Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 65 of 117
Found at i:12002786 original size:15 final size:14
Alignment explanation
Indices: 12002762--12002818 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
12002752 TAAAAAGGTT
*
12002762 ATTAAAAATAGAAA
1 ATTAAAAATAAAAA
12002776 ATTACAAAATAAAAA
1 ATTA-AAAATAAAAA
*
12002791 ATTAAACTAA-ACAAA
1 ATTAAA--AATAAAAA
*
12002806 ATTAAAATTAAAA
1 ATTAAAAATAAAA
12002819 GAAGAAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 1 0.03
14 9 0.26
15 23 0.66
16 2 0.06
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (14 bp):
ATTAAAAATAAAAA
Found at i:12005799 original size:16 final size:16
Alignment explanation
Indices: 12005770--12005808 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
12005760 CTAGGTATAA
12005770 AAATTAAAGGGCAAG-
1 AAATTAAAGGGCAAGT
*
12005785 AAATATAAAGTGCAAGT
1 AAAT-TAAAGGGCAAGT
12005802 AAATTAA
1 AAATTAA
12005809 CAAACAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 13 0.62
17 4 0.19
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (16 bp):
AAATTAAAGGGCAAGT
Found at i:12012554 original size:18 final size:19
Alignment explanation
Indices: 12012517--12012561 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
12012507 TTTTCATTTC
12012517 AAGAAGAAGGAAGAAAGAAA
1 AAGAA-AAGGAAGAAAGAAA
*
12012537 AAGAAAAGG-AGGAAGAAA
1 AAGAAAAGGAAGAAAGAAA
*
12012555 AGGAAAA
1 AAGAAAA
12012562 AAAGAAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (19 bp):
AAGAAAAGGAAGAAAGAAA
Found at i:12015922 original size:51 final size:48
Alignment explanation
Indices: 12015858--12015957 Score: 128
Period size: 48 Copynumber: 2.0 Consensus size: 48
12015848 AAATGATGTC
* *
12015858 TAGTCTTAACCTTTAAATGAGTATCATCAAGTTGCAATAGACAAGAGTTAT
1 TAGTCGTAACCTTTAAATGAG--T-ATCAAGTTCCAATAGACAAGAGTTAT
* * *
12015909 TAGTCGTATCCTTTGAATGAGTATCAAGTTCCAATAGTCAAGAGTTAT
1 TAGTCGTAACCTTTAAATGAGTATCAAGTTCCAATAGACAAGAGTTAT
12015957 T
1 T
12015958 CAGCATAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
48 25 0.57
49 1 0.02
51 18 0.41
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (48 bp):
TAGTCGTAACCTTTAAATGAGTATCAAGTTCCAATAGACAAGAGTTAT
Found at i:12017729 original size:2 final size:2
Alignment explanation
Indices: 12017724--12017764 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
12017714 TCTCTCTCTC
* * *
12017724 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TG TA TC TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12017765 GCGAGTGTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12020581 original size:11 final size:11
Alignment explanation
Indices: 12020560--12020594 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
12020550 TATGGATTGT
12020560 ACTATCAATTAC
1 ACTA-CAATTAC
12020572 ACTACAATTAC
1 ACTACAATTAC
12020583 ACTACAATTAC
1 ACTACAATTAC
12020594 A
1 A
12020595 TAGAAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.29
Consensus pattern (11 bp):
ACTACAATTAC
Found at i:12027210 original size:11 final size:10
Alignment explanation
Indices: 12027194--12027304 Score: 73
Period size: 10 Copynumber: 10.9 Consensus size: 10
12027184 AAGAAAAATA
12027194 TAAAAATTTTT
1 TAAAAA-TTTT
12027205 TAAAAATTTT
1 TAAAAATTTT
*
12027215 T-AAAATTAT
1 TAAAAATTTT
* *
12027224 AAAAAAATTT
1 TAAAAATTTT
*
12027234 TAAAAA-TTA
1 TAAAAATTTT
*
12027243 TAAAATAATTT
1 TAAAA-ATTTT
*
12027254 AAAATAATTTTT
1 TAAA-AA-TTTT
**
12027266 TAAAAATTCA
1 TAAAAATTTT
*
12027276 AAAAAATTTT
1 TAAAAATTTT
* *
12027286 AAAAAAATTT
1 TAAAAATTTT
12027296 TAAAAATTT
1 TAAAAATTT
12027305 GAAAACAAAC
Statistics
Matches: 77, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
9 14 0.18
10 42 0.55
11 14 0.18
12 7 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAAAATTTT
Found at i:12027219 original size:20 final size:20
Alignment explanation
Indices: 12027196--12027253 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
12027186 GAAAAATATA
* *
12027196 AAAATTTTTTAAAAATTTTT
1 AAAATTTATAAAAAATTTTT
*
12027216 AAAA-TTATAAAAAAATTTT
1 AAAATTTATAAAAAATTTTT
*
12027235 AAAAATTATAAAATAATTT
1 AAAATTTATAAAA-AATTT
12027254 AAAATAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 16 0.50
20 12 0.38
21 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAATTTATAAAAAATTTTT
Found at i:12027300 original size:20 final size:20
Alignment explanation
Indices: 12027194--12027309 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
12027184 AAGAAAAATA
**
12027194 TAAAAATTTTTTAAAAATTT
1 TAAAAATTTTAAAAAAATTT
* *
12027214 TTAAAATTATAAAAAAATTT
1 TAAAAATTTTAAAAAAATTT
* *
12027234 TAAAAATTATAAAATAATTT
1 TAAAAATTTTAAAAAAATTT
* ** *
12027254 AAAATAATTTTTTAAAAATTCA
1 TAAA-AATTTTAAAAAAATT-T
*
12027276 AAAAAATTTTAAAAAAATTT
1 TAAAAATTTTAAAAAAATTT
*
12027296 TAAAAATTTGAAAA
1 TAAAAATTTTAAAA
12027310 CAAACTAAAA
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 49 0.64
21 24 0.31
22 4 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
TAAAAATTTTAAAAAAATTT
Found at i:12027319 original size:62 final size:61
Alignment explanation
Indices: 12027198--12027322 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 61
12027188 AAAATATAAA
*** * **
12027198 AATTTTTTAAAAATTTTTAAAATTATAAAAAAATTTTAAAAATTATAAAATAATTTAAAAT
1 AATTTTTTAAAAATTAAAAAAATTATAAAAAAATTTTAAAAATTATAAAACAAACTAAAAT
*
12027259 AATTTTTTAAAAATTCAAAAAAATTTTAAAAAAATTTTAAAAATT-TGAAAACAAACTAAAAT
1 AATTTTTTAAAAATT-AAAAAAATTATAAAAAAATTTTAAAAATTAT-AAAACAAACTAAAAT
12027321 AA
1 AA
12027323 CAAAAATAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
61 16 0.29
62 39 0.71
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (61 bp):
AATTTTTTAAAAATTAAAAAAATTATAAAAAAATTTTAAAAATTATAAAACAAACTAAAAT
Found at i:12028436 original size:10 final size:10
Alignment explanation
Indices: 12028418--12028552 Score: 80
Period size: 10 Copynumber: 13.3 Consensus size: 10
12028408 ACAATTTCTG
12028418 AAAAA-TTTT
1 AAAAATTTTT
12028427 AAAAATTTTT
1 AAAAATTTTT
*
12028437 -AGAATTTTT
1 AAAAATTTTT
*
12028446 AAAAACTTCTT
1 AAAAA-TTTTT
12028457 AAAAATTTTT
1 AAAAATTTTT
*
12028467 TAAAATTTTT
1 AAAAATTTTT
12028477 AGAAATTATTTTT
1 A-AAA--ATTTTT
**
12028490 AAAAAAATTT
1 AAAAATTTTT
*
12028500 -AAATTTTTT
1 AAAAATTTTT
**
12028509 TGAAA-TTTT
1 AAAAATTTTT
**
12028518 AAATTTTTTT
1 AAAAATTTTT
* *
12028528 TAGAATTTTT
1 AAAAATTTTT
12028538 CAAAAAATTTTT
1 --AAAAATTTTT
12028550 AAA
1 AAA
12028553 TCTTTTTATA
Statistics
Matches: 93, Mismatches: 23, Indels: 19
0.69 0.17 0.14
Matches are distributed among these distances:
9 24 0.26
10 39 0.42
11 12 0.13
12 11 0.12
13 7 0.08
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (10 bp):
AAAAATTTTT
Found at i:12028476 original size:11 final size:11
Alignment explanation
Indices: 12028423--12028494 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 11
12028413 TTCTGAAAAA
12028423 TTTTAAAAA-T
1 TTTTAAAAATT
*
12028433 TTTT-AGAA-T
1 TTTTAAAAATT
*
12028442 TTTTAAAAACT
1 TTTTAAAAATT
*
12028453 TCTTAAAAATT
1 TTTTAAAAATT
12028464 TTTT-AAAA-T
1 TTTTAAAAATT
*
12028473 TTTTAGAAATTAT
1 TTTTA-AAAAT-T
12028486 TTTTAAAAA
1 TTTTAAAAA
12028495 AATTTAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
9 13 0.27
10 11 0.22
11 16 0.33
12 3 0.06
13 6 0.12
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TTTTAAAAATT
Found at i:12030599 original size:16 final size:17
Alignment explanation
Indices: 12030560--12030603 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
12030550 TAAACAACTT
12030560 AAATTAAACTAAAATTG
1 AAATTAAACTAAAATTG
* *
12030577 -TACTAAAC-AAAATTG
1 AAATTAAACTAAAATTG
12030592 AAATTAAACTAA
1 AAATTAAACTAA
12030604 TTAAACCTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
15 7 0.33
16 12 0.57
17 2 0.10
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (17 bp):
AAATTAAACTAAAATTG
Found at i:12031282 original size:25 final size:25
Alignment explanation
Indices: 12031253--12031310 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
12031243 AAACTCCCTC
12031253 AAGCAGCTCTCAAAGTCCTAACTTT
1 AAGCAGCTCTCAAAGTCCTAACTTT
12031278 AAGCAGCTCTCAAAGTCCTAACTTT
1 AAGCAGCTCTCAAAGTCCTAACTTT
12031303 AAGCAGCT
1 AAGCAGCT
12031311 TGCACCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.26
Consensus pattern (25 bp):
AAGCAGCTCTCAAAGTCCTAACTTT
Found at i:12035848 original size:31 final size:31
Alignment explanation
