Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold142
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: 1427168
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 17476 characters in sequence are not A, C, G, or T
File 6 of 8
Found at i:1021792 original size:11 final size:11
Alignment explanation
Indices: 1021772--1021802 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1021762 GGTTGATATT
*
1021772 ATAAACAAAAA
1 ATAAAAAAAAA
1021783 ATAAAAAAAAA
1 ATAAAAAAAAA
1021794 ATAAAAAAA
1 ATAAAAAAA
1021803 TAATTTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (11 bp):
ATAAAAAAAAA
Found at i:1025627 original size:255 final size:257
Alignment explanation
Indices: 1025173--1025680 Score: 797
Period size: 255 Copynumber: 2.0 Consensus size: 257
1025163 GGAATATTAA
* *
1025173 TTTTTTTTTCAAAATTTGCATTTATTTATAAGATTTTAAAAGATCATGTTTTTCGAAATATGTAT
1 TTTTTTTTTCAAAATTTACATTTATTTATAAGATTTTAAAAGATCATATTTTTCGAAATATGTAT
** * * *
1025238 TAGACATAGATATTAAACACGAAATACTTCGATGAAAAATGAAGAGTGCGATAAATTCATACGAA
66 TAGACATAGATATTAAACACGAAATACTTCGACAAAAAATGAAAAGTACGATAAATCCATACGAA
* *
1025303 AATTTGAAAGCGTTTTTTTGTAAACTAATCGATTGCATTTGCATGTGCATGAATTTGACATGAAA
131 AATTTGAAAGAG-TTTTTTGTAAACTAATCGATTGCATTTGCATGTACATGAATTTGACATGAAA
* * * *
1025368 TTGTCCTGTAAAATCAGAAGTAAACTGTAGATATCTAATTTCGTCCGGATCTTCTTTCAAAAT
195 TTGTCCTGTAAAATCAAAAGTAAACTGTAAACACCTAATTTCGTCCGGATCTTCTTTCAAAAT
* * *
1025431 TTTTTTTTTCAAAATTTACATTTATTTGTAGGATTTTTAAAAGATCATATTTTTCGAGATATGTA
1 TTTTTTTTTCAAAATTTACATTTATTTATAAGA-TTTTAAAAGATCATATTTTTCGAAATATGTA
*
1025496 TTAGACATAGATATTAAACAC-AAATACTT-GACAAAAAATGAAAAGTATGATAAATCCATACGA
65 TTAGACATAGATATTAAACACGAAATACTTCGACAAAAAATGAAAAGTACGATAAATCCATACGA
* *
1025559 AAATTTGAAAGAG-TTTTTGTAAAGTAATCGATTGCATTTGCATGTACATGAATTTGACATGGAA
130 AAATTTGAAAGAGTTTTTTGTAAACTAATCGATTGCATTTGCATGTACATGAATTTGACATGAAA
*
1025623 TTGTCTTGTAAAATCAAAAGTAAACTGTAAACACCTAATTTCGTCCGGATCTTCTTTC
195 TTGTCCTGTAAAATCAAAAGTAAACTGTAAACACCTAATTTCGTCCGGATCTTCTTTC
1025681 CTCGAAATGT
Statistics
Matches: 229, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
255 101 0.44
257 40 0.17
258 38 0.17
259 50 0.22
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (257 bp):
TTTTTTTTTCAAAATTTACATTTATTTATAAGATTTTAAAAGATCATATTTTTCGAAATATGTAT
TAGACATAGATATTAAACACGAAATACTTCGACAAAAAATGAAAAGTACGATAAATCCATACGAA
AATTTGAAAGAGTTTTTTGTAAACTAATCGATTGCATTTGCATGTACATGAATTTGACATGAAAT
TGTCCTGTAAAATCAAAAGTAAACTGTAAACACCTAATTTCGTCCGGATCTTCTTTCAAAAT
Found at i:1025983 original size:24 final size:24
Alignment explanation
Indices: 1025956--1026014 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
1025946 AAAATCAAGT
*
1025956 AATAAAAAAAATCAAAT-TCAAAAA
1 AATAAAAAAAAT-AAATATAAAAAA
1025980 AAT-AAAAAAATAAATATAAAAAA
1 AATAAAAAAAATAAATATAAAAAA
1026003 AATTAAAAAAAA
1 AA-TAAAAAAAA
1026015 ATCGAAGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 4 0.13
23 16 0.52
24 4 0.13
25 7 0.23
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (24 bp):
AATAAAAAAAATAAATATAAAAAA
Found at i:1026014 original size:12 final size:11
Alignment explanation
Indices: 1025938--1026016 Score: 59
Period size: 11 Copynumber: 6.5 Consensus size: 11
1025928 ATATATATAT
1025938 AAAATAAAAAA
1 AAAATAAAAAA
*
1025949 ATCAAGTAATAAAA
1 A--AAATAA-AAAA
1025963 AAAATCAAATTCAAA
1 AAAAT-AAA---AAA
1025978 AAAATAAAAAA
1 AAAATAAAAAA
*
1025989 ATAAATATAAAA
1 A-AAATAAAAAA
*
1026001 AAAATTAAAAA
1 AAAATAAAAAA
1026012 AAAAT
1 AAAAT
1026017 CGAAGATGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
11 18 0.33
12 14 0.25
13 7 0.13
14 8 0.15
15 8 0.15
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.18
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:1029972 original size:8 final size:8
Alignment explanation
Indices: 1029959--1030010 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
1029949 ATATATTTTA
1029959 ATTTAAAT
1 ATTTAAAT
1029967 ATTTAAAT
1 ATTTAAAT
*
1029975 TTTTAAATT
1 ATTTAAA-T
*
1029984 TTTTAAAT
1 ATTTAAAT
*
1029992 ATATAAAAT
1 AT-TTAAAT
*
1030001 AATTAAAT
1 ATTTAAAT
1030009 AT
1 AT
1030011 ATTTATATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 22 0.61
9 14 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTAAAT
Found at i:1029998 original size:17 final size:17
Alignment explanation
Indices: 1029963--1030012 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1029953 ATTTTAATTT
* *
1029963 AAATATTTAAATTTTTA
1 AAATATTTAAATATATA
* *
1029980 AATTTTTTAAATATATA
1 AAATATTTAAATATATA
*
1029997 AAATAATTAAATATAT
1 AAATATTTAAATATAT
1030013 TTATATTTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATATTTAAATATATA
Found at i:1030062 original size:15 final size:14
Alignment explanation
Indices: 1030042--1030083 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1030032 AATATTTATT
1030042 TAAATTTTAATAACA
1 TAAATTTTAATAA-A
1030057 TAAATTTTAATAAA
1 TAAATTTTAATAAA
*
1030071 TATATTTTTAATA
1 TA-AATTTTAATA
1030084 TTTTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 3 0.12
15 22 0.88
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAATTTTAATAAA
Found at i:1033001 original size:2 final size:2
Alignment explanation
Indices: 1032994--1033045 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
1032984 TTGAAGCAAC
*
1032994 AT AT AT AT AT AT AT AT AT AT AT A- AT CA- AT -T AT TT 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
1033034 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1033046 TCAATTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 3 0.07
2 40 0.91
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1033039 original size:28 final size:28
Alignment explanation
Indices: 1032999--1033055 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1032989 GCAACATATA
1032999 TATATATATATATATATAATCAATTATT
1 TATATATATATATATATAATCAATTATT
*
1033027 TATATATATATATATATATTCAATTATT
1 TATATATATATATATATAATCAATTATT
1033055 T
1 T
1033056 CAACTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (28 bp):
TATATATATATATATATAATCAATTATT
Found at i:1033520 original size:19 final size:20
Alignment explanation
Indices: 1033493--1033531 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1033483 ATTAATTGTA
1033493 ATTTGCCTTCAAA-TTCATT
1 ATTTGCCTTCAAATTTCATT
* *
1033512 ATTTTCCTTTAAATTTCATT
1 ATTTGCCTTCAAATTTCATT
1033532 TCGACTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTTGCCTTCAAATTTCATT
Found at i:1033812 original size:21 final size:21
Alignment explanation
Indices: 1033774--1033818 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1033764 TGTAAACAAA
*
1033774 ATATATTTATATAAATATAGT
1 ATATATTTATATAAATATACT
*
1033795 ATATCATTTATAT-TATATACT
1 ATAT-ATTTATATAAATATACT
1033816 ATA
1 ATA
1033819 CAATGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATATTTATATAAATATACT
Found at i:1035870 original size:2 final size:2
Alignment explanation
Indices: 1035863--1035894 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1035853 TCATAATAAC
1035863 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
1035895 GTCTCGGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1036010 original size:17 final size:16
Alignment explanation
Indices: 1035980--1036017 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
1035970 CAAATATAAA
*
1035980 TAATTAAATTTATATT
1 TAATTAAATATATATT
1035996 TAATATAAATATATATT
1 TAAT-TAAATATATATT
1036013 TAATT
1 TAATT
1036018 TCATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTAAATATATATT
Found at i:1036177 original size:2 final size:2
Alignment explanation
