Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 82 of 132
Found at i:24218578 original size:17 final size:17
Alignment explanation
Indices: 24218558--24218615 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
24218548 ATTGTCATCA
24218558 CATTTCTTTTGTCCTTG
1 CATTTCTTTTGTCCTTG
24218575 CATTT-TTATTGTCAC-TG
1 CATTTCTT-TTGTC-CTTG
* *
24218592 CATTTGCATTTGTCATTG
1 CATTT-CTTTTGTCCTTG
24218610 CATTTC
1 CATTTC
24218616 CATATATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 2 0.06
17 18 0.53
18 13 0.38
19 1 0.03
ACGTcount: A:0.14, C:0.21, G:0.12, T:0.53
Consensus pattern (17 bp):
CATTTCTTTTGTCCTTG
Found at i:24231457 original size:3 final size:3
Alignment explanation
Indices: 24231442--24231475 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
24231432 ATATGCAAGG
*
24231442 ACA ACA TCA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
24231476 TATTCACAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.32, G:0.00, T:0.03
Consensus pattern (3 bp):
ACA
Found at i:24234853 original size:17 final size:17
Alignment explanation
Indices: 24234828--24234870 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
24234818 ATGCATCTCA
24234828 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
* *
24234845 TTTAGTTGTCGTTGCAT
1 TTTAATTGTCATTGCAT
*
24234862 TTTACTTGT
1 TTTAATTGT
24234871 TAGTTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:24235478 original size:14 final size:13
Alignment explanation
Indices: 24235450--24235482 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
24235440 ACATATTTCT
24235450 AAAAA-AAAGAAG
1 AAAAAGAAAGAAG
24235462 AAAAAGAAAGCAAG
1 AAAAAGAAAG-AAG
24235476 AAAAAGA
1 AAAAAGA
24235483 GAAAAGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 4 0.21
14 10 0.53
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAGAAG
Found at i:24237060 original size:24 final size:23
Alignment explanation
Indices: 24237023--24237068 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
24237013 AACTACTCAT
24237023 TTTATCTTAATTTGCTTTGACAG
1 TTTATCTTAATTTGCTTTGACAG
*
24237046 TTTATTTTATATTTGCTTTGACA
1 TTTATCTTA-ATTTGCTTTGACA
24237069 AATTAACTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.57
Consensus pattern (23 bp):
TTTATCTTAATTTGCTTTGACAG
Found at i:24253471 original size:18 final size:19
Alignment explanation
Indices: 24253436--24253475 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
24253426 AAAAAAAAAA
24253436 TTTGCTTTTCTCTCTCTTC
1 TTTGCTTTTCTCTCTCTTC
* *
24253455 TTTGC-TTTCTTTTTCTTC
1 TTTGCTTTTCTCTCTCTTC
24253473 TTT
1 TTT
24253476 ACTATTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.00, C:0.25, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTGCTTTTCTCTCTCTTC
Found at i:24254564 original size:27 final size:26
Alignment explanation
Indices: 24254505--24254564 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
24254495 TGTTGGGGCA
24254505 TCTCCTTCTCTTCATTCTTGTCCTCT
1 TCTCCTTCTCTTCATTCTTGTCCTCT
* *
24254531 TCTTCCTTTTCTTC-TTCATTTTCCTTCT
1 TC-TCCTTCTCTTCATTC-TTGTCC-TCT
24254559 TCTCCT
1 TCTCCT
24254565 CAGGTTTCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 19 0.66
28 5 0.17
ACGTcount: A:0.03, C:0.37, G:0.02, T:0.58
Consensus pattern (26 bp):
TCTCCTTCTCTTCATTCTTGTCCTCT
Found at i:24258517 original size:22 final size:22
Alignment explanation
Indices: 24258492--24258539 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
24258482 AAATGATAGT
*
24258492 ATTTTCTTAAGCATTGCATCGA
1 ATTTTCATAAGCATTGCATCGA
* *
24258514 ATTTTCATAAGCTTTTCATCGA
1 ATTTTCATAAGCATTGCATCGA
24258536 ATTT
1 ATTT
24258540 CTTTCAGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (22 bp):
ATTTTCATAAGCATTGCATCGA
Found at i:24262342 original size:52 final size:52
Alignment explanation
Indices: 24262256--24262495 Score: 367
Period size: 52 Copynumber: 4.7 Consensus size: 52
24262246 ATTCCAATTA
* * * * *
24262256 ATACTCACGATGACAC--AGTCATCAGACCTCTTAATCCGTGAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
24262306 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* * *
24262358 AAACTCACGATGACTCATAGTCATCGGACCTTTTAATCCATAAAGGATTTAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
24262410 ATACTCACGATGACACATAGTCATCAGACCTTTTATTCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
24262462 ATACTCACGATGACACATAGCCATCGGACCTTTT
1 ATACTCACGATGACACATAGTCATCGGACCTTTT
24262496 TTTTATTTAC
Statistics
Matches: 173, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
50 16 0.09
52 157 0.91
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
Found at i:24263890 original size:199 final size:199
Alignment explanation
Indices: 24263544--24263943 Score: 746
Period size: 199 Copynumber: 2.0 Consensus size: 199
24263534 CTTTACAAAA
* *
24263544 TTATCCTATTTAACAGCCTAAATTAATAATCCATCATAAAATTTCAAGAATATACAAAAATCATC
1 TTATCATATTTAACAACCTAAATTAATAATCCATCATAAAATTTCAAGAATATACAAAAATCATC
*
24263609 AATGGAAAAATTCACAACATTTGATAGATTCACAAATTAGTCCTCGAGCTAGCTAGATTAAGCTA
66 AATGGAAAAATTCACAACATTTGATAGATTCACAAATTAGTCCTCGAGCTAGCTAGATTAAACTA
* *
24263674 ATACGGACTCAAAAACATAAAAATTACTAAAAACGGATGAAGTTTGCTCACCCAATCGAAGATAC
131 ATACGGACTCAAAAACATAAAAATTACTAAAAACGGACGAAGTTTGCTCACCCAATCGAAGACAC
24263739 AAGC
196 AAGC
24263743 TTATCATATTTAACAACCTAAATTAATAATCCATCATAAAATTTCAAGAATATACAAAAATCATC
1 TTATCATATTTAACAACCTAAATTAATAATCCATCATAAAATTTCAAGAATATACAAAAATCATC
*
24263808 AATGGAAAAATTCACAACATTTGATAGATTCACAAATTAGTCCTCGGGCTAGCTAGATTAAACTA
66 AATGGAAAAATTCACAACATTTGATAGATTCACAAATTAGTCCTCGAGCTAGCTAGATTAAACTA
24263873 ATACGGACTCAAAAACATAAAAATTACTAAAAACGGACGAAGTTTGCTCACCCAATCGAAGACAC
131 ATACGGACTCAAAAACATAAAAATTACTAAAAACGGACGAAGTTTGCTCACCCAATCGAAGACAC
24263938 AAGC
196 AAGC
24263942 TT
1 TT
24263944 GGACGATTGT
Statistics
Matches: 195, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
199 195 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (199 bp):
TTATCATATTTAACAACCTAAATTAATAATCCATCATAAAATTTCAAGAATATACAAAAATCATC
AATGGAAAAATTCACAACATTTGATAGATTCACAAATTAGTCCTCGAGCTAGCTAGATTAAACTA
ATACGGACTCAAAAACATAAAAATTACTAAAAACGGACGAAGTTTGCTCACCCAATCGAAGACAC
AAGC
Found at i:24268011 original size:16 final size:15
Alignment explanation
Indices: 24267990--24268028 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
24267980 CTAAACCAAA
*
24267990 AAATAAATACTTAAAT
1 AAATAAATA-ATAAAT
24268006 AAATAAATAATAAAT
1 AAATAAATAATAAAT
24268021 ATAATAAA
1 A-AATAAA
24268029 ATGAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAAATAATAAAT
Found at i:24271582 original size:24 final size:24
Alignment explanation
Indices: 24271543--24271589 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
24271533 ATTACATTGA
*
24271543 TTAAATGAAATAAAAATATATAAT
1 TTAAATGAAATAAAAATAAATAAT
24271567 TTAAAT-AAATAAAAAATAAATAA
1 TTAAATGAAAT-AAAAATAAATAA
24271590 AAAAGTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
TTAAATGAAATAAAAATAAATAAT
Found at i:24271585 original size:11 final size:11
Alignment explanation
Indices: 24271569--24271598 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
24271559 TATATAATTT
24271569 AAATAAATAAA
1 AAATAAATAAA
24271580 AAATAAATAAA
1 AAATAAATAAA
24271591 AAAGTAAA
1 AAA-TAAA
24271599 CTTTTATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:24273401 original size:45 final size:45
Alignment explanation
Indices: 24273350--24273485 Score: 182
Period size: 45 Copynumber: 3.0 Consensus size: 45
24273340 AGTGAAACGT
*
24273350 ATATCATGCAAATCATATAGCATAATCAATCAAATAATATTTACC
1 ATATCATGCATATCATATAGCATAATCAATCAAATAATATTTACC
* * *
24273395 ATATCATGCATATCATATAGCATAATCAACCAAATAATAATCACC
1 ATATCATGCATATCATATAGCATAATCAATCAAATAATATTTACC
* * ** * *
24273440 ATATTAAGCATATTGTACAGCATAATCAATCAAATAGTATTTACC
1 ATATCATGCATATCATATAGCATAATCAATCAAATAATATTTACC
24273485 A
1 A
24273486 CTCATCGGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (45 bp):
ATATCATGCATATCATATAGCATAATCAATCAAATAATATTTACC
Found at i:24275821 original size:17 final size:17
Alignment explanation
Indices: 24275801--24275834 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
24275791 TTAATGTATT
*
24275801 TTAAATTACATAATATA
1 TTAAATAACATAATATA
24275818 TTAAATAACATAATATA
1 TTAAATAACATAATATA
24275835 AAGATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAATAACATAATATA
Found at i:24276489 original size:40 final size:41
Alignment explanation
Indices: 24276429--24276523 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
24276419 GAATTTTACT
* *
24276429 TTAAGAAGAATTCTAGTCACCCAA-TCTAATAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
24276469 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
24276510 TTGACAAGAATTCT
1 TTAACAAGAATTCT
24276524 CTATGAACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 23 0.45
41 28 0.55
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.28
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:24281291 original size:18 final size:19
Alignment explanation
Indices: 24281260--24281295 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
24281250 AATAAAATAA
*
24281260 AAAATTGTGTAAATTGATG
1 AAAATTGTGAAAATTGATG
24281279 AAAA-TGTGAAAATTGAT
1 AAAATTGTGAAAATTGAT
24281296 TTTTAAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (19 bp):
AAAATTGTGAAAATTGATG
Found at i:24284607 original size:12 final size:12
Alignment explanation
Indices: 24284590--24284640 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 12
24284580 TGATTTTAAA
24284590 ATTTTTTAAATT
1 ATTTTTTAAATT
24284602 ATTTTTTAAAATAT
1 ATTTTTT-AAAT-T
24284616 AAAATTTTTTAAATT
1 ---ATTTTTTAAATT
24284631 ATTTTTTAAA
1 ATTTTTTAAA
24284641 ATATAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 17 0.50
