Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 71 of 93
Found at i:27426729 original size:19 final size:19
Alignment explanation
Indices: 27426691--27426730 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
27426681 GCGTGGCCCA
*
27426691 AGTTAAGTTAAGTTAAGTT
1 AGTTAAGTTAAGTCAAGTT
*
27426710 AGTTAAGTTAAGTCAGGTT
1 AGTTAAGTTAAGTCAAGTT
27426729 AG
1 AG
27426731 GTAGAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (19 bp):
AGTTAAGTTAAGTCAAGTT
Found at i:27426732 original size:5 final size:5
Alignment explanation
Indices: 27426690--27426722 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
27426680 TGCGTGGCCC
27426690 AAGTT AAGTT AAGTT AAGTT -AGTT AAGTT AAGT
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGT
27426723 CAGGTTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (5 bp):
AAGTT
Found at i:27430084 original size:13 final size:13
Alignment explanation
Indices: 27430066--27430091 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27430056 AGGAGAAATT
27430066 ATGATTTTATAAA
1 ATGATTTTATAAA
27430079 ATGATTTTATAAA
1 ATGATTTTATAAA
27430092 TTTTCTGGAA
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
ATGATTTTATAAA
Found at i:27437814 original size:16 final size:16
Alignment explanation
Indices: 27437793--27437825 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27437783 TAAAATAATA
27437793 TTATTTTATTATATTC
1 TTATTTTATTATATTC
*
27437809 TTATTTTATTTTATTC
1 TTATTTTATTATATTC
27437825 T
1 T
27437826 AACAGAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTATTATATTC
Found at i:27446450 original size:2 final size:2
Alignment explanation
Indices: 27446443--27446469 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27446433 TTCCAACTTT
27446443 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 T
27446470 TGTGACAAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27453042 original size:26 final size:25
Alignment explanation
Indices: 27453013--27453068 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
27453003 TATTATTATT
*
27453013 TATTTATTTCATATTTTAAATATTAA
1 TATTTATTT-ATAATTTAAATATTAA
*
27453039 TATTTTATTTATAATTTAATTATTAA
1 TA-TTTATTTATAATTTAAATATTAA
27453065 TATT
1 TATT
27453069 ATAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 18 0.67
27 7 0.26
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTTATTTATAATTTAAATATTAA
Found at i:27453062 original size:20 final size:19
Alignment explanation
Indices: 27453035--27453251 Score: 70
Period size: 20 Copynumber: 11.0 Consensus size: 19
27453025 ATTTTAAATA
27453035 TTAATATTTTATTTATAAT
1 TTAATATTTTATTTATAAT
* *
27453054 TTAATTATTAATATTATAAAATT
1 TTAA-TATT-TTATT-TATAA-T
*
27453077 TTAATATATTATTTATAAT
1 TTAATATTTTATTTATAAT
* * *
27453096 TCAA-ATGTTATTATGATTAT
1 TTAATATTTTATT-T-ATAAT
* * * **
27453116 TTTATTTTTTTTTTATTTT
1 TTAATATTTTATTTATAAT
*
27453135 TTAA-A---TATTAATAAT
1 TTAATATTTTATTTATAAT
** * *
27453150 TT-ATAACTTATCTAAAAT
1 TTAATATTTTATTTATAAT
27453168 ATTAATATTTGATCATTTAT-AT
1 -TTAATATTT--T-ATTTATAAT
* *
27453190 ATTAATATTTTGTTAATAAT
1 -TTAATATTTTATTTATAAT
* *
27453210 TTAATAATTTAAATTTTAAAAT
1 TTAAT-ATTT-TA-TTTATAAT
27453232 ATTAATATTTTATTTATAAT
1 -TTAATATTTTATTTATAAT
27453252 CTAAATATAT
Statistics
Matches: 142, Mismatches: 35, Indels: 41
0.65 0.16 0.19
Matches are distributed among these distances:
14 1 0.01
15 9 0.06
18 14 0.10
19 27 0.19
20 33 0.23
21 14 0.10
22 30 0.21
23 14 0.10
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTAATATTTTATTTATAAT
Found at i:27453243 original size:16 final size:16
Alignment explanation
Indices: 27453202--27453243 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
27453192 TAATATTTTG
*
27453202 TTAATAATTTAATAAT
1 TTAATATTTTAATAAT
27453218 TTAA-ATTTTAA-AAT
1 TTAATATTTTAATAAT
27453232 ATTAATATTTTA
1 -TTAATATTTTA
27453244 TTTATAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATATTTTAATAAT
Found at i:27453558 original size:18 final size:17
Alignment explanation
Indices: 27453511--27453569 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 17
27453501 TATTATAATA
27453511 TTTTATTTTTTA-TT-T
1 TTTTATTTTTTATTTAT
* *
27453526 TTCTCTTTTTT-TTTAT
1 TTTTATTTTTTATTTAT
27453542 TTTTATTTTTTAATTTAT
1 TTTTATTTTTT-ATTTAT
27453560 ATTTTCATTT
1 -TTTT-ATTT
27453570 AATAGTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 11 0.32
16 10 0.29
18 5 0.15
19 4 0.12
20 4 0.12
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTATTTTTTATTTAT
Found at i:27453668 original size:18 final size:19
Alignment explanation
Indices: 27453645--27453684 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
27453635 TATTTTAAAA
*
27453645 TATTAATAT-TTTATAATT
1 TATTAATATATTCATAATT
27453663 TATTAATATATTCATAATT
1 TATTAATATATTCATAATT
27453682 TAT
1 TAT
27453685 AATTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTAATATATTCATAATT
Found at i:27453683 original size:26 final size:26
Alignment explanation
Indices: 27453639--27453690 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
27453629 TATTTTTATT
*
27453639 TTAAAATATTAATATTTTATAATTTA
1 TTAAAATATTAATAATTTATAATTTA
* *
27453665 TTAATATATTCATAATTTATAATTTA
1 TTAAAATATTAATAATTTATAATTTA
27453691 AATATTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
TTAAAATATTAATAATTTATAATTTA
Found at i:27453688 original size:7 final size:7
Alignment explanation
Indices: 27453654--27453758 Score: 50
Period size: 7 Copynumber: 15.6 Consensus size: 7
27453644 ATATTAATAT
27453654 TTTATAA
1 TTTATAA
27453661 TTTATTAA
1 TTTA-TAA
27453669 --TAT-A
1 TTTATAA
*
27453673 TTCATAA
1 TTTATAA
27453680 TTTATAA
1 TTTATAA
27453687 TTTA-AA
1 TTTATAA
27453693 TATTA-ATA
1 T-TTATA-A
27453701 TTT-T-A
1 TTTATAA
27453706 TTTATAA
1 TTTATAA
27453713 TTTAATAA
1 TTT-ATAA
