Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 112 of 126
Found at i:22153810 original size:33 final size:35
Alignment explanation
Indices: 22153738--22153812 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
22153728 TTATCTAAGG
* *
22153738 AAAA-ATATGAATCTAATTCTTTAAGAATTAAGCA
1 AAAAGATATGAATCTAACTCTTTAAGAATTAAACA
* * *
22153772 GAAAGATATGAATTTAACTCTTT-A-AATTAAATA
1 AAAAGATATGAATCTAACTCTTTAAGAATTAAACA
22153805 AAAAGATA
1 AAAAGATA
22153813 CATTCACTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 14 0.41
34 4 0.12
35 16 0.47
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (35 bp):
AAAAGATATGAATCTAACTCTTTAAGAATTAAACA
Found at i:22156757 original size:18 final size:17
Alignment explanation
Indices: 22156734--22156767 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22156724 CCTGAACCAC
*
22156734 TCCCGTTGCCCTTGTTTT
1 TCCCGTT-CCCCTGTTTT
22156752 TCCCGTTCCCCTGTTT
1 TCCCGTTCCCCTGTTT
22156768 CTTCGTCAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.00, C:0.38, G:0.15, T:0.47
Consensus pattern (17 bp):
TCCCGTTCCCCTGTTTT
Found at i:22159267 original size:17 final size:17
Alignment explanation
Indices: 22159242--22159276 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22159232 ACTTTGAAAA
22159242 ATTAAAATAAAATAATT
1 ATTAAAATAAAATAATT
* *
22159259 ATTATAATAATATAATT
1 ATTAAAATAAAATAATT
22159276 A
1 A
22159277 AATAATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAAAATAAAATAATT
Found at i:22159282 original size:13 final size:13
Alignment explanation
Indices: 22159251--22159289 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
22159241 AATTAAAATA
22159251 AAATAAT-T-ATT
1 AAATAATATAATT
22159262 ATAATAATATAATT
1 A-AATAATATAATT
22159276 AAATAATATAATT
1 AAATAATATAATT
22159289 A
1 A
22159290 TGAAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.04
12 6 0.24
13 14 0.56
14 4 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATAATATAATT
Found at i:22159300 original size:30 final size:31
Alignment explanation
Indices: 22159241--22159301 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
22159231 AACTTTGAAA
*
22159241 AATTAAAATAAAATAATTATTATAATAATAT
1 AATTAAAATAAAATAATTATGATAATAATAT
*
22159272 AATT-AAATAATATAATTATGA-AATTAATAT
1 AATTAAAATAAAATAATTATGATAA-TAATAT
22159302 TAATGTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 21 0.78
31 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (31 bp):
AATTAAAATAAAATAATTATGATAATAATAT
Found at i:22159552 original size:1 final size:1
Alignment explanation
Indices: 22159546--22159583 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
22159536 AGCTAGAGAC
22159546 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22159584 CTTAGTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22164217 original size:27 final size:27
Alignment explanation
Indices: 22164187--22164279 Score: 73
Period size: 31 Copynumber: 3.3 Consensus size: 27
22164177 TTGTGCAGAG
22164187 AAAATTAATACTTTCAACTTTTTTCAA
1 AAAATTAATACTTTCAACTTTTTTCAA
* *
22164214 AAAA-T-ATTCTTTTAAAACTTTAATTTCGAGA
1 AAAATTAATAC-TTT-CAACTTT--TTTC-A-A
* *
22164245 AAAATTGATACTTTCAACTTTTCCTCAA
1 AAAATTAATACTTTCAACTTTT-TTCAA
22164273 AAAATTA
1 AAAATTA
22164280 TTTTTTTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 10 0.20
28 7 0.14
29 6 0.12
30 3 0.06
31 11 0.22
32 4 0.08
33 3 0.06
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (27 bp):
AAAATTAATACTTTCAACTTTTTTCAA
Found at i:22164335 original size:118 final size:118
Alignment explanation
Indices: 22164187--22164697 Score: 676
Period size: 118 Copynumber: 4.3 Consensus size: 118
22164177 TTGTGCAGAG
* ** * * * *
22164187 AAAATTAATACTTTCAACTTTTTTCAAAAAATATTCTTTTAAAACTTT-AATTTCGAGAAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTAAAACTTTCATTTTCAAGGAAAATT
*
22164251 GATACTTTCAACTTTTCCTCAAAAAATTATTTTTTTGAAAATTTATTTTTAAGG
66 GATACTTTCAACTTTTCCTC-AAAAATTATTTTTTTGAAAATTTATTTTTAAGA
** *
22164305 AAAATTGATACTTTCAACTTTTCCCCAAAAATATT-TTTGGAAACTTTTATTTTCAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTAAAACTTTCATTTTCAAGGAAAATT
*
22164369 GATACTTTCAACTTTTCCTCAAAAGTTGATTTTTTTG-AAATCTTATTTTTAAGA
66 GATACTTTCAACTTTTCCTCAAAAATT-ATTTTTTTGAAAAT-TTATTTTTAAGA
* * * *
22164423 AAAATTGATACTTTCAACTTTTCCTCAAAAACT-TTTTTTTGAAAA-TTTCTTTTTTAAGGAAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTCTTTT-AAAACTTTCATTTTCAAGGAAAA
** *
22164486 TTGATACTTTCAACTTTTCCTCAAAAACTT-TTTTTTTTTAAATTTATTTTTAAAA
64 TTGATACTTTCAACTTTTCCTCAAAAA-TTATTTTTTTGAAAATTTATTTTTAAGA
* * * *
22164541 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTCTTTGAAAACTTTGATTTTTAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTAAAACTTTCATTTTCAAGGAAAATT
**
22164606 GATACTTTCAACTTTTCCTCAAAAA-CCTTTTTTTGAAAATTTATTTTTAAGA
66 GATACTTTCAACTTTTCCTCAAAAATTATTTTTTTGAAAATTTATTTTTAAGA
* *
22164658 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTT
22164698 TTTATTTTTA
Statistics
Matches: 348, Mismatches: 34, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
117 83 0.24
118 211 0.61
119 49 0.14
120 5 0.01
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.46
Consensus pattern (118 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTAAAACTTTCATTTTCAAGGAAAATT
GATACTTTCAACTTTTCCTCAAAAATTATTTTTTTGAAAATTTATTTTTAAGA
Found at i:22164452 original size:27 final size:27
Alignment explanation
Indices: 22164363--22164453 Score: 65
Period size: 27 Copynumber: 3.1 Consensus size: 27
22164353 ATTTTCAAGG
22164363 AAAATTGATACTTTCAACTTTTCCTCA
1 AAAATTGATACTTTCAACTTTTCCTCA
* ** * ** *
22164390 AAAGTTGATTTTTTTGAAATCTTATTTTTAAGA
1 AAAATTGA-TACTTT-CAA-CTT-TTCCT--CA
22164423 AAAATTGATACTTTCAACTTTTCCTCA
1 AAAATTGATACTTTCAACTTTTCCTCA
22164450 AAAA
1 AAAA
22164454 CTTTTTTTTG
Statistics
Matches: 44, Mismatches: 14, Indels: 12
0.63 0.20 0.17
Matches are distributed among these distances:
27 12 0.27
28 4 0.09
29 5 0.11
30 6 0.14
31 5 0.11
32 4 0.09
33 8 0.18
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTCCTCA
Found at i:22164480 original size:59 final size:58
Alignment explanation
Indices: 22164187--22164698 Score: 597
Period size: 59 Copynumber: 8.7 Consensus size: 58
22164177 TTGTGCAGAG
* * * * * **
22164187 AAAATTAATACTTTCAACTTTT-TTCAAAAAATATTCTTTT-AAAACTTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACT-TTTTTTTGAAAA-TTTATTTTTAAGA
* *
22164245 AAAATTGATACTTTCAACTTTTCCTCAAAAAATTATTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAACT-TTTTTTTGAAAATTTATTTTTAAGA
* * * * * *
22164305 AAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTGGAAACTTTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTGAAA-ATTTATTTTTAAGA
**
22164363 AAAATTGATACTTTCAACTTTTCCTCAAAAGTTGATTTTTTTG-AAATCTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACT--TTTTTTTGAAAAT-TTATTTTTAAGA
* *
22164423 AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTGAAAATTTCTTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTGAAAATTT-ATTTTTAAGA
** *
22164482 AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTTTAAATTTATTTTTAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAC-TTTTTTTTGAAAATTTATTTTTAAGA
* * *
22164541 AAAATTGATACTTTCAACTTTT-CTCCAAAAA-TATTCTTTGAAAACTTTGATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAACTTTTTTTTGAAAA-TTT-ATTTTTAAGA
*
22164600 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTGAAAATTTATTTTTAAGA
*
22164658 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTT
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAA-CTTTTTTTT
22164699 TTATTTTTAT
Statistics
Matches: 395, Mismatches: 41, Indels: 35
0.84 0.09 0.07
Matches are distributed among these distances:
57 18 0.05
58 111 0.28
59 140 0.35
60 116 0.29
61 10 0.03
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.46
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTGAAAATTTATTTTTAAGA
Found at i:22164748 original size:30 final size:30
Alignment explanation
Indices: 22164714--22164801 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 30
22164704 TTTATTTAAA
22164714 GAAAATAGAAT-AATAAAACAAAATAAAAGT
1 GAAAATA-AATAAATAAAACAAAATAAAAGT
*
22164744 GAAAATAAATAAATAAAATAAAAT-AAAGT
1 GAAAATAAATAAATAAAACAAAATAAAAGT
* * *
22164773 -AAAACAAAAAAAATAAAATAAAGATAAAA
1 GAAAA-TAAATAAATAAAACAAA-ATAAAA
22164802 AGAATATTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
28 4 0.08
29 23 0.45
30 21 0.41
31 3 0.06
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (30 bp):
GAAAATAAATAAATAAAACAAAATAAAAGT
Found at i:22164755 original size:4 final size:4
Alignment explanation
Indices: 22164746--22164880 Score: 82
Period size: 4 Copynumber: 32.0 Consensus size: 4
22164736 ATAAAAGTGA
22164746 AAAT AAAT AAAT AAAAT AAAAT AAAGT AAA- ACAA- AAA- AAAT AAAAT
1 AAAT AAAT AAAT -AAAT -AAAT AAA-T AAAT A-AAT AAAT AAAT -AAAT
* * *
22164792 AAAGAT AAAA AGAAT -ATT AAAT AAACCT AATCT AA-T AAAT AAAAT AAAT
1 -AA-AT AAAT A-AAT AAAT AAAT AAA--T AA-AT AAAT AAAT -AAAT AAAT
* *
22164841 AAAT AAAT AAAT GAAT AAAC AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
22164881 TCAAAAAAAA
