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 124 of 129
Found at i:21423446 original size:18 final size:18
Alignment explanation
Indices: 21423423--21423458 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21423413 TTATTTTATA
21423423 AAAAATATATAAATTAAT
1 AAAAATATATAAATTAAT
*
21423441 AAAAATATATAATTTAAT
1 AAAAATATATAAATTAAT
21423459 TTGATTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAATATATAAATTAAT
Found at i:21423678 original size:20 final size:22
Alignment explanation
Indices: 21423653--21423699 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
21423643 ATTTCATAAG
21423653 ATATTACATTA-A-ACTAAATA
1 ATATTACATTAGACACTAAATA
* *
21423673 ATATTATATTAGACACTAATTA
1 ATATTACATTAGACACTAAATA
21423695 ATATT
1 ATATT
21423700 TTTCATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 1 0.04
22 12 0.52
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATTACATTAGACACTAAATA
Found at i:21432104 original size:32 final size:33
Alignment explanation
Indices: 21432036--21432114 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 33
21432026 TTTATTCATC
21432036 TTTTT-TTTTTT--ATATCTCAAAATTATATTA
1 TTTTTATTTTTTAAATATCTCAAAATTATATTA
*
21432066 TATTTTATTTTTTAAATATCT-AAAACTTTTATT-
1 T-TTTTATTTTTTAAATATCTCAAAA-TTATATTA
*
21432099 TTTTTATATTTTAAAT
1 TTTTTATTTTTTAAAT
21432115 TTATTTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 1 0.02
31 4 0.10
32 20 0.48
33 5 0.12
34 12 0.29
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (33 bp):
TTTTTATTTTTTAAATATCTCAAAATTATATTA
Found at i:21432107 original size:23 final size:23
Alignment explanation
Indices: 21432067--21432124 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
21432057 ATTATATTAT
21432067 ATTTTATTTTTTAAATATCTAAA
1 ATTTTATTTTTTAAATATCTAAA
* * *
21432090 ACTTTTATTTTTT-TATATTTTAA
1 A-TTTTATTTTTTAAATATCTAAA
21432113 A-TTTATTTTTTA
1 ATTTTATTTTTTA
21432125 TTTTTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 10 0.33
23 9 0.30
24 11 0.37
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTTATTTTTTAAATATCTAAA
Found at i:21432123 original size:20 final size:21
Alignment explanation
Indices: 21432093--21432132 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
21432083 ATCTAAAACT
21432093 TTTATTTTTTTATATTTTAAA
1 TTTATTTTTTTATATTTTAAA
*
21432114 TTTA-TTTTTTATTTTTTAA
1 TTTATTTTTTTATATTTTAA
21432133 TATTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTTTTTTATATTTTAAA
Found at i:21432142 original size:28 final size:28
Alignment explanation
Indices: 21432092--21432186 Score: 102
Period size: 28 Copynumber: 3.3 Consensus size: 28
21432082 TATCTAAAAC
* **
21432092 TTTTATTTTTTTATATTTTAAATTTATT
1 TTTTATTTTTTAATATTAAAAATTTATT
*
21432120 TTTTATTTTTTAATATTAAAAATTATAAAT
1 TTTTATTTTTTAATATTAAAAATT-T-ATT
* *
21432150 TTTTA-ATTTTAATATTAAATATATTATT
1 TTTTATTTTTTAATATTAAAAAT-TTATT
21432178 TTTTATTTT
1 TTTTATTTT
21432187 CATAAAATCC
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
28 28 0.51
29 19 0.35
30 8 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTATTTTTTAATATTAAAAATTTATT
Found at i:21432152 original size:29 final size:28
Alignment explanation
Indices: 21432092--21432186 Score: 75
Period size: 29 Copynumber: 3.3 Consensus size: 28
21432082 TATCTAAAAC
* ** **
21432092 TTTTATTTTTTTATATTTTAAATTTATT
1 TTTTATTTTTTAATATTAAAAATTTAAA
21432120 TTTTATTTTTTAATATTAAAAATTATAAA
1 TTTTATTTTTTAATATTAAAAATT-TAAA
* * **
21432149 TTTT-TAATTTTAATATTAAATATATTATT
1 TTTTAT-TTTTTAATATTAAAAAT-TTAAA
21432178 TTTTATTTT
1 TTTTATTTT
21432187 CATAAAATCC
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
28 22 0.42
29 29 0.55
30 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTATTTTTTAATATTAAAAATTTAAA
Found at i:21432177 original size:51 final size:51
Alignment explanation
Indices: 21432065--21432182 Score: 132
Period size: 50 Copynumber: 2.3 Consensus size: 51
21432055 AAATTATATT
* * ** *
21432065 ATATTTTATTTTTTAAATATCTAAAACTTTTATTTTTTTATATTTTAAATTT
1 ATATTTTATTTTTT-AATATCTAAAAATTATAAATTTTTATATTTTAAATTA
*
21432117 ATTTTTTATTTTTTAATAT-TAAAAATTATAAATTTTTA-ATTTTAATATTAA
1 ATATTTTATTTTTTAATATCTAAAAATTATAAATTTTTATATTTTAA-ATT-A
*
21432168 ATATATTATTTTTTA
1 ATATTTTATTTTTTA
21432183 TTTTCATAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
49 7 0.12
50 18 0.32
51 18 0.32
52 13 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (51 bp):
ATATTTTATTTTTTAATATCTAAAAATTATAAATTTTTATATTTTAAATTA
Found at i:21455379 original size:16 final size:16
Alignment explanation
Indices: 21455355--21455386 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21455345 CTCTCTGGAA
21455355 CCTGAAGCATCCCAAG
1 CCTGAAGCATCCCAAG
*
21455371 CCTGGAGCATCCCAAG
1 CCTGAAGCATCCCAAG
21455387 AGGGAAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.38, G:0.22, T:0.12
Consensus pattern (16 bp):
CCTGAAGCATCCCAAG
Found at i:21468474 original size:23 final size:23
Alignment explanation
Indices: 21468445--21468489 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
21468435 TAATTATTAT
21468445 TATTATAATTATAATTAAAAAAA
1 TATTATAATTATAATTAAAAAAA
* *
21468468 TATTATAGTTATGATTAAAAAA
1 TATTATAATTATAATTAAAAAA
21468490 TTTTCATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
TATTATAATTATAATTAAAAAAA
Found at i:21468524 original size:14 final size:13
Alignment explanation
Indices: 21468481--21468526 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
21468471 TATAGTTATG
21468481 ATTAAAAAATTTTC
1 ATTAAAAAA-TTTC
21468495 A-TAAAAAATTT-
1 ATTAAAAAATTTC
*
21468506 TTTAAATAAATTTC
1 ATTAAA-AAATTTC
21468520 ATTAAAA
1 ATTAAAA
21468527 TTAATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
12 7 0.26
13 14 0.52
14 6 0.22
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTAAAAAATTTC
Found at i:21468546 original size:23 final size:25
Alignment explanation
Indices: 21468512--21468557 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
21468502 ATTTTTTAAA
21468512 TAAATTTCATTAA-AAT-TAATATT
1 TAAATTTCATTAATAATCTAATATT
21468535 TAAA-TTCAATTAATAATCTAATA
1 TAAATTTC-ATTAATAATCTAATA
21468558 GGCTTAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.15
23 9 0.45
24 3 0.15
25 5 0.25
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAATTTCATTAATAATCTAATATT
Found at i:21473535 original size:24 final size:23
Alignment explanation
Indices: 21473503--21473569 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 23
21473493 TGCAGGGATT
* *
21473503 TTTTTTAATTAAATTAAATTAATA
1 TTTTATAATTAAAATAAATT-ATA
21473527 TTTTATAATTAAAAATAAATTATA
1 TTTTATAATT-AAAATAAATTATA
21473551 TTTTATAATTAAAAATAAA
1 TTTTATAATT-AAAATAAA
21473570 AATAAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
24 31 0.77
25 9 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTTATAATTAAAATAAATTATA
Found at i:21479258 original size:9 final size:9
Alignment explanation
Indices: 21479244--21479273 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
21479234 AATATTTTAT
21479244 TAATTAAAA
1 TAATTAAAA
21479253 TAATTAAAA
1 TAATTAAAA
21479262 TATATTAAAA
1 TA-ATTAAAA
21479272 TA
1 TA
21479274 TAAAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:21479270 original size:10 final size:10
Alignment explanation
Indices: 21479246--21479275 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21479236 TATTTTATTA
21479246 ATTAAAATA-
1 ATTAAAATAT
21479255 ATTAAAATAT
1 ATTAAAATAT
21479265 ATTAAAATAT
1 ATTAAAATAT
21479275 A
1 A
21479276 AAAATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:21481089 original size:19 final size:19
Alignment explanation
Indices: 21481065--21481101 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21481055 CACAGAAAAA
21481065 ATGAACAAG-GAGAAAAATG
1 ATGAACAAGTG-GAAAAATG
21481084 ATGAACAAGTGGAAAAAT
1 ATGAACAAGTGGAAAAAT
21481102 AAAAGGAAAG
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:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (19 bp):
ATGAACAAGTGGAAAAATG
Found at i:21485864 original size:22 final size:24
Alignment explanation
Indices: 21485839--21485887 Score: 84
Period size: 22 Copynumber: 2.1 Consensus size: 24
21485829 TTAGAAATAA
21485839 TATATACAAATA-T-AATATTAAT
1 TATATACAAATATTAAATATTAAT
21485861 TATATACAAATATTAAATATTAAT
1 TATATACAAATATTAAATATTAAT
21485885 TAT
1 TAT
21485888 CAATATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 12 0.48
23 1 0.04
24 12 0.48
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TATATACAAATATTAAATATTAAT
Found at i:21488779 original size:20 final size:19
Alignment explanation
Indices: 21488754--21488792 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
21488744 AAATTAACGG
*