* *
27453721 TTAATAT
1 TTTATAA
27453728 TTTAGT-A
1 TTTA-TAA
*
27453735 TGT-TAA
1 TTTATAA
27453741 TATT-TAA
1 T-TTATAA
27453748 TTTATAA
1 TTTATAA
27453755 TTTA
1 TTTA
27453759 AATATTATTA
Statistics
Matches: 76, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
4 1 0.01
5 6 0.08
6 12 0.16
7 45 0.59
8 12 0.16
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (7 bp):
TTTATAA
Found at i:27453708 original size:26 final size:26
Alignment explanation
Indices: 27453654--27453731 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 26
27453644 ATATTAATAT
* *
27453654 TTTATAATTTATTAA-T-ATATTCATAA
1 TTTATAATTTAATAATTAATATT--TTA
27453680 TTTATAATTTAA-ATATTAATATTTTA
1 TTTATAATTTAATA-ATTAATATTTTA
27453706 TTTATAATTTAATAATTAATATTTTA
1 TTTATAATTTAATAATTAATATTTTA
27453732 GTATGTTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 1 0.02
26 38 0.83
27 2 0.04
28 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTATAATTTAATAATTAATATTTTA
Found at i:27453897 original size:154 final size:154
Alignment explanation
Indices: 27453585--27453876 Score: 406
Period size: 159 Copynumber: 1.9 Consensus size: 154
27453575 TTTTAAAATT
* * *
27453585 AATATTTTATTTATACTTTAAATGTTATTATGATTATCTATTTTTATTTTTATTTTAAAATATTA
1 AATATTTAATTTATAATTTAAATATTATTATGATTATCTATTTTTATTTTTATTTTAAAATATTA
* * * ** *
27453650 ATATTTTATAATTTATTAATATATTCATAATTTATAATTTAAATATTAATATTTTATTTATAATT
66 ATAATTTATAATTAATTAAAATATTCATAATCGATAATTTAAATATTAATATTTTATTTATAAGT
* *
27453715 TAATAATTAATATTTTAGTATGTT
131 TAATAATTAATATTATAGTATGTA
* *
27453739 AATATTTAATTTATAATTTAAATATTATTATGATTATTTATTTTTATTTTATTTTATTTTTAAAT
1 AATATTTAATTTATAATTTAAATATTATTATGATTATCTATTTTTA---T-TTTTATTTTAAAAT
27453804 ATTAATAATTTATAATTAATTTAAAATATT-AGTAATCGATAATTTAAATATTAATATTTTATTT
62 ATTAATAATTTATAATTAA-TTAAAATATTCA-TAATCGATAATTTAAATATTAATATTTTATTT
27453868 ATAAGTTAA
125 ATAAGTTAA
27453877 ATGATATTAT
Statistics
Matches: 121, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
154 42 0.35
157 1 0.01
158 31 0.26
159 47 0.39
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (154 bp):
AATATTTAATTTATAATTTAAATATTATTATGATTATCTATTTTTATTTTTATTTTAAAATATTA
ATAATTTATAATTAATTAAAATATTCATAATCGATAATTTAAATATTAATATTTTATTTATAAGT
TAATAATTAATATTATAGTATGTA
Found at i:27453916 original size:159 final size:153
Alignment explanation
Indices: 27453601--27453910 Score: 365
Period size: 159 Copynumber: 2.0 Consensus size: 153
27453591 TTATTTATAC
* * *
27453601 TTTAAATGTTATTATGATTATCTATTTTTATTTTTATTTTAAAATATTAATATTTTATAATTTAT
1 TTTAAATATTATTATGATTATCTATTTTTATTTTTATTTTAAAATATTAATAATTTATAATTAAT
* ** * **
27453666 TAATATATTCATAATTTATAATTTAAATATTAATATTTTATTTATAATTTAATAATTAATATTTT
66 TAAAATATTCATAATCGATAATTTAAATATTAATATTTTATTTATAATTAAATAATTAATATTAA
* * *
27453731 AGTATGTTAATATTTAATTTATAA
131 AATATGATAATATTTAA-TTACAA
* *
27453755 TTTAAATATTATTATGATTATTTATTTTTATTTTATTTTATTTTTAAATATTAATAATTTATAAT
1 TTTAAATATTATTATGATTATCTATTTTTA---T-TTTTATTTTAAAATATTAATAATTTATAAT
27453820 TAATTTAAAATATT-AGTAATCGATAATTTAAATATTAATATTTTATTTATAAGTTAAATGATAT
62 TAA-TTAAAATATTCA-TAATCGATAATTTAAATATTAATATTTTATTTATAA-TTAAAT-A-AT
27453884 T-ATGATTAAAATATGGATAAT-TTTAAT
122 TAAT-ATTAAAATAT-GATAATATTTAAT
27453911 CAATTTTTTA
Statistics
Matches: 132, Mismatches: 13, Indels: 15
0.82 0.08 0.09
Matches are distributed among these distances:
154 28 0.21
157 1 0.01
158 31 0.23
159 43 0.33
160 5 0.04
161 4 0.03
162 15 0.11
163 5 0.04
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (153 bp):
TTTAAATATTATTATGATTATCTATTTTTATTTTTATTTTAAAATATTAATAATTTATAATTAAT
TAAAATATTCATAATCGATAATTTAAATATTAATATTTTATTTATAATTAAATAATTAATATTAA
AATATGATAATATTTAATTACAA
Found at i:27464808 original size:2 final size:2
Alignment explanation
Indices: 27464801--27464825 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27464791 TGAGTTAAAA
27464801 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
27464826 AATAACCAAT
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:27477785 original size:26 final size:27
Alignment explanation
Indices: 27477745--27477801 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
27477735 AATACAATAC
*
27477745 AAACTAAACTAAAAACAATTTAACA-TA
1 AAACTAAAATAAAAACAATTTAA-ATTA
27477772 AAACTAAAAT-AAAACAATTTAAATTA
1 AAACTAAAATAAAAACAATTTAAATTA
27477798 AAAC
1 AAAC
27477802 AACCCAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 1 0.04
26 18 0.64
27 9 0.32
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (27 bp):
AAACTAAAATAAAAACAATTTAAATTA
Found at i:27477794 original size:15 final size:15
Alignment explanation
Indices: 27477756--27477803 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
27477746 AACTAAACTA
*
27477756 AAAACAATTTAACAT
1 AAAACAATTTAAAAT
27477771 AAAAC----TAAAAT
1 AAAACAATTTAAAAT
*
27477782 AAAACAATTTAAATT
1 AAAACAATTTAAAAT
27477797 AAAACAA
1 AAAACAA
27477804 CCCAACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
11 10 0.37
15 17 0.63
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAACAATTTAAAAT
Found at i:27482846 original size:7 final size:7
Alignment explanation
Indices: 27482834--27482860 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
27482824 AGGTGCCACG
27482834 TTTGAAC
1 TTTGAAC
27482841 TTTGAAC
1 TTTGAAC
27482848 TTTGAAC
1 TTTGAAC
27482855 TTTGAA
1 TTTGAA
27482861 ATGTGGGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (7 bp):
TTTGAAC
Found at i:27491081 original size:27 final size:27
Alignment explanation
Indices: 27491029--27491081 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
27491019 AATGTCCTGG
*
27491029 TGGTGGAAAATTACAATTTTGCCCCTA
1 TGGTGGAAAATTACAATTTTGACCCTA
*
27491056 TGGTGGGAAAATTACCATTTT-ACCCT
1 TGGT-GGAAAATTACAATTTTGACCCT