Statistics
Matches: 109, Mismatches: 9, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
3 11 0.10
4 62 0.57
5 31 0.28
6 5 0.05
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:22164764 original size:5 final size:5
Alignment explanation
Indices: 22164725--22164801 Score: 79
Period size: 5 Copynumber: 15.4 Consensus size: 5
22164715 AAAATAGAAT
* *
22164725 AATAA AACAA AATAA AAGTGAA AAT-A AAT-A AATAA AATAA AATAA AGTAA
1 AATAA AATAA AATAA AA-T-AA AATAA AATAA AATAA AATAA AATAA AATAA
*
22164775 AACAA AA-AA AATAA AATAA AGATAA AA
1 AATAA AATAA AATAA AATAA A-ATAA AA
22164802 AGAATATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
4 12 0.19
5 39 0.63
6 7 0.11
7 4 0.06
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.16
Consensus pattern (5 bp):
AATAA
Found at i:22165926 original size:29 final size:29
Alignment explanation
Indices: 22165894--22165950 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
22165884 AAAGAGAGAA
* *
22165894 AAAAATATATAAA-ATAATAAAAATAAAAC
1 AAAAATATA-AAATACAAAAAAAATAAAAC
*
22165923 AAAAATGTAAAATACAAAAAAAATAAAA
1 AAAAATATAAAATACAAAAAAAATAAAA
22165951 ATAAAATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.18
Consensus pattern (29 bp):
AAAAATATAAAATACAAAAAAAATAAAAC
Found at i:22166398 original size:42 final size:42
Alignment explanation
Indices: 22166265--22166516 Score: 377
Period size: 42 Copynumber: 6.1 Consensus size: 42
22166255 TTTTTTCAAA
** *
22166265 GCTCCTCTAAACAGAGGTTCAACGACTTTG-GAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
*
22166306 GCTCCTCTAAACAGAGGCACCACAACTTTGA-AAAGT-AATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
* * *
22166346 GCTCCTCTAAACAAAGGTACCATGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
* *
22166388 GCTCCTCTAAATAGAGGCACCACGATTTTGA-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
* *
22166429 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
22166471 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
22166513 GCTC
1 GCTC
22166517 ATCGACTTTG
Statistics
Matches: 189, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
40 31 0.16
41 74 0.39
42 84 0.44
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
Found at i:22166472 original size:83 final size:83
Alignment explanation
Indices: 22166265--22166516 Score: 409
Period size: 83 Copynumber: 3.0 Consensus size: 83
22166255 TTTTTTCAAA
* *
22166265 GCTCCTCTAAACAGAGGTTCAACGACTTTG-GAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
22166329 AACTTTGAAAAGT-AATT
66 GACTTTGAAAAGTAAATT
* * *
22166346 GCTCCTCTAAACAAAGGTACCATGACTTTGAGAAAGTAAATTGCTCCTCTAAATAGAGGCACCAC
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
22166411 GATTTTGAAAAGTAAATT
66 GACTTTGAAAAGTAAATT
*
22166429 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
22166494 GACTTTGAGAAAGTAAATT
66 GACTTTGA-AAAGTAAATT
22166513 GCTC
1 GCTC
22166517 ATCGACTTTG
Statistics
Matches: 156, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
81 26 0.17
82 44 0.28
83 72 0.46
84 14 0.09
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (83 bp):
GCTCCTCTAAACAGAGGTACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
GACTTTGAAAAGTAAATT
Found at i:22166522 original size:26 final size:26
Alignment explanation
Indices: 22166493--22166542 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
22166483 AGAGGCACCA
*
22166493 CGACTTTGAGAAAGTAAATTGCTCAT
1 CGACTTTGAAAAAGTAAATTGCTCAT
22166519 CGACTTTGAAAAAGTAAATTGCTC
1 CGACTTTGAAAAAGTAAATTGCTC
22166543 CTCTAAACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (26 bp):
CGACTTTGAAAAAGTAAATTGCTCAT
Found at i:22166560 original size:68 final size:67
Alignment explanation
Indices: 22166451--22166583 Score: 257
Period size: 68 Copynumber: 2.0 Consensus size: 67
22166441 AGAGGTACCA
22166451 CGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCT
1 CGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAGTAAATTGCT
22166516 CAT
65 CAT
22166519 CGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTC
1 CGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTC
22166584 CTTGACAATC
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
67 15 0.23
68 50 0.77
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (67 bp):
CGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTC
AT
Found at i:22167606 original size:23 final size:23
Alignment explanation
Indices: 22167580--22167635 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
22167570 TTGAGTCTTC
22167580 TTTTTTCATTCACTT-TTTTTTCA
1 TTTTTTCATT-ACTTATTTTTTCA
** *
22167603 TTTTTTCATTTTTTATTTTTTTA
1 TTTTTTCATTACTTATTTTTTCA
22167626 TTTTTTCATT
1 TTTTTTCATT
22167636 TTTTTTCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTCATTACTTATTTTTTCA
Found at i:22167608 original size:8 final size:8
Alignment explanation
Indices: 22167595--22167639 Score: 74
Period size: 8 Copynumber: 5.8 Consensus size: 8
22167585 TCATTCACTT
22167595 TTTTTTCA
1 TTTTTTCA
22167603 TTTTTTCA
1 TTTTTTCA
22167611 TTTTTT-A
1 TTTTTTCA
*
22167618 TTTTTTTA
1 TTTTTTCA
22167626 TTTTTTCA
1 TTTTTTCA
22167634 TTTTTT
1 TTTTTT
22167640 TTCAAGCACA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
7 7 0.20
8 28 0.80
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTCA
Found at i:22167636 original size:23 final size:23
Alignment explanation
Indices: 22167596--22167639 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
22167586 CATTCACTTT
22167596 TTTTTCATTTTTTCATTTTTTAT
1 TTTTTCATTTTTTCATTTTTTAT
*
22167619 TTTTTTATTTTTTCATTTTTT
1 TTTTTCATTTTTTCATTTTTT
22167640 TTCAAGCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTCATTTTTTCATTTTTTAT
Found at i:22167640 original size:16 final size:16
Alignment explanation
Indices: 22167595--22167640 Score: 76
Period size: 15 Copynumber: 2.9 Consensus size: 16
22167585 TCATTCACTT
*
22167595 TTTTTTCATTTTTTCA
1 TTTTTTCATTTTTTTA
22167611 TTTTTT-ATTTTTTTA
1 TTTTTTCATTTTTTTA
22167626 TTTTTTCATTTTTTT
1 TTTTTTCATTTTTTT
22167641 TCAAGCACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTCATTTTTTTA
Found at i:22174889 original size:15 final size:15
Alignment explanation
Indices: 22174869--22174898 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
22174859 CTTTGTTAAG
22174869 TGTAATGAATGAAAA
1 TGTAATGAATGAAAA
22174884 TGTAATGAATGAAAA
1 TGTAATGAATGAAAA
22174899 ATGCATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (15 bp):
TGTAATGAATGAAAA
Found at i:22177500 original size:30 final size:31
Alignment explanation
Indices: 22177439--22177500 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
22177429 GCACATGCAT
*
22177439 ATGAATGACATAATTAACAAAATAAATAAAC
1 ATGAATGACATAATTAACAAAATAAACAAAC
* *
22177470 ATGAATGA-ATAA-TAACACATATATACAAAC
1 ATGAATGACATAATTAACA-AAATAAACAAAC
22177500 A
1 A
22177501 GGTTCAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.19
30 14 0.52
31 8 0.30
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (31 bp):
ATGAATGACATAATTAACAAAATAAACAAAC
Found at i:22178181 original size:17 final size:16
Alignment explanation
Indices: 22178146--22178184 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
22178136 CTTTTTCTCA
**
22178146 AAAATTTATTTTTTTG
1 AAAATTTATTTTTAGG
22178162 AAAATTTATTTTTAAGG
1 AAAATTTATTTTT-AGG
22178179 AAAATT
1 AAAATT
22178185 GATACTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
AAAATTTATTTTTAGG
Found at i:22178185 original size:60 final size:58
Alignment explanation
Indices: 22178061--22178454 Score: 506
Period size: 58 Copynumber: 6.7 Consensus size: 58
22178051 TTATGTAGGA
* *
22178061 AAAATTGATACTTTCAAC-TTTTCCCAAAAAATATTTTTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCCC-AAAAATATTTTTTTGAAACTTTATTTTCAAGG
* * *
22178119 AAAATTGATACTTTCAACTTTTTCTCAAAAATTTATTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAA--TATTTTTTTGAAACTTTATTTTCAAGG
* *
22178179 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTGAAATTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGAAACTTTATTTTCAAGG
*
22178237 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGGAAACTTTGATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTT-GAAACTTT-ATTTTCAAGG
* *
22178297 AAAATTGATACTTTCAACTTTTTCCCCAAAAATATTCTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTT-CCCAAAAATATTTTTTTGAAACTTT-ATTTTCAAGG
* ** * * * *
22178357 AATATTGATACTTTCAA-TTTTTCCTCAAAAACCTTTTTTTAAAAATTTATTTTTAAAG
1 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGAAACTTTATTTTCAAGG
* * *
22178415 AGAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTT
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTT
22178455 TATTTTTATT
Statistics
Matches: 300, Mismatches: 26, Indels: 20
0.87 0.08 0.06
Matches are distributed among these distances:
58 121 0.40
59 52 0.17
60 112 0.37
61 15 0.05
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAACTTTATTTTCAAGG
Found at i:22178209 original size:118 final size:116
Alignment explanation
Indices: 22178061--22178454 Score: 547
Period size: 118 Copynumber: 3.3 Consensus size: 116
22178051 TTATGTAGGA
* * *
