Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 28 of 64
Found at i:4272306 original size:45 final size:44
Alignment explanation
Indices: 4271995--4272306 Score: 288
Period size: 43 Copynumber: 7.3 Consensus size: 44
4271985 TGTCAATGGG
* * *
4271995 TGATATGTTTTTCAAAGTCGGTGAGCCTCTGTTTAGAGGAGCTT
1 TGATATATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTT
* *
4272039 T-ATTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTT
1 TGATATATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTT
* * *
4272082 T-ATTTATTTTTCAAAGTCGTAGAGCCTCTGATTAGATGAGC--
1 TGATATATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTT
* * * ** * *
4272123 -AATTTACTTCCCAAAAGTCGTTGAGCCTCTAATTAGAGGAAC--
1 TGATATATTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCTT
* * *
4272165 -CATTTA-TTTTCAAACTCGTTGAGCCTCTGATTAGAGGAGCTT
1 TGATATATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTT
* *
4272207 T-ATTTA-TTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTT
1 TGATATATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTT
* * *
4272249 TGTTTATGTTTTTCAAAGTCGTTGAGCCTCT-ACTTAGAGGAGTTT
1 TG-ATATATTTTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCTT
*
4272294 TGATCAAATTTTT
1 TGAT-ATATTTTT
4272307 AACACAAAAA
Statistics
Matches: 227, Mismatches: 31, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
40 26 0.11
41 11 0.05
42 70 0.31
43 75 0.33
44 5 0.02
45 40 0.18
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (44 bp):
TGATATATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTT
Found at i:4272496 original size:8 final size:7
Alignment explanation
Indices: 4272478--4272569 Score: 53
Period size: 8 Copynumber: 12.6 Consensus size: 7
4272468 AGGCCCATTC
4272478 TATTTTT
1 TATTTTT
4272485 TATTTTT
1 TATTTTT
*
4272492 GTATTTTA
1 -TATTTTT
*
4272500 TA-TTTG
1 TATTTTT
4272506 TA-TTTT
1 TATTTTT
*
4272512 TAGTTATT
1 TA-TTTTT
4272520 TATTTATT
1 TATTT-TT
4272528 TATTTTT
1 TATTTTT
* *
4272535 ATATATCT
1 -TATTTTT
*
4272543 TATGTATT
1 TAT-TTTT
*
4272551 TATTATT
1 TATTTTT
4272558 TATTTATT
1 TATTT-TT
4272566 TATT
1 TATT
4272570 ATTACTATTT
Statistics
Matches: 67, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
6 10 0.15
7 24 0.36
8 33 0.49
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.72
Consensus pattern (7 bp):
TATTTTT
Found at i:4272500 original size:13 final size:13
Alignment explanation
Indices: 4272482--4272511 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4272472 CCATTCTATT
*
4272482 TTTTATTTTTGTA
1 TTTTATATTTGTA
4272495 TTTTATATTTGTA
1 TTTTATATTTGTA
4272508 TTTT
1 TTTT
4272512 TAGTTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (13 bp):
TTTTATATTTGTA
Found at i:4272524 original size:4 final size:4
Alignment explanation
Indices: 4272510--4272644 Score: 75
Period size: 4 Copynumber: 33.5 Consensus size: 4
4272500 TATTTGTATT
* * *
4272510 TTTA GTTA TTTA TTTA TTTA -TT- TTTA TATA TCTTA TGTA TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA
* * *
4272556 TTTA TTTA TTTA -TTA TTACTA TTTA TTAATA TTTT TTTA TTTA TCTG
1 TTTA TTTA TTTA TTTA TT--TA TTTA TT--TA TTTA TTTA TTTA TTTA
* * * *
4272603 TTAATA TATA TGTA TTTA -TTA -TTA TTTA TCTA TTTA TATA TT
1 TT--TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
4272645 ATAATCTATC
Statistics
Matches: 100, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
3 16 0.16
4 71 0.71
5 3 0.03
6 10 0.10
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:4272607 original size:22 final size:22
Alignment explanation
Indices: 4272579--4272626 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
4272569 TATTACTATT
4272579 TATTAATATTTTTTTATTTATC
1 TATTAATATTTTTTTATTTATC
* * * *
4272601 TGTTAATATATATGTATTTAT-
1 TATTAATATTTTTTTATTTATC
4272622 TATTA
1 TATTA
4272627 TTTATCTATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (22 bp):
TATTAATATTTTTTTATTTATC
Found at i:4272622 original size:40 final size:39
Alignment explanation
Indices: 4272574--4272683 Score: 104
Period size: 40 Copynumber: 2.9 Consensus size: 39
4272564 TTTATTATTA
4272574 CTATTTATTAATATTTTTTTATTTATCTGTTAATATATAT
1 CTATTTATTAATATTTTTTTATTTATCTGTTAATATA-AT
* * * * * *
4272614 GTATTTATTATTATTTATCTATTTA--T-ATATTATAAT
1 CTATTTATTAATATTTTTTTATTTATCTGTTAATATAAT
* *
4272650 CTATCTATT-AT-TATTTTTATTTATCTGTTAATAT
1 CTATTTATTAATATTTTTTTATTTATCTGTTAATAT
4272684 TTTTGTTTAT
Statistics
Matches: 53, Mismatches: 14, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
34 9 0.17
35 1 0.02
36 10 0.19
37 11 0.21
38 1 0.02
40 21 0.40
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (39 bp):
CTATTTATTAATATTTTTTTATTTATCTGTTAATATAAT
Found at i:4272632 original size:32 final size:30
Alignment explanation
Indices: 4272554--4272643 Score: 83
Period size: 32 Copynumber: 2.9 Consensus size: 30
4272544 ATGTATTTAT
* * * *
4272554 TATTTATTTATTTAT-TATTACTATTTATTAA
1 TATTTTTTTATTTATCTATTAATATATA-T-G
*
4272585 TATTTTTTTATTTATCTGTTAATATATATG
1 TATTTTTTTATTTATCTATTAATATATATG
*
4272615 TATTTATTATTATTTATCTATTTATATAT
1 TATTT-TT-TTATTTATCTATTAATATAT
4272644 TATAATCTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
30 5 0.10
31 17 0.35
32 27 0.55
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (30 bp):
TATTTTTTTATTTATCTATTAATATATATG
Found at i:4272710 original size:42 final size:40
Alignment explanation
Indices: 4272651--4272729 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 40
4272641 TATTATAATC
* * *
4272651 TATCTATTATTATTTTTATTTATCTGTTAATATTTTTGTT
1 TATCTATTATTATTTTTAATTATCTATTAACATTTTTGTT
*
4272691 TATCTAATTATTTTCTTTTAATTATCTATTAACATTTTT
1 TATCT-ATTATTAT-TTTTAATTATCTATTAACATTTTT
4272730 TATTTGATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 5 0.15
41 7 0.21
42 21 0.64
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.65
Consensus pattern (40 bp):
TATCTATTATTATTTTTAATTATCTATTAACATTTTTGTT
Found at i:4273544 original size:5 final size:5
Alignment explanation
Indices: 4273534--4273579 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
4273524 GTTTAATACC
*
4273534 TTTTA TTTTA TTTT- TTAT- TTTTA TTTTA TTTTA -TTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
4273580 CTTTAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 10 0.27
5 27 0.73
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:4273560 original size:23 final size:25
Alignment explanation
Indices: 4273534--4273579 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
4273524 GTTTAATACC
4273534 TTTTATTTTA-TT-TTTTATTTTTA
1 TTTTATTTTATTTATTTTATTTTTA
4273557 TTTTATTTTATTTATTTTATTTT
1 TTTTATTTTATTTATTTTATTTT
4273580 CTTTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.48
24 2 0.10
25 9 0.43
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTTATTTTATTTATTTTATTTTTA
Found at i:4273584 original size:18 final size:19
Alignment explanation
Indices: 4273534--4273584 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
4273524 GTTTAATACC
4273534 TTTTATTTTATTT-TTTAT
1 TTTTATTTTATTTATTTAT
4273552 TTTTATTTTATTTTATTTA-
1 TTTTATTTTA-TTTATTTAT
*
4273571 TTTTATTTTCTTTA
1 TTTTATTTTATTTA
4273585 AATAAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 14 0.47
19 12 0.40
20 4 0.13
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTATTTTATTTATTTAT
Found at i:4273660 original size:60 final size:59
Alignment explanation
Indices: 4273596--4273813 Score: 280
Period size: 58 Copynumber: 3.7 Consensus size: 59
4273586 ATAAAATTCA
*
4273596 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTCT
1 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
* * * * *
4273655 -AAAAAATATTTTTGAGGAAAGGTTAAAAGTATTAATTTTCCTTGAAAATAAGCTTTTT
1 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
* * **
4273713 AAAAAAATATTTTTGAA-AAAAAGTTGAAAGTATCAATTTTCCTTTGAAAAGAAATTTTCT
1 AAAAAAATATTTTT-AAGGAAAAGTTGAAAGTATCAATTTTCC-TTGAAAATAAGCTTTCT
* *
4273773 AAAAAGATATTTTT-GGGAAAAAGTTGAAAGTATCAATTTTC
1 AAAAAAATATTTTTAAGG-AAAAGTTGAAAGTATCAATTTTC
4273814 TCTGTACAAA
Statistics
Matches: 136, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
58 52 0.38
59 34 0.25
60 50 0.37
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (59 bp):
AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
Found at i:4283365 original size:3 final size:3
Alignment explanation
Indices: 4283357--4283408 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
4283347 AAAAGAAAAG
4283357 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4283405 ATA A
1 ATA A
4283409 AAAAAGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4289563 original size:104 final size:104
Alignment explanation
Indices: 4289383--4289587 Score: 349
Period size: 104 Copynumber: 2.0 Consensus size: 104
4289373 ATAAACTTTT
*
4289383 GTGGATATTTCTAATGTATTGCATATGTGAAGTCCTTAGGTTTTTCAATTATAAATGCCAATAGA
1 GTGGATATTTCTAATGTATTGCATATGTGAAGTCCTTAGATTTTTCAATTATAAATGCCAATAGA
* * *
4289448 TAGTAAATAATCGGATATCAGTTATTATCCAATCTGTTA
66 TAGTAAATAATCAGATATCAGATACTATCCAATCTGTTA
*
4289487 GTGGATATTTCTAATGTATTGCATATGTGAAGTCCTTAGATTTTTCAATTATAAATGGCAATCAG
1 GTGGATATTTCTAATGTATTGCATATGTGAAGTCCTTAGATTTTTCAATTATAAATGCCAAT-AG
4289552 -TAGTAAATAATCAGATATCAGATACTATCCAATCTG
65 ATAGTAAATAATCAGATATCAGATACTATCCAATCTG
4289588 ATTACGTCAA
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 93 0.98
105 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (104 bp):
GTGGATATTTCTAATGTATTGCATATGTGAAGTCCTTAGATTTTTCAATTATAAATGCCAATAGA
TAGTAAATAATCAGATATCAGATACTATCCAATCTGTTA
Found at i:4297472 original size:12 final size:12
Alignment explanation
Indices: 4297455--4297485 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4297445 CAGAAACACC
4297455 ATTCAGCATACG
1 ATTCAGCATACG
4297467 ATTCAGCATACG
1 ATTCAGCATACG
4297479 ATTCAGC
1 ATTCAGC
4297486 CTCTCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (12 bp):
ATTCAGCATACG
Found at i:4298877 original size:356 final size:351
Alignment explanation
Indices: 4298218--4299006 Score: 959
Period size: 356 Copynumber: 2.2 Consensus size: 351
4298208 TAAAAAATTA
* * *
4298218 CCTTCACTAATTATCTACAAACTATGATAAAAATTATTAAAGACATCTTTCTTGAATATACGCCT
