Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 15 of 22
Found at i:6233541 original size:30 final size:29
Alignment explanation
Indices: 6233507--6233584 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
6233497 AATAATTATT
6233507 TATAAAAATTTATTTAATATAAAATAAAAA
1 TATAAAAATTTATTTAA-ATAAAATAAAAA
* ** *
6233537 TATAAAGATTTGA-TTAAATGTAATAAAAG
1 TATAAAAATTT-ATTTAAATAAAATAAAAA
* *
6233566 GATAAAAATTTATTCAAAT
1 TATAAAAATTTATTTAAAT
6233585 TTTTATAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.03
29 23 0.59
30 14 0.36
31 1 0.03
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.36
Consensus pattern (29 bp):
TATAAAAATTTATTTAAATAAAATAAAAA
Found at i:6239312 original size:2 final size:2
Alignment explanation
Indices: 6239305--6239352 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
6239295 ACAGAGTATA
* *
6239305 CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT GT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
6239347 TT CT CT
1 CT CT CT
6239353 TTCTGATTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.44, G:0.04, T:0.52
Consensus pattern (2 bp):
CT
Found at i:6243983 original size:24 final size:24
Alignment explanation
Indices: 6243914--6243989 Score: 98
Period size: 24 Copynumber: 3.2 Consensus size: 24
6243904 GTTTAGCTAG
6243914 GCCACAATCCCAGCCTCTGCAGCA
1 GCCACAATCCCAGCCTCTGCAGCA
* * * * *
6243938 GCCGCAGTCTCAGTCTTTGCAGCA
1 GCCACAATCCCAGCCTCTGCAGCA
*
6243962 GCCACAATCCCAGCCTCAGCAGCA
1 GCCACAATCCCAGCCTCTGCAGCA
6243986 GCCA
1 GCCA
6243990 GCCACTGGAG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.24, C:0.42, G:0.20, T:0.14
Consensus pattern (24 bp):
GCCACAATCCCAGCCTCTGCAGCA
Found at i:6248170 original size:33 final size:33
Alignment explanation
Indices: 6248133--6248329 Score: 109
Period size: 33 Copynumber: 6.1 Consensus size: 33
6248123 TTTGTAATGT
6248133 TATAAT-TAA-AATAAAAAATATCAAAATAAAATA
1 TATAATATAAGAATAAAAAAT-T-AAAATAAAATA
*
6248166 TATAATATAAGAATTAAAAATTAAAAT-AAA-A
1 TATAATATAAGAATAAAAAATTAAAATAAAATA
*
6248197 TA-AA-AT----ATAAAAAATTAAAAT---TTA
1 TATAATATAAGAATAAAAAATTAAAATAAAATA
* *
6248221 TATAATATAGGTAA-AAGAAATTAAAATAAAATA
1 TATAATATAAG-AATAAAAAATTAAAATAAAATA
* * *
6248254 TATAATATAAAAAATTATATTAAAAGATAAAAATAAAACA
1 TATAATAT--AAGA--ATA--AAAA-ATTAAAATAAAATA
* *
6248294 TATAATATTATAATAAAAAA-TAAAGATAAAATA
1 TATAATATAAGAATAAAAAATTAAA-ATAAAATA
6248327 TAT
1 TAT
6248330 GACATTAAAA
Statistics
Matches: 128, Mismatches: 14, Indels: 44
0.69 0.08 0.24
Matches are distributed among these distances:
24 3 0.02
25 16 0.12
26 2 0.02
29 2 0.02
30 14 0.11
31 4 0.03
32 6 0.05
33 32 0.25
34 9 0.07
35 10 0.08
36 4 0.03
37 1 0.01
38 2 0.02
39 3 0.02
40 20 0.16
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (33 bp):
TATAATATAAGAATAAAAAATTAAAATAAAATA
Found at i:6248227 original size:24 final size:25
Alignment explanation
Indices: 6248199--6248270 Score: 54
Period size: 30 Copynumber: 2.6 Consensus size: 25
6248189 AAATAAAATA
* *
6248199 AAATATAAAAAATTAAAATTTATATA
1 AAATATAAAAAATTAAAA-TAAAATA
*
6248225 ATATAGGTAAAAGAAATTAAAATAAAATA
1 AAATA--T-AAA-AAATTAAAATAAAATA
6248254 TATAATATAAAAAATTA
1 -A-AATATAAAAAATTA
6248271 TATTAAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
26 4 0.11
27 6 0.17
28 4 0.11
29 9 0.25
30 10 0.28
31 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (25 bp):
AAATATAAAAAATTAAAATAAAATA
Found at i:6248291 original size:55 final size:55
Alignment explanation
Indices: 6248139--6248291 Score: 129
Period size: 55 Copynumber: 2.8 Consensus size: 55
6248129 ATGTTATAAT
* * * * * *
6248139 TAAAATAAAAAATATCAAAA-TAAAATATATAATATAAGAAT-TAA-AAATTAAAA
1 TAAAATAAAATATA-AAAAATTAAAATTTATAAAATAAAAATAAAAGAAATTAAAA
* * **
6248192 TAAAATAAAATATAAAAAATTAAAATTTATATAATATAGGTAAAAGAAATTAAAA
1 TAAAATAAAATATAAAAAATTAAAATTTATAAAATAAAAATAAAAGAAATTAAAA
*
6248247 TAAAATATATAATATAAAAAATT-ATA-TTA-AAAGATAAAAATAAAA
1 TAAAATA-A-AATATAAAAAATTAAAATTTATAAA-ATAAAAATAAAA
6248292 CATATAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
52 4 0.05
53 27 0.34
54 4 0.05
55 28 0.35
56 3 0.04
57 13 0.16
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (55 bp):
TAAAATAAAATATAAAAAATTAAAATTTATAAAATAAAAATAAAAGAAATTAAAA
Found at i:6254710 original size:21 final size:22
Alignment explanation
Indices: 6254684--6254725 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
6254674 TTTTTTTTTA
6254684 AAAAAATAAAAATTTA-AAAAT
1 AAAAAATAAAAATTTATAAAAT
* *
6254705 AAAAAATTATAATTTATAAAA
1 AAAAAATAAAAATTTATAAAA
6254726 CATAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAATAAAAATTTATAAAAT
Found at i:6254725 original size:17 final size:17
Alignment explanation
Indices: 6254703--6254741 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
6254693 AAATTTAAAA
*
6254703 ATAAAAAATTATAATTT
1 ATAAAAAATAATAATTT
*
6254720 ATAAAACATAATAATTT
1 ATAAAAAATAATAATTT
*
6254737 TTAAA
1 ATAAA
6254742 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAAAATAATAATTT
Found at i:6258351 original size:21 final size:20
Alignment explanation
Indices: 6258313--6258351 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6258303 TTACAGTGAC
*
6258313 GCTTCAATTGATAAATTGAA
1 GCTTCAATTGAAAAATTGAA
6258333 GCTTCAATTGACAAAATTG
1 GCTTCAATTGA-AAAATTG
6258352 GATGAAGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
GCTTCAATTGAAAAATTGAA
Found at i:6265815 original size:33 final size:34
Alignment explanation
Indices: 6265763--6265827 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
6265753 GACACATACC
* *
6265763 TTATTAAAATATATTTATAA-AATTAATTAATTGA
1 TTATTAAAATAAATGTATAATAA-TAATTAATTGA
6265797 TTATT-AAATAAATGTATAATAATAATTAATT
1 TTATTAAAATAAATGTATAATAATAATTAATT
6265828 AACACCACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (34 bp):
TTATTAAAATAAATGTATAATAATAATTAATTGA
Found at i:6268329 original size:2 final size:2
Alignment explanation
Indices: 6268322--6268351 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6268312 ACTCCATTTC
6268322 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
6268352 TTTTGACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6270397 original size:25 final size:24
Alignment explanation
Indices: 6270369--6270426 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
6270359 ATAGTTACTT
6270369 ATAAAAATATTTTAATTTAAA-ATAA
1 ATAAAAATATTTTAA-TTAAATAT-A
6270394 ATAAATAA-ATTTTAATTAAATATA
1 ATAAA-AATATTTTAATTAAATATA
6270418 ATAAAAATA
1 ATAAAAATA
6270427 AATATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 2 0.07
24 12 0.40
25 14 0.47
26 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAAAAATATTTTAATTAAATATA
Found at i:6270404 original size:19 final size:20
Alignment explanation
Indices: 6270382--6270422 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
6270372 AAAATATTTT
6270382 AATTTAAAATAAATA-AATA
1 AATTTAAAATAAATATAATA
* *
6270401 AATTTTAATTAAATATAATA
1 AATTTAAAATAAATATAATA
6270421 AA
1 AA
6270423 AATAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTTAAAATAAATATAATA
Found at i:6272508 original size:2 final size:2
Alignment explanation
Indices: 6272501--6272538 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6272491 AAATAAAACC
6272501 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
6272539 GTAGGTGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6273657 original size:33 final size:33
Alignment explanation
Indices: 6273615--6273680 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
6273605 AGAATTCGAA
*
6273615 CGCTGTAGAGAATAATGCATCAATGAATCAAAT
1 CGCTGTAGAGAATAATGCATCAATCAATCAAAT
6273648 CGCTGTAGAGAATAATGCATCAATCAATCAAAT
1 CGCTGTAGAGAATAATGCATCAATCAATCAAAT
6273681 ACTTGAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (33 bp):
CGCTGTAGAGAATAATGCATCAATCAATCAAAT
Found at i:6274650 original size:2 final size:2
Alignment explanation
