Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 96 of 105
Found at i:17116262 original size:18 final size:19
Alignment explanation
Indices: 17116218--17116265 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
17116208 TAATTAATTT
*
17116218 TAAATAAAAAACTTCAACC
1 TAAATATAAAACTTCAACC
17116237 TAAATATAAAACTT-AA-C
1 TAAATATAAAACTTCAACC
17116254 TAGAATATAAAA
1 TA-AATATAAAA
17116266 TTATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 3 0.11
18 11 0.41
19 13 0.48
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.25
Consensus pattern (19 bp):
TAAATATAAAACTTCAACC
Found at i:17118708 original size:25 final size:22
Alignment explanation
Indices: 17118665--17118724 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 22
17118655 TTTTATTTAT
* *
17118665 ATATAATTTTTATCGATTTTAAATC
1 ATATTATTTTTATAGATTTT---TC
*
17118690 ATATTATTTTTATATATTTTTC
1 ATATTATTTTTATAGATTTTTC
17118712 ATATTATTTTTAT
1 ATATTATTTTTAT
17118725 GCTATATCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.47
25 17 0.53
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (22 bp):
ATATTATTTTTATAGATTTTTC
Found at i:17118722 original size:13 final size:12
Alignment explanation
Indices: 17118688--17118722 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
17118678 CGATTTTAAA
17118688 TCATATTATTTT
1 TCATATTATTTT
17118700 T-ATA-TATTTT
1 TCATATTATTTT
17118710 TCATATTATTTT
1 TCATATTATTTT
17118722 T
1 T
17118723 ATGCTATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 7 0.33
11 6 0.29
12 8 0.38
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (12 bp):
TCATATTATTTT
Found at i:17120216 original size:9 final size:9
Alignment explanation
Indices: 17120202--17120236 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
17120192 CCCCTTCCCA
*
17120202 CACCTGCTT
1 CACCTGCTC
17120211 CACCTGCTC
1 CACCTGCTC
17120220 CACCTGCTC
1 CACCTGCTC
17120229 CACCTGCT
1 CACCTGCT
17120237 TCTCTTCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.11, C:0.51, G:0.11, T:0.26
Consensus pattern (9 bp):
CACCTGCTC
Found at i:17121586 original size:25 final size:25
Alignment explanation
Indices: 17121552--17121627 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
17121542 CCCCTCCCCC
* *
17121552 TTTTATAAAAATTATA-AAAATTTTA
1 TTTTTTAAAAATTATATAAAA-ATTA
17121577 TTTTTTAAAAATTATATAAAAATTA
1 TTTTTTAAAAATTATATAAAAATTA
17121602 TTTTTT---AATTATAT-AAAATTA
1 TTTTTTAAAAATTATATAAAAATTA
17121623 TTTTT
1 TTTTT
17121628 AATTATTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
21 12 0.25
22 8 0.17
25 24 0.50
26 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTTTAAAAATTATATAAAAATTA
Found at i:17121626 original size:20 final size:22
Alignment explanation
Indices: 17121586--17121633 Score: 82
Period size: 20 Copynumber: 2.3 Consensus size: 22
17121576 ATTTTTTAAA
17121586 AATTATATAAAAATTATTTTTT
1 AATTATATAAAAATTATTTTTT
17121608 AATTATAT-AAAATTA-TTTTT
1 AATTATATAAAAATTATTTTTT
17121628 AATTAT
1 AATTAT
17121634 TAATTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 11 0.42
21 7 0.27
22 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTATATAAAAATTATTTTTT
Found at i:17121706 original size:23 final size:21
Alignment explanation
Indices: 17121648--17121708 Score: 79
Period size: 20 Copynumber: 2.8 Consensus size: 21
17121638 TTATATATTT
*
17121648 ATATATTTATATTTAAAAAATA
1 ATAT-TTTATATTTTAAAAATA
17121670 ATATTTTATA-TTTAAAAATA
1 ATATTTTATATTTTAAAAATA
17121690 ATATTTTATTAATTTTAAA
1 ATATTTTA-T-ATTTTAAA
17121709 TTAAATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
20 17 0.49
21 7 0.20
22 5 0.14
23 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTTTATATTTTAAAAATA
Found at i:17121715 original size:23 final size:20
Alignment explanation
Indices: 17121648--17121698 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
17121638 TTATATATTT
17121648 ATATATTTATATTTAAAAAATA
1 ATAT-TTTATATTT-AAAAATA
17121670 ATATTTTATATTTAAAAATA
1 ATATTTTATATTTAAAAATA
17121690 ATATTTTAT
1 ATATTTTAT
17121699 TAATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 16 0.55
21 9 0.31
22 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTTTATATTTAAAAATA
Found at i:17122295 original size:13 final size:14
Alignment explanation
Indices: 17122257--17122301 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
17122247 ATTTGTTAAA
17122257 ATTATTTTAAATAT
1 ATTATTTTAAATAT
*
17122271 ATAATTTATAAATAT
1 ATTATTT-TAAATAT
17122286 -TTATTTTAAAT-T
1 ATTATTTTAAATAT
17122298 ATTA
1 ATTA
17122302 GTTACTATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 1 0.04
13 8 0.30
14 11 0.41
15 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATTTTAAATAT
Found at i:17122315 original size:28 final size:29
Alignment explanation
Indices: 17122258--17122321 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
17122248 TTTGTTAAAA
* *
17122258 TTATTTTAAATATATAATTTATAAATA-T
1 TTATTTTAAATATATAAGTTATAAACATT
* *
17122286 TTATTTTAAAT-TATTAGTTACTATACATT
1 TTATTTTAAATATATAAGTTA-TAAACATT
17122315 TTATTTT
1 TTATTTT
17122322 TTATTTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.23
28 15 0.50
29 8 0.27
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (29 bp):
TTATTTTAAATATATAAGTTATAAACATT
Found at i:17126132 original size:15 final size:15
Alignment explanation
Indices: 17126114--17126199 Score: 50
Period size: 16 Copynumber: 5.5 Consensus size: 15
17126104 TATTAAAAGT
17126114 TTTTTTTCTCTTAAA
1 TTTTTTTCTCTTAAA
17126129 TTTTTTTTCTGCAAGTTAAA
1 -TTTTTTTCT-C---TTAAA
* *
17126149 --TTTATCTATTAAA
1 TTTTTTTCTCTTAAA
**
17126162 AATTTTTCTCTTAAAA
1 TTTTTTTCTCTT-AAA
* *
17126178 TTTTTTTTTCGTAAA
1 TTTTTTTCTCTTAAA
17126193 TTTTTTT
1 TTTTTTT
17126200 ATCCATCAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
13 5 0.09
15 18 0.33
16 20 0.36
17 7 0.13
20 5 0.09
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTTTTTCTCTTAAA
Found at i:17128405 original size:51 final size:51
Alignment explanation
Indices: 17128329--17128433 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
17128319 CTTTGCCCGA
*
17128329 CCTATAGAACCCCTTCCCACACCTGCTTCACCTGCTCCACCTGCTTCTCTT
1 CCTATAGAACCCCTTCCCACACCTGCTTCACCTCCTCCACCTGCTTCTCTT
* *
17128380 CCTATAGAACCCTTTCCCACGCCTGCTTCACCTCCTCCACCTGCTTCTCTT
1 CCTATAGAACCCCTTCCCACACCTGCTTCACCTCCTCCACCTGCTTCTCTT
17128431 CCT
1 CCT
17128434 CCACCAGGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.14, C:0.48, G:0.08, T:0.30
Consensus pattern (51 bp):
CCTATAGAACCCCTTCCCACACCTGCTTCACCTCCTCCACCTGCTTCTCTT
Found at i:17128424 original size:18 final size:18
Alignment explanation
Indices: 17128401--17128438 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17128391 CTTTCCCACG
17128401 CCTGCTTCACCTCCTCCA
1 CCTGCTTCACCTCCTCCA
* *
17128419 CCTGCTTCTCTTCCTCCA
1 CCTGCTTCACCTCCTCCA
17128437 CC
1 CC
17128439 AGGTAATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.55, G:0.05, T:0.32
Consensus pattern (18 bp):
CCTGCTTCACCTCCTCCA
Found at i:17129441 original size:13 final size:13
Alignment explanation
Indices: 17129423--17129496 Score: 50
Period size: 13 Copynumber: 5.9 Consensus size: 13
17129413 CTTTAATCAA
17129423 ATATTAAAATTAT
1 ATATTAAAATTAT
* *
17129436 ATATTATAATTCT
1 ATATTAAAATTAT
* *
17129449 -TATAAAAATTAA
1 ATATTAAAATTAT
*
17129461 ATA-TAAAA-TAG
1 ATATTAAAATTAT
17129472 ATATTTAAAATT-T
1 ATA-TTAAAATTAT
17129485 -TATTAAATATTA
1 ATATTAAA-ATTA
17129497 AATTCAATCA
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
11 10 0.22
12 17 0.37
13 18 0.39
14 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (13 bp):
ATATTAAAATTAT
Found at i:17129497 original size:37 final size:38
Alignment explanation
Indices: 17129421--17129499 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 38
17129411 CACTTTAATC
* *
17129421 AAATATTAAAATTATATATTATAATTCTTATAAAAATT
1 AAATATTAAAATGATATATTAAAATTCTTATAAAAATT
*
17129459 AAATA-TAAAATAGATAT-TTAAAATT-TTATTAAATATT
1 AAATATTAAAAT-GATATATTAAAATTCTTA-TAAAAATT
17129496 AAAT
1 AAAT
17129500 TCAATCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 3 0.08
37 24 0.67
38 9 0.25
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (38 bp):
AAATATTAAAATGATATATTAAAATTCTTATAAAAATT
Found at i:17131342 original size:21 final size:22
Alignment explanation
Indices: 17131302--17131347 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
17131292 CGATTAATTG
*