Indices: 12035807--12035872 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
12035797 ATACAACATT
*
12035807 TATAAAACATCCCATTGGGTAACAT-TATCAA
1 TATAAAACATCCCATTAGGTAACATGT-TCAA
*
12035838 TATAACACATCCCATTAGGTAACATGTTCAA
1 TATAAAACATCCCATTAGGTAACATGTTCAA
12035869 TATA
1 TATA
12035873 TATACAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (31 bp):
TATAAAACATCCCATTAGGTAACATGTTCAA
Found at i:12038445 original size:10 final size:10
Alignment explanation
Indices: 12038430--12038454 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12038420 TTTTGTTTCT
12038430 GTTGCCTTAC
1 GTTGCCTTAC
12038440 GTTGCCTTAC
1 GTTGCCTTAC
12038450 GTTGC
1 GTTGC
12038455 ATTTCCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.28, G:0.24, T:0.40
Consensus pattern (10 bp):
GTTGCCTTAC
Found at i:12039318 original size:20 final size:20
Alignment explanation
Indices: 12039293--12039331 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12039283 TTAATAAATA
12039293 TTTTAAAG-TTTAGTGGTTTG
1 TTTTAAAGATTTAG-GGTTTG
12039313 TTTTAAAGATTTAGGGTTT
1 TTTTAAAGATTTAGGGTTT
12039332 TTCATTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (20 bp):
TTTTAAAGATTTAGGGTTTG
Found at i:12039377 original size:18 final size:19
Alignment explanation
Indices: 12039340--12039384 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
12039330 TTTTCATTTC
12039340 AAGAAGAAGGAAGAAAGAAA
1 AAGAA-AAGGAAGAAAGAAA
*
12039360 AAGAAAAGG-AGGAAGAAA
1 AAGAAAAGGAAGAAAGAAA
*
12039378 AGGAAAA
1 AAGAAAA
12039385 AAAGAAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (19 bp):
AAGAAAAGGAAGAAAGAAA
Found at i:12039659 original size:67 final size:67
Alignment explanation
Indices: 12039551--12039682 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
12039541 ATCGAATTGG
* * *
12039551 TTAAACGCTCAATTTTGAATTAAACGTTTATGTGGTTGCTCAATTTAAGACTAAATATTTTATTT
1 TTAAACGCTCAATTTCGAATTAAACATTTAGGTGGTTGCTCAATTTAAGACTAAATATTTTATTT
12039616 GA
66 GA
*
12039618 TTAAACGCTCAATTTCGAATTAAACATTTGGGTGGTTGCTCAATTTAAGACTAAATATTTTATTT
1 TTAAACGCTCAATTTCGAATTAAACATTTAGGTGGTTGCTCAATTTAAGACTAAATATTTTATTT
12039683 TATGTGAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (67 bp):
TTAAACGCTCAATTTCGAATTAAACATTTAGGTGGTTGCTCAATTTAAGACTAAATATTTTATTT
GA
Found at i:12042753 original size:51 final size:48
Alignment explanation
Indices: 12042689--12042788 Score: 128
Period size: 48 Copynumber: 2.0 Consensus size: 48
12042679 AAATGATGTC
* *
12042689 TAGTCTTAACCTTTAAATGAGTATCATCAAGTTGCAATAGACAAGAGTTAT
1 TAGTCGTAACCTTTAAATGAG--T-ATCAAGTTCCAATAGACAAGAGTTAT
* * *
12042740 TAGTCGTATCCTTTGAATGAGTATCAAGTTCCAATAGTCAAGAGTTAT
1 TAGTCGTAACCTTTAAATGAGTATCAAGTTCCAATAGACAAGAGTTAT
12042788 T
1 T
12042789 CAGCATAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
48 25 0.57
49 1 0.02
51 18 0.41
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (48 bp):
TAGTCGTAACCTTTAAATGAGTATCAAGTTCCAATAGACAAGAGTTAT
Found at i:12049524 original size:21 final size:21
Alignment explanation
Indices: 12049490--12049541 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12049480 TGATATTTTT
* *
12049490 AAATA-TTTACATTTTAAAAA
1 AAATATTTTATATTTAAAAAA
*
12049510 TAATATTTTATATTTAAAAAA
1 AAATATTTTATATTTAAAAAA
12049531 AAATATTTTAT
1 AAATATTTTAT
12049542 TAATTTTGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTTTATATTTAAAAAA
Found at i:12054459 original size:9 final size:9
Alignment explanation
Indices: 12054446--12054541 Score: 57
Period size: 9 Copynumber: 9.7 Consensus size: 9
12054436 GGAAAACATA
12054446 AAAAAATTT
1 AAAAAATTT
*
12054455 TAAAAATTAT
1 AAAAAATT-T
*
12054465 AAAAAAATT
1 AAAAAATTT
12054474 ATAAAAATTAT
1 A-AAAAATT-T
*
12054485 AAAAAAATTCA
1 -AAAAAATT-T
12054496 AAATAATATTT
1 AAA-AA-ATTT
*
12054507 TAAAAATTCT
1 AAAAAATT-T
12054517 AAAAAAATTT
1 -AAAAAATTT
*
12054527 TAAAAATTT
1 AAAAAATTT
*
12054536 GAAAAA
1 AAAAAA
12054542 CAAACTAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 16
0.72 0.12 0.17
Matches are distributed among these distances:
9 25 0.37
10 20 0.29
11 19 0.28
12 4 0.06
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAAAATTT
Found at i:12054460 original size:11 final size:11
Alignment explanation
Indices: 12054444--12054532 Score: 66
Period size: 11 Copynumber: 8.5 Consensus size: 11
12054434 AAGGAAAACA
12054444 TAAAAAAATTT
1 TAAAAAAATTT
*
12054455 T--AAAAATTA
1 TAAAAAAATTT
12054464 TAAAAAAA--T
1 TAAAAAAATTT
* *
12054473 TATAAAAATTA
1 TAAAAAAATTT
12054484 TAAAAAAA-TT
1 TAAAAAAATTT
*
12054494 CAAAATAATATTT
1 TAAAA-AA-ATTT
*
12054507 T--AAAAATTC
1 TAAAAAAATTT
12054516 TAAAAAAATTT
1 TAAAAAAATTT
12054527 TAAAAA
1 TAAAAA
12054533 TTTGAAAAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
9 19 0.32
10 7 0.12
11 30 0.51
12 1 0.02
13 2 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAAAATTT
Found at i:12054468 original size:8 final size:9
Alignment explanation
Indices: 12054447--12054489 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
12054437 GAAAACATAA
*
12054447 AAAAATTTT
1 AAAAATTAT
12054456 AAAAATTAT
1 AAAAATTAT
12054465 AAAAAAATTAT
1 --AAAAATTAT
12054476 AAAAATTAT
1 AAAAATTAT
12054485 AAAAA
1 AAAAA
12054490 AATTCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 22 0.71
11 9 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:12054511 original size:21 final size:20
Alignment explanation
Indices: 12054444--12054534 Score: 81
Period size: 20 Copynumber: 5.0 Consensus size: 20
12054434 AAGGAAAACA
*
12054444 TAAAAAAATTTTAAAAATTA
1 TAAAAAAATTTTAAAAATTC
* *
12054464 TAAAAAAATTATAAAAATTA
1 TAAAAAAATTTTAAAAATTC
*
12054484 TAAAAAAA--TTCAAAA---
1 TAAAAAAATTTTAAAAATTC
*
12054499 T---AATATTTTAAAAATTC
1 TAAAAAAATTTTAAAAATTC
12054516 TAAAAAAATTTTAAAAATT
1 TAAAAAAATTTTAAAAATT
12054535 TGAAAAACAA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
12 3 0.05
14 6 0.11
15 1 0.02
17 1 0.02
18 5 0.09
20 41 0.72
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAAAATTTTAAAAATTC
Found at i:12054541 original size:20 final size:20
Alignment explanation
Indices: 12054443--12054493 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
12054433 AAAGGAAAAC
12054443 ATAAAAAAATTTTAAAAATT
1 ATAAAAAAATTTTAAAAATT
*
12054463 ATAAAAAAATTATAAAAATT
1 ATAAAAAAATTTTAAAAATT
12054483 ATAAAAAAATT
1 ATAAAAAAATT
12054494 CAAAATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAAAAATTTTAAAAATT
Found at i:12055663 original size:9 final size:9
Alignment explanation
Indices: 12055649--12055723 Score: 69
Period size: 9 Copynumber: 7.7 Consensus size: 9
12055639 CAATTTGTGA
12055649 AAAATTTTT
1 AAAATTTTT
12055658 AAAATTTTT
1 AAAATTTTT
*
12055667 AGAATTTTT
1 AAAATTTTT
**
12055676 AAAAACTTCTAAA
1 -AAAA-TT-T-TT
12055689 AAAATTTTT
1 AAAATTTTT
12055698 AAAATTTTTT
1 AAAA-TTTTT
12055708 AAAATTTTT
1 AAAATTTTT
12055717 AGAAATT
1 A-AAATT
12055724 ATTTTTAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
9 27 0.50
10 18 0.33
11 4 0.07
12 5 0.09
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (9 bp):
AAAATTTTT
Found at i:12055666 original size:10 final size:10
Alignment explanation
Indices: 12055648--12055757 Score: 62
Period size: 10 Copynumber: 10.7 Consensus size: 10
12055638 ACAATTTGTG
*
12055648 AAAAATTTTT
1 AAAATTTTTT
12055658 AAAA-TTTTT
1 AAAATTTTTT
* *
12055667 AGAATTTTTA
1 AAAATTTTTT
* **
12055677 AAAACTTCTAA
1 AAAA-TTTTTT
*
12055688 AAAAATTTTT
1 AAAATTTTTT
12055698 AAAATTTTTT
1 AAAATTTTTT
12055708 AAAA-TTTTT
1 AAAATTTTTT
12055717 AGAAATTATTTTT
1 A-AAA-T-TTTTT
***
12055730 AAAAAAATTT
1 AAAATTTTTT
*
12055740 AAATTTTTTT
1 AAAATTTTTT
12055750 GAAAATTT
1 -AAAATTT
12055758 AAATTTTTTT
Statistics
Matches: 75, Mismatches: 18, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
9 14 0.19
10 38 0.51
11 14 0.19
12 3 0.04
13 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:12055747 original size:18 final size:18
Alignment explanation
Indices: 12055724--12055765 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12055714 TTTAGAAATT
12055724 ATTTTTAAAAAAATTTAA
1 ATTTTTAAAAAAATTTAA
***
12055742 ATTTTTTTGAAAATTTAA
1 ATTTTTAAAAAAATTTAA
12055760 ATTTTT
1 ATTTTT
12055766 TTTAGAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTTTAAAAAAATTTAA
Found at i:12055775 original size:18 final size:18
Alignment explanation
Indices: 12055733--12055767 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12055723 TATTTTTAAA
