Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 49 of 54
Found at i:11587619 original size:11 final size:11
Alignment explanation
Indices: 11587581--11587667 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 11
11587571 TTTGATAAAA
11587581 TATAATATTT-T
1 TATAA-ATTTAT
*
11587592 TAATAATTTTAT
1 T-ATAAATTTAT
11587604 T-TAAATTTAT
1 TATAAATTTAT
11587614 TATAAATATT-T
1 TATAAAT-TTAT
11587625 TAATAATATTTTAT
1 T-ATAA-A-TTTAT
*
11587639 AATAAATTTA-
1 TATAAATTTAT
11587649 TATAAA--TAT
1 TATAAATTTAT
*
11587658 TTTAAATTTA
1 TATAAATTTA
11587668 AAAATTTTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
8 2 0.03
9 5 0.08
10 14 0.23
11 17 0.28
12 13 0.22
13 7 0.12
14 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATAAATTTAT
Found at i:11587653 original size:35 final size:35
Alignment explanation
Indices: 11587580--11587662 Score: 111
Period size: 35 Copynumber: 2.4 Consensus size: 35
11587570 ATTTGATAAA
*
11587580 ATAT-AATATTTT--TAATAATTTTATTTAAATTT
1 ATATAAATATTTTAATAATAATTTTATATAAATTT
11587612 ATTATAAATATTTTAATAAT-ATTTTATAATAAATTT
1 A-TATAAATATTTTAATAATAATTTTAT-ATAAATTT
11587648 ATATAAATATTTTAA
1 ATATAAATATTTTAA
11587663 ATTTAAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
32 1 0.02
33 3 0.07
34 8 0.18
35 21 0.47
36 12 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
ATATAAATATTTTAATAATAATTTTATATAAATTT
Found at i:11587688 original size:18 final size:18
Alignment explanation
Indices: 11587665--11587721 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 18
11587655 TATTTTAAAT
11587665 TTAAAAATTTTATTATTA
1 TTAAAAATTTTATTATTA
*
11587683 TTAAAATATTTATTATTTTTA
1 TTAAAA-A-TT-TTATTATTA
*
11587704 TATAATAATTTTATTATT
1 T-TAAAAATTTTATTATT
11587722 TATTTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.19
19 8 0.25
20 4 0.12
21 10 0.31
22 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAAAATTTTATTATTA
Found at i:11587704 original size:21 final size:22
Alignment explanation
Indices: 11587670--11587722 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 22
11587660 TAAATTTAAA
*
11587670 AATTTTATTATTATTA-A-AAT
1 AATTTTATTATTTTTATATAAT
11587690 -A-TTTATTATTTTTATATAAT
1 AATTTTATTATTTTTATATAAT
11587710 AATTTTATTATTT
1 AATTTTATTATTT
11587723 ATTTTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 12 0.43
19 2 0.07
20 3 0.11
21 1 0.04
22 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATTTTATTATTTTTATATAAT
Found at i:11588528 original size:24 final size:26
Alignment explanation
Indices: 11588486--11588535 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
11588476 AAAGAAAAAC
*
11588486 AAAAAAGGGAGAATCAAACCAAACAAG
1 AAAAAAGGGAGAA-CAAACAAAACAAG
11588513 AAAAAA-GGAGAA-AAACAAAACAA
1 AAAAAAGGGAGAACAAACAAAACAA
11588536 AGAGGAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.70, C:0.12, G:0.16, T:0.02
Consensus pattern (26 bp):
AAAAAAGGGAGAACAAACAAAACAAG
Found at i:11588530 original size:19 final size:20
Alignment explanation
Indices: 11588506--11588543 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
11588496 GAATCAAACC
11588506 AAACAAGAA-AAA-AGGAGAA
1 AAACAA-AACAAAGAGGAGAA
11588525 AAACAAAACAAAGAGGAGA
1 AAACAAAACAAAGAGGAGA
11588544 GAGTAGAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 9 0.53
20 6 0.35
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (20 bp):
AAACAAAACAAAGAGGAGAA
Found at i:11589603 original size:30 final size:30
Alignment explanation
Indices: 11589547--11589603 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
11589537 CATTGTGGTC
* *
11589547 TTTTAAATTTCTATTTGTAGTATTTTATTA
1 TTTTAAATTCCTATTTGTACTATTTTATTA
* *
11589577 TTTTAAATTCCTATTTTTACTGTTTTA
1 TTTTAAATTCCTATTTGTACTATTTTA
11589604 ATCTCTTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (30 bp):
TTTTAAATTCCTATTTGTACTATTTTATTA
Found at i:11590650 original size:20 final size:21
Alignment explanation
Indices: 11590611--11590660 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
11590601 TTTCTTAAAA
11590611 TATAATATTATGAATATATTT
1 TATAATATTATGAATATATTT
* *
11590632 TATAATTTTA-GATTATATTT
1 TATAATATTATGAATATATTT
*
11590652 GAT-ATATTA
1 TATAATATTA
11590661 AGTAACATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 5 0.20
20 11 0.44
21 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (21 bp):
TATAATATTATGAATATATTT
Found at i:11590691 original size:2 final size:2
Alignment explanation
Indices: 11590684--11590715 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11590674 TGTGAAAATA
11590684 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
11590716 GGTTAGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11595912 original size:21 final size:19
Alignment explanation
Indices: 11595865--11595912 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
11595855 AAAACTCCAA
* *
11595865 GATATTAATATTATTGTAT
1 GATATCAATATTATTGTAG
11595884 GAGTATCAATACTTACTTGTAG
1 GA-TATCAATA-TTA-TTGTAG
11595906 GATATCA
1 GATATCA
11595913 TTACCCTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 7 0.29
21 8 0.33
22 7 0.29
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (19 bp):
GATATCAATATTATTGTAG
Found at i:11596929 original size:33 final size:33
Alignment explanation
Indices: 11596881--11596947 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
11596871 TATGTGCAAA
*
11596881 TATACACAGTGAACCATGTAATATAGTAGTGAG
1 TATACACAGTCAACCATGTAATATAGTAGTGAG
*
11596914 TATACATAGTCAACCATGTAATATAGTAGTGAG
1 TATACACAGTCAACCATGTAATATAGTAGTGAG
11596947 T
1 T
11596948 GAGTATCGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (33 bp):
TATACACAGTCAACCATGTAATATAGTAGTGAG
Found at i:11599954 original size:133 final size:133
Alignment explanation
Indices: 11599716--11599961 Score: 429
Period size: 133 Copynumber: 1.8 Consensus size: 133
11599706 AACATTTGAA
* *
11599716 AAATTGATTTTGGCAAAACTCCACCTTACTAAAATGTTTAATGAAAAAGATACCAATTGTTGGAA
1 AAATTGATTTTGGAAAAACTCCACCTTACTAAAATGTTTAATGAAAAAGATACCAATTATTGGAA
* *
11599781 AATATGTGAAAATGTTCAGCTCCCCCTTTTTCATTTAGAAATTGAATTATATTTTTGGAAAACAT
66 AATATGTAAAAATGTTCAGCTCCCCCTTTTTCATTAAGAAATTGAATTATATTTTTGGAAAACAT
11599846 GTG
131 GTG
* *
11599849 AAATTGTTTTTGGAAAAACTCCCCCTTACTAAAATGTTTAATGAAAAAGATACCAATTATTGGAA
1 AAATTGATTTTGGAAAAACTCCACCTTACTAAAATGTTTAATGAAAAAGATACCAATTATTGGAA
*
11599914 AATATGTAAAAATGTTCAGCTCCCTCTTTTTCATTAAGAAATTGAATT
66 AATATGTAAAAATGTTCAGCTCCCCCTTTTTCATTAAGAAATTGAATT
11599962 TTTCAAACTC
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 106 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (133 bp):
AAATTGATTTTGGAAAAACTCCACCTTACTAAAATGTTTAATGAAAAAGATACCAATTATTGGAA
AATATGTAAAAATGTTCAGCTCCCCCTTTTTCATTAAGAAATTGAATTATATTTTTGGAAAACAT
GTG
Found at i:11602326 original size:20 final size:21
Alignment explanation
Indices: 11602289--11602328 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
11602279 AGCCGTTGGG
*
11602289 GCCTGATGGTATTAATACTAT
1 GCCTGATGGTATCAATACTAT
*
11602310 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCAATACTA
11602329 CTATAGAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
GCCTGATGGTATCAATACTAT
Found at i:11605042 original size:26 final size:26
Alignment explanation
Indices: 11605006--11605055 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
11604996 CCGTAGTGCT
* *
11605006 TACACATAAGGTTGTGTCCACCATAA
1 TACACATAAGGTCGTGCCCACCATAA
11605032 TACACATAAGGTCGTGCCCACCAT
1 TACACATAAGGTCGTGCCCACCAT
11605056 TTACACTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (26 bp):
TACACATAAGGTCGTGCCCACCATAA
Found at i:11606648 original size:31 final size:31
Alignment explanation
Indices: 11606610--11606672 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
11606600 AAATACCATT
*
11606610 AAACCAAGACACCTAAATCTTATCATCTTCC
1 AAACCAAGACACCTAAACCTTATCATCTTCC
* *
11606641 AAACCAAGACACCTCAACCTTATCATTTTCC
1 AAACCAAGACACCTAAACCTTATCATCTTCC
11606672 A
1 A
11606673 TAAGTCAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.33, G:0.03, T:0.25
Consensus pattern (31 bp):
AAACCAAGACACCTAAACCTTATCATCTTCC
Found at i:11611803 original size:2 final size:2
Alignment explanation
Indices: 11611796--11611849 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
11611786 GTTTGAAGTG
11611796 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
11611838 AT AT AT AT AT AT
1 AT AT AT AT AT AT
11611850 CAATGGAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11617258 original size:58 final size:59
Alignment explanation
Indices: 11617168--11617279 Score: 190
Period size: 58 Copynumber: 1.9 Consensus size: 59
11617158 TTTCAAAAAA
*
11617168 AAAAAACGAAAATATATTATCACTGAAATATTAT-AAATATCTAAAATATATGAATTTC
1 AAAAAACGAAAATAGATTATCACTGAAATATTATAAAATATCTAAAATATATGAATTTC
* *
11617226 AAAAAACGAAAATAGATTCTCACTGAATTATTATAAAATATCTAAAATATATGA
1 AAAAAACGAAAATAGATTATCACTGAAATATTATAAAATATCTAAAATATATGA
11617280 TAATTTTATG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
58 31 0.62
59 19 0.38
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (59 bp):
AAAAAACGAAAATAGATTATCACTGAAATATTATAAAATATCTAAAATATATGAATTTC
Found at i:11618363 original size:29 final size:31
Alignment explanation
Indices: 11618324--11618406 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
11618314 AGTGTCTTTA
* * *
11618324 AAAACATTAGACCCTTATTTGACCA-T-TTT
1 AAAAGATTAGACCCTTATTTGAACACTACTT
* * *
11618353 AAAAGATTAGATCCTTATATGAATACTACTT
1 AAAAGATTAGACCCTTATTTGAACACTACTT
*
11618384 AAAAGGTTAGACCCTTATTTGAA
1 AAAAGATTAGACCCTTATTTGAA