17131302 ATTAATTATTAAATTAATTTTA
1 ATTAATTATCAAATTAATTTTA
17131324 ATTAATTATCAAA-TAATTTTA
1 ATTAATTATCAAATTAATTTTA
17131345 ATT
1 ATT
17131348 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTAATTATCAAATTAATTTTA
Found at i:17131639 original size:15 final size:15
Alignment explanation
Indices: 17131615--17131651 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
17131605 AAAAAAATAA
*
17131615 TTTAATTAATTTAAT
1 TTTAAATAATTTAAT
17131630 TTTAAATAATTTAAT
1 TTTAAATAATTTAAT
*
17131645 TTAAAAT
1 TTTAAAT
17131652 TGATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAAATAATTTAAT
Found at i:17133766 original size:13 final size:14
Alignment explanation
Indices: 17133739--17133768 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
17133729 AAATTTGAAT
17133739 TTTATTGATAATTA
1 TTTATTGATAATTA
17133753 TTTATTGA-AATTA
1 TTTATTGATAATTA
17133766 TTT
1 TTT
17133769 TAAATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTATTGATAATTA
Found at i:17133770 original size:14 final size:15
Alignment explanation
Indices: 17133737--17133770 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
17133727 TTAAATTTGA
17133737 ATTTTATTGATAATT
1 ATTTTATTGATAATT
17133752 A-TTTATTGA-AATT
1 ATTTTATTGATAATT
17133765 ATTTTA
1 ATTTTA
17133771 AATATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.28
14 12 0.67
15 1 0.06
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
ATTTTATTGATAATT
Found at i:17134524 original size:8 final size:8
Alignment explanation
Indices: 17134499--17134547 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
17134489 ATAAAAATTA
17134499 ATATTT-T
1 ATATTTAT
17134506 AT-TTATAT
1 ATATT-TAT
17134514 ATATTTAT
1 ATATTTAT
*
17134522 ATAATTAT
1 ATATTTAT
*
17134530 ATATTTAA
1 ATATTTAT
17134538 ATATTTAT
1 ATATTTAT
17134546 AT
1 AT
17134548 TTAAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 2 0.06
7 3 0.09
8 28 0.80
9 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATATTTAT
Found at i:17134551 original size:14 final size:16
Alignment explanation
Indices: 17134511--17134565 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
17134501 ATTTTATTTA
*
17134511 TATATATTTATATAAT
1 TATATATTTAAATAAT
17134527 TATATATTTAAAT-AT
1 TATATATTTAAATAAT
*
17134542 T-TATATTTAAAAAAT
1 TATATATTTAAATAAT
*
17134557 AATAT-TTTA
1 TATATATTTA
17134566 TTAATTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 15 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:17144136 original size:17 final size:17
Alignment explanation
Indices: 17144098--17144140 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
17144088 TATGAAATAT
*
17144098 AAAATACATTTTCATACC
1 AAAATA-ATTTTCATACA
17144116 AAAATAATTTTCACT-CA
1 AAAATAATTTTCA-TACA
17144133 AAAATAAT
1 AAAATAAT
17144141 GAACCTTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAATTTTCATACA
Found at i:17147552 original size:19 final size:20
Alignment explanation
Indices: 17147522--17147562 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
17147512 TATAAACACA
*
17147522 AAATCAAAAGTACAAGCTTC
1 AAATCAAAAGTAAAAGCTTC
*
17147542 AAATC-AAAGTAAAAGTTTC
1 AAATCAAAAGTAAAAGCTTC
17147561 AA
1 AA
17147563 TAACTTTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.22
Consensus pattern (20 bp):
AAATCAAAAGTAAAAGCTTC
Found at i:17151201 original size:18 final size:18
Alignment explanation
Indices: 17151180--17151214 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17151170 GAATTTTGGG
*
17151180 TTTTTTGGTTTTTTTTCC
1 TTTTTTGGTCTTTTTTCC
17151198 TTTTTTGGTCTTTTTTC
1 TTTTTTGGTCTTTTTTC
17151215 TAGTAGTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.77
Consensus pattern (18 bp):
TTTTTTGGTCTTTTTTCC
Found at i:17151655 original size:26 final size:25
Alignment explanation
Indices: 17151610--17151673 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 25
17151600 AATATAATTG
17151610 TTAAAATATTAAAAATTATTTATTA
1 TTAAAATATTAAAAATTATTTATTA
*
17151635 TTAAAATATATCAAAATTATTTATTA
1 TTAAAATAT-TAAAAATTATTTATTA
17151661 TTAAAATTATTAA
1 TTAAAA-TATTAA
17151674 TATTAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 9 0.26
26 23 0.66
27 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TTAAAATATTAAAAATTATTTATTA
Found at i:17151682 original size:16 final size:16
Alignment explanation
Indices: 17151642--17151681 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
17151632 TTATTAAAAT
*
17151642 ATATCAAAATTATTTA
1 ATATTAAAATTATTTA
*
17151658 TTATTAAAATTA-TTA
1 ATATTAAAATTATTTA
17151673 ATATTAAAA
1 ATATTAAAA
17151682 AATAACTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTAAAATTATTTA
Found at i:17163430 original size:17 final size:18
Alignment explanation
Indices: 17163400--17163433 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17163390 AAATTTTAAA
*
17163400 TTATATTATTTTTATATT
1 TTATATTATATTTATATT
17163418 TTAT-TTATATTTATAT
1 TTATATTATATTTATAT
17163434 CATATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATATTATATTTATATT
Found at i:17164009 original size:14 final size:13
Alignment explanation
Indices: 17163990--17164029 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
17163980 AAATATCAAT
17163990 TTTAATAAAATATA
1 TTTAATAAAAT-TA
17164004 TTTAATATAAATTA
1 TTTAATA-AAATTA
*
17164018 TTTTATAAAATT
1 TTTAATAAAATT
17164030 TTCAATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 5 0.21
14 15 0.62
15 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAATAAAATTA
Found at i:17177338 original size:2 final size:2
Alignment explanation
Indices: 17177331--17177357 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17177321 ATTCATACAG
17177331 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 A
17177358 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17177362 original size:2 final size:2
Alignment explanation
Indices: 17177357--17177400 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
17177347 ATATATATAT
* *
17177357 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17177399 AG
1 AG
17177401 TATTACCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17189697 original size:2 final size:2
Alignment explanation
Indices: 17189690--17189723 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17189680 ACAGATATGT
17189690 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17189724 GGACTACAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17194771 original size:18 final size:17
Alignment explanation
Indices: 17194745--17194778 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17194735 AAAATTGCAA
*
17194745 AAAATAAAATAAAAAAT
1 AAAATAAAAGAAAAAAT
17194762 AAAATGAAAAGAAAAAA
1 AAAAT-AAAAGAAAAAA
17194779 AAGAAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAATAAAAGAAAAAAT
Found at i:17195153 original size:20 final size:20
Alignment explanation
Indices: 17195128--17195244 Score: 112
Period size: 20 Copynumber: 5.7 Consensus size: 20
17195118 ATTTTTTTTT
17195128 CAGAAATTC-AACTCCAAACC
1 CAGAAATTCAAAC-CCAAACC
* *
17195148 CAGAAATTCAAACCTAAACT
1 CAGAAATTCAAACCCAAACC
*
17195168 CAGAAATTCAAACCTAAACC
1 CAGAAATTCAAACCCAAACC
* *
17195188 CAGAACTTCAAACTCTCAATCC
1 CAGAAATTCAAAC-C-CAAACC
*
17195210 CA-AAACTTCAAACCTAAAACC
1 CAGAAA-TTCAAACC-CAAACC
*
17195231 AAGAAATTCAAACC
1 CAGAAATTCAAACC
17195245 ACTCTCAATC
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
20 45 0.55
21 21 0.26
22 16 0.20
ACGTcount: A:0.48, C:0.31, G:0.04, T:0.17
Consensus pattern (20 bp):
CAGAAATTCAAACCCAAACC
Found at i:17195276 original size:15 final size:15
Alignment explanation
Indices: 17195256--17195286 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17195246 CTCTCAATCG
*
17195256 CCAGAAACTTTAAAT
1 CCAGAAACTTCAAAT
17195271 CCAGAAACTTCAAAT
1 CCAGAAACTTCAAAT
17195286 C
1 C
17195287 TAGAGAGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (15 bp):
CCAGAAACTTCAAAT
Found at i:17196220 original size:12 final size:12
Alignment explanation
Indices: 17196183--17196231 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
17196173 TTGATTTCAG
*
17196183 CCTTCTCCGTTT
1 CCTTCTCCCTTT
* * *
17196195 CCTTTTCACGTT
1 CCTTCTCCCTTT
17196207 CCTTCTCCCTTT
1 CCTTCTCCCTTT
17196219 CCTTCTCCCTTT
1 CCTTCTCCCTTT
17196231 C
1 C
17196232 GTGTCTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.02, C:0.45, G:0.04, T:0.49
Consensus pattern (12 bp):
CCTTCTCCCTTT
Found at i:17196298 original size:6 final size:6
