Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 54 of 195
Found at i:11239973 original size:20 final size:19
Alignment explanation
Indices: 11239944--11239981 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 19
11239934 CTTGTTACGT
11239944 AAAAACTTGAAGCAAAAAAAG
1 AAAAACTTG-AG-AAAAAAAG
11239965 AAAAA-TTGAGAAAAAAA
1 AAAAACTTGAGAAAAAAA
11239982 ATTTGAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.41
19 2 0.12
20 3 0.18
21 5 0.29
ACGTcount: A:0.71, C:0.05, G:0.13, T:0.11
Consensus pattern (19 bp):
AAAAACTTGAGAAAAAAAG
Found at i:11248353 original size:1 final size:1
Alignment explanation
Indices: 11248349--11248391 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
11248339 AGAAAAAGAC
* * * *
11248349 AAAAAAAAAAACAAAAAAAAAGAAAAGATAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11248392 GAAAGACTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.91, C:0.02, G:0.05, T:0.02
Consensus pattern (1 bp):
A
Found at i:11248367 original size:22 final size:24
Alignment explanation
Indices: 11248341--11248393 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
11248331 TTTGCTTGAG
11248341 AAAAAGACAAAA-A-AAAAAACAAA
1 AAAAAGACAAAAGATAAAAAA-AAA
*
11248364 AAAAA-AGAAAAGATAAAAAAAAA
1 AAAAAGACAAAAGATAAAAAAAAA
11248387 AAAAAGA
1 AAAAAGA
11248394 AAGACTCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.19
23 14 0.54
24 7 0.27
ACGTcount: A:0.87, C:0.04, G:0.08, T:0.02
Consensus pattern (24 bp):
AAAAAGACAAAAGATAAAAAAAAA
Found at i:11248394 original size:22 final size:23
Alignment explanation
Indices: 11248341--11248395 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
11248331 TTTGCTTGAG
11248341 AAAAAGACAAAAAAAAAAACAAAA
1 AAAAAGA-AAAAAAAAAAACAAAA
* *
11248365 AAAAAGAAAAGATAAAAA-AAAA
1 AAAAAGAAAAAAAAAAAACAAAA
11248387 AAAAAGAAA
1 AAAAAGAAA
11248396 GACTCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 13 0.45
23 9 0.31
24 7 0.24
ACGTcount: A:0.87, C:0.04, G:0.07, T:0.02
Consensus pattern (23 bp):
AAAAAGAAAAAAAAAAAACAAAA
Found at i:11255893 original size:72 final size:73
Alignment explanation
Indices: 11255709--11255893 Score: 219
Period size: 73 Copynumber: 2.5 Consensus size: 73
11255699 ATCACCTTTT
* * * * ** * **
11255709 TGAACCAATCGATCCCCTCAAGGAAGGGATCGATCGGGTGAGCATTTTCAAAGGTGTAATTGGTT
1 TGAACCAATCGATCCCCTCATGGAAGGGATCGATCGGGTCAGAATTTTCAAACGCATAAATGGAA
11255774 CTAAAACA
66 CTAAAACA
** ** *
11255782 TGAACCAATCGATCTACTCATGGAAAAGATCGATCGGGTCATAATTTTCAAACGCATAAATGGAA
1 TGAACCAATCGATCCCCTCATGGAAGGGATCGATCGGGTCAGAATTTTCAAACGCATAAATGGAA
11255847 CT-AAACA
66 CTAAAACA
* *
11255854 TGAACCAATCGATCCCCTCATGGAAGGGATTGATTGGGTC
1 TGAACCAATCGATCCCCTCATGGAAGGGATCGATCGGGTC
11255894 TTGGGCAAAA
Statistics
Matches: 92, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
72 39 0.42
73 53 0.58
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (73 bp):
TGAACCAATCGATCCCCTCATGGAAGGGATCGATCGGGTCAGAATTTTCAAACGCATAAATGGAA
CTAAAACA
Found at i:11257094 original size:55 final size:54
Alignment explanation
Indices: 11256972--11257262 Score: 286
Period size: 49 Copynumber: 5.5 Consensus size: 54
11256962 AAAATGTATG
* * *
11256972 TTTAGGATGAGCCATTTTCAAATAAGATTTTTTAAAAAAAGGTTTCAAAGCCTCTG
1 TTTAGGAGGAGCCATTTTCAAACAAGATTTTTT-AAAAAA-GTTTCAAAGCCTCTA
*
11257028 TTTA-G-GGAGCCATTTTCAAACAAGATTTTTTAAAAAATGTTTCAAAGCTTCTA
1 TTTAGGAGGAGCCATTTTCAAACAAGATTTTTTAAAAAA-GTTTCAAAGCCTCTA
* ** *
11257081 TTTAGGAGGAGCCATTTACAAATGAGA--TTTT---ATAGTTTCAAAGCCTCTA
1 TTTAGGAGGAGCCATTTTCAAACAAGATTTTTTAAAAAAGTTTCAAAGCCTCTA
*
11257130 TTT-GGAAGGAGCCATTTTCAAACAAGATTTTTTTAAAAAAGTTTCTAAGCCTCTA
1 TTTAGG-AGGAGCCATTTTCAAACAAGA-TTTTTTAAAAAAGTTTCAAAGCCTCTA
* * * *
11257185 TTT-GAGATGAGTCATTTTCAAACAAGA--TTTT---AAAGTTTTAAAGCCTCGA
1 TTTAG-GAGGAGCCATTTTCAAACAAGATTTTTTAAAAAAGTTTCAAAGCCTCTA
* * *
11257234 TTTAAGAGAAGCCATTTTCAAATAAGATT
1 TTTAGGAGGAGCCATTTTCAAACAAGATT
11257263 AAAAAAATAA
Statistics
Matches: 197, Mismatches: 25, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
48 2 0.01
49 71 0.36
50 2 0.01
52 8 0.04
53 27 0.14
54 25 0.13
55 57 0.29
56 5 0.03
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (54 bp):
TTTAGGAGGAGCCATTTTCAAACAAGATTTTTTAAAAAAGTTTCAAAGCCTCTA
Found at i:11257174 original size:104 final size:103
Alignment explanation
Indices: 11257013--11257262 Score: 317
Period size: 104 Copynumber: 2.4 Consensus size: 103
11257003 TTAAAAAAAG
* * *
11257013 GTTTCAAAGCCTCTGTTTAGGGAGCCATTTTCAAACAAGA-TTTTTTAAAAAATGTTTCAAAGCT
1 GTTTCAAAGCCTCTATTTAAGGAGCCATTTTCAAACAAGATTTTTTTAAAAAATGTTTCAAAGCC
** *
11257077 TCTATTT-AGGAGGAGCCATTTACAAATGAGATTTTATA
66 TCTATTTGA-GAGGAGCCATTTACAAACAAGATTTTAAA
*
11257115 GTTTCAAAGCCTCTATTTGGAAGGAGCCATTTTCAAACAAGATTTTTTTAAAAAA-GTTTCTAAG
1 GTTTCAAAGCCTCTATTT--AAGGAGCCATTTTCAAACAAGATTTTTTTAAAAAATGTTTCAAAG
* * *
11257179 CCTCTATTTGAGATGAGTCATTTTCAAACAAGATTTTAAA
64 CCTCTATTTGAGAGGAGCCATTTACAAACAAGATTTTAAA
* * *
11257219 GTTTTAAAGCCTCGATTTAAGAGAAGCCATTTTCAAATAAGATT
1 GTTTCAAAGCCTCTATTTAAG-G-AGCCATTTTCAAACAAGATT
11257263 AAAAAAATAA
Statistics
Matches: 129, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
102 20 0.16
103 1 0.01
104 95 0.74
105 13 0.10
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (103 bp):
GTTTCAAAGCCTCTATTTAAGGAGCCATTTTCAAACAAGATTTTTTTAAAAAATGTTTCAAAGCC
TCTATTTGAGAGGAGCCATTTACAAACAAGATTTTAAA
Found at i:11259494 original size:16 final size:17
Alignment explanation
Indices: 11259469--11259518 Score: 68
Period size: 16 Copynumber: 3.0 Consensus size: 17
11259459 AATTTCTTTT
11259469 AAAAAAATAAATAGATG
1 AAAAAAATAAATAGATG
*
11259486 -AATAAATAAATAG-TAG
1 AAAAAAATAAATAGAT-G
11259502 AAAAAAATAAATAGATG
1 AAAAAAATAAATAGATG
11259519 TCCTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 1 0.04
16 13 0.46
17 13 0.46
18 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (17 bp):
AAAAAAATAAATAGATG
Found at i:11265672 original size:16 final size:16
Alignment explanation
Indices: 11265653--11265686 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11265643 AGAGGGTTTC
*
11265653 AAATATATTTTTATAA
1 AAATATAGTTTTATAA
*
11265669 AAATTTAGTTTTATAA
1 AAATATAGTTTTATAA
11265685 AA
1 AA
11265687 TATTCAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AAATATAGTTTTATAA
Found at i:11265840 original size:3 final size:3
Alignment explanation
Indices: 11265828--11265861 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
11265818 TATAATGTAA
11265828 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
11265862 ATAATAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:11270576 original size:26 final size:26
Alignment explanation
Indices: 11270472--11270566 Score: 88
Period size: 26 Copynumber: 3.6 Consensus size: 26
11270462 ATGTTATTAT
*
11270472 ATATTATTATTAGTATTATAGTATA-G
1 ATATTA-TATTATTATTATAGTATATG
* *
11270498 CATATTATATGATATTATTAT--TTTATT
1 -ATATTATAT--TATTATTATAGTATATG
*
11270525 ATTTTTATATTATTATTATAGTATATG
1 A-TATTATATTATTATTATAGTATATG
11270552 ATATTATATTATTAT
1 ATATTATATTATTAT
11270567 CTTGCTATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
25 9 0.16
26 20 0.36
27 18 0.33
28 8 0.15
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (26 bp):
ATATTATATTATTATTATAGTATATG
Found at i:11270579 original size:53 final size:49
Alignment explanation
Indices: 11270465--11270566 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 49
11270455 GTATAGTATG
*
11270465 TTATTATATATTATTATTAGTATTATAGTATAGCATATTATATGATATTA
1 TTATT-TATATTATTATTAGTATTATAGTATAGCATATGATATGATATTA
* * * *
11270515 TTATTT-TATTATTTTTA-TATTATTATTATAGTATATGATATTATATTA
1 TTATTTATATTATTATTAGTATTA-TAGTATAGCATATGATATGATATTA
11270563 TTAT
1 TTAT
11270567 CTTGCTATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
47 5 0.11
48 35 0.76
49 1 0.02
50 5 0.11
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (49 bp):
TTATTTATATTATTATTAGTATTATAGTATAGCATATGATATGATATTA
Found at i:11270584 original size:5 final size:5
Alignment explanation
Indices: 11270471--11270563 Score: 69
Period size: 5 Copynumber: 17.6 Consensus size: 5
11270461 TATGTTATTA
* * * *
11270471 TATAT TATTAT TAGTAT TATAG TATAG CATAT TATAT GATAT TATTAT
1 TATAT TA-TAT TA-TAT TATAT TATAT TATAT TATAT TATAT TA-TAT
* * * *
11270519 TTTAT TATTTT TATAT TATTAT TATAG TATAT GATAT TATAT TAT
1 TATAT TA-TAT TATAT TA-TAT TATAT TATAT TATAT TATAT TAT
11270564 TATCTTGCTA
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
5 46 0.67
6 23 0.33
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:11270646 original size:3 final size:3
Alignment explanation
Indices: 11270465--11270627 Score: 50
Period size: 3 Copynumber: 59.0 Consensus size: 3
11270455 GTATAGTATG
* * **
11270465 TTA TTA TATA TTA TTA TTA GTA TTA -TA GTA -TA GCA -TA TTA -TA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
11270507 TGA -TA TTA TTA TT- TTA TTA TTT TTA -TA TTA TTA TTA -TA GTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
11270550 TGA -TA TTA -TA TTA TTA -TC TTG CTA -TA TTA -TA TTA TTA CTA -TG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
11270592 TTA TTA CTA TTG TGA TTA CTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11270628 CATTATATAA
Statistics
Matches: 117, Mismatches: 27, Indels: 32
0.66 0.15 0.18
Matches are distributed among these distances:
2 25 0.21
