Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_pilon, 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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 73
Found at i:3930313 original size:19 final size:20
Alignment explanation
Indices: 3930270--3930321 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3930260 AATTTAAGGG
* *
3930270 AAGTTTCAAAGCTTTTATGA
1 AAGTTTCAAAACTATTATGA
3930290 AAGTTTCAAAACTATTAT-A
1 AAGTTTCAAAACTATTATGA
*
3930309 AAGTTTCTAAACT
1 AAGTTTCAAAACT
3930322 TCTAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (20 bp):
AAGTTTCAAAACTATTATGA
Found at i:3930543 original size:2 final size:2
Alignment explanation
Indices: 3930536--3930571 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3930526 AATATTTTTA
3930536 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
3930572 CATTCAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3935278 original size:29 final size:29
Alignment explanation
Indices: 3935240--3935303 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
3935230 AGGAGTTAAA
3935240 GATTCAGTTACAGGAACTATTGCAAAAAG
1 GATTCAGTTACAGGAACTATTGCAAAAAG
* * *
3935269 GATTCGGTTACATGAACTATTGGAAAAAG
1 GATTCAGTTACAGGAACTATTGCAAAAAG
3935298 GATTCA
1 GATTCA
3935304 TTAGACCAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (29 bp):
GATTCAGTTACAGGAACTATTGCAAAAAG
Found at i:3939140 original size:19 final size:20
Alignment explanation
Indices: 3939094--3939140 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
3939084 GATATTGAAC
* *
3939094 TCAAGAAAGTTCCGGAACAA
1 TCAAGAAAGTTCAGAAACAA
*
3939114 TTAA-AAAGTT-AGAAACAA
1 TCAAGAAAGTTCAGAAACAA
3939132 TCAAGAAAG
1 TCAAGAAAG
3939141 AGAAATTAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 9 0.41
19 10 0.45
20 3 0.14
ACGTcount: A:0.53, C:0.13, G:0.17, T:0.17
Consensus pattern (20 bp):
TCAAGAAAGTTCAGAAACAA
Found at i:3942407 original size:54 final size:53
Alignment explanation
Indices: 3942325--3942431 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 53
3942315 TATAGAAATA
*
3942325 CATCTCGACAAAGTAACTCTAACGATGAATGTTGGGTTGCACTGAATCAACTCC
1 CATCTCGACAAAATAACTCTAACGATGAATGTTGGGTTGCACTGAATC-ACTCC
*
3942379 CATCTCGACAAAATAACTCTAACGATGAATGTTGGGTTGTACTGAATCACTCC
1 CATCTCGACAAAATAACTCTAACGATGAATGTTGGGTTGCACTGAATCACTCC
3942432 TATAGATTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 5 0.10
54 46 0.90
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (53 bp):
CATCTCGACAAAATAACTCTAACGATGAATGTTGGGTTGCACTGAATCACTCC
Found at i:3942941 original size:15 final size:15
Alignment explanation
Indices: 3942923--3942953 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3942913 AAATTCTAAA
3942923 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
3942938 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
3942953 T
1 T
3942954 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:3945763 original size:15 final size:15
Alignment explanation
Indices: 3945745--3945779 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3945735 AAACGAAAAA
3945745 AAACTCAAATTCATT
1 AAACTCAAATTCATT
3945760 AAACTCAAATTCATT
1 AAACTCAAATTCATT
3945775 AAACT
1 AAACT
3945780 TGCATCAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTCAAATTCATT
Found at i:3948675 original size:33 final size:32
Alignment explanation
Indices: 3948637--3948754 Score: 105
Period size: 32 Copynumber: 3.7 Consensus size: 32
3948627 TGACTGAAAC
3948637 TAACTCGAACCAAAAGTAATCC-GAACCAAATTT
1 TAACTCGAACCAAAAGTAA-CCTGAACCAAA-TT
* * * *
3948670 TAACTCGATCCGAAAGCAACCTGAACTAAATT
1 TAACTCGAACCAAAAGTAACCTGAACCAAATT
* * * *
3948702 TAACCCGACCCAAAAGTAACCT-AAACAGAAAT
1 TAACTCGAACCAAAAGTAACCTGAACCA-AATT
* *
3948734 TAATTCGAACCGAAAGTAACC
1 TAACTCGAACCAAAAGTAACC
3948755 CAAACCGATT
Statistics
Matches: 68, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
31 3 0.04
32 42 0.62
33 23 0.34
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (32 bp):
TAACTCGAACCAAAAGTAACCTGAACCAAATT
Found at i:3948723 original size:32 final size:32
Alignment explanation
Indices: 3948605--3948723 Score: 100
Period size: 32 Copynumber: 3.7 Consensus size: 32
3948595 CAGACCGAAA
*
3948605 TTAACCCGAAGCAAAAGCAACCTG-ACTGAAA-
1 TTAACCCGAACCAAAAGCAACCTGAACT-AAAT
* * * *
3948636 CTAACTCGAACCAAAAGTAATCC-GAACCAAATT
1 TTAACCCGAACCAAAAGCAA-CCTGAACTAAA-T
* * *
3948669 TTAACTCGATCCGAAAGCAACCTGAACTAAAT
1 TTAACCCGAACCAAAAGCAACCTGAACTAAAT
* *
3948701 TTAACCCGACCCAAAAGTAACCT
1 TTAACCCGAACCAAAAGCAACCT
3948724 AAACAGAAAT
Statistics
Matches: 69, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
31 20 0.29
32 26 0.38
33 23 0.33
ACGTcount: A:0.43, C:0.28, G:0.12, T:0.18
Consensus pattern (32 bp):
TTAACCCGAACCAAAAGCAACCTGAACTAAAT
Found at i:3948747 original size:64 final size:64
Alignment explanation
Indices: 3948604--3948754 Score: 146
Period size: 64 Copynumber: 2.4 Consensus size: 64
3948594 CCAGACCGAA
* * * * *
3948604 ATTAACCCGAAGCAAAAGCAACCTGACTGAAACTAACTCGAACCAAAAGTAATCCGAACCAAAT
1 ATTAACTCGAACCGAAAGCAACCTGACTGAAACTAACCCGAACCAAAAGTAATCCGAAACAAAT
* * * * *
3948668 TTTAACTCGATCCGAAAGCAACCTGAACT-AAATTTAACCCGACCCAAAAGTAA-CCTAAACAGA
1 ATTAACTCGAACCGAAAGCAACCTG-ACTGAAA-CTAACCCGAACCAAAAGTAATCCGAAACA-A
3948731 A-
63 AT
* *
3948732 ATTAATTCGAACCGAAAGTAACC
1 ATTAACTCGAACCGAAAGCAACC
3948755 CAAACCGATT
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
64 48 0.69
65 22 0.31
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.17
Consensus pattern (64 bp):
ATTAACTCGAACCGAAAGCAACCTGACTGAAACTAACCCGAACCAAAAGTAATCCGAAACAAAT
Found at i:3949336 original size:14 final size:14
Alignment explanation
Indices: 3949313--3949342 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3949303 TTACATTGAG
3949313 TTTCTCAATAAAAC
1 TTTCTCAATAAAAC
*
3949327 TTTCTTAATAAAAC
1 TTTCTCAATAAAAC
3949341 TT
1 TT
3949343 AAAAGATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTCTCAATAAAAC
Found at i:3951729 original size:2 final size:2
Alignment explanation
Indices: 3951686--3951710 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3951676 CGATTGAAAC
3951686 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 A
3951711 GTATTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3952243 original size:28 final size:28
Alignment explanation
Indices: 3952203--3952258 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3952193 CGAGATTAAT
*
3952203 ATAAAATTTTGATAATAAATTCTAGCAC
1 ATAAAATTTTGATAACAAATTCTAGCAC
3952231 ATAAAATTTTGATAACAAATTCTAGCAC
1 ATAAAATTTTGATAACAAATTCTAGCAC
3952259 GTATTAACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (28 bp):
ATAAAATTTTGATAACAAATTCTAGCAC
Found at i:3952589 original size:16 final size:16
Alignment explanation
Indices: 3952568--3952601 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3952558 CAACCTATCA
3952568 AATATTGACCCGACCC
1 AATATTGACCCGACCC
* *
3952584 AATATTGATCCGATCC
1 AATATTGACCCGACCC
3952600 AA
1 AA
3952602 AAATCAACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (16 bp):
AATATTGACCCGACCC
Found at i:3954183 original size:95 final size:100
Alignment explanation
Indices: 3954075--3954353 Score: 343
Period size: 112 Copynumber: 2.7 Consensus size: 100
3954065 TTTTTGATAC
* *
3954075 TTACATCATCATCGACACATGAATCTTTCTTTGGAAGGGAATAAACTTTATAAATTAAAGAATAA
1 TTACATCATCATCGACACATGAATCTTTCTTTGGAAGGGAATAAGCTTTATAATTTAAAGAATAA
*
3954140 CCAAGAAA-ATTT-TAA-ATT-TTTT-AAGTTAAA
66 CCAAGAAATATTTATAATATTATTTTCAAGATAAA
*
3954170 TTACATCATCATCGACACATGAATCTTTCTTTGGAAAGGAATAAGCTTTATAATTTAAAGAATAA
1 TTACATCATCATCGACACATGAATCTTTCTTTGGAAGGGAATAAGCTTTATAATTTAAAGAATAA
* *
3954235 CCAATAAATTTTTTCATAACTTTTTGCATTAAATTTTCCAAGATAAA
66 CCAAGAAA-TATTT-ATAA-----T--ATT--ATTTT-CAAGATAAA
*
3954282 TTACATCATCATTGACACATGAATCTTTCTTTGGAAGGGAATAAGCTTTATAATTTAAAGAATAA
1 TTACATCATCATCGACACATGAATCTTTCTTTGGAAGGGAATAAGCTTTATAATTTAAAGAATAA
*
3954347 CAAAGAA
66 CCAAGAA
3954354 TTTTTTTTTC
Statistics
Matches: 157, Mismatches: 10, Indels: 17
0.85 0.05 0.09
Matches are distributed among these distances:
95 69 0.44
97 3 0.02
99 3 0.02
107 3 0.02
110 4 0.03
112 75 0.48
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (100 bp):
TTACATCATCATCGACACATGAATCTTTCTTTGGAAGGGAATAAGCTTTATAATTTAAAGAATAA
CCAAGAAATATTTATAATATTATTTTCAAGATAAA
Found at i:3954359 original size:112 final size:113
Alignment explanation
Indices: 3954151--3954392 Score: 369
Period size: 112 Copynumber: 2.1 Consensus size: 113
3954141 CAAGAAAATT
** *
3954151 TTAAATTTTTTAAGTTAAATTACATCATCATCGACACATGAATCTTTCTTTGGAAAGGAATAAGC
1 TTAAATTTTCCAAGATAAATTACATCATCATCGACACATGAATCTTTCTTTGGAAAGGAATAAGC
* * *
3954216 TTTATAATTTAAAGAATAACCAATAA-ATTTTTTCATAACTTTTTGCA
66 TTTATAATTTAAAGAATAACAAAGAATATTTTTTCATAACTTTTCGCA
* *
3954263 TTAAATTTTCCAAGATAAATTACATCATCATTGACACATGAATCTTTCTTTGGAAGGGAATAAGC
1 TTAAATTTTCCAAGATAAATTACATCATCATCGACACATGAATCTTTCTTTGGAAAGGAATAAGC
* *
3954328 TTTATAATTTAAAGAATAACAAAGAATTTTTTTTTCATCACTTTTCGCA
66 TTTATAATTTAAAGAATAACAAAGAA-TATTTTTTCATAACTTTTCGCA
*
3954377 TTAAATTTTCGAAGAT
1 TTAAATTTTCCAAGAT
3954393 TATCTTTTCC
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
112 84 0.72
114 33 0.28
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (113 bp):
TTAAATTTTCCAAGATAAATTACATCATCATCGACACATGAATCTTTCTTTGGAAAGGAATAAGC
TTTATAATTTAAAGAATAACAAAGAATATTTTTTCATAACTTTTCGCA
Found at i:3957765 original size:11 final size:11
Alignment explanation
Indices: 3957749--3957797 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
3957739 ATATGTATTT
3957749 TAAAATTTAAA
