Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 4 of 17
Found at i:600085 original size:17 final size:17
Alignment explanation
Indices: 600063--600097 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
600053 GTTTGGTTAC
600063 TTTAAAT-TTATATATTT
1 TTTAAATATT-TATATTT
600080 TTTAAATATTTATATTT
1 TTTAAATATTTATATTT
600097 T
1 T
600098 ATATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAAATATTTATATTT
Found at i:600119 original size:25 final size:26
Alignment explanation
Indices: 600068--600139 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
600058 GTTACTTTAA
**
600068 ATTTATATATTTTTTAAATATTTATAT
1 ATTTATATA-TTTTTAAATATAAATAT
600095 -TTTATATATTTTTAAATATAAATAT
1 ATTTATATATTTTTAAATATAAATAT
* *
600120 AATAATATAATTTTTAAATA
1 ATTTATAT-ATTTTTAAATA
600140 CTCTTTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 15 0.38
26 13 0.33
27 11 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTATATATTTTTAAATATAAATAT
Found at i:603872 original size:2 final size:2
Alignment explanation
Indices: 603867--603901 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
603857 TGTGTGTGTG
603867 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
603902 GCCCATGCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:605261 original size:2 final size:2
Alignment explanation
Indices: 605254--605288 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
605244 AAAGAGTTTC
605254 AT 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 AT A
605289 AAGAAGTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:606574 original size:19 final size:20
Alignment explanation
Indices: 606552--606593 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
606542 AATTTTAAAA
* *
606552 TTTTCATTAAAT-GAGTTTT
1 TTTTAATTAAATAGAATTTT
*
606571 TTTTAATTAGATAGAATTTT
1 TTTTAATTAAATAGAATTTT
606591 TTT
1 TTT
606594 ATATCATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (20 bp):
TTTTAATTAAATAGAATTTT
Found at i:607753 original size:18 final size:17
Alignment explanation
Indices: 607730--607775 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
607720 AATAATTATT
*
607730 AATATTTATATGATATAA
1 AATATTTATATAAT-TAA
*
607748 AATATTAAT-TAATTAA
1 AATATTTATATAATTAA
607764 AAT-TTTATATAA
1 AATATTTATATAA
607776 AAATATAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 3 0.12
18 8 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AATATTTATATAATTAA
Found at i:607763 original size:32 final size:32
Alignment explanation
Indices: 607694--607781 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 32
607684 TACTATTAAA
** * * *
607694 AATTAATATGAATAAGATATAAATAAAATAATT
1 AATTAATATTTATATGATATAAA-ATATTAATT
607727 -ATTAATATTTATATGATATAAAATATTAATT
1 AATTAATATTTATATGATATAAAATATTAATT
*
607758 AATTAAAATTT-TAT-ATA-AAAATAT
1 AATTAATATTTATATGATATAAAATAT
607782 AACTTAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
29 7 0.15
30 3 0.06
31 10 0.21
32 28 0.58
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (32 bp):
AATTAATATTTATATGATATAAAATATTAATT
Found at i:607796 original size:29 final size:28
Alignment explanation
Indices: 607742--607796 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
607732 TATTTATATG
*
607742 ATATAAAATATTAATTAATTAAAATTTT
1 ATATAAAATATTAATTAAATAAAATTTT
*
607770 ATATAAAA-ATATAACTTAAATACAATT
1 ATATAAAATAT-TAA-TTAAATAAAATT
607797 ATGACATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 11 0.48
29 10 0.43
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAAAATATTAATTAAATAAAATTTT
Found at i:609959 original size:24 final size:22
Alignment explanation
Indices: 609917--609977 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 22
609907 TAAAGATAAT
*
609917 TTTAATTTTAATAAAATAATATTA
1 TTTAA-TTTATTAAAATAA-ATTA
*
609941 TTTAATTTATTAAATATAAATTT
1 TTTAATTTATTAAA-ATAAATTA
609964 TATTAATATTATTA
1 T-TTAAT-TTATTA
609978 TCATTTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 12 0.38
24 14 0.44
25 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAATTTATTAAAATAAATTA
Found at i:610598 original size:17 final size:17
Alignment explanation
Indices: 610572--610627 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
610562 CGAGATTATC
*
610572 TAAAACATAAAAAAAAA
1 TAAAAAATAAAAAAAAA
*
610589 TAAAAAAT-AAAAAATA
1 TAAAAAATAAAAAAAAA
*
610605 -AAAAAATAAAAGAAAAC
1 TAAAAAATAAAA-AAAAA
610622 TAAAAA
1 TAAAAA
610628 GTAACCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 7 0.22
16 10 0.31
17 10 0.31
18 5 0.16
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (17 bp):
TAAAAAATAAAAAAAAA
Found at i:610602 original size:14 final size:15
Alignment explanation
Indices: 610583--610615 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
610573 AAAACATAAA
610583 AAAAAAT-AAAAAAT
1 AAAAAATAAAAAAAT
610597 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
610612 AAAA
1 AAAA
610616 GAAAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:610627 original size:7 final size:7
Alignment explanation
Indices: 610583--610615 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
610573 AAAACATAAA
610583 AAAAAAT
1 AAAAAAT
610590 AAAAAAT
1 AAAAAAT
610597 AAAAAAT
1 AAAAAAT
610604 AAAAAAAT
1 -AAAAAAT
610612 AAAA
1 AAAA
610616 GAAAACTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:610641 original size:26 final size:25
Alignment explanation
Indices: 610572--610642 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
610562 CGAGATTATC
* *
610572 TAAAACATAAAAAAAAATA-AAAAA
1 TAAAAAATAAAAAAAAAAAGAAAAA
*
610596 TAAAAAATAAAAAAATAAAAGAAAAC
1 TAAAAAATAAAAAAA-AAAAGAAAAA
* *
610622 TAAAAAGTAACCAAAAAAAAG
1 TAAAAAATAA-AAAAAAAAAG
610643 GGAAAAAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
24 14 0.36
25 3 0.08
26 18 0.46
27 4 0.10
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.11
Consensus pattern (25 bp):
TAAAAAATAAAAAAAAAAAGAAAAA
Found at i:612135 original size:2 final size:2
Alignment explanation
Indices: 612130--612163 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
612120 TTCGTGTGTA
* *
612130 AT AT AT AT AT AT AA AA 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
612164 TTTTTCTTCT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:613213 original size:17 final size:19
Alignment explanation
Indices: 613191--613336 Score: 63
Period size: 18 Copynumber: 7.6 Consensus size: 19
613181 CTAAATATTG
613191 AATATAATA-AAAAATA-A
1 AATATAATATAAAAATATA
*
613208 AATATAATATAAATATATA
1 AATATAATATAAAAATATA
* **
613227 AATAT--TTTAAATTTATA
1 AATATAATATAAAAATATA
613244 TAATATAA-ATAATTAATATATCA
1 -AATATAATATAA--AA-ATAT-A
* * ** *
613267 AAAATATTATATGAGTATA
1 AATATAATATAAAAATATA
* *
613286 AA-ATAATTTAAATATAATTA
1 AATATAATATAAAAAT-A-TA
*
613306 TAATATAATA-AAATATATA
1 -AATATAATATAAAAATATA
613325 AATATAATATAA
1 AATATAATATAA
613337 TTAAATAAAT
Statistics
Matches: 96, Mismatches: 18, Indels: 28
0.68 0.13 0.20
Matches are distributed among these distances:
17 19 0.20
18 27 0.28
19 17 0.18
20 6 0.06
21 10 0.10
22 13 0.14
23 4 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
AATATAATATAAAAATATA
Found at i:613251 original size:5 final size:5
Alignment explanation
Indices: 613191--613337 Score: 66
Period size: 5 Copynumber: 30.6 Consensus size: 5
613181 CTAAATATTG
* * *
613191 AATAT AATA- AA-A- AATAA AATAT AATAT AA-AT -ATAT AA-AT ATTTT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * *
613235 AA-ATT TATAT AATAT AA-AT AAT-T AATAT -ATCAAA AATAT TATAT
1 AATA-T AATAT AATAT AATAT AATAT AATAT AAT--AT AATAT AATAT
* * * *
613279 GAGTAT AAAAT AATTT AAATAT AATTAT AATAT AATAA AATAT -ATA-
1 -AATAT AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT AATAT
613325 AATAT AATAT AAT
1 AATAT AATAT AAT
613338 TAAATAAATT
Statistics
Matches: 106, Mismatches: 19, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
3 4 0.04
4 26 0.25
5 60 0.57
6 14 0.13
7 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:613307 original size:30 final size:29
Alignment explanation
Indices: 613191--613353 Score: 98
Period size: 28 Copynumber: 5.7 Consensus size: 29
613181 CTAAATATTG
*
613191 AATATAATAAAAAATA-AAATATAA-TAT
1 AATATAATAAAATATATAAATATAATTAT
* *
613218 AA-AT-ATATAAATATTTTAAAT-TTA-TAT
1 AATATAATA-AAATA-TATAAATATAATTAT
*
613245 AATATAAATAATTAATATATCAAAAAT-ATTAT
1 AATAT-AATAA--AATATAT-AAATATAATTAT
*
613277 -ATGAGT-ATAAAATAATTTAAATATAATTAT
1 AAT-A-TAATAAAAT-ATATAAATATAATTAT
613307 AATATAATAAAATATATAAATATAA-TAT
1 AATATAATAAAATATATAAATATAATTAT
*
613335 AAT-TAAATAAATTAT-TAAA
1 AATAT-AATAAAATATATAAA
613354 ATTTTTTATT
Statistics
Matches: 109, Mismatches: 9, Indels: 36
0.71 0.06 0.23
Matches are distributed among these distances:
25 3 0.03
26 6 0.06
27 15 0.14
28 21 0.19
29 21 0.19
30 21 0.19
31 16 0.15
32 5 0.05
33 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (29 bp):
AATATAATAAAATATATAAATATAATTAT
Found at i:613324 original size:61 final size:61
Alignment explanation
Indices: 613206--613356 Score: 145
Period size: 61 Copynumber: 2.6 Consensus size: 61
613196 AATAAAAAAT
* * *
613206 AAAATATAATATAAATATATAAATATTTTAAATTTATATAATATAAATAATTAATATATCA
1 AAAATATAATATAAATATATAAATAATTTAAATTAATATAATATAAATAAATAATATATCA
* * *
613267 AAAATATTATATGAGTATA-AAATAATTTAAATATAATTATAATAT-AAT-AA-AATATAT--
1 AAAATATAATATAAATATATAAATAATTTAAAT-TAA-TATAATATAAATAAATAATATATCA
* * * *
613324 -AAATATAATATAATTAAATAAATTATTAAAATT
1 AAAATATAATATAAATATATAAATAATTTAAATT
613357 TTTTATTACT
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
56 15 0.20
57 11 0.15
59 7 0.09
60 13 0.17
61 21 0.28
62 8 0.11
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (61 bp):
AAAATATAATATAAATATATAAATAATTTAAATTAATATAATATAAATAAATAATATATCA
Found at i:613330 original size:23 final size:23
Alignment explanation
