Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 5 of 190
Found at i:1416289 original size:5 final size:5
Alignment explanation
Indices: 1416279--1416306 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1416269 TGAGCATTCG
1416279 ATCGA ATCGA ATCGA ATCGA ATCGA ATC
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATC
1416307 AAAAATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (5 bp):
ATCGA
Found at i:1417098 original size:30 final size:30
Alignment explanation
Indices: 1417064--1417121 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1417054 AGGTGGGATG
*
1417064 GGAAGAGAATAAAAGTTTTAGGGGAAAAGT
1 GGAAGAGAATAAAAATTTTAGGGGAAAAGT
* * *
1417094 GGAAGGGAGTAAAAATTTTGGGGGAAAA
1 GGAAGAGAATAAAAATTTTAGGGGAAAA
1417122 TAAAAGGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (30 bp):
GGAAGAGAATAAAAATTTTAGGGGAAAAGT
Found at i:1417351 original size:9 final size:9
Alignment explanation
Indices: 1417337--1417364 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1417327 TATAGTTTGA
1417337 TATTCGAAT
1 TATTCGAAT
1417346 TATTCGAAT
1 TATTCGAAT
1417355 TATTCGAAT
1 TATTCGAAT
1417364 T
1 T
1417365 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1422922 original size:29 final size:28
Alignment explanation
Indices: 1422854--1422923 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 28
1422844 CAAATATAAT
*
1422854 AAATATATATTTTATTTTTTTAATTTTA
1 AAATATATTTTTTATTTTTTTAATTTTA
* *
1422882 AAATACTTTTTTTTATTTTTTTTATTTTTA
1 AAATA-TATTTTTTA-TTTTTTTAATTTTA
*
1422912 AAATAAATTTTT
1 AAATATATTTTT
1422924 GGTGTTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 5 0.14
29 12 0.34
30 18 0.51
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (28 bp):
AAATATATTTTTTATTTTTTTAATTTTA
Found at i:1423274 original size:17 final size:18
Alignment explanation
Indices: 1423240--1423276 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1423230 AAATATTGTG
1423240 AAAAAAAATAAAACACGA
1 AAAAAAAATAAAACACGA
*
1423258 AAAAAAAATGAAA-ACGA
1 AAAAAAAATAAAACACGA
1423275 AA
1 AA
1423277 TTATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.05
Consensus pattern (18 bp):
AAAAAAAATAAAACACGA
Found at i:1423594 original size:17 final size:17
Alignment explanation
Indices: 1423562--1423595 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1423552 CGAAAATACT
1423562 AACTACAATAATAACAA
1 AACTACAATAATAACAA
1423579 AACTAACAATAA-AACAA
1 AACT-ACAATAATAACAA
1423596 GTGTTATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.15
Consensus pattern (17 bp):
AACTACAATAATAACAA
Found at i:1424638 original size:15 final size:15
Alignment explanation
Indices: 1424620--1424658 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1424610 TATTTCATTT
*
1424620 TTAAATATTGTATTA
1 TTAAATATTATATTA
*
1424635 TTAAACATTATATTA
1 TTAAATATTATATTA
*
1424650 TTAACTATT
1 TTAAATATT
1424659 TTATCATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAAATATTATATTA
Found at i:1428238 original size:26 final size:25
Alignment explanation
Indices: 1428209--1428277 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 25
1428199 ATTTTAAACA
* *
1428209 AAAATTTAAAAATAATATATTATTT
1 AAAATTTAAAAATAATAAACTATTT
* *
1428234 GAAAATTTATGAAAAAAATAAACTCTTT
1 -AAAATTTA--AAAATAATAAACTATTT
1428262 AAAATTTAAAATATAA
1 AAAATTTAAAA-ATAA
1428278 ATTCATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 3 0.09
26 11 0.31
27 8 0.23
28 13 0.37
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (25 bp):
AAAATTTAAAAATAATAAACTATTT
Found at i:1430284 original size:37 final size:38
Alignment explanation
Indices: 1430222--1430319 Score: 103
Period size: 39 Copynumber: 2.6 Consensus size: 38
1430212 CATTTAATTA
* * *
1430222 ATTTTTAAAATTTTAAAATT-CAAAA-ATATAAAAACT
1 ATTTTTAAAATATTAAAATTAAAAAATATATAAAAAAT
1430258 ATTTTTAAAA-ATTAAAATTTTAAAAAATATATAAAAAAT
1 ATTTTTAAAATATTAAAA--TTAAAAAATATATAAAAAAT
* *
1430297 ATTTTTATAATTTTAAAAATTAA
1 ATTTTTAAAATATT-AAAATTAA
1430320 TTAAATAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
35 6 0.12
36 10 0.20
37 2 0.04
38 4 0.08
39 23 0.45
40 2 0.04
41 4 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (38 bp):
ATTTTTAAAATATTAAAATTAAAAAATATATAAAAAAT
Found at i:1430457 original size:13 final size:13
Alignment explanation
Indices: 1430441--1430469 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1430431 ATTCAATAAC
1430441 TAAAAAAATTAAA
1 TAAAAAAATTAAA
1430454 TAAAAAAATTAAA
1 TAAAAAAATTAAA
1430467 TAA
1 TAA
1430470 CATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAAAATTAAA
Found at i:1430675 original size:16 final size:15
Alignment explanation
Indices: 1430631--1430680 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1430621 TCGTAATACA
*
1430631 TATTTTTTATACTACT
1 TATTTTTTATATTA-T
*
1430647 TA-TTTTAATATTAT
1 TATTTTTTATATTAT
1430661 TATTTTTTATA--AT
1 TATTTTTTATATTAT
1430674 TATTTTT
1 TATTTTT
1430681 GAGTTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 9 0.30
14 3 0.10
15 16 0.53
16 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTATATTAT
Found at i:1446461 original size:31 final size:31
Alignment explanation
Indices: 1446391--1446467 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
1446381 TTCTTTAATT
* *
1446391 TGATTAATTTTGGTCTTAGTATTTTTTGAAA
1 TGATAAATTTTAGTCTTAGTATTTTTTGAAA
*
1446422 TGATAAATTTTAGTCTTTGTACTTTTTT-AAA
1 TGATAAATTTTAGTCTTAGTA-TTTTTTGAAA
*
1446453 -GTTGAAATTTTAGTC
1 TGAT-AAATTTTAGTC
1446468 CCGATCCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 2 0.05
31 32 0.80
32 6 0.15
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.53
Consensus pattern (31 bp):
TGATAAATTTTAGTCTTAGTATTTTTTGAAA
Found at i:1457370 original size:48 final size:48
Alignment explanation
Indices: 1457314--1457424 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 48
1457304 TGGTGTAATG
* * * * * *
1457314 CCTCGCAAGATTGCGAGGTGTTCTACCTCGTAAGGAGTTGATGTTCCA
1 CCTCGCAAGGTTGCGAAGCGTTCCACCTCGCAAGGAGTTGATATTCCA
* * * * *
1457362 CCTCGCAAGGTTGTGAAGCGTTCCATCTTGCGAGGTGTTGATATTCCA
1 CCTCGCAAGGTTGCGAAGCGTTCCACCTCGCAAGGAGTTGATATTCCA
1457410 CCTCGCAAGGTTGCG
1 CCTCGCAAGGTTGCG
1457425 GGGGGTTCCA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (48 bp):
CCTCGCAAGGTTGCGAAGCGTTCCACCTCGCAAGGAGTTGATATTCCA
Found at i:1457420 original size:23 final size:23
Alignment explanation
Indices: 1457338--1457420 Score: 62
Period size: 23 Copynumber: 3.5 Consensus size: 23
1457328 GAGGTGTTCT
* * *
1457338 ACCTCGTAAGGAGTTGATGTTCC
1 ACCTCGCAAGGTGTTGATATTCC
1457361 ACCTCGCAAGGT-TGTGA-AGCGTTCC
1 ACCTCGCAAGGTGT-TGATA---TTCC
* * *
1457386 ATCTTGCGAGGTGTTGATATTCC
1 ACCTCGCAAGGTGTTGATATTCC
1457409 ACCTCGCAAGGT
1 ACCTCGCAAGGT
1457421 TGCGGGGGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
22 1 0.02
23 26 0.58
25 16 0.36
26 2 0.04
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
ACCTCGCAAGGTGTTGATATTCC
Found at i:1458149 original size:54 final size:54
Alignment explanation
Indices: 1458090--1458226 Score: 184
Period size: 54 Copynumber: 2.5 Consensus size: 54
1458080 GGCAAAACGA
* **
1458090 AAGATTCTGAAAATCTTATAAGTATATGGTTGCGATCTTAAATTGGCGAACCGT
1 AAGATTCTGAAAATCTTATAAGTATATGGTCGCGATCTTAAATCAGCGAACCGT
* * * * *
1458144 AAGATTCTGAAAATCTTATAAATAAAAGGTCGCGATCTTAAATCAGTGAACTGT
1 AAGATTCTGAAAATCTTATAAGTATATGGTCGCGATCTTAAATCAGCGAACCGT
* *
1458198 AAGATTCTAAAAATCGTATAAGTATATGG
1 AAGATTCTGAAAATCTTATAAGTATATGG
1458227 CGGCTGTGAC
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (54 bp):
AAGATTCTGAAAATCTTATAAGTATATGGTCGCGATCTTAAATCAGCGAACCGT
Found at i:1458914 original size:17 final size:17
Alignment explanation
Indices: 1458894--1458940 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
1458884 GGATTCGTCA
*
1458894 TTTGGCAAACTCTAAGT
1 TTTGGCAAACTCTAAGG
*
1458911 TTTGGCAAACTCTAGGG
1 TTTGGCAAACTCTAAGG
*
1458928 TTTGGCCAACTCT
1 TTTGGCAAACTCT
1458941 TCTATTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (17 bp):
TTTGGCAAACTCTAAGG
Found at i:1463182 original size:25 final size:25
Alignment explanation
Indices: 1463130--1463235 Score: 74
Period size: 25 Copynumber: 4.3 Consensus size: 25
1463120 GTGCTCATTC
* * *
1463130 GAGCACATA-AACGGGAAGCTCTTTT
1 GAGC-CATATAACGAGAAGCTCCTGT
1463155 GAGCCATATAACGAGAAGCTCCTGT
1 GAGCCATATAACGAGAAGCTCCTGT
* * * * **
1463180 GAGCTATGTAACGGGAAGCTCATAC
1 GAGCCATATAACGAGAAGCTCCTGT
* *
1463205 GAGCCA-ATATA-GAGAAGCTCCAGA
1 GAGCCATATA-ACGAGAAGCTCCTGT
1463229 GAGCCAT
1 GAGCCAT
1463236 TAATTGGGAA
Statistics
Matches: 62, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
24 20 0.32
25 42 0.68
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACGAGAAGCTCCTGT
Found at i:1463248 original size:25 final size:24
Alignment explanation
Indices: 1463192--1463295 Score: 77
Period size: 25 Copynumber: 4.2 Consensus size: 24
1463182 GCTATGTAAC
* * *
1463192 GGGAAGCTCATACGAGCCAAT-ATA
1 GGGAAGCTCAGA-GAGCCATTAATT
*
1463216 GAGAAGCTCCAGAGAGCCATTAATT
1 GGGAAGCT-CAGAGAGCCATTAATT
* *
1463241 GGGAAGCTCATGAAGAGCCTTTAAAT
1 GGGAAGCTCA-G-AGAGCCATTAATT
*
1463267 GGGAAGCTTCAAAGAGCCA-TATATT
1 GGGAAGC-TCAGAGAGCCATTA-ATT
1463292 GGGA
1 GGGA
1463296 CGCTTATAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
24 18 0.28
25 25 0.39
26 18 0.28
27 3 0.05
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (24 bp):
GGGAAGCTCAGAGAGCCATTAATT
Found at i:1464692 original size:24 final size:23
Alignment explanation
Indices: 1464665--1464712 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 23
1464655 CTATTACATG
1464665 AGTTGTTATTTAAATTAATTATTT
1 AGTTGTT-TTTAAATTAATTATTT
1464689 A---GTTTTTAAATTAATTATTT
1 AGTTGTTTTTAAATTAATTATTT
1464709 AGTT
1 AGTT
1464713 TTGTAAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
20 17 0.81
21 3 0.14
24 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (23 bp):
AGTTGTTTTTAAATTAATTATTT
Found at i:1464698 original size:20 final size:20
Alignment explanation
Indices: 1464673--1464719 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
1464663 TGAGTTGTTA
1464673 TTTAAATTAATTATTTAGTT
1 TTTAAATTAATTATTTAGTT
1464693 TTTAAATTAATTATTTAGTT
1 TTTAAATTAATTATTTAGTT
1464713 TTGTAAA
1 TT-TAAA
1464720 GTATTGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TTTAAATTAATTATTTAGTT
Found at i:1467276 original size:23 final size:23
Alignment explanation
Indices: 1467226--1467276 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1467216 TTAATAATTC
1467226 AAAAA-ATAAAAAAATATTTTTA
1 AAAAATATAAAAAAATATTTTTA
1467248 AAAAATATAAAAAAATATTTTTA
1 AAAAATATAAAAAAATATTTTTA
1467271 AAAAAT
1 AAAAAT
1467277 TAGTTAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAATATAAAAAAATATTTTTA
Found at i:1470855 original size:14 final size:14
Alignment explanation
Indices: 1470838--1470871 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1470828 TTGGTTGAGA
1470838 AAATAATT-TAATTT
1 AAATAATTATAA-TT
1470852 AAATAATTATAATT
1 AAATAATTATAATT
1470866 AAATAA
1 AAATAA
1470872 ATAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATAATTATAATT
Found at i:1471547 original size:26 final size:26