1 TAAAATTTAAA
3957760 TAAAATTTAAA
1 TAAAATTTAAA
* *
3957771 TAATATTTTAA
1 TAAAATTTAAA
3957782 TACATAATTATAAA
1 TA-A-AATT-TAAA
3957796 TA
1 TA
3957798 TTTAGTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 22 0.71
12 1 0.03
13 3 0.10
14 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAAATTTAAA
Found at i:3957783 original size:22 final size:25
Alignment explanation
Indices: 3957753--3957797 Score: 60
Period size: 22 Copynumber: 1.9 Consensus size: 25
3957743 GTATTTTAAA
3957753 ATTTAAATA-A-AATT-TAAATAAT
1 ATTTAAATACATAATTATAAATAAT
*
3957775 ATTTTAATACATAATTATAAATA
1 ATTTAAATACATAATTATAAATA
3957798 TTTAGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 1 0.05
24 4 0.21
25 6 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATACATAATTATAAATAAT
Found at i:3960279 original size:15 final size:15
Alignment explanation
Indices: 3960261--3960301 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3960251 GACAAAAATT
3960261 AAATAATAAAAACAA
1 AAATAATAAAAACAA
* * *
3960276 AAATAAGAGAAATAA
1 AAATAATAAAAACAA
3960291 AAATAATAAAA
1 AAATAATAAAA
3960302 TTAAATAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (15 bp):
AAATAATAAAAACAA
Found at i:3960301 original size:24 final size:22
Alignment explanation
Indices: 3960261--3960314 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
3960251 GACAAAAATT
3960261 AAATAATAAAAACAAAAATAAGAG
1 AAATAA-AAAAACAAAAATAA-AG
* * *
3960285 AAATAAAAATAATAAAATTAAAT
1 AAATAAAAA-AACAAAAATAAAG
3960308 AAATAAA
1 AAATAAA
3960315 TAACAAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.19
Consensus pattern (22 bp):
AAATAAAAAAACAAAAATAAAG
Found at i:3961458 original size:12 final size:12
Alignment explanation
Indices: 3961408--3961460 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
3961398 TGGACCAAAG
*
3961408 AAAGAAAAACAA
1 AAAGAAAAAGAA
* * *
3961420 AAATAAATA-TA
1 AAAGAAAAAGAA
*
3961431 AAATAAAAAGAA
1 AAAGAAAAAGAA
3961443 AAAGAAAAAGAA
1 AAAGAAAAAGAA
3961455 AAAGAA
1 AAAGAA
3961461 TAAAATATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 9 0.26
12 25 0.74
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.08
Consensus pattern (12 bp):
AAAGAAAAAGAA
Found at i:3961543 original size:25 final size:25
Alignment explanation
Indices: 3961500--3961548 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
3961490 TACTATATAA
3961500 TATATAAATATATATTTTTAAAAAC
1 TATATAAATATATATTTTTAAAAAC
*
3961525 TATATAATATATATATTTTCAAAA
1 TATATAA-ATATATATTTTTAAAA
3961549 TATTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TATATAAATATATATTTTTAAAAAC
Found at i:3961568 original size:39 final size:38
Alignment explanation
Indices: 3961511--3961800 Score: 316
Period size: 37 Copynumber: 7.8 Consensus size: 38
3961501 ATATAAATAT
*
3961511 ATATTTTTAAAAACTATATA-ATATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATATATATATATTTTCAAA
3961548 ATATTTTCAAAAACTATATAT-TATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATATATATATATTTTCAAA
* * * *
3961585 A-A--CT-ATATA-T-TATATATATATATATATTCAAA
1 ATATTTTCAAAAACTATATATATATATATATTTTCAAA
*
3961617 ATGTTTTCAAAAACTATATAT-TATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATATATATATATTTTCAAA
* *
3961654 ATATTTTCAAAAACTATATATTATATATATGTTTTTAAA
1 ATATTTTCAAAAACTATATA-TATATATATATTTTCAAA
** *
3961693 ATGGTTTCAAAAACTATATAT-TATATATACTTTCAAA
1 ATATTTTCAAAAACTATATATATATATATATTTTCAAA
* * * *
3961730 ATATTTTTAAAAACTATATATTACATTTATGTTTTCAAA
1 ATATTTTCAAAAACTATATA-TATATATATATTTTCAAA
3961769 AT-TTTAT-AAAAACTATATATTATATACTATAT
1 ATATTT-TCAAAAACTATATA-TATATA-TATAT
3961801 ATATACTAAA
Statistics
Matches: 211, Mismatches: 28, Indels: 26
0.80 0.11 0.10
Matches are distributed among these distances:
31 5 0.02
32 17 0.08
33 3 0.01
34 1 0.00
35 1 0.00
36 4 0.02
37 101 0.48
38 28 0.13
39 51 0.24
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (38 bp):
ATATTTTCAAAAACTATATATATATATATATTTTCAAA
Found at i:3961605 original size:28 final size:26
Alignment explanation
Indices: 3961548--3961603 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
3961538 TATTTTCAAA
3961548 ATATTTTCAAAAACTATATATTATAT
1 ATATTTTCAAAAACTATATATTATAT
3961574 ATATTTTCAAAAACTATATATTATAT
1 ATATTTTCAAAAACTATATATTATAT
3961600 ATAT
1 ATAT
3961604 ATATATATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTTTCAAAAACTATATATTATAT
Found at i:3961701 original size:76 final size:75
Alignment explanation
Indices: 3961574--3961794 Score: 309
Period size: 76 Copynumber: 2.9 Consensus size: 75
3961564 TATATTATAT
*
3961574 ATATTTTCAAAAACTATATATTATATATATATATATATTCAAAATGTTTTCAAAAACTATATATT
1 ATATTTTCAAAAACTATATATTATATATATGT-T-T-TT-AAAATG-TTTCAAAAACTATATATT
*
3961639 ATATATATTTTCAAA
61 ATATATACTTTCAAA
3961654 ATATTTTCAAAAACTATATATTATATATATGTTTTTAAAATGGTTTCAAAAACTATATATTATAT
1 ATATTTTCAAAAACTATATATTATATATATGTTTTTAAAAT-GTTTCAAAAACTATATATTATAT
3961719 ATACTTTCAAA
65 ATACTTTCAAA
* * * * *
3961730 ATATTTTTAAAAACTATATATTACATTTATGTTTTCAAAAT-TTTATAAAAACTATATATTATAT
1 ATATTTTCAAAAACTATATATTATATATATGTTTTTAAAATGTTT-CAAAAACTATATATTATAT
3961794 A
65 A
3961795 CTATATATAT
Statistics
Matches: 132, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
74 3 0.02
75 19 0.14
76 74 0.56
77 3 0.02
78 1 0.01
79 1 0.01
80 31 0.23
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (75 bp):
ATATTTTCAAAAACTATATATTATATATATGTTTTTAAAATGTTTCAAAAACTATATATTATATA
TACTTTCAAA
Found at i:3970896 original size:15 final size:17
Alignment explanation
Indices: 3970875--3970923 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
3970865 TTTAATTGCG
3970875 TTTTTT-TATTTAATCA
1 TTTTTTATATTTAATCA
3970891 TTTTTTACTATTTAATCA
1 TTTTTTA-TATTTAATCA
*
3970909 TTTTGTACTATTTAA
1 TTTTTTA-TATTTAA
3970924 ATCTCATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 6 0.20
18 24 0.80
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTTTATATTTAATCA
Found at i:3970896 original size:18 final size:18
Alignment explanation
Indices: 3970881--3970923 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
3970871 TGCGTTTTTT
3970881 TATTTAATCATTTTTTAC
1 TATTTAATCATTTTTTAC
*
3970899 TATTTAATCATTTTGTAC
1 TATTTAATCATTTTTTAC
3970917 TATTTAA
1 TATTTAA
3970924 ATCTCATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTTAATCATTTTTTAC
Found at i:3974910 original size:32 final size:30
Alignment explanation
Indices: 3974850--3974911 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
3974840 ATGTTTTTTT
*
3974850 AAAAATTCAGGATCGGTTGGATTTTTTAAA
1 AAAAATTCAGGATCGGTCGGATTTTTTAAA
* *
3974880 AAAAATTCCAGGTTCGGGTCGGGTTTTTTAAA
1 AAAAATT-CAGGATC-GGTCGGATTTTTTAAA
3974912 GTTTGATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 7 0.26
31 6 0.22
32 14 0.52
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (30 bp):
AAAAATTCAGGATCGGTCGGATTTTTTAAA
Found at i:3974924 original size:28 final size:28
Alignment explanation
Indices: 3974892--3974960 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
3974882 AAATTCCAGG
*
3974892 TTCGGGTCGGGTTTTT-TAAAGTTTGATA
1 TTCGGGTCGGGTTTTTGT-AAGTGTGATA
3974920 TTCGGGTCGGGTTTTTGTAAGTGTGATA
1 TTCGGGTCGGGTTTTTGTAAGTGTGATA
*
3974948 TTCGGGTCAGGTT
1 TTCGGGTCGGGTT
3974961 CAGGTCTGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 37 0.97
29 1 0.03
ACGTcount: A:0.14, C:0.09, G:0.33, T:0.43
Consensus pattern (28 bp):
TTCGGGTCGGGTTTTTGTAAGTGTGATA
Found at i:3975071 original size:33 final size:34
Alignment explanation
Indices: 3975030--3975100 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
3975020 AATCGGGTTT
* *
3975030 GGGTCGGTTTTTTT-TAAGTGTGATATTCGGGTC
1 GGGTCGGTTTTTTTAAAAATGTGATATTCGGGTC
* *
3975063 GGGTCGGTTTTTTTAAAAATTTTATATTCGGGTC
1 GGGTCGGTTTTTTTAAAAATGTGATATTCGGGTC
3975097 GGGT
1 GGGT
3975101 TCAGGTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 14 0.42
34 19 0.58
ACGTcount: A:0.15, C:0.08, G:0.31, T:0.45
Consensus pattern (34 bp):
GGGTCGGTTTTTTTAAAAATGTGATATTCGGGTC
Found at i:3975604 original size:16 final size:18
Alignment explanation
Indices: 3975583--3975630 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
3975573 GTTTCAAATT
3975583 CAGATTCCAATTCC-T-A
1 CAGATTCCAATTCCTTCA
3975599 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
3975617 CAGATTCCAATTCC
1 CAGATTCCAATTCC
3975631 CTCATAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 14 0.47
17 1 0.03
18 15 0.50
ACGTcount: A:0.29, C:0.33, G:0.06, T:0.31
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:3983910 original size:20 final size:20
Alignment explanation
Indices: 3983871--3983911 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3983861 ACACACAAAG
* * *
3983871 ACAAAAATTAAATAATTAAA
1 ACAAAAATGAAAGAAATAAA
3983891 ACAAAAATGAAAGAAATAAA
1 ACAAAAATGAAAGAAATAAA
3983911 A
1 A
3983912 AATAATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (20 bp):
ACAAAAATGAAAGAAATAAA
Found at i:3983935 original size:28 final size:31
Alignment explanation
Indices: 3983880--3983942 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 31
3983870 GACAAAAATT
3983880 AAATAATTAAAACAAAAATGAAAGAAATAAA
1 AAATAATTAAAACAAAAATGAAAGAAATAAA
* * *
3983911 AAATAA-TAAAA-ATAAAT-AAATAAATAAC
1 AAATAATTAAAACAAAAATGAAAGAAATAAA
3983939 AAAT
1 AAAT
3983943 GTTGGATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 13 0.45
29 5 0.17
30 5 0.17
31 6 0.21
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (31 bp):
AAATAATTAAAACAAAAATGAAAGAAATAAA
Found at i:3985196 original size:26 final size:24
Alignment explanation
