9892174 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 24
9892112 ACGTGCAGTC
*
9892122 AATTTTATT-TATA-AAG-TTCAA
1 AATTTTATTCTATATAAGTTTAAA
*
9892143 AATTTT-TTCTATATGAGTTTAAA
1 AATTTTATTCTATATAAGTTTAAA
9892166 AATTTTATT
1 AATTTTATT
9892175 GCCTGCTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.08
21 10 0.38
22 2 0.08
23 10 0.38
24 2 0.08
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (24 bp):
AATTTTATTCTATATAAGTTTAAA
Found at i:9904763 original size:26 final size:27
Alignment explanation
Indices: 9904734--9904787 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
9904724 ATGTTTTTCC
* * *
9904734 CTTTTTTTGTATCTTT-TTCTTCTTCT
1 CTTTTTCTCTATCTTTCTTCTTCTACT
9904760 C-TTTTCTCTATCTTTCTTCTTCTACT
1 CTTTTTCTCTATCTTTCTTCTTCTACT
9904786 CT
1 CT
9904788 AAGATTAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.67
Consensus pattern (27 bp):
CTTTTTCTCTATCTTTCTTCTTCTACT
Found at i:9915367 original size:2 final size:2
Alignment explanation
Indices: 9915360--9915385 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9915350 TACTGTACAC
9915360 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
9915386 TTAGGGGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9919894 original size:16 final size:17
Alignment explanation
Indices: 9919873--9919904 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9919863 TATCCCACGT
9919873 GCCTCCT-CCGCCCTCC
1 GCCTCCTCCCGCCCTCC
9919889 GCCTCCTCCCGCCCTC
1 GCCTCCTCCCGCCCTC
9919905 TGATTCCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.69, G:0.12, T:0.19
Consensus pattern (17 bp):
GCCTCCTCCCGCCCTCC
Found at i:9920382 original size:24 final size:24
Alignment explanation
Indices: 9920350--9920396 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
9920340 TAGTAGTTTT
9920350 TCTTCAAAGAGAAAAGAATGATAC
1 TCTTCAAAGAGAAAAGAATGATAC
* *
9920374 TCTTCAAAGAGAGAAGGATGATA
1 TCTTCAAAGAGAAAAGAATGATA
9920397 TATATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (24 bp):
TCTTCAAAGAGAAAAGAATGATAC
Found at i:9925621 original size:54 final size:54
Alignment explanation
Indices: 9925540--9925653 Score: 178
Period size: 54 Copynumber: 2.1 Consensus size: 54
9925530 AACTTCATAA
* *
9925540 CCAGC-AGTGAAGGAATGCCATTACAAGCAGTTTCT-GGTTTTACACAGTTGCTG
1 CCAGCAAGTAAAGGAATGCCATTACAAGCAGTTTCTAGG-GTTACACAGTTGCTG
*
9925593 CCAGCAAGTAAAGGAATGCCATTACAAGCAGTTTCTAGGGTTACACATTTGCTG
1 CCAGCAAGTAAAGGAATGCCATTACAAGCAGTTTCTAGGGTTACACAGTTGCTG
9925647 CCAGCAA
1 CCAGCAA
9925654 TACCACGATT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
53 5 0.09
54 49 0.88
55 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (54 bp):
CCAGCAAGTAAAGGAATGCCATTACAAGCAGTTTCTAGGGTTACACAGTTGCTG
Found at i:9940851 original size:229 final size:230
Alignment explanation
Indices: 9940478--9940949 Score: 522
Period size: 229 Copynumber: 2.1 Consensus size: 230
9940468 AAGGTGTTGT
* * * *
9940478 AACTGGAACTACAAAATACAGTAAAAGCAGCAATATTATAACCAGACCTGGTGTTAAATCTATCC
1 AACTGGAGCTACAAAATACAGCAAAAGCAGCAATATTAGAACCAAACCTGGTGTTAAATCTATCC
* ** ** *
9940543 ACTAATTACACATCAATCTACAAATTATGTACCTGGAGCAATTGGCTCCGTAACAGGTGCTGTCT
66 ACGAAAAACACATCAATCTACAAATTATGTACCTGGAGCAATTGGCTCCGTAACAGGTGCCCTAT
* * * * * * * *
9940608 TATTTGATGAATTTCCTTGATTGGCACTTGGGGCCAAGGCA-TGTGGCTTACTGGAGTGAA-TAG
131 TACTTGACGAATTTCCTTGATTAGAAATTGGGGCCAAAGCACT-TCGCCTACTGGAGT-AAGTAG
* *
9940671 CTGGGGGATTTAGTGGTGGATTCCTCAATGGTGGTGC
194 CTGGGGAATTTAGTGGTGGATTCCTCAATGGCGGTGC
* * * * *
9940708 AACTGGAGCTACAAAATAGAGCAAAAGCAGCAGTATTAGAACCAAACTTGGTTTTAAATTTATCC
1 AACTGGAGCTACAAAATACAGCAAAAGCAGCAATATTAGAACCAAACCTGGTGTTAAATCTATCC
* * ** *
9940773 A-GAAAAAGACATCAAAT-TGCTGATTATGTACCTGGAGCAGTTGGCTCCAG-AACAGGTGCCCT
66 ACGAAAAACACATC-AATCTACAAATTATGTACCTGGAGCAATTGGCTCC-GTAACAGGTGCCCT
* ** * *
9940835 ATTACTTGACGAATTTCTTTGATTAGAAATTGGGGGGAAAGCACTTCGCCTGCTGGAGTAAGTGG
129 ATTACTTGACGAATTTCCTTGATTAGAAATTGGGGCCAAAGCACTTCGCCTACTGGAGTAAGTAG
* * *
9940900 GTGGGGAATTTTGTGGTGGATTCCTCAGTGGCGGTGC
194 CTGGGGAATTTAGTGGTGGATTCCTCAATGGCGGTGC
*
9940937 AAATGGAGCTACA
1 AACTGGAGCTACA
9940950 GATTATAATA
Statistics
Matches: 199, Mismatches: 39, Indels: 9
0.81 0.16 0.04
Matches are distributed among these distances:
228 2 0.01
229 135 0.68
230 62 0.31
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (230 bp):
AACTGGAGCTACAAAATACAGCAAAAGCAGCAATATTAGAACCAAACCTGGTGTTAAATCTATCC
ACGAAAAACACATCAATCTACAAATTATGTACCTGGAGCAATTGGCTCCGTAACAGGTGCCCTAT
TACTTGACGAATTTCCTTGATTAGAAATTGGGGCCAAAGCACTTCGCCTACTGGAGTAAGTAGCT
GGGGAATTTAGTGGTGGATTCCTCAATGGCGGTGC
Found at i:9953504 original size:8 final size:8
Alignment explanation
Indices: 9953486--9953533 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
9953476 AATATATTAA
*
9953486 AAATTTAT
1 AAATATAT
*
9953494 AAATATTT
1 AAATATAT
9953502 AAAATATAT
1 -AAATATAT
*
9953511 AAATAAAT
1 AAATATAT
*
9953519 AAAAATAT
1 AAATATAT
9953527 AAATATA
1 AAATATA
9953534 AATTAAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
8 25 0.78
9 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATATAT
Found at i:9953505 original size:17 final size:17
Alignment explanation
Indices: 9953474--9953556 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 17
9953464 TGAATAAAAA
*
9953474 ATAATATATTAAAAATTT
1 ATAA-ATATTAAAAATAT
*
9953492 ATAAATATTTAAAATAT
1 ATAAATATTAAAAATAT
*
9953509 ATAAATAAATAAAAATAT
1 ATAAAT-ATTAAAAATAT
9953527 A-AATATAAATTAAAAA-AT
1 ATAA-AT--ATTAAAAATAT
*
9953545 A-AAAAATTAAAA
1 ATAAATATTAAAA
9953557 TTAAGTTAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
15 7 0.12