11618407 GATTTAGTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
29 20 0.47
30 1 0.02
31 22 0.51
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (31 bp):
AAAAGATTAGACCCTTATTTGAACACTACTT
Found at i:11618914 original size:47 final size:47
Alignment explanation
Indices: 11618845--11618952 Score: 207
Period size: 47 Copynumber: 2.3 Consensus size: 47
11618835 TTATCGGATA
11618845 TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
1 TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
*
11618892 TCTCGGCGTCTTCTATATATGTTCGTTCAAAAGATGTTCATGGGAGC
1 TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
11618939 TCTCGGCGTCTTCT
1 TCTCGGCGTCTTCT
11618953 TCAGCCTTGG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.37
Consensus pattern (47 bp):
TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
Found at i:11619018 original size:35 final size:32
Alignment explanation
Indices: 11618934--11619019 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
11618924 GATGTTCATG
*
11618934 GGAGCTCTCGGCGTCTTCTTCAGCCTTGGGGT
1 GGAGTTCTCGGCGTCTTCTTCAGCCTTGGGGT
*
11618966 GGAGTTCTTGGCGTCTTCTTCAGCCTTGGGGT
1 GGAGTTCTCGGCGTCTTCTTCAGCCTTGGGGT
11618998 GGAGTTCTCGGCGTCTTCTTCA
1 GGAGTTCTCGGCGTCTTCTTCA
11619020 TCAGCATCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.07, C:0.26, G:0.33, T:0.35
Consensus pattern (32 bp):
GGAGTTCTCGGCGTCTTCTTCAGCCTTGGGGT
Found at i:11619227 original size:47 final size:49
Alignment explanation
Indices: 11619158--11619265 Score: 139
Period size: 51 Copynumber: 2.2 Consensus size: 49
11619148 AAAATGTTGC
* *
11619158 AAAAGTATTGGGCCCTAGCAATAAAC-AA-AAGCATATGTTTTATAAAAG
1 AAAAGT-TTGGGCCCTAGCAATAAACAAACAAGCACATATTTTATAAAAG
* *
11619206 AAAAGTTTGGTCCCTGGCAATAAACGAAAGCAAGCACATATTTTATAAAAG
1 AAAAGTTTGGGCCCTAGCAATAAAC-AAA-CAAGCACATATTTTATAAAAG
11619257 AAAAGTTTG
1 AAAAGTTTG
11619266 TTGTTATTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 17 0.33
48 6 0.12
49 2 0.04
51 27 0.52
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (49 bp):
AAAAGTTTGGGCCCTAGCAATAAACAAACAAGCACATATTTTATAAAAG
Found at i:11621473 original size:23 final size:22
Alignment explanation
Indices: 11621445--11621571 Score: 93
Period size: 23 Copynumber: 5.7 Consensus size: 22
11621435 TAATGATTTA
11621445 ACTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAAT-ATAATT
* *
11621468 ACTTTAATGATTTAATTTTAATG
1 ACTTTAATGATTTAA-TATAATT
* * * *
11621491 A-TTTAATAATAATTACTTTAATG
1 ACTTTAATGAT--TTAATATAATT
* *
11621514 A-TTTAAT-A-ATAAT-TACTT
1 ACTTTAATGATTTAATATAATT
11621532 AACTTTAATGATTTAATAATAATT
1 -ACTTTAATGATTTAAT-ATAATT
11621556 ACTTTAATGATTTAAT
1 ACTTTAATGATTTAAT
11621572 TTTAATGATT
Statistics
Matches: 85, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 6 0.07
21 1 0.01
22 13 0.15
23 50 0.59
24 8 0.09
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (22 bp):
ACTTTAATGATTTAATATAATT
Found at i:11621520 original size:37 final size:37
Alignment explanation
Indices: 11621427--11621520 Score: 179
Period size: 37 Copynumber: 2.5 Consensus size: 37
11621417 ATTATATTTC
*
11621427 AATTACTTTAATGATTTAACTTTAATGATTTAATAAT
1 AATTACTTTAATGATTTAATTTTAATGATTTAATAAT
11621464 AATTACTTTAATGATTTAATTTTAATGATTTAATAAT
1 AATTACTTTAATGATTTAATTTTAATGATTTAATAAT
11621501 AATTACTTTAATGATTTAAT
1 AATTACTTTAATGATTTAAT
11621521 AATAATTACT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.50
Consensus pattern (37 bp):
AATTACTTTAATGATTTAATTTTAATGATTTAATAAT
Found at i:11621577 original size:23 final size:23
Alignment explanation
Indices: 11621484--11621571 Score: 131
Period size: 23 Copynumber: 3.6 Consensus size: 23
11621474 ATGATTTAAT
11621484 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
11621507 TTTAATGATTTAATAATAATTACTTAAC
1 TTTAATGATTTAATAAT-A--A-TT-AC
11621535 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
11621558 TTTAATGATTTAAT
1 TTTAATGATTTAAT
11621572 TTTAATGATT
Statistics
Matches: 60, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
23 33 0.55
24 3 0.05
25 1 0.02
26 1 0.02
27 3 0.05
28 19 0.32
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (23 bp):
TTTAATGATTTAATAATAATTAC
Found at i:11621577 original size:37 final size:40
Alignment explanation
Indices: 11621530--11621631 Score: 131
Period size: 42 Copynumber: 2.6 Consensus size: 40
11621520 TAATAATTAC
*
11621530 TTAACTTTAATGATTTAATAATA-A-TT-ACTTTAATGAT
1 TTAATTTTAATGATTTAATAATATACTTGACTTTAATGAT
11621567 TTAATTTTAATGATTTAATAATAATTACTTGACTTTAATGAT
1 TTAATTTTAATGATTTAATAAT-A-TACTTGACTTTAATGAT
*
11621609 TT-ATATTTAATGATATAATAATA
1 TTAAT-TTTAATGATTTAATAATA
11621632 GTAAATATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
37 21 0.37
38 1 0.02
40 1 0.02
41 5 0.09
42 29 0.51
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (40 bp):
TTAATTTTAATGATTTAATAATATACTTGACTTTAATGAT
Found at i:11624116 original size:13 final size:13
Alignment explanation
Indices: 11624098--11624123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11624088 GTAATGTAAT
11624098 AACATATAATCAC
1 AACATATAATCAC
11624111 AACATATAATCAC
1 AACATATAATCAC
11624124 TAAACCTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
AACATATAATCAC
Found at i:11624429 original size:30 final size:32
Alignment explanation
Indices: 11624358--11624439 Score: 114
Period size: 33 Copynumber: 2.6 Consensus size: 32
11624348 ATCACCTCCC
*
11624358 ATGTGAAGAAAACGCCGAGCATTCCACCCCAA
1 ATGTGAAGAAAACGCCGAGCAATCCACCCCAA
*
11624390 ATTGTGAAGAAAACGCCGAGTAATCCA-CCCAA
1 A-TGTGAAGAAAACGCCGAGCAATCCACCCCAA
*
11624422 A-GTGAAGAAGACGCCGAG
1 ATGTGAAGAAAACGCCGAG
11624440 ACATCTTCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
30 16 0.35
32 7 0.15
33 23 0.50
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.12
Consensus pattern (32 bp):
ATGTGAAGAAAACGCCGAGCAATCCACCCCAA
Found at i:11624504 original size:20 final size:20
Alignment explanation
Indices: 11624479--11624517 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11624469 CTATTATCAA
*
11624479 CTCACCCCGTGAATTCCCTG
1 CTCACCACGTGAATTCCCTG
11624499 CTCACCACGTGAATTCCCT
1 CTCACCACGTGAATTCCCT
11624518 TTTGCGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.44, G:0.13, T:0.26
Consensus pattern (20 bp):
CTCACCACGTGAATTCCCTG
Found at i:11624948 original size:40 final size:39
Alignment explanation
Indices: 11624898--11624983 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 39
11624888 GGAAAATAAT
* *
11624898 TTGAAGACGCCGAGACCTCT-ATGTTTGAATGCAAATTGTG
1 TTGAAGACGCCGAGACATCTGAT-TTTGAATGC-AATTGTA
* * *
11624938 TTGAAGACGCCTAGAGATCTGATTTTGCATGCAATTGTA
1 TTGAAGACGCCGAGACATCTGATTTTGAATGCAATTGTA
11624977 TTGAAGA
1 TTGAAGA
11624984 TGCCTAGATC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 13 0.32
40 25 0.62
41 2 0.05
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (39 bp):
TTGAAGACGCCGAGACATCTGATTTTGAATGCAATTGTA
Found at i:11625809 original size:39 final size:40
Alignment explanation
Indices: 11625750--11625830 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
11625740 CATAACTACT
*
11625750 TCGACTTAAAAACTTAAAGAAATAACAATAT-TTTAATCA
1 TCGACTTAAAAACTCAAAGAAATAACAATATCTTTAATCA
* * *
11625789 TCGATTTAAAATCTCAAAGAAATAACAATCTCTTTAATCA
1 TCGACTTAAAAACTCAAAGAAATAACAATATCTTTAATCA
11625829 TC
1 TC
11625831 AATTCTACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 27 0.73
40 10 0.27
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (40 bp):
TCGACTTAAAAACTCAAAGAAATAACAATATCTTTAATCA
Found at i:11627589 original size:5 final size:5
Alignment explanation
Indices: 11627579--11627659 Score: 78
Period size: 5 Copynumber: 16.8 Consensus size: 5
11627569 AAGTGAAATA
* * * *
11627579 AAAAC AAAAC -AAAT AAAAC AAAGC AAAAC -AAAT AAAAC AAAGC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
* * *
11627627 -AAAT AAAAC AAAAC AAAAC AAAAT AAAAT AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
11627660 TAAAGGAAGA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
4 9 0.15
5 53 0.85
ACGTcount: A:0.78, C:0.14, G:0.02, T:0.06
Consensus pattern (5 bp):
AAAAC
Found at i:11627607 original size:19 final size:19
Alignment explanation
Indices: 11627583--11627654 Score: 126
Period size: 19 Copynumber: 3.7 Consensus size: 19
11627573 GAAATAAAAA
11627583 CAAAACAAATAAAACAAAG
1 CAAAACAAATAAAACAAAG
11627602 CAAAACAAATAAAACAAAG
1 CAAAACAAATAAAACAAAG
*
11627621 CAAAACAAATAAAACAAAA
1 CAAAACAAATAAAACAAAG
11627640 CAAAACAAAATAAAA
1 CAAAAC-AAATAAAA
11627655 TAAAATAAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 43 0.84
20 8 0.16
ACGTcount: A:0.76, C:0.15, G:0.03, T:0.06
Consensus pattern (19 bp):
CAAAACAAATAAAACAAAG
Found at i:11627660 original size:10 final size:10
Alignment explanation
Indices: 11627579--11627663 Score: 86
Period size: 10 Copynumber: 8.8 Consensus size: 10
11627569 AAGTGAAATA
*
11627579 AAAACAAAAC
1 AAAATAAAAC
11627589 -AAATAAAAC
1 AAAATAAAAC
**
11627598 AAAGCAAAAC
1 AAAATAAAAC
11627608 -AAATAAAAC
1 AAAATAAAAC
**
11627617 AAAGCAAAAC
1 AAAATAAAAC
11627627 -AAATAAAAC
1 AAAATAAAAC
*
11627636 AAAACAAAAC
1 AAAATAAAAC
*
11627646 AAAATAAAAT
1 AAAATAAAAC
11627656 AAAATAAA
1 AAAATAAA
11627664 GGAAGAAAAC
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
9 22 0.37
10 38 0.63
ACGTcount: A:0.78, C:0.13, G:0.02, T:0.07
Consensus pattern (10 bp):
AAAATAAAAC
Found at i:11627913 original size:3 final size:3
Alignment explanation
Indices: 11627895--11628075 Score: 119
Period size: 3 Copynumber: 61.7 Consensus size: 3
