Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 22 of 39
Found at i:3259419 original size:13 final size:13
Alignment explanation
Indices: 3259395--3259441 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
3259385 TTTTTATTTT
3259395 TTTAAGTATTTATA
1 TTTAA-TATTTATA
3259409 TTTAATATTTATA
1 TTTAATATTTATA
*
3259422 TTTGATATATT-T-
1 TTTAATAT-TTATA
3259434 TTTAATAT
1 TTTAATAT
3259442 GAATAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 7 0.23
13 16 0.53
14 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:3261913 original size:30 final size:32
Alignment explanation
Indices: 3261872--3261931 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
3261862 TTAATATTTT
* *
3261872 AAATATAAATATA-ATTTTTTTAATATATAAA
1 AAATATAAATATATATGTTTTGAATATATAAA
3261903 AAAT-TAAATATATATGTTTTGAATATATA
1 AAATATAAATATATATGTTTTGAATATATA
3261932 TTATATCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (32 bp):
AAATATAAATATATATGTTTTGAATATATAAA
Found at i:3263135 original size:51 final size:53
Alignment explanation
Indices: 3263059--3263166 Score: 202
Period size: 51 Copynumber: 2.1 Consensus size: 53
3263049 CCCTTCTCTC
3263059 TATACTTACATTGTACCTTAAATTTTTAA-TTTT-TTTAAAAATATTTTTATT
1 TATACTTACATTGTACCTTAAATTTTTAATTTTTATTTAAAAATATTTTTATT
3263110 TATACTTACATTGTACCTTAAATTTTTAATTTTTATTTAAAAATATTTTTATT
1 TATACTTACATTGTACCTTAAATTTTTAATTTTTATTTAAAAATATTTTTATT
3263163 TATA
1 TATA
3263167 TATACATCTA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 29 0.53
52 4 0.07
53 22 0.40
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (53 bp):
TATACTTACATTGTACCTTAAATTTTTAATTTTTATTTAAAAATATTTTTATT
Found at i:3264444 original size:15 final size:14
Alignment explanation
Indices: 3264419--3264448 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3264409 AAATTGTAAC
3264419 AAAATTAAAATTTT
1 AAAATTAAAATTTT
3264433 AAAATCTAAAATTTT
1 AAAAT-TAAAATTTT
3264448 A
1 A
3264449 TAATATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATTAAAATTTT
Found at i:3264679 original size:16 final size:17
Alignment explanation
Indices: 3264658--3264689 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3264648 TGCTTTTACT
3264658 AATTATA-TTATTAATC
1 AATTATATTTATTAATC
3264674 AATTATATTTATTAAT
1 AATTATATTTATTAAT
3264690 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTATATTTATTAATC
Found at i:3267130 original size:14 final size:15
Alignment explanation
Indices: 3267098--3267134 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3267088 TTGACCCTTC
3267098 ATTTG-TAAAATTTA
1 ATTTGATAAAATTTA
*
3267112 TTTTGATAAAA-TTA
1 ATTTGATAAAATTTA
3267126 ATTTGATAA
1 ATTTGATAA
3267135 CTCTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (15 bp):
ATTTGATAAAATTTA
Found at i:3269649 original size:14 final size:15
Alignment explanation
Indices: 3269619--3269651 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3269609 TAAGAGATAA
*
3269619 ATAATTTAATCAATT
1 ATAATTTAATAAATT
3269634 ATAATTTAA-AAATT
1 ATAATTTAATAAATT
3269648 ATAA
1 ATAA
3269652 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATTTAATAAATT
Found at i:3269675 original size:15 final size:16
Alignment explanation
Indices: 3269630--3269675 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
3269620 TAATTTAATC
3269630 AATTATAAT--TTAAA
1 AATTATAATAATTAAA
* *
3269644 AATTATAAAAATAAAA
1 AATTATAATAATTAAA
3269660 AATT-TAATAATTAAA
1 AATTATAATAATTAAA
3269675 A
1 A
3269676 TCTTAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 8 0.31
15 10 0.38
16 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTATAATAATTAAA
Found at i:3271288 original size:2 final size:2
Alignment explanation
Indices: 3271281--3271338 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
3271271 AGCGGCATTA
* *
3271281 AT AT AT AT AT AC AT AT AT AG AT AT AT AT AT A- AGT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
3271323 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3271339 GAAATATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3271839 original size:27 final size:27
Alignment explanation
Indices: 3271786--3271846 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
3271776 CCTCACATAA
* **
3271786 ATATA-TTT-AATTTTTTTAATATTTT
1 ATATATTTTAAATTTTTTTAAAAAATT
3271811 ATATATTTTAAATTTTTTTAAAAAATT
1 ATATATTTTAAATTTTTTTAAAAAATT
3271838 ATAT-TTTTA
1 ATATATTTTA
3271847 TATTCATGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.16
26 8 0.26
27 18 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
ATATATTTTAAATTTTTTTAAAAAATT
Found at i:3271979 original size:16 final size:17
Alignment explanation
Indices: 3271958--3272002 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
3271948 ATAAATCAGT
*
3271958 ATTTTACATTTATTA-A
1 ATTTTAAATTTATTATA
*
3271974 ATTTTAAATTTATTATG
1 ATTTTAAATTTATTATA
*
3271991 ATTTTATATTTA
1 ATTTTAAATTTA
3272003 ACTGAAGTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTTAAATTTATTATA
Found at i:3277719 original size:17 final size:16
Alignment explanation
Indices: 3277690--3277731 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3277680 TATATTTTTA
*
3277690 TAAT-TTTTTATAAGAT
1 TAATATTTTAATAA-AT
3277706 TAATATTTTAATAAAT
1 TAATATTTTAATAAAT
3277722 TAATTATTTT
1 TAA-TATTTT
3277732 TTATTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TAATATTTTAATAAAT
Found at i:3278563 original size:17 final size:16
Alignment explanation
Indices: 3278531--3278570 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3278521 ATAAAATTTT
3278531 TATAAATTTAATTTAA
1 TATAAATTTAATTTAA
*
3278547 TATAAATTATTATTTAA
1 TATAAATT-TAATTTAA
3278564 TAATAAA
1 T-ATAAA
3278571 AATTATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 8 0.38
18 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAAATTTAATTTAA
Found at i:3278623 original size:21 final size:20
Alignment explanation
Indices: 3278587--3278631 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3278577 ATTTTTATTT
3278587 AAATTTAATTATAAAATATA
1 AAATTTAATTATAAAATATA
3278607 AAATATTAA-TATAAAA-ATA
1 AAAT-TTAATTATAAAATATA
*
3278626 ATATTT
1 AAATTT
3278632 TAATAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 6 0.26
20 11 0.48
21 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATTTAATTATAAAATATA
Found at i:3278634 original size:19 final size:20
Alignment explanation
Indices: 3278590--3278636 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3278580 TTTATTTAAA
3278590 TTTAATTATAAAATATAAAAT
1 TTTAA-TATAAAATATAAAAT
* *
3278611 ATTAATATAAAA-ATAATAT
1 TTTAATATAAAATATAAAAT
3278630 TTTAATA
1 TTTAATA
3278637 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 12 0.52
20 7 0.30
21 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAATATAAAATATAAAAT
Found at i:3279604 original size:16 final size:17
Alignment explanation
Indices: 3279572--3279604 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3279562 ATTAATTTTA
*
3279572 AATATTTTTATATAATT
1 AATATTTTAATATAATT
3279589 AATATTTTAATA-AATT
1 AATATTTTAATATAATT
3279605 GATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATTTTAATATAATT
Found at i:3280736 original size:2 final size:2
Alignment explanation
Indices: 3280729--3280761 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3280719 AAAAGTATGA
3280729 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