27491082 TTTACTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (27 bp):
TGGTGGAAAATTACAATTTTGACCCTA
Found at i:27491152 original size:20 final size:20
Alignment explanation
Indices: 27491135--27491172 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
27491125 CCTCAAATCT
27491135 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
27491155 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
27491173 GGGGCTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:27498829 original size:30 final size:31
Alignment explanation
Indices: 27498785--27498842 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
27498775 ACTTTTTTTA
27498785 AAAAATCAACAAAATTAA-AAATATAATGAC
1 AAAAATCAACAAAATTAATAAATATAATGAC
* * *
27498815 AAAATTCAATAAAATTAATATATATAAT
1 AAAAATCAACAAAATTAATAAATATAAT
27498843 ATAGTGACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.28
Consensus pattern (31 bp):
AAAAATCAACAAAATTAATAAATATAATGAC
Found at i:27501044 original size:22 final size:22
Alignment explanation
Indices: 27501008--27501052 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
27500998 TATGAAAAGG
* *
27501008 AAAATTATTTCATT-ATAATGTT
1 AAAATTATATAATTAATAA-GTT
27501030 AAAATTATATAATTAATAAGTT
1 AAAATTATATAATTAATAAGTT
27501052 A
1 A
27501053 CTTTTTAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
AAAATTATATAATTAATAAGTT
Found at i:27501111 original size:2 final size:2
Alignment explanation
Indices: 27501104--27501136 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27501094 TTTAATGATC
27501104 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 A
27501137 AGATTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27502144 original size:43 final size:40
Alignment explanation
Indices: 27502082--27502167 Score: 127
Period size: 43 Copynumber: 2.1 Consensus size: 40
27502072 AACTTAATTT
*
27502082 TAATGGAAGAAGAGCAGAAGAAGATGAAGGGGTTGGAGAGAGA
1 TAATGGAAGAAGAGCAGAAGAAAATGAA---GTTGGAGAGAGA
*
27502125 TAATGGAAGAAGAGGAGAAGAAAATGAAGTTGGAGAGAGA
1 TAATGGAAGAAGAGCAGAAGAAAATGAAGTTGGAGAGAGA
27502165 TAA
1 TAA
27502168 AAGATGAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 15 0.37
43 26 0.63
ACGTcount: A:0.48, C:0.01, G:0.38, T:0.13
Consensus pattern (40 bp):
TAATGGAAGAAGAGCAGAAGAAAATGAAGTTGGAGAGAGA
Found at i:27502145 original size:40 final size:42
Alignment explanation
Indices: 27502082--27502167 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 42
27502072 AACTTAATTT
* **
27502082 TAATGGAAGAAGAGCAGAAGAAGATGAA-GGGGTTGGAGAGAGA
1 TAATGGAAGAAGAG-AGAAGAAGA-AAATGAAGTTGGAGAGAGA
27502125 TAATGGAAGAAGAG-G-AGAAGAAAATGAAGTTGGAGAGAGA
1 TAATGGAAGAAGAGAGAAGAAGAAAATGAAGTTGGAGAGAGA
27502165 TAA
1 TAA
27502168 AAGATGAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
39 2 0.05
40 22 0.56
41 1 0.03
43 14 0.36
ACGTcount: A:0.48, C:0.01, G:0.38, T:0.13
Consensus pattern (42 bp):
TAATGGAAGAAGAGAGAAGAAGAAAATGAAGTTGGAGAGAGA
Found at i:27503537 original size:2 final size:2
Alignment explanation
Indices: 27503530--27503574 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
27503520 AGTGGGCTCA
*
27503530 AT AT AT AT AC 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
27503572 AT A
1 AT A
27503575 ATTTTAGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27504892 original size:22 final size:20
Alignment explanation
Indices: 27504875--27504914 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27504865 TGTTAGGCAT
27504875 TGAGTCACTGGATATTAGGA
1 TGAGTCACTGGATATTAGGA
* *
27504895 TGTGTGACTGGATATTAGGA
1 TGAGTCACTGGATATTAGGA
27504915 ATCGTAACCT
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:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (20 bp):
TGAGTCACTGGATATTAGGA
Found at i:27505171 original size:102 final size:103
Alignment explanation
Indices: 27504946--27505199 Score: 330
Period size: 102 Copynumber: 2.5 Consensus size: 103
27504936 ATTAGGTACT
**
27504946 TGAATATTTGTTGAGCATTGTGTGAGTTCTTTATAGGCATTACGTGACTGAATATATGTTGAACG
1 TGAATATTTGTTGAGCATTGCATGAGTTCTTTATAGGCATTACGTGACTGAATATATGTTGAACG
** *
27505011 TTGCGTAACAGTTACTACGTGACTGAATATTACCTGAC
66 TTGCGTAACAGGCACTACGTGAATGAATATTACCTGAC
* * *
27505049 TGAATATTTGTTGAGCATTGCATTAGTTCTTTATAGGCATTACGTGACTGAATATTTGTT-AGCG
1 TGAATATTTGTTGAGCATTGCATGAGTTCTTTATAGGCATTACGTGACTGAATATATGTTGAACG
* * * *
27505113 TTGCGTGACAGGCATTACGTGAATTAATATTACGTGAC
66 TTGCGTAACAGGCACTACGTGAATGAATATTACCTGAC
* * ** * * *
27505151 TGAATATTTGTTGAGTATTGCGTGACCTATTTGTAGGCATTGCGTGACT
1 TGAATATTTGTTGAGCATTGCATGAGTTCTTTATAGGCATTACGTGACT
27505200 TTAGCTACCT
Statistics
Matches: 131, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
102 75 0.57
103 56 0.43
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TGAATATTTGTTGAGCATTGCATGAGTTCTTTATAGGCATTACGTGACTGAATATATGTTGAACG
TTGCGTAACAGGCACTACGTGAATGAATATTACCTGAC
Found at i:27505764 original size:30 final size:30
Alignment explanation
Indices: 27505728--27505787 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
27505718 GGAGGTGCCT
*
27505728 TTGAGTGTGAGGGACTAATTACACATATTC
1 TTGAGTGTGAGGGACCAATTACACATATTC
* *
27505758 TTGAGTGTGAGGGACCAGTTGCACATATTC
1 TTGAGTGTGAGGGACCAATTACACATATTC
27505788 CAGTAGAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (30 bp):
TTGAGTGTGAGGGACCAATTACACATATTC
Found at i:27506603 original size:111 final size:111
Alignment explanation
Indices: 27506422--27506852 Score: 491
Period size: 111 Copynumber: 3.8 Consensus size: 111
27506412 GGTGCGTGAC
* *
27506422 TGACTTGTGCAATTCAT-TGTTGCTTT-GAGGCTATTGTTCAGTAGTTTTTTAGGCAATGCGTGA
1 TGACTTGTGCAATTCATGTGTTG-TTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGC-TTGCGTGA
*
27506485 CTGGTTTTTATATATTGCGTTACCTGTTGTA-GCTAGAGTGGTGGCACG
64 CTGGTTTTTATATATTGCGTGACCTGTTGTATGCTAGAGTGGTGGC-CG
* * *