1 CCTTCACTAATTATCTACAAACTATGAT-AGAATTATTAAAGACGTCTTTCTTGGATATACGCCT
* * ** * *
4298283 TTAATAACCGTGTTAGAATTTGTGTAGCGGTATATAGAAGGCATTTTACACTAGAATATGCCTTT
65 TAAATAACCGTGTTAAAATTTGTGTAGCGGTATATAGAACACATTTTACACTAAAAGATGCCTTT
* * * * **
4298348 AATAATTCTCAAAATTTTTAGTGAGAAAATTTTGAAGGCGTCTGTTATTAACAAATGCCTTCAGT
130 AATAATTCCCAAAATTTTTAATGAAAAAATTTTGAAGGCGTCTGTTACTAACAAACACCTTCAGT
* * ** *
4298413 AATGGATTATTAAGTTTAAAGGTATATTGAAGGTGCATTTTTGAATAAATACCTTCCATAACTAT
195 AATGGATTACTAAGTTTAAAGGTATATTGAAGGTGCATTCTCAAATAAATACCTTCCATAACCAT
* * **
4298478 CGTGGTATATTAAAGGCATATCATAATAAAATACGTTTTTAATAATCCAAAAAAAAAGTTTTT-A
260 CGTGATATATTAAAGGCATATCATAATAAAAGACGCCTTTAATAAT-CAAAAAAAAAGTTTTTAA
* *
4298542 GGAAAATTATTGAAGGCATTGTTATCCT-ACTG
324 AG-AAATTATTGAA-G-A-CGTTAT-CTGACTG
* * *
4298574 CCTTCACTAATTATGTACAAACTATGATAGGAATTATTAAAAACGTCTTTCTCGGATATACGCCT
1 CCTTCACTAATTATCTACAAACTATGATA-GAATTATTAAAGACGTCTTTCTTGGATATACGCCT
* * * *
4298639 TCAATAACCGTGTTAAAATTTGTGT-GACGGTATATAGAACATATTTTATAGTAAAAGATGCCTT
65 TAAATAACCGTGTTAAAATTTGTGTAG-CGGTATATAGAACACATTTTACACTAAAAGATGCCTT
* *
4298703 TACTGATTCCCAAAATTTTTAATGAAAAAATTTTGAAGGCGTCTGTTACTAACAAACACCTTCAG
129 TAATAATTCCCAAAATTTTTAATGAAAAAATTTTGAAGGCGTCTGTTACTAACAAACACCTTCAG
* *
4298768 TAATGGATTACTAAGTTTAAAGGTATATTGAATGTGCCTTCTCAAATAAATACCTTCCATAACCA
194 TAATGGATTACTAAGTTTAAAGGTATATTGAAGGTGCATTCTCAAATAAATACCTTCCATAACCA
* * * ** * ** *
4298833 TTGTGATATGTTGAAGGTGGT-TCATAATAAAAGATGCCTTTAATAATCTGAAAAAAATTTTTTA
259 TCGTGATATATTAAAGG-CATATCATAATAAAAGACGCCTTTAATAATCAAAAAAAAAGTTTTTA
4298897 AAGAAATTATTGAAGACGTTATCTGGAACTG
323 AAGAAATTATTGAAGACGTTATCT-G-ACTG
* * *
4298928 CCTTCACTTATTATCTATAAAC--TG-T-G-A-TATTAAAGGCGTCTTTCTTGGATATACGCCTT
1 CCTTCACTAATTATCTACAAACTATGATAGAATTATTAAAGACGTCTTTCTTGGATATACGCCTT
4298987 AAATAACCGTGTTAAAATTT
66 AAATAACCGTGTTAAAATTT
4299007 ACGTGGCGAT
Statistics
Matches: 374, Mismatches: 52, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
347 48 0.13
348 1 0.00
349 1 0.00
351 3 0.01
352 7 0.02
353 1 0.00
354 24 0.06
355 26 0.07
356 262 0.70
357 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (351 bp):
CCTTCACTAATTATCTACAAACTATGATAGAATTATTAAAGACGTCTTTCTTGGATATACGCCTT
AAATAACCGTGTTAAAATTTGTGTAGCGGTATATAGAACACATTTTACACTAAAAGATGCCTTTA
ATAATTCCCAAAATTTTTAATGAAAAAATTTTGAAGGCGTCTGTTACTAACAAACACCTTCAGTA
ATGGATTACTAAGTTTAAAGGTATATTGAAGGTGCATTCTCAAATAAATACCTTCCATAACCATC
GTGATATATTAAAGGCATATCATAATAAAAGACGCCTTTAATAATCAAAAAAAAAGTTTTTAAAG
AAATTATTGAAGACGTTATCTGACTG
Found at i:4307437 original size:3 final size:3
Alignment explanation
Indices: 4307429--4307460 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4307419 GATTCTTGTG
4307429 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4307461 AAGGCACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4307866 original size:3 final size:3
Alignment explanation
Indices: 4307853--4307885 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
4307843 ATTATGAACT
*
4307853 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4307886 GCAACAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:4308776 original size:2 final size:2
Alignment explanation
Indices: 4308763--4308794 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4308753 CTTGCATGCT
*
4308763 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4308795 GGGAATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4314299 original size:2 final size:2
Alignment explanation
Indices: 4314287--4314329 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4314277 AAGAGTTTTC
*
4314287 AT AT AT CT 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
4314329 A
1 A
4314330 AAAGATTATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4315804 original size:22 final size:22
Alignment explanation
Indices: 4315779--4315819 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
4315769 TTGATAAATT
4315779 TTTTTTAAATATAAA-ATATTA
1 TTTTTTAAATATAAATATATTA
4315800 TTTTTTAAATATAAATATAT
1 TTTTTTAAATATAAATATAT
4315820 AAATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTTTAAATATAAATATATTA
Found at i:4317097 original size:16 final size:16
Alignment explanation
Indices: 4317057--4317190 Score: 56
Period size: 16 Copynumber: 8.0 Consensus size: 16
4317047 TTATTAAAAT
*
4317057 ATATTGAAATTATTTA
1 ATATTAAAATTATTTA
*
4317073 CTATTAAAATTA-TTA
1 ATATTAAAATTATTTA
* **
4317088 ATATTCAAAAATAAGTA
1 ATATT-AAAATTATTTA
*
4317105 TATTTTAATAATAATATTTA
1 -ATATTAA-AAT--TATTTA
4317125 ATATTAAAATATTATGTTA
1 ATATT-AAA-ATTAT-TTA
* * *
4317144 ATATAAAAAATACTTA
1 ATATTAAAATTATTTA
* *
4317160 A-AATAAAACTATTTA
1 ATATTAAAATTATTTA
* * *
4317175 TTATTTATATTATTTA
1 ATATTAAAATTATTTA
4317191 TTAATATATT
Statistics
Matches: 86, Mismatches: 22, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
15 17 0.20
16 30 0.35
17 7 0.08
18 12 0.14
19 12 0.14
20 8 0.09
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (16 bp):
ATATTAAAATTATTTA
Found at i:4317144 original size:19 final size:18
Alignment explanation
Indices: 4317067--4317160 Score: 56
Period size: 18 Copynumber: 5.4 Consensus size: 18
4317057 ATATTGAAAT
*
4317067 TATTTACTATTAAAAT--
1 TATTTAATATTAAAATAA
*
4317083 TA-TTAATATTCAAA-AA
1 TATTTAATATTAAAATAA
** *
4317099 TAAGTATATTTTAATAATAA
1 TATTTA-ATATTAA-AATAA
*
4317119 TATTTAATATTAAAATAT
1 TATTTAATATTAAAATAA
4317137 TATGTTAATA-TAAAA-AA
1 TAT-TTAATATTAAAATAA
*
4317154 TACTTAA
1 TATTTAA
4317161 AATAAAACTA
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
15 10 0.17
16 8 0.13
17 5 0.08
18 17 0.28
19 14 0.23
20 6 0.10
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (18 bp):
TATTTAATATTAAAATAA
Found at i:4317211 original size:23 final size:23
Alignment explanation
Indices: 4317181--4317323 Score: 85
Period size: 23 Copynumber: 6.4 Consensus size: 23
4317171 TTTATTATTT
4317181 ATATTATTTATTAATATATTATA
1 ATATTATTTATTAATATATTATA
*
4317204 ATATTATTTATAAATAATATTTATTA
1 ATATTATTTATTAAT-ATA-TTA-TA
*
4317230 ATA-TATTATATT-A-ATA--GT-
1 ATATTATT-TATTAATATATTATA
4317248 ATATTATTTATTAATA-A-TATA
1 ATATTATTTATTAATATATTATA
*
4317269 TTATTTATTTA-T-ATATTATTATA
1 ATA-TTATTTATTAATA-TATTATA
* *
4317292 ATATTTATTAATTAA-AT-TAATA
1 ATA-TTATTTATTAATATATTATA
4317314 ATATTTATTT
1 ATA-TTATTT
4317324 TTATTTATTT
Statistics
Matches: 96, Mismatches: 9, Indels: 31
0.71 0.07 0.23
Matches are distributed among these distances:
18 7 0.07
19 7 0.07
20 5 0.05
21 3 0.03
22 21 0.22
23 31 0.32
24 5 0.05
25 9 0.09
26 8 0.08
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (23 bp):
ATATTATTTATTAATATATTATA
Found at i:4317245 original size:49 final size:49
Alignment explanation
Indices: 4317161--4317355 Score: 144
Period size: 49 Copynumber: 4.1 Consensus size: 49
4317151 AAATACTTAA
* *
4317161 AATAAA-ACTATTTATTATTTATATTATTTATTAATATATTATAATATTATT
1 AATAAATAATATTTATTA-ATATATTA--TATTAATATATTATAATATTATT
* *
4317212 TATAAATAATATTTATTAATATATTATATTAATAGTA-TATTAT-TTATT
1 AATAAATAATATTTATTAATATATTATATTAATA-TATTATAATATTATT
* * *
4317260 AATAATATATTATTTATTTATATATTAT-TATAATAT-TTATTA-ATTA--
1 AATAA-ATAATATTTATTAATATATTATAT-TAATATATTATAATATTATT
* * * *
4317306 AATTAATAATATTTATT--TTTATT-TATTTAT-TAATATAATATTATT
1 AATAAATAATATTTATTAATATATTATATTAATATATTATAATATTATT
*
4317351 CATAA
1 AATAA
4317356 GTAAAATTAT
Statistics
Matches: 118, Mismatches: 15, Indels: 28
0.73 0.09 0.17
Matches are distributed among these distances:
41 1 0.01
42 8 0.07
43 10 0.08
45 14 0.12
46 4 0.03
48 19 0.16
49 38 0.32
50 2 0.02
51 12 0.10
52 10 0.08
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (49 bp):
AATAAATAATATTTATTAATATATTATATTAATATATTATAATATTATT
Found at i:4317319 original size:41 final size:40
Alignment explanation
Indices: 4317189--4317348 Score: 127
Period size: 41 Copynumber: 4.0 Consensus size: 40
4317179 TTATATTATT
* * *
4317189 TATTAATATATTATAATATTATTTATAAATAATATTTATTAA
1 TATTTATATATTATTATATTATTTATTAATAA-A-TTATTAA
* * *
4317231 TATATTATATTAATAGTATATTATTTATTAAT-AATATATTATT
1 TAT-TTATA-TATTATTATATTATTTATTAATAAAT-TATTA-A
* *
4317274 TATTTATATATTATTATAATATTTATTAATTAAATTAATAA
1 TATTTATATATTATTATATTATTTATTAA-TAAATTATTAA
4317315 TA-TT-TAT-TT-TTAT-TTATTTATTAATATAA-TATTA
1 TATTTATATATTATTATATTATTTATTAATA-AATTATTA
4317349 TTCATAAGTA
Statistics
Matches: 98, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
35 6 0.06
36 12 0.12
37 4 0.04
38 2 0.02
39 3 0.03
40 2 0.02
41 21 0.21
42 19 0.19
43 11 0.11
44 18 0.18
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (40 bp):
TATTTATATATTATTATATTATTTATTAATAAATTATTAA
Found at i:4317936 original size:25 final size:25
Alignment explanation
Indices: 4317908--4317956 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
4317898 ATTTTAAAGT
4317908 TAATATAAA-AATAAATTTTATTATA
1 TAATA-AAATAATAAATTTTATTATA
4317933 TAATAAAATAATAAATTTTATTAT
1 TAATAAAATAATAAATTTTATTAT
4317957 TACATTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TAATAAAATAATAAATTTTATTATA
Found at i:4321346 original size:23 final size:23
Alignment explanation
Indices: 4321318--4321367 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
4321308 AATCTAGAAG
4321318 ATAATAATTATTT-TTATATCAAA
1 ATAATAATTATTTCTTAT-TCAAA
4321341 ATAATAATTATTTCTTATTCAAA
1 ATAATAATTATTTCTTATTCAAA
4321364 ATAA
1 ATAA
4321368 AGTTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAATAATTATTTCTTATTCAAA
Found at i:4333472 original size:22 final size:22
Alignment explanation
Indices: 4333447--4333499 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
4333437 GTAAGTAACT
*
4333447 TTTTTTTTTCAAAAATAAAATA
1 TTTTATTTTCAAAAATAAAATA
4333469 TTTTATTTTCAAAAATAAAATA
1 TTTTATTTTCAAAAATAAAATA
4333491 TTTTATTTT
1 TTTTATTTT
4333500 GTTATGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATTTTCAAAAATAAAATA
Found at i:4335402 original size:5 final size:5
Alignment explanation
Indices: 4335389--4335422 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
4335379 TGTAAACATT
* *
4335389 AAAAG AAAAA AAAAA AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
4335423 ACGACTGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:4346969 original size:22 final size:23
