Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 153 of 163
Found at i:42251175 original size:27 final size:28
Alignment explanation
Indices: 42251134--42251186 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
42251124 TACAAATTGG
42251134 TAAAAAAAAATTTGGAGACCTTAAAAAC
1 TAAAAAAAAATTTGGAGACCTTAAAAAC
* *
42251162 TAAAAAACAA-TTGGAGGCCTTAAAA
1 TAAAAAAAAATTTGGAGACCTTAAAA
42251187 GTTGATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (28 bp):
TAAAAAAAAATTTGGAGACCTTAAAAAC
Found at i:42256693 original size:41 final size:41
Alignment explanation
Indices: 42256636--42256731 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 41
42256626 TTTTTCGTAG
* *
42256636 AGAATTCTTGTCAAGGTGGAGACTGTTAGAATT-AGGTGACT
1 AGAATTCTTGTTAAGGTGGAAACTGTTAGAATTGA-GTGACT
*
42256677 AGAATTCTTGTTAAGGTGGAAATTGTTAGAATTGAGTGACT
1 AGAATTCTTGTTAAGGTGGAAACTGTTAGAATTGAGTGACT
*
42256718 AGAATTTTTGTTAA
1 AGAATTCTTGTTAA
42256732 AATAAAATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 49 0.98
42 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAAACTGTTAGAATTGAGTGACT
Found at i:42258442 original size:33 final size:33
Alignment explanation
Indices: 42258405--42258472 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
42258395 TTTTTGAATC
*
42258405 AAACAAGTAGAGAGATGAAAT-TTCTAAAATTAA
1 AAACAAGTAGAGAGATGAAATCTT-AAAAATTAA
*
42258438 AAACAAGTAGAGAGATTAAATCTTAAAAATTAA
1 AAACAAGTAGAGAGATGAAATCTTAAAAATTAA
42258471 AA
1 AA
42258473 GTACAGGGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.57, C:0.06, G:0.13, T:0.24
Consensus pattern (33 bp):
AAACAAGTAGAGAGATGAAATCTTAAAAATTAA
Found at i:42262308 original size:27 final size:27
Alignment explanation
Indices: 42262259--42262325 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
42262249 TATATTCAAG
42262259 TAAATTATGATTTTTTTTAATATCCAAAA
1 TAAATTATG--TTTTTTTAATATCCAAAA
*
42262288 TAAATTATGTTTTTTTAATATCCAAAG
1 TAAATTATGTTTTTTTAATATCCAAAA
42262315 TAAATTATGTT
1 TAAATTATGTT
42262326 ACATTGGGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
27 28 0.76
29 9 0.24
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (27 bp):
TAAATTATGTTTTTTTAATATCCAAAA
Found at i:42274170 original size:19 final size:17
Alignment explanation
Indices: 42274138--42274172 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
42274128 TGTTTATCTC
42274138 TTTTTCTTTTTATATAA
1 TTTTTCTTTTTATATAA
42274155 TTTTCTCTTCTTTATATA
1 TTTT-TCTT-TTTATATA
42274173 TAACATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTCTTTTTATATAA
Found at i:42276728 original size:31 final size:31
Alignment explanation
Indices: 42276690--42276751 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
42276680 TACACAACAT
42276690 AAGTTTTGATGATCAAGAATCTGAAAGAACC
1 AAGTTTTGATGATCAAGAATCTGAAAGAACC
*
42276721 AAGTTTTGATGATCAAGAATCTGAAATAACC
1 AAGTTTTGATGATCAAGAATCTGAAAGAACC
42276752 TCAAGAATGC
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:0.13, G:0.18, T:0.27
Consensus pattern (31 bp):
AAGTTTTGATGATCAAGAATCTGAAAGAACC
Found at i:42285355 original size:105 final size:105
Alignment explanation
Indices: 42285191--42285405 Score: 396
Period size: 105 Copynumber: 2.0 Consensus size: 105
42285181 AGATGTAAAG
*
42285191 GAAGATGGTGAAACACATGATGTTATTGAAGAGGAATTGGTGGAAACAGGAGAGATTTTTGATGA
1 GAAGATGGTGAAACACATGATGTTATTGAAGAGGAATTGGTGGAAACAAGAGAGATTTTTGATGA
*
42285256 GATGGTAAGGGATATTGAGGAGCAGGGGCAGCAAACTGCT
66 GATGGTAAGGGATATTGAGCAGCAGGGGCAGCAAACTGCT
42285296 GAAGATGGTGAAACACATGATGTTATTGAAGAGGAATTGGTGGAAACAAGAGA-AGTTTTTGATG
1 GAAGATGGTGAAACACATGATGTTATTGAAGAGGAATTGGTGGAAACAAGAGAGA-TTTTTGATG
42285360 AGATGGTAAGGGATATTGAGCAGCAGGGGCAGCAAACTGCT
65 AGATGGTAAGGGATATTGAGCAGCAGGGGCAGCAAACTGCT
42285401 GAAGA
1 GAAGA
42285406 GGTTGAATTC
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
104 1 0.01
105 106 0.99
ACGTcount: A:0.35, C:0.08, G:0.34, T:0.22
Consensus pattern (105 bp):
GAAGATGGTGAAACACATGATGTTATTGAAGAGGAATTGGTGGAAACAAGAGAGATTTTTGATGA
GATGGTAAGGGATATTGAGCAGCAGGGGCAGCAAACTGCT
Found at i:42287764 original size:18 final size:18
Alignment explanation
Indices: 42287737--42287771 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42287727 CCCATTCATT
*
42287737 AATTTCAATCATCTTTTC
1 AATTTCAATCATATTTTC
*
42287755 AATTTGAATCATATTTT
1 AATTTCAATCATATTTT
42287772 ATTGCTAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTTCAATCATATTTTC
Found at i:42298295 original size:52 final size:52
Alignment explanation
Indices: 42298104--42298285 Score: 242
Period size: 52 Copynumber: 3.5 Consensus size: 52
42298094 GAAAAAGGGT
* * *
42298104 CCGATGATTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT-AGAGGC
1 CCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGC
*
42298155 CCGATGACTAAGTGTTATCGTGAGTATATGAAATCCTTTTATGGATTTAA-AGGC
1 CCGATGACTAAGTGTCATCGTGAGTATATG-AATCC-TTTATGGA-TTAAGAGGC
* * *
42298209 CCGATGACTAAATGTCATCTTGAGTATATGAATCCTTTATGGATTAAGAGGT
1 CCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGC
**
42298261 CCGATGACTCTGTGTCATCGTGAGT
1 CCGATGACTAAGTGTCATCGTGAGT
42298286 GTGCGAATCC
Statistics
Matches: 114, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
51 31 0.27
52 37 0.32
53 12 0.11
54 33 0.29
55 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (52 bp):
CCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGC
Found at i:42314724 original size:2 final size:2
Alignment explanation
Indices: 42314717--42314745 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42314707 AACCCTTCCC
42314717 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
42314746 ACACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:42328672 original size:19 final size:20
Alignment explanation
Indices: 42328594--42328674 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 20
42328584 TTAATCATAC
* *
42328594 AATA-AATTATTAATATTATT
1 AATATAATT-TTAATTTTAAT
* *
42328614 AATATAATTTATTATTTTAAA
1 AATATAATTT-TAATTTTAAT
42328635 AATATTTAATTTT-ATTTTAAT
1 AATA--TAATTTTAATTTTAAT
42328656 AATA-AATTTTAATTTTAAT
1 AATATAATTTTAATTTTAAT
42328675 TTATAACTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
18 6 0.12
19 8 0.16
20 5 0.10
21 25 0.49
22 1 0.02
23 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATAATTTTAATTTTAAT
Found at i:42334519 original size:11 final size:11
Alignment explanation
Indices: 42334493--42334526 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
42334483 TATTGAATTT
42334493 TTTTATATAGTTA
1 TTTTA-ATA-TTA
42334506 TTTTAATATTA
1 TTTTAATATTA
42334517 TTTTAATATT
1 TTTTAATATT
42334527 TACATTAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.62
12 3 0.14
13 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (11 bp):
TTTTAATATTA
Found at i:42344563 original size:70 final size:66
Alignment explanation
Indices: 42344438--42344569 Score: 156
Period size: 70 Copynumber: 1.9 Consensus size: 66
42344428 ATAAATAATA
* * * *
42344438 TAATGGTTTAGCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATAATTTTACTTTTTAAC
1 TAATGGTTTAGCTTTTAACTTAAAGGGTAAACATTTATAAAAACGACATAATTTTACCTTTTAAC
42344503 T
66 T
* * * *
42344504 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAATATTTATAAAAACGACGTAGTTTTACCTTT
1 TAATGGTTTAG-CTTTTAAC-TT--AAAGGGTAAACATTTATAAAAACGACATAATTTTACCTTT
42344569 T
62 T
42344570 CTTATTCGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
66 10 0.19
67 8 0.15
68 2 0.04
70 34 0.63
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (66 bp):
TAATGGTTTAGCTTTTAACTTAAAGGGTAAACATTTATAAAAACGACATAATTTTACCTTTTAAC
T
Found at i:42353923 original size:15 final size:16
Alignment explanation
Indices: 42353903--42353939 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
42353893 TTACAAAGGA
42353903 ATTAATAG-TTTTTTT
1 ATTAATAGATTTTTTT
42353918 ATTAATAGATTTTTTT
1 ATTAATAGATTTTTTT
42353934 -TTAATA
1 ATTAATA
42353940 ATGGTGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTAATAGATTTTTTT
Found at i:42355299 original size:13 final size:13
Alignment explanation
Indices: 42355281--42355310 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42355271 ATTCTATACG
42355281 GCTCGCACATCAA
1 GCTCGCACATCAA
*
42355294 GCTCGCACATTAA
1 GCTCGCACATCAA
42355307 GCTC
1 GCTC
42355311 ACGTATCGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.37, G:0.17, T:0.20
Consensus pattern (13 bp):
GCTCGCACATCAA
Found at i:42358755 original size:21 final size:21
Alignment explanation
Indices: 42358729--42358768 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
42358719 TTCCAGATCC