21488754 GATAATTTAAAATATAATAT
1 GATAATATAAAATA-AATAT
21488774 GATAATATAAAATAAATAT
1 GATAATATAAAATAAATAT
21488793 AATATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
GATAATATAAAATAAATAT
Found at i:21488793 original size:11 final size:11
Alignment explanation
Indices: 21488763--21488809 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
21488753 GGATAATTTA
*
21488763 AAATATAATAT
1 AAATATAAAAT
21488774 GATAATATAAAAT
1 -A-AATATAAAAT
*
21488787 AAATATAATAT
1 AAATATAAAAT
21488798 AAATATAAAAT
1 AAATATAAAAT
21488809 A
1 A
21488810 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 20 0.65
12 2 0.06
13 9 0.29
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:21488794 original size:24 final size:22
Alignment explanation
Indices: 21488763--21488831 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 22
21488753 GGATAATTTA
21488763 AAATATAATATGATAATATAAAAT
1 AAATATAATAT-A-AATATAAAAT
21488787 AAATATAATATAAATATAAAAT
1 AAATATAATATAAATATAAAAT
* *
21488809 ATTAAAATAATAT-AATTTAAAAT
1 A--AATATAATATAAATATAAAAT
21488832 TTTAATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
22 11 0.27
23 10 0.24
24 20 0.49
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (22 bp):
AAATATAATATAAATATAAAAT
Found at i:21488796 original size:16 final size:16
Alignment explanation
Indices: 21488775--21488831 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
21488765 ATATAATATG
21488775 ATAATATAAAATAAAT
1 ATAATATAAAATAAAT
21488791 ATAATATAAATATAAA-
1 ATAATATAAA-ATAAAT
21488807 AT-AT-TAAAAT-AAT
1 ATAATATAAAATAAAT
*
21488820 ATAATTTAAAAT
1 ATAATATAAAAT
21488832 TTTAATAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.05
13 4 0.11
14 6 0.16
15 8 0.22
16 12 0.32
17 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATATAAAATAAAT
Found at i:21488809 original size:29 final size:30
Alignment explanation
Indices: 21488764--21488829 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
21488754 GATAATTTAA
*
21488764 AATAT-AATATGATAATA-TAAAATAAATAT
1 AATATAAATATGAAAATATTAAAAT-AATAT
21488793 AATATAAATAT-AAAATATTAAAATAATAT
1 AATATAAATATGAAAATATTAAAATAATAT
*
21488822 AATTTAAA
1 AATATAAA
21488830 ATTTTAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 22 0.67
30 11 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AATATAAATATGAAAATATTAAAATAATAT
Found at i:21488841 original size:24 final size:23
Alignment explanation
Indices: 21488755--21488852 Score: 75
Period size: 24 Copynumber: 4.4 Consensus size: 23
21488745 AATTAACGGG
21488755 ATAATTTAAAATA-T--AAT-AT
1 ATAATTTAAAATATTAAAATAAT
* *
21488774 GATAATATAAAATA--AATATAAT
1 -ATAATTTAAAATATTAAAATAAT
*
21488796 ATAAATATAAAATATTAAAATAAT
1 AT-AATTTAAAATATTAAAATAAT
*
21488820 ATAATTTAAAATTTTAATAATAAT
1 ATAATTTAAAATATTAA-AATAAT
21488844 -TATATTTAA
1 ATA-ATTTAA
21488853 TTTAATAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
20 12 0.18
21 4 0.06
22 13 0.20
23 15 0.23
24 21 0.32
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (23 bp):
ATAATTTAAAATATTAAAATAAT
Found at i:21490488 original size:27 final size:26
Alignment explanation
Indices: 21490458--21490520 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 26
21490448 TAAAGATAAG
* * *
21490458 ATAATATTATTTTATTTTATTTTATTT
1 ATAATATTATTTTATTATATTCTA-TC
21490485 ATAATATTATTTTATTATATTCTATC
1 ATAATATTATTTTATTATATTCTATC
21490511 ATAATATTAT
1 ATAATATTAT
21490521 ATATTAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 11 0.33
27 22 0.67
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (26 bp):
ATAATATTATTTTATTATATTCTATC
Found at i:21500241 original size:134 final size:134
Alignment explanation
Indices: 21500057--21500331 Score: 437
Period size: 134 Copynumber: 2.1 Consensus size: 134
21500047 CCCCAATGTG
*
21500057 CTCATAGAAGTACAGTAGCAGAGCCCTTTTTCATATAAGTCCAGTTGCAGGAAGCATGCAGGGAT
1 CTCATAGAAGTACAGTAGCAGAGCCCTTTTTCATATAAGTCCAGTTGCAGGAAGCATGCAAGGAT
* * * *
21500122 ATCCTTTGATAAAAGATTTAGATATTGTTTAAGAACTTTCTCAAGCAACAGCATCATGATTTCTT
66 ATCCTTTGACAAAAGATCTAGATATTGTTTAAAAACTTTCTCAAGCAACAGAATCATGATTTCTT
21500187 AATA
131 AATA
* *
21500191 CTCATAGCAAG-ACAGTAGCAGAGCCCTTTTTCGTATAAGTCCAGTTGCAGGAAGCATGCAATGA
1 CTCATAG-AAGTACAGTAGCAGAGCCCTTTTTCATATAAGTCCAGTTGCAGGAAGCATGCAAGGA
* *
21500255 TATCCTTTGGCAAAAGATCTAGATATTGTTTAAAAACTTTCTCAAGCAACATAATCATGATTTCT
65 TATCCTTTGACAAAAGATCTAGATATTGTTTAAAAACTTTCTCAAGCAACAGAATCATGATTTCT
*
21500320 TAATG
130 TAATA
21500325 CT-ATAGA
1 CTCATAGA
21500332 TCCATCTTTA
Statistics
Matches: 130, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
132 1 0.01
133 4 0.03
134 122 0.94
135 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (134 bp):
CTCATAGAAGTACAGTAGCAGAGCCCTTTTTCATATAAGTCCAGTTGCAGGAAGCATGCAAGGAT
ATCCTTTGACAAAAGATCTAGATATTGTTTAAAAACTTTCTCAAGCAACAGAATCATGATTTCTT
AATA
Found at i:21502089 original size:2 final size:2
Alignment explanation
Indices: 21502082--21502116 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
21502072 GCCATTGAAA
*
21502082 TC TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
21502117 TCAGTGTAGC
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:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:21502806 original size:16 final size:14
Alignment explanation
Indices: 21502781--21502828 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
21502771 ATTTTAATAA
21502781 ATTTTAATATATATAT
1 ATTTTAATATA-A-AT
*
21502797 ATTTTGATATAAAT
1 ATTTTAATATAAAT
*
21502811 ATTTTTAATAAAAAT
1 A-TTTTAATATAAAT
21502826 ATT
1 ATT
21502829 AATAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 5 0.18
15 13 0.46
16 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
ATTTTAATATAAAT
Found at i:21502983 original size:14 final size:12
Alignment explanation
Indices: 21502949--21502992 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
21502939 AGTTATCGAT
*
21502949 TTAAATTTTTTA
1 TTAAAATTTTTA
21502961 TTAAAATTTTTA
1 TTAAAATTTTTA
21502973 TTAAATCATTTTTA
1 TTAAA--ATTTTTA
*
21502987 ATAAAA
1 TTAAAA
21502993 AATTTTACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 17 0.61
14 11 0.39
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAAAATTTTTA
Found at i:21511447 original size:19 final size:22
Alignment explanation
Indices: 21511408--21511448 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
21511398 TTTATTTAAA
21511408 ATTTAATAATATAATATTTTTT
1 ATTTAATAATATAATATTTTTT
21511430 ATTT-ATAAT-TAA-ATTTTTT
1 ATTTAATAATATAATATTTTTT
21511449 TATAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 3 0.16
21 5 0.26
22 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTAATAATATAATATTTTTT
Found at i:21517700 original size:24 final size:24
Alignment explanation
Indices: 21517670--21517724 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
21517660 CTGTGGAGAT
* *
21517670 TGATGATGCTT-TGGTGATTGAAGA
1 TGATGATACTTCTGATGA-TGAAGA
*
21517694 TGATGATATTTCTGATGATGAAGA
1 TGATGATACTTCTGATGATGAAGA
21517718 TGATGAT
1 TGATGAT
21517725 CATGATGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (24 bp):
TGATGATACTTCTGATGATGAAGA
Found at i:21533170 original size:17 final size:17
Alignment explanation
Indices: 21533148--21533182 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
21533138 CTTCAACTTT
21533148 ACTTCAGAAGAAGGGAA
1 ACTTCAGAAGAAGGGAA
*
21533165 ACTTCAGAAGATGGGAA
1 ACTTCAGAAGAAGGGAA
21533182 A
1 A
21533183 GCTCTCCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.29, T:0.14
Consensus pattern (17 bp):
ACTTCAGAAGAAGGGAA
Found at i:21533844 original size:2 final size:2
Alignment explanation
Indices: 21533837--21533868 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21533827 CCCTAAATCG
21533837 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
21533869 CTTCCTTCAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:21542285 original size:21 final size:20
Alignment explanation
Indices: 21542260--21542332 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 20
21542250 AAAAAGTAGA
21542260 AAAATCATAAAAAATAATTTT
1 AAAAT-ATAAAAAATAATTTT
21542281 AAAATATAAAAAATTAAGAATTTT
1 AAAATATAAAAAA-T---AATTTT
21542305 -AAATATTAAAAAAATAATTTT
1 AAAATA-T-AAAAAATAATTTT
*
21542326 AGAATAT
1 AAAATAT
21542333 TTCCAAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
20 8 0.18
21 13 0.30
22 4 0.09
23 5 0.11
24 8 0.18
25 6 0.14
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATATAAAAAATAATTTT
Found at i:21543928 original size:17 final size:17
Alignment explanation
Indices: 21543906--21543940 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21543896 TGAATTCTCC
*
21543906 TAATTATAATTTTAATT
1 TAATTAAAATTTTAATT
*
