Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397276.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_106.0, 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: 2845708
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.30
Warning! 346660 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:1459904 original size:9 final size:9
Alignment explanation
Indices: 1459860--1459904 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
1459850 GCACTGTCTC
*
1459860 TAGTAGTAG
1 TAGTAGTAA
*
1459869 TAGTAGTAG
1 TAGTAGTAA
*
1459878 TAGTAGTAG
1 TAGTAGTAA
1459887 TAGTAGTAA
1 TAGTAGTAA
*
1459896 TAGTGGTAA
1 TAGTAGTAA
1459905 CTATATTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (9 bp):
TAGTAGTAA
Found at i:1463204 original size:21 final size:20
Alignment explanation
Indices: 1463162--1463206 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1463152 ATAAAAAACT
* **
1463162 AATTATTAATTAATTACTAG
1 AATTATTAATTAATCAAAAG
1463182 AATTATTAATCTAATCAAAAG
1 AATTATTAAT-TAATCAAAAG
1463203 AATT
1 AATT
1463207 TAGTCACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (20 bp):
AATTATTAATTAATCAAAAG
Found at i:1476538 original size:19 final size:19
Alignment explanation
Indices: 1476489--1476536 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1476479 TTAATATTTT
1476489 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
*
1476508 AATATTATTTTATTTA-AA
1 AATATTATTTTATTCATAA
*
1476526 AATATTCTTTT
1 AATATTATTTT
1476537 TACTTGTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:1479293 original size:7 final size:7
Alignment explanation
Indices: 1479277--1479316 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
1479267 TCCAAGCCTT
*
1479277 TTTCTTC
1 TTTCTCC
1479284 TTTCTCC
1 TTTCTCC
*
1479291 TTTCTCT
1 TTTCTCC
*
1479298 TTTCTTC
1 TTTCTCC
1479305 TTTCTCC
1 TTTCTCC
1479312 TTTCT
1 TTTCT
1479317 TCCCTCTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTCTCC
Found at i:1479300 original size:21 final size:21
Alignment explanation
Indices: 1479276--1479316 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1479266 CTCCAAGCCT
1479276 TTTTCTTCTTTCTCCTTTCTC
1 TTTTCTTCTTTCTCCTTTCTC
1479297 TTTTCTTCTTTCTCCTTTCT
1 TTTTCTTCTTTCTCCTTTCT
1479317 TCCCTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTCTTCTTTCTCCTTTCTC
Found at i:1479324 original size:21 final size:21
Alignment explanation
Indices: 1479279--1479324 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1479269 CAAGCCTTTT
**
1479279 TCTTCTTTCTCCTTTCTCTTT
1 TCTTCTTTCTCCTTTCTCTCC
1479300 TCTTCTTTCTCCTTTCT-TCCC
1 TCTTCTTTCTCCTTTCTCT-CC
1479321 TCTT
1 TCTT
1479325 TTGTTCTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (21 bp):
TCTTCTTTCTCCTTTCTCTCC
Found at i:1480554 original size:116 final size:116
Alignment explanation
Indices: 1480417--1480649 Score: 448
Period size: 116 Copynumber: 2.0 Consensus size: 116
1480407 ATTCTTTTCA
*
1480417 CCCATCATCGTTTTTTGTCACTTAAATTTATATCAATTGACCCTTCATCTTATCAATTAGGTCTT
1 CCCATCATCGTTTTTTATCACTTAAATTTATATCAATTGACCCTTCATCTTATCAATTAGGTCTT
1480482 ATTGGTTTCTATTCGAGAGTACGGGGTGTTACATTATTAATGGGCTCATGT
66 ATTGGTTTCTATTCGAGAGTACGGGGTGTTACATTATTAATGGGCTCATGT
*
1480533 CCCATCATCGTTTTTTATCACTTAAATTTATATCAATTGACTCTTCATCTTATCAATTAGGTCTT
1 CCCATCATCGTTTTTTATCACTTAAATTTATATCAATTGACCCTTCATCTTATCAATTAGGTCTT
1480598 ATTGGTTTCTATTCGAGAGTACGGGGTGTTACATTATTAATGGGCTCATGT
66 ATTGGTTTCTATTCGAGAGTACGGGGTGTTACATTATTAATGGGCTCATGT
1480649 C
1 C
1480650 TATATGTGAA
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (116 bp):
CCCATCATCGTTTTTTATCACTTAAATTTATATCAATTGACCCTTCATCTTATCAATTAGGTCTT
ATTGGTTTCTATTCGAGAGTACGGGGTGTTACATTATTAATGGGCTCATGT
Found at i:1482441 original size:10 final size:11
Alignment explanation
Indices: 1482422--1482450 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1482412 AAAAGAGTTC
1482422 ATAGAAATAAA
1 ATAGAAATAAA
1482433 ATA-AAATAAA
1 ATAGAAATAAA
1482443 ATAGAAAT
1 ATAGAAAT
1482451 TGTTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (11 bp):
ATAGAAATAAA
Found at i:1482742 original size:23 final size:22
Alignment explanation
Indices: 1482699--1482755 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
1482689 AAATACAAGC
* **
1482699 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAAGATAATA
1482721 ATATTTTGTATTAGAAGATAATTA
1 ATATTTT-TATTAGAAGATAA-TA
1482745 A-ACTTTTTATT
1 ATA-TTTTTATT
1482756 GTAATTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.24
23 15 0.52
24 7 0.24
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (22 bp):
ATATTTTTATTAGAAGATAATA
Found at i:1488783 original size:16 final size:17
Alignment explanation
Indices: 1488757--1488789 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1488747 TCTTCTATTT
*
1488757 TCATCAAGCATTATCAA
1 TCATCAAGCATCATCAA
1488774 TCAT-AAGCATCATCAA
1 TCATCAAGCATCATCAA
1488790 ATCTTACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (17 bp):
TCATCAAGCATCATCAA
Found at i:1490827 original size:16 final size:17
Alignment explanation
Indices: 1490806--1490838 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1490796 TTGTAAACAA
1490806 TTAATT-AAAACTAAAT
1 TTAATTAAAAACTAAAT
1490822 TTAATTAGAAAACTAAA
1 TTAATTA-AAAACTAAA
1490839 CTAATTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAATTAAAAACTAAAT
Found at i:1490845 original size:17 final size:18
Alignment explanation
Indices: 1490812--1490845 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1490802 ACAATTAATT
*
1490812 AAAACTAAATTTAATTAG
1 AAAACTAAATCTAATTAG
1490830 AAAACTAAA-CTAATTA
1 AAAACTAAATCTAATTA
1490846 ATGAATACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAACTAAATCTAATTAG
Found at i:1492206 original size:21 final size:21
Alignment explanation
Indices: 1492182--1492228 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1492172 TTAATGTAAT
*
1492182 TTAAAATAATATAA-TATAAAA
1 TTAAAATAAAATAACT-TAAAA
*
1492203 TTAAACTAAAATAACTTAAAA
1 TTAAAATAAAATAACTTAAAA
1492224 TTAAA
1 TTAAA
1492229 CTACTTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAAATAAAATAACTTAAAA
Found at i:1498224 original size:504 final size:504
Alignment explanation
Indices: 1497264--1498272 Score: 1617
Period size: 504 Copynumber: 2.0 Consensus size: 504
1497254 TTGGCTTATC
* * ** *
1497264 TATGTGTTTCACGTTGTCACACACCTCAAGTGGGCTGTTTATGGGCCTTATCACCAAAAGGGGTC
1 TATGTGTTGCACATTGTCACACACCTCAAGTGGGCTGTTTATGGGCCACATCACCAAAAAGGGTC
* * *
1497329 ACCTCCCTATCTCATGCACTCAATGGAATGGAAATTATCTAAGGACCTTATTTATCACCCATGTA
66 ACCTCCCCATCTCATGCACTCAATGGAATGGAAATTATCTAAAGACCTTACTTATCACCCATGTA
*
1497394 CCTACTAAGCATGCTTATCTTCCTCCAACATCTTGAACCACGAGCCATGACACCCCTTTCCCCCT
131 CCTACTAAGCATGCTTATCTTCCTCCAACATCTTGAACCACGAGCCATGACACCCCTTTCCCCCC
*
1497459 ACTTAAGCTAGCAATGTCCTACTTGCCCCATGAAAAGCATTCACCTTACTTGGAACAGCCACAAG
196 ACTTAAGCTAGCAATGTCCTACTTGCCCCATGAAAAGCATCCACCTTACTTGGAACAGCCACAAG
*
1497524 TCCTCCACAGATTCCCAATTACCTTTATCCTTGGGTAGTCTTTTCCATTGCATAAGGTACTAATG
261 TCCTCCACAGATTCCCAATTACCTTTATCCTTGGGTAGTCTTTTCCATTGCACAAGGTACTAATG
* *
1497589 CTATGACATGTGATACTTCTATCTAAGTACCTTTTCAGACAGCACATCCTCTACTTCCCTTTCAT
326 CTATGACATGTGATACTTCTATCTAAGTACCTGTTCAGACAGCACATCCTCTACTTCCCTTTCAC
* *
1497654 ATGTAGCTTGGACCCCCCATCAATGCCATGTGGCTCAACCTTCTACTAGGGTTCTCCTTATCTCC
391 ATGTAGCTTGGACCCCCCATCAATGCCATGTGGCTCAACCTTCGACTAGGGTTCTACTTATCTCC
1497719 ATTATATGGCTTAAGCATACTCACATGGAAGATTGGGTGCACCTTGGGT
456 ATTATATGGCTTAAGCATACTCACATGGAAGATTGGGTGCACCTTGGGT
**
1497768 TATGTGTTGCACATTGTTGCACACCTCAAGTGGGCTGTTTATGGGCCACATCACCAAAAAGGGTC
1 TATGTGTTGCACATTGTCACACACCTCAAGTGGGCTGTTTATGGGCCACATCACCAAAAAGGGTC
* * *
1497833 ATCTCCCCATCTCATGCACTCAATGGAATGGAAATTATCTAAAGATCTTCCTTATCACCCATGTA
66 ACCTCCCCATCTCATGCACTCAATGGAATGGAAATTATCTAAAGACCTTACTTATCACCCATGTA
*
1497898 CCTACTAAGCATGCTTATCTTCCTCCAACATCTTGAACCATGAGCCATGACACCCCTTTCCCCCC
131 CCTACTAAGCATGCTTATCTTCCTCCAACATCTTGAACCACGAGCCATGACACCCCTTTCCCCCC
* * * * ** *
1497963 ACTTAAGTTGGCAGTGTCCTACTTGCCCCATGAAAGGCATCCATTTTACTTGGAATAGCCACAAG
196 ACTTAAGCTAGCAATGTCCTACTTGCCCCATGAAAAGCATCCACCTTACTTGGAACAGCCACAAG
* ** *
1498028 TCCTCCATAGATTCCCGTTTACCTTTATTCTTGGGTAGTCTTTTCCATTGCACAAGGTACTAATG
261 TCCTCCACAGATTCCCAATTACCTTTATCCTTGGGTAGTCTTTTCCATTGCACAAGGTACTAATG
* *
1498093 CTATGGCATGTGATACTTCTATCTAAGTACCCTGTT-AGATAGCACATCCTCTACTTCCCTTTCA
326 CTATGACATGTGATACTTCTATCTAAGTA-CCTGTTCAGACAGCACATCCTCTACTTCCCTTTCA
* * * * *
1498157 CATGTAGCTTGGACCCCCTATTAGTGCCATGTGGCTCAACCTTCGACTAGGGCTT-TATTTGTCT
390 CATGTAGCTTGGACCCCCCATCAATGCCATGTGGCTCAACCTTCGACTAGGG-TTCTACTTATCT
* *
1498221 CCATTATATGGCTTAGGCATTCTCACATGGAAGATTGGGTGCACCTTGGGT
454 CCATTATATGGCTTAAGCATACTCACATGGAAGATTGGGTGCACCTTGGGT
1498272 T
1 T
1498273 TGGGTGACAT
Statistics
Matches: 462, Mismatches: 41, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
504 455 0.98
505 7 0.02
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (504 bp):
TATGTGTTGCACATTGTCACACACCTCAAGTGGGCTGTTTATGGGCCACATCACCAAAAAGGGTC
ACCTCCCCATCTCATGCACTCAATGGAATGGAAATTATCTAAAGACCTTACTTATCACCCATGTA
CCTACTAAGCATGCTTATCTTCCTCCAACATCTTGAACCACGAGCCATGACACCCCTTTCCCCCC
ACTTAAGCTAGCAATGTCCTACTTGCCCCATGAAAAGCATCCACCTTACTTGGAACAGCCACAAG
TCCTCCACAGATTCCCAATTACCTTTATCCTTGGGTAGTCTTTTCCATTGCACAAGGTACTAATG
CTATGACATGTGATACTTCTATCTAAGTACCTGTTCAGACAGCACATCCTCTACTTCCCTTTCAC
ATGTAGCTTGGACCCCCCATCAATGCCATGTGGCTCAACCTTCGACTAGGGTTCTACTTATCTCC
ATTATATGGCTTAAGCATACTCACATGGAAGATTGGGTGCACCTTGGGT
Found at i:1507128 original size:67 final size:67
Alignment explanation
Indices: 1507055--1507216 Score: 290
Period size: 67 Copynumber: 2.4 Consensus size: 67
1507045 ATAAAGTTAT
*
1507055 TTATTATATGTTTATAAAAATTTTATAAAAATAAATTTATCAAACAGTTTTAATTTAATTTTAAA
1 TTATTATATGTTTATAAAAATTTTATAAAAATAAATTTACCAAACAGTTTTAATTTAATTTTAAA
1507120 AA
66 AA
1507122 TTATTATATGTTTATAAAAATTTTATAAAAATAAATTTACCAAACAGTTTTAATTTAATTTTAAA
1 TTATTATATGTTTATAAAAATTTTATAAAAATAAATTTACCAAACAGTTTTAATTTAATTTTAAA
1507187 AA
66 AA
*
1507189 TTATTATAT-TTTATAATAAACTTTATAA
1 TTATTATATGTTTATAA-AAATTTTATAA
1507217 TAATTTTTAC
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
66 7 0.08
67 85 0.92
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (67 bp):
TTATTATATGTTTATAAAAATTTTATAAAAATAAATTTACCAAACAGTTTTAATTTAATTTTAAA
AA
Found at i:1507189 original size:36 final size:35
Alignment explanation
Indices: 1507080--1507189 Score: 90
Period size: 36 Copynumber: 3.2 Consensus size: 35
1507070 AAAAATTTTA
1507080 TAAAAATAAATTTATCAAACAGTTTTAATTTAATTT
1 TAAAAATAAATTTA-CAAACAGTTTTAATTTAATTT
* * * *
1507116 TAAAAAT-TA-TT--ATA-TGTTTATAA--AAATTTT
1 TAAAAATAAATTTACAAACAGTTT-TAATTTAA-TTT
1507146 ATAAAAATAAATTTACCAAACAGTTTTAATTTAATTT
1 -TAAAAATAAATTTA-CAAACAGTTTTAATTTAATTT
1507183 TAAAAAT
1 TAAAAAT