12055733 AAAATTTAAATTTTTTTG
1 AAAATTTAAATTTTTTTG
12055751 AAAATTTAAATTTTTTT
1 AAAATTTAAATTTTTTT
12055768 TAGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AAAATTTAAATTTTTTTG
Found at i:12060257 original size:21 final size:21
Alignment explanation
Indices: 12060232--12060310 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
12060222 TAAGTGAATC
*
12060232 GATCAATCCATTTTTATAGAG
1 GATCAATCCATTTTCATAGAG
*** *
12060253 GATCAATTTGTTTTCAGA-ATG
1 GATCAATCCATTTTCATAGA-G
*
12060274 GATCAATCTATTTTCATAGAG
1 GATCAATCCATTTTCATAGAG
* *
12060295 GAACGATCCATTTTCA
1 GATCAATCCATTTTCA
12060311 GAATGGATCG
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.96
22 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
GATCAATCCATTTTCATAGAG
Found at i:12060293 original size:42 final size:42
Alignment explanation
Indices: 12060227--12060319 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
12060217 CATTGTAAGT
* * * ***
12060227 GAATCGATCAATCCATTTTTATAGAGGATCAATTTGTTTTCA
1 GAATGGATCAATCCATTTTCATAGAGGAACAATCCATTTTCA
* *
12060269 GAATGGATCAATCTATTTTCATAGAGGAACGATCCATTTTCA
1 GAATGGATCAATCCATTTTCATAGAGGAACAATCCATTTTCA
12060311 GAATGGATC
1 GAATGGATC
12060320 GTTCCATCTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (42 bp):
GAATGGATCAATCCATTTTCATAGAGGAACAATCCATTTTCA
Found at i:12060325 original size:21 final size:21
Alignment explanation
Indices: 12060263--12060326 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
12060253 GATCAATTTG
* *
12060263 TTTTCAGAATGGATCAATCTA
1 TTTTCAGAATGGATCGATCCA
* *
12060284 TTTTCATAGA-GGAACGATCCA
1 TTTTCAGA-ATGGATCGATCCA
*
12060305 TTTTCAGAATGGATCGTTCCA
1 TTTTCAGAATGGATCGATCCA
12060326 T
1 T
12060327 CTTATAAGCA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (21 bp):
TTTTCAGAATGGATCGATCCA
Found at i:12060984 original size:27 final size:27
Alignment explanation
Indices: 12060954--12061012 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
12060944 CCACCAATCT
* *
12060954 TTTTTAAGGTGTGATTAGTCACCT-AAA
1 TTTTT-AGCTGTGATTAGCCACCTAAAA
*
12060981 TTTTTTGCTGTGATTAGCCACCTAAAA
1 TTTTTAGCTGTGATTAGCCACCTAAAA
12061008 TTTTT
1 TTTTT
12061013 GTTCTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (27 bp):
TTTTTAGCTGTGATTAGCCACCTAAAA
Found at i:12061012 original size:26 final size:26
Alignment explanation
Indices: 12060963--12061013 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
12060953 TTTTTTAAGG
* *
12060963 TGTGATTAGTCACCTAAATTTTTTGC
1 TGTGATTAGCCACCTAAAATTTTTGC
12060989 TGTGATTAGCCACCTAAAATTTTTG
1 TGTGATTAGCCACCTAAAATTTTTG
12061014 TTCTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (26 bp):
TGTGATTAGCCACCTAAAATTTTTGC
Found at i:12061102 original size:29 final size:28
Alignment explanation
Indices: 12061064--12061121 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
12061054 TATTCTAATG
12061064 CTTAGAAATTAGTTCATTTGTTTTGTAAAA
1 CTTAGAAATTAGTTC-TTTGTTTTG-AAAA
**
12061094 CTTA-AAATTTTTTCTTTGTTTTGAAAA
1 CTTAGAAATTAGTTCTTTGTTTTGAAAA
12061121 C
1 C
12061122 AAATCAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.19
28 9 0.35
29 8 0.31
30 4 0.15
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (28 bp):
CTTAGAAATTAGTTCTTTGTTTTGAAAA
Found at i:12064560 original size:18 final size:19
Alignment explanation
Indices: 12064517--12064560 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
12064507 TCTTTCAAAG
12064517 TTGTTTCCAGGATGCAGTT
1 TTGTTTCCAGGATGCAGTT
* * *
12064536 CTGTTTCCA-GATTCTGTT
1 TTGTTTCCAGGATGCAGTT
12064554 TTGTTTC
1 TTGTTTC
12064561 GATTTTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (19 bp):
TTGTTTCCAGGATGCAGTT
Found at i:12071529 original size:18 final size:19
Alignment explanation
Indices: 12071486--12071529 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
12071476 TCTTTCAAAG
12071486 TTGTTTCCAGGATGCAGTT
1 TTGTTTCCAGGATGCAGTT
* * *
12071505 CTGTTTCCA-GATTCTGTT
1 TTGTTTCCAGGATGCAGTT
12071523 TTGTTTC
1 TTGTTTC
12071530 GATTTTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (19 bp):
TTGTTTCCAGGATGCAGTT
Found at i:12073602 original size:20 final size:21
Alignment explanation
Indices: 12073562--12073603 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12073552 TATTCTAAAC
*
12073562 AAAAAAAATTGAAATACCAAA
1 AAAAAAAATTGAAAAACCAAA
*
12073583 AAAAAAAATT-AAAAAGCAAA
1 AAAAAAAATTGAAAAACCAAA
12073603 A
1 A
12073604 GTTATGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAAAAAATTGAAAAACCAAA
Found at i:12074668 original size:20 final size:20
Alignment explanation
Indices: 12074643--12074723 Score: 144
Period size: 20 Copynumber: 4.0 Consensus size: 20
12074633 AGGGTTAGGG
12074643 TTGGGGTCTAGTTTAAGGTT
1 TTGGGGTCTAGTTTAAGGTT
12074663 TTGGGGTCTAGTTTAAGGTT
1 TTGGGGTCTAGTTTAAGGTT
12074683 TTGGGGTCTAGTTTAAGGTT
1 TTGGGGTCTAGTTTAAGGTT
* *
12074703 TTGGGGTTTGGTTTAAGGTT
1 TTGGGGTCTAGTTTAAGGTT
12074723 T
1 T
12074724 AGGATTTGGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.14, C:0.04, G:0.36, T:0.47
Consensus pattern (20 bp):
TTGGGGTCTAGTTTAAGGTT
Found at i:12074733 original size:19 final size:19
Alignment explanation
Indices: 12074693--12074745 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
12074683 TTGGGGTCTA
* *
12074693 GTTTAAGGTTTTGGGGTTTG
1 GTTTAAGG-TTTAGGATTTG
12074713 GTTTAAGGTTTAGGATTTG
1 GTTTAAGGTTTAGGATTTG
*
12074732 GTTTAGGGTTTAGG
1 GTTTAAGGTTTAGG
12074746 TTTATGTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (19 bp):
GTTTAAGGTTTAGGATTTG
Found at i:12074734 original size:12 final size:13
Alignment explanation
Indices: 12074718--12074830 Score: 53
Period size: 12 Copynumber: 9.1 Consensus size: 13
12074708 GTTTGGTTTA
12074718 AGGTTTAGGATTT
1 AGGTTTAGGATTT
*
12074731 -GGTTTAGGGTTT
1 AGGTTTAGGATTT
*
12074743 AGGTTTATG--TT
1 AGGTTTAGGATTT
*
12074754 AGAGTTAAGG-TTT
1 AG-GTTTAGGATTT
*
12074767 A-GTTTAGGGTTT
1 AGGTTTAGGATTT
*
12074779 GGGGTTT-GG-TTT
1 -AGGTTTAGGATTT
* *
12074791 AGGGTTA-GAGTT
1 AGGTTTAGGATTT
* *
12074803 AGGTTTTAGGCTTG
1 AGG-TTTAGGATTT
*
12074817 AGGATTAGGATTT
1 AGGTTTAGGATTT
12074830 A
1 A
12074831 TTATTTAGGG
Statistics
Matches: 74, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
11 15 0.20
12 27 0.36
13 23 0.31
14 9 0.12
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.44
Consensus pattern (13 bp):
AGGTTTAGGATTT
Found at i:12074749 original size:6 final size:6
Alignment explanation
Indices: 12074707--12074808 Score: 63
Period size: 6 Copynumber: 16.8 Consensus size: 6
12074697 AAGGTTTTGG
*
12074707 GGTTT- GGTTTAA GGTTTA GGATTT- GGTTTA GGGTTTA GGTTTA TG-TTA
1 GGTTTA GGTTT-A GGTTTA GG-TTTA GGTTTA -GGTTTA GGTTTA GGTTTA
* * *
12074755 GAGTTAA GGTTTA -GTTTA GGGTTTGG GGTTT- GGTTTA GGGTTA GAG-TTA
1 G-GTTTA GGTTTA GGTTTA -GGTTT-A GGTTTA GGTTTA GGTTTA G-GTTTA
12074804 GGTTT
1 GGTTT
12074809 TAGGCTTGAG
Statistics
Matches: 78, Mismatches: 6, Indels: 25
0.72 0.06 0.23
Matches are distributed among these distances:
5 22 0.28
6 29 0.37
7 27 0.35
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (6 bp):
GGTTTA
Found at i:12074767 original size:43 final size:42
Alignment explanation
Indices: 12074715--12074808 Score: 93
Period size: 43 Copynumber: 2.2 Consensus size: 42
12074705 GGGGTTTGGT
* * ***
12074715 TTAAGGTTTAGGATTT-GGTTTAGGGTTTAGGTTTATGTTAGAG
1 TTAAGGTTTA-G-TTTAGGTTTAGGGTTTGGTTTAGGGTTAGAG
*
12074758 TTAAGGTTTAGTTTAGGGTTTGGGGTTTGGTTTAGGGTTAGAG
1 TTAAGGTTTAGTTTA-GGTTTAGGGTTTGGTTTAGGGTTAGAG
12074801 TT-AGGTTT
1 TTAAGGTTT
12074809 TAGGCTTGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
41 3 0.07
42 7 0.16
43 33 0.77
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (42 bp):
TTAAGGTTTAGTTTAGGTTTAGGGTTTGGTTTAGGGTTAGAG
Found at i:12074790 original size:19 final size:19
Alignment explanation
Indices: 12074637--12074796 Score: 112
Period size: 20 Copynumber: 8.4 Consensus size: 19
12074627 TTAACTAGGG
*
12074637 TTAGGG-TTGGGGTCTAGT
1 TTAGGGTTTGGGGTTTAGT
* *
12074655 TTAAGGTTTTGGGGTCTAGT
1 TT-AGGGTTTGGGGTTTAGT
* *
12074675 TTAAGGTTTTGGGGTCTAGT
1 TT-AGGGTTTGGGGTTTAGT
* *
12074695 TTAAGGTTTTGGGGTTTGGT
1 TT-AGGGTTTGGGGTTTAGT
* * * *
12074715 TTAAGGTTTAGGATTTGGT
1 TTAGGGTTTGGGGTTTAGT
*
12074734 TTAGGGTTT-AGGTTTA-T
1 TTAGGGTTTGGGGTTTAGT
* **
12074751 GTTAGAG-TTAAGGTTTAGT
1 -TTAGGGTTTGGGGTTTAGT
*
12074770 TTAGGGTTTGGGGTTTGGT
1 TTAGGGTTTGGGGTTTAGT
12074789 TTAGGGTT
1 TTAGGGTT