Indices: 6274643--6274683 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6274633 TATCTGCACA
*
6274643 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6274684 CACACACATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6287900 original size:21 final size:21
Alignment explanation
Indices: 6287861--6287908 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6287851 TATAGGTTTT
* *
6287861 ATAATTTTATAATAATATA-A
1 ATAATTATATAAAAATATATA
6287881 ATAATTATATTAAAAATATATA
1 ATAATTATA-TAAAAATATATA
6287903 A-AATTA
1 ATAATTA
6287909 AGATAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 14 0.58
22 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAATTATATAAAAATATATA
Found at i:6287991 original size:18 final size:19
Alignment explanation
Indices: 6287970--6288014 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
6287960 TTTCTATCAC
6287970 TTTTATATT-TTTATTTAT
1 TTTTATATTATTTATTTAT
6287988 TTTTA-ATTATTTATTTAT
1 TTTTATATTATTTATTTAT
6288006 TTTT-TATTA
1 TTTTATATTA
6288015 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATATTATTTATTTAT
Found at i:6296490 original size:74 final size:75
Alignment explanation
Indices: 6296412--6296567 Score: 194
Period size: 74 Copynumber: 2.1 Consensus size: 75
6296402 AACCTATACG
* *
6296412 TATAAATA-TGTATTTATTAAATAATAAT-TATTAAAATATTTTTTATTATAATTATGAGTAAGA
1 TATAAATAGTGTATTCATCAAATAATAATCT-TTAAAATATTTTTTATTATAATTATGAGTAAGA
6296475 TTTATACCTA-T
65 TTTAT-CCTATT
* * * * *
6296486 TATAAA-AGTGTATTCATCAAATGATGATCTTTGAAATATTTTTTATTATAATTTTTAGTAAGAT
1 TATAAATAGTGTATTCATCAAATAATAATCTTTAAAATATTTTTTATTATAATTATGAGTAAGAT
*
6296550 TTATTCTATT
66 TTATCCTATT
6296560 TATAAATA
1 TATAAATA
6296568 AAAAATTTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
73 4 0.06
74 64 0.91
75 2 0.03
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (75 bp):
TATAAATAGTGTATTCATCAAATAATAATCTTTAAAATATTTTTTATTATAATTATGAGTAAGAT
TTATCCTATT
Found at i:6296626 original size:18 final size:19
Alignment explanation
Indices: 6296599--6296640 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
6296589 AATTTCATTA
*
6296599 AAATAATATT-TTTAATTT
1 AAATAATATTGTATAATTT
* *
6296617 TAATAGTATTGTATAATTT
1 AAATAATATTGTATAATTT
6296636 AAATA
1 AAATA
6296641 TTAATATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
AAATAATATTGTATAATTT
Found at i:6296676 original size:35 final size:35
Alignment explanation
Indices: 6296634--6296717 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
6296624 ATTGTATAAT
* *
6296634 TTAAATATTAATATTTTAA-ATTAATTATTTTAAAG
1 TTAAATATTAATATTATAATATTAAGTATTTT-AAG
* *
6296669 TTAAATATTAATA-TATAATTTTTAGTATTTTAAG
1 TTAAATATTAATATTATAATATTAAGTATTTTAAG
*
6296703 TTAAATATCAATATT
1 TTAAATATTAATATT
6296718 CATCAAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 19 0.45
35 23 0.55
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (35 bp):
TTAAATATTAATATTATAATATTAAGTATTTTAAG
Found at i:6299551 original size:21 final size:22
Alignment explanation
Indices: 6299509--6299552 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
6299499 TATAATTTTA
*
6299509 TTTTATTTAAAAAGTAATTAAT
1 TTTTATTTAAAAAGTAAATAAT
* *
6299531 TTTTATTT-TAAATTAAATAAT
1 TTTTATTTAAAAAGTAAATAAT
6299552 T
1 T
6299553 GATTTGATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTATTTAAAAAGTAAATAAT
Found at i:6300332 original size:27 final size:27
Alignment explanation
Indices: 6300302--6300359 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
6300292 GGAGGGAAAT
*
6300302 CCCTACATGGGTCTTGGTGGGCTGGCA
1 CCCTACATGGGTCTTGGAGGGCTGGCA
*
6300329 CCCTATATGGGTCTTGGAGGGCTGGCA
1 CCCTACATGGGTCTTGGAGGGCTGGCA
6300356 CCCT
1 CCCT
6300360 CTTGGGCCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.12, C:0.28, G:0.34, T:0.26
Consensus pattern (27 bp):
CCCTACATGGGTCTTGGAGGGCTGGCA
Found at i:6326499 original size:18 final size:17
Alignment explanation
Indices: 6326458--6326511 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
6326448 ATGATGAAAG
6326458 AAAGAA-GATAAAAAAA
1 AAAGAATGATAAAAAAA
*
6326474 AAAGAATGATAACAAAA
1 AAAGAATGATAAAAAAA
*
6326491 AATGAAATGA-AAATAAAA
1 AAAG-AATGATAAA-AAAA
6326509 AAA
1 AAA
6326512 ACCAAAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 6 0.19
17 14 0.45
18 11 0.35
ACGTcount: A:0.76, C:0.02, G:0.11, T:0.11
Consensus pattern (17 bp):
AAAGAATGATAAAAAAA
Found at i:6326506 original size:21 final size:19
Alignment explanation
Indices: 6326482--6326529 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
6326472 AAAAAGAATG
**
6326482 ATAACAAAAAATGAAATGAAA
1 ATAACAAAAAACCAAA-G-AA
6326503 ATAA-AAAAAACCAAAGAA
1 ATAACAAAAAACCAAAGAA
6326521 ATAACAAAA
1 ATAACAAAA
6326530 CGAAAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.25
19 5 0.21
20 9 0.38
21 4 0.17
ACGTcount: A:0.75, C:0.08, G:0.06, T:0.10
Consensus pattern (19 bp):
ATAACAAAAAACCAAAGAA
Found at i:6326555 original size:14 final size:14
Alignment explanation
Indices: 6326532--6326582 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
6326522 TAACAAAACG
6326532 AAAA-AGAAAAGAA
1 AAAAGAGAAAAGAA
*
6326545 AAAAGAGAAAAGAG
1 AAAAGAGAAAAGAA
6326559 AAAAGAGCAAAGAAGAA
1 AAAAGAG--AA-AAGAA
6326576 AAAAGAG
1 AAAAGAG
6326583 GACCAAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 4 0.12
14 15 0.47
16 2 0.06
17 11 0.34
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAAGAGAAAAGAA
Found at i:6326562 original size:21 final size:23
Alignment explanation
Indices: 6326531--6326582 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
6326521 ATAACAAAAC
6326531 GAAAA-AGAAAAGA-AAA-AAGA
1 GAAAAGAGAAAAGACAAAGAAGA
6326551 GAAAAGAGAAAAGAGCAAAGAAGA
1 GAAAAGAGAAAAGA-CAAAGAAGA
*
6326575 AAAAAGAG
1 GAAAAGAG
6326583 GACCAAAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 5 0.19
21 8 0.30
23 3 0.11
24 11 0.41
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (23 bp):
GAAAAGAGAAAAGACAAAGAAGA
Found at i:6326654 original size:19 final size:19
Alignment explanation
Indices: 6326616--6326654 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6326606 AAATGATGTT
*
6326616 AAAAAGAAAAAAAAATAGG
1 AAAAAGAAAAAAAAAGAGG
*
6326635 AAAAAGAAAAAGAAAGAGG
1 AAAAAGAAAAAAAAAGAGG
6326654 A
1 A
6326655 GATTCAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAAAAAAGAGG
Found at i:6328409 original size:5 final size:6
Alignment explanation
Indices: 6328393--6328419 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6328383 GGAAAAAAGG
6328393 GAAAAA GAAAAA GAAAAA GAAAAA GAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAA
6328420 CTGAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:6329920 original size:2 final size:2
Alignment explanation
Indices: 6329913--6329941 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6329903 GAGGGACCAG
6329913 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
6329942 TGAGATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6330396 original size:13 final size:14
Alignment explanation
Indices: 6330373--6330403 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
6330363 AAATAAGTAG
6330373 CTAAGATCCTAAGC
1 CTAAGATCCTAAGC
6330387 CTAA-ATCCTAAGC
1 CTAAGATCCTAAGC
6330400 CTAA
1 CTAA
6330404 TAACAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.23
Consensus pattern (14 bp):
CTAAGATCCTAAGC
Found at i:6333319 original size:18 final size:19
Alignment explanation
Indices: 6333296--6333342 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
6333286 TTTTAGACTT
6333296 CTTTAACTAGCTACTT-TC
1 CTTTAACTAGCTACTTCTC
* * *
6333314 CTTTAATTAGTTAGTTCTC
1 CTTTAACTAGCTACTTCTC
6333333 CTTTTAACTA
1 C-TTTAACTA
6333343 ATTGGGCCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 13 0.57
19 3 0.13
20 7 0.30
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.49
Consensus pattern (19 bp):
CTTTAACTAGCTACTTCTC
Found at i:6338502 original size:29 final size:27
