Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 74 of 129
Found at i:11738906 original size:95 final size:94
Alignment explanation
Indices: 11738739--11738911 Score: 233
Period size: 96 Copynumber: 1.8 Consensus size: 94
11738729 TGAAAGAATT
* * * *
11738739 TTTATAAAAAATAATTTTTAAATCCTACCGAACTATTAAAAGATTTAAACTTTTAAGTTAAGTCT
1 TTTATAAAAAATAATTTTTAAATCCTACCAAACTATTAAAAGATTTAAACTCTCAAGTTAAATCT
11738804 TACCAAACTATTGGAGAACTTAATAAATC
66 TACCAAACTATTGGAGAACTTAATAAATC
* * * *
11738833 TTTATAAAAAATTATTTTTTTCAATCCTACTAAACTATTGAAAA-ATTTAAA-TCTCGAGTTAAA
1 TTTATAAAAAA-TA-ATTTTTAAATCCTACCAAACTATT-AAAAGATTTAAACTCTCAAGTTAAA
11738896 TCTTACCAAACTATTG
63 TCTTACCAAACTATTG
11738912 AAAGATTTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
94 11 0.16
95 26 0.38
96 27 0.40
97 4 0.06
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (94 bp):
TTTATAAAAAATAATTTTTAAATCCTACCAAACTATTAAAAGATTTAAACTCTCAAGTTAAATCT
TACCAAACTATTGGAGAACTTAATAAATC
Found at i:11741788 original size:19 final size:19
Alignment explanation
Indices: 11741764--11741849 Score: 77
Period size: 19 Copynumber: 4.6 Consensus size: 19
11741754 ATCCAACACT
*
11741764 TTAAACCCTAAGTCAAACA
1 TTAAACCCTAAGTCAAACC
* * *
11741783 TTAAA-CTTTAGCCAAACC
1 TTAAACCCTAAGTCAAACC
*
11741801 TTAAACCCTAGGTCAAATCC
1 TTAAACCCTAAGTCAAA-CC
* **
11741821 -TAAACCATGTGTCAAACC
1 TTAAACCCTAAGTCAAACC
11741839 TTAAACCCTAA
1 TTAAACCCTAA
11741850 CATTGGTTAA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
18 16 0.32
19 32 0.64
20 2 0.04
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (19 bp):
TTAAACCCTAAGTCAAACC
Found at i:11741825 original size:37 final size:38
Alignment explanation
Indices: 11741764--11741849 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 38
11741754 ATCCAACACT
* *
11741764 TTAAACCCTAAGTCAAACATTAAA-C-TTTAGCCAAACC
1 TTAAACCCTAAGTCAAACACTAAACCATGT-GCCAAACC
* *
11741801 TTAAACCCTAGGTCAAATC-CTAAACCATGTGTCAAACC
1 TTAAACCCTAAGTCAAA-CACTAAACCATGTGCCAAACC
11741839 TTAAACCCTAA
1 TTAAACCCTAA
11741850 CATTGGTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
37 20 0.49
38 19 0.46
39 2 0.05
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (38 bp):
TTAAACCCTAAGTCAAACACTAAACCATGTGCCAAACC
Found at i:11741942 original size:20 final size:18
Alignment explanation
Indices: 11741891--11741942 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
11741881 CCTAAACCTT
*
11741891 AGTCAAATCCTAAAGTAAA
1 AGTCAAATCC-AAACTAAA
11741910 AGTCAAA-CTCAAACCTAAA
1 AGTCAAATC-CAAA-CTAAA
11741929 AGGTCAAATCCAAA
1 A-GTCAAATCCAAA
11741943 AATGAACCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.14
19 13 0.46
20 10 0.36
21 1 0.04
ACGTcount: A:0.52, C:0.21, G:0.10, T:0.17
Consensus pattern (18 bp):
AGTCAAATCCAAACTAAA
Found at i:11743752 original size:20 final size:21
Alignment explanation
Indices: 11743715--11743753 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
11743705 AAAAAAGAAA
11743715 AAGGAAGAAGAGAAATTTGAT
1 AAGGAAGAAGAGAAATTTGAT
11743736 AAGGAA-AAGA-AAGATTTG
1 AAGGAAGAAGAGAA-ATTTG
11743754 GGGTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.28, T:0.18
Consensus pattern (21 bp):
AAGGAAGAAGAGAAATTTGAT
Found at i:11744128 original size:60 final size:55
Alignment explanation
Indices: 11744063--11744174 Score: 127
Period size: 56 Copynumber: 1.9 Consensus size: 55
11744053 TTTTCTTTTC
*
11744063 TTAAAAATATTTTTAAATAAATTCATAAAT-CTTACTAAACTATTAGAAGAATTTCATGGG
1 TTAAAAAT-TATTT-AA-AAATT-ATAAATGC-TACTAAACTATTAG-AGAATTTCATGGG
* * *
11744123 TTAAAAATTATTTCAAAGTTATGAATGCTACTAAACTATTAGAGAATTTCAT
1 TTAAAAATTATTTAAAAATTATAAATGCTACTAAACTATTAGAGAATTTCAT
11744175 AACAAAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
55 10 0.21
56 19 0.40
57 5 0.11
58 1 0.02
59 4 0.09
60 8 0.17
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (55 bp):
TTAAAAATTATTTAAAAATTATAAATGCTACTAAACTATTAGAGAATTTCATGGG
Found at i:11744465 original size:96 final size:93
Alignment explanation
Indices: 11744199--11744465 Score: 247
Period size: 94 Copynumber: 2.8 Consensus size: 93
11744189 AAAAAATAAA
* * * * * *
11744199 ATTTTCTCAATCCTACAAGACTATTGGAGGATTCAAATCTCTAAATTAAGTCTTACTAAACTATT
1 ATTTTTTCAATCCTACAA-ACTATTGAAGAATTTAAATCTC-AAGTTAAGTCTTACCAAACTATT
* *
11744264 -AAGGGACTTAA-AGAATTTTTATAAAAAAT
64 GAA-AGACTTAATAGAATCTTTATAAAAAAT
* * * * *
11744293 AATTTTTAAATCCTACCAAACTATT-AAAAGATTTAAACTTTTAAGTTAAGTCTTACCAAACTAT
1 ATTTTTTCAATCCTA-CAAACTATTGAAGA-ATTTAAA-TCTCAAGTTAAGTCTTACCAAACTAT
*
11744357 TG-GAGAACTTAATA-AATCTTTATAAAAAATT
63 TGAAAG-ACTTAATAGAATCTTTATAAAAAA-T
* *
11744388 ATTTTTTTTCAATCCTACTAAACTATTGAAGAATTTAAATCTCGAGTTAAATCTTACCAAACTAT
1 A--TTTTTTCAATCCTAC-AAACTATTGAAGAATTTAAATCTCAAGTTAAGTCTTACCAAACTAT
*
11744453 TGAAAGATTTAAT
63 TGAAAGACTTAAT
11744466 GACTTTTTCC
Statistics
Matches: 138, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
93 2 0.01
94 65 0.47
95 8 0.06
96 31 0.22
97 29 0.21
98 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.37
Consensus pattern (93 bp):
ATTTTTTCAATCCTACAAACTATTGAAGAATTTAAATCTCAAGTTAAGTCTTACCAAACTATTGA
AAGACTTAATAGAATCTTTATAAAAAAT
Found at i:11747335 original size:19 final size:19
Alignment explanation
Indices: 11747311--11747396 Score: 77
Period size: 19 Copynumber: 4.6 Consensus size: 19
11747301 ATCCAACACT
*
11747311 TTAAACCCTAAGTCAAACA
1 TTAAACCCTAAGTCAAACC
* * *
11747330 TTAAA-CTTTAGCCAAACC
1 TTAAACCCTAAGTCAAACC
*
11747348 TTAAACCCTAGGTCAAATCC
1 TTAAACCCTAAGTCAAA-CC
* **
11747368 -TAAACCATGTGTCAAACC
1 TTAAACCCTAAGTCAAACC
11747386 TTAAACCCTAA
1 TTAAACCCTAA
11747397 CATTAGGTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
18 16 0.32
19 32 0.64
20 2 0.04
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (19 bp):
TTAAACCCTAAGTCAAACC
Found at i:11747372 original size:37 final size:38
Alignment explanation
Indices: 11747311--11747396 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 38
11747301 ATCCAACACT
* *
11747311 TTAAACCCTAAGTCAAACATTAAA-C-TTTAGCCAAACC
1 TTAAACCCTAAGTCAAACACTAAACCATGT-GCCAAACC
* *
11747348 TTAAACCCTAGGTCAAATC-CTAAACCATGTGTCAAACC
1 TTAAACCCTAAGTCAAA-CACTAAACCATGTGCCAAACC
11747386 TTAAACCCTAA
1 TTAAACCCTAA
11747397 CATTAGGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
37 20 0.49
38 19 0.46
39 2 0.05
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (38 bp):
TTAAACCCTAAGTCAAACACTAAACCATGTGCCAAACC
Found at i:11747490 original size:20 final size:18
Alignment explanation
Indices: 11747439--11747490 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
11747429 CCTAAACCTT
*
11747439 AGTCAAATCCTAAAGCAAA
1 AGTCAAATCC-AAACCAAA
11747458 AGTCAAA-CTCAAACCTAAA
1 AGTCAAATC-CAAACC-AAA
11747477 AGGTCAAATCCAAA
1 A-GTCAAATCCAAA
11747491 AATGAACCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 12 0.43
20 10 0.36
21 1 0.04
ACGTcount: A:0.52, C:0.23, G:0.10, T:0.15
Consensus pattern (18 bp):
AGTCAAATCCAAACCAAA
Found at i:11748306 original size:17 final size:17
Alignment explanation
Indices: 11748284--11748322 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
11748274 TGTAAAATAT
11748284 TTTTTGAGTTTTTTTAG
1 TTTTTGAGTTTTTTTAG
** *
11748301 TTTTTGCTTTTTTTTTG
1 TTTTTGAGTTTTTTTAG
11748318 TTTTT
1 TTTTT
11748323 CATTTTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.03, G:0.13, T:0.79
Consensus pattern (17 bp):
TTTTTGAGTTTTTTTAG
Found at i:11748328 original size:16 final size:17
Alignment explanation
Indices: 11748292--11748330 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
11748282 ATTTTTTGAG
*
11748292 TTTTTTTAGTTTTTGCT
1 TTTTTTTAGTTTTTGCA
*
11748309 TTTTTTTTGTTTTT-CA
1 TTTTTTTAGTTTTTGCA
11748325 TTTTTT
1 TTTTTT
11748331 GAAAACAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.05, C:0.05, G:0.08, T:0.82
Consensus pattern (17 bp):
TTTTTTTAGTTTTTGCA
Found at i:11750785 original size:20 final size:20
Alignment explanation
Indices: 11750749--11750786 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11750739 AAAACTTTTT
11750749 TTTAATATTTTAATAATTAC
1 TTTAATATTTTAATAATTAC
11750769 TTTAA-ATTTTAATTAATT
1 TTTAATATTTTAA-TAATT
11750787 TATAATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATATTTTAATAATTAC
Found at i:11750842 original size:15 final size:16
Alignment explanation
Indices: 11750815--11750844 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11750805 AATATCATAA
11750815 AAATTTAAATTTTTTT
1 AAATTTAAATTTTTTT
11750831 AAATTT-AATTTTTT
1 AAATTTAAATTTTTT
11750845 ATTCATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AAATTTAAATTTTTTT
Found at i:11751151 original size:23 final size:22
Alignment explanation
Indices: 11751111--11751196 Score: 120
Period size: 22 Copynumber: 3.8 Consensus size: 22
11751101 TCAAATCTGA
11751111 TTTAAAATTAATAAAATATTATTTT
1 TTTAAAA-T-ATAAAATATTA-TTT
*
11751136 TTTAAAATATAAAATATTACTT
1 TTTAAAATATAAAATATTATTT
11751158 TTTAAAATATAAAATATTATTT
1 TTTAAAATATAAAATATTATTT
11751180 TTT-AAATATAAATATAT
1 TTTAAAATATAAA-ATAT
11751197 AATTATATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
21 9 0.16
22 30 0.52
23 11 0.19
24 1 0.02
25 7 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAAAATATAAAATATTATTT
Found at i:11751211 original size:45 final size:45
Alignment explanation
Indices: 11751121--11751217 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
11751111 TTTAAAATTA
* *
11751121 ATAAAATATTATTTTTTTAAAATATAAAATATTACTTTTTAAAAT