Indices: 613297--613343 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
613287 AATAATTTAA
*
613297 ATATAATTATAATATAATAAAAT
1 ATATAAATATAATATAATAAAAT
*
613320 ATATAAATATAATATAATTAAAT
1 ATATAAATATAATATAATAAAAT
613343 A
1 A
613344 AATTATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATAAATATAATATAATAAAAT
Found at i:614128 original size:15 final size:15
Alignment explanation
Indices: 614090--614139 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
614080 TAATAATTTT
*
614090 AATATTTAAATTATA
1 AATATTTAAATAATA
614105 AATTATTTAAATAATA
1 AA-TATTTAAATAATA
*
614121 AATATTTAAATAAAA
1 AATATTTAAATAATA
614136 AATA
1 AATA
614140 AATCAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 18 0.56
16 14 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATTTAAATAATA
Found at i:614148 original size:31 final size:31
Alignment explanation
Indices: 614090--614151 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
614080 TAATAATTTT
* * * * *
614090 AATATTTAAATTATAAATTATTTAAATAATA
1 AATATTTAAATAAAAAATAAATCAAATAATA
614121 AATATTTAAATAAAAAATAAATCAAATAATA
1 AATATTTAAATAAAAAATAAATCAAATAATA
614152 TCAAAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (31 bp):
AATATTTAAATAAAAAATAAATCAAATAATA
Found at i:614793 original size:21 final size:19
Alignment explanation
Indices: 614769--614817 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
614759 TATTTTGTTT
614769 TATTATTTTTAATAATTTATA
1 TATTATTTTT-AT-ATTTATA
614790 TATT-TTTATTATATTTATA
1 TATTATTT-TTATATTTATA
*
614809 TATAATTTT
1 TATTATTTT
614818 ATTAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 11 0.44
20 8 0.32
21 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTATTTTTATATTTATA
Found at i:614804 original size:11 final size:10
Alignment explanation
Indices: 614766--614819 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
614756 TGTTATTTTG
614766 TTTTAT-TAT
1 TTTTATATAT
614775 TTTTA-ATA-
1 TTTTATATAT
*
614783 ATTTATATAT
1 TTTTATATAT
614793 TTTTATTATAT
1 TTTTA-TATAT
* *
614804 TTATATATAA
1 TTTTATATAT
614814 TTTTAT
1 TTTTAT
614820 TAAAATATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
8 4 0.11
9 10 0.28
10 13 0.36
11 9 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTATATAT
Found at i:614818 original size:21 final size:18
Alignment explanation
Indices: 614767--614822 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
614757 GTTATTTTGT
*
614767 TTTAT-TATTTTTAATAA
1 TTTATATATTTTTATTAA
614784 TTTATATATTTTTATTATA
1 TTTATATATTTTTATTA-A
614803 TTTATATATAATTTTATTAA
1 TTTATATAT--TTTTATTAA
614823 AATATTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.15
18 10 0.29
19 10 0.29
20 1 0.03
21 8 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATATATTTTTATTAA
Found at i:614820 original size:27 final size:27
Alignment explanation
Indices: 614766--614893 Score: 68
Period size: 30 Copynumber: 4.5 Consensus size: 27
614756 TGTTATTTTG
614766 TTTTATTAT-TTT-TA-ATAATTTATATAT
1 TTTTATTATATTTATATATAA-TT-T-TAT
614793 TTTTATTATATTTATATATAATTTTAT
1 TTTTATTATATTTATATATAATTTTAT
**
614820 TAAAATATTAATTATTTATATA-AATTTTAAT
1 T--TTTATT-A-TATTTATATATAATTTT-AT
* * *
614851 ATATTAAATATTTATTATATAATAATTTTA-
1 -T-TTTATTATAT-TTATAT-ATAATTTTAT
614881 TTTTATTATATTT
1 TTTTATTATATTT
614894 TAATTATTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
27 15 0.19
28 11 0.14
29 11 0.14
30 18 0.23
31 17 0.22
32 7 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTTATTATATTTATATATAATTTTAT
Found at i:614869 original size:16 final size:16
Alignment explanation
Indices: 614794--614888 Score: 52
Period size: 16 Copynumber: 5.8 Consensus size: 16
614784 TTTATATATT
*
614794 TTTATTATATT-TATA
1 TTTATTATATTAAATA
* *
614809 TATAATTTTATTAAAATA
1 T-TTATTATATT-AAATA
*
614827 TTAATTATTTATATAAAT-
1 TTTATTA--TAT-TAAATA
*
614845 TTTAATATATTAAATA
1 TTTATTATATTAAATA
*
614861 TTTATTATATAATAAT-
1 TTTATTATATTA-AATA
*
614877 TTTATTTTATTA
1 TTTATTATATTA
614889 TATTTTAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
15 6 0.10
16 31 0.50
17 8 0.13
18 9 0.15
19 7 0.11
20 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATTATATTAAATA
Found at i:614897 original size:21 final size:21
Alignment explanation
Indices: 614861--614917 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
614851 ATATTAAATA
**
614861 TTTATTATATAATAATT-TTAT
1 TTTATTATATTTTAATTATT-T
614882 TTTATTATATTTTAATTATTT
1 TTTATTATATTTTAATTATTT
*
614903 TTAAGTTATATTTTA
1 TTTA-TTATATTTTA
614918 TTTAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTATTATATTTTAATTATTT
Found at i:614911 original size:11 final size:11
Alignment explanation
Indices: 614873--614917 Score: 58
Period size: 10 Copynumber: 4.2 Consensus size: 11
614863 TATTATATAA
*
614873 TAATTTTATTT
1 TAATTATATTT
614884 T-ATTATATTT
1 TAATTATATTT
614894 TAATTAT-TTT
1 TAATTATATTT
614904 TAAGTTATATTT
1 TAA-TTATATTT
614916 TA
1 TA
614918 TTTAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 15 0.50
11 10 0.33
12 5 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TAATTATATTT
Found at i:616556 original size:2 final size:2
Alignment explanation
Indices: 616534--616581 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
616524 GTGCAGGCAG
* * * *
616534 AT AT AC AT AT AC AT TT AT AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
616576 AT AT AT
1 AT AT AT
616582 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:616810 original size:2 final size:2
Alignment explanation
Indices: 616803--616835 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
616793 GAACAGCAGC
616803 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
616836 AGAATTGATA
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:617345 original size:19 final size:18
Alignment explanation
Indices: 617318--617377 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
617308 ATATTATTAC
*
617318 ATAATTAAAAAAATATAAA
1 ATAAATAAAAAAAT-TAAA
*
617337 ATAAATAAAATAATTAAA
1 ATAAATAAAAAAATTAAA
*
617355 ATATAATATAATATAATTAAA
1 ATA-AATA-AA-AAAATTAAA
617376 AT
1 AT
617378 CTATGTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.19
19 16 0.44
20 2 0.06
21 11 0.31
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAAAAAAATTAAA
Found at i:617370 original size:21 final size:21
Alignment explanation
Indices: 617333--617414 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
617323 TAAAAAAATA
617333 TAAAATA-AATA-AA-ATAAT
1 TAAAATATAATATAATATAAT
617351 TAAAATATAATATAATATAAT
1 TAAAATATAATATAATATAAT
* *
617372 TAAAATCT-ATGTAAATATAAT
1 TAAAATATAATAT-AATATAAT
*
617393 TATAATATTAATATAATATAAT
1 TAAAATA-TAATATAATATAAT
617415 ATATAAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
18 7 0.13
19 4 0.08
20 5 0.09
21 25 0.47
22 9 0.17
23 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (21 bp):
TAAAATATAATATAATATAAT
Found at i:617411 original size:5 final size:5
Alignment explanation
Indices: 617329--617417 Score: 65
Period size: 5 Copynumber: 17.2 Consensus size: 5
617319 TAATTAAAAA
* * * *
617329 AATAT AAAAT AA-AT AAAAT AATTAA AATAT AATAT AATAT AAT-T AAAAT
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT
* *
617378 CTATGT AAATAT AATTAT AATATT AATAT AATAT AATAT A
1 -AATAT -AATAT AA-TAT AATA-T AATAT AATAT AATAT A
617418 TAAATTATTA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
4 7 0.10
5 42 0.63
6 18 0.27
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:622351 original size:25 final size:27
Alignment explanation
Indices: 622300--622361 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
622290 AATAATTTTT
622300 AAAATAAAATATATTTTAATACAAATAA
1 AAAAT-AAATATATTTTAATACAAATAA
*
622328 AAAATAAATAT-TTTTAATA-TAATAA
1 AAAATAAATATATTTTAATACAAATAA
622353 AAATATAAA
1 AAA-ATAAA
622362 AAAATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 8 0.25
26 13 0.41
27 6 0.19
28 5 0.16
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAATAAATATATTTTAATACAAATAA
Found at i:622369 original size:26 final size:24
Alignment explanation
Indices: 622322--622377 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 24
622312 ATTTTAATAC
* **
622322 AAATAAAAAATAAATATTTTTAAT
1 AAATAAAAAATAAAAAAATTTAAT
622346 ATAATAAAAATATAAAAAAATTTAA-
1 A-AATAAAAA-ATAAAAAAATTTAAT
622371 AAATAAA
1 AAATAAA
622378 TAGTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 7 0.26
25 9 0.33
26 11 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATAAAAAATAAAAAAATTTAAT
Found at i:624296 original size:43 final size:43
Alignment explanation
Indices: 624248--624334 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
624238 CTTATATTAA
*
624248 AGACCATACCATTTAGCTGAATGCATAATTTTATAAAGTATTT
1 AGACCACACCATTTAGCTGAATGCATAATTTTATAAAGTATTT
624291 AGACCACACCATTTAGCTGAATGCATAATTTTATAAAGTATTT
1 AGACCACACCATTTAGCTGAATGCATAATTTTATAAAGTATTT
624334 A
1 A
624335 CTATATTGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (43 bp):
AGACCACACCATTTAGCTGAATGCATAATTTTATAAAGTATTT
Found at i:629688 original size:2 final size:2
Alignment explanation
Indices: 629681--629710 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
629671 TGTAGACATT
629681 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
629711 TGGTACCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:632244 original size:2 final size:2
Alignment explanation
Indices: 632239--632274 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
632229 ATATATATAT
*
632239 AG AG AG AG AG AG AG AG GG 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 AG
632275 CGACGTTGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:632577 original size:12 final size:12
Alignment explanation
Indices: 632560--632602 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
632550 AGAGAAGAGC