12074797 AGAGTTAGGT
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
17 3 0.03
18 23 0.19
19 42 0.35
20 52 0.43
ACGTcount: A:0.15, C:0.02, G:0.37, T:0.46
Consensus pattern (19 bp):
TTAGGGTTTGGGGTTTAGT
Found at i:12077214 original size:42 final size:42
Alignment explanation
Indices: 12077085--12077301 Score: 167
Period size: 42 Copynumber: 5.2 Consensus size: 42
12077075 CCAAGGATTC
* *
12077085 ACAAAGTAAATGATTCACA---TAAAAGATTCTAGATTTACA
1 ACAAAGTAAATGATTCACAGCTTGAAAGACTCTAGATTTACA
* * * * * **
12077124 ATAAAGTAAATAATTCATAGATTGAATGACTCTAGATTCGCA
1 ACAAAGTAAATGATTCACAGCTTGAAAGACTCTAGATTTACA
**
12077166 GTAAAGTAAATGATTCACAGCTTGAAAGACTCTAGATTTACA
1 ACAAAGTAAATGATTCACAGCTTGAAAGACTCTAGATTTACA
* ** * *
12077208 ACAAAGTAAACGATTCACAATTTGAAAGACT-TTGAGTTGACA
1 ACAAAGTAAATGATTCACAGCTTGAAAGACTCTAGA-TTTACA
* * * * * *
12077250 ATAGAGCT-AATGATTCACAGCTTGGAATACT-TGGGATTTATA
1 ACAAAG-TAAATGATTCACAGCTTGAAAGACTCT-AGATTTACA
12077292 ACAAAGTAAA
1 ACAAAGTAAA
12077302 AGAATAAACA
Statistics
Matches: 137, Mismatches: 34, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
39 16 0.12
41 4 0.03
42 114 0.83
43 3 0.02
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (42 bp):
ACAAAGTAAATGATTCACAGCTTGAAAGACTCTAGATTTACA
Found at i:12077233 original size:84 final size:81
Alignment explanation
Indices: 12077087--12077238 Score: 198
Period size: 84 Copynumber: 1.8 Consensus size: 81
12077077 AAGGATTCAC
* * * * *
12077087 AAAGTAAATGATTCACATAAAAGATTCTAGATTTACAATAAAGTAAATAATTCATAGATTGAATG
1 AAAGTAAATGATTCACATAAAAGACTCTAGATTTACAACAAAGTAAACAATTCACAGATTGAAAG
12077152 ACTCTAGATTCGCAGT
66 ACTCTAGATTCGCAGT
* *
12077168 AAAGTAAATGATTCACAGCTTGAAAGACTCTAGATTTACAACAAAGTAAACGATTCACA-ATTTG
1 AAAGTAAATGATTCACA---TAAAAGACTCTAGATTTACAACAAAGTAAACAATTCACAGA-TTG
12077232 AAAGACT
62 AAAGACT
12077239 TTGAGTTGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
81 17 0.28
83 1 0.02
84 42 0.70
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (81 bp):
AAAGTAAATGATTCACATAAAAGACTCTAGATTTACAACAAAGTAAACAATTCACAGATTGAAAG
ACTCTAGATTCGCAGT
Found at i:12077675 original size:37 final size:37
Alignment explanation
Indices: 12077618--12077710 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
12077608 AAGGACTTGT
* ** *
12077618 AAATTTCAAAGTTTTGCAAGAGAGGTTAAAGATTCAC
1 AAATTTCAAAGATTCACAAGAAAGGTTAAAGATTCAC
*
12077655 AAATTTCAAAGATTCACAAGAAAGGTTAAAGATTCAT
1 AAATTTCAAAGATTCACAAGAAAGGTTAAAGATTCAC
* *
12077692 AAATTCCAGAGATTCACAA
1 AAATTTCAAAGATTCACAA
12077711 ATATAAATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (37 bp):
AAATTTCAAAGATTCACAAGAAAGGTTAAAGATTCAC
Found at i:12077687 original size:20 final size:20
Alignment explanation
Indices: 12077634--12077690 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
12077624 CAAAGTTTTG
*
12077634 CAAGAGAGGTTAAAGATTCA
1 CAAGAAAGGTTAAAGATTCA
*
12077654 C---AAA-TTTCAAAGATTCA
1 CAAGAAAGGTT-AAAGATTCA
12077671 CAAGAAAGGTTAAAGATTCA
1 CAAGAAAGGTTAAAGATTCA
12077691 TAAATTCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
16 2 0.07
17 12 0.41
20 13 0.45
21 2 0.07
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (20 bp):
CAAGAAAGGTTAAAGATTCA
Found at i:12079395 original size:26 final size:24
Alignment explanation
Indices: 12079347--12079430 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 24
12079337 GGTTTCTCCC
*
12079347 TTTCTTTTTCTTTTTCCCATTTCTT
1 TTTCTTTTTCTTTTTCTCATTT-TT
*
12079372 TTTCTTTTTC---CT-TCATTTTT
1 TTTCTTTTTCTTTTTCTCATTTTT
*
12079392 TTTCCTTTTCTTACTTTCTCATTTTT
1 TTTCTTTTTCTT--TTTCTCATTTTT
*
12079418 TTT-TTTTCCTTTT
1 TTTCTTTTTCTTTT
12079431 AAATGGATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
20 11 0.23
21 5 0.11
22 1 0.02
23 2 0.04
25 17 0.36
26 11 0.23
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTCTTTTTCTTTTTCTCATTTTT
Found at i:12079401 original size:20 final size:19
Alignment explanation
Indices: 12079343--12079401 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
12079333 CTTTGGTTTC
12079343 TCCC-TTTCTTTTTCTTTT
1 TCCCATTTCTTTTTCTTTT
12079361 TCCCATTTCTTTTTCTTTT
1 TCCCATTTCTTTTTCTTTT
*
12079380 TCCTTCATTT-TTTTTCCTTT
1 TCC--CATTTCTTTTTCTTTT
12079400 TC
1 TC
12079402 TTACTTTCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 4 0.11
19 17 0.46
20 11 0.30
21 5 0.14
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.69
Consensus pattern (19 bp):
TCCCATTTCTTTTTCTTTT
Found at i:12079746 original size:14 final size:14
Alignment explanation
Indices: 12079727--12079753 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12079717 TGAAGAAAGA
12079727 TTTTTTTATTTTAT
1 TTTTTTTATTTTAT
12079741 TTTTTTTATTTTA
1 TTTTTTTATTTTA
12079754 GGATTTCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTATTTTAT
Found at i:12079943 original size:8 final size:8
Alignment explanation
Indices: 12079932--12079978 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
12079922 ATCTTTTTCA
12079932 TCTTTGTT
1 TCTTTGTT
12079940 TCTTTGTT
1 TCTTTGTT
*
12079948 TTTTTGTT
1 TCTTTGTT
*
12079956 TCTTCTTTGT
1 TCTT-TGT-T
12079966 TCTTT-TT
1 TCTTTGTT
12079973 TCTTTG
1 TCTTTG
12079979 CATACCCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 6 0.18
8 19 0.58
9 3 0.09
10 5 0.15
ACGTcount: A:0.00, C:0.13, G:0.11, T:0.77
Consensus pattern (8 bp):
TCTTTGTT
Found at i:12079962 original size:27 final size:25
Alignment explanation
Indices: 12079927--12079978 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
12079917 TTTTCATCTT
*
12079927 TTTCATCTTTGTTTCTTTGTTTTTTTG
1 TTTCATCTTTG-TTCTTT-TTTCTTTG
*
12079954 TTTCTTCTTTGTTCTTTTTTCTTTG
1 TTTCATCTTTGTTCTTTTTTCTTTG
12079979 CATACCCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 6 0.26
27 10 0.43
ACGTcount: A:0.02, C:0.13, G:0.10, T:0.75
Consensus pattern (25 bp):
TTTCATCTTTGTTCTTTTTTCTTTG
Found at i:12089392 original size:50 final size:50
Alignment explanation
Indices: 12089338--12089439 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 50
12089328 AGAGGGTTTA
* * *
12089338 AAACTTTAAAAATCTCATCTTTGGAAAGCTCTTCCTAAACAGAA-GCTTTG
1 AAACTTTAAAAATCACATCTTTGAAAAGCTCTTCCCAAACA-AAGGCTTTG
* *
12089388 AAACTTTAAATATCACATCTTTGAAAAGCTCTTCCCAAATAAAGGCTTTG
1 AAACTTTAAAAATCACATCTTTGAAAAGCTCTTCCCAAACAAAGGCTTTG
12089438 AA
1 AA
12089440 TTTTAAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 2 0.04
50 44 0.96
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (50 bp):
AAACTTTAAAAATCACATCTTTGAAAAGCTCTTCCCAAACAAAGGCTTTG
Found at i:12089811 original size:31 final size:34
Alignment explanation
Indices: 12089776--12089857 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 34
12089766 CCAGTTAACT
*
12089776 TAGGCTTAAA-TCT-TATC-AGTGCCAACTAATC
1 TAGGCTTAAAGTCTCAATCGAGTGCCAACTAATC
12089807 TAGGCTTAAAGTCTCAATCTGAGTGCCAACTAAAT-
1 TAGGCTTAAAGTCTCAATC-GAGTGCCAACT-AATC
* *
12089842 TGGGCTTAAAATCTCA
1 TAGGCTTAAAGTCTCA
12089858 CTTTGGATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 10 0.23
32 3 0.07
33 3 0.07
35 24 0.56
36 3 0.07
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (34 bp):
TAGGCTTAAAGTCTCAATCGAGTGCCAACTAATC
Found at i:12089935 original size:31 final size:31
Alignment explanation
Indices: 12089881--12090120 Score: 124
Period size: 33 Copynumber: 7.5 Consensus size: 31
12089871 CTAAATTGGA
**** *
12089881 CTTAAATCTCATATGTACCAGCTAAACTGGG
1 CTTAAATCTCATATGGGTGAGCTAAACTAGG
*
12089912 CTTAAATCTCATATGGGTGAGCTAAACTAGA
1 CTTAAATCTCATATGGGTGAGCTAAACTAGG
* * *
12089943 CTTAAATCTAATTTGGGTGTCAGCTAAACTGGG
1 CTTAAATCTCATATGGGTG--AGCTAAACTAGG
* * * * * *
12089976 TTTAAATCTTATCTGGTTGTCAACTAAACTAGC
1 CTTAAATCTCATATGG--GTGAGCTAAACTAGG
* * * *
12090009 CTGAAATCTCTTTTGGGTGCCAACTAAACTAGG
1 CTTAAATCTCATATGGGTG--AGCTAAACTAGG
* * * *
12090042 CTTAATTCTCATCTGAGTGCTAGTTAAACTAGG
1 CTTAAATCTCATATGGGTG--AGCTAAACTAGG
* * * *
12090075 CTTAATTTTCTCTATAT--GTCAGTTAAACTGGG
1 CTTAA--ATCTC-ATATGGGTGAGCTAAACTAGG
12090107 CTTAAATCTCATAT
1 CTTAAATCTCATAT
12090121 AAATGCCAGT
Statistics
Matches: 164, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
29 4 0.02
30 4 0.02
31 44 0.27
32 16 0.10
33 84 0.51
34 2 0.01
35 7 0.04
36 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (31 bp):
CTTAAATCTCATATGGGTGAGCTAAACTAGG
Found at i:12090025 original size:66 final size:64
Alignment explanation
Indices: 12089756--12090056 Score: 185
Period size: 66 Copynumber: 4.6 Consensus size: 64