1 ATAAAATATTATTTTTTTAAAATATAAAATATTAATTTATAAAAT
11751166 ATAAAATATTA-TTTTTT-AAATAT-AAATATATAATTATATATAAAT
1 ATAAAATATTATTTTTTTAAAATATAAAATAT-TAATT-TATA-AAAT
*
11751211 AAAAAAT
1 ATAAAAT
11751218 TAAAAAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
42 6 0.13
43 10 0.22
44 9 0.20
45 21 0.46
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (45 bp):
ATAAAATATTATTTTTTTAAAATATAAAATATTAATTTATAAAAT
Found at i:11751213 original size:43 final size:44
Alignment explanation
Indices: 11751120--11751219 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 44
11751110 ATTTAAAATT
* *
11751120 AATAAAATATTATTTTTTTAAAATATAAAATATTACTTTTTAAA
1 AATAAAATATTATTTTTTTAAAATATAAAATATTAATTTATAAA
*
11751164 ATATAAAATATTA-TTTTTT-AAATAT-AAATATATAATTATATATA
1 A-ATAAAATATTATTTTTTTAAAATATAAAATAT-TAATT-TATAAA
*
11751208 AATAAAAAATTA
1 AATAAAATATTA
11751220 AAAAATAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
42 6 0.12
43 20 0.41
44 12 0.24
45 11 0.22
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (44 bp):
AATAAAATATTATTTTTTTAAAATATAAAATATTAATTTATAAA
Found at i:11751218 original size:18 final size:18
Alignment explanation
Indices: 11751185--11751219 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11751175 TATTTTTTAA
* *
11751185 ATATAAATATATAATTAT
1 ATATAAATAAAAAATTAT
11751203 ATATAAATAAAAAATTA
1 ATATAAATAAAAAATTA
11751220 AAAAATAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATAAATAAAAAATTAT
Found at i:11751695 original size:16 final size:16
Alignment explanation
Indices: 11751655--11751697 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
11751645 TTTAATTTTT
* *
11751655 TATTTATATATTTATA
1 TATTTATATTTTTAAA
* *
11751671 TAATGATATTTTTAAA
1 TATTTATATTTTTAAA
11751687 TATTTATATTT
1 TATTTATATTT
11751698 AAAAAATAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTTATATTTTTAAA
Found at i:11751715 original size:21 final size:22
Alignment explanation
Indices: 11751685--11751736 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
11751675 GATATTTTTA
11751685 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
11751705 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
*
11751727 ATTATTTTAT
1 AATATTTTAT
11751737 TAATTTCAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 19 0.66
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:11754070 original size:16 final size:16
Alignment explanation
Indices: 11754051--11754081 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11754041 TTTTTGTAGG
*
11754051 TTATTTTTTTAATTGA
1 TTATTGTTTTAATTGA
11754067 TTATTGTTTTAATTG
1 TTATTGTTTTAATTG
11754082 CATTTTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (16 bp):
TTATTGTTTTAATTGA
Found at i:11754326 original size:13 final size:13
Alignment explanation
Indices: 11754304--11754337 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
11754294 TAAGTAAATA
11754304 AAAAAATTTTTTG
1 AAAAAATTTTTTG
* *
11754317 AAAAATTTTTTTT
1 AAAAAATTTTTTG
11754330 AAAAAATT
1 AAAAAATT
11754338 AAAAAATACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AAAAAATTTTTTG
Found at i:11755886 original size:15 final size:15
Alignment explanation
Indices: 11755842--11755887 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
11755832 TTTTACTATT
*
11755842 ATAAATAAATATATA
1 ATAAATAAATAAATA
* **
11755857 ATAAATGAACCAATA
1 ATAAATAAATAAATA
11755872 ATAAATAAATAAATA
1 ATAAATAAATAAATA
11755887 A
1 A
11755888 ATGAGATTGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (15 bp):
ATAAATAAATAAATA
Found at i:11759060 original size:16 final size:18
Alignment explanation
Indices: 11759041--11759075 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
11759031 AAAAAAATAT
11759041 ATTTTATT-TA-ATTTAA
1 ATTTTATTATATATTTAA
11759057 ATTTTATTATATATTTAA
1 ATTTTATTATATATTTAA
11759075 A
1 A
11759076 AATATATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTATTATATATTTAA
Found at i:11760141 original size:22 final size:23
Alignment explanation
Indices: 11760108--11760152 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
11760098 TTTTTCTAAG
11760108 ATATCTTAAAATTATTT-TTTTTA
1 ATATCTTAAAATT-TTTATTTTTA
11760131 ATAT-TTAAAATTTTTATTTTTA
1 ATATCTTAAAATTTTTATTTTTA
11760153 TGATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.14
22 14 0.67
23 4 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATCTTAAAATTTTTATTTTTA
Found at i:11760233 original size:15 final size:15
Alignment explanation
Indices: 11760204--11760241 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
11760194 ATTTTATAAA
*
11760204 AAAATTTAA-ATATT
1 AAAATTAAATATATT
*
11760218 AATATTAAATATATT
1 AAAATTAAATATATT
11760233 AAAATTAAA
1 AAAATTAAA
11760242 AATTTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTAAATATATT
Found at i:11760252 original size:9 final size:11
Alignment explanation
Indices: 11760238--11760266 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
11760228 ATATTAAAAT
11760238 TAAAAATTTT-
1 TAAAAATTTTA
11760248 TAAAAATTTTA
1 TAAAAATTTTA
11760259 TAAAAATT
1 TAAAAATT
11760267 AATACATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TAAAAATTTTA
Found at i:11760644 original size:2 final size:2
Alignment explanation
Indices: 11760637--11760663 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11760627 GTGTTTGCAA
11760637 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
11760664 AGATACCCTT
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:11761007 original size:10 final size:9
Alignment explanation
Indices: 11760966--11761039 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 9
11760956 ATATTAATAT
11760966 AATTATTAA
1 AATTATTAA
11760975 AA-TATTTAA
1 AATTA-TTAA
11760984 AATTATT--
1 AATTATTAA
*
11760991 TATTATTAA
1 AATTATTAA
*
11761000 AATATATTGA
1 AAT-TATTAA
*
11761010 GATTATT--
1 AATTATTAA
*
11761017 TATTATTAA
1 AATTATTAA
11761026 AATTATTAA
1 AATTATTAA
*
11761035 TATTA
1 AATTA
11761040 AAAAGGAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
7 12 0.24
8 2 0.04
9 28 0.55
10 9 0.18
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (9 bp):
AATTATTAA
Found at i:11761021 original size:26 final size:26
Alignment explanation
Indices: 11760967--11761039 Score: 105
Period size: 25 Copynumber: 2.9 Consensus size: 26
11760957 TATTAATATA
11760967 ATTATTAAAATAT-TTAAAATTATTT
1 ATTATTAAAATATATTAAAATTATTT
* *
11760992 ATTATTAAAATATATTGAGATTATTT
1 ATTATTAAAATATATTAAAATTATTT
*
11761018 ATTATTAAAAT-TATTAATATTA
1 ATTATTAAAATATATTAAAATTA
11761040 AAAAGGAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 22 0.51
26 21 0.49
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (26 bp):
ATTATTAAAATATATTAAAATTATTT
Found at i:11761090 original size:19 final size:18
Alignment explanation
Indices: 11761013--11761100 Score: 58
Period size: 19 Copynumber: 4.9 Consensus size: 18
11761003 ATATTGAGAT
*
11761013 TATTTATTATTAAAAT--
1 TATTTAATATTAAAATAA
*
11761029 TA-TTAATATTAAAA-AG
1 TATTTAATATTAAAATAA
* * *
11761045 GAATTATATTTTAATAATAA
1 TATTTA-ATATTAA-AATAA
*
11761065 TATTTAATATTAAAATAT
1 TATTTAATATTAAAATAA
*
11761083 TATGTTAATATAAAAATA
1 TAT-TTAATATTAAAATA
11761101 CTTAAAATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
15 11 0.20
16 3 0.05
17 3 0.05
18 13 0.23
19 21 0.38
20 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TATTTAATATTAAAATAA
Found at i:11761186 original size:18 final size:17
Alignment explanation
Indices: 11761128--11761440 Score: 113
Period size: 18 Copynumber: 18.7 Consensus size: 17
11761118 TATTATTCTT
11761128 TATAT-TATT-TATTAA
1 TATATATATTATATTAA
* *
11761143 TATAT-TATAATATTATT
1 TATATATATTATATTA-A
11761160 TATTAATATATTATATTAA
1 TA-T-ATATATTATATTAA
11761179 TAGTATATTATT-TATTAA
1 TA-TATA-TATTATATTAA
*
11761197 TATAT-TATTATAAT-A
1 TATATATATTATATTAA
* *
11761212 TTTAT-TAATTAAATT-A
1 TATATAT-ATTATATTAA
*
11761228 -ATA-ATATT-TATTAT
1 TATATATATTATATTAA
11761242 TATAT-TATT-TATTAA
1 TATATATATTATATTAA
*
11761257 TATAATATTGTTATTTATTAA
1 TAT-ATA-TATTA--TATTAA
11761278 TAGTATATTATT-TATTAA
1 TA-TATA-TATTATATTAA
* *
11761296 -A-AT-TAATATATTAG
1 TATATATATTATATTAA
*
11761310 TATA-ATATT-TATTTA
1 TATATATATTATATTAA
11761325 TA-ATAATATT-TATTAA
1 TATAT-ATATTATATTAA
11761341 TATATATAATT-TATTAA
1 TATATAT-ATTATATTAA
*
11761358 TATAATATGATT-TATGAA
1 TAT-ATAT-ATTATATTAA
* *
11761376 TGTATTATAATGT-TATTTA
1 TATA-TAT-AT-TATATTAA
11761395 T-TAATATATTATATTAA
1 TAT-ATATATTATATTAA
*
11761412 TAGTATATTATT-TATTTA
1 TA-TATA-TATTATATTAA
11761430 TATA-ATATTAT
1 TATATATATTAT
11761441 TTATAAATAA
Statistics
Matches: 233, Mismatches: 29, Indels: 71
0.70 0.09 0.21
Matches are distributed among these distances:
13 6 0.03
14 9 0.04
15 49 0.21
16 38 0.16
17 31 0.13
18 54 0.23
19 21 0.09
20 9 0.04
21 15 0.06
22 1 0.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TATATATATTATATTAA
Found at i:11761196 original size:54 final size:54
Alignment explanation
Indices: 11761128--11761361 Score: 202
Period size: 54 Copynumber: 4.4 Consensus size: 54
11761118 TATTATTCTT
11761128 TATATTATTTATTAATATATTATAATATTATTTATTAAT-ATATTATATTAATA
1 TATATTATTTATTAATATATTATAATATTATTTATTAATAATATTATATTAATA
* * * *
11761181 GTATATTATTTATTAATATATTATTATAATATTTATTAATTAAATTAATAATATTTATTA
1 -TATATTATTTATTAATATATTATAATATTATTTATTAA-T-AA-T-ATTATA-TTAATA
* * *
11761241 TTATATTATTTATTAATATA--ATATTGTTATTTATTAATAGTATATTAT-TTATTA