27506533 TGACTTATGCAATTCATGTGTTGTTTTGAGGCTTTTGCTCAGTAGTTTTTTAGGCTTGCGTGACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * *
27506598 GGTTTTTATATATTGCGTTACTTGTTGTAATG-T-GAGTGGTGGCGCA
66 GGTTTTTATATATTGCGTGACCTGTTGT-ATGCTAGAGTGGTGGC-CG
* * * * *
27506644 TGACTTGTGCAATCCATGTGTTGTTTAGGGGCTTTTGTTAAGTAG-TTTTTAGGGTTACGTGA-T
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* *
27506707 CGATTTTTATATATTGCGTGACCTGTTGTTATGTATTGCGAGAGTGGTTGG-CG
66 -GGTTTTTATATATTGCGTGACC---TG-T-TGTA-TGCTAGAGTGG-TGGCCG
* * * *
27506760 TGACTTGTGCAATTCATGTGTTGTTTAGAGGTTTTTGTTCAGTAGTTTTTTAAGATTGCGTTACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* *
27506825 GGTTTTTATGTATTACGTGACCTGTTGT
66 GGTTTTTATATATTGCGTGACCTGTTGT
27506853 TATATATTGC
Statistics
Matches: 273, Mismatches: 31, Indels: 31
0.81 0.09 0.09
Matches are distributed among these distances:
109 1 0.00
110 34 0.12
111 105 0.38
112 36 0.13
113 4 0.01
114 4 0.01
115 5 0.02
116 42 0.15
117 38 0.14
118 4 0.01
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.45
Consensus pattern (111 bp):
TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
GGTTTTTATATATTGCGTGACCTGTTGTATGCTAGAGTGGTGGCCG
Found at i:27506804 original size:116 final size:117
Alignment explanation
Indices: 27506531--27506924 Score: 423
Period size: 117 Copynumber: 3.4 Consensus size: 117
27506521 AGTGGTGGCA
* * * *
27506531 CGTGACTTATGCAATTCATGTGTTGTTTTGAGGCTTTTGCTCAGTAGTTTTTTAGGCTTGCGTGA
1 CGTGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTGA
* * *
27506596 CTGGTTTTTATATATTGCGTTA-C--TTG-T-TGTAAT--GTGAGTGG-TGG
66 CTGGTTTTTATATATTGCGTGACCTGTTGTTATGTATTGCGAGAGTGGTTGG
* * * * *
27506640 CGCATGACTTGTGCAATCCATGTGTTGTTTAGGGGCTTTTGTTAAGTAG-TTTTTAGGGTTACGT
1 CG--TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGT
*
27506704 GA-TCGATTTTTATATATTGCGTGACCTGTTGTTATGTATTGCGAGAGTGGTTGG
64 GACT-GGTTTTTATATATTGCGTGACCTGTTGTTATGTATTGCGAGAGTGGTTGG
* * *
27506758 CGTGACTTGTGCAATTCATGTGTTGTTTAGAGGTTTTTGTTCAGTAGTTTTTTAAGATTGCGTTA
1 CGTGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTGA
* * * ** *
27506823 CTGGTTTTTATGTATTACGTGACCTGTTGTTATATATTGCGAGAGCAGTGGCG
66 CTGGTTTTTATATATTGCGTGACCTGTTGTTATGTATTGCGAGAGTGGTTG-G
* * * * *
27506876 CGTGACTTGTGCAATTC-TCCTTTTGTTTAGGGGCGTTTGTTCACTAGTT
1 CGTGACTTGTGCAATTCAT-GTGTTGTTTAGAGGCTTTTGTTCAGTAGTT
27506925 ATTAGGCATT
Statistics
Matches: 237, Mismatches: 33, Indels: 21
0.81 0.11 0.07
Matches are distributed among these distances:
109 3 0.01
110 33 0.14
111 40 0.17
113 3 0.01
114 1 0.00
115 5 0.02
116 41 0.17
117 63 0.27
118 48 0.20
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.44
Consensus pattern (117 bp):
CGTGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTGA
CTGGTTTTTATATATTGCGTGACCTGTTGTTATGTATTGCGAGAGTGGTTGG
Found at i:27506936 original size:118 final size:117
Alignment explanation
Indices: 27506422--27506936 Score: 337
Period size: 111 Copynumber: 4.5 Consensus size: 117
27506412 GGTGCGTGAC
* * *
27506422 TGACTTGTGCAA-T-TCATTGTTGCTTT-GAGGCTATTGTTCAGTAGTTTTTTAGGCAATGCGTG
1 TGACTTGTGCAATTCTCATT-TTG-TTTAGGGGCTTTTGTTCAGTAG-TTTTTAGG-ATTGCGTG
* * * * ** *
27506484 A-CTGGTTTTTATATATTGCGTTACCTGTTG-----TA--GCTAGAGTGGTGGCACG
62 ATC-GATTTTTATATATTACGTGACCTGTTGTTATATATTGCGAGAGCAGTGGCGCG
* * * * *
27506533 TGACTTATGCAA-T-TCATGTGTTGTTTTGAGGCTTTTGCTCAGTAGTTTTTTAGGCTTGCGTGA
1 TGACTTGTGCAATTCTCAT-T-TTGTTTAGGGGCTTTTGTTCAGTAG-TTTTTAGGATTGCGTGA
* * * * * * *
27506596 -CTGGTTTTTATATATTGCGTTA-C--TTGTTGTA-A-TGTGAGTG--GTGGCGCA
63 TC-GATTTTTATATATTACGTGACCTGTTGTTATATATTGCGAGAGCAGTGGCGCG
* * *
27506644 TGACTTGTGCAA-TC-CATGTGTTGTTTAGGGGCTTTTGTTAAGTAGTTTTTAGGGTTACGTGAT
1 TGACTTGTGCAATTCTCAT-T-TTGTTTAGGGGCTTTTGTTCAGTAGTTTTTAGGATTGCGTGAT
* * ** *
27506707 CGATTTTTATATATTGCGTGACCTGTTGTTATGTATTGCGAGAGTGGTTG-GCG
64 CGATTTTTATATATTACGTGACCTGTTGTTATATATTGCGAGAGCAGTGGCGCG
* * * *
27506760 TGACTTGTGCAA-T-TCATGTGTTGTTTAGAGGTTTTTGTTCAGTAGTTTTTTAAGATTGCGTTA
1 TGACTTGTGCAATTCTCAT-T-TTGTTTAGGGGCTTTTGTTCAGTAG-TTTTTAGGATTGCGTGA
* *
27506823 -CTGGTTTTTATGTATTACGTGACCTGTTGTTATATATTGCGAGAGCAGTGGCGCG
63 TC-GATTTTTATATATTACGTGACCTGTTGTTATATATTGCGAGAGCAGTGGCGCG
* * * *
27506878 TGACTTGTGCAATTCTCCTTTTGTTTAGGGGCGTTTGTTCACTAGTTATTAGGCATTGC
1 TGACTTGTGCAATTCTCATTTTGTTTAGGGGCTTTTGTTCAGTAGTTTTTAGG-ATTGC
27506937 AGTAATGTGT
Statistics
Matches: 334, Mismatches: 46, Indels: 41
0.79 0.11 0.10
Matches are distributed among these distances:
108 3 0.01
110 34 0.10
111 95 0.28
112 31 0.09
113 10 0.03
114 1 0.00
115 6 0.02
116 44 0.13
117 64 0.19
118 41 0.12
119 2 0.01
120 3 0.01
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.43
Consensus pattern (117 bp):
TGACTTGTGCAATTCTCATTTTGTTTAGGGGCTTTTGTTCAGTAGTTTTTAGGATTGCGTGATCG
ATTTTTATATATTACGTGACCTGTTGTTATATATTGCGAGAGCAGTGGCGCG
Found at i:27511368 original size:26 final size:26
Alignment explanation
Indices: 27511339--27511398 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
27511329 CCAACTACTT
* *
27511339 ACGCAATGCCTTAACAGAAACCAGTC
1 ACGCAATGACTTAACAAAAACCAGTC
* *
27511365 ACGCAATGACTTATCAAAAACTAGTC
1 ACGCAATGACTTAACAAAAACCAGTC
27511391 ACGCAATG
1 ACGCAATG
27511399 TCCAAAGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.18
Consensus pattern (26 bp):
ACGCAATGACTTAACAAAAACCAGTC
Found at i:27511411 original size:21 final size:21
Alignment explanation
Indices: 27511387--27511440 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
27511377 ATCAAAAACT
27511387 AGTCACGCAATGTCCAAAGTA
1 AGTCACGCAATGTCCAAAGTA
* * *
27511408 AGTCTCGCAATGTCTAAGGTA
1 AGTCACGCAATGTCCAAAGTA
*
27511429 AGTTACGCAATG
1 AGTCACGCAATG
27511441 GCTCATGTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (21 bp):
AGTCACGCAATGTCCAAAGTA
Found at i:27516110 original size:23 final size:23