632560 GCGTGGGATTGA
1 GCGTGGGATTGA
632572 GCGTGGGATTGA
1 GCGTGGGATTGA
* **
632584 GCGTGAGCGTGA
1 GCGTGGGATTGA
632596 GCGTGGG
1 GCGTGGG
632603 CGTGGGCGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.53, T:0.21
Consensus pattern (12 bp):
GCGTGGGATTGA
Found at i:632592 original size:6 final size:6
Alignment explanation
Indices: 632581--632614 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
632571 AGCGTGGGAT
* *
632581 TGAGCG TGAGCG TGAGCG TGGGCG TGGGCG TGAG
1 TGAGCG TGAGCG TGAGCG TGAGCG TGAGCG TGAG
632615 GTTGAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.12, C:0.15, G:0.56, T:0.18
Consensus pattern (6 bp):
TGAGCG
Found at i:632605 original size:12 final size:12
Alignment explanation
Indices: 632569--632612 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
632559 CGCGTGGGAT
**
632569 TGAGCGTGGGAT
1 TGAGCGTGGGCG
*
632581 TGAGCGTGAGCG
1 TGAGCGTGGGCG
632593 TGAGCGTGGGCG
1 TGAGCGTGGGCG
*
632605 TGGGCGTG
1 TGAGCGTG
632613 AGGTTGAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.11, C:0.14, G:0.55, T:0.20
Consensus pattern (12 bp):
TGAGCGTGGGCG
Found at i:632620 original size:24 final size:24
Alignment explanation
Indices: 632560--632620 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
632550 AGAGAAGAGC
*
632560 GCGTG-GGATTGAGCGTGGGATTGA
1 GCGTGAGG-TTGAGCGTGGGAGTGA
* *
632584 GCGTGAGCG-TGAGCGTGGGCGTGG
1 GCGTGAG-GTTGAGCGTGGGAGTGA
632608 GCGTGAGGTTGAG
1 GCGTGAGGTTGAG
632621 TTTTTTACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.03
24 28 0.90
25 1 0.03
26 1 0.03
ACGTcount: A:0.13, C:0.11, G:0.54, T:0.21
Consensus pattern (24 bp):
GCGTGAGGTTGAGCGTGGGAGTGA
Found at i:634674 original size:71 final size:71
Alignment explanation
Indices: 634594--634737 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
634584 TTTTAATATC
634594 ATGATTTATTTGATAATGAAAAAATTAAAGAAAAAATAACATGTAGTTAATTTTGACACCAATTT
1 ATGATTTATTTGATAATGAAAAAATTAAAGAAAAAATAACATGTAGTTAATTTTGACACCAATTT
634659 TTGCTG
66 TTGCTG
634665 ATGATTTATTTGATAATGAAAAAATTAAAGAAAAAATAACATGTAGTTAATTTTGACACCAATTT
1 ATGATTTATTTGATAATGAAAAAATTAAAGAAAAAATAACATGTAGTTAATTTTGACACCAATTT
634730 TTGCTG
66 TTGCTG
634736 AT
1 AT
634738 TAGAACATAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (71 bp):
ATGATTTATTTGATAATGAAAAAATTAAAGAAAAAATAACATGTAGTTAATTTTGACACCAATTT
TTGCTG
Found at i:642874 original size:21 final size:20
Alignment explanation
Indices: 642805--642874 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 20
642795 ATATTGATTA
642805 TTTTTAATATAATTTTTATAAC
1 TTTTT-ATATAA-TTTTATAAC
* * *
642827 ATTTGATATAATTTTAATAAAGT
1 TTTTTATATAATTTT-AT-AA-C
642850 TTTTTATATAATTTTAGTAAC
1 TTTTTATATAATTTTA-TAAC
642871 TTTT
1 TTTT
642875 GATGTCAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 4 0.11
21 12 0.32
22 8 0.21
23 14 0.37
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (20 bp):
TTTTTATATAATTTTATAAC
Found at i:642909 original size:9 final size:10
Alignment explanation
Indices: 642884--642984 Score: 57
Period size: 11 Copynumber: 9.8 Consensus size: 10
642874 TGATGTCAAC
642884 TTTGATAAAAT
1 TTTGAT-AAAT
642895 TTTGATAAA-
1 TTTGATAAAT
642904 TTTGATATAAT
1 TTTGATA-AAT
642915 CTTT-A-AAAT
1 -TTTGATAAAT
*
642924 TTATGATATTAT
1 TT-TGATA-AAT
*
642936 TTTGATAAGT
1 TTTGATAAAT
*
642946 TTTGATATGAT
1 TTTGATA-AAT
*
642957 TTT-ATAACT
1 TTTGATAAAT
*
642966 TGTGATATAAT
1 TTTGATA-AAT
*
642977 TTTAATAA
1 TTTGATAA
642985 TCTTTAATAT
Statistics
Matches: 69, Mismatches: 11, Indels: 21
0.68 0.11 0.21
Matches are distributed among these distances:
8 2 0.03
9 14 0.20
10 22 0.32
11 24 0.35
12 7 0.10
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (10 bp):
TTTGATAAAT
Found at i:642909 original size:20 final size:19
Alignment explanation
Indices: 642884--642980 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 19
642874 TGATGTCAAC
*
642884 TTTGATAAAATTTTGATAAA
1 TTTGATATAATTTT-ATAAA
642904 TTTGATATAATCTTTA-AAA
1 TTTGATATAAT-TTTATAAA
* *
642923 TTTATGATATTATTTTGATAAGT
1 -TT-TGATATAATTTT-ATAA-A
* *
642946 TTTGATATGATTTTATAAC
1 TTTGATATAATTTTATAAA
642965 TTGTGATATAATTTTA
1 TT-TGATATAATTTTA
642981 ATAATCTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
19 5 0.08
20 32 0.50
21 23 0.36
22 4 0.06
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (19 bp):
TTTGATATAATTTTATAAA
Found at i:642931 original size:41 final size:41
Alignment explanation
Indices: 642881--642984 Score: 113
Period size: 41 Copynumber: 2.6 Consensus size: 41
642871 TTTTGATGTC
*
642881 AACTT-TGATAAAATTTTGATAA-ATTTGATATAATCTTTAA
1 AACTTATGATATAATTTTGATAAGATTTGATATAAT-TTTAA
* * * * *
642921 AATTTATGATATTATTTTGATAAGTTTTGATATGATTTTAT
1 AACTTATGATATAATTTTGATAAGATTTGATATAATTTTAA
* *
642962 AACTTGTGATATAATTTTAATAA
1 AACTTATGATATAATTTTGATAA
642985 TCTTTAATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
40 4 0.08
41 38 0.73
42 10 0.19
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (41 bp):
AACTTATGATATAATTTTGATAAGATTTGATATAATTTTAA
Found at i:642951 original size:21 final size:19
Alignment explanation
Indices: 642884--643042 Score: 93
Period size: 21 Copynumber: 7.7 Consensus size: 19
642874 TGATGTCAAC
* *
642884 TTTGATAAAATTTTGATAAA
1 TTTGATATAATTTT-ATAAT
*
642904 TTTGATATAATCTTTAAAAT
1 TTTGATATAAT-TTTATAAT
*
642924 TTATGATATTATTTTGATAAGT
1 TT-TGATATAATTTT-ATAA-T
*
642946 TTTGATATGATTTTATAACT
1 TTTGATATAATTTTATAA-T
*
642966 TGTGATATAATTTTAATAAT
1 TTTGATATAATTTT-ATAAT
* ** *
642986 CTTTAATATCGTTTTGGTAAT
1 -TTTGATATAATTTT-ATAAT
**
643007 TTTTTTAATAATTTTTATAAT
1 TTTGAT-ATAA-TTTTATAAT
*
643028 TTTCAATATAATTTT
1 TTT-GATATAATTTT
643043 TGTAACTTTT
Statistics
Matches: 108, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
20 44 0.41
21 56 0.52
22 8 0.07
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTGATATAATTTTATAAT
Found at i:643019 original size:42 final size:42
Alignment explanation
Indices: 642971--643063 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
642961 TAACTTGTGA
** *
642971 TATAATTTTAATAATCTTT-AATATCGTTTTGGTAA-TTTTTT
1 TATAATTTTAATAAT-TTTCAATATAATTTTGGTAACTTTTAT
* *
643012 TAATAATTTTTATAATTTTCAATATAATTTTTGTAACTTTTAT
1 T-ATAATTTTAATAATTTTCAATATAATTTTGGTAACTTTTAT
643055 TATAATTTT
1 TATAATTTT
643064 GATATAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 4 0.09
42 34 0.77
43 6 0.14
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (42 bp):
TATAATTTTAATAATTTTCAATATAATTTTGGTAACTTTTAT
Found at i:643043 original size:21 final size:21
Alignment explanation
Indices: 642929--643063 Score: 71
Period size: 21 Copynumber: 6.5 Consensus size: 21
642919 AAAATTTATG
* * * *
642929 ATATTATTTTGATAAGTTTTG
1 ATATAATTTTTATAACTTTTA
* * *
642950 ATATGA-TTTTATAACTTGTG
1 ATATAATTTTTATAACTTTTA
*
642970 ATATAATTTTAATAA-TCTTTA
1 ATATAATTTTTATAACT-TTTA
** ** *
642991 ATATCGTTTTGGTAA-TTTTT
1 ATATAATTTTTATAACTTTTA
*
643011 TTAATAATTTTTATAA-TTTTCA
1 AT-ATAATTTTTATAACTTTT-A
*
643033 ATATAATTTTTGTAACTTTTA
1 ATATAATTTTTATAACTTTTA
*
643054 TTATAATTTT
1 ATATAATTTT
643064 GATATAATAT
Statistics
Matches: 87, Mismatches: 22, Indels: 10
0.73 0.18 0.08
Matches are distributed among these distances:
20 21 0.24
21 61 0.70
22 5 0.06
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.57
Consensus pattern (21 bp):
ATATAATTTTTATAACTTTTA
Found at i:643145 original size:21 final size:22
Alignment explanation
Indices: 643098--643147 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
643088 TTATAACTTG
* **
643098 TTGGTAACTTTTAATATATTTT
1 TTGGTAACATTTAATATATAGT
643120 TTGGTAACATTTAATATA-AGT
1 TTGGTAACATTTAATATATAGT
643141 TTGGTAA
1 TTGGTAA
643148 TTGTTGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.50
Consensus pattern (22 bp):
TTGGTAACATTTAATATATAGT
Found at i:644489 original size:2 final size:2
Alignment explanation
Indices: 644482--644510 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
644472 AAAGATTGGT
644482 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 T
644511 TTTTTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:645986 original size:431 final size:425
Alignment explanation
Indices: 645179--647467 Score: 1872
Period size: 418 Copynumber: 5.4 Consensus size: 425
645169 AAGGAAATTT
* * * * * * * * *
645179 TTTTTTTCTGAAAGTAGTATTAAAAA-AATATCTCAAAATAATATTAATATAACTATAGTAAAGG
1 TTTTTTT-TAAAAGTAATGTTAAAAAGAATGTCTTAAAAAAATATTAATATTACTATAATGAAGG
* ** * * * ** * *
645243 TAAAAATTATTTTAACGTTTTTTATTTTCAATAGGAGGAAGTAATTTGGCATATAAACTAAAAAA
65 CAAGTATTATTTTAACATTTTTTATTTTTAATA-AAAAAAGTAATTTAGCATATAAATTAAAAAA
* * ** * * * *
645308 GTAAAATCATTGCACAATTATGCTTAGTT-AGTTAGGATAGTATTAGC-TTTTGGTTTTCACTAT
129 GTAAAGTCATTGCATAATTATGCTTA-TTCAACTAGAATAATATTGGCTTTTTGGTTTTCACTAC
* * * *** *
645371 ATTAGTATTATGATGCGTTTGACAGTGAAAAAATTAAAAAAAATAACATGTAATTAATTTTGATA
193 CTTAGTATCATAATTTATTTGATAGTGAAAAAATT-AAAAAAATAACATGTAATTAATTTTGATA
* * * * * *
645436 TCAATTTTTTTTTGATTATAAAGTAACTTG-AAAGCCCATGATAAAATTTATAAGTAAAAATTTA
257 TCAA-TTTTTATCGATTATAAA-TATCTTGCAAAGCCCATGAAAAAATTTATTAGTAAAAA-CTA
* * * *
645500 TGTAATTGTTGATACAATAAAGGAAAATTAAAGTTT-ATCCAAATAGTTTATTTCTTTCTTCATT
319 TGTAATTGTTGATATAATAAAAGAAAA-TAAAGTTTAATCCAAATAGTTCATTTCTTTCATCATT
*
645564 CATATATCAAATATAATGGAAAAAAATAATTTTTCTTTCTTTCAC
383 CATATATCAAATATAAT--AAAAAAATAATTTTTCTTTCTCTCAC
* * * * *
645609 -TTTTTTTGAAAGTAATGTTAAAAAGAATGATTTTAAAAAAATATTAATATTGCTGTAGTGAAGG
1 TTTTTTTTAAAAGTAATGTTAAAAAGAATG-TCTTAAAAAAATATTAATATTACTATAATGAAGG
* * * *
645673 CAAGCATTATTTTAACATTTTTTCTTTTTAATAAAAAGAAATAA-TTGGCATATAAATTAAAAAA
65 CAAGTATTATTTTAACATTTTTTATTTTTAATAAAAA-AAGTAATTTAGCATATAAATTAAAAAA
* * * * *
645737 GTGAAGTTA-TGACATAATTATGGTTATTCAACTAGAATAATATTGGTTTTTTTGGTTTTTACTA
129 GTAAAGTCATTG-CATAATTATGCTTATTCAACTAGAATAATATTGG-CTTTTTGGTTTTCACTA