17 20 0.36
18 21 0.38
19 8 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAATATTAAAAATAT
Found at i:9953534 original size:18 final size:18
Alignment explanation
Indices: 9953476--9953556 Score: 66
Period size: 17 Copynumber: 4.7 Consensus size: 18
9953466 AATAAAAAAT
* *
9953476 AATATATTAAAAATTTATA
1 AATAAATTAAAAATATA-A
*
9953495 AAT--ATTTAAAATATATA
1 AATAAATTAAAAATATA-A
9953512 AATAAA-TAAAAATATAA
1 AATAAATTAAAAATATAA
9953529 ATATAAATTAAAAA-AT-A
1 A-ATAAATTAAAAATATAA
9953546 AA-AAATTAAAA
1 AATAAATTAAAA
9953557 TTAAGTTAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
15 9 0.16
16 1 0.02
17 19 0.35
18 16 0.29
19 10 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATTAAAAATATAA
Found at i:9954084 original size:13 final size:14
Alignment explanation
Indices: 9954062--9954106 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
9954052 TAAATAATGA
9954062 TAATAT-AATATAT
1 TAATATAAATATAT
*
9954075 TAAT-TAAATATAA
1 TAATATAAATATAT
*
9954088 TAATATAATTATA-
1 TAATATAAATATAT
9954101 TAATAT
1 TAATAT
9954107 TTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 1 0.04
13 20 0.71
14 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATATAAATATAT
Found at i:9954086 original size:18 final size:18
Alignment explanation
Indices: 9954062--9954106 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
9954052 TAAATAATGA
9954062 TAATATAATATAT-TAAT
1 TAATATAATATATATAAT
9954079 TAAATATAATA-ATATAAT
1 T-AATATAATATATATAAT
9954097 T-ATATAATAT
1 TAATATAATAT
9954107 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
17 3 0.12
18 14 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATATAATATATATAAT
Found at i:9954202 original size:27 final size:24
Alignment explanation
Indices: 9954155--9954212 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
9954145 TGATTAATGA
*
9954155 TATTATTAATAATAATTAATTAAC
1 TATTATTAATAAAAATTAATTAAC
9954179 TATTATTAATAAAAA--AATTAA-
1 TATTATTAATAAAAATTAATTAAC
9954200 -ATTA-TAATAAAAA
1 TATTATTAATAAAAA
9954213 ATTTATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 9 0.27
20 4 0.12
22 6 0.18
24 14 0.42
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TATTATTAATAAAAATTAATTAAC
Found at i:9955931 original size:41 final size:41
Alignment explanation
Indices: 9955873--9955969 Score: 176
Period size: 41 Copynumber: 2.3 Consensus size: 41
9955863 ATATGGAAGA
*
9955873 AATTATGACAAATAATTTTTTTGATAAGGGTATTTGAAAAAT
1 AATTATTA-AAATAATTTTTTTGATAAGGGTATTTGAAAAAT
9955915 AATTATTAAAATAATTTTTTTGATAAGGGTATTTGAAAAAT
1 AATTATTAAAATAATTTTTTTGATAAGGGTATTTGAAAAAT
9955956 AATTATTAAAATAA
1 AATTATTAAAATAA
9955970 ATTTAATTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 47 0.87
42 7 0.13
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.41
Consensus pattern (41 bp):
AATTATTAAAATAATTTTTTTGATAAGGGTATTTGAAAAAT
Found at i:9956608 original size:32 final size:31
Alignment explanation
Indices: 9956567--9956630 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
9956557 AACAACAATA
*
9956567 TTTTTTCAATATGACATGTAATAATAATTTTT
1 TTTTTTCAATATGACATGTAACAAT-ATTTTT
**
9956599 TTTTTTCAATATGGTATGTAACAATATTTTT
1 TTTTTTCAATATGACATGTAACAATATTTTT
9956630 T
1 T
9956631 AATCATGACG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (31 bp):
TTTTTTCAATATGACATGTAACAATATTTTT
Found at i:9956628 original size:29 final size:29
Alignment explanation
Indices: 9956539--9956630 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
9956529 TAATGAAATG
* * * *
9956539 TTTTTGAATATGAAATGTAACAACAATAT
1 TTTTTCAATATGAAATGTAACAATATTTT
* *
9956568 TTTTTCAATATGACATGTAATAATAATTTTTT
1 TTTTTCAATATGAAATGTAACAAT-A--TTTT
**
9956600 TTTTTCAATATGGTATGTAACAATATTTT
1 TTTTTCAATATGAAATGTAACAATATTTT
9956629 TT
1 TT
9956631 AATCATGACG
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
29 26 0.51
30 1 0.02
31 1 0.02
32 23 0.45
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (29 bp):
TTTTTCAATATGAAATGTAACAATATTTT
Found at i:9956736 original size:76 final size:76
Alignment explanation
Indices: 9956629--9956779 Score: 212
Period size: 76 Copynumber: 2.0 Consensus size: 76
9956619 ACAATATTTT
* * * * * * *
9956629 TTAATCATGACGTGTAATATGTTTTTATACATAATATGTAATAATAATATTTTTATTTAATATAA
1 TTAACCATAACGTGTAATATATTTTTATACATAACATATAACAATAATATTTTTATTTAACATAA
*
9956694 CGTGTAATAAC
66 CGTATAATAAC
* *
9956705 TTAACCATAACGTGTAATATATTTTTATACATAACGTATAACAATAATATTTTTTTTTAACATAA
1 TTAACCATAACGTGTAATATATTTTTATACATAACATATAACAATAATATTTTTATTTAACATAA
9956770 CGTATAATAA
66 CGTATAATAA
9956780 TCTAATTATG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 65 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (76 bp):
TTAACCATAACGTGTAATATATTTTTATACATAACATATAACAATAATATTTTTATTTAACATAA
CGTATAATAAC
Found at i:9956760 original size:30 final size:31
Alignment explanation
Indices: 9956719--9956776 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
9956709 CCATAACGTG
9956719 TAATATATTTTTAT-ACATAACGTATAACAA
1 TAATATATTTTTATAACATAACGTATAACAA
* *
9956749 TAATATTTTTTTTTAACATAACGTATAA
1 TAATATATTTTTATAACATAACGTATAA
9956777 TAATCTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (31 bp):
TAATATATTTTTATAACATAACGTATAACAA
Found at i:9956890 original size:15 final size:15
Alignment explanation
Indices: 9956872--9956900 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9956862 ATCATTATAT
9956872 ATAATTTTATTTAAA
1 ATAATTTTATTTAAA
9956887 ATAATTTTATTTAA
1 ATAATTTTATTTAA
9956901 TTTGATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTATTTAAA
Found at i:9962752 original size:3 final size:3