22178061 AAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTGAAACTTTAATTTCGAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAACTTTATTTTCAAGGAAAATTG
22178126 ATACTTTCAACTTTTTCTCAAAAATTTATTTTTTTGAAAATTTATTTTTAAGG
66 ATACTTTCAACTTTTTCTCAAAAA--TATTTTTTTGAAAATTTATTTTTAAGG
* * *
22178179 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTTATTTTTAAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAACTTTATTTTCAAGGAAAATTG
* * * *
22178244 ATACTTTCAACTTTTTCCCAAAAATATTTTTTTGGAAACTTTGATTTTCAAGA
66 ATACTTTCAACTTTTTCTCAAAAATATTTTTTT-GAAAATTT-ATTTTTAAGG
* * *
22178297 AAAATTGATACTTTCAACTTTTTCCCCAAAAATATTCTTTGGAAACTTTGATTTTCAAGGAATAT
1 AAAATTGATACTTTCAAC-TTTTCCCCAAAAATATTTTTTTGAAACTTT-ATTTTCAAGGAAAAT
** * *
22178362 TGATACTTTCAA-TTTTTCCTCAAAAACCTTTTTTTAAAAATTTATTTTTAAAG
64 TGATACTTTCAACTTTTT-CTCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
* *
22178415 AGAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
22178455 TATTTTTATT
Statistics
Matches: 243, Mismatches: 28, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
116 9 0.04
117 26 0.11
118 132 0.54
119 37 0.15
120 39 0.16
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (116 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAACTTTATTTTCAAGGAAAATTG
ATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
Found at i:22178503 original size:30 final size:30
Alignment explanation
Indices: 22178469--22178525 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
22178459 TTTATTTAAA
22178469 GAAAATAGAAT-AATAAAACAAAATAAAAGT
1 GAAAATA-AATAAATAAAACAAAATAAAAGT
*
22178499 GAAAATAAATAAATAAAATAAAATAAA
1 GAAAATAAATAAATAAAACAAAATAAA
22178526 GAAAAGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.18
Consensus pattern (30 bp):
GAAAATAAATAAATAAAACAAAATAAAAGT
Found at i:22178519 original size:5 final size:5
Alignment explanation
Indices: 22178480--22178564 Score: 68
Period size: 5 Copynumber: 16.4 Consensus size: 5
22178470 AAAATAGAAT
*
22178480 AATAA AACAA AATAA AAGTGAA AAT-A AAT-A AATAA AATAA AATAA AGA-AA
1 AATAA AATAA AATAA AA-T-AA AATAA AATAA AATAA AATAA AATAA A-ATAA
* *
22178530 AGTAA AACAAA AATAAA AATAA AATAA AGATAA AA
1 AATAA AA-TAA AAT-AA AATAA AATAA A-ATAA AA
22178565 AGAATATTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
4 8 0.12
5 37 0.56
6 17 0.26
7 4 0.06
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.15
Consensus pattern (5 bp):
AATAA
Found at i:22178595 original size:4 final size:4
Alignment explanation
Indices: 22178588--22178622 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
22178578 AACCTAATCT
*
22178588 AATA AATA AATA AATA AACA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT
22178623 TCAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:22179194 original size:9 final size:10
Alignment explanation
Indices: 22179171--22179195 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
22179161 TTCTCAGAAA
22179171 AAAAATCTCC
1 AAAAATCTCC
22179181 AAAAATCTCC
1 AAAAATCTCC
22179191 AAAAA
1 AAAAA
22179196 ATTTCTACTA
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:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATCTCC
Found at i:22179616 original size:24 final size:22
Alignment explanation
Indices: 22179572--22179617 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
22179562 AAAGAAGAAG
*
22179572 AAAAATAATAATAATAATAATA
1 AAAAAAAATAATAATAATAATA
*
22179594 AAAAAAAATATATACATATTAATA
1 AAAAAAAATA-ATA-ATAATAATA
22179618 GATATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAAAAAATAATAATAATAATA
Found at i:22179683 original size:15 final size:14
Alignment explanation
Indices: 22179663--22179727 Score: 53
Period size: 15 Copynumber: 4.5 Consensus size: 14
22179653 AAAGAGAGAG
22179663 AAAAT-ATATATATAT
1 AAAATAATA-ATA-AT
22179678 AAAATAATAATAAT
1 AAAATAATAATAAT
*
22179692 AAAAATAAAAATAA-
1 -AAAATAATAATAAT
* *
22179706 AAATAAAATAAAAAT
1 AAA-ATAATAATAAT
22179721 AAAATAA
1 AAAATAA
22179728 AAATGTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 3 0.07
14 12 0.29
15 23 0.56
16 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:22179689 original size:6 final size:6
Alignment explanation
Indices: 22179683--22179731 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
22179673 TATATAAAAT
*
22179683 AATAAT AATAAA AATAAA AATAAA AAT-AA AATAAA AAT-AA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
22179729 AAT
1 AAT
22179732 GTAAAATACA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
5 10 0.25
6 30 0.75
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:22179707 original size:11 final size:11
Alignment explanation
Indices: 22179683--22179731 Score: 80
Period size: 11 Copynumber: 4.3 Consensus size: 11
22179673 TATATAAAAT
22179683 AATAATAATAAA
1 AATAA-AATAAA
22179695 AATAAAAATAAA
1 AAT-AAAATAAA
22179707 AATAAAATAAA
1 AATAAAATAAA
22179718 AATAAAATAAA
1 AATAAAATAAA
22179729 AAT
1 AAT
22179732 GTAAAATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 22 0.61
12 12 0.33
13 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:22180433 original size:22 final size:22
Alignment explanation
Indices: 22180405--22180450 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
22180395 TTGATGCCAT
* *
22180405 GCCAACTAGGGGTGGACTCCAA
1 GCCAACTAGGAGTGCACTCCAA
22180427 GCCAACTAGGAGTGCACTCCAA
1 GCCAACTAGGAGTGCACTCCAA
22180449 GC
1 GC
22180451 AGATATACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.13
Consensus pattern (22 bp):
GCCAACTAGGAGTGCACTCCAA
Found at i:22181909 original size:29 final size:29
Alignment explanation
Indices: 22181861--22181939 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
22181851 TGAAGATTCG
* * *
22181861 GATTTTAAAGGTTTGGATTT-AAGTTTTGAG
1 GATTTT-AGGGTTTCGATTTAAAG-TTTGAA
* *
22181891 GGTTTTAGGGTTTTGATTTTAAAGTTTGAA
1 GATTTTAGGGTTTCGA-TTTAAAGTTTGAA
22181921 GATTTTAGGGTTTCGATTT
1 GATTTTAGGGTTTCGATTT
22181940 TTAAAATTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
29 11 0.27
30 27 0.66
31 3 0.07
ACGTcount: A:0.23, C:0.01, G:0.27, T:0.49
Consensus pattern (29 bp):
GATTTTAGGGTTTCGATTTAAAGTTTGAA
Found at i:22181940 original size:14 final size:14
Alignment explanation
Indices: 22181893--22182142 Score: 70
Period size: 15 Copynumber: 16.6 Consensus size: 14
22181883 GTTTTGAGGG
*
22181893 TTTTAGGGTTTTGA
1 TTTTAGGGTTTAGA
**
22181907 TTTTAAAGTTTGAAGA
1 TTTTAGGGTTT--AGA
*
22181923 TTTTAGGGTTTCGA
1 TTTTAGGGTTTAGA
*** * *
22181937 TTTTTAAAATTGAGG
1 -TTTTAGGGTTTAGA
* *
22181952 TTTGA-GGTTTTGA
1 TTTTAGGGTTTAGA
* *
22181965 TTTAAGGGTTTGGA
1 TTTTAGGGTTTAGA
22181979 TTTTAGGGATTTAGA
1 TTTTAGGG-TTTAGA
* * *
22181994 TTTAAGAGTTTAAA
1 TTTTAGGGTTTAGA
* * * *
22182008 GGTTTAAGATTTCGGA
1 -TTTTAGGGTTT-AGA
*
22182024 TTTTAGGGGGTTTTGGA
1 TTTTA--GGG-TTTAGA
22182041 TTTTAGGGGTTTAGA
1 TTTTA-GGGTTTAGA
* *
22182056 TTTAAGGGATTTTGGA
1 TTTTAGGG--TTTAGA
*
22182072 TTTTAGAGGTTTTGGA
1 TTTTAG-GG-TTTAGA
*
22182088 TTTTAGGATTTTAGA
1 TTTTAGG-GTTTAGA
** *
22182103 TTTTAAGATTTTGGA
1 TTTT-AGGGTTTAGA
22182118 TTTTAGGAGATTTTAGA
1 TTTTAGG-G--TTTAGA
22182135 TTTTAGGG
1 TTTTAGGG
22182143 GTTTTCGAAA
Statistics
Matches: 172, Mismatches: 46, Indels: 34
0.68 0.18 0.13
Matches are distributed among these distances:
13 7 0.04
14 39 0.23
15 58 0.34
16 42 0.24
17 23 0.13
18 3 0.02
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.48
Consensus pattern (14 bp):
TTTTAGGGTTTAGA
Found at i:22181983 original size:15 final size:15
Alignment explanation
Indices: 22181965--22182122 Score: 74
Period size: 15 Copynumber: 10.3 Consensus size: 15
22181955 GAGGTTTTGA
22181965 TTTAAGGGTTTGGAT
1 TTTAAGGGTTTGGAT
*
22181980 TTT-AGGGATTTAGA-
1 TTTAAGGG-TTTGGAT
* ** *
22181994 TTTAAGAGTTTAAAGG
1 TTTAAGGGTTTGGA-T
*
22182010 TTTAA-GATTTCGGAT
1 TTTAAGGGTTT-GGAT
*
22182025 TTTAGGGGGTTTTGGAT
1 TTTA-AGGG-TTTGGAT
* *
22182042 TTTAGGGGTTTAGA-
1 TTTAAGGGTTTGGAT
22182056 TTTAAGGGATTTTGGAT
1 TTTAAGGG--TTTGGAT
*
22182073 TTTAGAGGTTTTGGAT
1 TTTA-AGGGTTTGGAT
* *
22182089 TTT-AGGATTTTAGAT
1 TTTAAGG-GTTTGGAT
**
22182104 TTTAAGATTTTGGAT
1 TTTAAGGGTTTGGAT
22182119 TTTA
1 TTTA
22182123 GGAGATTTTA
Statistics
Matches: 112, Mismatches: 17, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
14 22 0.20
15 44 0.39
16 27 0.24
17 13 0.12
18 6 0.05
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.47
Consensus pattern (15 bp):
TTTAAGGGTTTGGAT
Found at i:22182069 original size:31 final size:31
Alignment explanation
Indices: 22182025--22182146 Score: 120
Period size: 31 Copynumber: 3.9 Consensus size: 31
22182015 GATTTCGGAT
* * * *
22182025 TTTAGGGGGTTTTGGATTTTAGGGGTTTAGA
1 TTTAAGGGATTTTAGATTTTAGGGGTTTGGA
* *
22182056 TTTAAGGGATTTTGGATTTTAGAGGTTTTGGA
1 TTTAAGGGATTTTAGATTTTAG-GGGTTTGGA
* * **
22182088 TTTTA-GGATTTTAGATTTTAAGATTTTGGA
1 TTTAAGGGATTTTAGATTTTAGGGGTTTGGA
*
22182118 TTTTAGGAGATTTTAGATTTTAGGGGTTT
1 TTTAAGG-GATTTTAGATTTTAGGGGTTT
22182147 TCGAAACCTA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
30 13 0.17
31 35 0.45
32 29 0.38
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (31 bp):