3 89 0.76
4 3 0.03
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:11283455 original size:56 final size:56
Alignment explanation
Indices: 11283269--11283455 Score: 207
Period size: 56 Copynumber: 3.3 Consensus size: 56
11283259 TCAATTTTTT
* * * *
11283269 CAGACTTACAGTTCAATCCTGGTCATCC-AACCTTGACTTGGTTCAGGTCAATTATC
1 CAGACTCACGGTTCAATCCTAGTCATCCGAA-CTTGACTCGGTTCAGGTCAATTATC
* * * *
11283325 TAGACTCGA-GGTTCAATCCTAGTCATCCGACCTTAACTCGGTTCAGGCCAATTATC
1 CAGACTC-ACGGTTCAATCCTAGTCATCCGAACTTGACTCGGTTCAGGTCAATTATC
* * * * * *
11283381 CAGACTCTCAGTTTAATCCTAGTCACCCGAACTTGACTCGGTTTAGGTCAATTGTC
1 CAGACTCACGGTTCAATCCTAGTCATCCGAACTTGACTCGGTTCAGGTCAATTATC
*
11283437 CAGACTCACGGCTCAATCC
1 CAGACTCACGGTTCAATCC
11283456 CTATCATTTT
Statistics
Matches: 106, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
56 104 0.98
57 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (56 bp):
CAGACTCACGGTTCAATCCTAGTCATCCGAACTTGACTCGGTTCAGGTCAATTATC
Found at i:11283617 original size:26 final size:27
Alignment explanation
Indices: 11283588--11283808 Score: 143
Period size: 26 Copynumber: 8.1 Consensus size: 27
11283578 TTTTTTATAG
*
11283588 TATAGTATGTTATTA-TATATTATTAT
1 TATAGTATATTATTATTATATTATTAT
**
11283614 TATAGTATAGCA-TATTATATGATATT-T
1 TATAGTATATTATTATTATAT--TATTAT
* * *
11283641 T-TACTTTATTACTATTATATTATTAT
1 TATAGTATATTATTATTATATTATTAT
*
11283667 TATAGTATATGA-TATTATATTATTATCTT
1 TATAGTATATTATTATTATATTATTA---T
* * *
11283696 GGTATATTATATTATTACTATATTATTAC
1 --TATAGTATATTATTATTATATTATTAT
* *
11283725 TATTGT-TATTACTATTATCATTATTAT
1 TATAGTATATTATTATTAT-ATTATTAT
** *
11283752 TATTTTATCATTATTATTACATTA-TAT
1 TATAGTAT-ATTATTATTATATTATTAT
* *
11283779 TATTGT-TGTTATTATTATTATTATTAT
1 TATAGTATATTATTATTA-TATTATTAT
11283806 TAT
1 TAT
11283809 TTTCATTTTT
Statistics
Matches: 153, Mismatches: 25, Indels: 33
0.73 0.12 0.16
Matches are distributed among these distances:
25 15 0.10
26 50 0.33
27 47 0.31
28 9 0.06
29 10 0.07
31 10 0.07
32 12 0.08
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (27 bp):
TATAGTATATTATTATTATATTATTAT
Found at i:11283661 original size:11 final size:11
Alignment explanation
Indices: 11283647--11283780 Score: 65
Period size: 11 Copynumber: 12.5 Consensus size: 11
11283637 ATTTTTACTT
11283647 TATTACTATTA
1 TATTACTATTA
*
11283658 TATTATTATTA
1 TATTACTATTA
* *
11283669 TAGTA-TATGA
1 TATTACTATTA
11283679 TATTA-TA-T-
1 TATTACTATTA
11283687 TATTATCT-TGGTA
1 TATTA-CTAT--TA
11283700 TATTA-TA-T-
1 TATTACTATTA
11283708 TATTACTA-TA
1 TATTACTATTA
*
11283718 TTATTACTATTGT
1 -TATTACTATT-A
11283731 TATTACTATTA
1 TATTACTATTA
*
11283742 TCATTATTATTA
1 T-ATTACTATTA
*
11283754 TTTTA-TCATTA
1 TATTACT-ATTA
11283765 TTATTAC-ATTA
1 -TATTACTATTA
11283776 TATTA
1 TATTA
11283781 TTGTTGTTAT
Statistics
Matches: 97, Mismatches: 10, Indels: 33
0.69 0.07 0.24
Matches are distributed among these distances:
8 10 0.10
9 4 0.04
10 17 0.18
11 35 0.36
12 26 0.27
13 5 0.05
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (11 bp):
TATTACTATTA
Found at i:11283666 original size:3 final size:3
Alignment explanation
Indices: 11283646--11283809 Score: 109
Period size: 3 Copynumber: 58.7 Consensus size: 3
11283636 TATTTTTACT
* * *
11283646 TTA TTA CTA TTA -TA TTA TTA TTA -TA GTA -TA TGA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
11283689 TTA -TC TTG GTA -TA TTA -TA TTA TTA CTA -TA TTA TTA CTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
11283733 TTA CTA TTA TCA TTA TTA TTA TT- TTA TCA TTA TTA TTA -CA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
11283778 TTA TTG TTG TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11283810 TTCATTTTTT
Statistics
Matches: 126, Mismatches: 23, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
2 21 0.17
3 105 0.83
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:11283704 original size:53 final size:51
Alignment explanation
Indices: 11283603--11283710 Score: 130
Period size: 53 Copynumber: 2.1 Consensus size: 51
11283593 TATGTTATTA
*
11283603 TATATTATTATTATAGTATAGCATATTATATGATATTTTTACTTTATTACTAT
1 TATATTATTATTATAGTATAGCATATTATAT-ATATTTTTACTATATTA-TAT
**
11283656 TATATTATTATTATAGTATATG-ATATTATAT-TATTATCTTGGTATATTATAT
1 TATATTATTATTATAGTATA-GCATATTATATATATT-T-TTACTATATTATAT
11283708 TAT
1 TAT
11283711 TACTATATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
51 4 0.08
52 7 0.14
53 37 0.76
54 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (51 bp):
TATATTATTATTATAGTATAGCATATTATATATATTTTTACTATATTATAT
Found at i:11283804 original size:54 final size:54
Alignment explanation
Indices: 11283702--11283811 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 54
11283692 TCTTGGTATA
*
11283702 TTATATTATTACTATATTATTACTATTGTTATTACTATTATCATTATTATTATT
1 TTATATTATTACTACATTATTACTATTGTTATTACTATTATCATTATTATTATT
* * * * *
11283756 TTATCATTATTATTACATTA-TATTATTGTTGTTATTATTATTATTATTATTATT
1 TTAT-ATTATTACTACATTATTACTATTGTTATTACTATTATCATTATTATTATT
11283810 TT
1 TT
11283812 CATTTTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
54 36 0.73
55 13 0.27
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (54 bp):
TTATATTATTACTACATTATTACTATTGTTATTACTATTATCATTATTATTATT
Found at i:11284322 original size:13 final size:11
Alignment explanation
Indices: 11284288--11284332 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
11284278 CGAAGTTTAG
11284288 ATTTTTTAAAA
1 ATTTTTTAAAA
11284299 ATTTTTT-AAA
1 ATTTTTTAAAA
11284309 ATTTTTCTAGAAA
1 ATTTTT-TA-AAA
*
11284322 ATTTTTGAAAA
1 ATTTTTTAAAA
11284333 TCTAGGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 9 0.30
11 11 0.37
12 1 0.03
13 9 0.30
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (11 bp):
ATTTTTTAAAA
Found at i:11284691 original size:18 final size:19
Alignment explanation
Indices: 11284663--11284709 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
11284653 TTTTTTTTCA
11284663 TTTTAATTTTAATTT-TAAT
1 TTTTAA-TTTAATTTATAAT
* *
11284682 TTTTGATTTAATTTATATT
1 TTTTAATTTAATTTATAAT
11284701 TTTTAATTT
1 TTTTAATTT
11284710 TTATTATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTAATTTAATTTATAAT
Found at i:11284716 original size:19 final size:19
Alignment explanation
Indices: 11284663--11284716 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
11284653 TTTTTTTTCA
*
11284663 TTTTAATTTTAATTTTAAT
1 TTTTAATTTTAATTATAAT
* *
11284682 TTTTGA-TTTAATTTATATT
1 TTTTAATTTTAA-TTATAAT
*
11284701 TTTTAATTTTTATTAT
1 TTTTAATTTTAATTAT
11284717 TACTATCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 5 0.18
19 19 0.68
20 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTAATTTTAATTATAAT
Found at i:11288736 original size:13 final size:13
Alignment explanation
Indices: 11288718--11288753 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
11288708 TATCTCTTCA
11288718 AATTAAAAAAAAT
1 AATTAAAAAAAAT
* *
11288731 AATTAAAATAGAT
1 AATTAAAAAAAAT
11288744 AATTAAAAAA
1 AATTAAAAAA
11288754 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (13 bp):
AATTAAAAAAAAT
Found at i:11289147 original size:18 final size:17
Alignment explanation
Indices: 11289109--11289148 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
11289099 TGTATAATAC
*
11289109 ATATATAAAAATTAAAT
1 ATATATAAAAATAAAAT
11289126 -TATATAAATAATAAAAT
1 ATATATAAA-AATAAAAT
11289143 ATATAT
1 ATATAT
11289149 TCTTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 8 0.40
17 7 0.35
18 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATATAAAAATAAAAT
Found at i:11289938 original size:2 final size:2
Alignment explanation
Indices: 11289931--11289955 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11289921 AGCAGTATTC
11289931 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
11289956 AGAAGAAATT
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:11298694 original size:21 final size:21
Alignment explanation
Indices: 11298644--11298694 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
11298634 GAAAGAGAAC
* *
11298644 AAGAGCGTGCTAGAATTGAAT
1 AAGAGCGTGCTAAAATTGAAG
*
11298665 AGGAGCGTGCTAAAATTGAAG
1 AAGAGCGTGCTAAAATTGAAG
*
11298686 AAGAACGTG
1 AAGAGCGTG
11298695 TTAGAATAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.10, G:0.31, T:0.20
Consensus pattern (21 bp):
AAGAGCGTGCTAAAATTGAAG
Found at i:11299643 original size:10 final size:10
Alignment explanation
Indices: 11299624--11299659 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
11299614 TGCATAAAAA
11299624 AATCATCAAG
1 AATCATCAAG
* *
11299634 ATTGATCAAG
1 AATCATCAAG
11299644 AATCATCAAG
1 AATCATCAAG
11299654 AATCAT
1 AATCAT
11299660 AAAAAATCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.25
Consensus pattern (10 bp):
AATCATCAAG
Found at i:11299667 original size:20 final size:20
Alignment explanation
Indices: 11299620--11299667 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
11299610 ATTATGCATA
* *
11299620 AAAAAATCATCAAGATTGAT
1 AAAAAATCATCAAGAATCAT
* *
11299640 CAAGAATCATCAAGAATCAT
1 AAAAAATCATCAAGAATCAT
11299660 AAAAAATC
1 AAAAAATC
11299668 TCCAAGATTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (20 bp):
AAAAAATCATCAAGAATCAT
Found at i:11303773 original size:17 final size:17
Alignment explanation
Indices: 11303751--11303797 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
