Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 64 of 77
Found at i:12824611 original size:19 final size:19
Alignment explanation
Indices: 12824589--12824707 Score: 59
Period size: 19 Copynumber: 5.9 Consensus size: 19
12824579 AATGATAATA
12824589 ATAATAATAAATAAAAAAT
1 ATAATAATAAATAAAAAAT
* * *
12824608 ATAA-AAAAAATTAATAGAT
1 ATAATAATAAA-TAAAAAAT
12824627 A-AATAA-AAAT-AAAAAT
1 ATAATAATAAATAAAAAAT
*
12824643 AATAGATAA-ATATAAAAAAT
1 -ATA-ATAATAAATAAAAAAT
12824663 ACATTAATAGATAAATAATAAAAAAT
1 --A-TAATA-AT--A-AATAAAAAAT
*
12824689 ATATTAATAAATAATAAAA
1 ATAATAATAAATAA-AAAA
12824708 ATGTAATATC
Statistics
Matches: 77, Mismatches: 9, Indels: 27
0.68 0.08 0.24
Matches are distributed among these distances:
16 4 0.05
17 2 0.03
18 11 0.14
19 25 0.32
20 11 0.14
21 4 0.05
22 5 0.06
23 4 0.05
24 1 0.01
25 1 0.01
26 9 0.12
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.26
Consensus pattern (19 bp):
ATAATAATAAATAAAAAAT
Found at i:12824634 original size:17 final size:15
Alignment explanation
Indices: 12824583--12824680 Score: 58
Period size: 16 Copynumber: 6.3 Consensus size: 15
12824573 CAAAAAAATG
12824583 ATAATAATAATAATAA
1 ATAA-AATAATAATAA
12824599 ATAAAA-AAT-ATAA
1 ATAAAATAATAATAA
*
12824612 AAAAAATTAATAGATAA
1 ATAAAA-TAATA-ATAA
*
12824629 ATAAAAATAAAAATAA
1 AT-AAAATAATAATAA
* *
12824645 TAGATAAAT-ATAAAAA
1 -ATA-AAATAATAATAA
* *
12824661 ATACATTAATAGATAA
1 ATAAAATAATA-ATAA
12824677 ATAA
1 ATAA
12824681 TAAAAAATAT
Statistics
Matches: 62, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
13 9 0.15
14 5 0.08
15 10 0.16
16 20 0.32
17 14 0.23
18 4 0.06
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAAAATAATAATAA
Found at i:12824689 original size:7 final size:7
Alignment explanation
Indices: 12824585--12824803 Score: 93
Period size: 7 Copynumber: 31.3 Consensus size: 7
12824575 AAAAAATGAT
12824585 AATAAT-
1 AATAATA
12824591 AATAATA
1 AATAATA
*
12824598 AATAAAA
1 AATAATA
*
12824605 AATATAAA
1 AATA-ATA
* *
12824613 AAAAATT
1 AATAATA
12824620 AATAGATA
1 AATA-ATA
12824628 AATAA-A
1 AATAATA
12824634 AATAA-A
1 AATAATA
12824640 AATAATA
1 AATAATA
*
12824647 GATAA-A
1 AATAATA
* *
12824653 TATAAAA
1 AATAATA
*
12824660 AATACATT
1 AATA-ATA
12824668 AATAGATA
1 AATA-ATA
12824676 AATAATA
1 AATAATA
*
12824683 AAAAATA
1 AATAATA
*
12824690 TATTAATA
1 -AATAATA
12824698 AATAATA
1 AATAATA
*
12824705 AA-AATGT
1 AATAAT-A
* *
12824712 AATATCTT
1 AATA-ATA
12824720 AATAGATA
1 AATA-ATA
12824728 AATAA-A
1 AATAATA
*
12824734 AA-AGATT
1 AATA-ATA
12824741 AATAGATA
1 AATA-ATA
12824749 AATAAT-
1 AATAATA
12824755 AATAA-A
1 AATAATA
12824761 AAT-ATA
1 AATAATA
* *
12824767 TATTTATA
1 -AATAATA
12824775 AATAGATA
1 AATA-ATA
12824783 AA-AATA
1 AATAATA
*
12824789 AAAAATA
1 AATAATA
12824796 AA-AATA
1 AATAATA
12824802 AA
1 AA
12824804 CAAATGGGCT
Statistics
Matches: 167, Mismatches: 27, Indels: 38
0.72 0.12 0.16
Matches are distributed among these distances:
5 2 0.01
6 50 0.30
7 59 0.35
8 55 0.33
9 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (7 bp):
AATAATA
Found at i:12824706 original size:48 final size:47
Alignment explanation
Indices: 12824604--12824761 Score: 164
Period size: 48 Copynumber: 3.3 Consensus size: 47
12824594 AATAAATAAA
*
12824604 AAATATAAAAAA-A-ATTAATAGATAAATAAAAATAAAAATAATAGAT
1 AAATATAAAAAATACATTAATAGATAAATAAAAA-AAATATAATAGAT
*
12824650 AAATATAAAAAATACATTAATAGATAAATAATAAAAAATATATTA-AT
1 AAATATAAAAAATACATTAATAGATAAATAA-AAAAAATATAATAGAT
*
12824697 AAATAATAAAAATGTAATATC-TTAATAGATAAATAAAAAAGAT-TAATAGAT
1 AAAT-AT-AAAA---AATA-CATTAATAGATAAATAAAAAAAATATAATAGAT
12824748 AAATAATAATAAAA
1 AAAT-ATAA-AAAA
12824762 ATATATATTT
Statistics
Matches: 97, Mismatches: 4, Indels: 20
0.80 0.03 0.17
Matches are distributed among these distances:
46 12 0.12
47 7 0.07
48 28 0.29
49 7 0.07
50 6 0.06
51 17 0.18
52 19 0.20
53 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.27
Consensus pattern (47 bp):
AAATATAAAAAATACATTAATAGATAAATAAAAAAAATATAATAGAT
Found at i:12824746 original size:73 final size:81
Alignment explanation
Indices: 12824642--12824787 Score: 209
Period size: 77 Copynumber: 1.9 Consensus size: 81
12824632 AAAATAAAAA
12824642 TAATAGATAAATATAAAAAATACATTAATAGAT-A-AATAATAAAAA-ATATATTAATAAATA-A
1 TAATAGATAAATATAAAAAATACATTAATAGATAATAATAATAAAAATATATATTAATAAATAGA
12824703 TAAAAATGTAATATCT
66 TAAAAATGTAATATCT
* *
12824719 TAATAGAT-AA-AT-AAAAA-AGATTAATAGATAAATAATAATAAAAATATATATTTATAAATAG
1 TAATAGATAAATATAAAAAATACATTAATAGAT-AATAATAATAAAAATATATATTAATAAATAG
12824780 ATAAAAAT
65 ATAAAAAT
12824788 AAAAAATAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
73 11 0.18
74 5 0.08
75 3 0.05
76 13 0.21
77 22 0.35
78 8 0.13
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (81 bp):
TAATAGATAAATATAAAAAATACATTAATAGATAATAATAATAAAAATATATATTAATAAATAGA
TAAAAATGTAATATCT
Found at i:12824776 original size:77 final size:78
Alignment explanation
Indices: 12824593--12824787 Score: 203
Period size: 77 Copynumber: 2.6 Consensus size: 78
12824583 ATAATAATAA
* * * * **
12824593 TAATAAATAAAAAATATAAAAA-AAATTAATAGATAAATAAAAA--TAA-A-AATAATAGATAAA
1 TAATAAATAAATAATA-AAAAATATATTAATAAATAGATAAAAATGTAATATCTTAATAGATAAA
12824653 TATAAAAAATACAT
65 TATAAAAAATACAT
*
12824667 TAATAGATAAATAATAAAAAATATATTAATAAATA-ATAAAAATGTAATATCTTAATAGATAAAT
1 TAATAAATAAATAATAAAAAATATATTAATAAATAGATAAAAATGTAATATCTTAATAGATAAAT
12824731 A-AAAAAGATTA-A-
66 ATAAAAA-A-TACAT
*
12824743 TAGATAAAT-AATAATAAAAATATATATTTATAAATAGATAAAAAT
1 TA-ATAAATAAATAATAAAAA-ATATATTAATAAATAGATAAAAAT
12824788 AAAAAATAAA
Statistics
Matches: 103, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
73 12 0.12
74 25 0.24
75 3 0.03
76 19 0.18
77 34 0.33
78 10 0.10
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (78 bp):
TAATAAATAAATAATAAAAAATATATTAATAAATAGATAAAAATGTAATATCTTAATAGATAAAT
ATAAAAAATACAT
Found at i:12824798 original size:13 final size:14
Alignment explanation
Indices: 12824780--12824808 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12824770 TTATAAATAG
12824780 ATAAAAATAAA-AA
1 ATAAAAATAAACAA
12824793 ATAAAAATAAACAA
1 ATAAAAATAAACAA
12824807 AT
1 AT
12824809 GGGCTTACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (14 bp):
ATAAAAATAAACAA
Found at i:12826491 original size:30 final size:30
Alignment explanation
Indices: 12826423--12826494 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
12826413 AATGTCTGTG
12826423 TTTT-GGAATTTATTTTACAGTGTTTTAGA
1 TTTTGGGAATTTATTTTACAGTGTTTTAGA
* *
12826452 -ATTGTGGAATTT-TTTGTACAGTGTTTTGGA
1 TTTTG-GGAATTTATTT-TACAGTGTTTTAGA
12826482 TTTTGGGAATTTA
1 TTTTGGGAATTTA
12826495 GATGATACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
28 2 0.06
29 3 0.09
30 27 0.77
31 3 0.09
ACGTcount: A:0.22, C:0.03, G:0.22, T:0.53
Consensus pattern (30 bp):
TTTTGGGAATTTATTTTACAGTGTTTTAGA
Found at i:12826535 original size:22 final size:22
Alignment explanation
Indices: 12826507--12826551 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
12826497 TGATACAATG
*
12826507 TCAGATGATATAATTTTGGAAT
1 TCAGATGATAAAATTTTGGAAT
12826529 TCAGATGATAAAATTTTGGAAT
1 TCAGATGATAAAATTTTGGAAT
12826551 T
1 T
12826552 TTGAAATGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (22 bp):
TCAGATGATAAAATTTTGGAAT
Found at i:12826554 original size:30 final size:30
Alignment explanation
Indices: 12826518--12826582 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
12826508 CAGATGATAT
* *
12826518 AATTTTGGAATTCAGATGATAAAATTTTGG
1 AATTTTGAAATGCAGATGATAAAATTTTGG
* **
12826548 AATTTTGAAATGCATATGATATCATTTTGG
1 AATTTTGAAATGCAGATGATAAAATTTTGG
12826578 AATTT
1 AATTT
12826583 ATATTTGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (30 bp):
AATTTTGAAATGCAGATGATAAAATTTTGG
Found at i:12833498 original size:12 final size:12
Alignment explanation
Indices: 12833474--12833508 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
12833464 AGGTTCGGAC
12833474 TTTAAATATTTTA
1 TTTAAA-ATTTTA
12833487 TTTAAAATTTTA
1 TTTAAAATTTTA
12833499 TTTAAAATTT
1 TTTAAAATTT
12833509 AAATGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAAAATTTTA
Found at i:12833565 original size:18 final size:19
Alignment explanation
Indices: 12833528--12833565 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12833518 TAAAATTTAT
12833528 ATTTAAATTTATTTAATGA
1 ATTTAAATTTATTTAATGA
* *
12833547 ATTTTAATTT-TTTATTGA
1 ATTTAAATTTATTTAATGA
12833565 A
1 A
12833566 ATCCTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTAAATTTATTTAATGA
Found at i:12833785 original size:16 final size:16
Alignment explanation
Indices: 12833760--12833794 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12833750 ACTTAAATTG
* *
12833760 TAATCGAAATATAATA
1 TAATCCAAATATAAAA
12833776 TAATCCAAATATAAAA
1 TAATCCAAATATAAAA
12833792 TAA
1 TAA
12833795 AAAAACATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAATCCAAATATAAAA
Found at i:12834048 original size:5 final size:5
Alignment explanation
Indices: 12834038--12834064 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12834028 TTGATTAATA
12834038 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
12834065 TATATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:12843163 original size:23 final size:24
Alignment explanation
Indices: 12843114--12843164 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
12843104 ATATTTGATG
* *
12843114 TATTATTAGTGAATAGATACTATA
1 TATTATTAGTGAATACATACAATA
12843138 TATTA-TAGTGAAT-CATACAATGA
1 TATTATTAGTGAATACATACAAT-A
12843161 TATT
1 TATT
12843165 TTATTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.25
23 13 0.54
24 5 0.21
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (24 bp):
TATTATTAGTGAATACATACAATA
Found at i:12846795 original size:12 final size:11
Alignment explanation
Indices: 12846765--12846801 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
12846755 CCTAATTGTA
12846765 AATTAAAGAAT
1 AATTAAAGAAT
12846776 AATTAAAGAAT
1 AATTAAAGAAT
*
12846787 ACTTTAAAGAAT
1 A-ATTAAAGAAT
12846799 AAT
1 AAT
12846802 GTTTGGAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (11 bp):
AATTAAAGAAT
Found at i:12846987 original size:137 final size:138
Alignment explanation
Indices: 12846834--12847083 Score: 387
Period size: 137 Copynumber: 1.8 Consensus size: 138
12846824 TTCAATTTTG
* * *
12846834 TACATAGTTTTAAATATAAATTCTTATTTTTACTATACGCTGCATACATATATTTGCAAATACA-