Indices: 1036170--1036227 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1036160 TAGTTCAATA
*
1036170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
1036212 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1036228 TTCAATTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1036793 original size:21 final size:21
Alignment explanation
Indices: 1036769--1036822 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
1036759 AAATTTAATT
*
1036769 ATAAAATATATAAATATCAA-A
1 ATAAAA-ATATAAATATAAATA
* *
1036790 ATAAAAATATTATTATAAATA
1 ATAAAAATATAAATATAAATA
1036811 ATAAAAAATATA
1 AT-AAAAATATA
1036823 TTCATATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.37
21 9 0.33
22 8 0.30
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAAAATATAAATATAAATA
Found at i:1037570 original size:12 final size:13
Alignment explanation
Indices: 1037543--1037575 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1037533 TAAAGGTAAA
*
1037543 TAAATTAAATATT
1 TAAATTTAATATT
1037556 TAAATTTAA-ATT
1 TAAATTTAATATT
1037568 TAAATTTA
1 TAAATTTA
1037576 TTAAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTTAATATT
Found at i:1037608 original size:12 final size:12
Alignment explanation
Indices: 1037593--1037617 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1037583 TAATATTTTC
1037593 AAAAATAATTAA
1 AAAAATAATTAA
1037605 AAAAATAATTAA
1 AAAAATAATTAA
1037617 A
1 A
1037618 TTAAATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATAATTAA
Found at i:1043410 original size:22 final size:21
Alignment explanation
Indices: 1043383--1043430 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1043373 ATTATTTAAA
1043383 TTTAATTA-TAAAAATATATTT
1 TTTAATTATTAAAAAT-TATTT
*
1043404 TATTAA-TATTAATAATTATTT
1 T-TTAATTATTAAAAATTATTT
1043425 TTTAAT
1 TTTAAT
1043431 ATTTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
20 4 0.17
21 9 0.39
22 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAATTATTAAAAATTATTT
Found at i:1043433 original size:31 final size:29
Alignment explanation
Indices: 1043398--1043458 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
1043388 TTATAAAAAT
*
1043398 ATATTTTATTAATATTAATAATTATTTTTTA
1 ATATTTTATTAAAATT--TAATTATTTTTTA
* *
1043429 ATATTTTTTTAAAATTTTATTATTTTTTA
1 ATATTTTATTAAAATTTAATTATTTTTTA
1043458 A
1 A
1043459 ATAATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 13 0.48
31 14 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
ATATTTTATTAAAATTTAATTATTTTTTA
Found at i:1044710 original size:19 final size:19
Alignment explanation
Indices: 1044669--1044713 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1044659 TTTATTTAAA
1044669 TTTAAT-TATAAAATATAT
1 TTTAATATATAAAATATAT
*
1044687 ATTAATATA-AAAATAATAT
1 TTTAATATATAAAAT-ATAT
1044706 TTTAATAT
1 TTTAATAT
1044714 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAATATATAAAATATAT
Found at i:1044712 original size:11 final size:11
Alignment explanation
Indices: 1044698--1044730 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1044688 TTAATATAAA
1044698 AATAATATTTT
1 AATAATATTTT
1044709 AAT-AT-TTTT
1 AATAATATTTT
1044718 AATAATATTTT
1 AATAATATTTT
1044729 AA
1 AA
1044731 ATTATCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 7 0.35
10 4 0.20
11 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AATAATATTTT
Found at i:1045168 original size:18 final size:18
Alignment explanation
Indices: 1045147--1045205 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
1045137 TACCTATAAT
*
1045147 AAAATCTTATAAAAATTA
1 AAAATATTATAAAAATTA
*
1045165 AAAATTTTAATAAAATATATA
1 AAAATATT-ATAAAA-AT-TA
1045186 AAAATAATTA-AAAAATTA
1 AAAAT-ATTATAAAAATTA
1045204 AA
1 AA
1045206 TAAAAAGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
18 11 0.31
19 8 0.23
20 6 0.17
21 8 0.23
22 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATATTATAAAAATTA
Found at i:1045196 original size:22 final size:21
Alignment explanation
Indices: 1045147--1045211 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
1045137 TACCTATAAT
*
1045147 AAAATCTT-ATAAAA-AT-TA
1 AAAATATTAATAAAATATATA
*
1045165 AAAATTTTAATAAAATATATA
1 AAAATATTAATAAAATATATA
*
1045186 AAAATAATTAA-AAAATTAAATA
1 AAAAT-ATTAATAAAA-TATATA
1045208 AAAA
1 AAAA
1045212 GTACTTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 7 0.18
19 6 0.15
20 2 0.05
21 11 0.28
22 13 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATATTAATAAAATATATA
Found at i:1045198 original size:31 final size:29
Alignment explanation
Indices: 1045143--1045210 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 29
1045133 AAAATACCTA
* * *
1045143 TAATAAAATCTTATAAAAATTAAAAATTT
1 TAATAAAATATTAAAAAAATTAAAAAATT
1045172 TAATAAAATATATAAAAATAATTAAAAAATT
1 TAATAAAATAT-TAAAAA-AATTAAAAAATT
*
1045203 AAATAAAA
1 TAATAAAA
1045211 AGTACTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 10 0.30
30 5 0.15
31 18 0.55
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (29 bp):
TAATAAAATATTAAAAAAATTAAAAAATT
Found at i:1045505 original size:27 final size:27
Alignment explanation
Indices: 1045475--1045586 Score: 79
Period size: 28 Copynumber: 4.1 Consensus size: 27
1045465 ATTTTTTTAA
1045475 TAAATTTAATAATTTATATATTTATAT
1 TAAATTTAATAATTTATATATTTATAT
*
1045502 TAAATTTATATATTTTATTATATTT-TAAT
1 TAAATTTA-ATAATTTA-TATATTTAT-AT
* * * *
1045531 T-ATTTTAAAAATATTTTATATTGATA-
1 TAAATTTAATAAT-TTATATATTTATAT
* *
1045557 TAAATTTTAATATATTAATA-ATTAATAT
1 TAAA-TTTAATA-ATTTATATATTTATAT
1045585 TA
1 TA
1045587 TATAAATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
26 1 0.02
27 25 0.38
28 27 0.42
29 12 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TAAATTTAATAATTTATATATTTATAT
Found at i:1045509 original size:19 final size:18
Alignment explanation
Indices: 1045485--1045526 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
1045475 TAAATTTAAT
1045485 AATTTATATATTTATATTA
1 AATTTATATATTT-TATTA
1045504 AATTTATATATTTTATTA
1 AATTTATATATTTTATTA
*
1045522 TATTT
1 AATTT
1045527 TAATTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTATATATTTTATTA
Found at i:1045528 original size:19 final size:19
Alignment explanation
Indices: 1045487--1045551 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
1045477 AATTTAATAA
*
1045487 TTTATATATTTATATTA-AA
1 TTTATATATTT-TATTATAT
1045506 TTTATATATTTTATTATAT
1 TTTATATATTTTATTATAT
**
1045525 TTTA-ATTATTTTAAAAATAT
1 TTTATA-TATTTT-ATTATAT
1045545 TTTATAT
1 TTTATAT
1045552 TGATATAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.15
19 22 0.56
20 10 0.26
21 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATATTTTATTATAT
Found at i:1045534 original size:9 final size:10
Alignment explanation
Indices: 1045458--1045548 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 10
1045448 TAAATAATTT
1045458 TATTTTAAT-
1 TATTTTAATA
*
1045467 TTTTTTAATA
1 TATTTTAATA
*
1045477 -AATTTAATA
1 TATTTTAATA
1045486 -A-TTT-ATA
1 TATTTTAATA
*
1045493 TATTTATATTA
1 TATTT-TAATA
*
1045504 -AATTT-ATA
1 TATTTTAATA
*
1045512 TATTTTATTA
1 TATTTTAATA
1045522 TATTTTAAT-
1 TATTTTAATA
*
1045531 TATTTTAAAAA
1 TATTTT-AATA
1045542 TATTTTA
1 TATTTTA
1045549 TATTGATATA
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
7 3 0.05
8 6 0.10
9 29 0.46
10 17 0.27
11 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATTTTAATA
Found at i:1045569 original size:18 final size:17
Alignment explanation
Indices: 1045496--1045598 Score: 61
Period size: 18 Copynumber: 5.9 Consensus size: 17
1045486 ATTTATATAT
1045496 TTATATTAAA-TTTATATA
1 TTATA-TAAATTTTA-ATA