Alignment explanation
Indices: 27516078--27516143 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 23
27516068 TTATCACATG
*
27516078 AATGAATACAAAGAATAATATGTA
1 AATG-ATACAAAGAATAATATGGA
27516102 AATGATACAACAAAGAATAATATGGA
1 AATGAT---ACAAAGAATAATATGGA
27516128 AATGATAC--AGAATAAT
1 AATGATACAAAGAATAAT
27516144 GTTAATGTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 8 0.21
23 4 0.11
24 4 0.11
26 22 0.58
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.23
Consensus pattern (23 bp):
AATGATACAAAGAATAATATGGA
Found at i:27516116 original size:26 final size:26
Alignment explanation
Indices: 27516085--27516136 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
27516075 ATGAATGAAT
*
27516085 ACAAAGAATAATATGTAAATGATACA
1 ACAAAGAATAATATGGAAATGATACA
27516111 ACAAAGAATAATATGGAAATGATACA
1 ACAAAGAATAATATGGAAATGATACA
27516137 GAATAATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (26 bp):
ACAAAGAATAATATGGAAATGATACA
Found at i:27517740 original size:24 final size:24
Alignment explanation
Indices: 27517713--27517826 Score: 110
Period size: 24 Copynumber: 4.9 Consensus size: 24
27517703 TCACCCGCTA
27517713 GATCTCCAACTGCATTGACTGTTG
1 GATCTCCAACTGCATTGACTGTTG
*
27517737 GATCTCCAATTGCATTGAC---TG
1 GATCTCCAACTGCATTGACTGTTG
* * * * * * *
27517758 CATTTGCATCTACA-TCACCAGTTG
1 GATCTCCAACTGCATTGA-CTGTTG
*
27517782 GATCTCCAACTGCACTGACTGTTG
1 GATCTCCAACTGCATTGACTGTTG
27517806 GATCTCCAACTGCATTGACTG
1 GATCTCCAACTGCATTGACTG
27517827 CATCTGCATC
Statistics
Matches: 69, Mismatches: 16, Indels: 10
0.73 0.17 0.11
Matches are distributed among these distances:
20 2 0.03
21 11 0.16
24 54 0.78
25 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (24 bp):
GATCTCCAACTGCATTGACTGTTG
Found at i:27517776 original size:69 final size:69
Alignment explanation
Indices: 27517683--27517837 Score: 229
Period size: 69 Copynumber: 2.2 Consensus size: 69
27517673 TGCTCATGAG
* * * * * *
27517683 TGACTGCGTCTGCGTCTGCATCACCCGCTAGATCTCCAACTGCATTGACTGTTGGATCTCCAATT
1 TGACTGCATCTGCATCTACATCACCAGCTAGATCTCCAACTGCACTGACTGTTGGATCTCCAACT
27517748 GCAT
66 GCAT
* * *
27517752 TGACTGCATTTGCATCTACATCACCAGTTGGATCTCCAACTGCACTGACTGTTGGATCTCCAACT
1 TGACTGCATCTGCATCTACATCACCAGCTAGATCTCCAACTGCACTGACTGTTGGATCTCCAACT
27517817 GCAT
66 GCAT
27517821 TGACTGCATCTGCATCT
1 TGACTGCATCTGCATCT
27517838 GCATATTCGT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 76 1.00
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.31
Consensus pattern (69 bp):
TGACTGCATCTGCATCTACATCACCAGCTAGATCTCCAACTGCACTGACTGTTGGATCTCCAACT
GCAT
Found at i:27518021 original size:15 final size:15
Alignment explanation
Indices: 27517986--27518026 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
27517976 GAGGAAGGGT
27517986 AGCAGCAGGAGTAGC
1 AGCAGCAGGAGTAGC
27518001 AGCAGCAGGAGTAGC
1 AGCAGCAGGAGTAGC
27518016 AGCAGCAGGAG
1 AGCAGCAGGAG
27518027 ATGCGCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.34, C:0.20, G:0.41, T:0.05
Consensus pattern (15 bp):
AGCAGCAGGAGTAGC
Found at i:27527978 original size:2 final size:2
Alignment explanation
Indices: 27527971--27528000 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27527961 ATAAGAGAAG
27527971 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
27528001 GATTTGCTTA
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:27533141 original size:9 final size:9
Alignment explanation
Indices: 27533127--27533165 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
27533117 ATTTTGTCTC
27533127 TAATAGTAG
1 TAATAGTAG
27533136 TAATAGTAG
1 TAATAGTAG
* *
27533145 TAGTAATAG
1 TAATAGTAG
27533154 TAATAGTAG
1 TAATAGTAG
27533163 TAA
1 TAA
27533166 CTATATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (9 bp):
TAATAGTAG
Found at i:27533147 original size:12 final size:12
Alignment explanation
Indices: 27533130--27533161 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
27533120 TTGTCTCTAA
27533130 TAGTAGTAATAG
1 TAGTAGTAATAG
27533142 TAGTAGTAATAG
1 TAGTAGTAATAG
*
27533154 TAATAGTA
1 TAGTAGTA
27533162 GTAACTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (12 bp):
TAGTAGTAATAG
Found at i:27543968 original size:66 final size:62
Alignment explanation
Indices: 27543889--27544025 Score: 148
Period size: 66 Copynumber: 2.1 Consensus size: 62
27543879 TCAGATGTAA
** * * * *
27543889 AATATTTTTTTAAAAATAATAAAATATTTTTATATTAAATTTATGAGTATAAATTTGATAAATAT
1 AATATTTAATTAAAAATAATAAAA-ATATTAATATTAAATTT-TAAATATAAATTT-A-AAATAT
27543954 T
62 T
* * * *
27543955 AATATTTAATTAAAAATATTAAAAATATTAATATTTAATTTTAAATTTTAATTTAAAATATT
1 AATATTTAATTAAAAATAATAAAAATATTAATATTAAATTTTAAATATAAATTTAAAATATT
27544017 AATATTTAA
1 AATATTTAA
27544026 ATTATACAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
62 16 0.26
63 1 0.02
64 9 0.15
65 14 0.23
66 21 0.34
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (62 bp):
AATATTTAATTAAAAATAATAAAAATATTAATATTAAATTTTAAATATAAATTTAAAATATT
Found at i:27544000 original size:29 final size:31
Alignment explanation
Indices: 27543948--27544025 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 31
27543938 TAAATTTGAT
27543948 AAATATTAATATTTAATTAAAAA-T-ATTAA
1 AAATATTAATATTTAATTAAAAATTAATTAA
** *
27543977 AAATATTAATATTTAATTTTAAATTTTAATTTA
1 AAATATTAATATTTAA--TTAAAAATTAATTAA
27544010 AAATATTAATATTTAA
1 AAATATTAATATTTAA
27544026 ATTATACAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 16 0.38
31 5 0.12
32 1 0.02
33 20 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
AAATATTAATATTTAATTAAAAATTAATTAA
Found at i:27544004 original size:13 final size:13
Alignment explanation
Indices: 27543988--27544028 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
27543978 AATATTAATA
27543988 TTTAATTTTAAAT