12089746 TGGGCTTTAA
* * * * * * * * * *
12089756 AATTTGGGGGCCAG-TTAACTTAGGCTTAAATCTTATCAGTGCCAACTAATCTAGGCTTAAAGTC
1 AATTTGGGTGCCAGCTAAAC-TGGGCTTAAATCTCATCTGGGTCAACTAAACTAGACTGAAA-TC
12089820 T
64 T
* * * * * * * * *
12089821 CAATCTGAGTGCCAACTAAATTGGGCTTAAAATCTCACTTTGGATACTAACTAAATTGGACTTAA
1 -AATTTGGGTGCCAGCTAAACTGGGCTT-AAATCTCA-TCTGGGT-C-AACTAAACTAGACTGAA
12089886 ATCT
61 ATCT
* * * * * * *
12089890 CATAT--GTACCAGCTAAACTGGGCTTAAATCTCATATGGGTGAGCTAAACTAGACTTAAATCT
1 AATTTGGGTGCCAGCTAAACTGGGCTTAAATCTCATCTGGGTCAACTAAACTAGACTGAAATCT
* * * *
12089952 AATTTGGGTGTCAGCTAAACTGGGTTTAAATCTTATCTGGTTGTCAACTAAACTAGCCTGAAATC
1 AATTTGGGTGCCAGCTAAACTGGGCTTAAATCTCATCTGG--GTCAACTAAACTAGACTGAAATC
12090017 T
64 T
** * * *
12090018 CTTTTGGGTGCCAACTAAACTAGGCTTAATTCTCATCTG
1 AATTTGGGTGCCAGCTAAACTGGGCTTAAATCTCATCTG
12090057 AGTGCTAGTT
Statistics
Matches: 179, Mismatches: 47, Indels: 18
0.73 0.19 0.07
Matches are distributed among these distances:
62 21 0.12
64 33 0.18
65 8 0.04
66 84 0.47
67 10 0.06
68 5 0.03
69 4 0.02
70 14 0.08
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (64 bp):
AATTTGGGTGCCAGCTAAACTGGGCTTAAATCTCATCTGGGTCAACTAAACTAGACTGAAATCT
Found at i:12090145 original size:33 final size:33
Alignment explanation
Indices: 12090033--12090152 Score: 125
Period size: 33 Copynumber: 3.6 Consensus size: 33
12090023 GGGTGCCAAC
* * * *
12090033 TAAACTAGGCTTAATTCTCATCTGAGTGCTAGT
1 TAAACTAGGCTTAAATCTCATCTAAATGCCAGT
* * * *
12090066 TAAACTAGGCTTAATTTTC-TCTATATGTCAGT
1 TAAACTAGGCTTAAATCTCATCTAAATGCCAGT
* *
12090098 TAAACTGGGCTTAAATCTCATATAAATGCCAGT
1 TAAACTAGGCTTAAATCTCATCTAAATGCCAGT
*
12090131 TAAATTAGGCTTAAAATCTCAT
1 TAAACTAGGCTT-AAATCTCAT
12090153 TTTGGTGCCA
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
32 24 0.34
33 38 0.54
34 9 0.13
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (33 bp):
TAAACTAGGCTTAAATCTCATCTAAATGCCAGT
Found at i:12090346 original size:32 final size:33
Alignment explanation
Indices: 12090243--12090493 Score: 181
Period size: 33 Copynumber: 7.6 Consensus size: 33
12090233 TATGTGCTGA
*
12090243 CTAAACTAGGTTTAAAATCTCAATTTGAGTGCTAG
1 CTAAACTAGGCTT-AAATCTC-ATTTGAGTGCTAG
** *
12090278 CTAAACTAAACTTAAATCTCATTTAAGTGCTAG
1 CTAAACTAGGCTTAAATCTCATTTGAGTGCTAG
*
12090311 CTAAACTAGGCTT-CATCTTC-TTTG-GTTGCTAG
1 CTAAACTAGGCTTAAATC-TCATTTGAG-TGCTAG
* * *
12090343 CTAAACTGGGTTTAAATCTCATTTGAGTGCTAA
1 CTAAACTAGGCTTAAATCTCATTTGAGTGCTAG
* * * *
12090376 CTAAACTAGGCTTAAAATCTCATATGGGTGCCAA
1 CTAAACTAGGCTT-AAATCTCATTTGAGTGCTAG
* * ** * * *
12090410 CTACACT-GTGTTTAAATCTCA-TCAAATGCCAT
1 CTAAACTAG-GCTTAAATCTCATTTGAGTGCTAG
* * *
12090442 CTCAACTAGGCTTAAATCTCATTT-AGGTGCCAA
1 CTAAACTAGGCTTAAATCTCATTTGA-GTGCTAG
* *
12090475 TTAAACTAGGTTTAAATCT
1 CTAAACTAGGCTTAAATCT
12090494 TTTTTTTTTC
Statistics
Matches: 172, Mismatches: 34, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
31 1 0.01
32 47 0.27
33 80 0.47
34 34 0.20
35 10 0.06
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (33 bp):
CTAAACTAGGCTTAAATCTCATTTGAGTGCTAG
Found at i:12090664 original size:11 final size:10
Alignment explanation
Indices: 12090648--12090706 Score: 66
Period size: 10 Copynumber: 5.7 Consensus size: 10
12090638 CCATGTTATA
12090648 CTTTTTTGTCT
1 CTTTTTT-TCT
*
12090659 CTTTTTTTTT
1 CTTTTTTTCT
12090669 CTTTCTTTTCT
1 CTTT-TTTTCT
12090680 -TTTTCTTTCT
1 CTTTT-TTTCT
*
12090690 ATTTTTTTCT
1 CTTTTTTTCT
12090700 CTTTTTT
1 CTTTTTT
12090707 CCAAATTCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
9 1 0.02
10 25 0.60
11 16 0.38
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (10 bp):
CTTTTTTTCT
Found at i:12090671 original size:10 final size:10
Alignment explanation
Indices: 12090648--12090706 Score: 57
Period size: 11 Copynumber: 5.7 Consensus size: 10
12090638 CCATGTTATA
*
12090648 CTTTTTTGTCT
1 CTTTTTT-TTT
12090659 CTTTTTTTTT
1 CTTTTTTTTT
*
12090669 C-TTTCTTTT
1 CTTTTTTTTT
*
12090678 CTTTTTCTTT
1 CTTTTTTTTT
12090688 CTATTTTTTTCT
1 CT-TTTTTTT-T
12090700 CTTTTTT
1 CTTTTTT
12090707 CCAAATTCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 8 0.20
10 11 0.28
11 18 0.45
12 3 0.08
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:12090682 original size:15 final size:14
Alignment explanation
Indices: 12090658--12090699 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
12090648 CTTTTTTGTC
12090658 TCTTTTTTTTTCTT
1 TCTTTTTTTTTCTT
12090672 TCTTTTCTTTTTCTT
1 TCTTTT-TTTTTCTT
*
12090687 TCTATTTTTTTCT
1 TCTTTTTTTTTCT
12090700 CTTTTTTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (14 bp):
TCTTTTTTTTTCTT
Found at i:12090682 original size:16 final size:16
Alignment explanation
Indices: 12090660--12090703 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
12090650 TTTTTGTCTC
12090660 TTTTTTTTTCTTTCT-
1 TTTTTTTTTCTTTCTA
*
12090675 TTTCTTTTTCTTTCTA
1 TTTTTTTTTCTTTCTA
*
12090691 TTTTTTTCTCTTT
1 TTTTTTTTTCTTT
12090704 TTTCCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTCTTTCTA
Found at i:12090683 original size:29 final size:29
Alignment explanation
Indices: 12090650--12090707 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
12090640 ATGTTATACT
* *
12090650 TTTTTGTCTCTTTTTTTTTCT-TTCTTTTC
1 TTTTTCTCTCTATTTTTTTCTCTT-TTTTC
*
12090679 TTTTTCTTTCTATTTTTTTCTCTTTTTTC
1 TTTTTCTCTCTATTTTTTTCTCTTTTTTC
12090708 CAAATTCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (29 bp):
TTTTTCTCTCTATTTTTTTCTCTTTTTTC
Found at i:12093310 original size:15 final size:15
Alignment explanation
Indices: 12093292--12093336 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
12093282 TTTCATTTCA
12093292 TTTCTTTTTTGTTTT
1 TTTCTTTTTTGTTTT
*
12093307 TTTCTCTTGTT-TTTT
1 TTTCT-TTTTTGTTTT
12093322 TTTC-TTTTTGTTTT
1 TTTCTTTTTTGTTTT
12093336 T
1 T
12093337 GTTTCCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 4 0.15
14 5 0.19
15 13 0.50
16 4 0.15
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (15 bp):
TTTCTTTTTTGTTTT
Found at i:12093949 original size:7 final size:7
Alignment explanation
Indices: 12093939--12093963 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12093929 AAAAAAAAAA
12093939 CTTTATT
1 CTTTATT
12093946 CTTTATT
1 CTTTATT
12093953 CTTTATT
1 CTTTATT
12093960 CTTT
1 CTTT
12093964 TCCCTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (7 bp):
CTTTATT
Found at i:12096607 original size:17 final size:16
Alignment explanation
Indices: 12096594--12096631 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
12096584 ATCTTTTTAT
12096594 TTCTTTTCTTTTTTTCA
1 TTCTTTT-TTTTTTTCA
12096611 TTCTTTTTTTTTCTTC-
1 TTCTTTTTTTTT-TTCA
12096627 TTCTT
1 TTCTT
12096632 CTATTACCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCTTTTTTTTTTTCA
Found at i:12096627 original size:13 final size:13
Alignment explanation
Indices: 12096585--12096628 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
12096575 ATTGGGTGGA
*
12096585 TCTTTTTATTTCT
1 TCTTTTTTTTTCT
12096598 T-TTCTTTTTTTCAT
1 TCTT-TTTTTTTC-T
12096612 TCTTTTTTTTTCT
1 TCTTTTTTTTTCT
12096625 TCTT
1 TCTT
12096629 CTTCTATTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.07
13 13 0.48
14 10 0.37
15 2 0.07
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TCTTTTTTTTTCT
Found at i:12096922 original size:17 final size:17
Alignment explanation
Indices: 12096897--12096932 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
12096887 CTTCTCACTT
*
12096897 TTTTTTCCTTTTTTTCA
1 TTTTCTCCTTTTTTTCA
12096914 TTTTCTCCTTTTTTTCA
1 TTTTCTCCTTTTTTTCA
12096931 TT
1 TT
12096933 GCCTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCTCCTTTTTTTCA
Found at i:12101912 original size:3 final size:3
Alignment explanation
Indices: 12101904--12101929 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12101894 CTTTTGTGCT
12101904 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12101930 TTTACTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12108750 original size:21 final size:21
Alignment explanation
Indices: 12108726--12108791 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
12108716 TTTTTAGATT
12108726 GGATCAATCCATTTTCATAGA
1 GGATCAATCCATTTTCATAGA
* ** *
12108747 GGATCGATATATTTTCA-AAA
1 GGATCAATCCATTTTCATAGA
*
12108767 TGGATCAATCCATTTT-ATAGG
1 -GGATCAATCCATTTTCATAGA
12108788 GGAT
1 GGAT
12108792 TGATCCCTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