Alignment explanation
Indices: 17196287--17196393 Score: 169
Period size: 6 Copynumber: 17.8 Consensus size: 6
17196277 CTGGTCAGCC
* * * *
17196287 TCTTTA TCTTTA TCTTTA TCTTCA TCTTCA TCTTCA TCTTCA TCTTTA
1 TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA
*
17196335 TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA CCTTTA
1 TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA
17196383 TCTTTA TCTTT
1 TCTTTA TCTTT
17196394 GTCTCTATCC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 97 1.00
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (6 bp):
TCTTTA
Found at i:17198503 original size:18 final size:18
Alignment explanation
Indices: 17198480--17198518 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17198470 AAAATTATTT
*
17198480 TTTAAAAAATTTATATAA
1 TTTAAAAAATTAATATAA
**
17198498 TTTAAATTATTAATATAA
1 TTTAAAAAATTAATATAA
17198516 TTT
1 TTT
17198519 TTAATGATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAAAAATTAATATAA
Found at i:17207883 original size:8 final size:8
Alignment explanation
Indices: 17207870--17207903 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
17207860 ACAAAAACGA
17207870 AATCAAAT
1 AATCAAAT
17207878 AATCAAAT
1 AATCAAAT
17207886 AATCAAAT
1 AATCAAAT
*
17207894 AATCACAT
1 AATCAAAT
17207902 AA
1 AA
17207904 GAGACAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (8 bp):
AATCAAAT
Found at i:17214093 original size:22 final size:22
Alignment explanation
Indices: 17214065--17214109 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
17214055 CCAATGACCG
17214065 ATTGATTCTTAAGAAAAGAGGA
1 ATTGATTCTTAAGAAAAGAGGA
17214087 ATTGATTCTTAAGAAAAGAGGA
1 ATTGATTCTTAAGAAAAGAGGA
17214109 A
1 A
17214110 GCAACATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (22 bp):
ATTGATTCTTAAGAAAAGAGGA
Found at i:17230844 original size:17 final size:17
Alignment explanation
Indices: 17230813--17230859 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
17230803 TTATTTATTT
17230813 ATTTATTTTTC-TTCTAG
1 ATTT-TTTTTCTTTCTAG
**
17230830 ATTTTTTTTCTTTCTTT
1 ATTTTTTTTCTTTCTAG
*
17230847 CTTTTTTTTCTTT
1 ATTTTTTTTCTTT
17230860 TTCAAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.77
Consensus pattern (17 bp):
ATTTTTTTTCTTTCTAG
Found at i:17231814 original size:22 final size:22
Alignment explanation
Indices: 17231767--17231815 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
17231757 TTTTTGTTTT
17231767 TTTTTAGTATTTTATTTATTTA
1 TTTTTAGTATTTTATTTATTTA
*
17231789 TTTTTATGTGTTTT-TTT-TTTA
1 TTTTTA-GTATTTTATTTATTTA
17231810 GTTTTT
1 -TTTTT
17231816 TTTTTTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (22 bp):
TTTTTAGTATTTTATTTATTTA
Found at i:17231855 original size:9 final size:9
Alignment explanation
Indices: 17231841--17231868 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
17231831 AATTTAGAAA
17231841 AAAAATAAT
1 AAAAATAAT
17231850 AAAAATAAT
1 AAAAATAAT
17231859 AAAAATAAT
1 AAAAATAAT
17231868 A
1 A
17231869 TTTTGAGAAT
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:17232052 original size:15 final size:16
Alignment explanation
Indices: 17232032--17232061 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17232022 TTTTCAAACA
17232032 AAAAAATA-AAAAATG
1 AAAAAATATAAAAATG
17232047 AAAAAATATAAAAAT
1 AAAAAATATAAAAAT
17232062 TGTGGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAAATATAAAAATG
Found at i:17232132 original size:25 final size:26
Alignment explanation
Indices: 17232087--17232137 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
17232077 CAAATTACCC
*
17232087 AATGATAAGATTCTTAAAAAT-TTTA
1 AATGATAAGATTCCTAAAAATCTTTA
*
17232112 AATGGTAA-ATTCCTAAGAAATCTTTA
1 AATGATAAGATTCCTAA-AAATCTTTA
17232138 GGTGAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 7 0.32
25 11 0.50
26 4 0.18
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (26 bp):
AATGATAAGATTCCTAAAAATCTTTA
Found at i:17232542 original size:16 final size:16
Alignment explanation
Indices: 17232517--17232550 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17232507 ATTTATTTTA
*
17232517 AATAAGAAAAAATGAT
1 AATAAGAAAAAATAAT
*
17232533 AATAATAAAAAATAAT
1 AATAAGAAAAAATAAT
17232549 AA
1 AA
17232551 ATAAACCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (16 bp):
AATAAGAAAAAATAAT
Found at i:17238529 original size:10 final size:10
Alignment explanation
Indices: 17238514--17238609 Score: 65
Period size: 10 Copynumber: 9.5 Consensus size: 10
17238504 TGAATGTATG
17238514 AAAAAAGAGA
1 AAAAAAGAGA
* *
17238524 AAAAAAAAAA
1 AAAAAAGAGA
17238534 GAAAAAAGA-A
1 -AAAAAAGAGA
17238544 ATAAAAAGAGA
1 A-AAAAAGAGA
17238555 AAAATAA-AG-
1 AAAA-AAGAGA
* *
17238564 AAAAAGGAAA
1 AAAAAAGAGA
* *
17238574 AAATAAAAAGG
1 AAA-AAAGAGA
17238585 AAAAAAGATG-
1 AAAAAAGA-GA
17238595 AAAAAAGAGA
1 AAAAAAGAGA
17238605 AAAAA
1 AAAAA
17238610 TAAAAAAAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
8 1 0.01
9 7 0.10
10 41 0.61
11 18 0.27
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAAAAGAGA
Found at i:17238550 original size:31 final size:31
Alignment explanation
Indices: 17238515--17238631 Score: 114
Period size: 31 Copynumber: 3.6 Consensus size: 31
17238505 GAATGTATGA
17238515 AAAAAGAGAAAAAAAA-AAAGAA-AAAAGAAAT
1 AAAAAGAGAAAAAAAAGAAA-AAGAAAA-AAAT
*
17238546 AAAAAGAGAAAAATAAAGAAAAAGGAAAAAAT
1 AAAAAGAGAAAAA-AAAGAAAAAGAAAAAAAT
*
17238578 AAAAAG-GAAAAAAGATGAAAAAAGAGAAAAAAT
1 AAAAAGAGAAAAAA-AAG-AAAAAGA-AAAAAAT
17238611 AAAAAAAGATGAAAAAAAAGA
1 --AAAAAGA-GAAAAAAAAGA
17238632 CTCAAATTAA
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
30 1 0.01
31 21 0.29
32 21 0.29
33 13 0.18
35 7 0.10
36 2 0.03
37 7 0.10
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (31 bp):
AAAAAGAGAAAAAAAAGAAAAAGAAAAAAAT
Found at i:17238557 original size:18 final size:17
Alignment explanation
Indices: 17238514--17238629 Score: 95
Period size: 18 Copynumber: 6.9 Consensus size: 17
17238504 TGAATGTATG
*
17238514 AAAAA-AGAGAAAAAA-
1 AAAAAGAGAAAAAAAAT
17238529 AAAAAGA-AAAAAGAAAT
1 AAAAAGAGAAAAA-AAAT
*
17238546 AAAAAGAGAAAAATAAAG
1 AAAAAGAGAAAAA-AAAT
17238564 AAAAAG-G--AAAAAAT
1 AAAAAGAGAAAAAAAAT
*
17238578 AAAAAG-GAAAAAAGAT
1 AAAAAGAGAAAAAAAAT
17238594 GAAAAAAGAGAAAAAATAA-
1 --AAAAAGAGAAAAAA-AAT
17238613 AAAAAGATGAAAAAAAA
1 AAAAAGA-GAAAAAAAA
17238630 GACTCAAATT
Statistics
Matches: 84, Mismatches: 6, Indels: 20
0.76 0.05 0.18
Matches are distributed among these distances:
14 10 0.12
15 12 0.14
16 10 0.12
17 17 0.20
18 27 0.32
19 7 0.08
20 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAAGAGAAAAAAAAT
Found at i:17238567 original size:50 final size:50
Alignment explanation
Indices: 17238513--17238629 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 50
17238503 GTGAATGTAT
17238513 GAAAAAAGAGAAAAAAAAAAA-GAAAAAAGA-AATAAAAAGAGAAAAATAAA
1 GAAAAAAGAGAAAAAAAAAAAGGAAAAAAGATAA-AAAAAGAGAAAAA-AAA
* *
17238563 G-AAAAAG-GAAAAAATAAAAAGGAAAAAAGATGAAAAAAGAGAAAAAATA
1 GAAAAAAGAGAAAAAA-AAAAAGGAAAAAAGATAAAAAAAGAGAAAAAAAA
17238612 -AAAAAAGATGAAAAAAAA
1 GAAAAAAGA-GAAAAAAAA
17238630 GACTCAAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
48 7 0.12
49 19 0.32
50 25 0.42
51 8 0.14
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (50 bp):
GAAAAAAGAGAAAAAAAAAAAGGAAAAAAGATAAAAAAAGAGAAAAAAAA
Found at i:17238644 original size:29 final size:27
Alignment explanation
Indices: 17238511--17238631 Score: 97
Period size: 27 Copynumber: 4.5 Consensus size: 27
17238501 GGGTGAATGT
* * *
17238511 ATGAAAAAAGAGAAAAAAAAAAAGAAAA
1 ATGAAAAAAAAGAAAAAATAAAA-AAAG
*
17238539 AAGAAATAAAAAGAGAAAAATAAAGAAAA-
1 ATGAAA-AAAAAGA-AAAAATAAA-AAAAG
* * **
17238568 A-G-GAAAAAA-TAAAAAGGAAAAAAG
1 ATGAAAAAAAAGAAAAAATAAAAAAAG
*
17238592 ATGAAAAAAGAGAAAAAATAAAAAAAG
1 ATGAAAAAAAAGAAAAAATAAAAAAAG
17238619 ATGAAAAAAAAGA
1 ATGAAAAAAAAGA
17238632 CTCAAATTAA
Statistics
Matches: 73, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
23 4 0.05
24 8 0.11
25 1 0.01
26 10 0.14
27 25 0.34
28 6 0.08
29 7 0.10
30 11 0.15
31 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.06
Consensus pattern (27 bp):
ATGAAAAAAAAGAAAAAATAAAAAAAG
Found at i:17240306 original size:41 final size:42
Alignment explanation
Indices: 17240248--17240348 Score: 143
Period size: 41 Copynumber: 2.4 Consensus size: 42
17240238 GTCAATGAGC
* *
17240248 ATTTATTTTTTCAAAGTTGTGGTACCTCTGTTTAGAGGAA-CA