42358729 TATGTCCTTCCCTGAAAATTT
1 TATGTCCTTCCCTGAAAATTT
42358750 TATGTCCTTCCCTGAAAAT
1 TATGTCCTTCCCTGAAAAT
42358769 CTATAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (21 bp):
TATGTCCTTCCCTGAAAATTT
Found at i:42370586 original size:17 final size:18
Alignment explanation
Indices: 42370559--42370592 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42370549 ACTCAAGCAT
*
42370559 TTGAGTCCATCTCCAAAC
1 TTGAGTCCATCACCAAAC
42370577 TTGA-TCCATCACCAAA
1 TTGAGTCCATCACCAAA
42370593 ATAACTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.26
Consensus pattern (18 bp):
TTGAGTCCATCACCAAAC
Found at i:42377775 original size:23 final size:23
Alignment explanation
Indices: 42377745--42377792 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
42377735 AGAAAATGTA
42377745 CTTAGTTTTTGCAATACTAGTGT
1 CTTAGTTTTTGCAATACTAGTGT
42377768 CTTAGTTTTTGCAATACTAGTGT
1 CTTAGTTTTTGCAATACTAGTGT
42377791 CT
1 CT
42377793 AATATGTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (23 bp):
CTTAGTTTTTGCAATACTAGTGT
Found at i:42380185 original size:18 final size:19
Alignment explanation
Indices: 42380152--42380187 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42380142 GATTTTAAGT
*
42380152 TTATTTTATTTATATTATA
1 TTATTTTATATATATTATA
42380171 TTATTTT-TATATATTAT
1 TTATTTTATATATATTAT
42380188 GTAATTTAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTTTATATATATTATA
Found at i:42383163 original size:18 final size:18
Alignment explanation
Indices: 42383140--42383178 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42383130 AAAAATCAAA
*
42383140 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
42383158 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
42383176 TTT
1 TTT
42383179 GTCCCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:42385937 original size:21 final size:21
Alignment explanation
Indices: 42385895--42385937 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
42385885 ATAAAGATTT
*
42385895 ATTGTGTGATTAATTTGTGAA
1 ATTGTGTGATTAATTTGGGAA
*
42385916 ATTGTG-GATTTATTTGAGGAA
1 ATTGTGTGATTAATTTG-GGAA
42385937 A
1 A
42385938 CAAAGGTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (21 bp):
ATTGTGTGATTAATTTGGGAA
Found at i:42386033 original size:6 final size:6
Alignment explanation
Indices: 42386022--42386078 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
42386012 TGATCAAAAT
*
42386022 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
42386070 TGAAAG TGA
1 TGAAAG TGA
42386079 CATGAATTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.32, T:0.19
Consensus pattern (6 bp):
TGAAAG
Found at i:42403864 original size:2 final size:2
Alignment explanation
Indices: 42403857--42403900 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
42403847 CAAACAGTCT
* * * *
42403857 TA TA TA TA TA TA GA TA TT TA GA TA TC TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42403899 TA
1 TA
42403901 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:42405064 original size:22 final size:22
Alignment explanation
Indices: 42405021--42405072 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
42405011 ATAATTTATA
*
42405021 TAATTTTTAAGAATTTTCA-TT
1 TAATTTTTAAGAATTTTAATTT
* *
42405042 TAATTTTATAATATTTTTAATTT
1 TAATTTT-TAAGAATTTTAATTT
42405065 TAATTTTT
1 TAATTTTT
42405073 TAAAAGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 7 0.27
22 10 0.38
23 9 0.35
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TAATTTTTAAGAATTTTAATTT
Found at i:42443692 original size:13 final size:13
Alignment explanation
Indices: 42443674--42443698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42443664 ATAATATTGA
42443674 AATTAATTTAATT
1 AATTAATTTAATT
42443687 AATTAATTTAAT
1 AATTAATTTAAT
42443699 CTTCGTATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTAATTTAATT
Found at i:42459333 original size:26 final size:26
Alignment explanation
Indices: 42459297--42459350 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
42459287 AAGTTGATTC
42459297 AACAGGGACTTCTAGCAGGACCATTG
1 AACAGGGACTTCTAGCAGGACCATTG
42459323 AACAGGGACTTCTAGCAGGACCATTG
1 AACAGGGACTTCTAGCAGGACCATTG
42459349 AA
1 AA
42459351 GTTATCAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (26 bp):
AACAGGGACTTCTAGCAGGACCATTG
Found at i:42471128 original size:21 final size:21
Alignment explanation
Indices: 42471089--42471128 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42471079 CAAGTAACGT
*
42471089 AAAATGAACTTGGAAACAAGA
1 AAAATGAACTTCGAAACAAGA
42471110 AAAATGAAC-TCGAATACAA
1 AAAATGAACTTCGAA-ACAA
42471129 TTGCTGAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.12, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAATGAACTTCGAAACAAGA
Found at i:42476554 original size:2 final size:2
Alignment explanation
Indices: 42476543--42476585 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
42476533 TTATGTGTCT
42476543 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42476584 TA
1 TA
42476586 GGTGAATACT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:42479522 original size:14 final size:15
Alignment explanation
Indices: 42479507--42479554 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
42479497 TGTATAATAA
42479507 TTAAAATATTTGAAT
1 TTAAAATATTTGAAT
*
42479522 TTAAATATTATTTAAAT
1 TTAAA-A-TATTTGAAT
*
42479539 TTATAATATTTGAAT
1 TTAAAATATTTGAAT
42479554 T
1 T
42479555 AAGAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.50
16 2 0.07
17 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (15 bp):
TTAAAATATTTGAAT
Found at i:42479539 original size:17 final size:18
Alignment explanation
Indices: 42479513--42479548 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
42479503 ATAATTAAAA
*
42479513 TATTTGAATTTA-AATAT
1 TATTTAAATTTATAATAT
42479530 TATTTAAATTTATAATAT
1 TATTTAAATTTATAATAT
42479548 T
1 T
42479549 TGAATTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTAAATTTATAATAT
Found at i:42495758 original size:30 final size:30
Alignment explanation
Indices: 42495722--42495782 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
42495712 CAACTTAACA
*
42495722 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
42495752 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
42495782 A
1 A
42495783 CAATAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:42496565 original size:2 final size:2
Alignment explanation
Indices: 42496558--42496605 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
42496548 TTTCACACTG
42496558 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
42496600 CT CT CT
1 CT CT CT
42496606 ACTTCAATTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:42502497 original size:16 final size:16
Alignment explanation
Indices: 42502473--42502515 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
42502463 CAAACCCGAT
42502473 AAAATCTGAACCTGAA
1 AAAATCTGAACCTGAA
*
42502489 AAGAA-CTGAATCTGAA
1 AA-AATCTGAACCTGAA
42502505 AAAATCTGAAC
1 AAAATCTGAAC
42502516 TCAAAAAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (16 bp):
AAAATCTGAACCTGAA
Found at i:42506468 original size:2 final size:2
Alignment explanation
Indices: 42506461--42506506 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
42506451 AGGAGGGAGG
42506461 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
42506503 GA GA
1 GA GA
42506507 AAAATGACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42514125 original size:6 final size:6
Alignment explanation
Indices: 42514088--42514124 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
42514078 GGTATACCAA
*
42514088 ATCTT- ATCTTG ATCTTG ATCTTG ATCTTG ATGTTG AT
1 ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG AT
42514125 GGACATCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (6 bp):
ATCTTG
Found at i:42519307 original size:19 final size:19
Alignment explanation
Indices: 42519292--42519340 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
42519282 GAGTTATATA
*
42519292 TTTTATATTATTTTATAAT
1 TTTTATAATATTTTATAAT
*
42519311 TTTTATAATATTTTAATAGT
1 TTTTATAATATTTT-ATAAT
42519331 TATTTATAAT
1 T-TTTATAAT
42519341 TCTTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 13 0.50
20 5 0.19
21 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATAATATTTTATAAT
Found at i:42519617 original size:2 final size:2
Alignment explanation
Indices: 42519610--42519657 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
42519600 AAAATAACAA
42519610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42519652 AT AT AT
1 AT AT AT