* * * * *
645801 CCTTAGTATGATAATTTGTTTGACAGTGAAAAAATTAAAGAAAGAATAACATATAGTTAATTTTG
192 CCTTAGTATCATAATTTATTTGATAGTGAAAAAATT-AA-AAA-AATAACATGTAATTAATTTTG
* * * ** *
645866 ATA-CTAATATTTATCGACTAT-AATATCTTACAAAGTTCATGACAAAATTTATTAGT-AAAACT
254 ATATC-AATTTTTATCGATTATAAATATCTTGCAAAGCCCATGAAAAAATTTATTAGTAAAAAC-
* * *
645928 TATGTAATTGTTGATATAATAAAAGAAAGATAAAGTGTAATCCAAGTAATTCATTTCTTTCATCA
317 TATGTAATTGTTGATATAATAAAAGAAA-ATAAAGTTTAATCCAAATAGTTCATTTCTTTCATCA
645993 TTCATATATCAAATATAATAAAAAATAATAATTTTTCTTTCTCTCAC
381 TTCATATATCAAATATAAT-AAAAA-AATAATTTTTCTTTCTCTCAC
* * * * *
646040 TTTTTTTTTTGAAAGTAATGTTAAAAAGAATGGCATCAAAGAATATTAATATTACTATAATGAAG
1 --TTTTTTTTAAAAGTAATGTTAAAAAGAATGTCTTAAAAAAATATTAATATTACTATAATGAAG
* * *
646105 GCAAGTATTATTTTAACATTCTTTACTTTGAATAAAATAAAGTAATTT-GACATATAAATTAAAA
64 GCAAGTATTATTTTAACATTTTTTATTTTTAATAAAA-AAAGTAATTTAG-CATATAAATTAAAA
* * * * * *
646169 AAGTAAAATCAATGCACAATTATGCTTATTCGACTAGAATAATATTAGATTTTTGGTTTTCACTA
127 AAGTAAAGTCATTGCATAATTATGCTTATTCAACTAGAATAATATTGGCTTTTTGGTTTTCACTA
* * * * * *
646234 CTTTAGTACCATGATTTTATTTGATAGTGAAAAAATGAAAAAAATAATATGTAATTAATTTTGAC
192 CCTTAGTATCAT-AATTTATTTGATAGTGAAAAAATTAAAAAAATAACATGTAATTAATTTTGAT
** *
646299 ATCAA-TTTT-T--A-T-T--A-A-CTTGCAAAGCCCACAAAAAAATTTATTAATAAAAAGCTAT
256 ATCAATTTTTATCGATTATAAATATCTTGCAAAGCCCATGAAAAAATTTATTAGTAAAAA-CTAT
* * * * *
646354 GTAATTATTGATATAATAAAAGGAAATTAAAATTTAATCTAAATAGTTTATTAT-TTTCATCATT
320 GTAATTGTTGATATAATAAAA-GAAAATAAAGTTTAATCCAAATAGTTCATT-TCTTTCATCATT
* * *
646418 CATATATCAATTATAATAAAAACATAA--TTT-TTTCTCTCTC
383 CATATATCAAATATAATAAAAAAATAATTTTTCTTTCTCTCAC
* * ** *
646458 TTCTTTTCCTAAAAGTAATGTTAAAAAAGAATG-CTTTAAAAAATATTAATATTGTTATAATAAA
1 TT-TTTT-TTAAAAGTAATGTT-AAAAAGAATGTCTTAAAAAAATATTAATATTACTATAATGAA
* * * ** *
646522 TGTAAGTATTATTTTAACATTCTTTATTTTTAATAGAAGGAAGTAATTTAGCATATAAACTAAAA
63 GGCAAGTATTATTTTAACATTTTTTATTTTTAATA-AAAAAAGTAATTTAGCATATAAATTAAAA
* * * *
646587 AAGTAAAGTCATTGTATAATTATGCTTATTTAACTAGAATAATGTTGGCTTTTTGGTTTTTACTA
127 AAGTAAAGTCATTGCATAATTATGCTTATTCAACTAGAATAATATTGGCTTTTTGGTTTTCACTA
* * *
646652 CTTTAGT-TGCATTATTTATTTGATAGTGTAAAAATTAAAAAAAT---ATGTAATTAA-TTTGAT
192 CCTTAGTAT-CATAATTTATTTGATAGTGAAAAAATTAAAAAAATAACATGTAATTAATTTTGAT
***
646712 ATCAATTTTTA-CTGATTATAAAATAAT-TTGCAAAGCTTTTGAAAAAATTTATTAGTAAAAA--
256 ATCAATTTTTATC-GATTAT-AAAT-ATCTTGCAAAGCCCATGAAAAAATTTATTAGTAAAAACT
* * * *
646773 ATATAA-TG--G-------AAAA-AAATTAAAGTTTAATCCAAACAGTTCATTTTTTTCATCATT
318 ATGTAATTGTTGATATAATAAAAGAAAATAAAGTTTAATCCAAATAGTTCATTTCTTTCATCATT
* *
646827 CATATATCAAATATAATAAAAAAATTTATTTTTTTATTTTTCTCTCAC
383 CATATATCAAATATAATAAAAAAA--TA--ATTTT-TCTTTCTCTCAC
* *
646875 TTTTTCTTCTAAAAGTAATGTTAAAAA-AATGTCTTAAAAAAATATTAATATAATTA-AAGTGAA
1 TTTTT-TT-TAAAAGTAATGTTAAAAAGAATGTCTTAAAAAAATATTAATATTACTATAA-TGAA
* *
646938 GACAAGTATTATTTTAACATTTTTTATTTTTAATAAGAAAAAGTAGTTTAGCATATAAATT-AAA
63 GGCAAGTATTATTTTAACATTTTTTATTTTTAATAA-AAAAAGTAATTTAGCATATAAATTAAAA
* * * * * * *
647002 AAGTGAAGCCATTGCATAATTGTGCTTCTTCAACTAAAATAGTATTGGCCTTTTGGTTTTCACTA
127 AAGTAAAGTCATTGCATAATTATGCTTATTCAACTAGAATAATATTGGCTTTTTGGTTTTCACTA
* * * * * * * *
647067 CCTTAGTATCATAATGTCTTTGATGGTGAAAAAAATAAAAAAATAACTTGTAGTTAATTCTGACA
192 CCTTAGTATCATAATTTATTTGATAGTGAAAAAATTAAAAAAATAACATGTAATTAATTTTGATA
* *
647132 TCAGTTTTTATC--------A-A-C-TGCAAAGCTCAT-AATAAAATTTATTAGTAAAAAACCTA
257 TCAATTTTTATCGATTATAAATATCTTGCAAAGCCCATGAA-AAAATTTATTAGT-AAAAA-CTA
* * * * * ** * * * *
647185 TGCAATTGTTAATATAATAAAA-AAATTAAAATATAATTTAAATAGTTTATTTTTTTCGTCATTT
319 TGTAATTGTTGATATAATAAAAGAAAATAAAGTTTAATCCAAATAGTTCATTTCTTTCATCATTC
* * *
647249 ATATATTAAATATAATAGAAAAAATAA--TTT-TTT-T-TAAA
384 ATATATCAAATATAATA-AAAAAATAATTTTTCTTTCTCTCAC
** * * * * *
647287 TTTTTTTTAAAAGTAATGTTAGGAAGAGTGGCTTAAAAGATTATT-ATA-TAGCTATAATGAAAG
1 TTTTTTTTAAAAGTAATGTTAAAAAGAATGTCTTAAAAAAATATTAATATTA-CTATAATGAAGG
* * * * * * * *
647350 TAAGTAATATTTTAACGTATTTAACTTTTAGTAAAAGAAGTAATTTA--A-ACTAAA--AAAAAA
65 CAAGTATTATTTTAACATTTTTTATTTTTAATAAAAAAAGTAATTTAGCATA-TAAATTAAAAAA
* * * * *
647410 G-AAA-TCATTACACAATTATACTTATTCAACTCA-AATAATATTGACTTTTTAGTTTTCA
129 GTAAAGTCATTGCATAATTATGCTTATTCAACT-AGAATAATATTGGCTTTTTGGTTTTCA
647468 TAAAATTTAA
Statistics
Matches: 1525, Mismatches: 244, Indels: 206
0.77 0.12 0.10
Matches are distributed among these distances:
404 42 0.03
405 3 0.00
406 9 0.01
407 28 0.02
408 7 0.00
409 69 0.05
410 53 0.03
411 29 0.02
412 9 0.01
413 11 0.01
414 17 0.01
415 102 0.07
416 89 0.06
417 58 0.04
418 174 0.11
419 31 0.02
420 4 0.00
421 63 0.04
422 35 0.02
423 73 0.05
424 36 0.02
425 1 0.00
426 1 0.00
427 1 0.00
428 20 0.01
429 60 0.04
430 109 0.07
431 154 0.10
432 18 0.01
433 113 0.07
434 104 0.07
435 2 0.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (425 bp):
TTTTTTTTAAAAGTAATGTTAAAAAGAATGTCTTAAAAAAATATTAATATTACTATAATGAAGGC
AAGTATTATTTTAACATTTTTTATTTTTAATAAAAAAAGTAATTTAGCATATAAATTAAAAAAGT
AAAGTCATTGCATAATTATGCTTATTCAACTAGAATAATATTGGCTTTTTGGTTTTCACTACCTT
AGTATCATAATTTATTTGATAGTGAAAAAATTAAAAAAATAACATGTAATTAATTTTGATATCAA
TTTTTATCGATTATAAATATCTTGCAAAGCCCATGAAAAAATTTATTAGTAAAAACTATGTAATT
GTTGATATAATAAAAGAAAATAAAGTTTAATCCAAATAGTTCATTTCTTTCATCATTCATATATC
AAATATAATAAAAAAATAATTTTTCTTTCTCTCAC
Found at i:650463 original size:29 final size:29
Alignment explanation
Indices: 650374--650469 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 29
650364 TTTCATTAAT
650374 AAAAAAT-ATATTTAATATATTATAGTTATTA
1 AAAAAATAATATTTAATA-ATTATA-TT-TTA
*
650405 AATAAAA-ATTAATTTAACTAATATATATTTTA
1 AA-AAAATAAT-ATTTAA-TAAT-TATATTTTA
*
650437 AAAAAATAATATTTAATACATTA-ATTTTG
1 AAAAAATAATATTTAATA-ATTATATTTTA
650466 AAAA
1 AAAA
650470 TTTTTAATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
29 9 0.16
30 4 0.07
31 14 0.25
32 12 0.22
33 10 0.18
34 6 0.11
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAAAATAATATTTAATAATTATATTTTA
Found at i:650601 original size:27 final size:27
Alignment explanation
Indices: 650571--650648 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
650561 TTAAAAACTC
* **
650571 AATTAATAATATATATAAATTTTTTTA
1 AATTAATAATATATATAAATTATTAAA
* * *
650598 AATTATTAATTTATTTAATATTATTAAA
1 AATTAATAATATATATAA-ATTATTAAA
*
650626 AATTAATTAATATTTATAAATTA
1 AATTAA-TAATATATATAAATTA
650649 AAAATCATAA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
27 15 0.38
28 15 0.38
29 9 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTAATAATATATATAAATTATTAAA
Found at i:650622 original size:18 final size:18
Alignment explanation
Indices: 650577--650624 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
650567 ACTCAATTAA
* *
650577 TAATATATATAAATTTTTT
1 TAATAT-TATTAATTTATT
650596 TAA-ATTATTAATTTATT
1 TAATATTATTAATTTATT
650613 TAATATTATTAA
1 TAATATTATTAA
650625 AAATTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.50
18 10 0.38
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATATTATTAATTTATT
Found at i:660495 original size:17 final size:16
Alignment explanation
Indices: 660454--660546 Score: 79
Period size: 15 Copynumber: 5.9 Consensus size: 16
660444 TGATTGAATT
*
660454 AAATATTTA-ATTAAA
1 AAATATTAATATTAAA
660469 AAAT-TTAATATTAAA
1 AAATATTAATATTAAA
660484 TAAATATTAATA-TAAA
1 -AAATATTAATATTAAA
* *
660500 ATAT-TTTATATTAAA
1 AAATATTAATATTAAA
660515 AAATATTAAATATGATAAA
1 AAATATT-AATAT--TAAA
*
660534 AAA-ATTTATATTA
1 AAATATTAATATTA
660547 CATAATAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 8 0.12
15 22 0.34
16 10 0.16
17 14 0.22
18 3 0.05
19 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
AAATATTAATATTAAA
Found at i:660533 original size:34 final size:31
Alignment explanation
Indices: 660453--660551 Score: 103
Period size: 31 Copynumber: 3.1 Consensus size: 31
660443 TTGATTGAAT
*
660453 TAAATATTTAAT-TAAAAAATTTAATATTAAA
1 TAAATA-TTAATATAAAAAATTTTATATTAAA
*
660484 TAAATATTAATATAAAATATTTTATATTAAA
1 TAAATATTAATATAAAAAATTTTATATTAAA
* *
660515 -AAATATTAAATATGATAAAAAAATTTATATTACA
1 TAAATATT--A-AT-ATAAAAAATTTTATATTAAA
660549 TAA
1 TAA
660552 TAAAAATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
30 12 0.21
31 23 0.40
32 1 0.02
33 2 0.04
34 17 0.30
35 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (31 bp):
TAAATATTAATATAAAAAATTTTATATTAAA
Found at i:661804 original size:32 final size:33
Alignment explanation
Indices: 661763--661841 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 33
661753 TATATATATA
* **
661763 TATATATATTATGATATGTCAATA-ATTTATTT
1 TATATATATTATAATAAATCAATATATTTATTT
* *
661795 TATATATATTTTAATAAATTAATATATTTATTT
1 TATATATATTATAATAAATCAATATATTTATTT
*
661828 TATATTTA-TATAAT
1 TATATATATTATAAT
661842 TTTTAAATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 24 0.62
33 15 0.38
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (33 bp):
TATATATATTATAATAAATCAATATATTTATTT
Found at i:661867 original size:39 final size:37
Alignment explanation
Indices: 661788--661860 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 37
661778 ATGTCAATAA
661788 TTTATTTTATATATATTTTAATAAATTAATATATTTAT
1 TTTATTTTATATATATTTT-ATAAATTAATATATTTAT
661826 TTTATATTTATATA-ATTTT-TAAATTAAATATATTT
1 TTTAT-TTTATATATATTTTATAAATT-AATATATTT
661861 TAATTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
36 6 0.18
37 9 0.27
38 10 0.30
39 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (37 bp):
TTTATTTTATATATATTTTATAAATTAATATATTTAT
Found at i:661908 original size:17 final size:16
Alignment explanation
Indices: 661854--661908 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
661844 TTAAATTAAA
*
661854 TATATTTTAATTTTTT
1 TATATTTTAAATTTTT
*
661870 TCATATCTTATAATTATTT
1 T-ATATTTTA-AATT-TTT
661889 TATATTTTAAATTTTCT
1 TATATTTTAAATTTT-T
661906 TAT
1 TAT