1 ATTTACTTTTTCAAAGTTGTGGTACCTCTATTTAGA-GAAGCA
* *
17240290 ATTTAC-TTTTCAAAGTTGTGGTGCCTCTATTTAGAGAAGTA
1 ATTTACTTTTTCAAAGTTGTGGTACCTCTATTTAGAGAAGCA
17240331 ATTTACTTTTTCAAAGTT
1 ATTTACTTTTTCAAAGTT
17240349 TTAGTGACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
40 3 0.06
41 34 0.64
42 16 0.30
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.45
Consensus pattern (42 bp):
ATTTACTTTTTCAAAGTTGTGGTACCTCTATTTAGAGAAGCA
Found at i:17240404 original size:44 final size:43
Alignment explanation
Indices: 17240332--17240483 Score: 123
Period size: 44 Copynumber: 3.4 Consensus size: 43
17240322 AGAGAAGTAA
* *
17240332 TTTACTTTTTCAAAGT-TTTAGTGACTCTGTCAATAAGAGCTTTGT
1 TTTA-TTTTTCAAAGTCGTT-GTGCCTCTGT-AATAAGAGCTTTGT
* *
17240377 TTTATTTTTCAAAGTCGTTGTGCCTCTG-ATTAGAGGAGCCTTG-
1 TTTATTTTTCAAAGTCGTTGTGCCTCTGTAATA-A-GAGCTTTGT
* * * * *
17240420 TTCATTTTTCAAAAGTCGTTGAGCCTTTGT-TTAGAGGAGCTTTAT
1 TTTATTTTTC-AAAGTCGTTGTGCCTCTGTAATA-A-GAGCTTTGT
17240465 TTTATTTTTCAAAGTCGTT
1 TTTATTTTTCAAAGTCGTT
17240484 ATACTTCTGA
Statistics
Matches: 91, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
42 3 0.03
43 10 0.11
44 63 0.69
45 15 0.16
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (43 bp):
TTTATTTTTCAAAGTCGTTGTGCCTCTGTAATAAGAGCTTTGT
Found at i:17240560 original size:43 final size:43
Alignment explanation
Indices: 17240377--17240761 Score: 366
Period size: 44 Copynumber: 8.9 Consensus size: 43
17240367 AGAGCTTTGT
* * *
17240377 TTTATTTTTCAAAGTCGTTGTGCCTCTGATTAGAGGAGCCTTG
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCTTA
* * *
17240420 TTCATTTTTCAAAAGTCGTTGAGCCTTTGTTTAGAGGAGCTTTA
1 TTTATTTTTC-AAAGTCGTTGAGCCTCTGTTTAGAGGAGCCTTA
* * * * *
17240464 TTTTATTTTTCAAAGTCGTT-ATACTTCTGATTAAAGGAGCCTTG
1 -TTTATTTTTCAAAGTCGTTGA-GCCTCTGTTTAGAGGAGCCTTA
* * * *
17240508 TTAATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGAAGTCTTA
1 TTTATTTTTC-AAAGTCGTTGAGCCTCTGTTTAGAGGAGCCTTA
*
17240552 TTTA-TTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCCTTA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCTTA
** * * * *
17240594 TTTATTTTTCAAAAGTTATTGAGCATCTGATTAGAGGAGCTTTG
1 TTTATTTTTC-AAAGTCGTTGAGCCTCTGTTTAGAGGAGCCTTA
* * * * **
17240638 TTTATTTTTTAAAGTTGTTGAGCTTCTGTTTAAAATAGCCTTA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCTTA
* * *
17240681 TTTATTTTTTAAAGTTGTTGAGCCTCTGTTTAGATGAG-C--A
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCTTA
* **
17240721 TTTATGTTTCTCAAAGTCATTGAGCCTCTACTTAGAGGAGC
1 TTTAT-TTT-TCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
17240762 TTTGACTAAA
Statistics
Matches: 280, Mismatches: 52, Indels: 20
0.80 0.15 0.06
Matches are distributed among these distances:
40 6 0.02
41 3 0.01
42 58 0.21
43 88 0.31
44 115 0.41
45 10 0.04
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (43 bp):
TTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCTTA
Found at i:17240623 original size:130 final size:129
Alignment explanation
Indices: 17240380--17240719 Score: 400
Period size: 130 Copynumber: 2.6 Consensus size: 129
17240370 GCTTTGTTTT
* * * * * *
17240380 ATTTTTCAAAGTCGTTGTGCCTCTGATTAGAGGAGCCTTGTTCATTTTTCAAAAGTCGTTGAGCC
1 ATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGAAGCCTTATTTATTTTTC-AAAGTTGTTGAGCC
* * * *
17240445 TTTGTTTAGAGGAGCTTTATTTTATTTTTCAAAGTCGTTATACTTCTGATTAAAGGAGCCTTGTT
65 TCTGTTTAGAGGAGCCTTATTTTATTTTTCAAAG-AGTTATACATCTGATTAAAGGAGCCTTGTT
17240510 A
129 A
* *
17240511 ATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGAAGTCTTATTTA-TTTTCAAAGTTGTTGAGCC
1 ATTTTTC-AAAGTCGTTGAGCCTCTGTTTAGAGAAGCCTTATTTATTTTTCAAAGTTGTTGAGCC
* *
17240575 TCTGTTTAGAGGAGCCTTA-TTTATTTTTCAAA-AGTTATTGAGCATCTGATTAGAGGAGCTTTG
65 TCTGTTTAGAGGAGCCTTATTTTATTTTTCAAAGAGTTA-T-A-CATCTGATTAAAGGAGCCTTG
*
17240638 TTT
127 TTA
* * * * *
17240641 ATTTTTTAAAGTTGTTGAGCTTCTGTTTA-AAATAGCCTTATTTATTTTTTAAAGTTGTTGAGCC
1 ATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGA-AGCCTTATTTATTTTTCAAAGTTGTTGAGCC
*
17240705 TCTGTTTAGATGAGC
65 TCTGTTTAGAGGAGC
17240720 ATTTATGTTT
Statistics
Matches: 180, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
127 4 0.02
128 3 0.02
129 43 0.24
130 88 0.49
131 12 0.07
132 30 0.17
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (129 bp):
ATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGAAGCCTTATTTATTTTTCAAAGTTGTTGAGCCT
CTGTTTAGAGGAGCCTTATTTTATTTTTCAAAGAGTTATACATCTGATTAAAGGAGCCTTGTTA
Found at i:17243686 original size:18 final size:15
Alignment explanation
Indices: 17243655--17243701 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
17243645 CATACACAAA
*
17243655 ATATAATAATTATTT
1 ATATAATAAATATTT
17243670 AATTATACATAAATA-TT
1 -A-TATA-ATAAATATTT
17243687 ATATAATAAATATTT
1 ATATAATAAATATTT
17243702 TATGCCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 2 0.07
17 6 0.22
18 6 0.22
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATAATAAATATTT
Found at i:17244772 original size:18 final size:15
Alignment explanation
Indices: 17244741--17244787 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
17244731 TGTGCAAAAA
*
17244741 ATATAATAATTATTT
1 ATATAATAAATATTT
17244756 AATCATACATAAATA-TT
1 -AT-ATA-ATAAATATTT
17244773 ATATAATAAATATTT
1 ATATAATAAATATTT
17244788 TATGGCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 7 0.26
15 5 0.19
16 4 0.15
17 5 0.19
18 6 0.22
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAATAAATATTT
Found at i:17255546 original size:14 final size:13
Alignment explanation
Indices: 17255521--17255554 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
17255511 TAATAAATTG
*
17255521 TAATATATATTTT
1 TAATAAATATTTT
17255534 TATATAAATATTTT
1 TA-ATAAATATTTT
17255548 TAATAAA
1 TAATAAA
17255555 ATTATTGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TAATAAATATTTT
Found at i:17256931 original size:26 final size:26
Alignment explanation
Indices: 17256902--17256953 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
17256892 CCACTAATAG
17256902 TTATACGGTTTCAATTATTCCTTAAA
1 TTATACGGTTTCAATTATTCCTTAAA
*
17256928 TTATAGGGTTTCAATTATTCCTTAAA
1 TTATACGGTTTCAATTATTCCTTAAA
17256954 AATTCCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (26 bp):
TTATACGGTTTCAATTATTCCTTAAA
Found at i:17258761 original size:3 final size:3
Alignment explanation
Indices: 17258755--17258784 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17258745 CACTTTTTAA
17258755 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17258785 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17258789 original size:3 final size:3
Alignment explanation
Indices: 17258783--17258823 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
17258773 AATAATAATA
17258783 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
17258824 ACGCAAATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17261206 original size:66 final size:66
Alignment explanation
Indices: 17261004--17261497 Score: 352
Period size: 66 Copynumber: 7.4 Consensus size: 66
17260994 CCGGACCCTC
* * * * * * * * * *
17261004 GGAGGCATTAAGAACTCTGGGCCAAGCCCTGGCG-AGGGACACAATTTAATTGACAGCTCGACTC
1 GGAGGCATTAAGGACTCCGGTCCAAGCCCTGGTGTA-GGAAACAAGTTAACTGATAGCTCTAATC
17261068 TT
65 TT
* * * * * ** * * *
17261070 GGAGGTATAAAGGACTCTGGCCCGAGCAATGGTGGTGAGGGACACAAGTTCACTGATAG-TCAAA
1 GGAGGCATTAAGGACTCCGGTCCAAGCCCTGGT-GT-A-GGAAACAAGTTAACTGATAGCTCTAA
*
17261134 CCCTT
63 -TCTT
* * * * *
17261139 GGAGGCATTAAGAACTCCGGTCCAAGCTCTGGT-AAGGGACACAAGATAACTGATAGCTCTAATC
1 GGAGGCATTAAGGACTCCGGTCCAAGCCCTGGTGTA-GGAAACAAGTTAACTGATAGCTCTAATC
17261203 TT
65 TT
* * * * * * * * **
17261205 GGAAGTATAAAGGACTCAGGCCCGAGCCCTGGTGTAGGAAACAAGTTTACCGATAGCTCTCCTCT
1 GGAGGCATTAAGGACTCCGGTCCAAGCCCTGGTGTAGGAAACAAGTTAACTGATAGCTCTAATCT
*
17261270 A
66 T
* * * * * *
17261271 GGTGGCATTAAGGACTCCGGTCCAAGTCCAGGTGTAGGAAATAAATTAACTGATAGCT-TCACTC
1 GGAGGCATTAAGGACTCCGGTCCAAGCCCTGGTGTAGGAAACAAGTTAACTGATAGCTCT-AATC
*
17261335 TA
65 TT
** * * *
17261337 GGAGGCATTAAAAACTCCGGTCCGAGCCCTGGTGTAGGAAACAGGCTAACTGATAGCT-TCAATC
1 GGAGGCATTAAGGACTCCGGTCCAAGCCCTGGTGTAGGAAACAAGTTAACTGATAGCTCT-AATC
17261401 TT
65 TT
* * * * *
17261403 GGAGGCATTAAGGATTCCGGTCCAAGCCCTGGTGTAGGAAACAAGTTAACGGACAGC-CAAACCA
1 GGAGGCATTAAGGACTCCGGTCCAAGCCCTGGTGTAGGAAACAAGTTAACTGATAGCTCTAATC-
*
17261467 TA
65 TT
* *
17261469 GGAGGCATCAAGGACTCTGGTCCAAGCCC
1 GGAGGCATTAAGGACTCCGGTCCAAGCCC
17261498 CGGAGCAGGA
Statistics