11303741 TATATTTAAA
11303751 TATTTATATAAAATAAT
1 TATTTATATAAAATAAT
*
11303768 TATTTATA-ATAATAAT
1 TATTTATATAAAATAAT
* *
11303784 TTTTTCT-TAAAATA
1 TATTTATATAAAATA
11303798 TATAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTTATATAAAATAAT
Found at i:11304008 original size:152 final size:159
Alignment explanation
Indices: 11303758--11304058 Score: 395
Period size: 152 Copynumber: 1.9 Consensus size: 159
11303748 AAATATTTAT
**
11303758 ATAAAATAATTATTTATAATAATAATTTTTTCTTAAAATATATAAAATATATTGATAATATATAA
1 ATAAAATAATTATTTATAATAATAATAATTTCTT---ATATATAAAATATATT-ATAATATATAA
* * *
11303823 AAAATCTTTAGGTGCAATATATAAAAATAAAATTCACAATTAT-A-AA-TAAAAAATATTATAAT
62 AAAATCTTTAGGTGCAATATATAAAAACAAAATTCAAAATTATAATAAGAAAAAAATATTATAAT
11303885 AAGAACATATAACATATAATAAACAAAACTCAC
127 AAGAACATATAACATATAATAAACAAAACTCAC
*
11303918 ATAAAATAATTATTTATAATAATAATAATTT-TT-TCT-TAAAATATA-T-TAATATATAAACAA
1 ATAAAATAATTATTTATAATAATAATAATTTCTTATATATAAAATATATTATAATATATAAA-AA
* *
11303978 AGT-TTTAGGTGCAATATGTAAAAACAAAATTCAAAATTATAATAAGAAAAAAATGTTATAATAA
65 A-TCTTTAGGTGCAATATATAAAAACAAAATTCAAAATTATAATAAGAAAAAAATATTATAATAA
* *
11304042 GAATATGTAACATATAA
129 GAACATATAACATATAA
11304059 GAAGAAAAAA
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
151 11 0.09
152 37 0.29
153 3 0.02
154 11 0.09
155 33 0.26
159 2 0.02
160 29 0.23
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.35
Consensus pattern (159 bp):
ATAAAATAATTATTTATAATAATAATAATTTCTTATATATAAAATATATTATAATATATAAAAAA
TCTTTAGGTGCAATATATAAAAACAAAATTCAAAATTATAATAAGAAAAAAATATTATAATAAGA
ACATATAACATATAATAAACAAAACTCAC
Found at i:11304460 original size:198 final size:195
Alignment explanation
Indices: 11303888--11304468 Score: 728
Period size: 201 Copynumber: 2.9 Consensus size: 195
11303878 TTATAATAAG
* * **
11303888 AACATATAACATATAATAAACAAA-ACTCACATAAAATAATTATTTATAATAATAATAATTTT--
1 AACATGTAACATATAATAAGCAAATACTCACATAAAATAATTATTTATAATAAT-ATTTTTTTAA
* * *
11303950 TTCT-TAAAATATATTAAT-A-TATAAACAAAGTTTTAGGTGCAATATGTAAAAACAAAATTCAA
65 TTATATAAAATATATTAATAATTATAAA-AAATTTTTAGGTGCAATATATAAAAACAAAATTCAA
* * *
11304012 AATTATAATAAGAAAAAAATGTTATAATAAGAATATGTAACATATAAGAAGAAAAAAAATGGAAC
129 AATTATAATAAG--AAAATTGTTATAATAAGAACATGTAACATATAATAAGAAAAAAAATGGAAC
11304077 ATAT
192 ATAT
* * ** *
11304081 GATATGTAACATATAATAAGCAAATACTCACATAAAATAATTATTTATTGTAGTATTTTTTTCTT
1 AACATGTAACATATAATAAGCAAATACTCACATAAAATAATTATTTATAATA--ATATTTTT-TT
* * * * *
11304146 AAAATATATAAAATTTATTAATAATATATATAAAAAATTTTAAGG-GTAATATATAAAAATAAAA
63 -AATTATATAAAATATATTAAT-A-AT-TATAAAAAATTTTTAGGTGCAATATATAAAAACAAAA
*
11304210 TTCAAAATTATAATAAAAAAATTGTTATAATAAGAACATGTAACATATAATAAGAAAAAAAATGG
124 TTCAAAATTATAATAAGAAAATTGTTATAATAAGAACATGTAACATATAATAAGAAAAAAAATGG
*
11304275 AACATGT
189 AACATAT
* * *
11304282 AACATGTAACATATAATAAGCAAATACTTACCTAAAATAAGTATTTATAATAATATTTTTTTACA
1 AACATGTAACATATAATAAGCAAATACTCACATAAAATAATTATTTATAATAATATTTTTTTA-A
*
11304347 TTATATAAAATATATTAATAATGTATAAAATAGATTTTTAGGTGCAATATATAAAAA-AAAAATC
65 TTATATAAAATATATTAATAAT-TATAAAA-A-ATTTTTAGGTGCAATATATAAAAACAAAATTC
*
11304411 AAAATTATAATAAGAAAATTGTTATAATAAGAACATGTATCATATAATAAGAAAAAAA
127 AAAATTATAATAAGAAAATTGTTATAATAAGAACATGTAACATATAATAAGAAAAAAA
11304469 TATTTGGTTG
Statistics
Matches: 333, Mismatches: 38, Indels: 29
0.83 0.09 0.07
Matches are distributed among these distances:
193 20 0.06
194 25 0.08
195 3 0.01
196 13 0.04
197 3 0.01
198 90 0.27
199 22 0.07
200 13 0.04
201 96 0.29
203 33 0.10
204 9 0.03
205 6 0.02
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (195 bp):
AACATGTAACATATAATAAGCAAATACTCACATAAAATAATTATTTATAATAATATTTTTTTAAT
TATATAAAATATATTAATAATTATAAAAAATTTTTAGGTGCAATATATAAAAACAAAATTCAAAA
TTATAATAAGAAAATTGTTATAATAAGAACATGTAACATATAATAAGAAAAAAAATGGAACATAT
Found at i:11319894 original size:12 final size:14
Alignment explanation
Indices: 11319878--11319914 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
11319868 TCCTACATTT
11319878 TACTAAAAAAAT-A
1 TACTAAAAAAATAA
*
11319891 -ACTATAAAAATAA
1 TACTAAAAAAATAA
11319904 TACTAAAAAAA
1 TACTAAAAAAA
11319915 ATTATTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 10 0.50
13 1 0.05
14 9 0.45
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (14 bp):
TACTAAAAAAATAA
Found at i:11321451 original size:15 final size:16
Alignment explanation
Indices: 11321431--11321462 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
11321421 CTCAATATGT
11321431 AAGCATAAAA-AAATA
1 AAGCATAAAAGAAATA
11321446 AAGCATAAAAGAAATA
1 AAGCATAAAAGAAATA
11321462 A
1 A
11321463 CACTGAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.12
Consensus pattern (16 bp):
AAGCATAAAAGAAATA
Found at i:11324693 original size:21 final size:21
Alignment explanation
Indices: 11324639--11324697 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
11324629 ATAATAGAGT
* *
11324639 AGCAACAATAACGACTTAATG
1 AGCAACAGTAATGACTTAATG
* * * *
11324660 AGCAAGAGCAATGGCTTCATG
1 AGCAACAGTAATGACTTAATG
11324681 AGCAACAGTAATGACTT
1 AGCAACAGTAATGACTT
11324698 GCAACATTGA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (21 bp):
AGCAACAGTAATGACTTAATG
Found at i:11324877 original size:16 final size:15
Alignment explanation
Indices: 11324856--11324885 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11324846 TTAAGTTATA
11324856 TTTTTTATTTATGTTT
1 TTTTTTATTT-TGTTT
11324872 TTTTTTATTTTGTT
1 TTTTTTATTTTGTT
11324886 ATAATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (15 bp):
TTTTTTATTTTGTTT
Found at i:11324896 original size:22 final size:22
Alignment explanation
Indices: 11324873--11324914 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
11324863 TTTATGTTTT
11324873 TTTTTAT-TTTG-TTATAATAA
1 TTTTTATATTTGTTTATAATAA
11324893 TTTTTATATTTGTTTATAATAA
1 TTTTTATATTTGTTTATAATAA
11324915 AATGTTCAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 4 0.20
22 9 0.45
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTTTATATTTGTTTATAATAA
Found at i:11325105 original size:27 final size:27
Alignment explanation
Indices: 11325073--11325124 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
11325063 GTCAGAGATT
* *
11325073 GATGCATTTTTTGATATAGAGATATTG
1 GATGCATTTTATGAGATAGAGATATTG
*
11325100 GATGCATTTTATGAGATGGAGATAT
1 GATGCATTTTATGAGATAGAGATAT
11325125 CGGCTATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.25, T:0.40
Consensus pattern (27 bp):
GATGCATTTTATGAGATAGAGATATTG
Found at i:11331313 original size:19 final size:19
Alignment explanation
Indices: 11331289--11331356 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
11331279 TTTTCAAGCT
11331289 CTAAACCACCCACCAAACC
1 CTAAACCACCCACCAAACC
* **
11331308 CTAAACCACCAATGAAACC
1 CTAAACCACCCACCAAACC
* * *
11331327 TTATACCACCCACTAAACC
1 CTAAACCACCCACCAAACC
*
11331346 CTCAACCACCC
1 CTAAACCACCC
11331357 TTCAAACACT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.40, C:0.47, G:0.01, T:0.12
Consensus pattern (19 bp):
CTAAACCACCCACCAAACC
Found at i:11331373 original size:38 final size:38
Alignment explanation
Indices: 11331293--11331382 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 38
11331283 CAAGCTCTAA
* *
11331293 ACCACCCACCAAACCCTAAACCACCAATGAAACCTTAT
1 ACCACCCACCAAACCCTAAACCACCAATCAAACCTTAC
* * **
11331331 ACCACCCACTAAACCCTCAACCACCCTTCAAACAC-TAC
1 ACCACCCACCAAACCCTAAACCACCAATCAAAC-CTTAC
*
11331369 ACCA-CCATCAAACC
1 ACCACCCACCAAACC
11331383 TTATACCCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
37 8 0.19
38 34 0.79
39 1 0.02
ACGTcount: A:0.40, C:0.47, G:0.01, T:0.12
Consensus pattern (38 bp):
ACCACCCACCAAACCCTAAACCACCAATCAAACCTTAC
Found at i:11331406 original size:26 final size:26
Alignment explanation
Indices: 11331377--11331432 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
11331367 ACACCACCAT
11331377 CAAACCTTATACCCTAAACCAAAACC
1 CAAACCTTATACCCTAAACCAAAACC
*
11331403 CAAACCTTATACCTTAAACCAAAACC
1 CAAACCTTATACCCTAAACCAAAACC
11331429 CAAA
1 CAAA
11331433 TCCCAAACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (26 bp):
CAAACCTTATACCCTAAACCAAAACC
Found at i:11331460 original size:18 final size:19
Alignment explanation
Indices: 11331437--11331478 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
11331427 CCCAAATCCC
*
11331437 AAACCA-CTGTGAAACCCT
1 AAACCACCTGTCAAACCCT
*
11331455 AAACCACCTTTCAAACCCT
1 AAACCACCTGTCAAACCCT
11331474 AAACC
1 AAACC
11331479 CTAAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.40, C:0.38, G:0.05, T:0.17
Consensus pattern (19 bp):
AAACCACCTGTCAAACCCT
Found at i:11331488 original size:19 final size:19
Alignment explanation
Indices: 11331466--11331601 Score: 84
Period size: 19 Copynumber: 7.2 Consensus size: 19
11331456 AACCACCTTT
*
11331466 CAAACCCTAAACCCTAAAA
1 CAAACCCTAAACCCTAAAC
* * *
11331485 CAAAACC-AAACCCGAAGC
1 CAAACCCTAAACCCTAAAC
*
11331503 TCTAACCC-AAACCCTAAAC
1 -CAAACCCTAAACCCTAAAC
*
11331522 CAAACCTTAAACCCT-AAC
1 CAAACCCTAAACCCTAAAC
* **
11331540 CTAAACCCTAAA-CTTACCC
1 C-AAACCCTAAACCCTAAAC
**
11331559 CAAACCCTAAAAACTCAAAC
1 CAAACCCTAAACCCT-AAAC
*
11331579 C-AACCCTCAAACCTTAAAAC
1 CAAACCCT-AAACCCT-AAAC
11331599 CAA
1 CAA
11331602 TCATGCATCT
Statistics
Matches: 87, Mismatches: 22, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
18 29 0.33
19 45 0.52
20 12 0.14
21 1 0.01