1 -TATATTATTTATTAATATATTATAATATTATTTATTAATA--ATATTATATTAATA
* * *
11761295 -AAATTA-ATA-T-AT-TAGTATAATATTTATTTA-TAATAATATT-TATTAATA
1 TATATTATTTATTAATATATTATAATA-TTATTTATTAATAATATTATATTAATA
*
11761343 TATATAATTTATTAATATA
1 TATATTATTTATTAATATA
11761362 ATATGATTTA
Statistics
Matches: 145, Mismatches: 18, Indels: 35
0.73 0.09 0.18
Matches are distributed among these distances:
47 1 0.01
48 12 0.08
49 6 0.04
50 12 0.08
51 10 0.07
52 7 0.05
53 2 0.01
54 42 0.29
55 1 0.01
56 5 0.03
57 3 0.02
58 15 0.10
59 5 0.03
60 24 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (54 bp):
TATATTATTTATTAATATATTATAATATTATTTATTAATAATATTATATTAATA
Found at i:11761246 original size:99 final size:101
Alignment explanation
Indices: 11761133--11761418 Score: 270
Period size: 99 Copynumber: 2.8 Consensus size: 101
11761123 TTCTTTATAT
11761133 TATTTATTAATATATTATAATATTATTTATTAATATATTATATTAATAGTATATTATTTATTAAT
1 TATTTATTAATATATTATAATATTATTTATTAATATATTATATTAATAGTATATTATTTATTAAT
* *
11761198 ATATTATTATAATA-TTTATTAATTAAAT-TAATAA
66 ATATTATTATAATAGTATAATAATTAAATATAATAA
* * * *
11761232 TATTTATTATTATATTAT-TTATTA-ATA-TAATATTGTTATTTATTAATAGTATATTATTTATT
1 TATTTATTAATATATTATAATATTATTTATTAATA-TATTA--TATTAATAGTATATTATTTATT
* * * **
11761294 AA-A-ATTAATATATTAGTATAATATTTATTTATAATAA
63 AATATATTATTATAATAGTATAATAATTAAATATAATAA
* * *
11761331 TATTTATTAATATA-TATAAT-TTATTAATATAATATGATTTATGAATGTATTA-TAATGTTATT
1 TATTTATTAATATATTATAATATTATTTAT-TAATAT-A-TTAT--AT-TAATAGT-ATATTATT
11761393 TATTAATATATTA-TATTAATAGTATA
59 TATTAATATATTATTA-TAATAGTATA
11761419 TTATTTATTT
Statistics
Matches: 150, Mismatches: 19, Indels: 30
0.75 0.10 0.15
Matches are distributed among these distances:
96 5 0.03
97 16 0.11
98 21 0.14
99 62 0.41
100 2 0.01
101 5 0.03
102 6 0.04
103 17 0.11
104 3 0.02
105 13 0.09
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (101 bp):
TATTTATTAATATATTATAATATTATTTATTAATATATTATATTAATAGTATATTATTTATTAAT
ATATTATTATAATAGTATAATAATTAAATATAATAA
Found at i:11761318 original size:29 final size:28
Alignment explanation
Indices: 11761278--11761365 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 28
11761268 TATTTATTAA
*
11761278 TAGTATATTATTTATTAAAATTAATATAT
1 TAGTATAATATTTATTAAAA-TAATATAT
*
11761307 TAGTATAATATTTATTTATAATAATATTTAT
1 TAGTATAATATTTA-TTAAAATAATA--TAT
* *
11761338 TAATATATATAATTTATTAATATAATAT
1 TAGTATA-AT-ATTTATTAAAATAATAT
11761366 GATTTATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
29 18 0.37
30 6 0.12
31 9 0.18
32 11 0.22
33 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
TAGTATAATATTTATTAAAATAATATAT
Found at i:11761335 original size:45 final size:46
Alignment explanation
Indices: 11761192--11761365 Score: 136
Period size: 52 Copynumber: 3.5 Consensus size: 46
11761182 TATATTATTT
* *
11761192 ATTAATATATTATTATAATATTTATTAATTAAATTAATAATATTTATTATTAT
1 ATTAATATATTAATATAATATTTA-T--TT--ATTAATAATATTTATTA--AA
*
11761245 ATT-ATTTATTAATATAATATTGTTATTTATTAATAGTATATTATTTATTAAA
1 ATTAATATATTAATATAATA-T-TTATTTATT-A-A-TA-A-TATTTATTAAA
*
11761297 ATTAATATATTAGTATAATATTTATTTA-TAATAATATTTATTAATA
1 ATTAATATATTAATATAATATTTATTTATTAATAATATTTATTAA-A
*
11761343 TATATAATTTATTAATATAATAT
1 -AT-TAATATATTAATATAATAT
11761366 GATTTATGAA
Statistics
Matches: 103, Mismatches: 7, Indels: 27
0.75 0.05 0.20
Matches are distributed among these distances:
45 10 0.10
46 2 0.02
47 4 0.04
48 18 0.17
49 4 0.04
50 2 0.02
51 10 0.10
52 21 0.20
53 20 0.19
54 12 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (46 bp):
ATTAATATATTAATATAATATTTATTTATTAATAATATTTATTAAA
Found at i:11762233 original size:17 final size:18
Alignment explanation
Indices: 11762192--11762234 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
11762182 ATTATTAATT
* *
11762192 ATTAATTAATAAATTTTG
1 ATTAATTAATAAATATTA
11762210 ATT-ATTAAT-AATATTA
1 ATTAATTAATAAATATTA
11762226 ATTAATTAA
1 ATTAATTAA
11762235 AACAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 8 0.36
17 11 0.50
18 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATTAATTAATAAATATTA
Found at i:11765897 original size:88 final size:88
Alignment explanation
Indices: 11765766--11765951 Score: 286
Period size: 89 Copynumber: 2.1 Consensus size: 88
11765756 AAATTTAATT
*
11765766 TTATGAATTAAAAATATATTTTTTATTTAAAAAAAATCTCTTTATAATCTTATT-TTTTAAAATA
1 TTAT-AATTAAAAATATATTTTTTATTTAAAAAAAATCTCTTTAAAATCTTATTATTTTAAAATA
*
11765830 TAAATTAATCATAATATAACATAA
65 TAAATTAATCATAATATAAAATAA
* *
11765854 TTATAATTAAAAATA-ATTCTTTTTATTTTAAAAAAATTTCTTTAAAATCTTATTATTTTAAAAT
1 TTATAATTAAAAATATA-T-TTTTTATTTAAAAAAAATCTCTTTAAAATCTTATTATTTTAAAAT
11765918 ATAAATTAATCATAATATAAAATAA
64 ATAAATTAATCATAATATAAAATAA
*
11765943 TTATCATTA
1 TTATAATTA
11765952 TATCTTTTAT
Statistics
Matches: 90, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
86 1 0.01
87 12 0.13
88 36 0.40
89 41 0.46
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (88 bp):
TTATAATTAAAAATATATTTTTTATTTAAAAAAAATCTCTTTAAAATCTTATTATTTTAAAATAT
AAATTAATCATAATATAAAATAA
Found at i:11767553 original size:2 final size:2
Alignment explanation
Indices: 11767548--11767597 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
11767538 ACAAAAAAAG
* *
11767548 GA GA GA GA GA GA -A G- GA GA -A GA AA GA GG GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
11767587 GA GA GA GA GA G
1 GA GA GA GA GA G
11767598 GGGGGAACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11768128 original size:12 final size:12
Alignment explanation
Indices: 11768107--11768151 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
11768097 ACGGGAACGG
11768107 GAACGAGATAGA
1 GAACGAGATAGA
* *
11768119 GAGCGGGATAGA
1 GAACGAGATAGA
11768131 GAACGAGATAGA
1 GAACGAGATAGA
*
11768143 GAAAGAGAT
1 GAACGAGAT
11768152 CGCTTGAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.47, C:0.07, G:0.38, T:0.09
Consensus pattern (12 bp):
GAACGAGATAGA
Found at i:11776235 original size:17 final size:19
Alignment explanation
Indices: 11776210--11776244 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
11776200 AAAATTTAAT
11776210 TTTTATAAAAATA-ATTTA
1 TTTTATAAAAATATATTTA
11776228 TTTT-TAAAAATATATTT
1 TTTTATAAAAATATATTT
11776245 TAATATGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTATAAAAATATATTTA
Found at i:11776246 original size:19 final size:19
Alignment explanation
Indices: 11776203--11776246 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
11776193 GAGATTCAAA
*
11776203 ATTTAATTTTTATAAAAAT
1 ATTTTATTTTTATAAAAAT
*
11776222 AATTTATTTTTA-AAAATAT
1 ATTTTATTTTTATAAAA-AT
11776241 ATTTTA
1 ATTTTA
11776247 ATATGTTGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTATTTTTATAAAAAT
Found at i:11776484 original size:16 final size:16
Alignment explanation
Indices: 11776463--11776497 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11776453 ATAATGATTT
* *
11776463 TTTTTATTTTAAAATA
1 TTTTTATATAAAAATA
11776479 TTTTTATATAAAAATA
1 TTTTTATATAAAAATA
11776495 TTT
1 TTT
11776498 ATAAATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTATATAAAAATA
Found at i:11776514 original size:21 final size:21
Alignment explanation
Indices: 11776498--11776546 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
11776488 AAAAATATTT
*
11776498 ATAAATGAATAACAAATATAA
1 ATAAATAAATAACAAATATAA
* *
11776519 ATAATTAAATAACAAACA-AA
1 ATAAATAAATAACAAATATAA
11776539 AT-AATAAA
1 ATAAATAAA
11776547 ATAAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 15 0.62
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22
Consensus pattern (21 bp):
ATAAATAAATAACAAATATAA
Found at i:11776542 original size:20 final size:21
Alignment explanation
Indices: 11776505--11776550 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
11776495 TTTATAAATG
* *
11776505 AATAACAAATATAAATAATTA
1 AATAACAAACATAAATAATAA
11776526 AATAACAAACA-AAATAATAA
1 AATAACAAACATAAATAATAA
11776546 AATAA
1 AATAA
11776551 AATTAATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.22
Consensus pattern (21 bp):
AATAACAAACATAAATAATAA
Found at i:11778013 original size:20 final size:20
Alignment explanation
Indices: 11777988--11778028 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
11777978 ATTTAGACAT
11777988 TGTCATAACTTTTTTTTTAA
1 TGTCATAACTTTTTTTTTAA
11778008 TGTCATAACTTTTTTTTTAA
1 TGTCATAACTTTTTTTTTAA
11778028 T
1 T
11778029 ATTATAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.61
Consensus pattern (20 bp):
TGTCATAACTTTTTTTTTAA
Found at i:11778040 original size:22 final size:20
Alignment explanation
Indices: 11777990--11778036 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
11777980 TTAGACATTG
*
11777990 TCATAACTTTTTTTTTAATG
1 TCATAACTTTTTTTTTAATA
11778010 TCATAACTTTTTTTTTAATA
1 TCATAACTTTTTTTTTAATA
*
11778030 TTATAAC
1 TCATAAC
11778037 ACTTCTTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (20 bp):
TCATAACTTTTTTTTTAATA
Found at i:11778923 original size:22 final size:22
Alignment explanation
Indices: 11778897--11778947 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
11778887 CTTAAAAGTA
11778897 TATTTTATGT-TAA-TATTTTAT
1 TATTTTATGTATAATTATTTT-T
* *
11778918 TAATTTGTGTATAATTATTTTT
1 TATTTTATGTATAATTATTTTT
11778940 TATTTTAT
1 TATTTTAT
11778948 AATGCTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 8 0.33
22 10 0.42
23 6 0.25
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (22 bp):