1 TACATAGTTTTAAATATAAATTCTTATTTTTACTATACACTGCATACATATATTTACAAACACAT
*
12846898 TTTTTA-TCAATGTAAACATTTTTGTATGTACATTATTTCATTTGTTTGTGAGTATCTTTGTCTT
66 TTTTTATTC-ATGTAAACATTTTTGTATGTACATTATTTCATTTATTTGTGAGTATCTTTGTCTT
12846962 TTGCAGTTT
130 TTGCAGTTT
* ** * * *
12846971 TACATAGTTTTGAATATAAATTCTTATTTTTACTATGTATTGCATACATGTATTTACATACACAT
1 TACATAGTTTTAAATATAAATTCTTATTTTTACTATACACTGCATACATATATTTACAAACACAT
12847036 TTTTTATTCATGTAAACATTTTTGTATGTACATTATTTCATTTATTTG
66 TTTTTATTCATGTAAACATTTTTGTATGTACATTATTTCATTTATTTG
12847084 GGGCTTTTTT
Statistics
Matches: 101, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
137 55 0.54
138 44 0.44
139 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.50
Consensus pattern (138 bp):
TACATAGTTTTAAATATAAATTCTTATTTTTACTATACACTGCATACATATATTTACAAACACAT
TTTTTATTCATGTAAACATTTTTGTATGTACATTATTTCATTTATTTGTGAGTATCTTTGTCTTT
TGCAGTTT
Found at i:12847138 original size:137 final size:137
Alignment explanation
Indices: 12846821--12847139 Score: 364
Period size: 137 Copynumber: 2.3 Consensus size: 137
12846811 CAATTTTTCC
*
12846821 CTTTT-CAATTTTGTACATAGTTTTAAATATAAATTCTTATTTTTACTATACGCTGCATACATAT
1 CTTTTGCAATTTTGTACATAGTTTTAAATATAAA-T-TTATTTTTACTATACACTGCATACATAT
* * *
12846885 ATTTGCAAATACATTTTTATCAATGTAAACATTTTTGTATGTACATTATTTCATTTGTTTGTGAG
64 ATTTACAAACACATTTTTATCAATGTAAACATTTTTGTATGTACATTATTTCATTTATTTGTGAG
12846950 TATCTTTGT
129 TATCTTTGT
* * ** * *
12846959 CTTTTGC-AGTTT-TACATAGTTTTGAATATAAATTCTTATTTTTACTATGTATTGCATACATGT
1 CTTTTGCAATTTTGTACATAGTTTTAAATATAAA-T-TTATTTTTACTATACACTGCATACATAT
*
12847022 ATTTACATACACATTTTTTATTC-ATGTAAACATTTTTGTATGTACATTATTTCATTTATTTG-G
64 ATTTACAAACACA-TTTTTA-TCAATGTAAACATTTTTGTATGTACATTATTTCATTTATTTGTG
* * *
12847085 GGCT-TTTTTTT
127 AG-TATCTTTGT
* *
12847096 TTTTTGCAATTTTGGTACATAAGTTTTAAATATGAATTT-TTTTT
1 CTTTTGCAATTTT-GTACAT-AGTTTTAAATATAAATTTATTTTT
12847140 CATAGAGGTA
Statistics
Matches: 155, Mismatches: 18, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
137 68 0.44
138 63 0.41
139 5 0.03
140 6 0.04
141 13 0.08
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.52
Consensus pattern (137 bp):
CTTTTGCAATTTTGTACATAGTTTTAAATATAAATTTATTTTTACTATACACTGCATACATATAT
TTACAAACACATTTTTATCAATGTAAACATTTTTGTATGTACATTATTTCATTTATTTGTGAGTA
TCTTTGT
Found at i:12848302 original size:8 final size:7
Alignment explanation
Indices: 12848273--12848316 Score: 54
Period size: 8 Copynumber: 6.0 Consensus size: 7
12848263 TGAAAACATG
12848273 AAAGAAA
1 AAAGAAA
12848280 AAA-AAA
1 AAAGAAA
12848286 CAAAGAAA
1 -AAAGAAA
12848294 AAGAGAAA
1 AA-AGAAA
12848302 AAATGAAA
1 AAA-GAAA
12848310 AAAGAAA
1 AAAGAAA
12848317 GATGAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 3 0.09
7 13 0.39
8 17 0.52
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:12850020 original size:22 final size:22
Alignment explanation
Indices: 12849995--12850075 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
12849985 AAACAAAAGA
12849995 ATGATTTATAAGACCTTTGGGC
1 ATGATTTATAAGACCTTTGGGC
*
12850017 ATGATTTGTAAGA-CTTCT-GGC
1 ATGATTTATAAGACCTT-TGGGC
* * * * *
12850038 ATAATTTTTAAGATCTTTGAGT
1 ATGATTTATAAGACCTTTGGGC
12850060 ATGATTTATAAGACCT
1 ATGATTTATAAGACCT
12850076 CCGAGCATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 18 0.38
22 30 0.62
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (22 bp):
ATGATTTATAAGACCTTTGGGC
Found at i:12850436 original size:22 final size:22
Alignment explanation
Indices: 12850411--12850566 Score: 145
Period size: 22 Copynumber: 7.1 Consensus size: 22
12850401 ATCTTTGGGT
12850411 ATTTATAAGACCTCTAAGCATG
1 ATTTATAAGACCTCTAAGCATG
* * * * *
12850433 ATTTAAAAGACTTTTAGGCATA
1 ATTTATAAGACCTCTAAGCATG
*
12850455 ATTTATAAGACCTCCAAGCATG
1 ATTTATAAGACCTCTAAGCATG
* *
12850477 ATTTATAAGA-TTTTCAAGCATG
1 ATTTATAAGACCTCT-AAGCATG
* * *
12850499 ATTTATAATACCTCCAAGCATA
1 ATTTATAAGACCTCTAAGCATG
* * *
12850521 ATCTAAAAGACATCTAAGCATG
1 ATTTATAAGACCTCTAAGCATG
*
12850543 ATTTATAAAACCT-TCAAGCATG
1 ATTTATAAGACCTCT-AAGCATG
12850565 AT
1 AT
12850567 CCATATGACT
Statistics
Matches: 102, Mismatches: 29, Indels: 6
0.74 0.21 0.04
Matches are distributed among these distances:
21 2 0.02
22 99 0.97
23 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (22 bp):
ATTTATAAGACCTCTAAGCATG
Found at i:12850474 original size:44 final size:44
Alignment explanation
Indices: 12850411--12850566 Score: 197
Period size: 44 Copynumber: 3.5 Consensus size: 44
12850401 ATCTTTGGGT
* * *
12850411 ATTTATAAGACCTCTAAGCATGATTTAAAAGACTTTTAGGCATA
1 ATTTATAAGACCTCCAAGCATGATTTAAAAGACTTTTAAGCATG
*
12850455 ATTTATAAGACCTCCAAGCATGATTTATAAGA-TTTTCAAGCATG
1 ATTTATAAGACCTCCAAGCATGATTTAAAAGACTTTT-AAGCATG
* * * * *
12850499 ATTTATAATACCTCCAAGCATAATCTAAAAGACATCTAAGCATG
1 ATTTATAAGACCTCCAAGCATGATTTAAAAGACTTTTAAGCATG
* *
12850543 ATTTATAAAACCTTCAAGCATGAT
1 ATTTATAAGACCTCCAAGCATGAT
12850567 CCATATGACT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
43 4 0.04
44 91 0.94
45 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (44 bp):
ATTTATAAGACCTCCAAGCATGATTTAAAAGACTTTTAAGCATG
Found at i:12850496 original size:66 final size:66
Alignment explanation
Indices: 12850411--12850566 Score: 170
Period size: 66 Copynumber: 2.4 Consensus size: 66
12850401 ATCTTTGGGT
* * ** * * * *
12850411 ATTTATAAGACC-TCTAAGCATGATTTAAAAGACTTTTAGGCATAATTTATAAGACCTCCAAGCA
1 ATTTATAAAACCTTC-AAGCATGATTTAAAAGACCTCCAAGCATAATCTAAAAGACATCCAAGCA
12850475 TG
65 TG
* ** * * *
12850477 ATTTATAAGATTTTCAAGCATGATTTATAATACCTCCAAGCATAATCTAAAAGACATCTAAGCAT
1 ATTTATAAAACCTTCAAGCATGATTTAAAAGACCTCCAAGCATAATCTAAAAGACATCCAAGCAT
12850542 G
66 G
12850543 ATTTATAAAACCTTCAAGCATGAT
1 ATTTATAAAACCTTCAAGCATGAT
12850567 CCATATGACT
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
66 72 0.97
67 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (66 bp):
ATTTATAAAACCTTCAAGCATGATTTAAAAGACCTCCAAGCATAATCTAAAAGACATCCAAGCAT
G
Found at i:12851079 original size:41 final size:41
Alignment explanation
Indices: 12851029--12851136 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
12851019 GAGAAGAGCT
* * *
12851029 TTTTAATTTTTCAAAGTTTCACAACATCTGGTGA-GAGGAACA
1 TTTTAA-TTTTCAAAGTTTCAAAACACCTGGTGATGA-CAACA
* *
12851071 TTTT-ATTTTCAAAAGTTTCAAAACCCCTGGTGATGACAGCA
1 TTTTAATTTTC-AAAGTTTCAAAACACCTGGTGATGACAACA
*
12851112 TTTTAAATTTTCAAAGTTTTAAAAC
1 TTTT-AATTTTCAAAGTTTCAAAAC
12851137 CCTTAATGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
40 5 0.09
41 27 0.48
42 18 0.32
43 6 0.11
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (41 bp):
TTTTAATTTTCAAAGTTTCAAAACACCTGGTGATGACAACA
Found at i:12851198 original size:41 final size:41
Alignment explanation
Indices: 12851064--12851216 Score: 127
Period size: 41 Copynumber: 3.7 Consensus size: 41
12851054 ATCTGGTGAG
* * **
12851064 AGGAA-CATTTT-ATTTTCAAAAGTTTCAAAACCCCTGGTG-
1 AGGAAGCATTTTAAATTTC-AAAGTTTCAAAACCCTTAATGA
* *
12851103 ATGACAGCATTTTAAATTTTCAAAGTTTTAAAACCCTTAATGA
1 AGGA-AGCATTTTAAA-TTTCAAAGTTTCAAAACCCTTAATGA
* * *
12851146 AGGAAGTATTTTAAATTTCAAAGTTGCAAAACCCTTGAT-A
1 AGGAAGCATTTTAAATTTCAAAGTTTCAAAACCCTTAATGA
* *
12851186 AGGGGAGCATTTT-AGTTTCCAAAGTTTCAAA
1 A-GGAAGCATTTTAAATTT-CAAAGTTTCAAA
12851217 GTCTCTATTA
Statistics
Matches: 92, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
39 3 0.03
40 7 0.08
41 47 0.51
42 28 0.30
43 7 0.08
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (41 bp):
AGGAAGCATTTTAAATTTCAAAGTTTCAAAACCCTTAATGA
Found at i:12865283 original size:21 final size:21
Alignment explanation
Indices: 12865245--12865284 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12865235 TGAGGTTTTA
*
12865245 TTTATAATCAAGTGTTATATC
1 TTTATAATCAAGTATTATATC
*
12865266 TTTATAATCAATTATTATA
1 TTTATAATCAAGTATTATA
12865285 CAGGGATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTATAATCAAGTATTATATC
Found at i:12866729 original size:32 final size:32
Alignment explanation
Indices: 12866665--12866731 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
12866655 TTTAGTTGAC
* *
12866665 GCCTAGATTATCTAGCAATAATAAAGTTTTAA
1 GCCTAGATTATCTAGCAACAATAAAGTCTTAA
12866697 GCCTAGATTATCTAG-AACCAATGAAA-TCTTAA
1 GCCTAGATTATCTAGCAA-CAAT-AAAGTCTTAA
12866729 GCC
1 GCC
12866732 CAGTGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 2 0.06
32 26 0.84
33 3 0.10
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (32 bp):
GCCTAGATTATCTAGCAACAATAAAGTCTTAA
Found at i:12866802 original size:82 final size:81
Alignment explanation
Indices: 12866665--12866814 Score: 203
Period size: 82 Copynumber: 1.8 Consensus size: 81
12866655 TTTAGTTGAC
* *
12866665 GCCTAGATTATCTAGCAATAATAAAGTTTTAAGCCTAGATTATCTAGAACCAATGAAATCTTAAG
1 GCCTAGATTATCTAGCAACAATAAAGTCTTAAGCCTAGATTATCTAGAACCAATGAAAT-TTAAG
12866730 CCCAGTGTAATTGGCAA
65 CCCAGTGTAATTGGCAA
* * * ** *
12866747 GCCTAGATTATCT-GACACCAATGAAGTCTTAAGCCTAGATTATCTAGCATTAATGAGATTTAAG
1 GCCTAGATTATCTAG-CAACAATAAAGTCTTAAGCCTAGATTATCTAGAACCAATGAAATTTAAG
12866811 CCCA
65 CCCA
12866815 TATTAGTTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
81 10 0.17
82 49 0.83
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (81 bp):
GCCTAGATTATCTAGCAACAATAAAGTCTTAAGCCTAGATTATCTAGAACCAATGAAATTTAAGC
CCAGTGTAATTGGCAA
Found at i:12866832 original size:22 final size:22
Alignment explanation
Indices: 12866807--12866886 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
12866797 TAATGAGATT
*
12866807 TAAGCCCATATTAGTTGACACA
1 TAAGCCCATATTAGTTGGCACA
**
12866829 TAAGCTTAGT-TTAGTTGGCACA
1 TAAGCCCA-TATTAGTTGGCACA
* * *
12866851 TAAGCCTAGATTAATTGGCACA
1 TAAGCCCATATTAGTTGGCACA
*
12866873 TAAGCCCAAATTAG
1 TAAGCCCATATTAG
12866887 CTAAAAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 46 0.98
23 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (22 bp):
TAAGCCCATATTAGTTGGCACA
Found at i:12867178 original size:34 final size:34
Alignment explanation
Indices: 12867131--12867275 Score: 127
Period size: 34 Copynumber: 4.3 Consensus size: 34
12867121 TTTAAGCCAA
*
12867131 AATTTATTTGGCACCAAAGAAAGATTTTAAACCC
1 AATTTACTTGGCACCAAAGAAAGATTTTAAACCC
* ** * *
12867165 AGTTTACTTGGCACTTGATGAAA-ATTTTAAATCC
1 AATTTACTTGGCAC-CAAAGAAAGATTTTAAACCC
* * **
12867199 AGTTTACTTGGCACCAATGAAAG--TTTAAGTCC
1 AATTTACTTGGCACCAAAGAAAGATTTTAAACCC
** *
12867231 AATTTA-TCTAACACCAAACAAAGATTTTAAACCC
1 AATTTACT-TGGCACCAAAGAAAGATTTTAAACCC
12867265 AATTTACTTGG
1 AATTTACTTGG
