Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 81 of 127
Found at i:15483522 original size:118 final size:119
Alignment explanation
Indices: 15483287--15483532 Score: 279
Period size: 118 Copynumber: 2.1 Consensus size: 119
15483277 GGTCAAAAAT
** * *
15483287 AAATGATCTAGACTAAGCCAAGATCAAATGATTGGGATGAAATCATAAGTCGAAATAAAGCAACC
1 AAATGATCTAGACTAAGCCAAGATCAAATGATCAGGATGAAATCACAAGTCGAAATAAAGCAACA
* * * *
15483352 CGAATCGAGTCAAGATAGAGAATAAATGATCGAGACGAAATCACAAATCATAAG
66 AGAACCGAGTCAAGATAGAGAATAAATGATCGAGACGAAATCACAAACCATAAA
* * *
15483406 AAATGATCTAGACTGAGCCAAGATCAAGTGGTCAGGATGAAA-CTACAAGTC-AAATAAAGCAAT
1 AAATGATCTAGACTAAGCCAAGATCAAATGATCAGGATGAAATC-ACAAGTCGAAATAAAGCAA-
* *
15483469 CAAG-ACCGAGTCAAGGTCA-AGAATAAATGATCGAGATGAAA-CTA-AGAACCATAAA
64 CAAGAACCGAGTCAAGAT-AGAGAATAAATGATCGAGACGAAATC-ACA-AACCATAAA
*
15483524 AAATAATCT
1 AAATGATCT
15483533 GGAAGTGAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
117 2 0.02
118 60 0.56
119 46 0.43
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.18
Consensus pattern (119 bp):
AAATGATCTAGACTAAGCCAAGATCAAATGATCAGGATGAAATCACAAGTCGAAATAAAGCAACA
AGAACCGAGTCAAGATAGAGAATAAATGATCGAGACGAAATCACAAACCATAAA
Found at i:15487842 original size:14 final size:14
Alignment explanation
Indices: 15487823--15487849 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15487813 ATTTTGATGG
15487823 TGGAATAAATGAAA
1 TGGAATAAATGAAA
15487837 TGGAATAAATGAA
1 TGGAATAAATGAA
15487850 TAAAACACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (14 bp):
TGGAATAAATGAAA
Found at i:15495233 original size:3 final size:3
Alignment explanation
Indices: 15495225--15495356 Score: 110
Period size: 3 Copynumber: 43.0 Consensus size: 3
15495215 AATAATGAAG
15495225 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GA-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * *
15495273 ATC ATA ATA ATA TATA AGA ATA A-A TATA CATA AAA ATA CTAA ATGA
1 ATA ATA ATA ATA -ATA ATA ATA ATA -ATA -ATA ATA ATA AT-A AT-A
* * *
15495319 AGGA A-A AT- ATA TTA ATA ATA ATA ACA ATA ATA ATA ATA
1 A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
15495357 CAATAAAATT
Statistics
Matches: 105, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
2 6 0.06
3 85 0.81
4 14 0.13
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:15499844 original size:13 final size:14
Alignment explanation
Indices: 15499824--15499862 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
15499814 AACTTCTGAA
15499824 TGTCTTTATATATG
1 TGTCTTTATATATG
*
15499838 T-TCTTTACATATG
1 TGTCTTTATATATG
15499851 TGT-TTTATATAT
1 TGTCTTTATATAT
15499863 ACACTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.59
Consensus pattern (14 bp):
TGTCTTTATATATG
Found at i:15501518 original size:159 final size:161
Alignment explanation
Indices: 15501024--15501769 Score: 685
Period size: 160 Copynumber: 4.6 Consensus size: 161
15501014 TGTTTACAAC
* * * * * * **
15501024 TTTTTGTGCCTTTACAAGGTAAAAATACAAATTT-ATAGTTATTGTTCTATTTTAATAGTTTTAA
1 TTTTTGTGTCGTTAAAAGGCAAAAATACAAATTTGCTA-TTATTGTTCTATTTTAACA-TTTGGA
* * * *
15501088 TAGTTTCAATACATGATATTAAA-TTTATTCAAATTATTGAACTTAGTTTCCA-AGGTTGATATG
64 TAGCTTCAATACATGATATTAAACTTT-TTCAAATGATTGAACTTAGTTTTCACA-GTTGATATA
* * **
15501151 TATGAAAAAGTTAATGTTTATGTCTATTTAAGAC-
127 TGTGAAAAAGTTATTGTTTACCTCTATTTAAGACT
* * * * *
15501185 CTTTTGTGTCGTTAATAGGTAATAATACAAATTTGCTATTATTGCTCTATTTTAACATTTGGATA
1 TTTTTGTGTCGTTAAAAGGCAAAAATACAAATTTGCTATTATTGTTCTATTTTAACATTTGGATA
* * * * * * *
15501250 GCTTCAATATATGATATTAAACTTGTCCGAATGATTGACCTTGGTTTTCACAGTTGATATGTGTG
66 GCTTCAATACATGATATTAAACTTTTTCAAATGATTGAACTTAGTTTTCACAGTTGATATATGTG
** *
15501315 AAAAAGTTATTGTTTATGTTTATTTAAGACT
131 AAAAAGTTATTGTTTACCTCTATTTAAGACT
* * * *
15501346 ATTTT-TG-CTGTTAAAATGCAAAAATAC-AATTTGCTATTATTATTCTATTTTAATCATTTGTA
1 TTTTTGTGTC-GTTAAAAGGCAAAAATACAAATTTGCTATTATTGTTCTATTTTAA-CATTTGGA
* * * * *
15501408 TGGCTCCATTACATGATATTAAA-TAGTTTT-GAATGATTAAACTTAGTTTTCACAGTTGATATA
64 TAGCTTCAATACATGATATTAAACT--TTTTCAAATGATTGAACTTAGTTTTCACAGTTGATATA
*
15501471 TGTG-AAAAGTTGTTGTTTACCTCTATTTAAGA-T
127 TGTGAAAAAGTTATTGTTTACCTCTATTTAAGACT
* * * * *
15501504 TTTTTGAGTCGTTAAAAGGCAAAAATATAAATTTACTATTATTGTT-TGTTTTAGCAGTTTGGAT
1 TTTTTGTGTCGTTAAAAGGCAAAAATACAAATTTGCTATTATTGTTCTATTTTAACA-TTTGGAT
* * * *
15501568 AGCTTCAATACATGATATTAAACTTTTTCAAAAGATTGAACTTGGTATTCACAATTGATATATGT
65 AGCTTCAATACATGATATTAAACTTTTTCAAATGATTGAACTTAGTTTTCACAGTTGATATATGT
* * * * * *
15501633 GACAAAGTTGTCGGTTACCTCTA-CTAGTGACT
130 GAAAAAGTTATTGTTTACCTCTATTTA-AGACT
* * * *** *
15501665 TTTTT-TGCCGTTAAAAGGCAAAAATACAAAGTTGCTATTAGTCACCATGTTTTAACAGTTTGGA
1 TTTTTGTGTCGTTAAAAGGCAAAAATACAAATTTGCTATTATTGTTC-TATTTTAACA-TTTGGA
* *
15501729 TAACTTCAATACATGATATTAAACTTATGT-AAATGATTGAA
64 TAGCTTCAATACATGATATTAAACTT-TTTCAAATGATTGAA
15501770 TTTGGTTTCC
Statistics
Matches: 484, Mismatches: 81, Indels: 39
0.80 0.13 0.06
Matches are distributed among these distances:
158 11 0.02
159 131 0.27
160 227 0.47
161 60 0.12
162 53 0.11
163 2 0.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (161 bp):
TTTTTGTGTCGTTAAAAGGCAAAAATACAAATTTGCTATTATTGTTCTATTTTAACATTTGGATA
GCTTCAATACATGATATTAAACTTTTTCAAATGATTGAACTTAGTTTTCACAGTTGATATATGTG
AAAAAGTTATTGTTTACCTCTATTTAAGACT
Found at i:15501672 original size:319 final size:321
Alignment explanation
Indices: 15501097--15501704 Score: 735
Period size: 319 Copynumber: 1.9 Consensus size: 321
15501087 ATAGTTTCAA
* * *
15501097 TACATGATATTAAATTTATTCAAATTATTGAACTTAGTTTCCAAGGTTGATATGTATGAAAAAGT
1 TACATGATATTAAATTTATTCAAATGATTAAACTTAGTTTCCAAGGTTGATATATATGAAAAAGT
** * * * * *
15501162 TAATGTTTATGTCTATTTAAGACCTTTTGTGTCGTTAATAGGTAATAATACAAATTTGCTATTAT
66 TAATGTTTACCTCTATTTAAGACCTTTTGAGTCGTTAAAAGGCAAAAATACAAATTTACTATTAT
* * * *
15501227 TGCTCTATTTTAACATTTGGATAGCTTCAATATATGATATTAAACTTGTCCGAATGATTGACCTT
131 TGCTCTATTTTAACATTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAAAGATTGAACTT
* * * * * ** * * *
15501292 GGTTTTCACAGTTGATATGTGTGAAAAAGTTATTGTTTATGTTTATTTAAGACTATTTTTGCTGT
196 GGTATTCACAATTGATATATGTGAAAAAGTTATCGGTTACCTCTATCTAAGACTATTTTTGCCGT
* *
15501357 TAAAATGCAAAAATAC-AATTTGCTATTATTATTCTATTTTAATCATTTGTATGGCTCCAT
261 TAAAAGGCAAAAATACAAAGTTGCTATTATTATTCTATTTTAATCATTTGTATGGCTCCAT
* * *
15501417 TACATGATATTAAATAGTT-TT-GAATGATTAAACTTAGTTTTCACA-GTTGATATATGTG-AAA
1 TACATGATATTAAAT--TTATTCAAATGATTAAACTTAGTTTCCA-AGGTTGATATATATGAAAA
** ** *
15501478 AGTTGTTGTTTACCTCTATTTAAGATTTTTTGAGTCGTTAAAAGGCAAAAATATAAATTTACTAT
63 AGTTAATGTTTACCTCTATTTAAGACCTTTTGAGTCGTTAAAAGGCAAAAATACAAATTTACTAT
* * * * *
15501543 TATTG-TTTGTTTTAGCAGTTTGGATAGCTTCAATACATGATATTAAACTTTTTCAAAAGATTGA
128 TATTGCTCTATTTTAACA-TTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAAAGATTGA
* * * *
15501607 ACTTGGTATTCACAATTGATATATGTGACAAAGTTGTCGGTTACCTCTA-CTAGTGACTTTTTTT
192 ACTTGGTATTCACAATTGATATATGTGAAAAAGTTATCGGTTACCTCTATCTA-AGACTATTTTT
15501671 GCCGTTAAAAGGCAAAAATACAAAGTTGCTATTA
256 GCCGTTAAAAGGCAAAAATACAAAGTTGCTATTA
15501705 GTCACCATGT
Statistics
Matches: 239, Mismatches: 43, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
318 11 0.05
319 168 0.70
320 55 0.23
321 3 0.01
322 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (321 bp):
TACATGATATTAAATTTATTCAAATGATTAAACTTAGTTTCCAAGGTTGATATATATGAAAAAGT
TAATGTTTACCTCTATTTAAGACCTTTTGAGTCGTTAAAAGGCAAAAATACAAATTTACTATTAT
TGCTCTATTTTAACATTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAAAGATTGAACTT
GGTATTCACAATTGATATATGTGAAAAAGTTATCGGTTACCTCTATCTAAGACTATTTTTGCCGT
TAAAAGGCAAAAATACAAAGTTGCTATTATTATTCTATTTTAATCATTTGTATGGCTCCAT
Found at i:15501793 original size:319 final size:314
Alignment explanation
Indices: 15501092--15501793 Score: 694
Period size: 319 Copynumber: 2.2 Consensus size: 314
15501082 TTTTAATAGT
* * *
15501092 TTCAATACATGATATTAAATTTATTCAAATTATTGAACTTAGTTTCCAAGGTTGATATGTATGAA
1 TTCAATACATGATATTAAA-TTATT-AAATGATTGAATTTGGTTTCC-A-GTTGATATG--TGAA
** * * * * *
15501157 AAAGTTAATGTTTATGTCTATTTAAGACCTTTTGTGTCGTTAATAGGTAATAATACAAATTTGCT
60 AAAGTTAATGTTTACCTCTATTTAAGACCTTTTGAGTCGTTAAAAGGCAAAAATACAAATTTACT
* * *
15501222 ATTATTGCTCTATTTTAACATTTGGATAGCTTCAATATATGATATTAAACTTGTCCGAATGATTG
125 ATTATTGCTCTATTTTAACATTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAAAGATTG
* * * * * * ** * *
15501287 ACCTTGGTTTTCACAGTTGATATGTGTGAAAAAGTTATTGTTTATGTTTATTTAAGACTATTTTT
190 AACTTGGTATTCACAATTGATATATGTGAAAAAGTTATCGGTTACCTCTATCTAAGACTATTTTT
* * * * * * **
15501352 GCTGTTAAAATGCAAAAATACAATTTGCTATTATTATTCTATTTTAATCATTTGTATGGC
255 GCCGTTAAAAGGCAAAAATACAAGTTGCTATTATCATCCTATTTTAATCATTTGGATAAC
* * * * * * *
15501412 TCCATTACATGATATTAAATAGTTTTGAATGATTAAACTTAGTTTTCACAGTTGATATATGTG-A
1 TTCAATACATGATATTAAAT--TATTAAATGATTGAA-TTTGGTTTC-CAGTTG--ATATGTGAA
** ** *
15501476 AAAGTTGTTGTTTACCTCTATTTAAGATTTTTTGAGTCGTTAAAAGGCAAAAATATAAATTTACT
60 AAAGTTAATGTTTACCTCTATTTAAGACCTTTTGAGTCGTTAAAAGGCAAAAATACAAATTTACT
* * * * *
15501541 ATTATTG-TTTGTTTTAGCAGTTTGGATAGCTTCAATACATGATATTAAACTTTTTCAAAAGATT
125 ATTATTGCTCTATTTTAACA-TTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAAAGATT
* * * *
15501605 GAACTTGGTATTCACAATTGATATATGTGACAAAGTTGTCGGTTACCTCTA-CTAGTGACTTTTT
189 GAACTTGGTATTCACAATTGATATATGTGAAAAAGTTATCGGTTACCTCTATCTA-AGACTATTT
*
15501669 TTGCCGTTAAAAGGCAAAAATACAAAGTTGCTATTAGTCA-CCATGTTTTAA-CAGTTTGGATAA
253 TTGCCGTTAAAAGGCAAAAATAC-AAGTTGCTATTA-TCATCC-TATTTTAATCA-TTTGGATAA
15501732 C
314 C
15501733 TTCAATACATGATATTAAACTTATGTAAATGATTGAATTTGGTTTCCATGATTGATATGTG
1 TTCAATACATGATATTAAA-TTAT-TAAATGATTGAATTTGGTTTCCA-G-TTGATATGTG
15501794 TGAAAGGCCA
Statistics
Matches: 306, Mismatches: 60, Indels: 33
0.77 0.15 0.08
Matches are distributed among these distances:
318 11 0.04
319 178 0.58
320 55 0.18
321 55 0.18
322 7 0.02
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (314 bp):
TTCAATACATGATATTAAATTATTAAATGATTGAATTTGGTTTCCAGTTGATATGTGAAAAAGTT
AATGTTTACCTCTATTTAAGACCTTTTGAGTCGTTAAAAGGCAAAAATACAAATTTACTATTATT
GCTCTATTTTAACATTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAAAGATTGAACTTG
GTATTCACAATTGATATATGTGAAAAAGTTATCGGTTACCTCTATCTAAGACTATTTTTGCCGTT
AAAAGGCAAAAATACAAGTTGCTATTATCATCCTATTTTAATCATTTGGATAAC
Found at i:15503575 original size:2 final size:2
Alignment explanation
Indices: 15503568--15503593 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15503558 CAAACATGCA
15503568 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
15503594 CTCTACCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15505874 original size:12 final size:13
Alignment explanation
Indices: 15505855--15505887 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
15505845 ATAATGATAG
15505855 TAAAATTT-ACAA
1 TAAAATTTAACAA
*
15505867 TTAAATTTAACAA
1 TAAAATTTAACAA
15505880 TAAAATTT
1 TAAAATTT
15505888 TCTTTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAAATTTAACAA
Found at i:15508620 original size:20 final size:22
Alignment explanation
Indices: 15508580--15508627 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 22
15508570 TTAAAATTAA
15508580 ATATATTTATATATAATTTTTC
1 ATATATTTATATATAATTTTTC
*
15508602 ATATA-TTAT-TAT-ATTTTTT
1 ATATATTTATATATAATTTTTC
15508621 AT-TATTT
1 ATATATTT
15508628 TTCATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.08
19 10 0.42
20 3 0.12
21 4 0.17
22 5 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
ATATATTTATATATAATTTTTC
Found at i:15508786 original size:3 final size:3
Alignment explanation
Indices: 15508762--15508820 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
15508752 ATTTTTAATT
*
15508762 TTA TTA TT- TATA TTTA TCA TTA TTA TTA -TA TTA TTA TTA TTA TT-