Matches: 335, Mismatches: 84, Indels: 18
0.77 0.19 0.04
Matches are distributed among these distances:
65 4 0.01
66 276 0.82
67 6 0.02
68 3 0.01
69 46 0.14
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.21
Consensus pattern (66 bp):
GGAGGCATTAAGGACTCCGGTCCAAGCCCTGGTGTAGGAAACAAGTTAACTGATAGCTCTAATCT
T
Found at i:17261213 original size:135 final size:135
Alignment explanation
Indices: 17260967--17261261 Score: 353
Period size: 135 Copynumber: 2.2 Consensus size: 135
17260957 GTCCAAGTCC
* * ** *
17260967 TGGTGGGGGACACAAGTTTACCGATAGCCGGACCCTCGGAGGCATTAAGAACTCTGGGCCAAGCC
1 TGGTGAGGGACACAAGTTCACCGATAGCCAAACCCTCGGAGGCATTAAGAACTCCGGGCCAAGCC
* ** * * * *
17261032 CTGGCGAGGGACACAATTTAATTGACAGCTCGACTCTTGGAGGTATAAAGGACTCTGGCCCGAGC
66 CTGGCAAGGGACACAAGATAACTGACAGCTCGAATCTTGGAAGTATAAAGGACTCAGGCCCGAGC
17261097 AATGG
131 AATGG
* * * * *
17261102 TGGTGAGGGACACAAGTTCACTGATAGTCAAACCCTTGGAGGCATTAAGAACTCCGGTCCAAGCT
1 TGGTGAGGGACACAAGTTCACCGATAGCCAAACCCTCGGAGGCATTAAGAACTCCGGGCCAAGCC
* * *
17261167 CTGGTAAGGGACACAAGATAACTGATAGCTCTAATCTTGGAAGTATAAAGGACTCAGGCCCGAGC
66 CTGGCAAGGGACACAAGATAACTGACAGCTCGAATCTTGGAAGTATAAAGGACTCAGGCCCGAGC
**
17261232 CCTGG
131 AATGG
* *
17261237 T-GT-A-GGAAACAAGTTTACCGATAGC
1 TGGTGAGGGACACAAGTTCACCGATAGC
17261262 TCTCCTCTAG
Statistics
Matches: 134, Mismatches: 26, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
132 17 0.13
133 1 0.01
134 2 0.01
135 114 0.85
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.20
Consensus pattern (135 bp):
TGGTGAGGGACACAAGTTCACCGATAGCCAAACCCTCGGAGGCATTAAGAACTCCGGGCCAAGCC
CTGGCAAGGGACACAAGATAACTGACAGCTCGAATCTTGGAAGTATAAAGGACTCAGGCCCGAGC
AATGG
Found at i:17262936 original size:19 final size:19
Alignment explanation
Indices: 17262912--17262949 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17262902 TTCTGCTTTT
17262912 GGCTTGATTTATGTTTTCA
1 GGCTTGATTTATGTTTTCA
17262931 GGCTTGATTTATGTTTTCA
1 GGCTTGATTTATGTTTTCA
17262950 CTTCTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.21, T:0.53
Consensus pattern (19 bp):
GGCTTGATTTATGTTTTCA
Found at i:17267074 original size:19 final size:17
Alignment explanation
Indices: 17267037--17267081 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
17267027 AAATATAAAA
*
17267037 TAAATTTTTTATTTTAT
1 TAAATTTTTTATATTAT
17267054 TAAATTTATTTATAATTAT
1 TAAATTT-TTTAT-ATTAT
17267073 TAAAATTTT
1 T-AAATTTT
17267082 AAATTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 5 0.21
19 6 0.25
20 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TAAATTTTTTATATTAT
Found at i:17270489 original size:14 final size:15
Alignment explanation
Indices: 17270457--17270493 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
17270447 CACATTTCTT
17270457 AAATAAAACTAAAAA
1 AAATAAAACTAAAAA
*
17270472 AAATAAAACT-ATAA
1 AAATAAAACTAAAAA
17270486 AAATAAAA
1 AAATAAAA
17270494 TTTTGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.16
Consensus pattern (15 bp):
AAATAAAACTAAAAA
Found at i:17270880 original size:11 final size:12
Alignment explanation
Indices: 17270847--17270892 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
17270837 ATACTGTTAA
17270847 TAATATTATTATT
1 TAATATT-TTATT
17270860 TAATATTTTATT
1 TAATATTTTATT
17270872 TAA-ATTTTATT
1 TAATATTTTATT
*
17270883 GTTATATTTT
1 -TAATATTTT
17270893 TAGAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 8 0.27
12 10 0.33
13 12 0.40
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
TAATATTTTATT
Found at i:17271861 original size:15 final size:15
Alignment explanation
Indices: 17271843--17271900 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
17271833 TATAAAAAAT
17271843 TATTTAATTTATTTA
1 TATTTAATTTATTTA
*
17271858 TATTTAATTTAATTA
1 TATTTAATTTATTTA
* * * *
17271873 AATAATAAATTATTCA
1 TAT-TTAATTTATTTA
17271889 TATTTAATTTAT
1 TATTTAATTTAT
17271901 ATTAAATTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 23 0.70
16 10 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTAATTTATTTA
Found at i:17271864 original size:40 final size:42
Alignment explanation
Indices: 17271820--17271919 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 42
17271810 TCGCTTATTT
* * *
17271820 TTTAAAATATTTATATAAAAAATTATTTA-ATTT-ATTTATA
1 TTTAAAATAATTAAATAAAAAATTATTCATATTTAATTTATA
** *
17271860 TTTAATTTAATTAAATAATAAATTATTCATATTTAATTTATA
1 TTTAAAATAATTAAATAAAAAATTATTCATATTTAATTTATA
*
17271902 -TTAAATTAAATTAAATAA
1 TTTAAAAT-AATTAAATAA
17271920 GATTATTCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 23 0.46
41 10 0.20
42 17 0.34
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (42 bp):
TTTAAAATAATTAAATAAAAAATTATTCATATTTAATTTATA
Found at i:17271886 original size:31 final size:30
Alignment explanation
Indices: 17271846--17271914 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
17271836 AAAAAATTAT
* *
17271846 TTAATTTATTTATATTTAATTTA-ATTAAA
1 TTAAATTATTCATATTTAATTTATATTAAA
17271875 TAATAAATTATTCATATTTAATTTATATTAAA
1 T--TAAATTATTCATATTTAATTTATATTAAA
17271907 TTAAATTA
1 TTAAATTA
17271915 AATAAGATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 1 0.03
30 7 0.20
31 20 0.57
32 7 0.20
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (30 bp):
TTAAATTATTCATATTTAATTTATATTAAA
Found at i:17271914 original size:42 final size:40
Alignment explanation
Indices: 17271834--17271919 Score: 118
Period size: 42 Copynumber: 2.1 Consensus size: 40
17271824 AAATATTTAT
* * *
17271834 ATAAAAAATTATTTAATTTATTTATATTTAATTTAATTAA
1 ATAAAAAATTATTCAATTTATTTATATTAAATTAAATTAA
*
17271874 ATAATAAATTATTCATATTTAATTTATATTAAATTAAATTAA
1 ATAAAAAATTATTCA-ATTT-ATTTATATTAAATTAAATTAA
17271916 ATAA
1 ATAA
17271920 GATTATTCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 13 0.32
41 4 0.10
42 23 0.57
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (40 bp):
ATAAAAAATTATTCAATTTATTTATATTAAATTAAATTAA
Found at i:17271973 original size:25 final size:25
Alignment explanation
Indices: 17271939--17271986 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
17271929 TAAATGTTAA
17271939 ATAAATAATAAACGAATCTTAAACT
1 ATAAATAATAAACGAATCTTAAACT
**
17271964 ATAAATAATAAATTAATCTTAAA
1 ATAAATAATAAACGAATCTTAAA
17271987 TAAATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.31
Consensus pattern (25 bp):
ATAAATAATAAACGAATCTTAAACT
Found at i:17272004 original size:19 final size:19
Alignment explanation
Indices: 17271965--17272009 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
17271955 TCTTAAACTA
*
17271965 TAAAT-AATAAATTAATCT
1 TAAATAAATAAATTAATAT
17271983 TAAATAAATAAATT-ATAAT
1 TAAATAAATAAATTAAT-AT
17272002 T-AATAAAT
1 TAAATAAAT
17272010 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATAAATAAATTAATAT
Found at i:17272042 original size:28 final size:28
Alignment explanation
Indices: 17272011--17272109 Score: 72
Period size: 29 Copynumber: 3.2 Consensus size: 28
17272001 TTAATAAATT
17272011 TAAATAAAATTTTTTTAAAAAATATAAA
1 TAAATAAAATTTTTTTAAAAAATATAAA
***
17272039 TAAATATAAATAAATTTAAAATAATATTAAAA
1 TAAATA-AAATTTTTTTAAAA-AATA-T-AAA
* * *
17272071 TAAAAATAAAATTTTATTAATATTATTATAAA
1 T--AAATAAAATTTTTTTAA-A-AAATATAAA
17272103 TAAATAA
1 TAAATAA
17272110 TAAACTAATG
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
28 6 0.11
29 11 0.20
30 10 0.19
31 1 0.02
32 8 0.15
33 9 0.17
34 9 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAATAAAATTTTTTTAAAAAATATAAA
Found at i:17274457 original size:29 final size:29
Alignment explanation
Indices: 17274385--17274473 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
17274375 AATTAATAGA
17274385 ATTTAAT-ATAAAAATTATTAA-AAATA-TT
1 ATTTAATAATAAAAA-T-TTAATAAATATTT
** *
17274413 ATTT-ATAATTTAAATTTAATCAATATTT
1 ATTTAATAATAAAAATTTAATAAATATTT
* *
17274441 ATTTAATAATAAAAATTTTATTAATATTT
1 ATTTAATAATAAAAATTTAATAAATATTT
17274470 -TTTA
1 ATTTA
17274474 TTAAAAATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
26 4 0.08
27 7 0.14
28 19 0.38
29 20 0.40
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTAATAATAAAAATTTAATAAATATTT
Found at i:17275597 original size:16 final size:17
Alignment explanation
Indices: 17275563--17275601 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
17275553 TGATATAAAT
*
17275563 ATAATATAAAATTAATA
1 ATAATTTAAAATTAATA
*
17275580 ATAATTTAAAATT-TTA
1 ATAATTTAAAATTAATA
17275596 ATAATT
1 ATAATT
17275602 ATTATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATTTAAAATTAATA
Found at i:17276534 original size:20 final size:19
Alignment explanation
Indices: 17276509--17276548 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17276499 ATTTGACTAC
*
17276509 TTTAATAGATGAGAAAAAAT
1 TTTAATA-ATCAGAAAAAAT
*
17276529 TTTAATAATCATAAAAAAT
1 TTTAATAATCAGAAAAAAT
17276548 T
1 T
17276549 ATAAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (19 bp):
TTTAATAATCAGAAAAAAT
Found at i:17276555 original size:20 final size:20
Alignment explanation
Indices: 17276522--17276560 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
17276512 AATAGATGAG
*
17276522 AAAAAATTTTAATA-ATCAT
1 AAAAAATTTAAATATATCAT
17276541 AAAAAATTATAAATATATCA
1 AAAAAATT-TAAATATATCA
17276561 AACAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATTTAAATATATCAT
Found at i:17279093 original size:21 final size:22
Alignment explanation
Indices: 17279068--17279112 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
17279058 TTGGTTTGAA
**
17279068 AAAATAAACTATAAAAAAA-TT
1 AAAATAAAAAATAAAAAAACTT
17279089 AAAATAAAAAATAAAAAAACTT
1 AAAATAAAAAATAAAAAAACTT
17279111 AA
1 AA
17279113 CTTTTAAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAATAAAAAATAAAAAAACTT
Found at i:17283927 original size:23 final size:23
Alignment explanation
Indices: 17283901--17283949 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
17283891 ATTTTTATTA
17283901 AATTTTTTAATCACAACTATAAT
1 AATTTTTTAATCACAACTATAAT
* *
17283924 AATTTTTTAATCATAATTATAAT
1 AATTTTTTAATCACAACTATAAT
17283947 AAT
1 AAT
17283950 AATAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTTTTAATCACAACTATAAT
Found at i:17285247 original size:2 final size:2
Alignment explanation
Indices: 17285242--17285268 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17285232 TCTCTCTCTC
17285242 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 T
17285269 TTCTTTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17286862 original size:17 final size:17
Alignment explanation
Indices: 17286840--17286874 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17286830 TAATATAATA
17286840 TTAAT-AAAATATTATTT
1 TTAATAAAAATA-TATTT
17286857 TTAATAAAAATATATTT
1 TTAATAAAAATATATTT
17286874 T
1 T
17286875 AATTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAATAAAAATATATTT
Found at i:17298587 original size:59 final size:59
Alignment explanation
Indices: 17298465--17298617 Score: 155
Period size: 59 Copynumber: 2.5 Consensus size: 59
17298455 GATATTTTTG
* * ** *** *
17298465 TAATTATGATAAAAAAATATTATAATTATTTTGATCAATTTTGATGGAAGAGTGTTTTTA
1 TAATTATGAT-AAAAAATATTATAATAATTTTAATCAATGATGATGGAAGACAATTTTCA
*
17298525 TAATTATGATAAAAAATATTATAATAATTTTAATCAATGATGGTGGTAA-ACAATTTTCA
1 TAATTATGATAAAAAATATTATAATAATTTTAATCAATGATGATGG-AAGACAATTTTCA
* * *
17298584 TAATTATAGTTAGAGAAATATTATAATATTTTTA
1 TAATTAT-GATA-AAAAATATTATAATAATTTTA
17298618 GCTTTATACA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 44 0.56
60 15 0.19
61 19 0.24
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (59 bp):
TAATTATGATAAAAAATATTATAATAATTTTAATCAATGATGATGGAAGACAATTTTCA
Found at i:17298810 original size:57 final size:57
Alignment explanation
Indices: 17298692--17298820 Score: 149
Period size: 57 Copynumber: 2.3 Consensus size: 57
17298682 TTGTAAGAAT
* *
17298692 TTTTTTTGTCATTTAAAAATAAAAAATATTATAATAATTTGACATTTATAAGGAGGG
1 TTTTTTTGTCATTTAAAAATAAAAAATATTATAATAATTTGACATTCATAAAGAGGG
* * *
17298749 TTTTTTTGTCATTTAAGAAATGAGAAA-ATTATAGTAATTT-A-ATTCA-AAAGAGGG
1 TTTTTTTGTCATTTAA-AAATAAAAAATATTATAATAATTTGACATTCATAAAGAGGG
* *
17298803 ATATTTTTGTCAATTAAA
1 -TTTTTTTGTCATTTAAA
17298821 TAGGAGAGCA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
54 8 0.13
55 18 0.29
56 1 0.02
57 28 0.44
58 8 0.13
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (57 bp):
TTTTTTTGTCATTTAAAAATAAAAAATATTATAATAATTTGACATTCATAAAGAGGG
Found at i:17303506 original size:61 final size:61
Alignment explanation
Indices: 17303411--17303532 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
17303401 GACAACCAAG
17303411 TTCCAATATAGCCTATGAAAAACAACAGGCAAGAGAATATCAAAACAGAGCACCCCAAGTA
1 TTCCAATATAGCCTATGAAAAACAACAGGCAAGAGAATATCAAAACAGAGCACCCCAAGTA
* *
17303472 TTCCAATATAGTCTATGAAAAACAACAGGCAAGAGAATTTCAAAACAGAGCACCCCAAGTA
1 TTCCAATATAGCCTATGAAAAACAACAGGCAAGAGAATATCAAAACAGAGCACCCCAAGTA
17303533 ATTGTGGACA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.47, C:0.22, G:0.15, T:0.16
Consensus pattern (61 bp):
TTCCAATATAGCCTATGAAAAACAACAGGCAAGAGAATATCAAAACAGAGCACCCCAAGTA
Found at i:17310064 original size:2 final size:2
Alignment explanation
Indices: 17310057--17310083 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17310047 TATCAAACAA
17310057 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 A
17310084 GTGGGTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17312721 original size:22 final size:22
Alignment explanation
Indices: 17312681--17312722 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
17312671 TTTATTTTTA
17312681 TTTCTAGAAAATTACATGTTAT
1 TTTCTAGAAAATTACATGTTAT
*
17312703 TTTCATAGAAGATTA-ATGTT
1 TTTC-TAGAAAATTACATGTT
17312723 GAATGAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (22 bp):
TTTCTAGAAAATTACATGTTAT
Found at i:17312870 original size:18 final size:19
Alignment explanation
Indices: 17312841--17312877 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
17312831 AATATGGTTA
17312841 ATTAATTATAAATTATTAT
1 ATTAATTATAAATTATTAT
17312860 ATTAA-TATAAATTATTAT
1 ATTAATTATAAATTATTAT
17312878 TATCTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTAATTATAAATTATTAT
Found at i:17315789 original size:36 final size:37
Alignment explanation
Indices: 17315722--17315793 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
17315712 CATTCTTAAG
17315722 AAGTTAATTTAATAAATTTAAATATTTAAATCTCAAC
1 AAGTTAATTTAATAAATTTAAATATTTAAATCTCAAC
17315759 AAGTTAATTTAATAAATTT-AATATTTAAATCTCAA
1 AAGTTAATTTAATAAATTTAAATATTTAAATCTCAA
17315794 TGTCTGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 16 0.46
37 19 0.54
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.42
Consensus pattern (37 bp):
AAGTTAATTTAATAAATTTAAATATTTAAATCTCAAC
Found at i:17328508 original size:85 final size:85
Alignment explanation
Indices: 17328419--17328582 Score: 265
Period size: 85 Copynumber: 1.9 Consensus size: 85
17328409 GAATGTTTGA
*
17328419 TATGAGATTATTCGTCTAAAAATCATGGTAATTTACATTTAGTAATTACATCACCTTATTTGATA
1 TATGAGATTATTCGTCTAAAAATCATGGTAATTTACATTTAATAATTACATCACCTTATTTGATA
*
17328484 ACAATTTACAAATCCCGTGG
66 ACAATTTAAAAATCCCGTGG
* * * *
17328504 TATGAGATTTTTTGTCTAAAAATCATGGTGATTTACATTTAATAATTACATCACCTTATTTGGTA
1 TATGAGATTATTCGTCTAAAAATCATGGTAATTTACATTTAATAATTACATCACCTTATTTGATA
*
17328569 ATAATTTAAAAATC
66 ACAATTTAAAAATC
17328583 TTATGTGATA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 72 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (85 bp):
TATGAGATTATTCGTCTAAAAATCATGGTAATTTACATTTAATAATTACATCACCTTATTTGATA
ACAATTTAAAAATCCCGTGG
Found at i:17329617 original size:15 final size:17
Alignment explanation
Indices: 17329585--17329622 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
17329575 TTTTTTATTA
17329585 TTTTTAAAATTTATAAT
1 TTTTTAAAATTTATAAT
*
17329602 TTTTTAATA-TTA-AAT
1 TTTTTAAAATTTATAAT
17329617 TTTTTA
1 TTTTTA
17329623 TTATACTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
17 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTAAAATTTATAAT
Found at i:17339451 original size:29 final size:30
Alignment explanation
Indices: 17339401--17339468 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
17339391 ATTCATATTA
*
17339401 ATATATTTAATTTTTTTAAAATTTAAATTT
1 ATATATTTAATTTTTTTAAAATTTAAAATT
17339431 ATATA-TT-ATTTTTATTAAAATTTAAAATT
1 ATATATTTAATTTTT-TTAAAATTTAAAATT
17339460 ATATCATTT
1 ATAT-ATTT
17339469 TTCATATCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.18
29 20 0.59
30 6 0.18
31 2 0.06
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (30 bp):
ATATATTTAATTTTTTTAAAATTTAAAATT
Found at i:17339462 original size:27 final size:28
Alignment explanation
Indices: 17339401--17339470 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
17339391 ATTCATATTA
* *
17339401 ATATATTTAATTTTTTTAAAATTTAAAT
1 ATATATATCATTTTTTTAAAATTTAAAT
* *
17339429 TTATATATTATTTTTATTAAAATTTAAA-
1 ATATATATCATTTTT-TTAAAATTTAAAT