* *
1045514 TTTTATTATATTTTAATTA
1 TTATA-TAAATTTTAA-TA
* * *
1045533 TTTTAAAAATATTTTATA
1 TTATATAAAT-TTTAATA
1045551 TTGATATAAATTTTAATA
1 TT-ATATAAATTTTAATA
*
1045569 -TAT-T-AATAATTAATA
1 TTATATAAAT-TTTAATA
1045584 TTATATAAATTTTAA
1 TTATATAAATTTTAA
1045599 AATATATTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
14 3 0.04
15 7 0.10
16 5 0.07
17 6 0.09
18 25 0.37
19 21 0.31
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (17 bp):
TTATATAAATTTTAATA
Found at i:1045871 original size:21 final size:19
Alignment explanation
Indices: 1045846--1045887 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
1045836 TTTAATTTTT
*
1045846 ATATTTTTTTATATATTTAAA
1 ATATTTTATT-TA-ATTTAAA
1045867 ATATTTTATTTAATTTAAA
1 ATATTTTATTTAATTTAAA
1045886 AT
1 AT
1045888 GATAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTTTATTTAATTTAAA
Found at i:1046126 original size:22 final size:21
Alignment explanation
Indices: 1046100--1046144 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1046090 TATATTAAAA
1046100 AAATAAAAATAAATTATAAATT
1 AAATAAAAATAAATT-TAAATT
* *
1046122 AAATAAAATTAAATTTAACTT
1 AAATAAAAATAAATTTAAATT
1046143 AA
1 AA
1046145 TTTAACTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAAAATAAATTTAAATT
Found at i:1046511 original size:21 final size:21
Alignment explanation
Indices: 1046468--1046519 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1046458 TAAAATATAA
*
1046468 ATTTTAATATTTATAATTTTTT
1 ATTTTAA-AATTATAATTTTTT
1046490 ATTTTAAAATTAT-ATTTATTT
1 ATTTTAAAATTATAATTT-TTT
*
1046511 ATTGTAAAA
1 ATTTTAAAA
1046520 AATAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 4 0.15
21 16 0.59
22 7 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTTAAAATTATAATTTTTT
Found at i:1052232 original size:13 final size:13
Alignment explanation
Indices: 1052214--1052240 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1052204 AGCTTTCTGA
1052214 CAGGATCAAATAT
1 CAGGATCAAATAT
1052227 CAGGATCAAATAT
1 CAGGATCAAATAT
1052240 C
1 C
1052241 TGCTGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (13 bp):
CAGGATCAAATAT
Found at i:1052732 original size:25 final size:26
Alignment explanation
Indices: 1052688--1052738 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
1052678 TAATTCGATC
1052688 ACTTATTAATTTTTTAAAATTTATAA
1 ACTTATTAATTTTTTAAAATTTATAA
1052714 ACTTATTAA-TTTTTAAAATTTATAA
1 ACTTATTAATTTTTTAAAATTTATAA
1052739 TCCAATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
ACTTATTAATTTTTTAAAATTTATAA
Found at i:1052897 original size:18 final size:18
Alignment explanation
Indices: 1052876--1052914 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1052866 TAAAATAATT
*
1052876 TTTTATTGATTTTA-TTAA
1 TTTTA-TGAATTTATTTAA
1052894 TTTTATGAATTTATTTAA
1 TTTTATGAATTTATTTAA
1052912 TTT
1 TTT
1052915 AATAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTATGAATTTATTTAA
Found at i:1052908 original size:17 final size:17
Alignment explanation
Indices: 1052876--1052927 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
1052866 TAAAATAATT
*
1052876 TTTTATTGATTTTATTAA
1 TTTTA-TGAATTTATTAA
1052894 TTTTATGAATTTATTTAA
1 TTTTATGAATTTA-TTAA
* *
1052912 TTTAATAAATTT-TTAA
1 TTTTATGAATTTATTAA
1052928 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 4 0.13
17 7 0.23
18 19 0.63
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTTATGAATTTATTAA
Found at i:1058023 original size:16 final size:16
Alignment explanation
Indices: 1057984--1058030 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1057974 TATATCATAA
*
1057984 TTATATTTA-AAATATT
1 TTATATTTATTAA-ATT
1058000 TTATATTTATATAAATT
1 TTATATTTAT-TAAATT
1058017 TTA-ATTTATTAAAT
1 TTATATTTATTAAAT
1058031 AAAAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 15 0.54
17 6 0.21
18 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATTTATTAAATT
Found at i:1058091 original size:49 final size:49
Alignment explanation
Indices: 1057982--1058092 Score: 115
Period size: 49 Copynumber: 2.3 Consensus size: 49
1057972 ATTATATCAT
1057982 AATTATATTTAAAATATTTTATATTTATATAAATTTTAATTTATTAAATAA
1 AATTATATTTAAAATA--TTATATTTATATAAATTTTAATTTATTAAATAA
* * *
1058033 AA-AAT-TTTAAAATA-TATTTTTAT-TATATTTTAA-TTATTTAATCATAA
1 AATTATATTTAAAATATTATATTTATATAAATTTTAATTTA-TTAA--ATAA
1058080 AATTATATTTAAA
1 AATTATATTTAAA
1058093 GAACAAATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
44 3 0.06
45 13 0.25
46 8 0.16
47 6 0.12
48 2 0.04
49 15 0.29
50 2 0.04
51 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (49 bp):
AATTATATTTAAAATATTATATTTATATAAATTTTAATTTATTAAATAA
Found at i:1065720 original size:18 final size:20
Alignment explanation
Indices: 1065690--1065726 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1065680 TATTAAAAAA
1065690 TATTTTTATTAAT-ATTTTT
1 TATTTTTATTAATAATTTTT
1065709 TATTTTTA-TAATAATTTT
1 TATTTTTATTAATAATTTT
1065727 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTTTATTAATAATTTTT
Found at i:1069746 original size:9 final size:8
Alignment explanation
Indices: 1069715--1069749 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
1069705 ATACAATAAA
*
1069715 TTAAAATT
1 TTAATATT
1069723 TTAATATT
1 TTAATATT
1069731 TTAATATT
1 TTAATATT
1069739 TATAATATT
1 T-TAATATT
1069748 TT
1 TT
1069750 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTAATATT
Found at i:1069746 original size:17 final size:16
Alignment explanation
Indices: 1069715--1069749 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1069705 ATACAATAAA
1069715 TTAAAATTTTAATATT
1 TTAAAATTTTAATATT
*
1069731 TTAATATTTATAATATT
1 TTAAAATTT-TAATATT
1069748 TT
1 TT
1069750 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAAATTTTAATATT
Found at i:1070071 original size:21 final size:20
Alignment explanation
Indices: 1070041--1070080 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1070031 TTTTATCAAA
1070041 TAATATAA-TTAATATTAAAG
1 TAATATAATTTAAT-TTAAAG
1070061 TAATAATAATTTAATTTAAA
1 TAAT-ATAATTTAATTTAAA
1070081 ATAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TAATATAATTTAATTTAAAG
Found at i:1070168 original size:8 final size:8
Alignment explanation
Indices: 1070155--1070179 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1070145 TGTTAGAAAA
1070155 TATATTTT
1 TATATTTT
1070163 TATATTTT
1 TATATTTT
1070171 TATATTTT
1 TATATTTT
1070179 T
1 T
1070180 TTATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATATTTT
Found at i:1070195 original size:40 final size:41
Alignment explanation
Indices: 1070127--1070216 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 41
1070117 ATGATTTTAA
* *
1070127 TTTTATCA-TTTTTTTAAATGTTAGAAAAT-ATATTTTTATAT
1 TTTTAT-ATTTTTTTTAAATGTTAGAAAATAAAATATTTAT-T
1070168 TTTTATATTTTTTTATAAAT-TTA-AAAATAAAATATTTATT
1 TTTTATATTTTTTT-TAAATGTTAGAAAATAAAATATTTATT
1070208 TTTTATATT
1 TTTTATATT
1070217 ATAAAATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
40 16 0.36
41 23 0.52
42 5 0.11
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (41 bp):
TTTTATATTTTTTTTAAATGTTAGAAAATAAAATATTTATT
Found at i:1071289 original size:2 final size:2
Alignment explanation
Indices: 1071282--1071318 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1071272 ACTAGTTCTC
1071282 AT 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 AT A
1071319 GATCATACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1072017 original size:14 final size:14
Alignment explanation
Indices: 1071978--1072018 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1071968 TTAATCTATA
1071978 TTTAAATATAAATAT