Alignment explanation
Indices: 9962744--9962768 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9962734 CTAAAGCTGT
9962744 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
9962769 AGATGATTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9967949 original size:28 final size:28
Alignment explanation
Indices: 9967909--9967971 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
9967899 ATCTTTTGAA
9967909 ATTATGTTATTGGCATTTCTCAGGCACC
1 ATTATGTTATTGGCATTTCTCAGGCACC
9967937 ATTATGTTATTGGCATTTCTCAGGCACC
1 ATTATGTTATTGGCATTTCTCAGGCACC
9967965 ATTATGT
1 ATTATGT
9967972 CAAGCATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (28 bp):
ATTATGTTATTGGCATTTCTCAGGCACC
Found at i:9972252 original size:7 final size:7
Alignment explanation
Indices: 9972240--9972276 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
9972230 GGGAGTGAAG
9972240 GGCTGAT
1 GGCTGAT
9972247 GGCTGAT
1 GGCTGAT
9972254 GGCTGAT
1 GGCTGAT
9972261 GGCTGAT
1 GGCTGAT
9972268 GGCTGAT
1 GGCTGAT
9972275 GG
1 GG
9972277 TGTTGTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.14, C:0.14, G:0.46, T:0.27
Consensus pattern (7 bp):
GGCTGAT
Found at i:9988323 original size:51 final size:53
Alignment explanation
Indices: 9988268--9988376 Score: 143
Period size: 51 Copynumber: 2.1 Consensus size: 53
9988258 ATTCGCCGGA
* * *
9988268 GGGGGAAGAAGTTAGGTCGGTGATGGG-GGGA-ATTAGGTCGGGACTC-GAGAG
1 GGGGGAAGAAGTTAGGTCGGCGATGGGTAGGAGATTAGGTCAGGACTCAGA-AG
* *
9988319 GGGGGAAGGAGTTAGGTCGGCGATGGGTAGGAGTTTAGGTCAGGACTCAGAAG
1 GGGGGAAGAAGTTAGGTCGGCGATGGGTAGGAGATTAGGTCAGGACTCAGAAG
9988372 GGGGG
1 GGGGG
9988377 GAATTAGTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
51 25 0.50
52 3 0.06
53 20 0.40
54 2 0.04
ACGTcount: A:0.23, C:0.08, G:0.51, T:0.17
Consensus pattern (53 bp):
GGGGGAAGAAGTTAGGTCGGCGATGGGTAGGAGATTAGGTCAGGACTCAGAAG
Found at i:9988539 original size:19 final size:19
Alignment explanation
Indices: 9988515--9988574 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
9988505 CCGATCGGAG
9988515 CAACCGACGGTTGAAAAAA
1 CAACCGACGGTTGAAAAAA
* * *
9988534 CAACCGTCGATT---ACAA
1 CAACCGACGGTTGAAAAAA
*
9988550 TAACCGACGGTTGAAAAAA
1 CAACCGACGGTTGAAAAAA
9988569 CAACCG
1 CAACCG
9988575 TCGATTACAA
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
16 12 0.40
19 18 0.60
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.13
Consensus pattern (19 bp):
CAACCGACGGTTGAAAAAA
Found at i:9988562 original size:35 final size:35
Alignment explanation
Indices: 9988516--9988593 Score: 156
Period size: 35 Copynumber: 2.2 Consensus size: 35
9988506 CGATCGGAGC
9988516 AACCGACGGTTGAAAAAACAACCGTCGATTACAAT
1 AACCGACGGTTGAAAAAACAACCGTCGATTACAAT
9988551 AACCGACGGTTGAAAAAACAACCGTCGATTACAAT
1 AACCGACGGTTGAAAAAACAACCGTCGATTACAAT
9988586 AACCGACG
1 AACCGACG
9988594 ATGGCGATCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.15
Consensus pattern (35 bp):
AACCGACGGTTGAAAAAACAACCGTCGATTACAAT
Found at i:9988595 original size:16 final size:16
Alignment explanation
Indices: 9988535--9988595 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
9988525 TTGAAAAAAC
*
9988535 AACCGTCGATTACAAT
1 AACCGACGATTACAAT
* * *
9988551 AACCGACGGTTGAAAAAAC
1 AACCGACGATT---ACAAT
*
9988570 AACCGTCGATTACAAT
1 AACCGACGATTACAAT
9988586 AACCGACGAT
1 AACCGACGAT
9988596 GGCGATCGGT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
16 21 0.64
19 12 0.36
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (16 bp):
AACCGACGATTACAAT
Found at i:9993295 original size:3 final size:3
Alignment explanation
Indices: 9993280--9993310 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
9993270 GAGACTTAAC
*
9993280 CAG CAG AAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
9993311 TCGAATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:10001937 original size:19 final size:21
Alignment explanation
Indices: 10001915--10001959 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
10001905 TTCATATATT
*
10001915 TAAATA-A-ATTTTTTTAAAA
1 TAAATACATATTTCTTTAAAA
10001934 TAAATACATATTTCTTTAAAA
1 TAAATACATATTTCTTTAAAA
10001955 -AAATA
1 TAAATA
10001960 GTTTATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
21 11 0.48
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATACATATTTCTTTAAAA
Found at i:10005641 original size:17 final size:19
Alignment explanation
Indices: 10005605--10005642 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
10005595 GCATATACAT
*
10005605 ATATATATATATATATAAA
1 ATATACATATATATATAAA
10005624 ATATACATA-ATATA-AAA
1 ATATACATATATATATAAA
10005641 AT
1 AT
10005643 TGACCACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATACATATATATATAAA
Found at i:10011874 original size:9 final size:9
Alignment explanation
Indices: 10011860--10011945 Score: 70
Period size: 9 Copynumber: 9.6 Consensus size: 9
10011850 ACTTTCTTCT
10011860 TCATCATCC
1 TCATCATCC
10011869 TCATCATCC
1 TCATCATCC
10011878 TCATCA---
1 TCATCATCC
10011884 TCATCATCC
1 TCATCATCC
*
10011893 TCATCCTCC
1 TCATCATCC
*
10011902 TCATCGTCTTC
1 TCATCATC--C
*
10011913 ATCCTCATCC
1 -TCATCATCC
* *
10011923 TCATCAACA
1 TCATCATCC
*
10011932 TCATCATCT
1 TCATCATCC
10011941 TCATC
1 TCATC
10011946 GTCATCTTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
6 6 0.10
9 48 0.77
10 1 0.02
11 1 0.02
12 6 0.10
ACGTcount: A:0.22, C:0.42, G:0.01, T:0.35
Consensus pattern (9 bp):
TCATCATCC
Found at i:10011881 original size:6 final size:6
Alignment explanation
Indices: 10011860--10011951 Score: 76
Period size: 6 Copynumber: 15.3 Consensus size: 6
10011850 ACTTTCTTCT