Alignment explanation
Indices: 4346917--4346971 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
4346907 TAGTTAAAAT
* *
4346917 TATTCATTTTGAACAGACTTATC
1 TATTTATTTTGAACAGACTTAAC
* *
4346940 TCTCTATTTT-AACAGACTTAAC
1 TATTTATTTTGAACAGACTTAAC
4346962 TATTTATTTT
1 TATTTATTTT
4346972 CAGTTTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.49
Consensus pattern (23 bp):
TATTTATTTTGAACAGACTTAAC
Found at i:4349070 original size:340 final size:340
Alignment explanation
Indices: 4348450--4349135 Score: 1363
Period size: 340 Copynumber: 2.0 Consensus size: 340
4348440 GAGATGTTCA
4348450 TTGAATAGTTGTTCTTAGCTTTTAGGCTTGCACACTGAAATCCTATTTAAAATGAATTTTATCCA
1 TTGAATAGTTGTTCTTAGCTTTTAGGCTTGCACACTGAAATCCTATTTAAAATGAATTTTATCCA
4348515 TTGACTTAAATCTTTTTTTCCCCTTCTTACGACTAGATTTTAGATACTGCAAAAGGCTCTATAAC
66 TTGACTTAAATCTTTTTTTCCCCTTCTTACGACTAGATTTTAGATACTGCAAAAGGCTCTATAAC
4348580 CGTGGAACTCTTCAGGCACAGTTCTTCTGAAGTTGTTTATAAATTCCTTGATTTATGGTAAGTTC
131 CGTGGAACTCTTCAGGCACAGTTCTTCTGAAGTTGTTTATAAATTCCTTGATTTATGGTAAGTTC
4348645 TGGACTCAATGTGTTCACTTACTTAAAATGATTGATTTTCTTTTATAGAACTATCATAAAATTCC
196 TGGACTCAATGTGTTCACTTACTTAAAATGATTGATTTTCTTTTATAGAACTATCATAAAATTCC
4348710 ATGTGGTTAATATTTGAACTGGAAATTAGGATGTAGATAGAGTTGATCAGATCGTGCTAGTGAAG
261 ATGTGGTTAATATTTGAACTGGAAATTAGGATGTAGATAGAGTTGATCAGATCGTGCTAGTGAAG
4348775 GAGTCAAGAACAGCT
326 GAGTCAAGAACAGCT
4348790 TTGAATAGTTGTTCTTAGCTTTTAGGCTTGCACACTGAAATCCTATTTAAAATGAATTTTATCCA
1 TTGAATAGTTGTTCTTAGCTTTTAGGCTTGCACACTGAAATCCTATTTAAAATGAATTTTATCCA
*
4348855 TTGACTTAACTCTTTTTTTCCCCTTCTTACGACTAGATTTTAGATACTGCAAAAGGCTCTATAAC
66 TTGACTTAAATCTTTTTTTCCCCTTCTTACGACTAGATTTTAGATACTGCAAAAGGCTCTATAAC
4348920 CGTGGAACTCTTCAGGCACAGTTCTTCTGAAGTTGTTTATAAATTCCTTGATTTATGGTAAGTTC
131 CGTGGAACTCTTCAGGCACAGTTCTTCTGAAGTTGTTTATAAATTCCTTGATTTATGGTAAGTTC
4348985 TGGACTCAATGTGTTCACTTACTTAAAATGATTGATTTTCTTTTATAGAACTATCATAAAATTCC
196 TGGACTCAATGTGTTCACTTACTTAAAATGATTGATTTTCTTTTATAGAACTATCATAAAATTCC
4349050 ATGTGGTTAATATTTGAACTGGAAATTAGGATGTAGATAGAGTTGATCAGATCGTGCTAGTGAAG
261 ATGTGGTTAATATTTGAACTGGAAATTAGGATGTAGATAGAGTTGATCAGATCGTGCTAGTGAAG
4349115 GAGTCAAGAACAGCT
326 GAGTCAAGAACAGCT
4349130 TTGAAT
1 TTGAAT
4349136 TATTTTCTGT
Statistics
Matches: 345, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
340 345 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (340 bp):
TTGAATAGTTGTTCTTAGCTTTTAGGCTTGCACACTGAAATCCTATTTAAAATGAATTTTATCCA
TTGACTTAAATCTTTTTTTCCCCTTCTTACGACTAGATTTTAGATACTGCAAAAGGCTCTATAAC
CGTGGAACTCTTCAGGCACAGTTCTTCTGAAGTTGTTTATAAATTCCTTGATTTATGGTAAGTTC
TGGACTCAATGTGTTCACTTACTTAAAATGATTGATTTTCTTTTATAGAACTATCATAAAATTCC
ATGTGGTTAATATTTGAACTGGAAATTAGGATGTAGATAGAGTTGATCAGATCGTGCTAGTGAAG
GAGTCAAGAACAGCT
Found at i:4354651 original size:19 final size:18
Alignment explanation
Indices: 4354626--4354675 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
4354616 CATATAATCT
4354626 AAGATGACATACTCATGA
1 AAGATGACATACTCATGA
*
4354644 ATAGATGAAATA-TCATGA
1 A-AGATGACATACTCATGA
4354662 AAGAATGATCATAC
1 AAG-ATGA-CATAC
4354676 ACCAAACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 2 0.08
18 12 0.46
19 12 0.46
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (18 bp):
AAGATGACATACTCATGA
Found at i:4354661 original size:18 final size:19
Alignment explanation
Indices: 4354627--4354662 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4354617 ATATAATCTA
*
4354627 AGATGACATACTCATGAAT
1 AGATGAAATACTCATGAAT
4354646 AGATGAAATA-TCATGAA
1 AGATGAAATACTCATGAA
4354663 AGAATGATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (19 bp):
AGATGAAATACTCATGAAT
Found at i:4359718 original size:17 final size:17
Alignment explanation
Indices: 4359696--4359728 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4359686 TCAATCTTAC
4359696 TTCTAAATCTTTTGAAA
1 TTCTAAATCTTTTGAAA
*
4359713 TTCTAAATTTTTTGAA
1 TTCTAAATCTTTTGAA
4359729 CCTTTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (17 bp):
TTCTAAATCTTTTGAAA
Found at i:4362975 original size:13 final size:13
Alignment explanation
Indices: 4362945--4362969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4362935 ATTCATCATT
4362945 TTTTTCATTTTTA
1 TTTTTCATTTTTA
4362958 TTTTTCATTTTT
1 TTTTTCATTTTT
4362970 TCTTTTTTGA
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCATTTTTA
Found at i:4362986 original size:21 final size:21
Alignment explanation
Indices: 4362939--4362986 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
4362929 TTAATCATTC
4362939 ATCATTTTTTTCATTTTTATTT
1 ATCA-TTTTTTCATTTTTATTT
* *
4362961 TTCATTTTTTCTTTTTTGA-TT
1 ATCATTTTTTCATTTTT-ATTT
4362982 ATCAT
1 ATCAT
4362987 ACTATGCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (21 bp):
ATCATTTTTTCATTTTTATTT
Found at i:4363330 original size:20 final size:22
Alignment explanation
Indices: 4363307--4363350 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
4363297 CTTAACTTAA
4363307 TCATTCATTT-CTT-TTTTTTT
1 TCATTCATTTCCTTCTTTTTTT
*
4363327 TCATTTATTTCCTTCTTTTTTT
1 TCATTCATTTCCTTCTTTTTTT
4363349 TC
1 TC
4363351 CCTGTTTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 3 0.14
22 9 0.43
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (22 bp):
TCATTCATTTCCTTCTTTTTTT
Found at i:4366231 original size:37 final size:37
Alignment explanation
Indices: 4366190--4366297 Score: 85
Period size: 37 Copynumber: 2.9 Consensus size: 37
4366180 TGAGGTAGAG
4366190 TGTATATGCTACCTATTAAGATTTGCATGAGATGGAA
1 TGTATATGCTACCTATTAAGATTTGCATGAGATGGAA
* * * * * * *
4366227 TGTATGTACTATCTATTGACA-TTG-GTGAGATAGAA
1 TGTATATGCTACCTATTAAGATTTGCATGAGATGGAA
* * * * *
4366262 TGCATTTGTTATCCTATTATGATATGCATGAGATGG
1 TGTATATGCTA-CCTATTAAGATTTGCATGAGATGG
4366298 GTTACATGTA
Statistics
Matches: 50, Mismatches: 18, Indels: 5
0.68 0.25 0.07
Matches are distributed among these distances:
35 16 0.32
36 9 0.18
37 18 0.36
38 7 0.14
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (37 bp):
TGTATATGCTACCTATTAAGATTTGCATGAGATGGAA
Found at i:4367505 original size:25 final size:25
Alignment explanation
Indices: 4367351--4367496 Score: 202
Period size: 25 Copynumber: 5.8 Consensus size: 25
4367341 AATATATAAT
**
4367351 AAATGACATAATTGGAATATGCATG
1 AAATGACATAATTAAAATATGCATG
*
4367376 AAATGACATAATCAAAATATGCATG
1 AAATGACATAATTAAAATATGCATG
* *
4367401 AAATCACATAATTAAAATATGCATA
1 AAATGACATAATTAAAATATGCATG
* *
4367426 AAATGACATAATTAAAATACGTATG
1 AAATGACATAATTAAAATATGCATG
* *
4367451 AAATGATATAATTAAAATATGTATG
1 AAATGACATAATTAAAATATGCATG
*
4367476 AAATGACATAACTAAAATATG
1 AAATGACATAATTAAAATATG
4367497 GAATAAATGT
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 107 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (25 bp):
AAATGACATAATTAAAATATGCATG
Found at i:4367505 original size:75 final size:74
Alignment explanation
Indices: 4367336--4367505 Score: 209
Period size: 75 Copynumber: 2.3 Consensus size: 74
4367326 AAAATAAAGA
* ** *
4367336 ATAAC-AATATAT-AATAAATGACATAATTGGAATATGCATGAAATGACATAATCAAAATATGCA
1 ATAACTAAAATATGAATAAATGACATAATTAAAATACGCATGAAATGACATAATCAAAATATGCA
4367399 TGAAATCAC
66 TGAAATCAC
* * * * * *
4367408 ATAATTAAAATATGCATAAAATGACATAATTAAAATACGTATGAAATGATATAATTAAAATATGT
1 ATAACTAAAATATGAAT-AAATGACATAATTAAAATACGCATGAAATGACATAATCAAAATATGC
*
4367473 ATGAAATGAC
65 ATGAAATCAC
4367483 ATAACTAAAATATGGAATAAATG
1 ATAACTAAAATAT-GAATAAATG
4367506 TAAAACACAC
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
72 4 0.05
73 6 0.07
74 2 0.02
75 66 0.81
76 3 0.04
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (74 bp):
ATAACTAAAATATGAATAAATGACATAATTAAAATACGCATGAAATGACATAATCAAAATATGCA
TGAAATCAC
Found at i:4373017 original size:33 final size:33
Alignment explanation
Indices: 4372980--4373044 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
4372970 GGAATTAAGT
* *
4372980 TTAAGGTTAGGGTTTTGGGTTTTGA-TTTAGGGC
1 TTAAGGTCAGGGTTTAGGG-TTTGATTTTAGGGC
*
4373013 TTAAGGTCATGGTTTAGGGTTTGATTTTAGGG
1 TTAAGGTCAGGGTTTAGGGTTTGATTTTAGGG
4373045 TTTTGATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.17, C:0.03, G:0.35, T:0.45
Consensus pattern (33 bp):
TTAAGGTCAGGGTTTAGGGTTTGATTTTAGGGC
Found at i:4373043 original size:13 final size:14
Alignment explanation
Indices: 4373025--4373053 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4373015 AAGGTCATGG
4373025 TTTAGGG-TTTGAT
1 TTTAGGGTTTTGAT
4373038 TTTAGGGTTTTGAT
1 TTTAGGGTTTTGAT
4373052 TT
1 TT
4373054 GAATTTAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.59
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:4373085 original size:51 final size:52
Alignment explanation
Indices: 4372986--4373114 Score: 129
Period size: 51 Copynumber: 2.5 Consensus size: 52
4372976 AAGTTTAAGG
* * * * *
4372986 TTAGGGTTTTGGGTTTTGATTTAGGGCTTAAGGTCATGGTTTAGGGTTTGATT
1 TTAGGGTTTT-GGATTTGATTTAGGGCTTAAGGTCATAGTTTAAGGTTTCAAT
*
4373039 TTAGGGTTTT-GATTTGAATTTAGGG-TTAAGGT-TTAGTTGTAAGGTTTCAAT
1 TTAGGGTTTTGGATTTG-ATTTAGGGCTTAAGGTCATAGTT-TAAGGTTTCAAT
* * *
4373090 TTAGGGTTTGGGATTAGGTTTAGGG
1 TTAGGGTTTTGGATTTGATTTAGGG
4373115 TTTATGATTA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
50 4 0.06
51 37 0.58
52 13 0.20
53 10 0.16
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.46
Consensus pattern (52 bp):
TTAGGGTTTTGGATTTGATTTAGGGCTTAAGGTCATAGTTTAAGGTTTCAAT
Found at i:4373123 original size:19 final size:19
Alignment explanation
Indices: 4373089--4373129 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
4373079 AAGGTTTCAA
* *
4373089 TTTAGGGTTTGGGATTAGG
1 TTTAGGGTTTAGGATTAAG
*
4373108 TTTAGGGTTTATGATTAAG
1 TTTAGGGTTTAGGATTAAG
4373127 TTT
1 TTT
4373130 TACAGTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.49
Consensus pattern (19 bp):
TTTAGGGTTTAGGATTAAG
Found at i:4373226 original size:24 final size:24
Alignment explanation
Indices: 4373199--4373250 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
4373189 TATGTTTAGG
*
4373199 GTTTCATGGGATTTAAGGTTTAAA
1 GTTTCATGGAATTTAAGGTTTAAA
* ** *
4373223 GTTTGATGGAATTTGGGGTTTCAA
1 GTTTCATGGAATTTAAGGTTTAAA
4373247 GTTT
1 GTTT