Alignment explanation
Indices: 6338446--6338502 Score: 62
Period size: 29 Copynumber: 2.0 Consensus size: 27
6338436 TCAAATTAAT
* *
6338446 TATATATAATAGCATATTATTCTTTTA
1 TATATATAATAGAATATTATTCTATTA
6338473 TATATATATATATGAATATTATAT-TATTA
1 TATATATA-ATA-GAATATTAT-TCTATTA
6338502 T
1 T
6338503 TATCAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 8 0.32
28 3 0.12
29 13 0.52
30 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (27 bp):
TATATATAATAGAATATTATTCTATTA
Found at i:6338768 original size:20 final size:20
Alignment explanation
Indices: 6338743--6338780 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6338733 GTGAAACAAT
6338743 TTATA-TATGTATATATTAAA
1 TTATATTATGT-TATATTAAA
6338763 TTATATTATGTTATATTA
1 TTATATTATGTTATATTA
6338781 TATTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTATATTATGTTATATTAAA
Found at i:6351126 original size:15 final size:15
Alignment explanation
Indices: 6351106--6351135 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6351096 TTAAGATTAT
6351106 CTCCAAAACCAAACA
1 CTCCAAAACCAAACA
6351121 CTCCAAAACCAAACA
1 CTCCAAAACCAAACA
6351136 AAAAGGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.40, G:0.00, T:0.07
Consensus pattern (15 bp):
CTCCAAAACCAAACA
Found at i:6354685 original size:209 final size:214
Alignment explanation
Indices: 6354316--6354709 Score: 600
Period size: 209 Copynumber: 1.9 Consensus size: 214
6354306 ATTTTAAACA
* *
6354316 TGCTGAAGCATAGTATTATTCTCCTCTCTTATGCTTCAAACGCCATACATGAATAGTGTTAATTG
1 TGCTGAAGCATAGTATTATTCGCCTCTCTTATGCTTCAAACGCCATACATGAATA--G-TAACTG
* * *
6354381 GTAAACCACTGTTAATATGAAAGTGATTGTGTTATCTAACTGAAAACTAAATGAACACAATAAAC
63 GTAAACCACTGTTAATATGAAAGTGATTATGTTACCTAACTGAAAACTAAATGAACACAATAAAA
* *
6354446 CAAGTTTAGGACTTGGGAAGAATTTTTTCCACATGTACCCCAAGTTG-AAATGCTTCTATAATTG
128 CAAGCTTAGGACTTGGGAAGAATGTTTTCCACATGTACCCCAAGTTGAAAATGCTTCTATAATTG
6354510 AAAAATTCTTGGAGTATGCTTT
193 AAAAATTCTTGGAGTATGCTTT
* *
6354532 TGCTGAAGCATAGTATTATTCGCCTTTCTTATGCTTCAAACGCTATACATG-A-A-T-ACTGGTA
1 TGCTGAAGCATAGTATTATTCGCCTCTCTTATGCTTCAAACGCCATACATGAATAGTAACTGGTA
* * *
6354593 AACCACTGTTAGTATGAAAGTGATTATGTTACCTAACTGAAAACTTAATGAACACGATAAAACAA
66 AACCACTGTTAATATGAAAGTGATTATGTTACCTAACTGAAAACTAAATGAACACAATAAAACAA
* *
6354658 GCTTATGACTTGGGAAGAATGTTTTCCACATGTAGCCCAAGTTGAAAATGCT
131 GCTTAGGACTTGGGAAGAATGTTTTCCACATGTACCCCAAGTTGAAAATGCT
6354710 GTTCTGAAAT
Statistics
Matches: 163, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
209 105 0.64
210 8 0.05
214 1 0.01
215 1 0.01
216 48 0.29
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (214 bp):
TGCTGAAGCATAGTATTATTCGCCTCTCTTATGCTTCAAACGCCATACATGAATAGTAACTGGTA
AACCACTGTTAATATGAAAGTGATTATGTTACCTAACTGAAAACTAAATGAACACAATAAAACAA
GCTTAGGACTTGGGAAGAATGTTTTCCACATGTACCCCAAGTTGAAAATGCTTCTATAATTGAAA
AATTCTTGGAGTATGCTTT
Found at i:6355427 original size:14 final size:14
Alignment explanation
Indices: 6355408--6355435 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6355398 TTGCCGGCAA
6355408 GGGCTCCAGCTACC
1 GGGCTCCAGCTACC
6355422 GGGCTCCAGCTACC
1 GGGCTCCAGCTACC
6355436 AGTCTGCCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (14 bp):
GGGCTCCAGCTACC
Found at i:6357247 original size:17 final size:17
Alignment explanation
Indices: 6357227--6357262 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
6357217 ATCAAATTTA
6357227 CTACAAAAAAAAATTAG
1 CTACAAAAAAAAATTAG
*
6357244 CTACAAAAAAATATTAG
1 CTACAAAAAAAAATTAG
6357261 CT
1 CT
6357263 TATAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (17 bp):
CTACAAAAAAAAATTAG
Found at i:6360606 original size:3 final size:3
Alignment explanation
Indices: 6360598--6360626 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6360588 AGTTTAATGC
6360598 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
6360627 ATGTAACTAA
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:6381208 original size:20 final size:20
Alignment explanation
Indices: 6381185--6381224 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6381175 AAGGTATCTT
6381185 CTAATTTTATTCTTATGTGA
1 CTAATTTTATTCTTATGTGA
*
6381205 CTAATTTTCTTCTTATGTGA
1 CTAATTTTATTCTTATGTGA
6381225 TTTTATTCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.12, G:0.10, T:0.55
Consensus pattern (20 bp):
CTAATTTTATTCTTATGTGA
Found at i:6384134 original size:24 final size:24
Alignment explanation
Indices: 6384089--6384134 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6384079 ATGCCATTGT
**
6384089 ATCTTTAACCATTTTAGTCCATGG
1 ATCTTTAACCATTTTAACCCATGG
*
6384113 ATCTTTAACTATTTTAACCCAT
1 ATCTTTAACCATTTTAACCCAT
6384135 TGAAATTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (24 bp):
ATCTTTAACCATTTTAACCCATGG
Found at i:6408244 original size:25 final size:25
Alignment explanation
Indices: 6408216--6408265 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
6408206 TAAATTGTTA
*
6408216 TAATT-AACTATTGATTAATTATTTT
1 TAATTAAAATATT-ATTAATTATTTT
*
6408241 TAATTAAAATATTATTTATTATTTT
1 TAATTAAAATATTATTAATTATTTT
6408266 ATATCTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TAATTAAAATATTATTAATTATTTT
Found at i:6414105 original size:25 final size:25
Alignment explanation
Indices: 6414066--6414130 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
6414056 TAGTTATAGG
* *
6414066 GTAATTGATAAATGTAATTAAAAGA
1 GTAATTGACAGATGTAATTAAAAGA
*
6414091 GTAATTGACAGATGTAATTAAAGGA
1 GTAATTGACAGATGTAATTAAAAGA
*
6414116 ATAATTGACAGATGT
1 GTAATTGACAGATGT
6414131 TAAATTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (25 bp):
GTAATTGACAGATGTAATTAAAAGA
Found at i:6418061 original size:18 final size:18
Alignment explanation
Indices: 6418027--6418061 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6418017 AATGTGCATG
*
6418027 TTGTTGATGGTACTATAA
1 TTGTTGATGATACTATAA
*
6418045 TTGTTGATGATATTATA
1 TTGTTGATGATACTATA
6418062 GACGTAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.49
Consensus pattern (18 bp):
TTGTTGATGATACTATAA
Found at i:6418093 original size:18 final size:18
Alignment explanation
Indices: 6418070--6418125 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
6418060 TAGACGTAAA
6418070 TGCTAATGTAAATGTTGT
1 TGCTAATGTAAATGTTGT
* *
6418088 TGCTAAAGTAAATG-TGAA
1 TGCTAATGTAAATGTTG-T
*
6418106 TGCTAATGTAAATATTGT
1 TGCTAATGTAAATGTTGT
6418124 TG
1 TG
6418126 ATAAAATGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 2 0.06
18 27 0.87
19 2 0.06
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (18 bp):
TGCTAATGTAAATGTTGT
Found at i:6419056 original size:362 final size:362
Alignment explanation
Indices: 6418383--6419098 Score: 944
Period size: 362 Copynumber: 2.0 Consensus size: 362
6418373 AGCCCATCTC
* * * * *
6418383 AAGGCAATTCTCTCTTCAGGAAGATAATGATGTTGATGGGTTATCTAATATTGGTAGTGATGTAA
1 AAGGAAATTCTCTATTCAGGAAGATAATGATATTAATGGGCTATCTAATATTGGTAGTGATGTAA
* *
6418448 ATAAGGAAAATCAAGCAAGCTCTAACTTTGATAGGAAAGATAGAGCTATTAATAGGTCAATGAGA
66 ATAAGGAAAATCAAGCAAGCTCTAACTTTGATAAGAAAGATAGAGCTATTAATAGGTCAATCAGA
* * * *
6418513 GGCATCATTTACACACTTGATGAGTGTCGGAAGGTAAGGCTTGCTGAAAACATGTTATTTAATAG
131 GGCATCACTTACACACTTGATAAGTGTCGGAAGGTAAGGCTTGCTAAAAACATGTTATTTAACAG
** * ** * *
6418578 TGTGCGGCACTTTAGGGAGGTGATGATAGATTACATAATTTAAGAAATGATTGAGTTATAGAGGG
196 TGTGCAACACTTTAAGGAAATGATGATAGATTACATAATTCAAGAAAAGATTGAGTTATAGAGGG
* * *
6418643 CTAAGAATGAAAAGACAAGGCATAGGGCATACTGTAAGGGGAATAAGTGTGAATGGATGGTTCAT
261 CTAAGAATGAAAAAACAAGACAAAGGGCATACTGTAAGGGGAATAAGTGTGAATGGATGGTTCAT
*
6418708 GCATCCCTTCGTTTGGATATGAAGACTTTTAAGTCTT
326 ACATCCCTTCGTTTGGATATGAAGACTTTTAAGTCTT
*
6418745 AAGGAAATTCTCTATTGAGGAAGATAATGATATTAATGGGCTATCTAATATTGGTAGTGACATGT
1 AAGGAAATTCTCTATTCAGGAAGATAATGATATTAATGGGCTATCTAATATTGGTAGTG--ATGT
* * * *
6418810 -AA-GAGGGAAATCAAGTAAGCTCTAACTTTGATAAGAAATG-TAGAGTTATTAATAGGTCAATC
64 AAATAAGGAAAATCAAGCAAGCTCTAACTTTGATAAGAAA-GATAGAGCTATTAATAGGTCAATC