Alignment explanation
Indices: 1471511--1471564 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1471501 AATCTGAAAG
1471511 TTTGCAGCAAGTTAACAACTACAATC
1 TTTGCAGCAAGTTAACAACTACAATC
1471537 TTTGCAGCAAGTTAACAACTACAATC
1 TTTGCAGCAAGTTAACAACTACAATC
1471563 TT
1 TT
1471565 AAACTTGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (26 bp):
TTTGCAGCAAGTTAACAACTACAATC
Found at i:1482861 original size:46 final size:46
Alignment explanation
Indices: 1482794--1482996 Score: 338
Period size: 46 Copynumber: 4.5 Consensus size: 46
1482784 TGATCAGTGA
* *
1482794 CAAGTGGCAAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
1482840 CAAGTGACAAAGTGATAAGTGGTAGATTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1482886 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* * *
1482932 CAAGTGACAAAGTAATAAGTGGTAGCCTTAGCTACAGTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1482978 CAAG-GAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
1482997 ATCATACATA
Statistics
Matches: 149, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
44 11 0.07
45 3 0.02
46 135 0.91
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:1484320 original size:49 final size:49
Alignment explanation
Indices: 1484243--1484384 Score: 176
Period size: 49 Copynumber: 2.9 Consensus size: 49
1484233 ATGTGAAAAT
*
1484243 GTGATTATGTGATCTCCGTGTAAGACCATAGCTGGGCTATGGCATCGATAA
1 GTGA-TATGTGAT-TACGTGTAAGACCATAGCTGGGCTATGGCATCGATAA
** * * * *
1484294 GTGATATGTGATTTTGTGTAAAACCATAGCTGGGCTATGCCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATAA
* * *
1484343 GTGATATGTGATTACATGTAAGACCATAGTTGGACTATGGCA
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCA
1484385 ATGTGAAAAC
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 66 0.85
50 8 0.10
51 4 0.05
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATAA
Found at i:1489159 original size:46 final size:46
Alignment explanation
Indices: 1489092--1489294 Score: 356
Period size: 46 Copynumber: 4.5 Consensus size: 46
1489082 TGATCAGTGA
*
1489092 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTGTCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
1489138 CAAGTGACAAAGTTATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1489184 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
1489230 CAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
1489276 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
1489295 ATCATACATA
Statistics
Matches: 152, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
44 12 0.08
45 5 0.03
46 135 0.89
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:1492973 original size:18 final size:18
Alignment explanation
Indices: 1492950--1492985 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1492940 GTTTTATTCA
1492950 AAGATTTCTAGGTTTTCT
1 AAGATTTCTAGGTTTTCT
* *
1492968 AAGATTTTTGGGTTTTCT
1 AAGATTTCTAGGTTTTCT
1492986 CATTCAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.53
Consensus pattern (18 bp):
AAGATTTCTAGGTTTTCT
Found at i:1493280 original size:11 final size:11
Alignment explanation
Indices: 1493266--1493316 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
1493256 TAATTATTTC
1493266 TTATATATATT
1 TTATATATATT
1493277 TTATATATAATT
1 TTATATAT-ATT
1493289 TT-TATA-ATTT
1 TTATATATA-TT
* *
1493299 TTATTTAGATT
1 TTATATATATT
1493310 TTATATA
1 TTATATA
1493317 GTTTTTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
9 1 0.03
10 4 0.12
11 23 0.68
12 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATATATATT
Found at i:1493294 original size:22 final size:21
Alignment explanation
Indices: 1493269--1493342 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
1493259 TTATTTCTTA
1493269 TATATATTTTATATATAATTTT
1 TATATATTTT-TATATAATTTT
*
1493291 TATA-ATTTTTATTTAGA-TTT
1 TATATATTTTTATATA-ATTTT
* *
1493311 TATATAGTTTTTTTCTCAATTTT
1 TATATA-TTTTTATAT-AATTTT
1493334 TATATATTT
1 TATATATTT
1493343 AATTACTTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
20 12 0.27
21 7 0.16
22 15 0.34
23 10 0.23
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TATATATTTTTATATAATTTT
Found at i:1493322 original size:11 final size:10
Alignment explanation
Indices: 1493269--1493342 Score: 51
Period size: 11 Copynumber: 6.9 Consensus size: 10
1493259 TTATTTCTTA
1493269 TATATATTTT
1 TATATATTTT
1493279 ATATATAATTTT
1 -TATAT-ATTTT
1493291 TATA-ATTTT
1 TATATATTTT
* *
1493300 TATTTAGATTT
1 TATATA-TTTT
1493311 TATATAGTTTT
1 TATATA-TTTT
* *
1493322 TTTCTCAATTTT
1 TATAT--ATTTT
1493334 TATATATTT
1 TATATATTT
1493343 AATTACTTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
9 8 0.16
10 5 0.10
11 24 0.48
12 12 0.24
13 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (10 bp):
TATATATTTT
Found at i:1508941 original size:23 final size:24
Alignment explanation
Indices: 1508911--1508966 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
1508901 AGATTATTAT
*
1508911 TAAAAATAATTTAATA-AAAATAA
1 TAAAAATAATTAAATATAAAATAA
**
1508934 TAAAAATAATTAAATATAATTTAA
1 TAAAAATAATTAAATATAAAATAA
1508958 T-AAAATAAT
1 TAAAAATAAT
1508967 ATATAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAAAATAATTAAATATAAAATAA
Found at i:1513692 original size:3 final size:3
Alignment explanation
Indices: 1513684--1513759 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
1513674 TACTATGACT
1513684 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1513732 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1513760 ATACGCATGT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1515781 original size:42 final size:41
Alignment explanation
Indices: 1515723--1516012 Score: 321
Period size: 42 Copynumber: 7.0 Consensus size: 41
1515713 GCGTTTACAG
** *
1515723 AAAAAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTCAGA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-A
* * * *
1515765 AAAAAAAGCCGTTAAAGATCATGTTCTTTAGCGACACTTTAA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAA
* * *
1515807 AAAAAATGCCGTTAAAGGTCATGTTCTTTAGCGGCGCTTAA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
* * *
1515848 AAAAAGACGCTGCTAAAGGTCATGTTCTTTCGCGGCGCTTAA
1 AAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
* *
1515890 AGAAAAACGCCCCTAAAGATCATGTT-TTTAGAGGCGCTTAA
1 A-AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
* * **
1515931 CGAAAAACGCCGCTAAAGATCATGCTCTTTAGCGGCGCTTTGC
1 -AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAA
* * *
1515974 ATAAAACACCGCGAAAGATCATGTTCTTTAGCGGCGCTT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
1516013 TTATCACAAA
Statistics
Matches: 211, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
41 46 0.22
42 157 0.74
43 8 0.04
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
Found at i:1516511 original size:21 final size:21
Alignment explanation
Indices: 1516487--1516537 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1516477 TTCTTTTGAA
*
1516487 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
1516508 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
*
1516529 CCTTTGCTT
1 CCTCTGCTT
1516538 TAAGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:1522016 original size:9 final size:9
Alignment explanation
Indices: 1522002--1522252 Score: 194
Period size: 9 Copynumber: 29.4 Consensus size: 9
1521992 TTTTTATGTA
1522002 TTATGTAAG
1 TTATGTAAG
1522011 TTATGTAAG
1 TTATGTAAG
*
1522020 TTATAT-A-
1 TTATGTAAG
1522027 TTATGT-A-
1 TTATGTAAG
1522034 TTATGTAAG
1 TTATGTAAG
1522043 -TACTGTAAG
1 TTA-TGTAAG
*
1522052 TAATGTAAG
1 TTATGTAAG
1522061 TTATGTAAG
1 TTATGTAAG
*
1522070 TAATGT-A-
1 TTATGTAAG
1522077 TTATGTAAG
1 TTATGTAAG
*
1522086 TTGTGTATA-
1 TTATGTA-AG
*
1522095 ATAT-TAA-
1 TTATGTAAG
*
1522102 TTATGTGAG
1 TTATGTAAG
*
1522111 TTGTGT-A-
1 TTATGTAAG
*
1522118 TAATGTAAG
1 TTATGTAAG
*
1522127 TTAAG-AAGG
1 TTATGTAA-G
1522136 TTATGT-A-
1 TTATGTAAG
*
1522143 TAATGTAAG
1 TTATGTAAG
1522152 TTATGTAAG
1 TTATGTAAG
* *
1522161 TTATTTAAT
1 TTATGTAAG
1522170 TTATGTAAG
1 TTATGTAAG
1522179 TTATGTAAG
1 TTATGTAAG
* *
1522188 TTATTTAAT
1 TTATGTAAG
1522197 TTATGTAAG
1 TTATGTAAG
* *
1522206 TTATTTAAT
1 TTATGTAAG
1522215 TTATGTAAG
1 TTATGTAAG
*
1522224 TTATGTAGG
1 TTATGTAAG
1522233 TTATGT-A-
1 TTATGTAAG
*
1522240 TTATGTTAG
1 TTATGTAAG
1522249 TTAT
1 TTAT
1522253 TATGTTATTA
Statistics
Matches: 192, Mismatches: 33, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
7 36 0.19
8 16 0.08
9 138 0.72
10 2 0.01
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1522065 original size:27 final size:26
Alignment explanation
Indices: 1522002--1522239 Score: 169
Period size: 25 Copynumber: 9.3 Consensus size: 26
1521992 TTTTTATGTA
*
1522002 TTATGTAAGTTATGTAAGT-TATATA-
1 TTATGTAAGTTATGTAAGTATGTA-AG
1522027 TTATGT-A-TTATGTAAGTACTGTAAG
1 TTATGTAAGTTATGTAAGTA-TGTAAG
*
1522052 TAATGTAAGTTATGTAAGTAATGT-A-
1 TTATGTAAGTTATGTAAGT-ATGTAAG
* *
1522077 TTATGTAAGTTGTGTATAATAT-TAA-
1 TTATGTAAGTTATGTA-AGTATGTAAG
* *
1522102 TTATGTGAGTTGTGT-A-TAATGTAAG
1 TTATGTAAGTTATGTAAGT-ATGTAAG
*
1522127 TTAAG-AAGGTTATGT-A-TAATGTAAG
1 TTATGTAA-GTTATGTAAGT-ATGTAAG
* *
1522152 TTATGTAAGTTATTTAATTTATGTAAG
1 TTATGTAAGTTATGTAA-GTATGTAAG
* *
1522179 TTATGTAAGTTATTTAATTTATGTAAG
1 TTATGTAAGTTATGTAA-GTATGTAAG
* * *
1522206 TTATTTAATTTATGTAAGTTATGTAGG
1 TTATGTAAGTTATGTAAG-TATGTAAG
1522233 TTATGTA
1 TTATGTA
1522240 TTATGTTAGT
Statistics
Matches: 179, Mismatches: 17, Indels: 32
0.79 0.07 0.14
Matches are distributed among these distances:
22 1 0.01
23 13 0.07
24 7 0.04
25 75 0.42
26 7 0.04
27 74 0.41
28 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (26 bp):
TTATGTAAGTTATGTAAGTATGTAAG
Found at i:1522392 original size:12 final size:11
Alignment explanation
Indices: 1522356--1522434 Score: 51
Period size: 12 Copynumber: 7.4 Consensus size: 11
1522346 GTTATTTAAG
*
1522356 TTATTATGTTA
1 TTATTATGTAA
*
1522367 TTA-TAT-AAA
1 TTATTATGTAA
*
1522376 GTATTATGTAA
1 TTATTATGTAA
*
1522387 TTTATTATGTTA
1 -TTATTATGTAA
1522399 TTA-TATGTAA
1 TTATTATGTAA
*
1522409 --GTTATGTAA
1 TTATTATGTAA
1522418 GTTATTATGTAA
1 -TTATTATGTAA
1522430 GTTAT
1 -TTAT
1522435 GCAAGCTTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
9 10 0.19
10 12 0.23
11 8 0.15
12 22 0.42
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (11 bp):
TTATTATGTAA
Found at i:1522451 original size:21 final size:20
Alignment explanation
Indices: 1522399--1522456 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
1522389 TATTATGTTA
*
1522399 TTATATGTAAGTTATGTAAG
1 TTATATGTAAGTTATGCAAG
1522419 TTATTATGTAAGTTATGCAAG
1 TTA-TATGTAAGTTATGCAAG
*
1522440 CTTATATATAAGTTATG
1 -TTATATGTAAGTTATG
1522457 TATTATAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 3 0.09
21 28 0.82
22 3 0.09
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.45
Consensus pattern (20 bp):
TTATATGTAAGTTATGCAAG
Found at i:1522487 original size:95 final size:95
Alignment explanation
Indices: 1522371--1522558 Score: 349
Period size: 95 Copynumber: 2.0 Consensus size: 95
1522361 ATGTTATTAT