4373251 TAAGGTTTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.04, G:0.29, T:0.44
Consensus pattern (24 bp):
GTTTCATGGAATTTAAGGTTTAAA
Found at i:4374775 original size:18 final size:18
Alignment explanation
Indices: 4374743--4374779 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4374733 CAATCAAGTT
4374743 TCAAAATTTTAAAAATCA
1 TCAAAATTTTAAAAATCA
4374761 TCAAATATTTT-AAAATCA
1 TCAAA-ATTTTAAAAATCA
4374779 T
1 T
4374780 GATCTTGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
TCAAAATTTTAAAAATCA
Found at i:4375441 original size:57 final size:57
Alignment explanation
Indices: 4375367--4375489 Score: 219
Period size: 57 Copynumber: 2.2 Consensus size: 57
4375357 CTTTATCTTT
*
4375367 CTTTATTCTACTTTTCGACTTAGCAACTTATGATACTTTACTTTCTTTAAGTTTTTG
1 CTTTATTCTACCTTTCGACTTAGCAACTTATGATACTTTACTTTCTTTAAGTTTTTG
*
4375424 CTTTATTCTACCTTTCGACTTAGTAACTTATGATACTTTACTTTCTTTAAGTTTTTG
1 CTTTATTCTACCTTTCGACTTAGCAACTTATGATACTTTACTTTCTTTAAGTTTTTG
*
4375481 CTTTCTTCT
1 CTTTATTCT
4375490 TTTTAAAGAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 63 1.00
ACGTcount: A:0.20, C:0.19, G:0.08, T:0.54
Consensus pattern (57 bp):
CTTTATTCTACCTTTCGACTTAGCAACTTATGATACTTTACTTTCTTTAAGTTTTTG
Found at i:4376151 original size:230 final size:233
Alignment explanation
Indices: 4375746--4376211 Score: 848
Period size: 230 Copynumber: 2.0 Consensus size: 233
4375736 CTTGACCATC
4375746 ACTTTTTGAGTTTATTACACAGTTCATTTTTAAATACTCTAATGTAGGATCCAATATGGGTCTCA
1 ACTTTTTGAGTTTATTACACAGTTCATTTTTAAATACTCTAATGTAGGATCCAATATGGGTCTCA
4375811 TAGTGAAGCCAGTTGTATAGGCCCAAATGAATGCCCAAAATGGCCCAATAAAAAGGCTTAATAAA
66 TAGTGAAGCCAGTTGTATAGGCCCAAATGAATGCCCAAAATGGCCCAATAAAAAGGCTTAATAAA
* *
4375876 AGACTTATCCTGAAAACCCATGAATGGCCCATTATTGAGCATTAAACAAAAAAAACCAAATAAAA
131 AGACTTATCCTGAAAACCCATGAATAGCCCATTATTGACCATTAAACAAAAAAAACCAAATAAAA
4375941 AAAATAT-A-AAA-AAAAAAAACTTGGCCTAAAATAAA
196 AAAATATAATAAATAAAAAAAACTTGGCCTAAAATAAA
*
4375976 ACTTTTTGAGTTTATTACACAGTTTATTTTTAAATACTCTAATGTAGGATCCAATATGGGTCTCA
1 ACTTTTTGAGTTTATTACACAGTTCATTTTTAAATACTCTAATGTAGGATCCAATATGGGTCTCA
4376041 TAGTGAAGCCAGTTGTATAGGCCCAAATGAATGCCCAAAATGGCCCAATAAAAAGGCTTAATAAA
66 TAGTGAAGCCAGTTGTATAGGCCCAAATGAATGCCCAAAATGGCCCAATAAAAAGGCTTAATAAA
*
4376106 AGACTTATCCTGAAAACCCATGAATAGCCCATTATTGACCATTAAACAAAAAAAGCCAAATAAAA
131 AGACTTATCCTGAAAACCCATGAATAGCCCATTATTGACCATTAAACAAAAAAAACCAAATAAAA
4376171 AAAATATAAAAATAAATAAAAAAAACTTGGCCTAAAATAAA
196 AAAATAT---AATAAATAAAAAAAACTTGGCCTAAAATAAA
4376212 TTCATGATAG
Statistics
Matches: 226, Mismatches: 4, Indels: 6
0.96 0.02 0.03
Matches are distributed among these distances:
230 198 0.88
234 1 0.00
235 3 0.01
236 24 0.11
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (233 bp):
ACTTTTTGAGTTTATTACACAGTTCATTTTTAAATACTCTAATGTAGGATCCAATATGGGTCTCA
TAGTGAAGCCAGTTGTATAGGCCCAAATGAATGCCCAAAATGGCCCAATAAAAAGGCTTAATAAA
AGACTTATCCTGAAAACCCATGAATAGCCCATTATTGACCATTAAACAAAAAAAACCAAATAAAA
AAAATATAATAAATAAAAAAAACTTGGCCTAAAATAAA
Found at i:4376918 original size:37 final size:38
Alignment explanation
Indices: 4376877--4376950 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 38
4376867 TACTAATGAA
*
4376877 AGAACAAAAAGAAA-CAAAAAAAAAAAGAACTAGTAAG
1 AGAACAAAAAGAAACCAAAAAAAAAAAGAAATAGTAAG
*
4376914 AGAACAAAAATAAACCCAAAAAAAAAAAGAAATAGTA
1 AGAACAAAAAGAAA-CCAAAAAAAAAAAGAAATAGTA
4376951 GTAGAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 13 0.39
39 20 0.61
ACGTcount: A:0.73, C:0.09, G:0.11, T:0.07
Consensus pattern (38 bp):
AGAACAAAAAGAAACCAAAAAAAAAAAGAAATAGTAAG
Found at i:4376976 original size:24 final size:26
Alignment explanation
Indices: 4376930--4376993 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 26
4376920 AAAATAAACC
4376930 CAAAAAAA-AAAAGAAATAGTAGTAG
1 CAAAAAAACAAAAGAAATAGTAGTAG
4376955 -AAAAAAACAAAAG-AAT-GATAGTAG
1 CAAAAAAACAAAAGAAATAG-TAGTAG
4376979 CAAAGAATAACAAAA
1 CAAA-AA-AACAAAA
4376994 AACCAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
23 1 0.03
24 16 0.47
25 8 0.24
26 2 0.06
27 7 0.21
ACGTcount: A:0.69, C:0.06, G:0.14, T:0.11
Consensus pattern (26 bp):
CAAAAAAACAAAAGAAATAGTAGTAG
Found at i:4378284 original size:3 final size:3
Alignment explanation
Indices: 4378276--4378340 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
4378266 ATTGAGAAAT
4378276 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4378324 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
4378341 GAGATTAATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4384347 original size:20 final size:21
Alignment explanation
Indices: 4384322--4384361 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4384312 CAAAGAAAAG
*
4384322 GAAAA-GAAAATGTGAAGAAT
1 GAAAAGGAAAATGTAAAGAAT
4384342 GAAAAGGAAAATGTAAAGAA
1 GAAAAGGAAAATGTAAAGAA
4384362 AAAAGAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAAAGGAAAATGTAAAGAAT
Found at i:4384370 original size:21 final size:21
Alignment explanation
Indices: 4384346--4384406 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
4384336 AAGAATGAAA
*
4384346 AGGAAAATGTAAAGAAAAAAG
1 AGGAAAAAGTAAAGAAAAAAG
4384367 AGGAAAAAG--AA-AAAAAAG
1 AGGAAAAAGTAAAGAAAAAAG
4384385 -GGAAAAAGTGAAAGAAAAAAG
1 AGGAAAAAGT-AAAGAAAAAAG
4384406 A
1 A
4384407 AAAAAAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
17 8 0.24
18 7 0.21
19 2 0.06
20 2 0.06
21 15 0.44
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (21 bp):
AGGAAAAAGTAAAGAAAAAAG
Found at i:4384435 original size:22 final size:20
Alignment explanation
Indices: 4384406--4384461 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 20
4384396 AAGAAAAAAG
4384406 AAAAAAAAAAGAAAGAAGAAC
1 AAAAAAAAAAGAAA-AAGAAC
4384427 AAAAGAAAAAAAGAAAAAGAA-
1 -AAA-AAAAAAAGAAAAAGAAC
* *
4384448 GAAAACAAAAGAAA
1 AAAAAAAAAAGAAA
4384462 TGATTGGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 10 0.32
20 2 0.06
22 8 0.26
23 11 0.35
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAGAAAAAGAAC
Found at i:4384439 original size:23 final size:22
Alignment explanation
Indices: 4384409--4384457 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
4384399 AAAAAAGAAA
*
4384409 AAAAAAAGAAAGAAGAACAAAAG
1 AAAAAAAGAAA-AAGAACAAAAC
*
4384432 AAAAAAAGAAAAAGAAGAAAAC
1 AAAAAAAGAAAAAGAACAAAAC
4384454 AAAA
1 AAAA
4384458 GAAATGATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAAAAGAACAAAAC
Found at i:4384445 original size:25 final size:26
Alignment explanation
Indices: 4384396--4384461 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 26
4384386 GAAAAAGTGA
4384396 AAGAA-AAAAGAAAAAAAAAAGAAAG
1 AAGAACAAAAGAAAAAAAAAAGAAAG
*
4384421 AAGAACAAAAGAAAAAAAGAA-AAAG
1 AAGAACAAAAGAAAAAAAAAAGAAAG
4384446 AAGAAAACAAAAGAAA
1 AAG--AACAAAAGAAA
4384462 TGATTGGGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 12 0.32
26 14 0.38
27 11 0.30
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (26 bp):
AAGAACAAAAGAAAAAAAAAAGAAAG
Found at i:4385636 original size:32 final size:32
Alignment explanation
Indices: 4385552--4385718 Score: 149
Period size: 32 Copynumber: 5.2 Consensus size: 32
4385542 CGAGAAATGA
* *
4385552 TTAAGCCCAGTTTAATTGGCACCTATGAAAAT
1 TTAAGCCCAGTTTAACTGGCACTTATGAAAAT
* ** *
4385584 TTAAACCCA-TATTAGTTGGCATTTATGAAAAT
1 TTAAGCCCAGT-TTAACTGGCACTTATGAAAAT
*
4385616 TTAAGCCCATTTTAACTGGCACTTAT-AAAGATT
1 TTAAGCCCAGTTTAACTGGCACTTATGAAA-A-T
** * * **
4385649 TTAAGTTCAGATTATCCAGCACTTATGAAAAT
1 TTAAGCCCAGTTTAACTGGCACTTATGAAAAT
* * *
4385681 TTAAGCCCAGTTTAGCTGGTACCTATGAAAAT
1 TTAAGCCCAGTTTAACTGGCACTTATGAAAAT
4385713 TTAAGC
1 TTAAGC
4385719 TCATCTTAAT
Statistics
Matches: 107, Mismatches: 23, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
31 4 0.04
32 78 0.73
33 22 0.21
34 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (32 bp):
TTAAGCCCAGTTTAACTGGCACTTATGAAAAT
Found at i:4386080 original size:34 final size:34
Alignment explanation
Indices: 4386010--4386096 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
4386000 GACTTGCATA
* **
4386010 TCAATCTCAGTCATCTTTA-TTTTTGGACTAGGGT
1 TCAATCTCAATCAT-TTTATTTTTTGGACTACAGT
4386044 TCAATCTCAATCATTTTATTTTTTGG-CTCACAGT
1 TCAATCTCAATCATTTTATTTTTTGGACT-ACAGT
*
4386078 TCAATC-CTAATCATCTTAT
1 TCAATCTC-AATCATTTTAT
4386097 CTCTCAATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 7 0.15
34 39 0.85
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (34 bp):
TCAATCTCAATCATTTTATTTTTTGGACTACAGT
Found at i:4388548 original size:3 final size:3
Alignment explanation
Indices: 4388540--4388569 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4388530 GTTGGAGAAT
4388540 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4388570 GGAGATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4388752 original size:19 final size:20
Alignment explanation
Indices: 4388710--4388761 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
4388700 TTTCATTTTT
*
4388710 ATGAAACCCGAAACCCTAAA
1 ATGAAACCCTAAACCCTAAA
*
4388730 ATGAAACCCTAAATCCT-AA
1 ATGAAACCCTAAACCCTAAA
*
4388749 ATGAAATCCTAAA
1 ATGAAACCCTAAA
4388762 ACCTCAAGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.50, C:0.25, G:0.08, T:0.17
Consensus pattern (20 bp):
ATGAAACCCTAAACCCTAAA
Found at i:4396767 original size:15 final size:16
Alignment explanation
Indices: 4396735--4396771 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4396725 TGAAAATGAT
4396735 ATTATTTTTATATCAA
1 ATTATTTTTATATCAA
*
4396751 ATTATTTTT-TATTAA
1 ATTATTTTTATATCAA
4396766 A-TATTT
1 ATTATTT
4396772 AAAAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 5 0.25
15 6 0.30
16 9 0.45
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATTTTTATATCAA
Found at i:4397280 original size:20 final size:20
Alignment explanation
Indices: 4397239--4397282 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4397229 TGAGATTAAA
* *
4397239 ATAT-CATATGTATGTATAT
1 ATATACATATATATGTACAT
*
4397258 ATATACATATATATGTACGT
1 ATATACATATATATGTACAT
4397278 ATATA
1 ATATA
4397283 TGTAGTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (20 bp):
ATATACATATATATGTACAT
Found at i:4397284 original size:12 final size:12
Alignment explanation
Indices: 4397244--4397290 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