TTTAAGGGATTTTAGATTTTAGGGGTTTGGA
Found at i:22182086 original size:47 final size:46
Alignment explanation
Indices: 22181957--22182146 Score: 181
Period size: 47 Copynumber: 4.1 Consensus size: 46
22181947 TGAGGTTTGA
* ** * *
22181957 GGTTTTGATTTAAGGGTTTGGATTTTA-G-GGATTTAGA-TTTAAG
1 GGTTTAGATTTAAGATTTTGGATTTTAGGAGGTTTTAGATTTTAGG
* * * * *
22182000 AGTTTAAAGGTTTAAGATTTCGGATTTTAGGGGGTTTTGGATTTTAGG
1 GGTTT--AGATTTAAGATTTTGGATTTTAGGAGGTTTTAGATTTTAGG
*
22182048 GGTTTAGATTTAAGGGATTTTGGATTTTA-GAGGTTTTGGATTTTAGG
1 GGTTTAGATTTAA--GATTTTGGATTTTAGGAGGTTTTAGATTTTAGG
** *
22182095 ATTTTAGATTTTAAGATTTTGGATTTTAGGAGATTTTAGATTTTAGG
1 GGTTTAGA-TTTAAGATTTTGGATTTTAGGAGGTTTTAGATTTTAGG
22182142 GGTTT
1 GGTTT
22182147 TCGAAACCTA
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
43 4 0.03
45 17 0.14
46 22 0.18
47 49 0.41
48 27 0.23
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (46 bp):
GGTTTAGATTTAAGATTTTGGATTTTAGGAGGTTTTAGATTTTAGG
Found at i:22182135 original size:7 final size:7
Alignment explanation
Indices: 22182063--22182140 Score: 66
Period size: 7 Copynumber: 10.1 Consensus size: 7
22182053 AGATTTAAGG
*
22182063 GATTTTG
1 GATTTTA
22182070 GATTTTA
1 GATTTTA
*
22182077 GAGGTTTTG
1 GA--TTTTA
22182086 GATTTTA
1 GATTTTA
22182093 GGATTTTA
1 -GATTTTA
22182101 GATTTTAA
1 GATTTT-A
*
22182109 GATTTTG
1 GATTTTA
22182116 GATTTTAGGA
1 GATTTT---A
22182126 GATTTTA
1 GATTTTA
22182133 GATTTTA
1 GATTTTA
22182140 G
1 G
22182141 GGGTTTTCGA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
7 33 0.56
8 14 0.24
9 6 0.10
10 6 0.10
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (7 bp):
GATTTTA
Found at i:22182135 original size:32 final size:31
Alignment explanation
Indices: 22182010--22182139 Score: 136
Period size: 32 Copynumber: 4.1 Consensus size: 31
22182000 AGTTTAAAGG
* * *
22182010 TTTAAGATTTCGGATTTTAGGGGGTTTTGGAT
1 TTTAAGATTTTGGATTTTA-GGGATTTTAGAT
* ** * * *
22182042 TTTAGGGGTTTAGATTTAAGGGATTTTGGAT
1 TTTAAGATTTTGGATTTTAGGGATTTTAGAT
*
22182073 TTTAGAGGTTTTGGATTTTA-GGATTTTAGAT
1 TTTA-AGATTTTGGATTTTAGGGATTTTAGAT
22182104 TTTAAGATTTTGGATTTTAGGAGATTTTAGAT
1 TTTAAGATTTTGGATTTTAGG-GATTTTAGAT
22182136 TTTA
1 TTTA
22182140 GGGGTTTTCG
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
30 14 0.17
31 30 0.37
32 38 0.46
ACGTcount: A:0.23, C:0.01, G:0.27, T:0.49
Consensus pattern (31 bp):
TTTAAGATTTTGGATTTTAGGGATTTTAGAT
Found at i:22182578 original size:18 final size:19
Alignment explanation
Indices: 22182531--22182580 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
22182521 ATCATGCATC
*
22182531 AATATA-AAAAAAATACTT
1 AATATATAAAAAAATACAT
22182549 AA-A-ATAACAAAAATA-AT
1 AATATATAA-AAAAATACAT
22182566 AATATATAAAAAAAT
1 AATATATAAAAAAAT
22182581 TCAAAAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 1 0.04
17 6 0.22
18 16 0.59
19 4 0.15
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (19 bp):
AATATATAAAAAAATACAT
Found at i:22184627 original size:23 final size:23
Alignment explanation
Indices: 22184598--22184646 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
22184588 CTAAAACATA
**
22184598 AAAAATATAAATTTCATAATTTT
1 AAAAATATAAATTAAATAATTTT
**
22184621 AAAAATATTTATTAAATAATTTT
1 AAAAATATAAATTAAATAATTTT
22184644 AAA
1 AAA
22184647 CAAAAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAATATAAATTAAATAATTTT
Found at i:22185669 original size:2 final size:2
Alignment explanation
Indices: 22185662--22185689 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22185652 AATAGCACTA
22185662 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
22185690 TTTAATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22185844 original size:68 final size:67
Alignment explanation
Indices: 22185771--22185985 Score: 179
Period size: 67 Copynumber: 3.2 Consensus size: 67
22185761 AATTTTATAA
* * * * *
22185771 AAAAAAAAAAAAAAGCTTTTTTAAGTGTTT-TTTTTTTATTTACAAAACTCAAAATTAAAACTTT
1 AAAAAAAATAAAAAGCTTTCTCAAATCTTTCTTTTTTT-TTT-CAAAACTCAAAATTAAAACTTT
*
22185835 ATTTT
64 A-CTT
* *
22185840 AAAAAAAATCAAAAGCTTTCTCAAATCTTTCTTTTTTTTTTCAAAACTTAAAATTAAAACTTTAC
1 AAAAAAAATAAAAAGCTTTCTCAAATCTTTCTTTTTTTTTTCAAAACTCAAAATTAAAACTTTAC
22185905 TT
66 TT
** * * * * *
22185907 AAAAAATTTTAAAA--TTCTCTCAAAT-TTAT-TTTTTTCATTTACAACATTCAAAATTAAAATT
1 AAAAAAAATAAAAAGCTT-TCTCAAATCTT-TCTTTTTT--TTTTCAAAACTCAAAATTAAAACT
22185968 TTACTT
62 TTACTT
* *
22185974 TAAAAAATTAAA
1 AAAAAAAATAAA
22185986 CTTTTTATTA
Statistics
Matches: 122, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
65 10 0.08
66 9 0.07
67 47 0.39
68 22 0.18
69 27 0.22
70 7 0.06
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.43
Consensus pattern (67 bp):
AAAAAAAATAAAAAGCTTTCTCAAATCTTTCTTTTTTTTTTCAAAACTCAAAATTAAAACTTTAC
TT
Found at i:22190008 original size:18 final size:20
Alignment explanation
Indices: 22189981--22190017 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
22189971 TTTTCTAATC
22189981 TTTTACTAAAAAT-TTTACT
1 TTTTACTAAAAATGTTTACT
22190000 TTTTA-TAAAAATGTTTAC
1 TTTTACTAAAAATGTTTAC
22190018 CTCTACCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTTACTAAAAATGTTTACT
Found at i:22190686 original size:31 final size:31
Alignment explanation
Indices: 22190648--22190709 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
22190638 TTTGTTGAAA
22190648 AAGAACATCTAGAGATTGGTAATCAGATCAT
1 AAGAACATCTAGAGATTGGTAATCAGATCAT
*
22190679 AAGAACATCTAGAGATTGGTAATTAGATCAT
1 AAGAACATCTAGAGATTGGTAATCAGATCAT
22190710 CATCATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.27
Consensus pattern (31 bp):
AAGAACATCTAGAGATTGGTAATCAGATCAT
Found at i:22204150 original size:2 final size:2
Alignment explanation
Indices: 22204145--22204174 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
22204135 ACACACAGAG
*
22204145 AT AT AT AT TT 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
22204175 TTTGAGCCAC
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:22204354 original size:27 final size:27
Alignment explanation
Indices: 22204311--22204395 Score: 152
Period size: 27 Copynumber: 3.1 Consensus size: 27
22204301 AAAATAAAAG
22204311 ATACAAAACATTGTTCACATAAAAGTAT
1 ATACAAAA-ATTGTTCACATAAAAGTAT
22204339 ATACAAAAATTGTTCACATAAAAGTAT
1 ATACAAAAATTGTTCACATAAAAGTAT
*
22204366 ATACAAAAATTGTTCACATTAAAGTAT
1 ATACAAAAATTGTTCACATAAAAGTAT
22204393 ATA
1 ATA
22204396 AAATATCTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
27 48 0.86
28 8 0.14
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.31
Consensus pattern (27 bp):
ATACAAAAATTGTTCACATAAAAGTAT
Found at i:22206334 original size:14 final size:16
Alignment explanation
Indices: 22206317--22206348 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
22206307 TGTGAAAAGC
22206317 ATTTTAAA-A-ATAAA
1 ATTTTAAATACATAAA
22206331 ATTTTAAATACATAAA
1 ATTTTAAATACATAAA
22206347 AT
1 AT
22206349 CGATGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTTAAATACATAAA
Found at i:22206682 original size:12 final size:12
Alignment explanation
Indices: 22206665--22206689 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22206655 TAATAATGTG
22206665 TAAAAAAATTAT
1 TAAAAAAATTAT
22206677 TAAAAAAATTAT
1 TAAAAAAATTAT
22206689 T
1 T
22206690 TATAATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAAAATTAT
Found at i:22207749 original size:22 final size:21
Alignment explanation
Indices: 22207707--22207769 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
22207697 TCAACTGGGC
* *
22207707 ATTTGTTTTTTTTCCTCTTTGG
1 ATTTGTTTTTTTTTCT-TTTTG
*
22207729 ATTTGTTTTTTTTTTTTTTTG
1 ATTTGTTTTTTTTTCTTTTTG
* * *
22207750 TTTTGTTTTGTTTTGTTTTT
1 ATTTGTTTTTTTTTCTTTTT
22207770 CTTTTGATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.03, C:0.05, G:0.13, T:0.79
Consensus pattern (21 bp):
ATTTGTTTTTTTTTCTTTTTG
Found at i:22207753 original size:10 final size:11
Alignment explanation
Indices: 22207730--22207775 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 11
22207720 CCTCTTTGGA
22207730 TTTGTTTTT-T
1 TTTGTTTTTCT
* *
22207740 TTTTTTTTTGT
1 TTTGTTTTTCT
*
22207751 TTTG-TTTTGT
1 TTTGTTTTTCT
22207761 TTTGTTTTTCT
1 TTTGTTTTTCT
22207772 TTTG
1 TTTG
22207776 ATTGGTAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 18 0.58
11 13 0.42
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (11 bp):
TTTGTTTTTCT
Found at i:22207754 original size:21 final size:21
Alignment explanation
Indices: 22207730--22207775 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
22207720 CCTCTTTGGA
* * *
22207730 TTTGTTTTTTTTTTTTTTTGT
1 TTTGTTTTGTTTTGTTTTTCT
22207751 TTTGTTTTGTTTTGTTTTTCT
1 TTTGTTTTGTTTTGTTTTTCT
22207772 TTTG
1 TTTG
22207776 ATTGGTAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (21 bp):
TTTGTTTTGTTTTGTTTTTCT
Found at i:22215125 original size:3 final size:3
Alignment explanation
Indices: 22215119--22215143 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
22215109 AAAAATAAAG
22215119 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
22215144 CGTCGTCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:22215999 original size:27 final size:26