3280762 AATGAAAGGT
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:3282925 original size:30 final size:28
Alignment explanation
Indices: 3282891--3282955 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
3282881 TCGAAAATAC
* *
3282891 TATTTTTTACTATATATTTAATAGTTAAAA
1 TATTTTTTA-TATAGAATTAATAGTT-AAA
* *
3282921 TATTTTTTATATCGAATTAATTGTTAAA
1 TATTTTTTATATAGAATTAATAGTTAAA
3282949 TATTTTT
1 TATTTTT
3282956 AATTAACTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 10 0.32
29 12 0.39
30 9 0.29
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (28 bp):
TATTTTTTATATAGAATTAATAGTTAAA
Found at i:3286126 original size:24 final size:24
Alignment explanation
Indices: 3286081--3286126 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3286071 CTTTTATATC
*
3286081 TATATAATTATATTATAAAAATGA
1 TATATAATTATATAATAAAAATGA
*
3286105 TATATAA-TATAATAATATAAAT
1 TATATAATTAT-ATAATAAAAAT
3286127 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TATATAATTATATAATAAAAATGA
Found at i:3287613 original size:17 final size:16
Alignment explanation
Indices: 3287576--3287627 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
3287566 TTTAACACAA
* *
3287576 TAATTTTTTAAATATA
1 TAATTTTTTAAAAATT
3287592 T-ATTTTTTATAAAATT
1 TAATTTTTTA-AAAATT
*
3287608 TAATTTATTAAAACATT
1 TAATTTTTTAAAA-ATT
3287625 TAA
1 TAA
3287628 AAATAGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.27
16 9 0.30
17 13 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATTTTTTAAAAATT
Found at i:3288214 original size:16 final size:15
Alignment explanation
Indices: 3288193--3288252 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
3288183 TATCTATTTG
3288193 AATTTTCAAAAATTAA
1 AATTTT-AAAAATTAA
*
3288209 AATTTTAATAATTTAA
1 AATTTTAA-AAATTAA
*
3288225 AA-TATAAATAATTAA
1 AATTTTAAA-AATTAA
*
3288240 AATTTTAATAATT
1 AATTTTAAAAATT
3288253 TGATTAATCA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 17 0.47
16 18 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTTAAAAATTAA
Found at i:3288239 original size:15 final size:15
Alignment explanation
Indices: 3288193--3288252 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
3288183 TATCTATTTG
*
3288193 AATTTTCAAAAATTAA
1 AATTTT-AATAATTAA
3288209 AATTTTAATAATTTAA
1 AATTTTAATAA-TTAA
* *
3288225 AATATAAATAATTAA
1 AATTTTAATAATTAA
3288240 AATTTTAATAATT
1 AATTTTAATAATT
3288253 TGATTAATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
15 19 0.50
16 19 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTTAATAATTAA
Found at i:3288274 original size:37 final size:33
Alignment explanation
Indices: 3288203--3288297 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 33
3288193 AATTTTCAAA
*
3288203 AATTAAAATTTTAATAATTT-A-AAATATAAAT
1 AATTAAAATTTTAATAATTTGATTAATATAAAT
3288234 AATTAAAATTTTAATAATTTGATTAATCAACTAAATT
1 AATTAAAATTTTAATAATTTGATTAAT--A-TAAA-T
3288271 AATTAAAATAATTT--TAATTTGATTAAT
1 AATTAAAAT--TTTAATAATTTGATTAAT
3288298 GTAATTTTCT
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
31 20 0.36
32 1 0.02
33 3 0.05
35 1 0.02
36 4 0.07
37 23 0.42
39 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (33 bp):
AATTAAAATTTTAATAATTTGATTAATATAAAT
Found at i:3288514 original size:26 final size:24
Alignment explanation
Indices: 3288446--3288518 Score: 65
Period size: 26 Copynumber: 2.9 Consensus size: 24
3288436 CCATAATGCA
* *
3288446 AAAAAAAAAAATATATATATATATC
1 AAAATAAAAAATATA-AAATATATC
* * *
3288471 AAAATATAAAGTACAAAATATATC
1 AAAATAAAAAATATAAAATATATC
*
3288495 ACCATATAAAAAATATAAAATATA
1 A--AAATAAAAAATATAAAATATA
3288519 AATTATTAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
24 9 0.24
25 11 0.30
26 17 0.46
ACGTcount: A:0.66, C:0.07, G:0.01, T:0.26
Consensus pattern (24 bp):
AAAATAAAAAATATAAAATATATC
Found at i:3288528 original size:24 final size:23
Alignment explanation
Indices: 3288504--3288551 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
3288494 CACCATATAA
*
3288504 AAAAT-ATAAAATATAAATTATT
1 AAAATAATATAATATAAATTATT
3288526 AAAATTAATATAATATAAATTATT
1 AAAA-TAATATAATATAAATTATT
3288550 AA
1 AA
3288552 CTTATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.17
23 1 0.04
24 18 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATAATATAATATAAATTATT
Found at i:3288564 original size:15 final size:14
Alignment explanation
Indices: 3288512--3288596 Score: 54
Period size: 16 Copynumber: 5.9 Consensus size: 14
3288502 AAAAAATATA
*
3288512 AAATATAAATTATT
1 AAATATTAATTATT
3288526 AAA-ATTAATATAATAT
1 AAATATTAAT-T-AT-T
3288542 AAATTATTAACTTATT
1 AAA-TATTAA-TTATT
3288558 AAATATT-A-TA-T
1 AAATATTAATTATT
*
3288569 AAATATATAATATTTT
1 AAATAT-TAAT-TATT
3288585 AAATATT-ATTAT
1 AAATATTAATTAT
3288597 AATATATAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 23
0.69 0.04 0.28
Matches are distributed among these distances:
11 7 0.12
12 3 0.05
13 8 0.14
14 7 0.12
15 8 0.14
16 15 0.26
17 2 0.04
18 6 0.11
19 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATATTAATTATT
Found at i:3289290 original size:21 final size:22
Alignment explanation
Indices: 3289265--3289324 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
3289255 AATACATCAA
3289265 TTAAAAATAAAATAAAATAA-C
1 TTAAAAATAAAATAAAATAAGC
* *
3289286 TTAAATATAAAAATAAAAAAAGC
1 TTAAAAAT-AAAATAAAATAAGC
*
3289309 --AAAAATAACATAAAAT
1 TTAAAAATAAAATAAAAT
3289325 TTAAAATGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.25
21 12 0.38
22 11 0.34
23 1 0.03
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.22
Consensus pattern (22 bp):
TTAAAAATAAAATAAAATAAGC
Found at i:3289891 original size:3 final size:3
Alignment explanation
Indices: 3289883--3289934 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
3289873 ATATTTAATT
* * *
3289883 TTA TTA TTA TAA TAA TTAA TT- TTA CTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
3289927 TTA TTA TT
1 TTA TTA TT
3289935 TTTAATCTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3289892 original size:21 final size:21
Alignment explanation
Indices: 3289854--3289933 Score: 101
Period size: 21 Copynumber: 3.8 Consensus size: 21
3289844 CATAACTTAT
3289854 TTTAATTTTATCTATTATAATA
1 TTTAATTTTAT-TATTATAATA
3289876 TTTAATTTTATTATTATAATA
1 TTTAATTTTATTATTATAATA
* * *
3289897 ATTAATTTTACTATTATATTA
1 TTTAATTTTATTATTATAATA
3289918 -TT-ATTATTATTATTAT
1 TTTAATT-TTATTATTAT
3289934 TTTTAATCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
19 3 0.06
20 11 0.21
21 28 0.53
22 11 0.21
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTAATTTTATTATTATAATA
Found at i:3297637 original size:3 final size:3
Alignment explanation
Indices: 3297616--3297677 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
3297606 GGACTTTCCT
* * * * * * *
3297616 CCA CCA CCG CCA CCT CCA CCA CCT CCA CCA CCG CCC CCG CCG CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
3297664 CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CC
3297678 TCCTCCACCG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.21, C:0.69, G:0.06, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:3298297 original size:20 final size:22
Alignment explanation
Indices: 3298272--3298350 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
3298262 TCTTACATAC
3298272 TATTTTTATAATA-TTAA-ATT
1 TATTTTTATAATATTTAATATT
*