4397234 TTAAAATATC
*
4397244 ATATGTATGTAT
1 ATATGTACGTAT
* *
4397256 ATATATACATAT
1 ATATGTACGTAT
4397268 ATATGTACGTAT
1 ATATGTACGTAT
4397280 ATATGTA-GTAT
1 ATATGTACGTAT
4397291 TCAAAAATTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 4 0.13
12 26 0.87
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (12 bp):
ATATGTACGTAT
Found at i:4407819 original size:46 final size:48
Alignment explanation
Indices: 4407764--4407888 Score: 155
Period size: 48 Copynumber: 2.6 Consensus size: 48
4407754 AAGCTCTTCC
** *
4407764 TCAATAAAGGTGTTAAAACTTTAAAAATT-ACAACAAAAAAATC-CCT
1 TCAATAAAGGCATTAAAACTTTAAAAATTCACAACAAAAAAATCACCA
* * * *
4407810 TCAATAAAGGCATTGAAATTTTAAAAATTCACAACAAAAAACTCATCA
1 TCAATAAAGGCATTAAAACTTTAAAAATTCACAACAAAAAAATCACCA
* *
4407858 TCAACAGAGGCATTAAAACTTTAAAAATTCA
1 TCAATAAAGGCATTAAAACTTTAAAAATTCA
4407889 AAAAGCTCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 25 0.38
47 13 0.20
48 28 0.42
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (48 bp):
TCAATAAAGGCATTAAAACTTTAAAAATTCACAACAAAAAAATCACCA
Found at i:4407898 original size:43 final size:43
Alignment explanation
Indices: 4407817--4407975 Score: 151
Period size: 43 Copynumber: 3.6 Consensus size: 43
4407807 CCTTCAATAA
*
4407817 AGGCATTGAAATTTTAAAAATTCACAACAAAAAACTCATCATCAACAG
1 AGGCATTGAAATTTTAAAAATT-----CAAAAAGCTCATCATCAACAG
* * *
4407865 AGGCATTAAAACTTTAAAAATTCAAAAAGCTCATCCTCAACAG
1 AGGCATTGAAATTTTAAAAATTCAAAAAGCTCATCATCAACAG
** * * * * *
4407908 AGGTTTTGAAATTTTAAAAATTTAAAAGGCTC--CTTTAACTAA
1 AGGCATTGAAATTTTAAAAATTCAAAAAGCTCATCATCAAC-AG
4407950 AGGCATTGAAATTTTAAAAATTCAAA
1 AGGCATTGAAATTTTAAAAATTCAAA
4407976 GTAAAAAAGC
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
41 5 0.05
42 24 0.26
43 45 0.48
48 20 0.21
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (43 bp):
AGGCATTGAAATTTTAAAAATTCAAAAAGCTCATCATCAACAG
Found at i:4408065 original size:133 final size:133
Alignment explanation
Indices: 4407814--4408067 Score: 300
Period size: 133 Copynumber: 1.9 Consensus size: 133
4407804 ATCCCTTCAA
4407814 TAAAGGCATTGAAATTTTAAAAATTCACAACAAAAAACTCATCATCAACAGAGGCATTAAAACTT
1 TAAAGGCATTGAAATTTTAAAAATTCACAACAAAAAACTCATCATCAACAGAGGCATTAAAACTT
** * *
4407879 TAAAAATTCAAAAAGCTCATCCTCAACAGAGGTTTTGAAATTTTAAAAATTTAAAAGGCTCCTTT
66 TAAAAATTCAAAAAGCTCATCCTCAACAGAGGCATTGAAACTTCAAAAATTTAAAAGGCTCCTTT
4407944 AAC
131 AAC
* * * * * * *
4407947 TAAAGGCATTGAAATTTTAAAAATTCA-AAGTAAAAAAGCTCTTCCTTAGCAGAGGTATTGAAAC
1 TAAAGGCATTGAAATTTTAAAAATTCACAA-CAAAAAA-CTCATCATCAACAGAGGCATTAAAAC
* * * * *
4408011 TTTAAGAATT-TAAAAGACTC-T-TTTAACCAGAGGCATTGAAACTTCAAAATTTTAAAA
64 TTTAAAAATTCAAAAAG-CTCATCCTCAA-CAGAGGCATTGAAACTTCAAAAATTTAAAA
4408068 TACTTTTCTA
Statistics
Matches: 101, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
132 5 0.05
133 64 0.63
134 32 0.32
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (133 bp):
TAAAGGCATTGAAATTTTAAAAATTCACAACAAAAAACTCATCATCAACAGAGGCATTAAAACTT
TAAAAATTCAAAAAGCTCATCCTCAACAGAGGCATTGAAACTTCAAAAATTTAAAAGGCTCCTTT
AAC
Found at i:4408815 original size:12 final size:12
Alignment explanation
Indices: 4408792--4408831 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
4408782 AGGTAAGCCC
4408792 ATTTTGTATTTTT
1 ATTTT-TATTTTT
4408805 ATTTTTA-TTTT
1 ATTTTTATTTTT
*
4408816 ATTTTTATTATT
1 ATTTTTATTTTT
4408828 ATTT
1 ATTT
4408832 ATCAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 11 0.44
12 9 0.36
13 5 0.20
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:4408820 original size:17 final size:17
Alignment explanation
Indices: 4408798--4408831 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4408788 GCCCATTTTG
*
4408798 TATTTTTATTTTTATTT
1 TATTTTTATTATTATTT
4408815 TATTTTTATTATTATTT
1 TATTTTTATTATTATTT
4408832 ATCAATATAT
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:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TATTTTTATTATTATTT
Found at i:4408847 original size:28 final size:26
Alignment explanation
Indices: 4408815--4408909 Score: 106
Period size: 28 Copynumber: 3.5 Consensus size: 26
4408805 ATTTTTATTT
4408815 TATTTTTATTATTATTTATCAATATATA
1 TATTTTTATT-TTATTTATC-ATATATA
4408843 TATTTTTATTATTATTTATC-TATTAATA
1 TATTTTTATT-TTATTTATCATA-T-ATA
*
4408871 TATTTTTA-TTTATCTATTCATATATA
1 TATTTTTATTTTATTTA-TCATATATA
4408897 T-TTTTTATTTTAT
1 TATTTTTATTTTAT
4408910 CTTTTTCTTG
Statistics
Matches: 61, Mismatches: 1, Indels: 12
0.82 0.01 0.16
Matches are distributed among these distances:
25 6 0.10
26 17 0.28
27 5 0.08
28 33 0.54
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (26 bp):
TATTTTTATTTTATTTATCATATATA
Found at i:4408852 original size:6 final size:6
Alignment explanation
Indices: 4408792--4408831 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
4408782 AGGTAAGCCC
*
4408792 ATTTTGT ATTTTT ATTTTT A-TTTT ATTTTT ATTATT ATTT
1 ATTTT-T ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT
4408832 ATCAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 5 0.17
6 20 0.67
7 5 0.17
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:4408879 original size:22 final size:24
Alignment explanation
Indices: 4408849--4408911 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 24
4408839 TATATATTTT
*
4408849 TATTATTATTTATCTATT-A-ATA
1 TATTTTTATTTATCTATTCATATA
4408871 TATTTTTATTTATCTATTCATATA
1 TATTTTTATTTATCTATTCATATA
4408895 TATTTTTTATTTTATCT
1 TA-TTTTTA-TTTATCT
4408912 TTTTCTTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 17 0.47
23 1 0.03
24 5 0.14
25 6 0.17
26 7 0.19
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTTTATTTATCTATTCATATA
Found at i:4408888 original size:14 final size:13
Alignment explanation
Indices: 4408792--4408888 Score: 60
Period size: 14 Copynumber: 7.2 Consensus size: 13
4408782 AGGTAAGCCC
4408792 ATTTTGTATTT-TT
1 ATTTT-TATTTATT
4408805 ATTTTTA-TT-TT
1 ATTTTTATTTATT
4408816 ATTTTTA-TTATT
1 ATTTTTATTTATT
* *
4408828 ATTTATCAATATATAT
1 ATTT-T-TATTTAT-T
4408844 ATTTTTA-TTATT
1 ATTTTTATTTATT
*
4408856 ATTTATCTATTAATAT
1 ATTT-T-TATTTAT-T
4408872 ATTTTTATTTATCT
1 ATTTTTATTTAT-T
4408886 ATT
1 ATT
4408889 CATATATATT
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
11 13 0.19
12 13 0.19
13 10 0.15
14 14 0.21
15 8 0.12
16 10 0.15
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (13 bp):
ATTTTTATTTATT
Found at i:4408897 original size:26 final size:26
Alignment explanation
Indices: 4408836--4408911 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 26
4408826 TTATTTATCA
*
4408836 ATATATATATTTTTA-TTAT-TATTT
1 ATATATATATTTTTATTTATCTATTC
4408860 ATCTATTAATATATTTTTATTTATCTATTC
1 A--TA-T-ATATATTTTTATTTATCTATTC
4408890 ATATATAT-TTTTTATTTTATCT
1 ATATATATATTTTTA-TTTATCT
4408912 TTTTCTTGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
24 1 0.02
25 6 0.14
26 13 0.30
27 2 0.05
28 13 0.30
29 4 0.09
30 5 0.11
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (26 bp):
ATATATATATTTTTATTTATCTATTC
Found at i:4409696 original size:5 final size:5
Alignment explanation
Indices: 4409686--4409732 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
4409676 TTGGTATTTC
*
4409686 TTATT TTATTT TTATT TT-TT TT-TC TTATTT TTATT TTATT TTATT TT
1 TTATT TTA-TT TTATT TTATT TTATT TTA-TT TTATT TTATT TTATT TT
4409733 TTTAATGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 7 0.19
5 21 0.57
6 9 0.24
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (5 bp):
TTATT
Found at i:4409711 original size:24 final size:25
Alignment explanation
Indices: 4409682--4409733 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 25
4409672 TTATTTGGTA
4409682 TTTCTTA-TTTTATTTTTATTTT-TT
1 TTTCTTATTTTTA-TTTTATTTTATT
4409706 TTTCTTATTTTTATTTTATTTTATT
1 TTTCTTATTTTTATTTTATTTTATT
4409731 TTT
1 TTT
4409734 TTAATGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTCTTATTTTTATTTTATTTTATT
Found at i:4409713 original size:19 final size:19
Alignment explanation
Indices: 4409691--4409736 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
4409681 ATTTCTTATT
* *
4409691 TTATTTTTATTTTTTTTTC
1 TTATTTTTATTTTATTTTA
4409710 TTATTTTTATTTTATTTTA
1 TTATTTTTATTTTATTTTA
4409729 TT-TTTTTA
1 TTATTTTTA
4409737 ATGATTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (19 bp):
TTATTTTTATTTTATTTTA
Found at i:4409908 original size:60 final size:60
Alignment explanation
Indices: 4409761--4409966 Score: 321
Period size: 60 Copynumber: 3.5 Consensus size: 60
4409751 AGAAAAAACT
* *
4409761 AAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-GA-TTTTTTA
1 AAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTTTTA
*
4409819 AAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTTTTA
1 AAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTTTTA
* * *
4409879 AAAAAATATTTTT-AAAGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAATTTTTTAA
1 AAAAAATATTTTTGAAA-AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTTTTA
4409939 AAAAAAT-TTTTTGAAAAAAAGTTGAAAG
1 AAAAAATATTTTTGAAAAAAAGTTGAAAG
4409967 CATCTCGAAA
Statistics
Matches: 136, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
58 47 0.35
59 19 0.14
60 70 0.51
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (60 bp):
AAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTTTTA
Found at i:4409955 original size:13 final size:14
Alignment explanation
Indices: 4409915--4409958 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 14
4409905 AAGTATCAAT
4409915 TTTTCTTAAAAATAAA
1 TTTT-TTAAAAA-AAA
4409931 TTTTTTAAAAAAAA
1 TTTTTTAAAAAAAA
4409945 TTTTTTGAAAAAAA
1 TTTTTT-AAAAAAA
4409959 GTTGAAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.33
15 14 0.52
16 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
TTTTTTAAAAAAAA
Found at i:4415946 original size:14 final size:14
Alignment explanation
Indices: 4415927--4415958 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4415917 CCTACTAAAA
4415927 GTATTGAACCAGAC
1 GTATTGAACCAGAC
4415941 GTATTGAACCAGAC
1 GTATTGAACCAGAC
4415955 GTAT
1 GTAT
4415959 GTGGCACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (14 bp):