TATTTTATGTATAATTATTTTT
Found at i:11780141 original size:16 final size:16
Alignment explanation
Indices: 11780107--11780179 Score: 87
Period size: 16 Copynumber: 4.6 Consensus size: 16
11780097 GCAATTGGAA
*
11780107 TTAAAA-AATTTAAATT
1 TTAAAATAATTCAAA-T
11780123 TTAAAATGAA-TCAAAT
1 TTAAAAT-AATTCAAAT
11780139 TTAAAATAATTCAAAT
1 TTAAAATAATTCAAAT
* *
11780155 TCAAAATAATTCAGAT
1 TTAAAATAATTCAAAT
11780171 TTAAAATAA
1 TTAAAATAA
11780180 CATAAATAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.04
16 42 0.84
17 4 0.08
18 2 0.04
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (16 bp):
TTAAAATAATTCAAAT
Found at i:11780963 original size:19 final size:18
Alignment explanation
Indices: 11780910--11780963 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
11780900 ATAAAATTCG
*
11780910 ATCAAATTCAAATTAAAA
1 ATCAAATTTAAATTAAAA
* * *
11780928 ATTAAATTATGAGTTAAAA
1 ATCAAATT-TAAATTAAAA
11780947 ATCAAATTTAAACTTAA
1 ATCAAATTTAAA-TTAA
11780964 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (18 bp):
ATCAAATTTAAATTAAAA
Found at i:11783722 original size:29 final size:29
Alignment explanation
Indices: 11783685--11783752 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
11783675 ACCTTTAAAC
*
11783685 TTTTAATTTGCATTCAAATAAATTTTTAA
1 TTTTAATTTGCATTCAAATAAAATTTTAA
*
11783714 TTTTAATTTGTATTCAAATAAAATTTTAA
1 TTTTAATTTGCATTCAAATAAAATTTTAA
11783743 TCTTTAATTT
1 T-TTTAATTT
11783753 ATACTTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 28 0.78
30 8 0.22
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTTAATTTGCATTCAAATAAAATTTTAA
Found at i:11783740 original size:30 final size:30
Alignment explanation
Indices: 11783685--11783770 Score: 106
Period size: 29 Copynumber: 2.9 Consensus size: 30
11783675 ACCTTTAAAC
*
11783685 TTTTAATTTGCATTCAAAT-AAATTTTTAA
1 TTTTAATTTGTATTCAAATAAAATTTTTAA
11783714 TTTTAATTTGTATTCAAATAAAA-TTTTAA
1 TTTTAATTTGTATTCAAATAAAATTTTTAA
*
11783743 TCTTTAATTTATACTT-AAATAAATATTT
1 T-TTTAATTTGTA-TTCAAATAAA-ATTT
11783771 AATCTAAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
29 25 0.50
30 20 0.40
31 3 0.06
32 2 0.04
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTTAATTTGTATTCAAATAAAATTTTTAA
Found at i:11783794 original size:16 final size:16
Alignment explanation
Indices: 11783757--11783801 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
11783747 TAATTTATAC
11783757 TTAAATAAATATTTAAT
1 TTAAATAAA-ATTTAAT
* *
11783774 CTAAATAAAATTTTAT
1 TTAAATAAAATTTAAT
11783790 TTAAATATAAAT
1 TTAAATA-AAAT
11783802 CAAAAGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATAAAATTTAAT
Found at i:11783817 original size:29 final size:27
Alignment explanation
Indices: 11783778--11783859 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 27
11783768 TTTAATCTAA
11783778 ATAAAATTTTATTTAAATATAAATCAAAAG
1 ATAAAA-TTTATTTAAATATAAA--AAAAG
* *
11783808 ATAAAATTTATTTAAGTATAAAAAAAT
1 ATAAAATTTATTTAAATATAAAAAAAG
*
11783835 ATAAAAATTTATTTTAAAAATAAAA
1 AT-AAAATTTA-TTTAAATATAAAA
11783860 TAATTAATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 6 0.13
28 8 0.17
29 26 0.57
30 6 0.13
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (27 bp):
ATAAAATTTATTTAAATATAAAAAAAG
Found at i:11790505 original size:3 final size:3
Alignment explanation
Indices: 11790497--11790525 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11790487 TTCAATCACG
11790497 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11790526 CAACAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11791009 original size:11 final size:11
Alignment explanation
Indices: 11790993--11791030 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
11790983 TTAAGTGTTT
11790993 TATATATTATA
1 TATATATTATA
11791004 TATATATTAT-
1 TATATATTATA
11791014 TATATA-TATA
1 TATATATTATA
11791024 T-TATATT
1 TATATATT
11791031 TTTTTGCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 7 0.28
10 8 0.32
11 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATATATTATA
Found at i:11791016 original size:14 final size:14
Alignment explanation
Indices: 11790993--11791027 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
11790983 TTAAGTGTTT
11790993 TATA-TATTATATA
1 TATATTATTATATA
11791006 TATATTATTATATA
1 TATATTATTATATA
11791020 TATATTAT
1 TATATTAT
11791028 ATTTTTTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATTATTATATA
Found at i:11791903 original size:4 final size:4
Alignment explanation
Indices: 11791892--11791921 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
11791882 ACATTAAAAA
11791892 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
11791922 AAGGAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:11792077 original size:57 final size:55
Alignment explanation
Indices: 11791955--11792294 Score: 281
Period size: 57 Copynumber: 5.9 Consensus size: 55
11791945 TTGTGCAAGA
* * * *
11791955 AAAATTGATACTTTCAACTTTTTC-TCAAAA-TATCTTTTGAAACTTTAATTTCTAAG
1 AAAATTGATACTTTCAACTTTTCCTTAAAAACT-TTTTTTGAAAATTT-ATTT-TAAG
11792011 AAAATTGATACTTTCAACTTTTCCTTAAAAACTTTTTTTGAAAATTTATTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTTAAAAACTTTTTTTGAAAATTTATTTTAA-G
** * ** *
11792067 AAAAATTGATACTTTCAAACTTTTTTTTCAAAAAATATTTTTTTTATGGAAAGCTTATTTTCAG
1 -AAAATTGATACTTTC-AACTTTTCCTT---AAAA-A-CTTTTTT-T-GAAAATTTATTTTAAG
* *
11792131 AAAATTGATACTTTCAACTTTTCCTCAAAATCTTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTTAAAAAC--TTTTTTTGAAAATTTA-TTTTAA-G
* * * * **
11792190 AAAATTGATACTTTTAAC-TTTCCTAAAAAATATTTTTTTGAAAACTTAATTCGAAG
1 AAAATTGATACTTTCAACTTTTCCTTAAAAA-CTTTTTTTGAAAA-TTTATTTTAAG
* * *
11792246 AAAATTGATACTTTCAACTTTTTCTCAAAATATTTCTTTTTGAAAATTT
1 AAAATTGATACTTTCAACTTTTCCTTAAAA-ACTT-TTTTTGAAAATTT
11792295 TTATTTTTGT
Statistics
Matches: 233, Mismatches: 30, Indels: 41
0.77 0.10 0.13
Matches are distributed among these distances:
55 3 0.01
56 46 0.20
57 68 0.29
58 40 0.17
59 28 0.12
61 4 0.02
62 9 0.04
63 21 0.09
64 2 0.01
65 12 0.05
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.46
Consensus pattern (55 bp):
AAAATTGATACTTTCAACTTTTCCTTAAAAACTTTTTTTGAAAATTTATTTTAAG
Found at i:11794298 original size:13 final size:13
Alignment explanation
Indices: 11794277--11794307 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11794267 AAAAAATGAT
11794277 AAATATGAAATAA
1 AAATATGAAATAA
*
11794290 AAATCTGAAATAA
1 AAATATGAAATAA
11794303 AAATA
1 AAATA
11794308 AATAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (13 bp):
AAATATGAAATAA
Found at i:11794687 original size:118 final size:110
Alignment explanation
Indices: 11794498--11794775 Score: 336
Period size: 118 Copynumber: 2.5 Consensus size: 110
11794488 TTTATTTTGC
* * *
11794498 TTTTTTTTTGTAATTTTGATCAAAGTTCCTCTAAGCAGAGGCTCCAACGACTTTGAGAAACATAA
1 TTTTTTTTTTTAA--TTGATCAAAGCTCCTCTAAACAGAGGCT-CAACGACTTTGAGAAACATAA
11794563 AAAAAGCTCCTCTAAACAGAGGCTCAACTTTTTCTTTTTGTTTTCTTGCTCTCTT
63 AAAAAGCTCCTCTAAACAGAGG-T-AA-TTTTT-TTTTTGTTTTCTTG-T-T-TT
* *
11794618 TTTTTTTTTTTAAATTGATCAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGAGAAACATAAAC
1 TTTTTTTTTTT-AATTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAAA
* *
11794683 AAAGCTCCTTTAAACAGAGGTAATTTTTTTTTTGTTTTTTTGTTTT
65 AAAGCTCCTCTAAACAGAGGTAATTTTTTTTTTGTTTTCTTGTTTT
11794729 TTTTTATTTTTT--TT--TC-AAGCTCCTCTAAACAGA-G-TCAACGACTTTGA
1 TTTTT-TTTTTTAATTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGA
11794776 AAGTAAATTG
Statistics
Matches: 148, Mismatches: 8, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
104 13 0.09
105 1 0.01
106 16 0.11
107 2 0.01
109 2 0.01
111 7 0.05
112 7 0.05
113 1 0.01
114 13 0.09
115 5 0.03
116 2 0.01
117 1 0.01
118 41 0.28
119 25 0.17
120 10 0.07
121 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (110 bp):
TTTTTTTTTTTAATTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAAAA
AAGCTCCTCTAAACAGAGGTAATTTTTTTTTTGTTTTCTTGTTTT
Found at i:11794730 original size:18 final size:18
Alignment explanation
Indices: 11794707--11794741 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11794697 CAGAGGTAAT
*
11794707 TTTTTTTTTGTTTTTTTG
1 TTTTTTTTTATTTTTTTG
11794725 TTTTTTTTTATTTTTTT
1 TTTTTTTTTATTTTTTT
11794742 TTCAAGCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (18 bp):
TTTTTTTTTATTTTTTTG
Found at i:11794730 original size:19 final size:19
Alignment explanation
Indices: 11794706--11794742 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
11794696 ACAGAGGTAA
11794706 TTTTTTTTT-TGTTTTTTTG
1 TTTTTTTTTAT-TTTTTTTG
11794725 TTTTTTTTTATTTTTTTT
1 TTTTTTTTTATTTTTTTT
11794743 TCAAGCTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.03, C:0.00, G:0.05, T:0.92
Consensus pattern (19 bp):
TTTTTTTTTATTTTTTTTG
Found at i:11794901 original size:41 final size:41
Alignment explanation
Indices: 11794747--11795026 Score: 421
Period size: 41 Copynumber: 6.9 Consensus size: 41
11794737 TTTTTTTCAA
*
11794747 GCTCCTCTAAACAGAGTCA--ACGACTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
11794785 G-TCCTCTAAACAGAGGCACCACGACTCTGAAAAGT-AATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
11794824 GCTCCTCTAAACAGTGGTACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
* *
11794866 GCTCCTCTAAACAAAGGCACCGCGACTTTGAAAAGTAAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGT-AAATT
11794908 GCTCCTCTAAACA-AGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