17339457 AT-TATATCATTTTT
1 ATATATATCATTTTT
17339471 CATATCGTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 11 0.31
28 13 0.36
29 12 0.33
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATATATCATTTTTTTAAAATTTAAAT
Found at i:17345469 original size:10 final size:10
Alignment explanation
Indices: 17345454--17345480 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
17345444 TAAATTTGTA
17345454 AAATTTTAAT
1 AAATTTTAAT
17345464 AAATTTTAAT
1 AAATTTTAAT
17345474 AAATTTT
1 AAATTTT
17345481 GATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AAATTTTAAT
Found at i:17345546 original size:29 final size:30
Alignment explanation
Indices: 17345506--17345594 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 30
17345496 ATAAATATTT
17345506 TTATT-AA-AAATATTAAT-ATAATTTTTA
1 TTATTAAATAAATATTAATAATAATTTTTA
* * *
17345533 TTATTAAATAAATATCAATCA-AATTTTAA
1 TTATTAAATAAATATTAATAATAATTTTTA
**
17345562 TTA-TAAAT-AATATTTTTAATAATTTTTA
1 TTATTAAATAAATATTAATAATAATTTTTA
17345590 -TATTA
1 TTATTA
17345595 TATTATATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
27 14 0.28
28 16 0.32
29 19 0.38
30 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
TTATTAAATAAATATTAATAATAATTTTTA
Found at i:17349890 original size:9 final size:9
Alignment explanation
Indices: 17349876--17349908 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
17349866 ATATTTGCTA
*
17349876 TTGTTGTTG
1 TTGTTGGTG
17349885 TTGTTGGTG
1 TTGTTGGTG
17349894 TTGTTGGTG
1 TTGTTGGTG
17349903 TT-TTGG
1 TTGTTGG
17349909 CTTTACTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.39, T:0.61
Consensus pattern (9 bp):
TTGTTGGTG
Found at i:17351465 original size:2 final size:2
Alignment explanation
Indices: 17351458--17351484 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17351448 ATAGAAAAGA
17351458 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 A
17351485 CATAATTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17351957 original size:22 final size:21
Alignment explanation
Indices: 17351927--17351981 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
17351917 TTATTATTAC
*
17351927 TATTATTTTATA-T-TATTGA
1 TATTATTTTTTATTGTATTGA
* *
17351946 TATTCTATTTTTATTGTATTTA
1 TATTAT-TTTTTATTGTATTGA
17351968 TATTATTTTTTATT
1 TATTATTTTTTATT
17351982 TGTTTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.17
20 5 0.17
21 9 0.31
22 10 0.34
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (21 bp):
TATTATTTTTTATTGTATTGA
Found at i:17351984 original size:22 final size:22
Alignment explanation
Indices: 17351927--17351989 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
17351917 TTATTATTAC
* *
17351927 TATTATTTTATAT-TATTGATAT
1 TATT-TTTTATTTGTATTTATAT
*
17351949 TCTATTTTTA-TTGTATTTATAT
1 TAT-TTTTTATTTGTATTTATAT
*
17351971 TATTTTTTATTTGTTTTTA
1 TATTTTTTATTTGTATTTA
17351990 ATGTATATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
21 7 0.21
22 25 0.76
23 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.70
Consensus pattern (22 bp):
TATTTTTTATTTGTATTTATAT
Found at i:17353448 original size:13 final size:14
Alignment explanation
Indices: 17353430--17353461 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
17353420 CAAATGGTAG
17353430 AAAATTTA-AAAAT
1 AAAATTTATAAAAT
17353443 AAAATTTATAAAAT
1 AAAATTTATAAAAT
17353457 AAAAT
1 AAAAT
17353462 AAATTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATTTATAAAAT
Found at i:17353467 original size:18 final size:19
Alignment explanation
Indices: 17353438--17353479 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
17353428 AGAAAATTTA
17353438 AAAATAAAATTTAT-AAAAT
1 AAAATAAAATTT-TGAAAAT
17353457 AAAAT-AAATTTTGAAAAT
1 AAAATAAAATTTTGAAAAT
17353475 AAAAT
1 AAAAT
17353480 TCTCAGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.05
18 16 0.73
19 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATAAAATTTTGAAAAT
Found at i:17354191 original size:26 final size:26
Alignment explanation
Indices: 17354161--17354212 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17354151 TTTTTTAAGT
17354161 AAGCAATAAGATAAAAAATTTAAAGA
1 AAGCAATAAGATAAAAAATTTAAAGA
17354187 AAGCAATAAGATAAAAAATTTAAAGA
1 AAGCAATAAGATAAAAAATTTAAAGA
17354213 TAAAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.19
Consensus pattern (26 bp):
AAGCAATAAGATAAAAAATTTAAAGA
Found at i:17354214 original size:15 final size:15
Alignment explanation
Indices: 17354168--17354231 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
17354158 AGTAAGCAAT
17354168 AAGATAAAAAATTTA
1 AAGATAAAAAATTTA
**
17354183 AAGA-AAGCAA--T-
1 AAGATAAAAAATTTA
17354194 AAGATAAAAAATTTA
1 AAGATAAAAAATTTA
*
17354209 AAGATAAAAAATTTT
1 AAGATAAAAAATTTA
17354224 AAGATAAA
1 AAGATAAA
17354232 TTAAATTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
11 4 0.10
12 5 0.12
14 5 0.12
15 26 0.65
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (15 bp):
AAGATAAAAAATTTA
Found at i:17354405 original size:18 final size:18
Alignment explanation
Indices: 17354382--17354418 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17354372 TTTTTAACTT
17354382 TTAGATCAATTTGATATA
1 TTAGATCAATTTGATATA
*
17354400 TTAGATCGATTTGATATA
1 TTAGATCAATTTGATATA
17354418 T
1 T
17354419 ACAATAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (18 bp):
TTAGATCAATTTGATATA
Found at i:17355910 original size:58 final size:56
Alignment explanation
Indices: 17355832--17356052 Score: 248
Period size: 58 Copynumber: 3.8 Consensus size: 56
17355822 ATTTTTAAAG
* *
17355832 GAAAAATTGAAAGTATCAATTTTTCTTGACAACA-AAAATTTTTAAAGAACATTTTTA
1 GAAAAATTAAAAGTATCAATTTTTCTT-A-AAAATAAAATTTTTAAAGAACATTTTTA
* * ** * *
17355889 GAAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAAACTTGAAGAAAAATATTTTTAAA
1 GAAAAA-TTAAAAGTATCAATTTTTCTTAAAAATAAAATTTTTA-AAGAACATTTTT--A
* *
17355949 GGAAAAATTGAAAGTATCAATTTTTCTTGACAACA-AAAATTTTTAAAGAACATTTTTA
1 -GAAAAATTAAAAGTATCAATTTTTCTT-A-AAAATAAAATTTTTAAAGAACATTTTTA
17356007 GAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTTTAAA
1 GAAAAA-TTAAAAGTATCAATTTTTCTTAAAAATAAAATTTTTAAA
17356053 ATAAAAAATT
Statistics
Matches: 136, Mismatches: 18, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
56 6 0.04
57 33 0.24
58 50 0.37
60 30 0.22
61 14 0.10
62 3 0.02
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (56 bp):
GAAAAATTAAAAGTATCAATTTTTCTTAAAAATAAAATTTTTAAAGAACATTTTTA
Found at i:17355952 original size:118 final size:118
Alignment explanation
Indices: 17355805--17356044 Score: 471
Period size: 118 Copynumber: 2.0 Consensus size: 118
17355795 TGGATGTATC
17355805 AAAACTTGAAGAAAAATATTTTTAAAGGAAAAATTGAAAGTATCAATTTTTCTTGACAACAAAAA
1 AAAACTTGAAGAAAAATATTTTTAAAGGAAAAATTGAAAGTATCAATTTTTCTTGACAACAAAAA
17355870 TTTTTAAAGAACATTTTTAGAAAAAGTTAAAAGTATCAATTTTCCTTAAAAAT
66 TTTTTAAAGAACATTTTTAGAAAAAGTTAAAAGTATCAATTTTCCTTAAAAAT
17355923 AAAACTTGAAGAAAAATATTTTTAAAGGAAAAATTGAAAGTATCAATTTTTCTTGACAACAAAAA
1 AAAACTTGAAGAAAAATATTTTTAAAGGAAAAATTGAAAGTATCAATTTTTCTTGACAACAAAAA
*
17355988 TTTTTAAAGAACATTTTTAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAAT
66 TTTTTAAAGAACATTTTTAGAAAAAGTTAAAAGTATCAATTTTCCTTAAAAAT
17356041 AAAA
1 AAAA
17356045 TTTTTAAAAT
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 121 1.00
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (118 bp):
AAAACTTGAAGAAAAATATTTTTAAAGGAAAAATTGAAAGTATCAATTTTTCTTGACAACAAAAA
TTTTTAAAGAACATTTTTAGAAAAAGTTAAAAGTATCAATTTTCCTTAAAAAT
Found at i:17359744 original size:16 final size:16
Alignment explanation
Indices: 17359725--17359756 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17359715 CTTAAAGATA
*
17359725 AAAAGAAAAGAAAAAT
1 AAAAGAAAAAAAAAAT
17359741 AAAAGAAAAAAAAAAT
1 AAAAGAAAAAAAAAAT
17359757 GAATGTCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAT
Found at i:17360144 original size:18 final size:18
Alignment explanation
Indices: 17360121--17360174 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
17360111 AAAAATGGAT
*
17360121 GAAAAAACAAGAAAAAGA
1 GAAAAAAAAAGAAAAAGA
*
17360139 GAAAAAAAAATGAAATA-A
1 GAAAAAAAAA-GAAAAAGA
*
17360157 GAAAAAATAAGAAAAAGA
1 GAAAAAAAAAGAAAAAGA
17360175 AAAGATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 5 0.17
18 20 0.67
19 5 0.17
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.06
Consensus pattern (18 bp):
GAAAAAAAAAGAAAAAGA
Found at i:17360161 original size:16 final size:16