11627885 AATAGTAAAA
*
11627895 AAT AAA AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * * * * *
11627940 AAT AAT AAT AAT AA- AAG AA- ACC AAA AAG AA- AAA AAT AGT AA- AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
11627984 AAG AAT CAA- AGT AAT AAA AAT AA- AAA ACAT AA- ATAT ATT TA- AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT
11628028 ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11628074 AA
1 AA
11628076 AAGGGCTAAA
Statistics
Matches: 144, Mismatches: 20, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
2 14 0.10
3 119 0.83
4 11 0.08
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:11645676 original size:32 final size:31
Alignment explanation
Indices: 11645651--11645727 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
11645641 AATAATAAAT
*
11645651 AAAACAAACTCAAATAAAGTGAAATAAAATAA
1 AAAACAAAAT-AAATAAAGTGAAATAAAATAA
* *
11645683 AAAACAAAATAAATAAA-TAAAACAAAATAAA
1 AAAACAAAATAAATAAAGTGAAATAAAAT-AA
*
11645714 TAAAATAAAATAAA
1 -AAAACAAAATAAA
11645728 AATAAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 9 0.23
31 9 0.23
32 21 0.54
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.16
Consensus pattern (31 bp):
AAAACAAAATAAATAAAGTGAAATAAAATAA
Found at i:11645682 original size:5 final size:5
Alignment explanation
Indices: 11645647--11645734 Score: 65
Period size: 5 Copynumber: 17.6 Consensus size: 5
11645637 AAAAAATAAT
* * * * * *
11645647 AAATA AAACA AACTC AAATA AAGTG AAATA AAATA AAA-A ACAAAA TAAAT-
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA A-AATA -AAATA
*
11645697 AAATA AAACA AAAT- AAATA AAATA AAATAA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA AAA
11645735 ATAAGGAAGA
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
4 10 0.16
5 45 0.70
6 8 0.12
7 1 0.02
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:11645708 original size:50 final size:49
Alignment explanation
Indices: 11645639--11645735 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 49
11645629 AATCTTCAAA
* * *
11645639 AAAATAATAAATAAAACAAACTCAAATAAAGTGAAAT-AAAATAAAAAAC
1 AAAATAATAAATAAAACAAAAT-AAATAAAATAAAATAAAAATAAAAAAC
11645688 AAAATAAATAAATAAAACAAAATAAATAAAATAAAATAAAAATAAAAA
1 AAAAT-AATAAATAAAACAAAATAAATAAAATAAAATAAAAATAAAAA
11645736 TAAGGAAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 17 0.40
50 26 0.60
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.16
Consensus pattern (49 bp):
AAAATAATAAATAAAACAAAATAAATAAAATAAAATAAAAATAAAAAAC
Found at i:11645892 original size:2 final size:2
Alignment explanation
Indices: 11645885--11645942 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
11645875 GGGTAAAAAC
11645885 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
11645927 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
11645943 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11645947 original size:2 final size:2
Alignment explanation
Indices: 11645942--11645980 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11645932 TATATATATA
11645942 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
11645981 ATATTCACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:11646076 original size:3 final size:3
Alignment explanation
Indices: 11646048--11646096 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
11646038 ATAGTAAAGA
*
11646048 AAT AAA AAT AAAT AA- AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11646091 AAT AAT
1 AAT AAT
11646097 GAAACCAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
4 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:11646177 original size:2 final size:2
Alignment explanation
Indices: 11646170--11646194 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11646160 ACAAAAATAA
11646170 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
11646195 ATAATAATAA
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:11647476 original size:30 final size:31
Alignment explanation
Indices: 11647440--11647498 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
11647430 TTAATTTATA
11647440 TATATATTTATT-TTTAAATAAATTTTAATT
1 TATATATTTATTGTTTAAATAAATTTTAATT
* *
11647470 TATATATTTATTGTTTAATTTAATTTTAA
1 TATATATTTATTGTTTAAATAAATTTTAA
11647499 ATAAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (31 bp):
TATATATTTATTGTTTAAATAAATTTTAATT
Found at i:11647986 original size:38 final size:38
Alignment explanation
Indices: 11647944--11648084 Score: 148
Period size: 38 Copynumber: 3.8 Consensus size: 38
11647934 AGGATAATAT
*
11647944 TATATTATTTGA-GAATTTATATTCAATTAAAATTTGAA
1 TATATTATTT-ACGAATTTATATTCAATTAAAATATGAA
* *
11647982 TATATTATTTATGAATTTATATT-ATATTGAAATATGAA
1 TATATTATTTACGAATTTATATTCA-ATTAAAATATGAA
* * * *
11648020 TATATTATTTA-TAATTTTTTATTTAATT-AAATACGAA
1 TATATTATTTACGAA-TTTATATTCAATTAAAATATGAA
*
11648057 TATATT-TTTACAAATTTATATTCAATTA
1 TATATTATTTACGAATTTATATTCAATTA
11648085 GAATGTTATA
Statistics
Matches: 89, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
36 15 0.17
37 20 0.22
38 53 0.60
39 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (38 bp):
TATATTATTTACGAATTTATATTCAATTAAAATATGAA
Found at i:11647998 original size:21 final size:21
Alignment explanation
Indices: 11647974--11648036 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 21
11647964 ATTCAATTAA
11647974 AATTTGAATATATTATTTATG
1 AATTTGAATATATTATTTATG
*
11647995 AA-TT---TATATTATAT-TG
1 AATTTGAATATATTATTTATG
*
11648011 AAATATGAATATATTATTTAT-
1 -AATTTGAATATATTATTTATG
11648032 AATTT
1 AATTT
11648037 TTTATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 13
0.65 0.08 0.27
Matches are distributed among these distances:
16 2 0.06
17 11 0.34
18 1 0.03
20 6 0.19
21 11 0.34
22 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
AATTTGAATATATTATTTATG
Found at i:11648007 original size:43 final size:40
Alignment explanation
Indices: 11647960--11648078 Score: 117
Period size: 37 Copynumber: 3.0 Consensus size: 40
11647950 ATTTGAGAAT
*
11647960 TTATATTCAATTAAAATTTGAATATATTATTTATGAATTTATA
1 TTATATT-AATT-AAATATGAATATATTATTTAT-AATTTATA
*
11648003 TTATA-T--TGAAATATGAATATATTATTTATAATTT-T-
1 TTATATTAATTAAATATGAATATATTATTTATAATTTATA
* *
11648038 TTAT-TTAATTAAATACGAATATATT-TTTACAAATTTATA
1 TTATATTAATTAAATATGAATATATTATTTA-TAATTTATA
11648077 TT
1 TT
11648079 CAATTAGAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
35 5 0.08
36 5 0.08
37 25 0.38
38 21 0.32
39 3 0.05
42 1 0.02
43 5 0.08
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (40 bp):
TTATATTAATTAAATATGAATATATTATTTATAATTTATA
Found at i:11648306 original size:37 final size:38
Alignment explanation
Indices: 11648241--11648315 Score: 134
Period size: 37 Copynumber: 2.0 Consensus size: 38
11648231 CTCAGGGAAC
11648241 TTTTTATCCTCTAGTTTTTCGGTAATAGATAAAGACAA
1 TTTTTATCCTCTAGTTTTTCGGTAATAGATAAAGACAA
*
11648279 TTTTTCTCCTCTAG-TTTTCGGTAATAGATAAAGACAA
1 TTTTTATCCTCTAGTTTTTCGGTAATAGATAAAGACAA
11648316 GGGTGTAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 23 0.64
38 13 0.36
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (38 bp):
TTTTTATCCTCTAGTTTTTCGGTAATAGATAAAGACAA
Found at i:11649566 original size:14 final size:14
Alignment explanation
Indices: 11649547--11649579 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
11649537 TTACTGATTT
11649547 GTTTCAAAATTTTA
1 GTTTCAAAATTTTA
11649561 GTTTCAAAATTTTA
1 GTTTCAAAATTTTA
11649575 GTTTC
1 GTTTC
11649580 TAACTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (14 bp):
GTTTCAAAATTTTA
Found at i:11650476 original size:32 final size:32
Alignment explanation
Indices: 11650406--11650478 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
11650396 AATGATGACA
* * * *
11650406 TGACATATGCCATGTCACCCAAAGTGAAGGTG
1 TGACATGTGCCAAGTCACCCAAAATGAAGGCG
*
11650438 TGACATGTGCCAAGTCACCCAAAATGAGGGCG
1 TGACATGTGCCAAGTCACCCAAAATGAAGGCG
11650470 TGACATGTG
1 TGACATGTG
11650479 TTGTGGTACC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (32 bp):
TGACATGTGCCAAGTCACCCAAAATGAAGGCG
Found at i:11652208 original size:23 final size:23
Alignment explanation
Indices: 11652182--11652260 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 23
11652172 CACCGGAGTG
11652182 CCACATAGAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* * * **
11652205 CCACATCGTATTGTCTTGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
***
11652228 CCGTGT-GAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* *
11652250 CCTCGTAGAAA
1 CCACATAGAAA
11652261 CCTCGACTCT
Statistics
Matches: 41, Mismatches: 14, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
22 16 0.39
23 25 0.61
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAGGA
Found at i:11652533 original size:18 final size:18
Alignment explanation
Indices: 11652501--11652547 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
11652491 TATCTTGTTC
*
11652501 TCATATAT-CCACATAGA
1 TCATATATAACACATAGA
* *
11652518 TCATGTATAACACATAGC
1 TCATATATAACACATAGA
11652536 TCATATATAACA
1 TCATATATAACA
11652548 GCACATGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (18 bp):
TCATATATAACACATAGA
Found at i:11672423 original size:2 final size:2
Alignment explanation
Indices: 11672418--11672445 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11672408 ATGCATATGC
11672418 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
11672446 CATCATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11672624 original size:23 final size:23
Alignment explanation