1 TTTAATTTTAAAT
*
27544001 TTTAATTTAAAAT
1 TTTAATTTTAAAT
*
27544014 ATTAATATTTAAAT
1 TTTAAT-TTTAAAT
27544028 T
1 T
27544029 ATACAACACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTAATTTTAAAT
Found at i:27544044 original size:33 final size:29
Alignment explanation
Indices: 27543976--27544046 Score: 52
Period size: 33 Copynumber: 2.2 Consensus size: 29
27543966 AAAAATATTA
* *
27543976 AAAATATTAATATTTAATTTTAAATTTTAATTT
1 AAAATATTAATATTTAATTATAAA--AT-A-TT
27544009 AAAATATTAATATTTAAATTATACAACACTATT
1 AAAATATTAATATTT-AATTATA-AA-A-TATT
27544042 AAAAT
1 AAAAT
27544047 TAAAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
33 22 0.69
34 7 0.22
35 3 0.09
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAATATTAATATTTAATTATAAAATATT
Found at i:27545149 original size:23 final size:24
Alignment explanation
Indices: 27545106--27545150 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
27545096 AATTTTGAGA
*
27545106 AATGAAGCTTTTTTCTTCTCTTGG
1 AATGAAGCTTTTTTCTCCTCTTGG
27545130 AATGAAGCTTTTTT-TCCTCTT
1 AATGAAGCTTTTTTCTCCTCTT
27545151 TCTTTCTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (24 bp):
AATGAAGCTTTTTTCTCCTCTTGG
Found at i:27546606 original size:21 final size:20
Alignment explanation
Indices: 27546578--27546627 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
27546568 GTCTTACGAA
27546578 AATA-TAAAAACTAAT-AAAT
1 AATACTAAAAA-TAATAAAAT
27546597 AATAACT-AAAATAATACAAAT
1 AAT-ACTAAAAATAATA-AAAT
27546618 AATACTAAAA
1 AATACTAAAA
27546628 TTTGCATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 7 0.27
20 8 0.31
21 11 0.42
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (20 bp):
AATACTAAAAATAATAAAAT
Found at i:27550501 original size:45 final size:46
Alignment explanation
Indices: 27550452--27550584 Score: 123
Period size: 45 Copynumber: 2.9 Consensus size: 46
27550442 GTGTTACTAC
* *
27550452 TTGATAGGGTATTACGTG-ATCGATTTTTAG-GCATTGTATGACTTG
1 TTGATAGGGCATTACGTGAAT-GATTTTTAGAGCATTGCATGACTTG
** * *
27550497 TTGATAGGGCATTGTGTGAATGGTTTTTAGAGCATTGCATGACTAGTT
1 TTGATAGGGCATTACGTGAATGATTTTTAGAGCATTGCATGACT--TG
* * *
27550545 TTGA-A-GGCATTGCATGACTGATTTTTAGA-CATTGCATGAC
1 TTGATAGGGCATTACGTGAATGATTTTTAGAGCATTGCATGAC
27550585 CAGTTTTAGT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
45 34 0.46
46 34 0.46
47 1 0.01
48 5 0.07
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (46 bp):
TTGATAGGGCATTACGTGAATGATTTTTAGAGCATTGCATGACTTG
Found at i:27550545 original size:23 final size:23
Alignment explanation
Indices: 27550475--27550718 Score: 148
Period size: 23 Copynumber: 10.9 Consensus size: 23
27550465 ACGTGATCGA
* *
27550475 TTTTTAG-GCATTGTATGACTTG
1 TTTTTAGAGCATTGCATGACTAG
** * ** * *
27550497 TTGATAGGGCATTGTGTGAATGG
1 TTTTTAGAGCATTGCATGACTAG
27550520 TTTTTAGAGCATTGCATGACTAG
1 TTTTTAGAGCATTGCATGACTAG
*
27550543 TTTTGA-AGGCATTGCATGACT-G
1 TTTTTAGA-GCATTGCATGACTAG
*
27550565 ATTTTTAGA-CATTGCATGACCAG
1 -TTTTTAGAGCATTGCATGACTAG
* *
27550588 -TTTTAG-TCATTGCATGACTGG
1 TTTTTAGAGCATTGCATGACTAG
** * * *
27550609 TTGATAGGGCATTGCATAACTGG
1 TTTTTAGAGCATTGCATGACTAG
** * *
27550632 TTGATAGTGCATT-CATGGCTAG
1 TTTTTAGAGCATTGCATGACTAG
* *
27550654 TTTTTA-AGCATTGCGTGACTGG
1 TTTTTAGAGCATTGCATGACTAG
* *
27550676 TTTTTA-AGGCATTTCATGATTAG
1 TTTTTAGA-GCATTGCATGACTAG
*
27550699 TTTTTAG-GCATTGCGTGACT
1 TTTTTAGAGCATTGCATGACT
27550719 GCTTAATAAG
Statistics
Matches: 173, Mismatches: 38, Indels: 22
0.74 0.16 0.09
Matches are distributed among these distances:
21 23 0.13
22 55 0.32
23 94 0.54
24 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (23 bp):
TTTTTAGAGCATTGCATGACTAG
Found at i:27550590 original size:45 final size:44
Alignment explanation
Indices: 27550520--27550625 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 44
27550510 GTGTGAATGG
*
27550520 TTTTTAGAGCATTGCATGACTAGTTTTGAAGGCATTGCATGACTGA
1 TTTTTAGAGCATTGCATGACCAGTTTT--AGGCATTGCATGACTGA
* *
27550566 TTTTTAGA-CATTGCATGACCAGTTTTAGTCATTGCATGACTGG
1 TTTTTAGAGCATTGCATGACCAGTTTTAGGCATTGCATGACTGA
** *
27550609 TTGATAGGGCATTGCAT
1 TTTTTAGAGCATTGCAT
27550626 AACTGGTTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 20 0.38
44 8 0.15
45 17 0.32
46 8 0.15
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (44 bp):
TTTTTAGAGCATTGCATGACCAGTTTTAGGCATTGCATGACTGA
Found at i:27550593 original size:112 final size:112
Alignment explanation
Indices: 27550475--27550733 Score: 290
Period size: 112 Copynumber: 2.3 Consensus size: 112
27550465 ACGTGATCGA
* * ** **
27550475 TTTTTAGGCATTGTATGACTTGTTGATAGGGCATTGTGTGAA-TGGTTTTTAGAGCATTGCATGA
1 TTTTTAGGCATTGCATGACTGGTTGATAGGGCATTGCAT-AACTGGTTGATAGAGCATT-CATGA
27550539 CTAGTTTTGAAGGCATTGCATGACTGATTTTT-AGACATTGCATGACCAG
64 CTAGTTTTGAA-GCATTGCATGACTGATTTTTAAGACATTGCATGACCAG
* * *
27550588 -TTTTAGTCATTGCATGACTGGTTGATAGGGCATTGCATAACTGGTTGATAGTGCATTCATGGCT
1 TTTTTAGGCATTGCATGACTGGTTGATAGGGCATTGCATAACTGGTTGATAGAGCATTCATGACT
* * * * * **
27550652 AGTTTTTAAGCATTGCGTGACTGGTTTTTAAGGCATTTCATGATTAG
66 AGTTTTGAAGCATTGCATGACTGATTTTTAAGACATTGCATGACCAG
* * * *
27550699 TTTTTAGGCATTGCGTGACTGCTTAATAAGGCATT
1 TTTTTAGGCATTGCATGACTGGTTGATAGGGCATT
27550734 ATGTGATTGG
Statistics
Matches: 122, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
110 18 0.15
111 29 0.24
112 75 0.61
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.39
Consensus pattern (112 bp):
TTTTTAGGCATTGCATGACTGGTTGATAGGGCATTGCATAACTGGTTGATAGAGCATTCATGACT
AGTTTTGAAGCATTGCATGACTGATTTTTAAGACATTGCATGACCAG
Found at i:27550710 original size:45 final size:45
Alignment explanation
Indices: 27550475--27550733 Score: 177
Period size: 45 Copynumber: 5.8 Consensus size: 45
27550465 ACGTGATCGA
* * ** * ** * *
27550475 TTTTTAGGCATTGTATGACTTGTTGATAGGGCATTGTGTGAATGG