1 TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15508806 TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TT
15508821 GTAAATAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
2 9 0.19
3 35 0.74
4 2 0.04
5 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:15509716 original size:12 final size:12
Alignment explanation
Indices: 15509699--15509745 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
15509689 AAGCAAATAA
15509699 AAATAAACAAAT
1 AAATAAACAAAT
*
15509711 AAATAAGCAAAT
1 AAATAAACAAAT
* *
15509723 CAATAAATAAA-
1 AAATAAACAAAT
15509734 AAATAAAACAAA
1 AAAT-AAACAAA
15509746 AACAAAATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 3 0.11
12 25 0.89
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.15
Consensus pattern (12 bp):
AAATAAACAAAT
Found at i:15509739 original size:7 final size:7
Alignment explanation
Indices: 15509727--15509769 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
15509717 GCAAATCAAT
15509727 AAATAAA
1 AAATAAA
15509734 AAATAAA
1 AAATAAA
*
15509741 ACAAAAACA
1 A-AATAA-A
15509750 AAAT-AA
1 AAATAAA
15509756 AAATAAA
1 AAATAAA
15509763 AAATAAA
1 AAATAAA
15509770 GAAAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
6 5 0.16
7 18 0.58
8 6 0.19
9 2 0.06
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.12
Consensus pattern (7 bp):
AAATAAA
Found at i:15510711 original size:106 final size:106
Alignment explanation
Indices: 15510587--15510803 Score: 416
Period size: 106 Copynumber: 2.0 Consensus size: 106
15510577 GTTAAATTTT
*
15510587 AATTTTTCACGAGAATAATTTTAATATATTTTGTAGACTATGATTTGTAATTGTTTAATTTTATA
1 AATTTTTCACGAGAATAATTTTAATATATTTTGTAGACTATGATTTGTAATTGTTTAATTCTATA
*
15510652 ATAAAAATGAATAATTTATTTATTCATTTAATTTTAGTTTA
66 ATAAAAATGAATAATTTATTTATTAATTTAATTTTAGTTTA
15510693 AATTTTTCACGAGAATAATTTTAATATATTTTGTAGACTATGATTTGTAATTGTTTAATTCTATA
1 AATTTTTCACGAGAATAATTTTAATATATTTTGTAGACTATGATTTGTAATTGTTTAATTCTATA
15510758 ATAAAAATGAATAATTTATTTATTAATTTAATTTTAGTTTA
66 ATAAAAATGAATAATTTATTTATTAATTTAATTTTAGTTTA
15510799 AATTT
1 AATTT
15510804 GAATGATTTA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 109 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (106 bp):
AATTTTTCACGAGAATAATTTTAATATATTTTGTAGACTATGATTTGTAATTGTTTAATTCTATA
ATAAAAATGAATAATTTATTTATTAATTTAATTTTAGTTTA
Found at i:15510815 original size:15 final size:16
Alignment explanation
Indices: 15510795--15510834 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
15510785 TTAATTTTAG
*
15510795 TTTAAATTT-GAATGA
1 TTTAAATTTAAAATGA
15510810 TTTAAATTTAAAATGA
1 TTTAAATTTAAAATGA
*
15510826 TTTAGATTT
1 TTTAAATTT
15510835 CATGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (16 bp):
TTTAAATTTAAAATGA
Found at i:15512628 original size:2 final size:2
Alignment explanation
Indices: 15512621--15512651 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15512611 GCAAAAAGAA
15512621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15512652 AATCATAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15513697 original size:29 final size:29
Alignment explanation
Indices: 15513647--15513707 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
15513637 TATGATTATT
* *
15513647 TTCAAAGATAATATTTGATAAATTTAAAA
1 TTCAAAGATAATACTTGATAAAATTAAAA
* *
15513676 TTCAAATATCAATACTTG-TAAAATTAGAA
1 TTCAAAGAT-AATACTTGATAAAATTAAAA
15513705 TTC
1 TTC
15513708 CTTCATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.38
Consensus pattern (29 bp):
TTCAAAGATAATACTTGATAAAATTAAAA
Found at i:15517741 original size:2 final size:2
Alignment explanation
Indices: 15517734--15517759 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15517724 GGATGGCTTT
15517734 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
15517760 ATTTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15527432 original size:35 final size:35
Alignment explanation
Indices: 15527381--15527456 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
15527371 TTCATCATTA
15527381 GGGTTAGGGTTAGTAAGGCCTTGATTTTATGTTAT
1 GGGTTAGGGTTAGTAAGGCCTTGATTTTATGTTAT
* *
15527416 GGGTTAGGGTTGGTAAGGCCTTGGTTTTATGTTAT
1 GGGTTAGGGTTAGTAAGGCCTTGATTTTATGTTAT
15527451 GGGTTA
1 GGGTTA
15527457 TTAAGGGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.17, C:0.05, G:0.36, T:0.42
Consensus pattern (35 bp):
GGGTTAGGGTTAGTAAGGCCTTGATTTTATGTTAT
Found at i:15527466 original size:35 final size:35
Alignment explanation
Indices: 15527393--15527467 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
15527383 GTTAGGGTTA
***
15527393 GTAAGGCCTTGATTTTATGTTATGGGTTAGGGTTG
1 GTAAGGCCTTGATTTTATGTTATGGGTTAGGAAGG
* **
15527428 GTAAGGCCTTGGTTTTATGTTATGGGTTATTAAGG
1 GTAAGGCCTTGATTTTATGTTATGGGTTAGGAAGG
15527463 GTAAG
1 GTAAG
15527468 TATTGTCTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.05, G:0.33, T:0.41
Consensus pattern (35 bp):
GTAAGGCCTTGATTTTATGTTATGGGTTAGGAAGG
Found at i:15531126 original size:26 final size:24
Alignment explanation
Indices: 15531089--15531136 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
15531079 ACATGCAAAA
15531089 TAAAAAAATTATTACATGATTTTTT
1 TAAAAAAATTATTACAT-ATTTTTT
* *
15531114 TAAAAAATTTTATTATATATTTT
1 TAAAAAA-ATTATTACATATTTT
15531137 AAAAGATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TAAAAAAATTATTACATATTTTTT
Found at i:15532977 original size:13 final size:13
Alignment explanation
Indices: 15532961--15532985 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15532951 AAAATAATTT
15532961 AATAAAAAACTAA
1 AATAAAAAACTAA
15532974 AATAAAAAACTA
1 AATAAAAAACTA
15532986 TTGCATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
AATAAAAAACTAA
Found at i:15547091 original size:22 final size:21
Alignment explanation
Indices: 15547043--15547091 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
15547033 AGGATAAACC
**
15547043 ATAATAAAAATTTAAAAATCAA
1 ATAA-AAAAATTTAAAAAAAAA
*
15547065 GTAAAAAAATTTAAAATAAAAA
1 ATAAAAAAATTTAAAA-AAAAA
15547087 ATAAA
1 ATAAA
15547092 TATATAATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
ATAAAAAAATTTAAAAAAAAA
Found at i:15547157 original size:16 final size:15
Alignment explanation
Indices: 15547134--15547189 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 15
15547124 TATGCTAAAT
*
15547134 AAAATAAAAATATAA
1 AAAATAAAAAAATAA
*
15547149 AATAATAAAAACATAA
1 AA-AATAAAAAAATAA
15547165 AAACATAAAAAAATAA
1 AAA-ATAAAAAAATAA
15547181 ATAAATAAA
1 A-AAATAAA
15547190 TAATTGAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
15 3 0.08
16 31 0.86
17 2 0.06
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAAAAAATAA
Found at i:15547167 original size:24 final size:24
Alignment explanation
Indices: 15547129--15547189 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
15547119 ATACATATGC
* *
15547129 TAAATAAAATAAAAATATAAAATAA
1 TAAAT-AAATAAAAACATAAAAAAA
15547154 TAAA-AACATAAAAACATAAAAAAA
1 TAAATAA-ATAAAAACATAAAAAAA
15547178 TAAATAAATAAA
1 TAAATAAATAAA
15547190 TAATTGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 2 0.06
24 24 0.75
25 6 0.19
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (24 bp):
TAAATAAATAAAAACATAAAAAAA
Found at i:15547192 original size:8 final size:7
Alignment explanation
Indices: 15547134--15547189 Score: 58
Period size: 8 Copynumber: 7.1 Consensus size: 7
15547124 TATGCTAAAT
15547134 AAAATAA
1 AAAATAA
15547141 AAATATAA
1 AAA-ATAA
15547149 AATAATAA
1 AA-AATAA
15547157 AAACATAA
1 AAA-ATAA
15547165 AAACATAAA
1 AAA-AT-AA
15547174 AAAATAA
1 AAAATAA
15547181 ATAAATAA
1 A-AAATAA
15547189 A
1 A
15547190 TAATTGAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.16
8 31 0.70
9 6 0.14
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAATAA
Found at i:15552958 original size:18 final size:18
Alignment explanation
Indices: 15552932--15552987 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
15552922 TTTTGTAAAT
* *
15552932 TTTTTTTATTATTTATTA
1 TTTTATTATTATTTAATA
*
15552950 TTTTATTATT-TTGAATA
1 TTTTATTATTATTTAATA
*
15552967 TATTTATAATTATTTTAATA
1 T-TTTATTATTA-TTTAATA
15552987 T
1 T
15552988 AAAAATAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.20
18 17 0.57
20 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTATTATTATTTAATA
Found at i:15556361 original size:35 final size:36
Alignment explanation
Indices: 15556274--15556361 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 36
15556264 ATTAGAGTAT
* * *
15556274 TTTTGGTTAGTTATGGTATGAGAGATATTATAATAA
1 TTTTGGTTAATTATGGTAGGAGAGACATTATAATAA
* * *
15556310 TTTTGGCTAATCATGGTAGGAG-GACATTATCATAA
1 TTTTGGTTAATTATGGTAGGAGAGACATTATAATAA
*
15556345 TTTTGATTAATTATGGT
1 TTTTGGTTAATTATGGT
15556362 GGTGGAGTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 25 0.58
36 18 0.42
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.43
Consensus pattern (36 bp):
TTTTGGTTAATTATGGTAGGAGAGACATTATAATAA
Found at i:15557424 original size:21 final size:21
Alignment explanation
Indices: 15557374--15557438 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
15557364 TGGTTAGGTT
* *
15557374 AGAGTATGAATTTTTAAAAAG
1 AGAGTATGAATTTTTAGAGAG
*
15557395 GGA-TAATGAATTTTTAGAGAG
1 AGAGT-ATGAATTTTTAGAGAG
*
15557416 AGAGTATGAATATTTAGAGAG
1 AGAGTATGAATTTTTAGAGAG
15557437 AG
1 AG
15557439 TATAAATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (21 bp):
AGAGTATGAATTTTTAGAGAG
Found at i:15557447 original size:17 final size:19
Alignment explanation
Indices: 15557412--15557449 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
15557402 GAATTTTTAG
15557412 AGAGAGAGTATGAATATTT
1 AGAGAGAGTATGAATATTT
15557431 AGAGAGAGTAT-AA-ATTT
1 AGAGAGAGTATGAATATTT
15557448 AG
1 AG
15557450 TTACGTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (19 bp):
AGAGAGAGTATGAATATTT
Found at i:15557586 original size:21 final size:21
Alignment explanation
Indices: 15557562--15557608 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
15557552 AATGGCGTGA
15557562 TTTTAGAGAGATAA-AATGAAT
1 TTTTAGAGAGA-AAGAATGAAT
*
15557583 TTTTAGAGAGAAAGTATGAAT
1 TTTTAGAGAGAAAGAATGAAT
15557604 TTTTA
1 TTTTA
15557609 AAAAGAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (21 bp):
TTTTAGAGAGAAAGAATGAAT
Found at i:15557615 original size:23 final size:21
Alignment explanation
Indices: 15557577--15557625 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
15557567 GAGAGATAAA
*
15557577 ATGAATTTTTAGAGAGAAAGT
1 ATGAATTTTTAAAGAGAAAGT
*
15557598 ATGAATTTTTAAAAAGAGAGAGT
1 ATGAATTTTT--AAAGAGAAAGT
15557621 ATGAA
1 ATGAA
15557626 ATCAGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
23 14 0.58
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (21 bp):
ATGAATTTTTAAAGAGAAAGT
Found at i:15559110 original size:15 final size:15
Alignment explanation
Indices: 15559090--15559124 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
15559080 TTCTATTCCA
15559090 TTTTATTTGTT-TTAT
1 TTTTATTT-TTATTAT
15559105 TTTTATTTTTATTAT
1 TTTTATTTTTATTAT
15559120 TTTTA
1 TTTTA
15559125 GATTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTATTTTTATTAT
Found at i:15567090 original size:25 final size:25
Alignment explanation
Indices: 15567056--15567108 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
15567046 GCTCAGGATG
*
15567056 ATATGAGTGGACTATCACAATCTAA
1 ATATGAGTGGACCATCACAATCTAA
15567081 ATATGAGTGGACCATCACAATCTAA
1 ATATGAGTGGACCATCACAATCTAA
15567106 ATA
1 ATA
15567109 GGGCTAGCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (25 bp):
ATATGAGTGGACCATCACAATCTAA
Found at i:15567208 original size:183 final size:182
Alignment explanation
Indices: 15566897--15567243 Score: 559