21543923 TAATTAAAATTTTTATT
1 TAATTAAAATTTTAATT
21543940 T
1 T
21543941 TTAATTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATTAAAATTTTAATT
Found at i:21549462 original size:16 final size:16
Alignment explanation
Indices: 21549441--21549496 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
21549431 TCCTTGCTCA
21549441 CTTTCTTTCTTCTTCT
1 CTTTCTTTCTTCTTCT
*
21549457 CTTTCTTTCTTCTCCT
1 CTTTCTTTCTTCTTCT
*
21549473 -TTTC-TCCTTCTTCT
1 CTTTCTTTCTTCTTCT
*
21549487 TTTTCCTTTC
1 CTTT-CTTTC
21549497 GGCCTTCACT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 8 0.24
15 7 0.21
16 16 0.48
17 2 0.06
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTCTTCTTCT
Found at i:21550762 original size:19 final size:19
Alignment explanation
Indices: 21550738--21550774 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21550728 GAGATTAACA
21550738 GAAAATTCAT-GAGGATTTG
1 GAAAATTC-TCGAGGATTTG
21550757 GAAAATTCTCGAGGATTT
1 GAAAATTCTCGAGGATTT
21550775 CGATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.32
Consensus pattern (19 bp):
GAAAATTCTCGAGGATTTG
Found at i:21552195 original size:21 final size:22
Alignment explanation
Indices: 21552147--21552214 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 22
21552137 TTGATCAGAT
* *
21552147 TTAATATTAA-TTCATATATATA
1 TTAATA-TAATTTTATATATAAA
21552169 -TAA-ATAATTTTATATATAAA
1 TTAATATAATTTTATATATAAA
21552189 TTAAATATAATTTTAT-TA-AAA
1 TT-AATATAATTTTATATATAAA
21552210 TTAAT
1 TTAAT
21552215 TTATTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.08
20 14 0.35
21 9 0.22
22 4 0.10
23 10 0.25
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATATAATTTTATATATAAA
Found at i:21552201 original size:23 final size:21
Alignment explanation
Indices: 21552172--21552213 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
21552162 ATATATATAA
21552172 ATAATTTTATATATAAATTAAAT
1 ATAATTTTAT-TA-AAATTAAAT
21552195 ATAATTTTATTAAAATTAA
1 ATAATTTTATTAAAATTAA
21552214 TTTATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATTTTATTAAAATTAAAT
Found at i:21552213 original size:57 final size:59
Alignment explanation
Indices: 21552147--21552258 Score: 138
Period size: 57 Copynumber: 1.9 Consensus size: 59
21552137 TTGATCAGAT
* *
21552147 TTAATATTAATTCATATATATATAAATAA-TTTT-ATATATAAATTAAATATAATTTTA
1 TTAAAATTAATTCATATATATATAAAAAATTTTTGATATATAAATTAAATATAATTTTA
* * * * * *
21552204 TTAAAATTAATTTATTTATTTTTAAAAAATTTTTGTTATATAAATTAAATTTAAT
1 TTAAAATTAATTCATATATATATAAAAAATTTTTGATATATAAATTAAATATAAT
21552259 AAAAAAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
57 23 0.51
58 4 0.09
59 18 0.40
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (59 bp):
TTAAAATTAATTCATATATATATAAAAAATTTTTGATATATAAATTAAATATAATTTTA
Found at i:21561979 original size:163 final size:164
Alignment explanation
Indices: 21561703--21562027 Score: 573
Period size: 163 Copynumber: 2.0 Consensus size: 164
21561693 TTCTCACCCT
21561703 AAATATCCATCAATTTTGCATCTTCAAGCCTTCAACTACTCTTGAAACTTATATATATGGTTATT
1 AAATATCCATCAATTTTGCATCTTCAAGCCTTCAACTACTCTTGAAACTTATATATATGGTTATT
* *
21561768 TACATGCATCTCAAATGACTTTTTGATAATTTTGATTTGAATAAGATTAAAAATAGTAGGTAGGG
66 TACATGCATCTCAAATGACTTTTTGATAATTTTGATTTGAATAAGATTAAAAATAGGAGCTAGGG
21561833 GAGTGAATATTTAACCT-TAACCTTCAAATAATCA
131 GAGTGAATATTTAA-CTATAACCTTCAAATAATCA
* *
21561867 AAATTTCCATCAATTTTGCATCTTCAAGCCTTCAACTGCTCTTGAAACTTA-ATATATGGTTATT
1 AAATATCCATCAATTTTGCATCTTCAAGCCTTCAACTACTCTTGAAACTTATATATATGGTTATT
* *
21561931 TACATGCTTCTCAAATGACTTTTTGATAATTTTGATTTGAATAAGATTAAATATAGGAGCTAGGG
66 TACATGCATCTCAAATGACTTTTTGATAATTTTGATTTGAATAAGATTAAAAATAGGAGCTAGGG
21561996 GAGTGAATATTTAACTATAACCTTCAAATAAT
131 GAGTGAATATTTAACTATAACCTTCAAATAAT
21562028 GATTTTTTTT
Statistics
Matches: 154, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
162 2 0.01
163 103 0.67
164 49 0.32
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (164 bp):
AAATATCCATCAATTTTGCATCTTCAAGCCTTCAACTACTCTTGAAACTTATATATATGGTTATT
TACATGCATCTCAAATGACTTTTTGATAATTTTGATTTGAATAAGATTAAAAATAGGAGCTAGGG
GAGTGAATATTTAACTATAACCTTCAAATAATCA
Found at i:21564883 original size:29 final size:29
Alignment explanation
Indices: 21564849--21564907 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
21564839 ATTCTTTTAA
**
21564849 TTGGATTCTCTCCAAA-CTTGTTTAATTCT
1 TTGGATTCTCT-CAAATCTAATTTAATTCT
21564878 TTGGATTCTCTCAAATCTAATTTAATTCT
1 TTGGATTCTCTCAAATCTAATTTAATTCT
21564907 T
1 T
21564908 CCTTAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (29 bp):
TTGGATTCTCTCAAATCTAATTTAATTCT
Found at i:21568631 original size:36 final size:37
Alignment explanation
Indices: 21568586--21568655 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
21568576 ATAAAATATT
*
21568586 TAAATATTTAAATTT-ATTTATTAAAAAATTAAATTAC
1 TAAATATTTAAATTTAATTTAAT-AAAAATTAAATTAC
*
21568623 TAAA-ATTTAAATTTAATTTAATAATAATTAAAT
1 TAAATATTTAAATTTAATTTAATAAAAATTAAAT
21568656 CAAATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (37 bp):
TAAATATTTAAATTTAATTTAATAAAAATTAAATTAC
Found at i:21568638 original size:21 final size:21
Alignment explanation
Indices: 21568614--21568655 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
21568604 TATTAAAAAA
*
21568614 TTAAATTACTAA-AATTTAAAT
1 TTAAATTAATAATAA-TTAAAT
*
21568635 TTAATTTAATAATAATTAAAT
1 TTAAATTAATAATAATTAAAT
21568656 CAAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAATTAATAATAATTAAAT
Found at i:21569163 original size:23 final size:22
Alignment explanation
Indices: 21569137--21569194 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
21569127 TTTTTTACAC
21569137 AATTTATATTATAAAAATTAATT
1 AATTTATATTATAAAAATTAA-T
* *
21569160 AATTAATATATTAT-TAATTTAAT
1 AATT--TATATTATAAAAATTAAT
21569183 AATTTA-ATTATA
1 AATTTATATTATA
21569195 TTTTATCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 5 0.17
21 2 0.07
23 9 0.30
24 6 0.20
25 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTATATTATAAAAATTAAT
Found at i:21569194 original size:25 final size:26
Alignment explanation
Indices: 21569140--21569196 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
21569130 TTTACACAAT
21569140 TTATATTATAAAAATTAATTAATTAA
1 TTATATTATAAAAATTAATTAATTAA
* *
21569166 -TATATTAT-TAATTTAA-TAATTTAA
1 TTATATTATAAAAATTAATTAA-TTAA
21569190 TTATATT
1 TTATATT
21569197 TTATCATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 3 0.11
24 10 0.37
25 14 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTATATTATAAAAATTAATTAATTAA
Found at i:21569722 original size:17 final size:18
Alignment explanation
Indices: 21569690--21569727 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
21569680 TTTTGATTAA
21569690 TATTTTTTAAGGTTAAATT
1 TATTTTTTAA-GTTAAATT
21569709 TATTTTTTAA-TTAAATT
1 TATTTTTTAAGTTAAATT
21569726 TA
1 TA
21569728 AAGAGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TATTTTTTAAGTTAAATT
Found at i:21569951 original size:26 final size:26
Alignment explanation
Indices: 21569904--21569975 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 26
21569894 CCCTAAGATA
* * *
21569904 TATATAAATAT-TATTTATTTAATTT
1 TATATTAATATATATTAATTTAATAT
21569929 TATATTAATATATATTAATTTAAATAT
1 TATATTAATATATATTAATTT-AATAT
21569956 TAT-TT-A-ATATATTAATTTAA
1 TATATTAATATATATTAATTTAA
21569976 GATGTTAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.05
24 12 0.29
25 11 0.26
26 10 0.24
27 7 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TATATTAATATATATTAATTTAATAT
Found at i:21569970 original size:24 final size:28
Alignment explanation
Indices: 21569938--21570002 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 28
21569928 TTATATTAAT
21569938 ATATATTAATTTAA-ATATT-A-TT-TA
1 ATATATTAATTTAAGATATTAATTTATA
*
21569962 ATATATTAATTTAAGATGTTAATTTATA
1 ATATATTAATTTAAGATATTAATTTATA
*
21569990 AAATATTAATTTA
1 ATATATTAATTTA
21570003 TAACTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 14 0.40
25 4 0.11
26 1 0.03
27 2 0.06
28 14 0.40
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
ATATATTAATTTAAGATATTAATTTATA
Found at i:21569996 original size:28 final size:24
Alignment explanation
Indices: 21569940--21570002 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 24
21569930 ATATTAATAT
*
21569940 ATATTAATTTAAATATTATTTAAT
1 ATATTAATTTAAATATTATTTAAA
*
21569964 ATATTAATTTAAGATGTTAATTTATAAA
1 ATATTAATTTAA-ATATT-A-TT-TAAA
21569992 ATATTAATTTA
1 ATATTAATTTA
21570003 TAACTTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 12 0.36
25 4 0.12
26 1 0.03
27 2 0.06
28 14 0.42
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (24 bp):
ATATTAATTTAAATATTATTTAAA
Found at i:21576906 original size:21 final size:20