ACGTcount: A:0.47, C:0.39, G:0.01, T:0.12
Consensus pattern (19 bp):
CAAACCCTAAACCCTAAAC
Found at i:11331522 original size:31 final size:31
Alignment explanation
Indices: 11331487--11331552 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
11331477 CCCTAAAACA
* *
11331487 AAACCAAACCCGAAGCTCTAACCCAAACCCT
1 AAACCAAACCCGAAACCCTAACCCAAACCCT
** *
11331518 AAACCAAACCTTAAACCCTAACCTAAACCCT
1 AAACCAAACCCGAAACCCTAACCCAAACCCT
11331549 AAAC
1 AAAC
11331553 TTACCCCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.39, G:0.03, T:0.12
Consensus pattern (31 bp):
AAACCAAACCCGAAACCCTAACCCAAACCCT
Found at i:11338911 original size:20 final size:21
Alignment explanation
Indices: 11338888--11338932 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
11338878 TATTCAATTA
*
11338888 ATTTACTTAATCAACT-AAAT
1 ATTTAATTAATCAACTAAAAT
* *
11338908 ATTTAATTAATTAATTAAAAT
1 ATTTAATTAATCAACTAAAAT
11338929 ATTT
1 ATTT
11338933 TTGATCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTAATTAATCAACTAAAAT
Found at i:11342317 original size:3 final size:3
Alignment explanation
Indices: 11342311--11342363 Score: 81
Period size: 3 Copynumber: 17.3 Consensus size: 3
11342301 TGTGTAAAAA
11342311 AAT AAT AA- AACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11342356 AACT AAT A
1 AA-T AAT A
11342364 CGCACACCAC
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:11342451 original size:2 final size:2
Alignment explanation
Indices: 11342446--11342492 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
11342436 GACATTGATC
* * *
11342446 CT CT CT -T C- CT CT CC CT CC CT AT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11342486 CT CT CT C
1 CT CT CT C
11342493 CAGTCTTCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.02, C:0.53, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:11343745 original size:2 final size:2
Alignment explanation
Indices: 11343738--11343773 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11343728 CAGGTACAAT
11343738 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11343774 AATGCATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:11345428 original size:19 final size:19
Alignment explanation
Indices: 11345406--11345444 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
11345396 TTATATAATC
* *
11345406 ATTAAATGATTAAAATTAA
1 ATTAAATAATTAAAAGTAA
11345425 ATTAAATAATTAAAAGTAA
1 ATTAAATAATTAAAAGTAA
11345444 A
1 A
11345445 ATAATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATTAAATAATTAAAAGTAA
Found at i:11345795 original size:8 final size:9
Alignment explanation
Indices: 11345771--11345865 Score: 50
Period size: 9 Copynumber: 9.8 Consensus size: 9
11345761 GTATTTTCGG
11345771 TATTTTTTA
1 TATTTTTTA
*
11345780 TAATTTTTTT
1 T-ATTTTTTA
11345790 TATTTTTTCA
1 TATTTTTT-A
*
11345800 TATTTTTTGC
1 TATTTTTT-A
11345810 TCAATTTTTATAA
1 T--ATTTTT-T-A
* *
11345823 TTTTTATTTC
1 TATTT-TTTA
11345833 TATTTTTTA
1 TATTTTTTA
*
11345842 TATATTTTA
1 TATTTTTTA
11345851 T-TTTATTT-
1 TATTT-TTTA
11345859 TATTTTT
1 TATTTTT
11345866 GTGTGAACTT
Statistics
Matches: 66, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
8 5 0.08
9 26 0.39
10 21 0.32
11 4 0.06
12 8 0.12
13 2 0.03
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (9 bp):
TATTTTTTA
Found at i:11345850 original size:22 final size:19
Alignment explanation
Indices: 11345771--11345859 Score: 81
Period size: 22 Copynumber: 4.3 Consensus size: 19
11345761 GTATTTTCGG
11345771 TATTTTTTATAATTTTTTT
1 TATTTTTTATAATTTTTTT
11345790 TATTTTTTCAT-ATTTTTTGCT
1 TATTTTTT-ATAATTTTTT--T
* *
11345811 CAATTTTTATAATTTTTATTT
1 TATTTTTTATAA-TTTT-TTT
11345832 CTATTTTTTATATATTTTATTT
1 -TATTTTTTATA-ATTTT-TTT
11345854 TATTTT
1 TATTTT
11345860 ATTTTTGTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
19 15 0.26
20 4 0.07
21 15 0.26
22 21 0.36
23 3 0.05
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73
Consensus pattern (19 bp):
TATTTTTTATAATTTTTTT
Found at i:11346223 original size:126 final size:127
Alignment explanation
Indices: 11346026--11346276 Score: 312
Period size: 126 Copynumber: 2.0 Consensus size: 127
11346016 TTAAAAAATG
* * * **
11346026 GCTAAGGAAAAAGTTAAAATATCAAATTTTCTTTAGAATAAAATTTTAAAAATATTTTTAAAAAA
1 GCTAAGAAAAAAGGTAAAATATCAAATTTTCTTCAGAATAAAATTTTAAAAATATTTAGAAAAAA
* * * * *
11346091 ATTGAAATATCAATTTTT-CTTAAATTTTTTAAGAATAAAAATAAAATAAGATAAATAAAACT
66 ATTGAAATATCAATTTTTACTAAAATTCTTCAAGAAT-AAAATAAAATAAAATAAACAAAACT
* * * *
11346153 GCTAAGAAAAAAGGTAAAATATTAATTTTTCCTTCA-AATGAAAA-TTT-GAAATATTTAGAGAA
1 GCTAAGAAAAAAGGTAAAATATCAAATTTT-CTTCAGAAT-AAAATTTTAAAAATATTTAGAAAA
*
11346215 AATTTGAAATATCAATTTTTACTAAAATTCTTCAAGAATAAAATAAAATAAAATAAACAAAA
64 AAATTGAAATATCAATTTTTACTAAAATTCTTCAAGAATAAAATAAAATAAAATAAACAAAA
11346277 TCAATTAAGG
Statistics
Matches: 106, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
126 51 0.48
127 47 0.44
128 8 0.08
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (127 bp):
GCTAAGAAAAAAGGTAAAATATCAAATTTTCTTCAGAATAAAATTTTAAAAATATTTAGAAAAAA
ATTGAAATATCAATTTTTACTAAAATTCTTCAAGAATAAAATAAAATAAAATAAACAAAACT
Found at i:11347555 original size:23 final size:23
Alignment explanation
Indices: 11347525--11347570 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
11347515 TTATTTTTAC
11347525 TAAAAAAA-GATTTATTTAAATAA
1 TAAAAAAATG-TTTATTTAAATAA
*
11347548 TAAAAAAATGTTTGTTTAAATAA
1 TAAAAAAATGTTTATTTAAATAA
11347571 ATCCCTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (23 bp):
TAAAAAAATGTTTATTTAAATAA
Found at i:11347722 original size:24 final size:24
Alignment explanation
Indices: 11347678--11347732 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
11347668 TTATTTATAT
* *
11347678 AATAAAAAATTGATGAAAATAAAA
1 AATAAAAAATAGATAAAAATAAAA
*
11347702 AATAAAAAATAG-TAAACAATAAAT
1 AATAAAAAATAGATAAA-AATAAAA
11347726 AA-AAAAA
1 AATAAAAA
11347733 TGTTTAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (24 bp):
AATAAAAAATAGATAAAAATAAAA
Found at i:11353746 original size:69 final size:69
Alignment explanation
Indices: 11353622--11353752 Score: 151
Period size: 69 Copynumber: 1.9 Consensus size: 69
11353612 TTACTAGATA
* * * * * * *
11353622 AATTTTGAGTTTGTTACCATCTTTTATGAAGAAAAATCGAGCATTAAGGTTGATAAGCCAATTCG
1 AATTTTGAGCTTGTCACCATCTTTTATGAAAAAAAATCAAGCATTAAGATGGATAACCCAATTCG
11353687 TATG
66 TATG
11353691 AATTTTGAGCTTGTCACCAT-TGTTTAT-AAAAAGAAATCAAGCATTATA-ATGGATAACCCAAT
1 AATTTTGAGCTTGTCACCATCT-TTTATGAAAAA-AAATCAAGCATTA-AGATGGATAACCCAAT
11353753 CTAAATGACT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
68 5 0.10
69 46 0.88
70 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (69 bp):
AATTTTGAGCTTGTCACCATCTTTTATGAAAAAAAATCAAGCATTAAGATGGATAACCCAATTCG
TATG
Found at i:11356251 original size:72 final size:72
Alignment explanation
Indices: 11356122--11356264 Score: 189
Period size: 72 Copynumber: 2.0 Consensus size: 72
11356112 TTGGCTCATG
* ** * * *
11356122 TTGATACCTTACTGGACAATACTGTTAGGCACTTTATATTTTCATTCATGGCTGGGTTTTTAGGT
1 TTGATACCTTACTGGACAACACCATTAGGCACTCTATATTTTCATTCATGGCTGGGTTCTTAGGC
11356187 TACAATA
66 TACAATA
* * *
11356194 TTGATACCTTAGTGGACAACACCATTAGGCACTCTCTATTTTCATTCAT-GATCGGGTTCTTAGG
1 TTGATACCTTACTGGACAACACCATTAGGCACTCTATATTTTCATTCATGGCT-GGGTTCTTAGG
11356258 CTACAAT
65 CTACAAT
11356265 CAAATCAAGA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 2 0.03
72 59 0.97
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (72 bp):
TTGATACCTTACTGGACAACACCATTAGGCACTCTATATTTTCATTCATGGCTGGGTTCTTAGGC
TACAATA
Found at i:11359996 original size:35 final size:33
Alignment explanation
Indices: 11359957--11360057 Score: 121
Period size: 34 Copynumber: 2.9 Consensus size: 33
11359947 TCTTTTAAAA
*
11359957 ACCATAGCCTCTGGTTATAAAAGTTTTCTTAAAGT
1 ACCATAGCCTCTGGTTATAAGAGTTTTC--AAAGT
* *
11359992 ACCATAGCCTCTGGTTAGAGGAGTTATTCAAAGT
1 ACCATAGCCTCTGGTTATAAGAGTT-TTCAAAGT
**
11360026 TTCATAGCCTCTGGTTATAAGAGTTTATCAAA
1 ACCATAGCCTCTGGTTATAAGAGTTT-TCAAA
11360058 TTTTAAAAGC
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
33 1 0.02
34 31 0.54
35 22 0.39
36 3 0.05
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (33 bp):
ACCATAGCCTCTGGTTATAAGAGTTTTCAAAGT
Found at i:11360213 original size:33 final size:34
Alignment explanation
Indices: 11360154--11360218 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
11360144 TTTTTGTTGT
* * * *
11360154 AAGTATCATAGCTTCTGGTTAGAAGAG-TTTTCA
1 AAGTATCATAACCTCTAGTTAAAAGAGCTTTTCA
11360187 AAGTATCATAACCTCTAGTTAAAAGAGCTTTT
1 AAGTATCATAACCTCTAGTTAAAAGAGCTTTT
11360219 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (34 bp):
AAGTATCATAACCTCTAGTTAAAAGAGCTTTTCA
Found at i:11360290 original size:165 final size:164
Alignment explanation
Indices: 11359988--11360383 Score: 431
Period size: 165 Copynumber: 2.4 Consensus size: 164
11359978 AGTTTTCTTA
* * * * *
11359988 AAGTACCATAGCCTCTGGTTAGAGGAGTTATTCAAAGTTTCATAGCCTCTGGTTATAAGAGTTTA
1 AAGTACCATAGCTTCTGGTTAGAAGAGTT-TTCAAAGTATCATAGCCTCTAGTTAAAAGAGTTT-
* * * * * * *
11360053 TCAAATTTTAAAAGCTTTTTAATAGAGGGCCCTTTCAAAATTAGGCATGATTTGTTAGATAAAAT
64 TTAAATTTTAAAAGCTTCTGAATAGAGGACCCTTTCAAAATTAAGCATGATTTGTAAGACAAAAT
* * *
11360118 GGCATAATCTATAAGAGCTATCAGATTTTTTGTTGT-
129 GGCATAATCTATAAGACCTATAAGATTTTTTATT-TC
* *
11360154 AAGTATCATAGCTTCTGGTTAGAAGAGTTTTCAAAGTATCATAACCTCTAGTTAAAAGAGCTTTT