1507190 TATTATATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 22
0.65 0.09 0.26
Matches are distributed among these distances:
29 2 0.04
30 7 0.13
31 12 0.22
32 1 0.02
33 2 0.04
34 2 0.04
35 1 0.02
36 19 0.35
37 7 0.13
38 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (35 bp):
TAAAAATAAATTTACAAACAGTTTTAATTTAATTT
Found at i:1515540 original size:70 final size:69
Alignment explanation
Indices: 1515449--1515595 Score: 186
Period size: 70 Copynumber: 2.1 Consensus size: 69
1515439 TTGCAACCAC
* * ** *
1515449 GGCATGTAACATGTTGCAGTCATGGCATGTAGCTTCCAACAGTCTTGCGTGTGTAGTTTGTTGGA
1 GGCATGTAACATCTTGCAGTCATGGCATGTAGCTTCCAACAGTCTAG-GTGTGTAACTTGTCGGA
1515514 GTCAT
65 GTCAT
* * * * *
1515519 GGCGTGTAACATCTTGTAGTCATGGCGTGTAGCTTCGAGCAGTCTAGGTGTGTAACTTGTCGGAG
1 GGCATGTAACATCTTGCAGTCATGGCATGTAGCTTCCAACAGTCTAGGTGTGTAACTTGTCGGAG
*
1515584 TCTT
66 TCAT
1515588 GGCATGTA
1 GGCATGTA
1515596 GCTTGTTAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
69 25 0.38
70 40 0.62
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (69 bp):
GGCATGTAACATCTTGCAGTCATGGCATGTAGCTTCCAACAGTCTAGGTGTGTAACTTGTCGGAG
TCAT
Found at i:1515562 original size:23 final size:23
Alignment explanation
Indices: 1515464--1515562 Score: 56
Period size: 23 Copynumber: 4.3 Consensus size: 23
1515454 GTAACATGTT
* *
1515464 GCAGTCATGGCATGTAGCTTCCA
1 GCAGTCATGGCGTGTAGCTTCGA
* * * * *
1515487 ACAGTCTTGCGTGTGTAG-TTTGTT
1 GCAGTCATG-GCGTGTAGCTTCG-A
* * * **
1515511 GGAGTCATGGCGTGTAACATCTT
1 GCAGTCATGGCGTGTAGCTTCGA
*
1515534 GTAGTCATGGCGTGTAGCTTCGA
1 GCAGTCATGGCGTGTAGCTTCGA
1515557 GCAGTC
1 GCAGTC
1515563 TAGGTGTGTA
Statistics
Matches: 52, Mismatches: 21, Indels: 6
0.66 0.27 0.08
Matches are distributed among these distances:
23 39 0.75
24 13 0.25
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.32
Consensus pattern (23 bp):
GCAGTCATGGCGTGTAGCTTCGA
Found at i:1515607 original size:23 final size:23
Alignment explanation
Indices: 1515489--1515641 Score: 78
Period size: 23 Copynumber: 6.6 Consensus size: 23
1515479 AGCTTCCAAC
* * *
1515489 AGTCTTGCGTGTGTAGTTTGTTGG
1 AGTCTTG-GCGTGTAGCTTGTTAG
* * * *
1515513 AGTCATGGCGTGTAACATCTT-G
1 AGTCTTGGCGTGTAGCTTGTTAG
*
1515535 TAGTCATGGCGTGTAGCTTCG--AG
1 -AGTCTTGGCGTGTAGCTT-GTTAG
* * * **
1515558 CAGTCTAGGTGTGTAACTTGTCGG
1 -AGTCTTGGCGTGTAGCTTGTTAG
*
1515582 AGTCTTGGCATGTAGCTTGTTAG
1 AGTCTTGGCGTGTAGCTTGTTAG
* * * *
1515605 AGTCATGGCGTGCAGTTTGTTAC
1 AGTCTTGGCGTGTAGCTTGTTAG
*
1515628 AATCTTGGCGTGTA
1 AGTCTTGGCGTGTA
1515642 ACTTCTGTGA
Statistics
Matches: 95, Mismatches: 29, Indels: 11
0.70 0.21 0.08
Matches are distributed among these distances:
22 2 0.02
23 86 0.91
24 7 0.07
ACGTcount: A:0.17, C:0.15, G:0.32, T:0.36
Consensus pattern (23 bp):
AGTCTTGGCGTGTAGCTTGTTAG
Found at i:1515696 original size:18 final size:18
Alignment explanation
Indices: 1515672--1515718 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
1515662 GCTGTTTACA
1515672 TTTTTATTATTTTGT--T
1 TTTTTATTATTTTGTCAT
*
1515688 TTCTT-TTATTTTTGTCAT
1 TTTTTATTA-TTTTGTCAT
1515706 TTTTTATTATTTT
1 TTTTTATTATTTT
1515719 AACTGTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 10 0.40
18 9 0.36
19 3 0.12
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTTTATTATTTTGTCAT
Found at i:1531603 original size:10 final size:10
Alignment explanation
Indices: 1531588--1531638 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
1531578 GGCTGGCGGG
1531588 GAAGAAGAAA
1 GAAGAAGAAA
*
1531598 GAAGAAGAAG
1 GAAGAAGAAA
1531608 GAAGAA-AAGGA
1 GAAGAAGAA--A
*
1531619 GAAAAAGAAA
1 GAAGAAGAAA
*
1531629 GAGGAAGAAA
1 GAAGAAGAAA
1531639 AAAAAGGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 2 0.06
10 24 0.73
11 5 0.15
12 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAA
Found at i:1531633 original size:15 final size:16
Alignment explanation
Indices: 1531592--1531644 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
1531582 GGCGGGGAAG
* *
1531592 AAGAAAGAAGAAGAAGG
1 AAGAAAGAGGAAGAA-A
1531609 AAGAAA-AGG-AGAAA
1 AAGAAAGAGGAAGAAA
1531623 AAGAAAGAGGAAGAAA
1 AAGAAAGAGGAAGAAA
1531639 AA-AAAG
1 AAGAAAG
1531645 GAAAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 6 0.19
15 11 0.34
16 9 0.28
17 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AAGAAAGAGGAAGAAA
Found at i:1531633 original size:24 final size:25
Alignment explanation
Indices: 1531593--1531639 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
1531583 GCGGGGAAGA
1531593 AGAAAGAAGAAGAAGGAAGAAAAGG
1 AGAAAGAAGAAGAAGGAAGAAAAGG
1531618 AGAAA-AAGAA-AGAGGAAGAAAA
1 AGAAAGAAGAAGA-AGGAAGAAAA
1531640 AAAAGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 1 0.05
24 15 0.71
25 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (25 bp):
AGAAAGAAGAAGAAGGAAGAAAAGG
Found at i:1531642 original size:27 final size:27
Alignment explanation
Indices: 1531590--1531664 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 27
1531580 CTGGCGGGGA
* *
1531590 AGAAGAAAG-AAGAAGAAGGAAGAAAAGG
1 AGAA-AAAGAAAGAGGAA-GAAAAAAAGG
1531618 AGAAAAAGAAAGAGGAAGAAAAAAAAGG
1 AGAAAAAGAAAGAGGAAG-AAAAAAAGG
*
1531646 A-AAATAA-AAGGAGGAAGAA
1 AGAAA-AAGAAAGAGGAAGAA
1531665 GAAGGGCAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
26 2 0.05
27 17 0.41
28 22 0.54
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (27 bp):
AGAAAAAGAAAGAGGAAGAAAAAAAGG
Found at i:1532123 original size:14 final size:14
Alignment explanation
Indices: 1532091--1532124 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1532081 GTTAGGAAAG
1532091 AATATATATATATA
1 AATATATATATATA
* *
1532105 CATATATATATGTA
1 AATATATATATATA
1532119 AATATA
1 AATATA
1532125 AAATATGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (14 bp):
AATATATATATATA
Found at i:1533105 original size:41 final size:41
Alignment explanation
Indices: 1533048--1533127 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
1533038 GGTGAGTTTA
1533048 TCGAGCATTTCTCCTAGGTGAGAGGATACTCTTGGATCCTT
1 TCGAGCATTTCTCCTAGGTGAGAGGATACTCTTGGATCCTT
1533089 TCGAGCATTTCTCCTAGGTGAGAGGATACTCTTGGATCC
1 TCGAGCATTTCTCCTAGGTGAGAGGATACTCTTGGATCC
1533128 CACCAGCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (41 bp):
TCGAGCATTTCTCCTAGGTGAGAGGATACTCTTGGATCCTT
Found at i:1534810 original size:15 final size:15
Alignment explanation
Indices: 1534774--1534803 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1534764 AGTTTTAATT
1534774 ATGGAAAGAATTAAA
1 ATGGAAAGAATTAAA
*
1534789 ATGGAAAGTATTAAA
1 ATGGAAAGAATTAAA
1534804 GAGGAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (15 bp):
ATGGAAAGAATTAAA
Found at i:1548778 original size:35 final size:35
Alignment explanation
Indices: 1548732--1548799 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
1548722 AAGAGAGGTA
1548732 AGATTTAGATGAAGTTGAAGGGATATTGTAATCGT
1 AGATTTAGATGAAGTTGAAGGGATATTGTAATCGT
1548767 AGATTTAGATGAAGTTGAAGGGATATTGTAATC
1 AGATTTAGATGAAGTTGAAGGGATATTGTAATC
1548800 CTACGCTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (35 bp):
AGATTTAGATGAAGTTGAAGGGATATTGTAATCGT
Found at i:1596758 original size:19 final size:19
Alignment explanation
Indices: 1596720--1596759 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1596710 TTCAAAAAAA
*
1596720 TTATAATTTTTTTGTACAT
1 TTATAATTTTTTCGTACAT
1596739 TTATAATTTTTTACGT-CAT
1 TTATAATTTTTT-CGTACAT
1596758 TT
1 TT
1596760 TTTACCCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.62
Consensus pattern (19 bp):
TTATAATTTTTTCGTACAT
Found at i:1596835 original size:21 final size:21
Alignment explanation
Indices: 1596789--1596834 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1596779 TTTTTTCAAT
*
1596789 TTTTAATTTTTACTATAATTA
1 TTTTAATTTTTACTATAATCA
*
1596810 TTTTAATTTTTATTATTAATCA
1 TTTTAATTTTTACTA-TAATCA
1596832 TTT
1 TTT
1596835 ATAAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTAATTTTTACTATAATCA
Found at i:1614339 original size:31 final size:31
Alignment explanation
Indices: 1614288--1614375 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 31
1614278 ATGGTTTGAC
*
1614288 CCCCA-TCTACCTTGGGCTGGCAATGTACAT
1 CCCCATTCAACCTTGGGCTGGCAATGTACAT
* * * *
1614318 CCCTATTCCACCTTGGACTGGCAACGTACAT
1 CCCCATTCAACCTTGGGCTGGCAATGTACAT
1614349 CCCCATTCAACCTTGGGCTGGCAATGT
1 CCCCATTCAACCTTGGGCTGGCAATGT
1614376 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 4 0.08
31 45 0.92
ACGTcount: A:0.20, C:0.34, G:0.19, T:0.26
Consensus pattern (31 bp):
CCCCATTCAACCTTGGGCTGGCAATGTACAT
Found at i:1618409 original size:22 final size:21
Alignment explanation
Indices: 1618384--1618430 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1618374 CTGCACTACC
**
1618384 ATAACAATTATAATAAATAATA
1 ATAACAAAGATAA-AAATAATA
*
1618406 ATAACAAAGATAAAAATAATT
1 ATAACAAAGATAAAAATAATA
1618427 ATAA
1 ATAA
1618431 GAAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (21 bp):
ATAACAAAGATAAAAATAATA
Found at i:1619564 original size:252 final size:253
Alignment explanation
Indices: 1618402--1619814 Score: 821
Period size: 254 Copynumber: 5.7 Consensus size: 253
1618392 TATAATAAAT
* * * * *
1618402 AATAATAACAAAGATAAAAATAATTATAA-GAAAAAAATAAG-AAAT-GACAATCCTTGGCGTAA
1 AATAATAACAAAAATAAAAATAATTATAATG---AAAATTAGCAATTGGA-AAACCTTGACGTAA
* * * * * * * * **
1618464 ACTTGTAAGAATTAATAT-AAAAGTTAACAAAGGTGGAATAAGCATATG--AAAATATTGATGTA
62 ACCTATAACAATGAATATAAAAAATT-ATAAAGGTGGAATAAGTAT-TGTCAAAATATTAACATA
* * * * * *** *
1618526 AATATGTGAGATTTAACATAACAAGTCAATTAAGTCAAAATAAATACAATTT-TTGTGAAACTCA
125 AATATGTGAGATTTAACGTAATAAGTCAATTAAGTC-AAATAAACATAATTTACTAAAAAACTTA
* * * * * * *
1618590 AACCTTTAAATTTATATTAT-TGAGCTAAAAGTATTTAACAATTTATAAATTTTAATTTATAAAG
189 AACATTTAAATTTATATTATCT-AACTAAAAATATTTAACAATTTACAAATTTGAAATTATAAAA
1618654 G
253 G
*** ** * * * * * ** *
1618655 AATAATAACACGGATAAAAATAATTATGGTGAAAACTAGGAACTGAAAAACATTGACGTGCACTT
1 AATAATAACAAAAATAAAAATAATTATAATGAAAATTAGCAATTGGAAAACCTTGACGTAAACCT
* * * * * * * * *
1618720 GTAAGAGTAAACATAAAAAATTATAAAAGTGGAACAAGTGTTGAT-AAAATATT---ATAAATTT
66 ATAACAATGAATATAAAAAATTATAAAGGTGGAATAAGTATTG-TCAAAATATTAACATAAATAT
** * * * * * * *
1618781 GTGAGATTTAGTGTAACAAGCCAATTAAGTTAAATTATA-ATAAATTT-TTGAGAAAA-TTATAC
130 GTGAGATTTAACGTAATAAGTCAATTAAGTCAAA-TAAACAT-AATTTACT-AAAAAACTTAAAC
* * * * * * * *
1618843 ATTTAAATTTATATGAT-TGAGTAAAAGTATTTAACGATTTATAAATTT-TAATTCATAAATG
192 ATTTAAATTTATATTATCTAACTAAAAATATTTAACAATTTACAAATTTGAAATT-ATAAAAG
* * ** * * ** *
1618904 AACAAT--CATAAGA-AAAAATAATTATTGTTAAAATTAGTAATTAAAAAATCTTGA-GTAAACC
1 AATAATAACA-AAAATAAAAATAATTATAATGAAAATTAGCAATTGGAAAACCTTGACGTAAACC
** * * * ** * ** * * *
1618965 CGTCAGAATTAATAT-AAAAA-TATAAAGGCAGAATAAGGATTACCAAAATATTGA-GTAAATGT
65 TATAACAATGAATATAAAAAATTATAAAGGTGGAATAAGTATTGTCAAAATATTAACATAAATAT
* ** ** *