12867276 TGCTTGATGA
Statistics
Matches: 87, Mismatches: 18, Indels: 12
0.74 0.15 0.10
Matches are distributed among these distances:
31 1 0.01
32 24 0.28
33 6 0.07
34 50 0.57
35 6 0.07
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.32
Consensus pattern (34 bp):
AATTTACTTGGCACCAAAGAAAGATTTTAAACCC
Found at i:12867354 original size:100 final size:100
Alignment explanation
Indices: 12867142--12867370 Score: 295
Period size: 100 Copynumber: 2.3 Consensus size: 100
12867132 ATTTATTTGG
* *
12867142 CACCAAAGAAAGATTTTAAACCCAGTTTACTTGGCACTTGATGAAAATTTTAAATCCAGTTTACT
1 CACCAAACAAAGATTTTAAACCCAATTTACTTGGCACTTGATGAAAATTTTAAATCCAGTTTACT
* *
12867207 TGGCACCAATGAAAGTTTAAGTCCAATTTATCTAA
66 TAGCACCAATGAAAATTTAAGTCCAATTTATCTAA
** *
12867242 CACCAAACAAAGATTTTAAACCCAATTTACTTGGTGCTTGATGAAAATTTTAAGTCCAGTTTACT
1 CACCAAACAAAGATTTTAAACCCAATTTACTTGGCACTTGATGAAAATTTTAAATCCAGTTTACT
* * *
12867307 TAGCATCAATGAAAATTTGAG-CCTAGTTT-TC-AA
66 TAGCACCAATGAAAATTTAAGTCC-AATTTATCTAA
*
12867340 GCCACTCAAA-AAAGATTTTAAACCTAATTTA
1 --CAC-CAAACAAAGATTTTAAACCCAATTTA
12867371 TCTAGCACCA
Statistics
Matches: 114, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
98 2 0.02
99 4 0.04
100 104 0.91
101 4 0.04
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (100 bp):
CACCAAACAAAGATTTTAAACCCAATTTACTTGGCACTTGATGAAAATTTTAAATCCAGTTTACT
TAGCACCAATGAAAATTTAAGTCCAATTTATCTAA
Found at i:12867428 original size:34 final size:34
Alignment explanation
Indices: 12867346--12867429 Score: 84
Period size: 34 Copynumber: 2.5 Consensus size: 34
12867336 TCAAGCCACT
12867346 CAAA-AAAGATTTTAAACCTAATTTATCTAGCAC
1 CAAAGAAAGATTTTAAACCTAATTTATCTAGCAC
* * * *
12867379 CAAAGAAAAAATTTAACCCTGATTTA-CTTAGCACC
1 CAAAGAAAGATTTTAAACCTAATTTATC-TAGCA-C
*
12867414 CAATG-AAGATTTTAAA
1 CAAAGAAAGATTTTAAA
12867430 GCCCAGCTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
33 5 0.12
34 30 0.75
35 5 0.12
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (34 bp):
CAAAGAAAGATTTTAAACCTAATTTATCTAGCAC
Found at i:12867555 original size:33 final size:33
Alignment explanation
Indices: 12867518--12867610 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 33
12867508 ATTGGCACTG
12867518 AATTTTAATTGTAGTTTATCT-AGCCCTTAATG-A
1 AATTTTAATT-TAGTTTATCTGA-CCCTTAATGAA
**
12867551 AATTTTAAGCCTAGTTTATCTGACCCTTAATGAA
1 AATTTTAA-TTTAGTTTATCTGACCCTTAATGAA
* *
12867585 AATTTTAAGTTCAGTTTATCTTACCC
1 AATTTTAA-TTTAGTTTATCTGACCC
12867611 CAATGTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
33 27 0.53
34 24 0.47
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (33 bp):
AATTTTAATTTAGTTTATCTGACCCTTAATGAA
Found at i:12867593 original size:34 final size:31
Alignment explanation
Indices: 12867529--12867610 Score: 101
Period size: 34 Copynumber: 2.5 Consensus size: 31
12867519 ATTTTAATTG
12867529 TAGTTTATCTAGCCCTTAATGAAATTTTAAGCC
1 TAGTTTATCTA-CCCTTAATGAAATTTTAAG-C
*
12867562 TAGTTTATCTGACCCTTAATGAAAATTTTAAGT
1 TAGTTTATCT-ACCCTTAATG-AAATTTTAAGC
12867595 TCAGTTTATCTTACCC
1 T-AGTTTATC-TACCC
12867611 CAATGTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
33 20 0.45
34 23 0.52
35 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.41
Consensus pattern (31 bp):
TAGTTTATCTACCCTTAATGAAATTTTAAGC
Found at i:12867938 original size:35 final size:35
Alignment explanation
Indices: 12867899--12868376 Score: 193
Period size: 35 Copynumber: 13.7 Consensus size: 35
12867889 GATCGTTTTC
* *
12867899 TTATTTTTTAACTTACGATTCAATCCCAATCATCT
1 TTATTTTTTGACTTACGATTCAATCTCAATCATCT
* * * * *
12867934 TTATTTTTTGACTTATGGTTCAATTTTAGTCAT-T
1 TTATTTTTTGACTTACGATTCAATCTCAATCATCT
* * * * *
12867968 TTCATTCTTTGACTTACGACTCAGTCTCAGTCATTT
1 TT-ATTTTTTGACTTACGATTCAATCTCAATCATCT
* * * * *
12868004 TTATTCTTCGACTTACAATTCAATCTCGATTATCT
1 TTATTTTTTGACTTACGATTCAATCTCAATCATCT
* * *
12868039 TTATTTTTTGACTCT-CAGCTT-AATCTTAATGATCT
1 TTATTTTTTGACT-TAC-GATTCAATCTCAATCATCT
** * ** * ** *
12868074 TTATCCTTTGACGTGTGATTTAATCTTGATCATTT
1 TTATTTTTTGACTTACGATTCAATCTCAATCATCT
* * * * * * *
12868109 TTATTTTTTGATTTACGACTCAGTTTCGATTATTT
1 TTATTTTTTGACTTACGATTCAATCTCAATCATCT
* * * * * *
12868144 TTATTCTTCGACTTGCAATTCAATCCCGATCATCT
1 TTATTTTTTGACTTACGATTCAATCTCAATCATCT
* * * *
12868179 TTATTTTTTGACTTTCGACTT-AGTTTCAATTATCT
1 TTATTTTTTGACTTACGA-TTCAATCTCAATCATCT
** * * * *
12868214 TTATCCTTTGACTTACGGTTCAATCTCAGTCTTTT
1 TTATTTTTTGACTTACGATTCAATCTCAATCATCT
* * * * * * *
12868249 TTTTTTTTTAACTT--GTAGCTCAGTCCCAAGCTTCT
1 TTATTTTTTGACTTACG-A-TTCAATCTCAATCATCT
* * *
12868284 TTATTTTTTAACTTAC-AGTTTAAT-TCTGATCATCT
1 TTATTTTTTGACTTACGA-TTCAATCTC-AATCATCT
* * * *
12868319 TTATTTTTTGACTCT-CCATTTAGTCCCAATCAT-T
1 TTATTTTTTGACT-TACGATTCAATCTCAATCATCT
* *
12868353 TTATCTTTTGACTTACGGTTCAAT
1 TTATTTTTTGACTTACGATTCAAT
12868377 TCCAGTTATT
Statistics
Matches: 319, Mismatches: 107, Indels: 35
0.69 0.23 0.08
Matches are distributed among these distances:
33 2 0.01
34 28 0.09
35 278 0.87
36 11 0.03
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.50
Consensus pattern (35 bp):
TTATTTTTTGACTTACGATTCAATCTCAATCATCT
Found at i:12868049 original size:70 final size:70
Alignment explanation
Indices: 12867975--12868240 Score: 230
Period size: 70 Copynumber: 3.8 Consensus size: 70
12867965 ATTTTCATTC
* * * * *
12867975 TTTGACTTACGACTCAGTCTCAGTCATTTTTATTCTTCGACTTACAATTCAATCTCGATTATCTT
1 TTTGACTTACGACTCAGTCTCAATTATCTTTATCCTTCGACTTACAATTCAATCTCGATCATCTT
12868040 TATTT
66 TATTT
* * * * * * *** * * *
12868045 TTTGACTCT-C-AGCTTAATCTTAATGATCTTTATCCTTTGACGTGTGATTTAATCTTGATCATT
1 TTTGACT-TACGA-CTCAGTCTCAATTATCTTTATCCTTCGACTTACAATTCAATCTCGATCATC
12868108 TTTATTT
64 TTTATTT
* * * * * * *
12868115 TTTGATTTACGACTCAGTTTCGATTATTTTTATTCTTCGACTTGCAATTCAATCCCGATCATCTT
1 TTTGACTTACGACTCAGTCTCAATTATCTTTATCCTTCGACTTACAATTCAATCTCGATCATCTT
12868180 TATTT
66 TATTT
* * * * **
12868185 TTTGACTTTCGACTTAGTTTCAATTATCTTTATCCTTTGACTTACGGTTCAATCTC
1 TTTGACTTACGACTCAGTCTCAATTATCTTTATCCTTCGACTTACAATTCAATCTC
12868241 AGTCTTTTTT
Statistics
Matches: 148, Mismatches: 44, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
69 2 0.01
70 144 0.97
71 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.10, T:0.49
Consensus pattern (70 bp):
TTTGACTTACGACTCAGTCTCAATTATCTTTATCCTTCGACTTACAATTCAATCTCGATCATCTT
TATTT
Found at i:12868239 original size:140 final size:142
Alignment explanation
Indices: 12867925--12868376 Score: 392
Period size: 140 Copynumber: 3.2 Consensus size: 142
12867915 GATTCAATCC
** *
12867925 CAATCATCTTTATTTTTTGACTTATGGTTCAAT-TTTAGTCATTTTCATTCTTTGACTTACGACT
1 CAATCATCTTTATCCTTTGACTTATGGTTCAATCTTGAGTCATTTTCATTCTTTGACTTACGACT
* *
12867989 CAGTCTCAGTCATTTTTATTCTTCGACTTACAATTCAATCTCGATTATCTTTATTTTTTGACTCT
66 CAGTCTCAGTCATTTTTATTCTTCGACTTACAATTCAATCCCGATCATCTTTATTTTTTGACTCT
12868054 CAGCTTAATCTT
131 CAGCTTAATCTT
* * * * * * * *
12868066 -AATGATCTTTATCCTTTGACGTGTGATTTAATCTTGA-TCATTTTTATTTTTTGATTTACGACT
1 CAATCATCTTTATCCTTTGACTTATGGTTCAATCTTGAGTCATTTTCATTCTTTGACTTACGACT
* * * *
12868129 CAGTTTC-GATTATTTTTATTCTTCGACTTGCAATTCAATCCCGATCATCTTTATTTTTTGACTT
66 CAGTCTCAG-TCATTTTTATTCTTCGACTTACAATTCAATCCCGATCATCTTTATTTTTTGACTC
*
12868193 TC-GACTTAGT-TT
130 TCAG-CTTAATCTT
* * * * ** * *
12868205 CAATTATCTTTATCCTTTGACTTACGGTTCAATC-TCAGTCTTTTTTTTTTTTTAACTT--GTAG
1 CAATCATCTTTATCCTTTGACTTATGGTTCAATCTTGAGTCATTTTCATTCTTTGACTTACG-A-
* * ** * * * *
12868267 CTCAGTCCCAAG-C-TTCTTTATTTTTTAACTTACAGTTTAATTCTGATCATCTTTATTTTTTGA
64 CTCAGTCTC-AGTCATT-TTTATTCTTCGACTTACAATTCAATCCCGATCATCTTTATTTTTTGA
* * *
12868330 CTCTCCA-TTTAGTC-C
127 CTCT-CAGCTTAATCTT
* *
12868345 CAATCAT-TTTATCTTTTGACTTACGGTTCAAT
1 CAATCATCTTTATCCTTTGACTTATGGTTCAAT
12868377 TCCAGTTATT
Statistics
Matches: 253, Mismatches: 45, Indels: 28
0.78 0.14 0.09
Matches are distributed among these distances:
138 1 0.00
139 33 0.13
140 214 0.85
141 4 0.02
142 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (142 bp):
CAATCATCTTTATCCTTTGACTTATGGTTCAATCTTGAGTCATTTTCATTCTTTGACTTACGACT
CAGTCTCAGTCATTTTTATTCTTCGACTTACAATTCAATCCCGATCATCTTTATTTTTTGACTCT
CAGCTTAATCTT
Found at i:12868445 original size:139 final size:140
Alignment explanation
Indices: 12867922--12868463 Score: 329
Period size: 140 Copynumber: 3.9 Consensus size: 140
12867912 TACGATTCAA
** * * * * * * * *
12867922 TCCCAATCATCTTTATTTTTTGACTTATGGTTCAATTTTAGTCATTTTCATTCTTTGACTTAC-G
1 TCCCAATCATCTTTATCCTTTGACTTACGGTTCAATCTCAGTCTTTTTTATTTTTTAACTTGCAG
* ** * * * * *
12867986 ACTCAGTCTCAGTCATT-TTTATTCTTCGACTTACAATTCAATCTCGATTATCTTTATTTTTTGA
66 -CTCAGTCCCAAAC-TTATTTATTCTTCAACTTACAGTTTAATCTTGATCATCTTTATTTTTTGA
*
12868050 CTCT-CAGCTTAA
129 CTCTCCA-CTTAG
** * * ** * * * * * * *
12868062 TCTTAATGATCTTTATCCTTTGACGTGTGATTTAATCT-TGATCATTTTTATTTTTTGATTTAC-
1 TCCCAATCATCTTTATCCTTTGACTTACGGTTCAATCTCAG-TCTTTTTTATTTTTTAACTTGCA
** * * * * * **
12868125 GACTCAGTTTC-GA-TTATTTTTATTCTTCGACTTGCAATTCAATCCCGATCATCTTTATTTTTT
65 G-CTCAGTCCCAAACTTA--TTTATTCTTCAACTTACAGTTTAATCTTGATCATCTTTATTTTTT
* *
12868188 GACTTTCGACTTAG
127 GACTCTCCACTTAG
** * * *
12868202 TTTCAATTATCTTTATCCTTTGACTTACGGTTCAATCTCAGTCTTTTTTTTTTTTTAACTTGTAG
1 TCCCAATCATCTTTATCCTTTGACTTACGGTTCAATCTCAGTCTTTTTTATTTTTTAACTTGCAG
* * * *
12868267 CTCAGTCCCAAGCTTCTTTATTTTTTAACTTACAGTTTAAT-TCTGATCATCTTTATTTTTTGAC
66 CTCAGTCCCAAACTTATTTATTCTTCAACTTACAGTTTAATCT-TGATCATCTTTATTTTTTGAC
*
12868331 TCTCCATTTAG
130 TCTCCACTTAG
*
12868342 TCCCAATCAT-TTTATCTTTTGACTTACGGTTCAAT-TCCAGT-TATTTTTATTTTTTAACTTGC
1 TCCCAATCATCTTTATCCTTTGACTTACGGTTCAATCT-CAGTCT-TTTTTATTTTTTAACTTGC
* * * * * *
12868404 AGCTTAGT-TCAAATTATATTTATTCTTCAGCTCGTA-A-TTTAATCTTAATCATTTTTATTT
64 AGCTCAGTCCCAAACT-TATTTATTCTTCAACT--TACAGTTTAATCTTGATCATCTTTATTT
12868464 CATGACTTGT
Statistics
Matches: 317, Mismatches: 69, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
137 2 0.01
138 6 0.02
139 85 0.27
140 217 0.68
141 5 0.02
142 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (140 bp):
TCCCAATCATCTTTATCCTTTGACTTACGGTTCAATCTCAGTCTTTTTTATTTTTTAACTTGCAG
CTCAGTCCCAAACTTATTTATTCTTCAACTTACAGTTTAATCTTGATCATCTTTATTTTTTGACT
CTCCACTTAG
Found at i:12868615 original size:6 final size:6
Alignment explanation
Indices: 12868604--12868630 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12868594 TTTTTCAAAG
12868604 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
12868631 CAAAACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:12868938 original size:22 final size:23