Alignment explanation
Indices: 21576877--21576925 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
21576867 TTAAACATAC
*
21576877 ATAAATATAAT-CATATATAT
1 ATAATTATAATACA-ATATAT
*
21576897 ATATATTATATTACAATATAT
1 ATA-ATTATAATACAATATAT
21576918 ATAATTAT
1 ATAATTAT
21576926 CAGATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 8 0.32
21 15 0.60
22 2 0.08
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATTATAATACAATATAT
Found at i:21577246 original size:19 final size:19
Alignment explanation
Indices: 21577209--21577260 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
21577199 AATTAACATG
21577209 AATA-TTTAAAT-TTATTAT
1 AATATTTTAAATATTA-TAT
21577227 AAT-TTTTAAAATATTATAT
1 AATATTTT-AAATATTATAT
21577246 AATATTTTAAATATT
1 AATATTTTAAATATT
21577261 TTTATAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.20
19 17 0.57
20 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTTTAAATATTATAT
Found at i:21577266 original size:20 final size:20
Alignment explanation
Indices: 21577209--21577267 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
21577199 AATTAACATG
*
21577209 AATA-TTTAAAT-TTATTAT
1 AATATTTTAAATATTTTTAT
*
21577227 AAT-TTTTAAA-ATATTATAT
1 AATATTTTAAATAT-TTTTAT
21577246 AATATTTTAAATATTTTTAT
1 AATATTTTAAATATTTTTAT
21577266 AA
1 AA
21577268 ATTATCTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 10 0.30
19 7 0.21
20 14 0.42
21 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATTTTAAATATTTTTAT
Found at i:21577633 original size:233 final size:230
Alignment explanation
Indices: 21577147--21577751 Score: 706
Period size: 233 Copynumber: 2.6 Consensus size: 230
21577137 ACGTAACCTT
* *
21577147 ATCTCAATTTAAAATTAATTTTAAAATAATTTATCTTTTTTAATTTATCTGA-AATTAACATGAA
1 ATCTAAATTTAAAACTAATTTTAAAATAATTTATCTTTTTTAATTTATCT-ACAATTAACATGAA
* * * * *
21577211 TATTTAAATTTATTATAATTTTTAAAATATTATATAATATTTTAAATATTTTTATAAATTATCTT
65 TATTTAAATTTATCACAACTTTTAAAATATTATTTAATATTTT-AATATTTTTATAAATAATCTT
** * * * *
21577276 TACATTATCTTTAGTTTTTAAATATATTTCATAAATAAAATGTGAAAAACAAAATATAAATATCA
129 TACATTATCTCCAGCTTTTAAATATATTTCAGAAATAAAATATGAAAAACAAAATATAAATACCA
* ** * * *
21577341 TAGTAACTTTAGGAAATATTCTCTTATATATCACCTC
194 AAACAACTTTAGAAAATATTCTATTATATATCACATC
* *
21577378 ATC-ATAATTTAAAACTAATTTTAAAATAATTTATTTTTTTTAATTTATCTACAATTAACATAAA
1 ATCTA-AATTTAAAACTAATTTTAAAATAATTTATCTTTTTTAATTTATCTACAATTAACATGAA
21577442 TATTTAAATTTATCACATA-TTTTAAAATTATTATTTAATATATTTAATATGTTTTATAAATAAT
65 TATTTAAATTTATCACA-ACTTTTAAAA-TATTATTTAATAT-TTTAATAT-TTTTATAAATAAT
*
21577506 CTTTACATTATCTCCAGCTTTTAAATATATTTCACGAAA-AAATATATG-AAAAGAAAATATAAA
126 CTTTACATTATCTCCAGCTTTTAAATATATTTCA-GAAATAAA-ATATGAAAAACAAAATATAAA
* * *
21577569 TACCAAAACAACTTCTA-AAAAGT-TTTTATTGTATTTCACATC
189 TACCAAAACAACTT-TAGAAAA-TATTCTATTATATATCACATC
* * * * *
21577611 ATCTAAATTTAAAACAAATTTTAAAATAATATATCATTTTTAATTTATCTACAGTTAATATGAAT
1 ATCTAAATTTAAAACTAATTTTAAAATAATTTATCTTTTTTAATTTATCTACAATTAACATGAAT
* *
21577676 ATTTAAAAATT-TCACAACTTTTAAAAATATTATTTCATATTTGTAATATTTTTTATAAATAAT-
66 ATTT-AAATTTATCACAACTTTT-AAAATATTATTTAATATTT-TAATA-TTTTTATAAATAATC
*
21577739 TATTGCATTATCT
127 T-TTACATTATCT
21577752 TTTTTAAATA
Statistics
Matches: 323, Mismatches: 34, Indels: 32
0.83 0.09 0.08
Matches are distributed among these distances:
230 1 0.00
231 80 0.25
232 22 0.07
233 199 0.62
234 21 0.07
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (230 bp):
ATCTAAATTTAAAACTAATTTTAAAATAATTTATCTTTTTTAATTTATCTACAATTAACATGAAT
ATTTAAATTTATCACAACTTTTAAAATATTATTTAATATTTTAATATTTTTATAAATAATCTTTA
CATTATCTCCAGCTTTTAAATATATTTCAGAAATAAAATATGAAAAACAAAATATAAATACCAAA
ACAACTTTAGAAAATATTCTATTATATATCACATC
Found at i:21578225 original size:2 final size:2
Alignment explanation
Indices: 21578218--21578246 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21578208 TAATCATCTA
21578218 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21578247 TACAACATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:21579182 original size:19 final size:18
Alignment explanation
Indices: 21579160--21579197 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 18
21579150 TATTTTTATT
21579160 AAAAATGATTAAAAATAAAA
1 AAAAAT-ATTAAAAA-AAAA
21579180 AAAAATATTAAAAAAAAA
1 AAAAATATTAAAAAAAAA
21579198 GTTTTTAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAATATTAAAAAAAAA
Found at i:21579562 original size:18 final size:20
Alignment explanation
Indices: 21579534--21579572 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
21579524 GCAAATAAAT
21579534 TGAAGAAAATATTTTT-TAA
1 TGAAGAAAATATTTTTATAA
21579553 TGAA-AAAATATTTTTATAA
1 TGAAGAAAATATTTTTATAA
21579572 T
1 T
21579573 TCTTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
TGAAGAAAATATTTTTATAA
Found at i:21579567 original size:19 final size:19
Alignment explanation
Indices: 21579534--21579572 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21579524 GCAAATAAAT
*
21579534 TGAAGAAAATATTTTTTAA
1 TGAAGAAAATATTTTATAA
21579553 TGAA-AAAATATTTTTATAA
1 TGAAGAAAATA-TTTTATAA
21579572 T
1 T
21579573 TCTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (19 bp):
TGAAGAAAATATTTTATAA
Found at i:21580000 original size:16 final size:15
Alignment explanation
Indices: 21579957--21579993 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
21579947 ATTATTCATA
21579957 AAAAAATAA--AA-T
1 AAAAAATAATTAATT
21579969 AAAAAATAATTAATT
1 AAAAAATAATTAATT
21579984 AAAAAATAAT
1 AAAAAATAAT
21579994 CTTATTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.41
14 2 0.09
15 11 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAAATAATTAATT
Found at i:21585125 original size:11 final size:11
Alignment explanation
Indices: 21585109--21585138 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21585099 ATCCCATAAA
21585109 AGATTTGTTTG
1 AGATTTGTTTG
21585120 AGATTTGTTTG
1 AGATTTGTTTG
*
21585131 GGATTTGT
1 AGATTTGT
21585139 CAGATATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (11 bp):
AGATTTGTTTG
Found at i:21585251 original size:52 final size:52
Alignment explanation
Indices: 21585163--21585319 Score: 210
Period size: 52 Copynumber: 3.0 Consensus size: 52
21585153 TGGACAAGAA
* * *
21585163 GACTTACAAAAGAAGAATT-TCAAAA-GAAAGAAGATTCTTAATAGGTAAGTTT
1 GACTTACAAGAGAAGAATTCT-AAAAGGAAAG-GGATTCTTAATAGGCAAGTTT
*
21585215 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTACAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
* * * *
21585267 GACTTACAGGAGAAGAATTCTAAATGGAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTACAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
21585319 G
1 G
21585320 TATGGTTATA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 88 0.94
53 6 0.06
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (52 bp):
GACTTACAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:21585848 original size:31 final size:31
Alignment explanation
Indices: 21585810--21585919 Score: 159
Period size: 31 Copynumber: 3.5 Consensus size: 31
21585800 TTAGCCCAAT
21585810 AAATGGTATCAGAGCTGTGGTGATCCTC-AAC
1 AAATGGTATCAGAGCTGTGGTGATCC-CAAAC
*
21585841 AAATGGTATCAGCGCTGTGGTGATCCCAAAC
1 AAATGGTATCAGAGCTGTGGTGATCCCAAAC
* *
21585872 AAGTGGTATCAGAGCTGTGGTGATCCCTAAC
1 AAATGGTATCAGAGCTGTGGTGATCCCAAAC
* *
21585903 AAGTGTTATCAGAGCTG
1 AAATGGTATCAGAGCTG
21585920 AACGTTCGAA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
30 1 0.01
31 72 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (31 bp):
AAATGGTATCAGAGCTGTGGTGATCCCAAAC
Found at i:21585951 original size:25 final size:26
Alignment explanation
Indices: 21585923--21586038 Score: 75
Period size: 25 Copynumber: 4.7 Consensus size: 26
21585913 AGAGCTGAAC
*
21585923 GTTCGAAACATGAGAAGAGTC-GAAT-
1 GTTCGAGACATGAGAAGAGTCTG-ATG
**
21585948 GTTCGAGATGTGAGAAGAG-CTGATG
1 GTTCGAGACATGAGAAGAGTCTGATG
* **
21585973 GTTCGAGACATGGGAAGAGT-TGACA
1 GTTCGAGACATGAGAAGAGTCTGATG
* * *
21585998 GTTCGAGATATGGGAAAAG-CT--TG
1 GTTCGAGACATGAGAAGAGTCTGATG
* *
21586021 GTTTGAGATATGAGAAGA
1 GTTCGAGACATGAGAAGA
21586039 AGTAAGCTTA
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
23 15 0.21
24 3 0.04
25 54 0.75
ACGTcount: A:0.34, C:0.09, G:0.34, T:0.23
Consensus pattern (26 bp):
GTTCGAGACATGAGAAGAGTCTGATG
Found at i:21586265 original size:11 final size:11
Alignment explanation
Indices: 21586249--21586278 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21586239 ATCCCATAAA
21586249 AGATTTGTTTG
1 AGATTTGTTTG
21586260 AGATTTGTTTG
1 AGATTTGTTTG
*
21586271 GGATTTGT
1 AGATTTGT
21586279 CAGATATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (11 bp):
AGATTTGTTTG