1 AAGTACCATAGCTTCTGGTTAGAAGAGTTTTCAAAGTATCATAGCCTCTAGTTAAAAGAG-TTTT
** **
11360219 TAAA-TTTAAAAGCCTATCTGGCT-GAGGACTTTTTCAAAATTAAGCATGATTTGTAAGACCAAA
65 TAAATTTTAAAAG-CT-TCTGAATAGAGGACCCTTTCAAAATTAAGCATGATTTGTAAGA-CAAA
11360282 A-GGCATAATCTATAAGACCTATAAGATTTTTTATTTC
127 ATGGCATAATCTATAAGACCTATAAGATTTTTTATTTC
* * * * * ** * *
11360319 ATGTGCTATAGCTTCTGGTTATAAGAGTTTTTAAAGTGCCATAGCCTCTACTTAGAAGAGTTTTT
1 AAGTACCATAGCTTCTGGTTAGAAGAGTTTTCAAAGTATCATAGCCTCTAGTTAAAAGAGTTTTT
11360384 TAAAGTGTCA
Statistics
Matches: 193, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
164 14 0.07
165 143 0.74
166 36 0.19
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (164 bp):
AAGTACCATAGCTTCTGGTTAGAAGAGTTTTCAAAGTATCATAGCCTCTAGTTAAAAGAGTTTTT
AAATTTTAAAAGCTTCTGAATAGAGGACCCTTTCAAAATTAAGCATGATTTGTAAGACAAAATGG
CATAATCTATAAGACCTATAAGATTTTTTATTTC
Found at i:11360408 original size:34 final size:33
Alignment explanation
Indices: 11360321--11360408 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 33
11360311 TTTATTTCAT
* * *
11360321 GTGCTATAGCTTCTGGTTATAAGAGTTTTTAAA
1 GTGCCATAGCCTCTGGTTAGAAGAGTTTTTAAA
**
11360354 GTGCCATAGCCTCTACTTAGAAGAGTTTTTTAAA
1 GTGCCATAGCCTCTGGTTAGAAGAG-TTTTTAAA
*
11360388 GTGTCATAGCCTCTGGTTAGA
1 GTGCCATAGCCTCTGGTTAGA
11360409 GGAATAGTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
33 20 0.43
34 26 0.57
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (33 bp):
GTGCCATAGCCTCTGGTTAGAAGAGTTTTTAAA
Found at i:11360925 original size:3 final size:3
Alignment explanation
Indices: 11360917--11360969 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
11360907 TTGTATTAGG
*
11360917 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11360965 TTA TT
1 TTA TT
11360970 TGACATCTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11361878 original size:6 final size:6
Alignment explanation
Indices: 11361869--11361921 Score: 72
Period size: 6 Copynumber: 8.7 Consensus size: 6
11361859 TCCTTTTCTA
*
11361869 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT-T GATTTGAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT --TTTTAT TTTTAT
11361918 TTTT
1 TTTT
11361922 GTTATTTGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 1 0.02
6 37 0.88
7 3 0.07
8 1 0.02
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:11364637 original size:3 final size:3
Alignment explanation
Indices: 11364629--11364672 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
11364619 AAGGATAAAC
11364629 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
11364673 GATGATGATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11364677 original size:3 final size:3
Alignment explanation
Indices: 11364671--11364696 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11364661 AATAATAATA
11364671 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
11364697 AAGGCAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:11366043 original size:60 final size:62
Alignment explanation
Indices: 11365969--11366108 Score: 146
Period size: 64 Copynumber: 2.3 Consensus size: 62
11365959 AAACATATTT
* * *
11365969 AATAATCCAC-TTCAAATTTTA-TGAGGTGATTATT-TAGGCCTTTTTG-TCA-AAAATGCTTTG
1 AATAATCC-CTTTCAAATTTTATTG-GG-GATTATTCAAGGCCTTTTTGCTCAGAAAACGCCTTG
* *
11366029 AATAATCCCTTTCAATTTTTTTATTGGGGATTATTCAAGGCGTTTTTGCTCAGAAAACGCCTTG
1 AATAATCCCTTTCAA--ATTTTATTGGGGATTATTCAAGGCCTTTTTGCTCAGAAAACGCCTTG
*
11366093 AATAATCCCTTGCAAA
1 AATAATCCCTTTCAAA
11366109 AAATTTAATG
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
59 1 0.02
60 13 0.20
61 7 0.11
62 17 0.26
63 5 0.08
64 23 0.35
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (62 bp):
AATAATCCCTTTCAAATTTTATTGGGGATTATTCAAGGCCTTTTTGCTCAGAAAACGCCTTG
Found at i:11366744 original size:149 final size:150
Alignment explanation
Indices: 11366428--11366737 Score: 378
Period size: 149 Copynumber: 2.1 Consensus size: 150
11366418 ATCGAAGGGG
* * * * * *
11366428 ATTATTCATAGCA-TTTTTAGCCAGAAATACTTTGAATAATTA-CATTCAATTTTTTGTAAGGGA
1 ATTATTCAAAGCATTTTTTA-TCAGAAACACTTTCAATAA-CACCATTCAAATTTTTGTAAGGGA
* * * *
11366491 TTATTGAATGTGTTTTCTGAGCAAAAACACCTTAAATAATCTCCTTAAATTTTTATGAGTTTAGA
64 TTATTCAAGGCGTTTTCTGAGCAAAAACACATTAAATAATCTCCTTAAATTTTTATGAGTTTAGA
*
11366556 GTTTAAAGTTTAGGGTTTAAAA
129 GTTTAAAGTTGAGGGTTTAAAA
*
11366578 ATTATTTAAAGCATTTTTTATCAGAAACACTTTCAATAACACCATTCAAATTTTT-TAAGGGATT
1 ATTATTCAAAGCATTTTTTATCAGAAACACTTTCAATAACACCATTCAAATTTTTGTAAGGGATT
* * *
11366642 ATTCAAGGCGTTTTCT-AGGCAAAAACGCATTGAATAATC-CCTTTAAGTTTTTATGAGTTTAGA
66 ATTCAAGGCGTTTTCTGA-GCAAAAACACATTAAATAATCTCC-TTAAATTTTTATGAGTTTAGA
** **
11366705 GTTTGGAGTTGAGGGTTTATGA
129 GTTTAAAGTTGAGGGTTTAAAA
11366727 ATTATTCAAAG
1 ATTATTCAAAG
11366738 TGTTTTTGGC
Statistics
Matches: 136, Mismatches: 20, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
148 3 0.02
149 88 0.65
150 39 0.29
151 6 0.04
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (150 bp):
ATTATTCAAAGCATTTTTTATCAGAAACACTTTCAATAACACCATTCAAATTTTTGTAAGGGATT
ATTCAAGGCGTTTTCTGAGCAAAAACACATTAAATAATCTCCTTAAATTTTTATGAGTTTAGAGT
TTAAAGTTGAGGGTTTAAAA
Found at i:11367402 original size:13 final size:13
Alignment explanation
Indices: 11367384--11367408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11367374 TGTGATGGTC
11367384 ATTTTTTTTGAAA
1 ATTTTTTTTGAAA
11367397 ATTTTTTTTGAA
1 ATTTTTTTTGAA
11367409 TAAAGATTTT
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
ATTTTTTTTGAAA
Found at i:11367474 original size:3 final size:3
Alignment explanation
Indices: 11367468--11367515 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
11367458 CAAAAAAAAA
* *
11367468 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11367516 TTCACAACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11370950 original size:12 final size:12
Alignment explanation
Indices: 11370933--11370958 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11370923 TTTAATACAT
11370933 TTAAAAAAATTA
1 TTAAAAAAATTA
11370945 TTAAAAAAATTA
1 TTAAAAAAATTA
11370957 TT
1 TT
11370959 TTACTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAAAAATTA
Found at i:11371227 original size:31 final size:30
Alignment explanation
Indices: 11371176--11371266 Score: 76
Period size: 31 Copynumber: 2.9 Consensus size: 30
11371166 AATCATTTGG
* * *
11371176 AAATTTCTACATAATATTTAACATGATAT-A
1 AAATTTTTACTTAATTTTTAA-ATGATATAA
* * * *
11371206 GAGTTTTTATTTAATTTTTTAAACCGATATAA
1 AAATTTTTACTTAA-TTTTTAAA-TGATATAA
11371238 AAATTTTTACTTAATTTTTAAAATGATAT
1 AAATTTTTACTTAATTTTT-AAATGATAT
11371267 GTAATTTTAA
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
30 10 0.22
31 21 0.46
32 15 0.33
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (30 bp):
AAATTTTTACTTAATTTTTAAATGATATAA
Found at i:11372561 original size:5 final size:5
Alignment explanation
Indices: 11372551--11372596 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
11372541 GTTTTTAAAA
* *
11372551 ATTTT ATTTT ATTTT ATTTTT ATTTT ATTTTT AATTT ATTGT ATTT
1 ATTTT ATTTT ATTTT A-TTTT ATTTT A-TTTT ATTTT ATTTT ATTT
11372597 GAAAACATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 25 0.71
6 10 0.29
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:11372573 original size:11 final size:11
Alignment explanation
Indices: 11372551--11372590 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
11372541 GTTTTTAAAA
11372551 ATTTTA-TTTT
1 ATTTTATTTTT
11372561 ATTTTATTTTT
1 ATTTTATTTTT
11372572 ATTTTATTTTT
1 ATTTTATTTTT
*
11372583 AATTTATT
1 ATTTTATT
11372591 GTATTTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 6 0.21
11 22 0.79
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:11372588 original size:16 final size:17
Alignment explanation
Indices: 11372553--11372596 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
11372543 TTTTAAAAAT
*
11372553 TTTATTTTA-TTTTATT
1 TTTATTTTATTTTTATA
11372569 TTTATTTTATTTTTA-A
1 TTTATTTTATTTTTATA
*
11372585 TTTATTGTATTT
1 TTTATTTTATTT
11372597 GAAAACATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTATTTTATTTTTATA
Found at i:11373540 original size:14 final size:13
Alignment explanation
Indices: 11373511--11373562 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 13
11373501 AATTGATTTT
*
11373511 TATATTTTTCAAA
1 TATATTTTTAAAA
11373524 TATATTTTGTAAAA
1 TATATTTT-TAAAA
*
11373538 TATTATAATTTAAAA
1 TA-TAT-TTTTAAAA
11373553 TAT-TTTTTAA
1 TATATTTTTAA
11373563 TTTTTATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 5 0.15
13 9 0.27
14 7 0.21
15 10 0.30
16 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (13 bp):
TATATTTTTAAAA
Found at i:11373707 original size:32 final size:31
Alignment explanation
Indices: 11373671--11373758 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
11373661 TTAAAATCAC
* *
11373671 ATATCATTTTAAAAAATTAAGTAAAAAGTTTT
1 ATATCATTTTAAAAAATTAAGTAAAAA-CTCT
* *
11373703 ATATC-TGTTTAAGAAATTAAATAAAAACTCT
1 ATATCAT-TTTAAAAAATTAAGTAAAAACTCT
* * *
11373734 ATATCATGTTAAAATATTATGTAAA
1 ATATCATTTTAAAAAATTAAGTAAA
11373759 TATTTTTGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
31 21 0.47
32 24 0.53
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.39
Consensus pattern (31 bp):
ATATCATTTTAAAAAATTAAGTAAAAACTCT
Found at i:11378279 original size:2 final size:2