3298292 TATTTTTATCATATTTAATATT
1 TATTTTTATAATATTTAATATT
* * * *
3298314 AATTTTTTAAAATTACTTAATATA
1 TA-TTTTTATAA-TATTTAATATT
3298338 TATTTTTA-AATAT
1 TATTTTTATAATAT
3298351 ATATATAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
20 12 0.26
21 6 0.13
22 6 0.13
23 13 0.28
24 10 0.21
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTTTATAATATTTAATATT
Found at i:3298451 original size:21 final size:21
Alignment explanation
Indices: 3298421--3298461 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3298411 TTTTAAAAAT
*
3298421 TAAAATATATATATATTTTTA
1 TAAAAAATATATATATTTTTA
* *
3298442 TAAAAAATATTTATGTTTTT
1 TAAAAAATATATATATTTTT
3298462 TGTTATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TAAAAAATATATATATTTTTA
Found at i:3298826 original size:8 final size:8
Alignment explanation
Indices: 3298769--3298840 Score: 53
Period size: 8 Copynumber: 8.9 Consensus size: 8
3298759 TTAAAATATT
3298769 ATATATTTA
1 ATAT-TTTA
3298778 TATATTTTA
1 -ATATTTTA
3298787 AT-TTATTA
1 ATATT-TTA
*
3298795 ATA-ATTA
1 ATATTTTA
3298802 AT-TTTATA
1 ATATTT-TA
*
3298810 TAAATTTTA
1 -ATATTTTA
3298819 ATATTTTA
1 ATATTTTA
3298827 ATATTTT-
1 ATATTTTA
3298834 ATATTTT
1 ATATTTT
3298841 TTATATTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
7 15 0.29
8 23 0.44
9 7 0.13
10 7 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATATTTTA
Found at i:3298849 original size:32 final size:32
Alignment explanation
Indices: 3298741--3298849 Score: 98
Period size: 32 Copynumber: 3.3 Consensus size: 32
3298731 ATTTGTTATA
* *
3298741 TTTATATTATAATTATATTTAAAATATTATATATT
1 TTTATATTTTAA-TAT-TTTAATATATTATAT-TT
*
3298776 TATATATTTTAAT-TTATTAATA-ATTA-ATTT
1 TTTATATTTTAATATT-TTAATATATTATATTT
* *
3298806 TATATAAATTTTAATATTTTAATATTTTATATTT
1 T-T-TATATTTTAATATTTTAATATATTATATTT
3298840 TTTATATTTT
1 TTTATATTTT
3298850 TTTATATTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
30 3 0.05
31 2 0.03
32 28 0.46
33 12 0.20
34 6 0.10
35 10 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTATATTTTAATATTTTAATATATTATATTT
Found at i:3298859 original size:24 final size:24
Alignment explanation
Indices: 3298814--3298859 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3298804 TTTATATAAA
*
3298814 TTTTAATATTTTAATATTTTATAT
1 TTTTAATATTTTAATATATTATAT
* **
3298838 TTTTTATATTTTTTTATATTAT
1 TTTTAATATTTTAATATATTAT
3298860 GTCATAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTTAATATTTTAATATATTATAT
Found at i:3298883 original size:16 final size:15
Alignment explanation
Indices: 3298773--3298902 Score: 72
Period size: 16 Copynumber: 8.4 Consensus size: 15
3298763 AATATTATAT
3298773 ATTTA-TATATTTTA
1 ATTTATTATATTTTA
*
3298787 ATTTATTA-ATAATTA
1 ATTTATTATAT-TTTA
*
3298802 ATTTTATATAAATTTTA
1 A-TTTAT-TATATTTTA
3298819 ATATT-TTAATATTTTA
1 AT-TTATT-ATATTTTA
*
3298835 TATTTTTTATATTTT-
1 -ATTTATTATATTTTA
* * **
3298850 TTTATATTATGTCATA
1 ATT-TATTATATTTTA
3298866 ATTTAATTATATTTTA
1 ATTT-ATTATATTTTA
*
3298882 ATTTTTTTATATTTT-
1 A-TTTATTATATTTTA
3298897 ATTTAT
1 ATTTAT
3298903 ATGATATAAT
Statistics
Matches: 89, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
14 13 0.15
15 16 0.18
16 43 0.48
17 15 0.17
18 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.65
Consensus pattern (15 bp):
ATTTATTATATTTTA
Found at i:3300177 original size:13 final size:12
Alignment explanation
Indices: 3300151--3300186 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
3300141 TTATAAAAAT
3300151 ATATAAATATTA
1 ATATAAATATTA
3300163 ATATAAATAATTA
1 ATATAAAT-ATTA
3300176 ATATAAA-ATTA
1 ATATAAATATTA
3300187 TTTTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.17
12 8 0.35
13 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATAAATATTA
Found at i:3301206 original size:24 final size:24
Alignment explanation
Indices: 3301179--3301229 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3301169 CATCAACATC
* *
3301179 TTTTTTATCTTTAAATTATAATTA
1 TTTTTTATATTTAAATTACAATTA
3301203 TTTTTTATATTTAAATTACAATTA
1 TTTTTTATATTTAAATTACAATTA
3301227 TTT
1 TTT
3301230 AATATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTTTATATTTAAATTACAATTA
Found at i:3301684 original size:22 final size:23
Alignment explanation
Indices: 3301647--3301693 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
3301637 TAATTTAAAT
3301647 AATTTAATTTATTAA-TAATAAA
1 AATTTAATTTATTAATTAATAAA
3301669 AATTTAA-TTATATAATTTAATAAA
1 AATTTAATTTAT-TAA-TTAATAAA
3301693 A
1 A
3301694 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 10 0.45
24 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTAATTTATTAATTAATAAA
Found at i:3301687 original size:30 final size:32
Alignment explanation
Indices: 3301651--3301715 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 32
3301641 TTAAATAATT
*
3301651 TAATTTATTAATAA-TAAAAATT-TAA-TTATA
1 TAATTTAATAA-AATTAAAAATTATAATTTATA
3301681 TAATTTAATAAAATTAAAAATTATAATTTATA
1 TAATTTAATAAAATTAAAAATTATAATTTATA
3301713 TAA
1 TAA
3301716 AAGTTAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 2 0.06
30 18 0.58
31 3 0.10
32 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
TAATTTAATAAAATTAAAAATTATAATTTATA
Found at i:3301727 original size:24 final size:23
Alignment explanation
Indices: 3301679--3301735 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
3301669 AATTTAATTA
3301679 TATAATTTAATAAAATTAAAAAT
1 TATAATTTAATAAAATTAAAAAT
*
3301702 TATAATTTATATAAAAGTT-AATAT
1 TATAATTTA-ATAAAA-TTAAAAAT
3301726 TA-AATTTAAT
1 TATAATTTAAT
3301736 TACTCAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 2 0.06
23 15 0.48
24 12 0.39
25 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TATAATTTAATAAAATTAAAAAT
Found at i:3301731 original size:36 final size:32
Alignment explanation
Indices: 3301656--3301731 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 32
3301646 TAATTTAATT
* *
3301656 TATTAATAATAAAAATTTAATTATATAATTTAA
1 TATTAA-ATTAAAAATTTAATTATATAAGTTAA
3301689 TA--AAATTAAAAATTATAATTTATATAAAAGTTAA
1 TATTAAATTAAAAATT-TAA-TTATAT--AAGTTAA
3301723 TATTAAATT
1 TATTAAATT
3301732 TAATTACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
30 9 0.26
31 5 0.14
32 6 0.17
33 2 0.06
34 8 0.23
36 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (32 bp):
TATTAAATTAAAAATTTAATTATATAAGTTAA
Found at i:3304552 original size:4 final size:4
Alignment explanation
Indices: 3304543--3304568 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3304533 ATCCAGTTGC
3304543 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
3304569 GTGGTTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:3306873 original size:17 final size:19
Alignment explanation
Indices: 3306851--3306893 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
3306841 TTATATTTAA
*
3306851 ATTTAAATAA-AAATA-TT
1 ATTTAAATAATAAATAGTG
*
3306868 ATTTAATTAATAAATAGTG
1 ATTTAAATAATAAATAGTG
3306887 ATTTAAA
1 ATTTAAA
3306894 CTGAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
18 5 0.24
19 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTTAAATAATAAATAGTG
Found at i:3310608 original size:23 final size:22
Alignment explanation
Indices: 3310554--3310610 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
3310544 ACATTACATT
* *
3310554 TAATAATTAATATTTATTTTAA
1 TAATAATTAATAATTATTATAA
*
3310576 TAATTTATTAATAATTATTATAA