1619027 GT-AGAGTAATAA--TATATAAGTCAATTAAGTCAAATAAAC-TAATTTTTTTGGAAAA-TCAAA
130 GTGAGA-T-TTAACGTA-ATAAGTCAATTAAGTCAAATAAACATAA-TTTACTAAAAAACTTAAA
* * ** ** * * * * * *
1619087 -ACTTAAATTTACATGCT-TGAGTTTAAAGTATTTAATAGTTTACAAATTTTAATTTAT-AAAG
191 CATTTAAATTTATATTATCT-AACTAAAAATATTTAACAATTTACAAATTTGAAATTATAAAAG
** * * *
1619148 CAATAAT-A-AATGATAAAAATAATT-TAATAAAAAATAGCAATTGAAAAACCTT-A--TATAA-
1 -AATAATAACAAAAATAAAAATAATTATAATGAAAATTAGCAATTGGAAAACCTTGACGTA-AAC
* ** * * * *
1619206 CTAATAA-AATTAACGTAAAAAATTATAAAGTTTGAATAAGTATTGTCAAAATATTGACCTAAAT
64 CT-ATAACAATGAATATAAAAAATTATAAAGGTGGAATAAGTATTGTCAAAATATTAACATAAAT
* * * * *
1619270 ATGTGAGATTGAATGTAACAAGTCAATTAAGTCAAATAAACATAA-TTACTATAAAATTTAAACA
128 ATGTGAGATTTAACGTAATAAGTCAATTAAGTCAAATAAACATAATTTACTAAAAAACTTAAACA
*
1619334 TTTAAATTTATATTATCTAACTAAAAATATTTAACGATTTACAAATTTGAAATTATAAAAG
193 TTTAAATTTATATTATCTAACTAAAAATATTTAACAATTTACAAATTTGAAATTATAAAAG
* * * *
1619395 AATAATAATAAAGATAAAAATAATTATAGT-AAAATATAG-AATTTTGAAAACCTTGACGTAAAC
1 AATAATAACAAAAATAAAAATAATTATAATGAAAAT-TAGCAA-TTGGAAAACCTTGACGTAAAC
* *
1619458 CTATAACAATGAATATAAAAAATTATAAAGGTGGAGTAAGTATTGTCAAAATATTAACATAGATA
64 CTATAACAATGAATATAAAAAATTATAAAGGTGGAATAAGTATTGTCAAAATATTAACATAAATA
* * ** ** *
1619523 TATGAGATTTAACGTAATAACTCAATTAAGT-ATCGTAAACATAATTTTTGTAAAAAACTTAAAT
129 TGTGAGATTTAACGTAATAAGTCAATTAAGTCA-AATAAACATAA-TTTACTAAAAAACTTAAAC
* * * * * *
1619587 GTTTAAATTTATATTATCTAGCTAAAAGTATTTAACAATTTACAAATTTTAATTTATAAAGG
192 ATTTAAATTTATATTATCTAACTAAAAATATTTAACAATTTACAAATTTGAAATTATAAAAG
* * *
1619649 AATAATAACAAAAATTAAAATAATTATAATGAAAATTAGCAATTGGAAAACCTTGATGTAAACTT
1 AATAATAACAAAAATAAAAATAATTATAATGAAAATTAGCAATTGGAAAACCTTGACGTAAACCT
* * * * * * * *
1619714 ATGAGAGTTAATGT-AAAAATTATTAAGGTGAAACAAAG-ATTGTCAAAATATTAACATAAATAT
66 ATAACAATGAATATAAAAAATTATAAAGGTGGAA-TAAGTATTGTCAAAATATTAACATAAATAT
* *
1619777 GTGATATTTAACGTAATAAGTCAATTAAGTCCAATAAA
130 GTGAGATTTAACGTAATAAGTCAATTAAGTCAAATAAA
1619815 TATTTCCTCA
Statistics
Matches: 909, Mismatches: 196, Indels: 110
0.75 0.16 0.09
Matches are distributed among these distances:
242 10 0.01
243 10 0.01
244 104 0.11
245 101 0.11
246 100 0.11
247 43 0.05
248 26 0.03
249 57 0.06
250 63 0.07
251 18 0.02
252 129 0.14
253 111 0.12
254 130 0.14
255 7 0.01
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (253 bp):
AATAATAACAAAAATAAAAATAATTATAATGAAAATTAGCAATTGGAAAACCTTGACGTAAACCT
ATAACAATGAATATAAAAAATTATAAAGGTGGAATAAGTATTGTCAAAATATTAACATAAATATG
TGAGATTTAACGTAATAAGTCAATTAAGTCAAATAAACATAATTTACTAAAAAACTTAAACATTT
AAATTTATATTATCTAACTAAAAATATTTAACAATTTACAAATTTGAAATTATAAAAG
Found at i:1619671 original size:254 final size:249
Alignment explanation
Indices: 1618402--1619814 Score: 895
Period size: 252 Copynumber: 5.7 Consensus size: 249
1618392 TATAATAAAT
* * * * *
1618402 AATAATAACAAAGATAAAAATAATTATAAGAAAAAAATAAG-AA-ATGACAATCCTTGGCGTAAA
1 AATAATAA-AAAGATAAAAATAATTATAA-TAAAATAT-AGCAATTTGA-AAACCTT-GAGTAAA
* * * * * * * **
1618465 CTTGTAAGAATTAATAT-AAAAGTTAACAAAGGTGGAATAAGCATATG--AAAATATTGATGTAA
61 CCTATAA-AATTAATGTAAAAAATT-ATAAAGGTGGAATAAGTAT-TGTCAAAATATTAACATAA
* * * * ** *** *
1618527 ATATGTGAGATTTAACATAACAAGTCAATTAAGTCAAAATAAATACAATTTTTGTGAAACTCAAA
123 ATATGTGAGATTTAACGTAATAAGTCAATTAAGTC-AAATAAACATAATTACTAAAAAACTTAAA
* * *
1618592 CCTTTAAATTTATATTAT-TGAGCTAAAAGTATTTAACAATTTATAAATTTTAATTTATAAAGG
187 CATTTAAATTTATATTATCT-AACTAAAAGTATTTAACAATTTACAAATTTTAATTTATAAAGG
** ** * * * * **
1618655 AATAATAACACGGATAAAAATAATTATGGTGAAAA-CTAGGAA-CTGAAAAACATTGACGTGCAC
1 AATAATAA-AAAGATAAAAATAATTATAAT-AAAATATAGCAATTTG-AAAACCTTGA-GTAAAC
* * * * ** * * *
1618718 TTGTAAGAGTAAACATAAAAAATTATAAAAGTGGAACAAGTGTTGAT-AAAATATT---ATAAAT
62 CTATAA-AATTAATGTAAAAAATTATAAAGGTGGAATAAGTATTG-TCAAAATATTAACATAAAT
* ** * * * * ** * *
1618779 TTGTGAGATTTAGTGTAACAAGCCAATTAAGTTAAATTATA-ATAAATTTTTGAGAAAA-TTATA
125 ATGTGAGATTTAACGTAATAAGTCAATTAAGTCAAA-TAAACAT-AATTACT-AAAAAACTTAAA
* * * * * * *
1618842 CATTTAAATTTATATGAT-TGAGTAAAAGTATTTAACGATTTATAAATTTTAATTCATAAATG
187 CATTTAAATTTATATTATCTAACTAAAAGTATTTAACAATTTACAAATTTTAATTTATAAAGG
* * * ** * ** * **
1618904 AACAATCATAAGA-AAAAATAATTATTGTTAAAAT-TAGTAATTAAAAAATCTTGAGTAAACCCG
1 AATAATAAAAAGATAAAAATAATTA-TAATAAAATATAGCAATTTGAAAACCTTGAGTAAACCTA
* * ** * ** * * *
1618967 TCAGAATTAATAT-AAAAA-TATAAAGGCAGAATAAGGATTACCAAAATATTGA-GTAAATGTGT
65 T-AAAATTAATGTAAAAAATTATAAAGGTGGAATAAGTATTGTCAAAATATTAACATAAATATGT
* ** ** *
1619029 -AGAGTAATAA--TATATAAGTCAATTAAGTCAAATAAAC-TAATTTTTTTGGAAAA-TCAAA-A
129 GAGA-T-TTAACGTA-ATAAGTCAATTAAGTCAAATAAACATAA--TTACTAAAAAACTTAAACA
* * ** ** * * * *
1619088 CTTAAATTTACATGCT-TGAGTTTAAAGTATTTAATAGTTTACAAATTTTAATTTATAAAGC
189 TTTAAATTTATATTATCT-AACTAAAAGTATTTAACAATTTACAAATTTTAATTTATAAAGG
* *
1619149 AATAAT-AAATGATAAAAATAATT-TAATAAAAAATAGCAA-TTGAAAAACCTT-A-TATAA-CT
1 AATAATAAAAAGATAAAAATAATTATAATAAAATATAGCAATTTG-AAAACCTTGAGTA-AACCT
* * * * *
1619208 AATAAAATTAACGTAAAAAATTATAAAGTTTGAATAAGTATTGTCAAAATATTGACCTAAATATG
64 -ATAAAATTAATGTAAAAAATTATAAAGGTGGAATAAGTATTGTCAAAATATTAACATAAATATG
* * * * *
1619273 TGAGATTGAATGTAACAAGTCAATTAAGTCAAATAAACATAATTACTATAAAATTTAAACATTTA
128 TGAGATTTAACGTAATAAGTCAATTAAGTCAAATAAACATAATTACTAAAAAACTTAAACATTTA
* * * * *
1619338 AATTTATATTATCTAACTAAAAATATTTAACGATTTACAAATTTGAAATTATAAAAG
193 AATTTATATTATCTAACTAAAAGTATTTAACAATTTACAAATTTTAATTTATAAAGG
*
1619395 AATAATAATAAAGATAAAAATAATTATAGTAAAATATAG-AATTTTGAAAACCTTGACGTAAACC
1 AATAATAA-AAAGATAAAAATAATTATAATAAAATATAGCAA-TTTGAAAACCTTGA-GTAAACC
* * * *
1619459 TATAACAATGAATATAAAAAATTATAAAGGTGGAGTAAGTATTGTCAAAATATTAACATAGATAT
63 TATAA-AATTAATGTAAAAAATTATAAAGGTGGAATAAGTATTGTCAAAATATTAACATAAATAT
* * ** ** **
1619524 ATGAGATTTAACGTAATAACTCAATTAAGT-ATCGTAAACATAATTTTTGTAAAAAACTTAAATG
127 GTGAGATTTAACGTAATAAGTCAATTAAGTCA-AATAAACATAA--TTACTAAAAAACTTAAACA
*
1619588 TTTAAATTTATATTATCTAGCTAAAAGTATTTAACAATTTACAAATTTTAATTTATAAAGG
189 TTTAAATTTATATTATCTAACTAAAAGTATTTAACAATTTACAAATTTTAATTTATAAAGG
* * * *
1619649 AATAATAACAAAAATTAAAATAATTATAATGAAAAT-TAGCAATTGGAAAACCTTGATGTAAACT
1 AATAATAA-AAAGATAAAAATAATTATAAT-AAAATATAGCAATTTGAAAACCTTGA-GTAAACC
* * * * *
1619713 TATGAGAGTTAATGT-AAAAATTATTAAGGTGAAACAAAG-ATTGTCAAAATATTAACATAAATA
63 TAT-AAAATTAATGTAAAAAATTATAAAGGTGGAA-TAAGTATTGTCAAAATATTAACATAAATA
* *
1619776 TGTGATATTTAACGTAATAAGTCAATTAAGTCCAATAAA
126 TGTGAGATTTAACGTAATAAGTCAATTAAGTCAAATAAA
1619815 TATTTCCTCA
Statistics
Matches: 908, Mismatches: 195, Indels: 114
0.75 0.16 0.09
Matches are distributed among these distances:
242 11 0.01
243 16 0.02
244 93 0.10
245 105 0.12
246 101 0.11
247 33 0.04
248 22 0.02
249 66 0.07
250 66 0.07
251 15 0.02
252 129 0.14
253 115 0.13
254 128 0.14
255 8 0.01
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (249 bp):
AATAATAAAAAGATAAAAATAATTATAATAAAATATAGCAATTTGAAAACCTTGAGTAAACCTAT
AAAATTAATGTAAAAAATTATAAAGGTGGAATAAGTATTGTCAAAATATTAACATAAATATGTGA
GATTTAACGTAATAAGTCAATTAAGTCAAATAAACATAATTACTAAAAAACTTAAACATTTAAAT
TTATATTATCTAACTAAAAGTATTTAACAATTTACAAATTTTAATTTATAAAGG
Found at i:1620533 original size:253 final size:251
Alignment explanation
Indices: 1619987--1620779 Score: 559
Period size: 254 Copynumber: 3.1 Consensus size: 251
1619977 ATCAAAGCAC
* * * * *
1619987 TGATGTAAATGTGTGAAATTTAACATAGCAAGTCCATTAAGTCAAAAT-ATATATAATT-TTTGT
1 TGATGTAAATAT-TGATATTT-ACATAACAAGTCAATTAAGTCAAAATGA-ATAT-ATTGTTTTT
* ** * * * * * * **
1620050 AAAAATTAAATGTTTAAGTTTATATTGT-TGAGCTAAAAGTTTTTAATTGTTTACAAATTTTAAT
62 GAAAATTAAAAATTAAAATTTATATTATCT-AACTAAAAGTATTAAATAATTTACAAATTTTAAT
* * * * * * * * * * * * * *
1620114 ATATAATGGAATAATAATGAGGATGAAAATACTTATAAT-TAAATTAGTAATTGATAAACCTTG-
126 TTATAAAGGAATAATAAAGAAGATAAAAATAATTATAGTGAAAAGTAGCAACTAAAAAAAC-TGA
* * * * * * * * ** * **
1620177 ACATAAACCTGTAAAAAGTACCGTAGAAAATAATAAAGGTGGAACTAGCATTATTAAAATAT
190 ACATAAACTTATAAAAATTAACATAAAAAATTATAAAAGTAAAACAAATATTATTAAAATAT
* * * *
1620239 TGACGTTAATGTCTAATATTTAACATAACAAGTCAATTAAGTCAAAAT-AAT-T-TT-TTTTTGA
1 TGATGTAAATAT-TGATATTT-ACATAACAAGTCAATTAAGTCAAAATGAATATATTGTTTTTG-
* * *
1620300 AAAAATTAAACATTTAAATTTATATTATC-AAGCTAAAAGTA-TAACATGCAGTTTACAAATTTT
63 -AAAATTAAAAATTAAAATTTATATTATCTAA-CTAAAAGTATTAA-AT--AATTTACAAATTTT
* * * * *
1620363 AATTTATAAATGAATAA-AAATAAGCATTAAAATAATTATAGTGACAATTAGCAACTAAAAAAAC
123 AATTTATAAAGGAATAATAAAGAAG-ATAAAAATAATTATAGTGAAAAGTAGCAACTAAAAAAAC
* * * * *
1620427 TTAACATAAACTTGTAAAAATTAGCATAAGAAATTATAAAAGTAAAACAAATATTGTTAAAATAT
187 TGAACATAAACTTATAAAAATTAACATAAAAAATTATAAAAGTAAAACAAATATTATTAAAATAT
* * *
1620492 TGATGTAAATATGTGATATTTACTATAATAAGTCTATTAAGTTAAAATGAATATAATTGTTTTTG
1 TGATGTAAATAT-TGATATTTAC-ATAACAAGTCAATTAAGTCAAAATGAATAT-ATTGTTTTTG
* * * *
1620557 AAAATTAAAAATTAAAATTTTTATTCTCTAATTAAAAGTATTTAATAATTTACAAATTTTAATTT
63 AAAATTAAAAATTAAAATTTATATTATCTAACTAAAAGTATTAAATAATTTACAAATTTTAATTT
* * * * * * *
1620622 ATAGAGGCATAATCACGAAGATAAAAATAATTATAGTGAAAAGTAGCAATTAAAAAACCTGGACA
128 ATAAAGGAATAATAAAGAAGATAAAAATAATTATAGTGAAAAGTAGCAACTAAAAAAACTGAACA
* * * * ** * *
1620687 TAAATTTATTAGAATTAACGTAAAAAATTATAAAAGTGGAATAAGTATTATTAAAATAT
193 TAAACTTATAAAAATTAACATAAAAAATTATAAAAGTAAAACAAATATTATTAAAATAT
* * *
1620746 TAATGTAAATA-TGATATTTAGCGTAGCAAGTCAA
1 TGATGTAAATATTGATATTTA-CATAACAAGTCAA
1620780 AATAATAAGT
Statistics
Matches: 428, Mismatches: 93, Indels: 40
0.76 0.17 0.07
Matches are distributed among these distances:
248 6 0.01
249 3 0.01
250 34 0.08
251 6 0.01
252 103 0.24
253 100 0.23
254 125 0.29
255 5 0.01
256 34 0.08
257 6 0.01
258 6 0.01
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (251 bp):
TGATGTAAATATTGATATTTACATAACAAGTCAATTAAGTCAAAATGAATATATTGTTTTTGAAA
ATTAAAAATTAAAATTTATATTATCTAACTAAAAGTATTAAATAATTTACAAATTTTAATTTATA
AAGGAATAATAAAGAAGATAAAAATAATTATAGTGAAAAGTAGCAACTAAAAAAACTGAACATAA
ACTTATAAAAATTAACATAAAAAATTATAAAAGTAAAACAAATATTATTAAAATAT
Found at i:1624311 original size:68 final size:68
Alignment explanation
Indices: 1624151--1624459 Score: 353
Period size: 68 Copynumber: 4.6 Consensus size: 68
1624141 CACATACATG
* * * *
1624151 CTTACTCATCTCATA-AGGTATACGGAATTTACATCATATACGTAATCTCATGGCATT--T-ATG
1 CTTAATCATCTCATATA-GTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCATG
*
1624212 CTTA
65 CATA
* * * * *
1624216 CTCAATCATCTCATGTAGGATATGGAATATACATCATATACATATTCTCATGGCATTAATGATGC
1 CTTAATCATCTCATATAGTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCATGC
1624281 ATA
66 ATA
* *
1624284 CTTAATCATCTCATGTAGTATATGGAATAATACATCATATACATATTCTCATGGCATTAATCATG
1 CTTAATCATCTCATATAGTATATGGAAT-TTACATCATATACATATTCTCATGGCATTAATCATG
1624349 CATA
65 CATA
* * * * *
1624353 CTTAATC-TCCTCATATGGTATATGGAATTTACATCATATACACCATCCT-ATAGTA-TACATCA
1 CTTAATCAT-CTCATATAGTATATGGAATTTACATCATATACA-TATTCTCATGGCATTA-ATCA
1624415 TGCATA
63 TGCATA