Period size: 183 Copynumber: 1.9 Consensus size: 182
15566887 AAAAATGTAC
* *
15566897 AAATATGAGTGGACTATCATAATCTAAATAAAGCTAGCCTGAAAGACAACTTTTCTTTATTGTAC
1 AAATATGAGTGGACCATCACAATCTAAATAAAGCTAGCCTGAAAGACAACTTTTCTTTATTGTAC
* * *
15566962 ATTGATATATTGGTAGATAATACAACCTAACATATGGTTTTCTCCTTTATGAATGGCTTCTCCAA
66 ATTGATACATTGGTAGATAATACAACCTAACATATGGTTTTCTCCTTTATGAATAGATTCTCCAA
15567027 CTATAATCAAATAAAGATGGCTCAGGATGATATGAGTGGACTATCACAATCT
131 CTATAATCAAATAAAGATGGCTCAGGATGATATGAGTGGACTATCACAATCT
** * *
15567079 AAATATGAGTGGACCATCACAATCTAAATAGGGCTAGCCTGAAAGATAACTTTTTTTTTATTGTA
1 AAATATGAGTGGACCATCACAATCTAAATAAAGCTAGCCTGAAAGACAAC-TTTTCTTTATTGTA
* * * *
15567144 TATTGATACATTGGTAGATAATACAACCTAACATGTGGTTTTCTCTTTTATGGATAGATTCTCCA
65 CATTGATACATTGGTAGATAATACAACCTAACATATGGTTTTCTCCTTTATGAATAGATTCTCCA
*
15567209 GCTATAATCAAATAAAGATGGCTCAGGATGATATG
130 ACTATAATCAAATAAAGATGGCTCAGGATGATATG
15567244 GGAACGATTA
Statistics
Matches: 150, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
182 45 0.30
183 105 0.70
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (182 bp):
AAATATGAGTGGACCATCACAATCTAAATAAAGCTAGCCTGAAAGACAACTTTTCTTTATTGTAC
ATTGATACATTGGTAGATAATACAACCTAACATATGGTTTTCTCCTTTATGAATAGATTCTCCAA
CTATAATCAAATAAAGATGGCTCAGGATGATATGAGTGGACTATCACAATCT
Found at i:15569055 original size:20 final size:20
Alignment explanation
Indices: 15569032--15569074 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
15569022 TAAGATGATG
*
15569032 CAAGAAATATGTA-CATAATT
1 CAAG-AATATATACCATAATT
*
15569052 CAAGATTATATACCATAATT
1 CAAGAATATATACCATAATT
15569072 CAA
1 CAA
15569075 CTCAATACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (20 bp):
CAAGAATATATACCATAATT
Found at i:15570529 original size:65 final size:65
Alignment explanation
Indices: 15570446--15570733 Score: 190
Period size: 65 Copynumber: 4.4 Consensus size: 65
15570436 TTTGACTCAG
* * * * **
15570446 TCCAGATCATTTTATTTTTCTAACTCATGGTTCGATTATGGTCACTTGTTTTGATCTTGGCTCGA
1 TCCAGATCATTTTATTTTTCTAACTCATGGTTCGATCATGGTAACCTGTTTTAATCTCAGCTCGA
* * * * * * *
15570511 TCTATATCATTTTATTTTTTTGACTCGTGGTTTGATCCTGGTAACCTGTTTTAATCTCAGCTCGA
1 TCCAGATCATTTTATTTTTCTAACTCATGGTTCGATCATGGTAACCTGTTTTAATCTCAGCTCGA
* * *** * *
15570576 TCCAGATCATTTTATTTTT-TACACTCGCT-GTTTGATCCCAGTCACCTGTTTTGATCTC-GACT
1 TCCAGATCATTTTATTTTTCTA-ACTC-ATGGTTCGATCATGGTAACCTGTTTTAATCTCAG-CT
* *
15570638 TGG
63 CGA
* * * * * * *
15570641 TCCAGATCGTTTTAATATTTTTTTGGACTCATGGTTCAATCCTGGTTA-CTAGTTTTGATCTC-G
1 TCCAGATC-ATTT--TATTTTTCT-AACTCATGGTTCGATCATGGTAACCT-GTTTTAATCTCAG
15570704 ACTCGA
61 -CTCGA
*
15570710 TCCAAATCATTTTATTTTTCTAAC
1 TCCAGATCATTTTATTTTTCTAAC
15570734 ATGTGGTTTG
Statistics
Matches: 176, Mismatches: 37, Indels: 20
0.76 0.16 0.09
Matches are distributed among these distances:
64 2 0.01
65 111 0.63
66 12 0.07
68 13 0.07
69 38 0.22
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.45
Consensus pattern (65 bp):
TCCAGATCATTTTATTTTTCTAACTCATGGTTCGATCATGGTAACCTGTTTTAATCTCAGCTCGA
Found at i:15570767 original size:134 final size:133
Alignment explanation
Indices: 15570523--15570768 Score: 306
Period size: 134 Copynumber: 1.8 Consensus size: 133
15570513 TATATCATTT
* ** *
15570523 TATTTTTTTGACTCGTGGTTTGATCCTGGTAACCTGTTTTAATCTCAGCTCGATCCAGATCATTT
1 TATTTTTTTGACTCATGGTTCAATCCTGGTAACCTGTTTTAATCTCAGCTCGATCCAAATCATTT
**
15570588 TATTTTTTACACTCGCTGTTTGATCCCAGTCACCTGTTTTGATCTCGACTTGGTCCAGATCGTTT
66 TATTTTTTACACTCGCTGTTTGATCCCAGTCACCTGTTTCAATCTCGACTTGGTCCAGATCGTTT
15570653 TAA
131 TAA
* *
15570656 TATTTTTTTGGACTCATGGTTCAATCCTGGTTA-CTAGTTTTGATCTC-GACTCGATCCAAATCA
1 TATTTTTTT-GACTCATGGTTCAATCCTGGTAACCT-GTTTTAATCTCAG-CTCGATCCAAATCA
*
15570719 TTTTATTTTTCTA-ACAT-G-TGGTTTGATTCCAGTCA-CTCGTTTCAATCTCG
63 TTTTATTTTT-TACAC-TCGCT-GTTTGATCCCAGTCACCT-GTTTCAATCTCG
15570769 GCTTAGCCTA
Statistics
Matches: 97, Mismatches: 9, Indels: 13
0.82 0.08 0.11
Matches are distributed among these distances:
133 15 0.15
134 79 0.81
135 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (133 bp):
TATTTTTTTGACTCATGGTTCAATCCTGGTAACCTGTTTTAATCTCAGCTCGATCCAAATCATTT
TATTTTTTACACTCGCTGTTTGATCCCAGTCACCTGTTTCAATCTCGACTTGGTCCAGATCGTTT
TAA
Found at i:15571185 original size:3 final size:3
Alignment explanation
Indices: 15571164--15571217 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
15571154 AGGCCCAATC
* **
15571164 ATT ATT ACT ATT ACA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
15571212 ATT ATT
1 ATT ATT
15571218 TCTTTTAGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:15572001 original size:20 final size:20
Alignment explanation
Indices: 15571950--15572002 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
15571940 TAAAATTTTC
15571950 TTATTTATTTCTATTTCTATT
1 TTATTTATTT-TATTTCTATT
* * *
15571971 TGATTTGTTTTATTTTTATTT
1 TTATTTATTTTATTTCTA-TT
15571992 TTATTT-TTTTA
1 TTATTTATTTTA
15572003 GGTTTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (20 bp):
TTATTTATTTTATTTCTATT
Found at i:15572096 original size:12 final size:13
Alignment explanation
Indices: 15572072--15572102 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
15572062 TTCATTTTTT
15572072 TAAAAAATAATAA
1 TAAAAAATAATAA
15572085 TAAAAAAT-ATAA
1 TAAAAAATAATAA
15572097 TAAAAA
1 TAAAAA
15572103 TATTTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAAATAATAA
Found at i:15573597 original size:25 final size:25
Alignment explanation
Indices: 15573569--15573617 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
15573559 TCTAAAAGTA
15573569 TTAAAAACGATTGACTAAAATACCT
1 TTAAAAACGATTGACTAAAATACCT
** * *
15573594 TTAAAATTGATTGAGTACAATACC
1 TTAAAAACGATTGACTAAAATACC
15573618 CTAATTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (25 bp):
TTAAAAACGATTGACTAAAATACCT
Found at i:15578776 original size:144 final size:141
Alignment explanation
Indices: 15578606--15579025 Score: 398
Period size: 145 Copynumber: 2.9 Consensus size: 141
15578596 GGGGTTTTCA
* * *
15578606 TGAAAAATTGA-TTTCAAAAATGTCAAATTACAAAAATACTTTGAAAGGGTATTTTGGTAATATC
1 TGAAAAATTGACATT-AAAAA-GTCAAATTATAAAAATACTTT-AAAGGGTATTTTGGTAATTTC
* *
15578670 ACTCATTTTAAGGTGCAATCAAAATTTTTAATGCATAAAAATTCATGAAATAATATTTAAACATG
63 ACTCTTTTTAAGGTGCAATCAAAATTTTTAATGCATCAAAATTCATGAAATAATATTTAAACATG
15578735 ATCAGTAGCATTTTG
128 ATCAG-AGCATTTTG
*
15578750 TGAAAAATTGACCTTAACAAAGTCAAATTATAAAAATATCTTTAAAGGGTATTTTGGTAATTTCA
1 TGAAAAATTGACATTAA-AAAGTCAAATTATAAAAATA-CTTTAAAGGGTATTTTGGTAATTTCA
* * * * * * * *
15578815 TTCTTTTTGAGGTGCAAT-AAATTCTTTCTATTTCATCAAAATTGATGTAATGATA-TTAAAGCA
64 CTCTTTTTAAGGTGCAATCAAAAT-TTT-TAATGCATCAAAATTCATGAAATAATATTTAAA-CA
* *
15578878 TGATTTAGAGCTTTTTG
126 TGA-TCAGAGCATTTTG
** ** * * * * ** *
15578895 CAAAAAATCAACATTAAGAAGATCACATTATGAAAATACTGCTAAAAAGTATTTTGGTAAATTTA
1 TGAAAAATTGACATTAAAAAG-TCAAATTATAAAAATACT-TTAAAGGGTATTTTGGT-AATTTC
** * * * *
15578960 ACT-TTTTTAAGGTGCAATCAAGGTTTTCAATGCACCAAAATTCATGGAATAATATTAAAACATG
63 ACTCTTTTTAAGGTGCAATCAAAATTTTTAATGCATCAAAATTCATGAAATAATATTTAAACATG
15579024 AT
128 AT
15579026 ATATTGCTTT
Statistics
Matches: 225, Mismatches: 39, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
143 5 0.02
144 103 0.46
145 104 0.46
146 13 0.06
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (141 bp):
TGAAAAATTGACATTAAAAAGTCAAATTATAAAAATACTTTAAAGGGTATTTTGGTAATTTCACT
CTTTTTAAGGTGCAATCAAAATTTTTAATGCATCAAAATTCATGAAATAATATTTAAACATGATC
AGAGCATTTTG
Found at i:15579677 original size:36 final size:35
Alignment explanation
Indices: 15579633--15579724 Score: 112
Period size: 36 Copynumber: 2.6 Consensus size: 35
15579623 AATGAACCGT
*
15579633 AAGTCAAAAAATTAAAAATATTTGAGATTAAATCCC
1 AAGTCAAAAAATTAAAAATA-CTGAGATTAAATCCC
* * * **
15579669 AATTCAAAAAATAAAAAATGACTGAGATTGAATCGT
1 AAGTCAAAAAATTAAAAAT-ACTGAGATTAAATCCC
15579705 AAGTCAAAAAATTAAAAATA
1 AAGTCAAAAAATTAAAAATA
15579725 ACCAAGACTA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
35 1 0.02
36 45 0.96
37 1 0.02
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.25
Consensus pattern (35 bp):
AAGTCAAAAAATTAAAAATACTGAGATTAAATCCC
Found at i:15579752 original size:72 final size:72
Alignment explanation
Indices: 15579625--15579806 Score: 184
Period size: 72 Copynumber: 2.5 Consensus size: 72
15579615 TGATCAATAA
* * ** * * *
15579625 TGAACCGTAAGTCAAAAAATTAAAAATATTTGAGATTAAATCCCAATTCAAAAAATAAAAAATGA
1 TGAATCGTAAGTCAAAAAATTAAAAATAATCAAGACTAAATCACAAGTCAAAAAATAAAAAATGA
*
15579690 CTGAGAT
66 CTGAGAC
* * * * * *
15579697 TGAATCGTAAGTCAAAAAATTAAAAATAACCAAGACTACATTACAAGTCAGAAAATTAAGAATGA
1 TGAATCGTAAGTCAAAAAATTAAAAATAATCAAGACTAAATCACAAGTCAAAAAATAAAAAATGA
* *
15579762 GTGGGAC
66 CTGAGAC
* * * *
15579769 TGAATTGCAAGTCAAAAATTTAAAAATAATCAGGACTA
1 TGAATCGTAAGTCAAAAAATTAAAAATAATCAAGACTA
15579807 TACCGTAAGT
Statistics
Matches: 89, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
72 89 1.00
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.24
Consensus pattern (72 bp):
TGAATCGTAAGTCAAAAAATTAAAAATAATCAAGACTAAATCACAAGTCAAAAAATAAAAAATGA
CTGAGAC
Found at i:15579805 original size:36 final size:35
Alignment explanation
Indices: 15579705--15579806 Score: 91
Period size: 36 Copynumber: 2.8 Consensus size: 35
15579695 ATTGAATCGT
* *
15579705 AAGTCAAAAAATTAAAAATAACCAAGACTACATTAC
1 AAGTC-AAAAATTAAAAATAATCAGGACTACATTAC
* * * *
15579741 AAGTCAGAAAATTAAGAATGAGT-GGGACTGA-ATTGC
1 AAGTCA-AAAATTAAAAAT-AATCAGGACT-ACATTAC
15579777 AAGTCAAAAATTTAAAAATAATCAGGACTA
1 AAGTCAAAAA-TTAAAAATAATCAGGACTA
15579807 TACCGTAAGT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
35 8 0.15
36 42 0.81
37 2 0.04
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.22
Consensus pattern (35 bp):
AAGTCAAAAATTAAAAATAATCAGGACTACATTAC
Found at i:15579889 original size:35 final size:35
Alignment explanation
Indices: 15579845--15580084 Score: 132
Period size: 35 Copynumber: 6.9 Consensus size: 35
15579835 AAACAAAATA
* *
15579845 GTAAATTAAAAAATAATGATGACTGAGACTGAATC
1 GTAAGTTAAAAAATAAAGATGACTGAGACTGAATC
**
15579880 GTAAGTTAAAAAAT-AAGAATGACT-AGGTTTGAATC
1 GTAAGTTAAAAAATAAAG-ATGACTGA-GACTGAATC
* * * * * *
15579915 GTAAGTTGACAAATAAAGATGATTGGGACTAAATG
1 GTAAGTTAAAAAATAAAGATGACTGAGACTGAATC
* * * * * *
15579950 GCAAGTCAAAAAATAAAGATAATTAAGATTGAATC
1 GTAAGTTAAAAAATAAAGATGACTGAGACTGAATC
** * * * *
15579985 ACAAGTTGAAAAATAAGGAT--CAG-GACTGAACC
1 GTAAGTTAAAAAATAAAGATGACTGAGACTGAATC
** * * * *
15580017 ACAAGTTAAAAAATAAAGTTGA-TCAGGATTGAACC
1 GTAAGTTAAAAAATAAAGATGACTGA-GACTGAATC
* * *
15580052 ATAAGTTAAAAAATAAGGATGACTGGGACTGAA
1 GTAAGTTAAAAAATAAAGATGACTGAGACTGAA
15580085 ATACAAGTTA
Statistics
Matches: 153, Mismatches: 43, Indels: 18
0.71 0.20 0.08
Matches are distributed among these distances:
32 24 0.16
34 3 0.02
35 122 0.80
36 4 0.03
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (35 bp):
GTAAGTTAAAAAATAAAGATGACTGAGACTGAATC
Found at i:15580093 original size:35 final size:35
Alignment explanation
Indices: 15579850--15580174 Score: 125
Period size: 35 Copynumber: 9.3 Consensus size: 35
15579840 AAATAGTAAA
*
15579850 TTAAAAAATAATGATGACT-GAGACTG-AAT-CGTAAG
1 TTAAAAAATAAAGATGACTAG-GACTGAAATAC--AAG
**
15579885 TTAAAAAAT-AAGAATGACTAGGTTTG-AAT-CGTAAG
1 TTAAAAAATAAAG-ATGACTAGGACTGAAATAC--AAG
* * * * *
15579920 TTGACAAATAAAGATGATTGGGACT-AAATGGCAAG
1 TTAAAAAATAAAGATGACTAGGACTGAAAT-ACAAG
* * * * *
15579955 TCAAAAAATAAAGATAATTAAGATTG-AATCACAAG
1 TTAAAAAATAAAGATGACTAGGACTGAAAT-ACAAG
* * **
15579990 TTGAAAAATAAGGAT--C-AGGACTGAACCACAAG
1 TTAAAAAATAAAGATGACTAGGACTGAAATACAAG
* * ** *
15580022 TTAAAAAATAAAGTTGA-TCAGGATTGAACCATAAG
1 TTAAAAAATAAAGATGACT-AGGACTGAAATACAAG
* *