42519658 TTTCAATATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42519711 original size:19 final size:17
Alignment explanation
Indices: 42519686--42519730 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
42519676 AGTTTTTATA
42519686 TAAATTTTAATATTTTTT
1 TAAATTTTAA-ATTTTTT
42519704 TAAGATTTCTAAATTTTTT
1 TAA-ATTT-TAAATTTTTT
42519723 TAAATTTT
1 TAAATTTT
42519731 TTTTAATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 7 0.28
19 14 0.56
20 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TAAATTTTAAATTTTTT
Found at i:42519827 original size:18 final size:18
Alignment explanation
Indices: 42519746--42519830 Score: 73
Period size: 18 Copynumber: 4.4 Consensus size: 18
42519736 ATTCTTTCAT
*
42519746 ATTTTGATAATATATTGATA
1 ATTTT-ATAATAT-TTAATA
*
42519766 ATGTATTATAATAATTAATA
1 AT-T-TTATAATATTTAATA
* *
42519786 TATTTAATAAAATTCTAA-A
1 -ATTTTATAATATT-TAATA
42519805 ATTTTATAATATTTAATA
1 ATTTTATAATATTTAATA
42519823 ATTTTATA
1 ATTTTATA
42519831 GTTTTTTCTA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
17 3 0.06
18 20 0.38
19 8 0.15
20 11 0.21
21 9 0.17
22 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (18 bp):
ATTTTATAATATTTAATA
Found at i:42520697 original size:17 final size:19
Alignment explanation
Indices: 42520672--42520706 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42520662 GACTAAAAAA
42520672 ATTTATTTTTAT-AAAACT
1 ATTTATTTTTATCAAAACT
42520690 ATTT-TTTTTATCAAAAC
1 ATTTATTTTTATCAAAAC
42520707 ACACAAGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTATTTTTATCAAAACT
Found at i:42523682 original size:11 final size:12
Alignment explanation
Indices: 42523668--42523696 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
42523658 ATTTATAATG
42523668 TATTTAATACA-
1 TATTTAATACAT
42523679 TATTTAATACAT
1 TATTTAATACAT
42523691 TATTTA
1 TATTTA
42523697 TTTCCCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTTAATACAT
Found at i:42524953 original size:29 final size:29
Alignment explanation
Indices: 42524920--42525065 Score: 104
Period size: 30 Copynumber: 4.9 Consensus size: 29
42524910 CTTTATAGGT
* *
42524920 CCCTAAACTATCCAAAAATTATATTTTGA
1 CCCTAAACTTTCCAAAAATTACATTTTGA
**
42524949 CCCTAAAACTTTTTAAAAATTACATTTTGA
1 CCCT-AAACTTTCCAAAAATTACATTTTGA
* *
42524979 CCTCCAAAC-TTCTAAAAAATTACCATTTT-A
1 CC-CTAAACTTTC-CAAAAATTA-CATTTTGA
* *
42525009 CCCCCAAACTTTCC-AAAATTCCATTTTTGA
1 -CCCTAAACTTTCCAAAAATTACA-TTTTGA
*
42525039 CCCT-AA-TTTCACCAAAAATTGCATTTT
1 CCCTAAACTTT--CCAAAAATTACATTTT
42525066 TTCCACCGAG
Statistics
Matches: 95, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
27 3 0.03
28 4 0.04
29 25 0.26
30 51 0.54
31 12 0.13
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATTACATTTTGA
Found at i:42525058 original size:59 final size:59
Alignment explanation
Indices: 42524993--42525180 Score: 193
Period size: 59 Copynumber: 3.2 Consensus size: 59
42524983 CAAACTTCTA
* *
42524993 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCTAATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGAACCTAATTTCACC
* * * * *
42525052 AAAAATT-GCATTTTTTCCACCGAGCTTTCCAAAATTCCATTTTTGAGCCTAATTTCACC
1 AAAAATTACCA-TTTTACCCCCGAACTTTCCAAAATTCCATTTTTGAACCTAATTTCACC
**** * * * *
42525111 AAAAATTGTGTTTTTGCCCTCGAACTTTCCAAAATTTCATTTTT-AACCTCGATTTC-CC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGAACCT-AATTTCACC
42525169 TAAAAATTACCA
1 -AAAAATTACCA
42525181 AAAATTCCTT
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
58 8 0.08
59 97 0.92
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGAACCTAATTTCACC
Found at i:42525064 original size:30 final size:30
Alignment explanation
Indices: 42525023--42525117 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
42525013 CAAACTTTCC
42525023 AAAATTCCATTTTTGACCCTAATTTCACCA
1 AAAATTCCATTTTTGACCCTAATTTCACCA
* ** * *
42525053 AAAATTGCATTTTTTCCACCGAGCTTT--CC-
1 AAAATTCCATTTTTGAC-CCTA-ATTTCACCA
*
42525082 AAAATTCCATTTTTGAGCCTAATTTCACCA
1 AAAATTCCATTTTTGACCCTAATTTCACCA
42525112 AAAATT
1 AAAATT
42525118 GTGTTTTTGC
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
27 3 0.06
28 3 0.06
29 15 0.31
30 22 0.45
31 3 0.06
32 3 0.06
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (30 bp):
AAAATTCCATTTTTGACCCTAATTTCACCA
Found at i:42525154 original size:29 final size:28
Alignment explanation
Indices: 42525015--42525154 Score: 88
Period size: 29 Copynumber: 4.8 Consensus size: 28
42525005 TTTACCCCCA
42525015 AACTTTCCAAAATTCCATTTTTGACCCT
1 AACTTTCCAAAATTCCATTTTTGACCCT
* ** *
42525043 AA-TTTCACCAAAAATTGCATTTTTTCCACCG
1 AACTTT--CC-AAAATTCCATTTTTGAC-CCT
* *
42525074 AGCTTTCCAAAATTCCATTTTTGAGCCT
1 AACTTTCCAAAATTCCATTTTTGACCCT
***
42525102 AA-TTTCACCAAAAATTGTGTTTTTG-CCCT
1 AACTTT--CC-AAAATTCCATTTTTGACCCT
*
42525131 CGAACTTTCCAAAATTTCATTTTT
1 --AACTTTCCAAAATTCCATTTTT
42525155 AACCTCGATT
Statistics
Matches: 83, Mismatches: 18, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
27 6 0.07
28 5 0.06
29 31 0.37
30 30 0.36
31 5 0.06
32 6 0.07
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (28 bp):
AACTTTCCAAAATTCCATTTTTGACCCT
Found at i:42525206 original size:40 final size:40
Alignment explanation
Indices: 42525141--42525220 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
42525131 CGAACTTTCC
* * *
42525141 AAAATTTCATTTTTAACCTCGATTTCCCT-AAAAATTACCA
1 AAAATTCCATTTTTAACCTCAATTT-CATAAAAAATTACCA
* *
42525181 AAAATTCCTTTTTTAACCTTAATTTCATAAAAAATTACCA
1 AAAATTCCATTTTTAACCTCAATTTCATAAAAAATTACCA
42525221 TTTTACCCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.40, C:0.20, G:0.01, T:0.39
Consensus pattern (40 bp):
AAAATTCCATTTTTAACCTCAATTTCATAAAAAATTACCA
Found at i:42530437 original size:26 final size:26
Alignment explanation
Indices: 42530408--42530464 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
42530398 CATTTAAAAT
42530408 TATTT-ATTATATTAAATGATAAATAA
1 TATTTAATTATATTAAATG-TAAATAA
* * *
42530434 TATTTAATTATTTTTAATGTTAATAA
1 TATTTAATTATATTAAATGTAAATAA
42530460 TATTT
1 TATTT
42530465 TATAACAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
TATTTAATTATATTAAATGTAAATAA
Found at i:42534397 original size:16 final size:17
Alignment explanation
Indices: 42534365--42534398 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
42534355 CGAAAATATA
42534365 ATTTAAATATAATTTTT
1 ATTTAAATATAATTTTT
*
42534382 ATTTAAA-ATTATTTTT
1 ATTTAAATATAATTTTT
42534398 A
1 A
42534399 AATAATAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTAAATATAATTTTT
Found at i:42540209 original size:23 final size:21
Alignment explanation
Indices: 42540167--42540209 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
42540157 GAGTTGAATA
* *
42540167 GGTATAATTTTAAAATATTAT
1 GGTATAAATTTAAAAGATTAT
42540188 GGTATAAAATTTAAATAGATTA
1 GGTAT-AAATTTAAA-AGATTA
42540210 AAAAAATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (21 bp):
GGTATAAATTTAAAAGATTAT
Found at i:42541474 original size:35 final size:35
Alignment explanation
Indices: 42541434--42541503 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
42541424 ATCTTATCTA
42541434 AAAAAGATGGTTGTGATTTAATCTTTTTGATTTGT
1 AAAAAGATGGTTGTGATTTAATCTTTTTGATTTGT
42541469 AAAAAGATGGTTGTGATTTAATCTTTTTGATTTGT
1 AAAAAGATGGTTGTGATTTAATCTTTTTGATTTGT
42541504 GCACAAGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.49
Consensus pattern (35 bp):
AAAAAGATGGTTGTGATTTAATCTTTTTGATTTGT
Found at i:42546546 original size:20 final size:21
Alignment explanation
Indices: 42546523--42546562 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
42546513 AAATAATACA
42546523 TTAAATTGAA-AAAATAAATC
1 TTAAATTGAAGAAAATAAATC
*
42546543 TTAATTTGAAGAAAATAAAT
1 TTAAATTGAAGAAAATAAAT
42546563 ATAATTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAATTGAAGAAAATAAATC
Found at i:42546567 original size:20 final size:20
Alignment explanation
Indices: 42546528--42546568 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
42546518 ATACATTAAA
*
42546528 TTGAAAAAATAAATCTTAAT
1 TTGAAAAAATAAATCATAAT
42546548 TTGAAGAAAATAAAT-ATAAT
1 TTGAA-AAAATAAATCATAAT
42546568 T
1 T
42546569 ATCTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (20 bp):
TTGAAAAAATAAATCATAAT
Found at i:42547640 original size:20 final size:21
Alignment explanation
Indices: 42547612--42547654 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
42547602 AAAATCTAAT
42547612 AAATATTAAAA-TATTCAAAA
1 AAATATTAAAAGTATTCAAAA
* *
42547632 AAATCTTAAAAGTGTTCAAAA
1 AAATATTAAAAGTATTCAAAA
42547653 AA
1 AA
42547655 CAATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (21 bp):