13 4 0.12
14 1 0.03
15 1 0.03
16 4 0.12
17 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTTTAAATT
Found at i:24284624 original size:17 final size:17
Alignment explanation
Indices: 24284602--24284650 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
24284592 TTTTTAAATT
24284602 ATTTTTTAAAATATAAA
1 ATTTTTTAAAATATAAA
24284619 ATTTTTT-AAAT-T---
1 ATTTTTTAAAATATAAA
24284631 ATTTTTTAAAATATAAA
1 ATTTTTTAAAATATAAA
24284648 ATT
1 ATT
24284651 ATTAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
14 1 0.04
15 1 0.04
16 4 0.15
17 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTTAAAATATAAA
Found at i:24284637 original size:30 final size:29
Alignment explanation
Indices: 24284586--24284693 Score: 155
Period size: 29 Copynumber: 3.7 Consensus size: 29
24284576 CAAATGATTT
24284586 TAAAATTTTTTAAATTATTTTTTAAAATA
1 TAAAATTTTTTAAATTATTTTTTAAAATA
24284615 TAAAATTTTTTAAATTATTTTTTAAAATA
1 TAAAATTTTTTAAATTATTTTTTAAAATA
* * *
24284644 TAAAATTATTAAAATTATTTTTTGAAATAA
1 TAAAATTTTTTAAATTATTTTTTAAAAT-A
* *
24284674 TAAAA-TTATTAAATAATTTT
1 TAAAATTTTTTAAATTATTTT
24284694 AATTTCCAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
29 65 0.92
30 6 0.08
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
TAAAATTTTTTAAATTATTTTTTAAAATA
Found at i:24285494 original size:18 final size:18
Alignment explanation
Indices: 24285471--24285507 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
24285461 AGTGCAGTCA
24285471 GTGAGGGTG-AGGGGAAGG
1 GTGAGGG-GAAGGGGAAGG
24285489 GTGAGGGGAAGGGGAAGG
1 GTGAGGGGAAGGGGAAGG
24285507 G
1 G
24285508 AAAGAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.24, C:0.00, G:0.68, T:0.08
Consensus pattern (18 bp):
GTGAGGGGAAGGGGAAGG
Found at i:24285507 original size:12 final size:12
Alignment explanation
Indices: 24285474--24285501 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
24285464 GCAGTCAGTG
24285474 AGGGTGAGGGGA
1 AGGGTGAGGGGA
24285486 AGGGTGAGGGGA
1 AGGGTGAGGGGA
24285498 AGGG
1 AGGG
24285502 GAAGGGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.68, T:0.07
Consensus pattern (12 bp):
AGGGTGAGGGGA
Found at i:24285587 original size:12 final size:11
Alignment explanation
Indices: 24285549--24285637 Score: 70
Period size: 11 Copynumber: 8.6 Consensus size: 11
24285539 GATGATGATT
24285549 ATAATTTTAAA
1 ATAATTTTAAA
24285560 ATAA-TTTAAA
1 ATAATTTTAAA
*
24285570 TTAATTTTAAA
1 ATAATTTTAAA
24285581 ATAAATTTT-AA
1 AT-AATTTTAAA
24285592 A-AATTTT---
1 ATAATTTTAAA
24285599 AT-ATTTTAAAAA
1 ATAATTTT--AAA
24285611 ATAATTTT--A
1 ATAATTTTAAA
24285620 ATAATTTTAAA
1 ATAATTTTAAA
*
24285631 ATTATTT
1 ATAATTT
24285638 ACTGATATGA
Statistics
Matches: 64, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
7 6 0.09
9 15 0.23
10 9 0.14
11 21 0.33
12 8 0.12
13 5 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:24285596 original size:21 final size:20
Alignment explanation
Indices: 24285549--24285599 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
24285539 GATGATGATT
24285549 ATAATTTTAAAATAATTTAA
1 ATAATTTTAAAATAATTTAA
24285569 ATTAATTTTAAAATAAATTTTAA
1 A-TAATTTTAAAAT-AA-TTTAA
24285592 A-AATTTTA
1 ATAATTTTA
24285600 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.04
21 19 0.68
22 2 0.07
23 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTAA
Found at i:24285609 original size:28 final size:29
Alignment explanation
Indices: 24285573--24285628 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
24285563 ATTTAAATTA
*
24285573 ATTTTAAAATA-AATTTTAAAAATTTTAT
1 ATTTTAAAAAATAATTTTAAAAATTTTAT
*
24285601 ATTTTAAAAAATAATTTTAATAATTTTA
1 ATTTTAAAAAATAATTTTAAAAATTTTA
24285629 AAATTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTTAAAAAATAATTTTAAAAATTTTAT
Found at i:24285849 original size:55 final size:56
Alignment explanation
Indices: 24285779--24285892 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
24285769 TTAATTTTGT
24285779 TATTATGCTAAAAAT-AAAAAAGTATGGCGCAATTGATTTGCTTAATAAAATCTAG
1 TATTATGCTAAAAATAAAAAAAGTATGGCGCAATTGATTTGCTTAATAAAATCTAG
24285834 TATTATGCTAAAAATAAAAAAAGTATGGCGCAATTGATTTGCTTAATAAAATCTAG
1 TATTATGCTAAAAATAAAAAAAGTATGGCGCAATTGATTTGCTTAATAAAATCTAG
24285890 TAT
1 TAT
24285893 GTAGAAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 15 0.26
56 43 0.74
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (56 bp):
TATTATGCTAAAAATAAAAAAAGTATGGCGCAATTGATTTGCTTAATAAAATCTAG
Found at i:24288867 original size:17 final size:17
Alignment explanation
Indices: 24288845--24288880 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
24288835 ATTTAATATA
*
24288845 AATATAGATAAATTATT
1 AATATAAATAAATTATT
*
24288862 AATATAAATAGATTATT
1 AATATAAATAAATTATT
24288879 AA
1 AA
24288881 AAGTTATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
AATATAAATAAATTATT
Found at i:24289362 original size:23 final size:23
Alignment explanation
Indices: 24289306--24289375 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
24289296 TCATTAACAT
* *
24289306 TGTTTGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* * *
24289330 TGTTCATGAACATATTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
24289353 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
24289376 GTTAAATAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 21 0.55
24 17 0.45
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:24289415 original size:15 final size:16
Alignment explanation
Indices: 24289395--24289424 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24289385 ATACGTTCGT
24289395 GAACATTAA-ACAAAC
1 GAACATTAACACAAAC
24289410 GAACATTAACACAAA
1 GAACATTAACACAAA
24289425 TGATTTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.20, G:0.07, T:0.13
Consensus pattern (16 bp):
GAACATTAACACAAAC
Found at i:24294295 original size:34 final size:34
Alignment explanation
Indices: 24294247--24294382 Score: 168
Period size: 34 Copynumber: 4.1 Consensus size: 34
24294237 ACACACTCGG
* * *
24294247 TGCTCGTATGAGCCAGTTCATCCAGCATACCAAA
1 TGCTCGTAAGAGCCAGTCCATCCAGCACACCAAA
* * *
24294281 TGCTAGTATGAGCCAATCCATCCAGCACACCAAA
1 TGCTCGTAAGAGCCAGTCCATCCAGCACACCAAA
* *
24294315 TGCTTGTAAGAGCTAGTCCATCCAGCACACCAAA
1 TGCTCGTAAGAGCCAGTCCATCCAGCACACCAAA
* *
24294349 CGCTCGTAAGAGCTAGTCCATCCAGCA-A-CAAA
1 TGCTCGTAAGAGCCAGTCCATCCAGCACACCAAA
24294381 TG
1 TG
24294383 GAGGACCTTG
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
32 5 0.05
33 1 0.01
34 85 0.93
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (34 bp):
TGCTCGTAAGAGCCAGTCCATCCAGCACACCAAA
Found at i:24295627 original size:49 final size:49
Alignment explanation
Indices: 24295553--24295653 Score: 132
Period size: 49 Copynumber: 2.1 Consensus size: 49
24295543 ATTAGTCGCA
* *
24295553 TTAATCACATGAGTACTTAAGCATTTAACACAAT-ACATATTAATCACAT
1 TTAATCAAATGAATACTTAAGCATTTAACAC-ATCACATATTAATCACAT
* * * *
24295602 TTAATCAAATGAATATTTTAGCATTTATCACATCACATATTAATTACAT
1 TTAATCAAATGAATACTTAAGCATTTAACACATCACATATTAATCACAT
24295651 TTA
1 TTA
24295654 GTCACATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 2 0.04
49 43 0.96
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (49 bp):
TTAATCAAATGAATACTTAAGCATTTAACACATCACATATTAATCACAT
Found at i:24295632 original size:33 final size:33
Alignment explanation
Indices: 24295595--24295703 Score: 98
Period size: 33 Copynumber: 3.2 Consensus size: 33
24295585 ATACATATTA
*
24295595 ATCACATTTAATCAAATGAATATTTTAGCATTT
1 ATCACATTTAATCATATGAATATTTTAGCATTT
* * *
24295628 ATCACA--TCA-CATATTAATTACATTTAGTCACATTT
1 ATCACATTTAATCATATGAA-TA-TTTTAG---CATTT
*
24295663 AATCACATTTAATCATATGAATATTTCAGCATTT
1 -ATCACATTTAATCATATGAATATTTTAGCATTT
24295697 ATCACAT
1 ATCACAT
24295704 CACATAATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 18
0.69 0.09 0.21
Matches are distributed among these distances:
30 6 0.10
31 4 0.07
32 5 0.08
33 13 0.22
34 5 0.08
35 5 0.08
36 6 0.10
37 4 0.07
38 4 0.07
39 7 0.12
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.40
Consensus pattern (33 bp):
ATCACATTTAATCATATGAATATTTTAGCATTT
Found at i:24295662 original size:10 final size:10
Alignment explanation
Indices: 24295633--24295677 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
24295623 CATTTATCAC
24295633 ATCACATATTA
1 ATCACAT-TTA
*
24295644 ATTACATTTA
1 ATCACATTTA
*
24295654 GTCACATTTA
1 ATCACATTTA
24295664 ATCACATTTA
1 ATCACATTTA
24295674 ATCA
1 ATCA
24295678 TATGAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 24 0.80
11 6 0.20
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (10 bp):
ATCACATTTA
Found at i:24295670 original size:20 final size:21
Alignment explanation
Indices: 24295634--24295739 Score: 65
Period size: 20 Copynumber: 4.8 Consensus size: 21
24295624 ATTTATCACA
*
24295634 TCACATATTAATTACATTTAG
1 TCACATATTAATCACATTTAG
*
24295655 TCACAT-TTAATCACATTTAA
1 TCACATATTAATCACATTTAG
* * *
24295675 TCATATGAATATTTCAGCATTTA-
1 TCACAT-ATTA-ATCA-CATTTAG
*
24295698 TCACATCACATAATAATCACGTTTAG
1 TCACAT---AT--TAATCACATTTAG
24295724 TCACAT-TTAATCACAT
1 TCACATATTAATCACAT
24295740 GAATATTTCA
Statistics
Matches: 65, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
20 25 0.38
21 6 0.09
22 3 0.05
23 8 0.12
24 6 0.09
25 6 0.09
26 9 0.14
27 2 0.03
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.39
Consensus pattern (21 bp):
TCACATATTAATCACATTTAG
Found at i:24295670 original size:36 final size:34
Alignment explanation
Indices: 24295623--24295739 Score: 91
Period size: 36 Copynumber: 3.4 Consensus size: 34
24295613 AATATTTTAG
*
24295623 CATTTATCACATCACATATTAATTACATTTAGTCA
1 CATTTATCACATCACATA-TAATCACATTTAGTCA
* *