Indices: 3985147--3985199 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
3985137 ATTATACTAT
* *
3985147 AAAATATATAAATATATTTTTTTA
1 AAAATATATAAATATATATATTTA
3985171 AAAACTATATAATATATATATATTTA
1 AAAA-TATATAA-ATATATATATTTA
3985197 AAA
1 AAA
3985200 TATTTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.16
25 7 0.28
26 14 0.56
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATATATAAATATATATATTTA
Found at i:3985205 original size:39 final size:38
Alignment explanation
Indices: 3985162--3985458 Score: 288
Period size: 37 Copynumber: 7.8 Consensus size: 38
3985152 ATATAAATAT
* *
3985162 ATTTTTTTAAAAACTATATAATATATATATATTT-AAA
1 ATTTTTTCAAAAACTATATATTATATATATATTTAAAA
* *
3985199 ATATTTTCAAAAACTATATATTACATATAT-TTTCAAAA
1 ATTTTTTCAAAAACTATATATTATATATATATTT-AAAA
* * * * *
3985237 ATTATAT-ATATA-TATATATATATATATATATTTTCAAA
1 ATTTTTTCAAAAACTATATAT-TATATATATA-TTTAAAA
*
3985275 ATGTTTTCAAAAACTATATATTAT-T-TATA-TTACAAA
1 ATTTTTTCAAAAACTATATATTATATATATATTTA-AAA
* * *
3985311 ATATTTTCAAAAACTATATATTATATATATGTTTTTAAA
1 ATTTTTTCAAAAACTATATATTATATATAT-ATTTAAAA
* *
3985350 ATGTTTTCAAAAACTATATATTATATATAT-TTTCAAA
1 ATTTTTTCAAAAACTATATATTATATATATATTTAAAA
* *
3985387 ATATTTTT-AAAAACTATATATTATATATATGTTTTCAAA
1 AT-TTTTTCAAAAACTATATATTATATATAT-ATTTAAAA
* *
3985426 ATTTTATAAAAAACTATATATTATATACTATAT
1 ATTTTTTCAAAAACTATATATTATATA-TATAT
3985459 ATATACTAAA
Statistics
Matches: 218, Mismatches: 25, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
35 2 0.01
36 36 0.17
37 72 0.33
38 26 0.12
39 70 0.32
40 12 0.06
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (38 bp):
ATTTTTTCAAAAACTATATATTATATATATATTTAAAA
Found at i:3985216 original size:26 final size:26
Alignment explanation
Indices: 3985187--3985296 Score: 86
Period size: 26 Copynumber: 4.3 Consensus size: 26
3985177 ATATAATATA
3985187 TATATATTTAAAATATTTTCAAAAAC
1 TATATATTTAAAATATTTTCAAAAAC
* *
3985213 TATATA-TTACATATATTTTCAAAAAT
1 TATATATTTA-AAATATTTTCAAAAAC
* * * * *
3985239 TATATATAT-ATATA-TAT-ATATA-
1 TATATATTTAAAATATTTTCAAAAAC
*
3985261 TATATATTTTCAAAATGTTTTCAAAAAC
1 TATATA-TTT-AAAATATTTTCAAAAAC
3985289 TATATATT
1 TATATATT
3985297 ATTTATATTA
Statistics
Matches: 64, Mismatches: 12, Indels: 15
0.70 0.13 0.16
Matches are distributed among these distances:
22 6 0.09
23 5 0.08
24 2 0.03
25 11 0.17
26 28 0.44
27 6 0.09
28 6 0.09
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (26 bp):
TATATATTTAAAATATTTTCAAAAAC
Found at i:3985244 original size:2 final size:2
Alignment explanation
Indices: 3985239--3985267 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3985229 TTTCAAAAAT
3985239 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3985268 TTTCAAAATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3985251 original size:25 final size:26
Alignment explanation
Indices: 3985199--3985255 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
3985189 TATATTTAAA
3985199 ATATTTTCAAAAACTATATATTACAT
1 ATATTTTCAAAAACTATATATTACAT
* *
3985225 ATATTTTCAAAAATTATATATATATAT
1 ATATTTTCAAAAACTATATAT-TACAT
3985252 ATAT
1 ATAT
3985256 ATATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTTTCAAAAACTATATATTACAT
Found at i:3985276 original size:76 final size:75
Alignment explanation
Indices: 3985166--3985452 Score: 379
Period size: 76 Copynumber: 3.8 Consensus size: 75
3985156 AAATATATTT
* * *
3985166 TTTTAAAAACTATATAATATATATATA-TTT-AAAATATTTTCAAAAACTATATATTACATATAT
1 TTTTAAAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
3985229 TTTCAAAA-A
66 TTTCAAAATA
* * *
3985238 TTATATATATA-TATATATATATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATTTA
1 TT-T-TAAAAACTATATAT-TATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATA
*
3985302 TA-TTACAAAATA
63 TATTTTCAAAATA
* *
3985314 TTTTCAAAAACTATATATTATATATATGTTTTTAAAATGTTTTCAAAAACTATATATTATATATA
1 TTTT-AAAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATA
3985379 TTTTCAAAATA
65 TTTTCAAAATA
* *
3985390 TTTTTAAAAACTATATATTATATATATGTTTTCAAAAT-TTTATAAAAAACTATATATTATATA
1 -TTTTAAAAACTATATATTATATATATATTTTCAAAATGTTT-TCAAAAACTATATATTATATA
3985453 CTATATATAT
Statistics
Matches: 189, Mismatches: 15, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
72 2 0.01
73 7 0.04
74 15 0.08
75 61 0.32
76 100 0.53
77 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (75 bp):
TTTTAAAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
TTTCAAAATA
Found at i:3985525 original size:9 final size:9
Alignment explanation
Indices: 3985511--3985541 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3985501 ATGGAAGACA
3985511 TTGTTTGAT
1 TTGTTTGAT
3985520 TTGTTTGAT
1 TTGTTTGAT
*
3985529 TTGTTTAAT
1 TTGTTTGAT
3985538 TTGT
1 TTGT
3985542 GGGTTTGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.19, T:0.68
Consensus pattern (9 bp):
TTGTTTGAT
Found at i:3988461 original size:46 final size:46
Alignment explanation
Indices: 3988394--3988485 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
3988384 AGATAAAATA
3988394 CTTTAAATACGTGAAGATAATCACTTGGTGCTTAGTTGAGAGAAAC
1 CTTTAAATACGTGAAGATAATCACTTGGTGCTTAGTTGAGAGAAAC
*
3988440 CTTTAAATATGTGAAGATAATCACTTGGTGCTTAGTTGAGAGAAAC
1 CTTTAAATACGTGAAGATAATCACTTGGTGCTTAGTTGAGAGAAAC
3988486 GTCATTTTAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (46 bp):
CTTTAAATACGTGAAGATAATCACTTGGTGCTTAGTTGAGAGAAAC
Found at i:3998530 original size:20 final size:20
Alignment explanation
Indices: 3998491--3998530 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3998481 CATTATAGTA
*
3998491 TAAATATTGAGATTGGTTTG
1 TAAATATTGAGATTAGTTTG
*
3998511 TAAATATTGAGATTATTTTG
1 TAAATATTGAGATTAGTTTG
3998531 ATACAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (20 bp):
TAAATATTGAGATTAGTTTG
Found at i:3999223 original size:14 final size:14
Alignment explanation
Indices: 3999204--3999230 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3999194 TCCCACACTT
3999204 GATATAATTTTAAA
1 GATATAATTTTAAA
3999218 GATATAATTTTAA
1 GATATAATTTTAA
3999231 CTAACAGTAG
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:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
GATATAATTTTAAA
Found at i:4001516 original size:21 final size:21
Alignment explanation
Indices: 4001490--4001534 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4001480 GATTTCTGGG
* *
4001490 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4001511 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4001532 CAA
1 CAA
4001535 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4003231 original size:25 final size:25
Alignment explanation
Indices: 4003195--4003263 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
4003185 GAGTAGAGGG
4003195 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
*
4003220 TCTACGCAGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
4003245 TCTACGCGGTCCTTCGGGA
1 TCTACGCGGTCCTTCGGGA
4003264 TATATATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.28
Consensus pattern (25 bp):
TCTACGCGGTCCTTCGGGACAATAT
Found at i:4003422 original size:23 final size:23
Alignment explanation
Indices: 4003378--4003422 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4003368 ATCATTATAT
*
4003378 GGCACTATGGTGCAATTCTACGC
1 GGCACTATGGTGCAATTATACGC
*
4003401 GGCACT-TCGGTGCATTTATACG
1 GGCACTAT-GGTGCAATTATACG
4003423 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTATGGTGCAATTATACGC
Found at i:4009875 original size:9 final size:10
Alignment explanation
Indices: 4009849--4009882 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
4009839 AATTTCTTTC
4009849 TATTTTTAAAA
1 TATTTTT-AAA
4009860 TATTTTTAAA
1 TATTTTTAAA
4009870 -ATTTTTAAA
1 TATTTTTAAA
4009879 TATT
1 TATT
4009883 ATAATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 6 0.27
11 7 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:4012248 original size:58 final size:58
Alignment explanation
Indices: 4012186--4012322 Score: 161
Period size: 58 Copynumber: 2.3 Consensus size: 58
4012176 AACAATTAGA
* ****
4012186 ATTTGTTGTAATTTATAAAAACA-ATTGG-AATTTGTTGTAATTTTTAATTTTTTTTGGC
1 ATTTGTTGTAATTTATAAAAA-ATATTGGTAATTTGTTGTAATTTATAA-AAAGTTTGGC
* * *
4012244 ATTTGTTGTAATTTATAAAAAATTTTGGTATTTTTTTGTAATTTATAAAAAGTTTGGC
1 ATTTGTTGTAATTTATAAAAAATATTGGTAATTTGTTGTAATTTATAAAAAGTTTGGC
4012302 ATTTGTTTGTAATTTATAAAA
1 ATTTG-TTGTAATTTATAAAA
4012323 GTTTTGGTCT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
57 1 0.01
58 36 0.53
59 31 0.46
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (58 bp):
ATTTGTTGTAATTTATAAAAAATATTGGTAATTTGTTGTAATTTATAAAAAGTTTGGC
Found at i:4012285 original size:30 final size:29
Alignment explanation
Indices: 4012186--4012352 Score: 135
Period size: 29 Copynumber: 5.8 Consensus size: 29
4012176 AACAATTAGA
** *
4012186 ATTTG-TTGTAATTTATAAAAACAATTGGA
1 ATTTGTTTGTAATTTATAAAAA-TTTTGGT
* *** *
4012215 ATTTG-TTGTAATTTTTAATTTTTTTTGGC
1 ATTTGTTTGTAATTTATAA-AAATTTTGGT
4012244 ATTTG-TTGTAATTTATAAAAAATTTTGGT
1 ATTTGTTTGTAATTTAT-AAAAATTTTGGT
* * *
4012273 ATTTTTTTGTAATTTATAAAAAGTTTGGC
1 ATTTGTTTGTAATTTATAAAAATTTTGGT
*
4012302 ATTTGTTTGTAATTTATAAAAGTTTTGGT
1 ATTTGTTTGTAATTTATAAAAATTTTGGT
* * * *
4012331 CTTT-ATTGTAATATATCAAAAT
1 ATTTGTTTGTAATTTATAAAAAT
4012353 ATTATTTTTA
Statistics
Matches: 111, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
28 14 0.13
29 84 0.76
30 13 0.12
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (29 bp):
ATTTGTTTGTAATTTATAAAAATTTTGGT
Found at i:4012328 original size:29 final size:30
Alignment explanation
Indices: 4012133--4012329 Score: 145