Found at i:21586390 original size:52 final size:52
Alignment explanation
Indices: 21586303--21586459 Score: 203
Period size: 52 Copynumber: 3.0 Consensus size: 52
21586293 TGGACAAGAA
* *
21586303 GACTTGCAAAAGAAGAATT-TCAAAA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCT-AAAAGGAAAG-GGATTCTTAATAGGCAAGTTT
21586355 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
* * * * *
21586407 AACTTACAGGAGAAGAATTCTAAATGGAGAGGGATTCTTAAT-GAGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAG-GCAAGTTT
21586459 G
1 G
21586460 TATGGTTATA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
51 1 0.01
52 87 0.93
53 6 0.06
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:21587531 original size:31 final size:31
Alignment explanation
Indices: 21587496--21587565 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
21587486 GCTCGATCAT
*
21587496 ATATTTATAATTT-ATTTGTTTATTT-TAAAAA
1 ATATTTATAATTTGATTCG--TATTTATAAAAA
*
21587527 ATATTT-GAATTTGATTCGTATTTAATAAAAA
1 ATATTTATAATTTGATTCGTATTT-ATAAAAA
21587558 ATATTTAT
1 ATATTTAT
21587566 TATATTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
29 5 0.16
30 5 0.16
31 22 0.69
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (31 bp):
ATATTTATAATTTGATTCGTATTTATAAAAA
Found at i:21587693 original size:25 final size:23
Alignment explanation
Indices: 21587650--21587702 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
21587640 TTATAAACGT
* * *
21587650 TAAATGAATGTATTCATAATATATA
1 TAAATGAATATAATAATAA-ATA-A
21587675 TAAATGAATATAATAATAAATAA
1 TAAATGAATATAATAATAAATAA
21587698 TAAAT
1 TAAAT
21587703 AAATTACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.24
24 3 0.12
25 16 0.64
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (23 bp):
TAAATGAATATAATAATAAATAA
Found at i:21587717 original size:15 final size:14
Alignment explanation
Indices: 21587696--21587734 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
21587686 AATAATAAAT
21587696 AATAAATAAA-TTA
1 AATAAATAAATTTA
21587709 CAATGAAATAAATTTA
1 -AAT-AAATAAATTTA
21587725 AATAAATAAA
1 AATAAATAAA
21587735 CAAATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.43
15 10 0.43
16 3 0.13
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (14 bp):
AATAAATAAATTTA
Found at i:21588563 original size:18 final size:16
Alignment explanation
Indices: 21588517--21588563 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
21588507 AAATTTTAAT
21588517 TATTGTATTTAATATAA
1 TATT-TATTTAATATAA
21588534 TA-TTATTATAATCCATAA
1 TATTTATT-TAAT--ATAA
21588552 TATTTATTTAAT
1 TATTTATTTAAT
21588564 TCTGAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 2 0.08
18 10 0.38
19 5 0.19
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (16 bp):
TATTTATTTAATATAA
Found at i:21589594 original size:11 final size:11
Alignment explanation
Indices: 21589564--21589660 Score: 60
Period size: 11 Copynumber: 8.9 Consensus size: 11
21589554 CGATAATTTA
*
21589564 AAATTTAATAT
1 AAATATAATAT
21589575 AGTAATATAATAT
1 A--AATATAATAT
21589588 AAATATAATAT
1 AAATATAATAT
* *
21589599 GAATAAAAATAT
1 AAAT-ATAATAT
*
21589611 AAAAATAATAT
1 AAATATAATAT
21589622 -AAT-T--TAT
1 AAATATAATAT
* *
21589629 AATTTTAATAAT
1 AAATATAAT-AT
*
21589641 AATTAT-ATAT
1 AAATATAATAT
21589651 AAATATAATA
1 AAATATAATA
21589661 AAAAAATATA
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
7 3 0.04
8 2 0.03
9 2 0.03
10 9 0.13
11 26 0.39
12 15 0.22
13 10 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAATATAATAT
Found at i:21589692 original size:71 final size:73
Alignment explanation
Indices: 21589617--21589758 Score: 168
Period size: 71 Copynumber: 2.0 Consensus size: 73
21589607 ATATAAAAAT
* * *
21589617 AATATAATTTATAATTTTAATAATAATTATATAT-AAATATAATA-AAA-AAATATATTTT-ATA
1 AATATAAATTATAA-TAT-ATAA-AATTATATATAAAATATAATATAAATAAATAAATTTTAATA
21589678 TTTT-TATATC
63 TTTTATATATC
* * *
21589688 AATATAAATTATAATATATAAATTTTTATATAAAATATAATATAAATATATAAATTTTAATATTT
1 AATATAAATTATAATATATAAAATTATATATAAAATATAATATAAATAAATAAATTTTAATATTT
21589753 TATATA
66 TATATA
21589759 ATTCGAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
68 8 0.13
69 14 0.23
70 5 0.08
71 22 0.37
72 7 0.12
73 4 0.07
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (73 bp):
AATATAAATTATAATATATAAAATTATATATAAAATATAATATAAATAAATAAATTTTAATATTT
TATATATC
Found at i:21589704 original size:48 final size:48
Alignment explanation
Indices: 21589592--21589709 Score: 118
Period size: 48 Copynumber: 2.4 Consensus size: 48
21589582 TAATATAAAT
*
21589592 ATAATATGAATAAAAATATAAAAATAATATAATTTATAATTTTAATAATA
1 ATAATAT--ATAAATATATAAAAATAATATAATTTATAATTTTAATAATA
* * *
21589642 ATTATATATAAATATAATAAAAA-AATATATTTTATATTTTTATATCAAT-
1 ATAATATATAAATAT-ATAAAAATAATATAATTTATAATTTTA-AT-AATA
21589691 ATAA-AT-TATAATATATAAA
1 ATAATATATA-AATATATAAA
21589710 TTTTTATATA
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
47 7 0.12
48 31 0.53
49 12 0.20
50 9 0.15
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (48 bp):
ATAATATATAAATATATAAAAATAATATAATTTATAATTTTAATAATA
Found at i:21589705 original size:12 final size:12
Alignment explanation
Indices: 21589688--21589740 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
21589678 TTTTTATATC
21589688 AATATAAATTAT
1 AATATAAATTAT
*
21589700 AATATATAAATTTT
1 -A-ATATAAATTAT
* *
21589714 TATATAAAATAT
1 AATATAAATTAT
21589726 AATATAAATATAT
1 AATATAAAT-TAT
21589739 AA
1 AA
21589741 ATTTTAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 16 0.50
13 6 0.19
14 10 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATAAATTAT
Found at i:21589718 original size:32 final size:32
Alignment explanation
Indices: 21589677--21589750 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
21589667 TATATTTTAT
*
21589677 ATTTTTATAT-CAATATAA-ATTATAATATATAA
1 ATTTTTATATAAAATATAATA-TA-AATATATAA
21589709 ATTTTTATATAAAATATAATATAAATATATAA
1 ATTTTTATATAAAATATAATATAAATATATAA
*
21589741 ATTTTAATAT
1 ATTTTTATAT
21589751 TTTATATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 28 0.74
33 9 0.24
34 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
ATTTTTATATAAAATATAATATAAATATATAA
Found at i:21589740 original size:39 final size:39
Alignment explanation
Indices: 21589683--21589759 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
21589673 TTATATTTTT
21589683 ATATCAATATAAATTATAATATATAAAT-TTTTATATAAA
1 ATATCAATATAAATTATAA-ATATAAATATTTTATATAAA
* *
21589722 ATAT-AATATAAATATATAAATTTTAATATTTTATATAA
1 ATATCAATATAAAT-TATAAATATAAATATTTTATATAA
21589760 TTCGAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 15 0.44
39 19 0.56
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (39 bp):
ATATCAATATAAATTATAAATATAAATATTTTATATAAA
Found at i:21589749 original size:14 final size:14
Alignment explanation
Indices: 21589689--21589750 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 14
21589679 TTTTATATCA
*
21589689 ATATAAATTATAAT
1 ATATAAATTTTAAT
*
21589703 ATATAAATTTTTAT
1 ATATAAATTTTAAT
21589717 ATA-AAATATAATATAAAT
1 ATATAAAT-T--T-T-AAT
21589735 ATATAAATTTTAAT
1 ATATAAATTTTAAT
21589749 AT
1 AT
21589751 TTTATATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
13 4 0.10
14 21 0.54
15 1 0.03
16 2 0.05
17 1 0.03
18 6 0.15
19 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATAAATTTTAAT
Found at i:21592011 original size:11 final size:11
Alignment explanation
Indices: 21591980--21592043 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
21591970 TATAAAATTT
*
21591980 TAATTTTATTA
1 TAATTTTTTTA
*
21591991 -AATTTATTTA
1 TAATTTTTTTA
21592001 TAATTTTTTTA
1 TAATTTTTTTA
* *
21592012 AAATTTTAAATTA
1 TAATTTT--TTTA
21592025 T-ATTATTTTTA
1 TAATT-TTTTTA
21592036 TAATTTTT
1 TAATTTTT
21592044 AGTCTTATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
10 8 0.20
11 22 0.54
12 6 0.15
13 5 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:21592638 original size:7 final size:7
Alignment explanation
Indices: 21592626--21592653 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
21592616 AAATTTTAAT
21592626 AAAAATA
1 AAAAATA
21592633 AAAAATA
1 AAAAATA
21592640 AAAAATA
1 AAAAATA
21592647 AAAAATA
1 AAAAATA
21592654 TATTTTTATA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:21592702 original size:20 final size:21
Alignment explanation
Indices: 21592664--21592703 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
21592654 TATTTTTATA
*
21592664 TTTATATAAATTATGAAATATT
1 TTTATATAAA-TATAAAATATT
21592686 TTTATATAAA-ATAAAATA
1 TTTATATAAATATAAAATA
21592704 AAAATACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TTTATATAAATATAAAATATT
Found at i:21600650 original size:17 final size:17