24295658 CATTTAATCACATTTA-ATCAT-ATGA-ATATT--TCA
1 CATTT-ATCACA-TCACAT-ATAATCACAT-TTAGTCA
*
24295691 GCATTTATCACATCACATAATAATCACGTTTAGTCA
1 -CATTTATCACATCACAT-ATAATCACATTTAGTCA
24295727 CATTTAATCACAT
1 CATTT-ATCACAT
24295740 GAATATTTCA
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
32 2 0.03
33 13 0.20
34 12 0.18
35 16 0.25
36 19 0.29
37 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (34 bp):
CATTTATCACATCACATATAATCACATTTAGTCA
Found at i:24295672 original size:69 final size:61
Alignment explanation
Indices: 24295587--24295911 Score: 378
Period size: 59 Copynumber: 5.3 Consensus size: 61
24295577 TTAACACAAT
*
24295587 ACATATTAATCACATTTAATCAAATGAATATTTTAGCATTTATCACATCACATATTAATTACATT
1 ACAT-TTAATCACATTTAATCAAATGAATATTTCAGCATTTATCACATCAC--ATTAATT--A--
24295652 TAGTC
59 -A-TC
*
24295657 ACATTTAATCACATTTAATCATATGAATATTTCAGCATTTATCACATCACA-TAA-TAATC
1 ACATTTAATCACATTTAATCAAATGAATATTTCAGCATTTATCACATCACATTAATTAATC
* * * * *
24295716 ACGTTTAGTCACATTTAATCACATGAATATTTCAACTTTTATCACATCACA-T-ATTAATC
1 ACATTTAATCACATTTAATCAAATGAATATTTCAGCATTTATCACATCACATTAATTAATC
* **
24295775 ACATTTAATCACATTTAATCACATGAATATTTCAATATTTATCACATCACA-T-ATTAATC
1 ACATTTAATCACATTTAATCAAATGAATATTTCAGCATTTATCACATCACATTAATTAATC
* * *
24295834 ACGTTTAGTCACATTTAATCAAATGAATATTTCAGCATTTATCACATCACA-T-ATCAATC
1 ACATTTAATCACATTTAATCAAATGAATATTTCAGCATTTATCACATCACATTAATTAATC
* *
24295893 ACATTTAGTCATATTTAAT
1 ACATTTAATCACATTTAAT
24295912 TAAGTTTAAT
Statistics
Matches: 235, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
58 1 0.00
59 179 0.76
60 1 0.00
63 1 0.00
65 1 0.00
66 3 0.01
67 1 0.00
69 44 0.19
70 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (61 bp):
ACATTTAATCACATTTAATCAAATGAATATTTCAGCATTTATCACATCACATTAATTAATC
Found at i:24295735 original size:59 final size:59
Alignment explanation
Indices: 24295655--24295911 Score: 381
Period size: 59 Copynumber: 4.4 Consensus size: 59
24295645 TTACATTTAG
* * *
24295655 TCACATTTAATCACATTTAATCATATGAATATTTCAGCATTTATCACATCACATAATAA
1 TCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCACATCACATAATAA
* * *
24295714 TCACGTTTAGTCACATTTAATCACATGAATATTTCAACTTTTATCACATCACATATTAA
1 TCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCACATCACATAATAA
* * *
24295773 TCACATTTAATCACATTTAATCACATGAATATTTCAATATTTATCACATCACATATTAA
1 TCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCACATCACATAATAA
* * *
24295832 TCACGTTTAGTCACATTTAATCAAATGAATATTTCAGCATTTATCACATCACAT-ATCAA
1 TCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCACATCACATAAT-AA
*
24295891 TCACATTTAGTCATATTTAAT
1 TCACATTTAGTCACATTTAAT
24295912 TAAGTTTAAT
Statistics
Matches: 179, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
58 1 0.01
59 178 0.99
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (59 bp):
TCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCACATCACATAATAA
Found at i:24295784 original size:10 final size:10
Alignment explanation
Indices: 24295761--24295798 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
24295751 CTTTTATCAC
24295761 ATCACATATTA
1 ATCACAT-TTA
24295772 ATCACATTTA
1 ATCACATTTA
24295782 ATCACATTTA
1 ATCACATTTA
24295792 ATCACAT
1 ATCACAT
24295799 GAATATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.74
11 7 0.26
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (10 bp):
ATCACATTTA
Found at i:24295786 original size:118 final size:118
Alignment explanation
Indices: 24295647--24295911 Score: 424
Period size: 118 Copynumber: 2.3 Consensus size: 118
24295637 CATATTAATT
* * *
24295647 ACAT-TTAGTCACATTTAATCACATTTAATCATATGAATATTTCAGCATTTATCACATCACATAA
1 ACATATTAATCACATTTAATCACATTTAATCACATGAATATTTCAACATTTATCACATCACATAA
* *
24295711 TAATCACGTTTAGTCACATTTAATCACATGAATATTTCAACTTTTATCACATC
66 TAATCACGTTTAGTCACATTTAATCAAATGAATATTTCAACATTTATCACATC
* *
24295764 ACATATTAATCACATTTAATCACATTTAATCACATGAATATTTCAATATTTATCACATCACATAT
1 ACATATTAATCACATTTAATCACATTTAATCACATGAATATTTCAACATTTATCACATCACATAA
*
24295829 TAATCACGTTTAGTCACATTTAATCAAATGAATATTTCAGCATTTATCACATC
66 TAATCACGTTTAGTCACATTTAATCAAATGAATATTTCAACATTTATCACATC
* * *
24295882 ACATATCAATCACATTTAGTCATATTTAAT
1 ACATATTAATCACATTTAATCACATTTAAT
24295912 TAAGTTTAAT
Statistics
Matches: 136, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 4 0.03
118 132 0.97
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (118 bp):
ACATATTAATCACATTTAATCACATTTAATCACATGAATATTTCAACATTTATCACATCACATAA
TAATCACGTTTAGTCACATTTAATCAAATGAATATTTCAACATTTATCACATC
Found at i:24295788 original size:26 final size:23
Alignment explanation
Indices: 24295724--24295788 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
24295714 TCACGTTTAG
*
24295724 TCACATTTAATCACATGAATATT
1 TCACATTTAATCACATCAATATT
*
24295747 TCA-ACTTTTATCACATCACATATT
1 TCACA-TTTAATCACATCA-ATATT
24295771 AATCACATTTAATCACAT
1 --TCACATTTAATCACAT
24295789 TTAATCACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 1 0.03
23 14 0.41
24 5 0.15
26 13 0.38
27 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (23 bp):
TCACATTTAATCACATCAATATT
Found at i:24295806 original size:26 final size:27
Alignment explanation
Indices: 24295777--24295847 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 27
24295767 TATTAATCAC
*
24295777 ATTTAATCACATTTAATCACATGA-AT
1 ATTTAATCACATTTAATCACATCACAT
24295803 ATTTCAAT---ATTT-ATCACATCACAT
1 ATTT-AATCACATTTAATCACATCACAT
* *
24295827 A-TTAATCACGTTTAGTCACAT
1 ATTTAATCACATTTAATCACAT
24295848 TTAATCAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
22 3 0.08
23 10 0.28
24 7 0.19
25 3 0.08
26 10 0.28
27 3 0.08
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.39
Consensus pattern (27 bp):
ATTTAATCACATTTAATCACATCACAT
Found at i:24296346 original size:36 final size:36
Alignment explanation
Indices: 24296306--24296465 Score: 205
Period size: 36 Copynumber: 4.4 Consensus size: 36
24296296 TTAGCACAAT
* * * *
24296306 ATATTTACTATCACATGGCCTGAATAACATATCCAC
1 ATATTTATTGTCACATGGCATGAATAACATACCCAC
* * *
24296342 ATATTTATTATCTCATGGTATGAATAACATACCCAC
1 ATATTTATTGTCACATGGCATGAATAACATACCCAC
* *
24296378 ATATTTACTGTCACATGGCATGAATAACATACCAAC
1 ATATTTATTGTCACATGGCATGAATAACATACCCAC
* *
24296414 ATATTTGTTGT-ATCATGACATGAATAACATACCCAC
1 ATATTTATTGTCA-CATGGCATGAATAACATACCCAC
24296450 ATATTTATTGTCACAT
1 ATATTTATTGTCACAT
24296466 AAGTCATCAT
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
35 1 0.01
36 105 0.98
37 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (36 bp):
ATATTTATTGTCACATGGCATGAATAACATACCCAC
Found at i:24296382 original size:72 final size:72
Alignment explanation
Indices: 24296306--24296465 Score: 232
Period size: 72 Copynumber: 2.2 Consensus size: 72
24296296 TTAGCACAAT
* * * **
24296306 ATATTTACTATCACATGGCCTGAATAACATATCC-ACATATTTATTATCTCATGGTATGAATAAC
1 ATATTTACTGTCACATGGCATGAATAACATA-CCAACATATTTATTATATCATGACATGAATAAC
24296370 ATACCCAC
65 ATACCCAC
* *
24296378 ATATTTACTGTCACATGGCATGAATAACATACCAACATATTTGTTGTATCATGACATGAATAACA
1 ATATTTACTGTCACATGGCATGAATAACATACCAACATATTTATTATATCATGACATGAATAACA
24296443 TACCCAC
66 TACCCAC
*
24296450 ATATTTATTGTCACAT
1 ATATTTACTGTCACAT
24296466 AAGTCATCAT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
71 2 0.03
72 77 0.97
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (72 bp):
ATATTTACTGTCACATGGCATGAATAACATACCAACATATTTATTATATCATGACATGAATAACA
TACCCAC
Found at i:24299082 original size:20 final size:21
Alignment explanation
Indices: 24299057--24299095 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24299047 GTAAGGAATT
24299057 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
24299077 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
24299096 TAAAAAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:24305581 original size:27 final size:26
Alignment explanation
Indices: 24305551--24305603 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
24305541 ATTAAAACCC
24305551 AAATTATTAATGAAAT-ATTTTATATTT
1 AAATTATTAA--AAATAATTTTATATTT
*
24305578 AAATTATTAAATATAATTTTATATTT
1 AAATTATTAAAAATAATTTTATATTT
24305604 TATTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 11 0.46
27 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AAATTATTAAAAATAATTTTATATTT
Found at i:24319050 original size:34 final size:34
Alignment explanation
Indices: 24319007--24319088 Score: 119
Period size: 34 Copynumber: 2.4 Consensus size: 34
24318997 AGTTAACCAA
* *** *
24319007 CCAGCACACCAGATGCTTTTATGAGCCAGTCCAT
1 CCAGCACACCAAATGCTCACATGAGCCAATCCAT
24319041 CCAGCACACCAAATGCTCACATGAGCCAATCCAT
1 CCAGCACACCAAATGCTCACATGAGCCAATCCAT
24319075 CCAGCACACCAAAT
1 CCAGCACACCAAAT
24319089 ACACATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.33, C:0.37, G:0.13, T:0.17
Consensus pattern (34 bp):
CCAGCACACCAAATGCTCACATGAGCCAATCCAT
Found at i:24319108 original size:34 final size:34
Alignment explanation
Indices: 24319030--24319120 Score: 110
Period size: 34 Copynumber: 2.7 Consensus size: 34
24319020 TGCTTTTATG
* * **
24319030 AGCCAGTCCATCCAGCACACCAAATGCTCACATG
1 AGCCAGTCCATCCAGCACACCAAATACACACAAA
* *
24319064 AGCCAATCCATCCAGCACACCAAATACACATAAA
1 AGCCAGTCCATCCAGCACACCAAATACACACAAA
* *
24319098 AGCTAGTCCATCTAGCACACCAA
1 AGCCAGTCCATCCAGCACACCAA
24319121 GTGCTCGTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.38, C:0.36, G:0.11, T:0.14
Consensus pattern (34 bp):
AGCCAGTCCATCCAGCACACCAAATACACACAAA
Found at i:24324803 original size:16 final size:15
Alignment explanation
Indices: 24324778--24324811 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
24324768 TCTTTTAGTT
24324778 TTTGTCTAATTACTTA
1 TTTGTCTAATTAC-TA
*
24324794 TTTGTTTAATTACTA