* * * * * *
10011860 TCATCA TCCTCA TCATCC TCATCA TCATCA TCCTCA TCCTCC TCATCG
1 TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA
* * * * * *
10011908 TCTTCA TCCTCA TCCTCA TCAACA TCATCA TCTTCA TCGTCA TC
1 TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TC
10011952 TTCTATCTCA
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.22, C:0.41, G:0.02, T:0.35
Consensus pattern (6 bp):
TCATCA
Found at i:10011891 original size:24 final size:24
Alignment explanation
Indices: 10011860--10011945 Score: 118
Period size: 24 Copynumber: 3.6 Consensus size: 24
10011850 ACTTTCTTCT
*
10011860 TCATCATCCTCATCATCCTCATCA
1 TCATCATCCTCATCCTCCTCATCA
*
10011884 TCATCATCCTCATCCTCCTCATCG
1 TCATCATCCTCATCCTCCTCATCA
* * *
10011908 TCTTCATCCTCATCCTCATCAACA
1 TCATCATCCTCATCCTCCTCATCA
*
10011932 TCATCATCTTCATC
1 TCATCATCCTCATC
10011946 GTCATCTTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.22, C:0.42, G:0.01, T:0.35
Consensus pattern (24 bp):
TCATCATCCTCATCCTCCTCATCA
Found at i:10036433 original size:28 final size:27
Alignment explanation
Indices: 10036391--10036446 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
10036381 TTAAATTTTT
* * *
10036391 AATGAAAATAGAAATTAAAAGATTAAAA
1 AATGAAAATACAAA-TAAAAAAATAAAA
10036419 AATGAAAATACAAATAAAAAAATAAAA
1 AATGAAAATACAAATAAAAAAATAAAA
10036446 A
1 A
10036447 GATATTGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (27 bp):
AATGAAAATACAAATAAAAAAATAAAA
Found at i:10037150 original size:2 final size:2
Alignment explanation
Indices: 10037143--10037171 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10037133 TTGCAGTAGT
10037143 AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10037172 GAGTTTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10042123 original size:497 final size:503
Alignment explanation
Indices: 10041181--10042214 Score: 1319
Period size: 497 Copynumber: 2.1 Consensus size: 503
10041171 TGTGCAAGAT
* * * *
10041181 TGCTTCAATCTCTTCCTTAGCTCTTTCTATCAAATTGGGGGCCTGGATACCATTTCCTGCCAATA
1 TGCTTCAATCTCTTCCTTAGCTCTTTCAATCAAACTGGGGGCCTGGACACCATTTCCTGCCAACA
** *
10041246 TACGAAATAAAAAAGCATGTATAGCGCTGAAGAAGTTTCTCATCATAACCTTAAAACTATCCATA
66 T---AAATAAAAAAGCACATATAGCGCT-AAGAAGTTTCTCATCATAACCTTAAAACTATCCAGA
* *
10041311 GCTTGAAAAAGATATCTAAGAAATAAGCATAAGCCAATAGACTAGCAAAGAACCTGGTTTCTCAT
127 GCTTGAAAAAGATATCTAAGAAATAAGCATAAGCCAAAAAACTAGCAAAGAACCTGGTTTCTCAT
* * * * *
10041376 GTTTCGGCTCTGCCTTGGGGGAATGGTCCCTGAAAATTCAGTGTGATGTTAGATTAAGTATCCAG
192 GTTTCGGCTCTGCCTTGGGAGAATGATCCCTGAAAATTCAGTGTGATGTGAAATTAAGTATACAG
* * * ** *
10041441 AAAAAGGCCCCTTTAAAAGTTCAATATTTGATTCTCATATTCAGTTCATCAGATTCCAACCTCTT
257 AAAAAGGCCCCTTTAAAACTTCAATATTTCAATCTCATAAGCAGATCATCAGATTCCAACCTCTT
*
10041506 ATCATCACGAGTGTGAGACTCTCTCTTGTGATGGATTGTTTCAACAAGAGCCTCAATCTCCTCCT
322 ATCATCACGAGTGTGAGACTCTCTCTTGTGATGGATTGTCTCAACAAGAGCCTCAATCTCCTCCT
* * *
10041571 TTGCTCGTTCAAACACATTAGGTGCTTTCACATCATCCAATGGGGTGTTTTCATCAATATCATTA
387 TTGCTCGTTCAAACACATTAGGCGCTTTCACATCATCCAATGGGGTATTTTCATCAATATCAATA
* * * *
10041636 CGCTTTCCATGAGTTTCCTTATG-GA-GATGTACTTTTCCGGTATGAATCAC
452 CGCTTTCCATGAGTTTCCTCATGAAATGAGGTACTTTTCCGGAATGAATCAC
*
10041686 TGCTTCAATCTCTTCCTTAGCTCTTTCAATCAAACTGGGGGCCTTGG-CACCATTTTCTGCCAAC
1 TGCTTCAATCTCTTCCTTAGCTCTTTCAATCAAACTGGGGGCC-TGGACACCATTTCCTGCCAAC
* * * * *
10041750 AT-AA-AACAGAGCACATATAGCTCT-A-AAG-TTCATCATCGTAGCCCTTAAAACTATCCAGAG
65 ATAAATAAAAAAGCACATATAGCGCTAAGAAGTTTC-TCATCATA-ACCTTAAAACTATCCAGAG
* * * *
10041810 CTTGAAAAAGATATTTAAGAAATAAGCATGAGGCAAAAAACTAGCAAAGAACCTGGTTTCTTATG
128 CTTGAAAAAGATATCTAAGAAATAAGCATAAGCCAAAAAACTAGCAAAGAACCTGGTTTCTCATG
* * * * *
10041875 TTT-TGATCCTGCCTTGGTAGAATGATCCCTGAAAATTCATTGTGATGTGAAATTCAGTATACAG
193 TTTCGGCT-CTGCCTTGGGAGAATGATCCCTGAAAATTCAGTGTGATGTGAAATTAAGTATACAG
** * *
10041939 -AAAAGGCACCCTCATT-TGACTCTC-ATA-TTCAAT-TCA-AAGGAGAAAT-ATTAGATTCCAA
257 AAAAAGGC-CCCT--TTAAAACT-TCAATATTTCAATCTCATAAGCAG--ATCATCAGATTCCAA
* * *
10041997 CCT-TTCATCATCATGAGTGTGAGACTCTTTCTTGTGATGGATTGTCTCAACAAGGGCCTCAATC
316 CCTCTT-ATCATCACGAGTGTGAGACTCTCTCTTGTGATGGATTGTCTCAACAAGAGCCTCAATC
* *
10042061 TCCTCCTTTGCTCGTTCAAACACATTAGGCGCTTTCACATCCTCCACTGGGGTATTTTCATCAAT
380 TCCTCCTTTGCTCGTTCAAACACATTAGGCGCTTTCACATCATCCAATGGGGTATTTTCATCAAT
*
10042126 ATCAATACGCTTTCCATGAGTTTCCTCATGAAAATGAGGTATTTTTCCGGAATGAATCAC
445 ATCAATACGCTTTCCATGAGTTTCCTCATG-AAATGAGGTACTTTTCCGGAATGAATCAC
*
10042186 TGCTTCAATCTCTTCCTTTGCTCTTTCAA
1 TGCTTCAATCTCTTCCTTAGCTCTTTCAA
10042215 ATATATTAGG
Statistics
Matches: 461, Mismatches: 54, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
496 8 0.02
497 179 0.39
498 137 0.30
499 6 0.01
500 69 0.15
501 2 0.00
505 57 0.12
506 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (503 bp):
TGCTTCAATCTCTTCCTTAGCTCTTTCAATCAAACTGGGGGCCTGGACACCATTTCCTGCCAACA
TAAATAAAAAAGCACATATAGCGCTAAGAAGTTTCTCATCATAACCTTAAAACTATCCAGAGCTT
GAAAAAGATATCTAAGAAATAAGCATAAGCCAAAAAACTAGCAAAGAACCTGGTTTCTCATGTTT
CGGCTCTGCCTTGGGAGAATGATCCCTGAAAATTCAGTGTGATGTGAAATTAAGTATACAGAAAA
AGGCCCCTTTAAAACTTCAATATTTCAATCTCATAAGCAGATCATCAGATTCCAACCTCTTATCA
TCACGAGTGTGAGACTCTCTCTTGTGATGGATTGTCTCAACAAGAGCCTCAATCTCCTCCTTTGC
TCGTTCAAACACATTAGGCGCTTTCACATCATCCAATGGGGTATTTTCATCAATATCAATACGCT
TTCCATGAGTTTCCTCATGAAATGAGGTACTTTTCCGGAATGAATCAC
Found at i:10043861 original size:3 final size:3
Alignment explanation
Indices: 10043853--10043882 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
10043843 AATTACACAA
10043853 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
10043883 TGGATGTTAT
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):