Period size: 29 Copynumber: 6.8 Consensus size: 30
4012123 CAAGTCATTA
* * ** *
4012133 TTGTAATTTATTAGAAGTTTTTTC-TTTGA
1 TTGTAATTTATAAAAAGTTTTGGCATTTGT
* *** * *
4012162 TTGCAATTTATAAAAACAATTAGAATTTG-
1 TTGTAATTTATAAAAAGTTTTGGCATTTGT
*** *
4012191 TTGTAATTTATAAAAACAATTGGAATTTG-
1 TTGTAATTTATAAAAAGTTTTGGCATTTGT
* ****
4012220 TTGTAATTTTTAATTTTTTTTGGCATTTG-
1 TTGTAATTTATAAAAAGTTTTGGCATTTGT
* * *
4012249 TTGTAATTTATAAAAAATTTTGGTATTTTT
1 TTGTAATTTATAAAAAGTTTTGGCATTTGT
4012279 TTGTAATTTATAAAAAG-TTTGGCATTTGT
1 TTGTAATTTATAAAAAGTTTTGGCATTTGT
4012308 TTGTAATTTAT-AAAAGTTTTGG
1 TTGTAATTTATAAAAAGTTTTGG
4012330 TCTTTATTGT
Statistics
Matches: 136, Mismatches: 29, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
28 5 0.04
29 111 0.82
30 20 0.15
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (30 bp):
TTGTAATTTATAAAAAGTTTTGGCATTTGT
Found at i:4012340 original size:87 final size:86
Alignment explanation
Indices: 4012133--4012351 Score: 194
Period size: 87 Copynumber: 2.5 Consensus size: 86
4012123 CAAGTCATTA
* * *
4012133 TTGTAATTTATTAGAAGTTTT-TTCTTTGATTGCAATTTATAAAAACAATTAGAATTTGTTGTAA
1 TTGTAATTTA-TAAAAGTTTTGGTCTTT-ATTGTAATTTATAAAAACAATTAGAATTTGTTGTAA
4012197 TTTATAAAAACAATTGGAATTTG
64 TTTATAAAAACAATTGGAATTTG
* *** * * * * *
4012220 TTGTAATTTTTAATTTTTTTTGG-CATTTGTTGTAATTTATAAAAA-ATTTTGGTATTTTTTTGT
1 TTGTAATTTATAA-AAGTTTTGGTC-TTTATTGTAATTTATAAAAACA-ATTAG-AATTTGTTGT
** *
4012283 AATTTATAAAAA-GTTTGGCATTTG
62 AATTTATAAAAACAATTGGAATTTG
* *
4012307 TTTGTAATTTATAAAAGTTTTGGTCTTTATTGTAATATATCAAAA
1 -TTGTAATTTATAAAAGTTTTGGTCTTTATTGTAATTTATAAAAA
4012352 TATTATTTTT
Statistics
Matches: 103, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
86 3 0.03
87 64 0.62
88 36 0.35
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.51
Consensus pattern (86 bp):
TTGTAATTTATAAAAGTTTTGGTCTTTATTGTAATTTATAAAAACAATTAGAATTTGTTGTAATT
TATAAAAACAATTGGAATTTG
Found at i:4025038 original size:17 final size:17
Alignment explanation
Indices: 4025016--4025068 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
4025006 AATTAAGAGT
*
4025016 TAGTTTGATTAATGCAC
1 TAGTTTGATTAATGAAC
* *
4025033 TAGTTTAATAAATGAAC
1 TAGTTTGATTAATGAAC
*
4025050 TAGTTTGATTAATAAAC
1 TAGTTTGATTAATGAAC
4025067 TA
1 TA
4025069 ACTTTACTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (17 bp):
TAGTTTGATTAATGAAC
Found at i:4025081 original size:34 final size:34
Alignment explanation
Indices: 4025016--4025085 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
4025006 AATTAAGAGT
** *
4025016 TAGTTTGATTAATGCACTAGTTTAATAAATGAAC
1 TAGTTTGATTAATAAACTACTTTAATAAATGAAC
*
4025050 TAGTTTGATTAATAAACTAACTTTACT-AATGAAC
1 TAGTTTGATTAATAAACT-ACTTTAATAAATGAAC
4025084 TA
1 TA
4025086 AATGCATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 25 0.81
35 6 0.19
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (34 bp):
TAGTTTGATTAATAAACTACTTTAATAAATGAAC
Found at i:4033306 original size:21 final size:22
Alignment explanation
Indices: 4033256--4033306 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
4033246 TAATGGTAAA
* *
4033256 AATATAAATAAATAAAATGACT
1 AATATAAAAAAATAAAAGGACT
**
4033278 ACGA-AAAAAAAT-AAAGGACT
1 AATATAAAAAAATAAAAGGACT
4033298 AATATAAAA
1 AATATAAAA
4033307 GAAAAAATAA
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
20 9 0.41
21 11 0.50
22 2 0.09
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.20
Consensus pattern (22 bp):
AATATAAAAAAATAAAAGGACT
Found at i:4035008 original size:98 final size:98
Alignment explanation
Indices: 4034839--4035023 Score: 289
Period size: 98 Copynumber: 1.9 Consensus size: 98
4034829 CTGGAACTGG
* *
4034839 GAAATTATTTGTCGACAATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGGGTCC
1 GAAATTATTTGTCGACAATCAGCCGCCCCTTCACTATGAAGTTGAGCTTGTGCTGTCTCGAGTCC
*
4034904 AATATCCTTCGCCGTGGAGTTGAGATTGGCTCC
66 AATATCCTTCGCCGTGAAGTTGAGATTGGCTCC
* * * * *
4034937 GAAATTGTTTTTCGACAGTCAGCCGCTCCTTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTCC
1 GAAATTATTTGTCGACAATCAGCCGCCCCTTCACTATGAAGTTGAGCTTGTGCTGTCTCGAGTCC
*
4035002 AATATCCTTCGCTGTGAAGTTG
66 AATATCCTTCGCCGTGAAGTTG
4035024 TTTGTTGACA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 78 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (98 bp):
GAAATTATTTGTCGACAATCAGCCGCCCCTTCACTATGAAGTTGAGCTTGTGCTGTCTCGAGTCC
AATATCCTTCGCCGTGAAGTTGAGATTGGCTCC
Found at i:4035287 original size:109 final size:109
Alignment explanation
Indices: 4035091--4035416 Score: 546
Period size: 109 Copynumber: 3.0 Consensus size: 109
4035081 CAATATCTTT
* *
4035091 GGCTTTGAAATTGGGAAA-TTGTTCATTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
1 GGCTCTGAAATT-GGAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
* * *
4035155 TGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATC
65 TGTTGTCTTGAGTGGCACGATATCCTCCGTCGTGGAGTTGAAATC
*
4035200 GGCTCTGAAATTGGAAAGTTGTTCGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGT
1 GGCTCTGAAATTGGAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGT
* * * *
4035265 GTTGTCTTGAGTGGCACGATATCTTTCATCATGGAGTTGAAATC
66 GTTGTCTTGAGTGGCACGATATCCTCCGTCGTGGAGTTGAAATC
4035309 GGCTCTGAAATTGGAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGT
1 GGCTCTGAAATTGGAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGT
4035374 GTTGTCTTGAGTGGCACGATATCCTCCGTCGTGGAGTTGAAAT
66 GTTGTCTTGAGTGGCACGATATCCTCCGTCGTGGAGTTGAAAT
4035417 TGTGGATGTT
Statistics
Matches: 201, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
108 5 0.02
109 196 0.98
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (109 bp):
GGCTCTGAAATTGGAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGT
GTTGTCTTGAGTGGCACGATATCCTCCGTCGTGGAGTTGAAATC
Found at i:4045707 original size:29 final size:30
Alignment explanation
Indices: 4045652--4045720 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
4045642 TGGTAATAAT
* *
4045652 ATAAATAAATAAAATGATTACGAAAAA-AA
1 ATAAATAAATAAAATGACTAAGAAAAAGAA
*
4045681 ATAAATAAATAAAA-GACTAATATAAAAGAA
1 ATAAATAAATAAAATGACTAAGA-AAAAGAA
4045711 A-AAATAAATA
1 ATAAATAAATA
4045721 TTGGGGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.14
29 27 0.77
30 3 0.09
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (30 bp):
ATAAATAAATAAAATGACTAAGAAAAAGAA
Found at i:4051050 original size:2 final size:2
Alignment explanation
Indices: 4051043--4051072 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4051033 ATTTTAGGGA
4051043 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
4051073 CATTTATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4051664 original size:34 final size:34
Alignment explanation
Indices: 4051511--4051649 Score: 170
Period size: 34 Copynumber: 4.1 Consensus size: 34
4051501 GGGGGCGACC
** * *
4051511 CCCCTTTGTGAGTTAATTCAAATTTTGGATGACT
1 CCCCTTTACGAGTTAAGTCAAATTATGGATGACT
* *
4051545 CCCCTTTACGAGTCAAGTCAGATTATGGATGACT
1 CCCCTTTACGAGTTAAGTCAAATTATGGATGACT
* * *
4051579 CCCTTTTACGAGTTAAGTCAGATTATGGACGACT
1 CCCCTTTACGAGTTAAGTCAAATTATGGATGACT
* * *
4051613 CCCCTTTACGTGTTAAGTAAAATTGTGGATGACT
1 CCCCTTTACGAGTTAAGTCAAATTATGGATGACT
4051647 CCC
1 CCC
4051650 TTTTGTGAGA
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 90 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (34 bp):
CCCCTTTACGAGTTAAGTCAAATTATGGATGACT
Found at i:4051664 original size:68 final size:68
Alignment explanation
Indices: 4051515--4051674 Score: 194
Period size: 68 Copynumber: 2.4 Consensus size: 68
4051505 GCGACCCCCC
* * * * *
4051515 TTTGTGAGTTAATTCAAATTTTGGATGACTCCCCTTTACGAGTCAAGTCAGATTATGGATGACTC
1 TTTGTGAGTTAAGTCAAATTATGGACGACTCCCCTTTACGAGTCAAGTAAAATTATGGATGACTC
4051580 CCT
66 CCT
** * * * *
4051583 TTTACGAGTTAAGTCAGATTATGGACGACTCCCCTTTACGTGTTAAGTAAAATTGTGGATGACTC
1 TTTGTGAGTTAAGTCAAATTATGGACGACTCCCCTTTACGAGTCAAGTAAAATTATGGATGACTC
4051648 CCT
66 CCT
* **
4051651 TTTGTGAGATAAGTTGAATTATGG
1 TTTGTGAGTTAAGTCAAATTATGG
4051675 TGCCCCTTTC
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
68 75 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (68 bp):
TTTGTGAGTTAAGTCAAATTATGGACGACTCCCCTTTACGAGTCAAGTAAAATTATGGATGACTC
CCT
Found at i:4054186 original size:2 final size:2
Alignment explanation
Indices: 4054179--4054205 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4054169 AAATACATAC
4054179 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 A
4054206 ACGTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4056594 original size:47 final size:45
Alignment explanation
Indices: 4056500--4056621 Score: 129
Period size: 47 Copynumber: 2.7 Consensus size: 45
4056490 TCATTTGGGG
* * * * * *
4056500 CATTCTTTCATGCCCATTAAGTATTGTTTACGTTTTTCTTTATGA
1 CATTCTTTCATACCAATTATGCATTGTTTACATTTTTCTCTATGA
*
4056545 CATTCATTT-ATTCCAATTATGCATTGTTGTACATTTTATCTCTATGA
1 CATTC-TTTCATACCAATTATGCATTGTT-TACATTTT-TCTCTATGA
* *
4056592 CATTCTTTCATACCACTTATGCACTGTTTA
1 CATTCTTTCATACCAATTATGCATTGTTTA
4056622 TATCAAAATG
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 20 0.31
46 15 0.23
47 29 0.45
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48
Consensus pattern (45 bp):
CATTCTTTCATACCAATTATGCATTGTTTACATTTTTCTCTATGA
Found at i:4057134 original size:46 final size:46
Alignment explanation
Indices: 4057078--4057474 Score: 569
Period size: 46 Copynumber: 8.6 Consensus size: 46
4057068 TTATTGATTA
* *
4057078 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
4057124 ATTACATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * * *
4057170 ATTTCATTTATGGCATCTTTTCATGCCTCAATGCATCCGTTCATGT
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
4057216 ATTTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 A-TTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
4057263 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
4057309 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
4057355 ATTTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGA
1 A-TTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
4057402 ATTTCAGTTATAGCATCCTTTTATGCCTTAATGCATCCGTTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
4057448 ATTTTTAGTTATGGCATCATTTCATGC
1 A-TTTCAGTTATGGCATCCTTTCATGC
4057475 ATTTCATTTA
Statistics
Matches: 315, Mismatches: 33, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
46 212 0.67
47 103 0.33
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (46 bp):
ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:4057248 original size:139 final size:139
Alignment explanation
Indices: 4057085--4057474 Score: 609
Period size: 139 Copynumber: 2.8 Consensus size: 139
4057075 TTAATTTCAT
* *
4057085 TTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTACATTTATGGCATCCTTTCATGC
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGC
* * * *
4057150 CTTAATGCATCATTTCATGCATTTCATTTATGGCATCTTTTCATGCCTCAATGCATCCGTTCATG
66 CTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCATTTCATGCCTCAATGCATCAGTTCATG
*
4057215 TATTTTTAA
131 CATTTTTAA
4057224 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGC
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGC
* * *
4057289 CTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
66 CTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCATTTCATGCCTCAATGCATCAGTTCATG
*
4057354 CATTTTTAG
131 CATTTTTAA
* * * * *
4057363 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGAATTTCAGTTATAGCATCCTTTTATGC
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGC
* *
4057428 CTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGC
66 CTTAATGCATCCTTTCATGCA-TTTCAGTTATGGCATCATTTCATGC
4057475 ATTTCATTTA
Statistics
Matches: 232, Mismatches: 18, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
139 209 0.90
140 23 0.10
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (139 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGC
CTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCATTTCATGCCTCAATGCATCAGTTCATG
CATTTTTAA
Found at i:4057266 original size:93 final size:92
Alignment explanation
Indices: 4057078--4057474 Score: 578
Period size: 93 Copynumber: 4.3 Consensus size: 92
4057068 TTATTGATTA
* *
4057078 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTACATTTATGGCATCCT
1 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCT
4057143 TTCATGCCTTAATGCATCATTTCATGC
66 TTCATGCCTTAATGCATCATTTCATGC
* * * * * *
4057170 ATTTCATTTATGGCATCTTTTCATGCCTCAATGCATCCGTTCATGTATTTTTAATTATGGCATCC
1 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCA-TTTCAGTTATGGCATCC
*
4057235 TTTCATGCCTTAATGCATCCTTTCATGC
65 TTTCATGCCTTAATGCATCATTTCATGC
*
4057263 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCT
1 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCT
4057328 TTCATGCCTTAATGCATCATTTCATGC
66 TTCATGCCTTAATGCATCATTTCATGC
* * * * * *
4057355 ATTTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGAATTTCAGTTATAGCATCC
1 A-TTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCC
* **
4057420 TTTTATGCCTTAATGCATCCGTTCATGC
65 TTTCATGCCTTAATGCATCATTTCATGC
* *
4057448 ATTTTTAGTTATGGCATCATTTCATGC
1 A-TTTCATTTATGGCATCATTTCATGC
4057475 ATTTCATTTA
Statistics
Matches: 278, Mismatches: 25, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
92 86 0.31
93 192 0.69
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (92 bp):
ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCT
TTCATGCCTTAATGCATCATTTCATGC
Found at i:4057479 original size:73 final size:72
Alignment explanation
Indices: 4057388--4057546 Score: 192
Period size: 73 Copynumber: 2.2 Consensus size: 72
4057378 ATGCCTTAAT
* * * * *
4057388 GCATCCTTTCATGAATTTCAGTTATAGCATCCTTTTATGCCTTAATGCATCCGTTCATGCATTTT
1 GCATCCTTTCATGCATTTCAGTTATAGCATCCTTTCATACCTTAATGCAACAGTTCATGCA-TTT
* *
4057453 TAGTTATG
65 CAATTATG
* * * * *
4057461 GCATCATTTCATGCATTTCATTTATGGCATCCTTTCATACCTTAATTCAACATTTCATGCATTTC
1 GCATCCTTTCATGCATTTCAGTTATAGCATCCTTTCATACCTTAATGCAACAGTTCATGCATTTC
*
4057526 AATTGTG
66 AATTATG
4057533 GCATCCTTTCATGC
1 GCATCCTTTCATGC
4057547 CTTAATGTAT
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
72 21 0.29
73 51 0.71
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (72 bp):
GCATCCTTTCATGCATTTCAGTTATAGCATCCTTTCATACCTTAATGCAACAGTTCATGCATTTC
AATTATG
Found at i:4057517 original size:139 final size:134
Alignment explanation
Indices: 4057091--4057520 Score: 456
Period size: 139 Copynumber: 3.1 Consensus size: 134
4057081 TCATTTATGG
*
4057091 CATCATTTCATGCCTTAATGCATCCTTTCATGCATTACATTTATGGCATCCTTTCATGCCTTAAT
1 CATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
* * * * *
4057156 GCATCATTTCATGCATTTCATTTATGGCATCTTTTCATGC-CTCA-ATGCATCCGTTCATGTATT
66 GCATCCTTTCATGCATTTCAGTTATGGCATCATTTCATGCTTTCATATGCATCCTTTCA--TA--
*
4057219 TTTAATTAT
127 CTTAA-TAT
*
4057228 GGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTA
1 --CATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTA
* * *
4057293 ATGCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTT-A-ATGCATCATTTCATGCA
64 ATGCATCCTTTCATGCATTTCAGTTATGGCATCATTTCATGCTTTCATATGCATCCTTTCAT--A
* *
4057356 TTTTTAGTTAT
127 --CTTA-ATAT
* * * * *
4057367 GACATCCTTTCATGCCTTAATGCATCCTTTCATGAATTTCAGTTATAGCATCCTTTTATGCCTTA
1 --CATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTA
* *
4057432 ATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCATTTCATTTATGGCATCCTTTC
64 ATGCATCCTTTCATGCA-TTTCAGTTATGGCATCATTTCATGC-TTTCA--TAT-GCATCCTTTC
4057497 ATACCTTAAT-T
124 ATA-CTTAATAT
*
4057508 CAACATTTCATGC
1 CATCATTTCATGC
4057521 ATTTCAATTG
Statistics
Matches: 256, Mismatches: 24, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
137 1 0.00
139 209 0.82
140 24 0.09
141 3 0.01
142 2 0.01
143 3 0.01
144 1 0.00
145 2 0.01
146 11 0.04
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (134 bp):
CATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
GCATCCTTTCATGCATTTCAGTTATGGCATCATTTCATGCTTTCATATGCATCCTTTCATACTTA
ATAT
Found at i:4057535 original size:46 final size:46
Alignment explanation
Indices: 4057465--4057552 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
4057455 GTTATGGCAT
*
4057465 CATTTCATGCATTTCATTTATGGCATCCTTTCATACCTTAATTCAA
1 CATTTCATGCATTTCAATTATGGCATCCTTTCATACCTTAATTCAA
* *
4057511 CATTTCATGCATTTCAATTGTGGCATCCTTTCATGCCTTAAT
1 CATTTCATGCATTTCAATTATGGCATCCTTTCATACCTTAAT
4057553 GTATTCGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (46 bp):
CATTTCATGCATTTCAATTATGGCATCCTTTCATACCTTAATTCAA
Found at i:4058180 original size:95 final size:95
Alignment explanation
Indices: 4057981--4058164 Score: 214
Period size: 96 Copynumber: 2.0 Consensus size: 95
4057971 ACTACCCTGG
* * * *
4057981 TATTGATACTTCTATACTATGGTACAGATACCCTCCTTTCAATATCGATACCATTTCTATATTTT
1 TATTGATACTACTATACTATGGTACAGATACCCTCCTTTCAATATCGATACCATTTCGACATTCT
* * *
4058046 GTGTTTCATGGTATCGATACCCTTCTCTCGG
66 GTGATCCATGGTATCGATA-CCTTCTCTCGA
* * * * * *
4058077 TATCGATACTACTCTACTATGGTACCGATACTC-CCTTTTAGTATCGATACCATTT-GACATTCT
1 TATTGATACTACTATACTATGGTACAGATACCCTCCTTTCAATATCGATACCATTTCGACATTCT
4058140 G-GATCCATGGTATCGATA-CTTCTCT
66 GTGATCCATGGTATCGATACCTTCTCT
4058165 TTGTTAATAT
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
91 7 0.09
93 15 0.20
94 6 0.08
95 20 0.26
96 28 0.37
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (95 bp):
TATTGATACTACTATACTATGGTACAGATACCCTCCTTTCAATATCGATACCATTTCGACATTCT
GTGATCCATGGTATCGATACCTTCTCTCGA
Found at i:4062227 original size:44 final size:47
Alignment explanation
Indices: 4062157--4062270 Score: 137
Period size: 46 Copynumber: 2.5 Consensus size: 47
4062147 TCATTTGGGG
* * * * *
4062157 CATCCTTTCATGCCCATTAAGTATTGTT-TACATTTT-TCTTTATGA
1 CATCCTTTCATACCAATTATGCATTGTTGTACATTTTATCTATATGA
4062202 CATCCATTT-ATA-CAATTATGCATTGTTGTACATTTTATCTATATGA
1 CATCC-TTTCATACCAATTATGCATTGTTGTACATTTTATCTATATGA
*
4062248 CATCCTTTCATACCACTTATGCA
1 CATCCTTTCATACCAATTATGCA
4062271 CCGTTTCTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
44 12 0.21
45 18 0.31
46 19 0.33
47 9 0.16
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (47 bp):
CATCCTTTCATACCAATTATGCATTGTTGTACATTTTATCTATATGA
Found at i:4062709 original size:12 final size:12
Alignment explanation
Indices: 4062683--4062717 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
4062673 AACATACCTT
4062683 TTTTTCTTATACA
1 TTTTTCTT-TACA
*
4062696 TTTTTCTTTTCA
1 TTTTTCTTTACA
4062708 TTTTTCTTTA
1 TTTTTCTTTA
4062718 GTAATTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTCTTTACA
Found at i:4062773 original size:20 final size:20
Alignment explanation
Indices: 4062750--4062914 Score: 78
Period size: 20 Copynumber: 7.3 Consensus size: 20
4062740 TATGGCATAT
4062750 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGCATCC
* *
4062770 TTTCATGGATTTCATTTATGGCATCC
1 TTTCAT-G----CCTTAAT-GCATCC
*
4062796 TTTCATTCCTTAATGCATCC
1 TTTCATGCCTTAATGCATCC
* *
4062816 TTTTATGCATTTCATTTATGGCATCC
1 TTTCATGC----C-TTAAT-GCATCC
*
4062842 TTTCATGCCTTAATGCATCA
1 TTTCATGCCTTAATGCATCC
* **
4062862 TTTCCTGCATTTCAGTTACGGCATCC
1 TTTCATGC----C--TTAATGCATCC