15580057 TTAAAAAATAAGGATGACTGGGACTGAAATACAAG
1 TTAAAAAATAAAGATGACTAGGACTGAAATACAAG
* * * * * * ** *
15580092 TTAGAAAATTAAAAATGATTAGTATTGAACTGTAGG
1 TTA-AAAAATAAAGATGACTAGGACTGAAATACAAG
** * * **
15580128 TCCAAAAATAAGGATGACAAGGACTGAACCACAAG
1 TTAAAAAATAAAGATGACTAGGACTGAAATACAAG
15580163 TTAAAAAATAAA
1 TTAAAAAATAAA
15580175 TATGGTCAAA
Statistics
Matches: 211, Mismatches: 65, Indels: 28
0.69 0.21 0.09
Matches are distributed among these distances:
32 22 0.10
33 1 0.00
34 2 0.01
35 158 0.75
36 27 0.13
37 1 0.00
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23
Consensus pattern (35 bp):
TTAAAAAATAAAGATGACTAGGACTGAAATACAAG
Found at i:15580222 original size:70 final size:70
Alignment explanation
Indices: 15580007--15580243 Score: 233
Period size: 70 Copynumber: 3.4 Consensus size: 70
15579997 ATAAGGATCA
* * *
15580007 GGACTGAACCACAAGTTAAAAAATAAAGT-TGATCAGGATTGAACCATAAGTTAAAAAATAAGGA
1 GGACTGAACCACAAGTTAAAAAATAAA-TATGATCAGAATTGAACCGTAAGTAAAAAAATAAGGA
15580071 TGACTG
65 TGACTG
** * * * * * * **
15580077 GGACTGAAATACAAGTTAGAAAATTAAAAATGATTAGTATTGAACTGTAGGTCCAAAAATAAGGA
1 GGACTGAACCACAAGTTA-AAAAATAAATATGATCAGAATTGAACCGTAAGTAAAAAAATAAGGA
**
15580142 TGACAA
65 TGACTG
* * * *
15580148 GGACTGAACCACAAGTTAAAAAATAAATATGGTCAAAATTGAACCGTAAATAAAAAAATATGGAT
1 GGACTGAACCACAAGTTAAAAAATAAATATGATCAGAATTGAACCGTAAGTAAAAAAATAAGGAT
*
15580213 GATTG
66 GACTG
*** *
15580218 GGACTGAATTGCAAGTCAAAAAATAA
1 GGACTGAACCACAAGTTAAAAAATAA
15580244 GAATGACTGT
Statistics
Matches: 131, Mismatches: 34, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
70 75 0.57
71 56 0.43
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (70 bp):
GGACTGAACCACAAGTTAAAAAATAAATATGATCAGAATTGAACCGTAAGTAAAAAAATAAGGAT
GACTG
Found at i:15581434 original size:17 final size:16
Alignment explanation
Indices: 15581412--15581469 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
15581402 TTAAGGTTTC
15581412 AAATTTGGGATTTCATG
1 AAATTTGGG-TTTCATG
*
15581429 AAATTT-AGTTTCATGG
1 AAATTTGGGTTTCAT-G
* *
15581445 AATTTTGGGTCTCATG
1 AAATTTGGGTTTCATG
15581461 AAATTTGGG
1 AAATTTGGG
15581470 GTCTCATGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 6 0.18
16 16 0.47
17 12 0.35
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (16 bp):
AAATTTGGGTTTCATG
Found at i:15581471 original size:17 final size:17
Alignment explanation
Indices: 15581412--15581477 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
15581402 TTAAGGTTTC
* *
15581412 AAATTTGGGATTTCATG
1 AAATTTGGGGTCTCATG
* *
15581429 AAATTT--AGTTTCATG
1 AAATTTGGGGTCTCATG
* *
15581444 GAATTTTGGGTCTCATG
1 AAATTTGGGGTCTCATG
15581461 AAATTTGGGGTCTCATG
1 AAATTTGGGGTCTCATG
15581478 GAATAATGCA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 12 0.30
17 28 0.70
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (17 bp):
AAATTTGGGGTCTCATG
Found at i:15585668 original size:2 final size:2
Alignment explanation
Indices: 15585663--15585687 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15585653 AAAAAAAAAA
15585663 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
15585688 AACTTAAACT
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:15590553 original size:43 final size:42
Alignment explanation
Indices: 15590445--15590604 Score: 153
Period size: 43 Copynumber: 3.8 Consensus size: 42
15590435 ACATTTATAA
* *
15590445 GACTCTAGG-TTCACAACAAAGTAAACGATTCATGGTTGGAAG
1 GACTCT-GGATTCACAACAAAGTAAATGATTCATAGTTGGAAG
* * **
15590487 GACTCTGGATTCATAACAAAGTAAATGATTAATAGTTGAGGGG
1 GACTCTGGATTCACAACAAAGTAAATGATTCATAGTTG-GAAG
* * * *
15590530 GATTCTGGATTCACAACAGAGTAAATCATTCATAGTTTGAA-
1 GACTCTGGATTCACAACAAAGTAAATGATTCATAGTTGGAAG
* * ** *
15590571 GACTATGGATTCATAGTAGAGTAAATGATTCATA
1 GACTCTGGATTCACAACAAAGTAAATGATTCATA
15590605 ATTTGGAGGA
Statistics
Matches: 96, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
41 30 0.31
42 32 0.33
43 34 0.35
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (42 bp):
GACTCTGGATTCACAACAAAGTAAATGATTCATAGTTGGAAG
Found at i:15590638 original size:42 final size:41
Alignment explanation
Indices: 15590538--15590642 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 41
15590528 GGGATTCTGG
* * * **
15590538 ATTCACAACAGAGTAAATCATTCATAGTTTGAAGACTATGG
1 ATTCACAATAGAGTAAATGATTCATAATTTGAAGACTATAA
* * * *
15590579 ATTCATAGTAGAGTAAATGATTCATAATTTGGAGGACTTTAA
1 ATTCACAATAGAGTAAATGATTCATAATTT-GAAGACTATAA
*
15590621 ATTCACAATAGAATAAATGATT
1 ATTCACAATAGAGTAAATGATT
15590643 TTCAATTTGA
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
41 25 0.49
42 26 0.51
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.32
Consensus pattern (41 bp):
ATTCACAATAGAGTAAATGATTCATAATTTGAAGACTATAA
Found at i:15590811 original size:19 final size:19
Alignment explanation
Indices: 15590746--15590813 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
15590736 AAAACTCTAA
*
15590746 ATTCACAATAGAGGGAACG
1 ATTCACAATAGAGGGAATG
* * **
15590765 ATTCAAAATTGGAGGGGCTCTAG
1 ATTCACAA-TAGA-GGG-AAT-G
15590788 ATTCACAATAGAGGGAATG
1 ATTCACAATAGAGGGAATG
15590807 ATTCACA
1 ATTCACA
15590814 GTTCAAAGGA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
19 15 0.42
20 4 0.11
21 6 0.17
22 3 0.08
23 8 0.22
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (19 bp):
ATTCACAATAGAGGGAATG
Found at i:15590902 original size:79 final size:77
Alignment explanation
Indices: 15590750--15590906 Score: 174
Period size: 79 Copynumber: 2.0 Consensus size: 77
15590740 CTCTAAATTC
* * *
15590750 ACAATAGAGGGAACGATTCAAAATTGGAGGGGCTCTAGATTCACAATAGAGGGAATGATTCACAG
1 ACAATAGAGGGAACAATTCAAAATT-GAGGGGCTCTAGATTCACAATAGAGGAAATGATTCAAAG
15590815 TTCAAAGGACTTTG
65 TTCAAAGGA-TTTG
* * * * *
15590829 ACAATAGAGGGAACAATTCATAGTT-AGGGGACTCTGGATTCATAATAGAGTAAATGATTTACAA
1 ACAATAGAGGGAACAATTCAAAATTGAGGGG-CTCTAGATTCACAATAGAGGAAATGA-TT-CAA
*
15590893 ATTTC-AAGGATTTG
63 AGTTCAAAGGATTTG
15590907 CAAGAGTCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
77 5 0.08
78 26 0.39
79 29 0.44
80 6 0.09
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (77 bp):
ACAATAGAGGGAACAATTCAAAATTGAGGGGCTCTAGATTCACAATAGAGGAAATGATTCAAAGT
TCAAAGGATTTG
Found at i:15590913 original size:34 final size:34
Alignment explanation
Indices: 15590875--15590946 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
15590865 GATTCATAAT
* *
15590875 AGAGT-AAATGATTTACAAATTTC-AAGGATTTGCA
1 AGAGTCAAA-GATTTAAAAATTTCAAAGG-TTCGCA
15590909 AGAGTCAAAGATTTAAAAATTTCAAAGGTTCGCA
1 AGAGTCAAAGATTTAAAAATTTCAAAGGTTCGCA
15590943 AGAG
1 AGAG
15590947 GGGTTAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 27 0.79
35 7 0.21
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (34 bp):
AGAGTCAAAGATTTAAAAATTTCAAAGGTTCGCA
Found at i:15591519 original size:34 final size:36
Alignment explanation
Indices: 15591454--15591543 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 36
15591444 CACAATAGAG
* *
15591454 TAAATGATTCATAAATTTCAAGGATTTGCAAG-A-GT
1 TAAA-GATTCAAAAATTTCAAGGATTCGCAAGAAGGT
*
15591489 TAAAGATTTAAAAATTTCAAAGG-TTCGCAAGAAGGGT
1 TAAAGATTCAAAAATTTC-AAGGATTCGCAAGAA-GGT
*
15591526 TAAAGATTCACAAATTTC
1 TAAAGATTCAAAAATTTC
15591544 CAAGATTTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
34 19 0.41
35 9 0.20
37 18 0.39
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (36 bp):
TAAAGATTCAAAAATTTCAAGGATTCGCAAGAAGGT
Found at i:15591915 original size:575 final size:575
Alignment explanation
Indices: 15590824--15593104 Score: 3836
Period size: 575 Copynumber: 4.0 Consensus size: 575
15590814 GTTCAAAGGA
* * *
15590824 CTTTGACAATAGAGGGAACAATTCATAGTTAGGGGACTCTGGATTCATAATAGAGTAAATGATTT
1 CTTTGACAATAGAGGGAACAATTCATAGTTAAGGGACTCTGGATTCACAATAGAGTAAATGATTC
*
15590889 ACAAATTTCAAGGATTTGCAAGAGTCAAAGATTTAAAAATTTCAAAGGTTCGCAAGAGGGGTTAA
66 ACAAATTTCAAGGATTTGCAAGAGTCAAAGATTTAAAAATTTCAAAGGTTCGCAAGAAGGGTTAA
*
15590954 AGATTCACAAATTTCTAAGATTTACAATCATAAATGATCAATCATCAAGATCTGGAATGCCAATG
131 AGATTCACAAATTTCCAAGATTTACAATCATAAATGATCAATCATCAAGATCTGGAATGCCAATG
* *
15591019 AGCTCTACTATGAAATGTCCCTAGGCAAATGCAAATGTTCTTTATAAGATGTACATTCAATAATG
196 AGCTCTACTATGAAATGTCCCTAGGCAAATGCAGATGTTCTTTATAAGATGTACATTCAATAACG
*
15591084 CAAATGCCTTTACATCGATACAAATACTTTCCCAATGTTGCAAATGTTTTATGCAATTATAGAAT
261 CAAATGCCTTTACATTGATACAAATACTTTCCCAATGTTGCAAATGTTTTATGCAATTATAGAAT
*
15591149 TTCATTTCAAAGATGCCAATGCTTATGAAAATGCAAGAACTTCATGATGTATATAGCCCTAACAT
326 TTCATTTCAAAGATGCCAATGCTTATGCAAATGCAAGAACTTCATGATGTATATAGCCCTAACAT
* ** * *
15591214 GAATGTAAACAATGAAAACATTACTTTTTTCAATAGAAATTTTTTTTCAATTCTGCTTATTTCCC
391 GAATGTAAACAATGAAAATATTACTTTTTTCAATAGAAAAATTTTCTCAATTCTACTTATTTCCC
* *
15591279 CTTACCATTCAATTAAATCTTCAACTTTTTTCTAAAAAGATCTCAACCTACCATTCTCTTACTTC
456 CTTACCATTCAATTAAATCTTCAACTTTTTTCTAGAAAGATCTCAACTTACCATTCTCTTACTTC
*
15591344 TTCACCCATTTCGTCTTGCTTTTTTACCAATTTCTACTAGGCTCTTTTGATTTTC
521 TTCACCCATTTCATCTTGCTTTTTTACCAATTTCTACTAGGCTCTTTTGATTTTC
* *
15591399 CTTTGACAATAGAGGGAACAATTCATAGTTAGGGGACTTTGGATTCACAATAGAGTAAATGATTC
1 CTTTGACAATAGAGGGAACAATTCATAGTTAAGGGACTCTGGATTCACAATAGAGTAAATGATTC
* *
15591464 ATAAATTTCAAGGATTTGCAAGAGTTAAAGATTTAAAAATTTCAAAGGTTCGCAAGAAGGGTTAA
66 ACAAATTTCAAGGATTTGCAAGAGTCAAAGATTTAAAAATTTCAAAGGTTCGCAAGAAGGGTTAA
15591529 AGATTCACAAATTTCCAAGATTTACAATCATAAATGATCAATCATCAAGATCTGGAATGCCAATG
131 AGATTCACAAATTTCCAAGATTTACAATCATAAATGATCAATCATCAAGATCTGGAATGCCAATG
* *
15591594 AGCTCTACTATGAAATGTCTCTAGGCAAATGCAGATGTTCTTTATAAGATGTACATTCAATAATG
196 AGCTCTACTATGAAATGTCCCTAGGCAAATGCAGATGTTCTTTATAAGATGTACATTCAATAACG
* *
15591659 TAAATGCCTTTACATTGATACAAATACTTTCCTAATGTTGCAAATGTTTTATGCAATTATAGAAT
261 CAAATGCCTTTACATTGATACAAATACTTTCCCAATGTTGCAAATGTTTTATGCAATTATAGAAT
15591724 TTCATTTCAAAGATGCCAATGCTTATGCAAATGCAAGAACTTCATGATGTATATAGCCCTAACAT
326 TTCATTTCAAAGATGCCAATGCTTATGCAAATGCAAGAACTTCATGATGTATATAGCCCTAACAT
**
15591789 GAATGTAAACAATGAAAATATTACTTTTTTCAATAGAAAAATTTTCTCAATTCTGTTTATTTCCC
391 GAATGTAAACAATGAAAATATTACTTTTTTCAATAGAAAAATTTTCTCAATTCTACTTATTTCCC
15591854 CTTACCATTCAATTAAATCTTCAACTTTTTTCTAGAAAGATCTCAACTTACCATTCTCTTACTTC
456 CTTACCATTCAATTAAATCTTCAACTTTTTTCTAGAAAGATCTCAACTTACCATTCTCTTACTTC
15591919 TTCACCCATTTCATCTTGCTTTTTTACCAATTTCTACTAGGCTCTTTTGATTTTC
521 TTCACCCATTTCATCTTGCTTTTTTACCAATTTCTACTAGGCTCTTTTGATTTTC
* *
15591974 CTTTGACAATAAAGGGAAGAATTCATAGTTAAGGGACTCTGGATTCACAATAGAGTAAATGATTC
1 CTTTGACAATAGAGGGAACAATTCATAGTTAAGGGACTCTGGATTCACAATAGAGTAAATGATTC
* *
15592039 ACAAATTTCAAGGATTCGTAAGAGTCAAAG--------ATTT---A-------AA-AA-----AA
66 ACAAATTTCAAGGATTTGCAAGAGTCAAAGATTTAAAAATTTCAAAGGTTCGCAAGAAGGGTTAA
* ** *
15592080 AGATTCACAAATTTCTAAGATTTACAATCATAAATGATCAATCATCAAGATCTGGAATGTTAATA
131 AGATTCACAAATTTCCAAGATTTACAATCATAAATGATCAATCATCAAGATCTGGAATGCCAATG
* *
15592145 AGCTCTACTATGAAATGTCCCTAGGCAAATGTAGATGTTCTTTATAAGATATACATTCAATAACG
196 AGCTCTACTATGAAATGTCCCTAGGCAAATGCAGATGTTCTTTATAAGATGTACATTCAATAACG
*
15592210 CAAATGCCTTTACATTGATACAAATACTTTCCCAATATTGCAAATGTTTTATGCAATTATAGAAT
261 CAAATGCCTTTACATTGATACAAATACTTTCCCAATGTTGCAAATGTTTTATGCAATTATAGAAT
*
15592275 TTCATTTCAAAGATGCCAATGCTTATGCAAATGTAAGAACTTCATGATGTATATAGCCCTAACAT
326 TTCATTTCAAAGATGCCAATGCTTATGCAAATGCAAGAACTTCATGATGTATATAGCCCTAACAT
* * *
15592340 GAATGTAAACAATGAAAATATTATTTTTTTCAATAGAAAATTTTTTTCAATTCTACTTATTTCCC
391 GAATGTAAACAATGAAAATATTACTTTTTTCAATAGAAAAATTTTCTCAATTCTACTTATTTCCC
* * * *
15592405 CTTACCATTCAATTAAATCTTTAACTTTTTTCTACAAAGATCTCAACTTATCATTCTCTTATTTC
456 CTTACCATTCAATTAAATCTTCAACTTTTTTCTAGAAAGATCTCAACTTACCATTCTCTTACTTC
15592470 TTCACCCATTTCATCTTGCTTTTTTACCAATTTCTACTAGGCTCTTTTGATTTTC
521 TTCACCCATTTCATCTTGCTTTTTTACCAATTTCTACTAGGCTCTTTTGATTTTC
* *