1 TTTAAATAT-AATAT
*
1071993 ATT-AATATAATAT
1 TTTAAATATAATAT
1072006 TTTAAATATAATA
1 TTTAAATATAATA
1072019 AAAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 7 0.30
14 14 0.61
15 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTAAATATAATAT
Found at i:1072057 original size:30 final size:30
Alignment explanation
Indices: 1072023--1072084 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1072013 ATAATAAAAA
* *
1072023 AATTAAAAATTAAAATGCACTTTACGTTTT
1 AATTAAAAATAAAAATGCACTTTACATTTT
1072053 AATTAAAAATAAAAATGCACTTTACATTTT
1 AATTAAAAATAAAAATGCACTTTACATTTT
1072083 AA
1 AA
1072085 GTTATTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (30 bp):
AATTAAAAATAAAAATGCACTTTACATTTT
Found at i:1077168 original size:170 final size:169
Alignment explanation
Indices: 1076860--1077191 Score: 488
Period size: 170 Copynumber: 2.0 Consensus size: 169
1076850 ATAGCACATT
* *
1076860 TTTAGTCCATGAAGTAAAAACAGGAATTAAAAAGCTCAAAAACCAAATGCCAATCAAAACTCTCA
1 TTTAGTCCATGAAGTAAAAACAGGAAATAAAAAGCTCAAAAACCAAAAGCCAATCAAAACTCTCA
* * * **
1076925 CAACATTAACCATTTCATCACAATCCAAATATTAACTTCCAAAAATGAAACACCATAACCTCAAA
66 CAACATTAACCATTTCAGCACAACCCAAAGATTAACTTCCAAAAATGAAACACCATAACCGAAAA
* *
1076990 TCACCAATCTACTTCTGAATAATTTCTGCAAAAACACCATA
131 TCACCAATCTAATTC--AATAATTACTGCAAAAACACCATA
* * *
1077031 TTTAGTCCATGAAGT-AAAATAGGAAATAAAAAGCTCAAAATCCAAAAGCCAATCAAAATTCTCA
1 TTTAGTCCATGAAGTAAAAACAGGAAATAAAAAGCTCAAAAACCAAAAGCCAATCAAAACTCTCA
* *
1077095 CTACATTAACCATTTTAGCACAACCCAAAGATTAACTTCCAAAAATGAAACACCATAACCGAAAA
66 CAACATTAACCATTTCAGCACAACCCAAAGATTAACTTCCAAAAATGAAACACCATAACCGAAAA
*
1077160 -CTACCAATCTAATTCAGTAATTACTGCAAAAA
131 TC-ACCAATCTAATTCAATAATTACTGCAAAAA
1077192 AAGAAACCAA
Statistics
Matches: 145, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
168 15 0.10
169 1 0.01
170 114 0.79
171 15 0.10
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (169 bp):
TTTAGTCCATGAAGTAAAAACAGGAAATAAAAAGCTCAAAAACCAAAAGCCAATCAAAACTCTCA
CAACATTAACCATTTCAGCACAACCCAAAGATTAACTTCCAAAAATGAAACACCATAACCGAAAA
TCACCAATCTAATTCAATAATTACTGCAAAAACACCATA
Found at i:1079855 original size:12 final size:12
Alignment explanation
Indices: 1079838--1079862 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1079828 TAATATCTGT
1079838 TTTTAATATAAA
1 TTTTAATATAAA
1079850 TTTTAATATAAA
1 TTTTAATATAAA
1079862 T
1 T
1079863 AAAAAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTAATATAAA
Found at i:1083352 original size:14 final size:15
Alignment explanation
Indices: 1083312--1083352 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1083302 ATATTTTTTA
1083312 TATATTTAAA-ATGT
1 TATATTTAAATATGT
**
1083326 TATATTTTTATAT-T
1 TATATTTAAATATGT
1083340 TATATTTAAATAT
1 TATATTTAAATAT
1083353 ATGTCAGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 20 0.91
15 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TATATTTAAATATGT
Found at i:1085515 original size:23 final size:21
Alignment explanation
Indices: 1085465--1085517 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
1085455 AATAGATTTG
1085465 ATAATT-TATATATTTGTATT
1 ATAATTATATATATTTGTATT
** *
1085485 ATGTTTATATATTTTATCGTATT
1 ATAATTATATATATT-T-GTATT
1085508 ATAATTATAT
1 ATAATTATAT
1085518 TTAAAATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.16
21 7 0.28
22 1 0.04
23 13 0.52
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (21 bp):
ATAATTATATATATTTGTATT
Found at i:1085615 original size:25 final size:25
Alignment explanation
Indices: 1085523--1085634 Score: 72
Period size: 25 Copynumber: 4.5 Consensus size: 25
1085513 TATATTTAAA
* *
1085523 ATATTTTATAATTTATATA-ATTTT
1 ATATTTAATAATTTATTTATATTTT
* *
1085547 AATATGTTAA-AATTTTATTT-TATATA
1 -ATAT-TTAATAA-TTTATTTATATTTT
* *
1085573 AAATTTAA-AATACATATTTATATTTT
1 ATATTTAATAAT--TTATTTATATTTT
*
1085599 ATATTTAATAATTTATTTATATTAT
1 ATATTTAATAATTTATTTATATTTT
*
1085624 AT-TTTTATAAT
1 ATATTTAATAAT
1085635 CGTATTCAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
23 1 0.01
24 14 0.21
25 27 0.40
26 23 0.34
27 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (25 bp):
ATATTTAATAATTTATTTATATTTT
Found at i:1085640 original size:25 final size:25
Alignment explanation
Indices: 1085587--1085640 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1085577 TTAAAATACA
* *
1085587 TATTTATATTTTATATTTAATAATT
1 TATTTATATTATATATTTAATAATG
*
1085612 TATTTATATTATAT-TTTTATAATCG
1 TATTTATATTATATATTTAATAAT-G
1085637 TATT
1 TATT
1085641 CAAAATTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
TATTTATATTATATATTTAATAATG
Found at i:1087307 original size:7 final size:7
Alignment explanation
Indices: 1087297--1087324 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1087287 TAAAAAGAAA
1087297 GAAAGAT
1 GAAAGAT
1087304 GAAAGAT
1 GAAAGAT
1087311 GAAAGAT
1 GAAAGAT
1087318 GAAAGAT
1 GAAAGAT
1087325 TAAACCGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (7 bp):
GAAAGAT
Found at i:1088035 original size:2 final size:2
Alignment explanation
Indices: 1088028--1088054 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1088018 CAAAAGTAAA
1088028 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1088055 CAGGTTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1092275 original size:2 final size:2
Alignment explanation
Indices: 1092268--1092299 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1092258 ATTTACAGAT
1092268 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1092300 GCGTATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1094134 original size:2 final size:2
Alignment explanation
Indices: 1094127--1094163 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1094117 GTAAATATTA
1094127 AG AG 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 AG AG A
1094164 ATGATTACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1095068 original size:12 final size:12
Alignment explanation
Indices: 1095050--1095139 Score: 74
Period size: 12 Copynumber: 7.0 Consensus size: 12
1095040 TCTGAGACAT
1095050 ACCTCCCCCTCC
1 ACCTCCCCCTCC
*
1095062 CCCTCCCCCTCC
1 ACCTCCCCCTCC
1095074 TACGCCTCCCATTCCTCC
1 -A--CCTCCC---CCTCC
*
1095092 ACCTCCACCTCC
1 ACCTCCCCCTCC
*
1095104 ACCTCCACCTCC
1 ACCTCCCCCTCC
*
1095116 ACCTCCACCTTCC
1 ACCTCC-CCCTCC
1095129 -CCTCCCCCTCC
1 ACCTCCCCCTCC
1095140 TCCACCAGGC
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
11 5 0.08
12 39 0.60
13 4 0.06
15 11 0.17
17 1 0.02
18 5 0.08
ACGTcount: A:0.10, C:0.69, G:0.01, T:0.20
Consensus pattern (12 bp):
ACCTCCCCCTCC
Found at i:1095069 original size:5 final size:6
Alignment explanation
Indices: 1095051--1095139 Score: 61
Period size: 6 Copynumber: 13.8 Consensus size: 6
1095041 CTGAGACATA
* *
1095051 CCTCCC CCTCCC CCTCCC CCTCCTAC GCCTCCC ATTCCTCCA CCTCCA
1 CCTCCC CCTCCC CCTCCC CCTCC--C -CCTCCC ---CCTCCC CCTCCC
* * * * *
1095099 CCTCCA CCTCCA CCTCCA CCTCCA CCTTCC CCTCCC CCTCC
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCTCC
1095140 TCCACCAGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
6 61 0.84
7 1 0.01
8 1 0.01
9 10 0.14
ACGTcount: A:0.09, C:0.70, G:0.01, T:0.20
Consensus pattern (6 bp):
CCTCCC
Found at i:1095108 original size:18 final size:18
Alignment explanation
Indices: 1095087--1095139 Score: 81
Period size: 18 Copynumber: 2.9 Consensus size: 18
1095077 GCCTCCCATT
1095087 CCTCCACCTCCACCTCCA
1 CCTCCACCTCCACCTCCA
1095105 CCTCCACCTCCACCTCCA
1 CCTCCACCTCCACCTCCA
*
1095123 CCTTCC-CCTCCCCCTCC
1 CC-TCCACCTCCACCTCC
1095140 TCCACCAGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 30 0.91