Indices: 11672598--11672691 Score: 98
Period size: 23 Copynumber: 4.1 Consensus size: 23
11672588 CATCGAAGTG
*
11672598 CCACATATAAATATCCCGAAGGA
1 CCACATAGAAATATCCCGAAGGA
* * * *
11672621 CCACATAGTATTGTCCCAAAGGA
1 CCACATAGAAATATCCCGAAGGA
* *
11672644 CCATATAGAAATGTCCCGAAGGA
1 CCACATAGAAATATCCCGAAGGA
* * *
11672667 CCACGTAGAATTATCCCGAAAGA
1 CCACATAGAAATATCCCGAAGGA
11672690 CC
1 CC
11672692 GCGTAAACCT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (23 bp):
CCACATAGAAATATCCCGAAGGA
Found at i:11680249 original size:45 final size:47
Alignment explanation
Indices: 11680191--11680279 Score: 128
Period size: 45 Copynumber: 1.9 Consensus size: 47
11680181 AATAAATGCT
*
11680191 TGCGAACTGGATATCATGCGGTTAGG-TTTATTTTT-TGAATAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAAGCA
* * *
11680236 TGCGAATTAGATATCATGCGGTTCGGATTTCTTTTTGTGAATAA
1 TGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAA
11680280 CAAAGCATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 23 0.61
46 8 0.21
47 7 0.18
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (47 bp):
TGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAAGCA
Found at i:11689906 original size:7 final size:7
Alignment explanation
Indices: 11689894--11690130 Score: 74
Period size: 7 Copynumber: 35.7 Consensus size: 7
11689884 TTCGCTTGAG
11689894 GAAAAAT
1 GAAAAAT
11689901 GAAAAAT
1 GAAAAAT
**
11689908 GATGAA-
1 GAAAAAT
11689914 -AAAAAT
1 GAAAAAT
11689920 G-AAAAT
1 GAAAAAT
*
11689926 AAAAAAT
1 GAAAAAT
*
11689933 GAAGAAAAG
1 G-A-AAAAT
11689942 GAAAAAT
1 GAAAAAT
*
11689949 -AAAAAA
1 GAAAAAT
*
11689955 AAGAAAAT
1 GA-AAAAT
*
11689963 GAAGAAAA
1 GAA-AAAT
11689971 G-AAAA-
1 GAAAAAT
11689976 G-AAAA-
1 GAAAAAT
11689981 G-AAAA-
1 GAAAAAT
11689986 G-AAAA-
1 GAAAAAT
11689991 GAAAAAAT
1 G-AAAAAT
11689999 GAAAAA-
1 GAAAAAT
11690005 GAAAAAAT
1 G-AAAAAT
11690013 GAAAAAT
1 GAAAAAT
11690020 ---AAAT
1 GAAAAAT
11690024 GAAAAAT
1 GAAAAAT
11690031 ---AAAT
1 GAAAAAT
11690035 GAAAAAT
1 GAAAAAT
* *
11690042 AAAAAAA
1 GAAAAAT
11690049 GAAAAA-
1 GAAAAAT
11690055 -AAAAA-
1 GAAAAAT
*
11690060 GAAAAAAA
1 G-AAAAAT
11690068 GAAAAAGT
1 GAAAAA-T
*
11690076 GAAAAAA
1 GAAAAAT
11690083 GAAGAAA-
1 GAA-AAAT
11690090 GAAGAAA-
1 GAA-AAAT
*
11690097 GAAGAAAGA
1 GAA-AAA-T
11690106 GAAAAAT
1 GAAAAAT
11690113 GAAAAAT
1 GAAAAAT
*
11690120 AAAAAAT
1 GAAAAAT
11690127 -AAAA
1 GAAAA
11690131 TGGGGTTCAA
Statistics
Matches: 185, Mismatches: 19, Indels: 53
0.72 0.07 0.21
Matches are distributed among these distances:
4 8 0.04
5 24 0.13
6 18 0.10
7 101 0.55
8 26 0.14
9 8 0.04
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (7 bp):
GAAAAAT
Found at i:11689931 original size:14 final size:13
Alignment explanation
Indices: 11689912--11690130 Score: 113
Period size: 14 Copynumber: 17.0 Consensus size: 13
11689902 AAAAATGATG
11689912 AAAAAAATGAAAA
1 AAAAAAATGAAAA
*
11689925 TAAAAAATGAAGAA
1 AAAAAAATGAA-AA
*
11689939 AAGGAAAAATAAAAA
1 AA--AAAAATGAAAA
11689954 AAAGAAAATGAAGAA
1 AAA-AAAATGAA-AA
*
11689969 AAGAAAA-G--AA
1 AAAAAAATGAAAA
*
11689979 AAGAAAA-GAAAA
1 AAAAAAATGAAAA
*
11689991 GAAAAAATGAAAA
1 AAAAAAATGAAAA
11690004 AGAAAAAATG--AA
1 A-AAAAAATGAAAA
*
11690016 AAATAAATG--AA
1 AAAAAAATGAAAA
*
11690027 AAATAAATGAAAA
1 AAAAAAATGAAAA
*
11690040 ATAAAAAAAG-AAA
1 A-AAAAAATGAAAA
11690053 AAAAAAA-GAAAA
1 AAAAAAATGAAAA
* **
11690065 AAAGAAAAAGTGAA
1 AAA-AAAATGAAAA
*
11690079 AAAAGAA-GAAAGA
1 AAAAAAATGAAA-A
* *
11690092 AGAAAGAA-GAAAG
1 A-AAAAAATGAAAA
*
11690105 AGAAAAATGAAAA
1 AAAAAAATGAAAA
11690118 ATAAAAAAT-AAAA
1 A-AAAAAATGAAAA
11690131 TGGGGTTCAA
Statistics
Matches: 166, Mismatches: 21, Indels: 38
0.74 0.09 0.17
Matches are distributed among these distances:
10 10 0.06
11 19 0.11
12 28 0.17
13 43 0.26
14 50 0.30
15 8 0.05
16 8 0.05
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAAAAATGAAAA
Found at i:11689954 original size:25 final size:25
Alignment explanation
Indices: 11689892--11690125 Score: 77
Period size: 25 Copynumber: 9.6 Consensus size: 25
11689882 ATTTCGCTTG
**
11689892 AGGAAAAATGAAAAATGATGAAAAAA
1 AGGAAAAAT-AAAAAAAATGAAAAAA
* *
11689918 ATG-AAAAT--AAAAAATGAAGAAA
1 AGGAAAAATAAAAAAAATGAAAAAA
*
11689940 AGGAAAAATAAAAAAAA-GAAAATGA
1 AGGAAAAATAAAAAAAATGAAAA-AA
*
11689965 A-GAAAAGA-AAAGAAAA-GAAAAGAA
1 AGGAAAA-ATAAAAAAAATGAAAA-AA
* **
11689989 AAGAAAAA-ATGAAAAA-G-AAAAA
1 AGGAAAAATAAAAAAAATGAAAAAA
* ** *
11690011 ATGAAAAAT-AAATGAA--AAATAA
1 AGGAAAAATAAAAAAAATGAAAAAA
* *
11690033 ATGAAAAATAAAAAAAGA-AAAAAAA
1 AGGAAAAATAAAAAAA-ATGAAAAAA
* *
11690058 AAGAAAAA-AAGAAAAAGTGAAAAAA
1 AGGAAAAATAA-AAAAAATGAAAAAA
* * *
11690083 GAAGAAAGAAGAAAGAAGAAA-GAGAAAA
1 -AGGAAA-AATAAA-AA-AAATGAAAAAA
*
11690111 ATGAAAAATAAAAAA
1 AGGAAAAATAAAAAA
11690126 TAAAATGGGG
Statistics
Matches: 161, Mismatches: 29, Indels: 38
0.71 0.13 0.17
Matches are distributed among these distances:
22 38 0.24
23 12 0.07
24 34 0.21
25 44 0.27
26 13 0.08
27 8 0.05
28 10 0.06
29 2 0.01
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (25 bp):
AGGAAAAATAAAAAAAATGAAAAAA
Found at i:11689977 original size:19 final size:18
Alignment explanation
Indices: 11689949--11690132 Score: 78
Period size: 19 Copynumber: 9.9 Consensus size: 18
11689939 AAGGAAAAAT
11689949 AAAA-AAAAGAAAATGAA
1 AAAAGAAAAGAAAATGAA
11689966 GAAAAGAAAAGAAAA-GAAAA
1 -AAAAGAAAAGAAAATG--AA
*
11689986 GAAAAGAAAAAATGAAAAAGAA
1 -AAAAG--AAAA-GAAAATGAA
11690008 AAAATGAAAA-ATAAATG-A
1 AAAA-GAAAAGA-AAATGAA
* * *
11690026 AAAATAAATGAAAAATAAA
1 AAAAGAAAAG-AAAATGAA
* *
11690045 AAAAGAAAAAAAAAAGAA
1 AAAAGAAAAGAAAATGAA
* *
11690063 AAAA-AGAA-AAAGTGAA
1 AAAAGAAAAGAAAATGAA
*
11690079 AAAAG--AAGAAAGAAGAA
1 AAAAGAAAAGAAA-ATGAA
*
11690096 AGAAGAAAGAGAAAAATGAA
1 AAAAGAAA-AG-AAAATGAA
* *
11690116 AAATAAAAAATAAAATG
1 AAA-AGAAAAGAAAATG
11690133 GGGTTCAAGA
Statistics
Matches: 127, Mismatches: 19, Indels: 39
0.69 0.10 0.21
Matches are distributed among these distances:
15 2 0.02
16 13 0.10
17 13 0.10
18 25 0.20
19 29 0.23
20 21 0.17
21 11 0.09
22 7 0.06
23 5 0.04
24 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAGAAAATGAA
Found at i:11689997 original size:50 final size:48
Alignment explanation
Indices: 11689913--11690072 Score: 141
Period size: 48 Copynumber: 3.2 Consensus size: 48
11689903 AAAATGATGA
* * *
11689913 AAAAAATGAAAATAAAAAATGAAGAAAAGGAAAAATAAAAAAAAGAAAATG
1 AAAAAA-GAAAA-GAAAAATAAAGAAAAGAAAAAATAAAAAAAA-AAAATG
*
11689964 AAGAAAAGAAAAGAAAAGA-AAAGAAAAGAAAAAATGAAAAAGAAAAAATG
1 AA-AAAAGAAAAGAAAA-ATAAAGAAAAGAAAAAAT-AAAAAAAAAAAATG
* *
11690014 -AAAAATAAATGAAAAATAAATGAAAA-ATAAAAA-AAGAAAAAAAAAA-G
1 AAAAAAGAAAAGAAAAATAAA-GAAAAGA-AAAAATAA-AAAAAAAAAATG
11690061 AAAAAAAGAAAA
1 -AAAAAAGAAAA
11690073 AGTGAAAAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
47 4 0.04
48 25 0.27
49 19 0.21
50 24 0.26
51 15 0.16
52 4 0.04
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.07
Consensus pattern (48 bp):
AAAAAAGAAAAGAAAAATAAAGAAAAGAAAAAATAAAAAAAAAAAATG
Found at i:11690009 original size:5 final size:5
Alignment explanation
Indices: 11689934--11689995 Score: 67
Period size: 5 Copynumber: 12.4 Consensus size: 5
11689924 ATAAAAAATG
*
11689934 AAGAA AAGGAA AA-ATA AAAAA AAGAA AATG-- AAGAA AAGAA AAGAA
1 AAGAA AA-GAA AAGA-A AAGAA AAGAA AA-GAA AAGAA AAGAA AAGAA
11689979 AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA AAGAA AA
11689996 AATGAAAAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
3 1 0.02
4 3 0.06
5 39 0.78
6 7 0.14
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:11690035 original size:36 final size:36
Alignment explanation
Indices: 11689922--11690099 Score: 120
Period size: 36 Copynumber: 4.9 Consensus size: 36
11689912 AAAAAAATGA
* * *
11689922 AAATAAAAAATGAAGAAAAGGAAAAATAAAAA-AAAGA-
1 AAATGAAAAA-GAA-AAAAAGAAAAA-AAAAAGAAAAAT
* *
11689959 AAATGAAGAA-AAGAAAAGAAAAGAAAAGAA-AAGAAA-
1 AAATGAAAAAGAAAAAAAGAAAA-AAAA-AAGAA-AAAT
* * *
11689995 AAATGAAAAAGAAAAAATGAAAAATAAATGAAAAAT
1 AAATGAAAAAGAAAAAAAGAAAAAAAAAAGAAAAAT
*
11690031 AAATGAAAAATAAAAAAAGAAAAAAAAAAG-AAAA-
1 AAATGAAAAAGAAAAAAAGAAAAAAAAAAGAAAAAT
*
11690065 AAA-GAAAAAGTGAAAAAAGAAGAAAGAAGAAAGAA
1 AAATGAAAAAG-AAAAAAAGAA-AAA-AA-AAAGAA
11690100 GAAAGAGAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
33 6 0.05
34 23 0.20
35 18 0.16
36 44 0.39
37 22 0.19
38 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (36 bp):
AAATGAAAAAGAAAAAAAGAAAAAAAAAAGAAAAAT
Found at i:11690056 original size:11 final size:11
Alignment explanation
Indices: 11689912--11690067 Score: 79
Period size: 11 Copynumber: 13.5 Consensus size: 11
11689902 AAAAATGATG
*
11689912 AAAAAAATGAA
1 AAAAAAAAGAA
11689923 AATAAAAAATGAA
1 AA-AAAAAA-GAA
*
11689936 GAAAAGGAAAA-AT
1 -AAAA--AAAAGAA
11689949 AAAAAAAAGAA
1 AAAAAAAAGAA
11689960 AATGAAGAAAAG-A
1 AA--AA-AAAAGAA
*
11689973 AAAGAAAAG-A
1 AAAAAAAAGAA
*
11689983 AAAGAAAAGAA
1 AAAAAAAAGAA
*
11689994 AAAATGAAA-AA
1 AAAA-AAAAGAA
* *
11690005 GAAAAAATGAA
1 AAAAAAAAGAA
* *
11690016 AAATAAATGAA
1 AAAAAAAAGAA
11690027 AAATAAATGAA-AA
1 AAA-AAA--AAGAA
11690040 ATAAAAAAAGAA
1 A-AAAAAAAGAA
11690052 AAAAAAAAGAA
1 AAAAAAAAGAA
11690063 AAAAA
1 AAAAA
11690068 GAAAAAGTGA
Statistics
Matches: 115, Mismatches: 13, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
10 21 0.18
11 46 0.40
12 17 0.15
13 17 0.15
14 10 0.09
15 4 0.03
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:11690073 original size:55 final size:53
Alignment explanation
Indices: 11689895--11690073 Score: 147