Alignment explanation
Indices: 22215969--22216026 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
22215959 TTATTTATTT
** * *
22215969 AATAATATTTATAATAATTATTTGTAA
1 AATAATATAAATAA-AATTATTCGCAA
22215996 AATAAATATAAATAAAATTATTCGCAA
1 AAT-AATATAAATAAAATTATTCGCAA
22216023 AATA
1 AATA
22216027 TTCGTTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.04
27 16 0.62
28 9 0.35
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (26 bp):
AATAATATAAATAAAATTATTCGCAA
Found at i:22221284 original size:24 final size:24
Alignment explanation
Indices: 22221257--22221304 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
22221247 ATTGACAATT
22221257 TGTGTATTCGTGTCGTGTTTTACA
1 TGTGTATTCGTGTCGTGTTTTACA
*
22221281 TGTGTATTCGTGTTGTGTTTTACA
1 TGTGTATTCGTGTCGTGTTTTACA
22221305 CGTAAATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.10, G:0.25, T:0.52
Consensus pattern (24 bp):
TGTGTATTCGTGTCGTGTTTTACA
Found at i:22243633 original size:2 final size:2
Alignment explanation
Indices: 22243626--22243651 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22243616 AAAACTACAG
22243626 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
22243652 TAAAACTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22249648 original size:354 final size:354
Alignment explanation
Indices: 22249194--22249872 Score: 940
Period size: 354 Copynumber: 1.9 Consensus size: 354
22249184 AAAAAGCCTC
* *
22249194 TATTCAAAAAAGCGTCTTCAATATACCTTTAAACTTGGTAATCCATTACTAAAGGCATTTGTTAA
1 TATTCAAAAAAGCATCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAGGCATTTGTTAA
* * *
22249259 TAACAGACACCTTTAAAATTTTCTCACTAAAAATTTT-GAGAATCATTAAAAGTATCTTCTACTG
66 TAACAGACACCTTTAAAAGTTTCTCACTAAAAATTTTAGA-AATCATTAAAAGCATCTTCTACTA
* * * *
22249323 TAAAATACTTTTTATATA-CTATCACACAAA-TTTAACAC-AGTTATTGAAGGCGTATATCCAAA
130 TAAAATACCTTCTATATATC-ATCACACAAATTTTAACACGA-TTATTAAAGGCATATATCCAAA
* * *
22249385 AAAGATGCCTTTAATAATTTCTATCATAGTTTTGTAGATAATTAATGAAGGCAGTTACAGATAAC
193 AAAGATACCTTTAATAATTTCTATCATAG-TTTATAGATAATT-ATCAAGGCAGTTACAGATAAC
* * *
22249450 AACGCCTTCAATAATTTTTTTAAAAAAAA-ATTTGGATTATTAAAGGCGTCTTTTATTATGAAAC
256 AACGCCTTCAATAA-TTTTCTAAAAAAAATATTTGGATTATTAAAGGCATATTTTATTATGAAAC
22249514 GCCTTATATATACCACAATGGTTATGAAAGGCATT
320 GCCTTATATATACCACAATGGTTATGAAAGGCATT
* * * *
22249549 TATTCGAAAAAGCATCTTCAATATA-CTTTAAACTTAGTAATCCATTATTGAAGGCGTTTGTTAA
1 TATTCAAAAAAGCATCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAGGCATTTGTTAA
* * * * *
22249613 TAATAGACA-CTTTCATAAGTTTCTCACTAAAAATTTTAGAAATTATTAAAGGCGTCTTCTACTA
66 TAACAGACACCTTT-AAAAGTTTCTCACTAAAAATTTTAGAAATCATTAAAAGCATCTTCTACTA
* * *
22249677 TAAAATACCTTCTATATATCGTCACACAAATTTTAATACGATTATTAAAGGCATATATCCAAGAA
130 TAAAATACCTTCTATATATCATCACACAAATTTTAACACGATTATTAAAGGCATATATCCAAAAA
* * * *
22249742 AGATACCTTTAATAATTTCTATCATAGTTTATAGATAATTGTCAAGGCTGTTGCAGATAACAATG
195 AGATACCTTTAATAATTTCTATCATAGTTTATAGATAATTATCAAGGCAGTTACAGATAACAACG
* *
22249807 CCTTTAATAATTTTCTAAAAAAAATTTTTTGGATTATTAAAGGCATATTTTATTATGAAACGCCT
260 CCTTCAATAATTTTCTAAAAAAAA-TATTTGGATTATTAAAGGCATATTTTATTATGAAACGCCT
22249872 T
324 T
22249873 TAATAATTTG
Statistics
Matches: 284, Mismatches: 33, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
352 13 0.05
353 33 0.12
354 157 0.55
355 80 0.28
356 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (354 bp):
TATTCAAAAAAGCATCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAGGCATTTGTTAA
TAACAGACACCTTTAAAAGTTTCTCACTAAAAATTTTAGAAATCATTAAAAGCATCTTCTACTAT
AAAATACCTTCTATATATCATCACACAAATTTTAACACGATTATTAAAGGCATATATCCAAAAAA
GATACCTTTAATAATTTCTATCATAGTTTATAGATAATTATCAAGGCAGTTACAGATAACAACGC
CTTCAATAATTTTCTAAAAAAAATATTTGGATTATTAAAGGCATATTTTATTATGAAACGCCTTA
TATATACCACAATGGTTATGAAAGGCATT
Found at i:22255045 original size:14 final size:14
Alignment explanation
Indices: 22255026--22255056 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
22255016 TGAAAGGCCA
22255026 CTACAAAACTGTCG
1 CTACAAAACTGTCG
22255040 CTACAAAACTGTCG
1 CTACAAAACTGTCG
22255054 CTA
1 CTA
22255057 ATACGTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (14 bp):
CTACAAAACTGTCG
Found at i:22255299 original size:11 final size:11
Alignment explanation
Indices: 22255265--22255301 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
22255255 TATTAGTATT
22255265 ATAATAAATGA
1 ATAATAAATGA
* *
22255276 ACAGTAAATGA
1 ATAATAAATGA
22255287 ATAATAAATGA
1 ATAATAAATGA
22255298 ATAA
1 ATAA
22255302 ATTTTAAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.24
Consensus pattern (11 bp):
ATAATAAATGA
Found at i:22259951 original size:30 final size:30
Alignment explanation
Indices: 22259915--22259973 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
22259905 ATCATATAAC
22259915 CTGATTTAACTTGAGTACCTAAACTGCCTA
1 CTGATTTAACTTGAGTACCTAAACTGCCTA
22259945 CTGATTTAACTTGAGTACCTAAACTGCCT
1 CTGATTTAACTTGAGTACCTAAACTGCCT
22259974 TAGTATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (30 bp):
CTGATTTAACTTGAGTACCTAAACTGCCTA
Found at i:22265638 original size:5 final size:6
Alignment explanation
Indices: 22265621--22265645 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22265611 TCAGCAAACA
22265621 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
22265646 ACTTCAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:22269904 original size:18 final size:18
Alignment explanation
Indices: 22269881--22269917 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
22269871 CTGATTAAAA
22269881 CCTAAAGGTTTCTTCAAT
1 CCTAAAGGTTTCTTCAAT
22269899 CCTAAAGGTTTCTTCAAT
1 CCTAAAGGTTTCTTCAAT
22269917 C
1 C
22269918 AATTGTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (18 bp):
CCTAAAGGTTTCTTCAAT
Found at i:22273620 original size:27 final size:29
Alignment explanation
Indices: 22273577--22273637 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
22273567 TTTAAAAATA
*
22273577 TTTTAATTTTTTAAAAATCCT-ATTTT-TT
1 TTTTAATTTTATAAAAA-CCTGATTTTATT
*
22273605 TTTTAATTTTAT-AAAACTTGATTTTATT
1 TTTTAATTTTATAAAAACCTGATTTTATT
22273633 TTTTA
1 TTTTA
22273638 GAAACAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 2 0.07
27 9 0.31
28 18 0.62
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (29 bp):
TTTTAATTTTATAAAAACCTGATTTTATT
Found at i:22273745 original size:8 final size:9
Alignment explanation
Indices: 22273649--22273755 Score: 69
Period size: 9 Copynumber: 11.4 Consensus size: 9
22273639 AAACAAATTT
22273649 TTTTTTATA
1 TTTTTTATA
22273658 TTTTTCT-TA
1 TTTTT-TATA
22273667 TTTTTTATA
1 TTTTTTATA
22273676 TAATTTTTATCAAA
1 T--TTTTTAT---A
* *
22273690 TTTTCTATG
1 TTTTTTATA
22273699 TATTTTTA-A
1 T-TTTTTATA
**
22273708 -TTTTTAGG
1 TTTTTTATA
22273716 TTTTTTATA
1 TTTTTTATA
*
22273725 TTATTTTACA
1 TT-TTTTATA
22273735 TTTTTT-TA
1 TTTTTTATA
22273743 TTTTTTATA
1 TTTTTTATA
22273752 TTTT
1 TTTT
22273756 AAAAAGTATT
Statistics
Matches: 77, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
7 6 0.08
8 8 0.10
9 34 0.44
10 14 0.18
11 7 0.09
12 6 0.08
14 2 0.03
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.71
Consensus pattern (9 bp):
TTTTTTATA
Found at i:22274191 original size:8 final size:8
Alignment explanation
Indices: 22274141--22274198 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
22274131 AAAAGGTAAA
*
22274141 TTTAATAT
1 TTTAAAAT
22274149 TTTAAAAT
1 TTTAAAAT
*
22274157 ATATAAAAT
1 -TTTAAAAT
22274166 TTCTAAAAAT
1 TT-T-AAAAT
*
22274176 TTTGAAAT
1 TTTAAAAT
*
22274184 ATTAAAAT
1 TTTAAAAT
22274192 TTTAAAA
1 TTTAAAA
22274199 AATATAATCT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
8 24 0.60
9 9 0.22
10 7 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (8 bp):
TTTAAAAT
Found at i:22274200 original size:27 final size:27
Alignment explanation
Indices: 22274147--22274199 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
22274137 TAAATTTAAT
22274147 ATTTTAAAATATATAAAATTTCTAAAA
1 ATTTTAAAATATATAAAATTTCTAAAA
*
22274174 ATTTTGAAATAT-TAAAATTT-TAAAA
1 ATTTTAAAATATATAAAATTTCTAAAA
22274199 A
1 A
22274200 ATATAATCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 6 0.24
26 8 0.32
27 11 0.44
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
ATTTTAAAATATATAAAATTTCTAAAA
Found at i:22274306 original size:42 final size:42
Alignment explanation
Indices: 22274227--22274307 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
22274217 AATTTTCAAA
* * * *
22274227 AAATATAACTTTTACAAAAATAGAATATTTTTTAAAAATATT
1 AAATATAACTTTTAAAAAAATAGAAAATTTCTAAAAAATATT
* * *
22274269 AAATTTAAGTTTTAAAAAAATGGAAAATTTCTAAAAAAT
1 AAATATAACTTTTAAAAAAATAGAAAATTTCTAAAAAAT
22274308 TACAAATATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.37
Consensus pattern (42 bp):
AAATATAACTTTTAAAAAAATAGAAAATTTCTAAAAAATATT
Found at i:22274906 original size:2 final size:2
Alignment explanation
Indices: 22274887--22274921 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
22274877 TTAAAAAGAA
* *
22274887 AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22274922 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:22276027 original size:3 final size:3