GTATTGAACCAGAC
Found at i:4418441 original size:541 final size:540
Alignment explanation
Indices: 4417305--4419464 Score: 3204
Period size: 540 Copynumber: 4.0 Consensus size: 540
4417295 AGATTGATTG
* * * *
4417305 AACAAGAAAATAAGCCAATTGAGCCTCACCATGAGATAATTGACTTAGTGAATCTGGGAGATGAA
1 AACAAGAAAAAAAGCC-ATTGAGCCTCATCAAGAGATAATTGACTTAGTGAATCTGAGAGATGAA
** * *
4417370 AAGAATAAGAAAGAAGTCAGAATCGGTACTTCACTTTTGTCGAAAGATAGGTAACGTTTAGAAAA
65 AAGAATAAGAAAGAAGTCAGAATCGACACTTCACTTTTGTCGAAAGATAGGCAACATTTAGAAAA
* * * *
4417435 TCTACTTCAAGAATTCATAAATGTATTTGTTTGGTCTTATCAGGATATGCCAGGGTAAGTACGGA
130 TCTACTTTAAGAATTCATAAATGTGTTTGCTTGGTCTTACCAGGATATGCCAGGGTAAGTACGGA
* * *
4417500 GATAGTGGAGTGCA-A-ACTGCCCTTAAAGCCAGAATGTAAGCCAATCCAGCAGAAATTAAGGTG
195 GATAGT--AGAGCATAGACTACCCTTAAAGCCAGAATGTAAGCCAGTCCAGCAGAAATTAAGGTG
* * * *
4417563 AATAAAGCCTGAAATGCTACTAAAAATTAAAGAAAAAGTGAAGAAGTAGTTTGATGCAGGCTTCT
258 AATGAAGCCTGAAATGCTACTAAAAATTTAAGAAAAAATAAAGAAGTAGTTTGATGCAGGCTTCT
* *
4417628 TACAAGTGGCTAAGTATCCATAGTGGGTGGTCAATATAGTACCAGTTCCTAAGAAAGATAAAAAT
323 TACAAGTGGCTAAGTATCCATAGTGGGTGGCCAATATAGTACCAGTTTCTAAGAAAGATAAAAAT
* * * *
4417693 GTATGAATTTATGTAGATTATCATGATTTGAATAGGGTTAG-CTCAAAGAATAACTTTTCTTTAC
388 GTATGAATTTGTGTAGATTATCATGATTTGAATAGGGCTAGAC-CAAAGGATAACTTTTTTTTAC
* *
4417757 CTCATATCGATACACTGGTAGATAACACGGCTAAACATTCAATGTTCTCTTTCGTGGATGGGTTC
452 CTCATATCGACACACTGGTAGATAACACGGCTAAACATTCAATGTTCTCTTTCATGGATGGGTTC
* *
4417822 TTAGGGTACAATCAGATAAAAATA
517 TCAAGGTACAATCAGATAAAAATA
* * *
4417846 AATAAGAAAAAAAGTCATTGAGCTTCATCAAGAGATAATTGACTTAGTGAATCTG-GAAGATGAA
1 AACAAGAAAAAAAGCCATTGAGCCTCATCAAGAGATAATTGACTTAGTGAATCTGAG-AGATGAA
* * * *
4417910 GAGAATAAGAAAGAAGTCAGAATCGACACTTCACTTTTGTCAAAAGATAGACAACCTTTAGAAAA
65 AAGAATAAGAAAGAAGTCAGAATCGACACTTCACTTTTGTCGAAAGATAGGCAACATTTAGAAAA
* * *
4417975 TCTACTTTAAAAATTCATAAATGTGTTTGCTTAGTCTTACCAGGATATGCCAGGGCAAGTACGGA
130 TCTACTTTAAGAATTCATAAATGTGTTTGCTTGGTCTTACCAGGATATGCCAGGGTAAGTACGGA
* * * *
4418040 GATAGTAGAGCATAGACTGCCCTTAAAGTCAGAATGTAAGCCAGTCCAACAGAAATTGAGGTGAA
195 GATAGTAGAGCATAGACTACCCTTAAAGCCAGAATGTAAGCCAGTCCAGCAGAAATTAAGGTGAA
4418105 TGAAGCCTGAAATGCTACTAAAAATTTAAGAAAAAAATAAAGAAGTAGTTTGATGCAGGCTTCTT
260 TGAAGCCTGAAATGCTACTAAAAATTTAAG-AAAAAATAAAGAAGTAGTTTGATGCAGGCTTCTT
4418170 ACAAGTGGCTAAGTATCCATAGTGGGTGGCCAATATAGTACCAGTTTCTAAGAAAAGATAAAAAT
324 ACAAGTGGCTAAGTATCCATAGTGGGTGGCCAATATAGTACCAGTTTCTAAG-AAAGATAAAAAT
* *
4418235 GTATGAATTTGTATAGATTATCATGATTTGAATAGGGCTAGACCAAAGGATAA-TTTTTTTTATC
388 GTATGAATTTGTGTAGATTATCATGATTTGAATAGGGCTAGACCAAAGGATAACTTTTTTTTACC
* * * *
4418299 TCATATCAACACACTGGTAGATAACACTGCTAAACATTCAATGTTTTCTTTTATGGATGGGTTCT
453 TCATATCGACACACTGGTAGATAACACGGCTAAACATTCAATGTTCTCTTTCATGGATGGGTTCT
4418364 CAAGGTACAATCAGATAAAAATA
518 CAAGGTACAATCAGATAAAAATA
* * * *
4418387 AACAAGAAAATAAGCCATTGAGCCTCAACAAAAGATAATTAACTTAGTGAATCTGAGAGATGAAA
1 AACAAGAAAAAAAGCCATTGAGCCTCATCAAGAGATAATTGACTTAGTGAATCTGAGAGATGAAA
* *
4418452 AGAATAAGAAAGAAGTCAGAATCGACACTTCACTTTTGTTGAAAGATAGGCAACATTTAGAAGAT
66 AGAATAAGAAAGAAGTCAGAATCGACACTTCACTTTTGTCGAAAGATAGGCAACATTTAGAAAAT
* * * *
4418517 CTACTTTAAGAATTCATAAATGTGTTTGCTTGATCTTACCAGTATATGCCAAGGTAAGTACGAAG
131 CTACTTTAAGAATTCATAAATGTGTTTGCTTGGTCTTACCAGGATATGCCAGGGTAAGTACGGAG
* * * *
4418582 ATAGTGGAGCATAGATTACCCTTAAAGCCAGAATGTAAGCTAGTCCAGTAGAAATTAAGGTGAAT
196 ATAGTAGAGCATAGACTACCCTTAAAGCCAGAATGTAAGCCAGTCCAGCAGAAATTAAGGTGAAT
* * ** * *
4418647 GAAGCCTAAAATGCTACTAAAAATTGAAGAAAAGGTGAAGAAATAGTTTGATGCAGGCTTCTTAC
261 GAAGCCTGAAATGCTACTAAAAATTTAAGAAAAAATAAAGAAGTAGTTTGATGCAGGCTTCTTAC
** * *
4418712 AAGTGGCTAAGTATCCATAGTACGTGGCCAATATAGTACCAGTTTCTAAAAAAGATAGAAATGTA
326 AAGTGGCTAAGTATCCATAGTGGGTGGCCAATATAGTACCAGTTTCTAAGAAAGATAAAAATGTA
*
4418777 CGAATTTGTGTAGATTATCATGATTTGAATAGGGCTA-ACCCAAAGGATAACTTTTTTTTACCTC
391 TGAATTTGTGTAGATTATCATGATTTGAATAGGGCTAGA-CCAAAGGATAACTTTTTTTTACCTC
* * * * *
4418841 ATATTGACACAGTGGTAGATAACACGGTTAAACATTCAATGTTCTTTTTCATAGATGGGTTCTCA
455 ATATCGACACACTGGTAGATAACACGGCTAAACATTCAATGTTCTCTTTCATGGATGGGTTCTCA
* *
4418906 AGGTACAATCAAATAAAAATG
520 AGGTACAATCAGATAAAAATA
* * * *
4418927 AATAAGAAAAAAAGCCATTGAACCTCATCAGGAGATAATTGACTTAGTGAATCTGAGAGATAAAA
1 AACAAGAAAAAAAGCCATTGAGCCTCATCAAGAGATAATTGACTTAGTGAATCTGAGAGATGAAA
* * *
4418992 AGAATAAGAAAGAAGTCAGAATCGACACTTCATTTTTGTCGAAAGATAGGCAATATTTAGAAGAT
66 AGAATAAGAAAGAAGTCAGAATCGACACTTCACTTTTGTCGAAAGATAGGCAACATTTAGAAAAT
4419057 CTACTTTAAGAATTCATAAATGTGTTTGCTTGGTCTTACCAGGATATGCCAGGGTAAGTACGGAG
131 CTACTTTAAGAATTCATAAATGTGTTTGCTTGGTCTTACCAGGATATGCCAGGGTAAGTACGGAG
* * * *
4419122 ATAGTAGAGCACAGACTACCCTTACAGCTATAATGTAAGCCAGTCCAGCAGAAATTGAA-GTGAA
196 ATAGTAGAGCATAGACTACCCTTAAAGCCAGAATGTAAGCCAGTCCAGCAGAAATT-AAGGTGAA
* * * *
4419186 TGAAGCTTGAAATGCTACTAAAAA-TAAAAAAAAAATAAAGAAGTAGTTTGATGTAGGCTTCTTA
260 TGAAGCCTGAAATGCTACTAAAAATTTAAGAAAAAATAAAGAAGTAGTTTGATGCAGGCTTCTTA
* **
4419250 CAAGTGGCTAAGTATCCATAGTGGGTGGCCAATATAGTACCAATTTCTAAGAAAGATGGAAATGT
325 CAAGTGGCTAAGTATCCATAGTGGGTGGCCAATATAGTACCAGTTTCTAAGAAAGATAAAAATGT
* * *
4419315 ATGAATTTGTGTAGATTATCATGATTTGAATAGGGCTAGCCCAAAGGATAACTTTTTTTTGCCTT
390 ATGAATTTGTGTAGATTATCATGATTTGAATAGGGCTAGACCAAAGGATAACTTTTTTTTACCTC
* * ** * *
4419380 ATATCGATACACTGGTTGATAAC-CGATTAAACATTCAATGTTCTATTTCATGGATGGGTTTTCA
455 ATATCGACACACTGGTAGATAACACGGCTAAACATTCAATGTTCTCTTTCATGGATGGGTTCTCA
4419444 AGGTACAATCAGATAAAAATA
520 AGGTACAATCAGATAAAAATA
4419465 GCTATAGATG
Statistics
Matches: 1460, Mismatches: 148, Indels: 25
0.89 0.09 0.02
Matches are distributed among these distances:
538 62 0.04
539 234 0.16
540 660 0.45
541 443 0.30
542 60 0.04
543 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (540 bp):
AACAAGAAAAAAAGCCATTGAGCCTCATCAAGAGATAATTGACTTAGTGAATCTGAGAGATGAAA
AGAATAAGAAAGAAGTCAGAATCGACACTTCACTTTTGTCGAAAGATAGGCAACATTTAGAAAAT
CTACTTTAAGAATTCATAAATGTGTTTGCTTGGTCTTACCAGGATATGCCAGGGTAAGTACGGAG
ATAGTAGAGCATAGACTACCCTTAAAGCCAGAATGTAAGCCAGTCCAGCAGAAATTAAGGTGAAT
GAAGCCTGAAATGCTACTAAAAATTTAAGAAAAAATAAAGAAGTAGTTTGATGCAGGCTTCTTAC
AAGTGGCTAAGTATCCATAGTGGGTGGCCAATATAGTACCAGTTTCTAAGAAAGATAAAAATGTA
TGAATTTGTGTAGATTATCATGATTTGAATAGGGCTAGACCAAAGGATAACTTTTTTTTACCTCA
TATCGACACACTGGTAGATAACACGGCTAAACATTCAATGTTCTCTTTCATGGATGGGTTCTCAA
GGTACAATCAGATAAAAATA
Found at i:4423373 original size:42 final size:40
Alignment explanation
Indices: 4423278--4423502 Score: 190
Period size: 40 Copynumber: 5.4 Consensus size: 40
4423268 ATGATTGTCA
* * *
4423278 AGGAGTATTTTACTTTTC-AAAGTTTTGTTGCCTTTATTTAG
1 AGGAGTA-TTTATTTTTCAAAAGTTCTGTT-CCTCTATTTAG
* **
4423319 AAGAGCCGTTTATTTTTTCAAAAGTTCTGTTCTCTCTATTTAG
1 AGGAG-TATTTA-TTTTTCAAAAGTTCTGTTC-CTCTATTTAG
* *
4423362 AGGAGTATTTATTTTT-TAAAGTTCTGGTACCTCTATTTAG
1 AGGAGTATTTATTTTTCAAAAGTTCT-GTTCCTCTATTTAG
* *
4423402 ATGAGTGATTTATTTTTCAAAAGTTCTGTTACCTCTATATAG
1 AGGAGT-ATTTATTTTTCAAAAGTTCTGTT-CCTCTATTTAG
*
4423444 AGGAGCATTTATTTTTC-AAAGTT-TCGTTGCCTCT-TATTAG
1 AGGAGTATTTATTTTTCAAAAGTTCT-GTT-CCTCTAT-TTAG
4423484 AGGAGCTTTATTTATTTTT
1 AGGAG---TATTTATTTTT
4423503 TAAAGTCGTT
Statistics
Matches: 151, Mismatches: 20, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
39 2 0.01
40 45 0.30
41 39 0.26
42 32 0.21
43 33 0.22
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (40 bp):
AGGAGTATTTATTTTTCAAAAGTTCTGTTCCTCTATTTAG
Found at i:4423477 original size:82 final size:82
Alignment explanation
Indices: 4423278--4423549 Score: 263
Period size: 82 Copynumber: 3.3 Consensus size: 82
4423268 ATGATTGTCA
* * * *
4423278 AGGAGTATTTTACTTTTCAAAGTTTTGTTGCCTTTATTTAGAAGAGCCG-TTTATTTTTTCAAAA
1 AGGAGTA-TTTATTTTTCAAAGTTTCGTTGCCTCTATTTAGAAGAGCTGATTTA-TTTTTCAAAA
4423342 GTTCTGTT-CTCTCTATTTAG
64 GTTCTGTTAC-CTCTA-TTAG
* * * *
4423362 AGGAGTATTTATTTTTTAAAG-TTCTGGTACCTCTATTTAGATGAG-TGATTTATTTTTCAAAAG
1 AGGAGTATTTATTTTTCAAAGTTTC-GTTGCCTCTATTTAGAAGAGCTGATTTATTTTTCAAAAG
4423425 TTCTGTTACCTCTATATAG
65 TTCTGTTACCTCTAT-TAG
* * * *
4423444 AGGAGCATTTATTTTTCAAAGTTTCGTTGCCTCT-TATTAGAGGAGCTTTATTTATTTTT-TAAA
1 AGGAGTATTTATTTTTCAAAGTTTCGTTGCCTCTAT-TTAGAAGAGC-TGATTTATTTTTCAAAA
*
4423507 G-TC-GTTAAGCCTCTGATTAT
64 GTTCTGTT-A-CCTCT-ATTAG
4423527 AGGAGTTATTTATTTTTCAAAGT
1 AGGAG-TATTTATTTTTCAAAGT
4423550 CGTTGAGCAT
Statistics
Matches: 159, Mismatches: 17, Indels: 24
0.80 0.09 0.12
Matches are distributed among these distances:
81 5 0.03
82 66 0.42
83 52 0.33
84 36 0.23
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (82 bp):
AGGAGTATTTATTTTTCAAAGTTTCGTTGCCTCTATTTAGAAGAGCTGATTTATTTTTCAAAAGT
TCTGTTACCTCTATTAG
Found at i:4423536 original size:41 final size:41
Alignment explanation
Indices: 4423429--4423576 Score: 155
Period size: 41 Copynumber: 3.6 Consensus size: 41
4423419 CAAAAGTTCT
4423429 GTTA-CCTCT-ATATAGAGGAGC--ATTTATTTTTCAAAGTTTC
1 GTTAGCCTCTGAT-TAGAGGAGCTTATTTATTTTTCAAAG--TC
* *
4423469 GTT-GCCTCTTATTAGAGGAGCTTTATTTATTTTTTAAAGTC
1 GTTAGCCTCTGATTAGAGGAGC-TTATTTATTTTTCAAAGTC
*
4423510 GTTAAGCCTCTGATTATAGGAG-TTATTTATTTTTCAAAGTC
1 GTT-AGCCTCTGATTAGAGGAGCTTATTTATTTTTCAAAGTC
* *
4423551 GTTGAGCATCTGCTTAGAGGAGCTTA
1 GTT-AGCCTCTGATTAGAGGAGCTTA
4423577 ATCAAAATTT
Statistics
Matches: 92, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
40 17 0.18
41 43 0.47
42 3 0.03
43 29 0.32
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.43
Consensus pattern (41 bp):
GTTAGCCTCTGATTAGAGGAGCTTATTTATTTTTCAAAGTC
Found at i:4423793 original size:26 final size:26
Alignment explanation
Indices: 4423764--4423882 Score: 115
Period size: 26 Copynumber: 4.7 Consensus size: 26
4423754 AATTTTATTT
*
4423764 TATTTTTATTTTTATTTATCAATATA
1 TATTTTTATTTTTATCTATCAATATA
* *
4423790 TATTTATTATTATTTATCTAT-TA-ATG
1 TATTT-TTATT-TTTATCTATCAATATA
*
4423816 TATTTTTA--TTTATCTATTAATATA
1 TATTTTTATTTTTATCTATCAATATA
*
4423840 T-TTTTTATTATTTATCTATTAATATA
1 TATTTTTATT-TTTATCTATCAATATA
4423866 TATTTTT-TATTTTATCT
1 TATTTTTAT-TTTTATCT
4423883 TTTATTTTAT
Statistics
Matches: 79, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
22 9 0.11
23 7 0.09
24 3 0.04
25 3 0.04
26 37 0.47
27 12 0.15
28 8 0.10
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (26 bp):
TATTTTTATTTTTATCTATCAATATA