11794949 GCTCCTCTAAACAGAGGCACCACGACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
11794990 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTA
11795027 CCATGACTTT
Statistics
Matches: 221, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
37 16 0.07
38 1 0.00
39 13 0.06
40 35 0.16
41 86 0.39
42 66 0.30
43 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:11794957 original size:83 final size:83
Alignment explanation
Indices: 11794747--11795026 Score: 425
Period size: 83 Copynumber: 3.5 Consensus size: 83
11794737 TTTTTTTCAA
*
11794747 GCTCCTCTAAACAGAGTCA--ACGACTTT--GAAAGTAAATTG-TCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
11794807 GACTCTGAAAAGT-AATT
66 GACTTTGAAAAGTAAATT
* * * *
11794824 GCTCCTCTAAACAGTGGTACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAAAGGCACCGC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
11794889 GACTTTGAAAAGTAAAATT
66 GACTTTGAAAAGT-AAATT
11794908 GCTCCTCTAAACA-AGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
11794972 GACTTTTG-AAAGTAAATT
66 GAC-TTTGAAAAGTAAATT
11794990 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTA
11795027 CCATGACTTT
Statistics
Matches: 184, Mismatches: 10, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
77 16 0.09
79 8 0.04
81 12 0.07
82 55 0.30
83 72 0.39
84 21 0.11
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (83 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
GACTTTGAAAAGTAAATT
Found at i:11795075 original size:58 final size:60
Alignment explanation
Indices: 11794967--11795082 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 60
11794957 AAACAGAGGC
*
11794967 ACCACGACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGT
1 ACCACGACTTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
* * *
11795026 ACCATGAC-TTTGAAAAATAAATTGCTCCTCT-AATAGAGGCACCATGACTTTGGAAAA
1 ACCACGACTTTTG-AAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA
11795083 TAAATTGCTC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 22 0.43
59 29 0.57
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (60 bp):
ACCACGACTTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
Found at i:11795127 original size:42 final size:42
Alignment explanation
Indices: 11795031--11795175 Score: 174
Period size: 42 Copynumber: 3.5 Consensus size: 42
11795021 AAAGTACCAT
* * *
11795031 GACTTTGAAAAATAAATTGCTCCTCT-AATAGAGGCACC-AT
1 GACTTTGAAAAATAAATTGCTCCTCTAAACAAAGGCACCTAC
*
11795071 GACTTTGGAAAATAAATTGCT-CTCTAAAACAAAGGCACCTAC
1 GACTTTGAAAAATAAATTGCTCCTCT-AAACAAAGGCACCTAC
*
11795113 GACTTTGAAAAATAAATTGCTCCTCTAAACAGCAGAGCA-CTAC
1 GACTTTGAAAAATAAATTGCTCCTCTAAACA-AAG-GCACCTAC
*
11795156 GACTTTGAAAGA-AAATTGCT
1 GACTTTGAAAAATAAATTGCT
11795176 TCTGATAATC
Statistics
Matches: 92, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
39 4 0.04
40 20 0.22
41 10 0.11
42 34 0.37
43 21 0.23
44 3 0.03
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (42 bp):
GACTTTGAAAAATAAATTGCTCCTCTAAACAAAGGCACCTAC
Found at i:11796892 original size:10 final size:10
Alignment explanation
Indices: 11796877--11796955 Score: 61
Period size: 10 Copynumber: 7.3 Consensus size: 10
11796867 TCTTTTTTCA
11796877 TTTTCTCATT
1 TTTTCTCATT
11796887 TTTTCTTC-TT
1 TTTTC-TCATT
11796897 TCTTTCTCATTT
1 T-TTTCTCA-TT
**
11796909 TTTTCTTTTT
1 TTTTCTCATT
*
11796919 TTTTCTAATTT
1 TTTTCTCA-TT
11796930 TTTTCATCATTTT
1 TTTTC-TCA--TT
11796943 TTTTCTCATT
1 TTTTCTCATT
11796953 TTT
1 TTT
11796956 CATCCATTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
10 23 0.40
11 18 0.32
12 8 0.14
13 8 0.14
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTCTCATT
Found at i:11796904 original size:21 final size:22
Alignment explanation
Indices: 11796877--11796955 Score: 99
Period size: 21 Copynumber: 3.6 Consensus size: 22
11796867 TCTTTTTTCA
11796877 TTTTCTCA-TTTTTTCTTCTTT
1 TTTTCTCATTTTTTTCTTCTTT
*
11796898 CTTTCTCATTTTTTTCTT-TTT
1 TTTTCTCATTTTTTTCTTCTTT
* *
11796919 TTTTCTAATTTTTTTCATCATTTT
1 TTTTCTCATTTTTTTCTTC--TTT
11796943 TTTTCTCATTTTT
1 TTTTCTCATTTTT
11796956 CATCCATTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
21 25 0.51
22 9 0.18
24 15 0.31
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTCTCATTTTTTTCTTCTTT
Found at i:11796913 original size:11 final size:11
Alignment explanation
Indices: 11796877--11796955 Score: 83
Period size: 11 Copynumber: 7.2 Consensus size: 11
11796867 TCTTTTTTCA
11796877 TTTTCTCA-TT
1 TTTTCTCATTT
11796887 TTTTCTTC-TTT
1 TTTTC-TCATTT
*
11796898 CTTTCTCATTT
1 TTTTCTCATTT
*
11796909 TTTTCT-TTTT
1 TTTTCTCATTT
*
11796919 TTTTCTAATTT
1 TTTTCTCATTT
11796930 TTTTCATCATTTT
1 TTTTC-TCA-TTT
11796943 TTTTCTCATTT
1 TTTTCTCATTT
11796954 TT
1 TT
11796956 CATCCATTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
10 16 0.28
11 29 0.50
12 5 0.09
13 8 0.14
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTCTCATTT
Found at i:11805050 original size:17 final size:17
Alignment explanation
Indices: 11805028--11805067 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
11805018 AGAGATTCAA
*
11805028 AATTTATTTTTATAAAT
1 AATTTATTTTTAAAAAT
11805045 AATTTATTTTTAAAAAT
1 AATTTATTTTTAAAAAT
11805062 ATATTT
1 A-ATTT
11805068 TAATATGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTATTTTTAAAAAT
Found at i:11805373 original size:22 final size:22
Alignment explanation
Indices: 11805331--11805376 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
11805321 ATAAATGAAT
* *
11805331 AACAAATATAAATAATTAAATA
1 AACAAACATAAATAATAAAATA
11805353 AACAAACA-AAATAAATAAAATA
1 AACAAACATAAAT-AATAAAATA
11805375 AA
1 AA
11805377 ATTAATTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.20
Consensus pattern (22 bp):
AACAAACATAAATAATAAAATA
Found at i:11806805 original size:21 final size:20
Alignment explanation
Indices: 11806781--11806827 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
11806771 ATCTTTTAAT
11806781 TTTTTTAGAAATTGTCATAAC
1 TTTTTTAGAAA-TGTCATAAC
***
11806802 TTTTTTTTTAATGTCATAAC
1 TTTTTTAGAAATGTCATAAC
11806822 TTTTTT
1 TTTTTT
11806828 TTTATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (20 bp):
TTTTTTAGAAATGTCATAAC
Found at i:11806840 original size:19 final size:20
Alignment explanation
Indices: 11806793--11806831 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
11806783 TTTTAGAAAT
11806793 TGTCATAACTTTTTTTTTAA
1 TGTCATAACTTTTTTTTTAA
11806813 TGTCATAACTTTTTTTTTA
1 TGTCATAACTTTTTTTTTA
11806832 TATTATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (20 bp):
TGTCATAACTTTTTTTTTAA
Found at i:11807151 original size:17 final size:17
Alignment explanation
Indices: 11807129--11807164 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
11807119 TTACTTTACC
11807129 TATATTTTTTATTAT-TT
1 TATATTTTTT-TTATATT
11807146 TATATTTTTTTTATATT
1 TATATTTTTTTTATATT
11807163 TA
1 TA
11807165 CATGAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TATATTTTTTTTATATT
Found at i:11807729 original size:22 final size:23
Alignment explanation
Indices: 11807704--11807754 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
11807694 CTTAAAGTAT
11807704 ATTTTATGT-TAA-TATTTTATTA
1 ATTTTATGTATAATTATTTT-TTA
* *
11807726 A-TTTGTGTATAATTATTTTTTT
1 ATTTTATGTATAATTATTTTTTA
11807748 ATTTTAT
1 ATTTTAT
11807755 AATGCTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
21 6 0.26
22 7 0.30
23 10 0.43
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (23 bp):
ATTTTATGTATAATTATTTTTTA
Found at i:11808947 original size:16 final size:16
Alignment explanation
Indices: 11808913--11808985 Score: 87
Period size: 16 Copynumber: 4.6 Consensus size: 16
11808903 GCAATTCGAA
*
11808913 TTAAAA-AATTTAAATT
1 TTAAAATAATTCAAA-T
11808929 TTAAAATGAA-TCAAAT
1 TTAAAAT-AATTCAAAT
11808945 TTAAAATAATTCAAAT
1 TTAAAATAATTCAAAT
* *
11808961 TCAAAATAATTCAGAT
1 TTAAAATAATTCAAAT
11808977 TTAAAATAA
1 TTAAAATAA
11808986 CATAAATAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.04
16 42 0.84
17 4 0.08
18 2 0.04
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (16 bp):
TTAAAATAATTCAAAT
Found at i:11808984 original size:32 final size:32
Alignment explanation
Indices: 11808894--11808985 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
11808884 TTAGTAACTT
** * *
11808894 AAATTCAAAGCAATTC-GAATTAAAA-AATTT
1 AAATTCAAAATAATTCAGATTTAAAATAATTC
* *
11808924 AAATTTTAAAATGAA-TCAAATTTAAAATAATTC
1 AAA-TTCAAAAT-AATTCAGATTTAAAATAATTC
11808957 AAATTCAAAATAATTCAGATTTAAAATAA
1 AAATTCAAAATAATTCAGATTTAAAATAA
11808986 CATAAATAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
30 3 0.06
31 9 0.18
32 30 0.61
33 7 0.14
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (32 bp):
AAATTCAAAATAATTCAGATTTAAAATAATTC
Found at i:11809768 original size:19 final size:18
Alignment explanation
Indices: 11809715--11809768 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
11809705 ATAAAATTCG
*
11809715 ATCAAATTCAAATTAAAA
1 ATCAAATTTAAATTAAAA
* * *
11809733 ATTAAATTATGAGTTAAAA
1 ATCAAATT-TAAATTAAAA
11809752 ATCAAATTTAAACTTAA
1 ATCAAATTTAAA-TTAA
11809769 TTTTTTATTA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (18 bp):
ATCAAATTTAAATTAAAA
Found at i:11810901 original size:30 final size:30
Alignment explanation
Indices: 11810848--11810923 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
11810838 TTTAATCTAA
*
11810848 TTAAAAGTTTAATTAAATTAAAATAAATGT