Period size: 56 Copynumber: 3.2 Consensus size: 53
11689885 TCGCTTGAGG
* *
11689895 AAAAATGAAAAATGATG-AAAAAAATG-AAAATAAAAAATGAAGAAAAGGAAAAATA-A
1 AAAAAAGAAAAATAATGAAAAAAAATGAAAAAT-AAAAA--AAGAAAA--AAAAA-AGA
11689951 AAAAAAG-AAAATGAA-GAAAAGAAAA-GAAAAGA-AAAGAAAAGAAAAAATGAAAAAGA
1 AAAAAAGAAAAAT-AATGAAAA-AAAATGAAAA-ATAAA-AAAAG-AAAAA--AAAAAGA
*
11690007 AAAAATGAAAAATAAATGAAAAATAAATGAAAAATAAAAAAAGAAAAAAAAAAGA
1 AAAAAAGAAAAAT-AATGAAAAA-AAATGAAAAATAAAAAAAGAAAAAAAAAAGA
11690062 AAAAAAGAAAAA
1 AAAAAAGAAAAA
11690074 GTGAAAAAAG
Statistics
Matches: 103, Mismatches: 5, Indels: 31
0.74 0.04 0.22
Matches are distributed among these distances:
54 1 0.01
55 28 0.27
56 29 0.28
57 22 0.21
58 15 0.15
59 8 0.08
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.08
Consensus pattern (53 bp):
AAAAAAGAAAAATAATGAAAAAAAATGAAAAATAAAAAAAGAAAAAAAAAAGA
Found at i:11690085 original size:78 final size:78
Alignment explanation
Indices: 11689976--11690125 Score: 175
Period size: 78 Copynumber: 1.9 Consensus size: 78
11689966 GAAAAGAAAA
* *
11689976 GAAAAGAAAAGAAAAGAAAAAATGAAAAAGAAAAAATGAA-AAATAAATGAAA-A-ATAAATGAA
1 GAAAAGAAAAAAAAAGAAAAAATGAAAAAGAAAAAA-GAAGAAA-AAA-GAAAGAGAAAAATGAA
11690038 AAATAAAAAAAGAAAA
63 AAATAAAAAAAGAAAA
* * *
11690054 -AAAA-AAGAAAAAAAGAAAAAGTGAAAAAAGAAGAAAGAAGAAAGAAGAAAGAGAAAAATGAAA
1 GAAAAGAA-AAAAAAAGAAAAAATG-AAAAAGAAAAAAGAAGAAAAAAGAAAGAGAAAAATGAAA
11690117 AATAAAAAA
64 AATAAAAAA
11690126 TAAAATGGGG
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
76 6 0.10
77 24 0.39
78 32 0.52
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (78 bp):
GAAAAGAAAAAAAAAGAAAAAATGAAAAAGAAAAAAGAAGAAAAAAGAAAGAGAAAAATGAAAAA
TAAAAAAAGAAAA
Found at i:11691544 original size:55 final size:55
Alignment explanation
Indices: 11691484--11691979 Score: 609
Period size: 55 Copynumber: 9.1 Consensus size: 55
11691474 GAAGCAAACT
*
11691484 CGTTTTATGAAGATTGTTCGAGTTCTATACTGTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
*
11691539 CGTTTTATTAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* *
11691594 TGTTTTATGAAGATTGTTCGAGTTATATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
*
11691649 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* *
11691704 CGTTTGT-TGAAGATTGTTTGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACC
1 CGTTT-TATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* * * * *
11691759 CGTTTGT-TGAAGATTGTTCGAGTTC--TACTCCCTGAAGCAAGAGGGAGC-AAGCC
1 CGTTT-TATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGA-CC
* * * *
11691812 CGTTTGT-TGAGGATTGTTCGAGTTCTATACTCTCTAAAGGAATAGAAAGCGGACA
1 CGTTT-TATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* * * * *
11691867 CGTTTGT-TGAAGATTGTTCGAG-TCTTATACTCCCTGAATGAATAGGGAGCAGACA
1 CGTTT-TATGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACC
* * * *
11691922 CG-TTTACTGAAGATTGGTCGAG-TCTTATACTCCCTGAAAGG-ATAGGGAGCAGACC
1 CGTTTTA-TGAAGATTGTTCGAGTTC-TATACTCTCTG-AAGGAATAGAGAGCGGACC
11691977 CGT
1 CGT
11691980 CATTCGAAGA
Statistics
Matches: 394, Mismatches: 37, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.00
53 45 0.11
54 4 0.01
55 339 0.86
56 5 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (55 bp):
CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
Found at i:11691991 original size:218 final size:219
Alignment explanation
Indices: 11691487--11692000 Score: 562
Period size: 218 Copynumber: 2.4 Consensus size: 219
11691477 GCAAACTCGT
* ** * * * **
11691487 TTTA-TGAAGATTGTTCGAGTTCTATACTGTCTGAAGGAATAGAGAGCGGACCCGT-TTTATTAA
1 TTTACTGAAGATTGGTCGAGTTCTATACTCCCTAAAGGAATAGAGAGCAGACCCGTATGT-CGAA
* * * * *
11691550 GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTTATGAAGATTGTTCGA
65 GATTGTTCGAGTTC-ATACTCCCTGAAGCAAGAGAGAGCAGACCCGTTTTATGAAGATTGTTCGA
* * *
11691615 GTTATATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACT
129 GTTATATACTCTCTAAAGGAATAGAAAGCGGACACGTTTTATGAAGATTGTTCGAGTTCTATACT
* * *
11691680 CTCTGAAAGAATAGAGAGCGGACCCG
194 CCCTGAAAGAATAGAGAGCAGACACG
** * * * * * *
11691706 TTTGTTGAAGATTGTTTGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACCCGTTTGTTGAAG
1 TTTACTGAAGATTGGTCGAGTTCTATACTCCCTAAAGGAATAGAGAGCAGACCCGTATGTCGAAG
* *
11691771 ATTGTTCGAGTTC-TACTCCCTGAAGCAAGAGGGAGCA-AGCCCGTTTGT-TGAGGATTGTTCGA
66 ATTGTTCGAGTTCATACTCCCTGAAGCAAGAGAGAGCAGA-CCCGTTT-TATGAAGATTGTTCGA
*
11691833 GTTCTATACTCTCTAAAGGAATAGAAAGCGGACACGTTTGT-TGAAGATTGTTCGAG-TCTTATA
129 GTTATATACTCTCTAAAGGAATAGAAAGCGGACACGTTT-TATGAAGATTGTTCGAGTTC-TATA
* *
11691896 CTCCCTGAATGAATAGGGAGCAGACACG
192 CTCCCTGAAAGAATAGAGAGCAGACACG
*
11691924 TTTACTGAAGATTGGTCGAG-TCTTATACTCCCTGAAAGG-ATAGGGAGCAGACCCGTCAT-TCG
1 TTTACTGAAGATTGGTCGAGTTC-TATACTCCCT-AAAGGAATAGAGAGCAGACCCGT-ATGTCG
* *
11691986 AAGATTTTTCAAGTT
63 AAGATTGTTCGAGTT
11692001 TCATTTATCC
Statistics
Matches: 253, Mismatches: 33, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
217 5 0.02
218 170 0.67
219 11 0.04
220 65 0.26
221 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (219 bp):
TTTACTGAAGATTGGTCGAGTTCTATACTCCCTAAAGGAATAGAGAGCAGACCCGTATGTCGAAG
ATTGTTCGAGTTCATACTCCCTGAAGCAAGAGAGAGCAGACCCGTTTTATGAAGATTGTTCGAGT
TATATACTCTCTAAAGGAATAGAAAGCGGACACGTTTTATGAAGATTGTTCGAGTTCTATACTCC
CTGAAAGAATAGAGAGCAGACACG
Found at i:11696994 original size:20 final size:21
Alignment explanation
Indices: 11696959--11697001 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
11696949 GAAGAAGAAG
*
11696959 TAATGTGGGTTATTTTGAATT
1 TAATGTGGGTTATTTTAAATT
*
11696980 TAATG-GGGTTGTTTTAAATT
1 TAATGTGGGTTATTTTAAATT
11697000 TA
1 TA
11697002 CACGTGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (21 bp):
TAATGTGGGTTATTTTAAATT
Found at i:11697666 original size:31 final size:31
Alignment explanation
Indices: 11697628--11697706 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
11697618 GACTTCGGTC
* *
11697628 AAATTTATAGGTCAAATTGATATTTTATTTA
1 AAATTTATAGGTCAAATTGATATTTCATCTA
*
11697659 AAATTTATGGGTCCAAA-TGATATTTCATCTA
1 AAATTTATAGGT-CAAATTGATATTTCATCTA
* *
11697690 AAGTTTA-AGTTCAAATT
1 AAATTTATAGGTCAAATT
11697707 AGTATCATAC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 4 0.10
30 3 0.08
31 29 0.73
32 4 0.10
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (31 bp):
AAATTTATAGGTCAAATTGATATTTCATCTA
Found at i:11714428 original size:20 final size:20
Alignment explanation
Indices: 11714403--11714461 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
11714393 GGTTTCAATT
*
11714403 CGGGTTAACCTTTAAATTTC
1 CGGGTTAACCTTTAGATTTC
* *
11714423 CGGGTTAGCCTTTAGATTTT
1 CGGGTTAACCTTTAGATTTC
* *
11714443 CAGGTCAACCTTTAGATTT
1 CGGGTTAACCTTTAGATTT
11714462 TTAAGTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
CGGGTTAACCTTTAGATTTC
Found at i:11717236 original size:18 final size:18
Alignment explanation
Indices: 11717213--11717247 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11717203 ACTGAAAATT
*
11717213 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
11717231 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
11717248 TATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:11722207 original size:26 final size:26
Alignment explanation
Indices: 11722150--11722201 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
11722140 CCAAGGGTGT
11722150 ACAATCCTTTGCCCAGCCTAGCACTG
1 ACAATCCTTTGCCCAGCCTAGCACTG
11722176 ACAATCCTTTGCCCAGCCTAGCACTG
1 ACAATCCTTTGCCCAGCCTAGCACTG
11722202 TTAATCACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (26 bp):
ACAATCCTTTGCCCAGCCTAGCACTG
Found at i:11722844 original size:14 final size:15
Alignment explanation
Indices: 11722822--11722855 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
11722812 GAAGCATCGG
*
11722822 AAATTTGAAATCT-A
1 AAATCTGAAATCTGA
11722836 AAATCTGAAATCTGA
1 AAATCTGAAATCTGA
11722851 AAATC
1 AAATC
11722856 AGATTGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (15 bp):
AAATCTGAAATCTGA
Found at i:11736192 original size:23 final size:23
Alignment explanation
Indices: 11736161--11736229 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
11736151 CACCACAGCT
* *
11736161 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
11736184 CGTAGAAATGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
11736207 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
11736230 TATAAGGTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:11737958 original size:24 final size:20
Alignment explanation
Indices: 11737885--11737962 Score: 120
Period size: 20 Copynumber: 3.7 Consensus size: 20
11737875 TTCCCCTTGA
11737885 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
11737905 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
11737925 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
11737948 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
11737963 CTACCCATGC
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
20 37 0.69
22 1 0.02
23 3 0.06
24 13 0.24
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:11741579 original size:23 final size:23
Alignment explanation
Indices: 11741553--11741617 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
11741543 CACCACAACT
*
11741553 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
11741576 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
11741599 CGTAGAAATGCACCGAAGT
1 CGTAGAAATGCACCGAAGT
11741618 TCCATATAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:11743300 original size:20 final size:22
Alignment explanation