Alignment explanation
Indices: 11378268--11378396 Score: 134
Period size: 2 Copynumber: 65.0 Consensus size: 2
11378258 AGTGTCCAAT
*
11378268 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
11378309 TA CA TA TA TA CA TA TA TA TG TA TA TA TG TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
11378351 TA CA CA TA TA TA TA TA CA TA TA TA TG TG TG TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11378393 TA TA
1 TA TA
11378397 ACAGCCGAGG
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
1 1 0.01
2 107 0.99
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:11379789 original size:15 final size:15
Alignment explanation
Indices: 11379769--11379798 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11379759 ACATACGTTT
11379769 GTTTGTTTATATTCA
1 GTTTGTTTATATTCA
11379784 GTTTGTTTATATTCA
1 GTTTGTTTATATTCA
11379799 TAGTAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (15 bp):
GTTTGTTTATATTCA
Found at i:11380387 original size:23 final size:23
Alignment explanation
Indices: 11380336--11380387 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
11380326 TTAATAAAAA
*
11380336 ATAAAAACAAAAATAAAAAAGTG
1 ATAAAAACAAAAATAAAAAAATG
* * *
11380359 AAAAAAATAAAAATAAAAAAATT
1 ATAAAAACAAAAATAAAAAAATG
11380382 ATAAAA
1 ATAAAA
11380388 GGTACCACGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (23 bp):
ATAAAAACAAAAATAAAAAAATG
Found at i:11380975 original size:21 final size:22
Alignment explanation
Indices: 11380950--11381005 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
11380940 ATAAAAAATC
*
11380950 AAGAAAAGGAAAAATAAA-AAG
1 AAGAAAAGGAAAAATAAACAAA
*
11380971 GAGAAAA-GAAAAATAAACAAA
1 AAGAAAAGGAAAAATAAACAAA
11380992 AAGAAAAAGGAAAA
1 AAG-AAAAGGAAAA
11381006 GAAAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.34
21 10 0.34
22 4 0.14
23 5 0.17
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (22 bp):
AAGAAAAGGAAAAATAAACAAA
Found at i:11384773 original size:12 final size:13
Alignment explanation
Indices: 11384756--11384789 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
11384746 AAAACTTAAG
11384756 AACTTAAAA-GAA
1 AACTTAAAAGGAA
11384768 AACTTAAAAGGAA
1 AACTTAAAAGGAA
11384781 AACTCTAAA
1 AACT-TAAA
11384790 GAACTAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 7 0.35
14 4 0.20
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.18
Consensus pattern (13 bp):
AACTTAAAAGGAA
Found at i:11385978 original size:23 final size:22
Alignment explanation
Indices: 11385948--11385994 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
11385938 CATTCCTCAA
*
11385948 TTTTTTTTCTTTTTTAGTTTTAG
1 TTTTTTTTATTTTTTAG-TTTAG
11385971 TTTTTTTTATTTTTTAGTTTAG
1 TTTTTTTTATTTTTTAGTTTAG
11385993 TT
1 TT
11385995 ATTGGCTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.79
Consensus pattern (22 bp):
TTTTTTTTATTTTTTAGTTTAG
Found at i:11386106 original size:18 final size:19
Alignment explanation
Indices: 11386072--11386112 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
11386062 AAAGTATTTT
*
11386072 TTTCAATATCTTTTTTTCA
1 TTTCAATATCTTGTTTTCA
*
11386091 TTTCAA-ATCTTGTTTTCT
1 TTTCAATATCTTGTTTTCA
11386109 TTTC
1 TTTC
11386113 TTAATTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTCAATATCTTGTTTTCA
Found at i:11389846 original size:24 final size:22
Alignment explanation
Indices: 11389783--11389849 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 22
11389773 TTACCTAATT
11389783 TAAAAAA-CAATAAA-C-AAAAA
1 TAAAAAAGCAA-AAAGCAAAAAA
*
11389803 TAAAAATGCAAAAAGCAAAAAA
1 TAAAAAAGCAAAAAGCAAAAAA
11389825 TATAAAAAGCATAAAGAG-AAAAAA
1 TA-AAAAAGCA-AAA-AGCAAAAAA
11389849 T
1 T
11389850 CTTCCCTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 9 0.23
21 4 0.10
22 7 0.18
23 7 0.18
24 10 0.26
25 2 0.05
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.12
Consensus pattern (22 bp):
TAAAAAAGCAAAAAGCAAAAAA
Found at i:11390209 original size:16 final size:16
Alignment explanation
Indices: 11390188--11390246 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
11390178 TAAATTAAGA
11390188 TATTAAATAATAACAT
1 TATTAAATAATAACAT
11390204 TATTAATATAAT-ACAT
1 TATTAA-ATAATAACAT
11390220 ATATATAAAT-ATAA-AT
1 -TAT-TAAATAATAACAT
*
11390236 AATTAAA-AATA
1 TATTAAATAATA
11390247 TAATTATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
14 7 0.19
15 2 0.05
16 14 0.38
17 11 0.30
18 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TATTAAATAATAACAT
Found at i:11390979 original size:17 final size:16
Alignment explanation
Indices: 11390953--11390987 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
11390943 ATAAATAAAC
11390953 AAAACAAAAAGAAATA
1 AAAACAAAAAGAAATA
*
11390969 AAAAGCAAAAAGAATTA
1 AAAA-CAAAAAGAAATA
11390986 AA
1 AA
11390988 TATAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAACAAAAAGAAATA
Found at i:11393326 original size:2 final size:2
Alignment explanation
Indices: 11393321--11393368 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
11393311 ACACACACAC
* *
11393321 AT AT AT AT AT AT AT AT AT AT -T AA AGC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
11393363 AT AT AT
1 AT AT AT
11393369 CTATTAGGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:11395149 original size:20 final size:21
Alignment explanation
Indices: 11395112--11395151 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
11395102 ATCTAAACTT
*
11395112 TTATGCAATAGAATATGCAAC
1 TTATGCAATAGAACATGCAAC
11395133 TTATGCAA-AGAACATGCAA
1 TTATGCAATAGAACATGCAA
11395152 TCATGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
TTATGCAATAGAACATGCAAC
Found at i:11404074 original size:20 final size:20
Alignment explanation
Indices: 11404037--11404086 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
11404027 ACCTAAACTT
* *
11404037 TTATGCAATAGAATATGCAAC
1 TTATGCAA-AGAACATGCAAA
11404058 TTATGCAAAGAACATGCAAA
1 TTATGCAAAGAACATGCAAA
*
11404078 TCATGCAAA
1 TTATGCAAA
11404087 TAGGTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (20 bp):
TTATGCAAAGAACATGCAAA
Found at i:11405439 original size:10 final size:10
Alignment explanation
Indices: 11405432--11405461 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
11405422 CGAGATTCTT
11405432 CAAGATTCAA
1 CAAGATTCAA
11405442 CAAGATTCAA
1 CAAGATTCAA
11405452 CAAGATTCAA
1 CAAGATTCAA
11405462 TCTTTTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.20, G:0.10, T:0.20
Consensus pattern (10 bp):
CAAGATTCAA
Found at i:11418271 original size:18 final size:18
Alignment explanation
Indices: 11418248--11418306 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
11418238 TTAATAAGTA
11418248 TCATAAAAATGAAATGTC
1 TCATAAAAATGAAATGTC
*** * * *
11418266 TCATAACTCTAAAAAGTA
1 TCATAAAAATGAAATGTC
11418284 TCATAAAAATGAAATGTC
1 TCATAAAAATGAAATGTC
11418302 TCATA
1 TCATA
11418307 TTCCAATGAA
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (18 bp):
TCATAAAAATGAAATGTC
Found at i:11432572 original size:88 final size:88
Alignment explanation
Indices: 11432423--11432591 Score: 311
Period size: 88 Copynumber: 1.9 Consensus size: 88
11432413 GAGTTGATGT
*
11432423 CTCACAATCATTAACATGGCTAAAGATAAATTTCTTAATTGACATCTTGCAATGTAATTCCACCA
1 CTCACAATCACTAACATGGCTAAAGATAAATTTCTTAATTGACATCTTGCAATGTAATTCCACCA
11432488 AATGAGCTATATTTATTGATCAA
66 AATGAGCTATATTTATTGATCAA
**
11432511 CTCACAATCACTAATGTGGCTAAAGATAAATTTCTTAATTGACATCTTGCAATGTAATTCCACCA
1 CTCACAATCACTAACATGGCTAAAGATAAATTTCTTAATTGACATCTTGCAATGTAATTCCACCA
11432576 AATGAGCTATATTTAT
66 AATGAGCTATATTTAT
11432592 CATTTTTTAG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (88 bp):
CTCACAATCACTAACATGGCTAAAGATAAATTTCTTAATTGACATCTTGCAATGTAATTCCACCA
AATGAGCTATATTTATTGATCAA
Found at i:11435699 original size:143 final size:140
Alignment explanation
Indices: 11435552--11435946 Score: 406
Period size: 144 Copynumber: 2.8 Consensus size: 140
11435542 TCAACATGTG
* * * *
11435552 TGAAATTACTAAAATACCCTT-ATGAGTACTTCTGTAATTTGACTTTCTTAATG-TCTGTTTTTC
1 TGAAATTACTAAAATACCCTTAAAGGGTATTTTTGTAATTTGACTTTCTTAA-GATCTGTTTTTC
11435615 ATAAAACATTACAAATCATAGTTTTATATTATTTTATGATTTTTAGTGCATTAAAAACCTTGATC
65 ATAAAAC-TT-CAAATCATAGTTTTATATTATTTTATGATTTTTAGTG-ATTAAAAACCTTGATC
* *
11435680 GCACCTTAGAACATA
127 GCACCTT-GAAAAAA
* ** * *
11435695 TGAAATTACTAAAATGCTTTTAAGGGGTATTTTTGTAATTTGA-TATTCTCAAGATCAAT-TTTT
1 TGAAATTACTAAAATACCCTTAAAGGGTATTTTTGTAATTTGACT-TTCTTAAGATC--TGTTTT
* * *
11435758 TGCA-AAATGCTTCAAATCATGGTTTTATATTATTTTATGATTTTTAGTGATTAAAAATCTTGAT
63 T-CATAAA-ACTTCAAATCATAGTTTTATATTATTTTATGATTTTTAGTGATTAAAAACCTTGAT
*
11435822 TGCACCTTGAAAAAA
126 CGCACCTTGAAAAAA
* * * *
11435837 TGTAAAATTACAAAAATATCCTTAAAAGGGTATTTTTGTAATTTGACCTTCCTAAGATC-GATTT
1 TG--AAATTACTAAAATACCCTT-AAAGGGTATTTTTGTAATTTGACTTTCTTAAGATCTG-TTT
* * * *
11435901 TTCATGAAACTTTCAAATCCTAATTTTATATTATTTTAAGATTTTT
62 TTCATAAAAC-TTCAAATCATAGTTTTATATTATTTTATGATTTTT
11435947 GGTGTTTGGA
Statistics
Matches: 208, Mismatches: 29, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
142 7 0.03
143 44 0.21
144 113 0.54
145 40 0.19
146 4 0.02
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (140 bp):
TGAAATTACTAAAATACCCTTAAAGGGTATTTTTGTAATTTGACTTTCTTAAGATCTGTTTTTCA
TAAAACTTCAAATCATAGTTTTATATTATTTTATGATTTTTAGTGATTAAAAACCTTGATCGCAC
CTTGAAAAAA
Found at i:11437306 original size:7 final size:7