661909 TACAGTATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.09
17 15 0.47
18 10 0.31
19 4 0.12
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTTTAAATTTTT
Found at i:662374 original size:28 final size:29
Alignment explanation
Indices: 662324--662382 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
662314 TCTGCGATTA
*
662324 AATTTAAAAATATAAAAATATAATATAAA
1 AATTTAAAAATATAAAAATATAATAAAAA
* **
662353 AATTTAAAAA-ATATATTTATAATAAAAA
1 AATTTAAAAATATAAAAATATAATAAAAA
662381 AA
1 AA
662383 CATAAATTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (29 bp):
AATTTAAAAATATAAAAATATAATAAAAA
Found at i:662747 original size:20 final size:20
Alignment explanation
Indices: 662724--662853 Score: 71
Period size: 20 Copynumber: 6.7 Consensus size: 20
662714 TTTATATTTA
662724 ATAATATAAAATATAATTAT
1 ATAATATAAAATATAATTAT
*
662744 ATAATA-AAAATAATTAA-AAT
1 ATAATATAAAAT-A-TAATTAT
662764 ATAATAT-AAA-A-AATTAT
1 ATAATATAAAATATAATTAT
* *
662781 ATAAATATATAAATAT-TTTAA
1 AT-AATATA-AAATATAATTAT
* * **
662802 ATTA-ATAATATATAAAAAT
1 ATAATATAAAATATAATTAT
*
662821 -TTATAT-AAATATAATTAT
1 ATAATATAAAATATAATTAT
*
662839 AATATTATAAAATAT
1 -ATAATATAAAATAT
662854 GAAAAGCTTA
Statistics
Matches: 81, Mismatches: 15, Indels: 27
0.66 0.12 0.22
Matches are distributed among these distances:
16 2 0.02
17 4 0.05
18 23 0.28
19 11 0.14
20 26 0.32
21 15 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAATATAAAATATAATTAT
Found at i:662756 original size:17 final size:17
Alignment explanation
Indices: 662729--662784 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
662719 ATTTAATAAT
662729 ATAAAATATAATTATATA
1 ATAAAA-ATAATTATATA
662747 ATAAAAATAATTAAAATATA
1 ATAAAAATAATT---ATATA
662767 ATATAAAA-AATTATATA
1 ATA-AAAATAATTATATA
662784 A
1 A
662785 ATATATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 12 0.35
18 6 0.18
20 12 0.35
21 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAAAAATAATTATATA
Found at i:662794 original size:17 final size:17
Alignment explanation
Indices: 662727--662833 Score: 56
Period size: 17 Copynumber: 6.6 Consensus size: 17
662717 ATATTTAATA
662727 ATATAAA-ATAT-AATT
1 ATATAAATATATAAATT
*
662742 ATAT-AATA-A-AAATA
1 ATATAAATATATAAATT
662756 AT-TAAA-ATAT-AA-T
1 ATATAAATATATAAATT
*
662769 ATAAAAAATTATATAAA-T
1 AT-ATAAA-TATATAAATT
*
662787 ATATAAATATTTTAAATT
1 ATATAAATA-TATAAATT
*
662805 A-ATAATATATAAAAATTT
1 ATATAA-ATATATAAA-TT
662823 ATATAAATATA
1 ATATAAATATA
662834 ATTATAATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 27
0.67 0.07 0.26
Matches are distributed among these distances:
13 4 0.06
14 13 0.19
15 8 0.11
16 2 0.03
17 21 0.30
18 18 0.26
19 4 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAAATATATAAATT
Found at i:662795 original size:40 final size:41
Alignment explanation
Indices: 662722--662834 Score: 126
Period size: 44 Copynumber: 2.7 Consensus size: 41
662712 AATTTATATT
662722 TAATAATATAAAATATAATTATAT-AATA-AAAATA-ATTAAAA
1 TAATAATAT-AAA-A-AATTATATAAATATAAAATATATTAAAA
* *
662763 T-ATAATATAAAAAATTATATAAATATATAAATATTTTAAAT
1 TAATAATATAAAAAATTATATAAATATA-AAATATATTAAAA
662804 TAATAATATATAAAAATTTATATAAATATAA
1 TAATAATATA-AAAAA-TTATATAAATATAA
662835 TTATAATATT
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
37 8 0.13
38 5 0.08
39 4 0.06
40 12 0.19
41 7 0.11
42 8 0.13
43 6 0.10
44 13 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (41 bp):
TAATAATATAAAAAATTATATAAATATAAAATATATTAAAA
Found at i:662816 original size:24 final size:26
Alignment explanation
Indices: 662774--662822 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
662764 ATAATATAAA
*
662774 AAATTATATAAATATATAAATATTTT
1 AAATTATATAAATATATAAAAATTTT
662800 AAATTA-AT-AATATATAAAAATTT
1 AAATTATATAAATATATAAAAATTT
662823 ATATAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 2 0.09
26 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATTATATAAATATATAAAAATTTT
Found at i:663143 original size:14 final size:15
Alignment explanation
Indices: 663121--663218 Score: 52
Period size: 14 Copynumber: 6.9 Consensus size: 15
663111 AATTATTTGA
*
663121 TTATAAAATTA-AAT
1 TTATTAAATTATAAT
663135 TTATTAAATTATAAT
1 TTATTAAATTATAAT
*
663150 TAATT--ATT-TAA-
1 TTATTAAATTATAAT
*
663161 TT-TTAAATTATTAT
1 TTATTAAATTATAAT
*
663175 AATATTAATATTA-AA-
1 -TTATTAA-ATTATAAT
* *
663190 ATATTAAATTTATATT
1 TTATTAAA-TTATAAT
663206 TTATT-AATTATAA
1 TTATTAAATTATAA
663219 AAATTAAATT
Statistics
Matches: 64, Mismatches: 9, Indels: 22
0.67 0.09 0.23
Matches are distributed among these distances:
10 2 0.03
11 1 0.02
12 6 0.09
13 6 0.09
14 25 0.39
15 11 0.17
16 9 0.14
17 4 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATTAAATTATAAT
Found at i:663197 original size:30 final size:29
Alignment explanation
Indices: 663163--663232 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
663153 TTATTTAATT
663163 TTAAA-TTATTATAATATTAA-TATTAAAATA
1 TTAAATTTA-TATAATATTAATTA-TAAAA-A
**
663193 TTAAATTTATATTTTATTAATTATAAAAA
1 TTAAATTTATATAATATTAATTATAAAAA
663222 TTAAATTTATA
1 TTAAATTTATA
663233 AAGATGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 12 0.33
30 19 0.53
31 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TTAAATTTATATAATATTAATTATAAAAA
Found at i:663824 original size:8 final size:8
Alignment explanation
Indices: 663811--663865 Score: 76
Period size: 8 Copynumber: 6.6 Consensus size: 8
663801 CATTAAATAA
663811 AAATATAT
1 AAATATAT
663819 AAATATAT
1 AAATATAT
663827 AAAAAATATAT
1 ---AAATATAT
663838 AAA-ATAT
1 AAATATAT
663845 AAATATAT
1 AAATATAT
663853 AAATATAT
1 AAATATAT
663861 AAATA
1 AAATA
663866 AAATAAATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.16
8 28 0.65
11 8 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATATAT
Found at i:665706 original size:2 final size:2
Alignment explanation
Indices: 665699--665731 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
665689 ATTAAAACAC
665699 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
665732 TATTTTGGTT
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:666483 original size:22 final size:22
Alignment explanation
Indices: 666458--666500 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
666448 ATGAAAAGAA
666458 TTTCAAGCACAAAGCAAGATCT
1 TTTCAAGCACAAAGCAAGATCT
666480 TTTCAAGCACAAAGCAAGATC
1 TTTCAAGCACAAAGCAAGATC
666501 AACTAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (22 bp):
TTTCAAGCACAAAGCAAGATCT
Found at i:666757 original size:3 final size:3
Alignment explanation
Indices: 666749--666773 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
666739 TAAAAGAATA
666749 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
666774 TATTTTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:668102 original size:21 final size:21
Alignment explanation
Indices: 668076--668124 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
668066 TAGTTTTAAC
668076 TTTT-AATATTAAATGGGTAAT
1 TTTTAAATA-TAAATGGGTAAT
* *
668097 TTTTAAATATAAGTGGGTAGT
1 TTTTAAATATAAATGGGTAAT
668118 TTTTAAA
1 TTTTAAA
668125 ATATTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (21 bp):
TTTTAAATATAAATGGGTAAT
Found at i:675711 original size:11 final size:11
Alignment explanation
Indices: 675695--675823 Score: 58
Period size: 11 Copynumber: 11.9 Consensus size: 11
675685 AATAATTTGC
*
675695 ATATTTATTTT
1 ATATTTATATT
675706 ATATTTATATT
1 ATATTTATATT
675717 AT-TTTATATT
1 ATATTTATATT
**
675727 A-A-AAATATT
1 ATATTTATATT
675736 AATAATTTATATT
1 -AT-ATTTATATT
675749 ATATATT-T-TT
1 ATAT-TTATATT
*
675759 -TA-ATATATT
1 ATATTTATATT
675768 AATAATTTATATT
1 -AT-ATTTATATT
* *
675781 ATTTTTATGTT
1 ATATTTATATT
* *
675792 GTATTT-TAAT
1 ATATTTATATT
*
675802 ATATTTTTATTT
1 ATATTTATA-TT
*
675814 ATATATATAT
1 ATATTTATAT
675824 AAACTAGCTA
Statistics
Matches: 87, Mismatches: 17, Indels: 28
0.66 0.13 0.21
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 9 0.10
10 19 0.22
11 30 0.34
12 16 0.18
13 11 0.13
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
ATATTTATATT
Found at i:675744 original size:32 final size:30
Alignment explanation
Indices: 675708--675786 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 30
675698 TTTATTTTAT
675708 ATTTATATTATTTTATATTAAAAATATTAATA
1 ATTTATATTATTTT-T-TTAAAAATATTAATA
* *
675740 ATTTATATTATATATTTTTTAATATATTAATA
1 ATTTATATTAT-T-TTTTTAAAAATATTAATA
675772 ATTTATATTATTTTT
1 ATTTATATTATTTTT
675787 ATGTTGTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 3 0.07
31 1 0.02
32 35 0.81
33 2 0.05
34 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTTATATTATTTTTTTAAAAATATTAATA
Found at i:675780 original size:25 final size:25
Alignment explanation
Indices: 675734--675785 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
675724 ATTAAAAATA
*
675734 TTAATAATTTATATTATATATT-TT
1 TTAATAATTAATATTATATATTATT
675758 TTAATATATTAATAATT-TATATTATT
1 TTAATA-ATTAAT-ATTATATATTATT
675784 TT
1 TT
675786 TATGTTGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 11 0.46
26 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTAATAATTAATATTATATATTATT
Found at i:675783 original size:16 final size:16
Alignment explanation
Indices: 675732--675783 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
675722 ATATTAAAAA
675732 TATTAATAATTTATAT
1 TATTAATAATTTATAT
* *
675748 TA-T-ATATTTTTTAAT
1 TATTAATAATTTAT-AT
675763 ATATTAATAATTTATAT
1 -TATTAATAATTTATAT
675780 TATT
1 TATT
675784 TTTATGTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 7 0.25
15 3 0.11
16 8 0.29
17 3 0.11
18 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTAATAATTTATAT
Found at i:678277 original size:20 final size:18
Alignment explanation
Indices: 678254--678308 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 18
678244 TGGTTACTTC