Alignment explanation
Indices: 22276019--22276045 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
22276009 TTAATATTGC
22276019 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
22276046 TTTTTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:22276481 original size:11 final size:10
Alignment explanation
Indices: 22276464--22276510 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
22276454 GTTAACATGA
22276464 AAAAAAATTC
1 AAAAAAATTC
22276474 AGAAAAAATTC
1 A-AAAAAATTC
*
22276485 AAAAAACTTC
1 AAAAAAATTC
*
22276495 AAATAAAATTT
1 AAA-AAAATTC
22276506 AAAAA
1 AAAAA
22276511 TTAAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 14 0.44
11 18 0.56
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:22276490 original size:21 final size:21
Alignment explanation
Indices: 22276464--22276510 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
22276454 GTTAACATGA
22276464 AAAAAAATTCAGAA-AAAATTC
1 AAAAAAATTCA-AATAAAATTC
* *
22276485 AAAAAACTTCAAATAAAATTT
1 AAAAAAATTCAAATAAAATTC
22276506 AAAAA
1 AAAAA
22276511 TTAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAAAAATTCAAATAAAATTC
Found at i:22276591 original size:9 final size:9
Alignment explanation
Indices: 22276555--22276773 Score: 73
Period size: 9 Copynumber: 22.6 Consensus size: 9
22276545 ATTTTTAAAA
*
22276555 AAAAAATTC
1 AAAAAATTT
*
22276564 AAAGAATTCT
1 AAAAAATT-T
*
22276574 ACAATAATTT
1 A-AAAAATTT
22276584 AAAAAATTAGT
1 AAAAAATT--T
* *
22276595 ATAAAATAT
1 AAAAAATTT
*
22276604 AAAAAAATT
1 AAAAAATTT
**
22276613 AAAACTTTAAAT
1 AAAAAATT---T
*
22276625 AAAAAATCT
1 AAAAAATTT
**
22276634 AAAATTTTTT
1 AAAA-AATTT
*
22276644 AAAAAATTCC
1 AAAAAATT-T
22276654 AAAAAATTTT
1 AAAAAA-TTT
*
22276664 AACAAATTTT
1 AA-AAAATTT
*
22276674 CAAAAATTCT
1 AAAAAATT-T
*
22276684 AAAAATTTT
1 AAAAAATTT
22276693 AAAATAATTT
1 AAAA-AATTT
22276703 CAAAAAATCTTT
1 -AAAAAA--TTT
* *
22276715 AGAAAATTC
1 AAAAAATTT
22276724 AAAAAA-TT
1 AAAAAATTT
22276732 -AAAAATTT
1 AAAAAATTT
**
22276740 TTAAAATTCT
1 AAAAAATT-T
*
22276750 GAAAAATTT
1 AAAAAATTT
*
22276759 TAAAAATTCT
1 AAAAAATT-T
22276769 AAAAA
1 AAAAA
22276774 CTCTAGAAAA
Statistics
Matches: 153, Mismatches: 37, Indels: 39
0.67 0.16 0.17
Matches are distributed among these distances:
7 5 0.03
8 3 0.02
9 63 0.41
10 46 0.30
11 27 0.18
12 9 0.06
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAAATTT
Found at i:22276648 original size:20 final size:19
Alignment explanation
Indices: 22276601--22276649 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
22276591 TAGTATAAAA
22276601 TATAAAAAAATTAAAACTT
1 TATAAAAAAATTAAAACTT
* *
22276620 TAAATAAAAAATCTAAAATTT
1 TATA-AAAAAAT-TAAAACTT
*
22276641 TTTAAAAAA
1 TATAAAAAA
22276650 TTCCAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.12
20 12 0.50
21 9 0.38
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
TATAAAAAAATTAAAACTT
Found at i:22276670 original size:10 final size:9
Alignment explanation
Indices: 22276655--22276802 Score: 93
Period size: 9 Copynumber: 15.6 Consensus size: 9
22276645 AAAAATTCCA
22276655 AAAAATTTT
1 AAAAATTTT
22276664 AACAAATTTT
1 AA-AAATTTT
*
22276674 CAAAAATTCT
1 -AAAAATTTT
22276684 AAAAATTTT
1 AAAAATTTT
*
22276693 AAAATAATTTCA
1 -AAA-AATTT-T
22276705 AAAAATCTTT
1 AAAAAT-TTT
*
22276715 AGAAAA-TTC
1 A-AAAATTTT
*
22276724 AAAAA-ATT
1 AAAAATTTT
22276732 AAAAATTTT
1 AAAAATTTT
* *
22276741 TAAAATTCTG
1 AAAAATT-TT
22276751 AAAAATTTT
1 AAAAATTTT
*
22276760 AAAAATTCT
1 AAAAATTTT
* *
22276769 AAAAACTCT
1 AAAAATTTT
**
22276778 AGAAAATTCC
1 A-AAAATTTT
22276788 AGAAAATTTT
1 A-AAAATTTT
22276798 AAAAA
1 AAAAA
22276803 AGTTCAAAAA
Statistics
Matches: 111, Mismatches: 18, Indels: 20
0.74 0.12 0.13
Matches are distributed among these distances:
8 10 0.09
9 43 0.39
10 42 0.38
11 16 0.14
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAAATTTT
Found at i:22276679 original size:30 final size:29
Alignment explanation
Indices: 22276625--22276708 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
22276615 AACTTTAAAT
* * *
22276625 AAAAAA-TCTAAAATTTTTTAAAAAATTCC
1 AAAAAATTTTAAAATATTTTCAAAAATT-C
22276654 AAAAAATTTTAACAA-ATTTTCAAAAATTC
1 AAAAAATTTTAA-AATATTTTCAAAAATTC
* *
22276683 TAAAAATTTTAAAATAATTTCAAAAA
1 AAAAAATTTTAAAATATTTTCAAAAA
22276709 ATCTTTAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 2 0.04
29 28 0.60
30 15 0.32
31 2 0.04
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAAAATTTTAAAATATTTTCAAAAATTC
Found at i:22276687 original size:8 final size:9
Alignment explanation
Indices: 22276645--22276802 Score: 86
Period size: 10 Copynumber: 16.6 Consensus size: 9
22276635 AAATTTTTTA
*
22276645 AAAAATTCCA
1 AAAAATT-CT
*
22276655 AAAAATTTT
1 AAAAATTCT
*
22276664 AACAAATTTT
1 AA-AAATTCT
22276674 CAAAAATTCT
1 -AAAAATTCT
*
22276684 AAAAATTTT
1 AAAAATTCT
*
22276693 AAAATAATTTCA
1 -AAA-AA-TTCT
*
22276705 AAAAATCTTT
1 AAAAAT-TCT
22276715 AGAAAATTC-
1 A-AAAATTCT
*
22276724 AAAAAAT-T
1 AAAAATTCT
*
22276732 AAAAATTTT
1 AAAAATTCT
*
22276741 TAAAATTCT
1 AAAAATTCT
*
22276750 GAAAAATTTT
1 -AAAAATTCT
22276760 AAAAATTCT
1 AAAAATTCT
*
22276769 AAAAACTCT
1 AAAAATTCT
*
22276778 AGAAAATTCC
1 A-AAAATTCT
*
22276788 AGAAAATTTT
1 A-AAAATTCT
22276798 AAAAA
1 AAAAA
22276803 AGTTCAAAAA
Statistics
Matches: 116, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
8 11 0.09
9 41 0.35
10 50 0.43
11 12 0.10
12 2 0.02
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATTCT
Found at i:22276803 original size:10 final size:10
Alignment explanation
Indices: 22276640--22276773 Score: 93
Period size: 10 Copynumber: 13.9 Consensus size: 10
22276630 ATCTAAAATT
22276640 TTTTAAAAAA
1 TTTTAAAAAA
**
22276650 TTCCAAAAAA
1 TTTTAAAAAA
*
22276660 TTTTAACAAA
1 TTTTAAAAAA
*
22276670 TTTTCAAAAA
1 TTTTAAAAAA
*
22276680 TTCT-AAAAA
1 TTTTAAAAAA
22276689 TTTTAAAATAA
1 TTTTAAAA-AA
*
22276700 TTTCAAAAAA
1 TTTTAAAAAA
*
22276710 TCTTTAGAAAA
1 T-TTTAAAAAA
*
22276721 -TTCAAAAAA
1 TTTTAAAAAA
22276730 --TT-AAAAA
1 TTTTAAAAAA
*
22276737 TTTT-TAAAA
1 TTTTAAAAAA
* *
22276746 TTCTGAAAAA
1 TTTTAAAAAA
22276756 TTTT-AAAAA
1 TTTTAAAAAA
*
22276765 TTCTAAAAA
1 TTTTAAAAA
22276774 CTCTAGAAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
7 5 0.05
8 1 0.01
9 32 0.33
10 43 0.44
11 16 0.16
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:22276888 original size:16 final size:16
Alignment explanation
Indices: 22276853--22276905 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
22276843 TATTTATAAA
22276853 TTTATAGAATTTAATAT
1 TTTATA-AATTTAATAT
22276870 TTTATAAAGTTTAAT-T
1 TTTATAAA-TTTAATAT
*
22276886 TTTATAAAATGTAATAT
1 TTTAT-AAATTTAATAT
22276903 TTT
1 TTT
22276906 TTTAATTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TTTATAAATTTAATAT
Found at i:22277179 original size:20 final size:18
Alignment explanation
Indices: 22277147--22277192 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
22277137 AATTGCTTAG
22277147 AATTTTTTTAAGTTTTTA
1 AATTTTTTTAAGTTTTTA
22277165 AATTCTTTTTGAAGTTTTTAA
1 AATT-TTTTT-AAGTTTTT-A
22277186 AATTTTT
1 AATTTTT
22277193 AGAGTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.16
19 5 0.20
20 11 0.44
21 5 0.20
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (18 bp):
AATTTTTTTAAGTTTTTA
Found at i:22277278 original size:20 final size:19
Alignment explanation
Indices: 22277243--22277285 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
22277233 AATTAATTTT
*
22277243 TTTTATAAATTTTAGACAA
1 TTTTATAAATTTTAGAAAA
22277262 TTTTA-AAATATTATAGAAAA
1 TTTTATAAAT-TT-TAGAAAA
22277282 TTTT
1 TTTT
22277286 CATATGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 7 0.33
20 10 0.48
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTTATAAATTTTAGAAAA
Found at i:22277337 original size:20 final size:19
Alignment explanation
Indices: 22277291--22277359 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
22277281 ATTTTCATAT
22277291 GTTTTTAAA-TTTTTTTAGA
1 GTTTTTAAATTTTTTTTA-A
*
22277310 ATTGTTTAGAATTTTTTTTAA
1 GTT-TTTA-AATTTTTTTTAA
*
22277331 GTTTTTACATTTTTTTTGAA
1 GTTTTTAAATTTTTTTT-AA
22277351 GTTTTTAAA
1 GTTTTTAAA
22277360 ATGTTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 11 0.26
20 18 0.43
21 5 0.12
22 8 0.19
ACGTcount: A:0.26, C:0.01, G:0.10, T:0.62
Consensus pattern (19 bp):
GTTTTTAAATTTTTTTTAA
Found at i:22277350 original size:173 final size:175
Alignment explanation
Indices: 22277044--22277380 Score: 425
Period size: 173 Copynumber: 1.9 Consensus size: 175
22277034 TTTAGTATTT
*
22277044 TTTTATAATTTATTGAAATTAAAATTTTTTTATAAATTTTGAAAAATTTTAAAATATGTTTAGAA
1 TTTTATAATTTATTGAAATTAAAATTTTTTTATAAATTTTGAAAAATTTTAAAATATGTATAGAA
** *
22277109 TTTTTTTCATGATTTAAAAAAAAATTGGAATTGCTTAGAATTTTTTTAAGTTTTTAAATTCTTTT
66 TTTTCATCATGATTTAAAAAAAAATTAGAATTGCTTAGAATTTTTTTAAGTTTTTAAATTCTTTT
* * *
22277174 TGAAGTTTTTAAAATTTTTAGAGTTT-TAAAAAAATTTTGGAATA
131 TGAAGTTTTTAAAATGTTTAAAATTTCTAAAAAAATTTTGGAATA
* *
22277218 TTTTATAATTT-TTGAAATT-AATTTTTTTTATAAATTTT-AGACAATTTTAAAATAT-TATAGA