19 3 0.09
ACGTcount: A:0.11, C:0.70, G:0.00, T:0.19
Consensus pattern (18 bp):
CCTCCACCTCCACCTCCA
Found at i:1097457 original size:24 final size:24
Alignment explanation
Indices: 1097403--1097457 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1097393 CAATATAAAT
*
1097403 TATTATTT-A-TTAATAAAAATAT
1 TATTATTTAATTTAATAAAAATAA
*
1097425 TTTTATTTAATTTAATATAAAATAA
1 TATTATTTAATTTAATA-AAAATAA
1097450 TATT-TTTA
1 TATTATTTA
1097458 GATAACTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.26
23 1 0.04
24 10 0.37
25 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTATTTAATTTAATAAAAATAA
Found at i:1097896 original size:2 final size:2
Alignment explanation
Indices: 1097883--1097913 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1097873 GAAATTTTAC
*
1097883 AT AT AC 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 A
1097914 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1098345 original size:73 final size:71
Alignment explanation
Indices: 1098254--1098395 Score: 178
Period size: 70 Copynumber: 2.0 Consensus size: 71
1098244 AAACTCAACC
*
1098254 TAATTCATAAACAAATCTTATTGTAATAATAAAAAAAAAAAAACTTTTCAG-CTTGGTAATAAAT
1 TAATCCATAAACAAATCTTATT-T--TAATAAAAAAAAAAAAACTTTTCAGACTTGGTAATAAAT
1098318 TTCTAACAA
63 TTCTAACAA
* * * * * **
1098327 TAATCCATGAACATATCTTATTTTAATGATAATAAAAAAACTTTTTGGACTTGGTAATAAATTTC
1 TAATCCATAAACAAATCTTATTTTAATAAAAAAAAAAAAACTTTTCAGACTTGGTAATAAATTTC
1098392 TAAC
66 TAAC
1098396 GATGCAAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
70 20 0.33
71 20 0.33
72 1 0.02
73 19 0.32
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (71 bp):
TAATCCATAAACAAATCTTATTTTAATAAAAAAAAAAAAACTTTTCAGACTTGGTAATAAATTTC
TAACAA
Found at i:1105684 original size:15 final size:15
Alignment explanation
Indices: 1105664--1105701 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1105654 AATTTGTATC
1105664 TTTATTT-TTATATAT
1 TTTATTTATTATA-AT
1105679 TTTATTTATTATAAT
1 TTTATTTATTATAAT
*
1105694 TATATTTA
1 TTTATTTA
1105702 AAATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATTTATTATAAT
Found at i:1105732 original size:21 final size:22
Alignment explanation
Indices: 1105665--1105735 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 22
1105655 ATTTGTATCT
**
1105665 TTAT-TTTTATATATTTTATTTA
1 TTATATTTTATAT-TTAAATTTA
* *
1105687 TTATA-ATTATATTTAAA-ATA
1 TTATATTTTATATTTAAATTTA
1105707 TTTATATTTTATA-TTAAATTTA
1 -TTATATTTTATATTTAAATTTA
1105729 TTATATT
1 TTATATT
1105736 AATAATTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 2 0.05
21 20 0.51
22 17 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATATTTTATATTTAAATTTA
Found at i:1105734 original size:27 final size:27
Alignment explanation
Indices: 1105673--1105801 Score: 89
Period size: 29 Copynumber: 4.4 Consensus size: 27
1105663 CTTTATTTTT
*
1105673 ATATATTT-TATTTATTATAATTATATTTA
1 ATATATTTATA-TT-TTAT-ATTAAATTTA
*
1105702 AAATATTTATATTTTATATTAAATTTA
1 ATATATTTATATTTTATATTAAATTTA
* *
1105729 TTATATTAATAATTTATATTATATAAATTTTA
1 ATATATTTAT-ATTT-TA-TAT-TAAA-TTTA
* * *
1105761 AAATATTTATATATTTATATTAATTTTT
1 ATATATTTATAT-TTTATATTAAATTTA
1105789 ATATTATATTATA
1 ATA-TAT-TTATA
1105802 ATTATTTTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
27 16 0.20
28 13 0.16
29 17 0.21
30 13 0.16
31 8 0.10
32 13 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
ATATATTTATATTTTATATTAAATTTA
Found at i:1105744 original size:58 final size:58
Alignment explanation
Indices: 1105682--1105794 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 58
1105672 TATATATTTT
*
1105682 ATTTATTATAAT-TATA-TTTAAAATATTTATAT-TTTATATTAAATTTATTATATTAATA
1 ATTTA-TATAATATAAATTTTAAAATATTTATATATTTATATT-AATTT-TTATATTAATA
*
1105740 ATTTATATTATATAAATTTTAAAATATTTATATATTTATATTAATTTTTATATTA
1 ATTTATATAATATAAATTTTAAAATATTTATATATTTATATTAATTTTTATATTA
1105795 TATTATAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
57 5 0.10
58 16 0.32
59 21 0.42
60 8 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (58 bp):
ATTTATATAATATAAATTTTAAAATATTTATATATTTATATTAATTTTTATATTAATA
Found at i:1105808 original size:22 final size:21
Alignment explanation
Indices: 1105727--1105836 Score: 70
Period size: 22 Copynumber: 5.2 Consensus size: 21
1105717 ATATTAAATT
*
1105727 TATTATATTAATAATTTATATTA
1 TATTATATT-ATAA-TTATTTTA
* * *
1105750 TA-TAAATTTTAA-AATATTTA
1 TATTATATTATAATTAT-TTTA
1105770 TA-TAT-TTAT-ATTAATTTTTA
1 TATTATATTATAATT-A-TTTTA
1105790 TATTATATTATAATTATTTTA
1 TATTATATTATAATTATTTTA
*
1105811 T-TTATATCATATAATTATATTA
1 TATTATAT--TATAATTATTTTA
1105833 TATT
1 TATT
1105837 TAATATTTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
18 1 0.01
19 5 0.07
20 20 0.29
21 13 0.19
22 23 0.33
23 7 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTATATTATAATTATTTTA
Found at i:1106105 original size:11 final size:11
Alignment explanation
Indices: 1106075--1106113 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1106065 CTTTAGAAAA
1106075 AATTAAAATA-
1 AATTAAAATAT
*
1106085 AGATTTAAATAT
1 A-ATTAAAATAT
1106097 AATTAAAATAT
1 AATTAAAATAT
1106108 AATTAA
1 AATTAA
1106114 GTTACGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 1 0.04
11 23 0.92
12 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AATTAAAATAT
Found at i:1106785 original size:20 final size:20
Alignment explanation
Indices: 1106735--1106785 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1106725 AATAAAAAAT
1106735 TATTTAAAATTAATTATATAA
1 TATTTAAAA-TAATTATATAA
*
1106756 -ATATATAAATAATTATATAA
1 TATTTA-AAATAATTATATAA
1106776 TATTTAAAAT
1 TATTTAAAAT
1106786 TTTTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTAAAATAATTATATAA
Found at i:1112083 original size:25 final size:25
Alignment explanation
Indices: 1112055--1112102 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1112045 TCATATAAAT
*
1112055 TATAATAAGTTGATA-ATTTATATTA
1 TATAA-AAGTTGATATATTAATATTA
*
1112080 TATAAAATTTGATATATTAATAT
1 TATAAAAGTTGATATATTAATAT
1112103 ATTCGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (25 bp):
TATAAAAGTTGATATATTAATATTA
Found at i:1112121 original size:27 final size:26
Alignment explanation
Indices: 1112073--1112150 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 26
1112063 GTTGATAATT
* *
1112073 TATATTATATAAAATTTGATATATTAA
1 TATATTATATTATATTT-ATATATTAA
* *
1112100 TATATTCGTATTATATTTATATTATT-T
1 TATATT-ATATTATATTTATA-TATTAA
*
1112127 TATGTTATATTATATTT-TATATTA
1 TATATTATATTATATTTATATATTA
1112151 TATTATATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
24 4 0.10
25 2 0.05
26 10 0.24
27 14 0.33
28 12 0.29
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (26 bp):
TATATTATATTATATTTATATATTAA
Found at i:1112124 original size:5 final size:5
Alignment explanation
Indices: 1112108--1112158 Score: 57
Period size: 5 Copynumber: 9.6 Consensus size: 5
1112098 AATATATTCG
* *
1112108 TATTA TATTTA TATTA TTTTA TGTTA TATTA TATTTTA TATTA TATTA
1 TATTA TA-TTA TATTA TATTA TATTA TATTA TA--TTA TATTA TATTA
1112156 TAT
1 TAT
1112159 ATTTTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
5 30 0.75
6 5 0.12
7 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (5 bp):
TATTA
Found at i:1112144 original size:17 final size:17
Alignment explanation
Indices: 1112110--1112158 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
1112100 TATATTCGTA
1112110 TTATATT-TA-TATTATT
1 TTATATTATATTA-TATT
*
1112126 TTATGTTATATTATATT
1 TTATATTATATTATATT
1112143 TTATATTATATTATAT
1 TTATATTATATTATAT