20 7 0.21
21 27 0.79
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (21 bp):
GGATCAATCCATTTTCATAGA
Found at i:12110124 original size:30 final size:30
Alignment explanation
Indices: 12110090--12110149 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
12110080 ATCTTGACCT
* * *
12110090 TAAACCCCAAACCAAAGCCTAACCTTAAAC
1 TAAACACCAAACCAAACCCTAACCCTAAAC
*
12110120 TAAACACCAAATCAAACCCTAACCCTAAAC
1 TAAACACCAAACCAAACCCTAACCCTAAAC
12110150 AATATCTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.48, C:0.37, G:0.02, T:0.13
Consensus pattern (30 bp):
TAAACACCAAACCAAACCCTAACCCTAAAC
Found at i:12114918 original size:17 final size:17
Alignment explanation
Indices: 12114893--12114926 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12114883 AAATACATGA
*
12114893 TTAAAATTTTGATAATC
1 TTAAAATTTTGAGAATC
*
12114910 TTAAGATTTTGAGAATC
1 TTAAAATTTTGAGAATC
12114927 ATCCAAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
TTAAAATTTTGAGAATC
Found at i:12117364 original size:22 final size:22
Alignment explanation
Indices: 12117323--12117388 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 22
12117313 GTTTTCCCTT
*
12117323 TTTTTGTTTATTTTCTATTTTGA
1 TTTTTGTTTATTTT-GATTTTGA
12117346 TTTTTGTTTATTTTGATTTTGA
1 TTTTTGTTTATTTTGATTTTGA
* *
12117368 TTTTTGATTTTTTTTGTTTTT
1 TTTTTG-TTTATTTTGATTTT
12117389 TATATATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
22 13 0.33
23 26 0.67
ACGTcount: A:0.11, C:0.02, G:0.11, T:0.77
Consensus pattern (22 bp):
TTTTTGTTTATTTTGATTTTGA
Found at i:12117381 original size:16 final size:15
Alignment explanation
Indices: 12117338--12117378 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 15
12117328 GTTTATTTTC
12117338 TATTTTGATTTTTGTT
1 TATTTTGA-TTTTGTT
*
12117354 TATTTTGATTTTG-A
1 TATTTTGATTTTGTT
12117368 T-TTTTGATTTT
1 TATTTTGATTTT
12117379 TTTTGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 5 0.21
16 8 0.33
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (15 bp):
TATTTTGATTTTGTT
Found at i:12122462 original size:17 final size:18
Alignment explanation
Indices: 12122431--12122464 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12122421 TGTAAAAAAA
*
12122431 AAAGCAAAAGAGAAAATG
1 AAAGAAAAAGAGAAAATG
12122449 AAAGAAAAAG-GAAAAT
1 AAAGAAAAAGAGAAAAT
12122465 TTAAATTGAA
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:0.71, C:0.03, G:0.21, T:0.06
Consensus pattern (18 bp):
AAAGAAAAAGAGAAAATG
Found at i:12126265 original size:22 final size:22
Alignment explanation
Indices: 12126237--12126278 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12126227 TCAACCAAGT
12126237 AATGTAATTGCATTCCATAAGC
1 AATGTAATTGCATTCCATAAGC
*
12126259 AATGTAATTGCATTTCATAA
1 AATGTAATTGCATTCCATAA
12126279 TCTATAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
AATGTAATTGCATTCCATAAGC
Found at i:12126320 original size:91 final size:90
Alignment explanation
Indices: 12126165--12126351 Score: 284
Period size: 91 Copynumber: 2.1 Consensus size: 90
12126155 ACATCAACCG
*
12126165 AGCAATGTAATTGCATTACATAATCAATAGACAGTGTAATGTAATCACATAACAAATAGACATCA
1 AGCAATGTAATTGCATTACATAATCAATAGACAGTGTAATATAATCACATAACAAATAGACATCA
*
12126230 ACCAAGTAATGTAATTGCATTCCATA
66 ACCAAGCAATG-AATTGCATTCCATA
* * * **
12126256 AGCAATGTAATTGCATTTCATAATCTATAGATAGTGTAATATAATTGCATAACAAATAGACATCA
1 AGCAATGTAATTGCATTACATAATCAATAGACAGTGTAATATAATCACATAACAAATAGACATCA
*
12126321 ACCGAGCAATGAATTGCATTCCATA
66 ACCAAGCAATGAATTGCATTCCATA
*
12126346 ATCAAT
1 AGCAAT
12126352 AGACAGTGTA
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 19 0.22
91 68 0.78
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (90 bp):
AGCAATGTAATTGCATTACATAATCAATAGACAGTGTAATATAATCACATAACAAATAGACATCA
ACCAAGCAATGAATTGCATTCCATA
Found at i:12126336 original size:34 final size:33
Alignment explanation
Indices: 12126298--12126402 Score: 94
Period size: 34 Copynumber: 3.2 Consensus size: 33
12126288 AGTGTAATAT
12126298 AATTGCATAACAAATAGACATCAACCGAGCAATG
1 AATTGCATAACAAATA-ACATCAACCGAGCAATG
* * ** *
12126332 AATTGCAT-TC-CAT-A-ATCAATAGA-CAGTG
1 AATTGCATAACAAATAACATCAACCGAGCAATG
*
12126360 TAATTGCATAACAAATATACATCAACCAAGCAATG
1 -AATTGCATAACAAATA-ACATCAACCGAGCAATG
12126395 AATTGCAT
1 AATTGCAT
12126403 TCCATATTCT
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
28 4 0.08
29 15 0.28
30 2 0.04
31 2 0.04
32 2 0.04
33 2 0.04
34 22 0.42
35 4 0.08
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (33 bp):
AATTGCATAACAAATAACATCAACCGAGCAATG
Found at i:12126346 original size:68 final size:63
Alignment explanation
Indices: 12126255--12126414 Score: 212
Period size: 63 Copynumber: 2.4 Consensus size: 63
12126245 TGCATTCCAT
* *
12126255 AAGCAATGTAATTGCATTTCATAATCTATAGATAGTGTAATATAATTGCATAACAAATAGACATC
1 AAGCAATG-AATTGCATTCCATAATCTATAGACAGTG-----TAATTGCATAACAAATAGACATC
12126320 AACC
60 AACC
* * *
12126324 GAGCAATGAATTGCATTCCATAATCAATAGACAGTGTAATTGCATAACAAATATACATCAACC
1 AAGCAATGAATTGCATTCCATAATCTATAGACAGTGTAATTGCATAACAAATAGACATCAACC
*
12126387 AAGCAATGAATTGCATTCCATATTCTAT
1 AAGCAATGAATTGCATTCCATAATCTAT
12126415 TAAGGTAGAC
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 51 0.61
68 25 0.30
69 7 0.08
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (63 bp):
AAGCAATGAATTGCATTCCATAATCTATAGACAGTGTAATTGCATAACAAATAGACATCAACC
Found at i:12135258 original size:21 final size:21
Alignment explanation
Indices: 12135233--12135274 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12135223 ATTTAACTTG
12135233 TAAGAGAAAAATTCTAAGAGA
1 TAAGAGAAAAATTCTAAGAGA
*
12135254 TAAGAGAAAAATTTTAAGAGA
1 TAAGAGAAAAATTCTAAGAGA
12135275 AAAAATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.19, T:0.21
Consensus pattern (21 bp):
TAAGAGAAAAATTCTAAGAGA
Found at i:12135921 original size:24 final size:25
Alignment explanation
Indices: 12135889--12135982 Score: 120
Period size: 25 Copynumber: 3.8 Consensus size: 25
12135879 AAAAAAACCG
*
12135889 AAAGTTTGAGACGT-GGAAGAGCTT
1 AAAGTTTGAGATGTGGGAAGAGCTT
*
12135913 AAAGTTTGAGATGTGGGAAGAGCTA
1 AAAGTTTGAGATGTGGGAAGAGCTT
*
12135938 AAAGTTCGAGATGTGGGAAGAGC-T
1 AAAGTTTGAGATGTGGGAAGAGCTT
* *
12135962 AAAGATTTAAGATATGGGAAG
1 AAAG-TTTGAGATGTGGGAAG
12135983 TGCATGGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
24 17 0.28
25 44 0.72
ACGTcount: A:0.37, C:0.05, G:0.34, T:0.23
Consensus pattern (25 bp):
AAAGTTTGAGATGTGGGAAGAGCTT
Found at i:12136424 original size:52 final size:51
Alignment explanation
Indices: 12136291--12136435 Score: 200
Period size: 52 Copynumber: 2.8 Consensus size: 51
12136281 ATTGTAAAAA
*
12136291 AAGAATTCTAAGAGAAAGGAGATTCTTAATAGGTAAGTTTGACTTATAAGAG
1 AAGAATTCTAAGAGAAAGG-GATTCTTAATAGGCAAGTTTGACTTATAAGAG
** *
12136343 AAGAATTCTAAGAGAAAAAAGATTCTTAATAGGCATGTTTGACTTATAAGAG
1 AAGAATTCTAAGAG-AAAGGGATTCTTAATAGGCAAGTTTGACTTATAAGAG
* * *
12136395 AAGAATTCTAAGAAGAGAGGGATTATTAATGGGCAAGTTTG
1 AAGAATTCTAAG-AGAAAGGGATTCTTAATAGGCAAGTTTG
12136436 TATGGTTATA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
52 76 0.94
53 5 0.06
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.28
Consensus pattern (51 bp):
AAGAATTCTAAGAGAAAGGGATTCTTAATAGGCAAGTTTGACTTATAAGAG
Found at i:12137137 original size:2 final size:2
Alignment explanation
Indices: 12137130--12137180 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
12137120 GTAGAGCAAA
12137130 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12137172 AG AG AG AG A
1 AG AG AG AG A
12137181 ATTGAAGCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12137557 original size:16 final size:15
Alignment explanation
Indices: 12137534--12137563 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12137524 TCCATCTTGC
12137534 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
12137549 TTTTCCTTTTTTTTT
1 TTTT-CTTTTTTTTT
12137564 AACCTTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:12137558 original size:15 final size:15
Alignment explanation
Indices: 12137534--12137563 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12137524 TCCATCTTGC
*
12137534 TTTTCTTTTTTTTTT
1 TTTTCCTTTTTTTTT
12137549 TTTTCCTTTTTTTTT
1 TTTTCCTTTTTTTTT
12137564 AACCTTTTGT
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:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCCTTTTTTTTT
Found at i:12138304 original size:21 final size:19
Alignment explanation