* *
1522371 ATAAAGTATTATGTAATTTATTATGTTATTATATGTAAGTTATGTAAGTTATTATGTAAGTTATG
1 ATAAAGTACTATGTAATTTATTATGTTATTATATATAAGTTATGTAAGTTATTATGTAAGTTATG
*
1522436 CAAGCTTATATATAAGTTATGTATTATAAC
66 CAAGCTTAAATATAAGTTATGTATTATAAC
1522466 ATAAAGTACTATGTAATTTATTATGTTATTATATATAAGTTATGTAAGTTATTATGTAAGTTATG
1 ATAAAGTACTATGTAATTTATTATGTTATTATATATAAGTTATGTAAGTTATTATGTAAGTTATG
1522531 CAAGCTTAAATATAAGTTATGTATTATA
66 CAAGCTTAAATATAAGTTATGTATTATA
1522559 TAAGTTTTGT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (95 bp):
ATAAAGTACTATGTAATTTATTATGTTATTATATATAAGTTATGTAAGTTATTATGTAAGTTATG
CAAGCTTAAATATAAGTTATGTATTATAAC
Found at i:1522522 original size:12 final size:12
Alignment explanation
Indices: 1522505--1522529 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1522495 TATATATAAG
1522505 TTATGTAAGTTA
1 TTATGTAAGTTA
1522517 TTATGTAAGTTA
1 TTATGTAAGTTA
1522529 T
1 T
1522530 GCAAGCTTAA
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:1522527 original size:21 final size:21
Alignment explanation
Indices: 1522497--1522553 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1522487 TATGTTATTA
1522497 TATATAAGTTATGTAAGTTAT
1 TATATAAGTTATGTAAGTTAT
* *
1522518 TATGTAAGTTATGCAAGCTTA-
1 TATATAAGTTATGTAAG-TTAT
*
1522539 AATATAAGTTATGTA
1 TATATAAGTTATGTA
1522554 TTATATAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.42
Consensus pattern (21 bp):
TATATAAGTTATGTAAGTTAT
Found at i:1522661 original size:61 final size:61
Alignment explanation
Indices: 1522585--1522853 Score: 369
Period size: 62 Copynumber: 4.4 Consensus size: 61
1522575 TGTATTATGT
* *
1522585 AACTTATGTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAA
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATACTAACAAATTTAGAA
** * *
1522646 AACTTATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATAC-AATTAAATTTAGAA
1 AACTTATTTAGAAAACTTA-TAAAATTAATACTAATAAATTTTAATACTAA-CAAATTTAGAA
* **
1522708 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTCTGTTACTAACAAATTTAGAA
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATACTAACAAATTTAGAA
* ** * * *
1522769 CACTTATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
1 AACTTATTTAGAAAACTTA-TAAAATTAATACTAATAAATTTTAATACTAACAAATTTAGAA
1522831 AACTTATTTAGAAAACTTATAAA
1 AACTTATTTAGAAAACTTATAAA
1522854 TTTAGAAAAC
Statistics
Matches: 179, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
61 72 0.40
62 107 0.60
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (61 bp):
AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATACTAACAAATTTAGAA
Found at i:1522671 original size:31 final size:30
Alignment explanation
Indices: 1522636--1522723 Score: 74
Period size: 31 Copynumber: 2.9 Consensus size: 30
1522626 TATTACTAAC
1522636 AAATTTAGAAAACTTATTTAGAAAACGAAGT
1 AAATTTAGAAAACTTATTTAGAAAAC-AAGT
* * * *
1522667 AAATTTA-ATACTAA-TAAATTT-TAATACAATT
1 AAATTTAGA-A--AACT-TATTTAGAAAACAAGT
1522698 AAATTTAGAAAACTTATTTAGAAAAC
1 AAATTTAGAAAACTTATTTAGAAAAC
1522724 TTATAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 15
0.66 0.11 0.23
Matches are distributed among these distances:
29 6 0.14
30 6 0.14
31 19 0.44
32 6 0.14
33 6 0.14
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (30 bp):
AAATTTAGAAAACTTATTTAGAAAACAAGT
Found at i:1522691 original size:16 final size:16
Alignment explanation
Indices: 1522666--1522703 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1522656 GAAAACGAAG
1522666 TAAA-TTTAATACTAA-
1 TAAATTTTAATAC-AAT
1522681 TAAATTTTAATACAAT
1 TAAATTTTAATACAAT
1522697 TAAATTT
1 TAAATTT
1522704 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTTTAATACAAT
Found at i:1522718 original size:13 final size:13
Alignment explanation
Indices: 1522700--1522727 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1522690 ATACAATTAA
1522700 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1522713 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1522726 AT
1 AT
1522728 AAAATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:1522804 original size:123 final size:123
Alignment explanation
Indices: 1522585--1522853 Score: 493
Period size: 123 Copynumber: 2.2 Consensus size: 123
1522575 TGTATTATGT
* *
1522585 AACTTATGTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAAAACT
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTCTATTACTAACAAATTTAGAAAACT
*
1522650 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAATTAAATTTAGAA
66 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
* *
1522708 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTCTGTTACTAACAAATTTAGAACACT
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTCTATTACTAACAAATTTAGAAAACT
1522773 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
66 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
1522831 AACTTATTTAGAAAACTTATAAA
1 AACTTATTTAGAAAACTTATAAA
1522854 TTTAGAAAAC
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 141 1.00
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (123 bp):
AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTCTATTACTAACAAATTTAGAAAACT
TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
Found at i:1522814 original size:16 final size:16
Alignment explanation
Indices: 1522789--1522826 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1522779 GAAAACGAAG
*
1522789 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
1522804 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
1522820 TAAATTT
1 TAAATTT
1522827 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:1522841 original size:13 final size:13
Alignment explanation
Indices: 1522823--1522850 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1522813 ATACAAATAA
1522823 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1522836 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1522849 AT
1 AT
1522851 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:1522858 original size:17 final size:17
Alignment explanation
Indices: 1522819--1522868 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
1522809 TTTAATACAA
1522819 ATAAATTTAGAAAAC-T
1 ATAAATTTAGAAAACTT
1522835 -T--ATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
1522849 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
1522866 ATA
1 ATA
1522869 TAGATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 2 0.07
17 16 0.53
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAAATTTAGAAAACTT
Found at i:1522883 original size:123 final size:123
Alignment explanation
Indices: 1522585--1522905 Score: 436
Period size: 123 Copynumber: 2.6 Consensus size: 123
1522575 TGTATTATGT
* * ** * *
1522585 AACTTATGTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAAAACT
1 AACTTATTTAGAAAACTTATAAAATTAAAACTAATAAATGATATTACAAACAAATTTAGAACACT
*
1522650 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAATTAAATTTAGAA
66 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
* ** * *
1522708 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTCTGTTACTAACAAATTTAGAACACT
1 AACTTATTTAGAAAACTTATAAAATTAAAACTAATAAATGATATTACAAACAAATTTAGAACACT
1522773 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
66 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
* * *
1522831 AACTTATTTAGAAAACTTATAAATTTAGAAAACTTATATA-GATATTA-AAACAATATTT---AC
1 AACTTATTTAGAAAACTTATAAAATT--AAAACTAATAAATGATATTACAAACAA-ATTTAGAAC
*
1522891 AATTATTTAGAAAAC
63 ACTTATTTAGAAAAC
1522906 TTACAAATTT
Statistics
Matches: 181, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
121 16 0.09
123 148 0.82
124 8 0.04
125 9 0.05
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.36
Consensus pattern (123 bp):
AACTTATTTAGAAAACTTATAAAATTAAAACTAATAAATGATATTACAAACAAATTTAGAACACT
TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
Found at i:1522889 original size:62 final size:58
Alignment explanation
Indices: 1522585--1522934 Score: 314
Period size: 62 Copynumber: 5.8 Consensus size: 58
1522575 TGTATTATGT
* *
1522585 AACTTATGTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAA-ATTTAGAA
1 AACTTATTTAGAAAACTTATAAATTTAATACTAATAAATTTTA--A--AACAATATTTAGAA
** *
1522646 AACTTATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAATTAAATTTAGAA
1 AACTTATTTAGAAAACTTA-TAAATTTAATACTAATAAATTTTAAAACAA-T--ATTTAGAA
* *
1522708 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTCTGTTACTAACAA-ATTTAGAA
1 AACTTATTTAGAAAACTTATAAATTTAATACTAATAAA-T-T-TTA-AAACAATATTTAGAA
* ** *
1522769 CACTTATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
1 AACTTATTTAGAAAACTTA-TAAATTTAATACTAATAAATTTTAAAAC-AAT--ATTTAGAA
* * * *
1522831 AACTTATTTAGAAAACTTATAAATTTAGAAAACTTATATAGATATTAAAACAATATTT--AC
1 AACTTATTTAGAAAACTTATAAATTT--AATAC-TA-ATAAATTTTAAAACAATATTTAGAA
* * * *
1522891 AA-TTATTTAGAAAACTTACAAATTTTATAGTAATAAGTTTTAAA
1 AACTTATTTAGAAAACTTATAAATTTAATACTAATAAATTTTAAA
1522935 TATAGGTTAT
Statistics
Matches: 240, Mismatches: 31, Indels: 42
0.77 0.10 0.13
Matches are distributed among these distances:
55 9 0.04
56 2 0.01
57 2 0.01
58 6 0.03
59 27 0.11
60 5 0.02
61 66 0.28
62 95 0.40
63 5 0.02
64 8 0.03
65 15 0.06
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (58 bp):
AACTTATTTAGAAAACTTATAAATTTAATACTAATAAATTTTAAAACAATATTTAGAA
Found at i:1526193 original size:7 final size:7
Alignment explanation
Indices: 1526144--1526174 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1526134 TTAAACACTG
1526144 AAACCCT
1 AAACCCT
1526151 AAACCCT
1 AAACCCT
1526158 AAACCCT
1 AAACCCT
1526165 AAACCCT
1 AAACCCT
1526172 AAA
1 AAA
1526175 TACTATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.48, C:0.39, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:1527170 original size:21 final size:20
Alignment explanation
Indices: 1527130--1527184 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
1527120 CGCTGAAATA
* * *
1527130 TAAACTCTAAACCTTAAACC
1 TAAACTCCAAGCCCTAAACC
*
1527150 TCAATCTCCAAGCCCTAAACC
1 T-AAACTCCAAGCCCTAAACC
*
1527171 TAAACTCTAAGCCC
1 TAAACTCCAAGCCC
1527185 AGAACACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.36, G:0.04, T:0.22
Consensus pattern (20 bp):
TAAACTCCAAGCCCTAAACC
Found at i:1527823 original size:114 final size:114
Alignment explanation
Indices: 1527623--1527835 Score: 340
Period size: 114 Copynumber: 1.9 Consensus size: 114
1527613 TATCCCAATA
*
1527623 TTTGCAGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAGCAATAAAACAGTAGCGTTTT
1 TTTGCAGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAATAAAACAGTAGCGTTTT
1527688 GTCCAAATTTTTTCCTCAAATTAGATATCTTTACTGGCCAATTCAATCT
66 GTCCAAATTTTTTCCTCAAATTAGATATCTTTACTGGCCAATTCAATCT
* * *
1527737 TTTGCGGCGTTTTTTACAATGCGCCACTAAAGCAATAAAATGAAACAATAAAACGGTA-CTGTTT
1 TTTGCAGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAATAAAACAGTAGC-GTTT
* *
1527801 TG-CTCAAATTTTTTCCTCAAATTCGTTATCTTTAC
65 TGTC-CAAATTTTTTCCTCAAATTAGATATCTTTAC
1527836 CGGCGTTTCT
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
113 2 0.02
114 89 0.98
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (114 bp):
TTTGCAGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAATAAAACAGTAGCGTTTT
GTCCAAATTTTTTCCTCAAATTAGATATCTTTACTGGCCAATTCAATCT
Found at i:1531671 original size:19 final size:19
Alignment explanation
Indices: 1531634--1531672 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1531624 TAGGCTCCCG
* *
1531634 AGTCCAATTTACGATTTCA
1 AGTCCAATTTACAAATTCA
*
1531653 AGTCCAATTTTCAAATTCA
1 AGTCCAATTTACAAATTCA
1531672 A
1 A
1531673 TTACCCATTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (19 bp):
AGTCCAATTTACAAATTCA
Found at i:1533775 original size:21 final size:20
Alignment explanation
Indices: 1533744--1533798 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 20
1533734 GACACGAAAA
1533744 TTTTGAAACACGAGATTTT-T
1 TTTTGAAACACGA-ATTTTCT
1533764 TTTTGAAAACACGAATTTTCT
1 TTTTG-AAACACGAATTTTCT
1533785 TTTTGAAACACGAA
1 TTTTGAAACACGAA
1533799 AATTATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
TTTTGAAACACGAATTTTCT
Found at i:1533776 original size:37 final size:37
Alignment explanation
Indices: 1533686--1533778 Score: 93
Period size: 39 Copynumber: 2.5 Consensus size: 37
1533676 ACACACAAAA
*
1533686 TTTTTTTAAAATAC-AAGAATTTTAGAAACACGAATT
1 TTTTTTTAAAACACGAAGAATTTTAGAAACACGAATT
**
1533722 TTTTTAAAAAAAGACACGAA-AATTTT-GAAACACGAGATT
1 TTTTT--TTAAA-ACACGAAGAATTTTAGAAACACGA-ATT
1533761 TTTTTTTGAAAACACGAA
1 TTTTTTT-AAAACACGAA
1533779 TTTTCTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
36 5 0.11
37 7 0.15
38 15 0.33
39 17 0.37
40 2 0.04
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (37 bp):
TTTTTTTAAAACACGAAGAATTTTAGAAACACGAATT
Found at i:1533832 original size:21 final size:20
Alignment explanation
Indices: 1533760--1533842 Score: 59
Period size: 21 Copynumber: 4.2 Consensus size: 20
1533750 AACACGAGAT
* *
1533760 TTTTTTTTGAAAACACGAAT
1 TTTTTTTTGAAAACACAAAA
1533780 TTTCTTTTTG-AAACACGAAAA
1 TTT-TTTTTGAAAACAC-AAAA
*
1533801 ---TTATT-AAAACACAAAA
1 TTTTTTTTGAAAACACAAAA
*
1533817 TTTGTTTTTGAAAACATAAAAA
1 TTT-TTTTTGAAAACA-CAAAA
1533839 TTTT
1 TTTT
1533843 GATAAAAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
16 4 0.08
17 10 0.20
20 13 0.27
21 15 0.31
22 7 0.14
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (20 bp):
TTTTTTTTGAAAACACAAAA
Found at i:1533839 original size:38 final size:37
Alignment explanation
Indices: 1533769--1533840 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
1533759 TTTTTTTTTG
* * *
1533769 AAAACACGAATTTTCTTTTTGAAACACGAAAATTATT
1 AAAACACAAAATTTCTTTTTGAAACACAAAAATTATT
* *
1533806 AAAACACAAAATTTGTTTTTGAAAACATAAAAATT
1 AAAACACAAAATTTCTTTTTG-AAACACAAAAATT
1533841 TTGATAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 18 0.62
38 11 0.38
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (37 bp):
AAAACACAAAATTTCTTTTTGAAACACAAAAATTATT
Found at i:1533917 original size:37 final size:35
Alignment explanation
Indices: 1533868--1534145 Score: 253
Period size: 38 Copynumber: 7.7 Consensus size: 35
1533858 ACGAGGATTT
*
1533868 TTTTTTG-AAACACGAAAATTTATGAAACACGGTCAA
1 TTTTTTGAAAACACGAAAATTTTTGAAACACGG--AA
*
1533904 TTTTTTGAAAACACGAAAATTTTTGAAAGACGAGAATA
1 TTTTTTGAAAACACGAAAATTTTTGAAACACG-G-A-A
* * *
1533942 TTTTTTTAAAACACGGAAATTTATGAAACACGGAA
1 TTTTTTGAAAACACGAAAATTTTTGAAACACGGAA
* *
1533977 TCTTTTTTGAAAACAAGAAAATTTTTGAAATACAGGAA
1 --TTTTTTGAAAACACGAAAATTTTTGAAACAC-GGAA
* *
1534015 -TTTTTAAAAACACGAAAATTTTTGAAACACTAGAA
1 TTTTTTGAAAACACGAAAATTTTTGAAACAC-GGAA
* *
1534050 --TTTTGAAAACACGAAGATTTTTGAAACATGAGAA
1 TTTTTTGAAAACACGAAAATTTTTGAAACACG-GAA
*
1534084 -TTTTTGAAAACAC-AAAATTTTTTTTTAAAACACGGAA
1 TTTTTTGAAAACACGAAAA----TTTTTGAAACACGGAA
* *
1534121 GTTTTTGAAACACAAGAAAATTTTT
1 TTTTTTGAAA-ACACGAAAATTTTT
1534146 TTTTGAAAAC
Statistics
Matches: 202, Mismatches: 25, Indels: 30
0.79 0.10 0.12
Matches are distributed among these distances:
34 32 0.16
35 43 0.21
36 13 0.06
37 53 0.26
38 54 0.27
39 3 0.01
40 4 0.02
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (35 bp):
TTTTTTGAAAACACGAAAATTTTTGAAACACGGAA
Found at i:1533928 original size:18 final size:18
Alignment explanation
Indices: 1533869--1534169 Score: 199
Period size: 17 Copynumber: 16.4 Consensus size: 18
1533859 CGAGGATTTT
1533869 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
1533886 TTTATG-AAACACGGTCAAT
1 TTTTTGAAAACAC-G-AAAA
1533905 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
1533923 TTTTTGAAAGACGA-GAATAT
1 TTTTTGAAA-AC-ACGAA-AA
* *
1533943 TTTTTTAAAACACGGAAA
1 TTTTTGAAAACACGAAAA
* **
1533961 TTTATG-AAACACGGAATCT
1 TTTTTGAAAACAC-GAA-AA
*
1533980 TTTTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
*
1533998 TTTTTGAAATACA-G-GAA
1 TTTTTGAAA-ACACGAAAA
*
1534015 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
1534033 TTTTTG-AAACACTAGAA
1 TTTTTGAAAACACGAAAA
*
1534050 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
* *
1534067 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGAAAA
1534084 TTTTTGAAAACAC-AAAA
1 TTTTTGAAAACACGAAAA
* * *
1534101 TTTTTTTTTAAAACACGGAAG
1 ---TTTTTGAAAACACGAAAA
*
1534122 TTTTTGAAACACAAGAAAA
1 TTTTTGAAA-ACACGAAAA
1534141 TTTTTTTTTGAAAACACGAAAA
1 ----TTTTTGAAAACACGAAAA
1534163 TTTTTGA
1 TTTTTGA
1534170 GACACGATTT
Statistics
Matches: 218, Mismatches: 41, Indels: 49
0.71 0.13 0.16
Matches are distributed among these distances:
16 8 0.04
17 62 0.28
18 62 0.28
19 34 0.16
20 33 0.15
21 2 0.01
22 8 0.04
23 9 0.04
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:1533946 original size:75 final size:74
Alignment explanation
Indices: 1533853--1534103 Score: 263
Period size: 75 Copynumber: 3.5 Consensus size: 74
1533843 GATAAAAAAC
* * *
1533853 GAAACACGAGGATTTTTTTTTGAAACACGAAAATTTATGAAACACGGTCAATTTTTTGAAAACAC
1 GAAACACGAGAATATTTTTTTAAAACACGAAAATTTATGAAACACGGT-AATTTTTTGAAAACAC
1533918 GAAAATTTTT
65 GAAAATTTTT
* *
1533928 GAAAGACGAGAATATTTTTTTAAAACACGGAAATTTATGAAACACGG-AATCTTTTTTGAAAACA
1 GAAACACGAGAATATTTTTTTAAAACACGAAAATTTATGAAACACGGTAA--TTTTTTGAAAACA
*
1533992 AGAAAATTTTT
64 CGAAAATTTTT
* * * * *
1534003 GAAATAC-AGGA-A-TTTTTAAAAACACGAAAATTTTTGAAACAC--TAGA-ATTTTGAAAACAC
1 GAAACACGAGAATATTTTTTTAAAACACGAAAATTTATGAAACACGGTA-ATTTTTTGAAAACAC
*
1534062 GAAGATTTTT
65 GAAAATTTTT
* *
1534072 GAAACATGAG-A-A-TTTTTGAAAACAC-AAAATTT
1 GAAACACGAGAATATTTTTTTAAAACACGAAAATTT
1534104 TTTTTTAAAA
Statistics
Matches: 154, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
68 7 0.05
69 39 0.25
70 2 0.01
71 1 0.01
72 28 0.18
73 3 0.02
74 3 0.02
75 71 0.46
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.31
Consensus pattern (74 bp):
GAAACACGAGAATATTTTTTTAAAACACGAAAATTTATGAAACACGGTAATTTTTTGAAAACACG
AAAATTTTT
Found at i:1534149 original size:23 final size:22
Alignment explanation
Indices: 1534122--1534167 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1534112 AACACGGAAG
1534122 TTTTTGAAACACAAGAAAATTTT
1 TTTTTGAAA-ACAAGAAAATTTT
*
1534145 TTTTTGAAAACACGAAAATTTT
1 TTTTTGAAAACAAGAAAATTTT
1534167 T
1 T
1534168 GAGACACGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (22 bp):
TTTTTGAAAACAAGAAAATTTT
Found at i:1534948 original size:46 final size:45
Alignment explanation
Indices: 1534857--1534951 Score: 111
Period size: 46 Copynumber: 2.1 Consensus size: 45
1534847 ATGGCCTGCA
** *
1534857 CTTTATTCTTTTTTTTTCCTTTCTTTCTTCCCCTTTCTTTTCTTT
1 CTTTATTCTTTTTTTAGCCTTTCTTTCTTCCCCTTTCTTTCCTTT
* * *
1534902 CTTTATTTCTTTTTTTCAGCCTTTTTTTCTTCTCTTTTC-TTCCTTT
1 CTTTA-TTCTTTTTTT-AGCCTTTCTTTCTTCCCCTTTCTTTCCTTT
1534948 CTTT
1 CTTT
1534952 CTTCCTCCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
45 5 0.12
46 20 0.48
47 17 0.40
ACGTcount: A:0.03, C:0.25, G:0.01, T:0.71
Consensus pattern (45 bp):
CTTTATTCTTTTTTTAGCCTTTCTTTCTTCCCCTTTCTTTCCTTT
Found at i:1535558 original size:58 final size:59
Alignment explanation
Indices: 1535453--1535588 Score: 177
Period size: 58 Copynumber: 2.3 Consensus size: 59
1535443 CAAAACTTTT
* * *
1535453 GGGGCCAAAATATAATTTTGAGAAAATTTAGGGCTTAAAATGTAATTTCAAAAAGCTTA
1 GGGGTCAAAATATAATTTTGAGAAAATTTAGGGCTCAAAATGCAATTTCAAAAAGCTTA
* * **
1535512 GGGGTCAAAATATAATTTT-AGGAAATTTTAGGG-TCAAAATGCAATTTTAAAAATTTTA
1 GGGGTCAAAATATAATTTTGA-GAAAATTTAGGGCTCAAAATGCAATTTCAAAAAGCTTA
*
1535570 GGGGTCAAAATGTAATTTT
1 GGGGTCAAAATATAATTTT
1535589 TTATTTTTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
58 39 0.57
59 29 0.43
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (59 bp):
GGGGTCAAAATATAATTTTGAGAAAATTTAGGGCTCAAAATGCAATTTCAAAAAGCTTA
Found at i:1535597 original size:29 final size:29
Alignment explanation
Indices: 1535444--1535588 Score: 143
Period size: 29 Copynumber: 5.0 Consensus size: 29
1535434 CAAACACAGC
* * *
1535444 AAAACTTTT-GGGGCCAAAATATAATTTT
1 AAAAATTTTAGGGGTCAAAATGTAATTTT
* * *
1535472 GAGAAAA-TTTAGGGCTTAAAATGTAATTTC
1 -A-AAAATTTTAGGGGTCAAAATGTAATTTT
** *
1535502 AAAAAGCTTAGGGGTCAAAATATAATTTT
1 AAAAATTTTAGGGGTCAAAATGTAATTTT
* *
1535531 AGGAAATTTTA-GGGTCAAAATGCAATTTT
1 A-AAAATTTTAGGGGTCAAAATGTAATTTT
1535560 AAAAATTTTAGGGGTCAAAATGTAATTTT
1 AAAAATTTTAGGGGTCAAAATGTAATTTT
1535589 TTATTTTTTG
Statistics
Matches: 93, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
28 12 0.13
29 58 0.62
30 23 0.25
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (29 bp):
AAAAATTTTAGGGGTCAAAATGTAATTTT
Found at i:1536388 original size:229 final size:227
Alignment explanation
Indices: 1535786--1537348 Score: 1284
Period size: 229 Copynumber: 6.6 Consensus size: 227
1535776 CTCGGCGTGC
* *
1535786 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAGGAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAGAAATTGAAAA-AAA
* *
1535851 TACCTCGGCATGTGACCCGAGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC-A
65 TACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAA
* * * * *
1535915 GCAATTGAAAAATAACTCGGCGTATGACCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
128 GAAATTGAAAAATACCTCGGCGTGTGACCCAAGGCTCAACTCACCTCTCGCATTATGAGTTGATT
* *
1535980 TTTTTG-AAAA-AGAAATTGAAAAATACCTTAGCGT
193 TTTTAGAAAAACAGAAATTG-AAAATACCTCAGCGT
** * *
1536014 GCGACATGGGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTAGAAAAACAGAAATTG---A
1 --GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAAA-AGAAATTGAAAA
* * *
1536076 AAATACCTCAGCGTGACCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTG-AAAA-A
62 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
* * **
1536139 AGAAATTGAAAAATAAATACCTCGGCATGCGACCTGAGGCTCAACTCACCTCTCGCATTATGAGT
127 AGAAATTG---AA-AAATACCTCGGCGTGTGACCCAAGGCTCAACTCACCTCTCGCATTATGAGT
1536204 TGA-TTTTTAGAAAAACAGAAATTGAAAATACCTCAGCGT
188 TGATTTTTTAGAAAAACAGAAATTGAAAATACCTCAGCGT
* * *
1536243 GACCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTGAAAAAAGAAATTGAAAATAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAGAAATTGAAAA-AAA
* * * *
1536308 TATCTCGGCATGTGAGCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACAA
65 TACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAA
* *
1536373 GCAATTGAAAAATACCTCGGCGTGTGACCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGA-T