Alignment explanation
Indices: 12868896--12868938 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12868886 TGAATTAATT
* *
12868896 ATTTTGAATTTAATTTTATTATC
1 ATTTAGAATTTAATTTAATTATC
12868919 ATTTAGAATTT-ATTTAATTA
1 ATTTAGAATTTAATTTAATTA
12868939 ATAGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (23 bp):
ATTTAGAATTTAATTTAATTATC
Found at i:12878320 original size:16 final size:17
Alignment explanation
Indices: 12878299--12878331 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12878289 AGAAATAAGA
12878299 TATTTTA-CATTAAATT
1 TATTTTATCATTAAATT
12878315 TATTTTATCATTAAATT
1 TATTTTATCATTAAATT
12878332 CTAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTATCATTAAATT
Found at i:12887131 original size:11 final size:11
Alignment explanation
Indices: 12887115--12887145 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
12887105 AATCCCATAA
12887115 GAGATTTGTTT
1 GAGATTTGTTT
12887126 GAGATTTGTTT
1 GAGATTTGTTT
12887137 GAGATTTGT
1 GAGATTTGT
12887146 CAGATATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:12887257 original size:52 final size:52
Alignment explanation
Indices: 12887170--12887326 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
12887160 TGGATAAAAA
* * * *
12887170 GACTTGCAAAAGAAGAATT-T-CAAGAGAAAGAAGATTTTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAG-GAAAG-AGATTCTTAATAGGCAAGTTT
12887222 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
* * * * *
12887274 GACTTACAGGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
12887326 G
1 G
12887327 TATGGTTATA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 85 0.90
53 6 0.06
54 3 0.03
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:12887837 original size:31 final size:31
Alignment explanation
Indices: 12887802--12887917 Score: 153
Period size: 31 Copynumber: 3.7 Consensus size: 31
12887792 AGGTTTTTAG
*
12887802 CCCAACAAATGGTATCGGAGCTGTGGTGTTT
1 CCCAACAAATGGTATCAGAGCTGTGGTGTTT
*
12887833 CCCAACAAATGGTATCAGAGCTATGGTG-TT
1 CCCAACAAATGGTATCAGAGCTGTGGTGTTT
* * * *
12887863 CCTTAATAAACGGTATCAGAGCTGTGGTGTTC
1 CC-CAACAAATGGTATCAGAGCTGTGGTGTTT
*
12887895 CCCAACAAGTGGTATCAGAGCTG
1 CCCAACAAATGGTATCAGAGCTG
12887918 AAGGTTTGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
30 4 0.06
31 65 0.90
32 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (31 bp):
CCCAACAAATGGTATCAGAGCTGTGGTGTTT
Found at i:12887963 original size:25 final size:25
Alignment explanation
Indices: 12887911--12887970 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
12887901 AAGTGGTATC
* *
12887911 AGAGCTGAAGGTTTGAAATGTGAGA
1 AGAGCTGAAGATTTAAAATGTGAGA
*
12887936 AGAGTTGAAGATTTAAAATGTG-GAA
1 AGAGCTGAAGATTTAAAATGTGAG-A
*
12887961 AGAGCCGAAG
1 AGAGCTGAAG
12887971 GTTCGAGACG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 1 0.03
25 28 0.97
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.22
Consensus pattern (25 bp):
AGAGCTGAAGATTTAAAATGTGAGA
Found at i:12888269 original size:11 final size:11
Alignment explanation
Indices: 12888253--12888283 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
12888243 AATCCCATAA
12888253 GAGATTTGTTT
1 GAGATTTGTTT
12888264 GAGATTTGTTT
1 GAGATTTGTTT
12888275 GAGATTTGT
1 GAGATTTGT
12888284 CAGATATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:12888395 original size:52 final size:52
Alignment explanation
Indices: 12888308--12888464 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
12888298 TGGATAAAAA
* * * *
12888308 GACTTGCAAAAGAAGAATT-T-CAAGAGAAAGAAGATTTTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAG-GAAAG-AGATTCTTAATAGGCAAGTTT
12888360 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
* * * * *
12888412 GACTTACAGGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
12888464 G
1 G
12888465 TATGGTTATA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 85 0.90
53 6 0.06
54 3 0.03
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:12892179 original size:3 final size:3
Alignment explanation
Indices: 12892166--12892198 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
12892156 CTAGTTTTAG
12892166 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
12892199 TTTGGCAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:12899655 original size:11 final size:11
Alignment explanation
Indices: 12899639--12899664 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12899629 ATTTTCAACA
12899639 AAAAAAATAAT
1 AAAAAAATAAT
12899650 AAAAAAATAAT
1 AAAAAAATAAT
12899661 AAAA
1 AAAA
12899665 CCTTTTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:12903674 original size:20 final size:20
Alignment explanation
Indices: 12903649--12903688 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12903639 GTGAATGAAT
12903649 GAAAAAA-AAAAGACAAAAAA
1 GAAAAAAGAAAAGA-AAAAAA
*
12903669 GAAAAAAGAAGAGAAAAAAA
1 GAAAAAAGAAAAGAAAAAAA
12903689 AATGGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (20 bp):
GAAAAAAGAAAAGAAAAAAA
Found at i:12903675 original size:19 final size:19
Alignment explanation
Indices: 12903651--12903687 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12903641 GAATGAATGA
12903651 AAAAAAAAAGACAAAAAAG
1 AAAAAAAAAGACAAAAAAG
* *
12903670 AAAAAAGAAGAGAAAAAA
1 AAAAAAAAAGACAAAAAA
12903688 AAATGGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGACAAAAAAG
Found at i:12905614 original size:42 final size:42
Alignment explanation
Indices: 12905550--12905979 Score: 364
Period size: 42 Copynumber: 10.0 Consensus size: 42
12905540 GATTGTCGAA
* * * *
12905550 GAGCAATTTATTTTTCTAAAGTTTTGTTACCTCTATTTAGAT
1 GAGCCATTTATTTTTCCAAAGTTTTGTTGCCTCTATTTAGAG
*
12905592 GAGCCATTTATTTTTCCAAAGTTTTGTTGCTTTGTTGCCTCTATTTAAAG
1 GAGCCATTTATTTTTCCAAA-----G-T--TTTGTTGCCTCTATTTAGAG
* * * * *
12905642 GAACCATTTATTTTTTCAAAGTTATGTTACGTCTATTTAGAG
1 GAGCCATTTATTTTTCCAAAGTTTTGTTGCCTCTATTTAGAG
* * * *
12905684 CAGGCATTTATTTTTCTAAAGTTGTGTTGCCTCTATTTAGAG
1 GAGCCATTTATTTTTCCAAAGTTTTGTTGCCTCTATTTAGAG
* * * * * *
12905726 GAGCAATTTATTTTTCCACAA-TTCTGTTACCTATATTCAGAT
1 GAGCCATTTATTTTTCCA-AAGTTTTGTTGCCTCTATTTAGAG
* * * *
12905768 AAGCAATTTATTTTTCCAAAGTTTTGTTGCCTATATTTATAG
1 GAGCCATTTATTTTTCCAAAGTTTTGTTGCCTCTATTTAGAG
* *
12905810 GAGCCATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAG
1 GAGCCATTTATTTTTCCAAAGTTTTGTTGCCTCTATTTAGAG
* * *
12905852 CAGCCATTTATTTTT-CAAAGTTGTGGTTGCCTTTATTTAGAG
1 GAGCCATTTATTTTTCCAAAGTT-TTGTTGCCTCTATTTAGAG
* ** ** * *
12905894 GAGCAATTTATTTTTTAAAAAAATCTGTTGCCTCTGTTTAGAG
1 GAGCCATTTA-TTTTTCCAAAGTTTTGTTGCCTCTATTTAGAG
* *
12905937 GAG-CAGTTTATTTTTCTAAAAGTTGTTG-AGCCTCTATTTAGAG
1 GAGCCA-TTTATTTTTC-CAAAGTT-TTGTTGCCTCTATTTAGAG
12905980 AAGCTTTGTT
Statistics
Matches: 312, Mismatches: 60, Indels: 31
0.77 0.15 0.08
Matches are distributed among these distances:
41 9 0.03
42 211 0.68
43 47 0.15
44 7 0.02
45 1 0.00
47 1 0.00
48 1 0.00
50 35 0.11
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (42 bp):
GAGCCATTTATTTTTCCAAAGTTTTGTTGCCTCTATTTAGAG
Found at i:12905649 original size:50 final size:50
Alignment explanation
Indices: 12905572--12905669 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 50
12905562 TTTCTAAAGT
* * * *
12905572 TTTGTTACCTCTATTTAGATGAGCCATTTATTTTTCCAAAGTTTTGTTGC
1 TTTGTTACCTCTATTTAAAGGAACCATTTATTTTTCCAAAGTTATGTTGC
* *
12905622 TTTGTTGCCTCTATTTAAAGGAACCATTTATTTTTTCAAAGTTATGTT
1 TTTGTTACCTCTATTTAAAGGAACCATTTATTTTTCCAAAGTTATGTT
12905670 ACGTCTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.50
Consensus pattern (50 bp):
TTTGTTACCTCTATTTAAAGGAACCATTTATTTTTCCAAAGTTATGTTGC
Found at i:12906725 original size:15 final size:15
Alignment explanation
Indices: 12906703--12906740 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
12906693 AGGTTCTGTT
12906703 AGAAAGAGAGGG-AG
1 AGAAAGAGAGGGAAG
12906717 AGAAA-AGAGGGGAAG
1 AGAAAGAGA-GGGAAG
12906732 AGAAAGAGA
1 AGAAAGAGA
12906741 ATGAAGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.14
14 8 0.38
15 7 0.33
16 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (15 bp):
AGAAAGAGAGGGAAG
Found at i:12907043 original size:17 final size:15
Alignment explanation
Indices: 12907023--12907080 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
12907013 CAAATTTTTT
12907023 TATTTATTTTATTTACG
1 TATTT-TTTTATTTA-G
* *
12907040 TATTTTATTTATGTATT
1 TATTTT-TTTATTTA-G
12907057 TATTTTTTTTATTTAG
1 TA-TTTTTTTATTTAG
12907073 TATTTTTT
1 TATTTTTT
12907081 CCTTTTCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 6 0.18
16 3 0.09
17 21 0.62
18 4 0.12
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (15 bp):
TATTTTTTTATTTAG
Found at i:12907071 original size:13 final size:13
Alignment explanation
Indices: 12907016--12907061 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
12907006 CCGCTTTCAA
*
12907016 ATTTT-TTTATTT
1 ATTTTATTTATGT
*
12907028 ATTTTATTTACGT
1 ATTTTATTTATGT
12907041 ATTTTATTTATGT
1 ATTTTATTTATGT
12907054 A-TTTATTT
1 ATTTTATTT
12907062 TTTTTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 12 0.40
13 18 0.60
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (13 bp):
ATTTTATTTATGT
Found at i:12907086 original size:20 final size:21
Alignment explanation
Indices: 12907016--12907086 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
12907006 CCGCTTTCAA
*
12907016 ATTT-TTTTATTTATTTTATTT
1 ATTTCTTTTATTTA-TGTATTT
** *
12907037 ACGTATTTTATTTATGTATTT
1 ATTTCTTTTATTTATGTATTT
*
12907058 ATTTTTTTTATTTA-GTATTT
1 ATTTCTTTTATTTATGTATTT
12907078 -TTTCCTTTT
1 ATTT-CTTTT
12907087 CTATTAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 3 0.07
20 10 0.24
21 19 0.46
22 9 0.22
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (21 bp):
ATTTCTTTTATTTATGTATTT
Found at i:12907086 original size:21 final size:21
Alignment explanation
Indices: 12907017--12907077 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
12907007 CGCTTTCAAA
* *
12907017 TTTTTTTATTTATTTTATTTAC
1 TTTTTTTATTTA-TGTATTTAT
* *
12907039 GTATTTTATTTATGTATTTAT
1 TTTTTTTATTTATGTATTTAT
12907060 TTTTTTTATTTA-GTATTT
1 TTTTTTTATTTATGTATTT
12907078 TTTCCTTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 6 0.18
21 17 0.52
22 10 0.30
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTTTTATTTATGTATTTAT
Found at i:12907330 original size:8 final size:9
Alignment explanation
Indices: 12907301--12907332 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