* ** * * *
6418872 AGAGGCATCCCTTACTTAC-TGAATAAGTGTGGGAAGGTGAGGCTTG-TCAAAAACATGTTGTTT
128 AGAGGCATCACTTACACACTTG-ATAAGTGTCGGAAGGTAAGGCTTGCT-AAAAACATGTTATTT
*
6418935 AGCAGTGCT-CAACACTTTAAGGAAATGATGATAGATTACATAATTC-AGAAAAAGATTGAGTTA
191 AACAGTG-TGCAACACTTTAAGGAAATGATGATAGATTACATAATTCAAG-AAAAGATTGAGTTA
* * *
6418998 T-GTAGGGCTAAGAATGAAAAAACAAGACAAAGGGTATATTGTAAGGGGAATGAGTGTGAATGGA
254 TAG-AGGGCTAAGAATGAAAAAACAAGACAAAGGGCATACTGTAAGGGGAATAAGTGTGAATGGA
* * *
6419062 TGGTTCATATATCCCTTTGTTTGTATATGAAGACTTT
318 TGGTTCATACATCCCTTCGTTTGGATATGAAGACTTT
6419099 AAAGATTAAA
Statistics
Matches: 306, Mismatches: 40, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
361 6 0.02
362 292 0.95
363 4 0.01
364 4 0.01
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (362 bp):
AAGGAAATTCTCTATTCAGGAAGATAATGATATTAATGGGCTATCTAATATTGGTAGTGATGTAA
ATAAGGAAAATCAAGCAAGCTCTAACTTTGATAAGAAAGATAGAGCTATTAATAGGTCAATCAGA
GGCATCACTTACACACTTGATAAGTGTCGGAAGGTAAGGCTTGCTAAAAACATGTTATTTAACAG
TGTGCAACACTTTAAGGAAATGATGATAGATTACATAATTCAAGAAAAGATTGAGTTATAGAGGG
CTAAGAATGAAAAAACAAGACAAAGGGCATACTGTAAGGGGAATAAGTGTGAATGGATGGTTCAT
ACATCCCTTCGTTTGGATATGAAGACTTTTAAGTCTT
Found at i:6427919 original size:2 final size:2
Alignment explanation
Indices: 6427912--6427947 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6427902 TCTAAGCAAC
6427912 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6427948 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6429253 original size:2 final size:2
Alignment explanation
Indices: 6429248--6429275 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6429238 TATATATATA
6429248 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
6429276 AGTGGTAGAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:6440750 original size:2 final size:2
Alignment explanation
Indices: 6440743--6440786 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
6440733 TATCCTCTCC
6440743 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
6440785 AT
1 AT
6440787 GAATTAAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6441323 original size:2 final size:2
Alignment explanation
Indices: 6441316--6441343 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6441306 AATTGATGAA
6441316 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
6441344 TTCCATTTGA
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:6445830 original size:19 final size:18
Alignment explanation
Indices: 6445784--6445840 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 18
6445774 CCTTACGCTC
**
6445784 TTTTTTAAAAAATTTTAT
1 TTTTTTAAAAAAAGTTAT
* *
6445802 TCTTTAAAAAAAAGTTACT
1 TTTTTTAAAAAAAGTTA-T
6445821 TTTTTTAAAAAAAGTT-T
1 TTTTTTAAAAAAAGTTAT
6445838 TTT
1 TTT
6445841 AAAATTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 4 0.12
18 13 0.41
19 15 0.47
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (18 bp):
TTTTTTAAAAAAAGTTAT
Found at i:6446283 original size:2 final size:2
Alignment explanation
Indices: 6446270--6446304 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6446260 TCTAAACTCA
*
6446270 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6446305 ATAGCAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6457257 original size:4 final size:4
Alignment explanation
Indices: 6457250--6457274 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6457240 AGACAGACAG
6457250 ACAA ACAA ACAA ACAA ACAA ACAA A
1 ACAA ACAA ACAA ACAA ACAA ACAA A
6457275 AACAACCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:6474336 original size:15 final size:15
Alignment explanation
Indices: 6474316--6474348 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6474306 GGCTGGAGAT
6474316 AACCTATAATTAAAG
1 AACCTATAATTAAAG
6474331 AACCTATAATTAAAG
1 AACCTATAATTAAAG
6474346 AAC
1 AAC
6474349 TAAAAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (15 bp):
AACCTATAATTAAAG
Found at i:6487586 original size:21 final size:21
Alignment explanation
Indices: 6487529--6487588 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
6487519 TCTCTGAAAT
*
6487529 TAAAGTTGCTTCC-TTGACTG
1 TAAAGTTGCTTCCTTTGAATG
*
6487549 TAAAAGTTGCGTCCTTTGAATG
1 T-AAAGTTGCTTCCTTTGAATG
*
6487571 TAAAGTTACTTCCTTTGA
1 TAAAGTTGCTTCCTTTGA
6487589 GTTTGGGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.03
21 26 0.76
22 7 0.21
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (21 bp):
TAAAGTTGCTTCCTTTGAATG
Found at i:6494127 original size:16 final size:16
Alignment explanation
Indices: 6494100--6494143 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
6494090 AATCGATTAA
*
6494100 CAAATT-ATATAAACT
1 CAAATTAATATAAAAT
6494115 CAAATTAATATAAAAT
1 CAAATTAATATAAAAT
*
6494131 TAAATTAAATATA
1 CAAATT-AATATA
6494144 CACACGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 6 0.24
16 13 0.52
17 6 0.24
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (16 bp):
CAAATTAATATAAAAT
Found at i:6500995 original size:31 final size:29
Alignment explanation
Indices: 6500953--6501016 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
6500943 ATTTTCTATC
*
6500953 TTAATCTTTAATTATAAAAAATTAAAAATAT
1 TTAATCATTAATTAT-AAAAATT-AAAATAT
* *
6500984 TTAATCATTAATTATTATAATTAAAATAT
1 TTAATCATTAATTATAAAAATTAAAATAT
6501013 TTAA
1 TTAA
6501017 CGTTTAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 11 0.37
30 5 0.17
31 14 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAATCATTAATTATAAAAATTAAAATAT
Found at i:6531171 original size:28 final size:28
Alignment explanation
Indices: 6531135--6531192 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
6531125 TTTGCATTGA
*
6531135 AGAATGATGATTTGTAAAAATAGAGAAG
1 AGAATGATGATTTGTAAAAACAGAGAAG
6531163 AGAATGATGATTTGTAAAAACAGAGAAG
1 AGAATGATGATTTGTAAAAACAGAGAAG
6531191 AG
1 AG
6531193 GGAGATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.50, C:0.02, G:0.26, T:0.22
Consensus pattern (28 bp):
AGAATGATGATTTGTAAAAACAGAGAAG
Found at i:6534456 original size:286 final size:284
Alignment explanation
Indices: 6533890--6534461 Score: 982
Period size: 284 Copynumber: 2.0 Consensus size: 284
6533880 TTTTTCATTT
*
6533890 TAAAATTTTTTTCTTGAAAAAAAGAACCTTCCAAGCTAGATATGGCCGACATTGGCATTATCCGA
1 TAAAATTTTTTTCTTGAAAAAAAAAACCTTCCAAGCTAGATATGGCCGACATTGGCATTATCCGA
*
6533955 CTAGATATGAACGGATCTGGCTGCGCTTCCCTGAGGGACCCTGAAAATGGCACTCCCTAAGGACG
66 CTAGATATGAACGGATCTGGCTGCGCTTCCCTGAGGGACCCTGAAAATGACACTCCCTAAGGACG
*
6534020 TGCGAATCTAGCTGGACGCCACATTCAGCTATATCTAGCTTGAAGGGAAAGTTTTTTTTTTTAAG
131 TGCGAATCTAGCTGGACGCCACATTCAGCTATATCTAGCTTGAAAGGAAAGTTTTTTTTTTTAAG
* * * **
6534085 AACAAAAATTTTAAATGCAAAATAAAAATGTATATAGTATTATAATTTTTGACTTGGTCGAGGTT
196 AACAAAAATTTTAAATGCAAAATAAAAATGCATATAGTATTATAATTTTTGACATAGTCGAAATT
6534150 AAAATTATTCAAAAATTATTACCA
261 AAAATTATTCAAAAATTATTACCA
*
6534174 TAAAATTTTTTTCTTGAAAAAAAAAACCTTCCAAGCTAGATTTGGCCGACATTGGCATTATCCGA
1 TAAAATTTTTTTCTTGAAAAAAAAAACCTTCCAAGCTAGATATGGCCGACATTGGCATTATCCGA
* *
6534239 CTAGATCTGAACGGATCTGGCTGCGCTTCCCTGAGGGACCGTGAAAATGACACTCCCTAAGGACG
66 CTAGATATGAACGGATCTGGCTGCGCTTCCCTGAGGGACCCTGAAAATGACACTCCCTAAGGACG
*
6534304 TGCGAATCTAGCTGGACGCCACATTCAGCTGTATCTAGCTTGAAAGGAAAGTTTTTTTTTTTTTA
131 TGCGAATCTAGCTGGACGCCACATTCAGCTATATCTAGCTTGAAAGGAAAG--TTTTTTTTTTTA
* * *
6534369 AGAATAAAAATTTTAAATGCAAAATAAAAGTGCATATAGTATTATAATTTTTGACATATTCGAAA
194 AGAACAAAAATTTTAAATGCAAAATAAAAATGCATATAGTATTATAATTTTTGACATAGTCGAAA
*
6534434 TTAAAATTATTTAAAAATTATTACCA
259 TTAAAATTATTCAAAAATTATTACCA
6534460 TA
1 TA
6534462 TTAAGAAATT
Statistics
Matches: 270, Mismatches: 16, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
284 174 0.64
286 96 0.36
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (284 bp):
TAAAATTTTTTTCTTGAAAAAAAAAACCTTCCAAGCTAGATATGGCCGACATTGGCATTATCCGA
CTAGATATGAACGGATCTGGCTGCGCTTCCCTGAGGGACCCTGAAAATGACACTCCCTAAGGACG