128 GAAATTGAAAAATACCTCGGCGTGTGACCCAAGGCTCAACTCACCTCTCGCATTATGAGTTGATT
*
1536437 TTTTAGAAAAACAGAAATTGCAAATACCTCAGCGT
193 TTTTAGAAAAACAGAAATTGAAAATACCTCAGCGT
* * *
1536472 GACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAGCAGAAATT-TAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA-AAGAAATTGAAAAAA
* ** *
1536536 ATACCTCAGCGTGACCCGAGGTTCAACTCACCTCT-ATATTATGAGTTGATTTTTTGAAAAAAAA
64 ATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG----AAAA
* * * * * *
1536600 AAACAGAAATTAAAAAAATACTTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAG
124 ACA-AGAAATT-GAAAAATACCTCGGCGTGTGACCCAAGGCTCAACTCACCTCTCGCATTATGAG
* *
1536662 TTGATTTTTTGAAAAAAACAGAAATTAAAAAAAATACCTCAGCGT
187 TTGATTTTTT-AGAAAAACAGAAATT---GAAAATACCTCAGCGT
* * * *
1536707 GACCCGAGGCTCAACTCACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAT
1 GACCCGAGGCTCAACTCACCT---C-T--CGC-A--AT--A-TGA-GT-TG-ATT-T---TTGA-
***** *
1536772 TTTTTGAAAAAAAATAGAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-G
46 AAAAAGAAA-----T-----TGAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCG
* * * * *
1536836 TATTATGAGTTGATTTTTTGAAAAA-AGCAGAAATTAAAAAAAATACCTCAGC--GTGACCCGAG
101 CAATATGAGTTGA-TTTTTGAAAAACA--AGAAATT--GAAAAATACCTCGGCGTGTGACCCAAG
* * *
1536898 GCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAAAACAGAAATTAAAAAAATACCT
161 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTT--AGAAAAACAGAAATT--GAAAATACCT
1536962 CAGCGT
222 CAGCGT
* * *
1536968 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTT-AAAAAA-AAGATAGAAATTAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAGAA-ATTG-AA--AA
* * *
1537030 AAATACCTCAGCGTGACTCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAA
62 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAAA
* * * * * *
1537094 CAGAAATTAAATTAAAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCT-TTGTATTATG
125 C---AA-GAAATT-GAAAAATACCTCGGCGTGTGACCCAAGGCTCAACTCACCTCTCGCATTATG
*** * *
1537156 AGTTGATTTGAAAAAAAAAGACATAAATT-ACAAATACCTCAGCGT
185 AGTTGATTT-TTTAGAAAA-ACAGAAATTGA-AAATACCTCAGCGT
* * * **
1537201 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTAATTTTT-AAAAAA-AAGACAGAAATTAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAGAA-ATTG-AA--AA
* *
1537263 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAA-
62 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAC
*
1537326 ATGCAGAAATTTAAAAATACCTC
126 A---AGAAATTGAAAAATACCTC
1537349 TTGAAAGAAA
Statistics
Matches: 1149, Mismatches: 102, Indels: 165
0.81 0.07 0.12
Matches are distributed among these distances:
225 19 0.02
226 59 0.05
227 66 0.06
228 21 0.02
229 216 0.19
230 82 0.07
231 89 0.08
232 95 0.08
233 156 0.14
234 8 0.01
235 99 0.09
236 5 0.00
237 1 0.00
238 3 0.00
239 2 0.00
240 1 0.00
241 4 0.00
242 1 0.00
244 2 0.00
245 3 0.00
246 3 0.00
247 3 0.00
248 3 0.00
249 5 0.00
250 2 0.00
251 1 0.00
253 9 0.01
257 1 0.00
258 2 0.00
259 1 0.00
260 13 0.01
261 99 0.09
262 15 0.01
263 1 0.00
264 59 0.05
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (227 bp):
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAGAAATTGAAAAAAAT
ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAGAA
ATTGAAAAATACCTCGGCGTGTGACCCAAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTT
TAGAAAAACAGAAATTGAAAATACCTCAGCGT
Found at i:1536629 original size:81 final size:77
Alignment explanation
Indices: 1535786--1537348 Score: 1039
Period size: 76 Copynumber: 19.9 Consensus size: 77
1535776 CTCGGCGTGC
** * *
1535786 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG--AAAAA-GGAAATTTAAAA
1 GACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTTTGAAAAAAACAGAAA-TTAAAA
*
1535847 GAAATACCTCGGCATGT
64 -AAATACCTCAGC--GT
* ** * * *
1535864 GACCCGAGGCTCAATTCACCTCTCGCAATATGAGTTGA-TTTTTG--AAAAACAGCAATT-GAAA
1 GACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAAAA
* *
1535925 AATAACTCGGCGTAT
65 AATACCTCAGCG--T
* * ** * *
1535940 GACCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTG---AAAA-AGAAATT-GAA
1 GACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGA-TTTTTTGAAAAAAACAGAAATTAAAA
*
1536000 AAATACCTTAGCGT
64 AAATACCTCAGCGT
** * ** * *
1536014 GCGACATGGGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTT-AGAAAAACAGAAATT--G
1 --GACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAA
1536075 AAAATACCTCAGCGT
63 AAAATACCTCAGCGT
* * **
1536090 GACCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGA-TTTTTG--AAAAA-AGAAATTGAAAA
1 GACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTTTGAAAAAAACAGAAATT--AAA
* *
1536151 ATAAATACCTCGGCATGC
63 A-AAATACCTCAGC--GT
* ** * *
1536169 GACCTGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTT-AGAAAAACAGAAATT--GAA
1 GACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAAAA
1536230 AATACCTCAGCGT
65 AATACCTCAGCGT
* * **
1536243 GACCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGA-TTTTTG--AAAAA-AGAAATTGAAAA
1 GACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTTTGAAAAAAACAGAAATT-AAAA
* *
1536304 TAAATATCTCGGCATGT
64 -AAATACCTCAGC--GT
* * ** * * * *
1536321 GAGCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGA-TTTTTGAAAAACA-AGCAATT-GAAA
1 GACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAAAA
*
1536383 AATACCTCGGCGTGT
65 AATACCTCAGC--GT
* * ** * **
1536398 GACCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGA-TTTTT-AGAAAAACAGAAATT--GCA
1 GACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAAAA
1536459 AATACCTCAGCGT
65 AATACCTCAGCGT
* ** * * *
1536472 GACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTG--AAAAGCAGAAATTTAAAA
1 GACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAAAA
1536535 AATACCTCAGCGT
65 AATACCTCAGCGT
*
1536548 GACCCGAGGTTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAAAAAAACAGAAATTAA
1 GACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTG----AAAAAAACAGAAATTAA
*
1536613 AAAAATACTTCAGCGT
62 AAAAATACCTCAGCGT
*
1536629 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAAAAA
1 GACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAAACAGAAATT-AAAAA
1536694 AATACCTCAGCGT
65 AATACCTCAGCGT
** * * ** ** * * ** ***
1536707 GACCCGAGGCTCAACTCACCTC-AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA
1 GACCCGAGGCTCAACTCACCTCTA-TATTA--TGA-G-TTGA-T--TTTTTG-A-AAAAAACAGA
** ** * ***
1536771 TTTTTTGAAAAAAAATAGAAATTAAAAAAAT
56 --AATT-AAAA-AAAT---ACCT--CAGCGT
* * * * *
1536802 -ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAG
1 GACC-C-GAG-G-CTC-A-ACTC-----ACCTCTATATTATGAGTTGATTTTTTGAAAAAAACAG
1536866 AAATTAAAAAAAATACCTCAGCGT
55 AAATT-AAAAAAATACCTCAGCGT
*
1536890 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAACAGAAATTAAAAA
1 GACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTG-AAAAAAACAGAAATTAAAAA
1536955 AATACCTCAGCGT
65 AATACCTCAGCGT
* ** *
1536968 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGATAGAAATT--AAA
1 GACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAA-ACAGAAATTAAAAA
1537031 AATACCTCAGCGT
65 AATACCTCAGCGT
* *
1537044 GACTCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AAAAAACAGAAATTAAATTA
1 GACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAAACAG-----AAATTA
1537108 AAAAAATACCTCAGCGT
61 AAAAAATACCTCAGCGT
* * * *
1537125 GACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGA---TTTGAAAAAAAAAGACA-TAAATTA
1 GACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAA--A
1537186 CAAATACCTCAGCGT
64 -AAATACCTCAGCGT
* * **
1537201 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTAATTTTTAAAAAAAAGACAGAAATT--AAA
1 GACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAA-ACAGAAATTAAAAA
1537264 AATACCTCAGCGT
65 AATACCTCAGCGT
* * *
1537277 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAATGCAGAAATT-TAAA
1 GACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAA-ACAGAAATTAAAAA
1537341 AATACCTC
65 AATACCTC
1537349 TTGAAAGAAA
Statistics
Matches: 1237, Mismatches: 155, Indels: 187
0.78 0.10 0.12
Matches are distributed among these distances:
72 14 0.01
73 14 0.01
74 141 0.11
75 30 0.02
76 364 0.29
77 116 0.09
78 239 0.19
79 80 0.06
80 22 0.02
81 130 0.11
82 2 0.00
83 4 0.00
84 1 0.00
85 5 0.00
86 2 0.00
87 6 0.00
88 3 0.00
89 9 0.01
90 6 0.00
93 6 0.00
94 9 0.01
95 3 0.00
96 7 0.01
97 2 0.00
98 5 0.00
99 1 0.00
100 4 0.00
101 2 0.00
102 1 0.00
103 2 0.00
105 7 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (77 bp):
GACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAAAAA
ATACCTCAGCGT
Found at i:1536735 original size:27 final size:27
Alignment explanation
Indices: 1536697--1536755 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
1536687 TAAAAAAAAT
1536697 ACCTCAGCGTGACCCGAGGCTCAACTC
1 ACCTCAGCGTGACCCGAGGCTCAACTC
1536724 ACCTCAGCGTGACCCGAGGCTCAACTC
1 ACCTCAGCGTGACCCGAGGCTCAACTC
1536751 ACCTC
1 ACCTC
1536756 TGTATTATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.42, G:0.20, T:0.15
Consensus pattern (27 bp):
ACCTCAGCGTGACCCGAGGCTCAACTC
Found at i:1536804 original size:105 final size:105
Alignment explanation
Indices: 1536622--1536833 Score: 399
Period size: 105 Copynumber: 2.0 Consensus size: 105
1536612 AAAAAATACT
1536622 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAAT
1 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAAT
1536687 TAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
66 TAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
*
1536727 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAATAGAAA
1 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AAAAAAACAGAAA
1536792 TT-AAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
65 TTAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
1536832 TC
1 TC
1536834 TGTATTATGA
Statistics
Matches: 105, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
105 91 0.87
106 14 0.13
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (105 bp):
TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAAT
TAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
Found at i:1536849 original size:183 final size:184
Alignment explanation
Indices: 1536538--1536911 Score: 678
Period size: 183 Copynumber: 2.0 Consensus size: 184
1536528 TTTAAAAAAT
*
1536538 ACCTCAGCGTGACCCGAGGTTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAAAAAAA
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTG--AAAAAAAAA
*
1536603 CAGAAATTAAAAAAATACTTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATT
64 CAGAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATT
1536668 TTTTGAAAAAAACAGAAATTAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTC
129 TTTTGAAAAAAACAGAAATTAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTC
* *
1536724 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AAAAAAAATA
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAAAAACA
1536788 GAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT
66 GAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT
*