Alignment explanation
Indices: 11437294--11437559 Score: 118
Period size: 7 Copynumber: 40.4 Consensus size: 7
11437284 ATTCTTCATG
11437294 AAACCCT
1 AAACCCT
*
11437301 AAACCCC
1 AAACCCT
11437308 AAACCC-
1 AAACCCT
* *
11437314 CAACCTT
1 AAACCCT
*
11437321 AAACCTT
1 AAACCCT
*
11437328 AAACTCT
1 AAACCCT
11437335 AAACCCT
1 AAACCCT
*
11437342 AAACCTT
1 AAACCCT
*
11437349 ACA-CCT
1 AAACCCT
11437355 AAA-CCT
1 AAACCCT
*
11437361 AAACCCC
1 AAACCCT
**
11437368 AAA-TTT
1 AAACCCT
11437374 AAACCCT
1 AAACCCT
11437381 AAACCCT
1 AAACCCT
* **
11437388 AAGCTTT
1 AAACCCT
*
11437395 AAACACT
1 AAACCCT
*
11437402 AAATCCT
1 AAACCCT
*
11437409 AAACTC-
1 AAACCCT
*
11437415 AAATCCT
1 AAACCCT
**
11437422 TGA-CCT
1 AAACCCT
11437428 AAACCCT
1 AAACCCT
*
11437435 AAACCCC
1 AAACCCT
11437442 AAA-CCT
1 AAACCCT
**
11437448 AAACTTT
1 AAACCCT
11437455 AAACCC-
1 AAACCCT
* *
11437461 AAATCTT
1 AAACCCT
11437468 AAACCCT
1 AAACCCT
11437475 AAACCC-
1 AAACCCT
*
11437481 AAATCCT
1 AAACCCT
* *
11437488 AAATCTT
1 AAACCCT
*
11437495 AAA-CCA
1 AAACCCT
11437501 AAACCCT
1 AAACCCT
11437508 -AA-CCT
1 AAACCCT
* *
11437513 AGACCTT
1 AAACCCT
11437520 AAA--CT
1 AAACCCT
*
11437525 -AACCCC
1 AAACCCT
11437531 AAACCCT
1 AAACCCT
11437538 AAA-CC-
1 AAACCCT
11437543 -AACCTCT
1 AAACC-CT
11437550 AAACCCT
1 AAACCCT
11437557 AAA
1 AAA
11437560 ACCACTTAAT
Statistics
Matches: 187, Mismatches: 54, Indels: 36
0.68 0.19 0.13
Matches are distributed among these distances:
4 4 0.02
5 5 0.03
6 50 0.27
7 124 0.66
8 4 0.02
ACGTcount: A:0.44, C:0.36, G:0.01, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:11437449 original size:20 final size:20
Alignment explanation
Indices: 11437425--11437509 Score: 91
Period size: 20 Copynumber: 4.2 Consensus size: 20
11437415 AAATCCTTGA
11437425 CCTAAACCCTAAACCCCAAA-
1 CCTAAACCCTAAA-CCCAAAT
**
11437445 CCTAAACTTTAAACCCAAAT
1 CCTAAACCCTAAACCCAAAT
*
11437465 CTTAAACCCTAAACCCAAAT
1 CCTAAACCCTAAACCCAAAT
* * * *
11437485 CCTAAATCTTAAACCAAAAC
1 CCTAAACCCTAAACCCAAAT
11437505 CCTAA
1 CCTAA
11437510 CCTAGACCTT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 6 0.11
20 48 0.89
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (20 bp):
CCTAAACCCTAAACCCAAAT
Found at i:11437449 original size:67 final size:67
Alignment explanation
Indices: 11437294--11437499 Score: 152
Period size: 67 Copynumber: 3.1 Consensus size: 67
11437284 ATTCTTCATG
** * * * *
11437294 AAACCCTAAACCCCAAACCCCAACCTTAAACCTTAAACTCTAAACCCTAAACCTTACACCTAAAC
1 AAACCCTAAACCCCAAACCTAAACCCTAAACCTTAAACACTAAACCCTAAACCTCAAACCTAAAC
11437359 CT
66 CT
* *** * * * **
11437361 AAACCCCAAA-TTTAAACCCTAAACCCTAAGCTTTAAACACTAAATCCTAAA-CTCAAATCCTTG
1 AAACCCTAAACCCCAAA-CCTAAACCCTAAACCTTAAACACTAAACCCTAAACCTCAAA-CCTAA
11437424 ACCT
64 ACCT
** * *
11437428 AAACCCTAAACCCCAAACCTAAACTTTAAACC-CAAATC-TTAAACCCTAAACC-CAAATCCTAA
1 AAACCCTAAACCCCAAACCTAAACCCTAAACCTTAAA-CACTAAACCCTAAACCTCAAA-CCTAA
*
11437490 ATCTT
64 A-CCT
11437495 AAACC
1 AAACC
11437500 AAAACCCTAA
Statistics
Matches: 104, Mismatches: 29, Indels: 12
0.72 0.20 0.08
Matches are distributed among these distances:
66 29 0.28
67 72 0.69
68 3 0.03
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.20
Consensus pattern (67 bp):
AAACCCTAAACCCCAAACCTAAACCCTAAACCTTAAACACTAAACCCTAAACCTCAAACCTAAAC
CT
Found at i:11437546 original size:18 final size:19
Alignment explanation
Indices: 11437519--11437559 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11437509 ACCTAGACCT
*
11437519 TAAACTAACC-CCAAACCC
1 TAAACCAACCTCCAAACCC
*
11437537 TAAACCAACCTCTAAACCC
1 TAAACCAACCTCCAAACCC
11437556 TAAA
1 TAAA
11437560 ACCACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (19 bp):
TAAACCAACCTCCAAACCC
Found at i:11440300 original size:29 final size:29
Alignment explanation
Indices: 11440238--11440316 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
11440228 TCCAAACCCT
*
11440238 CAAACCCTAAA-CTAGTCCCTAAACCTTAAA
1 CAAACCCTAAATCAAG--CCTAAACCTTAAA
*
11440268 CAAACCCTAAATCAAGCCTAAA-CTCTAAG
1 CAAACCCTAAATCAAGCCTAAACCT-TAAA
* *
11440297 CAAACCTTAAATTAAGCCTA
1 CAAACCCTAAATCAAGCCTA
11440317 GACTGTAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
28 2 0.05
29 27 0.63
30 11 0.26
31 3 0.07
ACGTcount: A:0.44, C:0.30, G:0.05, T:0.20
Consensus pattern (29 bp):
CAAACCCTAAATCAAGCCTAAACCTTAAA
Found at i:11440459 original size:20 final size:20
Alignment explanation
Indices: 11440400--11440459 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
11440390 TTAAATCGAG
*
11440400 CTTAAACC-CTAAACCCCAAA
1 CTTAAACCTC-AAACCCTAAA
* * *
11440420 C-TAAATCCTTAAATCTTAAA
1 CTTAAA-CCTCAAACCCTAAA
11440440 CTTAAACCTCAAACCCTAAA
1 CTTAAACCTCAAACCCTAAA
11440460 TCCTAAACCA
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (20 bp):
CTTAAACCTCAAACCCTAAA
Found at i:11440537 original size:29 final size:29
Alignment explanation
Indices: 11440451--11440567 Score: 105
Period size: 29 Copynumber: 4.0 Consensus size: 29
11440441 TTAAACCTCA
*
11440451 AACCCTAAATCC-TAAACCAAATCTTAAACC
1 AACCCTAAA-CCTTAAA-CAAACCTTAAACC
* *
11440481 AACCCCTAAACCCTAAAC-AAGCTCTAAACC
1 AA-CCCTAAACCTTAAACAAACCT-TAAACC
* * *
11440511 AAGCCTAAACCTTAAGCAAACCTTAAATC
1 AACCCTAAACCTTAAACAAACCTTAAACC
* *
11440540 AACCCAAAACC-TAAACTAACCTTAAACC
1 AACCCTAAACCTTAAACAAACCTTAAACC
11440568 CTAAACCAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
28 14 0.19
29 30 0.42
30 17 0.24
31 11 0.15
ACGTcount: A:0.46, C:0.34, G:0.03, T:0.17
Consensus pattern (29 bp):
AACCCTAAACCTTAAACAAACCTTAAACC
Found at i:11440583 original size:30 final size:29
Alignment explanation
Indices: 11440543--11440633 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 29
11440533 TTAAATCAAC
* *
11440543 CCAAAACCTAAACTAACCTTAAACCCTAAA
1 CCAAATCCTAAACTAACC-AAAACCCTAAA
11440573 CCAAATCCTAAACTAACCCCAAAACCCTAAA
1 CCAAATCCTAAACTAA--CCAAAACCCTAAA
* * * *
11440604 CC-AATCCCAAACAAACCCAAACCCCAAA
1 CCAAATCCTAAACTAACCAAAACCCTAAA
11440632 CC
1 CC
11440634 TAACCAAACT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.25
30 26 0.49
31 12 0.23
32 2 0.04
ACGTcount: A:0.48, C:0.41, G:0.00, T:0.11
Consensus pattern (29 bp):
CCAAATCCTAAACTAACCAAAACCCTAAA
Found at i:11441702 original size:22 final size:23
Alignment explanation
Indices: 11441645--11441712 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 23
11441635 TTTAATATAA
11441645 AAATATTTTAAATTT-TTTAGTTTT
1 AAATATTTTAAATTTATTT--TTTT
* *
11441669 AAAAAATATTAAATTTATTTTTTT
1 -AAATATTTTAAATTTATTTTTTT
* *
11441693 -AATATTTTAATTTTACTTTT
1 AAATATTTTAAATTTATTTTT
11441713 GAAAGCTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
22 16 0.44
24 4 0.11
25 13 0.36
26 3 0.08
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (23 bp):
AAATATTTTAAATTTATTTTTTT
Found at i:11441896 original size:23 final size:25
Alignment explanation
Indices: 11441866--11441923 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
11441856 TTTTTAAATT
11441866 TTTTATTTTTTC-AAA-ATTTAATA
1 TTTTATTTTTTCAAAATATTTAATA
** *
11441889 TTTTATTTAATCAAAATATTTAATT
1 TTTTATTTTTTCAAAATATTTAATA
*
11441914 TTTTGTTTTT
1 TTTTATTTTT
11441924 AACATTTTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 10 0.37
24 3 0.11
25 14 0.52
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTATTTTTTCAAAATATTTAATA
Found at i:11442984 original size:11 final size:12
Alignment explanation
Indices: 11442968--11443018 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 12
11442958 AGAGGCAAGC
11442968 TTTTAA-TATTT
1 TTTTAATTATTT
11442979 TTTTAATTTATTCTT
1 TTTTAA-TTA-T-TT
11442994 TTTTAAATTATTT
1 TTTT-AATTATTT
11443007 TTTT-ATTATTT
1 TTTTAATTATTT
11443018 T
1 T
11443019 AAATTCTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
11 14 0.40
13 8 0.23
14 2 0.06
15 9 0.26
16 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTAATTATTT
Found at i:11442997 original size:15 final size:14
Alignment explanation
Indices: 11442976--11443010 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
11442966 GCTTTTAATA
*
11442976 TTTTTTTAATTTAT
1 TTTTTTTAAATTAT
11442990 TCTTTTTTAAATTAT
1 T-TTTTTTAAATTAT
11443005 TTTTTT
1 TTTTTT
11443011 ATTATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTAAATTAT
Found at i:11449117 original size:2 final size:2
Alignment explanation
Indices: 11449112--11449136 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11449102 TATATATATA
11449112 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
11449137 ACTGTTCTTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:11449520 original size:27 final size:25
Alignment explanation
Indices: 11449490--11449541 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
11449480 ATGGATACAT
*
11449490 CATAAGCATATAGAACTTATTGTTCCC
1 CATAAGCACATAGAAC-T-TTGTTCCC
11449517 CATAAGCACATAGAACTTTGTTCCC
1 CATAAGCACATAGAACTTTGTTCCC
11449542 TTTTCCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.33
26 1 0.04
27 15 0.62
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.31
Consensus pattern (25 bp):
CATAAGCACATAGAACTTTGTTCCC
Found at i:11450954 original size:16 final size:15
Alignment explanation
Indices: 11450933--11450962 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11450923 AATATAAATA
11450933 AATTTATTATATTTAT
1 AATTTATT-TATTTAT
11450949 AATTTATTTATTTA
1 AATTTATTTATTTA