1112159 ATTTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 6 0.21
17 21 0.72
18 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTATATTATATTATATT
Found at i:1112146 original size:12 final size:12
Alignment explanation
Indices: 1112108--1112161 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
1112098 AATATATTCG
1112108 TATTATATTTATA
1 TATTATATTT-TA
* *
1112121 TTATTTTATGTTA
1 -TATTATATTTTA
1112134 TATTATATTTTA
1 TATTATATTTTA
*
1112146 TATTATATTATA
1 TATTATATTTTA
1112158 TATT
1 TATT
1112162 TTTTAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
12 25 0.71
13 2 0.06
14 8 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:1112715 original size:27 final size:28
Alignment explanation
Indices: 1112672--1112726 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
1112662 AGTTCGGTTT
1112672 AATTTTGATTATTATTT-ATTAATAAAAA
1 AATTTTGATTATTATTTAATT-ATAAAAA
1112700 AATTTT-ATT-TTAATTTAATTATAAAAA
1 AATTTTGATTATT-ATTTAATTATAAAAA
1112727 TATTAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 2 0.08
27 14 0.56
28 9 0.36
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
AATTTTGATTATTATTTAATTATAAAAA
Found at i:1113449 original size:18 final size:18
Alignment explanation
Indices: 1113428--1113466 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1113418 ATATAAAAGA
*
1113428 TAATTATA-AGTATTTATT
1 TAATTATATA-TAATTATT
1113446 TAATTATATATAATTATT
1 TAATTATATATAATTATT
1113464 TAA
1 TAA
1113467 AAAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TAATTATATATAATTATT
Found at i:1113850 original size:18 final size:17
Alignment explanation
Indices: 1113827--1113870 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1113817 ATTTTTAAAA
1113827 ATATTAAAAAATATTTTT
1 ATATTAAAAAATA-TTTT
* *
1113845 ATATTAATATATATTTT
1 ATATTAAAAAATATTTT
1113862 ATAATTAAA
1 AT-ATTAAA
1113871 TTTAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAAAAAATATTTT
Found at i:1116184 original size:24 final size:24
Alignment explanation
Indices: 1116155--1116201 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1116145 CAATTTCCCC
1116155 TTTTCTTCATCATTTCTTCATCAA
1 TTTTCTTCATCATTTCTTCATCAA
** *
1116179 TTTTCTTGGTCATTTCTTGATCA
1 TTTTCTTCATCATTTCTTCATCA
1116202 CTAATTTGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.21, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTTCTTCATCATTTCTTCATCAA
Found at i:1116955 original size:22 final size:24
Alignment explanation
Indices: 1116920--1116977 Score: 79
Period size: 22 Copynumber: 2.6 Consensus size: 24
1116910 TTAATAATTA
1116920 ATATTATATA--ATTTTTTATA-T
1 ATATTATATATTATTTTTTATATT
1116941 AT-TTATATATTATTTTTTATATT
1 ATATTATATATTATTTTTTATATT
*
1116964 ATATTATATTTTAT
1 ATATTATATATTAT
1116978 ATAATATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.22
21 2 0.06
22 10 0.31
23 3 0.09
24 10 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
ATATTATATATTATTTTTTATATT
Found at i:1116967 original size:19 final size:19
Alignment explanation
Indices: 1116920--1116990 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 19
1116910 TTAATAATTA
*
1116920 ATATTATATAATT-TTTTAT
1 ATATTATAT-ATTATTTTTT
1116939 ATATTTATATATTATTTTTT
1 ATA-TTATATATTATTTTTT
*
1116959 ATA-T-TATATTATATTTT
1 ATATTATATATTATTTTTT
* *
1116976 ATATAATATTTTATT
1 ATATTATATATTATT
1116991 GTAATTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 15 0.35
18 1 0.02
19 13 0.30
20 14 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTATATATTATTTTTT
Found at i:1116977 original size:12 final size:12
Alignment explanation
Indices: 1116906--1117000 Score: 55
Period size: 12 Copynumber: 8.4 Consensus size: 12
1116896 TAAAATTTAA
1116906 TATATTA-ATAAT
1 TATATTATAT-AT
1116918 TAATATTATATAAT
1 T-ATATTATAT-AT
1116932 T-T-TT-TATA-
1 TATATTATATAT
1116940 TAT-TTATATAT
1 TATATTATATAT
* *
1116951 TATTTTTTATAT
1 TATATTATATAT
*
1116963 TATATTATATTT
1 TATATTATATAT
1116975 TATA-TA-ATAT
1 TATATTATATAT
* *
1116985 TTTATTGTA-AT
1 TATATTATATAT
1116996 TATAT
1 TATAT
1117001 AATGTCTAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
8 1 0.01
9 4 0.06
10 13 0.19
11 14 0.21
12 23 0.34
13 6 0.09
14 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (12 bp):
TATATTATATAT
Found at i:1116984 original size:22 final size:22
Alignment explanation
Indices: 1116881--1117003 Score: 75
Period size: 22 Copynumber: 5.8 Consensus size: 22
1116871 CTGTTTAAAG
*
1116881 TATTATATATTTATATAAAATT-
1 TATTATAT-TTTATATAATATTA
* *
1116903 TAATATA-TTAATAATTAATATTA
1 TATTATATTTTAT-A-TAATATTA
* *
1116926 TATAATTTTTTATAT-AT-TTA
1 TATTATATTTTATATAATATTA
1116946 TA-TATTATTTT-T-T-ATATTA
1 TATTA-TATTTTATATAATATTA
*
1116965 TATTATATTTTATATAATATTT
1 TATTATATTTTATATAATATTA
* *
1116987 TATTGTA-ATTATATAAT
1 TATTATATTTTATATAAT
1117004 GTCTAAAGTT
Statistics
Matches: 79, Mismatches: 12, Indels: 21
0.71 0.11 0.19
Matches are distributed among these distances:
18 3 0.04
19 13 0.16
20 17 0.22
21 13 0.16
22 24 0.30
23 5 0.06
24 4 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (22 bp):
TATTATATTTTATATAATATTA
Found at i:1118802 original size:17 final size:19
Alignment explanation
Indices: 1118780--1118817 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
1118770 AAAATTAAAA
1118780 ATATTTGTA-TCGA-ATTT
1 ATATTTGTATTCGATATTT
1118797 ATATTTGTATTCGATATTT
1 ATATTTGTATTCGATATTT
1118816 AT
1 AT
1118818 TCTCGAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (19 bp):
ATATTTGTATTCGATATTT
Found at i:1122926 original size:15 final size:15
Alignment explanation
Indices: 1122893--1122937 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1122883 AATATTTATA
*
1122893 AAAATTTAAATTAAAT
1 AAAATTAAAATT-AAT
*
1122909 AAAATTATAATTAAT
1 AAAATTAAAATTAAT
*
1122924 AAATTTAAAATTAA
1 AAAATTAAAATTAA
1122938 AATTAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTAAAATTAAT
Found at i:1123222 original size:49 final size:47
Alignment explanation
Indices: 1123141--1123232 Score: 121
Period size: 49 Copynumber: 1.9 Consensus size: 47
1123131 ACACGTAAAA
*
1123141 AGATATATTTTTTAATTAAATCACTATAATAAATTATGAAAAAAAGT
1 AGATATATTTTTAAATTAAATCACTATAATAAATTATGAAAAAAAGT
* * * *
1123188 AGATATGATATTTTAAATTAAATTATTATGATAAATTATGTAAAA
1 AGATAT-AT-TTTTAAATTAAATCACTATAATAAATTATGAAAAA
1123233 TATGTCATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
47 6 0.16
48 2 0.05
49 30 0.79
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (47 bp):
AGATATATTTTTAAATTAAATCACTATAATAAATTATGAAAAAAAGT
Found at i:1123995 original size:10 final size:9
Alignment explanation
Indices: 1123974--1124031 Score: 62
Period size: 10 Copynumber: 5.9 Consensus size: 9
1123964 AACACATAAA
1123974 TTTTTTTCTC
1 TTTTTTT-TC
1123984 TTTTTCTTTC
1 TTTTT-TTTC
1123994 TTTCATTTTTC
1 TTT--TTTTTC
1124005 TTTTTTTTCC
1 TTTTTTTT-C
*
1124015 TTTTCTTTC
1 TTTTTTTTC
1124024 TTTTTTTT
1 TTTTTTTT
1124032 AGCCTTACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
9 13 0.31
10 18 0.43
11 9 0.21
12 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1124004 original size:15 final size:14
Alignment explanation
Indices: 1123982--1124031 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
1123972 AATTTTTTTC
1123982 TCTTTTTCTTTCTT
1 TCTTTTTCTTTCTT
*
1123996 TCATTTTTCTTTTTTT
1 TC-TTTTTC-TTTCTT
*
1124012 TCCTTTTCTTTCTT
1 TCTTTTTCTTTCTT
1124026 T-TTTTT
1 TCTTTTT
1124032 AGCCTTACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 4 0.13
14 8 0.27
15 11 0.37
16 7 0.23
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (14 bp):
TCTTTTTCTTTCTT
Found at i:1124017 original size:21 final size:19