TGCGAATCTAGCTGGACGCCACATTCAGCTATATCTAGCTTGAAAGGAAAGTTTTTTTTTTTAAG
AACAAAAATTTTAAATGCAAAATAAAAATGCATATAGTATTATAATTTTTGACATAGTCGAAATT
AAAATTATTCAAAAATTATTACCA
Found at i:6535886 original size:252 final size:250
Alignment explanation
Indices: 6535401--6536370 Score: 1078
Period size: 252 Copynumber: 3.9 Consensus size: 250
6535391 TACCTAAATA
* ** * * * * *
6535401 AATTAACGTAAAAAATTATAAAGGTTGATCAAATATTATCAAAATATTAACATAAATATATGAGA
1 AATTAACATAAAAAATTATAAAAATGGAACAAACATTGTCAAAATATTAACATAAACATATGAGA
* * *
6535466 TTTAACATAACAAGTCAATTATATTAAATAAACATAATTTTTTAAAAAATTAAACTTTTAAATTT
66 TTTAACATAACAAGTAAATTATATCAAATAAACATAATTTTTTAAAAAATTAAACATTTAAATTT
* * * * *
6535531 ATATTCTTAAGTTTAAAGTATTTAATGGTTTATAAATTTTAATTTATAAATGAATAACAGTAAGG
131 ATATTCTTGAGTTTAAAATATTTAATGATTTATAAATTTTAATTTATAAATAAATAATAGTAAGG
* * * *
6535596 ATAAAAATAATCATTGTGAAAATTAGGAATTAAAAAACCTTAACATAAACTTATAAG
196 ATAAAAA-AATTATAGTGAAAATTAGCAATTAAAAAACCTT-ACGTAAACTTATAAG
* ** ** ** ****
6535653 AATTAACATAAGAAATTATAATGATGGAACAAGTATTGTCAAAATATTAATGTAAATGCGTGAGA
1 AATTAACATAAAAAATTATAAAAATGGAACAAACATTGTCAAAATATTAACATAAACATATGAGA
** * * * *
6535718 TTTAATGTAACAAGTAAATTATGTCAAATAAACACAAGTTTTCTGAAAAATTAAACATTTAAATT
66 TTTAACATAACAAGTAAATTATATCAAATAAACATAA-TTTTTTAAAAAATTAAACATTTAAATT
* * *
6535783 TATACTCTTGAGTTTAAAATATTTAACGATTTATAAATTTTAATTTACAAATAAATAATAGTAAG
130 TATATTCTTGAGTTTAAAATATTTAATGATTTATAAATTTTAATTTATAAATAAATAATAGTAAG
* * *
6535848 GATAAAAAAATTATAGTGAAAATTAGTAATTGAAAAACCTCTACGTAAAAC-AATAAG
195 GATAAAAAAATTATAGTGAAAATTAGCAATTAAAAAACCT-TACGT-AAACTTATAAG
* * * * * *
6535905 AATTGATATAAAAAATTATAAAAA-GAGAACAAGCATTGTTAAAATATTGACATAAACATGTGAG
1 AATTAACATAAAAAATTATAAAAATG-GAACAAACATTGTCAAAATATTAACATAAACATATGAG
* *
6535969 ATTTAACATAACAAAG-AAATTA-AGTAAAAATAAATATAATTTTTTAAAAAATTAAACATTTAA
65 ATTTAACATAAC-AAGTAAATTATA-T-CAAATAAACATAATTTTTTAAAAAATTAAACATTTAA
* * * * * *
6536032 ATTTATGTTCTTGAGTTTAAAGTATTTAAT-AGTTTATAAATGTTAATTTATAAATGATTAATAA
127 ATTTATATTCTTGAGTTTAAAATATTTAATGA-TTTATAAATTTTAATTTATAAATAAATAATAG
* * * * * *
6536096 TAAGGGTAAAAAAATTATAATGAAAATTAGCAGTTAAAAAACATTGACGTAAAATTTTAATG
191 TAAGGATAAAAAAATTATAGTGAAAATTAGCAATTAAAAAACCTT-ACGTAAACTTATAA-G
* * * *
6536158 -ATTAACGTACAAAAATTATAAAAATGGAACAAACATTTTCAAAATGTTAACATAAACGTATGAG
1 AATTAACATA-AAAAATTATAAAAATGGAACAAACATTGTCAAAATATTAACATAAACATATGAG
* * * * * *
6536222 ATTTAACGTAATAAGTCAATTATATCAAATAAATATAATTTTTTAAACAATT-AATATTTAAATT
65 ATTTAACATAACAAGTAAATTATATCAAATAAACATAATTTTTTAAAAAATTAAACATTTAAATT
*
6536286 TATATTCTTGAGTTTAAAATATTTAATAATTTATAAATTTTAATTTATAAATAAAT-A-A-TAAG
130 TATATTCTTGAGTTTAAAATATTTAATGATTTATAAATTTTAATTTATAAATAAATAATAGTAAG
*
6536348 GATAAAAAAATTATAGTTAAAAT
195 GATAAAAAAATTATAGTGAAAAT
6536371 AATTATTTAT
Statistics
Matches: 603, Mismatches: 99, Indels: 36
0.82 0.13 0.05
Matches are distributed among these distances:
248 24 0.04
249 1 0.00
250 1 0.00
251 66 0.11
252 340 0.56
253 169 0.28
254 2 0.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (250 bp):
AATTAACATAAAAAATTATAAAAATGGAACAAACATTGTCAAAATATTAACATAAACATATGAGA
TTTAACATAACAAGTAAATTATATCAAATAAACATAATTTTTTAAAAAATTAAACATTTAAATTT
ATATTCTTGAGTTTAAAATATTTAATGATTTATAAATTTTAATTTATAAATAAATAATAGTAAGG
ATAAAAAAATTATAGTGAAAATTAGCAATTAAAAAACCTTACGTAAACTTATAAG
Found at i:6536083 original size:14 final size:15
Alignment explanation
Indices: 6536064--6536093 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6536054 TATTTAATAG
6536064 TTTATAAATG-TTAA
1 TTTATAAATGATTAA
6536078 TTTATAAATGATTAA
1 TTTATAAATGATTAA
6536093 T
1 T
6536094 AATAAGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
TTTATAAATGATTAA
Found at i:6536644 original size:203 final size:202
Alignment explanation
Indices: 6536296--6536888 Score: 765
Period size: 203 Copynumber: 3.0 Consensus size: 202
6536286 TATATTCTTG
* * * *
6536296 AGTTTAAAATATTTAATAATTTATAAATTTTAATTTATAAAT--A-AATAATAAGGATAAAAA-A
1 AGTTTAAAGTATTTAATAGTATATAAATTTTAATTTATAAATGAATAATAATAAAGATAAAAATA
* * * *
6536357 ATTATAGTTAAAATAATTATTTATTAAACTAAAATTTTAATACAATAGTTATTTCAAAATTTCTC
66 ATTATAGTTAAAATAATTATTTATTAAA-TAAATTTTTATTATAATAGTTATTTAAAAATTTCTC
* * * * *
6536422 AATGGTTAATATGTTTTAC-TCAAAATATAAATTTAAATGATTAATTTTAATAAAAATTCTGTTA
130 AATGGTTAATATTTTTTACTTGAGAATATAAATGTAAATGATTAATTTT-ATAAAAATTCTATTA
6536486 ATATACTCA
194 ATATACTCA
* * * *
6536495 AGTTTAAAGTTTTTAATGGT-TCGTAAATTTTAATTTATAAATGAATAATAATAAAAATAAAAAT
1 AGTTTAAAGTATTTAATAGTAT-ATAAATTTTAATTTATAAATGAATAATAATAAAGATAAAAAT
* * *
6536559 AATTATAGTTAAAATACTTATTTCTTAAATTAAATTTTTATTATAATAGTTACTTAAAAATTTCT
65 AATTATAGTTAAAATAATTATTTATTAAA-TAAATTTTTATTATAATAGTTATTTAAAAATTTCT
* *
6536624 CAACGGTTAATATTTTTTACTTGAGAATTTAAATGTAAATGATTAATTTTATAAAAATTCTATTA
129 CAATGGTTAATATTTTTTACTTGAGAATATAAATGTAAATGATTAATTTTATAAAAATTCTATTA
** *
6536689 ATATGTTCG
194 ATATACTCA
* * *
6536698 AGTTTAAAGTATTTAATAGTATATAAATTTTAATTTACACATGAATAATAATGAAGATAAAAATA
1 AGTTTAAAGTATTTAATAGTATATAAATTTTAATTTATAAATGAATAATAATAAAGATAAAAATA
* * *
6536763 CTTATAG-TAAAAGTAATTATTTATTAAAT---TTTTTATTATAATATTTATTTAAAAATTTCTT
66 ATTATAGTTAAAA-TAATTATTTATTAAATAAATTTTTATTATAATAGTTATTTAAAAATTTCTC
* *
6536824 AATGGTTACTATTTTTTACTTGAGAATATAAAAGTAAATGATTAATTTTTATAAAAATTCTATTA
130 AATGGTTAATATTTTTTACTTGAGAATATAAATGTAAATGATTAA-TTTTATAAAAATTCTATTA
6536889 TTCTCTTTAT
Statistics
Matches: 343, Mismatches: 42, Indels: 17
0.85 0.10 0.04
Matches are distributed among these distances:
198 1 0.00
199 105 0.31
200 19 0.06
201 1 0.00
202 21 0.06
203 170 0.50
204 26 0.08
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (202 bp):
AGTTTAAAGTATTTAATAGTATATAAATTTTAATTTATAAATGAATAATAATAAAGATAAAAATA
ATTATAGTTAAAATAATTATTTATTAAATAAATTTTTATTATAATAGTTATTTAAAAATTTCTCA
ATGGTTAATATTTTTTACTTGAGAATATAAATGTAAATGATTAATTTTATAAAAATTCTATTAAT
ATACTCA
Found at i:6551295 original size:1 final size:1
Alignment explanation
Indices: 6551289--6551318 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
6551279 GTGGCCCGGA
6551289 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
6551319 TGTTGTGCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:6554990 original size:28 final size:29
Alignment explanation
Indices: 6554944--6554998 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
6554934 ATTAATTTAA
6554944 AATAAAAATATAAAAATTTAATTAAATAT
1 AATAAAAATATAAAAATTTAATTAAATAT
** *
6554973 AATAAAAA-ATAATTATTTATTTAAAT
1 AATAAAAATATAAAAATTTAATTAAAT
6554999 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AATAAAAATATAAAAATTTAATTAAATAT
Found at i:6560503 original size:2 final size:2
Alignment explanation
Indices: 6560496--6560521 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6560486 ATATAAATCT
6560496 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6560522 GTATTGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6573210 original size:3 final size:3
Alignment explanation
Indices: 6573202--6573277 Score: 143
Period size: 3 Copynumber: 25.3 Consensus size: 3
6573192 CAACACAAAT
6573202 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
*
6573250 TTA TTA TTA TTA TTA TTA TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6573278 GGTTTTGTGG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6573964 original size:27 final size:27
Alignment explanation
Indices: 6573933--6573988 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
6573923 TATTTTATAT
6573933 TAATATTAT-A-TAATATAAAATAATAAA
1 TAATATTATAATTAA-ATAAAAT-ATAAA
*
6573960 TAATATTTTAATTAAATAAAATATAAA
1 TAATATTATAATTAAATAAAATATAAA
6573987 TA
1 TA
6573989 TTTAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 15 0.58
28 8 0.31
29 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TAATATTATAATTAAATAAAATATAAA
Found at i:6573985 original size:23 final size:23
Alignment explanation
Indices: 6573950--6573999 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