4062888 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGCATCC
*
4062908 GTTCATG
1 TTTCATG
4062915 TATTTTTTGT
Statistics
Matches: 108, Mismatches: 19, Indels: 36
0.66 0.12 0.22
Matches are distributed among these distances:
20 45 0.42
21 10 0.09
22 2 0.02
24 2 0.02
25 9 0.08
26 40 0.37
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.43
Consensus pattern (20 bp):
TTTCATGCCTTAATGCATCC
Found at i:4062784 original size:46 final size:46
Alignment explanation
Indices: 4062732--4062940 Score: 283
Period size: 46 Copynumber: 4.5 Consensus size: 46
4062722 TTACTCGTTA
** *
4062732 ATTTCATTTATGGCATATTTTCATGCCTTAATGCATCCTTTCATGG
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
4062778 ATTTCATTTATGGCATCCTTTCATTCCTTAATGCATCCTTTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
4062824 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCCTGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
4062870 ATTTCAGTTACGGCATCCTTTCATGCCTTAATGCATCCGTTCATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
** *
4062916 ATTTTTTGTTATGGCATCCTATCAT
1 ATTTCAT-TTATGGCATCCTTTCAT
4062941 CATTTCATGC
Statistics
Matches: 142, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 127 0.89
47 15 0.11
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:4062849 original size:26 final size:26
Alignment explanation
Indices: 4062764--4062895 Score: 99
Period size: 26 Copynumber: 5.5 Consensus size: 26
4062754 ATGCCTTAAT
*
4062764 GCATCCTTTCATGGATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
* *
4062790 GCATCC-TT--T-CA-TTCCTTAAT-
1 GCATCCTTTCATGCATTTCATTTATG
*
4062810 GCATCCTTTTATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
*
4062836 GCATCCTTTCATGC----C-TTAAT-
1 GCATCCTTTCATGCATTTCATTTATG
* * * *
4062856 GCATCATTTCCTGCATTTCAGTTACG
1 GCATCCTTTCATGCATTTCATTTATG
4062882 GCATCCTTTCATGC
1 GCATCCTTTCATGC
4062896 CTTAATGCAT
Statistics
Matches: 80, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
20 18 0.22
21 13 0.16
22 2 0.03
23 2 0.03
24 3 0.04
25 11 0.14
26 31 0.39
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.43
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTCATTTATG
Found at i:4062966 original size:25 final size:26
Alignment explanation
Indices: 4062938--4062998 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
4062928 GGCATCCTAT
* *
4062938 CATCATTTCATGCATTTCATTTAT-G
1 CATCCTTTCATGCATTTCAGTTATGG
*
4062963 CATCCTTTCATTCATTTCAGTTATGG
1 CATCCTTTCATGCATTTCAGTTATGG
4062989 CATCCTTTCA
1 CATCCTTTCA
4062999 CGCTCTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 21 0.66
26 11 0.34
ACGTcount: A:0.21, C:0.25, G:0.08, T:0.46
Consensus pattern (26 bp):
CATCCTTTCATGCATTTCAGTTATGG
Found at i:4067942 original size:2 final size:2
Alignment explanation
Indices: 4067935--4067969 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4067925 TCAATCTACA
*
4067935 AT AT AT AT AT AT AT AA 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
4067970 ATTTACGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4068169 original size:13 final size:13
Alignment explanation
Indices: 4068134--4068177 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
4068124 GCAATGAGCT
* *
4068134 TCATAAATGCGCT
1 TCATAAATGTGCA
* *
4068147 TTATAAATGTGTA
1 TCATAAATGTGCA
4068160 TCATAAATGTGCA
1 TCATAAATGTGCA
4068173 TCATA
1 TCATA
4068178 GATTTATGAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (13 bp):
TCATAAATGTGCA
Found at i:4069112 original size:24 final size:23
Alignment explanation
Indices: 4069085--4069211 Score: 85
Period size: 24 Copynumber: 5.3 Consensus size: 23
4069075 TATATCAAAA
*
4069085 ATCAAATAATAATTCAAGTCAAGT
1 ATCATATAA-AATTCAAGTCAAGT
* *
4069109 ATCATATAAAAATCTAGGTCAAGT
1 ATCATATAAAATTC-AAGTCAAGT
* *
4069133 ATCATATCAGAATCCAAGTCAAGT
1 ATCATAT-AAAATTCAAGTCAAGT
* * * *
4069157 ATCAGATCAGAATCCATGTCATA-T
1 ATCATAT-AAAATTCAAGTCA-AGT
* * *
4069181 ATCATATCAGAATCCATGTCAAGT
1 ATCATAT-AAAATTCAAGTCAAGT
4069205 ATCATAT
1 ATCATAT
4069212 TAGAAATCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
23 5 0.06
24 79 0.89
25 5 0.06
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (23 bp):
ATCATATAAAATTCAAGTCAAGT
Found at i:4069216 original size:24 final size:24
Alignment explanation
Indices: 4069102--4069216 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
4069092 AATAATTCAA
* * * *
4069102 GTCAAGTATCATATAAAAATCTAG
1 GTCAAGTATCATATCAGAATCCAT
*
4069126 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
*
4069150 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
4069174 GTCATA-TATCATATCAGAATCCAT
1 GTCA-AGTATCATATCAGAATCCAT
*
4069198 GTCAAGTATCATATTAGAA
1 GTCAAGTATCATATCAGAA
4069217 ATCAAATCGA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:4074039 original size:35 final size:35
Alignment explanation
Indices: 4073896--4074031 Score: 236
Period size: 35 Copynumber: 3.9 Consensus size: 35
4073886 CATCAGGTCC
* *
4073896 AGTAAGGCCCTGAGCACACAGTCGAGGAGACGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
4073931 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
*
4073966 AGTAAGGCCCTGAGCACATAGCCGAGGAGCCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
*
4074001 AGTAAGGCCCTGAGCAAACAGCCGAGGAGCC
1 AGTAAGGCCCTGAGCACACAGCCGAGGAGCC
4074032 TCCAAGTATT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 96 1.00
ACGTcount: A:0.30, C:0.26, G:0.34, T:0.10
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
Found at i:4074158 original size:24 final size:23
Alignment explanation
Indices: 4074119--4074243 Score: 74
Period size: 24 Copynumber: 5.2 Consensus size: 23
4074109 AATAATTCAC
* *
4074119 GTCAAGTATAATATCAAAAT-ATA
1 GTCAAGTATCAGATCAAAATCA-A
*
4074142 GTTCAAGTATCAGATCAGAATCCAA
1 G-TCAAGTATCAGATCAAAAT-CAA
* * *
4074167 GTCAAGTATCAGATTAGAATCCAT
1 GTCAAGTATCAGATCAAAAT-CAA
* * *
4074191 GT-AATATATCAGATCAGAATCCAT
1 GTCAA-GTATCAGATCAAAAT-CAA
*
4074215 GTCAAGTATTAGATCAGAAATCAA
1 GTCAAGTATCAGATCA-AAATCAA
*
4074239 ATCAA
1 GTCAA
4074244 AAATCAGGTA
Statistics
Matches: 84, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
23 3 0.04
24 73 0.87
25 7 0.08
26 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (23 bp):
GTCAAGTATCAGATCAAAATCAA
Found at i:4074250 original size:48 final size:48
Alignment explanation
Indices: 4074150--4074250 Score: 116
Period size: 48 Copynumber: 2.1 Consensus size: 48
4074140 TAGTTCAAGT
* * * *
4074150 ATCAGATCAGAATCCAAGTCAAGTATCAGATTAGAATCCATGTAATAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCAATGCAATAA
* *
4074198 ATCAGATCAGAATCCATGTCAAGTATTAGATCAGAAATCAAAT-CAA-AA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATC-AATGCAATAA
4074246 ATCAG
1 ATCAG
4074251 GTAAACTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 37 0.82
49 6 0.13
50 2 0.04
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.25
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCAATGCAATAA
Found at i:4079152 original size:24 final size:24
Alignment explanation
Indices: 4079089--4079203 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
4079079 AATAATTCAC
* *
4079089 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAT
*
4079113 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
* *
4079137 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCATATCAGAATCCAT
*
4079161 GTC-AGATATCATATCAGAATCTAT
1 GTCAAG-TATCATATCAGAATCCAT
*
4079185 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCATATCAGAA
4079204 ATCAAATCGA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.02
24 78 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:4080220 original size:26 final size:26
Alignment explanation
Indices: 4080191--4080243 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
4080181 TTTATTCTAT
*
4080191 TCATTTCAGAGCTCGAG-GATATCCAA
1 TCATTCCAGAGCTCG-GTGATATCCAA
* *
4080217 TCATTCCTGAGCTTGGTGATATCCAA
1 TCATTCCAGAGCTCGGTGATATCCAA
4080243 T
1 T
4080244 TTATTTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (26 bp):
TCATTCCAGAGCTCGGTGATATCCAA
Found at i:4088053 original size:12 final size:12
Alignment explanation
Indices: 4088028--4088097 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
4088018 ATGGAGATAT
* *
4088028 CAGAAATCAAAA
1 CAGAATTCAGAA
4088040 CAGAATTCAGAA
1 CAGAATTCAGAA
4088052 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
4088064 CAAAATCCAGAT
1 CAGAATTCAGAA
*
4088076 CAGAAATCAGAA
1 CAGAATTCAGAA
4088088 CAGAATTCAG
1 CAGAATTCAG
4088098 GTCATGTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:4088108 original size:24 final size:24
Alignment explanation
Indices: 4088026--4088120 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
4088016 AAATGGAGAT
* *
4088026 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* * *
4088050 AACAGATATCAGAACAAAATCCAG
1 ATCAGATATCAGAACAGAATTCAG
*
4088074 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* *
4088098 GTCATG-TATCAGAACATAATTCA
1 ATCA-GATATCAGAACAGAATTCA
4088121 AGTCGGAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
24 57 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGATATCAGAACAGAATTCAG
Found at i:4090485 original size:13 final size:13
Alignment explanation
Indices: 4090467--4090497 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4090457 GTCGGTCAAT
*
4090467 GGTCAACGGGTCG
1 GGTCAACGGGTAG
4090480 GGTCAACGGGTAG
1 GGTCAACGGGTAG
4090493 GGTCA
1 GGTCA
4090498 GGTCAACGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTAG
Found at i:4090501 original size:18 final size:18
Alignment explanation