* *
1624421 CTTGATCATCTCATATGGTATATGGAATTTACATCATAT
1 CTTAATCATCTCATATAGTATATGGAATTTACATCATAT
1624460 GCCGTCTATA
Statistics
Matches: 215, Mismatches: 20, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
65 47 0.22
66 1 0.00
67 3 0.01
68 96 0.45
69 68 0.32
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (68 bp):
CTTAATCATCTCATATAGTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCATGC
ATA
Found at i:1624391 original size:137 final size:133
Alignment explanation
Indices: 1624151--1624459 Score: 340
Period size: 137 Copynumber: 2.3 Consensus size: 133
1624141 CACATACATG
* * * * *
1624151 CTTACTCATCTCATA-AGGTATACGGAATTTACATCATATACGTAATCTCATGGCATTTATGCTT
1 CTTAATCATCTCATATA-GTATATGGAATATACATCATATACATAATCTCATGGCATTTATGCAT
* * * * *
1624215 ACTCAATCATCTCATGTAGGATATGGAATATACATCATATACA-TATTCTCATGGCATTA-ATGA
65 ACTCAATCATCTCATATAGGATATGGAATATACATCATATACACCATCCT-ATAGCA-TACATCA
1624278 TGCATA
128 TGCATA
* *
1624284 CTTAATCATCTCATGTAGTATATGGAATAATACATCATATACATATTCTCATGGCATTAATCATG
1 CTTAATCATCTCATATAGTATATGGAAT-ATACATCATATACATAATCTCATGGCATT--T-ATG
* * *
1624349 CATACTTAATC-TCCTCATAT-GGTATATGGAATTTACATCATATACACCATCCTATAGTATACA
62 CATACTCAATCAT-CTCATATAGG-ATATGGAATATACATCATATACACCATCCTATAGCATACA
1624412 TCATGCATA
125 TCATGCATA
* * *
1624421 CTTGATCATCTCATATGGTATATGGAATTTACATCATAT
1 CTTAATCATCTCATATAGTATATGGAATATACATCATAT
1624460 GCCGTCTATA
Statistics
Matches: 148, Mismatches: 19, Indels: 15
0.81 0.10 0.08
Matches are distributed among these distances:
133 23 0.16
134 27 0.18
136 16 0.11
137 78 0.53
138 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (133 bp):
CTTAATCATCTCATATAGTATATGGAATATACATCATATACATAATCTCATGGCATTTATGCATA
CTCAATCATCTCATATAGGATATGGAATATACATCATATACACCATCCTATAGCATACATCATGC
ATA
Found at i:1638924 original size:17 final size:16
Alignment explanation
Indices: 1638897--1638928 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1638887 TAACATGTTG
1638897 GTAATAAATATAAATA
1 GTAATAAATATAAATA
1638913 GTAATCAAATATAAAT
1 GTAAT-AAATATAAAT
1638929 TTCATAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
GTAATAAATATAAATA
Found at i:1642276 original size:25 final size:25
Alignment explanation
Indices: 1642243--1642290 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1642233 GTGGTCGCAA
* *
1642243 TCACTTATATCAACTTGTGGCCTAG
1 TCACGTATATCAACCTGTGGCCTAG
1642268 TCACGTATATCAACCTGTGGCCT
1 TCACGTATATCAACCTGTGGCCT
1642291 TGCCACATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (25 bp):
TCACGTATATCAACCTGTGGCCTAG
Found at i:1645271 original size:33 final size:31
Alignment explanation
Indices: 1645211--1645271 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
1645201 GTTAACAACA
**
1645211 AATAAAATATTAATATTTTAATTTTTTTATT
1 AATAAAATATTAATATTTTAAAATTTTTATT
*
1645242 AATAAAATATTATTTTATTTTAAAATTTTT
1 AATAAAATATTA--ATATTTTAAAATTTTT
1645272 CACTTGTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 12 0.48
33 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
AATAAAATATTAATATTTTAAAATTTTTATT
Found at i:1650093 original size:210 final size:213
Alignment explanation
Indices: 1649478--1650105 Score: 681
Period size: 214 Copynumber: 2.9 Consensus size: 213
1649468 TTCCTTAGGG
* * * *
1649478 GAGATACTTAGAAG-AAAATTTAA-TTTTTATTAATTTATTTTAATTTTTAAAAAAAATTAGTAC
1 GAGATACTTACAAGCAAAA-TTAATTTTTTATTAATTTA-TTTAATTTTTTAAAAAAATTAATAA
* * *
1649541 TGTTAACTTTTAAAAGCGTGCGACTCTTTCTTACATAT-AGAATATTTCTTAACGACTCGCGCGA
64 TATTAACTTTTAAAA-CGTGCGACTCTTTCTTACATATAAG-ATATTCCTTAACGACTCGTGCGA
* *
1649605 TTCATGAGAAGAGAACAAAGAATTTATTTTTTAGAAC-AGTGAAAAATATAGTAAGAGGGCAAAG
127 TTCATGAGAAGAGAA-TAAGAATTTATTTTTTAGAACAAG-G-AAAATATAGTAAGAGGCCAAAG
*
1649669 TACTAGGTTCCAAAAAGTTCGAAGA
189 TACTAGCTTCCAAAAAGTTCGAAGA
*
1649694 GAGATACTTACAAGCAAAA-TGATTTTTTATTAATTTATTTAA-TTTTTAAAAAAATTAATAATA
1 GAGATACTTACAAGCAAAATTAATTTTTTATTAATTTATTTAATTTTTTAAAAAAATTAATAATA
* * * * * * * *
1649757 GTAACTTTACAAAACGTGCTACTCTTTCTTACCTATATGGTATTCCTTAATC-ACTCATGTGA-T
66 TTAACTTT-TAAAACGTGCGACTCTTTCTTACATATAAGATATTCCTTAA-CGACTCGTGCGATT
* *
1649820 CTATGAGAAGTGAATAATGAATTTATTTTTTAGAATAATGGAAAATATAGTAAGAGGCCAAAGTA
129 C-ATGAGAAGAGAATAA-GAATTTATTTTTTAGAACAA-GGAAAATATAGTAAGAGGCCAAAGTA
***
1649885 CTAGCTTCCAAAAA-TTTTTAG-
191 CTAGCTTCCAAAAAGTTCGAAGA
* * * * *
1649906 G-GGTACTTGCAAGCAAAATTAATTTTTTATTAATTTATTGAATTTTTTTAAAAAA-TAATATTA
1 GAGATACTTACAAGCAAAATTAATTTTTTATTAATTTATTTAATTTTTTAAAAAAATTAATAATA
* *
1649969 TTAA-TTTTAAAACATGCGACTCTTTCTTACATATAAGATATTGCTTCAA-GACTCGTGCGATTC
66 TTAACTTTTAAAACGTGCGACTCTTTCTTACATATAAGATATTCCTT-AACGACTCGTGCGATTC
* * * * * * *
1650032 ATGTGACGAGAATGAAGAATTTATCTTTTAGGACAAGGAAATGTATAGTAAGAGTCCAAAGTAGT
130 ATGAGAAGAGAAT-AAGAATTTATTTTTTAGAACAAGGAAA-ATATAGTAAGAGGCCAAAGTACT
1650097 AGCTTCCAA
193 AGCTTCCAA
1650106 CAGGTTTTAA
Statistics
Matches: 347, Mismatches: 49, Indels: 38
0.80 0.11 0.09
Matches are distributed among these distances:
209 5 0.01
210 96 0.28
211 24 0.07
212 32 0.09
213 19 0.05
214 124 0.36
215 15 0.04
216 28 0.08
217 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (213 bp):
GAGATACTTACAAGCAAAATTAATTTTTTATTAATTTATTTAATTTTTTAAAAAAATTAATAATA
TTAACTTTTAAAACGTGCGACTCTTTCTTACATATAAGATATTCCTTAACGACTCGTGCGATTCA
TGAGAAGAGAATAAGAATTTATTTTTTAGAACAAGGAAAATATAGTAAGAGGCCAAAGTACTAGC
TTCCAAAAAGTTCGAAGA
Found at i:1657900 original size:8 final size:8
Alignment explanation
Indices: 1657866--1657971 Score: 66
Period size: 8 Copynumber: 14.2 Consensus size: 8
1657856 TCGGGTTAAC
1657866 CTTCCTTT
1 CTTCCTTT
*
1657874 C-TCTTTT
1 CTTCCTTT
1657881 CTT-C-TT
1 CTTCCTTT
*
1657887 CCTCCTTT
1 CTTCCTTT
1657895 CTTCCTTT
1 CTTCCTTT
*
1657903 CTTTCTTT
1 CTTCCTTT
* *
1657911 -GTCTTTT
1 CTTCCTTT
1657918 CTT-CTTT
1 CTTCCTTT
*
1657925 C-TCTTTT
1 CTTCCTTT
*
1657932 ATTCCTTT
1 CTTCCTTT
*
1657940 CTTTCTTT
1 CTTCCTTT
*
1657948 CTTTCTTT
1 CTTCCTTT
*
1657956 CTTTC-TT
1 CTTCCTTT
1657963 CTT-CTTT
1 CTTCCTTT
1657970 CT
1 CT
1657972 CAACTCTTCC
Statistics
Matches: 76, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
6 6 0.08
7 27 0.36
8 43 0.57
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.68
Consensus pattern (8 bp):
CTTCCTTT
Found at i:1657908 original size:4 final size:4
Alignment explanation
Indices: 1657891--1657971 Score: 73
Period size: 4 Copynumber: 21.5 Consensus size: 4
1657881 CTTCTTCCTC
* * * * * *
1657891 CTTT CTTC CTTT CTTT CTTT GTCT -TTT C-TT CTTT CTCT -TTT ATTC
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1657936 CTTT CTTT CTTT CTTT CTTT CTTT C-TT C-TT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
1657972 CAACTCTTCC
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
3 13 0.21
4 50 0.79
ACGTcount: A:0.01, C:0.27, G:0.01, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:1657917 original size:37 final size:37
Alignment explanation
Indices: 1657870--1657963 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
1657860 GTTAACCTTC
*
1657870 CTTTCTCTTTTCTTCTTCCTCCTTTCTTCCTTTCTTT
1 CTTTCTCTTTTCTTCTTCCTCCTTTATTCCTTTCTTT
* * *
1657907 CTTTGTCTTTTCTTCTTTCTCTTTTATTCCTTTCTTT
1 CTTTCTCTTTTCTTCTTCCTCCTTTATTCCTTTCTTT
*
1657944 CTTTCTTTCTTTCTTTCTTC
1 CTTTCTCT-TTTC-TTCTTC
1657964 TTCTTTCTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 39 0.81
38 4 0.08
39 5 0.10
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.68
Consensus pattern (37 bp):
CTTTCTCTTTTCTTCTTCCTCCTTTATTCCTTTCTTT
Found at i:1657924 original size:45 final size:44
Alignment explanation
Indices: 1657871--1657972 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 44
1657861 TTAACCTTCC
* *
1657871 TTTC-TCTTT-TCTTCTTCCTCCTTTCTTCCTTTCTTTCTTTGTCT
1 TTTCTTCTTTCTCTT-TTACTCCTTTCTTCCTTTCTTTCTTTCT-T
* *
1657915 TTTCTTCTTTCTCTTTTATTCCTTTCTTTCTTTCTTTCTTTCTT
1 TTTCTTCTTTCTCTTTTACTCCTTTCTTCCTTTCTTTCTTTCTT
1657959 TCTTCTTCTTTCTC
1 T-TTCTTCTTTCTC
1657973 AACTCTTCCT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
44 6 0.12
45 41 0.80
46 4 0.08
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (44 bp):
TTTCTTCTTTCTCTTTTACTCCTTTCTTCCTTTCTTTCTTTCTT
Found at i:1657982 original size:45 final size:45
Alignment explanation
Indices: 1657889--1657988 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
1657879 TTCTTCTTCC
* ***
1657889 TCCTTTCTTCCTTTCTTTCTTTGTCTTTTCTTCTTTCTCTTTTAT
1 TCCTTTCTTCCTTTCTTTCTTTCTCTTTTCTTCTTTCTCAACTAT
* *
1657934 TCCTTTCTTTCTTTCTTTCTTTCT-TTCTTCTTCTTTCTCAACTCT
1 TCCTTTCTTCCTTTCTTTCTTTCTCTT-TTCTTCTTTCTCAACTAT
*
1657979 TCCTCTCTTC
1 TCCTTTCTTC
1657989 TAGAGTGAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 2 0.04
45 44 0.96
ACGTcount: A:0.03, C:0.31, G:0.01, T:0.65
Consensus pattern (45 bp):
TCCTTTCTTCCTTTCTTTCTTTCTCTTTTCTTCTTTCTCAACTAT
Found at i:1672831 original size:23 final size:24
Alignment explanation
Indices: 1672797--1672845 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
1672787 ATCTTTTTAT
1672797 TTAAAAATTATTTATTAT-TTAATA
1 TTAAAAATTATTT-TTATATTAATA
1672821 TTAAAAA-TATTTTTATATTAATA
1 TTAAAAATTATTTTTATATTAATA
1672844 TT
1 TT
1672846 TTAACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 4 0.17
23 13 0.54
24 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAAAAATTATTTTTATATTAATA
Found at i:1688266 original size:58 final size:58
Alignment explanation
Indices: 1688181--1688293 Score: 181
Period size: 58 Copynumber: 1.9 Consensus size: 58
1688171 CATCTTTCCA
* * *
1688181 TGCATAGCATTTATTGAATCGCATAAAATAAATCTATCACATGCATACTACTTTGCAT
1 TGCATAGCATTCATTAAATCGCATAAAATAAATCTATCACATGCAAACTACTTTGCAT
* *
1688239 TGCATAGCATTCGTTAAATTGCATAAAATAAATCTATCACATGCAAACTACTTTG
1 TGCATAGCATTCATTAAATCGCATAAAATAAATCTATCACATGCAAACTACTTTG
1688294 GATGATTATG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (58 bp):
TGCATAGCATTCATTAAATCGCATAAAATAAATCTATCACATGCAAACTACTTTGCAT
Found at i:1708098 original size:12 final size:12
Alignment explanation
Indices: 1708081--1708120 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1708071 TTTGTGCTTT
1708081 ATTAATTATTTA
1 ATTAATTATTTA
1708093 ATTAATTATTT-
1 ATTAATTATTTA
1708104 ATT--TTAATTTA
1 ATTAATT-ATTTA
1708115 ATTAAT
1 ATTAAT
1708121 CCTTGGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
9 2 0.08
10 4 0.17
11 6 0.25
12 11 0.46
13 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTAATTATTTA
Found at i:1723550 original size:60 final size:60
Alignment explanation
Indices: 1723477--1723595 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
1723467 ATTTGAGTTT
*
1723477 CAACTAGCATTTGTATACCCTTCTAAAACTGAAGGAAAACTTGAGTAACAAATACCATAC
1 CAACTAGCATTTGTATACCCTTCTAAAACTGAAGGAAAACCTGAGTAACAAATACCATAC
1723537 CAACTAGCATTTGTATACCCTTCTAAAACTGAAGGAAAACCTGAGTAACAAATACCATA
1 CAACTAGCATTTGTATACCCTTCTAAAACTGAAGGAAAACCTGAGTAACAAATACCATA