AAT
Found at i:10044210 original size:60 final size:60
Alignment explanation
Indices: 10044137--10044326 Score: 193
Period size: 60 Copynumber: 3.2 Consensus size: 60
10044127 TTAATTATTA
**
10044137 AAATATAAATTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTT
1 AAATATATTTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTT
* *
10044197 AAATATATTTTTAATATCA--TATA--TTTTGTT-TTCATTTATTAT-T-ATA--ATCT-TAT
1 AAATATATTTTTAATAT-ATTTATATTTTTTATTATTAATTT-TTATATAATATCATCTCT-T
* * *
10044250 ATATTTTATTTTTAATATATTTATAATTTTTTATTATTAATTTTTATATAACATCATCTCTT
1 A-AATATATTTTTAATATATTTAT-ATTTTTTATTATTAATTTTTATATAATATCATCTCTT
*
10044312 AAATATTTTTTTAAT
1 AAATATATTTTTAAT
10044327 GTTATATATT
Statistics
Matches: 103, Mismatches: 12, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
52 1 0.01
53 7 0.07
54 14 0.14
55 6 0.06
56 8 0.08
57 10 0.10
58 10 0.10
59 11 0.11
60 17 0.17
61 12 0.12
62 6 0.06
63 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (60 bp):
AAATATATTTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTT
Found at i:10044295 original size:23 final size:23
Alignment explanation
Indices: 10044231--10044297 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
10044221 TTTGTTTTCA
* *
10044231 TTTATTATTATAATCTTAT-ATAT
1 TTTATTATTA-ATTTTTATAATAT
* *
10044254 TTTATTTTTAATATATTTATAATTT
1 TTTATTATTAAT-T-TTTATAATAT
10044279 TTTATTATTAATTTTTATA
1 TTTATTATTAATTTTTATA
10044298 TAACATCATC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 1 0.03
23 16 0.44
24 5 0.14
25 14 0.39
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTATTAATTTTTATAATAT
Found at i:10044299 original size:115 final size:114
Alignment explanation
Indices: 10044146--10044362 Score: 380
Period size: 115 Copynumber: 1.9 Consensus size: 114
10044136 AAAATATAAA
*
10044146 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAACATCATCTCTTAAATATATTTTTAA
*
10044211 TATCATATATTTTGTTTTCATTTATTATTATAATCTTATATATTTTATT
66 TATCATATATTTTATTTTCATTTATTATTATAATCTTATATATTTTATT
*
10044260 TTTAATATATTTATAATTTTTTATTATTAATTTTTATATAACATCATCTCTTAAATATTTTTTTA
1 TTTAATATATTTAT-ATTTTTTATTATTAATTTTTATATAACATCATCTCTTAAATATATTTTTA
* *
10044325 ATGTTATATATTTTATTTTCATTTATTATTATAATCTT
65 ATATCATATATTTTATTTTCATTTATTATTATAATCTT
10044363 TTTTTATTTC
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
114 14 0.14
115 83 0.86
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (114 bp):
TTTAATATATTTATATTTTTTATTATTAATTTTTATATAACATCATCTCTTAAATATATTTTTAA
TATCATATATTTTATTTTCATTTATTATTATAATCTTATATATTTTATT
Found at i:10044300 original size:25 final size:25
Alignment explanation
Indices: 10044231--10044297 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
10044221 TTTGTTTTCA
*
10044231 TTTATTATT-ATA-ATCTTAT-ATAT
1 TTTATTATTAATATAT-TTATAATTT
*
10044254 TTTATTTTTAATATATTTATAATTT
1 TTTATTATTAATATATTTATAATTT
10044279 TTTATTATTAAT-T-TTTATA
1 TTTATTATTAATATATTTATA
10044298 TAACATCATC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 14 0.37
24 8 0.21
25 16 0.42
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTATTATTAATATATTTATAATTT
Found at i:10044447 original size:24 final size:25
Alignment explanation
Indices: 10044420--10044494 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
10044410 TTGTTTTACC
10044420 TATATTATA-TAAATTTTAATTTTT
1 TATATTATATTAAATTTTAATTTTT
* **
10044444 TATATTTTATTTTATTTTAATTTTT
1 TATATTATATTAAATTTTAATTTTT
* *
10044469 GATTCTTATATTATATATTTT-ATTTT
1 TA-TATTATATTA-A-ATTTTAATTTT
10044495 AATATTTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
24 8 0.21
25 14 0.36
26 7 0.18
27 5 0.13
28 5 0.13
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (25 bp):
TATATTATATTAAATTTTAATTTTT
Found at i:10044504 original size:15 final size:15
Alignment explanation
Indices: 10044481--10044512 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10044471 TTCTTATATT
10044481 ATATATTTTATTTTA
1 ATATATTTTATTTTA
*
10044496 ATATTTTTTATTTTA
1 ATATATTTTATTTTA
10044511 AT
1 AT
10044513 TATAACAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:10046056 original size:16 final size:15
Alignment explanation
Indices: 10046037--10046078 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
10046027 GACTTAATTC
10046037 TATTTTTTTTATTTTT
1 TATTTTTTTTA-TTTT
*
10046053 TATTTATTTTATTTT
1 TATTTTTTTTATTTT
*
10046068 TATTTTATTTA
1 TATTTTTTTTA
10046079 CTATTGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TATTTTTTTTATTTT
Found at i:10046062 original size:20 final size:20
Alignment explanation
Indices: 10046037--10046078 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
10046027 GACTTAATTC
*
10046037 TATTTT-TTTTATTTTTTATT
1 TATTTTATTTT-TATTTTATT
10046057 TATTTTATTTTTATTTTATT
1 TATTTTATTTTTATTTTATT
10046077 TA
1 TA
10046079 CTATTGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (20 bp):
TATTTTATTTTTATTTTATT
Found at i:10046074 original size:11 final size:11
Alignment explanation
Indices: 10046042--10046077 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
10046032 AATTCTATTT
10046042 TTTTTATTTT-
1 TTTTTATTTTA
10046052 TTATTTATTTTA
1 TT-TTTATTTTA
10046064 TTTTTATTTTA
1 TTTTTATTTTA
10046075 TTT
1 TTT
10046078 ACTATTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.08
11 20 0.83
12 2 0.08
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:10058362 original size:2 final size:2
Alignment explanation
Indices: 10058355--10058410 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
10058345 GCTTTTCTAG
* *