Alignment explanation
Indices: 1123974--1124031 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
1123964 AACACATAAA
1123974 TTTTTTTCTCTTTTTCTTT-C
1 TTTTTTT-TCTTTTT-TTTCC
1123994 TTTCATTTTTCTTTTTTTTCC
1 TTT--TTTTTCTTTTTTTTCC
*
1124015 TTTTCTTTCTTTTTTTT
1 TTTTTTTTCTTTTTTTT
1124032 AGCCTTACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
19 13 0.38
20 6 0.18
21 11 0.32
22 4 0.12
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTTCTTTTTTTTCC
Found at i:1124424 original size:27 final size:24
Alignment explanation
Indices: 1124383--1124446 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 24
1124373 TACATATAAA
1124383 AATATATACATAAAATAAAATAAATTATT
1 AATATATA-A-AAAATAAAAT--ATT-TT
*
1124412 AATATATAAAAAATATAATATTTT
1 AATATATAAAAAATAAAATATTTT
1124436 AA-ATATAAAAA
1 AATATATAAAAA
1124447 TAATAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 9 0.26
24 4 0.12
25 3 0.09
27 9 0.26
28 1 0.03
29 8 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
AATATATAAAAAATAAAATATTTT
Found at i:1124445 original size:23 final size:24
Alignment explanation
Indices: 1124392--1124453 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
1124382 AAATATATAC
1124392 ATAAAATAAAATAAATTATTAATAT
1 ATAAAA-AAAATAAATTATTAATAT
*
1124417 ATAAAAAATATAATATT-TTAA-AT
1 ATAAAAAAAATAA-ATTATTAATAT
*
1124440 ATAAAAATAATAAA
1 ATAAAAAAAATAAA
1124454 AATGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 1 0.03
23 13 0.39
24 10 0.30
25 9 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
ATAAAAAAAATAAATTATTAATAT
Found at i:1124448 original size:22 final size:24
Alignment explanation
Indices: 1124392--1124446 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1124382 AAATATATAC
*
1124392 ATAAAATAAAATAAATTATTAATAT
1 ATAAAA-AATATAAATTATTAATAT
1124417 ATAAAAAATATAATATT-TTAA-AT
1 ATAAAAAATATAA-ATTATTAATAT
1124440 ATAAAAA
1 ATAAAAA
1124447 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 9 0.32
24 10 0.36
25 9 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAAAAATATAAATTATTAATAT
Found at i:1124486 original size:11 final size:10
Alignment explanation
Indices: 1124470--1124509 Score: 53
Period size: 11 Copynumber: 3.7 Consensus size: 10
1124460 AATCCATAAA
1124470 TTTTTTCTCTT
1 TTTTTTCT-TT
1124481 TTTTTTCTTTT
1 TTTTTTC-TTT
1124492 TTTCTTTCTTT
1 TTT-TTTCTTT
1124503 TTTTTTC
1 TTTTTTC
1124510 GATTGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 4 0.15
11 18 0.67
12 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1126437 original size:14 final size:14
Alignment explanation
Indices: 1126420--1126448 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1126410 GAAAAAAATT
1126420 AAAAATAAAAATAA
1 AAAAATAAAAATAA
1126434 AAAAATAAAAATAA
1 AAAAATAAAAATAA
1126448 A
1 A
1126449 TTTAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:1126492 original size:20 final size:20
Alignment explanation
Indices: 1126467--1126524 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1126457 TTATATATAA
1126467 ATTAATTAAAATTATTATTT
1 ATTAATTAAAATTATTATTT
*
1126487 ATTAATTAAAA-TAATATTT
1 ATTAATTAAAATTATTATTT
* *
1126506 -TTATTTAAATTTAATTATT
1 ATTAATTAAAATT-ATTATT
1126525 AAAAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.25
19 8 0.25
20 16 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTAATTAAAATTATTATTT
Found at i:1129732 original size:4 final size:4
Alignment explanation
Indices: 1129723--1129748 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1129713 CGGATTGGGA
1129723 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1129749 TTAACTTTTA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1135477 original size:19 final size:18
Alignment explanation
Indices: 1135453--1135504 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
1135443 TATTAATTTT
*
1135453 AAATATATATTAAAATATA
1 AAATATATAAT-AAATATA
*
1135472 AAATATTTAATAAATATA
1 AAATATATAATAAATATA
*
1135490 AAA-ATATTATAAATA
1 AAATATATAATAAATA
1135505 ATTTTAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 10 0.34
18 10 0.34
19 9 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATATATAATAAATATA
Found at i:1135714 original size:18 final size:17
Alignment explanation
Indices: 1135682--1135715 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1135672 GAATTTTAAT
*
1135682 ATTTTAATTTACTTTTA
1 ATTTTAATCTACTTTTA
1135699 ATTTTAGATCTACTTTT
1 ATTTTA-ATCTACTTTT
1135716 TGATTAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTTAATCTACTTTTA
Found at i:1136807 original size:8 final size:8
Alignment explanation
Indices: 1136796--1136820 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1136786 AAATATTAAT
1136796 ATATTTTA
1 ATATTTTA
1136804 ATATTTTA
1 ATATTTTA
1136812 ATATTTTA
1 ATATTTTA
1136820 A
1 A
1136821 ATAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATATTTTA
Found at i:1137183 original size:27 final size:28
Alignment explanation
Indices: 1137151--1137254 Score: 97
Period size: 28 Copynumber: 3.6 Consensus size: 28
1137141 TGAAATAATA
*
1137151 AAAAATAATATAATATAAATATATTTTT
1 AAAATTAATATAATATAAATATATTTTT
* *
1137179 AAAATTTATATAATATAAATTATTAATATATT
1 AAAATTAATATAATATAAA-TA-T-AT-TTTT
1137211 AAAATTAATATAAATATAAA-ATA-TTTT
1 AAAATTAATAT-AATATAAATATATTTTT
1137238 -AAATATAATTATAATAT
1 AAAAT-TAA-TATAATAT
1137255 GATAAATATA
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
26 4 0.06
27 11 0.17
28 20 0.31
29 3 0.05
30 2 0.03
31 3 0.05
32 13 0.20
33 8 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAATTAATATAATATAAATATATTTTT
Found at i:1137292 original size:23 final size:22
Alignment explanation
Indices: 1137259--1137302 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1137249 TAATATGATA
*
1137259 AATATACAAATATATATAAAATG
1 AATATACAAAT-TATAAAAAATG
*
1137282 AATATATAAATTATAAAAAAT
1 AATATACAAATTATAAAAAAT
1137303 TTCAAAACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
AATATACAAATTATAAAAAATG
Found at i:1137764 original size:17 final size:17
Alignment explanation
Indices: 1137738--1137778 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1137728 TATTTTATGA
1137738 ATATTAAATATGAATAT
1 ATATTAAATATGAATAT
* *
1137755 ATATTTAATATTAATAT
1 ATATTAAATATGAATAT
1137772 AT-TTAAA
1 ATATTAAA
1137779 AAATTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
ATATTAAATATGAATAT
Found at i:1138128 original size:9 final size:8
Alignment explanation
Indices: 1138113--1138137 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1138103 ATTGAATATT
1138113 GAAAAAAA
1 GAAAAAAA
1138121 GAAAAAAA
1 GAAAAAAA
1138129 GAAAAAAA
1 GAAAAAAA
1138137 G
1 G
1138138 GAGAATATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:1141850 original size:35 final size:36
Alignment explanation
Indices: 1141788--1141858 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1141778 AAAAAATAAT
* * * *
1141788 ATTTTATAATTTTAAAATTTATTATTTTTATATATA
1 ATTTAATAAATTTAAAATTTATAATTTTAATATATA
*
1141824 ATTTAATAAATTTAAATTTTA-AATTTTAATATATA
1 ATTTAATAAATTTAAAATTTATAATTTTAATATATA
1141859 TAAAGAAGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 12 0.40
36 18 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
ATTTAATAAATTTAAAATTTATAATTTTAATATATA
Found at i:1142809 original size:2 final size:2
Alignment explanation
Indices: 1142802--1142833 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1142792 TTCCAAATTC
1142802 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
1142834 GAATAATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1143200 original size:7 final size:7