Indices: 4090474--4090524 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
4090464 AATGGTCAAC
*
4090474 GGGTCGGGTCAACGGGTA
1 GGGTCAGGTCAACGGGTA
*
4090492 GGGTCAGGTCAACGGGTC
1 GGGTCAGGTCAACGGGTA
*
4090510 GGGTCAAGTCAACGG
1 GGGTCAGGTCAACGG
4090525 ATCGGGTCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.45, T:0.16
Consensus pattern (18 bp):
GGGTCAGGTCAACGGGTA
Found at i:4090529 original size:18 final size:18
Alignment explanation
Indices: 4090481--4090532 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
4090471 AACGGGTCGG
* *
4090481 GTCAACGGGTAGGGTCAG
1 GTCAACGGGTCGGGTCAA
4090499 GTCAACGGGTCGGGTCAA
1 GTCAACGGGTCGGGTCAA
*
4090517 GTCAACGGATCGGGTC
1 GTCAACGGGTCGGGTC
4090533 GGATTATGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.17
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCAA
Found at i:4092627 original size:24 final size:24
Alignment explanation
Indices: 4092600--4092680 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
4092590 AATCAAAAAT
* *
4092600 AGAATTCAGAACAGATATCATAAC
1 AGAATTCAGATCAGATATCAGAAC
* *
4092624 AGAATCCAGATCAGAAATCAGAAC
1 AGAATTCAGATCAGATATCAGAAC
*
4092648 AGAATTCAGGTCATG-TATCAGAAC
1 AGAATTCAGATCA-GATATCAGAAC
4092672 AGAATTCAG
1 AGAATTCAG
4092681 GTCGGAAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
24 48 0.98
25 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (24 bp):
AGAATTCAGATCAGATATCAGAAC
Found at i:4092653 original size:48 final size:48
Alignment explanation
Indices: 4092600--4092693 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
4092590 AATCAAAAAT
*
4092600 AGAATTCAGAACA-GATATCATAACAGAATCCAGATCAGAAATCAGAAC
1 AGAATTCAGAACATG-TATCAGAACAGAATCCAGATCAGAAATCAGAAC
** * * *
4092648 AGAATTCAGGTCATGTATCAGAACAGAATTCAGGTCGGAAATCAGA
1 AGAATTCAGAACATGTATCAGAACAGAATCCAGATCAGAAATCAGA
4092694 TAAAATATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (48 bp):
AGAATTCAGAACATGTATCAGAACAGAATCCAGATCAGAAATCAGAAC
Found at i:4092680 original size:12 final size:12
Alignment explanation
Indices: 4092600--4092680 Score: 67
Period size: 12 Copynumber: 6.8 Consensus size: 12
4092590 AATCAAAAAT
4092600 AGAATTCAGAAC
1 AGAATTCAGAAC
*
4092612 AG-ATATCATAAC
1 AGAAT-TCAGAAC
* *
4092624 AGAATCCAGATC
1 AGAATTCAGAAC
*
4092636 AGAAATCAGAAC
1 AGAATTCAGAAC
**
4092648 AGAATTCAGGTC
1 AGAATTCAGAAC
*
4092660 ATGTA-TCAGAAC
1 A-GAATTCAGAAC
4092672 AGAATTCAG
1 AGAATTCAG
4092681 GTCGGAAATC
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
11 4 0.08
12 43 0.84
13 4 0.08
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (12 bp):
AGAATTCAGAAC
Found at i:4092691 original size:24 final size:24
Alignment explanation
Indices: 4092600--4092693 Score: 100
Period size: 24 Copynumber: 3.9 Consensus size: 24
4092590 AATCAAAAAT
** * *
4092600 AGAATTCAGAACAGATATCATAAC
1 AGAATTCAGGTCAGAAATCAGAAC
* *
4092624 AGAATCCAGATCAGAAATCAGAAC
1 AGAATTCAGGTCAGAAATCAGAAC
*
4092648 AGAATTCAGGTCATG-TATCAGAAC
1 AGAATTCAGGTCA-GAAATCAGAAC
*
4092672 AGAATTCAGGTCGGAAATCAGA
1 AGAATTCAGGTCAGAAATCAGA
4092694 TAAAATATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.02
24 57 0.97
25 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (24 bp):
AGAATTCAGGTCAGAAATCAGAAC
Found at i:4098227 original size:19 final size:17
Alignment explanation
Indices: 4098190--4098250 Score: 58
Period size: 16 Copynumber: 3.7 Consensus size: 17
4098180 TAGTTATATG
4098190 AATATAAATAAATTAAA
1 AATATAAATAAATTAAA
*
4098207 AATATTAAAT-AACTATAA
1 AATA-TAAATAAATTA-AA
4098225 AA-ATAAAT-AATT-AA
1 AATATAAATAAATTAAA
*
4098239 AAGATAAATAAA
1 AATATAAATAAA
4098251 AATGATTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 4 0.11
15 6 0.16
16 10 0.26
17 9 0.24
18 9 0.24
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
AATATAAATAAATTAAA
Found at i:4098997 original size:51 final size:51
Alignment explanation
Indices: 4098950--4099134 Score: 261
Period size: 50 Copynumber: 3.7 Consensus size: 51
4098940 CATACATTCA
* * *
4098950 GTGTGAGTATGTGTTAAGTGCTATA-TTTTTTATTTTATTTACTTACATC-
1 GTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACATCG
* *
4098999 GTAGTAAGTATCTGTTAAGTGCTACACTTTTTTATTTTATTCACTTGCATCG
1 GT-GTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACATCG
*
4099051 GTGT-AGTATGTGTTAAGTGCTACACTTTTTTGTTTTATTCACTTACA-CTG
1 GTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACATC-G
*
4099101 GTGTAAGTATGTGTTAAGTGCTACATTTTTTTAT
1 GTGTAAGTATGTGTTAAGTGCTACACTTTTTTAT
4099135 GGTATGAATT
Statistics
Matches: 121, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
49 3 0.02
50 65 0.54
51 51 0.42
52 2 0.02
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.49
Consensus pattern (51 bp):
GTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACATCG
Found at i:4099131 original size:101 final size:101
Alignment explanation
Indices: 4098950--4099134 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 101
4098940 CATACATTCA
* *
4098950 GTGTGAGTATGTGTTAAGTGCTATATTTTTTATTTTATTTACTTACATCGTAGTAAGTATCTGTT
1 GTGTGAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCACTTACATCGTAGTAAGTATCTGTT
4099015 AAGTGCTACACTTTTTTATTTTATTCACTTGCATCG
66 AAGTGCTACACTTTTTTATTTTATTCACTTGCATCG
* * *
4099051 GTGT-AGTATGTGTTAAGTGCTACACTTTTTTGTTTTATTCACTTACACTGGT-GTAAGTATGTG
1 GTGTGAGTATGTGTTAAGTGCTACA-TTTTTTATTTTATTCACTTACA-TCGTAGTAAGTATCTG
*
4099114 TTAAGTGCTACATTTTTTTAT
64 TTAAGTGCTACACTTTTTTAT
4099135 GGTATGAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
100 19 0.25
101 54 0.71
102 3 0.04
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.49
Consensus pattern (101 bp):
GTGTGAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCACTTACATCGTAGTAAGTATCTGTT
AAGTGCTACACTTTTTTATTTTATTCACTTGCATCG
Found at i:4100201 original size:76 final size:75
Alignment explanation
Indices: 4100115--4100335 Score: 198
Period size: 76 Copynumber: 3.0 Consensus size: 75
4100105 AATTTTATTA
* *
4100115 TCACCCAATTCTTATTTATAATAATGTTATTCATCCTCCAAATATTGAATTTTGTTATTTATCAT
1 TCACCAAATTCTTATTTATAATAATGTTATTCATCATCCAAATATTGAATTTTGTTATTTATCAT
4100180 TATTTATTCT
66 TATTTATTCT
* * * *
4100190 TCTTCCAAATTCTTATTTATGAAT-A-G-T-TTCGA--AT---AAT-TT-TATTTATG-AAATTA
1 TC-ACCAAATTCTTATTTAT-AATAATGTTATTC-ATCATCCAAATATTGAATTT-TGTTATTTA
* * *
4100243 ACATAATTTTATT-A
62 TCATTA-TTTATTCT
* *
4100257 TCACCCAATTCTTATTTATAATAATGTTATTCATCTTCCAAATATTTGAATTTTGTTATTTATCA
1 TCACCAAATTCTTATTTATAATAATGTTATTCATCATCCAAATA-TTGAATTTTGTTATTTATCA
4100322 TTATTTATTCT
65 TTATTTATTCT
4100333 TCA
1 TCA
4100336 TTCTTTTTCT
Statistics
Matches: 109, Mismatches: 18, Indels: 37
0.66 0.11 0.23
Matches are distributed among these distances:
65 3 0.03
66 16 0.15
67 15 0.14
68 12 0.11
69 6 0.06
70 1 0.01
72 1 0.01
73 6 0.06
74 2 0.02
75 13 0.12
76 31 0.28
77 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.51
Consensus pattern (75 bp):
TCACCAAATTCTTATTTATAATAATGTTATTCATCATCCAAATATTGAATTTTGTTATTTATCAT
TATTTATTCT
Found at i:4101267 original size:3 final size:3
Alignment explanation
Indices: 4101259--4101296 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
4101249 TTATTTTAAT
*
4101259 TTA TTA TTA TTA TTA TTA TT- TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4101297 CAAATTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4101283 original size:20 final size:20
Alignment explanation
Indices: 4101244--4101296 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
4101234 CTTTTCTATA
*
4101244 TAATTTTATT-TTAATTTAT
1 TAATATTATTATTAATTTAT
* *
4101263 TATTATTATTATTATTTTAT
1 TAATATTATTATTAATTTAT
4101283 TAATATTATTATTA
1 TAATATTATTATTA
4101297 CAAATTTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TAATATTATTATTAATTTAT
Found at i:4101284 original size:17 final size:17
Alignment explanation
Indices: 4101262--4101295 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4101252 TTTTAATTTA
*
4101262 TTATTATTATTATTATT
1 TTATTAATATTATTATT
4101279 TTATTAATATTATTATT
1 TTATTAATATTATTATT
4101296 ACAAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTAATATTATTATT
Found at i:4102644 original size:27 final size:28
Alignment explanation
Indices: 4102609--4102700 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 28
4102599 TATTTGTTCA
* *
4102609 TTAGTCCCT-GATTTTTCTGTTTTTTATT
1 TTAGTCCCTAAATTTTTC-ATTTTTTATT
4102637 TTAG-CCCTAAATTTTTCATTTTTTA-T
1 TTAGTCCCTAAATTTTTCATTTTTTATT
* *
4102663 TTAGATCCTTTAA-TTTTCTATTTTTTTCATT
1 TTAG-TCCCTAAATTTTTC-A-TTTTTT-ATT
4102694 TTAGTCC
1 TTAGTCC
4102701 TTTAAACTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
26 5 0.09
27 16 0.30
28 17 0.32
29 6 0.11
30 4 0.08
31 5 0.09
ACGTcount: A:0.17, C:0.15, G:0.07, T:0.61
Consensus pattern (28 bp):
TTAGTCCCTAAATTTTTCATTTTTTATT
Found at i:4106231 original size:22 final size:20
Alignment explanation
Indices: 4106210--4106248 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4106200 ATTCCCTCTT
*
4106210 TTTGAGACCTTGAAACATTC
1 TTTGAGACATTGAAACATTC
*
4106230 TTTGTGACATTGAAACATT
1 TTTGAGACATTGAAACATT
4106249 GCATTTATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTGAGACATTGAAACATTC
Found at i:4106869 original size:11 final size:11
Alignment explanation
Indices: 4106824--4106871 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
4106814 TGCAGAGTAC
**
4106824 AAAGAAAAATC
1 AAAGAAAAAGA
4106835 AAAGAAAAATAGCA
1 AAAG-AAAA-AG-A
4106849 AAAGAAAAAGA
1 AAAGAAAAAGA
4106860 AAAGAAAAAGA
1 AAAGAAAAAGA
4106871 A
1 A
4106872 GACAAAAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 17 0.53