15592525 CTTTGACAATAGAGGGAAGAATTCATAGTTAAGAGACTCTGGATTCACAATAGAGTAAATGATTC
1 CTTTGACAATAGAGGGAACAATTCATAGTTAAGGGACTCTGGATTCACAATAGAGTAAATGATTC
* *
15592590 ACAAATTTCAAGGATTTGCAAGAGTCAAAGATTTAAAAATTTTAAAGGTTCGCAAGAGGGGTTAA
66 ACAAATTTCAAGGATTTGCAAGAGTCAAAGATTTAAAAATTTCAAAGGTTCGCAAGAAGGGTTAA
* *
15592655 AGATTCACAAATTTCCAAGATTTATAATCATAAATGATCAATCATCAAGATCTGGAATGCAAATG
131 AGATTCACAAATTTCCAAGATTTACAATCATAAATGATCAATCATCAAGATCTGGAATGCCAATG
* *
15592720 AGCTCTACTATGAAATGTCCCTAGGCAAATGCAGATGCTCTTTATAAGATGTACATTTAATAACG
196 AGCTCTACTATGAAATGTCCCTAGGCAAATGCAGATGTTCTTTATAAGATGTACATTCAATAACG
* *
15592785 TAAATGCCTTTACATTGATACAAATACTTTCCCAATGTTGCAAATGTTTTATGCAATTATAAAAT
261 CAAATGCCTTTACATTGATACAAATACTTTCCCAATGTTGCAAATGTTTTATGCAATTATAGAAT
15592850 TTCATTTCAAAGATGCCAATGCTTATGCAAATGCAAGAACTTCATGATGTATATAGCCCTAACAT
326 TTCATTTCAAAGATGCCAATGCTTATGCAAATGCAAGAACTTCATGATGTATATAGCCCTAACAT
* *
15592915 GAATTTAAACAATAAAAATATTACTTTTTTCAATAGAAAAATTTTTCTCAATTCTACTTATTTCC
391 GAATGTAAACAATGAAAATATTACTTTTTTCAATAGAAAAA-TTTTCTCAATTCTACTTATTTCC
* *
15592980 CCTTACCATTCAATTAAATCTTTAACTTTTTTCTAGAAAGATCTCAACTTACCATTCTTTTACTT
455 CCTTACCATTCAATTAAATCTTCAACTTTTTTCTAGAAAGATCTCAACTTACCATTCTCTTACTT
*
15593045 CTTCACCCATTTCATCTTGCTTTTTTTCCAATTTCTACTAGGCTCTTTTGATTTTC
520 CTTCACCCATTTCATCTTGCTTTTTTACCAATTTCTACTAGGCTCTTTTGATTTTC
15593101 CTTT
1 CTTT
15593105 CATTTTTGAT
Statistics
Matches: 1603, Mismatches: 78, Indels: 49
0.93 0.05 0.03
Matches are distributed among these distances:
551 517 0.32
556 2 0.00
557 2 0.00
559 4 0.00
562 1 0.00
564 1 0.00
567 4 0.00
569 2 0.00
570 1 0.00
575 927 0.58
576 142 0.09
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (575 bp):
CTTTGACAATAGAGGGAACAATTCATAGTTAAGGGACTCTGGATTCACAATAGAGTAAATGATTC
ACAAATTTCAAGGATTTGCAAGAGTCAAAGATTTAAAAATTTCAAAGGTTCGCAAGAAGGGTTAA
AGATTCACAAATTTCCAAGATTTACAATCATAAATGATCAATCATCAAGATCTGGAATGCCAATG
AGCTCTACTATGAAATGTCCCTAGGCAAATGCAGATGTTCTTTATAAGATGTACATTCAATAACG
CAAATGCCTTTACATTGATACAAATACTTTCCCAATGTTGCAAATGTTTTATGCAATTATAGAAT
TTCATTTCAAAGATGCCAATGCTTATGCAAATGCAAGAACTTCATGATGTATATAGCCCTAACAT
GAATGTAAACAATGAAAATATTACTTTTTTCAATAGAAAAATTTTCTCAATTCTACTTATTTCCC
CTTACCATTCAATTAAATCTTCAACTTTTTTCTAGAAAGATCTCAACTTACCATTCTCTTACTTC
TTCACCCATTTCATCTTGCTTTTTTACCAATTTCTACTAGGCTCTTTTGATTTTC
Found at i:15594624 original size:30 final size:30
Alignment explanation
Indices: 15594590--15594647 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
15594580 AACAAAACCA
* * *
15594590 AAAATCATAAAATCAGTATATTAAACTAAC
1 AAAATCATAAAAACAATATACTAAACTAAC
15594620 AAAATCATAAAAACAATATACTAAACTA
1 AAAATCATAAAAACAATATACTAAACTA
15594648 GCACTTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (30 bp):
AAAATCATAAAAACAATATACTAAACTAAC
Found at i:15596855 original size:42 final size:42
Alignment explanation
Indices: 15596805--15596928 Score: 167
Period size: 42 Copynumber: 3.0 Consensus size: 42
15596795 CATCAGATTC
* * *
15596805 AATGATTCACAATTGTAAGACTCTAGATTCACAACTAAAGCT
1 AATGATTCACAGTTGTAGGACTCTAGATTCACAACTAAAGCA
* * * *
15596847 AATGATTCACAGTTGCAGGATTCTGGATTCACAACTAGAGCA
1 AATGATTCACAGTTGTAGGACTCTAGATTCACAACTAAAGCA
* *
15596889 AATGATTCATAGTTGTAGGACTCTAGATTCATAACTAAAG
1 AATGATTCACAGTTGTAGGACTCTAGATTCACAACTAAAG
15596929 TTTTTGGATT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (42 bp):
AATGATTCACAGTTGTAGGACTCTAGATTCACAACTAAAGCA
Found at i:15596977 original size:104 final size:104
Alignment explanation
Indices: 15596868--15597087 Score: 287
Period size: 104 Copynumber: 2.1 Consensus size: 104
15596858 GTTGCAGGAT
* * * *
15596868 TCTGGATTCACAACTAGAGCAAATGATTCATAGTTGTAGGACTCTAGATTCATAACTAAAGTTTT
1 TCTGGATTCACAACTAAAGCAAACGATTCATAGTTGTAGAACTCTAGATTCATAACTAAAGTTTC
**
15596933 TGGATTCACATCAGATTCAATGATTCATAATTGTTGGAC
66 TGGATTCACATCAGATTCAATGATTCATAATTGTAAGAC
*** * * * * *
15596972 TCTGGATTTGTAACTAAAGTAAACGATTCATAGTTGTAGAATTCTGGATTCATGACTAGAGTTTC
1 TCTGGATTCACAACTAAAGCAAACGATTCATAGTTGTAGAACTCTAGATTCATAACTAAAGTTTC
* *
15597037 TGGATTTACATCAGATTCAATGATTCATAGTTGTAAGAC
66 TGGATTCACATCAGATTCAATGATTCATAATTGTAAGAC
*
15597076 TTTGGATTCACA
1 TCTGGATTCACA
15597088 TCATAGTTTT
Statistics
Matches: 96, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (104 bp):
TCTGGATTCACAACTAAAGCAAACGATTCATAGTTGTAGAACTCTAGATTCATAACTAAAGTTTC
TGGATTCACATCAGATTCAATGATTCATAATTGTAAGAC
Found at i:15596987 original size:146 final size:147
Alignment explanation
Indices: 15596763--15597032 Score: 373
Period size: 146 Copynumber: 1.8 Consensus size: 147
15596753 ATTGCAGAAT
* *
15596763 TCTAGATTCACCACTAAAATTTTTTGGATTCACATCAGATTCAATGATTCACAATTGTAAGACTC
1 TCTAGATTCACAACTAAAAGTTTTTGGATTCACATCAGATTCAATGATTCACAATTGTAAGACTC
* *
15596828 TAGATTCACAACTAAAGCT-AATGATTCACAGTTGCAGGATTCTGGATTCACAACTAGAGCAAAT
66 TAGATTCACAACTAAAG-TAAACGATTCACAGTTGCAGAATTCTGGATTCACAACTAGAGCAAAT
15596892 GATTCATAGTTGTAGGAC
130 GATTCATAGTTGTAGGAC
* * **
15596910 TCTAGATTCATAACT-AAAGTTTTTGGATTCACATCAGATTCAATGATTCATAATTGTTGGACTC
1 TCTAGATTCACAACTAAAAGTTTTTGGATTCACATCAGATTCAATGATTCACAATTGTAAGACTC
* *** * * **
15596974 TGGATTTGTAACTAAAGTAAACGATTCATAGTTGTAGAATTCTGGATTCATGACTAGAG
66 TAGATTCACAACTAAAGTAAACGATTCACAGTTGCAGAATTCTGGATTCACAACTAGAG
15597033 TTTCTGGATT
Statistics
Matches: 106, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
145 1 0.01
146 92 0.87
147 13 0.12
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (147 bp):
TCTAGATTCACAACTAAAAGTTTTTGGATTCACATCAGATTCAATGATTCACAATTGTAAGACTC
TAGATTCACAACTAAAGTAAACGATTCACAGTTGCAGAATTCTGGATTCACAACTAGAGCAAATG
ATTCATAGTTGTAGGAC
Found at i:15597319 original size:68 final size:67
Alignment explanation
Indices: 15597247--15597374 Score: 152
Period size: 68 Copynumber: 1.9 Consensus size: 67
15597237 AAAGATTCAA
* * * *
15597247 AAAAGTCAAATATTTGTAACTTGCAAAGA-TCTGCAAGAATCAAAGAT-TCACAAATTCTAAAGA
1 AAAAGTCAAAGATTTATAAATTGCAAAGATTC-ACAAGAATCAAAGATGT-ACAAATT-TAAAGA
15597310 ATCGT
63 ATCGT
* * *
15597315 AAAAGTCAAGGGTTTATAAATTTCAAAGATTCACAAGAATCAAAGATGTACAAATTTAAA
1 AAAAGTCAAAGATTTATAAATTGCAAAGATTCACAAGAATCAAAGATGTACAAATTTAAA
15597375 AAATTTGCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
67 4 0.08
68 44 0.86
69 3 0.06
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (67 bp):
AAAAGTCAAAGATTTATAAATTGCAAAGATTCACAAGAATCAAAGATGTACAAATTTAAAGAATC
GT
Found at i:15597390 original size:68 final size:68
Alignment explanation
Indices: 15597280--15597413 Score: 157
Period size: 68 Copynumber: 2.0 Consensus size: 68
15597270 CAAAGATCTG
* * * * *
15597280 CAAGAATCAAAGATTCACAAATTCTAAAGAATCGTAAAAGTCA-AGGGTTTATAAATTTCAAAGA
1 CAAGAATCAAAGATTCACAAATTCTAAAAAATCGCAAAAGTCACA-GATTCATAAATATCAAAGA
15597344 TTCA
65 TTCA
* *
15597348 CAAGAATCAAAGATGT-ACAAATT-TAAAAAATTTGCAAGAGTCACAGATTCATAAATATCAAAG
1 CAAGAATCAAAGAT-TCACAAATTCTAAAAAA-TCGCAAAAGTCACAGATTCATAAATATCAAAG
15597411 ATT
64 ATT
15597414 TGCAATAAGG
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
67 6 0.11
68 48 0.86
69 2 0.04
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (68 bp):
CAAGAATCAAAGATTCACAAATTCTAAAAAATCGCAAAAGTCACAGATTCATAAATATCAAAGAT
TCA
Found at i:15597913 original size:32 final size:32
Alignment explanation
Indices: 15597877--15597940 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
15597867 TTCTAACTAA
* *
15597877 AGTGCAAATGCTTATTTTATTGATGCAATTGC
1 AGTGCAAATGCTTATTTCAATGATGCAATTGC
*
15597909 AGTGCAAATTCTTATTTCAATGATGCAATTGC
1 AGTGCAAATGCTTATTTCAATGATGCAATTGC
15597941 TTTTTTCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (32 bp):
AGTGCAAATGCTTATTTCAATGATGCAATTGC
Found at i:15597935 original size:21 final size:21
Alignment explanation
Indices: 15597915--15597954 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15597905 TTGCAGTGCA
15597915 AATT-CTTATTTCAATGATGC
1 AATTGCTTATTTCAATGATGC
* *
15597935 AATTGCTTTTTTCTATGATG
1 AATTGCTTATTTCAATGATG
15597955 ATGATGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (21 bp):
AATTGCTTATTTCAATGATGC
Found at i:15599444 original size:27 final size:27
Alignment explanation
Indices: 15599414--15599472 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
15599404 TTTCCTTTTG
* *
15599414 TTTTTTTTCTTC-TCTTTTCTTCTTCA
1 TTTTTTTTTTTCACCTTTTCTTCTTCA
* * *
15599440 TTTTTCTTTTTCACCTTTTTTTTTTCA
1 TTTTTTTTTTTCACCTTTTCTTCTTCA
15599467 TTTTTT
1 TTTTTT
15599473 CCCATTTCCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTTTTTTTTCACCTTTTCTTCTTCA
Found at i:15599472 original size:13 final size:13
Alignment explanation
Indices: 15599391--15599472 Score: 51
Period size: 13 Copynumber: 6.2 Consensus size: 13
15599381 CACTCAACCA
*
15599391 TTTTATTCATTTT
1 TTTTTTTCATTTT
*
15599404 TTTCCTTTT-GTTTT
1 TTT--TTTTCATTTT
*
15599418 TTTTCTTC-TCTTT
1 TTTTTTTCAT-TTT
* *
15599431 TCTTCTTCATTTT
1 TTTTTTTCATTTT
* *
15599444 TCTTTTTCACCTTT
1 TTTTTTTCA-TTTT
15599458 TTTTTTTCATTTT
1 TTTTTTTCATTTT
15599471 TT
1 TT
15599473 CCCATTTCCA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.07
13 29 0.53
14 19 0.35
15 3 0.05
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (13 bp):
TTTTTTTCATTTT
Found at i:15600854 original size:7 final size:7
Alignment explanation
Indices: 15600817--15600933 Score: 63
Period size: 7 Copynumber: 17.7 Consensus size: 7
15600807 TTTGGGATTT
15600817 AGTTTA-
1 AGTTTAG
15600823 AGTTTAG
1 AGTTTAG
* *
15600830 GGTTTAA
1 AGTTTAG
15600837 AGTTTAG
1 AGTTTAG
15600844 -GTTTAG
1 AGTTTAG
15600850 AGTTT-G
1 AGTTTAG
* *
15600856 GGGTTACG
1 AGTTTA-G
15600864 A-TTTAG
1 AGTTTAG
15600870 -GTTTAG
1 AGTTTAG
*
15600876 GGTTT-G
1 AGTTTAG
15600882 AGGTTT-G
1 A-GTTTAG
*
15600889 GGTTTAG
1 AGTTTAG
15600896 -GTTTAG
1 AGTTTAG
*
15600902 TGTTTAG
1 AGTTTAG
15600909 AGTTT-G
1 AGTTTAG
*
15600915 GGTTTAG
1 AGTTTAG
*
15600922 GGTTTAG
1 AGTTTAG
*
15600929 GGTTT
1 AGTTT
15600934 CATGGGTGGT
Statistics
Matches: 89, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
6 38 0.43
7 50 0.56
8 1 0.01
ACGTcount: A:0.18, C:0.01, G:0.35, T:0.46
Consensus pattern (7 bp):
AGTTTAG
Found at i:15600894 original size:20 final size:20
Alignment explanation
Indices: 15600769--15600933 Score: 107
Period size: 20 Copynumber: 8.5 Consensus size: 20
15600759 TGATTCGGGT
*
15600769 TTTAGGGTTT-GGG-GTAGG
1 TTTAGGGTTTAGGGTTTAGG
* **
15600787 TTTAGGGTCTAGGGAAT-GG
1 TTTAGGGTTTAGGGTTTAGG
* *
15600806 TTTTGGGATTTA--GTTTAAG
1 TTTAGGG-TTTAGGGTTTAGG
**
15600825 TTTAGGGTTTAAAGTTTAGG
1 TTTAGGGTTTAGGGTTTAGG
* * *
15600845 TTTAGAGTTT-GGGGTTACGA
1 TTTAGGGTTTAGGGTTTA-GG
15600865 TTTA-GGTTTAGGGTTTGAGG
1 TTTAGGGTTTAGGGTTT-AGG
15600885 TTT-GGGTTTA-GGTTTAGTG
1 TTTAGGGTTTAGGGTTTAG-G
*
15600904 TTTAGAGTTT-GGGTTTAGGG
1 TTTAGGGTTTAGGGTTTA-GG
15600924 TTTAGGGTTT
1 TTTAGGGTTT
15600934 CATGGGTGGT
Statistics
Matches: 114, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
18 17 0.15
19 35 0.31
20 60 0.53
21 2 0.02
ACGTcount: A:0.17, C:0.01, G:0.37, T:0.45
Consensus pattern (20 bp):
TTTAGGGTTTAGGGTTTAGG
Found at i:15600913 original size:26 final size:25
Alignment explanation
Indices: 15600838--15600933 Score: 102
Period size: 26 Copynumber: 3.7 Consensus size: 25
15600828 AGGGTTTAAA
* * **
15600838 GTTTAGGTTTAGAGTTTGGGGTTACG
1 GTTTAGGTTTAGGGTTT-GAGTTTGG
*
15600864 ATTTAGGTTTAGGGTTTGAGGTTTGG
1 GTTTAGGTTTAGGGTTTGA-GTTTGG
*
15600890 GTTTAGGTTTAGTGTTTAGAGTTTGG
1 GTTTAGGTTTAGGGTTT-GAGTTTGG
15600916 GTTTAGGGTTTAGGGTTT
1 GTTTA-GGTTTAGGGTTT
15600934 CATGGGTGGT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.02
26 45 0.76
27 13 0.22
ACGTcount: A:0.15, C:0.01, G:0.38, T:0.47
Consensus pattern (25 bp):
GTTTAGGTTTAGGGTTTGAGTTTGG
Found at i:15602759 original size:22 final size:21