Alignment explanation
Indices: 1143188--1143219 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1143178 TTAATTGATG
1143188 TTTAAAA
1 TTTAAAA
1143195 TTTAAAA
1 TTTAAAA
1143202 TTTAAAA
1 TTTAAAA
*
1143209 TTTAATA
1 TTTAAAA
1143216 TTTA
1 TTTA
1143220 TATATTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
TTTAAAA
Found at i:1145571 original size:22 final size:22
Alignment explanation
Indices: 1145528--1145601 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
1145518 AATTATTGAT
1145528 TAAATATATAAATGATTTATTA
1 TAAATATATAAATGATTTATTA
1145550 TAAATA-AT-AATGATATTAATTA
1 TAAATATATAAATGAT-TT-ATTA
* *
1145572 TAAAATTATTTAAAT-ATTTTTTAA
1 T-AAA-TATATAAATGATTTATT-A
1145596 TAAATA
1 TAAATA
1145602 AAAAATATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
20 6 0.14
21 4 0.09
22 13 0.30
23 8 0.19
24 6 0.14
25 3 0.07
26 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (22 bp):
TAAATATATAAATGATTTATTA
Found at i:1145830 original size:27 final size:28
Alignment explanation
Indices: 1145800--1145871 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
1145790 ATAATACTGA
1145800 AATTTTAATTAATTTTAAAAT-TATTTT
1 AATTTTAATTAATTTTAAAATATATTTT
*
1145827 AATTATT-ATTAA-ATTAAAATATATTTT
1 AATT-TTAATTAATTTTAAAATATATTTT
*
1145854 AA-TTTAAATATATTTTAA
1 AATTTTAATTA-ATTTTAA
1145872 TTTAAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 2 0.05
26 11 0.30
27 18 0.49
28 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AATTTTAATTAATTTTAAAATATATTTT
Found at i:1145862 original size:16 final size:16
Alignment explanation
Indices: 1145838--1145887 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
1145828 ATTATTATTA
*
1145838 AATTAAAATATATTTT
1 AATTTAAATATATTTT
1145854 AATTTAAATATATTTT
1 AATTTAAATATATTTT
1145870 AATTTAAATATATTTT
1 AATTTAAATATATTTT
1145886 AA
1 AA
1145888 ATAATTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTAAATATATTTT
Found at i:1145899 original size:32 final size:32
Alignment explanation
Indices: 1145838--1145900 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1145828 ATTATTATTA
*
1145838 AATTAAAATATATTTTAATTTAAATATATTTT
1 AATTAAAATATATTTTAATATAAATATATTTT
* *
1145870 AATTTAAATATATTTTAA-ATAATTAATATTT
1 AATTAAAATATATTTTAATATAAAT-ATATTT
1145901 GTTGTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
AATTAAAATATATTTTAATATAAATATATTTT
Found at i:1145977 original size:21 final size:22
Alignment explanation
Indices: 1145951--1145993 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1145941 TATGTTATTT
*
1145951 TTATTT-AAAATAAATTAATTA
1 TTATTTAAAAATAAATAAATTA
1145972 TTATTTAAAAATAAATAAATTA
1 TTATTTAAAAATAAATAAATTA
1145994 AATAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATTTAAAAATAAATAAATTA
Found at i:1146570 original size:25 final size:24
Alignment explanation
Indices: 1146538--1146585 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1146528 TAAATAAATT
1146538 TTTAAATTTAAATAA-ATAATTTAA
1 TTTAAA-TTAAATAATATAATTTAA
*
1146562 TTTATAATTAAATAATTTAATTTA
1 TTTA-AATTAAATAATATAATTTA
1146586 TAAATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAAATTAAATAATATAATTTAA
Found at i:1146591 original size:16 final size:19
Alignment explanation
Indices: 1146542--1146595 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1146532 TAAATTTTTA
1146542 AATTTA-AATAAATAATTT
1 AATTTATAATAAATAATTT
1146560 AATTTATAATTAAATAATTT
1 AATTTATAA-TAAATAATTT
1146580 AATTTATAAATAAATA
1 AATTTAT-AATAAATA
1146596 TGTTTGATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.18
19 2 0.06
20 23 0.70
21 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTTATAATAAATAATTT
Found at i:1147126 original size:13 final size:13
Alignment explanation
Indices: 1147082--1147127 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
1147072 TTATATAATT
*
1147082 TAAAATAATTATA
1 TAAAATATTTATA
1147095 TAAATATATTATATA
1 TAAA-ATATT-TATA
*
1147110 TAAAATATTTATT
1 TAAAATATTTATA
1147123 TAAAA
1 TAAAA
1147128 GATGTATCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 12 0.41
14 9 0.31
15 8 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAAATATTTATA
Found at i:1147260 original size:19 final size:19
Alignment explanation
Indices: 1147223--1147294 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
1147213 TTTAATTTTA
* *
1147223 AAATCAAATAAATCAAATT
1 AAATCAATTAAATTAAATT
1147242 AAATCAATTAAATTTAATTAATT
1 AAATCAATTAAA-TT-A--AATT
* * *
1147265 TAATCAATTAAATTGATTT
1 AAATCAATTAAATTAAATT
*
1147284 AAATCGATTAA
1 AAATCAATTAA
1147295 TTTCATCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 23 0.55
20 1 0.02
21 1 0.02
22 2 0.05
23 15 0.36
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATCAATTAAATTAAATT
Found at i:1147285 original size:23 final size:23
Alignment explanation
Indices: 1147238--1147285 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1147228 AAATAAATCA
*
1147238 AATTAAATCAATTAAATTTAATT
1 AATTAAATCAATTAAATTGAATT
* *
1147261 AATTTAATCAATTAAATTGATTT
1 AATTAAATCAATTAAATTGAATT
1147284 AA
1 AA
1147286 ATCGATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
AATTAAATCAATTAAATTGAATT
Found at i:1149366 original size:30 final size:30
Alignment explanation
Indices: 1149332--1149477 Score: 229
Period size: 30 Copynumber: 4.9 Consensus size: 30
1149322 CTAACGATGT
*
1149332 CAAAGAAGTGAAGGAAAATGGTGTTGCAGA
1 CAAAGATGTGAAGGAAAATGGTGTTGCAGA
*
1149362 CAAAGATGTGAAAGAAAATGGTGTTGCAGA
1 CAAAGATGTGAAGGAAAATGGTGTTGCAGA
* *
1149392 CAGAGATGTGAAGGACAATGGTGTTGCAGA
1 CAAAGATGTGAAGGAAAATGGTGTTGCAGA
* *
1149422 CAAAGATGTGAAAGAAAATGGTGTTGCTGA
1 CAAAGATGTGAAGGAAAATGGTGTTGCAGA
*
1149452 CAAAAATGTGAAGGAAAATGGTGTTG
1 CAAAGATGTGAAGGAAAATGGTGTTG
1149478 ATGTGAAAGA
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 105 1.00
ACGTcount: A:0.40, C:0.07, G:0.32, T:0.21
Consensus pattern (30 bp):
CAAAGATGTGAAGGAAAATGGTGTTGCAGA
Found at i:1149423 original size:15 final size:15
Alignment explanation
Indices: 1149348--1149424 Score: 52
Period size: 15 Copynumber: 5.1 Consensus size: 15
1149338 AGTGAAGGAA
1149348 AATGGTGTTGCAGAC
1 AATGGTGTTGCAGAC
* * * *
1149363 AAAGATG-TGAAAGAA
1 AATGGTGTTG-CAGAC
1149378 AATGGTGTTGCAGAC
1 AATGGTGTTGCAGAC
* *
1149393 AGA-GATG-TGAAGGAC
1 A-ATGGTGTTGCA-GAC
1149408 AATGGTGTTGCAGAC
1 AATGGTGTTGCAGAC
1149423 AA
1 AA
1149425 AGATGTGAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 12
0.65 0.18 0.18
Matches are distributed among these distances:
14 6 0.14
15 32 0.73
16 6 0.14
ACGTcount: A:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (15 bp):
AATGGTGTTGCAGAC
Found at i:1149483 original size:21 final size:21
Alignment explanation
Indices: 1149457--1149496 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1149447 GCTGACAAAA
*
1149457 ATGTGAAGGAAAATGGTGTTG
1 ATGTGAAAGAAAATGGTGTTG
1149478 ATGTGAAAGAAAATGGTGT
1 ATGTGAAAGAAAATGGTGT
1149497 CAGCCATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.28
Consensus pattern (21 bp):
ATGTGAAAGAAAATGGTGTTG
Found at i:1150986 original size:13 final size:12
Alignment explanation
Indices: 1150968--1151030 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 12
1150958 TCATACATAT
1150968 AAAAATATAATA
1 AAAAATATAATA
1150980 CAAAAATATAAT-
1 -AAAAATATAATA
*
1150992 TAAAATATAATA
1 AAAAATATAATA
1151004 TAAAAATAACATAATA
1 -AAAAAT---ATAATA
1151020 AAAATATATAA
1 AAAA-ATATAA
1151031 ATATAATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
11 10 0.24
13 20 0.48
15 4 0.10
16 8 0.19
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAAATATAATA
Done.