1723596 ATTCTTTGTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (60 bp):
CAACTAGCATTTGTATACCCTTCTAAAACTGAAGGAAAACCTGAGTAACAAATACCATAC
Found at i:1726793 original size:15 final size:17
Alignment explanation
Indices: 1726773--1726805 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1726763 TGTAGGTTCA
1726773 ATACTTT-TA-TTTTTT
1 ATACTTTCTAGTTTTTT
1726788 ATACTTTCTAGTTTTTT
1 ATACTTTCTAGTTTTTT
1726805 A
1 A
1726806 CCATTAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.67
Consensus pattern (17 bp):
ATACTTTCTAGTTTTTT
Found at i:1730399 original size:28 final size:28
Alignment explanation
Indices: 1730335--1730400 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
1730325 CTACTAATTA
1730335 AAGGTTCAAGGATAACCATTGTCTTTTC
1 AAGGTTCAAGGATAACCATTGTCTTTTC
** * *
1730363 AAGAATCAAGTATAACTATTGTCTTTTC
1 AAGGTTCAAGGATAACCATTGTCTTTTC
1730391 AAGGTTCAAG
1 AAGGTTCAAG
1730401 CACAACCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (28 bp):
AAGGTTCAAGGATAACCATTGTCTTTTC
Found at i:1731314 original size:13 final size:13
Alignment explanation
Indices: 1731296--1731322 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1731286 TCTTTTCACA
1731296 AACAAGTTCAAAG
1 AACAAGTTCAAAG
1731309 AACAAGTTCAAAG
1 AACAAGTTCAAAG
1731322 A
1 A
1731323 TCATTCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
AACAAGTTCAAAG
Found at i:1732521 original size:10 final size:10
Alignment explanation
Indices: 1732488--1732570 Score: 58
Period size: 10 Copynumber: 7.9 Consensus size: 10
1732478 ATCATTAGTT
1732488 ATCAAGCATC
1 ATCAAGCATC
*
1732498 ATTCCTAATCATC
1 A-T-C-AAGCATC
*
1732511 ATCAAGGATC
1 ATCAAGCATC
*
1732521 ATTAAGCATTC
1 ATCAAGCA-TC
***
1732532 ATCAATTTTC
1 ATCAAGCATC
*
1732542 ATCAAGGATC
1 ATCAAGCATC
*
1732552 ATTAAGCATC
1 ATCAAGCATC
1732562 ATCAAGCAT
1 ATCAAGCAT
1732571 TACCAAGCAA
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
10 37 0.69
11 8 0.15
12 2 0.04
13 7 0.13
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (10 bp):
ATCAAGCATC
Found at i:1732545 original size:31 final size:30
Alignment explanation
Indices: 1732509--1732566 Score: 107
Period size: 31 Copynumber: 1.9 Consensus size: 30
1732499 TTCCTAATCA
1732509 TCATCAAGGATCATTAAGCATTCATCAATTT
1 TCATCAAGGATCATTAAGCA-TCATCAATTT
1732540 TCATCAAGGATCATTAAGCATCATCAA
1 TCATCAAGGATCATTAAGCATCATCAA
1732567 GCATTACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (30 bp):
TCATCAAGGATCATTAAGCATCATCAATTT
Found at i:1737583 original size:18 final size:18
Alignment explanation
Indices: 1737552--1737586 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1737542 AGATTTCTCA
* *
1737552 ATTAGTATCTAGCTTTAC
1 ATTAGCATCAAGCTTTAC
1737570 ATTAGCATCAAGCTTTA
1 ATTAGCATCAAGCTTTA
1737587 AATTGATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (18 bp):
ATTAGCATCAAGCTTTAC
Found at i:1740991 original size:34 final size:34
Alignment explanation
Indices: 1740953--1741082 Score: 113
Period size: 34 Copynumber: 3.9 Consensus size: 34
1740943 ATGTTGAATG
**
1740953 TTGTGCTTGATTATTTGAAAAGGCATTGTGAGGA
1 TTGTGCTTGATCCTTTGAAAAGGCATTGTGAGGA
* *
1740987 TTGTGCTTGA-CCCTTGAAAAGGCATTGTGA-AA
1 TTGTGCTTGATCCTTTGAAAAGGCATTGTGAGGA
* * ** * *
1741019 GTTATGCTTAATTTTTTGAAAGGGCATTATGAAGG-
1 -TTGTGCTTGATCCTTTGAAAAGGCATTGTG-AGGA
* *
1741054 TTGTACTTGATCCTTTGAAAAGGTATTGT
1 TTGTGCTTGATCCTTTGAAAAGGCATTGT
1741083 AAAGATTATG
Statistics
Matches: 72, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
32 1 0.01
33 25 0.35
34 45 0.62
35 1 0.01
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.38
Consensus pattern (34 bp):
TTGTGCTTGATCCTTTGAAAAGGCATTGTGAGGA
Found at i:1741027 original size:33 final size:35
Alignment explanation
Indices: 1740967--1741097 Score: 101
Period size: 34 Copynumber: 3.9 Consensus size: 35
1740957 GCTTGATTAT
* *
1740967 TTGAAAAGGCATTGTG-AGGATTGTGCTTGA-CCC
1 TTGAAAAGGCATTGTGAAAGATTATGCTTGATCCC
* ***
1741000 TTGAAAAGGCATTGTGAAAG-TTATGCTTAATTTT
1 TTGAAAAGGCATTGTGAAAGATTATGCTTGATCCC
* * * * * *
1741034 TTGAAAGGGCATTATG-AAGGTTGTACTTGATCCT
1 TTGAAAAGGCATTGTGAAAGATTATGCTTGATCCC
* *
1741068 TTGAAAAGGTATTGT-AAAGATTATGTTTGA
1 TTGAAAAGGCATTGTGAAAGATTATGCTTGA
1741098 GTCTTGAAAA
Statistics
Matches: 74, Mismatches: 20, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
33 27 0.36
34 47 0.64
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.37
Consensus pattern (35 bp):
TTGAAAAGGCATTGTGAAAGATTATGCTTGATCCC
Found at i:1741045 original size:67 final size:68
Alignment explanation
Indices: 1740947--1741092 Score: 172
Period size: 67 Copynumber: 2.2 Consensus size: 68
1740937 AAGATAATGT
* * * * *
1740947 TGAATGTTGTGCTTGATTATTTGAAAAGGCATTGTG-AGGATTGTGCTTGA-CCCTTGAAAAGGC
1 TGAAAGTTATGCTTAATTATTTGAAAAGGCATTATGAAGG-TTGTACTTGATCCCTTGAAAAGGC
1741010 ATTG
65 ATTG
* * * *
1741014 TGAAAGTTATGCTTAATTTTTTGAAAGGGCATTATGAAGGTTGTACTTGATCCTTTGAAAAGGTA
1 TGAAAGTTATGCTTAATTATTTGAAAAGGCATTATGAAGGTTGTACTTGATCCCTTGAAAAGGCA
1741079 TTG
66 TTG
1741082 T-AAAGATTATG
1 TGAAAG-TTATG
1741093 TTTGAGTCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
67 43 0.64
68 24 0.36
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (68 bp):
TGAAAGTTATGCTTAATTATTTGAAAAGGCATTATGAAGGTTGTACTTGATCCCTTGAAAAGGCA
TTG
Found at i:1741105 original size:67 final size:67
Alignment explanation
Indices: 1740967--1741107 Score: 153
Period size: 67 Copynumber: 2.1 Consensus size: 67
1740957 GCTTGATTAT
* * *
1740967 TTGAAAAGGCATTGTGAGGATTGTGCTTGACCCTTGAAAAGGCATTGTGAAAGTTATGCTTAATT
1 TTGAAAAGGCATTATGAGGATTGTACTTGACCCTTGAAAAGGCATTGTGAAAGTTATGCTTAATG
*
1741032 TT
66 TC
* * * * *
1741034 TTGAAAGGGCATTATGAAGG-TTGTACTTGATCCTTTGAAAAGGTATTGT-AAAGATTATGTTTG
1 TTGAAAAGGCATTATG-AGGATTGTACTTGA-CCCTTGAAAAGGCATTGTGAAAG-TTATGCTTA
1741097 A-GTC
63 ATGTC
1741101 TTGAAAA
1 TTGAAAA
1741108 AGTATTTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
67 34 0.56
68 27 0.44
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (67 bp):
TTGAAAAGGCATTATGAGGATTGTACTTGACCCTTGAAAAGGCATTGTGAAAGTTATGCTTAATG
TC
Found at i:1743505 original size:19 final size:20
Alignment explanation
Indices: 1743478--1743515 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1743468 TCTAACGCCG
1743478 GGGCATTGT-AAAGACACTT
1 GGGCATTGTGAAAGACACTT
* *
1743497 GGGCGTTGTGAAGGACACT
1 GGGCATTGTGAAAGACACT
1743516 AATCGTGACG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGCATTGTGAAAGACACTT
Found at i:1748048 original size:2 final size:2
Alignment explanation
Indices: 1748041--1748070 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1748031 TGTGAAGTCA
1748041 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
1748071 CAATTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1751449 original size:16 final size:17
Alignment explanation
Indices: 1751428--1751460 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1751418 TAATATATTT
1751428 TTATGTCATAT-TAATA
1 TTATGTCATATATAATA
*
1751444 TTATGTGATATATAATA
1 TTATGTCATATATAATA
1751461 AAATAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (17 bp):
TTATGTCATATATAATA
Found at i:1753622 original size:54 final size:54
Alignment explanation
Indices: 1753539--1753646 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
1753529 TGTAAAACAA
1753539 CAATAGCGAGCTATGCTCATACGTATATCAATCTCACAGCATTGAGTTCCCAAG
1 CAATAGCGAGCTATGCTCATACGTATATCAATCTCACAGCATTGAGTTCCCAAG
*
1753593 CAATAGCGAGCTATGCTCATACGTGTATCAATCTCACAGCATTGAGTTCCCAAG
1 CAATAGCGAGCTATGCTCATACGTATATCAATCTCACAGCATTGAGTTCCCAAG
1753647 GCCAAAAAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (54 bp):
CAATAGCGAGCTATGCTCATACGTATATCAATCTCACAGCATTGAGTTCCCAAG
Found at i:1754317 original size:16 final size:16
Alignment explanation
Indices: 1754296--1754335 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1754286 TAACGTCTCA
1754296 TACCTTGATCTAGGTC
1 TACCTTGATCTAGGTC
*
1754312 TACCTTGATCTGGGTC
1 TACCTTGATCTAGGTC
1754328 TACCTTGA
1 TACCTTGA
1754336 CCATGATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (16 bp):
TACCTTGATCTAGGTC
Found at i:1756367 original size:20 final size:19
Alignment explanation
Indices: 1756319--1756368 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1756309 ATGTTGGAAG
*
1756319 GCTCAAAGAAATTAATTGGA
1 GCTC-AAGAAAGTAATTGGA
**
1756339 GCTTGAGAAAGTAATTTGGA
1 GCTCAAGAAAGTAA-TTGGA
1756359 GCTCAAGAAA
1 GCTCAAGAAA
1756369 CTATTGGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (19 bp):
GCTCAAGAAAGTAATTGGA
Found at i:1759329 original size:80 final size:79
Alignment explanation
Indices: 1759241--1759529 Score: 346
Period size: 80 Copynumber: 3.6 Consensus size: 79
1759231 TATCATCATA
* * * *
1759241 CTTAGCCCATAGTGTATATGACTATCTCAACACATATATCTCATGGCATACATTTCATAACTTCT
1 CTTAGCCCATAGTGTACATGA-TATCTCAACACATACATCTCATGGCATACATTTCATAACCTCA
1759306 TAAATCACTTACATG
65 TAAATCACTTACATG
* * *** * * * *
1759321 CTTAGCCCATAGTATATATGACTATCTCAATGTATTC-TCTTATGGTATACATTTCAAAACCTCA
1 CTTAGCCCATAGTGTACATGA-TATCTCAACACATACATCTCATGGCATACATTTCATAACCTCA
*
1759385 TAGATCACTTACATG
65 TAAATCACTTACATG
* * *
1759400 CTTAGCCCATAGTGTACATGATATACTTATCACATACATCTCACGGCATACATTTCATAACCTCA
1 CTTAGCCCATAGTGTACATGATAT-CTCAACACATACATCTCATGGCATACATTTCATAACCTCA
*
1759465 TAAATCACTTACACG
65 TAAATCACTTACATG
* * *
1759480 CGTAGCCCATAGTGTACATGATACACTTAACACATACATCTCATGGCATA
1 CTTAGCCCATAGTGTACATGATA-TCTCAACACATACATCTCATGGCATA
1759530 TATGTTACAA
Statistics
Matches: 176, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
78 3 0.02
79 61 0.35
80 112 0.64
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (79 bp):
CTTAGCCCATAGTGTACATGATATCTCAACACATACATCTCATGGCATACATTTCATAACCTCAT
AAATCACTTACATG
Found at i:1761329 original size:74 final size:73
Alignment explanation
Indices: 1761234--1761415 Score: 206
Period size: 74 Copynumber: 2.5 Consensus size: 73
1761224 CTCTTAGTTG
* * *
1761234 ACTAACATACTTCTTAGTTGACTAAGTCTTTTCTATCTTCT-ACTCT-CAGTTTTTGGAAGTGAG
1 ACTAACATACTTCTTGGTTGACTAAGTCTTTTCTATCTTCTGA-T-TGAAGTTTCTGGAAGTGAG
*
1761297 CATTTAGTCA
64 CACTTAGTCA
* * **
1761307 ACTAATCATACTTCTTGGTTGACTAAGTCTTTTCTATTTTTTGATTGAAGTTTCTGGCTGTGAGC
1 ACTAA-CATACTTCTTGGTTGACTAAGTCTTTTCTATCTTCTGATTGAAGTTTCTGGAAGTGAGC
*
1761372 ACTTAGTCG
65 ACTTAGTCA
* * *
1761381 ACTAACCATGCTTCTTGGTCGACTACGTCTTTTCT
1 ACTAA-CATACTTCTTGGTTGACTAAGTCTTTTCT
1761416 GTTTCTGGAT
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
73 6 0.06
74 86 0.92
75 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (73 bp):
ACTAACATACTTCTTGGTTGACTAAGTCTTTTCTATCTTCTGATTGAAGTTTCTGGAAGTGAGCA
CTTAGTCA
Found at i:1766133 original size:2 final size:2
Alignment explanation
Indices: 1766126--1766154 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1766116 TCTTCATGTT