*
678254 TTTTGTTTTTTTATTTTGAT
1 TTTTGTTTTTTTATTCT--T
678274 TTTTGTTTTTTTACTTCTT
1 TTTTGTTTTTTTA-TTCTT
678293 TTTTGCTTTTTTTATT
1 TTTTG-TTTTTTTATT
678309 AGAAAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.25
20 21 0.66
21 3 0.09
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTGTTTTTTTATTCTT
Found at i:678487 original size:20 final size:20
Alignment explanation
Indices: 678464--678509 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
678454 ATAATTTTTT
678464 AAAATTTTAATAAATTAATA
1 AAAATTTTAATAAATTAATA
678484 AAAATTTTAATAAATTAATA
1 AAAATTTTAATAAATTAATA
*
678504 ATAATT
1 AAAATT
678510 ACATAAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTTTAATAAATTAATA
Found at i:678515 original size:11 final size:11
Alignment explanation
Indices: 678471--678507 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
678461 TTTAAAATTT
678471 TAATAAATTAA
1 TAATAAATTAA
*
678482 TAA-AAATT-T
1 TAATAAATTAA
678491 TAATAAATTAA
1 TAATAAATTAA
678502 TAATAA
1 TAATAA
678508 TTACATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 3 0.14
10 10 0.45
11 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAATTAA
Found at i:678628 original size:27 final size:27
Alignment explanation
Indices: 678579--678630 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
678569 ATTAAAAATA
*
678579 ATTATTTTTATTCATTATTATATAATT
1 ATTATTTTTATTCATTATAATATAATT
*
678606 ATTATTTTTATTTA-TATGAATATAA
1 ATTATTTTTATTCATTAT-AATATAA
678631 GTTGAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
ATTATTTTTATTCATTATAATATAATT
Found at i:681735 original size:99 final size:99
Alignment explanation
Indices: 681564--681766 Score: 406
Period size: 99 Copynumber: 2.1 Consensus size: 99
681554 ACTCTGATTA
681564 AGATCGTACAGTGCAATGCTACTGTTGTCAAACAAATTAGAGGATGAACATTCTTGGAGAACTTT
1 AGATCGTACAGTGCAATGCTACTGTTGTCAAACAAATTAGAGGATGAACATTCTTGGAGAACTTT
681629 TGAGGAAAGTACTTAGTCCTTACATTCACTTTCT
66 TGAGGAAAGTACTTAGTCCTTACATTCACTTTCT
681663 AGATCGTACAGTGCAATGCTACTGTTGTCAAACAAATTAGAGGATGAACATTCTTGGAGAACTTT
1 AGATCGTACAGTGCAATGCTACTGTTGTCAAACAAATTAGAGGATGAACATTCTTGGAGAACTTT
681728 TGAGGAAAGTACTTAGTCCTTACATTCACTTTCT
66 TGAGGAAAGTACTTAGTCCTTACATTCACTTTCT
681762 AGATC
1 AGATC
681767 CTAGAAACTT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 104 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (99 bp):
AGATCGTACAGTGCAATGCTACTGTTGTCAAACAAATTAGAGGATGAACATTCTTGGAGAACTTT
TGAGGAAAGTACTTAGTCCTTACATTCACTTTCT
Found at i:682707 original size:433 final size:430
Alignment explanation
Indices: 681904--682762 Score: 1515
Period size: 433 Copynumber: 2.0 Consensus size: 430
681894 GGTAAATTTA
* *
681904 GACATTTTAACTCTGTTTTTTTCTTCCATAGTAGTAGCGATGGACTAGAAAATATTCTTTTCTAG
1 GACATTTTAACTCTGTTTTTTTCTTCCATAGTAGTAGCGATGGACCAGAAAATATTCGTTTCTAG
681969 GTTATCTAAGGATTGACCGCATTTATTGTTTTTTTATTGGATATAGGGCAGGCACTGAAAACTAT
66 GTTATCTAAGGATTGACCGCATTTATTGTTTTTTTATTGGATATAGGGCAGGCACTGAAAACTAT
*
682034 TTTATTCATCCTTCTTTTATGTTTTCATGAATAAATAGTCTCAGATGCTCAGTAAACATGCTAAT
131 TTTATTCATCCTTCTTTGATGTTTTCATGAATAAATAGTCTCAGATGCTCAGTAAACATGCTAAT
*
682099 TTCATATTACCCGCTCTCACTACCTTCTTTTTTTCTTTTTTAATATTTATTATTGTGAAATAATA
196 TTCATATTACCCACTCTCACTACCTTCTTTTTTTCTTTTTTAATATTTATTATTGTGAAATAATA
* *
682164 TTTTTATTATTAATGCTGGAAATGGATTGTCTGAGTCTGATGCAGGAGAGGGTGCAATCCAACGG
261 TTTTTATTATTAATGCTGGAAATGGATTGTCTGAGTATGATGCAGGAGAGGGTGCAATCCAACAG
*
682229 TTTTCTTGGAATTTAATTTGACAGTCACGAACATGATTTTAGGATATATCCCTGCTTTCCTTTCG
326 TTTTCTTGGAAGTTAATTTGACAGTCACGAACATGATTTTAGGATATATCCCTGCTTTCCTTTCG
* *
682294 GCTGACCTTTGTGAGGCTTCCTTGTGTCTCGGTTGCGATG
391 ACTGACCTTTGTGAGGCTTCCTTGTGTCCCGGTTGCGATG
682334 GACATTTTAA-TGCTGTTTTTTTCTTCCATAGTAGTAGCGATGGACCAGAAAATATTCGTTTCTA
1 GACATTTTAACT-CTGTTTTTTTCTTCCATAGTAGTAGCGATGGACCAGAAAATATTCGTTTCTA
682398 GGTTATCTAAGGATTGACCGCATTTATTGTTTTTTTTTATTGGATATAGGGCAGGCACTGAAAAC
65 GGTTATCTAAGGATTGACCGCATTTATTG--TTTTTTTATTGGATATAGGGCAGGCACTGAAAAC
*
682463 TATTTTATTCATCCTTCTTTGATGTTTTCATGAATAAAATAGTCTCAGATGCTCGGTAAACATGC
128 TATTTTATTCATCCTTCTTTGATGTTTTCATGAAT-AAATAGTCTCAGATGCTCAGTAAACATGC
682528 TAATTTCATATTACCCACTCTCACTACCTTCTTTTTTT-TCTTTTTAATATTTATTATTGTGAAA
192 TAATTTCATATTACCCACTCTCACTACCTTCTTTTTTTCT-TTTTTAATATTTATTATTGTGAAA
* * * *
682592 TAATATTTTTATTATTAATGCTTGAAATGGATTGTCTGAGTATGATGCATGAGAGGGTGCAGTCT
256 TAATATTTTTATTATTAATGCTGGAAATGGATTGTCTGAGTATGATGCAGGAGAGGGTGCAATCC
* *
682657 AACAGTTTTCTTGGAAGTTAATTTGACTGTCATGAACATGATTTTAGGATATATCCCTGCTTTCC
321 AACAGTTTTCTTGGAAGTTAATTTGACAGTCACGAACATGATTTTAGGATATATCCCTGCTTTCC
682722 TTTCGACTGACCTTTGTGAGGCTTCCTTGTGTCCCGGTTGC
386 TTTCGACTGACCTTTGTGAGGCTTCCTTGTGTCCCGGTTGC
682763 CTCATTCCCC
Statistics
Matches: 408, Mismatches: 16, Indels: 7
0.95 0.04 0.02
Matches are distributed among these distances:
429 1 0.00
430 89 0.22
432 69 0.17
433 249 0.61
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.42
Consensus pattern (430 bp):
GACATTTTAACTCTGTTTTTTTCTTCCATAGTAGTAGCGATGGACCAGAAAATATTCGTTTCTAG
GTTATCTAAGGATTGACCGCATTTATTGTTTTTTTATTGGATATAGGGCAGGCACTGAAAACTAT
TTTATTCATCCTTCTTTGATGTTTTCATGAATAAATAGTCTCAGATGCTCAGTAAACATGCTAAT
TTCATATTACCCACTCTCACTACCTTCTTTTTTTCTTTTTTAATATTTATTATTGTGAAATAATA
TTTTTATTATTAATGCTGGAAATGGATTGTCTGAGTATGATGCAGGAGAGGGTGCAATCCAACAG
TTTTCTTGGAAGTTAATTTGACAGTCACGAACATGATTTTAGGATATATCCCTGCTTTCCTTTCG
ACTGACCTTTGTGAGGCTTCCTTGTGTCCCGGTTGCGATG
Found at i:684014 original size:285 final size:282
Alignment explanation
Indices: 683507--684073 Score: 1044
Period size: 285 Copynumber: 2.0 Consensus size: 282
683497 ATTATTTTGC
683507 CAAATTTGCTGCTGATATGTAATATGAAATGGTCTAGGTATTTTAATGTCTTTGTTTTATGTCCT
1 CAAATTTGCTGCTGATATGTAATATGAAATGGTCTAGGTATTTTAATGTCTTTGTTTTATGTCCT
683572 GTCTTTTTCTCATTTTGTCTTTTCCTTCCAAAGGAAGTGCTTTCTTAATCCATCCATGAAAGAAT
66 GTCTTTTTCTCATTTTGTCTTTTCCTTCCAAAGGAAGTGCTTTCTTAATCCATCCATGAAAGAAT
*
683637 ATATGCATAGTAGTTAGAATTGAATAGAAACTAGGAATTCTGATGTGCTCAGTTAAATGTCGAAA
131 ATATGCATAGTAGTTAGAATTGAATAGAAACTAGGAATTCTGATGGGCTCAGTTAAATGTCGAAA
683702 TTTTTAGATATTGTTTGGGGAACTCTGAATGTGCTTAGTTAAATGACAAAATACTAAGTAGATTG
196 TTTTTAGATATTGTTTGGGGAACTCTGAATGTGCTTAGTTAAATGACAAAATACTAAGTAGATTG
683767 CTATGACAATCGTAGAAAAGAG
261 CTATGACAATCGTAGAAAAGAG
*
683789 CAAATTTGCTGCTGATATGTAATATGAAATGGTCTAGGTATTTTAGTGTCTTTGTTTTTATGTCC
1 CAAATTTGCTGCTGATATGTAATATGAAATGGTCTAGGTATTTTAATGTCTTTG-TTTTATGTCC
683854 TGTCTTTTTCTCATTTTGTCTTTTCCTTCCAAAGGAAGTGCTTTCTTAATCTCCATCCATGAAAG
65 TGTCTTTTTCTCATTTTGTCTTTTCCTTCCAAAGGAAGTGCTTTCTTAA--TCCATCCATGAAAG
**
683919 AATATATGCATAGTAGTTAGAATTGAATAGAAACTAGGAATTCTGATGGGCTGGGTTAAATGTCG
128 AATATATGCATAGTAGTTAGAATTGAATAGAAACTAGGAATTCTGATGGGCTCAGTTAAATGTCG
* *
683984 AAATTTTTAGATTTTGTTTGGGGAACTCTGAATGTGCTTAGTTAAATGACGAAATACTAAGTAGA
193 AAATTTTTAGATATTGTTTGGGGAACTCTGAATGTGCTTAGTTAAATGACAAAATACTAAGTAGA
*
684049 TTGCTATGACGATCGTAGAAAAGAG
258 TTGCTATGACAATCGTAGAAAAGAG
684074 TAAAATGATT
Statistics
Matches: 275, Mismatches: 7, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
282 53 0.19
283 59 0.21
285 163 0.59
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (282 bp):
CAAATTTGCTGCTGATATGTAATATGAAATGGTCTAGGTATTTTAATGTCTTTGTTTTATGTCCT
GTCTTTTTCTCATTTTGTCTTTTCCTTCCAAAGGAAGTGCTTTCTTAATCCATCCATGAAAGAAT
ATATGCATAGTAGTTAGAATTGAATAGAAACTAGGAATTCTGATGGGCTCAGTTAAATGTCGAAA
TTTTTAGATATTGTTTGGGGAACTCTGAATGTGCTTAGTTAAATGACAAAATACTAAGTAGATTG
CTATGACAATCGTAGAAAAGAG
Found at i:686030 original size:2 final size:2
Alignment explanation
Indices: 686023--686060 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
686013 TAGAAGTTTT
686023 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
686061 TATGCATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:688410 original size:14 final size:14
Alignment explanation
Indices: 688391--688418 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
688381 TGCTGTTTCA
688391 TAACCTTTTCCCCT
1 TAACCTTTTCCCCT
688405 TAACCTTTTCCCCT
1 TAACCTTTTCCCCT
688419 GAATGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (14 bp):
TAACCTTTTCCCCT
Found at i:688939 original size:582 final size:582
Alignment explanation
Indices: 687835--688990 Score: 2312
Period size: 582 Copynumber: 2.0 Consensus size: 582
687825 TTGAACCATT
687835 CTGAATGTTTCAATTGTCATGCTTAAAATTGTTTATTGGATAACATGGTGCTTTTGATTTTTGTT
1 CTGAATGTTTCAATTGTCATGCTTAAAATTGTTTATTGGATAACATGGTGCTTTTGATTTTTGTT
687900 TGAAGTCCTTTTCTCCAGCCTTTCCTTTTTTGTAATTGTGGTGCATTATCCTATTTTGTTTGTCC
66 TGAAGTCCTTTTCTCCAGCCTTTCCTTTTTTGTAATTGTGGTGCATTATCCTATTTTGTTTGTCC
687965 CGACCATACTGTCTCAGGATGTAGAAATGTGATTTTGGAACAGTGAAGTGGATATATTTTTTAAA
131 CGACCATACTGTCTCAGGATGTAGAAATGTGATTTTGGAACAGTGAAGTGGATATATTTTTTAAA
688030 CTAGAGAACACTTGCTAGTTATTGACATTTTCACTAATGGCAGCTGTCTCTGGGTTTTTGCCTTA
196 CTAGAGAACACTTGCTAGTTATTGACATTTTCACTAATGGCAGCTGTCTCTGGGTTTTTGCCTTA
688095 TATGAAAATAACTTGAATATTCCATGTGGATGATTTTGTACTTTATAATATGTAGAAAATTTAAT
261 TATGAAAATAACTTGAATATTCCATGTGGATGATTTTGTACTTTATAATATGTAGAAAATTTAAT
688160 TCAAACTAAATTATGTTTCTATGGATGTTGATATAGCTCAGGCCTTATACATTGAAATTTGGTCT
326 TCAAACTAAATTATGTTTCTATGGATGTTGATATAGCTCAGGCCTTATACATTGAAATTTGGTCT
688225 CGTTTGTTAGTTGTGGTCATGTATTTTATGTGAAGAAATTTAGATGGAACTCTTGAGTGGCTATA
391 CGTTTGTTAGTTGTGGTCATGTATTTTATGTGAAGAAATTTAGATGGAACTCTTGAGTGGCTATA
688290 TCAGGAATTTTTTGATTAAAAGAGGTTTTGCAATATATTTTTTGTAAAATTAGCATCTAGAAACT
456 TCAGGAATTTTTTGATTAAAAGAGGTTTTGCAATATATTTTTTGTAAAATTAGCATCTAGAAACT
688355 GCCATATGAGATTACATTGTGATGTTTGCTGTTTCATAACCTTTTCCCCTTAACCTTTTCCC
521 GCCATATGAGATTACATTGTGATGTTTGCTGTTTCATAACCTTTTCCCCTTAACCTTTTCCC
688417 CTGAATGTTTCAATTGTCATGCTTAAAATTGTTTATTGGATAACATGGTGCTTTTGATTTTTGTT
1 CTGAATGTTTCAATTGTCATGCTTAAAATTGTTTATTGGATAACATGGTGCTTTTGATTTTTGTT
688482 TGAAGTCCTTTTCTCCAGCCTTTCCTTTTTTGTAATTGTGGTGCATTATCCTATTTTGTTTGTCC