1 TTTTTAGGCATTGCATGACTGGTTTTTAAGGCATTGCATGACTAG
* *
27550520 TTTTTAGAGCATTGCATGACTAGTTTTGAAGGCATTGCATGACT-G
1 TTTTTAG-GCATTGCATGACTGGTTTTTAAGGCATTGCATGACTAG
* ** * *
27550565 ATTTTTAGACATTGCATGACCAG-TTTT-AGTCATTGCATGACTGG
1 -TTTTTAGGCATTGCATGACTGGTTTTTAAGGCATTGCATGACTAG
** * ** *
27550609 TTGATAGGGCATTGCATAACTGGTTGAT-AGTGCATT-CATGGCTAG
1 TTTTTA-GGCATTGCATGACTGGTTTTTAAG-GCATTGCATGACTAG
* * * *
27550654 TTTTTAAGCATTGCGTGACTGGTTTTTAAGGCATTTCATGATTAG
1 TTTTTAGGCATTGCATGACTGGTTTTTAAGGCATTGCATGACTAG
* * **
27550699 TTTTTAGGCATTGCGTGACTGCTTAATAAGGCATT
1 TTTTTAGGCATTGCATGACTGGTTTTTAAGGCATT
27550734 ATGTGATTGG
Statistics
Matches: 169, Mismatches: 37, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
43 18 0.11
44 37 0.22
45 76 0.45
46 38 0.22
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.39
Consensus pattern (45 bp):
TTTTTAGGCATTGCATGACTGGTTTTTAAGGCATTGCATGACTAG
Found at i:27550739 original size:23 final size:23
Alignment explanation
Indices: 27550704--27550765 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 23
27550694 ATTAGTTTTT
** *
27550704 AGGCATTGCGTGACTGCTTAAT-A
1 AGGCATTATGTGACTG-GTAATGA
* *
27550727 AGGCATTATGTGATTGGTAATGT
1 AGGCATTATGTGACTGGTAATGA
*
27550750 AGGTATTATGTGACTG
1 AGGCATTATGTGACTG
27550766 ATTTCTAGGC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (23 bp):
AGGCATTATGTGACTGGTAATGA
Found at i:27560560 original size:2 final size:2
Alignment explanation
Indices: 27560553--27560586 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
27560543 TTTCTATTGC
* *
27560553 AT AT AT AT AT AT AT AT AT AT AC AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27560587 GAACACCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:27561596 original size:19 final size:20
Alignment explanation
Indices: 27561572--27561619 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
27561562 AAATTATCAG
*
27561572 TATTTTTATCTTC-TTCATT
1 TATTTTTATCCTCATTCATT
*
27561591 TA-TTTTACCCTCATTCATT
1 TATTTTTATCCTCATTCATT
27561610 TATTTCTTAT
1 TATTT-TTAT
27561620 GCCTACTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 8 0.35
19 10 0.43
20 2 0.09
21 3 0.13
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTATCCTCATTCATT
Found at i:27563870 original size:6 final size:6
Alignment explanation
Indices: 27563859--27563883 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27563849 GCTCATAATC
27563859 TATAAA TATAAA TATAAA TATAAA T
1 TATAAA TATAAA TATAAA TATAAA T
27563884 TCTTAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:27576421 original size:19 final size:20
Alignment explanation
Indices: 27576394--27576439 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
27576384 AGGAGACAAG
*
27576394 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
27576413 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
27576432 ATAATATT
1 ATAATATT
27576440 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:27578253 original size:13 final size:13
Alignment explanation
Indices: 27578235--27578259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27578225 GGAGAAATTG
27578235 TGATTTTATAAAA
1 TGATTTTATAAAA
27578248 TGATTTTATAAA
1 TGATTTTATAAA
27578260 TTTTCTAGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:27584151 original size:22 final size:22
Alignment explanation
Indices: 27584132--27584189 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
27584122 ATGTGTCATG
27584132 CAATACCT-AAAACTCAGTCAAA
1 CAATACCTAAAAAC-CAGTCAAA
*
27584154 CAATGCCTAAAAACCAGTCAAA
1 CAATACCTAAAAACCAGTCAAA
* *
27584176 CAATGCATAAAAAC
1 CAATACCTAAAAAC
27584190 AAGACACGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.16
Consensus pattern (22 bp):
CAATACCTAAAAACCAGTCAAA
Found at i:27584188 original size:23 final size:23
Alignment explanation
Indices: 27584140--27584189 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
27584130 TGCAATACCT
*
27584140 AAAACTCAGTCAAACAATGCCTA
1 AAAACTCAGTCAAACAATGCATA
27584163 AAAAC-CAGTCAAACAATGCATA
1 AAAACTCAGTCAAACAATGCATA
27584185 AAAAC
1 AAAAC
27584190 AAGACACGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.54, C:0.24, G:0.08, T:0.14
Consensus pattern (23 bp):
AAAACTCAGTCAAACAATGCATA
Found at i:27584343 original size:38 final size:38
Alignment explanation
Indices: 27584301--27584399 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 38
27584291 TCATGTAATA
* * *
27584301 CCTAAGTCACGCAATGCCTAAAAATCAGTCACGTAAAG
1 CCTAAGTCACGCAATGCCTAAAAACCAGACACGCAAAG
* * * *
27584339 CCTAAGTTAAGCAATGCCTAAAAACCAGAGACGCAATG
1 CCTAAGTCACGCAATGCCTAAAAACCAGACACGCAAAG
**
27584377 ATTAAGTCACGCAATGCCTAAAA
1 CCTAAGTCACGCAATGCCTAAAA
27584400 GCATGTCTCA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.18
Consensus pattern (38 bp):
CCTAAGTCACGCAATGCCTAAAAACCAGACACGCAAAG
Found at i:27584449 original size:41 final size:41
Alignment explanation
Indices: 27584383--27584460 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
27584373 AATGATTAAG
*
27584383 TCACGCAATGCCTAAAAGCATGTCTCACAATACCTAAGTGA
1 TCACGCAATGCCTAAAAACATGTCTCACAATACCTAAGTGA
* * *
27584424 TCACGTAATGCCTAAAAAC-TAGTCTCTCAATGCCTAA
1 TCACGCAATGCCTAAAAACAT-GTCTCACAATACCTAA
27584461 AAGCCAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.03
41 31 0.97
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (41 bp):
TCACGCAATGCCTAAAAACATGTCTCACAATACCTAAGTGA
Found at i:27584498 original size:22 final size:21
Alignment explanation
Indices: 27584451--27584503 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
27584441 ACTAGTCTCT
*
27584451 CAATGCCTAAAAGCCAATGATG
1 CAATGCCTAAAAACCAATGA-G
27584473 CAATGCCTAAAAACCAATTGCA-
1 CAATGCCTAAAAACCAA-TG-AG
27584495 CAATGCCTA
1 CAATGCCTA
27584504 TTAATTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 25 0.89