12907291 AAACAAATGA
12907301 AAAAAT-AT
1 AAAAATAAT
12907309 AAAAATAAT
1 AAAAATAAT
12907318 AAAAATAAT
1 AAAAATAAT
12907327 AAAAAT
1 AAAAAT
12907333 TTTGAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAATAAT
Found at i:12907450 original size:210 final size:205
Alignment explanation
Indices: 12907097--12907497 Score: 465
Period size: 210 Copynumber: 1.9 Consensus size: 205
12907087 CTATTAAATT
* ** *
12907097 AAATAAAAAATAATAAAAATAAATATTTTGAGAATAAATATTAATTATCCAATGATGGAATTTAT
1 AAATAAAAAATAATAAAAATAAAAATTTTGAGAATAAATACAAATTATCCAAGGATGGAATTTAT
* * * *
12907162 AAAAATTTCAAATAGTAAGTTCTATAAAATTCTTAGGTGATAAATTTTATCTAAATTTGTCCAAA
66 AAAAATTTCAAATAGTAAGTTCTATAAAATTCTTAGGTGAGAAATTTCATATAAATTTGGCCAAA
* *
12907227 ATGGTGGAATAATTTAGATAAAGTTTCAATAACAA-TAATTACTATT-TATTTTTAAACAAAAAA
131 ATGGTGAAATAATTTAGATAAAGTTTCAATAA-AAGTAATT-CTATTCT-TTTCTAAACAAAAAA
12907290 TAAACAAATGAAA
193 TAAACAAATGAAA
*
12907303 AAATATAAAAATAATAAAAATAATAAAAATTTTGA-ATTAAATACAAATTATCCAAGGAT-GAGA
1 AAATA-AAAAATAAT--AAA-AATAAAAATTTTGAGAATAAATACAAATTATCCAAGGATGGA-A
* * * *
12907366 TTCT-TAGAAATTTCAAATGGTAAATTTCTA-AGAAA-TCTCTAGGTGAGAAATTTCCTATAAAT
61 TT-TATAAAAATTTCAAATAGT-AAGTTCTATA-AAATTCT-TAGGTGAGAAATTTCATATAAAT
* * * * *
12907428 TTGGCCCAAATTGTGAAATAATTTAGATGAAGTTTCCATAAAAGTAATTGTATTCTTTTCTAAAC
122 TTGGCCAAAATGGTGAAATAATTTAGATAAAGTTTCAATAAAAGTAATTCTATTCTTTTCTAAAC
12907493 AAAAA
187 AAAAA
12907498 CTTTTGGTTG
Statistics
Matches: 164, Mismatches: 20, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
206 5 0.03
207 9 0.05
208 2 0.01
209 64 0.39
210 84 0.51
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (205 bp):
AAATAAAAAATAATAAAAATAAAAATTTTGAGAATAAATACAAATTATCCAAGGATGGAATTTAT
AAAAATTTCAAATAGTAAGTTCTATAAAATTCTTAGGTGAGAAATTTCATATAAATTTGGCCAAA
ATGGTGAAATAATTTAGATAAAGTTTCAATAAAAGTAATTCTATTCTTTTCTAAACAAAAAATAA
ACAAATGAAA
Found at i:12917316 original size:14 final size:14
Alignment explanation
Indices: 12917297--12917325 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12917287 TAAACGCTGC
12917297 AAATATATATATAT
1 AAATATATATATAT
12917311 AAATATATATATAT
1 AAATATATATATAT
12917325 A
1 A
12917326 TAAAGGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATATATAT
Found at i:12922212 original size:58 final size:58
Alignment explanation
Indices: 12922149--12922265 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
12922139 GTTGGCTGAA
12922149 CCAAATATATTTGTGTGTTTTTATTATTGATTTGAGCTTGTTATTTTGTGTGTGGTTG
1 CCAAATATATTTGTGTGTTTTTATTATTGATTTGAGCTTGTTATTTTGTGTGTGGTTG
*
12922207 CCAAATATATTTGTGTGTTTTTATTCTTGATTTGAGCTTGTTATTTTGTGTGTGGTTG
1 CCAAATATATTTGTGTGTTTTTATTATTGATTTGAGCTTGTTATTTTGTGTGTGGTTG
12922265 C
1 C
12922266 TGCGCGTGGG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.16, C:0.07, G:0.22, T:0.55
Consensus pattern (58 bp):
CCAAATATATTTGTGTGTTTTTATTATTGATTTGAGCTTGTTATTTTGTGTGTGGTTG
Found at i:12926238 original size:22 final size:22
Alignment explanation
Indices: 12926213--12926340 Score: 114
Period size: 22 Copynumber: 5.7 Consensus size: 22
12926203 TTTCTTATTT
*
12926213 AATGATAATTTAGTAGTTAATC
1 AATGATAATTTAATAGTTAATC
* * * * *
12926235 AATGAAAACTTAAAAGTAAATA
1 AATGATAATTTAATAGTTAATC
12926257 AAT-ATAACTTTAATAGTAATTAATC
1 AATGATAA-TTTAATAG---TTAATC
** *
12926282 AACAATAACTTAATAGTTAATC
1 AATGATAATTTAATAGTTAATC
*
12926304 AATGATAATTTAATAGTAAATC
1 AATGATAATTTAATAGTTAATC
*
12926326 ATTGATAATTTAATA
1 AATGATAATTTAATA
12926341 TAAAAAATGG
Statistics
Matches: 83, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.04
22 63 0.76
25 13 0.16
26 4 0.05
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (22 bp):
AATGATAATTTAATAGTTAATC
Found at i:12926280 original size:47 final size:47
Alignment explanation
Indices: 12926223--12926322 Score: 123
Period size: 47 Copynumber: 2.1 Consensus size: 47
12926213 AATGATAATT
* *
12926223 TAGTAGTTAATCAATGAA-AACTTAAAAGTAAATAAAT-ATAACTTTAA
1 TAGTAATTAATCAA-CAATAACTTAAAAGTAAATAAATGATAA-TTTAA
* * *
12926270 TAGTAATTAATCAACAATAACTTAATAGTTAATCAATGATAATTTAA
1 TAGTAATTAATCAACAATAACTTAAAAGTAAATAAATGATAATTTAA
12926317 TAGTAA
1 TAGTAA
12926323 ATCATTGATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
46 2 0.04
47 40 0.87
48 4 0.09
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.34
Consensus pattern (47 bp):
TAGTAATTAATCAACAATAACTTAAAAGTAAATAAATGATAATTTAA
Found at i:12926529 original size:22 final size:22
Alignment explanation
Indices: 12926423--12926522 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
12926413 TCAAAAATTA
*
12926423 AATAGTAAATCAATGATAACAT
1 AATAGTAAATCATTGATAACAT
* * *
12926445 AATTGTAAAT-TTATAATAACAT
1 AATAGTAAATCAT-TGATAACAT
* * *
12926467 AACAATAAATCATTGATAA-TT
1 AATAGTAAATCATTGATAACAT
* * *
12926488 TATATGTAAATTATTGATAACTT
1 AATA-GTAAATCATTGATAACAT
12926511 AATAGTAAATCA
1 AATAGTAAATCA
12926523 CTAATAATTA
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
21 3 0.05
22 49 0.84
23 6 0.10
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (22 bp):
AATAGTAAATCATTGATAACAT
Found at i:12926659 original size:22 final size:21
Alignment explanation
Indices: 12926634--12926803 Score: 117
Period size: 22 Copynumber: 7.8 Consensus size: 21
12926624 ACTTTATAAC
12926634 AAATCATCAATAACTTAGTAGT
1 AAATCAT-AATAACTTAGTAGT
* * * *
12926656 AAATTATCAACAATTTTGTAGT
1 AAATCAT-AATAACTTAGTAGT
* *
12926678 AAATCAATCATAAATTAGTAGT
1 AAATC-ATAATAACTTAGTAGT
* * *
12926700 AAATCAATACTAATTTAGTATT
1 AAATC-ATAATAACTTAGTAGT
* * * *
12926722 AAATAATGATAATTTAATAGT
1 AAATCATAATAACTTAGTAGT
*
12926743 ATAA-CATTAATAGCTTAGTAGT
1 A-AATCA-TAATAACTTAGTAGT
* *
12926765 AAATCATTAATAACATAATAGT
1 AAATCA-TAATAACTTAGTAGT
12926787 AAATCAATAATAACTTA
1 AAATC-ATAATAACTTA
12926804 ATTGTTAATC
Statistics
Matches: 116, Mismatches: 27, Indels: 10
0.76 0.18 0.07
Matches are distributed among these distances:
21 16 0.14
22 97 0.84
23 3 0.03
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35
Consensus pattern (21 bp):
AAATCATAATAACTTAGTAGT
Found at i:12926715 original size:44 final size:44
Alignment explanation
Indices: 12926667--12926795 Score: 120
Period size: 43 Copynumber: 3.0 Consensus size: 44
12926657 AATTATCAAC
* *
12926667 AATTTTGTAGTAAATCAATCATAAATTAGTAGTAAATCAATACT
1 AATTTAGTAGTAAATCAATCATAAATTAATAGTAAATCAATACT
* * * * *
12926711 AATTTAGTATTAAAT-AATGATAATTTAATAGTATAA-CATTAAT
1 AATTTAGTAGTAAATCAATCATAAATTAATAGTA-AATCAATACT
** * *
12926754 AGCTTAGTAGTAAATCATTAATAACA-TAATAGTAAATCAATA
1 AATTTAGTAGTAAATCAATCATAA-ATTAATAGTAAATCAATA
12926796 ATAACTTAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
43 34 0.51
44 33 0.49
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (44 bp):
AATTTAGTAGTAAATCAATCATAAATTAATAGTAAATCAATACT
Found at i:12926798 original size:44 final size:43
Alignment explanation
Indices: 12926673--12926823 Score: 126
Period size: 44 Copynumber: 3.5 Consensus size: 43
12926663 CAACAATTTT
* * * *
12926673 GTAGTAAATCAATCATAAATTAGTAGTAAATCAATACTAATTTA
1 GTAGTAAATCAATGATAAA-TAATAGTAAATCAATAATAACTTA
* * * *
12926717 GTATTAAAT-AATGATAATTTAATAGTATAA-CATTAATAGCTTA
1 GTAGTAAATCAATGATAA-ATAATAGTA-AATCAATAATAACTTA
* *
12926760 GTAGTAAATCATTAATAACATAATAGTAAATCAATAATAACTTA
1 GTAGTAAATCAATGATAA-ATAATAGTAAATCAATAATAACTTA
* * * *
12926804 ATTGTTAATCATTGATAAAT
1 GTAGTAAATCAATGATAAAT
12926824 TTTTTTAAAC
Statistics
Matches: 84, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
43 35 0.42
44 49 0.58
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (43 bp):
GTAGTAAATCAATGATAAATAATAGTAAATCAATAATAACTTA
Found at i:12926821 original size:22 final size:22
Alignment explanation
Indices: 12926736--12926821 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
12926726 AATGATAATT
* *
12926736 TAATAGTATAA-CATTAATAGCT
1 TAATAGTA-AATCATTAATAACA
*
12926758 TAGTAGTAAATCATTAATAACA
1 TAATAGTAAATCATTAATAACA
* *
12926780 TAATAGTAAATCAATAATAACT
1 TAATAGTAAATCATTAATAACA
* * *
12926802 TAATTGTTAATCATTGATAA
1 TAATAGTAAATCATTAATAA
12926822 ATTTTTTTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 2 0.04
22 51 0.96
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (22 bp):
TAATAGTAAATCATTAATAACA
Found at i:12928702 original size:23 final size:24
Alignment explanation
Indices: 12928657--12928702 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
12928647 ACAAATCTTG
*
12928657 AATTATACTTTGTCATAACATAAA
1 AATTATACTTTGTCATAAAATAAA
*
12928681 AATTATTCTTT-TCATAAAATAA
1 AATTATACTTTGTCATAAAATAA
12928703 TGGAATCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (24 bp):
AATTATACTTTGTCATAAAATAAA
Found at i:12929482 original size:21 final size:21
Alignment explanation
Indices: 12929453--12929521 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
12929443 TAATGGTTAT
* *
12929453 CAAAGTTATATCATAAGGTAC
1 CAAAATTATATCAAAAGGTAC
*
12929474 CAAAATTATATC-GAAGGTTAC
1 CAAAATTATATCAAAAGG-TAC
* * *
12929495 CAAAATTTTATCAAAAGTTAT
1 CAAAATTATATCAAAAGGTAC
12929516 CAAAAT
1 CAAAAT
12929522 CAAAATTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 4 0.10
21 33 0.82
22 3 0.08
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.30
Consensus pattern (21 bp):
CAAAATTATATCAAAAGGTAC
Found at i:12929537 original size:27 final size:27
Alignment explanation
Indices: 12929495--12929548 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
12929485 CGAAGGTTAC
* * * *
12929495 CAAAATTTTATCAAAAGTTATCAAAAT
1 CAAAATTATATAAAAAATAATCAAAAT
12929522 CAAAATTATATAAAAAATAATCAAAAT
1 CAAAATTATATAAAAAATAATCAAAAT
12929549 TTACTTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (27 bp):
CAAAATTATATAAAAAATAATCAAAAT
Found at i:12939550 original size:16 final size:16
Alignment explanation
Indices: 12939529--12939559 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12939519 CAGACGAAAA
12939529 AAGGATCGAATGCGAT
1 AAGGATCGAATGCGAT
12939545 AAGGATCGAATGCGA
1 AAGGATCGAATGCGA
12939560 GATAAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.32, T:0.16
Consensus pattern (16 bp):
AAGGATCGAATGCGAT
Found at i:12946962 original size:18 final size:18
Alignment explanation
Indices: 12946939--12946988 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
12946929 CCGGATTTTC
12946939 CTCCAAGTTCAAGTTCTG
1 CTCCAAGTTCAAGTTCTG
12946957 CTCCAAGTTCACA-TTCTG
1 CTCCAAGTTCA-AGTTCTG
12946975 CTCCAAGTTCAAGT
1 CTCCAAGTTCAAGT
12946989 CATGCTGCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.03