1 TAA-TAATTAATAATTATTATAA
3310599 TACATAATTAAT
1 TA-ATAATTAAT
3310611 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 3 0.10
23 25 0.86
24 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATAATTAATAATTATTATAA
Found at i:3312595 original size:15 final size:15
Alignment explanation
Indices: 3312577--3312611 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3312567 TAAGGATGCT
**
3312577 TATCCCCCGCCGGGA
1 TATCCCCCGCAAGGA
3312592 TATCCCCCGCAAGGA
1 TATCCCCCGCAAGGA
3312607 TATCC
1 TATCC
3312612 TCAGGGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.17
Consensus pattern (15 bp):
TATCCCCCGCAAGGA
Found at i:3313106 original size:15 final size:15
Alignment explanation
Indices: 3313078--3313118 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3313068 TAAAAAAATT
* *
3313078 TATATAATATTTTTA
1 TATATTATAATTTTA
3313093 TATATTATAATTTTA
1 TATATTATAATTTTA
3313108 TA-ATTA-AATTT
1 TATATTATAATTT
3313119 AAATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 5 0.21
14 4 0.17
15 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTATAATTTTA
Found at i:3314709 original size:10 final size:10
Alignment explanation
Indices: 3314681--3314721 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
3314671 TCGATCGGTT
3314681 AATTTTAATA
1 AATTTTAATA
*
3314691 GAATTTTAATT
1 -AATTTTAATA
*
3314702 ATTTTTAATA
1 AATTTTAATA
3314712 AATTTTAATA
1 AATTTTAATA
3314722 TTAAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (10 bp):
AATTTTAATA
Found at i:3314749 original size:22 final size:22
Alignment explanation
Indices: 3314710--3314751 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3314700 TTATTTTTAA
*
3314710 TAAATTTTAATATTAAATATAT
1 TAAATTTTAATATAAAATATAT
3314732 TAAATTATTAATA-AAAATAT
1 TAAATT-TTAATATAAAATAT
3314752 GTATTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTTTAATATAAAATATAT
Found at i:3315616 original size:42 final size:42
Alignment explanation
Indices: 3315557--3315644 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
3315547 ATTTTTACAT
3315557 AATTTATTTACTATAAACTACATAAAATTTTACATGTATTCG
1 AATTTATTTACTATAAACTACATAAAATTTTACATGTATTCG
*
3315599 AATTTATTTACTGTAAACTACATAAAATTTTACATGTATTCG
1 AATTTATTTACTATAAACTACATAAAATTTTACATGTATTCG
3315641 AATT
1 AATT
3315645 CAATTACATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (42 bp):
AATTTATTTACTATAAACTACATAAAATTTTACATGTATTCG
Found at i:3315649 original size:22 final size:21
Alignment explanation
Indices: 3315582--3315649 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 21
3315572 AACTACATAA
3315582 AATTTTACATGTATTCGAATT
1 AATTTTACATGTATTCGAATT
* ** * *
3315603 TA-TTTAC-TGTAAACTACATAA
1 AATTTTACATGTATTCGA-AT-T
3315624 AATTTTACATGTATTCGAATT
1 AATTTTACATGTATTCGAATT
3315645 CAATT
1 -AATT
3315650 ACATTGCGAT
Statistics
Matches: 32, Mismatches: 10, Indels: 9
0.63 0.20 0.18
Matches are distributed among these distances:
19 6 0.19
20 7 0.22
21 2 0.06
22 11 0.34
23 6 0.19
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (21 bp):
AATTTTACATGTATTCGAATT
Found at i:3316700 original size:18 final size:18
Alignment explanation
Indices: 3316632--3316698 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
3316622 TGTTTTTGTA
* *
3316632 TAATTGAAATAAAA-TCT
1 TAATTAAAATAAAATTTT
* *
3316649 TAATATAAATTAATA-TTT
1 TAAT-TAAAATAAAATTTT
*
3316667 TATTTAAAATAAAATTTT
1 TAATTAAAATAAAATTTT
3316685 TAATTAAATATAAA
1 TAATTAAA-ATAAA
3316699 TTAAATAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 12 0.31
18 22 0.56
19 5 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (18 bp):
TAATTAAAATAAAATTTT
Found at i:3320864 original size:2 final size:2
Alignment explanation
Indices: 3320857--3320889 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3320847 GCTTATTTGT
3320857 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3320890 TGCATTTATG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3321802 original size:22 final size:22
Alignment explanation
Indices: 3321758--3321802 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
3321748 TTACTTATAA
*
3321758 ATTTGATAAATTAAATATAATT
1 ATTTGATAAATTAAATAAAATT
*
3321780 ATTT-ATAAATTTAATAAATATT
1 ATTTGATAAATTAAATAAA-ATT
3321802 A
1 A
3321803 AATAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTGATAAATTAAATAAAATT
Found at i:3321812 original size:32 final size:32
Alignment explanation
Indices: 3321727--3321834 Score: 123
Period size: 32 Copynumber: 3.4 Consensus size: 32
3321717 AACATAAACT
* * *
3321727 TTTAA-AAAAATTAAATTAATATTACTTATAAA
1 TTTAATAAATATTAAA-TAAAATTATTTATAAA
* *
3321759 TTTGAT-AA-ATTAAATATAATTATTTATAAA
1 TTTAATAAATATTAAATAAAATTATTTATAAA
**
3321789 TTTAATAAATATTAAATAAAATTATTCGTAAA
1 TTTAATAAATATTAAATAAAATTATTTATAAA
3321821 TTTAATAAATATTA
1 TTTAATAAATATTA
3321835 GTACTTAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
30 18 0.28
31 8 0.12
32 39 0.60
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
TTTAATAAATATTAAATAAAATTATTTATAAA
Found at i:3323179 original size:2 final size:2
Alignment explanation
Indices: 3323172--3323205 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3323162 TTTACAGTGA
3323172 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
3323206 GTTCATTGCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3323465 original size:24 final size:23
Alignment explanation
Indices: 3323431--3323486 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
3323421 AATTAAAATA
3323431 AATTTATTTATATATTAATATTT-AT
1 AATTT-TTTATA-ATTAA-ATTTAAT
3323456 AATTTTTTATAATTAAATTTAAAT
1 AATTTTTTATAATTAAATTT-AAT
3323480 AATTTTT
1 AATTTTT
3323487 ATTTATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.14
23 5 0.17
24 15 0.52
25 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTTTTTATAATTAAATTTAAT
Found at i:3324110 original size:8 final size:8
Alignment explanation
Indices: 3324097--3324136 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
3324087 AATCGATATC
3324097 TATATCTA
1 TATATCTA
3324105 TATATCTA
1 TATATCTA
*
3324113 TATATATA
1 TATATCTA
*
3324121 TATATATA
1 TATATCTA
3324129 TATATCTA
1 TATATCTA
3324137 AAGTGGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (8 bp):
TATATCTA
Found at i:3324130 original size:14 final size:14
Alignment explanation
Indices: 3324092--3324133 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
3324082 CTGCAAATCG
*
3324092 ATATCTATATCTAT
1 ATATCTATATATAT
3324106 ATATCTATATATAT
1 ATATCTATATATAT
*
3324120 ATATATATATATAT
1 ATATCTATATATAT
3324134 CTAAAGTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATCTATATATAT
Found at i:3333318 original size:17 final size:19
Alignment explanation
Indices: 3333284--3333320 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
3333274 TATTCATATG
*
3333284 TAAAAAAATTAATTATTTT
1 TAAAAAAATTAATCATTTT
3333303 TAAAAAAA-T-ATCATTTT
1 TAAAAAAATTAATCATTTT
3333320 T
1 T
3333321 TGTCGCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAAAAATTAATCATTTT
Found at i:3333624 original size:30 final size:29
Alignment explanation
Indices: 3333564--3333625 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
3333554 TAAGATAAAT
* **
3333564 TTTAATATTTATTTAATTTGATAATCATA
1 TTTAATATTTATTTAAATAAATAATCATA
* *
3333593 TTTAATATTTTATTTAAATAAATTATTATA
1 TTTAATA-TTTATTTAAATAAATAATCATA
3333623 TTT
1 TTT