Indices: 11743275--11743332 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
11743265 TTCCCCTTGA
11743275 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
11743295 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
11743318 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
11743333 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:11743407 original size:64 final size:63
Alignment explanation
Indices: 11743320--11743460 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
11743310 TCTTTAACAT
* *
11743320 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
11743383 GATGCATCGATGTACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
11743447 GTGCATCGATGCAC
1 GTGCATCGATGCAC
11743461 ATTGAATTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 20 0.30
64 46 0.70
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:11744270 original size:44 final size:44
Alignment explanation
Indices: 11744207--11744302 Score: 192
Period size: 44 Copynumber: 2.2 Consensus size: 44
11744197 TCAAGTTGAG
11744207 AGGTATTGTGCAAGACTGGTGGTCAAAGGATATGCTCAAAAAGA
1 AGGTATTGTGCAAGACTGGTGGTCAAAGGATATGCTCAAAAAGA
11744251 AGGTATTGTGCAAGACTGGTGGTCAAAGGATATGCTCAAAAAGA
1 AGGTATTGTGCAAGACTGGTGGTCAAAGGATATGCTCAAAAAGA
11744295 AGGTATTG
1 AGGTATTG
11744303 ATTTCAATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.24
Consensus pattern (44 bp):
AGGTATTGTGCAAGACTGGTGGTCAAAGGATATGCTCAAAAAGA
Found at i:11747844 original size:18 final size:18
Alignment explanation
Indices: 11747821--11747856 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11747811 ATTTCTCTAT
11747821 TTTCATCTCCTTGAATTG
1 TTTCATCTCCTTGAATTG
11747839 TTTCATCTCCTTGAATTG
1 TTTCATCTCCTTGAATTG
11747857 AGTTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.11, T:0.50
Consensus pattern (18 bp):
TTTCATCTCCTTGAATTG
Found at i:11748747 original size:12 final size:11
Alignment explanation
Indices: 11748730--11748772 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
11748720 ATATGTATTT
11748730 ATGAACAGTACC
1 ATGAACAGTA-C
11748742 ATGAACAGTA-
1 ATGAACAGTAC
*
11748752 ATGAACAATATC
1 ATGAACAGTA-C
11748764 ATGAACAGT
1 ATGAACAGT
11748773 TCTATAGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (11 bp):
ATGAACAGTAC
Found at i:11748758 original size:22 final size:22
Alignment explanation
Indices: 11748730--11748772 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11748720 ATATGTATTT
*
11748730 ATGAACAGTACCATGAACAGTA
1 ATGAACAATACCATGAACAGTA
*
11748752 ATGAACAATATCATGAACAGT
1 ATGAACAATACCATGAACAGT
11748773 TCTATAGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (22 bp):
ATGAACAATACCATGAACAGTA
Found at i:11748942 original size:6 final size:6
Alignment explanation
Indices: 11748931--11748959 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11748921 TTCATTACTA
11748931 TACATT TACATT TACATT TACATT TACAT
1 TACATT TACATT TACATT TACATT TACAT
11748960 AAACACGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
TACATT
Found at i:11749266 original size:6 final size:6
Alignment explanation
Indices: 11749255--11749282 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
11749245 AATAAAATGC
11749255 ATACAT ATACAT ATACAT ATACAT ATAC
1 ATACAT ATACAT ATACAT ATACAT ATAC
11749283 CATCATCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACAT
Found at i:11749734 original size:32 final size:32
Alignment explanation
Indices: 11749587--11749751 Score: 153
Period size: 32 Copynumber: 5.2 Consensus size: 32
11749577 CCGAAGAACC
* * *
11749587 TAGGTAAAT-TGTCCATATGTTCAT-TAGAATA
1 TAGGTAATTCTGTCCATATGTTC-TGTAAAACA
* **
11749618 TAGGT-ATAT-TGTCTATATG-TCTCAAAAGACA
1 TAGGTAAT-TCTGTCCATATGTTCTGTAAA-ACA
* * *
11749649 TAGGTAATTCTGTCCATATGTCCCG-AAAGGCA
1 TAGGTAATTCTGTCCATATGTTCTGTAAA-ACA
11749681 TAGGTAATTCTGTCCATATGTTCTGTAAAACA
1 TAGGTAATTCTGTCCATATGTTCTGTAAAACA
* *
11749713 TAGGTAATTCTGTCCATATGTTCCGTAGAACA
1 TAGGTAATTCTGTCCATATGTTCTGTAAAACA
11749745 TAGGTAA
1 TAGGTAA
11749752 ACCCTCGACT
Statistics
Matches: 112, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
29 1 0.01
30 5 0.04
31 23 0.21
32 79 0.71
33 4 0.04
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (32 bp):
TAGGTAATTCTGTCCATATGTTCTGTAAAACA
Found at i:11749747 original size:64 final size:64
Alignment explanation
Indices: 11749587--11749751 Score: 180
Period size: 64 Copynumber: 2.6 Consensus size: 64
11749577 CCGAAGAACC
* ** * *
11749587 TAGGTAAAT-TGTCCATATGTTCATTAGAATATAGGT-ATATTGTCTATATGTCTCAAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAATATTGTCCATATGTCTCAAAAGACA
* **
11749649 TAGGTAATTCTGTCCATATGTCCCG-A-AAGGCATAGGTAAT-TCTGTCCATATGTTCTGTAAA-
1 TAGGTAATTCTGTCCATATGTTCCGTAGAA--CATAGGTAATAT-TGTCCATATG-TCTCAAAAG
11749710 ACA
62 ACA
11749713 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAA
11749752 ACCCTCGACT
Statistics
Matches: 86, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
61 2 0.02
62 9 0.10
63 19 0.22
64 47 0.55
65 7 0.08
66 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (64 bp):
TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAATATTGTCCATATGTCTCAAAAGACA
Found at i:11752448 original size:3 final size:3
Alignment explanation
Indices: 11752440--11752477 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
11752430 AAATATTAAT
*
11752440 TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11752478 TACATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11754626 original size:24 final size:24
Alignment explanation
Indices: 11754599--11754669 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
11754589 CACCACAGCT
*
11754599 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* ** *
11754623 CGTAGAATTTTAACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
*
11754647 CGTAGAAA-TGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
11754670 TATAAGATTG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 11 0.30
24 26 0.70
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:11754817 original size:23 final size:23
Alignment explanation
Indices: 11754783--11754848 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
11754773 ACACATATAC
11754783 GTCCCGAAGGACCACGTAGAATT
1 GTCCCGAAGGACCACGTAGAATT
*
11754806 GTCTCGAAGGACCACGTAGAATT
1 GTCCCGAAGGACCACGTAGAATT
* * *
11754829 TTCCCGAATGACCGCGTAGA
1 GTCCCGAAGGACCACGTAGA
11754849 CCCTCTACTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
GTCCCGAAGGACCACGTAGAATT
Found at i:11755677 original size:2 final size:2
Alignment explanation
Indices: 11755670--11755722 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
11755660 GTTACCATTT
11755670 AC AC AC AC A- AC AC AC AC AC AC AC AC AC A- AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
11755710 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
11755723 TATATATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11755694 original size:19 final size:19
Alignment explanation
Indices: 11755670--11755722 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
11755660 GTTACCATTT
11755670 ACACACACAACACACACAC
1 ACACACACAACACACACAC
11755689 ACACACACAACACACACAC
1 ACACACACAACACACACAC
11755708 ACACACAC-ACACACA
1 ACACACACAACACACA
11755723 TATATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 7 0.21
19 27 0.79
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (19 bp):
ACACACACAACACACACAC
Found at i:11755727 original size:2 final size:2
Alignment explanation
Indices: 11755722--11755758 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11755712 ACACACACAC
11755722 AT AT AT 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 AT AT AT A
11755759 CGTTTAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11757173 original size:3 final size:3
Alignment explanation
Indices: 11757165--11757212 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
11757155 GGTTCACGGT
*
11757165 GAA GAA GAA GAAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
11757211 GA
1 GA
11757213 GAGTTTTCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11759330 original size:15 final size:15
Alignment explanation
Indices: 11759310--11759356 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
11759300 AATTTCACCG
*
11759310 AAAATAAAAGATTGA
1 AAAATAAAAGATTTA
*
11759325 AAAATAAAA-ATTTC
1 AAAATAAAAGATTTA
*
11759339 AAAATATAAGATTTA
1 AAAATAAAAGATTTA
11759354 AAA
1 AAA
11759357 TTAATATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (15 bp):
AAAATAAAAGATTTA
Found at i:11761416 original size:13 final size:13
Alignment explanation
Indices: 11761398--11761429 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
11761388 TTTGGTCAAA
11761398 GTCAACGAGCTTG
1 GTCAACGAGCTTG
*
11761411 GTCAACGAGTTTG
1 GTCAACGAGCTTG
11761424 GTCAAC
1 GTCAAC
11761430 AGTGAATGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (13 bp):
GTCAACGAGCTTG
Found at i:11761467 original size:13 final size:13
Alignment explanation
Indices: 11761449--11761473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11761439 GCAAGTCAAC
11761449 GGTCAATGGGTTA
1 GGTCAATGGGTTA
11761462 GGTCAATGGGTT
1 GGTCAATGGGTT
11761474 GACTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.40, T:0.32
Consensus pattern (13 bp):
GGTCAATGGGTTA
Found at i:11764213 original size:25 final size:25
Alignment explanation
Indices: 11764185--11764234 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
11764175 ACTAAATATT
*
11764185 AATTATAATTTTAAAA-AAATTAAAA
1 AATTA-AATATTAAAATAAATTAAAA