1766126 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1766155 TTTTATTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1768253 original size:22 final size:22
Alignment explanation
Indices: 1768225--1768275 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1768215 TAGCTTTTAC
1768225 TATGTATACT-CATATATATATA
1 TATGTATA-TGCATATATATATA
* *
1768247 TATGTATATGTATATATATGTA
1 TATGTATATGCATATATATATA
1768269 TATGTAT
1 TATGTAT
1768276 GTATAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (22 bp):
TATGTATATGCATATATATATA
Found at i:1768272 original size:6 final size:6
Alignment explanation
Indices: 1768239--1768275 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1768229 TATACTCATA
*
1768239 TATATA TATATG TATATG TATA-- TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TAT
1768276 GTATAATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
4 4 0.14
6 24 0.86
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:1768272 original size:16 final size:16
Alignment explanation
Indices: 1768236--1768280 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1768226 ATGTATACTC
*
1768236 ATATATATATATATGT
1 ATATGTATATATATGT
1768252 ATATGTATATATATGT
1 ATATGTATATATATGT
*
1768268 ATATGTATGTATA
1 ATATGTATATATA
1768281 ATTCATGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (16 bp):
ATATGTATATATATGT
Found at i:1768276 original size:10 final size:10
Alignment explanation
Indices: 1768237--1768280 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
1768227 TGTATACTCA
*
1768237 TATATATATA
1 TATATATATG
*
1768247 TATGTATATG
1 TATATATATG
1768257 TATATATATG
1 TATATATATG
*
1768267 TATATGTATG
1 TATATATATG
1768277 TATA
1 TATA
1768281 ATTCATGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:1776948 original size:21 final size:21
Alignment explanation
Indices: 1776922--1776978 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
1776912 TGCTCATGCT
1776922 ATTCATGAAAAAGACTGATAC
1 ATTCATGAAAAAGACTGATAC
* *
1776943 ATTCAT-AACAAAGATTGATGC
1 ATTCATGAA-AAAGACTGATAC
*
1776964 AGTT-ATGATAAAGAC
1 A-TTCATGAAAAAGAC
1776979 AAATGCCTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 2 0.07
21 24 0.83
22 3 0.10
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (21 bp):
ATTCATGAAAAAGACTGATAC
Found at i:1787310 original size:28 final size:28
Alignment explanation
Indices: 1787270--1787326 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1787260 AAGTCCCATA
*
1787270 TAAAGCTTTTCCAGGAAACCAAAAGAAT
1 TAAAGCTTTTCCAAGAAACCAAAAGAAT
*
1787298 TAAAGCTTTTCCAAGAAACCAGAAGAAT
1 TAAAGCTTTTCCAAGAAACCAAAAGAAT
1787326 T
1 T
1787327 CTATCATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.23
Consensus pattern (28 bp):
TAAAGCTTTTCCAAGAAACCAAAAGAAT
Found at i:1807981 original size:31 final size:33
Alignment explanation
Indices: 1807941--1808001 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1807931 CTCTCAACAT
*
1807941 AATGCCTTTT-AGGGATAA-GCACAACCTTCAC
1 AATGCCTTTTAAAGGATAAGGCACAACCTTCAC
* *
1807972 AATGGCTTTTAAAGGCTAAGGCACAACCTT
1 AATGCCTTTTAAAGGATAAGGCACAACCTT
1808002 TTCTCTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.36
32 6 0.24
33 10 0.40
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (33 bp):
AATGCCTTTTAAAGGATAAGGCACAACCTTCAC
Found at i:1808608 original size:22 final size:21
Alignment explanation
Indices: 1808579--1808620 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1808569 AACAAGTTCT
1808579 AAAATCATTAAAGCAATTTTC
1 AAAATCATTAAAGCAATTTTC
* *
1808600 AAAACTCATTCAAGTAATTTT
1 AAAA-TCATTAAAGCAATTTT
1808621 GGAACTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAATCATTAAAGCAATTTTC
Found at i:1808702 original size:21 final size:21
Alignment explanation
Indices: 1808676--1808742 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1808666 AAAAAAGCTG
1808676 AAAAACTATTTAAACAAGTTC
1 AAAAACTATTTAAACAAGTTC
* * *
1808697 AAAAACTCATTCAAA-TAGCTTT
1 AAAAACT-ATTTAAACAAG-TTC
*
1808719 AAAAAAT-TTTCAAACAAGTTC
1 AAAAACTATTT-AAACAAGTTC
1808740 AAA
1 AAA
1808743 GATCATTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
20 2 0.06
21 17 0.49
22 16 0.46
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAACTATTTAAACAAGTTC
Found at i:1808894 original size:21 final size:21
Alignment explanation
Indices: 1808870--1808910 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1808860 CAAAAGTTTT
* *
1808870 TCAAACAATTTCAAGGATCAC
1 TCAAACAAGTTCAAAGATCAC
*
1808891 TCAAAGAAGTTCAAAGATCA
1 TCAAACAAGTTCAAAGATCA
1808911 TTGAAGAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (21 bp):
TCAAACAAGTTCAAAGATCAC
Found at i:1815136 original size:24 final size:23
Alignment explanation
Indices: 1815109--1815156 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1815099 TCCAAATAGT
1815109 TCTTG-GCTTCTCCTTTGCTGCCTC
1 TCTTGCGCTTCT-C-TTGCTGCCTC
1815133 TCTTGCTGCTTCTCTTGCTGCCTC
1 TCTTGC-GCTTCTCTTGCTGCCTC
1815157 AAAAATCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 15 0.68
25 1 0.05
26 6 0.27
ACGTcount: A:0.00, C:0.38, G:0.17, T:0.46
Consensus pattern (23 bp):
TCTTGCGCTTCTCTTGCTGCCTC
Found at i:1815140 original size:12 final size:12
Alignment explanation
Indices: 1815123--1815156 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1815113 GGCTTCTCCT
1815123 TTGCTGCCTCTC
1 TTGCTGCCTCTC
*
1815135 TTGCTGCTTCTC
1 TTGCTGCCTCTC
1815147 TTGCTGCCTC
1 TTGCTGCCTC
1815157 AAAAATCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.38, G:0.18, T:0.44
Consensus pattern (12 bp):
TTGCTGCCTCTC
Found at i:1830975 original size:33 final size:33
Alignment explanation
Indices: 1830938--1831010 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
1830928 AAAGGTTTAA
1830938 CTTGATCCCATGAAAA-GCATCGTAAGGGTTT-T
1 CTTGATCCCAT-AAAATGCATCGTAAGGGTTTCT
* *
1830970 GCTTGATCCCATAAAATGCATTGTGAGGGTTTCT
1 -CTTGATCCCATAAAATGCATCGTAAGGGTTTCT
1831004 CTTGATC
1 CTTGATC
1831011 TCGTAAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 4 0.11
33 31 0.86
34 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (33 bp):
CTTGATCCCATAAAATGCATCGTAAGGGTTTCT
Found at i:1837215 original size:23 final size:23
Alignment explanation
Indices: 1837189--1837234 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1837179 TCCCCTTGTT
*
1837189 TCATTTGTTTCCTTGATTTGGGG
1 TCATTTATTTCCTTGATTTGGGG
1837212 TCATTTATTTCCTTGATTTGGGG
1 TCATTTATTTCCTTGATTTGGGG
1837235 ACGGCAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.13, G:0.24, T:0.52
Consensus pattern (23 bp):
TCATTTATTTCCTTGATTTGGGG
Found at i:1838553 original size:22 final size:22
Alignment explanation
Indices: 1838525--1838571 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1838515 GCACAATACG
1838525 ACTGTGCTTGCTTGTCTGTCGT
1 ACTGTGCTTGCTTGTCTGTCGT
*
1838547 ACTGTGCTTGCTTGTCTGTTGT
1 ACTGTGCTTGCTTGTCTGTCGT
1838569 ACT
1 ACT
1838572 TTTATTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.06, C:0.21, G:0.26, T:0.47
Consensus pattern (22 bp):
ACTGTGCTTGCTTGTCTGTCGT
Found at i:1840268 original size:41 final size:42
Alignment explanation
Indices: 1840210--1840298 Score: 171
Period size: 41 Copynumber: 2.1 Consensus size: 42
1840200 TATTGAATCA
1840210 GAGAGTAAAATGAAGTCTTATCTATTAGACCTAGTAACTAAT
1 GAGAGTAAAATGAAGTCTTATCTATTAGACCTAGTAACTAAT
1840252 -AGAGTAAAATGAAGTCTTATCTATTAGACCTAGTAACTAAT
1 GAGAGTAAAATGAAGTCTTATCTATTAGACCTAGTAACTAAT
1840293 GAGAGT
1 GAGAGT
1840299 TGCCAAAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 41 0.89
42 5 0.11
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.30
Consensus pattern (42 bp):
GAGAGTAAAATGAAGTCTTATCTATTAGACCTAGTAACTAAT
Found at i:1841145 original size:17 final size:16
Alignment explanation
Indices: 1841114--1841155 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
1841104 TAAATTAAAC
*
1841114 ATATGAAATTGACTTT
1 ATATGATATTGACTTT
1841130 ATATGATATCTGACTTT
1 ATATGATAT-TGACTTT
1841147 ATATGATAT
1 ATATGATAT
1841156 ATATTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (16 bp):
ATATGATATTGACTTT
Found at i:1859674 original size:65 final size:65
Alignment explanation
Indices: 1859600--1859775 Score: 192
Period size: 65 Copynumber: 2.7 Consensus size: 65
1859590 TGGAAAATGT
* * * *
1859600 TATCA-TCATCATACTACACGTAATCAACTCATGTGGCATGTTGCCTTACACCATATGAAAGCAC
1 TATCATTCATCACACTAAACGTAATCAACTCATGTGGCATGTTACCTCACACCATATGAAAGCAC
* * ** **
1859664 TATCATTCATCACACTAAAGGTAATCAATTTGTGTGGCATGTTACCTCACACCATATGAAAGTGC
1 TATCATTCATCACACTAAACGTAATCAACTCATGTGGCATGTTACCTCACACCATATGAAAGCAC
* * * * ** *
1859729 TATCATTCATCACATTAGATGCAATCAACTTGTGTGGAATGTTACCT
1 TATCATTCATCACACTAAACGTAATCAACTCATGTGGCATGTTACCT
1859776 TCCATAGTAT
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 5 0.05
65 90 0.95
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (65 bp):
TATCATTCATCACACTAAACGTAATCAACTCATGTGGCATGTTACCTCACACCATATGAAAGCAC
Found at i:1859789 original size:65 final size:65
Alignment explanation
Indices: 1859621--1859775 Score: 193
Period size: 65 Copynumber: 2.4 Consensus size: 65
1859611 TACTACACGT
** * * * *
1859621 AATCAACTCATGTGGCATGTTGCCTTACACCATATGAAAGCACTATCATTCATCACACTAAAGGT
1 AATCAACTTGTGTGGAATGTTACCTCACACCATATGAAAGCACTATCATTCATCACACTAAAGGC
* * ** * * *
1859686 AATCAATTTGTGTGGCATGTTACCTCACACCATATGAAAGTGCTATCATTCATCACATTAGATGC
1 AATCAACTTGTGTGGAATGTTACCTCACACCATATGAAAGCACTATCATTCATCACACTAAAGGC
1859751 AATCAACTTGTGTGGAATGTTACCT
1 AATCAACTTGTGTGGAATGTTACCT
1859776 TCCATAGTAT
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 77 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (65 bp):
AATCAACTTGTGTGGAATGTTACCTCACACCATATGAAAGCACTATCATTCATCACACTAAAGGC
Found at i:1860169 original size:13 final size:13
Alignment explanation
Indices: 1860151--1860189 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1860141 TTGAAAACTA
1860151 ATACATAGTAATG
1 ATACATAGTAATG
1860164 ATACATAGT-A--
1 ATACATAGTAATG
1860174 ATACATAGTAATG
1 ATACATAGTAATG
1860187 ATA
1 ATA
1860190 TTTACCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
12 1 0.04
13 12 0.52
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.31
Consensus pattern (13 bp):
ATACATAGTAATG
Found at i:1875186 original size:23 final size:24
Alignment explanation
Indices: 1875135--1875192 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1875125 GTTATGTGTT
* *
1875135 TTTATTGATTTTTATTTGTGTTTC
1 TTTATTTATTTTTATTTGTGTATC
1875159 TTTATTTATTTTTATTTGCT-TATC
1 TTTATTTATTTTTATTTG-TGTATC
1875183 -TTATTTATTT
1 TTTATTTATTT
1875193 GTTTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 10 0.32
24 20 0.65
25 1 0.03
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (24 bp):
TTTATTTATTTTTATTTGTGTATC
Found at i:1876642 original size:16 final size:16