3333626 TGAATTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTAATATTTATTTAAATAAATAATCATA
Found at i:3335450 original size:16 final size:16
Alignment explanation
Indices: 3335429--3335459 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3335419 ATGAGCTTTT
3335429 AGTTTAAATTTAAATA
1 AGTTTAAATTTAAATA
3335445 AGTTTAAATTTAAAT
1 AGTTTAAATTTAAAT
3335460 TTATATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
AGTTTAAATTTAAATA
Found at i:3335810 original size:2 final size:2
Alignment explanation
Indices: 3335803--3335835 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3335793 TATGAGTTAT
3335803 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3335836 TCAAGTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3336070 original size:8 final size:8
Alignment explanation
Indices: 3336047--3336082 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
3336037 GTATTTTTTA
3336047 AATTTAAT
1 AATTTAAT
*
3336055 -ACTTAAT
1 AATTTAAT
3336062 AATTTAAT
1 AATTTAAT
3336070 AATTTAAT
1 AATTTAAT
3336078 AATTT
1 AATTT
3336083 TTATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (8 bp):
AATTTAAT
Found at i:3337778 original size:18 final size:19
Alignment explanation
Indices: 3337747--3337784 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3337737 TGTTTATAAA
3337747 TATTAATTACAAAT-TATT
1 TATTAATTACAAATATATT
3337765 TATTAATTTA-AAATATATT
1 TATTAA-TTACAAATATATT
3337784 T
1 T
3337785 TTTTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTAATTACAAATATATT
Found at i:3337817 original size:22 final size:21
Alignment explanation
Indices: 3337763--3337820 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
3337753 TTACAAATTA
3337763 TTTATT-AATTTAAAATATAT
1 TTTATTAAATTTAAAATATAT
* **
3337783 TTTTTTATGTTTAATAAT-TAAT
1 TTTATTAAATTTAA-AATAT-AT
3337805 TTTATTAAATTTAAAA
1 TTTATTAAATTTAAAA
3337821 AAATATTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 5 0.17
21 8 0.28
22 16 0.55
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTATTAAATTTAAAATATAT
Found at i:3338034 original size:26 final size:24
Alignment explanation
Indices: 3338004--3338059 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3337994 AAATTTAATT
*
3338004 TTTATACTATTAATAAATTAAATGA
1 TTTATACTATTAA-AAATAAAATGA
** *
3338029 TGTTATTTTATTAAAAATAAAATTA
1 T-TTATACTATTAAAAATAAAATGA
3338054 TTTATA
1 TTTATA
3338060 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 4 0.16
25 11 0.44
26 10 0.40
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (24 bp):
TTTATACTATTAAAAATAAAATGA
Found at i:3338063 original size:25 final size:26
Alignment explanation
Indices: 3338011--3338065 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
3338001 ATTTTTATAC
*
3338011 TATTAATAAATTAAATGATGTTATTT
1 TATTAATAAATAAAATGATGTTATTT
*
3338037 TATTAA-AAATAAAATTAT-TTATATT
1 TATTAATAAATAAAATGATGTTAT-TT
3338062 TATT
1 TATT
3338066 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 16 0.62
26 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
TATTAATAAATAAAATGATGTTATTT
Found at i:3338416 original size:22 final size:19
Alignment explanation
Indices: 3338389--3338440 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 19
3338379 AATTACCAAC
*
3338389 TTTTAAAAAATTAATTGTATT
1 TTTTAAAAAATT-ACT-TATT
*
3338410 TTATTAAAAAAATACTTATT
1 TT-TTAAAAAATTACTTATT
3338430 TTTTAAAAAAT
1 TTTTAAAAAAT
3338441 ATATTCAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.30
20 6 0.22
21 4 0.15
22 9 0.33
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TTTTAAAAAATTACTTATT
Found at i:3340452 original size:22 final size:24
Alignment explanation
Indices: 3340400--3340453 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
3340390 GTTCATATAC
* *
3340400 AATTGAGCATTTTTTTTACTGGAT
1 AATTAAGCAATTTTTTTACTGGAT
* *
3340424 AAGTAAGCAATTTTTTT-CT-GTT
1 AATTAAGCAATTTTTTTACTGGAT
3340446 AATTAAGC
1 AATTAAGC
3340454 TACATTTGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 9 0.36
23 2 0.08
24 14 0.56
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (24 bp):
AATTAAGCAATTTTTTTACTGGAT
Found at i:3341195 original size:25 final size:25
Alignment explanation
Indices: 3341167--3341216 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3341157 ATTCTAAAAA
3341167 TAAATTGGCAAATGGAA-TATAATTT
1 TAAATTGGCAAATGGAACTA-AATTT
* *
3341192 TAAATTTGCACATGGAACTAAATTT
1 TAAATTGGCAAATGGAACTAAATTT
3341217 GATATTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (25 bp):
TAAATTGGCAAATGGAACTAAATTT
Found at i:3341435 original size:21 final size:20
Alignment explanation
Indices: 3341398--3341438 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3341388 TATTAGTTAT
* *
3341398 TTTATATTTTTACTTATTAA
1 TTTATATTGTTAATTATTAA
3341418 TTTATCATTGTTAATTATTAA
1 TTTAT-ATTGTTAATTATTAA
3341439 AATAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTATATTGTTAATTATTAA
Found at i:3341516 original size:18 final size:19
Alignment explanation
Indices: 3341493--3341529 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
3341483 ATCGAGTGCC
3341493 AAAATTTAAT-ATAAAATT
1 AAAATTTAATAATAAAATT
3341511 AAAATTTAATAATAAAATT
1 AAAATTTAATAATAAAATT
3341530 CAATTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTTAATAATAAAATT
Found at i:3341709 original size:19 final size:19
Alignment explanation
Indices: 3341673--3341723 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
3341663 ATAAATATAA
*
3341673 AAAT-ATAT-TTAAATTTT
1 AAATAATATGTTAAAATTT
*
3341690 AATTAATATGTTAAAATTT
1 AAATAATATGTTAAAATTT
3341709 AAATAA-ATGTATAAA
1 AAATAATATGT-TAAA
3341724 TGACAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.11
18 8 0.29
19 17 0.61
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
AAATAATATGTTAAAATTT
Found at i:3342528 original size:15 final size:14
Alignment explanation
Indices: 3342510--3342554 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
3342500 TTCAAAAGTA
3342510 TAAAGATTAAAATAT
1 TAAA-ATTAAAATAT
*
3342525 TAAATTTAATAATAT
1 TAAAATTAA-AATAT
*
3342540 AAAAATTAAAATAT
1 TAAAATTAAAATAT
3342554 T
1 T
3342555 TCGTTTACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
TAAAATTAAAATAT
Found at i:3342571 original size:31 final size:29
Alignment explanation
Indices: 3342491--3342578 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 29
3342481 TTTTCTTATT
3342491 TATTATAATTTCAA-AAGTATAAAGATTAAAA
1 TATTA-AATTT-AATAA-TATAAAGATTAAAA
*
3342522 TATTAAATTTAATAATATAAAAATTAAAA
1 TATTAAATTTAATAATATAAAGATTAAAA
***
3342551 TATTTCGTTTACTATAATATAAAGATTA
1 TATTAAATTTA--ATAATATAAAGATTA
3342579 CTAGTAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 23 0.47
30 7 0.14
31 19 0.39
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (29 bp):
TATTAAATTTAATAATATAAAGATTAAAA
Found at i:3343006 original size:14 final size:14
Alignment explanation
Indices: 3342988--3343054 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
3342978 TATATAGGTA
3342988 AATATATTAAAATT
1 AATATATTAAAATT
* *
3343002 TATATAATAAAAATAGT
1 AATAT-ATTAAAAT--T
*
3343019 AATATACTAAAATT
1 AATATATTAAAATT
*
3343033 --TATA-TAAAAAT
1 AATATATTAAAATT
3343044 AATATATTAAA
1 AATATATTAAA
3343055 TATAATTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
11 6 0.15
12 4 0.10
13 4 0.10
14 9 0.22
15 7 0.17
16 6 0.15
17 5 0.12