Alignment explanation
Indices: 15602732--15602774 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
15602722 ATATTTTATT
15602732 ATAATTA-TAAAATGAATAAAAA
1 ATAATTATTAAAA--AATAAAAA
15602754 ATAATTATTAAAAAATAAAAA
1 ATAATTATTAAAAAATAAAAA
15602775 TTAAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 7 0.35
23 5 0.25
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
ATAATTATTAAAAAATAAAAA
Found at i:15602781 original size:22 final size:22
Alignment explanation
Indices: 15602729--15602782 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
15602719 AAAATATTTT
15602729 ATTATAATTATAAAATGAATAAAA
1 ATTA-AATTATAAAA-GAATAAAA
*
15602753 AAT-AATTATTAAAA-AATAAAA
1 ATTAAATTA-TAAAAGAATAAAA
15602774 ATTAAATTA
1 ATTAAATTA
15602783 ATATCTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 9 0.35
22 10 0.38
23 5 0.19
24 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATTAAATTATAAAAGAATAAAA
Found at i:15602813 original size:15 final size:15
Alignment explanation
Indices: 15602795--15602832 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
15602785 ATCTAATAAA
15602795 TTATTAT-AAATATAT
1 TTATTATAAAATAT-T
15602810 TTATTTATAAAATATT
1 TTA-TTATAAAATATT
15602826 TTATTAT
1 TTATTAT
15602833 TTCATTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTATAAAATATT
Found at i:15603597 original size:19 final size:19
Alignment explanation
Indices: 15603573--15603621 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 19
15603563 AGTTAACCGA
15603573 AATAAATATTATATTAATT
1 AATAAATATTATATTAATT
15603592 AAT-AA-ATT-TA-TAATT
1 AATAAATATTATATTAATT
15603607 --TAAATATTATATTAA
1 AATAAATATTATATTAA
15603622 AGATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
13 1 0.04
14 2 0.08
15 8 0.31
16 4 0.15
17 6 0.23
18 2 0.08
19 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAAATATTATATTAATT
Found at i:15605429 original size:52 final size:52
Alignment explanation
Indices: 15605372--15605480 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 52
15605362 TTTTTTCTTG
* * * *
15605372 TAAGTCAAATTTGCCTATTAAGAA-TTTTTTTCTTCTTTGAATTCTTCTATTA
1 TAAGTCAAACTTACCTATTAAAAATTTTTTTTCTT-TTAGAATTCTTCTATTA
*
15605424 TAAGTCAAACTTACCTATTAAAAATTTTTTTTCTTTTAGAATTCTTCTTTTA
1 TAAGTCAAACTTACCTATTAAAAATTTTTTTTCTTTTAGAATTCTTCTATTA
*
15605476 CAAGT
1 TAAGT
15605481 TTTTTATCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
52 40 0.80
53 10 0.20
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.50
Consensus pattern (52 bp):
TAAGTCAAACTTACCTATTAAAAATTTTTTTTCTTTTAGAATTCTTCTATTA
Found at i:15607213 original size:10 final size:10
Alignment explanation
Indices: 15607198--15607245 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
15607188 TGGGATGTCA
15607198 ATATCTATAT
1 ATATCTATAT
15607208 ATATCTATAT
1 ATATCTATAT
*
15607218 CTA--TATAT
1 ATATCTATAT
*
15607226 ATATATATAT
1 ATATCTATAT
15607236 ATATCTATAT
1 ATATCTATAT
15607246 TTATATACAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 7 0.21
10 26 0.79
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATCTATAT
Found at i:15607216 original size:6 final size:6
Alignment explanation
Indices: 15607198--15607251 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
15607188 TGGGATGTCA
* *
15607198 ATATCT ATA--T ATATCT ATATCT ATA--T ATATAT ATATAT ATATCT
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATATCT ATATCT ATATCT
*
15607242 ATATTT ATAT
1 ATATCT ATAT
15607252 ACACACACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 8 0.19
6 34 0.81
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (6 bp):
ATATCT
Found at i:15607219 original size:16 final size:16
Alignment explanation
Indices: 15607198--15607252 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
15607188 TGGGATGTCA
15607198 ATATCTATATATATCT
1 ATATCTATATATATCT
15607214 ATATCTATATATA--T
1 ATATCTATATATATCT
15607228 ATA--TATATATATCT
1 ATATCTATATATATCT
*
15607242 ATATTTATATA
1 ATATCTATATA
15607253 CACACACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.23
14 8 0.23
16 19 0.54
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATCTATATATATCT
Found at i:15616002 original size:11 final size:11
Alignment explanation
Indices: 15615946--15616006 Score: 56
Period size: 11 Copynumber: 5.8 Consensus size: 11
15615936 CCTATCAATG
*
15615946 ATATTTTAGTA
1 ATATTTTAATA
*
15615957 ATATTTTGATA
1 ATATTTTAATA
*
15615968 ATATTTTAA-C
1 ATATTTTAATA
*
15615978 ATA--ATAATA
1 ATATTTTAATA
*
15615987 TTATTTTAATA
1 ATATTTTAATA
15615998 ATATTTTAA
1 ATATTTTAA
15616007 ATTAATTTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
8 3 0.08
9 2 0.05
10 3 0.08
11 30 0.79
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (11 bp):
ATATTTTAATA
Found at i:15616034 original size:33 final size:34
Alignment explanation
Indices: 15615987--15616068 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 34
15615977 CATAATAATA
* * * *
15615987 TTATTTTAATAATATTTTAA-ATTAATTTTATAT
1 TTATTTAAAAAATATTTAAATATTAATTTGATAT
*
15616020 TTATTTAAAGAATA-TTAAATATTAATTTGATAT
1 TTATTTAAAAAATATTTAAATATTAATTTGATAT
* *
15616053 TAAATTAAAAAATATT
1 TTATTTAAAAAATATT
15616069 GGATATTGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 4 0.10
33 35 0.88
34 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (34 bp):
TTATTTAAAAAATATTTAAATATTAATTTGATAT
Found at i:15620515 original size:33 final size:33
Alignment explanation
Indices: 15620486--15620561 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
15620476 GTAATATTCT
*
15620486 AGATTGATTTGATATTTATTTAGAGAATATTAG
1 AGATTGATTTGATATTGATTTAGAGAATATTAG
* *
15620519 ATATTGATTTGATATTGATTTAGAGAATATTAA
1 AGATTGATTTGATATTGATTTAGAGAATATTAG
*
15620552 ATATTGATTT
1 AGATTGATTT
15620562 AGTTGATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (33 bp):
AGATTGATTTGATATTGATTTAGAGAATATTAG
Found at i:15620532 original size:11 final size:11
Alignment explanation
Indices: 15620488--15620539 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
15620478 AATATTCTAG
15620488 ATTGATTTGAT
1 ATTGATTTGAT
* *
15620499 ATTTATTTAGAG
1 ATTGATTT-GAT
* *
15620511 AAT-ATTAGAT
1 ATTGATTTGAT
15620521 ATTGATTTGAT
1 ATTGATTTGAT
15620532 ATTGATTT
1 ATTGATTT
15620540 AGAGAATATT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
10 4 0.12
11 24 0.75
12 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (11 bp):
ATTGATTTGAT
Found at i:15622138 original size:129 final size:128
Alignment explanation
Indices: 15621945--15622272 Score: 426
Period size: 129 Copynumber: 2.5 Consensus size: 128
15621935 TCATGAGAAG
* * * * * *
15621945 TTGACATATGATAATTTGTTTCAAAATTACTATAAAACCTCTATTAAATTATATATTAAATTTTA
1 TTGACATGTGATATTTTATTTAAAAATTACTATAATA-CTCTATTAAATTACATATTAAATTTTA
* *
15622010 ACATAATATAAAATTAACCACATATTAAATTA-TGAAAATATCATTACAATTGCTTTATAAAAAT
65 ACATAATATAAAATTAACCACATATTAAATTACT-AAAATACCATTACAATTGCTTCATAAAAAT
* * *
15622074 TTGGCATGTGATATTTTATTTAAAAATTACTATACTACTCATATTAAATTACATATGAAATTTTA
1 TTGACATGTGATATTTTATTTAAAAATTACTATAATACTC-TATTAAATTACATATTAAATTTTA
*** * *
15622139 ACATAATATAAAATTAATTTCATATTAAATTACTAAAATACCTTTACCATTGCTTCATAAAAAT
65 ACATAATATAAAATTAACCACATATTAAATTACTAAAATACCATTACAATTGCTTCATAAAAAT
* * * *
15622203 TTGACATGTGAAATTTTATTTAAAATTTACTATAATACCCTTATTAAATTACTTATTAAATTTTA
1 TTGACATGTGATATTTTATTTAAAAATTACTATAATACTC-TATTAAATTACATATTAAATTTTA
15622268 A-ATAA
65 ACATAA
15622273 CATATATTAA
Statistics
Matches: 173, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
128 7 0.04
129 165 0.95
130 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.41
Consensus pattern (128 bp):
TTGACATGTGATATTTTATTTAAAAATTACTATAATACTCTATTAAATTACATATTAAATTTTAA
CATAATATAAAATTAACCACATATTAAATTACTAAAATACCATTACAATTGCTTCATAAAAAT
Found at i:15627052 original size:12 final size:13
Alignment explanation
Indices: 15627032--15627064 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
15627022 CCATGACTTA
15627032 GAAAAAGCGGG-G
1 GAAAAAGCGGGCG
*
15627044 GAAATAGCGGGCG
1 GAAAAAGCGGGCG
15627057 GAAAAAGC
1 GAAAAAGC
15627065 AGGGACTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.42, C:0.12, G:0.42, T:0.03
Consensus pattern (13 bp):
GAAAAAGCGGGCG
Found at i:15631873 original size:30 final size:30
Alignment explanation
Indices: 15631837--15631904 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
15631827 AGGAATTAAC
15631837 AGCTGAATAGGAAGCAGATAGGGA-GTCAGT
1 AGCTGAATAGGAAGCAGAT-GGGAGGTCAGT
* *
15631867 AGCTGAATAGGAAGCTGATGGGAGGTTAGT
1 AGCTGAATAGGAAGCAGATGGGAGGTCAGT
*
15631897 AACTGAAT
1 AGCTGAAT
15631905 GAAAAGCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (30 bp):
AGCTGAATAGGAAGCAGATGGGAGGTCAGT
Found at i:15633169 original size:31 final size:31
Alignment explanation
Indices: 15633134--15633196 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
15633124 CTTATCCCTA
15633134 ACAAATTCTCAAATACTAAAATCCCATAAAC
1 ACAAATTCTCAAATACTAAAATCCCATAAAC
* *
15633165 ACAAATTCTTAAATACTGAAATCCCATAAAC
1 ACAAATTCTCAAATACTAAAATCCCATAAAC
15633196 A
1 A
15633197 TGTTCAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.24
Consensus pattern (31 bp):
ACAAATTCTCAAATACTAAAATCCCATAAAC
Found at i:15635126 original size:28 final size:27
Alignment explanation
Indices: 15635067--15635136 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
15635057 AATTTTTTTG
15635067 AAAATATTTTAAAATTGAAAAAAAAAT
1 AAAATATTTTAAAATTGAAAAAAAAAT
* *
15635094 AAAATCTTTTGAAAATT-AAAAAAAATT
1 AAAATATTTT-AAAATTGAAAAAAAAAT
*
15635121 AGAAATTTTTTTAAAA
1 A-AAA-TATTTTAAAA
15635137 ATTTTTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 19 0.51
28 13 0.35
29 5 0.14
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (27 bp):
AAAATATTTTAAAATTGAAAAAAAAAT
Found at i:15635267 original size:20 final size:20
Alignment explanation
Indices: 15635234--15635288 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
15635224 ATAGAAATCC
* *
15635234 AAAAGAATTGAAAATTTTTAT
1 AAAAAAATT-AAAATTTATAT
*
15635255 -AAAAAATTCAAAA-ATATAT
1 AAAAAAATT-AAAATTTATAT
15635274 AAAAAAATTAAAATT
1 AAAAAAATTAAAATT
15635289 GCAAGATTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAAAAATTAAAATTTATAT
Found at i:15635324 original size:11 final size:10
Alignment explanation
Indices: 15635304--15635353 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
15635294 ATTCAAAAAA
15635304 TAAAAATTTT
1 TAAAAATTTT
*
15635314 CAAAAATTTT
1 TAAAAATTTT
*
15635324 TAAAACTTTT
1 TAAAAATTTT
*
15635334 TTAAAATTTT
1 TAAAAATTTT
*
15635344 TTAAAATTTT
1 TAAAAATTTT
15635354 AGATTTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (10 bp):
TAAAAATTTT
Found at i:15635507 original size:25 final size:25
Alignment explanation
Indices: 15635479--15635527 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
15635469 AAGTTTCCTT
* * *
15635479 AATTTTTATTTTTTAAAAATATTTC
1 AATTTGTAATTTTTAAAAAAATTTC
15635504 AATTTGTAATTTTTAAAAAAATTT
1 AATTTGTAATTTTTAAAAAAATTT
15635528 TAAAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
AATTTGTAATTTTTAAAAAAATTTC
Found at i:15635772 original size:3 final size:3
Alignment explanation
Indices: 15635764--15635794 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
15635754 ATACTTTTAC
15635764 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
15635795 TATTTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:15636651 original size:29 final size:26
Alignment explanation
Indices: 15636586--15636665 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 26
15636576 CACAGGTTTT
*
15636586 TTTTTTTCATTTTCATTTTATTTTCTAAT
1 TTTTTTT-ATTTT-ATTTTATTTT-TAAA
15636615 TTTATTTTATTTTATTTTATTTTTAACCCA
1 TTT-TTTTATTTTATTTTATTTTTAA---A