18 28 0.93
19 1 0.03
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (18 bp):
CTCCAAGTTCAAGTTCTG
Found at i:12946981 original size:36 final size:36
Alignment explanation
Indices: 12946939--12947019 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
12946929 CCGGATTTTC
12946939 CTCCAAGTTCAAGTTC-TGCTCCAAGTTCACATTCTG
1 CTCCAAGTTCAAG-TCATGCTCCAAGTTCACATTCTG
* * ***
12946975 CTCCAAGTTCAAGTCATGCTGCAGGTTTGGATTCTG
1 CTCCAAGTTCAAGTCATGCTCCAAGTTCACATTCTG
12947011 CTCCAAGTT
1 CTCCAAGTT
12947020 ATCAGGTTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 2 0.05
36 37 0.95
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (36 bp):
CTCCAAGTTCAAGTCATGCTCCAAGTTCACATTCTG
Found at i:12946994 original size:18 final size:17
Alignment explanation
Indices: 12946939--12946994 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 17
12946929 CCGGATTTTC
12946939 CTCCAAGTTCAAGTTCTG
1 CTCCAAGTTCAAG-TCTG
*
12946957 CTCCAAGTTCACATTCTG
1 CTCCAAGTTCA-AGTCTG
12946975 CTCCAAGTTCAAGTCATG
1 CTCCAAGTTCAAGTC-TG
12946993 CT
1 CT
12946995 GCAGGTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 3 0.09
18 30 0.88
19 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.32
Consensus pattern (17 bp):
CTCCAAGTTCAAGTCTG
Found at i:12952704 original size:12 final size:11
Alignment explanation
Indices: 12952678--12952777 Score: 50
Period size: 10 Copynumber: 9.2 Consensus size: 11
12952668 TGGGGTAAAC
*
12952678 TTATTTTCTTTT
1 TTATTTT-TTAT
12952690 TTATTTTTGTAT
1 TTATTTTT-TAT
*
12952702 TTACATTTTTAT
1 TTA-TTTTTTAT
*
12952714 TTA-TTTATAT
1 TTATTTTTTAT
* *
12952724 ATA-TATTTAT
1 TTATTTTTTAT
*
12952734 TT-TTTTTTCT
1 TTATTTTTTAT
12952744 TTA-TTTTTAT
1 TTATTTTTTAT
*
12952754 CTTATGTATTTA-
1 -TTAT-TTTTTAT
12952766 TT-TTTTTTAT
1 TTATTTTTTAT
12952776 TT
1 TT
12952778 TTATTACTAT
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
9 5 0.07
10 30 0.44
11 6 0.09
12 18 0.26
13 9 0.13
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (11 bp):
TTATTTTTTAT
Found at i:12952710 original size:20 final size:19
Alignment explanation
Indices: 12952687--12952738 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
12952677 CTTATTTTCT
*
12952687 TTTTTATTTTTGTATTTACA
1 TTTTTATTTTT-TATATACA
*
12952707 TTTTTATTTATTTATATATA
1 TTTTTATTT-TTTATATACA
*
12952727 TATTTATTTTTT
1 TTTTTATTTTTT
12952739 TTTCTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 23 0.82
21 2 0.07
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTATTTTTTATATACA
Found at i:12952753 original size:36 final size:36
Alignment explanation
Indices: 12952711--12952844 Score: 132
Period size: 36 Copynumber: 3.6 Consensus size: 36
12952701 TTTACATTTT
12952711 TATTTATTTATATATATATTTATTTTTTTTTCT-TTA
1 TATTTA-TTATATATATATTTATTTTTTTTTCTATTA
* * *
12952747 TTTTTATCTTATGTATTTATTT-TTTTTATTTT-TATTA
1 TATTTA--TTATATATATATTTATTTTT-TTTTCTATTA
*
12952784 CTATTTATTATATATATATCCTTATTTTTTTTTCTGTTAA
1 -TATTTATTATATATATAT--TTATTTTTTTTTCTATT-A
12952824 TATTTA-TATATATATATTTAT
1 TATTTATTATATATATATTTAT
12952845 CTGGGATTAT
Statistics
Matches: 81, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
36 25 0.31
37 19 0.23
38 22 0.27
39 14 0.17
40 1 0.01
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (36 bp):
TATTTATTATATATATATTTATTTTTTTTTCTATTA
Found at i:12952881 original size:18 final size:18
Alignment explanation
Indices: 12952858--12952916 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
12952848 GGATTATATA
12952858 TTATAATTTATCTATTAT
1 TTATAATTTATCTATTAT
*
12952876 TTATAATTTATCTGTTAAT
1 TTATAATTTATCTATT-AT
* ** *
12952895 TTTTGGTTTATCGATTAT
1 TTATAATTTATCTATTAT
12952913 TTAT
1 TTAT
12952917 TTATTAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 20 0.61
19 13 0.39
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (18 bp):
TTATAATTTATCTATTAT
Found at i:12953500 original size:18 final size:18
Alignment explanation
Indices: 12953468--12953509 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
12953458 GTTTCTAGAG
12953468 AGAAGGAGAGAAGAGAAA
1 AGAAGGAGAGAAGAGAAA
*
12953486 AGAA-GAGAGAGAGAGGAA
1 AGAAGGAGAGA-AGAGAAA
12953504 AGAAGG
1 AGAAGG
12953510 CTTCTGCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 14 0.67
19 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (18 bp):
AGAAGGAGAGAAGAGAAA
Found at i:12953878 original size:19 final size:18
Alignment explanation
Indices: 12953829--12953879 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 18
12953819 AAATGTTTAA
12953829 CATTTTTA-TTATTTATT
1 CATTTTTATTTATTTATT
*
12953846 --TTTTAATTTA-TTATT
1 CATTTTTATTTATTTATT
12953861 CATTTTTATTCTATTTATT
1 CATTTTTATT-TATTTATT
12953880 TTATTTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 7 0.26
18 2 0.07
19 5 0.19
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (18 bp):
CATTTTTATTTATTTATT
Found at i:12953882 original size:32 final size:31
Alignment explanation
Indices: 12953829--12953899 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
12953819 AAATGTTTAA
*
12953829 CATTTTTATTATTTATTTTTTAATTTATTATT
1 CATTTTTATTATTTA-TTTTTAATTTATCATT
*
12953861 CATTTTTATTCTATTTA-TTTTATTTTATCATT
1 CATTTTTA-T-TATTTATTTTTAATTTATCATT
*
12953893 TATTTTT
1 CATTTTT
12953900 TTTTAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 27 0.79
33 1 0.03
34 6 0.18
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.72
Consensus pattern (31 bp):
CATTTTTATTATTTATTTTTAATTTATCATT
Found at i:12954042 original size:59 final size:60
Alignment explanation
Indices: 12953958--12954184 Score: 255
Period size: 60 Copynumber: 3.7 Consensus size: 60
12953948 TAAGAATAAA
* *
12953958 TTTCAAAAAAAAATGTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAGT
1 TTTCAAAAAATAGT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAGT
* * * *
12954019 TTTCAAAAACTA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA-T-AAA-T
1 TTTCAAAAAATAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAGT
* * * *
12954075 TTTCAAAAAAAAAAAAGGCGTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAGAAG
1 TTTC----AAAAAATA-G-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAG
12954140 T
60 T
* *
12954141 TTTCAAAAAATATTTTTTAAGGAAAAGTTGAAAGTATCAATTTT
1 TTTCAAAAAATAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTT
12954185 CCCTTGTACA
Statistics
Matches: 139, Mismatches: 17, Indels: 21
0.79 0.10 0.12
Matches are distributed among these distances:
56 5 0.04
57 3 0.02
58 1 0.01
59 35 0.25
60 36 0.26
61 10 0.07
62 7 0.05
63 34 0.24
64 1 0.01
65 2 0.01
66 5 0.04
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (60 bp):
TTTCAAAAAATAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAGT
Found at i:12954122 original size:122 final size:118
Alignment explanation
Indices: 12953923--12954186 Score: 381
Period size: 122 Copynumber: 2.2 Consensus size: 118
12953913 TATTTTGAGA
* *
12953923 AAAAGTTAAAAAGTATCAA-TTTCCTTAAGAATAAATTTCAAAAAAAAATGTTTTGAGGAAAAGT
1 AAAAGTT-GAAAGTATCAATTTTCCTTAAGAATAAATTTCAAAAAAAAACGTTTTGAGGAAAAGT
* **
12953987 TGAAAGTATCAATTTTTCTCAAAATTAAAAGTTTTCAAAAACTA-TTTTTGGGG
65 TGAAAGTATCAATTTTTCTCAAAATTAAAAGTTTTCAAAAAATATTTTTTAAGG
12954040 AAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAATTTTCAAAAAAAAAAAAGGCGTTTTGAGGA
1 AAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAA-TTTC---AAAAAAAAA--CGTTTTGAGGA
* *
12954104 AAAGTTGAAAGTATCAATTTTTCTCGAAATTAGAAGTTTTCAAAAAATATTTTTTAAGG
60 AAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAGTTTTCAAAAAATATTTTTTAAGG
12954163 AAAAGTTGAAAGTATCAATTTTCC
1 AAAAGTTGAAAGTATCAATTTTCC
12954187 CTTGTACAAA
Statistics
Matches: 132, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
116 16 0.12
117 20 0.15
120 9 0.07
122 56 0.42
123 31 0.23
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (118 bp):
AAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTCAAAAAAAAACGTTTTGAGGAAAAGTT
GAAAGTATCAATTTTTCTCAAAATTAAAAGTTTTCAAAAAATATTTTTTAAGG
Found at i:12966262 original size:16 final size:16
Alignment explanation
Indices: 12966241--12966278 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
12966231 GCTTTTTATG
12966241 AACTTACACTAAATCA
1 AACTTACACTAAATCA
12966257 AACTTACACTAAATCA
1 AACTTACACTAAATCA
12966273 AACTTA
1 AACTTA
12966279 ACAGCCTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (16 bp):
AACTTACACTAAATCA
Found at i:12968363 original size:18 final size:18
Alignment explanation
Indices: 12968340--12968389 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
12968330 CCGGATTTTC
12968340 CTCCAAGTTCAAGTTCTG
1 CTCCAAGTTCAAGTTCTG
12968358 CTCCAAGTTCACA-TTCTG
1 CTCCAAGTTCA-AGTTCTG
12968376 CTCCAAGTTCAAGT
1 CTCCAAGTTCAAGT
12968390 CATGCTGCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.03
18 28 0.93
19 1 0.03
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (18 bp):
CTCCAAGTTCAAGTTCTG
Found at i:12968382 original size:36 final size:36
Alignment explanation
Indices: 12968340--12968420 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
12968330 CCGGATTTTC
12968340 CTCCAAGTTCAAGTTC-TGCTCCAAGTTCACATTCTG
1 CTCCAAGTTCAAG-TCATGCTCCAAGTTCACATTCTG
* * ***
12968376 CTCCAAGTTCAAGTCATGCTGCAGGTTTGGATTCTG
1 CTCCAAGTTCAAGTCATGCTCCAAGTTCACATTCTG
12968412 CTCCAAGTT
1 CTCCAAGTT
12968421 ATCAGGTTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 2 0.05
36 37 0.95
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (36 bp):
CTCCAAGTTCAAGTCATGCTCCAAGTTCACATTCTG
Found at i:12968395 original size:18 final size:17
Alignment explanation
Indices: 12968340--12968395 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 17
12968330 CCGGATTTTC
12968340 CTCCAAGTTCAAGTTCTG
1 CTCCAAGTTCAAG-TCTG
*
12968358 CTCCAAGTTCACATTCTG
1 CTCCAAGTTCA-AGTCTG
12968376 CTCCAAGTTCAAGTCATG
1 CTCCAAGTTCAAGTC-TG
12968394 CT
1 CT
12968396 GCAGGTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 3 0.09
18 30 0.88
19 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.32
Consensus pattern (17 bp):
CTCCAAGTTCAAGTCTG
Found at i:12974100 original size:6 final size:6
Alignment explanation
Indices: 12974081--12974189 Score: 51
Period size: 6 Copynumber: 16.8 Consensus size: 6
12974071 ATGGGTAAAC
* * * *
12974081 TTATTT TCTTTTT TTATTTT TGTATTT TACATTT TTA-TT TTATTT ATATAT
1 TTATTT T-TATTT TTA-TTT T-TATTT T-TATTT TTATTT TTATTT TTATTT
* * *
12974132 ATATTT ATT-TTT TTTTCTT TTATTT TTATCTT ATGTATTT ATTTTTT