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (14 bp):
AATATATTAAAATT
Found at i:3343023 original size:31 final size:31
Alignment explanation
Indices: 3342988--3343047 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
3342978 TATATAGGTA
*
3342988 AATATATTAAAATTTATATAATAAA-AATAGT
1 AATATACTAAAATTTATATAA-AAATAATAGT
3343019 AATATACTAAAATTTATATAAAAATAATA
1 AATATACTAAAATTTATATAAAAATAATA
3343048 TATTAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (31 bp):
AATATACTAAAATTTATATAAAAATAATAGT
Found at i:3343097 original size:19 final size:19
Alignment explanation
Indices: 3343042--3343090 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
3343032 TTATATAAAA
* *
3343042 ATAATATATTAAATATAATT
1 ATAATATA-AAAAAATAATT
3343062 ATAATATAAAAAAATAA-T
1 ATAATATAAAAAAATAATT
3343080 ATAA-ATAAAAA
1 ATAATATAAAAA
3343091 TACATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 5 0.19
19 7 0.26
20 8 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATATAAAAAAATAATT
Found at i:3348243 original size:28 final size:29
Alignment explanation
Indices: 3348209--3348272 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
3348199 TTAATATTTA
3348209 TTTTTTAGCCATT-AAATTGT-ATTATTAT
1 TTTTTTAG-CATTAAAATTGTAATTATTAT
** *
3348237 TTTTTTAGTGTTAAAATTTTAATTATTAT
1 TTTTTTAGCATTAAAATTGTAATTATTAT
3348266 TTTTTTA
1 TTTTTTA
3348273 ACAGTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 14 0.45
29 15 0.48
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.62
Consensus pattern (29 bp):
TTTTTTAGCATTAAAATTGTAATTATTAT
Found at i:3348426 original size:15 final size:14
Alignment explanation
Indices: 3348394--3348434 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
3348384 TATTATGTGG
3348394 AATTAAGTTTAGCGT
1 AATT-AGTTTAGCGT
*
3348409 AATTAGTTTAGGGAT
1 AATTAGTTTAGCG-T
3348424 AATTAGTTTAG
1 AATTAGTTTAG
3348435 AGCTTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.41
Consensus pattern (14 bp):
AATTAGTTTAGCGT
Found at i:3349829 original size:36 final size:36
Alignment explanation
Indices: 3349780--3349904 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 36
3349770 CTCGGATTAG
3349780 TTGTTGATAGTAGTAATGTGAAATATGCAGAAACAT
1 TTGTTGATAGTAGTAATGTGAAATATGCAGAAACAT
* * * * ** *
3349816 TTGTTGATTGTAGTTATCGTGCAGATTATTTCAG-ATTAG
1 TTGTTGATAGTAGTAAT-GTG-A-AATA-TGCAGAAACAT
*
3349855 TTGTTGATAGTAGCAATGTGAAATATGCAGAAACAT
1 TTGTTGATAGTAGTAATGTGAAATATGCAGAAACAT
* *
3349891 TTGTTAATTGTAGT
1 TTGTTGATAGTAGT
3349905 TATCATGCAG
Statistics
Matches: 66, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
35 4 0.06
36 31 0.47
37 4 0.06
38 4 0.06
39 19 0.29
40 4 0.06
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.39
Consensus pattern (36 bp):
TTGTTGATAGTAGTAATGTGAAATATGCAGAAACAT
Found at i:3349864 original size:75 final size:75
Alignment explanation
Indices: 3349759--3350003 Score: 382
Period size: 75 Copynumber: 3.3 Consensus size: 75
3349749 AATGTGAAAT
*
3349759 ATGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGAT
1 ATGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAAT
3349824 TGTAGTTATC
66 TGTAGTTATC
* * * *
3349834 GTGCAGATTATTTCAGATTAGTTGTTGATAGTAGCAATGTGAAATATGCAGAAACATTTGTTAAT
1 ATGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAAT
3349899 TGTAGTTATC
66 TGTAGTTATC
* * ** *
3349909 ATGCAGATTATCTCGGATTAGTTGTTAATAGTAGTATTGTGAAATATGTTGAAATATTTGTTAAT
1 ATGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAAT
*
3349974 TGTAATTATC
66 TGTAGTTATC
*
3349984 AAGCAGATTATCTCGGATTA
1 ATGCAGATTATCTCGGATTA
3350004 TCGTTTCATC
Statistics
Matches: 154, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 154 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (75 bp):
ATGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAAT
TGTAGTTATC
Found at i:3350127 original size:32 final size:33
Alignment explanation
Indices: 3350086--3350150 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3350076 GTCCATTAGA
*
3350086 ATGCGCTGAAGC-GGGTAGCGCATCCTACGTGG
1 ATGCGCTGAAGCACGGTAGCGCATCCTACGTGG
**
3350118 ATGCGCTGAAGCACTTTAGCGCATCCTACGTGG
1 ATGCGCTGAAGCACGGTAGCGCATCCTACGTGG
3350151 CACGCCACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.20, C:0.26, G:0.32, T:0.22
Consensus pattern (33 bp):
ATGCGCTGAAGCACGGTAGCGCATCCTACGTGG
Found at i:3351125 original size:20 final size:19
Alignment explanation
Indices: 3351089--3351146 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 19
3351079 ATTTTTTTTA
3351089 ATTAAA-AAA-AATTAAAT
1 ATTAAATAAATAATTAAAT
3351106 ATTAAATAAATAATTTAAAT
1 ATTAAATAAATAA-TTAAAT
*
3351126 ATTAAATAAAT-AGTAAAT
1 ATTAAATAAATAATTAAAT
3351144 ATT
1 ATT
3351147 GTATTTTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
17 6 0.16
18 11 0.30
19 3 0.08
20 17 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
ATTAAATAAATAATTAAAT
Found at i:3351293 original size:23 final size:22
Alignment explanation
Indices: 3351257--3351303 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
3351247 TCAAACTCAA
*
3351257 TTTTTTTAAAAATTTTACCTTAT
1 TTTTTTTAAAAATTTAACC-TAT
**
3351280 TTTTTTTACTAATTTAACCTAT
1 TTTTTTTAAAAATTTAACCTAT
3351302 TT
1 TT
3351304 CTCATTAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTTTAAAAATTTAACCTAT
Found at i:3355934 original size:2 final size:2
Alignment explanation
Indices: 3355881--3355916 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3355871 AATATGTATG
3355881 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
3355917 AAGGATTATA
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):
TA
Found at i:3360095 original size:18 final size:20
Alignment explanation
Indices: 3360054--3360095 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
3360044 ATATGATTAT
*
3360054 TTAAAAAATTTTTAAATACA
1 TTAAAAAATTTTTAAATAAA
3360074 -TAAAAAA-TTTTAAA-AAA
1 TTAAAAAATTTTTAAATAAA
3360091 TTAAA
1 TTAAA
3360096 TATATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 2 0.10
18 11 0.55
19 7 0.35
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAAAAATTTTTAAATAAA
Found at i:3360621 original size:31 final size:29
Alignment explanation
Indices: 3360539--3360621 Score: 71
Period size: 32 Copynumber: 2.7 Consensus size: 29
3360529 ACATTAAAAA
*
3360539 TATATAAAT-ATAAATTATATAATATATTTT
1 TATA-AAATAATAATTTATA-AATATATTTT
*
3360569 TATAAAA-AATTATTAAATATAAATATAATTTT
1 TATAAAATAATAATT---TATAAATAT-ATTTT
3360601 TACTAAAATAATAATTTATAA
1 TA-TAAAATAATAATTTATAA
3360622 TTTATTGATA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
29 7 0.16
30 4 0.09
31 10 0.23
32 11 0.26
33 5 0.12
34 6 0.14
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (29 bp):
TATAAAATAATAATTTATAAATATATTTT
Found at i:3362302 original size:17 final size:16
Alignment explanation
Indices: 3362280--3362344 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
3362270 TAAAAATTAA
3362280 AAATAATTTTAATATAT
1 AAATAATTTTAA-ATAT
3362297 AAATAATAATTTAAAT-T
1 AAATAAT--TTTAAATAT
*
3362314 AAATTATTTTAAATTAT
1 AAATAATTTTAAA-TAT
*
3362331 AAAATATTTTTAAA
1 -AAATAATTTTAAA
3362345 ATTTATTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 6 0.15
16 1 0.03
17 15 0.38
18 13 0.32
19 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATAATTTTAAATAT
Found at i:3362813 original size:42 final size:42
Alignment explanation