Alignment explanation
Indices: 21600628--21600682 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
21600618 TTTAGATAAT
**
21600628 AATATTAAATTTATTTA
1 AATATTAAATAAATTTA
21600645 AATATTTAAATAAATTTA
1 AATA-TTAAATAAATTTA
21600663 AATATT--ATAAATATTA
1 AATATTAAATAAAT-TTA
21600679 AATA
1 AATA
21600683 GATTATGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 6 0.18
16 7 0.21
17 6 0.18
18 15 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATTAAATAAATTTA
Found at i:21600655 original size:18 final size:18
Alignment explanation
Indices: 21600640--21600675 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
21600630 TATTAAATTT
21600640 ATTTAAATATTTAAATAA
1 ATTTAAATATTTAAATAA
21600658 ATTTAAATATTATAAATA
1 ATTTAAATATT-TAAATA
21600676 TTAAATAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAAATATTTAAATAA
Found at i:21600675 original size:9 final size:8
Alignment explanation
Indices: 21600639--21600682 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
21600629 ATATTAAATT
21600639 TATTTAAA
1 TATTTAAA
21600647 TATTTAAA
1 TATTTAAA
21600655 TAAATTTAAA
1 T--ATTTAAA
21600665 TATTATAAA
1 TATT-TAAA
21600674 TA-TTAAA
1 TATTTAAA
21600681 TA
1 TA
21600683 GATTATGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 6 0.18
8 13 0.39
9 6 0.18
10 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TATTTAAA
Found at i:21604947 original size:18 final size:18
Alignment explanation
Indices: 21604924--21604975 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
21604914 CCATCACTGC
*
21604924 TTTCATCTTCACCATCCT
1 TTTCATCTTCATCATCCT
*
21604942 TTTCATCATCATCAT-CT
1 TTTCATCTTCATCATCCT
*
21604959 TCGTCATCTTCATCATC
1 T-TTCATCTTCATCATC
21604976 AGTCATGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 3 0.11
18 25 0.89
ACGTcount: A:0.19, C:0.35, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTCATCTTCATCATCCT
Found at i:21613147 original size:71 final size:71
Alignment explanation
Indices: 21613016--21613153 Score: 158
Period size: 71 Copynumber: 1.9 Consensus size: 71
21613006 TATATTTGTA
* * *
21613016 TTATATGAAATATTAATAATTTATATATTTATTTTATATTTTATATAAAAATTATGTATTATAAT
1 TTATATGAAATATTAATAATATATATATTTATTTTATAATTTATATAAAAATTATGTATTAAAAT
21613081 TTATAC
66 TTATAC
* * *
21613087 TTATATGAAA-ATATAA-AATATATATTTTTTATTTTATTAAATTTATTTATAAATT-T-TATTA
1 TTATATGAAATAT-TAATAATATATA-TATTTATTTTA-T-AATTTATATAAAAATTATGTATTA
21613148 AAATTT
62 AAATTT
21613154 TAAATTATGT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
70 9 0.16
71 33 0.58
72 2 0.04
73 13 0.23
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (71 bp):
TTATATGAAATATTAATAATATATATATTTATTTTATAATTTATATAAAAATTATGTATTAAAAT
TTATAC
Found at i:21617361 original size:19 final size:19
Alignment explanation
Indices: 21617336--21617401 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
21617326 TATGAAATCC
21617336 TTAAAAATATTGTAAAGTT
1 TTAAAAATATTGTAAAGTT
* *
21617355 CTAAAAAAAACTATG-AAA-TCT
1 -TTAAAAATA-T-TGTAAAGT-T
21617376 TTAAAAATATTGTAAAGTT
1 TTAAAAATATTGTAAAGTT
21617395 TTAAAAA
1 TTAAAAA
21617402 AACTATGTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
18 2 0.05
19 12 0.32
20 16 0.43
21 5 0.14
22 2 0.05
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.35
Consensus pattern (19 bp):
TTAAAAATATTGTAAAGTT
Found at i:21617371 original size:40 final size:39
Alignment explanation
Indices: 21617326--21617408 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 39
21617316 CACATGTCAA
21617326 TATGAAATCCTTAAAAATATTGTAAAGTTCTAAAAAAAAC
1 TATGAAATCCTTAAAAATATTGTAAAGTT-TAAAAAAAAC
* *
21617366 TATGAAATCTTTAAAAATATTGTAAAGTTTTAAAAAAAC
1 TATGAAATCCTTAAAAATATTGTAAAGTTTAAAAAAAAC
21617405 TATG
1 TATG
21617409 TACACCTAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 13 0.32
40 28 0.68
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.34
Consensus pattern (39 bp):
TATGAAATCCTTAAAAATATTGTAAAGTTTAAAAAAAAC
Found at i:21620077 original size:18 final size:18
Alignment explanation
Indices: 21620054--21620089 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21620044 ACTTATTTGA
*
21620054 CATAAAGTAAAGATGACT
1 CATAAAGTAAACATGACT
21620072 CATAAAGTAAACATGACT
1 CATAAAGTAAACATGACT
21620090 TGACTTAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (18 bp):
CATAAAGTAAACATGACT
Found at i:21624982 original size:27 final size:27
Alignment explanation
Indices: 21624950--21625003 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
21624940 TGAAGTCGTC
*
21624950 AGTTGCCA-AAGCCTTGATCGTACTACT
1 AGTTGCCAGAA-CCTTGACCGTACTACT
*
21624977 AGTTGCCAGAACCTTTACCGTACTACT
1 AGTTGCCAGAACCTTGACCGTACTACT
21625004 TGTCGCTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (27 bp):
AGTTGCCAGAACCTTGACCGTACTACT
Found at i:21631079 original size:17 final size:17
Alignment explanation
Indices: 21631057--21631090 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21631047 TTTTACAATT
21631057 AAAATTACAATAACATC
1 AAAATTACAATAACATC
21631074 AAAATTACAATAACATC
1 AAAATTACAATAACATC
21631091 CTCTTATTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATTACAATAACATC
Found at i:21634416 original size:23 final size:23
Alignment explanation
Indices: 21634381--21634425 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21634371 TTTTAATTGA
*
21634381 TTTAAAATTAATA-AAATATTATT
1 TTTAAAATAAATATAAA-ATTATT
*
21634404 TTTAATATAAATATAAAATTAT
1 TTTAAAATAAATATAAAATTAT
21634426 ATAAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAAAATAAATATAAAATTATT
Found at i:21647781 original size:22 final size:22
Alignment explanation
Indices: 21647741--21647814 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
21647731 AATATTTTTA
*
21647741 AATA-TTTATA-TCTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
21647761 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
21647783 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
21647805 AATATTTTAT
1 AATATTTTAT
21647815 TAATTTCAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 4 0.08
21 6 0.12
22 41 0.80
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:21655473 original size:47 final size:47
Alignment explanation
Indices: 21655399--21655494 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
21655389 TTTTGACGAG
* * *
21655399 ATGATGTCTGTGAAGAATTTTGTTAGAGTTACAACTAGGATTACTGT
1 ATGATGTCTGTAAAGAATTTTGGTAGAGTTACAACTAGGATTAATGT
21655446 ATGATGTCTGTAAAGAATTTTGGTAGAGTTACAACTAGGATTAATGT
1 ATGATGTCTGTAAAGAATTTTGGTAGAGTTACAACTAGGATTAATGT
21655493 AT
1 AT
21655495 TTTACTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (47 bp):
ATGATGTCTGTAAAGAATTTTGGTAGAGTTACAACTAGGATTAATGT
Found at i:21655953 original size:2 final size:2
Alignment explanation
Indices: 21655946--21655990 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
21655936 TGCTTTAACG
* *
21655946 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21655988 AT A
1 AT A
21655991 GATTCTAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:21665623 original size:35 final size:38
Alignment explanation
Indices: 21665556--21665651 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 38
21665546 TTTGATAATT
* * ** *
21665556 TAAAATATAATATAATAATATAATTTAAAA-TTTT-TG
1 TAAAATATTATATAAAAATATAACATAAAATTTTTATA
*
21665592 TAAAAT-TTATATAAAAATATAACATATAATTTTTATA
1 TAAAATATTATATAAAAATATAACATAAAATTTTTATA
*
21665629 TAAAATATTATATAAATATATAA
1 TAAAATATTATATAAAAATATAA
21665652 ATTATTCGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 18 0.36
36 10 0.20
37 7 0.14
38 15 0.30
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (38 bp):
TAAAATATTATATAAAAATATAACATAAAATTTTTATA
Found at i:21665645 original size:11 final size:12
Alignment explanation
Indices: 21665556--21665649 Score: 57
Period size: 13 Copynumber: 7.7 Consensus size: 12
21665546 TTTGATAATT
*
21665556 TAAAATATAATA
1 TAAAATATTATA
* *
21665568 TAATAATATAATT
1 TAA-AATATTATA
* *
21665581 TAAAAT-TTTTG
1 TAAAATATTATA
21665592 TAAAAT-TTATA
1 TAAAATATTATA
* *
21665603 TAAAAATATAACA
1 T-AAAATATTATA
* *
21665616 TATAATTTTTATA
1 TA-AAATATTATA
21665629 TAAAATATTATA
1 TAAAATATTATA
21665641 TAAATATAT
1 TAAA-ATAT
21665650 AAATTATTCG
Statistics
Matches: 63, Mismatches: 14, Indels: 9
0.73 0.16 0.10
Matches are distributed among these distances:
11 12 0.19
12 24 0.38
13 27 0.43
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (12 bp):
TAAAATATTATA
Found at i:21666433 original size:3 final size:3
Alignment explanation
Indices: 21666425--21666472 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
21666415 GAGAAGAGTT
* * *
21666425 TGA TGA TGA TTA TGA TGA TGA TGA TGA TGA TGA GGA TGA TTA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