11764210 AATTAAATATTAAAATAAATTAAAA
1 AATTAAATATTAAAATAAATTAAAA
11764235 TTAATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
AATTAAATATTAAAATAAATTAAAA
Found at i:11767887 original size:14 final size:14
Alignment explanation
Indices: 11767868--11767904 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
11767858 CCCTCCCCTC
11767868 TCCCCTTCTCCTTT
1 TCCCCTTCTCCTTT
11767882 TCCCCTTCTCCTTT
1 TCCCCTTCTCCTTT
11767896 TCCCCTTCT
1 TCCCCTTCT
11767905 ATAGTCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (14 bp):
TCCCCTTCTCCTTT
Found at i:11768288 original size:18 final size:19
Alignment explanation
Indices: 11768249--11768289 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
11768239 ATAATTTCAG
* *
11768249 TAAA-AAATTAGTTTTTTA
1 TAAATAAATTAATCTTTTA
11768267 TAAATAAATTAATCTTTT-
1 TAAATAAATTAATCTTTTA
11768285 TAAAT
1 TAAAT
11768290 TTTTTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TAAATAAATTAATCTTTTA
Found at i:11768450 original size:18 final size:19
Alignment explanation
Indices: 11768411--11768451 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
11768401 ATAATTTCAG
* *
11768411 TAAA-AAATTAGTTTTTTA
1 TAAATAAATTAATCTTTTA
11768429 TAAATAAATTAATCTTTT-
1 TAAATAAATTAATCTTTTA
11768447 TAAAT
1 TAAAT
11768452 TTTTTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TAAATAAATTAATCTTTTA
Found at i:11768492 original size:162 final size:165
Alignment explanation
Indices: 11768225--11768551 Score: 633
Period size: 162 Copynumber: 2.0 Consensus size: 165
11768215 AAATTTTAGT
11768225 TTTTAGGGTTTTTTATAATTTCAGTAAAAAATTAGTTTTTTATAAATAAATTAATCTTTTTAAAT
1 TTTTAGGGTTTTTTATAATTTCAGTAAAAAATTAGTTTTTTATAAATAAATTAATCTTTTTAAAT
11768290 TTTTTCTTTTTGTAAATAATATTTTTATTTAAAAAAATAAAATAAATTAAAAATATAT-ACAAT-
66 TTTTTCTTTTTGTAAATAATATTTTTATTTAAAAAAATAAAATAAATTAAAAATATATAACAATA
11768353 TGCACCTAAAAATATAACTG-AAAAAATTAACCAC
131 TGCACCTAAAAATATAACTGAAAAAAATTAACCAC
11768387 TTTTAGGGTTTTTTATAATTTCAGTAAAAAATTAGTTTTTTATAAATAAATTAATCTTTTTAAAT
1 TTTTAGGGTTTTTTATAATTTCAGTAAAAAATTAGTTTTTTATAAATAAATTAATCTTTTTAAAT
11768452 TTTTTCTTTTTGTAAATAATATTTTTATTTAAAAAAATAAAATAAATTAAAAATATATAACAATA
66 TTTTTCTTTTTGTAAATAATATTTTTATTTAAAAAAATAAAATAAATTAAAAATATATAACAATA
11768517 TGCACCTAAAAATATAACTGAAAAAAATTAACCAC
131 TGCACCTAAAAATATAACTGAAAAAAATTAACCAC
11768552 CTATTTTTAA
Statistics
Matches: 162, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
162 123 0.76
163 5 0.03
164 20 0.12
165 14 0.09
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (165 bp):
TTTTAGGGTTTTTTATAATTTCAGTAAAAAATTAGTTTTTTATAAATAAATTAATCTTTTTAAAT
TTTTTCTTTTTGTAAATAATATTTTTATTTAAAAAAATAAAATAAATTAAAAATATATAACAATA
TGCACCTAAAAATATAACTGAAAAAAATTAACCAC
Found at i:11769871 original size:25 final size:24
Alignment explanation
Indices: 11769840--11769886 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
11769830 TTACATCCAG
11769840 AGCCCAACAACAACATCAAATTCGA
1 AGCCCAACAACAAC-TCAAATTCGA
* *
11769865 AGCCCAAGAACAGCTCAAATTC
1 AGCCCAACAACAACTCAAATTC
11769887 AACCCGTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.45, C:0.32, G:0.11, T:0.13
Consensus pattern (24 bp):
AGCCCAACAACAACTCAAATTCGA
Found at i:11770631 original size:2 final size:2
Alignment explanation
Indices: 11770626--11770660 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
11770616 GTTGAGAGAG
11770626 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11770661 CCTCATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:11771203 original size:58 final size:57
Alignment explanation
Indices: 11771136--11771263 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 57
11771126 CCCTTACATG
* *
11771136 TTTTA-TTTTATTTCAATT-TTGTCATGATAATTTAATAATTTATGATTTAGCCCTAT
1 TTTTATTTTTATTTCAATTCTTG-CATGATAATCTAATAATTTATGATTTAGCCCTAC
* * * * * *
11771192 TTTTAGTTTTTATTTTAATTCTTGCATGATAGTCTGATTATTTATGTTTTAGTCCTAC
1 TTTTA-TTTTTATTTCAATTCTTGCATGATAATCTAATAATTTATGATTTAGCCCTAC
11771250 TTTTATTTTTATTT
1 TTTTATTTTTATTT
11771264 TATTTTTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
56 5 0.08
57 9 0.15
58 44 0.72
59 3 0.05
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.59
Consensus pattern (57 bp):
TTTTATTTTTATTTCAATTCTTGCATGATAATCTAATAATTTATGATTTAGCCCTAC
Found at i:11773259 original size:23 final size:23
Alignment explanation
Indices: 11773229--11773272 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
11773219 GCAAGTTTTA
11773229 TCGATTAATT-ATATTATGATTGT
1 TCGATTAATTCAT-TTATGATTGT
11773252 TCGATTAATTCATTTATGATT
1 TCGATTAATTCATTTATGATT
11773273 ATTTACCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (23 bp):
TCGATTAATTCATTTATGATTGT
Found at i:11781449 original size:231 final size:232
Alignment explanation
Indices: 11781028--11781490 Score: 903
Period size: 231 Copynumber: 2.0 Consensus size: 232
11781018 TGGTGGAAAA
11781028 CACTATCCTTTTATCATCCGATTGAATTTTGATTACACGAATAACATGGCCAAGTATGAAGCATG
1 CACTATCCTTTTATCATCCGATTGAATTTTGATTACACGAATAACATGGCCAAGTATGAAGCATG
11781093 TATTATGGGTCTTAGAGCTGCCATTGAGCATAAAGTGAAAACACTCAAAGTATATGAGGATTCAA
66 TATTATGGGTCTTAGAGCTGCCATTGAGCATAAAGTGAAAACACTCAAAGTATATGAGGATTCAA
11781158 CTTGGTAATTTATCAACTCAAAGGTGATAGGAAACAAAGGATATAAAGTTGGCGGGAATACCGTA
131 CTTGGTAATTTATCAACTCAAAGGTGATAGGAAACAAAGGATATAAAGTTGGCGGGAATACCGTA
11781223 AGTTGGTCATAGAGCTTATTC-AAAATTCGAGAAGGT
196 AGTTGGTCATAGAGCTTATTCAAAAATTCGAGAAGGT
11781259 CACTATCCTTTTATCATCCGATTGAATTTTGATTACACGAATAACATGGCCAAGTATGAAGCATG
1 CACTATCCTTTTATCATCCGATTGAATTTTGATTACACGAATAACATGGCCAAGTATGAAGCATG
11781324 TATTATGGGTCTTAGAGCTGCCATTGAGCATAAAGTGAAAACACTCAAAGTATATGAGGATTCAA
66 TATTATGGGTCTTAGAGCTGCCATTGAGCATAAAGTGAAAACACTCAAAGTATATGAGGATTCAA
11781389 CTTGGTAATTTATCAACTCAAAGGTGAATAGGAAACAAAGGATATAAAGTTGGC-GGAATACCGT
131 CTTGGTAATTTATCAACTCAAAGGTG-ATAGGAAACAAAGGATATAAAGTTGGCGGGAATACCGT
11781453 AAGTTGGTCATAGAGCTTATTCAAAAATTCGAGAAGGT
195 AAGTTGGTCATAGAGCTTATTCAAAAATTCGAGAAGGT
11781491 GACATTTCAT
Statistics
Matches: 230, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
231 188 0.82
232 42 0.18
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (232 bp):
CACTATCCTTTTATCATCCGATTGAATTTTGATTACACGAATAACATGGCCAAGTATGAAGCATG
TATTATGGGTCTTAGAGCTGCCATTGAGCATAAAGTGAAAACACTCAAAGTATATGAGGATTCAA
CTTGGTAATTTATCAACTCAAAGGTGATAGGAAACAAAGGATATAAAGTTGGCGGGAATACCGTA
AGTTGGTCATAGAGCTTATTCAAAAATTCGAGAAGGT
Found at i:11783933 original size:111 final size:111
Alignment explanation
Indices: 11783587--11784260 Score: 740
Period size: 111 Copynumber: 6.1 Consensus size: 111
11783577 CGATCCTGAC
* * * * * *
11783587 TCAATGGTTCAACTCCCCCTATATCTGATATTCCC-ATAGAAGAAGC-GAA-ACAT-ATCACTTA
1 TCAATGGATCAACTCCCCC-ATATATGATATTCCCTTTAGAAGAAGCAGAACAAATCATCTCTTC
* ** * *
11783648 CAAGATTTGATATTCCCTGAGTGAAAATGGAACAAGTCTGCCCCAAT
65 CAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTGCCCCGAT
* * * * *
11783695 TCAATGGATGAACTCCCTCAAATATGATATTCCCTTTCA-AAGAAGCAGAACAAATCCCTCTTTT
1 TCAATGGATCAACTCCCCCATATATGATATTCCCTTT-AGAAGAAGCAGAACAAAT-CATCTCTT
* * *
11783759 CCAAGATTTTGATATTCCCTGAGTGATAGTGGAACAAGTCTGCCCCGAT
64 CCAAGA-TTTGATATTCCCTGAGTGACAGCGAAACAAGTCTGCCCCGAT
* * * *
11783808 TCAACGGATGAACTCCCCCATATTTGATATTCCCTTTCA-AAGAAGCAGAACATATCATCTCTTC
1 TCAATGGATCAACTCCCCCATATATGATATTCCCTTT-AGAAGAAGCAGAACAAATCATCTCTTC
* * *
11783872 AAAGATTTGATATTCCCTGAGTGACATCGAAACAAGTCTGCCTCGAT
65 CAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTGCCCCGAT
* * * * *
11783919 TCAATGGATCAACTCCCCTATATCTGATATTCCCTTTCA-AATAAG-TGAA-ACAATCTCTCTCT
1 TCAATGGATCAACTCCCCCATATATGATATTCCCTTT-AGAAGAAGCAGAACA-AATC-ATCTCT
* * *
11783981 TCCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAGTCTGCCCAGAT
63 TCCAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTGCCCCGAT
* * * * *
11784030 TCAATGGATCAACTCCCCCAGATTTGATATTCCCTTTAGAAAAAGCGGAACAAATCCCTCTCTTC
1 TCAATGGATCAACTCCCCCATATATGATATTCCCTTTAGAAGAAGCAGAACAAAT-CATCTCTTC
* * * *
11784095 CAAGATTTGGTATTCCCTGAGTGACAGC-AGAACGAGTATGCCCAGAT
65 CAAGATTTGATATTCCCTGAGTGACAGCGA-AACAAGTCTGCCCCGAT
* *
11784142 TCAATGGATCAACTCCCCCATATATGATATTCCC-TTAGAAGAAGCGGAACAGATCACTCTCTTC
1 TCAATGGATCAACTCCCCCATATATGATATTCCCTTTAGAAGAAGCAGAACAAATCA-TCTCTTC
* * *
11784206 TAAGATTTGATATTCCCAGAGTGACAGCGAAATAAGTCTGCCCCGAT
65 CAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTGCCCCGAT
11784253 TCAATGGA
1 TCAATGGA
11784261 ACAAGTATGA
Statistics
Matches: 487, Mismatches: 63, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
107 13 0.03
108 24 0.05
109 5 0.01
110 11 0.02
111 235 0.48
112 108 0.22
113 91 0.19
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (111 bp):
TCAATGGATCAACTCCCCCATATATGATATTCCCTTTAGAAGAAGCAGAACAAATCATCTCTTCC
AAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTGCCCCGAT
Found at i:11784172 original size:223 final size:220
Alignment explanation
Indices: 11783648--11784260 Score: 759
Period size: 223 Copynumber: 2.7 Consensus size: 220
11783638 ATATCACTTA
* * *
11783648 CAAGATTTGATATTCCCTGAGTGAAAATGGAACAAGTCTGCCCCA-ATTCAATGGATGAACTCCC
1 CAAGATTTGATATTCCCTGAGTGACAA-CGAACAAGTCTG-CCCAGATTCAATGGATCAACTCCC
* * * * *
11783712 TCAAATATGATATTCCCTTTCAAAGAAGCAGAACAAATCCCTCTTTTCCAAGATTTTGATATTCC
64 CCATATATGATATTCCCTTTCAAAGAAGGA-AAC-AATCACTCTCTTCCAAGA-TTTGATATTCC
* * * * *
11783777 CTGAGTGATAGTGGAACAAGTCTGCCCCGATTCAACGGATGAACTCCCCCATATTTGATATTCCC
126 CTGAGTGACAGAGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCCCAGATTTGATATTCCC
* *
11783842 TTTCAAAGAAGCAGAACATATCATCTCTTC
191 TTTCAAAAAAGCAGAACAAATCATCTCTTC