15636645 TTTTTTTA-TTT-TTTTATTTTT
1 TTTTTTTATTTTATTTTATTTTT
15636666 TTAAAAAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
27 13 0.28
28 13 0.28
29 13 0.28
30 7 0.15
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTTTTATTTTATTTTATTTTTAAA
Found at i:15636656 original size:5 final size:5
Alignment explanation
Indices: 15636584--15636637 Score: 54
Period size: 5 Copynumber: 9.8 Consensus size: 5
15636574 ATCACAGGTT
*
15636584 TTTTT TTTTCA TTTTCA TTTTA TTTTCTAA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTT-A TTTT-A TTTTA -TTT-T-A TTTTA TTTTA TTTTA TTTTA
15636634 TTTT
1 TTTT
15636638 TAACCCATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
5 25 0.57
6 14 0.32
7 4 0.09
8 1 0.02
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:15636659 original size:9 final size:8
Alignment explanation
Indices: 15636644--15636668 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
15636634 TTTTTAACCC
15636644 ATTTTTTT
1 ATTTTTTT
15636652 ATTTTTTT
1 ATTTTTTT
15636660 ATTTTTTT
1 ATTTTTTT
15636668 A
1 A
15636669 AAAAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:15647993 original size:119 final size:119
Alignment explanation
Indices: 15647780--15648534 Score: 705
Period size: 119 Copynumber: 6.3 Consensus size: 119
15647770 CATTTTGCAA
* * ** *
15647780 GATTCATGG-TTCTATCCCGATCATTCATTTTTTACCTTGACTTGGTCCTGGTCGTTTTATTTTG
1 GATTCATGGTTTC-ATCCCGATCATTCATTTTTAACCTCGACTCAGTCCTGGTCATTTTATTTTG
* * * * * *
15647844 ACTCATGGTTTCATCCTGATTGTTTAATTTTGGCTCAATCCAAATCATTTCTTAT
65 ACTCGTGATTTCATCCCGATCGTTTGATCTTGGCTCAATCCAAATCATTTCTTAT
* * * *
15647899 GATTCATGGTTTCATCCCGATTATTCATTTTCAACATCGACTCAATCCTGGTCATTTTATTTTGA
1 GATTCATGGTTTCATCCCGATCATTCATTTTTAACCTCGACTCAGTCCTGGTCATTTTATTTTGA
* ** * * * * * * * *
15647964 TTTTTGATTTCGTCCAGGTCGTTTGATTTTGGCTTAGTCTAAATCATTTTTTAT
66 CTCGTGATTTCATCCCGATCGTTTGATCTTGGCTCAATCCAAATCATTTCTTAT
** * * * * *
15648018 GATTTGTGGTTTCGTCCTGATCATTCATTTTTTGACCTCGACT-TGATCCTGGTTATTTTATTTT
1 GATTCATGGTTTCATCCCGATCATTCA-TTTTTAACCTCGACTCAG-TCCTGGTCATTTTATTTT
* ** * * *
15648082 GATTCGTGATTTTGTCCCGATCATTTGATCTTGGCTCAGTCCAGATCATTTCTTAT
64 GACTCGTGATTTCATCCCGATCGTTTGATCTTGGCTCAATCCAAATCATTTCTTAT
* * ** * *
15648138 GATTCATGGTTCCGTCTTGGTCATTCATTTTTAACCTCAACTCAGTCCTGGTCATTTTATTTTGA
1 GATTCATGGTTTCATCCCGATCATTCATTTTTAACCTCGACTCAGTCCTGGTCATTTTATTTTGA
* ** * *
15648203 CTCGTGGTTTCAT-CTTAGTCGTTTGATATTGGCTCGATCCAAATCATTTCTTAT
66 CTCGTGATTTCATCCCGA-TCGTTTGATCTTGGCTCAATCCAAATCATTTCTTAT
* ** * * *
15648257 AATTCATGG-TTCTATCTTGATCATTCATTTTTTGACCTCGACTCAGTCTTGATCATTTTATTTT
1 GATTCATGGTTTC-ATCCCGATCATTCA-TTTTTAACCTCGACTCAGTCCTGGTCATTTTATTTT
* * * * * * * *
15648321 AATTCATGGTTTCATCCCGATCATTTGATCTTGGCTCAGTCCAGATAATTTCTTAT
64 GACTCGTGATTTCATCCCGATCGTTTGATCTTGGCTCAATCCAAATCATTTCTTAT
* *
15648377 GATTCATGG-TTCTATCCCGATCATTCATTTTCT-ACCTCGACTCGGTCCTGGTCTTTTTATTTT
1 GATTCATGGTTTC-ATCCCGATCATTCATTTT-TAACCTCGACTCAGTCCTGGTCATTTTATTTT
* * * * *
15648440 GACTTGTGATTTCATCCCGGTCGCTTGATCTTGGCTCAATCTAAATCATTTTTTAT
64 GACTCGTGATTTCATCCCGATCGTTTGATCTTGGCTCAATCCAAATCATTTCTTAT
* * * * *
15648496 GATT-GTGGTTTCGTCCCAATTATTCATTTTTTACCTCGA
1 GATTCATGGTTTCATCCCGATCATTCATTTTTAACCTCGA
15648535 TTCGATCTTG
Statistics
Matches: 518, Mismatches: 107, Indels: 23
0.80 0.17 0.04
Matches are distributed among these distances:
117 1 0.00
118 29 0.06
119 287 0.55
120 199 0.38
121 2 0.00
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (119 bp):
GATTCATGGTTTCATCCCGATCATTCATTTTTAACCTCGACTCAGTCCTGGTCATTTTATTTTGA
CTCGTGATTTCATCCCGATCGTTTGATCTTGGCTCAATCCAAATCATTTCTTAT
Found at i:15648189 original size:239 final size:238
Alignment explanation
Indices: 15647798--15648534 Score: 856
Period size: 239 Copynumber: 3.1 Consensus size: 238
15647788 GTTCTATCCC
* * * * *
15647798 GATCATTCATTTTTTACCTTGACTTGGTCCTGGTCGTTTTATTTTGACTCATGGTTTCATCCTGA
1 GATCATTCATTTTTTACCTCGACTTGATCCTGGTCATTTTATTTTGATTCATGGTTTCATCCCGA
** * * * * * *
15647863 TTGTTTAATTTTGGCTCAATCCAAATCATTTCTTATGATTCATGGTTTCATCCCGATTATTCATT
66 TCATTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTCCATCCCGATCATTCATT
* * * * * * *
15647928 TTCAACATCGACTCAATCCTGGTCATTTTATTTTGATTTTTGATTTCGTCCAGGTCGTTTGATTT
131 TTTAACCTCGACTCAGTCCTGGTCATTTTATTTTGACTTGTGATTTCATCCAGGTCGTTTGATAT
15647993 TGGCTTAGTCTAAATCATTTTTTATGATTTGTGGTTTCGTCCT
196 TGGCTTAGTCTAAATCATTTTTTATGATTTGTGGTTTCGTCCT
* * * **
15648036 GATCATTCATTTTTTGACCTCGACTTGATCCTGGTTATTTTATTTTGATTCGTGATTTTGTCCCG
1 GATCATTCATTTTTT-ACCTCGACTTGATCCTGGTCATTTTATTTTGATTCATGGTTTCATCCCG
* ** *
15648101 ATCATTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTCCGTCTTGGTCATTCAT
65 ATCATTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTCCATCCCGATCATTCAT
* * * *
15648166 TTTTAACCTCAACTCAGTCCTGGTCATTTTATTTTGACTCGTGGTTTCATCTTA-GTCGTTTGAT
130 TTTTAACCTCGACTCAGTCCTGGTCATTTTATTTTGACTTGTGATTTCATC-CAGGTCGTTTGAT
* * * * ** * *
15648230 ATTGGC-TCGATCCAAATCATTTCTTATAATTCATGG-TTCTATCTT
194 ATTGGCTTAG-TCTAAATCATTTTTTATGATTTGTGGTTTC-GTCCT
* * * *
15648275 GATCATTCATTTTTTGACCTCGAC-TCAGTCTTGATCATTTTATTTTAATTCATGGTTTCATCCC
1 GATCATTCATTTTTT-ACCTCGACTTGA-TCCTGGTCATTTTATTTTGATTCATGGTTTCATCCC
* *
15648339 GATCATTTGATCTTGGCTCAGTCCAGATAATTTCTTATGATTCATGGTTCTATCCCGATCATTCA
64 GATCATTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTCCATCCCGATCATTCA
* * * *
15648404 TTTTCT-ACCTCGACTCGGTCCTGGTCTTTTTATTTTGACTTGTGATTTCATCCCGGTCGCTTGA
129 TTTT-TAACCTCGACTCAGTCCTGGTCATTTTATTTTGACTTGTGATTTCATCCAGGTCGTTTGA
* * * *
15648468 TCTTGGCTCAATCTAAATCATTTTTTATGA-TTGTGGTTTCGTCCC
193 TATTGGCTTAGTCTAAATCATTTTTTATGATTTGTGGTTTCGTCCT
* *
15648513 AATTATTCATTTTTTACCTCGA
1 GATCATTCATTTTTTACCTCGA
15648535 TTCGATCTTG
Statistics
Matches: 412, Mismatches: 78, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
237 7 0.02
238 41 0.10
239 362 0.88
240 2 0.00
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (238 bp):
GATCATTCATTTTTTACCTCGACTTGATCCTGGTCATTTTATTTTGATTCATGGTTTCATCCCGA
TCATTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTCCATCCCGATCATTCATT
TTTAACCTCGACTCAGTCCTGGTCATTTTATTTTGACTTGTGATTTCATCCAGGTCGTTTGATAT
TGGCTTAGTCTAAATCATTTTTTATGATTTGTGGTTTCGTCCT
Found at i:15648416 original size:358 final size:357
Alignment explanation
Indices: 15647744--15648532 Score: 856
Period size: 358 Copynumber: 2.2 Consensus size: 357
15647734 ATTATCTCAT
* * * *
15647744 TCACTTGATCTTGGCTCTGTCAAGATCATTTTGCAAGATTCATGGTTCTATCCCGATCATTCATT
1 TCACTTGATCTTGGCTCAGTCAAGATCATTTT-TATGATTCATGGTTCCATCCCGATCATTCATT
* ** ** * * *
15647809 TTTTACCTTGACTTGGTCCTGGTCGTTTTATTTTGACTCATGGTTTCATCCTGATTGTTTAATTT
65 TTTAACCTCAACTCAGTCCTGGTCATTTTATTTTGACTCATGGTTTCATCCTGATCGTTTAATAT
* *
15647874 TGGCTCAATCCAAATCATTTCTTATGATTCATGGTTTCATCCCGATTATTCATTTTCAACATCGA
130 TGGCTCAATCCAAATCATTTCTTATAATTCATGGTTTCATCCCGATCATTCATTTTCAACATCGA
* * ** * * * * * *
15647939 CTCAATCCTGGTCATTTTATTTTGATTTTTGATTTCGTCCAGGTCGTTTGATTTTGGCTTAGTCT
195 CTCAATCCTGATCATTTTATTTTAATTCATGATTTCATCCAGATCATTTGATCTTGGCTCAGTCC
* * ** * * * *
15648004 AAATCATTTTTTATGATTTGTGGTTTCGTCCTGATCATTCATTTTTTGACCTCGACTTGATCCTG
260 AAATAATTTCTTATGATTCATGGTTTCATCCCGATCATTCATTTTCTGACCTCGACTCGATCCTG
**
15648069 GT-TATTTTATTTTGA-TTCGTGATTTTGTCCCGA
325 GTCT-TTTTATTTTGACTT-GTGATTTCATCCCGA
* * * ** *
15648102 TCATTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGGTTCCGTCTTGGTCATTCATT
1 TCACTTGATCTTGGCTCAGTCAAGATCATTT-TTATGATTCATGGTTCCATCCCGATCATTCATT
* * *
15648167 TTTAACCTCAACTCAGTCCTGGTCATTTTATTTTGACTCGTGGTTTCAT-CTTAGTCGTTTGATA
65 TTTAACCTCAACTCAGTCCTGGTCATTTTATTTTGACTCATGGTTTCATCCTGA-TCGTTTAATA
* ** ** *
15648231 TTGGCTCGATCCAAATCATTTCTTATAATTCATGG-TTCTATCTTGATCATTCATTTTTTGACCT
129 TTGGCTCAATCCAAATCATTTCTTATAATTCATGGTTTC-ATCCCGATCATTCA-TTTTCAACAT
* * * *
15648295 CGACTCAGTCTTGATCATTTTATTTTAATTCATGGTTTCATCCCGATCATTTGATCTTGGCTCAG
192 CGACTCAATCCTGATCATTTTATTTTAATTCATGATTTCATCCAGATCATTTGATCTTGGCTCAG
* *
15648360 TCCAGATAATTTCTTATGATTCATGG-TTCTATCCCGATCATTCATTTTCT-ACCTCGACTCGGT
257 TCCAAATAATTTCTTATGATTCATGGTTTC-ATCCCGATCATTCATTTTCTGACCTCGACTCGAT
*
15648423 CCTGGTCTTTTTATTTTGACTTGTGATTTCATCCCGG
321 CCTGGTCTTTTTATTTTGACTTGTGATTTCATCCCGA
* * * * * * *
15648460 TCGCTTGATCTTGGCTCAATCTAA-ATCATTTTTTATGATT-GTGGTTTCGTCCCAATTATTCAT
1 TCACTTGATCTTGGCTCAGTC-AAGATCA-TTTTTATGATTCATGGTTCCATCCCGATCATTCAT
*
15648523 TTTTTACCTC
64 TTTTAACCTC
15648533 GATTCGATCT
Statistics
Matches: 354, Mismatches: 68, Indels: 19
0.80 0.15 0.04
Matches are distributed among these distances:
357 31 0.09
358 219 0.62
359 104 0.29
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (357 bp):
TCACTTGATCTTGGCTCAGTCAAGATCATTTTTATGATTCATGGTTCCATCCCGATCATTCATTT
TTAACCTCAACTCAGTCCTGGTCATTTTATTTTGACTCATGGTTTCATCCTGATCGTTTAATATT
GGCTCAATCCAAATCATTTCTTATAATTCATGGTTTCATCCCGATCATTCATTTTCAACATCGAC
TCAATCCTGATCATTTTATTTTAATTCATGATTTCATCCAGATCATTTGATCTTGGCTCAGTCCA
AATAATTTCTTATGATTCATGGTTTCATCCCGATCATTCATTTTCTGACCTCGACTCGATCCTGG
TCTTTTTATTTTGACTTGTGATTTCATCCCGA
Found at i:15648763 original size:26 final size:26
Alignment explanation
Indices: 15648712--15648782 Score: 101
Period size: 26 Copynumber: 2.7 Consensus size: 26
15648702 ATCCGAGCAT
15648712 AATTAGGCCCATTTTGG-CTTGAGCCC
1 AATTAGGCCCATTTTGGTCTT-AGCCC
15648738 AATTAGGCCCATTTTGGTC-TATGCCC
1 AATTAGGCCCATTTTGGTCTTA-GCCC
*
15648764 AATTAGGCCCATTCTGGTC
1 AATTAGGCCCATTTTGGTC
15648783 AGGCCCGCCA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 1 0.02
26 40 0.95
27 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (26 bp):
AATTAGGCCCATTTTGGTCTTAGCCC
Found at i:15649676 original size:18 final size:17
Alignment explanation
Indices: 15649650--15649695 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
15649640 CGATTGCAGG
*
15649650 TTTTTTTTTTCATTTTTA
1 TTTTATTTTTCA-TTTTA
*
15649668 TTTTATTTTTTGATTTTA
1 TTTTA-TTTTTCATTTTA
15649686 TTTTATTTTT
1 TTTTATTTTT
15649696 AACCCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 14 0.56
19 6 0.24
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTATTTTTCATTTTA
Found at i:15649723 original size:18 final size:17
Alignment explanation
Indices: 15649650--15649724 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
15649640 CGATTGCAGG
*
15649650 TTTTT-TTTTTCATTTT
1 TTTTTATTTTTTATTTT
15649666 TATTTTATTTTTTGATTTT
1 T-TTTTATTTTTT-ATTTT
* * ***
15649685 ATTTTATTTTTAACCCT
1 TTTTTATTTTTTATTTT
15649702 TTTTTATTTTTTATTTT
1 TTTTTATTTTTTATTTT
*
15649719 CTTTTA
1 TTTTTA
15649725 AAAAATATAT
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
16 1 0.02
17 23 0.52
18 15 0.34
19 5 0.11
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (17 bp):
TTTTTATTTTTTATTTT
Found at i:15653760 original size:17 final size:18
Alignment explanation
Indices: 15653732--15653766 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
15653722 TTAAAATTTA
15653732 AAATATAAAAAATCATCT
1 AAATATAAAAAATCATCT
*
15653750 AAATA-AAAAAATTATCT
1 AAATATAAAAAATCATCT
15653767 TCCAAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATAAAAAATCATCT
Found at i:15660584 original size:18 final size:19
Alignment explanation
Indices: 15660561--15660596 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
15660551 TGAAATTTCA
*
15660561 AAAAAATTTA-ATTTTAAG
1 AAAAAATTAATATTTTAAG
15660579 AAAAAATTAATATTTTAA
1 AAAAAATTAATATTTTAA
15660597 CTTTTTCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAAAATTAATATTTTAAG
Found at i:15660687 original size:54 final size:54
Alignment explanation
Indices: 15660622--15660876 Score: 192
Period size: 55 Copynumber: 4.5 Consensus size: 54
15660612 ATTGGCATTG
* *
15660622 TTTTAAAAAAAATTGATATTTCAATTTTTCCTCAAATCTTTGAAATTATTTTCA