66 TGAAGTCCTTTTCTCCAGCCTTTCCTTTTTTGTAATTGTGGTGCATTATCCTATTTTGTTTGTCC
688547 CGACCATACTGTCTCAGGATGTAGAAATGTGATTTTGGAACAGTGAAGTGGATATATTTTTTAAA
131 CGACCATACTGTCTCAGGATGTAGAAATGTGATTTTGGAACAGTGAAGTGGATATATTTTTTAAA
688612 CTAGAGAACACTTGCTAGTTATTGACATTTTCACTAATGGCAGCTGTCTCTGGGTTTTTGCCTTA
196 CTAGAGAACACTTGCTAGTTATTGACATTTTCACTAATGGCAGCTGTCTCTGGGTTTTTGCCTTA
688677 TATGAAAATAACTTGAATATTCCATGTGGATGATTTTGTACTTTATAATATGTAGAAAATTTAAT
261 TATGAAAATAACTTGAATATTCCATGTGGATGATTTTGTACTTTATAATATGTAGAAAATTTAAT
688742 TCAAACTAAATTATGTTTCTATGGATGTTGATATAGCTCAGGCCTTATACATTGAAATTTGGTCT
326 TCAAACTAAATTATGTTTCTATGGATGTTGATATAGCTCAGGCCTTATACATTGAAATTTGGTCT
688807 CGTTTGTTAGTTGTGGTCATGTATTTTATGTGAAGAAATTTAGATGGAACTCTTGAGTGGCTATA
391 CGTTTGTTAGTTGTGGTCATGTATTTTATGTGAAGAAATTTAGATGGAACTCTTGAGTGGCTATA
688872 TCAGGAATTTTTTGATTAAAAGAGGTTTTGCAATATATTTTTTGTAAAATTAGCATCTAGAAACT
456 TCAGGAATTTTTTGATTAAAAGAGGTTTTGCAATATATTTTTTGTAAAATTAGCATCTAGAAACT
688937 GCCATATGAGATTACATTGTGATGTTTGCTGTTTCATAACCTTTTCCCCTTAAC
521 GCCATATGAGATTACATTGTGATGTTTGCTGTTTCATAACCTTTTCCCCTTAAC
688991 TTCTCTTCTA
Statistics
Matches: 574, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
582 574 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (582 bp):
CTGAATGTTTCAATTGTCATGCTTAAAATTGTTTATTGGATAACATGGTGCTTTTGATTTTTGTT
TGAAGTCCTTTTCTCCAGCCTTTCCTTTTTTGTAATTGTGGTGCATTATCCTATTTTGTTTGTCC
CGACCATACTGTCTCAGGATGTAGAAATGTGATTTTGGAACAGTGAAGTGGATATATTTTTTAAA
CTAGAGAACACTTGCTAGTTATTGACATTTTCACTAATGGCAGCTGTCTCTGGGTTTTTGCCTTA
TATGAAAATAACTTGAATATTCCATGTGGATGATTTTGTACTTTATAATATGTAGAAAATTTAAT
TCAAACTAAATTATGTTTCTATGGATGTTGATATAGCTCAGGCCTTATACATTGAAATTTGGTCT
CGTTTGTTAGTTGTGGTCATGTATTTTATGTGAAGAAATTTAGATGGAACTCTTGAGTGGCTATA
TCAGGAATTTTTTGATTAAAAGAGGTTTTGCAATATATTTTTTGTAAAATTAGCATCTAGAAACT
GCCATATGAGATTACATTGTGATGTTTGCTGTTTCATAACCTTTTCCCCTTAACCTTTTCCC
Found at i:694754 original size:2 final size:2
Alignment explanation
Indices: 694747--694787 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
694737 TAAGGTTTGG
*
694747 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
694788 CCCCCTCCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:1019204 original size:2 final size:2
Alignment explanation
Indices: 1019197--1019227 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1019187 AGGTTTAGCT
1019197 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 T
1019228 TTCCCCTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1021128 original size:241 final size:242
Alignment explanation
Indices: 1020705--1021163 Score: 712
Period size: 241 Copynumber: 1.9 Consensus size: 242
1020695 CTTATATATC
** *
1020705 ATCCACTTGTAAACTGTTGCCTCTTTTTTATTATTATTATTAATTTTTTTTTCCTATCTTTTGAT
1 ATCCACTTGTAAACTGGGGCCTCTTTTTTATTATTATTATTAATTTTTTTTTCCTATCTTTAGAT
1020770 ATCAGTATTTTTTCTTTTGATTGCTATATATCTTAATTTTTCCTGTAAATTTACATATCTGTAGA
66 ATCAGTATTTTTTCTTTTGATTGCTATATATCTTAATTTTTCCTGTAAATTTACATATCTGTAGA
*
1020835 ACCACCTTTCTCCTAATGTGCGTTCAATGATTTGAGAAGGGGCTTGAAATATCCAAAGTTCCCAC
131 ACCAACTTTCTCCTAATGTGCGTTCAATGATTTGAGAAGGGGCTTGAAATATCCAAAGTTCCCAC
1020900 TTTCATGA-TTTGAGCAGCTATTTTCTTCCAATCCATCCTATACAAT
196 TTTCATGATTTTGAGCAGCTATTTTCTTCCAATCCATCCTATACAAT
1020946 ATCCACTTGTAAACTGGGGGCCTC-TTTTT-TTATTATTATTAATTTTCTTTTTTCCTATCTTTA
1 ATCCACTTGTAAACT-GGGGCCTCTTTTTTATTATTATTATTAA-TTT-TTTTTTCCTATCTTTA
* * * * *
1021009 GATATCATTATTTTTGT-TTTTTATTGCTATATATTTTAA-TTTTCCTGTAAGTTTACGTATCTG
63 GATATCAGTATTTTT-TCTTTTGATTGCTATATATCTTAATTTTTCCTGTAAATTTACATATCTG
* * *
1021072 TAGAACGAACTTTCTCCTAATGTGTGTTCAATGATTTGAGAAGGGGCTTGAAATATCCGAAGTTC
127 TAGAACCAACTTTCTCCTAATGTGCGTTCAATGATTTGAGAAGGGGCTTGAAATATCCAAAGTTC
* * *
1021137 CTATTTTCATGATTTTGAGCAGTTATT
192 CCACTTTCATGATTTTGAGCAGCTATT
1021164 GATTTTCTTC
Statistics
Matches: 198, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
240 13 0.07
241 116 0.59
242 68 0.34
243 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (242 bp):
ATCCACTTGTAAACTGGGGCCTCTTTTTTATTATTATTATTAATTTTTTTTTCCTATCTTTAGAT
ATCAGTATTTTTTCTTTTGATTGCTATATATCTTAATTTTTCCTGTAAATTTACATATCTGTAGA
ACCAACTTTCTCCTAATGTGCGTTCAATGATTTGAGAAGGGGCTTGAAATATCCAAAGTTCCCAC
TTTCATGATTTTGAGCAGCTATTTTCTTCCAATCCATCCTATACAAT
Found at i:1033307 original size:14 final size:14
Alignment explanation
Indices: 1033290--1033340 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
1033280 TAATATATTT
1033290 TTAAAATATAAATA
1 TTAAAATATAAATA
1033304 TTAAAATATTAAAT-
1 TTAAAATA-TAAATA
*
1033318 TTAATAATA-AAAAA
1 TTAA-AATATAAATA
1033332 TTAAAATAT
1 TTAAAATAT
1033341 TTTTTCACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 7 0.22
14 16 0.50
15 9 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAATATAAATA
Found at i:1039200 original size:13 final size:14
Alignment explanation
Indices: 1039168--1039206 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
1039158 TAAAAAAAAA
1039168 TTATTTTTTACATAT
1 TTATTTTTTA-ATAT
*
1039183 TTATTTATTAAT-T
1 TTATTTTTTAATAT
1039196 TTATTTTTTAA
1 TTATTTTTTAA
1039207 AAAATATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 2 0.09
15 9 0.41
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTTTTAATAT
Found at i:1045492 original size:58 final size:57
Alignment explanation
Indices: 1045401--1045512 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 57
1045391 AATGCCATGC
*
1045401 TATGTCTTGGAATTAGAAATTACTTGCTACTGTATTTGCAGGCTTAAACAGATCCTGT
1 TATGTCTTGGAATTAGAAATTACTTGCTACTGTA-TTGCAGGCATAAACAGATCCTGT
* * * **
1045459 TATGTCTTGGAATTGGAAATTACTTGTTTCTGTATTGGTGGCATAAACAGATCC
1 TATGTCTTGGAATTAGAAATTACTTGCTACTGTATTGCAGGCATAAACAGATCC
1045513 AGTAACCGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 17 0.35
58 31 0.65
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (57 bp):
TATGTCTTGGAATTAGAAATTACTTGCTACTGTATTGCAGGCATAAACAGATCCTGT
Found at i:1055683 original size:23 final size:22
Alignment explanation
Indices: 1055652--1055697 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
1055642 GGGGGCGTCA
1055652 TTTTTATTGTTATTAATTTTGT
1 TTTTTATTGTTATTAATTTTGT
1055674 TTTTTAATTGTTATTAATTTTGT
1 TTTTT-ATTGTTATTAATTTTGT
1055697 T
1 T
1055698 CTTCCTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (22 bp):
TTTTTATTGTTATTAATTTTGT
Found at i:1056403 original size:240 final size:239
Alignment explanation
Indices: 1055962--1056417 Score: 711
Period size: 240 Copynumber: 1.9 Consensus size: 239
1055952 CTTGTATATC
** *
1055962 ATCCACTTGTAAACTGTTGCCTCTTTTTTTTTATTATTATTAATTTTGTTTTTCCTATATTTTGA
1 ATCCACTTGTAAACTGAGGCCTC-TTTTCTTTATTATTATTAATTTTGTTTTTCCTATATTTTGA
*
1056027 TATCAATTTTGTTTTTGATTGCTACATATCTTAATTTTTCCTGTAAATTTACACAGCTGTAGAAC
65 TATCAATTTTGTTTTTGATTGCTACATATCTTAATTTTTCCTGTAAATTTACACAGCAGTAGAAC
* *
1056092 CACCTTTCTCCTATTGTGTGTTCAATGATTTGAGAAGGGGCTTGAAATATCCAAAGTTCCTACTT
130 CAACTTTCTCCTAATGTGTGTTCAATGATTTGAGAAGGGGCTTGAAATATCCAAAGTTCCTACTT
1056157 TCATGA-TTTGAGCAGTTATTTTCTTCCGACCCATCCTATACAGT
195 TCATGATTTTGAGCAGTTATTTTCTTCCGACCCATCCTATACAGT
*
1056201 ATCCACTTGTAAACTAGAGGCCTC-TTTCTTTATTATTATTAATTTTGTTTTTCCTATCTTTTGA
1 ATCCACTTGTAAACT-GAGGCCTCTTTTCTTTATTATTATTAATTTTGTTTTTCCTATATTTTGA
* * ** *
1056265 TATCATTATTTTTGTTTTTGATTGCTATATATCTTAA-TTTTCCTGTAAGTTTACGTATCAGTAG
65 TATCA--A-TTTTGTTTTTGATTGCTACATATCTTAATTTTTCCTGTAAATTTACACAGCAGTAG
* *
1056329 AACCAACTTTCTCCTAATGTGTGTTCAATGATTTGAGAAGGGGCTTGAGATATCCGAAGTTCCTA
127 AACCAACTTTCTCCTAATGTGTGTTCAATGATTTGAGAAGGGGCTTGAAATATCCAAAGTTCCTA
*
1056394 TTTTCATGATTTTGAGCAGTTATT
192 CTTTCATGATTTTGAGCAGTTATT
1056418 GATTTTCTTC
Statistics
Matches: 197, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
238 43 0.22
239 15 0.08
240 98 0.50
241 41 0.21
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (239 bp):
ATCCACTTGTAAACTGAGGCCTCTTTTCTTTATTATTATTAATTTTGTTTTTCCTATATTTTGAT
ATCAATTTTGTTTTTGATTGCTACATATCTTAATTTTTCCTGTAAATTTACACAGCAGTAGAACC
AACTTTCTCCTAATGTGTGTTCAATGATTTGAGAAGGGGCTTGAAATATCCAAAGTTCCTACTTT
CATGATTTTGAGCAGTTATTTTCTTCCGACCCATCCTATACAGT
Found at i:1056855 original size:18 final size:17
Alignment explanation
Indices: 1056833--1056873 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1056823 CTTTTGTCTT
*
1056833 CAATTTTTCTTCTTTCTC
1 CAATTTTT-GTCTTTCTC
*
1056851 TAATTTTTGTCTTTCTC
1 CAATTTTTGTCTTTCTC
1056868 CAATTT
1 CAATTT
1056874 GTGAATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.15, C:0.22, G:0.02, T:0.61
Consensus pattern (17 bp):
CAATTTTTGTCTTTCTC
Found at i:1060069 original size:19 final size:20
Alignment explanation
Indices: 1060022--1060069 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
1060012 AAAAAAATTT
1060022 ATGT-TATTTTTTTCATAAC
1 ATGTGTATTTTTTTCATAAC
*
1060041 ATGTTCGTATTTTTTT-ATATC
1 ATG-T-GTATTTTTTTCATAAC
1060062 ATGTGTAT
1 ATGTGTAT
1060070 ATGTTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 7 0.28
20 2 0.08
21 7 0.28
22 9 0.36
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.58
Consensus pattern (20 bp):
ATGTGTATTTTTTTCATAAC
Found at i:1060367 original size:29 final size:30
Alignment explanation
Indices: 1060315--1060392 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
1060305 TAGGTCGATA
* *
1060315 AAAATAATAATATTTTGTTAAATT-ATTTT
1 AAAATAACAATATTTTGATAAATTAATTTT
1060344 AAAATAACAATATTTTTGAT-AATTAATTTT
1 AAAATAACAATA-TTTTGATAAATTAATTTT
* *
1060374 ATAAA-AAAAATAGTTTGAT
1 A-AAATAACAATATTTTGAT
1060393 CAATCTGCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 21 0.50
30 18 0.43
31 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (30 bp):
AAAATAACAATATTTTGATAAATTAATTTT
Found at i:1061929 original size:66 final size:66
Alignment explanation
Indices: 1061807--1061931 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 66
1061797 GAAGAGGTTT
* * *
1061807 GGGAAAGCAGGACGACTTCGGATCAAGATGAGAGCAATGTTGCCCTCAATCTTCCAATTTCGGCT