6573940 ATATAATATA
6573950 AAATAATAAAT-AATATTTTAATT
1 AAATAATAAATAAATA-TTTAATT
6573973 AAATAA-AATATAAATATTTAATT
1 AAATAATAA-ATAAATATTTAATT
6573996 AAAT
1 AAAT
6574000 GTAATCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 2 0.08
23 19 0.76
24 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATAATAAATAAATATTTAATT
Found at i:6584107 original size:21 final size:21
Alignment explanation
Indices: 6584066--6584105 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
6584056 AATAAAATTA
* *
6584066 AAACTTAAATAACTTTTAAAT
1 AAACTTAAATAAATTTAAAAT
6584087 AAAC-TAAATAAATTTAAAA
1 AAACTTAAATAAATTTAAAA
6584106 ATTATCTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AAACTTAAATAAATTTAAAAT
Found at i:6593065 original size:38 final size:41
Alignment explanation
Indices: 6593023--6593101 Score: 128
Period size: 38 Copynumber: 2.0 Consensus size: 41
6593013 CATAAGAGAA
*
6593023 TGGCTACTCAACCTTATCTTAC-A-A-CTTTGATTATCTGG
1 TGGCTACACAACCTTATCTTACAACAGCTTTGATTATCTGG
6593061 TGGCTACACAACCTTATCTTACAACAGCTTTGATTATCTGG
1 TGGCTACACAACCTTATCTTACAACAGCTTTGATTATCTGG
6593102 AATTCTGGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
38 21 0.57
39 1 0.03
40 1 0.03
41 14 0.38
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (41 bp):
TGGCTACACAACCTTATCTTACAACAGCTTTGATTATCTGG
Found at i:6602004 original size:31 final size:31
Alignment explanation
Indices: 6601976--6602037 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
6601966 CACAAACAAG
*
6601976 CACAGCAAGAGTGCAAGACAACAAAAACACA
1 CACAGCAAGAGTGCAAGAAAACAAAAACACA
*
6602007 CACAGCAAGAGTGCAAGAAAACCAAAACACA
1 CACAGCAAGAGTGCAAGAAAACAAAAACACA
6602038 TGGCCCATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.55, C:0.26, G:0.16, T:0.03
Consensus pattern (31 bp):
CACAGCAAGAGTGCAAGAAAACAAAAACACA
Found at i:6602791 original size:12 final size:11
Alignment explanation
Indices: 6602777--6602827 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
6602767 TGCGATAAAT
*
6602777 AAGAGAGAGAAT
1 AAGA-AGAGAAG
6602789 AAGAAGAAGAAG
1 AAGAAG-AGAAG
*
6602801 AAGAAGAGGAG
1 AAGAAGAGAAG
*
6602812 AAGAGGAGAAG
1 AAGAAGAGAAG
6602823 -AGAAG
1 AAGAAG
6602828 GCCACCATCG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 4 0.12
11 15 0.45
12 14 0.42
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (11 bp):
AAGAAGAGAAG
Found at i:6613999 original size:28 final size:28
Alignment explanation
Indices: 6613959--6614016 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
6613949 GAAGTAATTG
*
6613959 TGTCTGTTGTTCCTCAGTTCTGTACAGC
1 TGTCTGTTATTCCTCAGTTCTGTACAGC
6613987 TGTCTGTTATTCCTCAGTTCTGTACAGC
1 TGTCTGTTATTCCTCAGTTCTGTACAGC
6614015 TG
1 TG
6614017 GTACATGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (28 bp):
TGTCTGTTATTCCTCAGTTCTGTACAGC
Found at i:6616949 original size:3 final size:3
Alignment explanation
Indices: 6616935--6616972 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
6616925 CCAAAGCTCC
* *
6616935 CAG CAA CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
6616973 ACAACATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.39, C:0.34, G:0.26, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:6616953 original size:9 final size:9
Alignment explanation
Indices: 6616935--6616978 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
6616925 CCAAAGCTCC
6616935 CAGCAACAG
1 CAGCAACAG
*
6616944 CAGCAGCAG
1 CAGCAACAG
*
6616953 CAGCAGCAG
1 CAGCAACAG
6616962 CAGCAACAG
1 CAGCAACAG
*
6616971 CAACAACA
1 CAGCAACA
6616979 TATTGGATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.43, C:0.34, G:0.23, T:0.00
Consensus pattern (9 bp):
CAGCAACAG
Found at i:6618043 original size:24 final size:24
Alignment explanation
Indices: 6618011--6618059 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
6618001 TATATTCTCA
*
6618011 ATTTTCTTCATTTCTTTGTCTTTT
1 ATTTGCTTCATTTCTTTGTCTTTT
* * *
6618035 ATTTGCTTCTTTTTTTTTTCTTTT
1 ATTTGCTTCATTTCTTTGTCTTTT
6618059 A
1 A
6618060 GATTTGGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.08, C:0.14, G:0.04, T:0.73
Consensus pattern (24 bp):
ATTTGCTTCATTTCTTTGTCTTTT
Found at i:6621813 original size:63 final size:63
Alignment explanation
Indices: 6621714--6621839 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
6621704 AAAAAAGGAT
*
6621714 GACAATGTTGCCATATATTTTAATCAATCTGCTGGATAATGTCAGGTATGTGAAATAATGCAA
1 GACAATGTTGCCATATATTTTAATCAATCTGCTGGATAATGTCAGGTATATGAAATAATGCAA
6621777 GACAATGTTGCCATATATTTTAATCAATCTGCTGGATAATGTCAGGTATATGAAATAATGCAA
1 GACAATGTTGCCATATATTTTAATCAATCTGCTGGATAATGTCAGGTATATGAAATAATGCAA
6621840 CCTCTGGTTG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (63 bp):
GACAATGTTGCCATATATTTTAATCAATCTGCTGGATAATGTCAGGTATATGAAATAATGCAA
Found at i:6629303 original size:2 final size:2
Alignment explanation
Indices: 6629296--6629335 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6629286 TTATTTGTTT
6629296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6629336 GTAGGAAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6637466 original size:13 final size:13
Alignment explanation
Indices: 6637448--6637481 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
6637438 TTAAAATAAT
6637448 ATTTAAATTTTTA
1 ATTTAAATTTTTA
6637461 ATTTAAATTTTTA
1 ATTTAAATTTTTA
6637474 ATTTAAAT
1 ATTTAAAT
6637482 AAAAAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTAAATTTTTA
Found at i:6642687 original size:19 final size:19
Alignment explanation
Indices: 6642663--6642711 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
6642653 TTCACCCTTC
6642663 GGCTTTTTCGTTTTTTCAA
1 GGCTTTTTCGTTTTTTCAA
6642682 GGCTTTTTCGTTTTTTCAA
1 GGCTTTTTCGTTTTTTCAA
6642701 GGCTTTTTCGT
1 GGCTTTTTCGT
6642712 CAATCTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.08, C:0.16, G:0.18, T:0.57
Consensus pattern (19 bp):
GGCTTTTTCGTTTTTTCAA
Found at i:6652247 original size:28 final size:28
Alignment explanation
Indices: 6652196--6652249 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
6652186 TTAATTTTAA
*
6652196 AATAAAATATAAATATTTAATTAAATAT
1 AATAAAATATAAATAATTAATTAAATAT
*
6652224 AATAAAATAATAAA-AATTATTTAAAT
1 AATAAAAT-ATAAATAATTAATTAAAT
6652250 TTATTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AATAAAATATAAATAATTAATTAAATAT
Found at i:6656363 original size:3 final size:3
Alignment explanation
Indices: 6656355--6656402 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
6656345 AAACAATATT
*
6656355 TAA TAA TAA -AA TAA AAA TAA T-A TAA TAA T-A TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6656399 TAA T
1 TAA T
6656403 TTAATATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 8 0.21
3 31 0.79
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:6656367 original size:8 final size:8
Alignment explanation
Indices: 6656356--6656401 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
6656346 AACAATATTT
6656356 AATAATAA
1 AATAATAA
6656364 AAT-A-AA
1 AATAATAA
*
6656370 AATAATAT
1 AATAATAA
*
6656378 AATAATAT
1 AATAATAA
6656386 AATAATAA
1 AATAATAA
6656394 AATAATAA
1 AATAATAA
6656402 TTTAATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 5 0.15
7 2 0.06
8 27 0.79
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AATAATAA
Found at i:6656401 original size:11 final size:11
Alignment explanation
Indices: 6656355--6656402 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
6656345 AAACAATATT
6656355 TAATAATAAAA
1 TAATAATAAAA
*
6656366 TAA-AA-ATAA
1 TAATAATAAAA
*
6656375 T-ATAATAATA
1 TAATAATAAAA
6656385 TAATAATAAAA
1 TAATAATAAAA
6656396 TAATAAT
1 TAATAAT
6656403 TTAATATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
8 1 0.03
9 6 0.20
10 5 0.17
11 18 0.60
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:6656402 original size:19 final size:19
Alignment explanation
Indices: 6656356--6656408 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