10058355 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT AT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
10058397 CA CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
10058411 ATATATATGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.04, C:0.46, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10059439 original size:22 final size:21
Alignment explanation
Indices: 10059414--10059468 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
10059404 GGCATACATT
10059414 AATTTTAAGCATAA-TATTTAAA
1 AATTTTAA--ATAACTATTTAAA
*
10059436 AATTTTAATTAACTATTTAAA
1 AATTTTAAATAACTATTTAAA
*
10059457 ATTTTTAAATAA
1 AATTTTAAATAA
10059469 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.10
21 18 0.62
22 8 0.28
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTTTAAATAACTATTTAAA
Found at i:10059475 original size:21 final size:21
Alignment explanation
Indices: 10059426--10059475 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
10059416 TTTTAAGCAT
*
10059426 AATATTTAAAAATTTTAATTA
1 AATATTTAAAAATTTTAAATA
* *
10059447 ACTATTTAAAATTTTTAAATA
1 AATATTTAAAAATTTTAAATA
*
10059468 AATTTTTA
1 AATATTTA
10059476 TTTTTTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTTAAAAATTTTAAATA
Found at i:10059525 original size:28 final size:28
Alignment explanation
Indices: 10059461--10059532 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
10059451 TTTAAAATTT
10059461 TTAAATAA-ATTTTTATTTTTTATTACA
1 TTAAATAATATTTTTATTTTTTATTACA
* **
10059488 TTCAATTAATATTTTTA-TTTTTATTTTTA
1 TT-AAATAATATTTTTATTTTTTA-TTACA
10059517 TTAAATAAT-TTTTTAT
1 TTAAATAATATTTTTAT
10059533 AAATAATGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
27 8 0.22
28 17 0.46
29 12 0.32
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (28 bp):
TTAAATAATATTTTTATTTTTTATTACA
Found at i:10060831 original size:19 final size:19
Alignment explanation
Indices: 10060790--10060831 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
10060780 GATTTTATTA
*
10060790 AAATAATATTTTTAATTGT
1 AAATAATATTTATAATTGT
10060809 -AATAATATTGTATAATT-T
1 AAATAATATT-TATAATTGT
10060827 AAATA
1 AAATA
10060832 TTAATATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (19 bp):
AAATAATATTTATAATTGT
Found at i:10061489 original size:2 final size:2
Alignment explanation
Indices: 10061477--10061513 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
10061467 TGGCCTAGCA
* *
10061477 TC TC TC GC TC TC TC TC TC TC TC TC TA TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
10061514 ATCAAACCCA
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:0.03, C:0.46, G:0.03, T:0.49
Consensus pattern (2 bp):
TC
Found at i:10075755 original size:5 final size:5
Alignment explanation
Indices: 10075738--10075771 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
10075728 AAAGCGGCGA
*
10075738 AGAGC AGAAC AGAGC AGAGC AGAGC AGAGC AGAG
1 AGAGC AGAGC AGAGC AGAGC AGAGC AGAGC AGAG
10075772 ACAAGAGCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.38, T:0.00
Consensus pattern (5 bp):
AGAGC
Found at i:10088453 original size:2 final size:2
Alignment explanation
Indices: 10088446--10088478 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10088436 AATTCTTCTT
10088446 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 T
10088479 GAAAAAAAGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10100066 original size:29 final size:28
Alignment explanation
Indices: 10100006--10100066 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
10099996 ATATGACATT
* *
10100006 TTCACCATTCCAACAAAGGCCCACTATT
1 TTCACCATTCCAACAAAGACCCACTATC
* *
10100034 TTCACCATTCCAAACAAAGATCCATTATC
1 TTCACCATTCC-AACAAAGACCCACTATC
10100063 TTCA
1 TTCA
10100067 GTGTCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.34, C:0.33, G:0.05, T:0.28
Consensus pattern (28 bp):
TTCACCATTCCAACAAAGACCCACTATC
Found at i:10101590 original size:12 final size:12
Alignment explanation
Indices: 10101575--10101622 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
10101565 AAGATATTAT
10101575 TTAATTAATAAA
1 TTAATTAATAAA
*
10101587 TTAATCAATAAA
1 TTAATTAATAAA
* *
10101599 TTAATTTATATA
1 TTAATTAATAAA
10101611 TTAATTAATAAA
1 TTAATTAATAAA
10101623 AAATTAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAATTAATAAA
Found at i:10101602 original size:24 final size:24
Alignment explanation
Indices: 10101575--10101630 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
10101565 AAGATATTAT
10101575 TTAATTAATAAATTAATCAATAAA
1 TTAATTAATAAATTAATCAATAAA
* * *
10101599 TTAATTTATATATTAATTAATAAA
1 TTAATTAATAAATTAATCAATAAA
*
10101623 -AAATTAAT
1 TTAATTAAT
10101631 TTATGAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAATTAATAAATTAATCAATAAA
Found at i:10102413 original size:16 final size:17
Alignment explanation
Indices: 10102392--10102439 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
10102382 AAATAGATTA
10102392 AAAATATT-ATTTAATT
1 AAAATATTAATTTAATT
*
10102408 AAAATAATTCATTT-ATT
1 AAAAT-ATTAATTTAATT
10102425 -AAATATTAATTTAAT
1 AAAATATTAATTTAAT
10102440 GAGTGACAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.25
16 11 0.39
17 6 0.21
18 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATATTAATTTAATT
Found at i:10114073 original size:282 final size:282
Alignment explanation
Indices: 10113438--10114762 Score: 2357
Period size: 282 Copynumber: 4.7 Consensus size: 282
10113428 TGACTCATTG
*
10113438 AGGTAAAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
1 AGGTAGAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
10113503 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