Indices: 12138278--12138318 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
12138268 TACCTACTAT
12138278 TAGAAAAAATAAATAAAATAA
1 TAGAAAAAAT-AA-AAAATAA
*
12138299 TAGAAATAATAAAAAATAA
1 TAGAAAAAATAAAAAATAA
12138318 T
1 T
12138319 TTTGATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (19 bp):
TAGAAAAAATAAAAAATAA
Found at i:12141390 original size:15 final size:15
Alignment explanation
Indices: 12141372--12141402 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12141362 TCAAATAATT
12141372 ATAATAATTTATATA
1 ATAATAATTTATATA
*
12141387 ATAATTATTTATATA
1 ATAATAATTTATATA
12141402 A
1 A
12141403 ACAATTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATAATTTATATA
Found at i:12142930 original size:23 final size:23
Alignment explanation
Indices: 12142895--12142939 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12142885 ATTTATATTA
* *
12142895 TTAAAATTTTAATAATATAATTT
1 TTAAAATTCTAATAATAAAATTT
*
12142918 TTAATATTCTAATAATAAAATT
1 TTAAAATTCTAATAATAAAATT
12142940 ACATAAAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAAATTCTAATAATAAAATTT
Found at i:12150202 original size:22 final size:22
Alignment explanation
Indices: 12150174--12150216 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12150164 CTGATTGGGA
12150174 CATTCTGCAAGTGCATAGGCTG
1 CATTCTGCAAGTGCATAGGCTG
*
12150196 CATTCTGGAAGTGCATAGGCT
1 CATTCTGCAAGTGCATAGGCT
12150217 AAACAAGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (22 bp):
CATTCTGCAAGTGCATAGGCTG
Found at i:12152939 original size:15 final size:15
Alignment explanation
Indices: 12152905--12152940 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12152895 TATTTTTTGA
12152905 AAAAAATCAAAAAAT
1 AAAAAATCAAAAAAT
* *
12152920 CAAAAATCAAAAAGT
1 AAAAAATCAAAAAAT
12152935 AAAAAA
1 AAAAAA
12152941 AAAATTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.78, C:0.08, G:0.03, T:0.11
Consensus pattern (15 bp):
AAAAAATCAAAAAAT
Found at i:12156267 original size:9 final size:9
Alignment explanation
Indices: 12156253--12156287 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
12156243 TGATTTATGA
12156253 AAAAAAAAG
1 AAAAAAAAG
12156262 AAAAAAAAG
1 AAAAAAAAG
* *
12156271 AAAAAGATG
1 AAAAAAAAG
12156280 AAAAAAAA
1 AAAAAAAA
12156288 AGAGTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:12157150 original size:21 final size:21
Alignment explanation
Indices: 12157121--12157214 Score: 64
Period size: 21 Copynumber: 4.3 Consensus size: 21
12157111 GAAGATGAAC
*
12157121 AAGAAGATGAAGATAAAGATA
1 AAGAAGATGAAGAAAAAGATA
* * *
12157142 AAGATGATGACGAAAAAGATG
1 AAGAAGATGAAGAAAAAGATA
**
12157163 AAGAA-AAAAATGAAAAAGATAAAA
1 AAGAAGATGAA-GAAAAAGAT---A
* * *
12157187 AAGAAGATGATGAAGAAGAAA
1 AAGAAGATGAAGAAAAAGATA
12157208 AAGAAGA
1 AAGAAGA
12157215 AGAATAGGAA
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
20 2 0.04
21 38 0.70
24 12 0.22
25 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.23, T:0.11
Consensus pattern (21 bp):
AAGAAGATGAAGAAAAAGATA
Found at i:12157398 original size:22 final size:22
Alignment explanation
Indices: 12157373--12157418 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12157363 GGTGTATGTT
12157373 TTTAAATATATTATT-AAATATA
1 TTTAAAT-TATTATTGAAATATA
* *
12157395 TTTACATTATTATTGATATATA
1 TTTAAATTATTATTGAAATATA
12157417 TT
1 TT
12157419 ATATTTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTAAATTATTATTGAAATATA
Found at i:12159262 original size:25 final size:25
Alignment explanation
Indices: 12159210--12159296 Score: 72
Period size: 25 Copynumber: 3.4 Consensus size: 25
12159200 ATTTTTACAG
12159210 AAAATAAAAA-AC-ATCCAAAAAAGTTA
1 AAAATAAAAAGACAAT-CAAAAAA--TA
12159236 AAAATAAAAAGACAATCAAAAAATA
1 AAAATAAAAAGACAATCAAAAAATA
* ** *
12159261 AAAA-AAGAAAGAGAAAGAAAAAAGA
1 AAAATAA-AAAGACAATCAAAAAATA
*
12159286 AAAAGAAAAAG
1 AAAATAAAAAG
12159297 GAAAATTTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
24 2 0.04
25 28 0.53
26 12 0.23
27 9 0.17
28 2 0.04
ACGTcount: A:0.76, C:0.06, G:0.10, T:0.08
Consensus pattern (25 bp):
AAAATAAAAAGACAATCAAAAAATA
Found at i:12159266 original size:27 final size:26
Alignment explanation
Indices: 12159210--12159265 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
12159200 ATTTTTACAG
*
12159210 AAAATAAAAAACATCCAAAAAAGTTA
1 AAAATAAAAAACATCCAAAAAAGTAA
12159236 AAAATAAAAAGACAAT-CAAAAAA-TAA
1 AAAATAAAAA-AC-ATCCAAAAAAGTAA
12159262 AAAA
1 AAAA
12159266 AGAAAGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 16 0.59
27 9 0.33
28 2 0.07
ACGTcount: A:0.75, C:0.09, G:0.04, T:0.12
Consensus pattern (26 bp):
AAAATAAAAAACATCCAAAAAAGTAA
Found at i:12159283 original size:17 final size:17
Alignment explanation
Indices: 12159261--12159293 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12159251 TCAAAAAATA
*
12159261 AAAAAAGAAAGAGAAAG
1 AAAAAAGAAAAAGAAAG
12159278 AAAAAAGAAAAAGAAA
1 AAAAAAGAAAAAGAAA
12159294 AAGGAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAGAAAG
Found at i:12159290 original size:13 final size:13
Alignment explanation
Indices: 12159253--12159301 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
12159243 AAAGACAATC
*
12159253 AAAAAATAAAAA-
1 AAAAAAGAAAAAG
* *
12159265 AAGAAAGAGAAAG
1 AAAAAAGAAAAAG
12159278 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
*
12159291 AAAAAGGAAAA
1 AAAAAAGAAAA
12159302 TTTACCAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 9 0.30
13 21 0.70
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:12160190 original size:24 final size:24
Alignment explanation
Indices: 12160151--12160213 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
12160141 GACTTTATGG
* *
12160151 GAAAATAGAAAAAAAT-ACTAAAAA
1 GAAAATA-AAATAAATAAATAAAAA
12160175 GAAGAATAAAATAAATAAATAAAAA
1 GAA-AATAAAATAAATAAATAAAAA
*
12160200 TAAAATAAACATAA
1 GAAAATAAA-ATAA
12160214 TTATATTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (24 bp):
GAAAATAAAATAAATAAATAAAAA
Found at i:12161169 original size:66 final size:64
Alignment explanation
Indices: 12161030--12161182 Score: 166
Period size: 66 Copynumber: 2.4 Consensus size: 64
12161020 AGTTATGGGT
* * * * *
12161030 GCCAACTAAATTAGGCTT-AAGAAATCTCATTAATGCCAACTTAACTACACTTAAAATCTTAAA
1 GCCAACTAGATTAGGCTTAAAAAAATCTCATTAATGCCAAATTAACTACACTTAAAATATCAAA
* * * *
12161093 GCCAACTAGATTGGGTTTAAAAAAATCTCATCTAATGGCCAAATTAACTAGACTTAAAATATCAT
1 GCCAACTAGATTAGGCTTAAAAAAATCTCAT-TAAT-GCCAAATTAACTACACTTAAAATATCAA
*
12161158 T
64 A
*
12161159 G-CAAGTTAGATTAGGCTTAAAAAA
1 GCCAA-CTAGATTAGGCTTAAAAAA
12161183 TCTAAACCCA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
63 15 0.21
64 11 0.15
65 7 0.10
66 40 0.55
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (64 bp):
GCCAACTAGATTAGGCTTAAAAAAATCTCATTAATGCCAAATTAACTACACTTAAAATATCAAA
Found at i:12161625 original size:16 final size:16
Alignment explanation
Indices: 12161606--12161647 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
12161596 CCTTTTTTGT
*
12161606 TTTTTTCTTAACAAAC
1 TTTTTTCTTAACAAAA
*
12161622 TTTTTTCCTTAATAAAA
1 TTTTTT-CTTAACAAAA
12161639 TTTTTTCTT
1 TTTTTTCTT
12161648 TTTATTTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTTCTTAACAAAA
Found at i:12161629 original size:32 final size:33
Alignment explanation
Indices: 12161556--12161631 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
12161546 TTTCTTTTTC
*
12161556 CTTTTTT-CTTTTATTGCTTTTTTCTTTACAAA
1 CTTTTTTCCTTTTATTGCTTTTTTCTTAACAAA
*
12161588 CTTTTTTTCCTTTT-TTGTTTTTTTCTTAACAAA
1 C-TTTTTTCCTTTTATTGCTTTTTTCTTAACAAA
12161621 CTTTTTTCCTT
1 CTTTTTTCCTT
12161632 AATAAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 11 0.28
33 24 0.60
34 5 0.12
ACGTcount: A:0.13, C:0.17, G:0.03, T:0.67
Consensus pattern (33 bp):
CTTTTTTCCTTTTATTGCTTTTTTCTTAACAAA
Found at i:12165176 original size:112 final size:112
Alignment explanation
Indices: 12165026--12165250 Score: 441
Period size: 112 Copynumber: 2.0 Consensus size: 112
12165016 TGAGATAGGA
12165026 TCACTTTGAGTAAGAAGGCTTTCTAGGTTTTGTAGGGATAGTGAAAATCATATGACTATTGACAA
1 TCACTTTGAGTAAGAAGGCTTTCTAGGTTTTGTAGGGATAGTGAAAATCATATGACTATTGACAA
12165091 GTAAAGGAAAAAGCAATGCATAAGATATTAAAAGTGAGTGGTGTGTT
66 GTAAAGGAAAAAGCAATGCATAAGATATTAAAAGTGAGTGGTGTGTT
*
12165138 TCACTTTGAGTAAGGAGGCTTTCTAGGTTTTGTAGGGATAGTGAAAATCATATGACTATTGACAA
1 TCACTTTGAGTAAGAAGGCTTTCTAGGTTTTGTAGGGATAGTGAAAATCATATGACTATTGACAA