6656346 AACAATATTT
* *
6656356 AATAATAAAATAAAAATAA
1 AATAATAATATAATAATAA
*
6656375 TATAATAATATAATAATAA
1 AATAATAATATAATAATAA
*
6656394 AATAATAATTTAATA
1 AATAATAATATAATA
6656409 TTTATGGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAATAATATAATAATAA
Found at i:6676172 original size:23 final size:22
Alignment explanation
Indices: 6676146--6676188 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
6676136 GTTTCTTTGG
*
6676146 AAATTATAAATTTATTTATCCAA
1 AAATTATAAA-TTAGTTATCCAA
6676169 AAATTATAAATTAGTTATCC
1 AAATTATAAATTAGTTATCC
6676189 GCTTCTCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATTATAAATTAGTTATCCAA
Found at i:6677650 original size:27 final size:27
Alignment explanation
Indices: 6677619--6677722 Score: 163
Period size: 27 Copynumber: 3.9 Consensus size: 27
6677609 TCAACATGGA
* *
6677619 CATGGTGGAGAGTACAAGGAAGGTCAC
1 CATGGTGGAGAGCACAAGGAAGGTTAC
*
6677646 CATGGTGGTGAGCACAAGGAAGGTTAC
1 CATGGTGGAGAGCACAAGGAAGGTTAC
*
6677673 TATGGTGGAGAGCACAAGGAAGGTTAC
1 CATGGTGGAGAGCACAAGGAAGGTTAC
*
6677700 TATGGTGGAGAGCACAAGGAAGG
1 CATGGTGGAGAGCACAAGGAAGG
6677723 CCAGCACAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.33, C:0.12, G:0.38, T:0.16
Consensus pattern (27 bp):
CATGGTGGAGAGCACAAGGAAGGTTAC
Found at i:6677809 original size:3 final size:3
Alignment explanation
Indices: 6677803--6677834 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6677793 GACGGGGAGG
*
6677803 AGA AGA AGA AGA AGA AGA AGG AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
6677835 CACGAGGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6686496 original size:2 final size:2
Alignment explanation
Indices: 6686489--6686524 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6686479 CACCACTGTA
6686489 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
6686525 TTGATAGGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6693259 original size:19 final size:18
Alignment explanation
Indices: 6693227--6693271 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
6693217 ATACGAAAAT
6693227 TATTTTTA-TCATAATTCA
1 TATTTTTATTCATAATT-A
*
6693245 TATTTTTATTTATAATTA
1 TATTTTTATTCATAATTA
*
6693263 TAATTTTAT
1 TATTTTTAT
6693272 AAAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTTATTCATAATTA
Found at i:6700252 original size:7 final size:7
Alignment explanation
Indices: 6700240--6700275 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
6700230 AAATCCAATC
6700240 GAGAATG
1 GAGAATG
6700247 GAGAATG
1 GAGAATG
6700254 GAGAATG
1 GAGAATG
6700261 GAGAATG
1 GAGAATG
6700268 GAGAATG
1 GAGAATG
6700275 G
1 G
6700276 GCTAGAGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (7 bp):
GAGAATG
Found at i:6701620 original size:25 final size:24
Alignment explanation
Indices: 6701574--6701620 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6701564 ATTTTCATTG
* **
6701574 ATAAATTAATAATTTATTAAATTT
1 ATAAAATAATAATTTAAAAAATTT
6701598 ATAAAATAATATATTTAAAAAAT
1 ATAAAATAATA-ATTTAAAAAAT
6701621 ATTTATAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAAAATAATAATTTAAAAAATTT
Found at i:6714383 original size:2 final size:2
Alignment explanation
Indices: 6714376--6714410 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6714366 CCGATTGAAG
6714376 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
6714411 GGGGGGACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6715341 original size:6 final size:7
Alignment explanation
Indices: 6715324--6715348 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6715314 TTAAAGAAAG
6715324 AAAAAAT
1 AAAAAAT
6715331 AAAAAAT
1 AAAAAAT
6715338 AAAAAAT
1 AAAAAAT
6715345 AAAA
1 AAAA
6715349 GTTTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:6729355 original size:20 final size:21
Alignment explanation
Indices: 6729327--6729365 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
6729317 GATTTTTTAA
6729327 TTTATATTAT-TATTTATTTGT
1 TTTATATTATAT-TTTATTTGT
6729348 TTTA-ATTATATTTTATTT
1 TTTATATTATATTTTATTT
6729366 ACTCAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTATATTATATTTTATTTGT
Found at i:6731049 original size:3 final size:3
Alignment explanation
Indices: 6731037--6731093 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
6731027 TTTTGGGGGC
6731037 GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
6731084 GAA GGA GAA G
1 GAA GAA GAA G
6731094 GACTTGGGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6731247 original size:62 final size:60
Alignment explanation
Indices: 6731166--6731288 Score: 194
Period size: 62 Copynumber: 2.0 Consensus size: 60
6731156 GCATTCTCAT
*
6731166 TGATCATCCATGATACTGAC-ATGCCCAAGATAATATTTTTTTATATCCAACATGGTAATCAG
1 TGATCATCCATGATACTGACAAT-CCCAAGATAATA-TTTTTT-TATCAAACATGGTAATCAG
*
6731228 TGATTATCCATGATACTGACAATCCCAAGATAATATTTTTTTATCAAACATGGTAATCAG
1 TGATCATCCATGATACTGACAATCCCAAGATAATATTTTTTTATCAAACATGGTAATCAG
6731288 T
1 T
6731289 TGGAAATGTG
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
60 19 0.33
61 6 0.10
62 31 0.53
63 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (60 bp):
TGATCATCCATGATACTGACAATCCCAAGATAATATTTTTTTATCAAACATGGTAATCAG
Found at i:6737825 original size:2 final size:2
Alignment explanation
Indices: 6737818--6737853 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6737808 ATCCAAACCC
6737818 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
6737854 TGCTTCATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6741711 original size:11 final size:12
Alignment explanation
Indices: 6741695--6741732 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6741685 AATTTACATG
6741695 AAAAGTGATTA-
1 AAAAGTGATTAT
*
6741706 AAAAGTAATTAT
1 AAAAGTGATTAT
*
6741718 AAAAATGATTAT
1 AAAAGTGATTAT
6741730 AAA
1 AAA
6741733 TATAATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (12 bp):
AAAAGTGATTAT
Found at i:6741722 original size:24 final size:24
Alignment explanation
Indices: 6741695--6741746 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
6741685 AATTTACATG
* *
6741695 AAAAGTGATTA-AAA-AGTAATTAT
1 AAAAATGATTATAAATA-TAATAAT
6741718 AAAAATGATTATAAATATAATAAT
1 AAAAATGATTATAAATATAATAAT
6741742 AAAAA
1 AAAAA
6741747 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.40
24 14 0.56
25 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (24 bp):
AAAAATGATTATAAATATAATAAT
Found at i:6741728 original size:12 final size:12
Alignment explanation
Indices: 6741704--6741746 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
6741694 GAAAAGTGAT
6741704 TAAAAAGTAATTA
1 TAAAAA-TAATTA
*
6741717 TAAAAATGATTA
1 TAAAAATAATTA
* *
6741729 TAAATATAATAA
1 TAAAAATAATTA
6741741 TAAAAA
1 TAAAAA
6741747 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 19 0.76
13 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (12 bp):
TAAAAATAATTA
Found at i:6749843 original size:36 final size:36
Alignment explanation
Indices: 6749792--6749863 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
6749782 ATTTTAATGG
* *
6749792 GACTAATTAAGATTAGCCCCACTCTAGTAAAATATT
1 GACTAATTAACATTAGCCCCAATCTAGTAAAATATT
* *
6749828 GACTAATTAACATTAGCTCCAATCTAGTTAAATATT
1 GACTAATTAACATTAGCCCCAATCTAGTAAAATATT
6749864 TAAGAAGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (36 bp):
GACTAATTAACATTAGCCCCAATCTAGTAAAATATT
Found at i:6751714 original size:22 final size:22
Alignment explanation
Indices: 6751652--6751723 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
6751642 TACGTTATTG
* *
6751652 GTTTTTAGGCATTACGTGATTA
1 GTTTTTAGGCATTGCATGATTA
* **
6751674 G-TTATAACCATTGCATGATTA
1 GTTTTTAGGCATTGCATGATTA
*
6751695 GTTTTTAGGCATTGCTTGATT-
1 GTTTTTAGGCATTGCATGATTA
6751716 GATTTTTA
1 G-TTTTTA
6751724 AGCAATGTCT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 17 0.44
22 22 0.56
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (22 bp):