AAATATTAAAAGTATTCAAAA
Found at i:42556299 original size:3 final size:3
Alignment explanation
Indices: 42556287--42556331 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
42556277 AATTAAAAGT
42556287 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
42556332 AAGTAAAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:42557013 original size:13 final size:14
Alignment explanation
Indices: 42556986--42557026 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
42556976 TACACAATCA
42556986 ATTTTTATAAAAAT
1 ATTTTTATAAAAAT
*
42557000 ATTTTT-TAATAAT
1 ATTTTTATAAAAAT
*
42557013 ATTTTAATAAAAAT
1 ATTTTTATAAAAAT
42557027 TGAATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTTTATAAAAAT
Found at i:42558184 original size:20 final size:20
Alignment explanation
Indices: 42558161--42558201 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
42558151 TTTGAAAATG
42558161 ATATCTCCTTTTTTATTAAC
1 ATATCTCCTTTTTTATTAAC
42558181 ATATCTCCTTTTTTATTAAC
1 ATATCTCCTTTTTTATTAAC
42558201 A
1 A
42558202 GACAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATCTCCTTTTTTATTAAC
Found at i:42561175 original size:12 final size:13
Alignment explanation
Indices: 42561153--42561185 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
42561143 TATTCCAAAT
42561153 TAAAAACTATTAA
1 TAAAAACTATTAA
42561166 TAAAAA-TATTAA
1 TAAAAACTATTAA
42561178 -AAAAACTA
1 TAAAAACTA
42561186 AAAGTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.26
12 8 0.42
13 6 0.32
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (13 bp):
TAAAAACTATTAA
Found at i:42562367 original size:15 final size:15
Alignment explanation
Indices: 42562344--42562373 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42562334 TATTTTCACT
*
42562344 ATATTATTATTTTTA
1 ATATCATTATTTTTA
42562359 ATATCATTATTTTTA
1 ATATCATTATTTTTA
42562374 TTTATAGAAT
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:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATCATTATTTTTA
Found at i:42568210 original size:55 final size:55
Alignment explanation
Indices: 42568126--42568236 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
42568116 GTATTCTATA
42568126 TATTTTATCCCATTTACAAGTAGCATACTCCTCTATATATATAGGAAGATTCAAC
1 TATTTTATCCCATTTACAAGTAGCATACTCCTCTATATATATAGGAAGATTCAAC
42568181 TATTTTATCCCATTTACAAGTAGCATACTCCTCTATATATATAGGAAGATTCAAC
1 TATTTTATCCCATTTACAAGTAGCATACTCCTCTATATATATAGGAAGATTCAAC
42568236 T
1 T
42568237 CTTCATATTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (55 bp):
TATTTTATCCCATTTACAAGTAGCATACTCCTCTATATATATAGGAAGATTCAAC
Found at i:42589093 original size:57 final size:58
Alignment explanation
Indices: 42589026--42589146 Score: 174
Period size: 57 Copynumber: 2.1 Consensus size: 58
42589016 ATTTCCAAGT
*
42589026 TATTTTCATTTCCATTTTGGAGAAAACCACATTCATTGCCATA-TGTTT-TTATTTCTC
1 TATTTTCATTTCCATTTTGGAGAAAACCACATTCATTGCCA-AGTGTTTGCTATTTCTC
* * *
42589083 TATTTTCATTTTCATTTTGGAGAAAATCACATTCATTTCCAAGTGTTTGCTATTTCTC
1 TATTTTCATTTCCATTTTGGAGAAAACCACATTCATTGCCAAGTGTTTGCTATTTCTC
*
42589141 CATTTT
1 TATTTT
42589147 GACCATTTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
56 1 0.02
57 43 0.75
58 13 0.23
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (58 bp):
TATTTTCATTTCCATTTTGGAGAAAACCACATTCATTGCCAAGTGTTTGCTATTTCTC
Found at i:42590802 original size:58 final size:59
Alignment explanation
Indices: 42590738--42590919 Score: 296
Period size: 58 Copynumber: 3.1 Consensus size: 59
42590728 ATTTTTTACT
*
42590738 TTCGGGGGTAAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATGGAATATTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAG
*
42590796 TTCGGGGGTAAAATGATAATTTTTGGTGAAATTGGGGTT-AAAATGGAATTTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAG
* * * *
42590854 TTCGGGGGCAAAATGGTAATTTTTGATGAAATCGGGATTAAAAATGGAATTTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAG
42590913 TTCGGGG
1 TTCGGGG
42590920 TCAAAATATA
Statistics
Matches: 115, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
58 70 0.61
59 45 0.39
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.32
Consensus pattern (59 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAG
Found at i:42590917 original size:29 final size:28
Alignment explanation
Indices: 42590738--42590926 Score: 147
Period size: 30 Copynumber: 6.5 Consensus size: 28
42590728 ATTTTTTACT
*
42590738 TTCGGGGGTAAAATGGTAATTTTGGTGAAA
1 TTCGGGGTTAAAATGG-AATTTT-GTGAAA
*
42590768 TT-GGGGTTAAAAATGGAATATTG-GAAA
1 TTCGGGGTT-AAAATGGAATTTTGTGAAA
* *
42590795 GTTCGGGGGTAAAATGATAATTTTTGGTGAAA
1 -TTCGGGGTTAAAATG-GAA-TTTT-GTGAAA
42590827 TT-GGGGTTAAAATGGAATTTTG-GAAA
1 TTCGGGGTTAAAATGGAATTTTGTGAAA
**
42590853 GTTCGGGGGCAAAATGGTAATTTTTGATGAAA
1 -TTCGGGGTTAAAATGG-AA-TTTTG-TGAAA
*
42590885 -TCGGGATTAAAAATGGAATTTTG-GAAA
1 TTCGGGGTT-AAAATGGAATTTTGTGAAA
*
42590912 GTTCGGGGTCAAAAT
1 -TTCGGGGTTAAAAT
42590927 ATAATTTCTG
Statistics
Matches: 129, Mismatches: 14, Indels: 34
0.73 0.08 0.19
Matches are distributed among these distances:
26 4 0.03
27 11 0.09
28 29 0.22
29 32 0.25
30 35 0.27
31 10 0.08
32 8 0.06
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.32
Consensus pattern (28 bp):
TTCGGGGTTAAAATGGAATTTTGTGAAA
Found at i:42591909 original size:21 final size:21
Alignment explanation
Indices: 42591863--42591902 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42591853 AATATTATTA
* *
42591863 ATTATTATTAATGCATTTAAT
1 ATTATTATTAAAGCAATTAAT
42591884 ATTATTATTAAAGCAATTA
1 ATTATTATTAAAGCAATTA
42591903 TCATTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTATTATTAAAGCAATTAAT
Found at i:42592799 original size:6 final size:6
Alignment explanation
Indices: 42592788--42592869 Score: 71
Period size: 6 Copynumber: 13.8 Consensus size: 6
42592778 TTAAATTTGA
* * *
42592788 TTAAAT TTAAAT TTAAA- GTAAAA TTAAAT AGGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
* * *
42592836 ATAAAT TTAAAT TTAAA- ATCAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
42592870 ATCAATTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
5 11 0.18
6 44 0.73
8 5 0.08
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:42592814 original size:17 final size:17
Alignment explanation
Indices: 42592789--42592880 Score: 109
Period size: 17 Copynumber: 5.6 Consensus size: 17
42592779 TAAATTTGAT
*
42592789 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
* **
42592806 TAAAATTAAA--T-AGG
1 TAAATTTAAATTTAAAA
42592820 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
42592837 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
42592854 TCAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
42592871 TCAATTTAAA
1 TAAATTTAAA
42592881 CTTTTAATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 1 0.02
17 53 0.80
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:42592827 original size:31 final size:31
Alignment explanation
Indices: 42592789--42592847 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
42592779 TAAATTTGAT
*
42592789 TAAATTTAAATTTAAAGTAAAATTAAATAGG
1 TAAATTTAAATTTAAAATAAAATTAAATAGG
*
42592820 TAAATTTAAATTTAAAATAAATTTAAAT
1 TAAATTTAAATTTAAAATAAAATTAAAT
42592848 TTAAAATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (31 bp):
TAAATTTAAATTTAAAATAAAATTAAATAGG
Found at i:42596864 original size:7 final size:7
Alignment explanation
Indices: 42596852--42596877 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42596842 ATAAAAATAC
42596852 ATTTACT
1 ATTTACT
42596859 ATTTACT
1 ATTTACT
42596866 ATTTACT
1 ATTTACT
42596873 ATTTA
1 ATTTA
42596878 TGGAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTACT
Found at i:42597218 original size:6 final size:6
Alignment explanation
Indices: 42597182--42597289 Score: 80
Period size: 6 Copynumber: 18.0 Consensus size: 6
42597172 TTAAATTGAT
* * * *
42597182 TTTAAA TTT--A TTTGAA TTTAGA TTT-AT TTTAAA TTTAAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA-A
* ** *
42597229 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
42597277 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
42597290 AGTCCAAATG
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 49 0.60
7 21 0.26
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:42597238 original size:31 final size:31
Alignment explanation
Indices: 42597197--42597259 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
42597187 ATTTATTTGA
* *
42597197 ATTTAGATTTATTTTAAATTTAAAATTAAAT
1 ATTTAAATTTAATTTAAATTTAAAATTAAAT
* *
42597228 ATTTAAATTTAATTTGAATTTAAATTTAAAT