11450963 ATTAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTATTTATTTAT
Found at i:11455232 original size:5 final size:5
Alignment explanation
Indices: 11455207--11455351 Score: 71
Period size: 5 Copynumber: 27.2 Consensus size: 5
11455197 TTTTAGTTTG
* * * * *
11455207 TATAT TATTAC TATAT TATAT GATAT TATAT TATCT TACTAT TATAG TATAG
1 TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT
* * * *
11455259 TATAT TA-A- TATAC TATAT GATATAG TGTAT TATAT TATTAT TACCAT
1 TATAT TATAT TATAT TATAT --TATAT TATAT TATAT TA-TAT TA-TAT
*
11455306 TATTAC TATTAT TATAT TAT-T ATATTAT TATCAT TATTAT TATAT T
1 TA-TAT TA-TAT TATAT TATAT -TA-TAT TAT-AT TA-TAT TATAT T
11455352 TTACTATTAT
Statistics
Matches: 109, Mismatches: 19, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
3 2 0.02
4 3 0.03
5 62 0.57
6 36 0.33
7 6 0.06
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:11455299 original size:3 final size:3
Alignment explanation
Indices: 11455286--11455365 Score: 80
Period size: 3 Copynumber: 28.3 Consensus size: 3
11455276 TGATATAGTG
* * *
11455286 TAT TA- TAT TAT TAT TAC CAT TAT TAC TAT TAT TA- TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
11455331 TAT TAT CAT TAT TAT TA- TAT T-T TAC TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11455366 TGTATTTTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
2 10 0.16
3 52 0.84
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:11455309 original size:9 final size:8
Alignment explanation
Indices: 11455207--11455364 Score: 81
Period size: 8 Copynumber: 18.4 Consensus size: 8
11455197 TTTTAGTTTG
11455207 TATATTAT
1 TATATTAT
11455215 TACTA-TAT
1 TA-TATTAT
11455223 TATATGATAT
1 TATAT--TAT
11455233 TATATTAT
1 TATATTAT
*
11455241 CT-TACTAT
1 -TATATTAT
*
11455249 TATAGTATAG
1 TATA-T-TAT
*
11455259 TATATTAA
1 TATATTAT
*
11455267 TATACTA-
1 TATATTAT
*
11455274 TATGATATAG
1 TAT-AT-TAT
*
11455284 TGTATTA-
1 TATATTAT
11455291 TATTATTAT
1 TA-TATTAT
*
11455300 TACCATTAT
1 TA-TATTAT
11455309 TACTATTAT
1 TA-TATTAT
11455318 TATATTAT
1 TATATTAT
11455326 TATATTAT
1 TATATTAT
11455334 TATCATTAT
1 TAT-ATTAT
*
11455343 TATTATATTT
1 TA-TAT-TAT
11455353 TACTATTAT
1 TA-TATTAT
11455362 TAT
1 TAT
11455365 TTGTATTTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 32
0.72 0.08 0.19
Matches are distributed among these distances:
7 7 0.06
8 51 0.43
9 38 0.32
10 24 0.20
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (8 bp):
TATATTAT
Found at i:11455371 original size:25 final size:27
Alignment explanation
Indices: 11455207--11455371 Score: 85
Period size: 26 Copynumber: 6.0 Consensus size: 27
11455197 TTTTAGTTTG
*
11455207 TATATTATTACTA-TATTATATGA-TAT
1 TATATTATTA-TATTATTATATTAGTAT
* * *
11455233 TATATTATCT-TACTATTATAGTA-TAG
1 TATATTAT-TATATTATTATATTAGTAT
* *
11455259 TATATTAATATACTA-TATGATATAGTGTAT
1 TATATTATTATATTATTAT-AT-TA--GTAT
** * *
11455289 TATATTATTATTACCATTATTACTATTAT
1 TATATTATTA-TATTATTA-TATTAGTAT
*
11455318 TATATTATTATATTATTATCATTATTAT
1 TATATTATTATATTATTAT-ATTAGTAT
11455346 TATATT-TTACTATTATTAT-TT-GTAT
1 TATATTATTA-TATTATTATATTAGTAT
11455371 T
1 T
11455372 TTTATTTTTT
Statistics
Matches: 112, Mismatches: 14, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
25 10 0.09
26 33 0.29
27 7 0.06
28 28 0.25
29 13 0.12
30 11 0.10
31 6 0.05
32 3 0.03
33 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.55
Consensus pattern (27 bp):
TATATTATTATATTATTATATTAGTAT
Found at i:11456204 original size:19 final size:19
Alignment explanation
Indices: 11456176--11456218 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
11456166 CGATCGTAGG
* * *
11456176 TTTTTCTTTTTTCATTTTA
1 TTTTTATTTTTTAATTTAA
11456195 TTTTTATTTTTTAATTTAA
1 TTTTTATTTTTTAATTTAA
11456214 TTTTT
1 TTTTT
11456219 TAAGCTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTATTTTTTAATTTAA
Found at i:11456379 original size:17 final size:18
Alignment explanation
Indices: 11456353--11456397 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
11456343 AAAAAAAGAA
11456353 ACAAATATAAAAAATCTTT
1 ACAAA-ATAAAAAATCTTT
*
11456372 -CCAAAT-AAAAATCTTT
1 ACAAAATAAAAAATCTTT
11456388 ACAAAATAAA
1 ACAAAATAAA
11456398 TTCATGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 10 0.45
17 7 0.32
18 5 0.23
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (18 bp):
ACAAAATAAAAAATCTTT
Found at i:11460429 original size:13 final size:13
Alignment explanation
Indices: 11460390--11460448 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
11460380 AAGAGAAATG
*
11460390 AAAAAAAGTGAGA
1 AAAAAAAGTGAAA
* *
11460403 AAAAGATGTGAAA
1 AAAAAAAGTGAAA
*
11460416 AAAAAAAGTAAAAAA
1 AAAAAAAGT--GAAA
11460431 AAAAAAAG-GAAA
1 AAAAAAAGTGAAA
11460443 AAAAAA
1 AAAAAA
11460449 GACTTAAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
12 9 0.24
13 17 0.46
15 11 0.30
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAAAAAGTGAAA
Found at i:11460431 original size:15 final size:15
Alignment explanation
Indices: 11460413--11460448 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
11460403 AAAAGATGTG
*
11460413 AAAAAAAAAAGTAAA
1 AAAAAAAAAAGGAAA
11460428 AAAAAAAAAAGGAAA
1 AAAAAAAAAAGGAAA
11460443 AAAAAA
1 AAAAAA
11460449 GACTTAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.08, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAGGAAA
Found at i:11462584 original size:5 final size:5
Alignment explanation
Indices: 11462568--11462703 Score: 82
Period size: 5 Copynumber: 26.2 Consensus size: 5
11462558 TTAGTTTGTG
* * * *
11462568 TATTA TTATTA TATTA TATGA TATTA TATTA TCTTA CTATTA TAGTA TAGTA
1 TATTA -TATTA TATTA TATTA TATTA TATTA TATTA -TATTA TATTA TATTA
* * *
11462620 TATTA -A-TA TATTA TATGGCA TAGTG TATTA TATTA TTATTA TTATTA
1 TATTA TATTA TATTA TAT--TA TATTA TATTA TATTA -TATTA -TATTA
* *
11462667 TCA-T- TATTA CTATTA TTATTT TATTT TATTA TATTA T
1 T-ATTA TATTA -TATTA -TATTA TATTA TATTA TATTA T
11462704 TATCATTACT
Statistics
Matches: 105, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
3 3 0.03
4 4 0.04
5 65 0.62
6 30 0.29
7 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:11462594 original size:18 final size:17
Alignment explanation
Indices: 11462571--11462703 Score: 77
Period size: 18 Copynumber: 7.8 Consensus size: 17
11462561 GTTTGTGTAT
11462571 TATTATTATATTATAT-
1 TATTATTATATTATATA
* *
11462587 GA-TATTATATTATCT-
1 TATTATTATATTATATA
* *
11462602 TACTATTATAGTATAGTA
1 TATTATTATATTATA-TA
*
11462620 TATTAATATATTATATGGCA
1 TATTATTATATTATAT---A
11462640 TAGTGTATTATATTAT-TA
1 TA-T-TATTATATTATATA
11462658 TTATTATTATCATTAT-TA
1 -TATTATTAT-ATTATATA
11462676 CTATTATTAT-TT-TAT-
1 -TATTATTATATTATATA
11462691 T-TTATTATATTAT
1 TATTATTATATTAT
11462704 TATCATTACT
Statistics
Matches: 94, Mismatches: 10, Indels: 27
0.72 0.08 0.21
Matches are distributed among these distances:
13 7 0.07
14 3 0.03
15 15 0.16
16 14 0.15
17 8 0.09
18 30 0.32
19 2 0.02
20 3 0.03
21 2 0.02
22 10 0.11
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (17 bp):
TATTATTATATTATATA
Found at i:11462594 original size:21 final size:21
Alignment explanation
Indices: 11462568--11462737 Score: 91
Period size: 21 Copynumber: 7.8 Consensus size: 21
11462558 TTAGTTTGTG
*
11462568 TATTATTATTATATTATATGA
1 TATTATTATTATATTATATTA
*
11462589 TATTA-TATTATCTTACTATTA
1 TATTATTATTATATTA-TATTA
* *
11462610 TAGTA-TAGTATATTA-A-TA
1 TATTATTATTATATTATATTA
* * *
11462628 TATTA-TATGGCATAGTGTATTA
1 TATTATTAT--TATATTATATTA
11462650 TATTATTATTATTATTATCATTA
1 TATTATTATTA-TATTAT-ATTA
* * *
11462673 TTACTATTATTATTTTATTTTA
1 -TATTATTATTATATTATATTA
11462695 T-TATATTATTATCATTACTATTA
1 TAT-TATTATTAT-ATTA-TATTA
*
11462718 TACTTTATTTTTATTATTAT
1 TA--TTATTATTA-TATTAT
11462738 TTTTATTTTT
Statistics
Matches: 113, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
18 8 0.07
19 1 0.01
20 13 0.12
21 33 0.29
22 17 0.15
23 17 0.15
24 11 0.10
25 11 0.10
26 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.58
Consensus pattern (21 bp):
TATTATTATTATATTATATTA
Found at i:11462658 original size:3 final size:3
Alignment explanation
Indices: 11462645--11462744 Score: 95
Period size: 3 Copynumber: 35.3 Consensus size: 3
11462635 TGGCATAGTG
* *
11462645 TAT TA- TAT TAT TAT TAT TAT TAT CAT TAT TAC TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
11462691 T-T TAT TA- TAT TAT TAT CAT TAC TAT TA- TAC T-T TAT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
11462735 TAT TTT TAT T
1 TAT TAT TAT T
11462745 TTTTTCTTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
2 11 0.14
3 67 0.86
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:11462704 original size:18 final size:20
Alignment explanation
Indices: 11462650--11462738 Score: 80
Period size: 19 Copynumber: 4.7 Consensus size: 20
11462640 TAGTGTATTA
*
11462650 TATTATTATTATTATTATCAT
1 TATTATTATTATTATT-TTAT
*
11462671 TATTACTATTATTATTTTAT
1 TATTATTATTATTATTTTAT
11462691 T-TTATTA-TATTA--TTAT
1 TATTATTATTATTATTTTAT
* * *
11462707 CATTACTATTA-TACTTTAT
1 TATTATTATTATTATTTTAT
*
11462726 TTTTATTATTATT
1 TATTATTATTATT
11462739 TTTATTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
16 4 0.07
17 7 0.13
18 7 0.13
19 17 0.31
20 5 0.09
21 15 0.27
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTATTATTATTTTAT
Done.