GTTTTTAGGCATTGCATGATTA
Found at i:6751761 original size:23 final size:23
Alignment explanation
Indices: 6751735--6751783 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6751725 GCAATGTCTA
*
6751735 AGTCACACAATACCTTGCTAACT
1 AGTCACACAATACCTTACTAACT
* **
6751758 AGTCACGCAATGTCTTACTAACT
1 AGTCACACAATACCTTACTAACT
6751781 AGT
1 AGT
6751784 TAGGTAATGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (23 bp):
AGTCACACAATACCTTACTAACT
Found at i:6751792 original size:23 final size:23
Alignment explanation
Indices: 6751752--6751815 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
6751742 CAATACCTTG
* *
6751752 CTAACTAGTCACGCAATGTCTTA
1 CTAACTAGTTACGCAATGGCTTA
* *
6751775 CTAACTAGTTAGGTAATGGCTTA
1 CTAACTAGTTACGCAATGGCTTA
* *
6751798 CTAACAAGTTACACAATG
1 CTAACTAGTTACGCAATG
6751816 CCTACCAACT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (23 bp):
CTAACTAGTTACGCAATGGCTTA
Found at i:6752410 original size:21 final size:21
Alignment explanation
Indices: 6752381--6752420 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6752371 TTTGAAGTAT
6752381 ATAAATATTTATGATTAATAA
1 ATAAATATTTATGATTAATAA
* *
6752402 ATAATTATTTATTATTAAT
1 ATAAATATTTATGATTAAT
6752421 CAAAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
ATAAATATTTATGATTAATAA
Found at i:6754587 original size:21 final size:20
Alignment explanation
Indices: 6754557--6754595 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
6754547 TCCCCCAAAA
*
6754557 TTTTTAAATTTTTTTAATCT
1 TTTTTAAATTTTCTTAATCT
6754577 TTTTATAAATTTTCTTAAT
1 TTTT-TAAATTTTCTTAAT
6754596 GGTCTTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAAATTTTCTTAATCT
Found at i:6756261 original size:16 final size:16
Alignment explanation
Indices: 6756246--6756277 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6756236 ATTTTTTAAT
6756246 TATTTT-TTAAAATAA
1 TATTTTATTAAAATAA
6756261 TATTTTATTAAAA-AA
1 TATTTTATTAAAATAA
6756276 TA
1 TA
6756278 ATAAAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTTATTAAAATAA
Found at i:6756271 original size:27 final size:27
Alignment explanation
Indices: 6756220--6756271 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
6756210 AAATTTTAAA
* *
6756220 ATTTTTTATATATTATATTTTTTAATT
1 ATTTTTTATAAATAATATTTTTTAATT
6756247 ATTTTTTA-AAATAATATTTTATTAA
1 ATTTTTTATAAATAATATTTT-TTAA
6756272 AAAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTTTTATAAATAATATTTTTTAATT
Found at i:6756608 original size:15 final size:16
Alignment explanation
Indices: 6756588--6756618 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6756578 TCTACTATGT
6756588 GAATTTT-ATTTTTAA
1 GAATTTTAATTTTTAA
6756603 GAATTTTAATTTTTAA
1 GAATTTTAATTTTTAA
6756619 AAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
GAATTTTAATTTTTAA
Found at i:6756801 original size:21 final size:22
Alignment explanation
Indices: 6756777--6756823 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
6756767 GTTTTACATT
*
6756777 TTATATTTAGT-TAA-AAGGAAA
1 TTATATTGAGTATAAGAA-GAAA
*
6756798 TTATCTTGAGTATAAGAAGAAA
1 TTATATTGAGTATAAGAAGAAA
6756820 TTAT
1 TTAT
6756824 TAATTCTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 9 0.41
22 11 0.50
23 2 0.09
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATATTGAGTATAAGAAGAAA
Found at i:6758856 original size:2 final size:2
Alignment explanation
Indices: 6758849--6758881 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6758839 AGGAATGGAC
6758849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6758882 GCTTGACTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6761483 original size:28 final size:27
Alignment explanation
Indices: 6761412--6761517 Score: 95
Period size: 28 Copynumber: 3.9 Consensus size: 27
6761402 ACACCTGACG
* * *
6761412 TTAAAAATACAAGTATTACATATTATA
1 TTAAAAATATAATTATTATATATTATA
* * *
6761439 ATATATATATAATTATTATATATTATA
1 TTAAAAATATAATTATTATATATTATA
** *
6761466 TTAAAAAATATAATTATTATACGTTATG
1 TT-AAAAATATAATTATTATATATTATA
* *
6761494 TTGAAAAATTTAATTATTAGATAT
1 TT-AAAAATATAATTATTATATAT
6761518 CTTAATAAAG
Statistics
Matches: 61, Mismatches: 17, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
27 22 0.36
28 39 0.64
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (27 bp):
TTAAAAATATAATTATTATATATTATA
Found at i:6766287 original size:33 final size:33
Alignment explanation
Indices: 6766242--6766309 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
6766232 CATTAGACTA
* *
6766242 ATGTGGTATGCTAAAATATTATAACTGATTATG
1 ATGTGGTATGCTAAAATATCATAACTGATAATG
* *
6766275 ATGTGG-ATTGCTAATATATCATAATTGATAATG
1 ATGTGGTA-TGCTAAAATATCATAACTGATAATG
6766308 AT
1 AT
6766310 ATAACATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.40
Consensus pattern (33 bp):
ATGTGGTATGCTAAAATATCATAACTGATAATG
Found at i:6768767 original size:24 final size:25
Alignment explanation
Indices: 6768740--6768787 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
6768730 ACTAGATTAT
6768740 AATA-TTATATAAT-ATCTCTAACTA
1 AATAGTTATATAATCATCT-TAACTA
6768764 AATAGTTTATATAATCATCTTAAC
1 AATAG-TTATATAATCATCTTAAC
6768788 AATTTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.19
26 13 0.62
27 4 0.19
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (25 bp):
AATAGTTATATAATCATCTTAACTA
Found at i:6771289 original size:21 final size:21
Alignment explanation
Indices: 6771265--6771308 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
6771255 GTGCCCGCCA
*
6771265 CAACAACTGAAACTTGGGCAC
1 CAACAACTCAAACTTGGGCAC
** *
6771286 CAACTCCTCAACCTTGGGCAC
1 CAACAACTCAAACTTGGGCAC
6771307 CA
1 CA
6771309 GCTCCTCAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (21 bp):
CAACAACTCAAACTTGGGCAC
Found at i:6771313 original size:21 final size:21
Alignment explanation
Indices: 6771277--6771328 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
6771267 ACAACTGAAA
6771277 CTTGGGCACCAACTCCTCAAC
1 CTTGGGCACCAACTCCTCAAC
*
6771298 CTTGGGCACCAGCTCCTCAAC
1 CTTGGGCACCAACTCCTCAAC
*
6771319 CTTGGACACC
1 CTTGGGCACC
6771329 GGTTCCATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.42, G:0.17, T:0.19
Consensus pattern (21 bp):
CTTGGGCACCAACTCCTCAAC
Found at i:6773837 original size:20 final size:20
Alignment explanation
Indices: 6773797--6773837 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6773787 CATTATTTCT
* **
6773797 TTATTTTTTAAAATTTTTAA
1 TTATTTTTTAAAAATAATAA
6773817 TTATTTTTTAAAAATAATAA
1 TTATTTTTTAAAAATAATAA
6773837 T
1 T
6773838 AAAAGTATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTTTTTAAAAATAATAA
Found at i:6782977 original size:33 final size:33
Alignment explanation
Indices: 6782938--6783006 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
6782928 TCTCATTCTC
*
6782938 GCTTTCCTTCTCCATTGACCCAATATGGGTAGT
1 GCTTTCCTTCTCCATTGACCCAATATAGGTAGT
*
6782971 GCTTTCCTTCTCTATTGACCCAATATAGGTAGT
1 GCTTTCCTTCTCCATTGACCCAATATAGGTAGT
6783004 GCT
1 GCT
6783007 GCAAATTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (33 bp):
GCTTTCCTTCTCCATTGACCCAATATAGGTAGT
Found at i:6786006 original size:82 final size:80
Alignment explanation
Indices: 6785846--6786007 Score: 279
Period size: 82 Copynumber: 2.0 Consensus size: 80
6785836 TCTGCTTAAA
* **
6785846 ATGGTTTTGCCTGGCCTCACTTTGGAACTGTGCTTTCTATAGATTTGCATGGTTAGTGTGTTGTT
1 ATGGTTTTGCCTGGCCCCACTTTGGAACTGTGCTTTCTATAGATTTGCATGGTTAACGTGTTGTT
6785911 TTCACCACCTGCATG
66 TTCACCACCTGCATG
6785926 ATGGTTTTGCCTGGCCCCACTTTGGAACTGTGCTTTCTATATAGATTTGCATGGTTAACGTGTTG
1 ATGGTTTTGCCTGGCCCCACTTTGGAACTGTGCTTTC--TATAGATTTGCATGGTTAACGTGTTG
6785991 TTTTCACCACCTGCATG
64 TTTTCACCACCTGCATG
6786008 TGCTAATATT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
80 36 0.47
82 41 0.53
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (80 bp):
ATGGTTTTGCCTGGCCCCACTTTGGAACTGTGCTTTCTATAGATTTGCATGGTTAACGTGTTGTT
TTCACCACCTGCATG
Done.