1 TTTGTCTAATTACTA
24324809 TTT
1 TTT
24324812 TACCCTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTGTCTAATTACTA
Found at i:24325906 original size:50 final size:52
Alignment explanation
Indices: 24325847--24325956 Score: 170
Period size: 50 Copynumber: 2.2 Consensus size: 52
24325837 TTATTAAGGT
* *
24325847 CATGCATTATGTAACTTTCATG-TTAGTTAAGTATGCATCA-TAAATAATGA
1 CATGCATTATGTAACTCTCATGATTAGTTAAGTATGCATCATTAAATAAAGA
* *
24325897 CATGCATTATGTAACTCTCATGATTAGTTAAGTTTGCATCATTAAATAAAGT
1 CATGCATTATGTAACTCTCATGATTAGTTAAGTATGCATCATTAAATAAAGA
24325949 CATGCATT
1 CATGCATT
24325957 TAGTAATCCA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 21 0.39
51 17 0.31
52 16 0.30
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (52 bp):
CATGCATTATGTAACTCTCATGATTAGTTAAGTATGCATCATTAAATAAAGA
Found at i:24327626 original size:24 final size:24
Alignment explanation
Indices: 24327593--24327647 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
24327583 GTTAAGAGTA
24327593 AAAATTGTCAGTGCAAATGTAATAC
1 AAAA-TGTCAGTGCAAATGTAATAC
* *
24327618 AAAATGTCAGTGCAATTGTAATAT
1 AAAATGTCAGTGCAAATGTAATAC
24327642 AAAATG
1 AAAATG
24327648 AATTGATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.29
Consensus pattern (24 bp):
AAAATGTCAGTGCAAATGTAATAC
Found at i:24333536 original size:29 final size:30
Alignment explanation
Indices: 24333490--24333547 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
24333480 ATTAAAATTA
*
24333490 TTTAATAATTTTATTATTTCAAAAAATAAT
1 TTTAATAATTTTATTATTTAAAAAAATAAT
*
24333520 TTTATTAATTTTA-TATTTAAAAAAATAA
1 TTTAATAATTTTATTATTTAAAAAAATAA
24333548 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTAATAATTTTATTATTTAAAAAAATAAT
Found at i:24333555 original size:29 final size:30
Alignment explanation
Indices: 24333495--24333556 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
24333485 AATTATTTAA
* ****
24333495 TAATTTTATTATTTCAAAAAATAATTTTAT
1 TAATTTTATTATTTAAAAAAATAAAAAAAT
24333525 TAATTTTA-TATTTAAAAAAATAAAAAAAT
1 TAATTTTATTATTTAAAAAAATAAAAAAAT
24333554 TAA
1 TAA
24333557 AATCATTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
TAATTTTATTATTTAAAAAAATAAAAAAAT
Found at i:24339597 original size:21 final size:22
Alignment explanation
Indices: 24339553--24339598 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
24339543 CTAAATTTTA
*
24339553 TTTGTCATTAACTTGTTTCCTT
1 TTTGTCATTAACTTGTTTCATT
* *
24339575 TTTGTTATTTACTT-TTTCATT
1 TTTGTCATTAACTTGTTTCATT
24339596 TTT
1 TTT
24339599 TTAGTGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (22 bp):
TTTGTCATTAACTTGTTTCATT
Found at i:24342485 original size:34 final size:34
Alignment explanation
Indices: 24342447--24342512 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
24342437 CTGTAGTATA
*
24342447 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
* *
24342481 ATTGTCGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
24342513 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:24342486 original size:17 final size:17
Alignment explanation
Indices: 24342455--24342512 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
24342445 TAATTGTCCC
* *
24342455 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
24342472 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
24342489 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
24342506 TGCATTT
1 TGCATTT
24342513 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:24345531 original size:16 final size:18
Alignment explanation
Indices: 24345499--24345536 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
24345489 TTTCTTTCTT
24345499 TTATATTTATAAATATTA
1 TTATATTTATAAATATTA
24345517 TTATA-TTAT-AATATTA
1 TTATATTTATAAATATTA
24345533 TTAT
1 TTAT
24345537 TAATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATTTATAAATATTA
Found at i:24351414 original size:21 final size:20
Alignment explanation
Indices: 24351382--24351420 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
24351372 ATTCAAAGAT
* *
24351382 TAATGCTATCCATTCATTAC
1 TAATGCAATCCAATCATTAC
24351402 TAATGCAATTCCAATCATT
1 TAATGCAA-TCCAATCATT
24351421 CATTCAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.38
Consensus pattern (20 bp):
TAATGCAATCCAATCATTAC
Found at i:24351740 original size:18 final size:18
Alignment explanation
Indices: 24351711--24351754 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
24351701 AAATGTACTA
24351711 ACAAAT-AAAATGCAATG
1 ACAAATAAAAATGCAATG
24351728 ACAAATAAAAATGCAATG
1 ACAAATAAAAATGCAATG
24351746 ACAAATAAA
1 ACAAATAAA
24351755 TGCTATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.64, C:0.11, G:0.09, T:0.16
Consensus pattern (18 bp):
ACAAATAAAAATGCAATG
Found at i:24352753 original size:16 final size:17
Alignment explanation
Indices: 24352732--24352775 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
24352722 TGGGCGCATA
24352732 TTCTTTCTTCT-CCTTT
1 TTCTTTCTTCTCCCTTT
24352748 TTCTTTCCTT-TCCCTTT
1 TTCTTT-CTTCTCCCTTT
*
24352765 TTCCTTCTTCT
1 TTCTTTCTTCT
24352776 TAGGCACCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCTTTCTTCTCCCTTT
Found at i:24364747 original size:37 final size:37
Alignment explanation
Indices: 24364665--24364810 Score: 166
Period size: 37 Copynumber: 3.9 Consensus size: 37
24364655 GTGTAATCCG
* *
24364665 GAAGTGCTCATGTGGCGACAGTTTTTGGGCGCAATCTA
1 GAAGTGCTCATGCGGCGACA-TGTTTGGGCGCAATCTA
* * *
24364703 GAGGTGCTCATGCGGCGACATGTTTGGGCACAGTCTA
1 GAAGTGCTCATGCGGCGACATGTTTGGGCGCAATCTA
* * *
24364740 AAAGTGCTCATGCGACGAAATGTTTGGGCGCAATCTA
1 GAAGTGCTCATGCGGCGACATGTTTGGGCGCAATCTA
* * * * *
24364777 GAAGTACTTATGCAGCAACATGTTTAGGCGCAAT
1 GAAGTGCTCATGCGGCGACATGTTTGGGCGCAAT
24364811 TCTGGATTAA
Statistics
Matches: 89, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
37 71 0.80
38 18 0.20
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (37 bp):
GAAGTGCTCATGCGGCGACATGTTTGGGCGCAATCTA
Found at i:24364922 original size:15 final size:15
Alignment explanation
Indices: 24364898--24364942 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
24364888 TCAAGACGCA
*
24364898 ATACTAACACTAAAT
1 ATACTGACACTAAAT
24364913 ATACTGACACTAAAT
1 ATACTGACACTAAAT
**
24364928 ATGGTGACACTAAAT
1 ATACTGACACTAAAT
24364943 GCAATTACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.27
Consensus pattern (15 bp):
ATACTGACACTAAAT
Found at i:24365930 original size:17 final size:17
Alignment explanation
Indices: 24365910--24365943 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24365900 GATAATGTAG
*
24365910 ATGCAGCGACAATAAAA
1 ATGCAGCAACAATAAAA
*
24365927 ATGCAGTAACAATAAAA
1 ATGCAGCAACAATAAAA
24365944 TGTAGGGACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (17 bp):
ATGCAGCAACAATAAAA
Found at i:24367805 original size:14 final size:15
Alignment explanation
Indices: 24367768--24367807 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
24367758 CATATTTCAC
24367768 TAAAA-GAAA-AATG
1 TAAAAGGAAACAATG
*
24367781 TAAAAGTAAACAATG
1 TAAAAGGAAACAATG
24367796 -AAAAGGAAACAA
1 TAAAAGGAAACAA
24367808 GTTAGTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 5 0.22
14 14 0.61
15 4 0.17
ACGTcount: A:0.68, C:0.05, G:0.15, T:0.12
Consensus pattern (15 bp):
TAAAAGGAAACAATG
Found at i:24369149 original size:37 final size:37
Alignment explanation
Indices: 24369033--24369151 Score: 139
Period size: 37 Copynumber: 3.2 Consensus size: 37
24369023 TGCAGTGACA
* *
24369033 GTTTTGGTGCAATCTGGAAGTGCTCATGTGGCAACAGT
1 GTTTGGGTGCAATCTAGAAGTGCTCATGTGGCAACA-T
* *** * **
24369071 TTTTGGACCCAATCTAGAGGTGCTCATACGGCAACAT
1 GTTTGGGTGCAATCTAGAAGTGCTCATGTGGCAACAT
*
24369108 GTTTGGGTGCAATCTAGAAGTGCTCATGTGGCGACAT
1 GTTTGGGTGCAATCTAGAAGTGCTCATGTGGCAACAT
24369145 GTTTGGG
1 GTTTGGG
24369152 CTTAATTCTG
Statistics
Matches: 64, Mismatches: 17, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
37 37 0.58
38 27 0.42
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (37 bp):
GTTTGGGTGCAATCTAGAAGTGCTCATGTGGCAACAT
Found at i:24372528 original size:20 final size:21
Alignment explanation
Indices: 24372503--24372541 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24372493 TGGAGTTTAA
*
24372503 GCATTTT-TAACTTAGTGACT
1 GCATTTTCTAACTCAGTGACT
24372523 GCATTTTCTAACTCAGTGA
1 GCATTTTCTAACTCAGTGA
24372542 AGCTCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGACT
Found at i:24391861 original size:44 final size:44
Alignment explanation
Indices: 24391793--24391882 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
24391783 TTCGAGGAAG
* *
24391793 TATCTCTAGGCCGACTATTATTGTGAATAACTTTGAAATTAAGC
1 TATCACTAGGCCAACTATTATTGTGAATAACTTTGAAATTAAGC
*
24391837 TATCACTAGGCCAACTATTGTTGTGAATAACTTTGAAATTAAGC
1 TATCACTAGGCCAACTATTATTGTGAATAACTTTGAAATTAAGC
24391881 TA
1 TA
24391883 ACCATGATCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (44 bp):
TATCACTAGGCCAACTATTATTGTGAATAACTTTGAAATTAAGC
Found at i:24399306 original size:22 final size:23
Alignment explanation
Indices: 24399278--24399320 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
24399268 CCTAATCACT
*
24399278 ATGTCACGACAT-GAGACAAGCG
1 ATGTCACAACATAGAGACAAGCG
*
24399300 ATGTCACAACATAGGGACAAG
1 ATGTCACAACATAGAGACAAG
24399321 AATCAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.14
Consensus pattern (23 bp):
ATGTCACAACATAGAGACAAGCG
Found at i:24406502 original size:50 final size:50
Alignment explanation
Indices: 24406443--24406542 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
24406433 GTTTCATCAT
24406443 AAATCTAAACAAGATTTCATGAACATTAACAAAAAACTCAGAATCAGGAA
1 AAATCTAAACAAGATTTCATGAACATTAACAAAAAACTCAGAATCAGGAA
*
24406493 AAATCTAAACAAGATTTCATGAACATTAACAGAAAACTCAGAATCAGGAA