1 TTAAAAGTTTAATTAAATAAAAATAAATGT
* *
11810878 TTAAAA-TTTCAATTTAATAAAAATAAATAT
1 TTAAAAGTTT-AATTAAATAAAAATAAATGT
* *
11810908 TTGAGAGTTTAATTAA
1 TTAAAAGTTTAATTAA
11810924 TTACAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 3 0.08
30 32 0.84
31 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (30 bp):
TTAAAAGTTTAATTAAATAAAAATAAATGT
Found at i:11811251 original size:22 final size:23
Alignment explanation
Indices: 11811208--11811251 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
11811198 GTATTTAACA
* * *
11811208 TTTACTTTGTATCTAAATAAAAT
1 TTTAATTTGTATCAAAAAAAAAT
11811231 TTTAATTTGTAT-AAAAAAAAA
1 TTTAATTTGTATCAAAAAAAAA
11811252 GTCTTTAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (23 bp):
TTTAATTTGTATCAAAAAAAAAT
Found at i:11811319 original size:27 final size:28
Alignment explanation
Indices: 11811280--11811367 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 28
11811270 AAATTATTTG
* *
11811280 AAATAAGAGTTTATTTATA-TATAAT-TA
1 AAATAAGAATTTATTTA-AGTATAATAAA
11811307 AAATAAGAATTTATTTAAGTATAATAAA
1 AAATAAGAATTTATTTAAGTATAATAAA
* *
11811335 AATATAAGAATTTATCTAAATA-AATAATA
1 AA-ATAAGAATTTATTTAAGTATAATAA-A
11811364 AAAT
1 AAAT
11811368 TCCAAAGTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.02
27 22 0.42
28 10 0.19
29 20 0.38
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.38
Consensus pattern (28 bp):
AAATAAGAATTTATTTAAGTATAATAAA
Found at i:11811385 original size:2 final size:2
Alignment explanation
Indices: 11811378--11811407 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11811368 TCCAAAGTGT
11811378 TA TA TA TA TA T- 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 T
11811408 TTTTAGCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11812689 original size:30 final size:30
Alignment explanation
Indices: 11812654--11812722 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
11812644 ACCTTTAAAC
*
11812654 TTTTAATTTGCATTCAAATAAATTTTTAAT
1 TTTTAATTTGCATTCAAATAAAATTTTAAT
*
11812684 TTTTAATTTGTATTCAAATAAAATTTTAAT
1 TTTTAATTTGCATTCAAATAAAATTTTAAT
*
11812714 CTTTAATTT
1 TTTTAATTT
11812723 ATACTTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTTAATTTGCATTCAAATAAAATTTTAAT
Found at i:11812733 original size:30 final size:30
Alignment explanation
Indices: 11812655--11812745 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 30
11812645 CCTTTAAACT
** * *
11812655 TTTAATTTGCATTCAAATAAATTTTTAATT
1 TTTAATTTATATTCAAATAAAATTTTAATC
*
11812685 TTTAATTTGTATTCAAATAAAATTTTAATC
1 TTTAATTTATATTCAAATAAAATTTTAATC
11812715 TTTAATTTATACTT-AAAT-AAATATTTAATC
1 TTTAATTTATA-TTCAAATAAAAT-TTTAATC
11812745 T
1 T
11812746 AAATAAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
29 4 0.07
30 49 0.89
31 2 0.04
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTAATTTATATTCAAATAAAATTTTAATC
Found at i:11812764 original size:16 final size:16
Alignment explanation
Indices: 11812727--11812771 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
11812717 TAATTTATAC
11812727 TTAAATAAATATTTAAT
1 TTAAATAAA-ATTTAAT
* *
11812744 CTAAATAAAATTTTAT
1 TTAAATAAAATTTAAT
11812760 TTAAATATAAAT
1 TTAAATA-AAAT
11812772 CAAAAGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATAAAATTTAAT
Found at i:11812787 original size:29 final size:27
Alignment explanation
Indices: 11812748--11812829 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 27
11812738 TTTAATCTAA
11812748 ATAAAATTTTATTTAAATATAAATCAAAAG
1 ATAAAA-TTTATTTAAATATAAA--AAAAG
* *
11812778 ATAAAATTTATTTAAGTATAAAAAAAT
1 ATAAAATTTATTTAAATATAAAAAAAG
*
11812805 ATAAAAATTTATTTTAAAAATAAAA
1 AT-AAAATTTA-TTTAAATATAAAA
11812830 TAATTAATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 6 0.13
28 8 0.17
29 26 0.57
30 6 0.13
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (27 bp):
ATAAAATTTATTTAAATATAAAAAAAG
Found at i:11819472 original size:3 final size:3
Alignment explanation
Indices: 11819464--11819495 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11819454 TTCAATCACG
11819464 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11819496 CAACAACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11819984 original size:14 final size:14
Alignment explanation
Indices: 11819965--11819993 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11819955 CCTTAAAGTG
11819965 TTTATATATATATA
1 TTTATATATATATA
11819979 TTTATATATATATA
1 TTTATATATATATA
11819993 T
1 T
11819994 ATTTTTTTTT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATATATATATA
Found at i:11820976 original size:57 final size:57
Alignment explanation
Indices: 11820919--11821257 Score: 339
Period size: 60 Copynumber: 5.8 Consensus size: 57
11820909 TTGTGCAAGA
* *
11820919 AAAATTGATACTTTTAACTTTTTCTCAAAATA-TCTTTTGAAACTTTAATTTCGAAG
1 AAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTTGAAACTTTAATTTCGAAG
* * **
11820975 AAAATTGATACTTTCAACTTTTTCTTAAAA-ACTTTTTTTGAAAATTT-ATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAATA-TTTTTTTGAAACTTTAATTTCGAA-G
* *
11821032 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTTATGGAAAGC-TTATTTTC-AAG
1 AAAATTGATACTTTCAACTTTTTCTC-AAAATA--TTTTTT-T-GAAA-CTTTAATTTCGAAG
* * * **
11821093 AAAAATTGATACTTTCAACTTTTCCTCAAAATCTTTTTTTTTTGAAAATTT-ATTTTTAAGG
1 -AAAATTGATACTTTCAACTTTTTCTCAAAA---TATTTTTTTGAAACTTTAATTTCGAA-G
* * *
11821154 AAAATTGATACTTTTAACTTTTCCTAAAAATATTTTTTTGAAAACTTTAATTTCGAAG
1 AAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTTG-AAACTTTAATTTCGAAG
11821212 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTCTTTTTGAAA
1 AAAATTGATACTTTCAACTTTTTCTC-AAAATA-TT-TTTTTGAAA
11821258 ATTTTTATTT
Statistics
Matches: 234, Mismatches: 27, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
55 1 0.00
56 34 0.15
57 46 0.20
58 34 0.15
59 16 0.07
60 47 0.20
61 14 0.06
62 38 0.16
63 3 0.01
64 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTTGAAACTTTAATTTCGAAG
Found at i:11821130 original size:119 final size:115
Alignment explanation
Indices: 11820919--11821261 Score: 453
Period size: 119 Copynumber: 2.9 Consensus size: 115
11820909 TTGTGCAAGA
*
11820919 AAAATTGATACTTTTAACTTTTTCTC-AAAATA-TCTTTTGAAACTTTAATTTCGAAGAAAATTG
1 AAAATTGATACTTTTAACTTTTTCTCAAAAATATTTTTTTGAAACTTTAATTTCGAAGAAAATTG
* *
11820982 ATACTTTCAACTTTTTCTTAAAAACTTTTTTTGAAAATTTATTTTTAAGG
66 ATACTTTCAACTTTTTCTCAAAATCTTTTTTTGAAAATTTATTTTTAAGG
* * *
11821032 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTTATGGAAAGC-TTATTTTC-AAGAA
1 AAAATTGATACTTTTAACTTTTTCTCAAAAATA--TTTTTT-T-GAAA-CTTTAATTTCGAAG-A
*
11821095 AAATTGATACTTTCAACTTTTCCTCAAAATCTTTTTTTTTTGAAAATTTATTTTTAAGG
60 AAATTGATACTTTCAACTTTTTCTCAAAATC---TTTTTTTGAAAATTTATTTTTAAGG
*
11821154 AAAATTGATACTTTTAACTTTTCCT-AAAAATATTTTTTTGAAAACTTTAATTTCGAAGAAAATT
1 AAAATTGATACTTTTAACTTTTTCTCAAAAATATTTTTTTG-AAACTTTAATTTCGAAGAAAATT
*
11821218 GATACTTTCAACTTTTTCTCAAAAATATTTCTTTTTGAAAATTT
65 GATACTTTCAACTTTTTCTC-AAAAT-CTT-TTTTTGAAAATTT
11821262 TTATTTTTTG
Statistics
Matches: 200, Mismatches: 13, Indels: 29
0.83 0.05 0.12
Matches are distributed among these distances:
113 24 0.12
114 6 0.03
117 8 0.04
118 53 0.26
119 54 0.27
120 1 0.00
121 7 0.04
122 47 0.23
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (115 bp):
AAAATTGATACTTTTAACTTTTTCTCAAAAATATTTTTTTGAAACTTTAATTTCGAAGAAAATTG
ATACTTTCAACTTTTTCTCAAAATCTTTTTTTGAAAATTTATTTTTAAGG
Found at i:11823261 original size:13 final size:13
Alignment explanation
Indices: 11823240--11823270 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11823230 AAAAAATGAT
11823240 AAATATGAAATAA
1 AAATATGAAATAA
*
11823253 AAATCTGAAATAA
1 AAATATGAAATAA
11823266 AAATA
1 AAATA
11823271 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (13 bp):
AAATATGAAATAA
Found at i:11823640 original size:118 final size:112
Alignment explanation
Indices: 11823459--11823766 Score: 348
Period size: 118 Copynumber: 2.8 Consensus size: 112
11823449 TTTATTTTGC
* *
11823459 TTTTTTTTTTAATTTTGATCAAAGTTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAAA
1 TTTTTTTTTTAA--TTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAAA
**
11823524 AAAGCTCCTCTAAACAGAGGCTCAACTTTTTCTTTTTGTTTTCTTGCTCTCTT-T
64 AAAGCTCCTCTAAACAGAGGCT-AA-TTTTT-TTTACGTTTTCTTG-T-T-TTAT
* *
11823578 TTTTTTTTTTAAATTGATCAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGAGAAACATAAACA
1 TTTTTTTTTT-AATTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAAAA
* * *
11823643 AAGCTCCTTTAAATAGAGG-TAATTTTTTTTACGTTTTTTTGTTTTAT
65 AAGCTCCTCTAAACAGAGGCTAATTTTTTTTACGTTTTCTTGTTTTAT
*
11823690 TTTTATTTTTT--TT--TCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGA-AAA-GT--AAA
1 TTTT-TTTTTTAATTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAAAA
**
11823747 TTGCTCCTCTAAACAGAGGC
65 AAGCTCCTCTAAACAGAGGC
11823767 ACCACGACTC
Statistics
Matches: 169, Mismatches: 16, Indels: 22
0.82 0.08 0.11
Matches are distributed among these distances:
104 17 0.10
106 1 0.01
107 3 0.02
108 35 0.21
110 2 0.01
111 2 0.01
112 6 0.04
113 7 0.04
114 11 0.07
115 5 0.03
116 2 0.01
117 1 0.01
118 65 0.38
119 10 0.06
120 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.40
Consensus pattern (112 bp):
TTTTTTTTTTAATTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAAAAA
AGCTCCTCTAAACAGAGGCTAATTTTTTTTACGTTTTCTTGTTTTAT
Found at i:11823839 original size:42 final size:41
Alignment explanation
Indices: 11823708--11823993 Score: 473