Found at i:4423824 original size:22 final size:22
Alignment explanation
Indices: 4423770--4423875 Score: 106
Period size: 22 Copynumber: 4.6 Consensus size: 22
4423760 ATTTTATTTT
* *
4423770 TATTTTTATTTATCAATATATATT
1 TATTTTTATTTATCTAT-TA-ATA
* *
4423794 TATTATTATTTATCTATTAATG
1 TATTTTTATTTATCTATTAATA
4423816 TATTTTTATTTATCTATTAATA
1 TATTTTTATTTATCTATTAATA
4423838 TATTTTTTATTATTTATCTATTAATA
1 TA---TTT-TTATTTATCTATTAATA
*
4423864 TATATTT-TTTAT
1 TATTTTTATTTAT
4423876 TTTATCTTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
21 5 0.07
22 26 0.36
23 4 0.06
24 15 0.21
25 3 0.04
26 19 0.26
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (22 bp):
TATTTTTATTTATCTATTAATA
Found at i:4423849 original size:48 final size:46
Alignment explanation
Indices: 4423770--4423875 Score: 151
Period size: 48 Copynumber: 2.3 Consensus size: 46
4423760 ATTTTATTTT
*
4423770 TATTTTTATTTATCAATATATATTTATTATTATTTATCTATTAATG
1 TATTTTTATTTATCAATATATATTTATTATTATTTATCTATTAATA
* *
4423816 TATTTTTATTTATCTATTAATATATTTTTTATTATTTATCTATTAATA
1 TATTTTTATTTATC-AAT-ATATATTTATTATTATTTATCTATTAATA
*
4423864 TATATTT-TTTAT
1 TATTTTTATTTAT
4423876 TTTATCTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
46 14 0.26
47 7 0.13
48 33 0.61
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (46 bp):
TATTTTTATTTATCAATATATATTTATTATTATTTATCTATTAATA
Found at i:4424583 original size:3 final size:3
Alignment explanation
Indices: 4424575--4424663 Score: 60
Period size: 3 Copynumber: 29.7 Consensus size: 3
4424565 TTCCAAAGGT
* **
4424575 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA -GA TTA GAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * *
4424620 TT- TGGTA TTCT TTA TT- TTA TTA TTA TTT TTA TTG TTA TT- TTA TT
1 TTA T--TA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4424664 TTTTTAATGA
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
2 6 0.09
3 53 0.80
4 6 0.09
5 1 0.02
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4424652 original size:17 final size:17
Alignment explanation
Indices: 4424625--4424666 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
4424615 AATTATTTGG
4424625 TATTCTTTATT-TTATTAT
1 TATT-TTTATTGTTATT-T
4424643 TATTTTTATTGTTATTT
1 TATTTTTATTGTTATTT
4424660 TATTTTT
1 TATTTTT
4424667 TTAATGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
TATTTTTATTGTTATTT
Found at i:4424866 original size:15 final size:14
Alignment explanation
Indices: 4424846--4424881 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
4424836 AAGTATCAAT
4424846 TTTTTTTAAAAATAA
1 TTTTTTTAAAAA-AA
4424861 TTTTTTTAAAAAAA
1 TTTTTTTAAAAAAA
*
4424875 TATTTTT
1 TTTTTTT
4424882 GAGGAAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTTTTAAAAAAA
Found at i:4424900 original size:59 final size:58
Alignment explanation
Indices: 4424673--4424900 Score: 322
Period size: 58 Copynumber: 4.0 Consensus size: 58
4424663 TTTTTTAATG
**
4424673 ATTTTC-TT-AAAATAAAATTCT-AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCA
1 ATTTTCTTTGAAAATAATTTTCTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCA
* *
4424728 ATTTTCCTTGAAAATAAGTTTTCT-AAAAAATATTTTCGA-GAAAATGTTGAAAGTATCA
1 ATTTTCTTTGAAAATAA-TTTTCTAAAAAAATATTTTTGAGGAAAA-GTTGAAAGTATCA
*
4424786 ATTTTCTTTGAAAATAATTTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCA
1 ATTTTCTTTGAAAATAATTTTCTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCA
* * *
4424844 ATTTTTTTTAAAAATAATTTTTTTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTAT
1 ATTTTCTTTGAAAATAA-TTTTCTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTAT
4424901 ATCGAAATTA
Statistics
Matches: 156, Mismatches: 10, Indels: 10
0.89 0.06 0.06
Matches are distributed among these distances:
55 6 0.04
56 2 0.01
57 18 0.12
58 89 0.57
59 41 0.26
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (58 bp):
ATTTTCTTTGAAAATAATTTTCTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCA
Found at i:4428255 original size:11 final size:11
Alignment explanation
Indices: 4428239--4428271 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4428229 CTTACACAAA
4428239 CCCAACTTGCC
1 CCCAACTTGCC
4428250 CCCAACTTAG-C
1 CCCAACTT-GCC
4428261 CCCAACTTGCC
1 CCCAACTTGCC
4428272 TGAAATCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.21, C:0.52, G:0.09, T:0.18
Consensus pattern (11 bp):
CCCAACTTGCC
Found at i:4428963 original size:31 final size:31
Alignment explanation
Indices: 4428927--4428991 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
4428917 AGTTTTTTCT
* *
4428927 TTTCTGCCCATTCATGAATCCACTAGTTTTG
1 TTTCTGCCCATACATGAATCAACTAGTTTTG
* *
4428958 TTTCTGCCTATACATGAATGAACTAGTTTTG
1 TTTCTGCCCATACATGAATCAACTAGTTTTG
4428989 TTT
1 TTT
4428992 TGAGCATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (31 bp):
TTTCTGCCCATACATGAATCAACTAGTTTTG
Found at i:4435477 original size:21 final size:21
Alignment explanation
Indices: 4435453--4435497 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4435443 GTAAACAAAA
*
4435453 AAAAAAGTAATTTTTAAATTT
1 AAAAAAGTAATTTTTAAACTT
***
4435474 AAAAGTTTAATTTTTAAACTT
1 AAAAAAGTAATTTTTAAACTT
4435495 AAA
1 AAA
4435498 TAAAAATGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (21 bp):
AAAAAAGTAATTTTTAAACTT
Found at i:4438296 original size:59 final size:58
Alignment explanation
Indices: 4438219--4438333 Score: 135
Period size: 59 Copynumber: 2.0 Consensus size: 58
4438209 ATTAAGTCCC
* * * *
4438219 TATACTATTATTTCATCTATATA-AGTTTCTTAACTCTTATTTTTCATTATCCAAACCTT
1 TATACTATTATTTCATCTAAATACA-TATCTCAACTCTTA-TTTTCACTATCCAAACCTT
* *
4438278 TATATTATTATTAT-ATCTAAATACATATCTCAACTCTTATTTTCACTATCTAAACC
1 TATACTATTATT-TCATCTAAATACATATCTCAACTCTTATTTTCACTATCCAAACC
4438334 CTTCTACAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
58 15 0.31
59 31 0.65
60 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.01, T:0.48
Consensus pattern (58 bp):
TATACTATTATTTCATCTAAATACATATCTCAACTCTTATTTTCACTATCCAAACCTT
Found at i:4439769 original size:40 final size:40
Alignment explanation
Indices: 4439725--4439805 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
4439715 CTAATTACAT
4439725 AAAAATACAAAAATA-ACGATATGTTCCAAATCCTTAACAA
1 AAAAATACAAAAATACA-GATATGTTCCAAATCCTTAACAA
*
4439765 AAAAATACAAAAATACATATATGTTCCAAATCCTTAACAA
1 AAAAATACAAAAATACAGATATGTTCCAAATCCTTAACAA
4439805 A
1 A
4439806 CATTTGGTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.56, C:0.17, G:0.04, T:0.23
Consensus pattern (40 bp):
AAAAATACAAAAATACAGATATGTTCCAAATCCTTAACAA
Found at i:4441265 original size:103 final size:109
Alignment explanation
Indices: 4441156--4441352 Score: 282
Period size: 113 Copynumber: 1.8 Consensus size: 109
4441146 AAAAAAGTTT
*
4441156 AAAAATTTTAAAATATAATTGT-AAA-AT-ACAAA-AAAAA-TAGATA-TAAAAAAAA-ATAATT
1 AAAAATTTTAAAATATAATTGTAAAATATAAAAAATAAAAATTAGATATTAAAAAAAACATAATT
*
4441214 TTGAAACATCTCAAAAAATTAATAAAAAATAAAATAGGAGTATAA
66 TTGAAACATCTCAAAAAA-AAATAAAAAATAAAATAGGAGTATAA
*
4441259 AAAAATTTTAAAATATAATTTTAAAATATAAAAAATAAAAATTTTAGATATTAAAAAAAATCATA
1 AAAAATTTTAAAATATAATTGTAAAATATAAAAAATAAAAA--TTAGATATTAAAAAAAA-CATA
4441324 ATTTTGAAACATCTCAAAAAAAAATAAAA
63 ATTTTGAAACATCTCAAAAAAAAATAAAA
4441353 TAGAAGGAGT
Statistics
Matches: 81, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
103 21 0.26
104 3 0.04
105 2 0.02
106 4 0.05
107 5 0.06
110 6 0.07
111 9 0.11
112 7 0.09
113 24 0.30
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (109 bp):
AAAAATTTTAAAATATAATTGTAAAATATAAAAAATAAAAATTAGATATTAAAAAAAACATAATT
TTGAAACATCTCAAAAAAAAATAAAAAATAAAATAGGAGTATAA
Found at i:4441278 original size:13 final size:13
Alignment explanation
Indices: 4441262--4441289 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4441252 AGTATAAAAA
4441262 AATTTTAAAATAT
1 AATTTTAAAATAT
4441275 AATTTTAAAATAT
1 AATTTTAAAATAT
4441288 AA
1 AA
4441290 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTTTAAAATAT
Found at i:4441293 original size:22 final size:25
Alignment explanation
Indices: 4441268--4441328 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
4441258 AAAAAATTTT
*
4441268 AAAAT-ATAATTTTA-A-AATATAA
1 AAAATAATAATTTTAGATAATAAAA
* *
4441290 AAAATAAAAATTTTAGATATTAAAA
1 AAAATAATAATTTTAGATAATAAAA
*
4441315 AAAATCATAATTTT
1 AAAATAATAATTTT
4441329 GAAACATCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 5 0.16
23 8 0.26
24 1 0.03
25 17 0.55
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
AAAATAATAATTTTAGATAATAAAA
Found at i:4441407 original size:23 final size:20
Alignment explanation
Indices: 4441380--4441434 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
4441370 TTTGATTGTC
4441380 TAAAATTTTTTATATATATATTT
1 TAAAATTTTTTATA-AT-T-TTT
4441403 TAAAATTATATTTATAATTTTT
1 TAAAATT-T-TTTATAATTTTT
*
4441425 TAAACTTTTT
1 TAAAATTTTT
4441435 ATCTTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.07
21 1 0.03
22 9 0.31
23 8 0.28
24 3 0.10
25 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TAAAATTTTTTATAATTTTT
Found at i:4441493 original size:2 final size:2
Alignment explanation
Indices: 4441486--4441523 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4441476 ATCATATAAT
4441486 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4441524 GTGATGGCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4441751 original size:2 final size:2
Alignment explanation
Indices: 4441744--4441782 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4441734 TTTTCTCTGC
*
4441744 CT CT CT CT CT CT CT CT CT CT CT AT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4441783 AGTAGCCACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:4443806 original size:16 final size:15
Alignment explanation
Indices: 4443781--4443812 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
4443771 TAAAAAAATT
4443781 ATTTTTTTATTTTTA
1 ATTTTTTTATTTTTA
4443796 ATTTTTCTTATTTTTA
1 ATTTTT-TTATTTTTA
4443812 A
1 A
4443813 AAATATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTTTTTATTTTTA
Found at i:4444118 original size:21 final size:20
Alignment explanation
Indices: 4444075--4444118 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