1 GGGAAAGCAGGACGACTTCGGATCAAGATGAGAGCAATGCTGCCCTCAACCATCCAATTTCGGCT
1061872 G
66 G
* * *
1061873 GGGAAAGCAGGACGA-TATCGGATCTAGATCTG-GA-CGATGCTGCCCTTAACCATCCAATT
1 GGGAAAGCAGGACGACT-TCGGATCAAGA--TGAGAGCAATGCTGCCCTCAACCATCCAATT
1061932 CTGGAGCCAG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
65 1 0.02
66 45 0.90
67 2 0.04
68 2 0.04
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.22
Consensus pattern (66 bp):
GGGAAAGCAGGACGACTTCGGATCAAGATGAGAGCAATGCTGCCCTCAACCATCCAATTTCGGCT
G
Found at i:1073678 original size:45 final size:45
Alignment explanation
Indices: 1073594--1073679 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
1073584 AATATATATG
* *
1073594 TATATAAAGAATAATTATTTAATATATTAATAGTGAAATTTAATT
1 TATATAAAGAATAATTATTTAATATATTAATAATAAAATTTAATT
* *
1073639 TATATATAAG-ATAATTATTTGATATATTGATAATAAAATTT
1 TATATA-AAGAATAATTATTTAATATATTAATAATAAAATTT
1073680 TTTATTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 33 0.92
46 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (45 bp):
TATATAAAGAATAATTATTTAATATATTAATAATAAAATTTAATT
Found at i:1074161 original size:17 final size:18
Alignment explanation
Indices: 1074129--1074164 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1074119 AATTTAAAAT
1074129 ATTATATTTAAAATTTTA
1 ATTATATTTAAAATTTTA
*
1074147 ATTAT-TTTTAAATTTTA
1 ATTATATTTAAAATTTTA
1074164 A
1 A
1074165 CAATATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATATTTAAAATTTTA
Found at i:1074428 original size:42 final size:42
Alignment explanation
Indices: 1074369--1074451 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1074359 GTATACACAG
*
1074369 TGAGCCAACTGACAGTCATGTTGAGCTAATGTCCAAGCCCAC
1 TGAGCCAACTGACAGTCATGTTGAGCGAATGTCCAAGCCCAC
*
1074411 TGAGCCAACTTACAGTCATGTTGAGCGAATGTCCAAGCCCA
1 TGAGCCAACTGACAGTCATGTTGAGCGAATGTCCAAGCCCA
1074452 AGTTTTTACC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (42 bp):
TGAGCCAACTGACAGTCATGTTGAGCGAATGTCCAAGCCCAC
Found at i:1076569 original size:40 final size:39
Alignment explanation
Indices: 1076514--1076594 Score: 144
Period size: 40 Copynumber: 2.1 Consensus size: 39
1076504 AGTGTAAAAC
*
1076514 ATTTGTTTAACACTGCCAGAAATTGATTGTCAAAATTAAT
1 ATTTGTTTAAAACTGCCAGAAATTGATTGTCAAAA-TAAT
1076554 ATTTGTTTAAAACTGCCAGAAATTGATTGTCAAAATAAT
1 ATTTGTTTAAAACTGCCAGAAATTGATTGTCAAAATAAT
1076593 AT
1 AT
1076595 AGTTTCTTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 6 0.15
40 34 0.85
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (39 bp):
ATTTGTTTAAAACTGCCAGAAATTGATTGTCAAAATAAT
Found at i:1077051 original size:32 final size:32
Alignment explanation
Indices: 1077010--1077074 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1077000 TGTCGTTGTC
1077010 ATTGTCCTTGTCCTTGCCTTCTTTTCTTTTAT
1 ATTGTCCTTGTCCTTGCCTTCTTTTCTTTTAT
1077042 ATTGTCCTTGTCCTTGCCTTCTTTTCTTTTAT
1 ATTGTCCTTGTCCTTGCCTTCTTTTCTTTTAT
1077074 A
1 A
1077075 ATTTCATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.08, C:0.25, G:0.09, T:0.58
Consensus pattern (32 bp):
ATTGTCCTTGTCCTTGCCTTCTTTTCTTTTAT
Found at i:1077425 original size:34 final size:34
Alignment explanation
Indices: 1077387--1077462 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 34
1077377 AAAAATGAAA
1077387 ATAAAAATG-TAATTAT-TATAATATTTTTAATTTT
1 ATAAAAATGATAATTATATATAA-ATTTTT-ATTTT
* *
1077421 ATAAAAATGATTAATTATATGTAAATTTTTTTTTT
1 ATAAAAATGA-TAATTATATATAAATTTTTATTTT
1077456 A-AAAAAT
1 ATAAAAAT
1077463 AAAAGATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
34 15 0.41
35 5 0.14
36 13 0.35
37 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (34 bp):
ATAAAAATGATAATTATATATAAATTTTTATTTT
Found at i:1078293 original size:16 final size:16
Alignment explanation
Indices: 1078276--1078315 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1078266 AATATTTATA
1078276 AAATTAAAT-AAATTT
1 AAATTAAATCAAATTT
*
1078291 AAATCAAATCAAATTT
1 AAATTAAATCAAATTT
1078307 AAATTAAAT
1 AAATTAAAT
1078316 TTATTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTAAATCAAATTT
Found at i:1078486 original size:17 final size:16
Alignment explanation
Indices: 1078448--1078490 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1078438 TTATTATATT
1078448 ATATTTTTATAAAATA
1 ATATTTTTATAAAATA
*
1078464 AAATTTTTA-AAAATA
1 ATATTTTTATAAAATA
1078479 TATTATTTTTAT
1 -A-TATTTTTAT
1078491 TTAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.27
16 9 0.41
17 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTTTATAAAATA
Found at i:1079047 original size:2 final size:2
Alignment explanation
Indices: 1079042--1079074 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1079032 GAGAAAGGGA
1079042 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1079075 AAACTGTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1079176 original size:3 final size:3
Alignment explanation
Indices: 1079168--1079214 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
1079158 TCAACCTCAC
* * *
1079168 CAA CAA CAA CAG CAG CAG CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
1079215 TTGCCTTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.60, C:0.34, G:0.06, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:1083376 original size:52 final size:52
Alignment explanation
Indices: 1083263--1083366 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
1083253 CATATTATTC
1083263 AAACAGAAATGGGAAATAGAGAATAAGATGACCAGTAATGTAGTTGAACATT
1 AAACAGAAATGGGAAATAGAGAATAAGATGACCAGTAATGTAGTTGAACATT
1083315 AAACAGAAATGGGAAATAGAGAATAAGATGACCAGTAATGTAGTTGAACATT
1 AAACAGAAATGGGAAATAGAGAATAAGATGACCAGTAATGTAGTTGAACATT
1083367 CATAGGAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.21
Consensus pattern (52 bp):
AAACAGAAATGGGAAATAGAGAATAAGATGACCAGTAATGTAGTTGAACATT
Found at i:1087803 original size:2 final size:2
Alignment explanation
Indices: 1087796--1087823 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1087786 GAAGCACATT
1087796 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
1087824 GCTGAATGAA
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):
TA
Found at i:1090915 original size:2 final size:2
Alignment explanation
Indices: 1090908--1090985 Score: 129
Period size: 2 Copynumber: 39.0 Consensus size: 2
1090898 TATAAACTTG
*
1090908 CA CA CA CA CA CA CA CT CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
* *
1090950 CT CA CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1090986 TATATATATA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.47, C:0.49, G:0.00, T:0.04
Consensus pattern (2 bp):
CA
Found at i:1094391 original size:3 final size:3
Alignment explanation
Indices: 1094378--1094443 Score: 51
Period size: 3 Copynumber: 22.0 Consensus size: 3
1094368 CAACTTCAAA
* * * * * * *
1094378 TTC TCC TTC TTC TTC TTC GTC TTC TTC TTC TTC ATC ATC ATC ATC ATC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
1094426 ATC TTC TAC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC
1094444 ACATCCTTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.11, C:0.35, G:0.02, T:0.53
Consensus pattern (3 bp):
TTC
Found at i:1095914 original size:28 final size:29
Alignment explanation
Indices: 1095860--1095919 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
1095850 CATGTCTTTA
1095860 TTTAAATGTTATGTCTTTACATAACAA-T
1 TTTAAATGTTATGTCTTTACATAACAACT
*
1095888 TTTAAATGTTGTGTTCTTT-CA-ACACAACT
1 TTTAAATGTTATG-TCTTTACATA-ACAACT
1095917 TTT
1 TTT
1095920 TGATGCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.04
28 18 0.64
29 9 0.32
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (29 bp):
TTTAAATGTTATGTCTTTACATAACAACT
Found at i:1095991 original size:17 final size:17
Alignment explanation
Indices: 1095954--1096005 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1095944 TAATATTTCG
*
1095954 AATTAAAT-ATTAATA-
1 AATTAAATAAATAATAT
1095969 AA-TAAATAAATAATAT
1 AATTAAATAAATAATAT
1095985 AATTAAAATAAA-AATAT
1 AATT-AAATAAATAATAT
1096002 AATT
1 AATT
1096006 GCATCTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 2 0.06
17 10 0.31
18 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTAAATAAATAATAT
Found at i:1097684 original size:17 final size:18
Alignment explanation
Indices: 1097662--1097695 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1097652 TTAAAGATGC
1097662 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
1097679 AATTATATTATTTATTT
1 AATTATATTATTTATTT
1097696 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:1097696 original size:17 final size:17
Alignment explanation
Indices: 1097662--1097713 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1097652 TTAAAGATGC
1097662 AATTATATT-TTTATTTT
1 AATTATATTATTTA-TTT
1097679 AATTATATTATTTATTT
1 AATTATATTATTTATTT
*
1097696 -ATT-TATTA-ATATTT
1 AATTATATTATTTATTT
1097710 AATT
1 AATT
1097714 CGAAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 3 0.09
17 12 0.38
18 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTATATTATTTATTT
Found at i:1100081 original size:17 final size:17
Alignment explanation
Indices: 1100059--1100096 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1100049 GCAGAAAACC
1100059 AAGTTTAAATTATTTTA
1 AAGTTTAAATTATTTTA
1100076 AAGTTTAAATTATTTTA
1 AAGTTTAAATTATTTTA
1100093 AAGT
1 AAGT
1100097 ATGGGGGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (17 bp):
AAGTTTAAATTATTTTA
Found at i:1103513 original size:18 final size:19
Alignment explanation
Indices: 1103487--1103523 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1103477 TTAATTTACA
*
1103487 TTTACTAATTTTATGTAAT
1 TTTACTAATTTTATCTAAT
1103506 TTTA-TAATTTTATCTAAT
1 TTTACTAATTTTATCTAAT
1103524 ACAATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTACTAATTTTATCTAAT
Done.