21666473 CAAAGTTGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:21667275 original size:17 final size:17
Alignment explanation
Indices: 21667253--21667287 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21667243 TTGTTTTTGA
21667253 ATTTTTATAT-TATATTT
1 ATTTTT-TATCTATATTT
21667270 ATTTTTTATCTATATTT
1 ATTTTTTATCTATATTT
21667287 A
1 A
21667288 AAATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTATCTATATTT
Found at i:21667483 original size:26 final size:26
Alignment explanation
Indices: 21667419--21667553 Score: 75
Period size: 25 Copynumber: 5.2 Consensus size: 26
21667409 TTTTTATCTT
* * * *
21667419 ATATATTTAAATA-ATTTTTTACAAAT
1 ATATA-TTAATTATATTTTTAATAAAA
21667445 ATATATTAA-TATATTTTTAATAAAA
1 ATATATTAATTATATTTTTAATAAAA
* *
21667470 ATATATTAATTATA--ATTAATTTAAA
1 ATATATTAATTATATTTTTAA-TAAAA
21667495 ATA-A-TAATTTATATTATTTAATAAAAA
1 ATATATTAA-TTATATT-TTTAAT-AAAA
* * * * * *
21667522 ATTTATTTATTAAATATATAAAAAAA
1 ATATATTAATTATATTTTTAATAAAA
21667548 ATATAT
1 ATATAT
21667554 AATACAAATA
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
23 3 0.04
24 12 0.14
25 30 0.35
26 19 0.22
27 13 0.15
28 6 0.07
29 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATATTAATTATATTTTTAATAAAA
Found at i:21667517 original size:20 final size:19
Alignment explanation
Indices: 21667481--21667542 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
21667471 TATATTAATT
*
21667481 ATAATTAATTTA--AAATA
1 ATAATTTATTTATTAAATA
*
21667498 ATAATTTATATTATTTAATAA
1 ATAATTTAT-TTATTAAAT-A
*
21667519 AAAATTTATTTATTAAATA
1 ATAATTTATTTATTAAATA
21667538 TATAA
1 -ATAA
21667543 AAAAAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 8 0.23
18 3 0.09
19 1 0.03
20 14 0.40
21 9 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATTTATTTATTAAATA
Found at i:21668796 original size:3 final size:3
Alignment explanation
Indices: 21668638--21668776 Score: 102
Period size: 3 Copynumber: 46.3 Consensus size: 3
21668628 CATCACCACT
* * * * * *
21668638 ATC AAC ATC TTC ATC ACC ATC ATC GTC ATC ATC ATC GTC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * *
21668686 ATC GTC GTC ATC ATC GAT- GTC ATC ATA AAC ATC ATC ATA ATC ATC
1 ATC ATC ATC ATC ATC -ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* ** *
21668731 ATC A-C TATC ATC TTC CCC ATC ATC ATC ATC ATC ATC ATC AAC ATC
1 ATC ATC -ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
21668776 A
1 A
21668777 AAAAAAGTAT
Statistics
Matches: 103, Mismatches: 29, Indels: 8
0.74 0.21 0.06
Matches are distributed among these distances:
2 2 0.02
3 98 0.95
4 3 0.03
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:21672061 original size:2 final size:2
Alignment explanation
Indices: 21672054--21672078 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21672044 TTCTAAAAGA
21672054 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 A
21672079 ATTCAGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21673945 original size:15 final size:15
Alignment explanation
Indices: 21673895--21673952 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 15
21673885 TGTTTATTAG
*
21673895 TAATATAATAAATTT
1 TAATTTAATAAATTT
21673910 TAA-TTAATAAATTT
1 TAATTTAATAAATTT
21673924 ATAAATTTAA-AATATTT
1 -T-AATTTAATAA-ATTT
21673941 TAA-TTAATAAAT
1 TAATTTAATAAAT
21673953 AAAATTAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
14 16 0.43
15 8 0.22
16 5 0.14
17 8 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTTAATAAATTT
Found at i:21678005 original size:34 final size:34
Alignment explanation
Indices: 21677964--21678044 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
21677954 CATAAATTGT
* *
21677964 GAAAATAAATTTTTAAAAAATTATTAATT-TTTTC
1 GAAAATAAATTTTCAAAAAATTA-TAATTCTTTAC
*
21677998 -ATAAATAAATTTTCAAAATATTATAATTCTTTAC
1 GA-AAATAAATTTTCAAAAAATTATAATTCTTTAC
21678032 GAAAATAAATTTT
1 GAAAATAAATTTT
21678045 AAATAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.15
34 34 0.83
35 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (34 bp):
GAAAATAAATTTTCAAAAAATTATAATTCTTTAC
Found at i:21693595 original size:18 final size:20
Alignment explanation
Indices: 21693555--21693595 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
21693545 TTTTATATAT
* *
21693555 TATTTTAATATAATTTAATA
1 TATTTAAATATAATCTAATA
21693575 TATTTAAATA-AATCTAA-A
1 TATTTAAATATAATCTAATA
21693593 TAT
1 TAT
21693596 AAAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 4 0.21
19 6 0.32
20 9 0.47
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTTAAATATAATCTAATA
Found at i:21702938 original size:17 final size:16
Alignment explanation
Indices: 21702909--21702984 Score: 75
Period size: 16 Copynumber: 4.8 Consensus size: 16
21702899 TTAATTGCTT
*
21702909 AAATGATTT-AATTATA
1 AAATAATTTAAATT-TA
*
21702925 AAATAACTTAAATTTA
1 AAATAATTTAAATTTA
* *
21702941 AAATAATTTAAAATTC
1 AAATAATTTAAATTTA
21702957 AAATAATTTAAATTCT-
1 AAATAATTTAAATT-TA
*
21702973 AAATAATCTAAA
1 AAATAATTTAAA
21702985 AAAATAGTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
16 46 0.90
17 5 0.10
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (16 bp):
AAATAATTTAAATTTA
Found at i:21702961 original size:32 final size:32
Alignment explanation
Indices: 21702925--21702985 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
21702915 TTTAATTATA
*
21702925 AAATAACTTAAATT-TAAAATAATTTAAAATTC
1 AAATAACTTAAATTCT-AAATAATCTAAAATTC
*
21702957 AAATAATTTAAATTCTAAATAATCTAAAA
1 AAATAACTTAAATTCTAAATAATCTAAAA
21702986 AAATAGTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (32 bp):
AAATAACTTAAATTCTAAATAATCTAAAATTC
Found at i:21704646 original size:15 final size:16
Alignment explanation
Indices: 21704616--21704649 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21704606 TATGATATAA
21704616 ATATAATATAAAAATT
1 ATATAATATAAAAATT
*
21704632 ATATAAT-TTAAAATT
1 ATATAATATAAAAATT
21704647 ATA
1 ATA
21704650 ATTATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAATATAAAAATT
Found at i:21704654 original size:6 final size:6
Alignment explanation
Indices: 21704633--21704679 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
21704623 ATAAAAATTA
* *
21704633 TATAATT TAAAAT TATAAT TATAAT TATAAT TAT-A- TATAAT TTTAAT
1 TATAA-T TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT
21704680 AAAATAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
4 3 0.09
5 2 0.06
6 26 0.74
7 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TATAAT
Found at i:21705550 original size:39 final size:37
Alignment explanation
Indices: 21705464--21705553 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 37
21705454 TGATATGATC
*
21705464 ATTTATATATTTATATTTTATAAAATAGTTAAATTTAT
1 ATTTATATATTT-TATTTTATAAAATAATTAAATTTAT
**
21705502 ATATT-TATATTTTATTTTATATAAA-AATTACGTATTAT
1 AT-TTATATATTTTATTTTATA-AAATAATTAAAT-TTAT
21705540 AATTTATATATTTT
1 -ATTTATATATTTT
21705554 TATATTAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
37 14 0.32
38 18 0.41
39 12 0.27
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (37 bp):
ATTTATATATTTTATTTTATAAAATAATTAAATTTAT
Found at i:21708469 original size:405 final size:400
Alignment explanation
Indices: 21707550--21708734 Score: 1576
Period size: 401 Copynumber: 2.9 Consensus size: 400
21707540 TAGAAATCAA
* * * *
21707550 TCCATGATTTGATTGAGTTGAAACTTTGTTAATAAATTTATGATTCAAAATTTTACATTTTAAAT
1 TCCATGATTCGATTGAGTTGAAACTTTGTCAACAAATTTATGATTCAAAATTTTACATTTTGAAT
* * * *
21707615 GATAAAGATTGGTTTTGAAGCTCTTTAAGAATAAA-TCAAATGTGTATTTGTTGAGTCACTTATT
66 GGTAAAGATCGGATTTGAAGCTCTCTAAGAATAAATTC-AATGTGTATTTGTTGAGTCACTTATT
* * *
21707679 TAATGAGATTTCTCAAATTATCTTTTTAATTGTTGATTAGTTATAGTTTTAGTTAAAGAATAACT
130 TAGTGAGATTTCTCAAATTATCTCTTTAGTTGTTGATTAGTTATAGTTTTAGTTAAAGAATAACT
21707744 TTGTATATTCATTATTTGATAGTAAAGATTTTTT--TACGGTCCGTGATTTTTTTT-TATACACT
195 TTGTATATTCATTATTTGATAGTAAAGATTTTTTGGTA--GTCCGTGATTTTTTTTATATAC-C-
*
21707806 GAAAGATTTTTCACATAAATCTTGATGTATTTTATTTTTTTACATTGCTGATTATTAATTGTTAT
256 GAAAGATTTTTCACATAAATCTTGATGTATTTTATTTTTTTGCATTGCTGATTATTAATTGTTAT
* * *
21707871 TTATTACTATAAATTTATTGCAACATATTATTTCTATGTTATTGTGTTTATTATTTCAGGTCCAA
321 TTATTACTATAAATTTATTGCGACATATTATTTTTATGTTATTGTGTTTATTACTTCAGGTCCAA
21707936 TAATTGAATCCGTGG
386 TAATTGAATCCGTGG
* * * * * * * *
21707951 TCCGTGATCCGATTGAGTTAAAACTTTGTCAACGAGTTTATGATTCAGAATTCTACATTTTGAAC
1 TCCATGATTCGATTGAGTTGAAACTTTGTCAACAAATTTATGATTCAAAATTTTACATTTTGAAT
* * * * * * *
21708016 AGTAAAAATC-GAGTTTGAAGCTTTCTATGAACAAATTCAATGTGTATTTATCGAGTCACTTATT
66 GGTAAAGATCGGA-TTTGAAGCTCTCTAAGAATAAATTCAATGTGTATTTGTTGAGTCACTTATT