1 TTATTT -TTATTT TTAT-TT TTATTT TTAT-TT -T-TATTT -TTATTT
12974179 TTATTT TTATT
1 TTATTT TTATT
12974190 ACTATTTATT
Statistics
Matches: 81, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
5 7 0.09
6 34 0.42
7 30 0.37
8 7 0.09
9 3 0.04
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:12974108 original size:13 final size:12
Alignment explanation
Indices: 12974081--12974189 Score: 51
Period size: 13 Copynumber: 8.4 Consensus size: 12
12974071 ATGGGTAAAC
*
12974081 TTATTTTCTTTTT
1 TTATTTT-TTATT
12974094 TTATTTTTGTATT
1 TTATTTTT-TATT
*
12974107 TTACATTTTTATT
1 TTA-TTTTTTATT
12974120 TTATTTATATATATAT
1 TTATTT-T-T-TAT-T
*
12974136 TTATTTTTTTTT
1 TTATTTTTTATT
* *
12974148 CTTTTATTTTTATC
1 -TTAT-TTTTTATT
*
12974162 TTATGTATTTATT
1 TTAT-TTTTTATT
*
12974175 TT-TTTTAT-TT
1 TTATTTTTTATT
12974185 TTATT
1 TTATT
12974190 ACTATTTATT
Statistics
Matches: 74, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
10 4 0.05
11 5 0.07
12 5 0.07
13 37 0.50
14 12 0.16
15 4 0.05
16 7 0.09
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (12 bp):
TTATTTTTTATT
Found at i:12974262 original size:18 final size:21
Alignment explanation
Indices: 12974234--12974294 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
12974224 CTGTTAATAT
12974234 TTATATATATATATTTATCTGA
1 TTATATATATA-ATTTATCTGA
12974256 TTATATATTATAATTTATCT-A
1 TTATATA-TATAATTTATCTGA
12974277 TTAT-T-TATAATTTATCTG
1 TTATATATATAATTTATCTG
12974295 TTAATTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
18 12 0.32
20 1 0.03
21 5 0.14
22 15 0.41
23 4 0.11
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (21 bp):
TTATATATATAATTTATCTGA
Found at i:12974354 original size:19 final size:19
Alignment explanation
Indices: 12974332--12974376 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
12974322 TTTATTAAAA
12974332 TTTTTTATTATTATTTGAT
1 TTTTTTATTATTATTTGAT
* *
12974351 TTTTTTATTATTTTTTTAT
1 TTTTTTATTATTATTTGAT
12974370 TTCTTTT
1 TT-TTTT
12974377 TTTTCGGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTATTATTATTTGAT
Found at i:12974909 original size:16 final size:16
Alignment explanation
Indices: 12974874--12974910 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
12974864 TCGGGTTTCT
*
12974874 AGAGAG-AAGGAAGAG
1 AGAGAGAAAAGAAGAG
12974889 A-AGAGAAAAGAAGAG
1 AGAGAGAAAAGAAGAG
12974904 AGAGAGA
1 AGAGAGA
12974911 GGAAAGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 10 0.53
16 5 0.26
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (16 bp):
AGAGAGAAAAGAAGAG
Found at i:12975257 original size:10 final size:10
Alignment explanation
Indices: 12975242--12975306 Score: 55
Period size: 10 Copynumber: 6.3 Consensus size: 10
12975232 AACATTTTTA
12975242 TTATTTATTT
1 TTATTTATTT
12975252 TTATTTATTT
1 TTATTTATTT
*
12975262 TCATTT-TTAT
1 TTATTTATT-T
12975272 TCTATTTA-TT
1 T-TATTTATTT
12975282 TTATTTTATCATT
1 TTA-TTTAT--TT
12975295 TTATTT-TTT
1 TTATTTATTT
12975304 TTA
1 TTA
12975307 AATAAAATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
9 9 0.20
10 23 0.50
11 6 0.13
12 3 0.07
13 5 0.11
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (10 bp):
TTATTTATTT
Found at i:12975279 original size:21 final size:21
Alignment explanation
Indices: 12975237--12975306 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 21
12975227 TGTTTAACAT
*
12975237 TTTTATTATTTATTTTTATTTA
1 TTTTATT-TTTATTTCTATTTA
12975259 TTTTCATTTTTA-TTCTATTTA
1 TTTT-ATTTTTATTTCTATTTA
*
12975280 TTTTATTTTATCATTT-TATTTT
1 TTTTATTTT-T-ATTTCTATTTA
12975302 TTTTA
1 TTTTA
12975307 AATAAAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 5 0.12
21 13 0.31
22 19 0.45
23 5 0.12
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTATTTTTATTTCTATTTA
Found at i:12975381 original size:59 final size:59
Alignment explanation
Indices: 12975318--12975593 Score: 281
Period size: 59 Copynumber: 4.5 Consensus size: 59
12975308 ATAAAATTAT
*
12975318 TTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTAAGAATAAA-TTTTCAAAAAAAAATG
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAAGTTTTCAAAAAAAAATG
* * **
12975377 TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAGTTTTC-AAAAACTAT-
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA-T-AAAGTTTTCAAAAAAAAATG
* * *
12975436 TTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAA-TTTTAAAAAAAAAAAAAGGCG
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAAGTTTT---CAAAAAAAAA--TG
* * * * * *
12975499 TTTTGAGGAAAAGTTGAAAGTATCAATTTTTTCTCGAAATTAGAAGTTTTCAAAAAATATTT
1 TTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCT-TAAAATA-AAGTTTTCAAAAAAAAATG
*
12975561 TTTTAAGGGAAAAGTTGAAAGTATCAATTTTCC
1 TTTTGA-GGAAAAGTTGAAAGTATCAATTTTCC
12975594 CTTGTACAAA
Statistics
Matches: 179, Mismatches: 23, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
56 4 0.02
57 3 0.02
58 3 0.02
59 69 0.39
60 16 0.09
61 5 0.03
62 10 0.06
63 45 0.25
64 13 0.07
65 5 0.03
66 2 0.01
67 4 0.02
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (59 bp):
TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAAGTTTTCAAAAAAAAATG
Found at i:12986014 original size:8 final size:8
Alignment explanation
Indices: 12986001--12986048 Score: 71
Period size: 9 Copynumber: 5.9 Consensus size: 8
12985991 TATGCTTGAA
12986001 GAAAAAAT
1 GAAAAAAT
12986009 GAAAAAAAT
1 G-AAAAAAT
12986018 GAAAAAAAT
1 G-AAAAAAT
12986027 GAAAAAAT
1 GAAAAAAT
12986035 GAAAAAA-
1 GAAAAAAT
12986042 GAAAAAA
1 GAAAAAA
12986049 AGTGAATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.18
8 15 0.38
9 17 0.44
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:12986016 original size:9 final size:9
Alignment explanation
Indices: 12986002--12986054 Score: 76
Period size: 8 Copynumber: 6.1 Consensus size: 9
12985992 ATGCTTGAAG
12986002 AAAAAATGA
1 AAAAAATGA
12986011 AAAAAATGA
1 AAAAAATGA
12986020 AAAAAATG-
1 AAAAAATGA
12986028 AAAAAATG-
1 AAAAAATGA
12986036 AAAAAA-GA
1 AAAAAATGA
12986044 AAAAAAGTGA
1 AAAAAA-TGA
12986054 A
1 A
12986055 TGAAAAAGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
7 1 0.02
8 20 0.49
9 17 0.41
10 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.09
Consensus pattern (9 bp):
AAAAAATGA
Found at i:12986023 original size:17 final size:17
Alignment explanation
Indices: 12986001--12986054 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
12985991 TATGCTTGAA
12986001 GAAAAAATGAAAAAAAT
1 GAAAAAATGAAAAAAAT
12986018 GAAAAAAATG-AAAAAAT
1 G-AAAAAATGAAAAAAAT
12986035 GAAAAAA-GAAAAAAAGT
1 GAAAAAATGAAAAAAA-T
12986052 GAA
1 GAA
12986055 TGAAAAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.03
16 12 0.35
17 13 0.38
18 8 0.24
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (17 bp):
GAAAAAATGAAAAAAAT
Found at i:12987247 original size:45 final size:42
Alignment explanation
Indices: 12987039--12987259 Score: 273
Period size: 42 Copynumber: 5.1 Consensus size: 42
12987029 GATTGTCAAT
* *
12987039 GAGCCATTTACTTTTCAAAAGTCGTTGAGCCTCTGATTAGAG
1 GAGCCATTTATTTTTCCAAAGTCGTTGAGCCTCTGATTAGAG
*
12987081 GAGCCATTTATTTTTCCAAAGTCGTTGAGCCTCTAATTAGAG
1 GAGCCATTTATTTTTCCAAAGTCGTTGAGCCTCTGATTAGAG
* *
12987123 GAGCCATTTATCTTTCCAAAGTCGTTGACGAGCCTCTAATTAGAG
1 GAGCCATTTATTTTTCCAAAGTCGTT---GAGCCTCTGATTAGAG
*
12987168 GAGCCATTTATTTTTCCAAAGTCATTGAGCCTCTGATTAGAG
1 GAGCCATTTATTTTTCCAAAGTCGTTGAGCCTCTGATTAGAG
* * * *
12987210 GAG-CATTGTTTATGTTTTTCAAAATTGTTGAGCCTCTGCTTAGAG
1 GAGCCA---TTTAT-TTTTCCAAAGTCGTTGAGCCTCTGATTAGAG
*
12987255 AAGCC
1 GAGCC
12987260 TTGATCAAAT
Statistics
Matches: 158, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
41 2 0.01
42 82 0.52
44 5 0.03
45 68 0.43
46 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (42 bp):
GAGCCATTTATTTTTCCAAAGTCGTTGAGCCTCTGATTAGAG
Found at i:12987253 original size:87 final size:84
Alignment explanation
Indices: 12987039--12987259 Score: 275
Period size: 87 Copynumber: 2.6 Consensus size: 84
12987029 GATTGTCAAT
12987039 GAGCCATTTA-CTTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCCAAAGT
1 GAGCCATTTATCTTTTCAAAA-TCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCCAAAGT
*
12987103 CGTTGAGCCTCTAATTAGAG
65 CATTGAGCCTCTAATTAGAG
* * *
12987123 GAGCCATTTATCTTTCCAAAGTCGTTGACGAGCCTCTAATTAGAGGAGCCATTTATTTTTCCAAA
1 GAGCCATTTATCTTTTCAAAATCGTT---GAGCCTCTGATTAGAGGAGCCATTTATTTTTCCAAA
*
12987188 GTCATTGAGCCTCTGATTAGAG
63 GTCATTGAGCCTCTAATTAGAG
* * * *
12987210 GAG-CATTGTTTATGTTTTTCAAAATTGTTGAGCCTCTGCTTAGAGAAGCC
1 GAGCCA---TTTAT-CTTTTCAAAATCGTTGAGCCTCTGATTAGAGGAGCC
12987260 TTGATCAAAT
Statistics
Matches: 117, Mismatches: 12, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
84 15 0.13
85 8 0.07
86 2 0.02
87 76 0.65
89 5 0.04
90 11 0.09
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (84 bp):
GAGCCATTTATCTTTTCAAAATCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCCAAAGTC
ATTGAGCCTCTAATTAGAG
Found at i:12987452 original size:6 final size:6
Alignment explanation
Indices: 12987443--12987564 Score: 70
Period size: 6 Copynumber: 19.3 Consensus size: 6
12987433 CCATTTTCCT
* * * *
12987443 TTTTTA TTTTTGTA TTTTACA TTTTTA -TTTTA TTTATA TATTT- TTATTA
1 TTTTTA -TTTT-TA TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * *
12987492 TTTTTA TTATTA TTATTA TTTATA TTTTTT TCTTTTA TTTTTA TCTTATGTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T-TTTTA TTTTTA T-TT-T-TA
12987544 TTTATTA TTATTT- TTTTTA TT
1 TTT-TTA TT-TTTA TTTTTA TT
12987565 ACTATTTATT
Statistics
Matches: 91, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
5 11 0.12
6 43 0.47
7 26 0.29
8 8 0.09
9 3 0.03
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:12987460 original size:13 final size:12
Alignment explanation
Indices: 12987444--12987559 Score: 65
Period size: 13 Copynumber: 8.9 Consensus size: 12
12987434 CATTTTCCTT
12987444 TTTTATTTTTGTA
1 TTTTATTTTT-TA
*
12987457 TTTTACATTTTTA
1 TTTTA-TTTTTTA
*
12987470 TTTTATTTATATA
1 TTTTATTT-TTTA
12987483 TTTTTATTATTTTTA
1 -TTTTA-T-TTTTTA
*
12987498 TTATTA-TTATTA
1 TT-TTATTTTTTA
*
12987510 TTTATATTTTTTTC
1 TTT-TA-TTTTTTA
12987524 TTTTA-TTTTTA
1 TTTTATTTTTTA
* *
12987535 TCTTATGTATTTA
1 TTTTAT-TTTTTA
12987548 TTATTATTTTTT
1 TT-TTATTTTTT
12987560 TTATTACTAT
Statistics
Matches: 79, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
11 10 0.13
12 11 0.14
13 27 0.34
14 22 0.28
15 7 0.09
16 2 0.03
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:12987484 original size:26 final size:25