1 AAATCTAAACAAGATTTCATGAACATTAACAAAAAACTCAGAATCAGGAA
24406543 GTTTCCTTCC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.20
Consensus pattern (50 bp):
AAATCTAAACAAGATTTCATGAACATTAACAAAAAACTCAGAATCAGGAA
Found at i:24409999 original size:14 final size:14
Alignment explanation
Indices: 24409971--24410013 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
24409961 AATTCGAATT
*
24409971 TCGAGTTAATCGAA
1 TCGAGTTATTCGAA
*
24409985 TCGAGTTATTTGAA
1 TCGAGTTATTCGAA
* *
24409999 TTGAATTATTCGAA
1 TCGAGTTATTCGAA
24410013 T
1 T
24410014 TATTCGAGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (14 bp):
TCGAGTTATTCGAA
Found at i:24410250 original size:18 final size:21
Alignment explanation
Indices: 24410218--24410261 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
24410208 TCAAAACTTG
*
24410218 AAAATAATTT-TTAAAATTC-
1 AAAATAATTTATAAAAATTCT
24410237 AAAAT-ATTTATAAAAATTCT
1 AAAATAATTTATAAAAATTCT
24410257 AAAAT
1 AAAAT
24410262 TTGTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 13 0.59
20 5 0.23
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATAATTTATAAAAATTCT
Found at i:24410324 original size:45 final size:44
Alignment explanation
Indices: 24410224--24410325 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 44
24410214 CTTGAAAATA
* * *
24410224 ATTTTTAAAATTCAAAATATTTATAAAAATTCTAAAATTTGTAT
1 ATTTTTAAAATTCAAAATATTTATAAAAAATCTAAAATATATAT
* * * *
24410268 TTTTTTAAAAATT-ATAATTTTTTTAAAAAATCTAAAAGTATATAT
1 ATTTTT-AAAATTCAAAATATTTATAAAAAATCTAAAA-TATATAT
24410313 ATTTGTTAAAATT
1 ATTT-TTAAAATT
24410326 TTATAAAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
44 25 0.53
45 20 0.43
46 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (44 bp):
ATTTTTAAAATTCAAAATATTTATAAAAAATCTAAAATATATAT
Found at i:24410658 original size:21 final size:21
Alignment explanation
Indices: 24410634--24410673 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
24410624 ACTTTTTCCA
24410634 AAGTT-AAAAGTTAAAACTACC
1 AAGTTAAAAAG-TAAAACTACC
24410655 AAGTTAAAAAGTAAAACTA
1 AAGTTAAAAAGTAAAACTA
24410674 TTTCATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAAGTAAAACTACC
Found at i:24413992 original size:21 final size:22
Alignment explanation
Indices: 24413966--24414009 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
24413956 TTTTAATACT
24413966 AAAAATGAA-TAATTTTTTTAA
1 AAAAATGAATTAATTTTTTTAA
* *
24413987 AAAAATTAATTTATTTTTTTAA
1 AAAAATGAATTAATTTTTTTAA
24414009 A
1 A
24414010 TAAAGCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AAAAATGAATTAATTTTTTTAA
Found at i:24416988 original size:2 final size:2
Alignment explanation
Indices: 24416981--24417013 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24416971 AAATTGATTC
24416981 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24417014 AAGTTCTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24421450 original size:98 final size:98
Alignment explanation
Indices: 24421320--24421517 Score: 396
Period size: 98 Copynumber: 2.0 Consensus size: 98
24421310 ATGGGAAAAA
24421320 TTGAGGAAGCCTATCTATTTTTAGTCTTTTATTATTATTGAATTAGAACAAAAAATTGAAAGTAT
1 TTGAGGAAGCCTATCTATTTTTAGTCTTTTATTATTATTGAATTAGAACAAAAAATTGAAAGTAT
24421385 GGAGTGAAATGCAGGAAAATACTTCAATGGCCG
66 GGAGTGAAATGCAGGAAAATACTTCAATGGCCG
24421418 TTGAGGAAGCCTATCTATTTTTAGTCTTTTATTATTATTGAATTAGAACAAAAAATTGAAAGTAT
1 TTGAGGAAGCCTATCTATTTTTAGTCTTTTATTATTATTGAATTAGAACAAAAAATTGAAAGTAT
24421483 GGAGTGAAATGCAGGAAAATACTTCAATGGCCG
66 GGAGTGAAATGCAGGAAAATACTTCAATGGCCG
24421516 TT
1 TT
24421518 TTATGGCACG
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (98 bp):
TTGAGGAAGCCTATCTATTTTTAGTCTTTTATTATTATTGAATTAGAACAAAAAATTGAAAGTAT
GGAGTGAAATGCAGGAAAATACTTCAATGGCCG
Found at i:24421531 original size:12 final size:12
Alignment explanation
Indices: 24421509--24421537 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24421499 AAATACTTCA
24421509 ATGGC-CGTTTT
1 ATGGCACGTTTT
24421520 ATGGCACGTTTT
1 ATGGCACGTTTT
24421532 ATGGCA
1 ATGGCA
24421538 AAACTTGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (12 bp):
ATGGCACGTTTT
Found at i:24425526 original size:52 final size:52
Alignment explanation
Indices: 24425440--24425683 Score: 371
Period size: 52 Copynumber: 4.7 Consensus size: 52
24425430 ATTTCATTTC
* *
24425440 ATTCATATACTCACGATGACACATAGCCACCGGACCTCATAATCCGTAAAAG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* *
24425492 ATTCATATACTCATGATGACACATAACCATCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
*
24425544 ATTCATATACTCACGATGACACATAGCCATCGGACGTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* * * * *
24425596 ATTCAGATACTCACGTTGACACATAGTCATCGCACCTCATAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* **
24425648 ATTCATATACTCACGATGACACTTAATCATCGGACC
1 ATTCATATACTCACGATGACACATAGCCATCGGACC
24425684 CTTTTTCATT
Statistics
Matches: 174, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 174 1.00
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
Found at i:24426983 original size:3 final size:3
Alignment explanation
Indices: 24426975--24427016 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
24426965 GCCAAAGATT
24426975 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
24427017 AAATAAGGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:24430974 original size:43 final size:43
Alignment explanation
Indices: 24430911--24431300 Score: 315
Period size: 43 Copynumber: 9.1 Consensus size: 43
24430901 GGAAAAACGT
* * *
24430911 CGCTATAGAACATGATCTTTAGTGGCGCTTTTCCCTCAAACTC
1 CGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACTC
* *
24430954 CACTATAGAACATGGTCTTTAGCGGCGTTTTTCCCA-AAACGT-
1 CGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC-TC
* * *
24430996 CGCTATAGAGCATGGTCTTTAGCGGCACTTTTCCCACAAACGC
1 CGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACTC
* * * * * * *
24431039 TGCTATAGAGCATGATCTTTAGCGGTGTTTTTACCATAAA-TGC
1 CGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACT-C
* *
24431082 CGCTATAGAACATGGTCTTTAGCGACGCTTTTCCCACAAACGC
1 CGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACTC
* * * * * * *
24431125 AGCTATAGAGCATGGTAC-TTAACGACGTTTTTACCACAAACGC
1 CGCTATAGAACATGGT-CTTTAGCGGCGCTTTTCCCACAAACTC
* * * ** *
24431168 TGCTATAGAACATGATCTTTAACAACGCTTTTCCCATAAA-TGC
1 CGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACT-C
* * * * *
24431211 CGCTATAGGACAT-GTCTTTAGCAGCGTTTTTACCACAAACGC
1 CGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACTC
* * * * ** * *
24431253 CACTATAAAACATGTTATTTAGCGTTGTTTTTCCCACAAACAC
1 CGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACTC
24431296 CGCTA
1 CGCTA
24431301 ATATTGACAA
Statistics
Matches: 277, Mismatches: 60, Indels: 20
0.78 0.17 0.06
Matches are distributed among these distances:
42 68 0.25
43 208 0.75
44 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (43 bp):
CGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACTC
Found at i:24431115 original size:86 final size:86
Alignment explanation
Indices: 24430905--24431300 Score: 422
Period size: 85 Copynumber: 4.6 Consensus size: 86
24430895 TTATGTGGAA
* * * * * * *
24430905 AAACGTCGCTATAGAACATGATCTTTAGTGGCGCTTTTCCCTCAAACTCCACTATAGAACATGGT
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGAGCATGGT
*
24430970 CTTTAGCGGCGTTTTTCCCA-
66 CTTTAGCGGCGTTTTTACCAC
* * * * * * *
24430990 AAACGTCGCTATAGAGCATGGTCTTTAGCGGCACTTTTCCCACAAACGCTGCTATAGAGCATGAT
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGAGCATGGT
* *
24431055 CTTTAGCGGTGTTTTTACCAT
66 CTTTAGCGGCGTTTTTACCAC
* * *
24431076 AAATGCCGCTATAGAACATGGTCTTTAGCGACGCTTTTCCCACAAACGCAGCTATAGAGCATGGT
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGAGCATGGT
* *
24431141 AC-TTAACGACGTTTTTACCAC
66 -CTTTAGCGGCGTTTTTACCAC
* * * * *
24431162 AAACGCTGCTATAGAACATGATCTTTAACAACGCTTTTCCCATAAATGCCGCTATAG-GACAT-G
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGAG-CATGG
*
24431225 TCTTTAGCAGCGTTTTTACCAC
65 TCTTTAGCGGCGTTTTTACCAC
* * * * ** * *
24431247 AAACGCCACTATAAAACATGTTATTTAGCGTTGTTTTTCCCACAAACACCGCTA
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTTCCCACAAACGCCGCTA
24431301 ATATTGACAA
Statistics
Matches: 260, Mismatches: 47, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
84 1 0.00
85 133 0.51
86 125 0.48
87 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (86 bp):
AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGAGCATGGT
CTTTAGCGGCGTTTTTACCAC
Found at i:24431182 original size:129 final size:127
Alignment explanation
Indices: 24430912--24431252 Score: 413
Period size: 129 Copynumber: 2.7 Consensus size: 127
24430902 GAAAAACGTC
* * *
24430912 GCTATAGAACATGATCTTTAGTGGCGCTTTTCCCTCAAACT-CCACTATAGAACATGGTCTTTAG
1 GCTATAGAACATGATCTTTAGCGGCGCTTTTCCAT-AAA-TGCCGCTATAGAACATGGTCTTTAG
* * * *
24430976 CGGCGTTTTTCCCA-AAACGTCGCTATAGAGCATGGTCTTTAGCGGCACTTTTCCCACAAACGCT
64 CGACGTTTTTCCCACAAACG-CGCTATAGAGCATGGTCTTTAACGACACTTTTACCACAAACGCT
* * *
24431040 GCTATAGAGCATGATCTTTAGCGGTGTTTTTACCATAAATGCCGCTATAGAACATGGTCTTTAGC
1 GCTATAGAACATGATCTTTAGCGGCGCTTTT-CCATAAATGCCGCTATAGAACATGGTCTTTAGC
* **
24431105 GACGCTTTTCCCACAAACGCAGCTATAGAGCATGGTAC-TTAACGACGTTTTTACCACAAACGCT
65 GACGTTTTTCCCACAAACGC-GCTATAGAGCATGGT-CTTTAACGACACTTTTACCACAAACGCT
* ** *
24431169 GCTATAGAACATGATCTTTAACAACGCTTTTCCCATAAATGCCGCTATAGGACAT-GTCTTTAGC
1 GCTATAGAACATGATCTTTAGCGGCGCTTTT-CCATAAATGCCGCTATAGAACATGGTCTTTAGC
*
24431233 -AGCGTTTTTACCACAAACGC
65 GA-CGTTTTTCCCACAAACGC
24431253 CACTATAAAA
Statistics
Matches: 184, Mismatches: 23, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
127 2 0.01
128 90 0.49
129 91 0.49