1 TTTTATAATTTATTGAAATTAAAATTTTTTTATAAATTTTGA-AAAATTTTAAAATATGTATAG-
* * ***** * * *
22277279 AAATTTTCAT-ATGTTTTTAAATTTTTTTAGAATTGTTTAGAATTTTTTTTAAGTTTTTACATTT
64 -AATTTTCATCATGATTTAAAAAAAAATTAGAATTGCTTAGAA-TTTTTTTAAGTTTTTAAATTC
22277343 TTTTTGAAGTTTTTAAAATGTTTAAAATTTCTAAAAAA
127 TTTTTGAAGTTTTTAAAATGTTTAAAATTTCTAAAAAA
22277381 TTAAAAAAAA
Statistics
Matches: 139, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
171 5 0.04
172 55 0.40
173 61 0.44
174 18 0.13
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (175 bp):
TTTTATAATTTATTGAAATTAAAATTTTTTTATAAATTTTGAAAAATTTTAAAATATGTATAGAA
TTTTCATCATGATTTAAAAAAAAATTAGAATTGCTTAGAATTTTTTTAAGTTTTTAAATTCTTTT
TGAAGTTTTTAAAATGTTTAAAATTTCTAAAAAAATTTTGGAATA
Found at i:22277410 original size:10 final size:10
Alignment explanation
Indices: 22277397--22277457 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
22277387 AAAATTATAT
22277397 ATTTTTTAAA
1 ATTTTTTAAA
*
22277407 A-TTTTTAAT
1 ATTTTTTAAA
*
22277416 ATTTTTGAGAA
1 ATTTTTTA-AA
22277427 ATTTTTTAAA
1 ATTTTTTAAA
*
22277437 ACCTTTTTTTATA
1 A---TTTTTTAAA
22277450 ATTTTTTA
1 ATTTTTTA
22277458 GAAAATTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
9 8 0.20
10 16 0.39
11 8 0.20
13 9 0.22
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:22277417 original size:19 final size:20
Alignment explanation
Indices: 22277395--22277432 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
22277385 AAAAAATTAT
*
22277395 ATATTTTTTA-AAATTTTTA
1 ATATTTTTGAGAAATTTTTA
22277414 ATATTTTTGAGAAATTTTT
1 ATATTTTTGAGAAATTTTT
22277433 TAAAACCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
ATATTTTTGAGAAATTTTTA
Found at i:22278571 original size:13 final size:13
Alignment explanation
Indices: 22278553--22278578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22278543 AACGAGATTC
22278553 TTTTAATATATAT
1 TTTTAATATATAT
22278566 TTTTAATATATAT
1 TTTTAATATATAT
22278579 ATATATAAGC
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAATATATAT
Found at i:22283455 original size:27 final size:28
Alignment explanation
Indices: 22283422--22283482 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
22283412 TAGTTATTAA
22283422 ATTTAT-AATTCAAATA-CTAAATTAAAT
1 ATTTATAAATTCAAATATC-AAATTAAAT
* *
22283449 ATTTATAAAATTCAAGTATCATATTAAAT
1 ATTTAT-AAATTCAAATATCAAATTAAAT
22283478 ATTTA
1 ATTTA
22283483 ACCATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.21
29 22 0.76
30 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (28 bp):
ATTTATAAATTCAAATATCAAATTAAAT
Found at i:22285831 original size:17 final size:17
Alignment explanation
Indices: 22285811--22285863 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
22285801 CATGTATTTT
22285811 ATTTTATACTTTAAAAA
1 ATTTTATACTTTAAAAA
* *
22285828 ATTTTGTA-TTT----T
1 ATTTTATACTTTAAAAA
22285840 ATTTTATACTTTAAAAA
1 ATTTTATACTTTAAAAA
22285857 ATTTTAT
1 ATTTTAT
22285864 TGGTTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
12 7 0.26
13 3 0.11
16 3 0.11
17 14 0.52
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATACTTTAAAAA
Found at i:22285845 original size:29 final size:29
Alignment explanation
Indices: 22285803--22285861 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
22285793 TATTGATGCA
22285803 TGTATTTTATTTTATACTTTAAAAAATTT
1 TGTATTTTATTTTATACTTTAAAAAATTT
22285832 TGTATTTTATTTTATACTTTAAAAAATTT
1 TGTATTTTATTTTATACTTTAAAAAATTT
22285861 T
1 T
22285862 ATTGGTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (29 bp):
TGTATTTTATTTTATACTTTAAAAAATTT
Found at i:22286109 original size:30 final size:30
Alignment explanation
Indices: 22286048--22286124 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 30
22286038 TTGTTTTCCC
*
22286048 TAATTTTTATTACTTTTATTAATAATTTTAGT
1 TAATTTTTATT--TTTAATTAATAATTTTAGT
22286080 TAATTTTTATTTTTAATT-ATAATTTTTAGT
1 TAATTTTTATTTTTAATTAATAA-TTTTAGT
*
22286110 TAATTCTTATTTTTA
1 TAATTTTTATTTTTA
22286125 TTTTATAGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 4 0.10
30 27 0.64
32 11 0.26
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (30 bp):
TAATTTTTATTTTTAATTAATAATTTTAGT
Found at i:22286384 original size:13 final size:15
Alignment explanation
Indices: 22286358--22286389 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
22286348 TTTTCATTTA
22286358 TTATTATTAGTTATT
1 TTATTATTAGTTATT
22286373 TTATT-TTA-TTATT
1 TTATTATTAGTTATT
22286386 TTAT
1 TTAT
22286390 AAAGTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TTATTATTAGTTATT
Found at i:22286550 original size:17 final size:17
Alignment explanation
Indices: 22286518--22286570 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
22286508 GTAGTAAAAG
22286518 AAAAAAAT-AAATAAATA
1 AAAAAAATCAAA-AAATA
* *
22286535 AGAAATATCAAAAAATA
1 AAAAAAATCAAAAAATA
*
22286552 AAAAAAATGAAAAAA-A
1 AAAAAAATCAAAAAATA
22286568 AAA
1 AAA
22286571 TTAAATTGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 4 0.13
17 23 0.77
18 3 0.10
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (17 bp):
AAAAAAATCAAAAAATA
Found at i:22287099 original size:22 final size:22
Alignment explanation
Indices: 22287065--22287116 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
22287055 TTTTTTTTGA
* *
22287065 ATTTTTTGTGTAGG-TGAAATG
1 ATTTTTTTTGTAGGCTAAAATG
22287086 ATTTTTTTTAGTAGGCTAAAATG
1 ATTTTTTTT-GTAGGCTAAAATG
22287109 ATTTTTTT
1 ATTTTTTT
22287117 CTTAATAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 8 0.30
22 5 0.19
23 14 0.52
ACGTcount: A:0.25, C:0.02, G:0.19, T:0.54
Consensus pattern (22 bp):
ATTTTTTTTGTAGGCTAAAATG
Found at i:22288051 original size:50 final size:51
Alignment explanation
Indices: 22287953--22288085 Score: 133
Period size: 51 Copynumber: 2.6 Consensus size: 51
22287943 ACTCAAAGCT
* * ***
22287953 TTTTAAAATTCTTATATTGAAAAAAGACTCTTTTAAGCGGATGTTCGAT-AA
1 TTTTAAAATTTTTATATTG-AAAAAGACTCTTTTAAGCAGAAACTCGATGAA
** * *
22288004 TTTTAAAATTTTTATATTGAAAAAGGTTTTTTTAAGCAGAAACTCGATGAC
1 TTTTAAAATTTTTATATTGAAAAAGACTCTTTTAAGCAGAAACTCGATGAA
* * * *
22288055 TTTAAAAATTTTCATATTAAAAAAAACTCTT
1 TTTTAAAATTTTTATATTGAAAAAGACTCTT
22288086 CTAAACAAAT
Statistics
Matches: 65, Mismatches: 16, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
50 22 0.34
51 43 0.66
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.41
Consensus pattern (51 bp):
TTTTAAAATTTTTATATTGAAAAAGACTCTTTTAAGCAGAAACTCGATGAA
Found at i:22288163 original size:50 final size:50
Alignment explanation
Indices: 22288059--22288163 Score: 111
Period size: 50 Copynumber: 2.1 Consensus size: 50
22288049 GATGACTTTA
* * * **
22288059 AAAATTTTCATATTAAAAAAAACTCTTCTAAACAAATGCTCAAAAACTTT
1 AAAATTCTCATATTAAAAAAAACTCATCTAAACAAAGGCTCAAAAACTAC
** ** * *
22288109 AAAATTCTCATATTAAAAAAGGCTCATCTAAGTAAAGGCTTAATAACTAC
1 AAAATTCTCATATTAAAAAAAACTCATCTAAACAAAGGCTCAAAAACTAC
22288159 AAAAT
1 AAAAT
22288164 CTTTATCTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.30
Consensus pattern (50 bp):
AAAATTCTCATATTAAAAAAAACTCATCTAAACAAAGGCTCAAAAACTAC
Found at i:22292972 original size:13 final size:13
Alignment explanation
Indices: 22292954--22292978 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22292944 TCTCTTTTCT
22292954 TTATTTTCATTCA
1 TTATTTTCATTCA
22292967 TTATTTTCATTC
1 TTATTTTCATTC
22292979 TGTCCCCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTTCATTCA
Found at i:22296814 original size:22 final size:23
Alignment explanation
Indices: 22296789--22296844 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
22296779 GGACATAAGC
*
22296789 TTTTTTTTTGGCA-TTTTTTGGT
1 TTTTTTTTTGGCAGTTTTTTAGT
* *
22296811 TTTTTTTTTTGTAGTTTTTTAGT
1 TTTTTTTTTGGCAGTTTTTTAGT
22296834 TTGTTTTTTTG
1 TT-TTTTTTTG
22296845 CTAGAGTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 11 0.39
23 10 0.36
24 7 0.25
ACGTcount: A:0.05, C:0.02, G:0.16, T:0.77
Consensus pattern (23 bp):
TTTTTTTTTGGCAGTTTTTTAGT
Found at i:22296872 original size:18 final size:18
Alignment explanation
Indices: 22296851--22296887 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
22296841 TTTGCTAGAG
**
22296851 TTTTTTTTTTTTTTTTGA
1 TTTTTTTTGGTTTTTTGA
22296869 TTTTTTTTGGTTTTTTGA
1 TTTTTTTTGGTTTTTTGA
22296887 T
1 T
22296888 AAAGTTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.05, C:0.00, G:0.11, T:0.84
Consensus pattern (18 bp):
TTTTTTTTGGTTTTTTGA
Found at i:22296882 original size:23 final size:23
Alignment explanation
Indices: 22296789--22296884 Score: 81
Period size: 23 Copynumber: 4.2 Consensus size: 23
22296779 GGACATAAGC
**
22296789 TTTTTTTTTGGCATTTTTTGGTT
1 TTTTTTTTTGATATTTTTTGGTT
*
22296812 TTTTTTTTTG-TAGTTTTTTAGTT
1 TTTTTTTTTGATA-TTTTTTGGTT
* * *
22296835 TGTTTTTTTGCTAGAGTTTTT--TT
1 TTTTTTTTTG--ATATTTTTTGGTT
*
22296858 TTTTTTTTTGATTTTTTTTGGTT
1 TTTTTTTTTGATATTTTTTGGTT
22296881 TTTT
1 TTTT
22296885 GATAAAGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
21 6 0.10
22 1 0.02
23 45 0.78
25 5 0.09
26 1 0.02
ACGTcount: A:0.06, C:0.02, G:0.15, T:0.77
Consensus pattern (23 bp):
TTTTTTTTTGATATTTTTTGGTT
Found at i:22296883 original size:41 final size:42