1 TTTTAAGAAAAATTGATATTTCAATTTTTCCTCAAATCTTTGAAATTATTTTTA
* * * *
15660676 TTTTAAGAAAAATGGATATTTTATCTTTTTCCTCATAGT-TTTGAAATTATTTTT-
1 TTTTAAGAAAAATTGATATTTCA-ATTTTTCCTCA-AATCTTTGAAATTATTTTTA
* * * * *
15660730 GTTTAAAAAAAATTTGATATTTCACCTTTTTCCTCCAAACATTTTTGCAATTATTTTTA
1 TTTTAAGAAAAA-TTGATATTTCA-ATTTTTCCT-C-AA-ATCTTTGAAATTATTTTTA
* * * ** **
15660789 TTTTAAGAAAAAAATTAATATTTTAAAATTTTCCTCATTTC-TCAAAATTATTTTTTA
1 TTTTAAG--AAAAATTGATA-TTTCAATTTTTCCTCAAATCTTTGAAATTA-TTTTTA
* *
15660846 TATATAAGAAAAAATTGATATTTTAATTTTT
1 T-TTTAAG-AAAAATTGATATTTCAATTTTT
15660877 TTTTCAATTT
Statistics
Matches: 159, Mismatches: 29, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
54 30 0.19
55 42 0.26
56 19 0.12
57 21 0.13
58 20 0.13
59 6 0.04
60 12 0.08
61 9 0.06
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.49
Consensus pattern (54 bp):
TTTTAAGAAAAATTGATATTTCAATTTTTCCTCAAATCTTTGAAATTATTTTTA
Found at i:15660893 original size:57 final size:57
Alignment explanation
Indices: 15660778--15660905 Score: 147
Period size: 57 Copynumber: 2.3 Consensus size: 57
15660768 ACATTTTTGC
* *
15660778 AATTA-TTTTTATTTTAAGAAAAAAATTAATATTTTAAAATTTTCCTCATTTCTCAA
1 AATTATTTTTTATTATAAGAAAAAAATTAATATTTTAAAATTTTCCTCATTTCTAAA
* ** **
15660834 AATTATTTTTTATATATAAG-AAAAAATTGATATTTTAATTTTTTTTTCAATTT-TAAA
1 AATTATTTTTTAT-TATAAGAAAAAAATTAATATTTTAAAATTTTCCTC-ATTTCTAAA
15660891 AATTA-TTTTTATTAT
1 AATTATTTTTTATTAT
15660906 TTTTTAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
55 3 0.05
56 12 0.19
57 38 0.61
58 9 0.15
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (57 bp):
AATTATTTTTTATTATAAGAAAAAAATTAATATTTTAAAATTTTCCTCATTTCTAAA
Found at i:15662525 original size:5 final size:5
Alignment explanation
Indices: 15662515--15662584 Score: 72
Period size: 5 Copynumber: 13.4 Consensus size: 5
15662505 AAACAATAAT
*
15662515 AAATA AAATA AAATA AAATA AAGATA AAAT- AAAT- GAATA AAATAA ATAATA
1 AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA AAAT-A A-AATA
15662566 AAGATA AAATAA AAATA AA
1 AA-ATA AAAT-A AAATA AA
15662585 GATTTATACA
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
4 7 0.12
5 28 0.49
6 19 0.33
7 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:15662543 original size:11 final size:11
Alignment explanation
Indices: 15662517--15662584 Score: 74
Period size: 11 Copynumber: 6.5 Consensus size: 11
15662507 ACAATAATAA
15662517 ATAAAATAAA-
1 ATAAAATAAAG
15662527 ATAAAATAAAG
1 ATAAAATAAAG
15662538 ATAAAATAAATG
1 ATAAAATAAA-G
15662550 AATAAAAT-AA-
1 -ATAAAATAAAG
15662560 AT--AATAAAG
1 ATAAAATAAAG
*
15662569 ATAAAATAAAA
1 ATAAAATAAAG
15662580 ATAAA
1 ATAAA
15662585 GATTTATACA
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
7 3 0.06
8 2 0.04
9 4 0.08
10 10 0.20
11 21 0.42
12 3 0.06
13 7 0.14
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (11 bp):
ATAAAATAAAG
Found at i:15662556 original size:13 final size:13
Alignment explanation
Indices: 15662526--15662573 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
15662516 AATAAAATAA
15662526 AATAAAATAAA-G
1 AATAAAATAAATG
15662538 -ATAAAATAAATG
1 AATAAAATAAATG
15662550 AATAAAATAAAT-
1 AATAAAATAAATG
15662562 AATAAAGATAAA
1 AATAAA-ATAAA
15662574 ATAAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.30
12 7 0.21
13 16 0.48
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (13 bp):
AATAAAATAAATG
Found at i:15662565 original size:20 final size:17
Alignment explanation
Indices: 15662509--15662587 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 17
15662499 CTTTATAAAC
15662509 AATAATAAATAAA-ATAA
1 AATAA-AAATAAAGATAA
15662526 AAT-AAAATAAAGATAA
1 AATAAAAATAAAGATAA
*
15662542 AAT--AAAT-GA-ATAA
1 AATAAAAATAAAGATAA
15662555 AATAAATAATAAAGATAA
1 AATAAA-AATAAAGATAA
15662573 AATAAAAATAAAGAT
1 AATAAAAATAAAGAT
15662588 TTATACAATG
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
13 7 0.13
14 1 0.02
15 12 0.22
16 11 0.20
17 13 0.24
18 10 0.19
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (17 bp):
AATAAAAATAAAGATAA
Found at i:15662569 original size:31 final size:30
Alignment explanation
Indices: 15662512--15662578 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
15662502 TATAAACAAT
15662512 AATAAATAAAATAAAATAAAATAAAGATAA
1 AATAAATAAAATAAAATAAAATAAAGATAA
*
15662542 AATAAAT-GAATAAAATAAATAATAAAGATAA
1 AATAAATAAAATAAAAT-AA-AATAAAGATAA
15662573 AATAAA
1 AATAAA
15662579 AATAAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 8 0.24
30 9 0.26
31 17 0.50
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (30 bp):
AATAAATAAAATAAAATAAAATAAAGATAA
Found at i:15662580 original size:24 final size:23
Alignment explanation
Indices: 15662503--15662584 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 23
15662493 CCTTTTCTTT
15662503 ATAAACAAT-AATAAATAAAATAAA
1 ATAAA-AATAAAT-AATAAAATAAA
*
15662527 AT-AAAATAAA-GATAAAAT-AA
1 ATAAAAATAAATAATAAAATAAA
15662547 ATGAATAAAATAAATAATAAAGATAAA
1 AT--A-AAAATAAATAATAAA-ATAAA
15662574 ATAAAAATAAA
1 ATAAAAATAAA
15662585 GATTTATACA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
20 4 0.08
21 7 0.15
22 3 0.06
23 4 0.08
24 18 0.38
25 6 0.12
26 2 0.04
27 4 0.08
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (23 bp):
ATAAAAATAAATAATAAAATAAA
Found at i:15662615 original size:48 final size:46
Alignment explanation
Indices: 15662503--15662619 Score: 125
Period size: 48 Copynumber: 2.5 Consensus size: 46
15662493 CCTTTTCTTT
15662503 ATAAACAATAATAA-ATAAAATAAAATAAAATAAAGATAAAATAAATG
1 ATAAA-AATAA-AATATAAAATAAAATAAAATAAAGATAAAATAAATG
**
15662550 A-ATAAAAT-AAATAATAAAGATAAAATAAAAATAAAGAT-TTATACAATG
1 ATA-AAAATAAAAT-ATAAA-ATAAAAT-AAAATAAAGATAAAATA-AATG
15662598 ATAAAAATAAAATATAAAATAA
1 ATAAAAATAAAATATAAAATAA
15662620 TGATAAGCAC
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
44 2 0.03
45 1 0.02
46 9 0.15
47 17 0.28
48 26 0.43
49 5 0.08
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (46 bp):
ATAAAAATAAAATATAAAATAAAATAAAATAAAGATAAAATAAATG
Found at i:15663664 original size:7 final size:7
Alignment explanation
Indices: 15663652--15663813 Score: 57
Period size: 7 Copynumber: 24.4 Consensus size: 7
15663642 GCCACCATGC
15663652 AAACCCT
1 AAACCCT
15663659 AAACCCCT
1 AAA-CCCT
*
15663667 AAACCACAGA
1 AAACC-C--T
15663677 AAACCCT
1 AAACCCT
*
15663684 AAACCCC
1 AAACCCT
*
15663691 AAACATCT
1 AAAC-CCT
15663699 -AACCCT
1 AAACCCT
*
15663705 AAACCAT
1 AAACCCT
*
15663712 -AA-CCA
1 AAACCCT
*
15663717 AAACCTT
1 AAACCCT
15663724 AAA-CCT
1 AAACCCT
15663730 AAA--CT
1 AAACCCT
15663735 AAACCCT
1 AAACCCT
**
15663742 AAA-AAT
1 AAACCCT
*
15663748 AAACACCC
1 AAAC-CCT
15663756 AAACCCT
1 AAACCCT
*
15663763 AAA-GC-
1 AAACCCT
*
15663768 AAACCTT
1 AAACCCT
15663775 AAA-CC-
1 AAACCCT
*
15663780 -AATCCT
1 AAACCCT
15663786 AAACCCT
1 AAACCCT
15663793 AAA-CCT
1 AAACCCT
15663799 -AA-CCT
1 AAACCCT
15663804 AAACCCT
1 AAACCCT
15663811 AAA
1 AAA
15663814 AACTCAAACC
Statistics
Matches: 113, Mismatches: 23, Indels: 38
0.65 0.13 0.22
Matches are distributed among these distances:
4 2 0.02
5 16 0.14
6 22 0.19
7 54 0.48
8 13 0.12
9 1 0.01
10 5 0.04
ACGTcount: A:0.49, C:0.36, G:0.01, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:15663744 original size:18 final size:18
Alignment explanation
Indices: 15663699--15663813 Score: 80
Period size: 18 Copynumber: 6.5 Consensus size: 18
15663689 CCAAACATCT
* *
15663699 AACCCTAAACCATAACCAA
1 AACCCTAAACC-TAAACTA
*
15663718 AACCTTAAACCTAAACTA
1 AACCCTAAACCTAAACTA
**
15663736 AACCCTAAAAATAAAC--
1 AACCCTAAACCTAAACTA
15663752 -ACCC-AAACCCTAAAGC-A
1 AACCCTAAA-CCTAAA-CTA
* *
15663769 AACCTTAAACC-AATCCTA
1 AACCCTAAACCTAA-ACTA
*
15663787 AACCCTAAACCTAACCTA
1 AACCCTAAACCTAAACTA
15663805 AACCCTAAA
1 AACCCTAAA
15663814 AACTCAAACC
Statistics
Matches: 77, Mismatches: 11, Indels: 17
0.73 0.10 0.16
Matches are distributed among these distances:
14 3 0.04
15 8 0.10
16 1 0.01
17 3 0.04
18 47 0.61
19 15 0.19
ACGTcount: A:0.50, C:0.34, G:0.01, T:0.15
Consensus pattern (18 bp):
AACCCTAAACCTAAACTA
Found at i:15669457 original size:24 final size:22
Alignment explanation
Indices: 15669430--15669474 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
15669420 AGAATGAGAA
*
15669430 AATAAGAAAAAAATAGAATAAAAG
1 AATAA-AAAAAAA-AGAAGAAAAG
15669454 AATAAAAAAAAAAGAAGAAAA
1 AATAAAAAAAAAAGAAGAAAA
15669475 AAAAGGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (22 bp):
AATAAAAAAAAAAGAAGAAAAG
Found at i:15669468 original size:14 final size:14
Alignment explanation
Indices: 15669449--15669478 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
15669439 AAAATAGAAT
*
15669449 AAAAGAATAAAAAA
1 AAAAGAAGAAAAAA
15669463 AAAAGAAGAAAAAA
1 AAAAGAAGAAAAAA
15669477 AA
1 AA
15669479 GGGAAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAAGAAGAAAAAA
Found at i:15669476 original size:24 final size:24
Alignment explanation
Indices: 15669430--15669477 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
15669420 AGAATGAGAA
* *
15669430 AATAAGAAAAAAATAGAATAAAAG
1 AATAAAAAAAAAAAAGAATAAAAG
*
15669454 AATAAAAAAAAAAGAAGAAAAAAA
1 AATAAAAAAAAAA-AAGAATAAAA
15669478 AGGGAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.08
Consensus pattern (24 bp):
AATAAAAAAAAAAAAGAATAAAAG
Found at i:15670551 original size:12 final size:13
Alignment explanation
Indices: 15670522--15670551 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15670512 GTTGATTGAG
15670522 AAAAAAAAAGAAC
1 AAAAAAAAAGAAC
*
15670535 AAAAAAAAAGTAC
1 AAAAAAAAAGAAC
15670548 AAAA
1 AAAA
15670552 TATTTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.07, G:0.07, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAGAAC
Found at i:15672092 original size:126 final size:125
Alignment explanation
Indices: 15671737--15672275 Score: 608
Period size: 125 Copynumber: 4.3 Consensus size: 125
15671727 TTTTGTCAAA
* *
15671737 GGTGATA-TCTAAGTATCCAAGTTTGAATTTCTTAAAAAAATTTTCAATGATGATATCCGAGCGT
1 GGTGATATTC-AAGTATCCAAGTTTGAATTTCTTAAAAAAATTTTCAATGATGATATCTGAGCAT
* * * * * * * **
15671801 TTAAGTTTGAATTTCATTTTCTCAATAGCGAAATTCGACCCTTCATTAGAACT-TTTTCGGT
65 TCAAGTTTGAATTTCATTTTCTTAATGGCAAAATTCAACCCTTCATTAAAACTCTCTT-AAT
* *
15671862 GGTGATATTCGAGTATCCAAGTTTGAATTTCTT--AAAAATTTTC-TTGGTAATGATAT-TCGAG
1 GGTGATATTCAAGTATCCAAGTTTGAATTTCTTAAAAAAATTTTCAAT-G--ATGATATCT-GAG
* ** ** *
15671923 CATTCAAGTTTGAATTTCATTATCTCGATGGTGAAATTCAACCCTGCATTAAAACTCTCTTAAT
62 CATTCAAGTTTGAATTTCATTTTCTTAATGGCAAAATTCAACCCTTCATTAAAACTCTCTTAAT
* * *
15671987 GGTAATATTCAAGTATCCAAGTTTGAATTTCTTAAAAAAAATTTACAATGGTGATATCTGAGCAT
1 GGTGATATTCAAGTATCCAAGTTTGAATTTCTT-AAAAAAATTTTCAATGATGATATCTGAGCAT
* * * *
15672052 TCAAGTTAGAATTTCATTTTCTTATTGGCAAAATCCAACCCTTCATTAAAACTCCCTTAAT
65 TCAAGTTTGAATTTCATTTTCTTAATGGCAAAATTCAACCCTTCATTAAAACTCTCTTAAT
* * * * *
15672113 GATGATATTCAATTATTCAAGTTTGAATTTCTTAAAAAAATTTTCAATGATGATATTTGAACATT
1 GGTGATATTCAAGTATCCAAGTTTGAATTTCTTAAAAAAATTTTCAATGATGATATCTGAGCATT
* * * *
15672178 CAAGTTTGAATTTTATTTTCTTAATGGCAAAATAT-GACCCTTCATTAAAACTCTCTCAGT
66 CAAGTTTGAATTTCATTTTCTTAATGGCAAAAT-TCAACCCTTCATTAAAACTCTCTTAAT
*
15672238 GGTGATACTTAAAGTATCCAAGTTTGAGATTT-TTAAAA
1 GGTGATA-TTCAAGTATCCAAGTTTGA-ATTTCTTAAAA
15672276 TTTTTTCAAT
Statistics
Matches: 350, Mismatches: 50, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
122 1 0.00
123 11 0.03
125 203 0.58
126 119 0.34
127 5 0.01
128 10 0.03
129 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (125 bp):
GGTGATATTCAAGTATCCAAGTTTGAATTTCTTAAAAAAATTTTCAATGATGATATCTGAGCATT
CAAGTTTGAATTTCATTTTCTTAATGGCAAAATTCAACCCTTCATTAAAACTCTCTTAAT
Done.