130 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (127 bp):
GCTATAGAACATGATCTTTAGCGGCGCTTTTCCATAAATGCCGCTATAGAACATGGTCTTTAGCG
ACGTTTTTCCCACAAACGCGCTATAGAGCATGGTCTTTAACGACACTTTTACCACAAACGCT
Found at i:24431231 original size:171 final size:171
Alignment explanation
Indices: 24430905--24431293 Score: 428
Period size: 171 Copynumber: 2.3 Consensus size: 171
24430895 TTATGTGGAA
* * * *
24430905 AAACGTCGCTATAGAACATGATCTTTAGTGGCGCTTTTCCCTCAAACTCCACTATAGAACATGGT
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTTCCCACAAACTCCACTATAGAACATGGT
* * * * * * **
24430970 CTTTAGCGGCGTTTTTCCCAAAACGTCGCTATAGAGCATGGTCTTTAGCGGCACTTTTCCCACAA
66 CTTTAACGACGTTTTTACCAAAACGTCGCTATAGAACATGATCTTTAACAACACTTTTCCCACAA
* * * *
24431035 ACGCTGCTATAGAGCATGATCTTTAGCGGTGTTTTTACCAT
131 ACGCCGCTATAGAGCATGATCTTTAGCAGCGTTTTTACCAC
* * * *
24431076 AAATGCCGCTATAGAACATGGTCTTTAGCGACGCTTTTCCCACAAAC-GCAGCTATAGAGCATGG
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTTCCCACAAACTCCA-CTATAGAACATGG
*
24431140 TAC-TTAACGACGTTTTTACCACAAACG-CTGCTATAGAACATGATCTTTAACAACGCTTTTCCC
65 T-CTTTAACGACGTTTTTACCA-AAACGTC-GCTATAGAACATGATCTTTAACAACACTTTTCCC
* *
24431203 ATAAATGCCGCTATAG-GACATG-TCTTTAGCAGCGTTTTTACCAC
127 ACAAACGCCGCTATAGAG-CATGATCTTTAGCAGCGTTTTTACCAC
* * * * ** *
24431247 AAACGCCACTATAAAACATGTTATTTAGCGTTGTTTTTCCCACAAAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTTCCCACAAAC
24431294 ACCGCTAATA
Statistics
Matches: 182, Mismatches: 31, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
170 2 0.01
171 129 0.71
172 51 0.28
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (171 bp):
AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTTCCCACAAACTCCACTATAGAACATGGT
CTTTAACGACGTTTTTACCAAAACGTCGCTATAGAACATGATCTTTAACAACACTTTTCCCACAA
ACGCCGCTATAGAGCATGATCTTTAGCAGCGTTTTTACCAC
Found at i:24438100 original size:6 final size:6
Alignment explanation
Indices: 24438089--24438128 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
24438079 ACATTATGGT
24438089 TTATAA TTATAA TTATAA TT-TAA TTTATAA TTATTAA TTA
1 TTATAA TTATAA TTATAA TTATAA -TTATAA TTA-TAA TTA
24438129 AAAATTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 3 0.10
6 19 0.61
7 9 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTATAA
Found at i:24438449 original size:29 final size:29
Alignment explanation
Indices: 24438383--24438452 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
24438373 TTAATAAAGT
* * *
24438383 TTGACTTAAAAAAAGTTGTGTTAATTTTA
1 TTGATTTAAAAAAAGTTGCGTTAATTTGA
* * *
24438412 TTGTTTTTAAAAAATGTTGCGTTAATTTGG
1 TTG-ATTTAAAAAAAGTTGCGTTAATTTGA
24438442 TTGATTTAAAA
1 TTGATTTAAAA
24438453 TAGAGTTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (29 bp):
TTGATTTAAAAAAAGTTGCGTTAATTTGA
Found at i:24438645 original size:89 final size:89
Alignment explanation
Indices: 24438547--24438709 Score: 233
Period size: 89 Copynumber: 1.8 Consensus size: 89
24438537 ACTCACTTGG
* * *
24438547 ATACTTGAACTTTCAAAATAGAT-AAAAAAGATCCTCAAAC-TTTAAAAAAAAATAATTAAGC-C
1 ATACTTGAACTTTCAAAATACATCAAAAAA-A-CCTCAAACTTTTAAAAAAAAACAATTAAACTC
24438609 CATGCTTTTTTTTTTGCACTCAAATGA
64 C-TGCTTTTTTTTTTGCACTCAAATGA
**
24438636 ATACTTGAACTTTCAAAATACATCAAAAAAACCTCAAACTTTTTCAAAAAAACAATTAAACTCCT
1 ATACTTGAACTTTCAAAATACATCAAAAAAACCTCAAACTTTTAAAAAAAAACAATTAAACTCCT
24438701 GCTTTTTTT
66 GCTTTTTTT
24438710 GTACTTAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
88 8 0.12
89 50 0.76
90 8 0.12
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.33
Consensus pattern (89 bp):
ATACTTGAACTTTCAAAATACATCAAAAAAACCTCAAACTTTTAAAAAAAAACAATTAAACTCCT
GCTTTTTTTTTTGCACTCAAATGA
Found at i:24438852 original size:21 final size:20
Alignment explanation
Indices: 24438826--24438869 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
24438816 TTAAGGTTAT
24438826 AAAAATTATAAAATTTTAATA
1 AAAAATTATAAAATTTTAA-A
24438847 AAAAATTATAAAATTTTAAA
1 AAAAATTATAAAATTTTAAA
24438867 AAA
1 AAA
24438870 TCATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTATAAAATTTTAAA
Found at i:24438859 original size:10 final size:10
Alignment explanation
Indices: 24438822--24438879 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
24438812 TCAATTAAGG
24438822 TTAT-AAAAA
1 TTATAAAAAA
**
24438831 TTATAAAATT
1 TTATAAAAAA
24438841 TTAATAAAAAA
1 TT-ATAAAAAA
24438852 TTAT--AAAA
1 TTATAAAAAA
*
24438860 TTTTAAAAAA
1 TTATAAAAAA
*
24438870 TCATAAAAAA
1 TTATAAAAAA
24438880 CATATAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
8 7 0.18
9 4 0.11
10 19 0.50
11 8 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:24438953 original size:10 final size:9
Alignment explanation
Indices: 24438844--24438959 Score: 51
Period size: 9 Copynumber: 12.7 Consensus size: 9
24438834 TAAAATTTTA
24438844 ATAAAAAAT
1 ATAAAAAAT
*
24438853 -TATAAAATT
1 ATA-AAAAAT
*
24438862 TTAAAAAAT
1 ATAAAAAAT
*
24438871 CATAAAAAAC
1 -ATAAAAAAT
* *
24438881 ATATAATAT
1 ATAAAAAAT
*
24438890 AT-ATAAAT
1 ATAAAAAAT
24438898 AT-AAAAAT
1 ATAAAAAAT
*
24438906 AT-AAAATT
1 ATAAAAAAT
* * *
24438914 TTATAAAGT
1 ATAAAAAAT
24438923 CATAAGAAAAAT
1 -AT-A-AAAAAT
24438935 ATAAAAAAT
1 ATAAAAAAT
*
24438944 GTAAAGAAAT
1 ATAAA-AAAT
24438954 ATAAAA
1 ATAAAA
24438960 TACGTAAAAA
Statistics
Matches: 79, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
8 20 0.25
9 33 0.42
10 19 0.24
11 3 0.04
12 4 0.05
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:24438966 original size:19 final size:19
Alignment explanation
Indices: 24438931--24438967 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24438921 GTCATAAGAA
*
24438931 AAATATAAAAAATGTAAAG
1 AAATATAAAAAACGTAAAG
*
24438950 AAATATAAAATACGTAAA
1 AAATATAAAAAACGTAAA
24438968 AAAAAATTAC
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:0.68, C:0.03, G:0.08, T:0.22
Consensus pattern (19 bp):
AAATATAAAAAACGTAAAG
Found at i:24439208 original size:19 final size:19
Alignment explanation
Indices: 24439184--24439262 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 19
24439174 GTTAAAGGGT
24439184 ATTTTTGATGGA-TTTTATA
1 ATTTTTGAT-GATTTTTATA
*
24439203 ATTTTTTATGATTTTTATAAA
1 ATTTTTGATGATTTTTAT--A
24439224 ATTTTAT-AT-ATTTTTAT-
1 ATTTT-TGATGATTTTTATA
* * *
24439241 ATTTTTTAAGATTTATATA
1 ATTTTTGATGATTTTTATA
24439260 ATT
1 ATT
24439263 ATTTTTTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
16 1 0.02
17 6 0.12
18 9 0.18
19 17 0.34
20 8 0.16
21 8 0.16
22 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (19 bp):
ATTTTTGATGATTTTTATA
Found at i:24439209 original size:10 final size:10
Alignment explanation
Indices: 24439196--24439336 Score: 55
Period size: 10 Copynumber: 14.3 Consensus size: 10
24439186 TTTTGATGGA
24439196 TTTTATAATT
1 TTTTATAATT
*
24439206 TTTTATGA-T
1 TTTTATAATT
**
24439215 TTTTATAAAA
1 TTTTATAATT
24439225 TTTTAT-ATAT
1 TTTTATAAT-T
24439235 TTTTAT-ATT
1 TTTTATAATT
24439244 TTTTA-AGA-T
1 TTTTATA-ATT
*
24439253 TTATATAATT
1 TTTTATAATT
*
24439263 ATTTTTTCAATT
1 -TTTTAT-AATT
* *
24439275 TTTAAAAATT
1 TTTTATAATT
24439285 TTATTAT--TT
1 TT-TTATAATT
* *
24439294 TTTAATATTT
1 TTTTATAATT
**
24439304 TTTTATTAAAA
1 TTTTA-TAATT
**
24439315 TTCAATAA-T
1 TTTTATAATT
24439324 TTTTATAATT
1 TTTTATAATT
24439334 TTT
1 TTT
24439337 ATTGATTTTT
Statistics
Matches: 95, Mismatches: 23, Indels: 26
0.66 0.16 0.18
Matches are distributed among these distances:
8 3 0.03
9 31 0.33
10 43 0.45
11 14 0.15
12 4 0.04
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:24439326 original size:59 final size:57
Alignment explanation
Indices: 24439200--24439359 Score: 143
Period size: 59 Copynumber: 2.8 Consensus size: 57
24439190 GATGGATTTT
* *
24439200 ATAATTTTTTATGATTTTTATAAAATTTTATATATTTTTATATTTTTTAAGATTTATATA
1 ATAATTTTTTA--ATTTTTATAAAATTTTATATATTTTTATATTTTTT-AGATTAAAATA
* *
24439260 ATTATTTTTTCAATTTTTA-AAAATTTTAT-TATTTTTTAATATTTTTT-TATTAAAATTCA
1 ATAATTTTTT-AATTTTTATAAAATTTTATATA-TTTTT-ATATTTTTTAGATTAAAA-T-A
**
24439319 ATAATTTTTATAATTTTTAT-TGATTTT-TAT-TTTTTATATTT
1 ATAATTTTT-TAATTTTTATAAAATTTTATATATTTTTATATTT
24439360 CTTTTGCCAC
Statistics
Matches: 85, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
56 6 0.07
57 12 0.14
58 17 0.20
59 39 0.46
60 10 0.12
61 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (57 bp):
ATAATTTTTTAATTTTTATAAAATTTTATATATTTTTATATTTTTTAGATTAAAATA
Found at i:24439335 original size:8 final size:9
Alignment explanation
Indices: 24439196--24439356 Score: 68
Period size: 9 Copynumber: 17.8 Consensus size: 9
24439186 TTTTGATGGA
24439196 TTTTATAATT
1 TTTTATAA-T
*
24439206 TTTTATGAT
1 TTTTATAAT
*
24439215 TTTTATAAAA
1 TTTTAT-AAT
24439225 TTTTATATAT
1 TTTTATA-AT
*
24439235 TTTTATATT
1 TTTTATAAT
24439244 TTTTA-AGAT
1 TTTTATA-AT
*
24439253 TTATATAATT
1 TTTTATAA-T
*
24439263 ATTTTTTCAAT
1 -TTTTAT-AAT
* *
24439274 TTTTAAAAA
1 TTTTATAAT
*
24439283 TTTTATTAT
1 TTTTATAAT
24439292 TTTT-TAAT
1 TTTTATAAT
24439300 ATTTT-T--T
1 -TTTTATAAT
* *
24439307 TATTA-AAA
1 TTTTATAAT
**
24439315 TTCAATAAT
1 TTTTATAAT
24439324 TTTTATAAT
1 TTTTATAAT
*
24439333 TTTTATTGAT
1 TTTTA-TAAT
24439343 TTTTAT--T
1 TTTTATAAT
24439350 TTTTATA
1 TTTTATA
24439357 TTTCTTTTGC
Statistics
Matches: 112, Mismatches: 25, Indels: 30
0.67 0.15 0.18
Matches are distributed among these distances:
6 3 0.03
7 8 0.07
8 6 0.05
9 52 0.46
10 36 0.32
11 5 0.04
12 2 0.02
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:24439358 original size:19 final size:19
Alignment explanation
Indices: 24439196--24439348 Score: 65
Period size: 19 Copynumber: 8.3 Consensus size: 19
24439186 TTTTGATGGA
24439196 TTTTATAATTTTT-TATGAT
1 TTTTATAATTTTTAT-TGAT
*
24439215 TTTTATAAAATTTTATAT-AT