Indices: 3362767--3362850 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
3362757 AAAAATTTTA
* * *
3362767 ATCACTTTAGTTACATGTTTAATTTAATTTTTTATTAGTTTG
1 ATCACTTTAATTACATGTTTAATTTAATTTTTAATTAATTTG
*
3362809 ATCACTTTAATTATATGTTTAATTTAATTTTTAATTAATTTG
1 ATCACTTTAATTACATGTTTAATTTAATTTTTAATTAATTTG
3362851 TGATCTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.57
Consensus pattern (42 bp):
ATCACTTTAATTACATGTTTAATTTAATTTTTAATTAATTTG
Found at i:3363941 original size:68 final size:68
Alignment explanation
Indices: 3363829--3363955 Score: 218
Period size: 68 Copynumber: 1.9 Consensus size: 68
3363819 CTCAGGCTCA
*
3363829 ACCCACACCTTCGACGATCGTATCAAGCTCAATGTTCAACTCCATTGTAAGTAACGAGTCTAGGC
1 ACCCACACCTTCGACGATCGTATCAAGCTCAATATTCAACTCCATTGTAAGTAACGAGTCTAGGC
3363894 GGT
66 GGT
* * *
3363897 ACCCACACCTTCTACGATCGTATCAAGCTCAATATTCAATTCCATTGTAAGTAATGAGT
1 ACCCACACCTTCGACGATCGTATCAAGCTCAATATTCAACTCCATTGTAAGTAACGAGT
3363956 AACTCAACCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (68 bp):
ACCCACACCTTCGACGATCGTATCAAGCTCAATATTCAACTCCATTGTAAGTAACGAGTCTAGGC
GGT
Found at i:3364456 original size:2 final size:2
Alignment explanation
Indices: 3364449--3364476 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3364439 AGCCTTTAAA
3364449 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
3364477 GGAAAAACTT
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:3364947 original size:21 final size:21
Alignment explanation
Indices: 3364921--3364963 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3364911 TACTTATTAA
*
3364921 ATTTAAAA-AATTTATTTTATT
1 ATTTAAAATAATAT-TTTTATT
3364942 ATTTAAAATAATATTTTTATT
1 ATTTAAAATAATATTTTTATT
3364963 A
1 A
3364964 AAATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAAAATAATATTTTTATT
Found at i:3365234 original size:15 final size:14
Alignment explanation
Indices: 3365214--3365293 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 14
3365204 TTTGAGAAAT
3365214 TTTTAATTTGAATTA
1 TTTTAATTT-AATTA
*
3365229 TTTTAATTTTTAGTTA
1 TTTTAA--TTTAATTA
**
3365245 TCTCGAATTTAAGTTA
1 T-TTTAATTTAA-TTA
3365261 TTTTAATTTAAATTA
1 TTTTAATTT-AATTA
3365276 TTTTAATTTAATTTA
1 TTTTAATTTAA-TTA
3365291 TTT
1 TTT
3365294 CAGGTTTATA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
14 2 0.04
15 34 0.64
16 11 0.21
17 6 0.11
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (14 bp):
TTTTAATTTAATTA
Found at i:3367884 original size:2 final size:2
Alignment explanation
Indices: 3367877--3367944 Score: 100
Period size: 2 Copynumber: 34.0 Consensus size: 2
3367867 ACATATCAAG
* * *
3367877 TA TA TA TA TA TA TA TA TA TA CA CA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3367919 TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3367945 AACACTGTAG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3373198 original size:21 final size:21
Alignment explanation
Indices: 3373172--3373227 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3373162 ATCGATCCAT
*
3373172 TTAATTTACTTAAATTAAAAA
1 TTAATTTAATTAAATTAAAAA
* *
3373193 TTAATTTAATTAAATTTAATA
1 TTAATTTAATTAAATTAAAAA
*
3373214 TTAAAATTAATTAA
1 TT-AATTTAATTAA
3373228 TTATATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAATTTAATTAAATTAAAAA
Found at i:3373370 original size:11 final size:12
Alignment explanation
Indices: 3373356--3373387 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3373346 TTATTATTTT
3373356 ATTTTAATT-AA
1 ATTTTAATTAAA
3373367 ATTTTAATTAAA
1 ATTTTAATTAAA
3373379 ATTTTAATT
1 ATTTTAATT
3373388 TAAGTTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTAATTAAA
Found at i:3373430 original size:23 final size:22
Alignment explanation
Indices: 3373404--3373462 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
3373394 CATACGTTGC
* * *
3373404 TTAAGTTAAATTTAGATGAGTTT
1 TTAACTTAAATTTAAATAAG-TT
*
3373427 TTAATTTAAATTTAAATAAGTT
1 TTAACTTAAATTTAAATAAGTT
*
3373449 TAAACTTAAATTTA
1 TTAACTTAAATTTA
3373463 TATTTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (22 bp):
TTAACTTAAATTTAAATAAGTT
Found at i:3373460 original size:22 final size:23
Alignment explanation
Indices: 3373409--3373462 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
3373399 GTTGCTTAAG
* * * *
3373409 TTAAATTTAGATGAGTTTTTAAT
1 TTAAATTTAAATAAGTTTTAAAC
3373432 TTAAATTTAAATAAG-TTTAAAC
1 TTAAATTTAAATAAGTTTTAAAC
3373454 TTAAATTTA
1 TTAAATTTA
3373463 TATTTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (23 bp):
TTAAATTTAAATAAGTTTTAAAC
Found at i:3373532 original size:9 final size:9
Alignment explanation
Indices: 3373520--3373602 Score: 73
Period size: 9 Copynumber: 9.0 Consensus size: 9
3373510 TAATAATTTA
*
3373520 AAATTGATT
1 AAATTAATT
3373529 AAATTAATT
1 AAATTAATT
3373538 -AATTAAATT
1 AAATT-AATT
3373547 AATATT--TT
1 AA-ATTAATT
3373555 AAATTAATT
1 AAATTAATT
3373564 AAAATTTAAATT
1 -AAA-TT-AATT
3373576 AAATTAATT
1 AAATTAATT
*
3373585 AATTTAATT
1 AAATTAATT
*
3373594 TAATTAATT
1 AAATTAATT
3373603 TTTCGATTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
7 3 0.05
8 8 0.13
9 33 0.53
10 6 0.10
11 8 0.13
12 4 0.06
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (9 bp):
AAATTAATT
Found at i:3373542 original size:13 final size:13
Alignment explanation
Indices: 3373521--3373600 Score: 72
Period size: 13 Copynumber: 5.8 Consensus size: 13
3373511 AATAATTTAA
*
3373521 AATTGATTAAATT
1 AATTAATTAAATT
3373534 AATTAATTAAATT
1 AATTAATTAAATT
*
3373547 AA-TATTTTAAATT
1 AATTA-ATTAAATT
3373560 AATTAAAATTTAAATT
1 AATT--AA-TTAAATT
*
3373576 AAATTAATTAATTT
1 -AATTAATTAAATT
3373590 AATTTAATTAA
1 AA-TTAATTAA
3373601 TTTTTCGATT
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
12 2 0.04
13 25 0.45
14 15 0.27
15 2 0.04
16 8 0.14
17 4 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (13 bp):
AATTAATTAAATT
Found at i:3373556 original size:17 final size:17
Alignment explanation
Indices: 3373536--3373618 Score: 80
Period size: 17 Copynumber: 4.8 Consensus size: 17
3373526 ATTAAATTAA
3373536 TTAATTAAATTAATATT
1 TTAATTAAATTAATATT
*
3373553 TTAAATT-AATTAAAATT
1 TT-AATTAAATTAATATT
* *
3373570 TAAATTAAATTAATTAAT
1 TTAATTAAATTAA-TATT
*
3373588 TTAATTTAATTAAT-TT
1 TTAATTAAATTAATATT
*
3373604 TTCGATTAAATTAAT
1 TT-AATTAAATTAAT
3373619 TTTAATCGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
16 7 0.13
17 29 0.55
18 17 0.32
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
TTAATTAAATTAATATT
Found at i:3373566 original size:35 final size:33
Alignment explanation
Indices: 3373509--3373618 Score: 94
Period size: 35 Copynumber: 3.2 Consensus size: 33
3373499 ATTTTATATT
* * *
3373509 TTAATAATTTAAAATTGATTAAATTAATTAATTAAA
1 TTAAT-ATTTTAAATTAATTAAATT--TAAATTAAA
3373545 TTAATATTTTAAATTAATTAAAATTTAAATTAAA
1 TTAATATTTTAAATTAATT-AAATTTAAATTAAA
* * * **
3373579 TTAATTAATTTAATTTAATTAATTTTTCGATTAAA
1 TTAA-TATTTTAAATTAATTAA-ATTTAAATTAAA
3373614 TTAAT
1 TTAAT
3373619 TTTAATCGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
34 15 0.24
35 38 0.60
36 10 0.16
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (33 bp):
TTAATATTTTAAATTAATTAAATTTAAATTAAA
Found at i:3373603 original size:9 final size:9
Alignment explanation
Indices: 3373473--3373602 Score: 60
Period size: 9 Copynumber: 14.3 Consensus size: 9
3373463 TATTTTAAAT
*
3373473 ATTATTTTA
1 ATTAATTTA
3373482 ATT-ATTTA
1 ATTAATTTA