1 ATTTAAATTTAATTTAAATTTAAAATTAAAT
42597259 A
1 A
42597260 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTTAAATTTAATTTAAATTTAAAATTAAAT
Found at i:42597247 original size:11 final size:11
Alignment explanation
Indices: 42597172--42597258 Score: 52
Period size: 11 Copynumber: 7.5 Consensus size: 11
42597162 GACTTTTGAG
* *
42597172 TTAAATTGATT
1 TTAAATTTAAT
42597183 TTAAATTT-AT
1 TTAAATTTAAT
*
42597193 TTGAATTTAGAT
1 TTAAATTTA-AT
*
42597205 TT-ATTTTAAAT
1 TTAAATTT-AAT
*
42597216 TTAAAATTAAATAT
1 TT-AAATT-TA-AT
42597230 TTAAATTTAAT
1 TTAAATTTAAT
*
42597241 TTGAATTTAAAT
1 TTAAATTT-AAT
42597253 TTAAAT
1 TTAAAT
42597259 AAAAATTAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
10 8 0.14
11 24 0.41
12 14 0.24
13 9 0.15
14 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:42597268 original size:48 final size:48
Alignment explanation
Indices: 42597182--42597288 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
42597172 TTAAATTGAT
* ** * *
42597182 TTTAAATTT-ATTTGAATTTAGATTTATTTTAAATTTAAAAT-TAAATA
1 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATATAAA-A
*
42597229 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATATTAAA
1 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATATAAAA
42597277 TTTAACATTTAA
1 TTTAA-ATTTAA
42597289 AAGTCCAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
47 9 0.18
48 33 0.65
49 9 0.18
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.49
Consensus pattern (48 bp):
TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATATAAAA
Found at i:42597279 original size:31 final size:30
Alignment explanation
Indices: 42597209--42597289 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
42597199 TTAGATTTAT
* * *
42597209 TTTAAATTTAAAATTAAATATTTAAATTTAA
1 TTTAAATTTAAATTTAAATA-TAAAATTAAA
*
42597240 TTTGAATTTAAATTTAAATA-AAAATTAAAA
1 TTTAAATTTAAATTTAAATATAAAATT-AAA
42597270 TATTAAATTTAACATTTAAA
1 T-TTAAATTTAA-ATTTAAA
42597290 AGTCCAAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 5 0.12
30 3 0.07
31 27 0.64
32 7 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
TTTAAATTTAAATTTAAATATAAAATTAAA
Found at i:42598989 original size:161 final size:163
Alignment explanation
Indices: 42598810--42599104 Score: 445
Period size: 162 Copynumber: 1.8 Consensus size: 163
42598800 TTATAATTTA
** *
42598810 GTCCTTTGACTGTTTGACTGTGCCAGAGGTTGCCACGTGTCA-TGTATTGGAT-TATTTATGCAT
1 GTCCTTTGACTGTTTGACTGCACCAAAGGTTGCCACGTGTCATTGTATTGGATAT-TTTATGCAT
*
42598873 TTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCC-CAAATCAACTTTGT-TTTAATTACGA
65 TTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTT-TATTTAATTACAA
42598936 AATTGGCCCCATAATTTTTCGAGGTTTATAAACTG
129 AATTGGCCCCATAATTTTTCGAGGTTTATAAACTG
* * * *
42598971 GTCCTTTGACTTTTTGACTGCACCAAAGGTTGCCACGTGTCATTTTTTTGGATATTTTCTGCATT
1 GTCCTTTGACTGTTTGACTGCACCAAAGGTTGCCACGTGTCATTGTATTGGATATTTTATGCATT
* * *
42599036 TAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACAAAA
66 TAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAA
42599101 TTGG
131 TTGG
42599105 TCCAAAATTT
Statistics
Matches: 119, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
161 38 0.32
162 54 0.45
163 27 0.23
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (163 bp):
GTCCTTTGACTGTTTGACTGCACCAAAGGTTGCCACGTGTCATTGTATTGGATATTTTATGCATT
TAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAA
TTGGCCCCATAATTTTTCGAGGTTTATAAACTG
Found at i:42599174 original size:162 final size:160
Alignment explanation
Indices: 42598832--42599150 Score: 394
Period size: 162 Copynumber: 2.0 Consensus size: 160
42598822 TTTGACTGTG
42598832 CCAGAGGTTGCCACGTGTCATGTATTGGATTATTTATGCATTTAGTCCTTTTCATTTTTAATTTG
1 CCAGAGGTTGCCACGTGTCATGTATTGGATTATTTATGCATTTAGTCCTTTTCATTTTTAATTTG
* * * *
42598897 TTTTAATTTAATCCCAAATCAACTTTGTTTTAATTACGAAATTGGCCCCATAATTTTTCGAGGTT
66 TTTTAATTTAATCCCAAATCAACTTTGTTTTAATTACAAAATTGGCCCCAAAATTTTTCAAGATT
* * * *
42598962 TATAAACTGGTCCTTTGACTTTTTGACTGCA
131 TATAAACTGGTCCCTTGACCTCTGGACT-CA
* * * * *
42598993 CCAAAGGTTGCCACGTGTCATTTTTTTGGA-TATTTTCTGCATTTAGTCCTTTTTATTTTTAATT
1 CCAGAGGTTGCCACGTGTCA-TGTATTGGATTA-TTTATGCATTTAGTCCTTTTCATTTTTAATT
* * *
42599057 TGTTTTAATTTAATCCTTAAATCGACTTT-TATTTAATTACAAAATTGG-TCCAAAATTTTTTCA
64 TGTTTTAATTTAATCC-CAAATCAACTTTGT-TTTAATTACAAAATTGGCCCCAAAA-TTTTTCA
*
42599120 AGATTT-TCAAATTGGTCCCTTGACCTCTGGA
126 AGATTTAT-AAACTGGTCCCTTGACCTCTGGA
42599151 TACCTGTGAG
Statistics
Matches: 135, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
161 21 0.16
162 59 0.44
163 55 0.41
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (160 bp):
CCAGAGGTTGCCACGTGTCATGTATTGGATTATTTATGCATTTAGTCCTTTTCATTTTTAATTTG
TTTTAATTTAATCCCAAATCAACTTTGTTTTAATTACAAAATTGGCCCCAAAATTTTTCAAGATT
TATAAACTGGTCCCTTGACCTCTGGACTCA
Found at i:42599279 original size:25 final size:25
Alignment explanation
Indices: 42599249--42599299 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
42599239 AACTTTTCTA
*
42599249 AAATTCCATTTTTAACCCCAATTTC
1 AAATTCCATTTTTAACCACAATTTC
** *
42599274 AAATTCTGTTTTTAACCACGATTTC
1 AAATTCCATTTTTAACCACAATTTC
42599299 A
1 A
42599300 CCGAAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (25 bp):
AAATTCCATTTTTAACCACAATTTC
Found at i:42599317 original size:30 final size:30
Alignment explanation
Indices: 42599283--42599788 Score: 234
Period size: 30 Copynumber: 17.1 Consensus size: 30
42599273 CAAATTCTGT
* *
42599283 TTTTAACCACGATTTCACCGAAAATTATCA
1 TTTTAACCCCGATTTCACCGAAAATTACCA
* * **** **
42599313 TTTTACCCCCGA-ATCTTTTAAAATT-CTGT
1 TTTTAACCCCGATTTCACCGAAAATTAC-CA
**
42599342 TTTTAACCATGATTTCACCGAAAATTACCA
1 TTTTAACCCCGATTTCACCGAAAATTACCA
* * ****
42599372 TTTTACCCCCGA-ATCTTTTAAAATT-CCA
1 TTTTAACCCCGATTTCACCGAAAATTACCA
42599400 TTTTTAACCCCGATTTCACCGAAAATTACCA
1 -TTTTAACCCCGATTTCACCGAAAATTACCA
* ** ** *
42599431 TTTTACCCCCGA-AGCTTCTAAAATT-CCA
1 TTTTAACCCCGATTTCACCGAAAATTACCA
*
42599459 TTTTTAACCCCGATTTCACTGAAAATTACCA
1 -TTTTAACCCCGATTTCACCGAAAATTACCA
** ** * * **
42599490 TTTT-ACCCTCGA-AGCTTCTAAAATTTCGT
1 TTTTAACCC-CGATTTCACCGAAAATTACCA
* *
42599519 TTTTAACCCCGATTTCATCAAAAATTACCA
1 TTTTAACCCCGATTTCACCGAAAATTACCA
* * **** *
42599549 TTTTACCCCCGA-ATCTTTTAAAATT-CCGT
1 TTTTAACCCCGATTTCACCGAAAATTACC-A
42599578 TTTTAACCCCGATTTCACCGAAAATTACCA
1 TTTTAACCCCGATTTCACCGAAAATTACCA
* * ** ** * * **
42599608 TTTTATCCTCGA-AGCTTCTAAAATTTCGT
1 TTTTAACCCCGATTTCACCGAAAATTACCA
*
42599637 TTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTAACCCCGATTTCACCGAAAATTACCA
* ** ** *
42599667 TTTTACCCCCGA-AGCTTCTAAAATT-CCA
1 TTTTAACCCCGATTTCACCGAAAATTACCA
*
42599695 TTTTTAACCCCGATTTCATCGAAAATTACCA
1 -TTTTAACCCCGATTTCACCGAAAATTACCA
** ****
42599726 TTTT-ACCCTCGA-AGCTTTTAAAATT-CCA
1 TTTTAACCC-CGATTTCACCGAAAATTACCA
42599754 TTTTTAACCCCGATTTCACCGAAAATTACCA
1 -TTTTAACCCCGATTTCACCGAAAATTACCA
42599785 TTTT
1 TTTT
42599789 GCCCTCGGGT
Statistics
Matches: 334, Mismatches: 118, Indels: 48
0.67 0.24 0.10
Matches are distributed among these distances:
28 14 0.04
29 151 0.45
30 154 0.46
31 15 0.04
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (30 bp):
TTTTAACCCCGATTTCACCGAAAATTACCA
Found at i:42599346 original size:59 final size:59
Alignment explanation
Indices: 42599274--42599788 Score: 778
Period size: 59 Copynumber: 8.7 Consensus size: 59
42599264 CCCCAATTTC
* * * * *
42599274 AAATTCTGTTTTTAACCACGATTTCACCGAAAATTATCATTTTACCCCCGAATCTTTTA
1 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTA
* ** * *
42599333 AAATTCTGTTTTTAACCATGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTA
1 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTA
*
42599392 AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTA
1 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTA
* * *
42599451 AAATTCCATTTTTAACCCCGATTTCACTGAAAATTACCATTTTACCCTCGAAGCTTCTA
1 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTA
* * * * *
42599510 AAATTTCGTTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATCTTTTA
1 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTA
* *
42599569 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTATCCTCGAAGCTTCTA
1 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTA
* *
42599628 AAATTTCGTTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCTA
1 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTA
* * * *
42599687 AAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCTCGAAGCTTTTA
1 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTA
*