* * * *
21708080 TAGTGAGATTTATCAAATTATCTCTTTAGTTATTGATTAATTATAGTTTTAGTTAAAGAAGAACT
130 TAGTGAGATTTCTCAAATTATCTCTTTAGTTGTTGATTAGTTATAGTTTTAGTTAAAGAATAACT
*
21708145 TTGTATATTCATTATTTGATAGTAAAGATTTTTTGGTAATCCGTGATTTTTTTCTATATACCGAA
195 TTGTATATTCATTATTTGATAGTAAAGATTTTTTGGTAGTCCGTGATTTTTTT-TATATACCGAA
21708210 AGATTTTTCACATAAATCTTGATGTATTTTATTTTTTTTTTTGCATTGCTGATTATTAATTGTTA
259 AGATTTTTCACATAAATCTTGATGTATTTTA----TTTTTTTGCATTGCTGATTATTAATTGTTA
*
21708275 TTTATTACTGTAAATTTATTGCGACATATTATTTTTATGTTATTGTGTTTATTACTTCAGGTCCA
320 TTTATTACTATAAATTTATTGCGACATATTATTTTTATGTTATTGTGTTTATTACTTCAGGTCCA
* *
21708340 GTAATTGAATCTGTGG
385 ATAATTGAATCCGTGG
* * * *
21708356 TCCATAATTCGATTAAGTTGAAACTTTATCAGCAAATTTATGATTCAAAATTTTACATTTTGAAT
1 TCCATGATTCGATTGAGTTGAAACTTTGTCAACAAATTTATGATTCAAAATTTTACATTTTGAAT
* *
21708421 GGTAAAGATCGGATTTAAAGCTCTCTAAGAATAAATTCAATGTGTATTTGTTGAGTTACTTATTT
66 GGTAAAGATCGGATTTGAAGCTCTCTAAGAATAAATTCAATGTGTATTTGTTGAGTCACTTATTT
* * * ***
21708486 -GATGAGATTTCTCCAATTATCTCTTTAGTTGTTGATTAGCTATAATTTTAGTTAAA-AATTTTT
131 AG-TGAGATTTCTCAAATTATCTCTTTAGTTGTTGATTAGTTATAGTTTTAGTTAAAGAATAACT
* * * * ** *
21708549 TTGTATATTTATTGTTTGATAGTAAAAATTTTTTTGGTGGTCATTAATTTTTTTT-TATACACGT
195 TTGTATATTCATTATTTGATAGTAAAGA-TTTTTTGGTAGTCCGTGATTTTTTTTATATAC-CG-
* * * * * *
21708613 GAAGATTTTTCATATAAATCTTGATATATTTTATTTTTTTGTATTGTTGATTATTAATTATTATT
257 AAAGATTTTTCACATAAATCTTGATGTATTTTATTTTTTTGCATTGCTGATTATTAATTGTTATT
** * *
21708678 TATTACTATAAATTTATTATGATATATTATTTTTATGTTATTGTGTTTATTGCTTCA
322 TATTACTATAAATTTATTGCGACATATTATTTTTATGTTATTGTGTTTATTACTTCA
21708735 TATTGAATAA
Statistics
Matches: 681, Mismatches: 88, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
400 1 0.00
401 322 0.47
402 4 0.01
403 12 0.02
404 32 0.05
405 308 0.45
406 2 0.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (400 bp):
TCCATGATTCGATTGAGTTGAAACTTTGTCAACAAATTTATGATTCAAAATTTTACATTTTGAAT
GGTAAAGATCGGATTTGAAGCTCTCTAAGAATAAATTCAATGTGTATTTGTTGAGTCACTTATTT
AGTGAGATTTCTCAAATTATCTCTTTAGTTGTTGATTAGTTATAGTTTTAGTTAAAGAATAACTT
TGTATATTCATTATTTGATAGTAAAGATTTTTTGGTAGTCCGTGATTTTTTTTATATACCGAAAG
ATTTTTCACATAAATCTTGATGTATTTTATTTTTTTGCATTGCTGATTATTAATTGTTATTTATT
ACTATAAATTTATTGCGACATATTATTTTTATGTTATTGTGTTTATTACTTCAGGTCCAATAATT
GAATCCGTGG
Found at i:21711091 original size:155 final size:155
Alignment explanation
Indices: 21710809--21711118 Score: 561
Period size: 155 Copynumber: 2.0 Consensus size: 155
21710799 GCCGCTCAAC
*
21710809 AGCTCTTCCCATTTGTTATTTTCTTCTATATCGGGTCAAGTTTCTATTTGTGATGGTTAAATAAA
1 AGCTCTTCCCATTTGTTATTTTCTTCTATATCGGGTCAAGTTTCTATTTGAGATGGTTAAATAAA
*
21710874 TTGATTATAAATTTTCATGTTAATCATGTGTTTTGTTTTATATGCTAATATCGTTTCGATTTCCT
66 TTGATTATAAATTTTCATGTTAATCATGTGTTTTGTTTTATATACTAATATCGTTTCGATTTCCT
21710939 GTTTCCTTTTCAT-ATCCTCCAATTG
131 GTTTCCTTTTC-TCATCCTCCAATTG
21710964 AGCTCTTCCCATTTGTTATTTTCTTCTATAGT-GGGTCAAGTTTCTATTTGAGATGGTTAAATAA
1 AGCTCTTCCCATTTGTTATTTTCTTCTATA-TCGGGTCAAGTTTCTATTTGAGATGGTTAAATAA
*
21711028 ATTGATTATAAATTTTCATGTTAATCATGTGTTTTGTTTTATATACTAATATTGTTTCGATTTCC
65 ATTGATTATAAATTTTCATGTTAATCATGTGTTTTGTTTTATATACTAATATCGTTTCGATTTCC
21711093 TGTTTCCTTTTCTCATCCTCCAATTG
130 TGTTTCCTTTTCTCATCCTCCAATTG
21711119 TTGTCTGGCA
Statistics
Matches: 150, Mismatches: 3, Indels: 4
0.96 0.02 0.03
Matches are distributed among these distances:
154 1 0.01
155 148 0.99
156 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.50
Consensus pattern (155 bp):
AGCTCTTCCCATTTGTTATTTTCTTCTATATCGGGTCAAGTTTCTATTTGAGATGGTTAAATAAA
TTGATTATAAATTTTCATGTTAATCATGTGTTTTGTTTTATATACTAATATCGTTTCGATTTCCT
GTTTCCTTTTCTCATCCTCCAATTG
Found at i:21720304 original size:18 final size:18
Alignment explanation
Indices: 21720248--21720306 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
21720238 AATTTTTTTA
21720248 TTTA-ATTTGAATTAAA-
1 TTTAGATTTGAATTAAAT
*
21720264 TTTAGATGTT--ATATATAT
1 TTTAGAT-TTGAAT-TAAAT
*
21720282 ATTAGATTTGAATTAAAT
1 TTTAGATTTGAATTAAAT
21720300 TTTAGAT
1 TTTAGAT
21720307 AAAAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 18 0.55
19 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (18 bp):
TTTAGATTTGAATTAAAT
Found at i:21729134 original size:19 final size:19
Alignment explanation
Indices: 21729110--21729170 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 19
21729100 ATATAATATT
21729110 TATAAATTATTATTTTTA-A
1 TATAAATTA-TATTTTTATA
21729129 TATAAATTATATCTTAATTATA
1 TATAAATTATAT-TT--TTATA
21729151 TATAAATATAATATTTTTAT
1 TATAAAT-T-ATATTTTTAT
21729171 TAAGTTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 3 0.08
19 11 0.31
21 7 0.19
22 8 0.22
23 3 0.08
24 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TATAAATTATATTTTTATA
Found at i:21730724 original size:16 final size:17
Alignment explanation
Indices: 21730691--21730724 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21730681 AGAAATTAAG
21730691 AATTTAAACTATAATTT
1 AATTTAAACTATAATTT
*
21730708 AATTTAAA-TATATTTT
1 AATTTAAACTATAATTT
21730724 A
1 A
21730725 TTATTCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTAAACTATAATTT
Found at i:21731039 original size:15 final size:14
Alignment explanation
Indices: 21731003--21731050 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
21730993 ATGAAATTAA
21731003 TAAAATATTAAATT
1 TAAAATATTAAATT
*
21731017 TAAAATATTAATTTT
1 TAAAATATTAA-ATT
* *
21731032 TTAAATA-TAAATA
1 TAAAATATTAAATT
21731045 TAAAAT
1 TAAAAT
21731051 TAAATAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 6 0.21
14 14 0.50
15 8 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAATATTAAATT
Found at i:21731044 original size:6 final size:6
Alignment explanation
Indices: 21731033--21731090 Score: 66
Period size: 6 Copynumber: 9.7 Consensus size: 6
21731023 ATTAATTTTT
* *
21731033 TAAATA TAAATA TAAA-A TTAAATA -AATATA TAAATA TATATA AAAATA
1 TAAATA TAAATA TAAATA -TAAATA TAA-ATA TAAATA TAAATA TAAATA
21731081 TAAATA TAAA
1 TAAATA TAAA
21731091 ATTAAAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 3 0.07
6 38 0.86
7 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATA
Found at i:21731055 original size:18 final size:18
Alignment explanation
Indices: 21731032--21731096 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 18
21731022 TATTAATTTT
21731032 TTAAATATAAATATAAAA
1 TTAAATATAAATATAAAA
21731050 TTAAATA-AATATATAAATATA
1 TTAAATATAA-ATAT-AA-A-A
21731071 TATAAAAATATAAATATAAAA
1 T-T--AAATATAAATATAAAA
21731092 TTAAA
1 TTAAA
21731097 AAAGTAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
17 2 0.05
18 14 0.36
19 2 0.05
20 2 0.05
21 4 0.10
22 2 0.05
23 2 0.05
24 9 0.23
25 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAATATAAATATAAAA
Found at i:21732395 original size:35 final size:35
Alignment explanation
Indices: 21732356--21732422 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
21732346 TTTTATTAGT
* *
21732356 TTTATATATATTTTAAATTTTTATAAAATAAAAGA
1 TTTATAAATATTTTAAACTTTTATAAAATAAAAGA
21732391 TTTATAAATATTTTAAACTTTTATAAAATAAA
1 TTTATAAATATTTTAAACTTTTATAAAATAAA
21732423 TTAATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (35 bp):
TTTATAAATATTTTAAACTTTTATAAAATAAAAGA
Found at i:21732415 original size:19 final size:19
Alignment explanation
Indices: 21732355--21732417 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
21732345 TTTTTATTAG
* *
21732355 TTTTATATATATTTTAAAT
1 TTTTATAAATATTTTAAAC
* *
21732374 TTTTATAAA-A--TAAAAG
1 TTTTATAAATATTTTAAAC
*
21732390 ATTTATAAATATTTTAAAC
1 TTTTATAAATATTTTAAAC
21732409 TTTTATAAA
1 TTTTATAAA
21732418 ATAAATTAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 12 0.35
17 1 0.03
18 1 0.03
19 20 0.59
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTATAAATATTTTAAAC
Found at i:21733191 original size:15 final size:15
Alignment explanation
Indices: 21733157--21733194 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
21733147 ACACTGTTTA
21733157 TTTATTTTTAGCTTTT
1 TTTATTTTTA-CTTTT
21733173 TTTATTTTTA-TTTT
1 TTTATTTTTACTTTT
21733187 GTTTATTT
1 -TTTATTT
21733195 ACATAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 7 0.33
16 10 0.48
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTATTTTTACTTTT
Found at i:21733233 original size:28 final size:28
Alignment explanation
Indices: 21733194--21733250 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
21733184 TTTGTTTATT
*
21733194 TACATAATTTTT-TATAAAAATATATTAA
1 TACATAATTTTTCAATAAAAA-ATATTAA
*
21733222 TACATATTTTTTCAATAAAAAATATTAA
1 TACATAATTTTTCAATAAAAAATATTAA
21733250 T
1 T
21733251 TTTAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (28 bp):
TACATAATTTTTCAATAAAAAATATTAA
Done.