66 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
*
10113568 AATTGAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
131 AATTAAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
*** *
10113633 TATGTGTTCAAC-AAAAATTTTTTTGTAAGACAGAATATTTATTTCGAGAACTAATTGACTCATT
196 TATGTGTTCAACAAAAAAAAATTTT-TAAGACAGAATATTTATTTCGAGAACTAATTGACCCATT
10113697 GAAAATTTCGATTAAAACTTAAA
260 GAAAATTTCGATTAAAACTTAAA
10113720 AGGTAGAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
1 AGGTAGAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
*
10113785 AAAAAATTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
66 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
*
10113850 AATTAAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAAATATTACGATTTTATATT
131 AATTAAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
10113915 TATGTGTTCAACAAAAAAAAAATTTTTAAGACAGAATATTTATTTCGAGAACTAATTGACCCATT
196 TATGTGTTCAAC-AAAAAAAAATTTTTAAGACAGAATATTTATTTCGAGAACTAATTGACCCATT
10113980 GAAAATTTCGATTAAAACTTAAA
260 GAAAATTTCGATTAAAACTTAAA
10114003 AGGTAGAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
1 AGGTAGAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
10114068 AAAAA-TTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
66 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
*
10114132 AATTAAGATAACATTAAATACATTAAGATTTTATATATATATGAAAAAATATTACGATTTTATAT
131 AATTAAGATAACATTAAATACATTAAGATTTTATATATAT-TGAAAAACTATTACGATTTTATAT
*
10114197 TTATGTGTTCAACAAAAAAAAAAATTTTAAGACAGAATATTTATTTCGAGAACTAATTGACCCAT
195 TTATGTGTTCAAC-AAAAAAAAATTTTTAAGACAGAATATTTATTTCGAGAACTAATTGACCCAT
10114262 TGAAAATTTCGATTAAAACTTAAA
259 TGAAAATTTCGATTAAAACTTAAA
*
10114286 AGGTAGAAGTATTTTATCTTAATTTGTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
1 AGGTAGAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
*
10114351 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGCTTTTTAACTATTCAATGTCAATAA
66 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
* *
10114416 AATTGAGATAACATTAAATGCATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
131 AATTAAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
****** *
10114481 TATGTGTTCAACAAATTTTTTTTTTTAAGACAGAATGTTTATTTCGAGAACTAATTGACCCATTG
196 TATGTGTTCAACAAAAAAAAATTTTTAAGACAGAATATTTATTTCGAGAACTAATTGACCCATTG
*
10114546 AAAATTTTGATTAAAACTTAAA
261 AAAATTTCGATTAAAACTTAAA
*
10114568 AGGTAAAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
1 AGGTAGAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
* *
10114633 AAAAATTTTAATCTATAAATATCAGTGTCAATAAAAATTGCTTTTTAACTATTCAATGTCAATAA
66 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
* *
10114698 AATTAAGATAACATTAAATATATTAAGATTTTATATATATTGAAAAACTATTAAGATTTTATATT
131 AATTAAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
10114763 AAAATGATAT
Statistics
Matches: 1009, Mismatches: 30, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
282 556 0.55
283 348 0.34
284 105 0.10
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (282 bp):
AGGTAGAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
AATTAAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
TATGTGTTCAACAAAAAAAAATTTTTAAGACAGAATATTTATTTCGAGAACTAATTGACCCATTG
AAAATTTCGATTAAAACTTAAA
Found at i:10114645 original size:566 final size:565
Alignment explanation
Indices: 10113438--10114762 Score: 2368
Period size: 566 Copynumber: 2.3 Consensus size: 565
10113428 TGACTCATTG
10113438 AGGTAAAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
1 AGGTAAAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
10113503 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
66 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
*
10113568 AATTGAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
131 AATTAAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
**** *
10113633 TATGTGTTCAACAAAAATTTTTTTGTAAGACAGAATATTTATTTCGAGAACTAATTGACTCATTG
196 TATGTGTTCAACAAAAAAAAATTTGTAAGACAGAATATTTATTTCGAGAACTAATTGACCCATTG
*
10113698 AAAATTTCGATTAAAACTTAAAAGGTAGAAGTATTTTATCTTAATTTTTTTAATATAATCATCAA
261 AAAATTTCGATTAAAACTTAAAAGGTAGAAGTATTTTATCTTAATTTGTTTAATATAATCATCAA
*
10113763 CTTATATGAATTTCAAGTAATAAAAAAATTTAATCTATAAATATCAATGTCAATAAAAATTGTTT
326 CTTATATGAATTTCAAGTAATAAAAAAATTTAATCTATAAATATCAATGTCAATAAAAATTGCTT
10113828 TTTAACTATTCAATGTCAATAAAATTAAGATAACATTAAATACATTAAGATTTTATATATATTGA
391 TTTAACTATTCAATGTCAATAAAATTAAGATAACATTAAATACATTAAGATTTTATATATATTGA
10113893 AAAAATATTACGATTTTATATTTATGTGTTCAACAAAAAAAAAATTTTTAAGACAGAATATTTAT
456 AAAAATATTACGATTTTATATTTATGTGTTCAACAAAAAAAAAATTTTTAAGACAGAATATTTAT
10113958 TTCGAGAACTAATTGACCCATTGAAAATTTCGATTAAAACTTAAA
521 TTCGAGAACTAATTGACCCATTGAAAATTTCGATTAAAACTTAAA
*
10114003 AGGTAGAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
1 AGGTAAAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
10114068 AAAAA-TTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
66 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
*
10114132 AATTAAGATAACATTAAATACATTAAGATTTTATATATATATGAAAAAATATTACGATTTTATAT
131 AATTAAGATAACATTAAATACATTAAGATTTTATATATAT-TGAAAAACTATTACGATTTTATAT
10114197 TTATGTGTTCAACAAAAAAAAAAATTT-TAAGACAGAATATTTATTTCGAGAACTAATTGACCCA
195 TTATGTGTTCAAC--AAAAAAAAATTTGTAAGACAGAATATTTATTTCGAGAACTAATTGACCCA
10114261 TTGAAAATTTCGATTAAAACTTAAAAGGTAGAAGTATTTTATCTTAATTTGTTTAATATAATCAT
258 TTGAAAATTTCGATTAAAACTTAAAAGGTAGAAGTATTTTATCTTAATTTGTTTAATATAATCAT
*
10114326 CAACTTATATGAATTTCAAGTAATAAAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTG
323 CAACTTATATGAATTTCAAGTAATAAAAAAATTTAATCTATAAATATCAATGTCAATAAAAATTG
* *
10114391 CTTTTTAACTATTCAATGTCAATAAAATTGAGATAACATTAAATGCATTAAGATTTTATATATAT
388 CTTTTTAACTATTCAATGTCAATAAAATTAAGATAACATTAAATACATTAAGATTTTATATATAT
* ****** *
10114456 TGAAAAACTATTACGATTTTATATTTATGTGTTCAAC-AAATTTTTTTTTTTAAGACAGAATGTT
453 TGAAAAAATATTACGATTTTATATTTATGTGTTCAACAAAAAAAAAATTTTTAAGACAGAATATT
*
10114520 TATTTCGAGAACTAATTGACCCATTGAAAATTTTGATTAAAACTTAAA
518 TATTTCGAGAACTAATTGACCCATTGAAAATTTCGATTAAAACTTAAA
10114568 AGGTAAAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
1 AGGTAAAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
* *
10114633 AAAAATTTTAATCTATAAATATCAGTGTCAATAAAAATTGCTTTTTAACTATTCAATGTCAATAA
66 AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
* *
10114698 AATTAAGATAACATTAAATATATTAAGATTTTATATATATTGAAAAACTATTAAGATTTTATATT
131 AATTAAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
10114763 AAAATGATAT
Statistics
Matches: 728, Mismatches: 28, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
564 98 0.13
565 264 0.36
566 358 0.49
567 8 0.01
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (565 bp):
AGGTAAAAGTATTTTATCTTAATTTTTTTAATATAATCATCAACTTATATGAATTTCAAGTAATA
AAAAATTTTAATCTATAAATATCAATGTCAATAAAAATTGTTTTTTAACTATTCAATGTCAATAA
AATTAAGATAACATTAAATACATTAAGATTTTATATATATTGAAAAACTATTACGATTTTATATT
TATGTGTTCAACAAAAAAAAATTTGTAAGACAGAATATTTATTTCGAGAACTAATTGACCCATTG
AAAATTTCGATTAAAACTTAAAAGGTAGAAGTATTTTATCTTAATTTGTTTAATATAATCATCAA
CTTATATGAATTTCAAGTAATAAAAAAATTTAATCTATAAATATCAATGTCAATAAAAATTGCTT
TTTAACTATTCAATGTCAATAAAATTAAGATAACATTAAATACATTAAGATTTTATATATATTGA
AAAAATATTACGATTTTATATTTATGTGTTCAACAAAAAAAAAATTTTTAAGACAGAATATTTAT
TTCGAGAACTAATTGACCCATTGAAAATTTCGATTAAAACTTAAA
Found at i:10115820 original size:2 final size:2
Alignment explanation
Indices: 10115813--10115848 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10115803 CGGTCAAGAC
10115813 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
10115849 TCTTTGTTTG
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:10125050 original size:24 final size:27
Alignment explanation
Indices: 10124994--10125054 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
10124984 CAAAAATTGC
* *
10124994 CTAAAATAATAAATTAATACTTTTTTTG
1 CTAAAATAATAAATCAATAC-TTTTTAG
10125022 CTAAAATAATAAATCAAT-C-TTTTAG
1 CTAAAATAATAAATCAATACTTTTTAG
10125047 -TAAAATAA
1 CTAAAATAA
10125055 ATAGATATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 8 0.26
25 5 0.16
27 1 0.03
28 17 0.55
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.39
Consensus pattern (27 bp):
CTAAAATAATAAATCAATACTTTTTAG
Found at i:10125793 original size:27 final size:27
Alignment explanation
Indices: 10125663--10125868 Score: 86
Period size: 25 Copynumber: 7.6 Consensus size: 27
10125653 AAGTGTAACA
*
10125663 ATTTTTTTTAACATG-TCGTGTAATAAT
1 ATTTTTTTTAACATGAT-GTATAATAAT
*
10125690 AATATTTTTTTAACATAGTGTGTAATAATAAT
1 -AT-TTTTTTTAACAT-G-ATGT-ATAATAAT
* * ** * * *
10125722 ATTTTTTTCAGCATGGCGCACAA-CAT
1 ATTTTTTTTAACATGATGTATAATAAT
* *
10125748 A-TTTTTGT-ACATGACATGTACAATAAT
1 ATTTTTTTTAACATG--ATGTATAATAAT
10125775 ATTTTTTTTAACATGATGTATAAT-A-
1 ATTTTTTTTAACATGATGTATAATAAT
* * *
10125800 ATTTTTTTTAATCATAACGTGTAAT-AT
1 ATTTTTTTTAA-CATGATGTATAATAAT
* ** * * *
10125827 GTTTTTGGT-ACATAACGTGTAATAAT
1 ATTTTTTTTAACATGATGTATAATAAT
*
10125853 AATTTTTTTAACATGA
1 ATTTTTTTTAACATGA
10125869 CGTGTAACAA
Statistics
Matches: 137, Mismatches: 27, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
24 4 0.03
25 29 0.21
26 28 0.20
27 25 0.18
28 10 0.07
29 18 0.13
30 11 0.08
31 4 0.03
32 8 0.06
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (27 bp):
ATTTTTTTTAACATGATGTATAATAAT
Found at i:10125831 original size:25 final size:24
Alignment explanation
Indices: 10125771--10125902 Score: 95
Period size: 25 Copynumber: 5.2 Consensus size: 24
10125761 ACATGTACAA
* * *
10125771 TAATATTTTTTTTAACATGATGTA
1 TAATATTTTTTTTAACATAACGTG
10125795 TAATAATTTTTTTTAATCATAACGTG
1 TAAT-ATTTTTTTTAA-CATAACGTG
*
10125821 TAATATGTTTTTGGT-ACATAACGTG
1 TAATAT-TTTTT-TTAACATAACGTG
*
10125846 TAATAATAATTTTTTTAACATGACGTG
1 TAAT-AT--TTTTTTTAACATAACGTG
* ** * *
10125873 TAACAACTTTTTTAACCATAGCGCG
1 TAATATTTTTTTTAA-CATAACGTG
10125898 TAATA
1 TAATA
10125903 ATAACATTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
24 12 0.14
25 36 0.42
26 20 0.23
27 18 0.21
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (24 bp):
TAATATTTTTTTTAACATAACGTG
Found at i:10125871 original size:27 final size:27
Alignment explanation
Indices: 10125665--10125875 Score: 118
Period size: 29 Copynumber: 7.8 Consensus size: 27
10125655 GTGTAACAAT
*
10125665 TTTTTTTAACATGTCGTGTAATAATAATA
1 TTTTTTTAACATGACGTGTAATAAT-A-A
*
10125694 TTTTTTTAACAT-AGTGTGTAATAATAATA
1 TTTTTTTAACATGA-CGTGTAATAAT-A-A
* * *** *
10125723 TTTTTTTCAGCATGGCGCACAA-CAT-A
1 TTTTTTT-AACATGACGTGTAATAATAA
* * *
10125749 TTTTTGT-ACATGACATGTACAATAATAT
1 TTTTTTTAACATGACGTGT--AATAATAA
10125777 TTTTTTTAACATGA--TGT-ATAATAA
1 TTTTTTTAACATGACGTGTAATAATAA
* *
10125801 TTTTTTTTAATCATAACGTGTAAT-AT-G
1 -TTTTTTTAA-CATGACGTGTAATAATAA
* *
10125828 TTTTTGGT-ACATAACGTGTAATAATAA
1 TTTTT-TTAACATGACGTGTAATAATAA
10125855 TTTTTTTAACATGACGTGTAA
1 TTTTTTTAACATGACGTGTAA
10125876 CAACTTTTTT
Statistics
Matches: 139, Mismatches: 26, Indels: 36
0.69 0.13 0.18
Matches are distributed among these distances:
24 11 0.08
25 22 0.16
26 22 0.16
27 23 0.17
28 11 0.08
29 43 0.31
30 7 0.05
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (27 bp):
TTTTTTTAACATGACGTGTAATAATAA
Done.