42599746 AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTT
1 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTT
42599789 GCCCTCGGGT
Statistics
Matches: 420, Mismatches: 36, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 420 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (59 bp):
AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTA
Found at i:42609039 original size:20 final size:20
Alignment explanation
Indices: 42609016--42609053 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42609006 ATGATTTTTG
42609016 TTAATTAAATCAA-CATTAGT
1 TTAATT-AATCAACCATTAGT
42609036 TTAATTAATCAACCATTA
1 TTAATTAATCAACCATTA
42609054 ACTATACCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
TTAATTAATCAACCATTAGT
Found at i:42620272 original size:15 final size:16
Alignment explanation
Indices: 42620242--42620275 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
42620232 AAAATGTAAT
42620242 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
42620258 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
42620273 TTT
1 TTT
42620276 TTAAAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:42620732 original size:29 final size:29
Alignment explanation
Indices: 42620699--42620755 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
42620689 TTTAAACAAT
42620699 TATTG-ATATA-AAATCATATTATATTTATA
1 TATTGAATATATAAAT-A-ATTATATTTATA
42620728 TATTGAATATATAAATAATTATATTTAT
1 TATTGAATATATAAATAATTATATTTAT
42620756 CCGATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 16 0.62
30 6 0.23
31 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (29 bp):
TATTGAATATATAAATAATTATATTTATA
Found at i:42622097 original size:3 final size:3
Alignment explanation
Indices: 42622091--42622121 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
42622081 TTTGCAAAAA
42622091 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
42622122 GCTGTATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42649469 original size:18 final size:18
Alignment explanation
Indices: 42649446--42649480 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
42649436 TATTTATTTA
42649446 ATCGAATTGTATAAATTG
1 ATCGAATTGTATAAATTG
42649464 ATCGAATTGTATAAATT
1 ATCGAATTGTATAAATT
42649481 ATCAATTTAA
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:0.06, G:0.14, T:0.40
Consensus pattern (18 bp):
ATCGAATTGTATAAATTG
Found at i:42650280 original size:20 final size:21
Alignment explanation
Indices: 42650244--42650285 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
42650234 ATTGAAAACA
*
42650244 AAATAACATGATGTTTT-TTT
1 AAATAACATAATGTTTTATTT
42650264 AAATAATCATAAT-TTTTATTT
1 AAATAA-CATAATGTTTTATTT
42650285 A
1 A
42650286 TTCAGGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
AAATAACATAATGTTTTATTT
Found at i:42661917 original size:3 final size:3
Alignment explanation
Indices: 42661911--42661955 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
42661901 AAAGATACTA
42661911 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42661956 TCTAGACTTC
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:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42666491 original size:13 final size:13
Alignment explanation
Indices: 42666473--42666524 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
42666463 AAAATCAACT
42666473 GTCAACGATCAAA
1 GTCAACGATCAAA
* *
42666486 GTCAACAATCAATG
1 GTCAACGATCAA-A
*
42666500 GTCAACGGTCAAA
1 GTCAACGATCAAA
42666513 GTCAACGATCAA
1 GTCAACGATCAA
42666525 CGGTTTGACT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 22 0.69
14 10 0.31
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (13 bp):
GTCAACGATCAAA
Found at i:42666503 original size:27 final size:27
Alignment explanation
Indices: 42666465--42666525 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
42666455 TTGAAAAAAA
42666465 AATCAACTGTCAACGATCAAAGTCAAC
1 AATCAACTGTCAACGATCAAAGTCAAC
*
42666492 AATCAA-TGGTCAACGGTCAAAGTCAAC
1 AATCAACT-GTCAACGATCAAAGTCAAC
*
42666519 GATCAAC
1 AATCAAC
42666526 GGTTTGACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.18
Consensus pattern (27 bp):
AATCAACTGTCAACGATCAAAGTCAAC
Found at i:42671981 original size:32 final size:32
Alignment explanation
Indices: 42671936--42672018 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
42671926 TTGCTAAATA
* *
42671936 TCTTCCTTAAAATTAATGCTTTTTGTCTAATT
1 TCTTCTTTAAAATTAATGCTTTTTGCCTAATT
42671968 T-TCTCATTT-AAATTAATGCTTTTTGCCTAATT
1 TCT-TC-TTTAAAATTAATGCTTTTTGCCTAATT
42672000 TCTTCTTTAAAATTAATGC
1 TCTTCTTTAAAATTAATGC
42672019 CTTTATGGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
31 4 0.09
32 38 0.84
33 3 0.07
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.52
Consensus pattern (32 bp):
TCTTCTTTAAAATTAATGCTTTTTGCCTAATT
Found at i:42673268 original size:16 final size:15
Alignment explanation
Indices: 42673242--42673271 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42673232 TTTGTTGTGT
42673242 TTTCAATAAATTTTC
1 TTTCAATAAATTTTC
42673257 TTTCACATAAATTTT
1 TTTCA-ATAAATTTT
42673272 TTTTGCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTCAATAAATTTTC
Found at i:42675841 original size:15 final size:16
Alignment explanation
Indices: 42675812--42675843 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42675802 AGTTTAATAA
42675812 TTTTATTTTTGACTTC
1 TTTTATTTTTGACTTC
42675828 TTTTATTTTT-ACTTC
1 TTTTATTTTTGACTTC
42675843 T
1 T
42675844 CCTGTATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTATTTTTGACTTC
Found at i:42677880 original size:17 final size:18
Alignment explanation
Indices: 42677845--42677882 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
42677835 ATAAAATTTT
*
42677845 ATATTATTAATATTTTAA
1 ATATTATTAATATTCTAA
*
42677863 ATATTA-TAGTATTCTAA
1 ATATTATTAATATTCTAA
42677880 ATA
1 ATA
42677883 CTAGTTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATTATTAATATTCTAA
Found at i:42683659 original size:165 final size:165
Alignment explanation
Indices: 42683387--42683718 Score: 664
Period size: 165 Copynumber: 2.0 Consensus size: 165
42683377 TTTTTCATTT
42683387 TAAAGGGGTCGGATCCCTACCAACCCCTGATTGTAGATTAAATCACGTATAAACGTGAATCTTTG
1 TAAAGGGGTCGGATCCCTACCAACCCCTGATTGTAGATTAAATCACGTATAAACGTGAATCTTTG
42683452 TGAATAAAATTTATATAAAGTGAATGATGTAAGCTCAAGCGAATATTCTTCAACTATATAGTGCT
66 TGAATAAAATTTATATAAAGTGAATGATGTAAGCTCAAGCGAATATTCTTCAACTATATAGTGCT
42683517 CTTCTACCAAAAATATAAAAGTATTTGGTGTTGTA
131 CTTCTACCAAAAATATAAAAGTATTTGGTGTTGTA
42683552 TAAAGGGGTCGGATCCCTACCAACCCCTGATTGTAGATTAAATCACGTATAAACGTGAATCTTTG
1 TAAAGGGGTCGGATCCCTACCAACCCCTGATTGTAGATTAAATCACGTATAAACGTGAATCTTTG
42683617 TGAATAAAATTTATATAAAGTGAATGATGTAAGCTCAAGCGAATATTCTTCAACTATATAGTGCT
66 TGAATAAAATTTATATAAAGTGAATGATGTAAGCTCAAGCGAATATTCTTCAACTATATAGTGCT
42683682 CTTCTACCAAAAATATAAAAGTATTTGGTGTTGTA
131 CTTCTACCAAAAATATAAAAGTATTTGGTGTTGTA
42683717 TA
1 TA
42683719 GAGGCGAAGT
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 167 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (165 bp):
TAAAGGGGTCGGATCCCTACCAACCCCTGATTGTAGATTAAATCACGTATAAACGTGAATCTTTG
TGAATAAAATTTATATAAAGTGAATGATGTAAGCTCAAGCGAATATTCTTCAACTATATAGTGCT
CTTCTACCAAAAATATAAAAGTATTTGGTGTTGTA
Found at i:42689972 original size:23 final size:23
Alignment explanation
Indices: 42689946--42690089 Score: 168
Period size: 23 Copynumber: 6.2 Consensus size: 23
42689936 ACACTAGCGC
42689946 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
42689969 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
* *
42689992 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
42690015 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
42690040 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
42690063 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
42690086 GCTC
1 GCTC
42690090 AGTACTTTGT
Statistics
Matches: 109, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.04
23 85 0.78
24 1 0.01
25 16 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:42690089 original size:71 final size:69
Alignment explanation
Indices: 42689946--42690078 Score: 196
Period size: 71 Copynumber: 1.9 Consensus size: 69
42689936 ACACTAGCGC
* * *
42689946 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTTAGCACGTC
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCTCTCTGATTAGCACGTC
42690011 TCGT
66 TCGT
*
42690015 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGT-GTGCTCTCTGATTAGCAC
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTC-TCGTGCTCTCTGATTAGCAC
42690079 TTTGTGTGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