1 TTTTAT-AATTTTTAT-TGAT
* *
24439235 TTTTATATTTTTTA-AGAT
1 TTTTATAATTTTTATTGAT
* * *
24439253 TTATATAATTATTTTTTCAAT
1 TTTTATAATT-TTTATT-GAT
* *
24439274 TTTTAAAAATTTTATT-AT
1 TTTTATAATTTTTATTGAT
*
24439292 TTTT-TAATATTT-TT--T
1 TTTTATAATTTTTATTGAT
* * * * *
24439307 TATTA-AA-ATTCAATAAT
1 TTTTATAATTTTTATTGAT
24439324 TTTTATAATTTTTATTGAT
1 TTTTATAATTTTTATTGAT
24439343 TTTTAT
1 TTTTAT
24439349 TTTTTATATT
Statistics
Matches: 98, Mismatches: 24, Indels: 24
0.67 0.16 0.16
Matches are distributed among these distances:
14 3 0.03
15 7 0.07
16 2 0.02
17 10 0.10
18 18 0.18
19 27 0.28
20 19 0.19
21 12 0.12
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTATTGAT
Found at i:24442114 original size:18 final size:18
Alignment explanation
Indices: 24442091--24442138 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
24442081 ACAATTCATA
24442091 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* * *
24442109 TCACTTTCACTTTCAGTT
1 TCACTTTCAATTCCAATT
24442127 TCACTTTCAATT
1 TCACTTTCAATT
24442139 TTGATCACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.02, T:0.48
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:24442116 original size:6 final size:6
Alignment explanation
Indices: 24442091--24442135 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
24442081 ACAATTCATA
* * * *
24442091 TCACTT TCAATT CCAATT TCACTT TCACTT TCAGTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
24442136 ATTTTGATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.22, C:0.29, G:0.02, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:24442122 original size:12 final size:12
Alignment explanation
Indices: 24442091--24442139 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
24442081 ACAATTCATA
24442091 TCACTTTCAATT
1 TCACTTTCAATT
* * *
24442103 CCAATTTCACTT
1 TCACTTTCAATT
*
24442115 TCACTTTCAGTT
1 TCACTTTCAATT
24442127 TCACTTTCAATT
1 TCACTTTCAATT
24442139 T
1 T
24442140 TGATCACAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.22, C:0.27, G:0.02, T:0.49
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:24443849 original size:44 final size:45
Alignment explanation
Indices: 24443786--24443873 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 45
24443776 AATCCTTGAA
* * *
24443786 TTTTCTTAACCTTTCTTA-TTTAGACTACACATTCTAATTCTTAAT
1 TTTTCCTAACCTTTCTTATTTTA-ACCACACATTCTAACTCTTAAT
* *
24443831 TTTTCCTAATCTTT-TTATTTTAACCACATATTCTAACTCTTAA
1 TTTTCCTAACCTTTCTTATTTTAACCACACATTCTAACTCTTAA
24443874 CTCGATACTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 21 0.57
45 16 0.43
ACGTcount: A:0.27, C:0.20, G:0.01, T:0.51
Consensus pattern (45 bp):
TTTTCCTAACCTTTCTTATTTTAACCACACATTCTAACTCTTAAT
Found at i:24447633 original size:18 final size:18
Alignment explanation
Indices: 24447610--24447646 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24447600 ACAATTCATA
24447610 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
24447628 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
24447646 T
1 T
24447647 TGACCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:24451100 original size:2 final size:2
Alignment explanation
Indices: 24451093--24451151 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
24451083 GTATACATAC
24451093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24451135 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
24451152 AAAGTCAGGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24451727 original size:15 final size:14
Alignment explanation
Indices: 24451677--24451732 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
24451667 GTATAAATTT
* *
24451677 TTATAAATTATAAA
1 TTATAATTTATATA
24451691 TTATAAATTTATATA
1 TTAT-AATTTATATA
* *
24451706 ATCTAATTTAATATA
1 TTATAATTT-ATATA
24451721 TTATAA-TTATAT
1 TTATAATTTATAT
24451733 TAATTATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
13 4 0.12
14 11 0.32
15 19 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATAATTTATATA
Found at i:24464317 original size:15 final size:15
Alignment explanation
Indices: 24464292--24464331 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
24464282 AATTCAATCG
* *
24464292 TATGTTTATTTATGT
1 TATGGTTATTTATAT
*
24464307 TATTGTTATTTATAT
1 TATGGTTATTTATAT
24464322 TATGGTTATT
1 TATGGTTATT
24464332 ATGAAGTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (15 bp):
TATGGTTATTTATAT
Found at i:24478916 original size:138 final size:138
Alignment explanation
Indices: 24478619--24479223 Score: 954
Period size: 138 Copynumber: 4.4 Consensus size: 138
24478609 GGAGAAAATC
* * *
24478619 AATATATGAAATTT-ATTCGTACAAAATATTAATTGTATATATTTTACCAAAATTATTAATATAA
1 AATATATG-AATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAA
* *
24478683 ATAGTTATAATAATTAATTTCGGTC-AAATATAAAAGACATG-AAATTAATATTCTTTTGGAATG
65 ATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAG
24478746 AATATAATT
130 AATATAATT
* *
24478755 AATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATGTAAA
1 AATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAA
* *
24478820 -ATGTTATATTAATAAATTTCGGTCAAAATATAAAATACATGAAAATTAATATTCTTTTGGAAAG
66 TA-GTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAG
24478884 AATATAATT
130 AATATAATT
* * *
24478893 AATATATGAATTTGATTCATACAACATATTAATTGTATATATTTTATCGAATTTATAAATATAAA
1 AATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAA
* * *
24478958 CAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTTTTTTGGAAAGA
66 TAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGA
24479023 ATAT-A--
131 ATATAATT
* **
24479028 AATATATGAATTTGATTCATACAAAATACTAATTGTATATATTTTAAAGAATTTATTAATATAAA
1 AATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAA
* *
24479093 TAGTTATATTAATTGATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAACA
66 TAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGA
24479158 ATATAATT
131 ATATAATT
*
24479166 AATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTA
1 AATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTA
24479224 TATTAATTAA
Statistics
Matches: 429, Mismatches: 32, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
135 130 0.30
136 75 0.17
137 16 0.04
138 207 0.48
139 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (138 bp):
AATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAA
TAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGA
ATATAATT
Found at i:24479114 original size:273 final size:272
Alignment explanation
Indices: 24478619--24479289 Score: 942
Period size: 273 Copynumber: 2.5 Consensus size: 272
24478609 GGAGAAAATC
* * * *
24478619 AATATATGAAATTTATTCGTACAAAATATTAATTGTATATATTTTACCAAAATTATTAATATAAA
1 AATATATG-AATTTATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATAAATATAAA
* * *
24478684 TAGTTATAATAATTAATTTCGGTCAAATATAAAAGACATGAAATTAATATTCTTTTGGAATGAAT
65 CAGTTATAATAATTAATTTCGATCAAATATAAAAGACATGAAATTAATATTCTTTTGGAAAGAAT
* **
24478749 ATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAA
130 ATAA-TAATATATAAATTTGATTCATACAAAATACTAATTGTATATATTTTAAAGAATTTATTAA
* *
24478814 TGTAAAATGTTATATTAATAAATTTCGGTCAAAATATAAAATACATGAAAATTAATATTCTTTTG
194 TATAAAATGTTATATTAATAAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTG
*
24478879 GAAAGAATATAATT
259 GAAACAATATAATT
* *
24478893 AATATATGAATTTGATTCATACAACATATTAATTGTATATATTTTATCGAATTTATAAATATAAA
1 AATATATGAATTT-ATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATAAATATAAA
* *
24478958 CAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTTTTTTGGAAAGA
65 CAGTTATAATAATTAATTTCGATC-AAATATAAAAGACATG-AAATTAATATTCTTTTGGAAAGA
*
24479023 ATAT-A-AATATATGAATTTGATTCATACAAAATACTAATTGTATATATTTTAAAGAATTTATTA
128 ATATAATAATATATAAATTTGATTCATACAAAATACTAATTGTATATATTTTAAAGAATTTATTA
**
24479086 ATAT-AAATAGTTATATTAATTGATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
193 ATATAAAAT-GTTATATTAATAAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
24479150 TGGAAACAATATAATT
257 TGGAAACAATATAATT
24479166 AATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACCGAA-TT-T--AT-T---
1 AATATATGAATTT-ATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATAAATATAAA
* * *
24479223 -A--TAT--TAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAAAATTCTTTTGAAAAGA
65 CAGTTATAATAATTAATTTCGATC-AAATATAAAAGACAT-GAAATTAATATTCTTTTGGAAAGA
24479283 ATATAAT
128 ATATAAT
24479290 TCATTTTTCT
Statistics
Matches: 363, Mismatches: 27, Indels: 26
0.87 0.06 0.06
Matches are distributed among these distances:
260 54 0.15
261 2 0.01
262 3 0.01
264 1 0.00
268 1 0.00
269 2 0.01
271 1 0.00
272 6 0.02
273 177 0.49
274 74 0.20
275 17 0.05
276 25 0.07
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (272 bp):
AATATATGAATTTATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATAAATATAAAC
AGTTATAATAATTAATTTCGATCAAATATAAAAGACATGAAATTAATATTCTTTTGGAAAGAATA
TAATAATATATAAATTTGATTCATACAAAATACTAATTGTATATATTTTAAAGAATTTATTAATA
TAAAATGTTATATTAATAAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
AACAATATAATT
Found at i:24479765 original size:19 final size:18
Alignment explanation
Indices: 24479711--24479790 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 18
24479701 TATAGATACT
*
24479711 TATAAAAAG-AATAAAAA
1 TATAATAAGAAATAAAAA
* * *
24479728 TATAATAAGCATTAGAAA
1 TATAATAAGAAATAAAAA
24479746 TATATATAAGAAATAAAAA
1 TATA-ATAAGAAATAAAAA
* *
24479765 TATAATACAGTAATAGAAA
1 TATAATA-AGAAATAAAAA
24479784 TAATAAT
1 T-ATAAT
24479791 GCATATTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
17 8 0.16
18 13 0.25
19 25 0.49
20 5 0.10
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (18 bp):
TATAATAAGAAATAAAAA