Period size: 41 Copynumber: 6.9 Consensus size: 41
11823698 TTTTTTCAAA
* *
11823708 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
11823749 GCTCCTCTAAACAGAGGCACCACGACTCTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
11823790 GCTCCTCTAAACAGTGGTACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
* *
11823832 GCTCCTCTAAACAAAGGCACCGCGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
11823873 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
*
11823915 GCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
11823957 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTA
11823994 CCATGACTTT
Statistics
Matches: 228, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
41 115 0.50
42 109 0.48
43 4 0.02
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:11823850 original size:83 final size:82
Alignment explanation
Indices: 11823708--11823993 Score: 473
Period size: 83 Copynumber: 3.5 Consensus size: 82
11823698 TTTTTTCAAA
* *
11823708 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
11823773 ACTCTGAAAAGTAAATT
66 ACTTTGAAAAGTAAATT
* * * *
11823790 GCTCCTCTAAACAGTGGTACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAAAGGCACCGC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
11823855 GACTTTGAAAAGTAAATT
65 GACTTTGAAAAGTAAATT
11823873 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
11823938 GACTTTTGGAAAGTAAATT
65 GAC-TTTGAAAAGTAAATT
11823957 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTA
11823994 CCATGACTTT
Statistics
Matches: 190, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
82 27 0.14
83 118 0.62
84 45 0.24
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAGTAAATT
Found at i:11824032 original size:59 final size:61
Alignment explanation
Indices: 11823933--11824050 Score: 177
Period size: 59 Copynumber: 2.0 Consensus size: 61
11823923 AAACAGAGGC
* *
11823933 ACCACGACTTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGT
1 ACCACGACTTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
* * *
11823993 ACCATGAC-TTTGAAAAATAAATTGCTCCTCTAAATAGAGGCACCATGACTTTGGAAAA
1 ACCACGACTTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA
11824051 TAAATTGCTC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 40 0.77
60 12 0.23
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (61 bp):
ACCACGACTTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
Found at i:11824051 original size:41 final size:41
Alignment explanation
Indices: 11823993--11824141 Score: 228
Period size: 41 Copynumber: 3.6 Consensus size: 41
11823983 TTTGAAAAGT
* *
11823993 ACCATGACTTTGAAAAATAAATTGCTCCTCTAAATAGAGGC
1 ACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGC
* * *
11824034 ACCATGACTTTGGAAAATAAATTGCTCCTCTAAACAAAGGC
1 ACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGC
11824075 ACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGC
1 ACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGC
*
11824116 ACTACGACTTTGAAAAGA-AAATTGCT
1 ACCACGACTTTGAAAA-ATAAATTGCT
11824142 TCTTGATAAT
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
41 99 0.99
42 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (41 bp):
ACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGC
Found at i:11824083 original size:100 final size:102
Alignment explanation
Indices: 11823891--11824090 Score: 332
Period size: 100 Copynumber: 2.0 Consensus size: 102
11823881 AAACAGAGGC
* *
11823891 ACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGTAAAT
1 ACCACGACTTTGAGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAATAAAT
*
11823956 TGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGT
66 TGCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGT
* * *
11823993 ACCATGACTTTGA-AAAATAAATTGCTCCTCTAAATAGAGGCACCATGAC-TTTGGAAAATAAAT
1 ACCACGACTTTGAGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAATAAAT
11824056 TGCTCCTCTAAACAAAGGCACCACGACTTTGAAAA
66 TGCTCCTCTAAACAAAGGCACCACGACTTTGAAAA
11824091 ATAAATTGCT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 47 0.51
101 33 0.36
102 12 0.13
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (102 bp):
ACCACGACTTTGAGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAATAAAT
TGCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGT
Found at i:11825872 original size:21 final size:22
Alignment explanation
Indices: 11825846--11825922 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
11825836 CTTTTTTTCA
11825846 TTTTCTCA-TTTTTTCTTCTTT
1 TTTTCTCATTTTTTTCTTCTTT
*
11825867 CTTTCTCATTTTTTTCTT-TTT
1 TTTTCTCATTTTTTTCTTCTTT
*
11825888 TTTTCT-ATTTTTTTCATCATTT
1 TTTTCTCATTTTTTTCTTC-TTT
11825910 TTTTCTCATTTTT
1 TTTTCTCATTTTT
11825923 CATCCATTGT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
20 10 0.20
21 15 0.31
22 18 0.37
23 6 0.12
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTCTCATTTTTTTCTTCTTT
Found at i:11825882 original size:11 final size:11
Alignment explanation
Indices: 11825846--11825922 Score: 90
Period size: 11 Copynumber: 7.2 Consensus size: 11
11825836 CTTTTTTTCA
11825846 TTTTCTCA-TT
1 TTTTCTCATTT
11825856 TTTTCTTC-TTT
1 TTTTC-TCATTT
*
11825867 CTTTCTCATTT
1 TTTTCTCATTT
*
11825878 TTTTCT-TTTT
1 TTTTCTCATTT
11825888 TTTTCT-ATTT
1 TTTTCTCATTT
11825898 TTTTCATCATTT
1 TTTTC-TCATTT
11825910 TTTTCTCATTT
1 TTTTCTCATTT
11825921 TT
1 TT
11825923 CATCCATTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
10 24 0.41
11 25 0.43
12 9 0.16
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTCTCATTT
Found at i:11825898 original size:12 final size:11
Alignment explanation
Indices: 11825846--11825922 Score: 54
Period size: 10 Copynumber: 7.2 Consensus size: 11
11825836 CTTTTTTTCA
*
11825846 TTTTCTCATTT
1 TTTTTTCATTT
*
11825857 TTTCTTC-TTT
1 TTTTTTCATTT
* *
11825867 CTTTCTCA--T
1 TTTTTTCATTT
11825876 TTTTTTC-TTT
1 TTTTTTCATTT
11825886 TTTTTTCTATTT
1 TTTTTTC-ATTT
*
11825898 TTTTCATCATTT
1 TTTT-TTCATTT
*
11825910 TTTTCTCATTT
1 TTTTTTCATTT
11825921 TT
1 TT
11825923 CATCCATTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
9 6 0.12
10 15 0.29
11 13 0.25
12 15 0.29
13 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:11825922 original size:32 final size:32
Alignment explanation
Indices: 11825846--11825922 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
11825836 CTTTTTTTCA
11825846 TTTTCTCATTTTTTCTTCTTTCTTTCTCATTT
1 TTTTCTCATTTTTTCTTCTTTCTTTCTCATTT
**
11825878 TTTTCTTTTTTTTTCTAT-TTT-TTTCATCATTT
1 TTTTCTCATTTTTTCT-TCTTTCTTTC-TCATTT
11825910 TTTTCTCATTTTT
1 TTTTCTCATTTTT
11825923 CATCCATTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 4 0.10
32 34 0.87
33 1 0.03
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (32 bp):
TTTTCTCATTTTTTCTTCTTTCTTTCTCATTT
Found at i:11825923 original size:21 final size:21
Alignment explanation
Indices: 11825846--11825926 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
11825836 CTTTTTTTCA
*
11825846 TTTTCTCATTTTTTCTTCTTT
1 TTTTCTCATTTTTTCATCTTT
*
11825867 CTTTCTCATTTTTT--TCTTT
1 TTTTCTCATTTTTTCATCTTT
*
11825886 TTTTTTCTATTTTTTTCATCATTT
1 TTTTCTC-A-TTTTTTCATC-TTT
11825910 TTTTCTCA-TTTTTCATC
1 TTTTCTCATTTTTTCATC
11825927 CATTGTTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
19 10 0.20
20 1 0.02
21 28 0.55
23 3 0.06
24 9 0.18
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTCTCATTTTTTCATCTTT
Found at i:11833605 original size:1 final size:1
Alignment explanation
Indices: 11833599--11833630 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
11833589 AGTACCCCAA
11833599 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
11833631 AAAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:11835809 original size:3 final size:3
Alignment explanation
Indices: 11835801--11835830 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
11835791 TTCAATCACG
11835801 AAT AAT AAT AAT AAT AAT ATAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AA
11835831 ACAACAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11836308 original size:2 final size:2
Alignment explanation
Indices: 11836301--11836335 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11836291 TTAAAGTGTT
*
11836301 TA TA TA TA TA TA TA TA TA TT 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
11836336 TTTTTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:11837447 original size:61 final size:56
Alignment explanation
Indices: 11837253--11837597 Score: 329
Period size: 61 Copynumber: 5.9 Consensus size: 56
11837243 TGTTTTTGTG
* * *
11837253 CAAGAAAAATTGATACTTTCAACTTTTTTCTCAAAATA--TCTTTTGAAACTTTAATTT
1 CAAG-AAAATTGATACTTTCAAC-TTTTCCTCAAAATATTTTTTTTGAAAC-TTATTTT
* * *
11837310 CGAAGAAAATTGATACTTTCAACTTTTCCTTAAAA-ACTTTTTTTGAAATTTATTTT
1 C-AAGAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTTGAAACTTATTTT
* **
11837366 TAAGGAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTTATGGAAAGCTTATTTT
1 CAA-G-AAAATTGATACTTTCAACTTTTCCTC-AAAATA-TTTTTTT-T-GAAA-CTTATTTT
* *
11837429 CAAGAAAATTGATACTTTCAACTTTTCCTCAAAATCTTTTTTTTTTGAAAATTTATTTT
1 CAAGAAAATTGATACTTTCAACTTTTCCTCAAAA--TATTTTTTTTG-AAACTTATTTT
* * * *
11837488 TAAGGGAAAATTGATACTTTTAACTTTTCCTAAAAATA-TTTTTTTGAAAACTTTAATTT
1 CAA--GAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTTG-AAAC-TTATTTT
*
11837547 CGAAGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTCTTTTTGAAA
1 C-AAGAAAATTGATACTTTCAACTTTTCCTC-AAAATATTT-TTTTTGAAA
11837598 ATTTTTATTT
Statistics
Matches: 241, Mismatches: 26, Indels: 39
0.79 0.08 0.13
Matches are distributed among these distances:
55 3 0.01
56 17 0.07
57 51 0.21
58 43 0.18
59 24 0.10
60 21 0.09
61 67 0.28
62 6 0.02
63 9 0.04
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (56 bp):
CAAGAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTTGAAACTTATTTT
Found at i:11839606 original size:13 final size:13
Alignment explanation
Indices: 11839585--11839615 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11839575 AAAAAATGAT
11839585 AAATATGAAATAA
1 AAATATGAAATAA
*
11839598 AAATCTGAAATAA
1 AAATATGAAATAA
11839611 AAATA
1 AAATA
11839616 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (13 bp):
AAATATGAAATAA
Found at i:11839993 original size:119 final size:109
Alignment explanation
Indices: 11839798--11840110 Score: 372
Period size: 119 Copynumber: 2.8 Consensus size: 109
11839788 GCCTATTTTA
* *
11839798 TTTTGTTTTTTTTTTTTAATTTTGATCAAAGTTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAA
1 TTTT-TTTTTTTTTTTTAA--TTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAA
11839863 CATAAAAAAAGCTCCTCTAAACAGAGGCTCAACTTTTTCTTTTTGTTTTCTTG
63 CAT-AAAAAAGCTCCTCTAAACAGAGGCT-AA---TTT-TTTTTGTTTTCTTG
*
11839916 CTCTCTTTTTTTTTTTTTTAAATTGATCAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGAGAA
1 -T-T-TTTTTTTTTTTTTT-AATTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAA
* *
11839981 ACATAAACAAAGCTCCTTTAAACAGAGG-TAATTTTTTTTGTTTTTTTG
62 ACATAAA-AAAGCTCCTCTAAACAGAGGCTAATTTTTTTTGTTTTCTTG
*
11840029 TTTTTTTTTTTTTTTT--TT--TCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGA-AAA-GT
1 TTTTTTTTTTTTTTTTAATTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACAT
**
11840088 -AAATTGCTCCTCTAAACAGAGGC
66 AAAAAAGCTCCTCTAAACAGAGGC
11840111 ACCACGACTC
Statistics
Matches: 179, Mismatches: 10, Indels: 27
0.83 0.05 0.12
Matches are distributed among these distances:
101 17 0.09
102 2 0.01
103 1 0.01
104 3 0.02
105 35 0.20
107 2 0.01
110 14 0.08
111 1 0.01
112 1 0.01
113 13 0.07
114 3 0.02
117 2 0.01
118 4 0.02
119 64 0.36
120 13 0.07
121 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (109 bp):
TTTTTTTTTTTTTTTTAATTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACAT
AAAAAAGCTCCTCTAAACAGAGGCTAATTTTTTTTGTTTTCTTG
Found at i:11840018 original size:1 final size:1
Alignment explanation
Indices: 11840012--11840047 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
11840002 ACAGAGGTAA
* *
11840012 TTTTTTTTGTTTTTTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11840048 CAAAGCTCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:11840183 original size:42 final size:41
Alignment explanation
Indices: 11840052--11840339 Score: 427
Period size: 41 Copynumber: 6.9 Consensus size: 41
11840042 TTTTTTCAAA
* *
11840052 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
11840093 GCTCCTCTAAACAGAGGCACCACGACTCTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
11840134 GCTCCTCTAAACAGTGGTACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
* *
11840176 GCTCCTCTAAACAAAGGCACCGCGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
11840217 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
*
11840259 GCT-C-CTAAAGCAGAGGCACCCACGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAA-CAGAGGCA-CCACGAC-TTTGAAAAGTAAATT
11840301 GCTCCTCTAAAACAGAGGCACCACGACTTCTGAAAAGTA
1 GCTCCTCT-AAACAGAGGCACCACGACTT-TGAAAAGTA
11840340 CCATGACTTT
Statistics
Matches: 224, Mismatches: 14, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
40 5 0.02
41 114 0.51
42 72 0.32
43 20 0.09
44 10 0.04
45 3 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:11840194 original size:83 final size:82
Alignment explanation
Indices: 11840052--11840339 Score: 427
Period size: 83 Copynumber: 3.5 Consensus size: 82
11840042 TTTTTTCAAA
* *
11840052 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
11840117 ACTCTGAAAAGTAAATT
66 ACTTTGAAAAGTAAATT
* * * *
11840134 GCTCCTCTAAACAGTGGTACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAAAGGCACCGC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
11840199 GACTTTGAAAAGTAAATT
65 GACTTTGAAAAGTAAATT
11840217 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCT-C-CTAAAGCAGAGGCACCC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATTGCTCCTCTAAA-CAGAGGCA-CC
*
11840280 ACGACTTTTGGAAAGTAAATT
63 ACGAC-TTTGAAAAGTAAATT
11840301 GCTCCTCTAAAACAGAGGCACCACGACTTCTGAAAAGTA
1 GCTCCTCT-AAACAGAGGCACCACGACTT-TGAAAAGTA
11840340 CCATGACTTT
Statistics
Matches: 188, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
81 5 0.03
82 35 0.19
83 97 0.52
84 22 0.12
85 26 0.14
86 3 0.02
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAGTAAATT
Found at i:11840437 original size:44 final size:43
Alignment explanation
Indices: 11840339--11840463 Score: 164
Period size: 44 Copynumber: 2.9 Consensus size: 43
11840329 TCTGAAAAGT
* *
11840339 ACCATGACTTTAGAAAAATAAATTGCTCCCTCTAAA-TAGAGGC
1 ACCATGACTTT-GAAAAATAAATTGCTCCCTCTAAACAAAAGGC
*
11840382 ACCATGACTTTGGAAAATAAATTGCTTCCCTCTAAACAAAAGGC
1 ACCATGACTTTGAAAAATAAATTGC-TCCCTCTAAACAAAAGGC
*
11840426 ACCACGACTTTGAAAAATAAATTGCAGT-CCTCTAAACA
1 ACCATGACTTTGAAAAATAAATTGC--TCCCTCTAAACA
11840464 GAGGCCCACT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
42 13 0.18
43 21 0.29
44 38 0.52
45 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (43 bp):
ACCATGACTTTGAAAAATAAATTGCTCCCTCTAAACAAAAGGC
Found at i:11842225 original size:10 final size:10
Alignment explanation
Indices: 11842210--11842285 Score: 75
Period size: 10 Copynumber: 7.3 Consensus size: 10
11842200 CTTTTTTTCA
11842210 TTTTCTCATT
1 TTTTCTCATT
11842220 TTTTCTTC-TT
1 TTTTC-TCATT
11842230 TCTTTCTCATT
1 T-TTTCTCATT
**
11842241 TTTTCTTTTT
1 TTTTCTCATT
11842251 TTTTCT-ATTT
1 TTTTCTCA-TT
11842261 TTTTCATCATTT
1 TTTTC-TCA-TT
11842273 TTTTCTCATT
1 TTTTCTCATT
11842283 TTT
1 TTT
11842286 CATCCATTGT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
10 35 0.61
11 13 0.23
12 9 0.16
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTCTCATT
Found at i:11842236 original size:21 final size:21
Alignment explanation
Indices: 11842210--11842285 Score: 102
Period size: 20 Copynumber: 3.6 Consensus size: 21
11842200 CTTTTTTTCA
11842210 TTTTCTCATTTTTTCTTCTTT
1 TTTTCTCATTTTTTCTTCTTT
*
11842231 CTTTCTCATTTTTTCTT-TTT
1 TTTTCTCATTTTTTCTTCTTT
*
11842251 TTTTCT-ATTTTTTTCATCATTT
1 TTTTCTCA-TTTTTTCTTC-TTT
11842273 TTTTCTCATTTTT
1 TTTTCTCATTTTT
11842286 CATCCATTGT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 1 0.02
20 16 0.33
21 16 0.33
22 14 0.29
23 1 0.02
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTCTCATTTTTTCTTCTTT
Found at i:11842245 original size:31 final size:32
Alignment explanation
Indices: 11842210--11842285 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
11842200 CTTTTTTTCA
11842210 TTTTCTCATTTTTTCT-TCTTTCTTTC-TCA-TT
1 TTTTCTCATTTTTTCTAT-TTT-TTTCATCATTT
**
11842241 TTTTCTTTTTTTTTCTATTTTTTTCATCATTT
1 TTTTCTCATTTTTTCTATTTTTTTCATCATTT
11842273 TTTTCTCATTTTT
1 TTTTCTCATTTTT
11842286 CATCCATTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 4 0.11
31 20 0.53
32 14 0.37
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (32 bp):
TTTTCTCATTTTTTCTATTTTTTTCATCATTT
Found at i:11842248 original size:18 final size:19
Alignment explanation
Indices: 11842220--11842263 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
11842210 TTTTCTCATT
11842220 TTTTCTTCTTTCTTTCTC-A
1 TTTT-TTCTTTCTTTCTCTA
* *
11842239 TTTTTTCTTTTTTTTTCTA
1 TTTTTTCTTTCTTTCTCTA
11842258 TTTTTT
1 TTTTTT
11842264 TCATCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTCTTTCTTTCTCTA
Found at i:11842253 original size:11 final size:10
Alignment explanation
Indices: 11842201--11842285 Score: 54
Period size: 11 Copynumber: 8.4 Consensus size: 10
11842191 TTTGAATATC
11842201 TTTTTTTCA-
1 TTTTTTTCAT
*
11842210 -TTTTCTCAT
1 TTTTTTTCAT
11842219 TTTTTCTTC-T
1 TTTTT-TTCAT
*
11842229 TTCTTTCTCA-
1 TT-TTTTTCAT
*
11842239 -TTTTTTCTT
1 TTTTTTTCAT
11842248 TTTTTTTCTAT
1 TTTTTTTC-AT
11842259 TTTTTTCATCAT
1 TTTTTT--TCAT
11842271 TTTTTTCTCAT
1 TTTTTT-TCAT
11842282 TTTT
1 TTTT
11842286 CATCCATTGT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
8 12 0.20
9 1 0.02
10 16 0.27
11 20 0.34
12 8 0.14
13 2 0.03
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:11842286 original size:21 final size:21
Alignment explanation
Indices: 11842210--11842289 Score: 94
Period size: 21 Copynumber: 3.9 Consensus size: 21
11842200 CTTTTTTTCA
*
11842210 TTTTCTCATTTTTTCTTCTTT
1 TTTTCTCATTTTTTCATCTTT
* *
11842231 CTTTCTCATTTTTTC-TTTTT
1 TTTTCTCATTTTTTCATCTTT
11842251 TTTTCT-ATTTTTTTCATCATTT
1 TTTTCTCA-TTTTTTCATC-TTT
11842273 TTTTCTCA-TTTTTCATC
1 TTTTCTCATTTTTTCATC
11842290 CATTGTTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.02
20 16 0.31
21 24 0.47
22 9 0.18
23 1 0.02
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCTCATTTTTTCATCTTT
Found at i:11846667 original size:4 final size:4
Alignment explanation
Indices: 11846658--11846688 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
11846648 TTTAACATTA
11846658 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
11846689 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Done.