4444065 CCTGATTAGT
* *
4444075 AAAGTTAATGCTACATTAAC
1 AAAGTTAACGCTACATCAAC
*
4444095 AAAGTTAACGACTACATCATC
1 AAAGTTAACG-CTACATCAAC
4444116 AAA
1 AAA
4444119 TCAAAGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.25
Consensus pattern (20 bp):
AAAGTTAACGCTACATCAAC
Found at i:4457796 original size:22 final size:22
Alignment explanation
Indices: 4457748--4457804 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
4457738 AAAAAATTCG
*
4457748 TCGATAATAATTA-AAATTCCA
1 TCGATAATATTTATAAATTCCA
*
4457769 TCGATAATATTTATAATTTCCA
1 TCGATAATATTTATAAATTCCA
*
4457791 TTGATAATATTTAT
1 TCGATAATATTTAT
4457805 TTTTCAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (22 bp):
TCGATAATATTTATAAATTCCA
Found at i:4457914 original size:17 final size:17
Alignment explanation
Indices: 4457892--4457924 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4457882 TATGAATACT
*
4457892 AAAAAATACATAAATAG
1 AAAAAATAAATAAATAG
4457909 AAAAAATAAATAAATA
1 AAAAAATAAATAAATA
4457925 AAACATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAAATAAATAAATAG
Found at i:4459651 original size:13 final size:13
Alignment explanation
Indices: 4459635--4459662 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4459625 ACTACTTATT
4459635 CAGAATCTTAAAA
1 CAGAATCTTAAAA
4459648 CAGAATCTTAAAA
1 CAGAATCTTAAAA
4459661 CA
1 CA
4459663 ATCTTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.18, G:0.07, T:0.21
Consensus pattern (13 bp):
CAGAATCTTAAAA
Found at i:4461387 original size:20 final size:20
Alignment explanation
Indices: 4461362--4461399 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4461352 TGATTGGAGG
*
4461362 ATAACAGATGGGTGTTCATA
1 ATAACAGACGGGTGTTCATA
*
4461382 ATAACAGGCGGGTGTTCA
1 ATAACAGACGGGTGTTCA
4461400 CAACAAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (20 bp):
ATAACAGACGGGTGTTCATA
Found at i:4463658 original size:19 final size:19
Alignment explanation
Indices: 4463636--4463676 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
4463626 TTAGGTTAGA
4463636 GTTTAGGGTTAGCTTTAAG
1 GTTTAGGGTTAGCTTTAAG
* *
4463655 GTTTAGGGTTTGTTTTAAG
1 GTTTAGGGTTAGCTTTAAG
4463674 GTT
1 GTT
4463677 CGAGTAGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.02, G:0.32, T:0.49
Consensus pattern (19 bp):
GTTTAGGGTTAGCTTTAAG
Found at i:4463735 original size:30 final size:30
Alignment explanation
Indices: 4463701--4463817 Score: 91
Period size: 30 Copynumber: 3.9 Consensus size: 30
4463691 GGCTTGACTA
*
4463701 AGGTTTGGGGTTT-GGTTTAGGGTTTAGGCT
1 AGGTTTAGGGTTTAGG-TTAGGGTTTAGGCT
* *
4463731 AGGTTTAGTGTTTAGGTTAGGGTTTAGGGT
1 AGGTTTAGGGTTTAGGTTAGGGTTTAGGCT
** *
4463761 GAAATTTA-GG-TTAGGCTTTAGTGTTTAGGCT
1 -AGGTTTAGGGTTTAGG--TTAGGGTTTAGGCT
4463792 AGGTTTTAGGGTTT-GAG-TAGGGTTTA
1 AGG-TTTAGGGTTTAG-GTTAGGGTTTA
4463818 AGGTTTAATG
Statistics
Matches: 68, Mismatches: 11, Indels: 16
0.72 0.12 0.17
Matches are distributed among these distances:
29 5 0.07
30 34 0.50
31 23 0.34
32 3 0.04
33 3 0.04
ACGTcount: A:0.17, C:0.03, G:0.38, T:0.43
Consensus pattern (30 bp):
AGGTTTAGGGTTTAGGTTAGGGTTTAGGCT
Found at i:4463756 original size:19 final size:19
Alignment explanation
Indices: 4463714--4463817 Score: 79
Period size: 19 Copynumber: 5.3 Consensus size: 19
4463704 TTTGGGGTTT
*
4463714 GGTTTAGGGTTTAGGCTA-
1 GGTTTAGTGTTTAGGCTAG
*
4463732 GGTTTAGTGTTTAGGTTAG
1 GGTTTAGTGTTTAGGCTAG
*
4463751 GGTTTAGGGTGAAATTTAGGTTAG
1 GGTTTA--GTG---TTTAGGCTAG
*
4463775 GCTTTAGTGTTTAGGCTAG
1 GGTTTAGTGTTTAGGCTAG
* *
4463794 GTTTTAGGGTTT-GAG-TAG
1 GGTTTAGTGTTTAG-GCTAG
4463812 GGTTTA
1 GGTTTA
4463818 AGGTTTAATG
Statistics
Matches: 72, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
18 25 0.35
19 26 0.36
21 3 0.04
22 3 0.04
24 15 0.21
ACGTcount: A:0.18, C:0.03, G:0.37, T:0.42
Consensus pattern (19 bp):
GGTTTAGTGTTTAGGCTAG
Found at i:4463782 original size:43 final size:42
Alignment explanation
Indices: 4463723--4463803 Score: 126
Period size: 43 Copynumber: 1.9 Consensus size: 42
4463713 TGGTTTAGGG
*
4463723 TTTAGGCTAGGTTTAGTGTTTAGGTTAGGGTTTAGGGTGAAA
1 TTTAGGCTAGGTTTAGTGTTTAGGCTAGGGTTTAGGGTGAAA
* *
4463765 TTTAGGTTAGGCTTTAGTGTTTAGGCTAGGTTTTAGGGT
1 TTTAGGCTAGG-TTTAGTGTTTAGGCTAGGGTTTAGGGT
4463804 TTGAGTAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 10 0.29
43 25 0.71
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.43
Consensus pattern (42 bp):
TTTAGGCTAGGTTTAGTGTTTAGGCTAGGGTTTAGGGTGAAA
Found at i:4463891 original size:37 final size:35
Alignment explanation
Indices: 4463827--4463908 Score: 92
Period size: 37 Copynumber: 2.3 Consensus size: 35
4463817 AAGGTTTAAT
* * * *
4463827 GTTTTTAGGGTTTTTGGTTTAAAGTTAGGTTTTAGGG
1 GTTTTTA-GGCTTTTGATATAAAGTTAGGGTTTA-GG
*
4463864 AGTTTTTAGGCTTTTGATATAATGTTAGGGTTTAGG
1 -GTTTTTAGGCTTTTGATATAAAGTTAGGGTTTAGG
4463900 GTTTTTAGG
1 GTTTTTAGG
4463909 GTTTGGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 9 0.23
36 2 0.05
37 21 0.54
38 7 0.18
ACGTcount: A:0.18, C:0.01, G:0.30, T:0.50
Consensus pattern (35 bp):
GTTTTTAGGCTTTTGATATAAAGTTAGGGTTTAGG
Found at i:4466667 original size:143 final size:141
Alignment explanation
Indices: 4466365--4466667 Score: 342
Period size: 143 Copynumber: 2.1 Consensus size: 141
4466355 ATATTCATGA
* * ** *
4466365 TTTTAATGGATCAAAATTCATAAAACAATATCTAATTATGATCTGAAGCTTTTCATGAAAAACCA
1 TTTTAATGCATCAAAATTCACAAAACAATATCTAAACATGATCTGAAGCTTTACA-GAAAAACCA
** * * ** * *
4466430 ACCTTAAAAAGATAAATTATAAAAATGCCCCTAAAGGTATTTTTGCAATTTTACTCCTTTTGAGG
65 ACCCCAAAAAGATAAATTACAAAAATACCCCTAAAGGTATTTAAGCAATTTCACTCCTTTCGAGG
4466495 GACAATCAAGAT
130 GACAATCAAGAT
* * *
4466507 TTTTAATGCATCAAAATTCACAAAATAATATTTAAACATGATCTGCAATGCTTTACA-AAAAATC
1 TTTTAATGCATCAAAATTCACAAAACAATATCTAAACATGATCTG-AA-GCTTTACAGAAAAACC
* * * *
4466571 AACCCCAAAAAGGTTAAATTACAAAAATACCCTTAAAAGGTATTTAAGTAATTTCA-TCGTTTCG
64 AACCCCAAAAA-GATAAATTACAAAAATACCCCT-AAAGGTATTTAAGCAATTTCACTCCTTTCG
4466635 AGGTG-CAATCAAGAT
127 AGG-GACAATCAAGAT
*
4466650 TTTTAATGCATAAAAATT
1 TTTTAATGCATCAAAATT
4466668 TATACAATGA
Statistics
Matches: 135, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
142 54 0.40
143 56 0.41
144 25 0.19
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (141 bp):
TTTTAATGCATCAAAATTCACAAAACAATATCTAAACATGATCTGAAGCTTTACAGAAAAACCAA
CCCCAAAAAGATAAATTACAAAAATACCCCTAAAGGTATTTAAGCAATTTCACTCCTTTCGAGGG
ACAATCAAGAT
Found at i:4467620 original size:14 final size:15
Alignment explanation
Indices: 4467590--4467627 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
4467580 TACTTTCAAC
4467590 TTTTCTTTTAAATAT
1 TTTTCTTTTAAATAT
*
4467605 TTTTCTTTTGAA-AT
1 TTTTCTTTTAAATAT
*
4467619 TTTTATTTT
1 TTTTCTTTT
4467628 CAAGGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTCTTTTAAATAT
Found at i:4467756 original size:58 final size:59
Alignment explanation
Indices: 4467572--4467830 Score: 298
Period size: 58 Copynumber: 4.4 Consensus size: 59
4467562 TCATACATGA
* *
4467572 AAAATTGCTACTTTCAACTTTTCTTTTAAA-TATTTTTCTTTTGAAATTTTTAT-TTTCAAGG
1 AAAATTGATACTTTCAACTTTTC-TTTAAAGTATTTTTC--TTGAAATTTTGATCTTT-AAGG
* *
4467633 AAAATTGATACTTTCAACTTTTCCTTAAAGTATTTTTTCTTGAAA-TTTGATCTTCAAGG
1 AAAATTGATACTTTCAACTTTTCTTTAAAGTA-TTTTTCTTGAAATTTTGATCTTTAAGG
*
4467692 AAAATTGATACTTTCAACTTTTCTTTAAAGCATTTTTCTTGAAA-TTTGATCTTTAAGG
1 AAAATTGATACTTTCAACTTTTCTTTAAAGTATTTTTCTTGAAATTTTGATCTTTAAGG
* * * * * * *
4467750 AAAATTGATGCTTTCAACTTTTCCTCAAAGTA-TTCT-TTGAAATTTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCTTTAAAGTATTTTTCTTGAAATTTTGATCTTTAAGG
* *
4467807 AAAATTAATTCTTT-AACTTTTCTT
1 AAAATTGATACTTTCAACTTTTCTT
4467831 GAAAATTTGA
Statistics
Matches: 176, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
56 15 0.09
57 26 0.15
58 53 0.30
59 39 0.22
60 13 0.07
61 24 0.14
62 6 0.03
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCTTTAAAGTATTTTTCTTGAAATTTTGATCTTTAAGG
Found at i:4467939 original size:3 final size:3
Alignment explanation
Indices: 4467931--4467958 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4467921 AGAAAAAGAA
4467931 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4467959 CTNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4469278 original size:60 final size:60
Alignment explanation
Indices: 4469109--4469280 Score: 227
Period size: 60 Copynumber: 2.9 Consensus size: 60
4469099 AGTGACCGAG
*
4469109 CTAGATTGGGTTTAAAACTCAACTGATGCCAACTTCATTAGGCTTAAACCTCTATGCTAT
1 CTAGATTGGGTTTAAAACTCAACTGATGCCAACTTCATTAGGCTTAAACGTCTATGCTAT
* * * ** * * *
4469169 CTATATTAGGTTTAAAACTCAACTAATGATAGCTTCATTGGGCCTAAACGTCTATGCTAT
1 CTAGATTGGGTTTAAAACTCAACTGATGCCAACTTCATTAGGCTTAAACGTCTATGCTAT
* * * *
4469229 CTAGATTGGGCTTAAAACTTAATTGATGCCAACTTCACTAGGCTTAAACGTC
1 CTAGATTGGGTTTAAAACTCAACTGATGCCAACTTCATTAGGCTTAAACGTC
4469281 AATACCAAGC
Statistics
Matches: 91, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 91 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (60 bp):
CTAGATTGGGTTTAAAACTCAACTGATGCCAACTTCATTAGGCTTAAACGTCTATGCTAT
Found at i:4469401 original size:64 final size:64
Alignment explanation
Indices: 4469311--4469430 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 64
4469301 TAAATTTGTC
* * * *
4469311 ATCTAGTACCAATTTAGCTAGTCTTAATAATCCAAATGCTAGCTAGATTAGGCTTACATCTCTT
1 ATCTAGTACCAATTTAACTAGGCTTAACAATCCAAATGCCAGCTAGATTAGGCTTACATCTCTT
* ***
4469375 ATCTAGTGCCAATTTAACTAGGCTTAACAATTTTAATGCCAGCTAGATTAGGCTTA
1 ATCTAGTACCAATTTAACTAGGCTTAACAATCCAAATGCCAGCTAGATTAGGCTTA
4469431 AAAACTCATC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (64 bp):
ATCTAGTACCAATTTAACTAGGCTTAACAATCCAAATGCCAGCTAGATTAGGCTTACATCTCTT
Found at i:4469659 original size:24 final size:25
Alignment explanation
Indices: 4469632--4469683 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
4469622 TTATTTTCCC
*
4469632 TTTAATAGACT-TTT-TTTTTTGTTT
1 TTTAATA-ACTCTTTCTTTTTTATTT
*
4469656 TTTACTAACTCTTTCTTTTTTATTT
1 TTTAATAACTCTTTCTTTTTTATTT
4469681 TTT
1 TTT
4469684 TGCATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.12
24 9 0.38
25 12 0.50
ACGTcount: A:0.15, C:0.10, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTAATAACTCTTTCTTTTTTATTT
Done.