*
3373490 ATTTATTTA
1 ATTAATTTA
3373499 ATTTTATATTTTA
1 A--TTA-A-TTTA
3373512 A-TAATTTA
1 ATTAATTTA
*
3373520 A--AA-TTG
1 ATTAATTTA
*
3373526 ATTAAATTA
1 ATTAATTTA
*
3373535 ATTAATTAA
1 ATTAATTTA
3373544 ATTAATATT-
1 ATTAAT-TTA
*
3373553 -TTAAATTA
1 ATTAATTTA
3373561 ATTAAAATTTAA
1 ATT--AATTT-A
*
3373573 ATTAAATTA
1 ATTAATTTA
3373582 ATTAATTTA
1 ATTAATTTA
3373591 ATTTAA-TTA
1 A-TTAATTTA
3373600 ATT
1 ATT
3373603 TTTCGATTAA
Statistics
Matches: 95, Mismatches: 11, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
6 3 0.03
7 4 0.04
8 20 0.21
9 41 0.43
10 11 0.12
11 6 0.06
12 5 0.05
13 5 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (9 bp):
ATTAATTTA
Found at i:3373617 original size:5 final size:5
Alignment explanation
Indices: 3373526--3373600 Score: 52
Period size: 5 Copynumber: 15.0 Consensus size: 5
3373516 TTTAAAATTG
3373526 ATTAA ATT-A ATT-A ATTAA ATTAA TATTTTAA ATT-A ATTAAA ATTTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA -A--TTAA ATTAA ATT-AA A-TTAA
* *
3373573 ATTAA ATT-A ATT-A ATTTA ATTTA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
3373601 TTTTTCGATT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
4 20 0.33
5 28 0.46
6 6 0.10
7 3 0.05
8 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (5 bp):
ATTAA
Found at i:3373619 original size:35 final size:35
Alignment explanation
Indices: 3373538--3373619 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 35
3373528 TAAATTAATT
*
3373538 AATTAAATTAA-TATTTTAAATTAATTAAAATTTA
1 AATTAAATTAATTAATTTAAATTAATTAAAATTTA
* ** *
3373572 AATTAAATTAATTAATTTAATTTAATTAATTTTTC
1 AATTAAATTAATTAATTTAAATTAATTAAAATTTA
*
3373607 GATTAAATTAATT
1 AATTAAATTAATT
3373620 TTAATCGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 11 0.27
35 30 0.73
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (35 bp):
AATTAAATTAATTAATTTAAATTAATTAAAATTTA
Found at i:3374580 original size:25 final size:23
Alignment explanation
Indices: 3374552--3374609 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
3374542 ATAAAAATTT
3374552 ATATATTATTAATAAATTTAATATC
1 ATATATTATT--TAAATTTAATATC
*
3374577 ATATATAATATTTAAATTTAATATT
1 ATATAT--TATTTAAATTTAATATC
*
3374602 TTATATTA
1 ATATATTA
3374610 AAATTATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 2 0.07
25 23 0.79
27 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATTATTTAAATTTAATATC
Found at i:3374584 original size:18 final size:18
Alignment explanation
Indices: 3374540--3374591 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
3374530 TTTTATTTTA
* *
3374540 ATATAAAAATTTATATATT
1 ATATATAAATTTA-ATATC
3374559 AT-TAATAAATTTAATATC
1 ATAT-ATAAATTTAATATC
3374577 ATATATAATATTTAA
1 ATATATAA-ATTTAA
3374592 ATTTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATATAAATTTAATATC
Found at i:3375816 original size:18 final size:18
Alignment explanation
Indices: 3375785--3375836 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
3375775 ATTTAATTTT
3375785 AAATTTT-TTAAAATTTAA
1 AAATTTTATT-AAATTTAA
* *
3375803 TAATTTTATTAAATATAA
1 AAATTTTATTAAATTTAA
* *
3375821 AAAATTAATTAAATTT
1 AAATTTTATTAAATTT
3375837 TATTCAAGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATTTTATTAAATTTAA
Found at i:3375869 original size:20 final size:20
Alignment explanation
Indices: 3375846--3375885 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3375836 TTATTCAAGT
3375846 AATTAAAATAA-TTAATTTAA
1 AATT-AAATAATTTAATTTAA
*
3375866 AATTAATTAATTTAATTTAA
1 AATTAAATAATTTAATTTAA
3375886 TTAGTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTAAATAATTTAATTTAA
Found at i:3375874 original size:15 final size:14
Alignment explanation
Indices: 3375848--3375880 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
3375838 ATTCAAGTAA
3375848 TTAAAATAATTAAT
1 TTAAAATAATTAAT
3375862 TTAAAATTAATTAAT
1 TTAAAA-TAATTAAT
3375877 TTAA
1 TTAA
3375881 TTTAATTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAAATAATTAAT
Found at i:3378917 original size:11 final size:11
Alignment explanation
Indices: 3378903--3378927 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3378893 TTAATATTAT
3378903 ATTTAAATTTA
1 ATTTAAATTTA
3378914 ATTTAAATTTA
1 ATTTAAATTTA
3378925 ATT
1 ATT
3378928 GAACATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:3379082 original size:2 final size:2
Alignment explanation
Indices: 3379077--3379106 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3379067 TATATATATA
3379077 TG 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 TG
3379107 AGAAAATGAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3379983 original size:23 final size:22
Alignment explanation
Indices: 3379936--3379988 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
3379926 CGTTTTAAAA
*
3379936 ATTTTTCATAAATTTTATTTTT
1 ATTTTTAATAAATTTTATTTTT
* *
3379958 ATTTTTAATTAATTTT-TTATT
1 ATTTTTAATAAATTTTATTTTT
*
3379979 ATATTTAATA
1 ATTTTTAATA
3379989 TTATCTGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTTTAATAAATTTTATTTTT
Found at i:3383583 original size:19 final size:19
Alignment explanation
Indices: 3383561--3383600 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
3383551 TATTTTTATT
3383561 TAAAT-TTAATTATAAAATA
1 TAAATATTAA-TATAAAATA
3383580 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
3383599 TA
1 TA
3383601 TTTTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATATTAATATAAAATA
Found at i:3384204 original size:21 final size:21
Alignment explanation
Indices: 3384150--3384204 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
3384140 TTAATTGATT
3384150 TATTAAAATAAT-ATTTTAAA
1 TATTAAAATAATAATTTTAAA
3384170 TATTTAAAA-AATAATTTT-AA
1 TA-TTAAAATAATAATTTTAAA
3384190 TATTAAATATAATAA
1 TATTAAA-ATAATAA
3384205 ATAATTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 5 0.16
20 10 0.32
21 16 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTAAAATAATAATTTTAAA
Found at i:3385557 original size:15 final size:15
Alignment explanation
Indices: 3385516--3385559 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 15
3385506 TTATTAAGAT
3385516 ATATTTAATAAATTTTA
1 ATATTT-AT-AATTTTA
3385533 AT-TTTA-AATTTTA
1 ATATTTATAATTTTA
3385546 ATATTTATAATTTT
1 ATATTTATAATTTT
3385560 TTTGATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.36
14 4 0.16
15 7 0.28
16 3 0.12
17 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTTATAATTTTA
Found at i:3387788 original size:2 final size:2
Alignment explanation
Indices: 3387781--3387814 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3387771 CCTTTTGGAG
*
3387781 AT AT AT AT AC 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
3387815 TAATGTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3395470 original size:36 final size:36
Alignment explanation
Indices: 3395422--3395504 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 36
3395412 ATCTAAATCT
3395422 CCCCATGCCTGTTGACGATTTCGATCTGAACCTTTC
1 CCCCATGCCTGTTGACGATTTCGATCTGAACCTTTC
* *
3395458 CCCCATGGCTGTTGACGATTTCGATCTGAATCTTTC
1 CCCCATGCCTGTTGACGATTTCGATCTGAACCTTTC
3395494 CTCCC-TGCCTG
1 C-CCCATGCCTG
3395505 GCCTTGACTC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 40 0.93
37 3 0.07
ACGTcount: A:0.14, C:0.34, G:0.18, T:0.34
Consensus pattern (36 bp):
CCCCATGCCTGTTGACGATTTCGATCTGAACCTTTC
Done.