Alignment explanation
Indices: 17360121--17360187 Score: 64
Period size: 18 Copynumber: 4.0 Consensus size: 16
17360111 AAAAATGGAT
*
17360121 GAAAAAACAAGAAAAAGA
1 GAAAAAATAAG-AAAA-A
*
17360139 GAAAAAAAAATGAAATAA
1 GAAAAAATAA-GAAA-AA
17360157 GAAAAAATAAGAAAAA
1 GAAAAAATAAGAAAAA
*
17360173 GAAAAGATAA-AAAAA
1 GAAAAAATAAGAAAAA
17360188 ACTCAAATTG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.11
16 11 0.25
17 4 0.09
18 22 0.50
19 2 0.05
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.06
Consensus pattern (16 bp):
GAAAAAATAAGAAAAA
Found at i:17361318 original size:21 final size:20
Alignment explanation
Indices: 17361291--17361410 Score: 88
Period size: 21 Copynumber: 6.0 Consensus size: 20
17361281 TTAAATAATC
17361291 TTCAAATGAGAATCTTTGAG
1 TTCAAATGAGAATCTTTGAG
*
17361311 TGTCAAATAAGAATCTTTGAGG
1 T-TCAAATGAGAATCTTTGA-G
* ** *
17361333 TGTGAAACCCA-AA-ATTT-A-
1 T-TCAAA-TGAGAATCTTTGAG
* *
17361351 -TCAAATGAGAATCTTCGAA
1 TTCAAATGAGAATCTTTGAG
*
17361370 TTCAAATGAGAATCTTTGAAT
1 TTCAAATGAGAATCTTTG-AG
17361391 TTCAAATGAGAATCTTTGAG
1 TTCAAATGAGAATCTTTGAG
17361411 ATGTGAAACC
Statistics
Matches: 78, Mismatches: 13, Indels: 18
0.72 0.12 0.17
Matches are distributed among these distances:
15 1 0.01
16 6 0.08
17 2 0.03
18 1 0.01
20 19 0.24
21 39 0.50
22 9 0.12
23 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (20 bp):
TTCAAATGAGAATCTTTGAG
Found at i:17361376 original size:20 final size:21
Alignment explanation
Indices: 17361351--17361406 Score: 96
Period size: 20 Copynumber: 2.7 Consensus size: 21
17361341 CCAAAATTTA
17361351 TCAAATGAGAATCTTCGAA-T
1 TCAAATGAGAATCTTCGAATT
*
17361371 TCAAATGAGAATCTTTGAATT
1 TCAAATGAGAATCTTCGAATT
17361392 TCAAATGAGAATCTT
1 TCAAATGAGAATCTT
17361407 TGAGATGTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (21 bp):
TCAAATGAGAATCTTCGAATT
Found at i:17361602 original size:114 final size:114
Alignment explanation
Indices: 17361469--17361740 Score: 429
Period size: 114 Copynumber: 2.4 Consensus size: 114
17361459 AGTTTTGAAC
*
17361469 TTTTGGATGTGAATCTCCAAAATTCAAACGAAAAGCTTTGAACTCAACTTTTGGATATGAATCTC
1 TTTTGGATGTGAATCTCCAAAATTCAAACGAAAAGCTTTGAACTCAACTTTTGGATACGAATCTC
*
17361534 TAAATTTTTTAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATT
66 TAAATTTTTGAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATT
* *
17361583 TTTTGGATGTGAATCTCCAAAATTCAAACGAAAAGCTTTGAACTCAACTTTTGGATGCGCATCTC
1 TTTTGGATGTGAATCTCCAAAATTCAAACGAAAAGCTTTGAACTCAACTTTTGGATACGAATCTC
*
17361648 TAAATTTTTGAGTGAGTACCTTTGAACTTAGATGTGAAACTCTAAGATT
66 TAAATTTTTGAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATT
* * ****
17361697 TCTTGAATGTGAA-CGTTTTGAATTCAAACGAAAAGCTTTGAACT
1 TTTTGGATGTGAATC-TCCAAAATTCAAACGAAAAGCTTTGAACT
17361741 TTTGGATGAG
Statistics
Matches: 146, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 1 0.01
114 145 0.99
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (114 bp):
TTTTGGATGTGAATCTCCAAAATTCAAACGAAAAGCTTTGAACTCAACTTTTGGATACGAATCTC
TAAATTTTTGAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATT
Found at i:17362581 original size:121 final size:121
Alignment explanation
Indices: 17362438--17362727 Score: 476
Period size: 121 Copynumber: 2.4 Consensus size: 121
17362428 TTTTGTGCAG
17362438 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATGTTTTTTTTTTTGAAACTTTGATTTTTAAGG
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAA--TTTTTTTTTTTGAAACTTTGATTTTTAAGG
* * *
17362503 AAAATTGATACTTTCAACTTTTCTC-AAAAATA-TTTTTTGGAAATTTTGATTTTCAA
64 AAAATTGAAACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTTCAA
*
17362559 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAATTTTTTTTTTGAAACTTTGATTTTTAAGGAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTTTGAAACTTTGATTTTTAAGGAA
17362624 AATTGAAACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTTCAA
66 AATTGAAACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTTCAA
* * * *
17362680 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATTCTTTTTTTTGAAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTTTGAAA
17362728 TTTTTTTTAA
Statistics
Matches: 158, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
119 52 0.33
120 7 0.04
121 99 0.63
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (121 bp):
GAAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTTTGAAACTTTGATTTTTAAGGAA
AATTGAAACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTTCAA
Found at i:17362844 original size:4 final size:4
Alignment explanation
Indices: 17362837--17362868 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
17362827 AACCTAATCT
17362837 AATA AATA AATA AATAA AATA AATA AATA AAT
1 AATA AATA AATA AAT-A AATA AATA AATA AAT
17362869 TCAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:17362858 original size:13 final size:13
Alignment explanation
Indices: 17362840--17362867 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17362830 CTAATCTAAT
17362840 AAATAAATAAATA
1 AAATAAATAAATA
17362853 AAATAAATAAATA
1 AAATAAATAAATA
17362866 AA
1 AA
17362868 TTCAAAAAAA
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:17363344 original size:24 final size:22
Alignment explanation
Indices: 17363317--17363368 Score: 52
Period size: 24 Copynumber: 2.2 Consensus size: 22
17363307 TGAAATTTGG
17363317 AATTTTCCAAAAAT-TCTCAAAAA
1 AATTTT-CAAAAATCT-TCAAAAA
*
17363340 TAATTCGTCAAAAATCTTCAAAAA
1 -AATT-TTCAAAAATCTTCAAAAA
17363364 AATTT
1 AATTT
17363369 CTGCTAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
23 4 0.17
24 18 0.75
25 2 0.08
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (22 bp):
AATTTTCAAAAATCTTCAAAAA
Found at i:17363808 original size:25 final size:24
Alignment explanation
Indices: 17363758--17363827 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
17363748 AAGATAAAAA
*
17363758 ATAATAATAATAAT-AA-ATAAATT
1 ATAAT-ATAATAATAAATATAAACT
17363781 ATAATATAATAATAAATATATAACT
1 ATAATATAATAATAAATATA-AACT
* *
17363806 ATATAAATAA-AATACATATAAA
1 ATA-ATATAATAATAAATATAAA
17363828 TATTAACAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 8 0.20
23 7 0.17
24 5 0.12
25 15 0.38
26 5 0.12
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAATATAATAATAAATATAAACT
Found at i:17363809 original size:22 final size:22
Alignment explanation
Indices: 17363751--17363811 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
17363741 ATATTACAAG
*
17363751 ATAAAAAATAATAATAATAATAA
1 ATAAATAATAAT-ATAATAATAA
*
17363774 ATAAATTATAATATAATAATAA
1 ATAAATAATAATATAATAATAA
*
17363796 ATATATAACT-ATATAA
1 ATAAATAA-TAATATAA
17363812 ATAAAATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 22 0.67
23 11 0.33
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAATAATAATATAATAATAA
Found at i:17363814 original size:28 final size:26
Alignment explanation
Indices: 17363756--17363829 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
17363746 ACAAGATAAA
17363756 AAATAATAATAATAATAAATAAATTAT
1 AAAT-ATAATAATAATAAATAAATTAT
* *
17363783 -AATATAATAATAAATATATAACTATAT
1 AAATATAATAAT-AATAAATAAAT-TAT
*
17363810 AAATAAAATACAT-ATAAATA
1 AAATATAATA-ATAATAAATA
17363830 TTAACAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 8 0.21
26 12 0.31
27 9 0.23
28 8 0.21
29 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (26 bp):
AAATATAATAATAATAAATAAATTAT
Found at i:17364128 original size:15 final size:14
Alignment explanation
Indices: 17364106--17364136 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
17364096 TCATCTTTTA
17364106 TTTTTTTTTTGTTT
1 TTTTTTTTTTGTTT
17364120 TTTTGTTTTTTGTTT
1 TTTT-TTTTTTGTTT
17364135 TT
1 TT
17364137 AATTTTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Found at i:17364232 original size:42 final size:43
Alignment explanation
Indices: 17364150--17364252 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 43
17364140 TTTTACCAAA
* * ** * *
17364150 GCTCATCTAAACAGAGGCTCAACGACTTTTAGAAACATAAATG
1 GCTCCTCTAAACAGAGGCTCAACAACTTAAAAAAAAATAAATG
* *
17364193 GCTCCTCTAATCAG-GGCTCAACAACTTAAAAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCTCAACAACTTAAAAAAAAATAAATG
*
17364235 ACTCCTCTAAACAGAGGC
1 GCTCCTCTAAACAGAGGC
17364253 ACCACGATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
42 34 0.69
43 15 0.31
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (43 bp):
GCTCCTCTAAACAGAGGCTCAACAACTTAAAAAAAAATAAATG
Done.