* *
11783872 AAAGATTTGATATTCCCTGAGTGACATCGAAACAAGTCTGCCTC-GATTCAATGGATCAACTCCC
1 CAAGATTTGATATTCCCTGAGTGACAACG-AACAAGTCTGCC-CAGATTCAATGGATCAACTCCC
* * * *
11783936 CTATATCTGATATTCCCTTTCAAATAAGTGAAACAATCTCTCTCTTCCAAGATTTGATATTCCCT
64 CCATATATGATATTCCCTTTCAAAGAAG-GAAACAATCACTCTCTTCCAAGATTTGATATTCCCT
*
11784001 GAGTGACAGAGGAACAAGTCTGCCCAGATTCAATGGATCAACTCCCCCAGATTTGATATTCCCTT
128 GAGTGACAGAGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCCCAGATTTGATATTCCCTT
* *
11784066 T-AGAAAAAGCGGAACAAATCCCTCTCTTC
193 TCA-AAAAAGCAGAACAAAT-CATCTCTTC
* * * *
11784095 CAAGATTTGGTATTCCCTGAGTGACAGCAGAACGAGTATGCCCAGATTCAATGGATCAACTCCCC
1 CAAGATTTGATATTCCCTGAGTGACAAC-GAACAAGTCTGCCCAGATTCAATGGATCAACTCCCC
* *
11784160 CATATATGATATTCCC-TT-AGAAGAAGCGGAACAGATCACTCTCTTCTAAGATTTGATATTCCC
65 CATATATGATATTCCCTTTCA-AAGAAG-GAAACA-ATCACTCTCTTCCAAGATTTGATATTCCC
* * * *
11784223 AGAGTGACAGCGAAATAAGTCTGCCCCGATTCAATGGA
127 TGAGTGACAGAGGAACAAGTCTGCCCCGATTCAATGGA
11784261 ACAAGTATGA
Statistics
Matches: 339, Mismatches: 40, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
221 2 0.01
222 99 0.29
223 157 0.46
224 80 0.24
225 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (220 bp):
CAAGATTTGATATTCCCTGAGTGACAACGAACAAGTCTGCCCAGATTCAATGGATCAACTCCCCC
ATATATGATATTCCCTTTCAAAGAAGGAAACAATCACTCTCTTCCAAGATTTGATATTCCCTGAG
TGACAGAGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCCCAGATTTGATATTCCCTTTCA
AAAAAGCAGAACAAATCATCTCTTC
Found at i:11788663 original size:104 final size:103
Alignment explanation
Indices: 11788496--11788692 Score: 349
Period size: 104 Copynumber: 1.9 Consensus size: 103
11788486 TCTTTGGTTG
* *
11788496 CCCAAATTGGTTCGAGGTTAGTTATGTACATGTTAATTCTTTTGAGTTTATGAAATGTGATGCAT
1 CCCAAATTGGTTCGAGGTTAGTTATGTACATGTTAATTCTTCTGAGTTTATGAAATATGATGCAT
*
11788561 ATTGGTTAGTTATGAAATGCTTCACCATTCTTCAGTTA
66 ATTGGTTAGTTATGAAATGCTTAACCATTCTTCAGTTA
*
11788599 CCCAAATTGGTTCGAGGTTAGTTCATGTACATGTTAATTCTTCTGATTTTATGAAATATGATGCA
1 CCCAAATTGGTTCGAGGTTAGTT-ATGTACATGTTAATTCTTCTGAGTTTATGAAATATGATGCA
11788664 TATTGGTTAGTTATGAAATGCTTAACCAT
65 TATTGGTTAGTTATGAAATGCTTAACCAT
11788693 GATTTGTTCT
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
103 23 0.26
104 66 0.74
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (103 bp):
CCCAAATTGGTTCGAGGTTAGTTATGTACATGTTAATTCTTCTGAGTTTATGAAATATGATGCAT
ATTGGTTAGTTATGAAATGCTTAACCATTCTTCAGTTA
Found at i:11789294 original size:40 final size:41
Alignment explanation
Indices: 11789220--11789311 Score: 143
Period size: 40 Copynumber: 2.3 Consensus size: 41
11789210 GTTGTACAAT
*
11789220 TATATAAAGTTGACCAAAATTTTCATTCAAAATTAACAAAA
1 TATATAAAGTTGACCAAAATTTCCATTCAAAATTAACAAAA
11789261 TATATAAAGTT-ACC-AAATTTCCATTCAATAATTAACAAAA
1 TATATAAAGTTGACCAAAATTTCCATTCAA-AATTAACAAAA
*
11789301 TACATAAAGTT
1 TATATAAAGTT
11789312 TAACTAAAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
39 13 0.27
40 24 0.50
41 11 0.23
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (41 bp):
TATATAAAGTTGACCAAAATTTCCATTCAAAATTAACAAAA
Found at i:11789461 original size:15 final size:15
Alignment explanation
Indices: 11789417--11789482 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
11789407 TACTTCCATG
* *
11789417 GTGTTGTTGCATGTG
1 GTGTTGCTGCATGTT
* *
11789432 GTGATGATGCATGTT
1 GTGTTGCTGCATGTT
11789447 GTGTTGCTG-ATTGTT
1 GTGTTGCTGCA-TGTT
*
11789462 GTGTTGTTGCATGTT
1 GTGTTGCTGCATGTT
11789477 GTGTTG
1 GTGTTG
11789483 GTGCCTCTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
14 1 0.02
15 41 0.95
16 1 0.02
ACGTcount: A:0.09, C:0.06, G:0.36, T:0.48
Consensus pattern (15 bp):
GTGTTGCTGCATGTT
Found at i:11789493 original size:15 final size:15
Alignment explanation
Indices: 11789460--11789506 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
11789450 TTGCTGATTG
* * *
11789460 TTGTGTTGTTGCATG
1 TTGTGTTGGTGCCTC
11789475 TTGTGTTGGTGCCTC
1 TTGTGTTGGTGCCTC
*
11789490 TTGTATTGGTGCCTC
1 TTGTGTTGGTGCCTC
11789505 TT
1 TT
11789507 CTATTGGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.04, C:0.15, G:0.30, T:0.51
Consensus pattern (15 bp):
TTGTGTTGGTGCCTC
Found at i:11789511 original size:15 final size:15
Alignment explanation
Indices: 11789480--11789515 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
11789470 GCATGTTGTG
*
11789480 TTGGTGCCTCTTGTA
1 TTGGTGCCTCTTCTA
11789495 TTGGTGCCTCTTCTA
1 TTGGTGCCTCTTCTA
11789510 TTGGTG
1 TTGGTG
11789516 TATGTTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.06, C:0.19, G:0.28, T:0.47
Consensus pattern (15 bp):
TTGGTGCCTCTTCTA
Found at i:11791783 original size:41 final size:41
Alignment explanation
Indices: 11791722--11791824 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
11791712 TCTCACTGTT
* *
11791722 AGCCTTACCCTTAGCACCCTCACCCTC-ATTGTTAGACTTCTC
1 AGCCTCACCC-TAGCACCCTCACCATCAATT-TTAGACTTCTC
*
11791764 AGCCTCACCCTAGCACCCTCACCATCAATTTTAGGCTTCTC
1 AGCCTCACCCTAGCACCCTCACCATCAATTTTAGACTTCTC
*
11791805 AGCCTCACCCTGATCACCCT
1 AGCCTCACCCT-AGCACCCT
11791825 TGGTCTCACT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
41 36 0.65
42 19 0.35
ACGTcount: A:0.20, C:0.43, G:0.10, T:0.27
Consensus pattern (41 bp):
AGCCTCACCCTAGCACCCTCACCATCAATTTTAGACTTCTC
Found at i:11796934 original size:23 final size:23
Alignment explanation
Indices: 11796904--11796966 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
11796894 ATCGAATTTA
11796904 CACCGAAGTACCACATAGGTTTG
1 CACCGAAGTACCACATAGGTTTG
* *
11796927 CACCGAAGTGCAACATAGGTTTG
1 CACCGAAGTACCACATAGGTTTG
11796950 CACCGAAGTACCACATA
1 CACCGAAGTACCACATA
11796967 ATTGTCCCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (23 bp):
CACCGAAGTACCACATAGGTTTG
Found at i:11797605 original size:184 final size:185
Alignment explanation
Indices: 11797295--11797662 Score: 668
Period size: 184 Copynumber: 2.0 Consensus size: 185
11797285 AATTAAATGT
*
11797295 TTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
11797360 ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
*
11797425 GGGTTTTAAATGGTTTGGGTTGAGCCCATATGTTATATATAATATATTTAATATA
131 GGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATATA
*
11797480 TTTTAATT-AAAAAAATAGTTTACAATTAATTTAAATAATATTTAATTATAAAATAAAAATTT-A
1 TTTTAATTCAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCA
* *
11797543 TATAAATTTTTTAATTAATTAATATTGATTTATGTTTAAAAGTTATTGGATCTTAAATTATTAAT
65 GATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAAT
11797608 TGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
130 TGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
11797663 TTAAAATTTA
Statistics
Matches: 177, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
184 125 0.71
185 52 0.29
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (185 bp):
TTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
GGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATATA
Found at i:11798722 original size:17 final size:16
Alignment explanation
Indices: 11798700--11798733 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
11798690 TAAAGACAGT
11798700 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
11798717 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
11798733 A
1 A
11798734 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:11799251 original size:24 final size:24
Alignment explanation
Indices: 11799207--11799256 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
11799197 ATAAAGAACC
* *
11799207 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCACTA
*
11799231 AAAATAAAGTTTAAACA-ACCACTA
1 AAAATAAA-CTTAAACATACCACTA
11799255 AA
1 AA
11799257 TCAACCACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCACTA
Found at i:11802605 original size:25 final size:26
Alignment explanation
Indices: 11802546--11802605 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 26
11802536 GAGAAAAAGT
11802546 TAAAGTTAACATGAAAGAGAAAAAAAA
1 TAAAGTTAA-ATGAAAGAGAAAAAAAA
*
11802573 TGAA--TAAA-GAAAGAGAAAAGAAAA
1 TAAAGTTAAATGAAAGAGAAAA-AAAA
11802597 -AAAGTTAAA
1 TAAAGTTAAA
11802606 AATTTGGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
23 13 0.46
24 5 0.18
25 7 0.25
27 3 0.11
ACGTcount: A:0.68, C:0.02, G:0.17, T:0.13
Consensus pattern (26 bp):
TAAAGTTAAATGAAAGAGAAAAAAAA
Found at i:11808961 original size:17 final size:16
Alignment explanation
Indices: 11808939--11808972 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
11808929 TAAAGGTAGT
11808939 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
11808956 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
11808972 A
1 A
11808973 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:11809491 original size:24 final size:24
Alignment explanation
Indices: 11809447--11809496 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
11809437 ATAAAGAACC
11809447 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAATATACCATTA
*
11809471 AAAATAAAGTTTAAATA-ACCATTA
1 AAAATAAA-CTTAAATATACCATTA
11809495 AA
1 AA
11809497 TCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAATATACCATTA
Found at i:11813458 original size:21 final size:21
Alignment explanation
Indices: 11813432--11813486 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
11813422 TCACATAGTT
11813432 AGTGTACCGATACACTAAGGA
1 AGTGTACCGATACACTAAGGA
*
11813453 AGTGTAGCGATACACTAAGGA
1 AGTGTACCGATACACTAAGGA
*
11813474 AGTGTATCGATAC
1 AGTGTACCGATAC
11813487 CCCCTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (21 bp):
AGTGTACCGATACACTAAGGA
Done.