12165203 GTAAAGGAAAAAGCAATGCATAAGATATTAAAAGTGAGTGGTGTGTT
66 GTAAAGGAAAAAGCAATGCATAAGATATTAAAAGTGAGTGGTGTGTT
12165250 T
1 T
12165251 TAACTCTCTT
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (112 bp):
TCACTTTGAGTAAGAAGGCTTTCTAGGTTTTGTAGGGATAGTGAAAATCATATGACTATTGACAA
GTAAAGGAAAAAGCAATGCATAAGATATTAAAAGTGAGTGGTGTGTT
Found at i:12167881 original size:9 final size:8
Alignment explanation
Indices: 12167852--12167882 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
12167842 AATTTTCATC
12167852 TATTTTTA
1 TATTTTTA
12167860 TATTTTTA
1 TATTTTTA
12167868 TATTTTTA
1 TATTTTTA
12167876 TAATTTT
1 T-ATTTT
12167883 GTTGTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTTTTA
Found at i:12169367 original size:3 final size:3
Alignment explanation
Indices: 12169359--12169387 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12169349 ATTTATTTAT
12169359 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12169388 TCTTCATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12169422 original size:20 final size:19
Alignment explanation
Indices: 12169373--12169422 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
12169363 TATTATTATT
12169373 ATTATTATTATTATTTCTTC
1 ATTATTATT-TTATTTCTTC
* *
12169393 ATCATTATTTTCATTTCTTT
1 ATTATTATTTT-ATTTCTTC
*
12169413 TTTATTATTT
1 ATTATTATTT
12169423 AAAATATACC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTATTATTTTATTTCTTC
Found at i:12169910 original size:29 final size:28
Alignment explanation
Indices: 12169865--12169919 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
12169855 TTTTTTAAGA
12169865 AAAAAAACAAAAATGAAAAAAATAAAAG
1 AAAAAAACAAAAATGAAAAAAATAAAAG
* * *
12169893 AAAAAAATAAAACTTGAAAAATATAAA
1 AAAAAAACAAAA-ATGAAAAAAATAAA
12169920 TAAAATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (28 bp):
AAAAAAACAAAAATGAAAAAAATAAAAG
Found at i:12169911 original size:16 final size:14
Alignment explanation
Indices: 12169874--12169919 Score: 58
Period size: 13 Copynumber: 3.2 Consensus size: 14
12169864 AAAAAAAACA
12169874 AAAATGAAAAAAAT
1 AAAATGAAAAAAAT
12169888 AAAA-GAAAAAAAT
1 AAAATGAAAAAAAT
*
12169901 AAAACTTGAAAAATAT
1 AAAA--TGAAAAAAAT
12169917 AAA
1 AAA
12169920 TAAAATGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 13 0.46
14 4 0.14
16 11 0.39
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAATGAAAAAAAT
Found at i:12170428 original size:20 final size:20
Alignment explanation
Indices: 12170403--12170451 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
12170393 AGATCAAAAT
*
12170403 TTTTGTTTTTGGTTTT-TTTG
1 TTTTGTTTTT-GTTTTGTTTC
*
12170423 TTTTGTTTCTGTTTTGTTTC
1 TTTTGTTTTTGTTTTGTTTC
12170443 TTTT-TTTTT
1 TTTTGTTTTT
12170452 TAGAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (20 bp):
TTTTGTTTTTGTTTTGTTTC
Found at i:12170448 original size:11 final size:11
Alignment explanation
Indices: 12170403--12170447 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
12170393 AGATCAAAAT
*
12170403 TTTTGTTTTTG
1 TTTTGTTTCTG
*
12170414 GTTT-TTT-TG
1 TTTTGTTTCTG
12170423 TTTTGTTTCTG
1 TTTTGTTTCTG
12170434 TTTTGTTTCT-
1 TTTTGTTTCTG
12170444 TTTT
1 TTTT
12170448 TTTTTAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 5 0.17
10 10 0.33
11 15 0.50
ACGTcount: A:0.00, C:0.04, G:0.16, T:0.80
Consensus pattern (11 bp):
TTTTGTTTCTG
Found at i:12174709 original size:27 final size:27
Alignment explanation
Indices: 12174679--12174733 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
12174669 GGAAAAGAAG
12174679 AATAAAATAGAACAATTTAATTTATTT
1 AATAAAATAGAACAATTTAATTTATTT
*
12174706 AATAAAATAGAACAATTTAATTTGTTT
1 AATAAAATAGAACAATTTAATTTATTT
12174733 A
1 A
12174734 TAACAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (27 bp):
AATAAAATAGAACAATTTAATTTATTT
Found at i:12175876 original size:146 final size:145
Alignment explanation
Indices: 12175650--12175911 Score: 343
Period size: 146 Copynumber: 1.8 Consensus size: 145
12175640 CAGCAATACA
* *
12175650 CCAAGAAGTGTGAAATTACCAAAAACCCTTTAAGGGGTATTTTCATAATTTGGCTTTTTCGAGAT
1 CCAAAAAGTGTGAAATTACCAAAAACCCTTTAAGGGGTATTTTCATAATTTGCCTTTTTCGAGAT
* *
12175715 TGGAATATCATGAAACCTTCCAAATCTCAA-TTCTATAATATTCCATGATTTTTTATGCATTTAA
66 TGGAATATAACGAAACCTTCCAAATCTCAATTTC-ATAATATTCCATGATTTTTTATGCATTTAA
12175779 AATCACAATAGTACCC
130 AATCACAATAGTACCC
*
12175795 CCAAAAAGTGTGAAATTACCAAAATACCCTTATAA-GGGTATTTTCGTAATTTAGCCTTTTT-GA
1 CCAAAAAGTGTGAAATTACCAAAA-ACCCTT-TAAGGGGTATTTTCATAATTT-GCCTTTTTCGA
* * * * * **
12175858 G-TTCGGATTTTAACGAAACTTTTCAAATCTTAATTTCATAATATTTTATGATTT
63 GATT-GGAATATAACGAAACCTTCCAAATCTCAATTTCATAATATTCCATGATTT
12175912 GTGGTGCTTT
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
145 25 0.25
146 62 0.62
147 13 0.13
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (145 bp):
CCAAAAAGTGTGAAATTACCAAAAACCCTTTAAGGGGTATTTTCATAATTTGCCTTTTTCGAGAT
TGGAATATAACGAAACCTTCCAAATCTCAATTTCATAATATTCCATGATTTTTTATGCATTTAAA
ATCACAATAGTACCC
Found at i:12178548 original size:24 final size:25
Alignment explanation
Indices: 12178516--12178564 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
12178506 TTATCAATAA
12178516 TTATCA-TTTACAAAGAATGTTATT
1 TTATCATTTTACAAAGAATGTTATT
* *
12178540 TTATTATTTTTAGAAAGAATGTTAT
1 TTATCA-TTTTACAAAGAATGTTAT
12178565 GATAATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
26 16 0.76
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (25 bp):
TTATCATTTTACAAAGAATGTTATT
Found at i:12182825 original size:14 final size:15
Alignment explanation
Indices: 12182770--12182825 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 15
12182760 AATTTAAATT
*
12182770 TTATTATAAATAAA-
1 TTATTAAAAATAAAC
12182784 TTATTAAAAAAATAAAC
1 TTATT--AAAAATAAAC
* *
12182801 TTATTACAAATAATC
1 TTATTAAAAATAAAC
12182816 -TATTAAAAAT
1 TTATTAAAAAT
12182826 GTTATAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 14 0.40
15 8 0.23
16 8 0.23
17 5 0.14
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
TTATTAAAAATAAAC
Found at i:12183301 original size:13 final size:13
Alignment explanation
Indices: 12183267--12183311 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
12183257 ATTCTCATTC
12183267 ACTTTAAAATTTT
1 ACTTTAAAATTTT
*
12183280 ATTTTTAAAATTTT
1 A-CTTTAAAATTTT
12183294 ACTTTAAAATTTT
1 ACTTTAAAATTTT
12183307 ACTTT
1 ACTTT
12183312 GTTTTCTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (13 bp):
ACTTTAAAATTTT
Found at i:12188918 original size:11 final size:11
Alignment explanation
Indices: 12188902--12188930 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
12188892 CACTAGGTTC
12188902 TCTTTTTTTTT
1 TCTTTTTTTTT
12188913 TC-TTTTTTTT
1 TCTTTTTTTTT
12188923 TCTTTTTT
1 TCTTTTTT
12188931 GTTTACCGTT
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:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:12188920 original size:10 final size:10
Alignment explanation
Indices: 12188905--12188930 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12188895 TAGGTTCTCT
12188905 TTTTTTTTTC
1 TTTTTTTTTC
12188915 TTTTTTTTTC
1 TTTTTTTTTC
12188925 TTTTTT
1 TTTTTT
12188931 GTTTACCGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:12193265 original size:48 final size:46
Alignment explanation
Indices: 12193194--12193286 Score: 132
Period size: 48 Copynumber: 2.0 Consensus size: 46
12193184 ATATGCATCA
*
12193194 ATGCATCATACCTATATGGACCCTCTCAATCTCCTCTAGTCCACTCAC
1 ATGCATCATACCTATATAGACCCTCTCAATCT-C-CTAGTCCACTCAC
* * *
12193242 ATGCATTATACCTATGTAGACCCTCTTAATCTCCTAGTCCACTCA
1 ATGCATCATACCTATATAGACCCTCTCAATCTCCTAGTCCACTCA
12193287 TAAACATACA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 12 0.29
47 1 0.02
48 28 0.68
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (46 bp):
ATGCATCATACCTATATAGACCCTCTCAATCTCCTAGTCCACTCAC
Found at i:12194102 original size:34 final size:33
Alignment explanation
Indices: 12194062--12194132 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
12194052 CTCCTCTAAT
*
12194062 CCTATGAAGTA-TTCTCAACCCAAACAAACACATA
1 CCTATG-AGTACTT-TCAACACAAACAAACACATA
*
12194096 CCTATGAGTACCCTTTCAACACAACCAAACACATA
1 CCTATGAGTA--CTTTCAACACAAACAAACACATA
12194131 CC
1 CC
12194133 CATATGCACC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 4 0.12
34 6 0.19
35 20 0.62
36 2 0.06
ACGTcount: A:0.41, C:0.34, G:0.06, T:0.20
Consensus pattern (33 bp):
CCTATGAGTACTTTCAACACAAACAAACACATA
Done.