Found at i:24479803 original size:19 final size:20
Alignment explanation
Indices: 24479720--24479804 Score: 56
Period size: 19 Copynumber: 4.5 Consensus size: 20
24479710 TTATAAAAAG
*
24479720 AATAAAAAT-ATAATA-AGC
1 AATAAAAATAATAATACAGT
* * *
24479738 ATTAGAAAT-ATATATA-AGA
1 AATAAAAATAATA-ATACAGT
24479757 AATAAAAAT-ATAATACAGT
1 AATAAAAATAATAATACAGT
* *
24479776 AATAGAAATAATAATGCA-T
1 AATAAAAATAATAATACAGT
*
24479795 ATTAAAAATA
1 AATAAAAATA
24479805 TAAAGAATAA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
18 13 0.24
19 34 0.63
20 7 0.13
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (20 bp):
AATAAAAATAATAATACAGT
Found at i:24480743 original size:29 final size:29
Alignment explanation
Indices: 24480688--24480747 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
24480678 TTGGGGGATC
* **
24480688 CTTCTAGTGCCTTAAACAGCTGGTTGATT
1 CTTCTAGTGCCTTAAACAACTAATTGATT
* *
24480717 CTTCTTGTGCCTTAGACAACTAATTGATT
1 CTTCTAGTGCCTTAAACAACTAATTGATT
24480746 CT
1 CT
24480748 AGAACAATCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.40
Consensus pattern (29 bp):
CTTCTAGTGCCTTAAACAACTAATTGATT
Found at i:24481015 original size:27 final size:27
Alignment explanation
Indices: 24480962--24481016 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
24480952 ATCTGTTGAG
*
24480962 TCAGCACTCCCAAGATTGACGTGACAA
1 TCAGCACTCCCAAGATTGACATGACAA
* * *
24480989 TCAGCACTCCCAGGATTGCCATTACAA
1 TCAGCACTCCCAAGATTGACATGACAA
24481016 T
1 T
24481017 AAAATTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (27 bp):
TCAGCACTCCCAAGATTGACATGACAA
Found at i:24489986 original size:14 final size:15
Alignment explanation
Indices: 24489959--24489996 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
24489949 TTGTTTTTAG
24489959 TGCGAGAAAATTAAA
1 TGCGAGAAAATTAAA
*
24489974 TGCG-GAAATTTAAA
1 TGCGAGAAAATTAAA
*
24489988 TGCAAGAAA
1 TGCGAGAAA
24489997 GTAATTTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (15 bp):
TGCGAGAAAATTAAA
Found at i:24489996 original size:15 final size:14
Alignment explanation
Indices: 24489966--24490047 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
24489956 TAGTGCGAGA
*
24489966 AAATTAAATGC-GG
1 AAATTAAATGCAAG
24489979 AAATTTAAATGCAAG
1 AAA-TTAAATGCAAG
* *
24489994 AAAGTAATTTGCAAG
1 AAATTAA-ATGCAAG
*
24490009 AAAATAAAGTGCAAG
1 AAATTAAA-TGCAAG
* *
24490024 AATTTAAATTGCAAC
1 AAATTAAA-TGCAAG
*
24490039 AAAGTAAAT
1 AAATTAAAT
24490048 CGGTAAACAG
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
13 3 0.06
14 12 0.22
15 39 0.72
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.24
Consensus pattern (14 bp):
AAATTAAATGCAAG
Found at i:24490036 original size:30 final size:29
Alignment explanation
Indices: 24489984--24490047 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
24489974 TGCGGAAATT
* *
24489984 TAAATGCAAGAAAGTAATTTGCAAGAAAA
1 TAAATGCAAGAAAGTAAATTGCAACAAAA
** *
24490013 TAAAGTGCAAGAATTTAAATTGCAACAAAG
1 TAAA-TGCAAGAAAGTAAATTGCAACAAAA
24490043 TAAAT
1 TAAAT
24490048 CGGTAAACAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.53, C:0.08, G:0.16, T:0.23
Consensus pattern (29 bp):
TAAATGCAAGAAAGTAAATTGCAACAAAA
Found at i:24490726 original size:29 final size:29
Alignment explanation
Indices: 24490688--24490746 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
24490678 TGGGGGCTCA
24490688 TTCTAGTGCCTTAGACAGCTGGTTGATTC
1 TTCTAGTGCCTTAGACAGCTGGTTGATTC
* *
24490717 TTCTTGTGCCTTAGACAGTTGGTTGATTC
1 TTCTAGTGCCTTAGACAGCTGGTTGATTC
24490746 T
1 T
24490747 AGAACAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (29 bp):
TTCTAGTGCCTTAGACAGCTGGTTGATTC
Found at i:24494079 original size:12 final size:12
Alignment explanation
Indices: 24494062--24494086 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24494052 AATGCACTTC
24494062 ACCTAAAAATTA
1 ACCTAAAAATTA
24494074 ACCTAAAAATTA
1 ACCTAAAAATTA
24494086 A
1 A
24494087 TCTTTTCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ACCTAAAAATTA
Found at i:24495212 original size:122 final size:120
Alignment explanation
Indices: 24495010--24495227 Score: 298
Period size: 122 Copynumber: 1.8 Consensus size: 120
24495000 AAAACAGGAA
* * *
24495010 AAGATAATATTTAACCAGAATCAGCAGATTTTCTGTTTCACATCACTATACCATACGTGGCCAGT
1 AAGATAATATTAAACCAGAATCAGCAGATTTTATGTTTCACATCACTATACCATACGTAGCCAGT
24495075 GCTCTCAAGAAAATTTAATAGTGAAACAGAAGAAAATGTTCCTAAAAAGTAGAAC
66 GCTCTCAAGAAAATTTAATAGTGAAACAGAAGAAAATGTTCCTAAAAAGTAGAAC
* * *
24495130 AAGATAATATTAAACCAGAATC-GCCATATTTTTATAGTTTCACATCCCTATTCCATA-GTTAGC
1 AAGATAATATTAAACCAGAATCAG-CAGA-TTTTAT-GTTTCACATCACTATACCATACG-TAGC
* *
24495193 CAGTGGC-CTTAAGAAAATTTAATAGTGAAAGAGAA
62 CAGT-GCTCTCAAGAAAATTTAATAGTGAAACAGAA
24495228 TAAGAAAATG
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
119 1 0.01
120 24 0.28
121 6 0.07
122 52 0.61
123 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (120 bp):
AAGATAATATTAAACCAGAATCAGCAGATTTTATGTTTCACATCACTATACCATACGTAGCCAGT
GCTCTCAAGAAAATTTAATAGTGAAACAGAAGAAAATGTTCCTAAAAAGTAGAAC
Found at i:24500479 original size:96 final size:96
Alignment explanation
Indices: 24500315--24500512 Score: 378
Period size: 96 Copynumber: 2.1 Consensus size: 96
24500305 ACTTTACTCA
*
24500315 TTAAATCAAAAAAATCCCGCCATAGTCCTCATAAACCATATGGGGCTTTTATAATAGGGTTTCCA
1 TTAAATCAAAAAAATCCAGCCATAGTCCTCATAAACCATATGGGGCTTTTATAATAGGGTTTCCA
24500380 TCTATTACTCTATCCTTCTCGCTTTGGTAAT
66 TCTATTACTCTATCCTTCTCGCTTTGGTAAT
24500411 TTAAATCAAAAAAATCCAGCCATAGTCCTCATAAACCATATGGGGCTTTTATAATAGGGTTTCCA
1 TTAAATCAAAAAAATCCAGCCATAGTCCTCATAAACCATATGGGGCTTTTATAATAGGGTTTCCA
24500476 TCTATTACTCTATCCTTCTCGCTTTGGTAAT
66 TCTATTACTCTATCCTTCTCGCTTTGGTAAT
24500507 TCTAAA
1 T-TAAA
24500513 CTTTTTCCTA
Statistics
Matches: 100, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
96 96 0.96
97 4 0.04
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (96 bp):
TTAAATCAAAAAAATCCAGCCATAGTCCTCATAAACCATATGGGGCTTTTATAATAGGGTTTCCA
TCTATTACTCTATCCTTCTCGCTTTGGTAAT
Found at i:24507300 original size:157 final size:151
Alignment explanation
Indices: 24506977--24507434 Score: 746
Period size: 151 Copynumber: 3.0 Consensus size: 151
24506967 AATTCAACTG
* *
24506977 TGCATCTTAAATGGTAGCAAAGGTTTAATTTTAAATTTTAAAATCTTTTTAGCCTAGAGAGGAGC
1 TGCATCTTAAATGGTAGCAAAGGTTTAATTTTAAATTTTAAAATCATTTTAGCCTAGAAAGGAGC
*
24507042 ATTGCAAGGTTGGAATCCTCTCTCCCCTCTTAGACTTCC----ATGTATTTAGGAAAGGATAACA
66 AATGCAAGGTTGGAATCCTCTCTCCCCTCTTAGACTTCCTTATATGTATTTAGGAAAGGATAACA
*
24507103 GCCATCTATCATCAGTACATA
131 GGCATCTATCATCAGTACATA
*
24507124 TGCATCTTAAATGGTAGCAAAGGTTTAATTTTAAATTTTAAATTTTAAATCATTTTAGCCAAGAA
1 TGCATCTTAAATGGTAGCAAAGGTTTAATTTTAAATTTT--A----AAATCATTTTAGCCTAGAA
24507189 AGGAGCAATGCAAGGTTGGAATCCTCTCTCCCCTCTTAGACTTCCTTATATGTATTTAGGAAAGG
60 AGGAGCAATGCAAGGTTGGAATCCTCTCTCCCCTCTTAGACTTCCTTATATGTATTTAGGAAAGG
24507254 ATAACAGGCATCTATCATCAGTACATA
125 ATAACAGGCATCTATCATCAGTACATA
24507281 TGCATCTTAAATGGTAGCAAAGGTTTAATTTTAAATTTTAAAATCATTTTAGCCTAGAGAA-GAG
1 TGCATCTTAAATGGTAGCAAAGGTTTAATTTTAAATTTTAAAATCATTTTAGCCTAGA-AAGGAG
* * *
24507345 CAATGAAAGGTTGGAATCCTCTCTCCCCTCTTAGACTTCCTTATAAGTATTTAGGAAGGGATAAC
65 CAATGCAAGGTTGGAATCCTCTCTCCCCTCTTAGACTTCCTTATATGTATTTAGGAAAGGATAAC
24507410 AGGCATCTATCATCAGTACATA
130 AGGCATCTATCATCAGTACATA
24507432 TGC
1 TGC
24507435 TTCATAATTC
Statistics
Matches: 291, Mismatches: 9, Indels: 18
0.92 0.03 0.06
Matches are distributed among these distances:
147 39 0.13
149 1 0.00
151 107 0.37
152 2 0.01
153 60 0.21
155 1 0.00
157 81 0.28
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (151 bp):
TGCATCTTAAATGGTAGCAAAGGTTTAATTTTAAATTTTAAAATCATTTTAGCCTAGAAAGGAGC
AATGCAAGGTTGGAATCCTCTCTCCCCTCTTAGACTTCCTTATATGTATTTAGGAAAGGATAACA
GGCATCTATCATCAGTACATA
Found at i:24529114 original size:27 final size:27
Alignment explanation
Indices: 24529076--24529132 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
24529066 TTCGACATTA
24529076 TTCACCATAATTCTTCTTGTTTTAACT
1 TTCACCATAATTCTTCTTGTTTTAACT
24529103 TTCACCATAATTCTTCTTGTTTTAACT
1 TTCACCATAATTCTTCTTGTTTTAACT
24529130 TTC
1 TTC
24529133 TTTGCATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.04, T:0.53
Consensus pattern (27 bp):
TTCACCATAATTCTTCTTGTTTTAACT
Found at i:24536839 original size:12 final size:12
Alignment explanation
Indices: 24536818--24536853 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
24536808 GGAGACAGAT
24536818 GAGGAAAAAGAA
1 GAGGAAAAAGAA
* *
24536830 GAGGACAAAGAG
1 GAGGAAAAAGAA
24536842 GAGGAAAAAGAA
1 GAGGAAAAAGAA
24536854 AAAGATAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.61, C:0.03, G:0.36, T:0.00
Consensus pattern (12 bp):
GAGGAAAAAGAA
Found at i:24537962 original size:21 final size:22
Alignment explanation
Indices: 24537933--24537975 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
24537923 TATTGATTAT
*
24537933 AAATAGGTTTAA-TAAAGGTTAA
1 AAATAGG-TTAATTAAAGCTTAA
24537955 AAAT-GGTTAATTAAAGCTTAA
1 AAATAGGTTAATTAAAGCTTAA
24537976 TGATGAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (22 bp):
AAATAGGTTAATTAAAGCTTAA
Found at i:24539719 original size:21 final size:21
Alignment explanation
Indices: 24539652--24539720 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
24539642 ACTTGAGTTG
*
24539652 TATCGGTAG-TTGAATTACA-A
1 TATCGGTAGTTTGTA-TACATA
24539672 GTATCGGTAGTTT-T-TAGCAT-
1 -TATCGGTAGTTTGTATA-CATA
24539692 T-TCGGTAGTTTGTATACATA
1 TATCGGTAGTTTGTATACATA
24539712 TATCGGTAG
1 TATCGGTAG
24539721 AAATTGCAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
18 10 0.25
19 7 0.17
20 5 0.12
21 16 0.40
22 2 0.05
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (21 bp):
TATCGGTAGTTTGTATACATA
Done.