Alignment explanation
Indices: 12987444--12987556 Score: 86
Period size: 26 Copynumber: 4.3 Consensus size: 25
12987434 CATTTTCCTT
* *
12987444 TTTTATTTTTGTATTTTACATTTTTA
1 TTTTATTTAT-TATTTTATATTTTTA
12987470 TTTTATTTATATATTTTTATTATTTTTA
1 TTTTATTTAT-TA-TTTTA-TATTTTTA
* *
12987498 TTATTA-TTATTATTTATATTTTTTTC
1 TT-TTATTTATTATTT-TATATTTTTA
* * *
12987524 TTTTATTT-TTATCTTATGTATTTA
1 TTTTATTTATTATTTTATATTTTTA
12987548 TTATTATTT
1 TT-TTATTT
12987557 TTTTTATTAC
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
24 9 0.12
25 14 0.19
26 24 0.33
27 9 0.12
28 13 0.18
29 3 0.04
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTATTTATTATTTTATATTTTTA
Found at i:12987493 original size:9 final size:9
Alignment explanation
Indices: 12987463--12987564 Score: 79
Period size: 9 Copynumber: 11.3 Consensus size: 9
12987453 TGTATTTTAC
12987463 ATTTTTATT
1 ATTTTTATT
12987472 -TTATTTATAT
1 ATT-TTTAT-T
12987482 ATTTTTATT
1 ATTTTTATT
12987491 ATTTTTATT
1 ATTTTTATT
*
12987500 ATTATTATT
1 ATTTTTATT
*
12987509 ATTTATATT
1 ATTTTTATT
*
12987518 -TTTTTCTT
1 ATTTTTATT
12987526 -TTATTT-TT
1 ATT-TTTATT
*
12987534 A-TCTTATGT
1 ATTTTTAT-T
12987543 ATTTATTATT
1 ATTT-TTATT
*
12987553 ATTTTTTTT
1 ATTTTTATT
12987562 ATT
1 ATT
12987565 ACTATTTATT
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
7 2 0.03
8 14 0.18
9 42 0.55
10 12 0.16
11 6 0.08
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.75
Consensus pattern (9 bp):
ATTTTTATT
Found at i:12987530 original size:37 final size:37
Alignment explanation
Indices: 12987457--12987565 Score: 104
Period size: 37 Copynumber: 3.0 Consensus size: 37
12987447 TATTTTTGTA
* *
12987457 TTTTACATTTTTATT-TTATTTATA-TATTTTTATTAT
1 TTTTAC-TTATTATTATTATTTATATTTTTTTTATTAT
*
12987493 TTTTA-TTATTATTATTATTTATATTTTTTTCTTTTAT
1 TTTTACTTATTATTATTATTTATATTTTTTT-TATTAT
12987530 TTTTATCTTATGTA-T-TTA-TTATTATTTTTTTTATTA
1 TTTTA-CTTAT-TATTATTATTTA-TATTTTTTTTATTA
12987566 CTATTTATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
34 7 0.11
35 9 0.15
36 10 0.16
37 17 0.27
38 12 0.19
39 5 0.08
40 2 0.03
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (37 bp):
TTTTACTTATTATTATTATTTATATTTTTTTTATTAT
Found at i:12987573 original size:38 final size:33
Alignment explanation
Indices: 12987466--12987573 Score: 78
Period size: 33 Copynumber: 3.2 Consensus size: 33
12987456 ATTTTACATT
* * *
12987466 TTTATTTTATT-TATATATTTTTATTATTTT-TA
1 TTTATCTTATTATTTATATTTTT-TTCTTTTATA
* *
12987498 -TTATTATTATTATTTATATTTTTTTCTTTTATT
1 TTTA-TCTTATTATTTATATTTTTTTCTTTTATA
*
12987531 TTTATCTTATGTATTTATTATTATTTTTTTTATTACTA
1 TTTATCTTAT-TATTTA-TATT-TTTTTCTT-TTA-TA
12987569 TTTAT
1 TTTAT
12987574 TAATATATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
31 3 0.05
32 12 0.20
33 16 0.27
34 9 0.15
35 4 0.07
36 7 0.12
37 3 0.05
38 6 0.10
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (33 bp):
TTTATCTTATTATTTATATTTTTTTCTTTTATA
Found at i:12987581 original size:65 final size:59
Alignment explanation
Indices: 12987465--12987579 Score: 158
Period size: 62 Copynumber: 1.9 Consensus size: 59
12987455 TATTTTACAT
*
12987465 TTTTATTTTATTTATATATTTTTATTATTTTTATTATTATTATTATTTATATTTTTTTC
1 TTTTATTTTATTTATATATTTTTATTATTTTTATTATTACTATTATTTATATTTTTTTC
* * *
12987524 TTTTATTTTTATCTTATGTATTTATTATTATTTTTTTTATTACTATTTATTAATAT
1 TTTTA-TTTTAT-TTATATATTT-TTATTATTTTTATTATTACTA-TTATTTATAT
12987580 ATATATCCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 5 0.10
60 6 0.12
61 9 0.19
62 19 0.40
63 9 0.19
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (59 bp):
TTTTATTTTATTTATATATTTTTATTATTTTTATTATTACTATTATTTATATTTTTTTC
Found at i:12987595 original size:65 final size:60
Alignment explanation
Indices: 12987465--12987602 Score: 152
Period size: 62 Copynumber: 2.2 Consensus size: 60
12987455 TATTTTACAT
* * * * *
12987465 TTTTA-TTTTATTTATATATTTTTATTATTTTTATTATTATTATTATTTATATTTTTTTC
1 TTTTATTTTTATTTATATATTTTTATTATTTTTATTATTACTATTATTAATATTATATCC
* *
12987524 TTTTATTTTTATCTTATGTATTTATTATTATTTTTTTTATTACTATTTATTAATATATATATCC
1 TTTTATTTTTAT-TTATATATTT-TTATTATTTTTATTATTACTA-TTATTAATAT-TATATCC
*
12987588 TTATTATTATTATTT
1 TT-TTATTTTTATTT
12987603 TTTTCCTGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 5 0.08
60 6 0.09
61 9 0.14
62 19 0.29
63 9 0.14
64 8 0.12
65 9 0.14
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (60 bp):
TTTTATTTTTATTTATATATTTTTATTATTTTTATTATTACTATTATTAATATTATATCC
Found at i:12987597 original size:6 final size:6
Alignment explanation
Indices: 12987467--12987601 Score: 57
Period size: 6 Copynumber: 22.3 Consensus size: 6
12987457 TTTTACATTT
* *
12987467 TTATT- TTATTTA TATATTT TTATTA TTTTTA TTATTA TTATTA TT-TATA
1 TTATTA TTA-TTA T-TATTA TTATTA TTATTA TTATTA TTATTA TTAT-TA
* * * * * *
12987516 TT-TTT TTCTT- TTATTT TTA-TC TTATGTA TTTATTA TTATTT TTTTTA
1 TTATTA TTATTA TTATTA TTATTA TTAT-TA -TTATTA TTATTA TTATTA
* * **
12987563 TTACTA TTTATTA ATA-TA TATATCC TTATTA TTATTA TT
1 TTATTA -TTATTA TTATTA T-TATTA TTATTA TTATTA TT
12987602 TTTTTCCTGT
Statistics
Matches: 98, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
5 17 0.17
6 62 0.63
7 13 0.13
8 6 0.06
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.70
Consensus pattern (6 bp):
TTATTA
Found at i:12987626 original size:46 final size:45
Alignment explanation
Indices: 12987545--12987646 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 45
12987535 TCTTATGTAT
* *
12987545 TTATTATTATTTTTTTTATTACTATTTATTAATATATATATCCTTA
1 TTATTATTATTTTTTTTATTAATATTTATTAATATATATAT-CTGA
* *
12987591 TTATTATTATTTTTTTCCTGTTAATATTTA-T-ATATATTTATCTGA
1 TTATTATTATTTTTTT--TATTAATATTTATTAATATATATATCTGA
12987636 TTATATATTAT
1 TTAT-TATTAT
12987647 AATTTATCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
45 7 0.14
46 31 0.63
47 1 0.02
48 10 0.20
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (45 bp):
TTATTATTATTTTTTTTATTAATATTTATTAATATATATATCTGA
Found at i:12987641 original size:18 final size:20
Alignment explanation
Indices: 12987616--12987674 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 20
12987606 TCCTGTTAAT
12987616 ATTTATATAT-ATTTATCTG
1 ATTTATATATAATTTATCTG
12987635 ATTATATATTATAATTTATCT-
1 ATT-TATA-TATAATTTATCTG
*
12987656 A-TTATTTATAATTTATCTG
1 ATTTATATATAATTTATCTG
12987675 TTAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 12 0.34
19 6 0.17
20 5 0.14
21 4 0.11
22 8 0.23
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTATATATAATTTATCTG
Found at i:12987720 original size:14 final size:14
Alignment explanation
Indices: 12987697--12987751 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
12987687 TTTATCTGAT
*
12987697 TATTTATTTATTAA
1 TATTTTTTTATTAA
*
12987711 TATTTTTTTATTATT
1 TATTTTTTTATTA-A
12987726 TGATTTTTTTTATT-A
1 T-A-TTTTTTTATTAA
12987741 T-TTTTTTTATT
1 TATTTTTTTATT
12987752 TCTTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 10 0.29
14 12 0.34
15 2 0.06
16 1 0.03
17 10 0.29
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (14 bp):
TATTTTTTTATTAA
Found at i:12987722 original size:18 final size:18
Alignment explanation
Indices: 12987699--12987743 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
12987689 TATCTGATTA
12987699 TTTATTTA-TTAATATTTT
1 TTTATTTATTTAAT-TTTT
*
12987717 TTTA-TTATTTGATTTTT
1 TTTATTTATTTAATTTTT
12987734 TTTA-TTATTT
1 TTTATTTATTT
12987744 TTTTTATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTATTTATTTAATTTTT
Found at i:12987744 original size:26 final size:24
Alignment explanation
Indices: 12987695--12987761 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
12987685 AGTTTATCTG
**
12987695 ATTATTTATTTATTAATATTTTTTT
1 ATTATTTATTT-TTTTTATTTTTTT
12987720 ATTATTTGATTTTTTTTATTATTTTT
1 ATTATTT-ATTTTTTTTATT-TTTTT
* *
12987746 TTTATTTCTTTTTTTT
1 ATTATTTATTTTTTTT
12987762 CGTCTGAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 21 0.58
26 15 0.42
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.78
Consensus pattern (24 bp):
ATTATTTATTTTTTTTATTTTTTT
Found at i:12988649 original size:21 final size:19
Alignment explanation
Indices: 12988623--12988679 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
12988613 TTGTTTAACA
12988623 TTTTTATTATTTATTTTTTT
1 TTTTTATT-TTTATTTTTTT
*
12988643 TTATTTATTTTCATTTTTATT
1 TT-TTTATTTTTATTTTT-TT
12988664 CTTTTTA-TTTTATTTT
1 -TTTTTATTTTTATTTT
12988680 ATCATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 18 0.56
21 12 0.38
22 2 0.06
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTATTTTTATTTTTTT
Found at i:12988653 original size:26 final size:27
Alignment explanation
Indices: 12988624--12988698 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 27
12988614 TGTTTAACAT
12988624 TTTTATTATTTATTTTTTTTTA-TTTA
1 TTTTATTATTTATTTTTTTTTATTTTA
*
12988650 TTTTCATT-TTTA-TTCTTTTTATTTTA
1 TTTT-ATTATTTATTTTTTTTTATTTTA
*
12988676 TTTTATCATTTTATTATTTTTTT
1 TTTTATTA-TTTATT-TTTTTTT
12988699 TTAATAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
25 10 0.25
26 16 0.40
27 7 0.17
28 1 0.03
29 6 0.15
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTATTATTTATTTTTTTTTATTTTA
Found at i:12988692 original size:21 final size:19
Alignment explanation
Indices: 12988624--12988701 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 19
12988614 TGTTTAACAT
12988624 TTTTATTA-TTTATTTTT-
1 TTTTATTATTTTATTTTTA
12988641 TTTTATTTATTTTCATTTTTA
1 TTTTA-TTATTTT-ATTTTTA
*
12988662 TTCTTTTTATTTTATTTTATCA
1 TT-TTATTATTTTATTTT-T-A
12988684 TTTTATTATTTT-TTTTTA
1 TTTTATTATTTTATTTTTA
12988702 ATAAAATTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.10
18 4 0.08
19 4 0.08
20 15 0.29
21 19 0.37
22 5 0.10
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATTATTTTATTTTTA
Found at i:12988698 original size:19 final size:19
Alignment explanation
Indices: 12988623--12988698 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 19
12988613 TTGTTTAACA
12988623 TTTTTATT-A-TTTATTTT
1 TTTTTATTCATTTTATTTT
*
12988640 TTTTTATTTATTTTCA----
1 TTTTTATTCATTTT-ATTTT
*
12988656 TTTTTATTCTTTTTATTTT
1 TTTTTATTCATTTTATTTT
*
12988675 ATTTTA-TCATTTTATTATT
1 TTTTTATTCATTTTATT-TT
12988694 TTTTT
1 TTTTT
12988699 TTAATAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
15 1 0.02
16 12 0.26
17 8 0.17
18 10 0.22
19 14 0.30
20 1 0.02
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTATTCATTTTATTTT
Done.