69 8 0.14
71 48 0.84
72 1 0.02
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.38
Consensus pattern (69 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCTCTCTGATTAGCACGTC
TCGT
Found at i:42690118 original size:39 final size:39
Alignment explanation
Indices: 42690054--42690128 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
42690044 TCCGATTAGC
*
42690054 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
42690093 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
42690129 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:42690123 original size:23 final size:23
Alignment explanation
Indices: 42690088--42690181 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
42690078 CTTTGTGTGC
*
42690088 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
42690111 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
42690134 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
42690159 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
42690181 T
1 T
42690182 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:42691297 original size:23 final size:23
Alignment explanation
Indices: 42691271--42691315 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
42691261 AGTTTTGAAT
**
42691271 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
42691294 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
42691316 GAATTTTTTT
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:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:42703905 original size:73 final size:73
Alignment explanation
Indices: 42703816--42703962 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
42703806 GCAATTAGGA
*
42703816 ATTCATGAACATGGAGATATGGGTTTAATTTTTTTTTCTTTTTGTCTTTGTTTGGATGAAATAAG
1 ATTCATGAACATGGAGATATGGGTTTAATCTTTTTTTCTTTTTGTCTTTGTTTGGATGAAATAAG
42703881 GTCCGGAC
66 GTCCGGAC
42703889 ATTCATGAACATGGAGATATGGGTTTAATCTTTTTTTCTTTTTGTCTTTGTTTGGATGAAATAAG
1 ATTCATGAACATGGAGATATGGGTTTAATCTTTTTTTCTTTTTGTCTTTGTTTGGATGAAATAAG
42703954 GTCCGGAC
66 GTCCGGAC
42703962 A
1 A
42703963 ATTTTGGCAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (73 bp):
ATTCATGAACATGGAGATATGGGTTTAATCTTTTTTTCTTTTTGTCTTTGTTTGGATGAAATAAG
GTCCGGAC
Found at i:42708387 original size:7 final size:7
Alignment explanation
Indices: 42708375--42708409 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
42708365 TTACTCCTAG
42708375 TGCCTGC
1 TGCCTGC
42708382 TGCCTGC
1 TGCCTGC
42708389 TGCCTGC
1 TGCCTGC
42708396 TGCCTGC
1 TGCCTGC
42708403 TGCCTGC
1 TGCCTGC
42708410 CCCTTTTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.00, C:0.43, G:0.29, T:0.29
Consensus pattern (7 bp):
TGCCTGC
Found at i:42716676 original size:4 final size:4
Alignment explanation
Indices: 42716669--42716706 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
42716659 ACCTACCACA
42716669 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
42716707 GAAATCATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:42719197 original size:15 final size:17
Alignment explanation
Indices: 42719164--42719202 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
42719154 ACCAAATAAT
42719164 TTTTC-TTTAATATTTA
1 TTTTCATTTAATATTTA
42719180 TTTTCATTTAA-A-TTA
1 TTTTCATTTAATATTTA
42719195 TTTT-ATTT
1 TTTTCATTT
42719203 TTAAAATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 7 0.32
16 6 0.27
17 5 0.23
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTCATTTAATATTTA
Found at i:42722819 original size:142 final size:142
Alignment explanation
Indices: 42721685--42722811 Score: 1975
Period size: 142 Copynumber: 7.9 Consensus size: 142
42721675 ATTAAGTGAG
* * * *
42721685 GAAATCTAGGCCACATTTGGGCATTACTTGCAAACAAGGGCTTATTGTAACCGTTACTTAGGACG
1 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
* *
42721750 GTCCTCGAACTATATTGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
66 GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
42721815 AATCAGTGAATT
131 AATCAGTGAATT
* * *
42721827 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTGTTGTAACCGTTACCTAAGGCG
1 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
*
42721892 GTCCTCGAACTATGTTGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
66 GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
42721957 AATCAGTGAATT
131 AATCAGTGAATT
42721969 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
1 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
* *
42722034 GTCCTCTAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGCGAAGG
66 GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
42722099 AATCAGTGAATT
131 AATCAGTGAATT
*
42722111 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGATG
1 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
42722176 GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
66 GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
42722241 AATCAGTGAATT
131 AATCAGTGAATT
* * * * *
42722253 GAAATCTTGGCCACATTTGGACATAACTTGCAAACGAGGGTTTGTTGTAACCGTTACCTAAGGCG
1 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
*
42722318 GTCCTCGAACTATGTTGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
66 GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
42722383 AATCAGTGAATT
131 AATCAGTGAATT
42722395 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
1 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
*
42722460 GTCCTCTAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
66 GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
42722525 AATCAGTGAATT
131 AATCAGTGAATT
*
42722537 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGATG
1 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
42722602 GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
66 GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
42722667 AATCAGTGAATT
131 AATCAGTGAATT
* * * * * *
42722679 GAAATCTTGGCCACATTTGGACATTACTTGTAAACAAGGGCTTATTATAACCGTTACTTAAGATG
1 GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
* * * *
42722744 GTCCTCGAACTATGTGGTCAGTTCTAAATGAAATGAACTTGTAACCGATGCTTACATAGGGAAGG
66 GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
42722809 AAT
131 AAT
42722812 TGGTGAATCC
Statistics
Matches: 943, Mismatches: 42, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 943 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (142 bp):
GAAATCTAGGCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACG
GTCCTCGAACTATGTGGTCGGTTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGG
AATCAGTGAATT
Found at i:42725542 original size:28 final size:26
Alignment explanation
Indices: 42725511--42725572 Score: 61
Period size: 28 Copynumber: 2.3 Consensus size: 26
42725501 AGAAAATGTA
42725511 AAAAAATTATTAAATATTTAAATAAAAT
1 AAAAAATTA-TAAATATTTAAA-AAAAT
* * *
42725539 AAAATAAATATATATTTTTAAAAAAAT
1 AAAA-AATTATAAATATTTAAAAAAAT
*
42725566 TAAAAAT
1 AAAAAAT
42725573 AATATGGGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 2 0.07
27 8 0.29
28 14 0.50
29 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAAATTATAAATATTTAAAAAAAT
Found at i:42735623 original size:220 final size:221
Alignment explanation
Indices: 42735241--42735683 Score: 800
Period size: 220 Copynumber: 2.0 Consensus size: 221
42735231 AGTATCTACT
42735241 CATACTTTCTTAAAAAGCACACCCATTTTGCACACACAACCGCTCAAACCCGGGACCCTTAGGAT
1 CATACTTTCTTAAAAAGCACACCCATTTTGCACACACAACCGCTCAAACCCGGGACCCTTAGGAT
42735306 GAACAATATTCTCTTTTTCACTGGAGTCACTTGTTGGATTCAATGTAAATTTATTATTGATTGAA
66 GAACAATATTCTCTTTTTCACTGGAGTCACTTGTTGGATTCAATGTAAATTTATTATTGATTGAA
42735371 TATGATTGATAAAATTTTCATGTGACCTTAACTATGTGATCC-AATAATAATAATAATAATTTGT
131 TATGATTGATAAAATTTTCATGTGACCTTAACTATGTGATCCAAATAATAATAATAATAATTTGT
42735435 ATCATTACTTCGACAAAAACAATTAA
196 ATCATTACTTCGACAAAAACAATTAA
*
42735461 CATACTTTCTTAAAAAGCACACCCATTTTGCACACACAATCGCTCAAACCCGGGACCCTTAGGAT
1 CATACTTTCTTAAAAAGCACACCCATTTTGCACACACAACCGCTCAAACCCGGGACCCTTAGGAT
* * *
42735526 GAATAATATTCTC-TTTTCTATTGGAGTCATTTGTTGGATTCAATGTAAATTTATTATTGATTGA
66 GAACAATATTCTCTTTTTC-ACTGGAGTCACTTGTTGGATTCAATGTAAATTTATTATTGATTGA
*
42735590 ATATGATTGATAAGATTTTCATGTGACCTTAACTATGTGATCCAATAATAATAATAATAATAATT
130 ATATGATTGATAAAATTTTCATGTGACCTTAACTATGTGATCC-A-AATAATAATAATAATAATT
42735655 TGTATCATTACTTCGACAAAAACAATTAA
193 TGTATCATTACTTCGACAAAAACAATTAA
42735684 TAATTTTATT
Statistics
Matches: 214, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
219 5 0.02
220 161 0.75
223 48 0.22
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (221 bp):