Alignment explanation
Indices: 1876623--1876672 Score: 100
Period size: 16 Copynumber: 3.1 Consensus size: 16
1876613 CAAATGATGT
1876623 GATTCTTAAATCATGG
1 GATTCTTAAATCATGG
1876639 GATTCTTAAATCATGG
1 GATTCTTAAATCATGG
1876655 GATTCTTAAATCATGG
1 GATTCTTAAATCATGG
1876671 GA
1 GA
1876673 AAGCTAAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (16 bp):
GATTCTTAAATCATGG
Found at i:1892760 original size:2 final size:2
Alignment explanation
Indices: 1892753--1892782 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1892743 AAGAGTTCTT
*
1892753 TA TA TA TA CA 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
1892783 AATTAAGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1907381 original size:73 final size:69
Alignment explanation
Indices: 1907223--1907356 Score: 178
Period size: 73 Copynumber: 1.9 Consensus size: 69
1907213 GATAGTGTTA
** * *
1907223 GTTGACTAAGAGTTTACTGCCAGAAACTGAGTTCAGAGACAAAAATGACTTAATCGACTAAAAAG
1 GTTGACTAAGAGCCTACTGCCAAAAACTGAGTTCAGAGACAAAAACGACTTAATCGACTAAAAAG
1907288 TTTT
66 TTTT
* *
1907292 GTGAGTCGACTAAGAGCCTACTGCCAAAAACTGGGTTCAGAGACAAAGACGACTTAATCGACTAA
1 GT---T-GACTAAGAGCCTACTGCCAAAAACTGAGTTCAGAGACAAAAACGACTTAATCGACTAA
1907357 GTAGCAATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
69 2 0.04
72 1 0.02
73 52 0.95
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (69 bp):
GTTGACTAAGAGCCTACTGCCAAAAACTGAGTTCAGAGACAAAAACGACTTAATCGACTAAAAAG
TTTT
Found at i:1911401 original size:12 final size:13
Alignment explanation
Indices: 1911382--1911407 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1911372 ATGTCAAATA
1911382 GAAAAAAATTTTG
1 GAAAAAAATTTTG
1911395 GAAAAAAATTTTG
1 GAAAAAAATTTTG
1911408 TCATGTCAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
GAAAAAAATTTTG
Found at i:1917370 original size:71 final size:71
Alignment explanation
Indices: 1917267--1917787 Score: 338
Period size: 71 Copynumber: 7.2 Consensus size: 71
1917257 TTGTTAGTTC
* * * * * * *
1917267 TCGTTTACATCTTGTAGTGACACGCCT-TGTCATTGCAGTATTGTGGGTTGACACACCACGCTTG
1 TCGTTGACATCTTGTGGTGACAC-ACTGAGTCATTGCAGTATTATGGGTTGACACGCCACGCTTA
1917331 TTAGATG
65 TTAGATG
* * * * *
1917338 TCGTTAACATCTTGTGGTGATACGA-TCAGTCATTGTAGTATTATGGGGTT-ACATGCCACGCTT
1 TCGTTGACATCTTGTGGTGACAC-ACTGAGTCATTGCAGTATTAT-GGGTTGACACGCCACGCTT
1917401 ATTAGATG
64 ATTAGATG
* *
1917409 TCGTTGACATCTTGTGGTGACACACTGAGTCACTGCAGTATTATGCAG-TGACACGCCACGCTTA
1 TCGTTGACATCTTGTGGTGACACACTGAGTCATTGCAGTATTATG-GGTTGACACGCCACGCTTA
1917473 TTAGATG
65 TTAGATG
* * * * * *
1917480 TTGTTGACATCTTGTTGTGACACATTGAGTCGTTGCAGTATTACGGG-TGACAC-CCAATGCTCC
1 TCGTTGACATCTTGTGGTGACACACTGAGTCATTGCAGTATTATGGGTTGACACGCC-A--C-GC
* *
1917543 AATTGTTAGATT
62 --TTATTAGATG
* * * * * * * * *
1917555 TGGTAGGGCATCTTATGGTGACACACTAAGTCATTGCAGTATTCTGGGGTGACACGCCATGCTTG
1 TCGT-TGACATCTTGTGGTGACACACTGAGTCATTGCAGTATTATGGGTTGACACGCCACGCTTA
**
1917620 TTAGACA
65 TTAGATG
* * *** * * *
1917627 TCGTTGATATCTTATGGTGACATGTTGAGTCATTGTAGTATTATGGGGTGACACGCCACACTCCA
1 TCGTTGACATCTTGTGGTGACACACTGAGTCATTGCAGTATTATGGGTTGACACG-C-CAC-GC-
* *
1917692 ATTGTTAGATT
62 -TTATTAGATG
* * * * * * * *
1917703 TGGTAAGGCATCTTGTGGTGGCACGCTAAGTCATTGCAGTATTAT-GG-TGACACGCCACACTTG
1 TCGT-TGACATCTTGTGGTGACACACTGAGTCATTGCAGTATTATGGGTTGACACGCCACGCTTA
* *
1917766 TCAGTTG
65 TTAGATG
* *
1917773 TCATTTACATCTTGT
1 TCGTTGACATCTTGT
1917788 CATGACACGC
Statistics
Matches: 356, Mismatches: 74, Indels: 42
0.75 0.16 0.09
Matches are distributed among these distances:
69 10 0.03
70 21 0.06
71 192 0.54
72 19 0.05
73 6 0.02
74 3 0.01
75 18 0.05
76 47 0.13
77 38 0.11
78 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (71 bp):
TCGTTGACATCTTGTGGTGACACACTGAGTCATTGCAGTATTATGGGTTGACACGCCACGCTTAT
TAGATG
Found at i:1917607 original size:147 final size:147
Alignment explanation
Indices: 1917295--1917760 Score: 441
Period size: 147 Copynumber: 3.2 Consensus size: 147
1917285 GACACGCCTT
* * * ** * * *
1917295 GTCATTGCAGTATTGTGGGTTGACACACCACGCTTGTTAGATGTCGTTAACATCTTGTGGTGATA
1 GTCATTGCAGTATTATGGG-TGACACGCCACGCTTATTAGACATCGTTGACATCTTATGGTGACA
* * * * * * * * * * *
1917360 CGA-TCAGTCATTGTAGTATTATGGGGTTACATG-C-CAC-GC--TTATTAGATGTCGT-TGACA
65 C-ATTGAGTCATTGCAGTATTATCGGGTGACACGCCACACTCCAATTGTTAGATTTGGTAAGGCA
*
1917418 TCTTGTGGTGACACACTGA
129 TCTTGTGGTGACACACTAA
* * ** * * *
1917437 GTCACTGCAGTATTATGCAGTGACACGCCACGCTTATTAGATGTTGTTGACATCTTGTTGTGACA
1 GTCATTGCAGTATTATG-GGTGACACGCCACGCTTATTAGACATCGTTGACATCTTATGGTGACA
* *
1917502 CATTGAGTCGTTGCAGTATTA-CGGGTGACAC-CCA-ATGCTCCAATTGTTAGATTTGGTAGGGC
65 CATTGAGTCATTGCAGTATTATCGGGTGACACGCCACA--CTCCAATTGTTAGATTTGGTAAGGC
*
1917564 ATCTTATGGTGACACACTAA
128 ATCTTGTGGTGACACACTAA
* * * *
1917584 GTCATTGCAGTATTCTGGGGTGACACGCCATGCTTGTTAGACATCGTTGATATCTTATGGTGACA
1 GTCATTGCAGTATTAT-GGGTGACACGCCACGCTTATTAGACATCGTTGACATCTTATGGTGACA
** * *
1917649 TGTTGAGTCATTGTAGTATTATGGGGTGACACGCCACACTCCAATTGTTAGATTTGGTAAGGCAT
65 CATTGAGTCATTGCAGTATTATCGGGTGACACGCCACACTCCAATTGTTAGATTTGGTAAGGCAT
* *
1917714 CTTGTGGTGGCACGCTAA
130 CTTGTGGTGACACACTAA
1917732 GTCATTGCAGTATTAT-GGTGACACGCCAC
1 GTCATTGCAGTATTATGGGTGACACGCCAC
1917761 ACTTGTCAGT
Statistics
Matches: 265, Mismatches: 45, Indels: 24
0.79 0.13 0.07
Matches are distributed among these distances:
141 10 0.04
142 70 0.26
143 2 0.01
144 1 0.00
146 23 0.09
147 89 0.34
148 66 0.25
149 3 0.01
150 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (147 bp):
GTCATTGCAGTATTATGGGTGACACGCCACGCTTATTAGACATCGTTGACATCTTATGGTGACAC
ATTGAGTCATTGCAGTATTATCGGGTGACACGCCACACTCCAATTGTTAGATTTGGTAAGGCATC
TTGTGGTGACACACTAA
Found at i:1920699 original size:5 final size:5
Alignment explanation
Indices: 1920689--1920717 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1920679 AAAAAACTTA
1920689 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
1920718 CTTATTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:1924125 original size:26 final size:26
Alignment explanation
Indices: 1924096--1924178 Score: 148
Period size: 26 Copynumber: 3.2 Consensus size: 26
1924086 TTGTTACACA
*
1924096 CCAATACTGAGCTATGTCGTGGCACG
1 CCAATGCTGAGCTATGTCGTGGCACG
*
1924122 CCAATGCTGAGCTATGTCGTGGCAGG
1 CCAATGCTGAGCTATGTCGTGGCACG
1924148 CCAATGCTGAGCTATGTCGTGGCACG
1 CCAATGCTGAGCTATGTCGTGGCACG
1924174 CCAAT
1 CCAAT
1924179 CATTATAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.23
Consensus pattern (26 bp):
CCAATGCTGAGCTATGTCGTGGCACG
Found at i:1924801 original size:23 final size:23
Alignment explanation
Indices: 1924773--1924839 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
1924763 TTTTTTCTAT
*
1924773 TTCAAGCCATGGCGTGTCACATA
1 TTCAAGCCATGGCATGTCACATA
* *
1924796 TTCAAGTCATGGCTTGTCACATA
1 TTCAAGCCATGGCATGTCACATA
*
1924819 TTCAAGCCATGCCATGTCACA
1 TTCAAGCCATGGCATGTCACA
1924840 ATATCTCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (23 bp):
TTCAAGCCATGGCATGTCACATA
Found at i:1924851 original size:23 final size:23
Alignment explanation
Indices: 1924825--1924954 Score: 77
Period size: 23 Copynumber: 5.7 Consensus size: 23
1924815 CATATTCAAG
1924825 CCATGCCATGTCACAATATCTCA
1 CCATGCCATGTCACAATATCTCA
* * *
1924848 CCATGCAATGTCATACTATCTCA
1 CCATGCCATGTCACAATATCTCA
** * * *
1924871 CCATATCGTGTCACCGAT-TTTCA
1 CCATGCCATGTCA-CAATATCTCA
*** *
1924894 CCATGTTGTGTCACACA-ATTTCA
1 CCATGCCATGTCACA-ATATCTCA
* *
1924917 ACATG-CAGTGTCACAATTTCTCA
1 CCATGCCA-TGTCACAATATCTCA
*
1924940 CAATGCCATGTCACA
1 CCATGCCATGTCACA
1924955 CATTCCCACA
Statistics
Matches: 80, Mismatches: 21, Indels: 12
0.71 0.19 0.11
Matches are distributed among these distances:
22 2 0.03
23 75 0.94
24 3 0.04
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (23 bp):
CCATGCCATGTCACAATATCTCA
Found at i:1924964 original size:23 final size:23
Alignment explanation
Indices: 1924925--1924978 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1924915 CAACATGCAG
*
1924925 TGTCACAATTTCTCACAATGCCA
1 TGTCACAATTTCCCACAATGCCA
* *
1924948 TGTCACACA-TTCCCACAATGGCG
1 TGTCACA-ATTTCCCACAATGCCA
1924971 TGTCACAA
1 TGTCACAA
1924979 ACTCTAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 25 0.93
24 1 0.04
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (23 bp):
TGTCACAATTTCCCACAATGCCA
Found at i:1925297 original size:23 final size:23
Alignment explanation
Indices: 1925243--1925416 Score: 133
Period size: 23 Copynumber: 7.7 Consensus size: 23
1925233 CATGTCACAA
*
1925243 TCATGTCACATATGCTCACCATG
1 TCATGTCACATATTCTCACCATG
*
1925266 -C-TGTCTCACATATTCTTACCATG
1 TCATG--TCACATATTCTCACCATG
*
1925289 TCATGTCACATATTCACACCATG
1 TCATGTCACATATTCTCACCATG
*
1925312 GCATGTCAC--ATTCTCA-CACTG
1 TCATGTCACATATTCTCACCA-TG
* *
1925333 GCATGTCACATATTCTCAGCATG
1 TCATGTCACATATTCTCACCATG
* * * * * *
1925356 TCGTCTCACATATTCCCTCTAAG
1 TCATGTCACATATTCTCACCATG
* * *
1925379 TCGTGTCACATATTCTCACCCTA
1 TCATGTCACATATTCTCACCATG
* *
1925402 CCGTGTCACATATTC
1 TCATGTCACATATTC
1925417 CCTTCATAGT
Statistics
Matches: 121, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.02
21 19 0.16
22 1 0.01
23 94 0.78
24 3 0.02
25 2 0.02
ACGTcount: A:0.24, C:0.32, G:0.11, T:0.33
Consensus pattern (23 bp):
TCATGTCACATATTCTCACCATG
Found at i:1925365 original size:44 final size:43
Alignment explanation
Indices: 1925244--1925366 Score: 122
Period size: 44 Copynumber: 2.7 Consensus size: 43
1925234 ATGTCACAAT
* * *
1925244 CATGTCACATATGCTCACCATGCTGTCTCACATATTCTTACCATGT
1 CATGTCACATATTCTCACCATGC-GTCTCAC--ATTCTCACCATGG
* * *
1925290 CATGTCACATATTCACACCATGGCATGTCACATTCTCA-CACTGG
1 CATGTCACATATTCTCACCAT-GCGTCTCACATTCTCACCA-TGG
*
1925334 CATGTCACATATTCTCAGCATGTCGTCTCACAT
1 CATGTCACATATTCTCACCATG-CGTCTCACAT
1925367 ATTCCCTCTA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
43 3 0.05
44 35 0.55
46 24 0.38
47 2 0.03
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (43 bp):
CATGTCACATATTCTCACCATGCGTCTCACATTCTCACCATGG
Found at i:1925409 original size:90 final size:90
Alignment explanation
Indices: 1925244--1925412 Score: 207
Period size: 90 Copynumber: 1.9 Consensus size: 90
1925234 ATGTCACAAT
* *
1925244 CATGTCACATATGCTCACCATGCTGTCTCACATATTCTTACCATGTCATGTCACATATTCACACC
1 CATGTCACATATGCTCACCATGCTGTCTCACATATTCCTACCAAGTCATGTCACATATTCACACC
**
1925309 ATGGCATGTCACATTCTCACACTGG
66 ATACCATGTCACATTCTCACACTGG
* * * * *
1925334 CATGTCACATATTCTCAGCATG-TCGTCTCACATATTCCCT-CTAAGTCGTGTCACATATTCTCA
1 CATGTCACATATGCTCACCATGCT-GTCTCACATATT-CCTACCAAGTCATGTCACATATTCACA
* *
1925397 CCCTACCGTGTCACAT
64 CCATACCATGTCACAT
1925413 ATTCCCTTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
89 1 0.02
90 63 0.95
91 2 0.03
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (90 bp):
CATGTCACATATGCTCACCATGCTGTCTCACATATTCCTACCAAGTCATGTCACATATTCACACC
ATACCATGTCACATTCTCACACTGG