Alignment explanation
Indices: 22296810--22296896 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 42
22296800 CATTTTTTGG
* * * *
22296810 TTTTTTTTTTTGTAGTTTTTTAGTTTGTTTTTTTGCTAGAGTT
1 TTTTTTTTTTTGTAGATTTTTA-TTTGGTTTTTTGATAAAGTT
* *
22296853 TTTTTTTTTTTTTTGATTTTT-TTTGGTTTTTTGATAAAGTT
1 TTTTTTTTTTTGTAGATTTTTATTTGGTTTTTTGATAAAGTT
22296894 TTT
1 TTT
22296897 CTCCCTTTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 20 0.53
43 18 0.47
ACGTcount: A:0.10, C:0.01, G:0.14, T:0.75
Consensus pattern (42 bp):
TTTTTTTTTTTGTAGATTTTTATTTGGTTTTTTGATAAAGTT
Found at i:22299378 original size:18 final size:18
Alignment explanation
Indices: 22299357--22299391 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22299347 TTCTATGCAT
*
22299357 ATTAAAAACATGTAAAAC
1 ATTAAAAAAATGTAAAAC
22299375 ATTAAAAAAATGTAAAA
1 ATTAAAAAAATGTAAAA
22299392 GTTTTTGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (18 bp):
ATTAAAAAAATGTAAAAC
Found at i:22303963 original size:24 final size:24
Alignment explanation
Indices: 22303936--22303984 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
22303926 TCAATATAAC
* *
22303936 AAAAACTTATAATATTAAATAAATA
1 AAAAATTTA-AATATCAAATAAATA
22303961 AAAAATTTAAATATCAAATAAATA
1 AAAAATTTAAATATCAAATAAATA
22303985 CAAATACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAAATTTAAATATCAAATAAATA
Found at i:22304295 original size:18 final size:19
Alignment explanation
Indices: 22304261--22304296 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22304251 TAACATGCTA
*
22304261 CTTTTATATATATTTTAAC
1 CTTTTAAATATATTTTAAC
22304280 CTTTTAAATA-ATTTTAA
1 CTTTTAAATATATTTTAA
22304297 AATTGATGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
CTTTTAAATATATTTTAAC
Found at i:22305523 original size:22 final size:22
Alignment explanation
Indices: 22305498--22305547 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
22305488 ATTTTTTAAA
*
22305498 TTTTTTATGTAGGC-AAAATGAT
1 TTTTTTA-GTAAGCTAAAATGAT
22305520 TTTTTTAGTAAGCTAAAATGAT
1 TTTTTTAGTAAGCTAAAATGAT
22305542 TTTTTT
1 TTTTTT
22305548 TCTTAATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (22 bp):
TTTTTTAGTAAGCTAAAATGAT
Found at i:22305676 original size:35 final size:35
Alignment explanation
Indices: 22305608--22305676 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
22305598 ATTTTTGATC
*
22305608 TTTTTTTTTTTTGTTTTCTTTCGTAAAATTTTTCTT
1 TTTTTTTTTTTTGTTTTCTTTCGT-AAAGTTTTCTT
* *
22305644 TTTTTTTTTTTTGTTCTTTTTTGGT-AAGTTTTC
1 TTTTTTTTTTTTGTT-TTCTTTCGTAAAGTTTTC
22305677 CCTTTCTCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 7 0.24
36 15 0.52
37 7 0.24
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.75
Consensus pattern (35 bp):
TTTTTTTTTTTTGTTTTCTTTCGTAAAGTTTTCTT
Found at i:22306385 original size:50 final size:49
Alignment explanation
Indices: 22306324--22306605 Score: 189
Period size: 50 Copynumber: 5.6 Consensus size: 49
22306314 TTAAATAGCT
22306324 TCTT-TAAGTAGAGGCTCTACAACTTTAAAATTTTTATATTAAAAAAGGC
1 TCTTCTAAGTAGAGGCT-TACAACTTTAAAATTTTTATATTAAAAAAGGC
* * * * *
22306373 TCCTCTAAGTAGATGCTTA-ATGACTTTAAAAATTCTTATATT-GAAAAGGT
1 TCTTCTAAGTAGAGGCTTACA--ACTTT-AAAATTTTTATATTAAAAAAGGC
* * * * *
22306423 TCTTCTAAGCAGAGGTTTGAGAATTTTAAAATTTTTATATTAAAAAAGGT
1 TCTTCTAAGTAGAGGCTT-ACAACTTTAAAATTTTTATATTAAAAAAGGC
* * * * *
22306473 TTTTCTAAG-GGAAAGCTTGACAACTTTAAAAATTCTCATATTGAAAAAA-GC
1 TCTTCTAAGTAG-AGGCTT-ACAACTTT-AAAATTTTTATATT-AAAAAAGGC
* * * * * * *
22306524 TTTTTTAAGCAAAGGCTCAACAACTTTAAAATTTTCATATTAAAAAGGGC
1 TCTTCTAAGTAGAGGCT-TACAACTTTAAAATTTTTATATTAAAAAAGGC
* * *
22306574 TCATT-TAAGTAAATGCTTAACAACTATAAAAT
1 TC-TTCTAAGTAGAGGCTT-ACAACTTTAAAAT
22306606 CTTCATTTTT
Statistics
Matches: 185, Mismatches: 33, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
48 1 0.01
49 24 0.13
50 104 0.56
51 49 0.26
52 7 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (49 bp):
TCTTCTAAGTAGAGGCTTACAACTTTAAAATTTTTATATTAAAAAAGGC
Found at i:22306569 original size:100 final size:99
Alignment explanation
Indices: 22306320--22306604 Score: 277
Period size: 100 Copynumber: 2.8 Consensus size: 99
22306310 AAATTTAAAT
* * * *
22306320 AGCTTCTTTAAGTAGAGGCTCTACAACTTTAAAATTTTTATATTAAAAAAGGCTCCTCTAAGTAG
1 AGCTTTTTTAAGCAGAGGCTCAACAACTTTAAAATTTTTATATTAAAAAAGGCTCCTCTAAGGAG
* ** *
22306385 ATGCTTAATGACTTTAAAAATTCTTATATTGAAA
66 AAGCTTAACAACTTTAAAAATTCTCATATTGAAA
* * * ** * * * **
22306419 AGGTTCTTCTAAGCAGAGGTTTGAGAATTTTAAAATTTTTATATTAAAAAAGGTTTTTCTAAGG-
1 AGCTT-TTTTAAGCAGAGGCTCAACAACTTTAAAATTTTTATATTAAAAAAGGCTCCTCTAAGGA
*
22306483 GAAAGCTTGACAACTTTAAAAATTCTCATATTGAAAAA
65 G-AAGCTTAACAACTTTAAAAATTCTCATATTG--AAA
* * * * * *
22306521 AGCTTTTTTAAGCAAAGGCTCAACAACTTTAAAATTTTCATATTAAAAAGGGCTCATTTAAGTA-
1 AGCTTTTTTAAGCAGAGGCTCAACAACTTTAAAATTTTTATATTAAAAAAGGCTCCTCTAAGGAG
*
22306585 AATGCTTAACAACTATAAAA
66 AA-GCTTAACAACTTTAAAA
22306605 TCTTCATTTT
Statistics
Matches: 145, Mismatches: 35, Indels: 10
0.76 0.18 0.05
Matches are distributed among these distances:
99 5 0.03
100 74 0.51
101 59 0.41
102 7 0.05
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (99 bp):
AGCTTTTTTAAGCAGAGGCTCAACAACTTTAAAATTTTTATATTAAAAAAGGCTCCTCTAAGGAG
AAGCTTAACAACTTTAAAAATTCTCATATTGAAA
Found at i:22311280 original size:4 final size:4
Alignment explanation
Indices: 22311273--22311327 Score: 101
Period size: 4 Copynumber: 13.5 Consensus size: 4
22311263 AGAGAGAAAC
22311273 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGAA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG-A
22311322 AAGA AA
1 AAGA AA
22311328 AGAGAAGAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 46 0.92
5 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:22312600 original size:10 final size:10
Alignment explanation
Indices: 22312585--22312632 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
22312575 TGCATTTATT
22312585 AAAAAAATGA
1 AAAAAAATGA
*
22312595 AAAAAAAAGA
1 AAAAAAATGA
22312605 AAAAAAATTGTA
1 AAAAAAA-TG-A
22312617 CTAAAAAAATGA
1 --AAAAAAATGA
22312629 AAAA
1 AAAA
22312633 TAAAGAGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 20 0.62
11 1 0.03
12 2 0.06
13 2 0.06
14 7 0.22
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.12
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:22312697 original size:3 final size:3
Alignment explanation
Indices: 22312689--22312718 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
22312679 ATATTTAAAA
22312689 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
22312719 GGTTGTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:22315230 original size:3 final size:3
Alignment explanation
Indices: 22315218--22315277 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
22315208 GCTCAATAAA
22315218 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22315265 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
22315278 TGTGTGTAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22316015 original size:3 final size:3
Alignment explanation
Indices: 22316007--22316051 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
22315997 GGAAAAGAAC
22316007 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
22316052 TTATATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ACT
Found at i:22318710 original size:3 final size:3
Alignment explanation
Indices: 22318704--22318747 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
22318694 CTACTACTAC
*
22318704 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
22318748 TATTATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:22318754 original size:3 final size:3
Alignment explanation
Indices: 22318748--22318790 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
22318738 AATAATAATA
22318748 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
22318791 GTTGTTGTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:22318795 original size:3 final size:3
Alignment explanation
Indices: 22318789--22318820 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
22318779 ATTATTATTA
*
22318789 TTG TTG TTG TTG TTC TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
22318821 TTATCTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.28, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:22319057 original size:19 final size:19
Alignment explanation
Indices: 22319033--22319077 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
22319023 ATCAGTTTCT
22319033 TATTTTAAAAATAATAAAA
1 TATTTTAAAAATAATAAAA
** *
22319052 TATTTTATTATTAATAAAA
1 TATTTTAAAAATAATAAAA
22319071 TATTTTA
1 TATTTTA
22319078 TTTTGATCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTTTAAAAATAATAAAA
Found at i:22325539 original size:26 final size:23
Alignment explanation
Indices: 22325501--22325548 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
22325491 AAGAAATTTT
22325501 AAATATTAGAATTTGATAAGATAAA
1 AAATATTAGAA-TTGATAA-ATAAA
*
22325526 AAATAATTATAATTGATAAATAA
1 AAAT-ATTAGAATTGATAAATAA
22325549 TGATATCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (23 bp):
AAATATTAGAATTGATAAATAAA
Done.