CATACTTTCTTAAAAAGCACACCCATTTTGCACACACAACCGCTCAAACCCGGGACCCTTAGGAT
GAACAATATTCTCTTTTTCACTGGAGTCACTTGTTGGATTCAATGTAAATTTATTATTGATTGAA
TATGATTGATAAAATTTTCATGTGACCTTAACTATGTGATCCAAATAATAATAATAATAATTTGT
ATCATTACTTCGACAAAAACAATTAA
Found at i:42745163 original size:16 final size:16
Alignment explanation
Indices: 42745138--42745179 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
42745128 ATTAATAAAT
*
42745138 TTAACAATTAAAT-TA
1 TTAAAAATTAAATATA
*
42745153 TTAAAATATTAATTATA
1 TTAAAA-ATTAAATATA
42745170 TTAAAAATTA
1 TTAAAAATTA
42745180 TGAAAAGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAAATTAAATATA
Found at i:42751144 original size:20 final size:19
Alignment explanation
Indices: 42751107--42751150 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
42751097 ACGTATTTAG
*
42751107 TTATTTTATTATTCAGTAA
1 TTATTTTATTATTAAGTAA
42751126 TATATTTCTATT-TTAAGTAA
1 T-TATTT-TATTATTAAGTAA
42751146 TTATT
1 TTATT
42751151 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 5 0.23
20 13 0.59
21 4 0.18
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATTTTATTATTAAGTAA
Found at i:42755229 original size:17 final size:17
Alignment explanation
Indices: 42755207--42755239 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42755197 AACAATAAAT
42755207 AAATTTCTTTTA-CTTTC
1 AAATTT-TTTTATCTTTC
42755224 AAATTTTTTTATCTTT
1 AAATTTTTTTATCTTT
42755240 TCTACCAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (17 bp):
AAATTTTTTTATCTTTC
Found at i:42756878 original size:28 final size:27
Alignment explanation
Indices: 42756834--42756889 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
42756824 TTAAAAAAAC
42756834 ATCAAATTGAATATTTTTCAAAAGGTTG
1 ATCAAATTGAATATTTTT-AAAAGGTTG
* *
42756862 ATCAAATTTGACT-TTTTTAAAAGTTTG
1 ATCAAA-TTGAATATTTTTAAAAGGTTG
42756889 A
1 A
42756890 GAGCCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.36
28 11 0.44
29 5 0.20
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (27 bp):
ATCAAATTGAATATTTTTAAAAGGTTG
Found at i:42757189 original size:18 final size:18
Alignment explanation
Indices: 42757162--42757213 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
42757152 TATATATGAT
42757162 TAAT-ATAAAAAT-AATAA
1 TAATAATAAAAATAAAT-A
*
42757179 TAATAATAAAATTAAATA
1 TAATAATAAAAATAAATA
*
42757197 TTATAATATAAAATAAA
1 TAATAATA-AAAATAAA
42757214 AAATAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 4 0.14
18 15 0.52
19 10 0.34
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATAATAAAAATAAATA
Found at i:42764194 original size:15 final size:15
Alignment explanation
Indices: 42764158--42764199 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
42764148 ATTTGATCTC
42764158 TCGACTGTC-GACCCT
1 TCGACT-TCTGACCCT
*
42764173 TCGACTTTTGACCCT
1 TCGACTTCTGACCCT
*
42764188 TGGACTTCTGAC
1 TCGACTTCTGAC
42764200 TTCTCGATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.14, C:0.33, G:0.19, T:0.33
Consensus pattern (15 bp):
TCGACTTCTGACCCT
Found at i:42765356 original size:30 final size:30
Alignment explanation
Indices: 42765300--42765420 Score: 113
Period size: 30 Copynumber: 4.1 Consensus size: 30
42765290 TCAAATTTAA
* * *
42765300 CCCCAAGTTTTCT-AAATTTTAGTTTTGAC
1 CCCCAAATTTTCTAAAATTTCATTTTTGAC
42765329 CCCCAAATTTTCTAAAATTTCATTTTTGA-
1 CCCCAAATTTTCTAAAATTTCATTTTTGAC
* *
42765358 CCCCAAACTATT-TATAATTTCATTTTTTGAC
1 CCCCAAA-TTTTCTAAAATTTCA-TTTTTGAC
* * * * *
42765389 TCTCAAACTATCTAAAATTACATTTTTGAC
1 CCCCAAATTTTCTAAAATTTCATTTTTGAC
42765419 CC
1 CC
42765421 TTAATCTTTC
Statistics
Matches: 74, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
29 28 0.38
30 33 0.45
31 13 0.18
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (30 bp):
CCCCAAATTTTCTAAAATTTCATTTTTGAC
Found at i:42765433 original size:30 final size:30
Alignment explanation
Indices: 42765322--42765475 Score: 143
Period size: 30 Copynumber: 5.1 Consensus size: 30
42765312 TAAATTTTAG
* * *
42765322 TTTTGACCCCCAAATTTTCTAAAATTTCAT
1 TTTTGACCCTCAAACTTTCTAAAATTACAT
* *
42765352 TTTTGACCC-CAAACTATT-TATAATTTCATT
1 TTTTGACCCTCAAACT-TTCTAAAATTACA-T
* *
42765382 TTTTGACTCTCAAACTATCTAAAATTACAT
1 TTTTGACCCTCAAACTTTCTAAAATTACAT
* *
42765412 TTTTGACCCTTAATCTTTCTAAAAATTACA-
1 TTTTGACCCTCAAACTTTCT-AAAATTACAT
* *
42765442 TTTTAACCCTTAAACTTTCTAAAAAATTACAT
1 TTTTGACCCTCAAACTTTCT--AAAATTACAT
42765474 TT
1 TT
42765476 CAGCCTCTAA
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
29 14 0.13
30 56 0.53
31 33 0.31
32 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTTGACCCTCAAACTTTCTAAAATTACAT
Found at i:42765437 original size:31 final size:32
Alignment explanation
Indices: 42765402--42765475 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 32
42765392 CAAACTATCT
* *
42765402 AAAATTACATTTTTGACCCTTAATCTTTCT-A
1 AAAATTACATTTTTAACCCTTAAACTTTCTAA
42765433 AAAATTACA-TTTTAACCCTTAAACTTTCTAA
1 AAAATTACATTTTTAACCCTTAAACTTTCTAA
42765464 AAAATTACATTT
1 AAAATTACATTT
42765476 CAGCCTCTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
30 18 0.46
31 19 0.49
32 2 0.05
ACGTcount: A:0.39, C:0.18, G:0.01, T:0.42
Consensus pattern (32 bp):
AAAATTACATTTTTAACCCTTAAACTTTCTAA
Found at i:42773783 original size:14 final size:14
Alignment explanation
Indices: 42773764--42773790 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42773754 TTAATACACT
42773764 ATCAAACTCGATTA
1 ATCAAACTCGATTA
42773778 ATCAAACTCGATT
1 ATCAAACTCGATT
42773791 TGACTTACAA
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:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (14 bp):
ATCAAACTCGATTA
Found at i:42801407 original size:3 final size:3
Alignment explanation
Indices: 42801399--42801435 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
42801389 CTCTAGAGAG
42801399 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
42801436 ACTGACACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:42804428 original size:7 final size:7
Alignment explanation
Indices: 42804413--42804443 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
42804403 CATGCTGCTC
42804413 TTTCCAA
1 TTTCCAA
*
42804420 TTACCAA
1 TTTCCAA
42804427 TTTCCAA
1 TTTCCAA
42804434 TTTCCAA
1 TTTCCAA
42804441 TTT
1 TTT
42804444 AAAAGCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (7 bp):
TTTCCAA
Found at i:42809776 original size:21 final size:21
Alignment explanation
Indices: 42809752--42809791 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42809742 TAAAACAATG
**
42809752 TAGTTTTGCCTTTTAACTTAA
1 TAGTTTTAACTTTTAACTTAA
42809773 TAGTTTTAACTTTTAACTT
1 TAGTTTTAACTTTTAACTT
42809792 TAGAAAAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (21 bp):
TAGTTTTAACTTTTAACTTAA
Found at i:42815757 original size:18 final size:18
Alignment explanation
Indices: 42815717--42815768 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
42815707 TTTTTAGTTG
*
42815717 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
42815735 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
42815753 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
42815769 CTCATCCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:42842915 original size:20 final size:20
Alignment explanation
Indices: 42842890--42842988 Score: 83
Period size: 20 Copynumber: 5.0 Consensus size: 20
42842880 TGTATCTAAG
42842890 TTTTGGTACTTCCTCATAAT
1 TTTTGGTACTTCCTCATAAT
* * ** *
42842910 TTTTGGTAATTCTTTGTATT
1 TTTTGGTACTTCCTCATAAT
* *
42842930 TTTTTGCACTTCCTCATAAAT
1 TTTTGGTACTTCCTCAT-AAT
* * *
42842951 TTTT-ATACATCCTCATAAG
1 TTTTGGTACTTCCTCATAAT
*
42842970 TTTTGGTACTTTCTCATAA
1 TTTTGGTACTTCCTCATAA
42842989 CTCTTGGTAT
Statistics
Matches: 58, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
19 6 0.10
20 46 0.79
21 6 0.10
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (20 bp):
TTTTGGTACTTCCTCATAAT
Found at i:42845217 original size:2 final size:2
Alignment explanation
Indices: 42845210--42845240 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42845200 AGATAAATTG
42845210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42845241 CAGAGAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42849927 original size:18 final size:18
Alignment explanation
Indices: 42849900--42849934 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42849890 CGGGTTTTGT
*
42849900 GGTGGAAGTGGCGGTGGC
1 GGTGGAAGTGGCAGTGGC
*
42849918 GGTGGCAGTGGCAGTGG
1 GGTGGAAGTGGCAGTGG
42849935 TGGAGTTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.11, G:0.60, T:0.17
Consensus pattern (18 bp):
GGTGGAAGTGGCAGTGGC
Done.