Found at i:1925430 original size:23 final size:21
Alignment explanation
Indices: 1925361--1925433 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 21
1925351 GCATGTCGTC
1925361 TCACATATTCCCTCTAAGTCGTG
1 TCACATATTCCCTCT-AGT-GTG
* **
1925384 TCACATATTCTCACCCTACCGTG
1 TCACATATTC-C-CTCTAGTGTG
1925407 TCACATATTCCCTTCATAGTGTG
1 TCACATATTCCC-TC-TAGTGTG
1925430 TCAC
1 TCAC
1925434 TAACTCTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 1 0.03
22 2 0.05
23 32 0.80
24 2 0.05
25 3 0.08
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.34
Consensus pattern (21 bp):
TCACATATTCCCTCTAGTGTG
Found at i:1925487 original size:23 final size:23
Alignment explanation
Indices: 1925461--1925528 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1925451 GTGTCAAAGC
* *
1925461 CATGTCACATATTCTCACCATGA
1 CATGTCACACATTCCCACCATGA
* *
1925484 CATGTAACACATTCCCACCATGT
1 CATGTCACACATTCCCACCATGA
*
1925507 CGTGTCACACATTCCCACCATG
1 CATGTCACACATTCCCACCATG
1925529 GCGTTTCACA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.35, G:0.10, T:0.26
Consensus pattern (23 bp):
CATGTCACACATTCCCACCATGA
Found at i:1925537 original size:23 final size:23
Alignment explanation
Indices: 1925463--1925538 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
1925453 GTCAAAGCCA
* * * *
1925463 TGTCACATATTCTCACCATGACA
1 TGTCACACATTCCCACCATGGCG
* *
1925486 TGTAACACATTCCCACCATGTCG
1 TGTCACACATTCCCACCATGGCG
1925509 TGTCACACATTCCCACCATGGCG
1 TGTCACACATTCCCACCATGGCG
*
1925532 TTTCACA
1 TGTCACA
1925539 AGCTCTAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.26, C:0.34, G:0.12, T:0.28
Consensus pattern (23 bp):
TGTCACACATTCCCACCATGGCG
Found at i:1927206 original size:64 final size:64
Alignment explanation
Indices: 1927132--1927288 Score: 217
Period size: 64 Copynumber: 2.5 Consensus size: 64
1927122 ATTAACACAA
* *
1927132 TATATGGAATGTTACCTCACACCATGTGAAATGCTATCATCATCATACTAGGCACAATTCACCAC
1 TATATGGAATGTTACCTCACACCATGTGAAACGCTATCATCATCATACTAGACACAATTCACC-C
* * * ** *
1927197 -ATATGGAATGTTACCTCACACCATGTGGAGCGTTATCATCATCATACTAGATGCAATTCGCCC
1 TATATGGAATGTTACCTCACACCATGTGAAACGCTATCATCATCATACTAGACACAATTCACCC
*
1927260 TATGTGGAATGTTACCTCACACCATGTGA
1 TATATGGAATGTTACCTCACACCATGTGA
1927289 TAGCTCTAGG
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
63 1 0.01
64 80 0.99
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (64 bp):
TATATGGAATGTTACCTCACACCATGTGAAACGCTATCATCATCATACTAGACACAATTCACCC
Found at i:1932566 original size:18 final size:18
Alignment explanation
Indices: 1932528--1932567 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1932518 CGGGATTTAT
*
1932528 TTTTTTATTAAATAATTA
1 TTTTTTATTAAATAATAA
* *
1932546 TTTTTTATTTAATTATAA
1 TTTTTTATTAAATAATAA
1932564 TTTT
1 TTTT
1932568 AAATTATATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTATTAAATAATAA
Found at i:1932723 original size:19 final size:18
Alignment explanation
Indices: 1932701--1932739 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1932691 TGTGAAAAGC
*
1932701 TTTTTAAAAAAAAAAAAT
1 TTTTTTAAAAAAAAAAAT
*
1932719 TTTTTTAAAAAACAAAAT
1 TTTTTTAAAAAAAAAAAT
1932737 TTT
1 TTT
1932740 AAAAAAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTTTTAAAAAAAAAAAT
Found at i:1932746 original size:18 final size:17
Alignment explanation
Indices: 1932701--1932746 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
1932691 TGTGAAAAGC
1932701 TTTTTAAAAAAAAAAAA
1 TTTTTAAAAAAAAAAAA
* *
1932718 TTTTTTTAAAAAACAAAA
1 -TTTTTAAAAAAAAAAAA
1932736 -TTTTAAAAAAA
1 TTTTTAAAAAAA
1932747 GCTTAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.40
18 15 0.60
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTTTAAAAAAAAAAAA
Found at i:1933256 original size:17 final size:18
Alignment explanation
Indices: 1933236--1933271 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1933226 CTTTTTTTAG
1933236 AAAACAAA-ATTAAAAAA
1 AAAACAAAGATTAAAAAA
*
1933253 AAAACAAAGCTTAAAAAA
1 AAAACAAAGATTAAAAAA
1933271 A
1 A
1933272 CCTTCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.78, C:0.08, G:0.03, T:0.11
Consensus pattern (18 bp):
AAAACAAAGATTAAAAAA
Found at i:1933742 original size:7 final size:7
Alignment explanation
Indices: 1933713--1933754 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1933703 TATTAAGGTA
*
1933713 TTATTTC
1 TTATTTT
*
1933720 TTCTTTT
1 TTATTTT
1933727 TT-TTGTT
1 TTATT-TT
1933734 TTATTTT
1 TTATTTT
1933741 TTATTTT
1 TTATTTT
1933748 TTATTTT
1 TTATTTT
1933755 GCTTTGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 2 0.06
7 27 0.87
8 2 0.06
ACGTcount: A:0.10, C:0.05, G:0.02, T:0.83
Consensus pattern (7 bp):
TTATTTT
Found at i:1934128 original size:14 final size:14
Alignment explanation
Indices: 1934109--1934143 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1934099 GGTTACCAAA
1934109 TCAATAGATAATTT
1 TCAATAGATAATTT
1934123 TCAATAGATAATTT
1 TCAATAGATAATTT
1934137 TCAATAG
1 TCAATAG
1934144 GAAAATGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (14 bp):
TCAATAGATAATTT
Found at i:1937112 original size:63 final size:64
Alignment explanation
Indices: 1937002--1937156 Score: 163
Period size: 63 Copynumber: 2.4 Consensus size: 64
1936992 CCTAGAGCTT
* * * * *
1937002 TTCACAAGGTGTGAGGTAACATTCCACACAAGGTGAATTTTATCTAGTATAATGATGATAACAC
1 TTCACATGCTGTGAGGTAACATTCCATACAAGGTGAATTATACCTAGTATAATGATGATAACAC
* * *
1937066 TTCACAT-CTGTGAGGTAACATTCCATAGGC-A-GTGAATTATGCCTAGTATGATGATGATAGCA
1 TTCACATGCTGTGAGGTAACATTCCATA--CAAGGTGAATTATACCTAGTATAATGATGATAACA
*
1937128 T
64 C
* * *
1937129 TTTACATGGTGTGAAGTAACATTCCATA
1 TTCACATGCTGTGAGGTAACATTCCATA
1937157 TGTCGTGCTA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 50 0.66
64 25 0.33
65 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (64 bp):
TTCACATGCTGTGAGGTAACATTCCATACAAGGTGAATTATACCTAGTATAATGATGATAACAC
Found at i:1939969 original size:251 final size:253
Alignment explanation
Indices: 1939371--1940024 Score: 653
Period size: 254 Copynumber: 2.6 Consensus size: 253
1939361 TTAACGGTTT
* * *
1939371 ACAAATTTTAATTTATAATGAAATAATAATAAGGATAAAAATACA-TATAATGAAAATTCACAAT
1 ACAAATTTTAATTTAAAATGAAATAATAATAAGGATAAAAATA-ATTATAGTGAAAATTAACAAT
* * * * * * *
1939435 TGAAAAACATTGACATAAACTTGCAAGAA-ATAACGTAAAATATAATAAAAGTGGAACTAGT-AT
65 TGAAAAACCTTGACCTAAACTTGTAAGAATA-AACGTAAAAAATTATAAAGGTGGAAC-AATCAT
* * * * * *
1939498 TGTCAAAATATTGACTTAAATGTACGAAATTTAACGTAACAAGTTAATGAAGTTAAAATAAATAT
128 TGTTAAAATATTGA-TTAAATGCACGAAATTTAACATAACAAATTAATGAAGTCAAAACAAATAT
* * * * ** * * * * *
1939563 ATTTTTAAAAAAATTAAACATTTAAATTTATATTGTTGAGCTAAAAGTATAACGTACAATTT
192 ATTTTTAAAAAAATTAAAAATGTAAATGTATATTCTCAAACTAAAAGAATAACGAACAACTC
* * ** * * *
1939625 GCAAATTTTAACTTATAAATG-AATAGCAATAAGGATAAAAATAATTATAGTAAAAATTAGCAAC
1 ACAAATTTTAATTTA-AAATGAAATAATAATAAGGATAAAAATAATTATAGTGAAAATTAACAAT
* * *
1939689 TGAAAAATCTTGATGC-AAACATGTAAGAATAAACGTAAAAAATTATAAAGGTGGAACAATCATT
65 TGAAAAACCTTGA-CCTAAACTTGTAAGAATAAACGTAAAAAATTATAAAGGTGGAACAATCATT
* * *
1939753 GTTAAAATATTGATGTAAATGCATGAAATTTAATATAACAAATCTAGT-AAGTCAAAACAAATAT
129 GTTAAAATATTGAT-TAAATGCACGAAATTTAACATAACAAAT-TAATGAAGTCAAAACAAATAT
** * * *
1939817 AATTTTT-TGAAAGTTAAAAATGTAAATGTATATTCTCAAATTAAAA-AAT-TC-AACAACTC
192 -ATTTTTAAAAAAATTAAAAATGTAAATGTATATTCTCAAACTAAAAGAATAACGAACAACTC
* * *
1939876 ACAAATTTTAATTTAAAAAGAAAAAATAATAAAGATAAAAATAATTATAGTGAAAATTAACAATT
1 ACAAATTTTAATTTAAAATGAAATAATAATAAGGATAAAAATAATTATAGTGAAAATTAACAATT
* * * * * * *
1939941 GAAAAACCTTGACCTAAACTTATAAGAATTAACATAAAAAATTATAAAGGTAGAATAAGCATTTT
66 GAAAAACCTTGACCTAAACTTGTAAGAATAAACGTAAAAAATTATAAAGGTGGAACAATCATTGT
1940006 TAAAATATTGATATAAATG
131 TAAAATATTGAT-TAAATG
1940025 TGTGAGATTT
Statistics
Matches: 324, Mismatches: 66, Indels: 23
0.78 0.16 0.06
Matches are distributed among these distances:
250 5 0.02
251 126 0.39
252 1 0.00
253 6 0.02
254 172 0.53
255 14 0.04
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.31
Consensus pattern (253 bp):
ACAAATTTTAATTTAAAATGAAATAATAATAAGGATAAAAATAATTATAGTGAAAATTAACAATT
GAAAAACCTTGACCTAAACTTGTAAGAATAAACGTAAAAAATTATAAAGGTGGAACAATCATTGT
TAAAATATTGATTAAATGCACGAAATTTAACATAACAAATTAATGAAGTCAAAACAAATATATTT
TTAAAAAAATTAAAAATGTAAATGTATATTCTCAAACTAAAAGAATAACGAACAACTC
Found at i:1947216 original size:35 final size:35
Alignment explanation
Indices: 1947142--1947301 Score: 167
Period size: 35 Copynumber: 4.5 Consensus size: 35
1947132 NNNNNNNNNA
****
1947142 AATTTAATCAATTAGGCCCAATAACTTAATTGTTT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * *
1947177 AATTTAATTAATGAGGCCTAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * ** * *
1947212 AATTTGATCAATTAAGTTCAATAACTTGATTAAAAA
1 AATTTAATCAATTAGGCCCAATAACTTAATT-AAAC
* *
1947248 AATTTAATCAATTAAGCCCAATAACTTGATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
1947283 AAATTTAATCAATTAGGCC
1 -AATTTAATCAATTAGGCC
1947302 NNNNNNNNNN
Statistics
Matches: 102, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
35 54 0.53
36 48 0.47
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:1952425 original size:30 final size:29
Alignment explanation
Indices: 1952369--1952429 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
1952359 GCCTCATCGA
*
1952369 TTATTTGATTTAAAATAAAAATATAAAAGT
1 TTATTTAATTTAAAATAAAAATAT-AAAGT
* *
1952399 TTATTTAATTTAATATAATTAA-ATAAAGT
1 TTATTTAATTTAAAATAA-AAATATAAAGT
1952428 TT
1 TT
1952430 GATTGAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.26
30 18 0.67
31 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
TTATTTAATTTAAAATAAAAATATAAAGT
Found at i:1958116 original size:15 final size:15
Alignment explanation
Indices: 1958096--1958133 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1958086 ACTTCCACTA
1958096 AGCTTTTACAAGGTG
1 AGCTTTTACAAGGTG
1958111 AGCTTTTACAAGGTG
1 AGCTTTTACAAGGTG
1958126 AGCTTTTA
1 AGCTTTTA
1958134 ACTCAAGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (15 bp):
AGCTTTTACAAGGTG
Found at i:1960069 original size:64 final size:64
Alignment explanation
Indices: 1959918--1960070 Score: 164
Period size: 64 Copynumber: 2.4 Consensus size: 64
1959908 ACGACATATA
* * *
1959918 GAATGTTACTTTACACCATGTGAAATGCTATCATCACCATACTAGGCACAATTCACTACGTGTG
1 GAATGTTACCTCACACCATGTGAAATGCTATCATCACCATACTAGACACAATTCACTACGTGTG
* * * * * ** * * *
1959982 GAATGTTACCTCACAGCAAGTGAAGTGTTATCATCATCATACTAGATGCAATTTACCT-TGTGTT
1 GAATGTTACCTCACACCATGTGAAATGCTATCATCACCATACTAGACACAATTCA-CTACGTGTG
*
1960046 GAATGTTACCTCACACCTTGTGAAA
1 GAATGTTACCTCACACCATGTGAAA
1960071 AGCTCTAGGA
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
64 69 0.97
65 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (64 bp):
GAATGTTACCTCACACCATGTGAAATGCTATCATCACCATACTAGACACAATTCACTACGTGTG
Done.