1536853 TTGAAAAAAGCAGAAATTAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTC
131 TTGAAAAAAACAGAAATTAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTC
1536907 ACCTC
1 ACCTC
1536912 TGTATTATGA
Statistics
Matches: 183, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
183 131 0.72
186 52 0.28
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (184 bp):
ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAAAAACA
GAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT
TTGAAAAAAACAGAAATTAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTC
Found at i:1536853 original size:78 final size:78
Alignment explanation
Indices: 1536724--1537348 Score: 952
Period size: 78 Copynumber: 8.1 Consensus size: 78
1536714 GGCTCAACTC
*
1536724 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAATAG
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAACAG
1536789 AAATTAAAAAAAT
66 AAATTAAAAAAAT
*
1536802 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AAAAAAGCAG
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAACAG
1536866 AAATTAAAAAAAAT
66 AAATT-AAAAAAAT
1536880 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAACAG
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAACAG
1536945 AAATTAAAAAAAT
66 AAATTAAAAAAAT
* *
1536958 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTAAAAAAAAGATA
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAA-ACA
1537022 GAAATT--AAAAAT
65 GAAATTAAAAAAAT
* *
1537034 ACCTCAGCGTGACTCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACAGAA
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA-A-AC
*
1537099 ATTAAATTAAAAAAAT
64 A-GAAATTAAAAAAAT
*
1537115 ACCTCAGCGTGACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGA---TTTGAAAAAAAA-AG
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAACAG
*
1537176 ACA-TAAATTACAAAT
66 AAATTAAA--A-AAAT
* *
1537191 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT-AATTTTTAAAAAAAAGACA
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAA-ACA
1537255 GAAATT--AAAAAT
65 GAAATTAAAAAAAT
**
1537267 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAATGCAG
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAACAG
*
1537332 AAATT-TAAAAAT
66 AAATTAAAAAAAT
1537344 ACCTC
1 ACCTC
1537349 TTGAAAGAAA
Statistics
Matches: 508, Mismatches: 20, Indels: 39
0.90 0.04 0.07
Matches are distributed among these distances:
73 4 0.01
74 2 0.00
75 3 0.01
76 158 0.31
77 61 0.12
78 203 0.40
79 21 0.04
80 4 0.01
81 52 0.10
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (78 bp):
ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAACAG
AAATTAAAAAAAT
Found at i:1538231 original size:16 final size:15
Alignment explanation
Indices: 1538196--1538258 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 15
1538186 TTCATCTTGA
1538196 TTTTTTC-TTTCTTTT
1 TTTTTTCTTTTC-TTT
1538211 CTTTTTTCTTTTCTATT
1 -TTTTTTCTTTTCT-TT
*
1538228 TTTTTGT-TTTTGTTT
1 TTTTT-TCTTTTCTTT
1538243 TTTTTTCTTTT-TTT
1 TTTTTTCTTTTCTTT
1538257 TT
1 TT
1538259 AGGCATAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
14 6 0.14
15 11 0.26
16 18 0.43
17 7 0.17
ACGTcount: A:0.02, C:0.10, G:0.03, T:0.86
Consensus pattern (15 bp):
TTTTTTCTTTTCTTT
Found at i:1549285 original size:19 final size:20
Alignment explanation
Indices: 1549261--1549449 Score: 86
Period size: 19 Copynumber: 10.0 Consensus size: 20
1549251 CAACTTTTTC
1549261 TTTTTTTTGAAAACAC-AAA
1 TTTTTTTTGAAAACACGAAA
* *
1549280 TTTTTTTTTAAAATAC-AAGA
1 TTTTTTTTGAAAACACGAA-A
* *
1549300 --ATTTTAG-AAACACG-AA
1 TTTTTTTTGAAAACACGAAA
*
1549316 TTTTTTTTAAAAAGACACGAAA
1 TTTTTTTT-GAAA-ACACGAAA
* *
1549338 ---ATTTTG-AAACACGAGA
1 TTTTTTTTGAAAACACGAAA
*
1549354 -TTTTTTTGAAAACACGAAT
1 TTTTTTTTGAAAACACGAAA
1549373 TTTCTTTTTG-AAACACGAAA
1 TTT-TTTTTGAAAACACGAAA
* * *
1549393 --ATTATT-AAAACACAAAA
1 TTTTTTTTGAAAACACGAAA
**
1549410 TTTGTTTTTGAAAACATAAAA
1 TTT-TTTTTGAAAACACGAAA
* *
1549431 TTTTTTAT-AAAAAACGAAA
1 TTTTTTTTGAAAACACGAAA
1549450 CACGAGGATT
Statistics
Matches: 126, Mismatches: 26, Indels: 36
0.67 0.14 0.19
Matches are distributed among these distances:
16 8 0.06
17 21 0.17
18 13 0.10
19 36 0.29
20 22 0.17
21 24 0.19
22 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (20 bp):
TTTTTTTTGAAAACACGAAA
Found at i:1549318 original size:36 final size:36
Alignment explanation
Indices: 1549265--1549365 Score: 114
Period size: 36 Copynumber: 2.7 Consensus size: 36
1549255 TTTTTCTTTT
* * * *
1549265 TTTTGAAAACACAAATTTTTTTTTAAAATACA-AGAA
1 TTTTG-AAACACGAATTTTTTTTAAAAAGACACAAAA
1549301 TTTTAGAAACACGAATTTTTTTTAAAAAGACACGAAAA
1 TTTT-GAAACACGAATTTTTTTTAAAAAGACAC-AAAA
*
1549339 TTTTGAAACACGAGATTTTTTTGAAAA
1 TTTTGAAACACGA-ATTTTTTTTAAAA
1549366 CACGAATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
36 27 0.48
37 10 0.18
38 19 0.34
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (36 bp):
TTTTGAAACACGAATTTTTTTTAAAAAGACACAAAA
Found at i:1549367 original size:56 final size:58
Alignment explanation
Indices: 1549307--1549445 Score: 151
Period size: 56 Copynumber: 2.4 Consensus size: 58
1549297 AGAATTTTAG
* * *
1549307 AAACACGAATTTTTTTTAAAAAGACACGAAAATT-TTGAAACACGAGA-TT-TTTTTGA
1 AAACACGAATTTTTTTTAAAAA-ACACGAAAATTATTAAAACACAAAATTTGTTTTTGA
**
1549363 AAACACGAATTTTCTTTT-TGAAACACGAAAATTATTAAAACACAAAATTTGTTTTTGA
1 AAACACGAATTTT-TTTTAAAAAACACGAAAATTATTAAAACACAAAATTTGTTTTTGA
** *
1549421 AAACATAAAATTTTTTATAAAAAAC
1 AAACA-CGAATTTTTTTTAAAAAAC
1549446 GAAACACGAG
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
55 11 0.16
56 25 0.37
57 6 0.09
58 15 0.22
59 10 0.15
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (58 bp):
AAACACGAATTTTTTTTAAAAAACACGAAAATTATTAAAACACAAAATTTGTTTTTGA
Found at i:1549386 original size:20 final size:17
Alignment explanation
Indices: 1549339--1549391 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 17
1549329 GACACGAAAA
1549339 TTTTGAAACACGAGATTT
1 TTTTGAAACACGA-ATTT
1549357 TTTTGAAAACACGAATTTTCT
1 TTTTG-AAACACGAA--TT-T
1549378 TTTTGAAACACGAA
1 TTTTGAAACACGAA
1549392 AATTATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.19
19 8 0.26
20 11 0.35
21 6 0.19
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (17 bp):
TTTTGAAACACGAATTT
Found at i:1549418 original size:37 final size:39
Alignment explanation
Indices: 1549339--1549422 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 39
1549329 GACACGAAAA
** * * *
1549339 TTTTGAAACACGAGATTTTTTTGAAAACACGAATTTTCT
1 TTTTGAAACACGAGAAATTATTGAAAACACAAAATTTCT
*
1549378 TTTTGAAACACGA-AAATTATT-AAAACACAAAATTTGT
1 TTTTGAAACACGAGAAATTATTGAAAACACAAAATTTCT
1549415 TTTTGAAA
1 TTTTGAAA
1549423 ACATAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 21 0.54
38 5 0.13
39 13 0.33
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (39 bp):
TTTTGAAACACGAGAAATTATTGAAAACACAAAATTTCT
Found at i:1549488 original size:17 final size:17
Alignment explanation
Indices: 1549462--1549768 Score: 159
Period size: 17 Copynumber: 16.8 Consensus size: 17
1549452 CGAGGATTTT
1549462 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* * *
1549479 TTTATGAAACACGGTCAAT
1 TTTTTGAAACAC-G-AAAA
1549498 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* *
1549516 TTTTTGAAAGACGAGAATGTT
1 TTTTTGAAACACGA-AA---A
* *
1549537 TTTTTAAAACACGGAAA
1 TTTTTGAAACACGAAAA
* **
1549554 TTTATGAAACACAGAATCT
1 TTTTTGAAACAC-GAA-AA
*
1549573 TTTTTGAAAACAAGAAAA
1 TTTTTG-AAACACGAAAA
* *
1549591 TTTTTGAAATAC-AGGAA
1 TTTTTGAAACACGA-AAA
*
1549608 TTTTTAAAAACACGAAAA
1 TTTTT-GAAACACGAAAA
* *
1549626 TTTTTGAAACACTAGAA
1 TTTTTGAAACACGAAAA
*
1549643 -TTTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
* *
1549660 TTTTTGAAACATGAGAA
1 TTTTTGAAACACGAAAA
**
1549677 TTTTTGAAAACACGAATTTT
1 TTTTTG-AAACACGAA--AA
* * *
1549697 TTTTTAAAACACGGAAG
1 TTTTTGAAACACGAAAA
*
1549714 TTTTTGAAACACAAGAAATTTTT
1 TTTTTGAAACAC--GAAA----A
1549737 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
*
1549755 TTTTTGAGACACGA
1 TTTTTGAAACACGA
1549769 TTTTTTTTAA
Statistics
Matches: 216, Mismatches: 49, Indels: 50
0.69 0.16 0.16
Matches are distributed among these distances:
16 6 0.03
17 88 0.41
18 49 0.23
19 28 0.13
20 18 0.08
21 11 0.05
22 4 0.02
23 6 0.03
24 6 0.03
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:1549510 original size:37 final size:35
Alignment explanation
Indices: 1549461--1549737 Score: 240
Period size: 37 Copynumber: 7.7 Consensus size: 35
1549451 ACGAGGATTT
*
1549461 TTTTTTG-AAACACGAAAATTTATGAAACACGGTCAA
1 TTTTTTGAAAACACGAAAATTTTTGAAACACGG--AA
*
1549497 TTTTTTGAAAACACGAAAATTTTTGAAAGACGAGAA
1 TTTTTTGAAAACACGAAAATTTTTGAAACACG-GAA
* * * *
1549533 TGTTTTTTTAAAACACGGAAATTTATGAAACACAGAA
1 --TTTTTTGAAAACACGAAAATTTTTGAAACACGGAA
* *
1549570 TCTTTTTTGAAAACAAGAAAATTTTTGAAATACAGGAA
1 --TTTTTTGAAAACACGAAAATTTTTGAAACAC-GGAA
* *
1549608 -TTTTTAAAAACACGAAAATTTTTGAAACACTAGAA
1 TTTTTTGAAAACACGAAAATTTTTGAAACAC-GGAA
* *
1549643 --TTTTGAAAACACGAAGATTTTTGAAACATGAGAA
1 TTTTTTGAAAACACGAAAATTTTTGAAACACG-GAA
** *
1549677 -TTTTTGAAAACACGAATTTTTTTTTAAAACACGGAA
1 TTTTTTGAAAACACGAA--AATTTTTGAAACACGGAA
* * *
1549713 GTTTTTGAAACACAAGAAATTTTTT
1 TTTTTTGAAA-ACACGAAAATTTTT
1549738 TTTTGAAAAC
Statistics
Matches: 201, Mismatches: 29, Indels: 22
0.80 0.12 0.09
Matches are distributed among these distances:
34 29 0.14
35 45 0.22
36 18 0.09
37 72 0.36
38 37 0.18
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (35 bp):
TTTTTTGAAAACACGAAAATTTTTGAAACACGGAA
Found at i:1549521 original size:18 final size:18
Alignment explanation
Indices: 1549462--1549761 Score: 186
Period size: 18 Copynumber: 16.4 Consensus size: 18
1549452 CGAGGATTTT
1549462 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
1549479 TTTATG-AAACACGGTCAAT
1 TTTTTGAAAACAC-G-AAAA
1549498 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
1549516 TTTTTGAAAGACGA-GAATGT
1 TTTTTGAAA-AC-ACGAA-AA
* *
1549536 TTTTTTAAAACACGGAAA
1 TTTTTGAAAACACGAAAA
* **
1549554 TTTATG-AAACACAGAATCT
1 TTTTTGAAAACAC-GAA-AA
*
1549573 TTTTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
*
1549591 TTTTTGAAATACA-G-GAA
1 TTTTTGAAA-ACACGAAAA
*
1549608 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
1549626 TTTTTG-AAACACTAGAA
1 TTTTTGAAAACACGAAAA
*
1549643 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
* *
1549660 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGAAAA
**
1549677 TTTTTGAAAACACGAATTT
1 TTTTTGAAAACACGAA-AA
* * *
1549696 TTTTTTAAAACACGGAAG
1 TTTTTGAAAACACGAAAA
* *
1549714 TTTTTGAAACACAAGAAATTTTT
1 TTTTTGAAA-ACACGAAA----A
1549737 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
1549755 TTTTTGA
1 TTTTTGA
1549762 GACACGATTT
Statistics
Matches: 214, Mismatches: 47, Indels: 43
0.70 0.15 0.14
Matches are distributed among these distances:
16 8 0.04
17 59 0.28
18 63 0.29
19 48 0.22
20 20 0.09
22 7 0.03
23 9 0.04
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:1549539 original size:75 final size:72
Alignment explanation
Indices: 1549446--1549681 Score: 250
Period size: 75 Copynumber: 3.2 Consensus size: 72