12 6 0.19
13 5 0.16
14 4 0.12
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:4107750 original size:22 final size:21
Alignment explanation
Indices: 4107725--4107790 Score: 60
Period size: 24 Copynumber: 2.9 Consensus size: 21
4107715 TGAAAGGAGC
4107725 AATATTTTCAAACTTTTGATT
1 AATATTTTCAAACTTTTGATT
*
4107746 AAATATTTTTCAAAACTCTTTTAATT
1 -AATA-TTTTC-AAA--CTTTTGATT
* *
4107772 GATATTTTCATACTTTTGA
1 AATATTTTCAAACTTTTGA
4107791 AAATACAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
21 6 0.17
22 4 0.11
23 7 0.19
24 8 0.22
25 3 0.08
26 8 0.22
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.52
Consensus pattern (21 bp):
AATATTTTCAAACTTTTGATT
Found at i:4108680 original size:36 final size:34
Alignment explanation
Indices: 4108640--4108741 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 34
4108630 TGTTTCTTTC
4108640 AAAACAAACTTTGTCTCGCTTGAGACAATTTCTCTA
1 AAAACAAA-TTTGTCTCG-TTGAGACAATTTCTCTA
* * * *
4108676 AAAACAATTTTTGTCTCGTTTAAAACAATTTCTCTT
1 AAAACAA-ATTTGTCTCG-TTGAGACAATTTCTCTA
4108712 AAAACAAATGTTGTCTCAGTTGAGACAATT
1 AAAACAAAT-TTGTCTC-GTTGAGACAATT
4108742 CTCCAAATTA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
35 1 0.02
36 53 0.96
37 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (34 bp):
AAAACAAATTTGTCTCGTTGAGACAATTTCTCTA
Found at i:4108919 original size:30 final size:29
Alignment explanation
Indices: 4108845--4108928 Score: 69
Period size: 30 Copynumber: 2.8 Consensus size: 29
4108835 GTGAAAAAAT
* * * * *
4108845 CTTTGAGTCCTTTCTTTTCAAACACCTAT
1 CTTTGAGTCATTTCTATTAAAACACCCAC
* * *
4108874 CTTTGAGTTAATTTCTCTTGAAACACCCAC
1 CTTTGAG-TCATTTCTATTAAAACACCCAC
*
4108904 CTTTGAGATCGTTTCTATTAAAACA
1 CTTTGAG-TCATTTCTATTAAAACA
4108929 AATATTATTT
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 7 0.16
30 36 0.84
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (29 bp):
CTTTGAGTCATTTCTATTAAAACACCCAC
Found at i:4109276 original size:64 final size:64
Alignment explanation
Indices: 4109189--4109328 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 64
4109179 ATTTTCTGAA
*
4109189 AAACAAAGTTTTGTCTATCTTGAGACAATTTCTTTT-GAAAAATCATTGAATATGTTTCTTTGGG
1 AAACAAAATTTTGTCTATCTTGAGACAATTTCTTTTAGAAAAATCATTGAATATGTTTCTTT-GG
* * * * * * * *
4109253 AAATAAAATTTTGTCTCTTTTGAGATAGTTTCTTTTAAGAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAACAAAATTTTGTCTATCTTGAGACAATTTCTTTT-AGAAAAATCATTGAATATGTTTCTTTGG
4109318 AAACAAAATTT
1 AAACAAAATTT
4109329 ACCATCTTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
64 30 0.47
65 12 0.19
66 22 0.34
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.44
Consensus pattern (64 bp):
AAACAAAATTTTGTCTATCTTGAGACAATTTCTTTTAGAAAAATCATTGAATATGTTTCTTTGG
Found at i:4109817 original size:43 final size:40
Alignment explanation
Indices: 4109706--4109822 Score: 101
Period size: 43 Copynumber: 2.9 Consensus size: 40
4109696 AAGATGGCCA
* *
4109706 AGAACTCTTCCTCATGTATGAGCAGTGTCATCCCTCGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
** * * * *
4109746 AGATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAGACGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC-T---CGACC
* *
4109789 CGAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC
4109823 CAACAACCAA
Statistics
Matches: 56, Mismatches: 16, Indels: 6
0.72 0.21 0.08
Matches are distributed among these distances:
39 3 0.05
40 23 0.41
43 27 0.48
44 3 0.05
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
Found at i:4109997 original size:3 final size:3
Alignment explanation
Indices: 4109989--4110026 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
4109979 TTATTTTAAT
*
4109989 TTA TTA TTA TTA TTA TTA TT- TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4110027 CAAATTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4110013 original size:20 final size:20
Alignment explanation
Indices: 4109974--4110026 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
4109964 TTTTTCTATA
*
4109974 TAATTTTATT-TTAATTTAT
1 TAATATTATTATTAATTTAT
* *
4109993 TATTATTATTATTATTTTAT
1 TAATATTATTATTAATTTAT
4110013 TAATATTATTATTA
1 TAATATTATTATTA
4110027 CAAATTTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TAATATTATTATTAATTTAT
Found at i:4110014 original size:17 final size:17
Alignment explanation
Indices: 4109992--4110025 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4109982 TTTTAATTTA
*
4109992 TTATTATTATTATTATT
1 TTATTAATATTATTATT
4110009 TTATTAATATTATTATT
1 TTATTAATATTATTATT
4110026 ACAAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTAATATTATTATT
Found at i:4117274 original size:15 final size:15
Alignment explanation
Indices: 4117254--4117307 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
4117244 CTCGCTTGAG
*
4117254 ACAATTTCTCTAAAA
1 ACAATTTCTCTTAAA
4117269 ACAATTTTGTCTCGTTTAAA
1 ACAA--TT-TCTC--TTAAA
4117289 ACAATTTCTCTTAAA
1 ACAATTTCTCTTAAA
4117304 ACAA
1 ACAA
4117308 ATGTTGTCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
15 13 0.39
17 6 0.18
18 6 0.18
20 8 0.24
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (15 bp):
ACAATTTCTCTTAAA
Found at i:4117333 original size:35 final size:35
Alignment explanation
Indices: 4117230--4117330 Score: 123
Period size: 35 Copynumber: 2.8 Consensus size: 35
4117220 TGTTTCTTTC
4117230 AAAACAAACTTTGTCTCGCTTGAGACAATTTCTCTA
1 AAAACAAA-TTTGTCTCGCTTGAGACAATTTCTCTA
* * * * *
4117266 AAAACAATTTTGTCTCGTTTAAAACAATTTCTCTT
1 AAAACAAATTTGTCTCGCTTGAGACAATTTCTCTA
4117301 AAAACAAATGTTGTCTCAG-TTGAGACAATT
1 AAAACAAAT-TTGTCTC-GCTTGAGACAATT
4117331 CTCCAAATTA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 31 0.56
36 23 0.42
37 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (35 bp):
AAAACAAATTTGTCTCGCTTGAGACAATTTCTCTA
Found at i:4117508 original size:30 final size:29
Alignment explanation
Indices: 4117434--4117517 Score: 69
Period size: 30 Copynumber: 2.8 Consensus size: 29
4117424 GTGAAAAAAT
* * * * *
4117434 CTTTGAGTCCTTTCTTTTCAAACACCTAT
1 CTTTGAGTCATTTCTATTAAAACACCCAC
* * *
4117463 CTTTGAGTTAATTTCTCTTGAAACACCCAC
1 CTTTGAG-TCATTTCTATTAAAACACCCAC
*
4117493 CTTTGAGATCGTTTCTATTAAAACA
1 CTTTGAG-TCATTTCTATTAAAACA
4117518 AATATTATTT
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 7 0.16
30 36 0.84
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (29 bp):
CTTTGAGTCATTTCTATTAAAACACCCAC
Found at i:4117574 original size:31 final size:31
Alignment explanation
Indices: 4117539--4117599 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
4117529 CCTTGAGGCA
*
4117539 GTTTCTCTAGAAAATCAAA-ATCTTTGAGTTT
1 GTTTCTCTAG-AAATAAAACATCTTTGAGTTT
*
4117570 GTTTCTCTTGAAATAAAACCATCTTTGAGT
1 GTTTCTCTAGAAATAAAA-CATCTTTGAGT
4117600 CGTTTCCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 9 0.35
32 10 0.38
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (31 bp):
GTTTCTCTAGAAATAAAACATCTTTGAGTTT
Found at i:4117853 original size:64 final size:64
Alignment explanation
Indices: 4117777--4117916 Score: 183
Period size: 64 Copynumber: 2.2 Consensus size: 64
4117767 AATTTTCTGA
*
4117777 AAACAAAGTTTTGTCTATCTTGAGACAATTTCTTTT-GAAAAATCATTGAATATGTTTCTTTGGG
1 AAACAAAATTTTGTCTATCTTGAGACAATTTCTTTTAGAAAAATCATTGAATATGTTTCTTT-GG
* * * * * * *
4117841 AAACAAAATTTTGTCTCTTTTGAGATAGTTTCTTTTAAGAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAACAAAATTTTGTCTATCTTGAGACAATTTCTTTT-AGAAAAATCATTGAATATGTTTCTTTGG
4117906 AAACAAAATTT
1 AAACAAAATTT
4117917 ACCATCTTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 31 0.47
65 13 0.20
66 22 0.33
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (64 bp):
AAACAAAATTTTGTCTATCTTGAGACAATTTCTTTTAGAAAAATCATTGAATATGTTTCTTTGG
Found at i:4117928 original size:64 final size:64
Alignment explanation
Indices: 4117796--4117925 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 64
4117786 TTTGTCTATC
**
4117796 TTGAGACAATTTCTTTTGAAAAATCATTGAATATGTTTCTTTGGGAAACAAAATTTTGTCTCTT
1 TTGAGACAATTTCTTTTGAAAAATCATTGAATATGTTTCTTTGGGAAACAAAATTTTACCTCTT
* * * * *
4117860 TTGAGATAGTTTCTTTTAAGAAAAATCTTTGAGTTTGTTTCTTT-GGAAACAAAA-TTTACCATC
1 TTGAGACAATTTCTTTT--GAAAAATCATTGAATATGTTTCTTTGGGAAACAAAATTTTACC-TC
4117923 TT
63 TT
4117925 T
1 T
4117926 GAGTTTGTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
64 19 0.34
65 15 0.27
66 22 0.39
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (64 bp):
TTGAGACAATTTCTTTTGAAAAATCATTGAATATGTTTCTTTGGGAAACAAAATTTTACCTCTT
Found at i:4118588 original size:3 final size:3
Alignment explanation
Indices: 4118580--4118617 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
4118570 TTATTTTAAT
*
4118580 TTA TTA TTA TTA TTA TTA TT- TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4118618 CAAATTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4118604 original size:20 final size:20
Alignment explanation
Indices: 4118565--4118617 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
4118555 TTTTTCTATA
*
4118565 TAATTTTATT-TTAATTTAT
1 TAATATTATTATTAATTTAT
* *
4118584 TATTATTATTATTATTTTAT
1 TAATATTATTATTAATTTAT
4118604 TAATATTATTATTA
1 TAATATTATTATTA
4118618 CAAATTTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TAATATTATTATTAATTTAT
Found at i:4118605 original size:17 final size:17
Alignment explanation
Indices: 4118583--4118616 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4118573 TTTTAATTTA
*
4118583 TTATTATTATTATTATT
1 TTATTAATATTATTATT
4118600 TTATTAATATTATTATT
1 TTATTAATATTATTATT
4118617 ACAAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTAATATTATTATT
Done.