1549436 TATAAAAAAC
* *
1549446 GAAACACGAGGATTTTTTTTTGAAACACGAAAATTTATGAAACACGGTCAATTTTTTGAAAACAC
1 GAAACACGA-GAATTTTTTTTAAAACACGAAAATTTATGAAACAC-GT-AATTTTTTGAAAACAC
1549511 GAAAATTTTT
63 GAAAATTTTT
* *
1549521 GAAAGACGAGAATGTTTTTTTAAAACACGGAAATTTATGAAACACAG-AATCTTTTTTGAAAACA
1 GAAACACGAGAAT-TTTTTTTAAAACACGAAAATTTATGAAACAC-GTAA--TTTTTTGAAAACA
*
1549585 AGAAAATTTTT
62 CGAAAATTTTT
* * * *
1549596 GAAATAC-AGGAA--TTTTTAAAAACACGAAAATTTTTGAAACAC-TAGA-ATTTTGAAAACACG
1 GAAACACGA-GAATTTTTTTTAAAACACGAAAATTTATGAAACACGTA-ATTTTTTGAAAACACG
*
1549656 AAGATTTTT
64 AAAATTTTT
*
1549665 GAAACATGAGAATTTTT
1 GAAACACGAGAATTTTT
1549682 GAAAACACGA
Statistics
Matches: 137, Mismatches: 15, Indels: 22
0.79 0.09 0.13
Matches are distributed among these distances:
69 28 0.20
70 1 0.01
71 4 0.03
72 28 0.20
73 2 0.01
74 4 0.03
75 70 0.51
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (72 bp):
GAAACACGAGAATTTTTTTTAAAACACGAAAATTTATGAAACACGTAATTTTTTGAAAACACGAA
AATTTTT
Found at i:1549739 original size:22 final size:22
Alignment explanation
Indices: 1549714--1549759 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1549704 AACACGGAAG
*
1549714 TTTTTGAAACACAAGAAATTTTT
1 TTTTTGAAA-ACAAGAAATATTT
*
1549737 TTTTTGAAAACACGAAA-ATTT
1 TTTTTGAAAACAAGAAATATTT
1549758 TT
1 TT
1549760 GAGACACGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 7 0.33
23 9 0.43
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTTTGAAAACAAGAAATATTT
Found at i:1549741 original size:23 final size:22
Alignment explanation
Indices: 1549714--1549759 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1549704 AACACGGAAG
*
1549714 TTTTTGAAACACAAGAAATTTTT
1 TTTTTGAAA-ACAAGAAAATTTT
*
1549737 TTTTTGAAAACACGAAAATTTT
1 TTTTTGAAAACAAGAAAATTTT
1549759 T
1 T
1549760 GAGACACGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTTTGAAAACAAGAAAATTTT
Found at i:1550542 original size:46 final size:45
Alignment explanation
Indices: 1550451--1550545 Score: 111
Period size: 46 Copynumber: 2.1 Consensus size: 45
1550441 ATGGCCTGCA
** *
1550451 CTTTATTCTTTTTTTTTCCTTTCTTTCTTCCCCTTTCTTTTCTTT
1 CTTTATTCTTTTTTTAGCCTTTCTTTCTTCCCCTTTCTTTCCTTT
* * *
1550496 CTTTATTTCTTTTTTTCAGCCTTTTTTTCTTCTCTTTTC-TTCCTTT
1 CTTTA-TTCTTTTTTT-AGCCTTTCTTTCTTCCCCTTTCTTTCCTTT
1550542 CTTT
1 CTTT
1550546 CTTCCTCCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
45 5 0.12
46 20 0.48
47 17 0.40
ACGTcount: A:0.03, C:0.25, G:0.01, T:0.71
Consensus pattern (45 bp):
CTTTATTCTTTTTTTAGCCTTTCTTTCTTCCCCTTTCTTTCCTTT
Found at i:1551107 original size:29 final size:29
Alignment explanation
Indices: 1551037--1551182 Score: 154
Period size: 29 Copynumber: 5.0 Consensus size: 29
1551027 GCAAACACAG
* * *
1551037 TAAAACTTTT-GGGGCCAAAATATAATTT
1 TAAAAATTTTAGGGGTCAAAATGTAATTT
*
1551065 TGAGAAAA-TTTAGGGCTCAAAATGTAATTT
1 T-A-AAAATTTTAGGGGTCAAAATGTAATTT
* ** *
1551095 CAAAAAGCTTAGGGGTCAAAATATAATTT
1 TAAAAATTTTAGGGGTCAAAATGTAATTT
* *
1551124 TAGGAAATTTTA-GGGTCAAAATGCAATTT
1 TA-AAAATTTTAGGGGTCAAAATGTAATTT
1551153 TAAAAATTTTAGGGGTCAAAATGTAATTT
1 TAAAAATTTTAGGGGTCAAAATGTAATTT
1551182 T
1 T
1551183 TTATTTTTGT
Statistics
Matches: 96, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
28 13 0.14
29 59 0.61
30 24 0.25
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (29 bp):
TAAAAATTTTAGGGGTCAAAATGTAATTT
Found at i:1551158 original size:58 final size:59
Alignment explanation
Indices: 1551047--1551182 Score: 186
Period size: 58 Copynumber: 2.3 Consensus size: 59
1551037 TAAAACTTTT
* *
1551047 GGGGCCAAAATATAATTTTGAGAAAATTTAGGGCTCAAAATGTAATTTCAAAAAGCTTA
1 GGGGTCAAAATATAATTTTGAGAAAATTTAGGGCTCAAAATGCAATTTCAAAAAGCTTA
* * **
1551106 GGGGTCAAAATATAATTTT-AGGAAATTTTAGGG-TCAAAATGCAATTTTAAAAATTTTA
1 GGGGTCAAAATATAATTTTGA-GAAAATTTAGGGCTCAAAATGCAATTTCAAAAAGCTTA
*
1551164 GGGGTCAAAATGTAATTTT
1 GGGGTCAAAATATAATTTT
1551183 TTATTTTTGT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 40 0.58
59 29 0.42
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (59 bp):
GGGGTCAAAATATAATTTTGAGAAAATTTAGGGCTCAAAATGCAATTTCAAAAAGCTTA
Found at i:1551898 original size:16 final size:15
Alignment explanation
Indices: 1551877--1551917 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1551867 GCACGATGGA
1551877 TATTTTTTCTTTTAAC
1 TATTTTTTCTTTT-AC
1551893 TATTTTTT-TTTTAC
1 TATTTTTTCTTTTAC
1551907 T-TTTCTTTCTT
1 TATTT-TTTCTT
1551918 ATCTGACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.13
14 6 0.26
15 6 0.26
16 8 0.35
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTTTCTTTTAC
Found at i:1560666 original size:13 final size:12
Alignment explanation
Indices: 1560643--1560686 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1560633 TTATTAAAAA
*
1560643 ATAATAAAATTT
1 ATAAAAAAATTT
1560655 ATAAACAAAATTT
1 ATAAA-AAAATTT
*
1560668 ATAAAAAAAGTT
1 ATAAAAAAATTT
1560680 ATAAAAA
1 ATAAAAA
1560687 GTTTACAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (12 bp):
ATAAAAAAATTT
Found at i:1561246 original size:22 final size:23
Alignment explanation
Indices: 1561210--1561253 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
1561200 AATTTTGTTT
1561210 ATAATTTTTATAATTTTAAAAAA
1 ATAATTTTTATAATTTTAAAAAA
1561233 ATAATTTTTA-AATTTTAAAAA
1 ATAATTTTTATAATTTTAAAAA
1561254 GGATTAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAATTTTTATAATTTTAAAAAA
Found at i:1567512 original size:22 final size:21
Alignment explanation
Indices: 1567470--1567522 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1567460 AATATTAAAA
**
1567470 ATATATT-TTATAATATTTTT
1 ATATATTATTATAATAAATTT
1567490 ATATATTATTATAATTAAATTT
1 ATATATTATTATAA-TAAATTT
* *
1567512 AAATAATATTA
1 ATATATTATTA
1567523 GTAAACATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.26
21 6 0.22
22 14 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATATTATTATAATAAATTT
Found at i:1569310 original size:2 final size:2
Alignment explanation
Indices: 1569305--1569332 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1569295 ATATAATGCA
1569305 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
1569333 GGCAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1571198 original size:43 final size:43
Alignment explanation
Indices: 1571112--1571278 Score: 183
Period size: 43 Copynumber: 3.9 Consensus size: 43
1571102 GTTTTAACGA
* * * *
1571112 AAACGCCGCTAAAGAACCTGATCTATGGCGGCAC-TTCGACCAC
1 AAACGCCGCTAAAGAACCTGATCTTTAGCGGCGCTTTC-TCCAC
* *
1571155 AAACACCACTAAAGAACCTGATCTTTAGCGGCGCTTTCTCCAC
1 AAACGCCGCTAAAGAACCTGATCTTTAGCGGCGCTTTCTCCAC
* * * * *
1571198 AAACGCCGCTAAATACCCTTAGCTTTAGCAGCGCTTTCTCCAC
1 AAACGCCGCTAAAGAACCTGATCTTTAGCGGCGCTTTCTCCAC
* * *
1571241 AAACGCCGCTAAATACCCTTATCTTTTAGCGGCGCTTT
1 AAACGCCGCTAAAGAACCTGATC-TTTAGCGGCGCTTT
1571279 TTGTCGAAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
43 91 0.85
44 16 0.15
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACCTGATCTTTAGCGGCGCTTTCTCCAC
Found at i:1573995 original size:3 final size:3
Alignment explanation
Indices: 1573987--1574021 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1573977 TGATTAAGGT
1573987 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1574022 GTTAAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1579390 original size:18 final size:17
Alignment explanation
Indices: 1579367--1579404 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
1579357 AAAAAAATGT
1579367 AATAATGTAATCTCATGC
1 AATAATGTAATCTCAT-C
1579385 AATAATGTAATCTCATC
1 AATAATGTAATCTCATC
1579402 AAT
1 AAT
1579405 TACACTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (17 bp):
AATAATGTAATCTCATC
Found at i:1582150 original size:2 final size:2
Alignment explanation
Indices: 1582143--1582191 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1582133 CAAAGCATTA
1582143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1582185 AT AT AT A
1 AT AT AT A
1582192 CGAGATAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1588060 original size:16 final size:16
Alignment explanation
Indices: 1588039--1588091 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
1588029 AAAAGATCCA
**
1588039 AGCCCGAGAAAATTTG
1 AGCCCGAGAAAACCTG
*
1588055 AGCCCGACAAAACCTG
1 AGCCCGAGAAAACCTG
*
1588071 AGCCTGAGAAAACCTG
1 AGCCCGAGAAAACCTG
1588087 AGCCC
1 AGCCC
1588092 ATAACAAACT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.36, C:0.30, G:0.23, T:0.11
Consensus pattern (16 bp):
AGCCCGAGAAAACCTG
Found at i:1588828 original size:15 final size:15
Alignment explanation
Indices: 1588799--1588842 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 15
1588789 AGAATGTATT
1588799 ATTATTATATATAATA
1 ATTATTAT-TATAATA
1588815 ATTATTATTATAAT-
1 ATTATTATTATAATA
1588829 A-TA-TATTATAATA
1 ATTATTATTATAATA
1588842 A
1 A
1588843 AAGATATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.33
13 3 0.11
14 1 0.04
15 6 0.22
16 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATTATTATAATA
Found at i:1589120 original size:235 final size:239
Alignment explanation
Indices: 1588583--1589179 Score: 627
Period size: 239 Copynumber: 2.5 Consensus size: 239
1588573 TATAATTATT
* * * * ** *
1588583 ATAATATAGATTATAATAAAAAAGATATAGTTTTACATGATATTATGATGCTTAATTGTCGATGC
1 ATAATATAGATTATAATAAAAGA-ATATAGTATTACATGATATTATAATGTTTAATCATTGATGC
* * *
1588648 ATATATATAAATTATTAATATA-T-TATACGATATGATATAACATTATATAATATAGTAAGAGGG
65 ATATATATAAACTATTAATATAGTATATACTATATGATATAACATTATATAATATAATAAGAGGG
* * * *
1588711 CTAACTTTCAAATATACGAAATGTATAGAGACTTAAAACATGTTTCAACAAAAAATAATAATATA
130 CTAACTTTCAAATATACGAAAAGTATAAAGACTTAAAACATATTTCAACAAAAAATAATAATAAA
* * * *
1588776 TAATAAGTAAAATAGAATGTATTATTATTATATATAATAATTATTATT
195 CAATAAGTAAAATAGAA-GTA-TATTA-TATATATAATAACTACTATC
* ** *
1588824 ATAATATATATTATAATAAAAG-ATATAGTATTACATGATAACATAATGTTTAACCATTGATGCA
1 ATAATATAGATTATAATAAAAGAATATAGTATTACATGATATTATAATGTTTAATCATTGATGCA
* * * *
1588888 TATATAAAAACTATAAATATAGTATATACTATATGATATAACATTATGTAATATAATAGGAGGGC
66 TATATATAAACTATTAATATAGTATATACTATATGATATAACATTATATAATATAATAAGAGGGC
* * * * * * * **
1588953 T-GCTTTTAAATGTACGAAAAGTATAAAGTCTTAAAGCGTATTTCAAC-CAGTATAATAATAAAC
131 TAACTTTCAAATATACGAAAAGTATAAAGACTTAAAACATATTTCAACAAAAAATAATAATAAAC
* * * *
1589016 AATAA-TATATTATAA-TA-ATTA-ATATATAATGTACTACTATC
196 AATAAGTAAAATAGAAGTATATTATATATATAAT-AACTACTATC
* * * *
1589057 ATATTATAGAATATAATAAAAGATATATAGTATTACATTATATTACAATGTTTAATCATTGATGC
1 ATAATATAGATTATAATAAAAGA-ATATAGTATTACATGATATTATAATGTTTAATCATTGATGC
* *
1589122 ATATACATAAACTATTAACATAGTATATACTACATGATATGATATAACATTATATAAT
65 ATATATATAAACTATTAATATAG--TATA-TAC-T-ATATGATATAACATTATATAAT
1589180 CTAAGTCTGA
Statistics
Matches: 294, Mismatches: 52, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
232 9 0.03
233 25 0.09
234 4 0.01
235 55 0.19
236 2 0.01
237 4 0.01
238 10 0.03
239 68 0.23
240 59 0.20
241 58 0.20
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (239 bp):
ATAATATAGATTATAATAAAAGAATATAGTATTACATGATATTATAATGTTTAATCATTGATGCA
TATATATAAACTATTAATATAGTATATACTATATGATATAACATTATATAATATAATAAGAGGGC
TAACTTTCAAATATACGAAAAGTATAAAGACTTAAAACATATTTCAACAAAAAATAATAATAAAC
AATAAGTAAAATAGAAGTATATTATATATATAATAACTACTATC
Found at i:1595932 original size:13 final size:13
Alignment explanation
Indices: 1595914--1595940 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1595904 TATGAACACC
1595914 AATACTTAAAGAT
1 AATACTTAAAGAT
1595927 AATACTTAAAGAT
1 AATACTTAAAGAT
1595940 A
1 A
1595941 GAGAAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
AATACTTAAAGAT
Found at i:1597438 original size:187 final size:186
Alignment explanation
Indices: 1597123--1597506 Score: 660
Period size: 187 Copynumber: 2.1 Consensus size: 186
1597113 TCATGCATGG
*
1597123 TATGTGATTTTGGCCCCGTTTTTAATAATTTTTATGTTTTGGAGATCGTTACAACTATGTCCAAC
1 TATGTGATTTTGGCCCCGTTTTTAATAATTTTTATGTTTTGGAGATCGTTACAACTAGGTCCAAC
1597188 TAACCCGTACCTTCGATTTTGAAACTGTCAAAGAATTTGAATGTTGCCATCAATGAACCTTGTGA
66 TAACCCGTACCTTCGATTTTGAAACTGTCAAAGAATTTGAATGTTGCCATCAATGAACCTTGTGA
*
1597253 TGTTAGATGTTAAATGGTGAATTTAAAATATTATTTTTTTATTTAAAAGTATTTTAT
131 TGTTAGATGTTAAATGATGAATTTAAAATATTA-TTTTTTATTTAAAAGTATTTTAT
*
1597310 TATGTGATTTTGGCCCCGTTTTTAATAATTTTTATGTTTTGGAGATCGTTACAACTAGGTCCAGC
1 TATGTGATTTTGGCCCCGTTTTTAATAATTTTTATGTTTTGGAGATCGTTACAACTAGGTCCAAC
* * * * *
1597375 TAGCTCGTACCTTCGCTTTTGAAACTGTTAAAGAATTTGAATGTTGCCATCAGTGAACCTTGTGA
66 TAACCCGTACCTTCGATTTTGAAACTGTCAAAGAATTTGAATGTTGCCATCAATGAACCTTGTGA
* *
1597440 TTTTAGATGTTAAATGATGAATTTAAAATATTATTTTTTATTTAAATGTATTTTAT
131 TGTTAGATGTTAAATGATGAATTTAAAATATTATTTTTTATTTAAAAGTATTTTAT
*
1597496 TAAGTGATTTT
1 TATGTGATTTT
1597507 TGATAATTTT
Statistics
Matches: 186, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
186 32 0.17
187 154 0.83
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (186 bp):
TATGTGATTTTGGCCCCGTTTTTAATAATTTTTATGTTTTGGAGATCGTTACAACTAGGTCCAAC
TAACCCGTACCTTCGATTTTGAAACTGTCAAAGAATTTGAATGTTGCCATCAATGAACCTTGTGA
TGTTAGATGTTAAATGATGAATTTAAAATATTATTTTTTATTTAAAAGTATTTTAT
Found at i:1597947 original size:2 final size:2
Alignment explanation
Indices: 1597940--1597978 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1597930 NNNNNNTTAC
1597940 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1597979 TCCATTGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1606866 original size:63 final size:63
Alignment explanation
Indices: 1606795--1606920 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
1606785 GAACTATACT
1606795 GATGATCCCCGAGTTCGTAACGCGTCTCCAAAATCTATAAAAAAAAACAAATGAACGAAAATA
1 GATGATCCCCGAGTTCGTAACGCGTCTCCAAAATCTATAAAAAAAAACAAATGAACGAAAATA
1606858 GATGATCCCCGAGTTCGTAACGCGTCTCCAAAATCTATAAAAAAAAACAAATGAACGAAAATA
1 GATGATCCCCGAGTTCGTAACGCGTCTCCAAAATCTATAAAAAAAAACAAATGAACGAAAATA
1606921 AACGAAGTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.19
Consensus pattern (63 bp):
GATGATCCCCGAGTTCGTAACGCGTCTCCAAAATCTATAAAAAAAAACAAATGAACGAAAATA
Found at i:1607545 original size:41 final size:40
Alignment explanation
Indices: 1607417--1607584 Score: 160
Period size: 41 Copynumber: 4.1 Consensus size: 40
1607407 TAAAAACAGA
* * * * * *
1607417 TTCACCGGTATTTAGCCTGCTAGGCTTAAAGCCTGATTCAA
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATT-AT
* * * *
1607458 TACACCGGCACTT-AGCCTGCTAGACATATAGTCCGA-TAT
1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATTAT
1607497 GTATCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAT
1 -T-TCACCGGCATTAAGCCTGCTAGACGTAAAGTCTG-ATTAT
* *
1607540 TTCACCGGCATCAAGCCTGCTAGACGTAAAGTCTAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCT-GATTAT
1607581 TTCA
1 TTCA
1607585 ATCACTTTAA
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
39 1 0.01
40 4 0.04
41 94 0.89
42 4 0.04
43 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (40 bp):
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATTAT
Found at i:1609204 original size:3 final size:3
Alignment explanation
Indices: 1609196--1609234 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1609186 ATAAACACAC
1609196 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1609235 TTTTTCTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1613390 original size:23 final size:24
Alignment explanation
Indices: 1613364--1613427 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 24
1613354 AAATTTTATT
1613364 TTTAAATTTAAATAAAATAAT-AA
1 TTTAAATTTAAATAAAATAATAAA
**
1613387 TTTAAAAATAAATAAAATAATAAA
1 TTTAAATTTAAATAAAATAATAAA
*
1613411 ATTACATATTTAAATAA
1 TTTA-A-ATTTAAATAA
1613428 TACAATTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 19 0.58
24 5 0.15
25 1 0.03
26 8 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
TTTAAATTTAAATAAAATAATAAA
Found at i:1613401 original size:18 final size:17
Alignment explanation
Indices: 1613368--1613401 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1613358 TTTATTTTTA
*
1613368 AATTTAAATAAAATAAT
1 AATTTAAAAAAAATAAT
1613385 AATTTAAAAATAAATAA
1 AATTTAAAAA-AAATAA
1613402 AATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATTTAAAAAAAATAAT
Found at i:1613410 original size:12 final size:12
Alignment explanation
Indices: 1613372--1613410 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1613362 TTTTTAAATT
1613372 TAAATAAAATAA
1 TAAATAAAATAA
* *
1613384 TAATTTAAA-AA
1 TAAATAAAATAA
1613395 TAAATAAAATAA
1 TAAATAAAATAA
1613407 TAAA
1 TAAA
1613411 ATTACATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAATAAAATAA
Found at i:1627819 original size:13 final size:14
Alignment explanation
Indices: 1627803--1627843 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
1627793 TTTCAATTTT
1627803 ATTTTAATAATA-A
1 ATTTTAATAATATA
1627816 ATTTTAA-AATGATA
1 ATTTTAATAAT-ATA
1627830 ATTTTAAATAATAT
1 ATTTT-AATAATAT
1627844 TCTTCACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.12
13 8 0.33
14 6 0.25
15 4 0.17
16 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:1627895 original size:15 final size:15
Alignment explanation
Indices: 1627875--1627931 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
1627865 ATTCAATATT
1627875 AATATTTTAATAATA
1 AATATTTTAATAATA
*
1627890 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
1627909 AATATATTAATAATA
1 AATATTTTAATAATA
1627924 AATATTTT
1 AATATTTT
1627932 TATAGTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:1631008 original size:13 final size:13
Alignment explanation
Indices: 1630943--1631008 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
1630933 AGTTCTTCAT
1630943 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
1630956 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
1630969 TACTGTGGAAAAG
1 TGCTTTTGAAAAG
*
1630982 TACTTTT-AAGAAG
1 TGCTTTTGAA-AAG
1630995 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
1631008 T
1 T
1631009 TTGGTTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 2 0.05
13 39 0.91
14 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:1632062 original size:21 final size:20
Alignment explanation
Indices: 1632022--1632064 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1632012 TTTGAAAATC
*
1632022 AAAATAATAAAAATATATTA
1 AAAATAATAAAAATAAATTA
1632042 AAAATTAA-AAAAATTAAATTA
1 AAAA-TAATAAAAA-TAAATTA
1632063 AA
1 AA
1632065 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATAATAAAAATAAATTA
Found at i:1633318 original size:38 final size:37
Alignment explanation
Indices: 1633243--1633337 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 37
1633233 AATTTTATTG
* * *
1633243 GGGTGAATTTTGGTTTTTGTTCCAACCCAGTGTCACT
1 GGGTTAATTATGGTTTTTGTTCCAACCCAGTGACACT
* ** *
1633280 GGGTTAATTGTGGTTTTTGTTTCTGACCCATTGACACT
1 GGGTTAATTATGGTTTTTG-TTCCAACCCAGTGACACT
*
1633318 GAGATTAATTATGGTTTTTG
1 G-GGTTAATTATGGTTTTTG
1633338 ATATTTGCCA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
37 17 0.35
38 15 0.31
39 16 0.33
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44
Consensus pattern (37 bp):
GGGTTAATTATGGTTTTTGTTCCAACCCAGTGACACT
Found at i:1633333 original size:39 final size:37
Alignment explanation
Indices: 1633248--1633337 Score: 99
Period size: 39 Copynumber: 2.4 Consensus size: 37
1633238 TATTGGGGTG
* * *
1633248 AATTTTGGTTTTTGTTCCAACCCAGTGTCACTGGGTT
1 AATTATGGTTTTTGTTCCAACCCAGTGACACTGGATT
* ** *
1633285 AATTGTGGTTTTTGTTTCTGACCCATTGACACTGAGATT
1 AATTATGGTTTTTG-TTCCAACCCAGTGACACTG-GATT
1633324 AATTATGGTTTTTG
1 AATTATGGTTTTTG
1633338 ATATTTGCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 13 0.30
38 15 0.34
39 16 0.36
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.46
Consensus pattern (37 bp):
AATTATGGTTTTTGTTCCAACCCAGTGACACTGGATT
Found at i:1634523 original size:10 final size:11
Alignment explanation
Indices: 1634507--1634556 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
1634497 TATATTTTCA
1634507 AAAAAATATAT
1 AAAAAATATAT
* *
1634518 -AAAAATTTCT
1 AAAAAATATAT
* *
1634528 AAAAAATTTCT
1 AAAAAATATAT
1634539 AAAAAATATAT
1 AAAAAATATAT
1634550 AAAAAAT
1 AAAAAAT
1634557 TTAAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 8 0.24
11 26 0.76
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAAAATATAT
Found at i:1634532 original size:11 final size:11
Alignment explanation
Indices: 1634518--1634558 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
1634508 AAAAATATAT
1634518 AAAAATTTCTA
1 AAAAATTTCTA
1634529 AAAAATTTCTA
1 AAAAATTTCTA
* *
1634540 AAAAATATATA
1 AAAAATTTCTA
1634551 AAAAATTT
1 AAAAATTT
1634559 AAAATTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAAATTTCTA
Found at i:1634546 original size:32 final size:31
Alignment explanation
Indices: 1634502--1634562 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
1634492 AAATTTATAT
*
1634502 TTTCAAAAAAATATATAAAAATTTCTAAAAAA
1 TTTCAAAAAAATATATAAAAAATT-TAAAAAA
*
1634534 TTTCTAAAAAATATATAAAAAATTTAAAA
1 TTTCAAAAAAATATATAAAAAATTTAAAA
1634563 TTTTCTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (31 bp):
TTTCAAAAAAATATATAAAAAATTTAAAAAA
Found at i:1634640 original size:3 final size:3
Alignment explanation
Indices: 1634632--1634660 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1634622 ACTAAAGTAT
1634632 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1634661 TTGCTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1635582 original size:15 final size:17
Alignment explanation
Indices: 1635557--1635594 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
1635547 ATGTAATTTT
*
1635557 CTATTTGAACA-TACAA
1 CTATTTCAACATTACAA
1635573 -TATTTCAACATTACAA
1 CTATTTCAACATTACAA
1635589 CTATTT
1 CTATTT
1635595 TTAATCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 5 0.26
17 5 0.26
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (17 bp):
CTATTTCAACATTACAA
Found at i:1643932 original size:14 final size:14
Alignment explanation
Indices: 1643913--1643946 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1643903 ATCATTTTGC
1643913 TATTATATTATTAT
1 TATTATATTATTAT
* *
1643927 TATTATATTGTTGT
1 TATTATATTATTAT
1643941 TATTAT
1 TATTAT
1643947 TTGAATATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
TATTATATTATTAT
Done.