23 2 0.07
24 1 0.04
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (21 bp):
CAATGCCTAAAAACCAATGAG
Found at i:27619119 original size:23 final size:23
Alignment explanation
Indices: 27619091--27619137 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
27619081 TTCATTCTTC
*
27619091 TCTTTAATTATTCTTTCAAGTTA
1 TCTTTAATTATTATTTCAAGTTA
* * *
27619114 TCTTTATTTGTTATTTTAAGTTA
1 TCTTTAATTATTATTTCAAGTTA
27619137 T
1 T
27619138 ATTTTTATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.09, G:0.06, T:0.62
Consensus pattern (23 bp):
TCTTTAATTATTATTTCAAGTTA
Found at i:27626749 original size:21 final size:21
Alignment explanation
Indices: 27626719--27626760 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27626709 CCTAGGGAGA
27626719 ATATTGTGGTTGA-ATTTGATG
1 ATATTGTGG-TGATATTTGATG
*
27626740 ATATTTTGGTGATATTTGATG
1 ATATTGTGGTGATATTTGATG
27626761 TTAGGTGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (21 bp):
ATATTGTGGTGATATTTGATG
Found at i:27628267 original size:22 final size:23
Alignment explanation
Indices: 27628224--27628268 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
27628214 AGCTTTTACG
27628224 CTACAAAAATTATTTACGTATAACT
1 CTACAAAAATTATTTA--TATAACT
*
27628249 CTACAAATATTATTT-TATAA
1 CTACAAAAATTATTTATATAA
27628269 GAAAATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
25 14 0.74
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (23 bp):
CTACAAAAATTATTTATATAACT
Found at i:27630538 original size:45 final size:47
Alignment explanation
Indices: 27630484--27630575 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 47
27630474 ATTGAGTAGC
27630484 TTTATTAGTCCTATAATTATTATCATA-TTTTTCTCAAAACCAAACT
1 TTTATTAGTCCTATAATTATTATCATATTTTTTCTCAAAACCAAACT
27630530 TTTA-TAGTCCTATAATTATTATCATATTTTTTCTCAAAACCAAACT
1 TTTATTAGTCCTATAATTATTATCATATTTTTTCTCAAAACCAAACT
27630576 CTTAATATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 22 0.49
46 23 0.51
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (47 bp):
TTTATTAGTCCTATAATTATTATCATATTTTTTCTCAAAACCAAACT
Found at i:27696903 original size:97 final size:97
Alignment explanation
Indices: 27696768--27696960 Score: 289
Period size: 97 Copynumber: 2.0 Consensus size: 97
27696758 AGAAAACACT
* *
27696768 AAGATTATCCACAAAAGAGACAAGAAAATCAGCAACAAAACAAATATTGAAGATTAAATTTGAAA
1 AAGATTATACACAAAAAAGACAAGAAAATCAGCAACAAAACAAATATTGAAGATTAAATTTGAAA
27696833 AAAAAGAA-GCAAAAATTAACAACAAAGCAAGG
66 AAAAA-AAGGCAAAAATTAACAACAAAGCAAGG
* * * * *
27696865 AAGATTTTACACAAAAAAGACAAGAAAATTAGCTACAAAACAAGTATTGAATATTAAATTTGAAA
1 AAGATTATACACAAAAAAGACAAGAAAATCAGCAACAAAACAAATATTGAAGATTAAATTTGAAA
*
27696930 AAAAAAAGGGCAAAAATTAGCAACAAAGCAA
66 AAAAAAA-GGCAAAAATTAACAACAAAGCAA
27696961 AGATTGAATG
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
96 2 0.02
97 63 0.73
98 21 0.24
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (97 bp):
AAGATTATACACAAAAAAGACAAGAAAATCAGCAACAAAACAAATATTGAAGATTAAATTTGAAA
AAAAAAAGGCAAAAATTAACAACAAAGCAAGG
Found at i:27696946 original size:53 final size:54
Alignment explanation
Indices: 27696889--27696990 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 54
27696879 AAAAGACAAG
* *
27696889 AAAATTAGCTACAAAAC-AAGTATTGAATATTAAATTTG-AAAAAAAAAAGGGCA
1 AAAATTAGCAACAAAACAAAG-ATTGAATATTAAACTTGTAAAAAAAAAAGGGCA
* *
27696942 AAAATTAGCAACAAAGCAAAGATTGAATGTTAAACTTGTAAAAAAAAAA
1 AAAATTAGCAACAAAACAAAGATTGAATATTAAACTTGTAAAAAAAAAA
27696991 ATGTAAAGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
53 30 0.70
54 13 0.30
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.22
Consensus pattern (54 bp):
AAAATTAGCAACAAAACAAAGATTGAATATTAAACTTGTAAAAAAAAAAGGGCA
Found at i:27697066 original size:68 final size:67
Alignment explanation
Indices: 27696980--27697107 Score: 206
Period size: 68 Copynumber: 1.9 Consensus size: 67
27696970 GTTAAACTTG
27696980 TAAAAAAAAAAATGTAAAGCAAAGGAGAAGG-TTTGGTTGCATGGAAGAAAATTAAAACAATTTT
1 TAAAAAAAAAAATGTAAAGCAAAGGAG-AGGTTTTGGTTGCATGGAAGAAAATTAAAACAATTTT
27697044 TTT
65 TTT
*
27697047 TAAAAAAAAAGGAA-GTAAAGGAAAGGAGAGGTTTTGGTTGCATGGAAGAAAATTAAAACAA
1 TAAAAAAAAA--AATGTAAAGCAAAGGAGAGGTTTTGGTTGCATGGAAGAAAATTAAAACAA
27697108 AAATAAGAAG
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
67 13 0.23
68 42 0.74
69 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.23
Consensus pattern (67 bp):
TAAAAAAAAAAATGTAAAGCAAAGGAGAGGTTTTGGTTGCATGGAAGAAAATTAAAACAATTTTT
TT
Found at i:27702224 original size:19 final size:19
Alignment explanation
Indices: 27702200--27702237 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
27702190 CTGCCAAACC
*
27702200 CTCAAATTATACTCCAATA
1 CTCAAATAATACTCCAATA
27702219 CTCAAATAATACTCCAATA
1 CTCAAATAATACTCCAATA
27702238 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATAATACTCCAATA
Found at i:27709873 original size:20 final size:20
Alignment explanation
Indices: 27709847--27709887 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
27709837 TTTTTAGTTG
27709847 TTTTTA-TA-ATTA-TTTAA
1 TTTTTATTATATTATTTTAA
*
27709864 TTTTTATTATGTTATTTTAA
1 TTTTTATTATATTATTTTAA
27709884 TTTT
1 TTTT
27709888 ATGTTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 2 0.10
19 3 0.15
20 9 0.45
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTATTATATTATTTTAA
Found at i:27712925 original size:20 final size:20
Alignment explanation
Indices: 27712900--27712945 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
27712890 TTTTGACCCC
27712900 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
27712920 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
27712940 ATTTGA
1 ATTTGA
27712946 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:27713021 original size:28 final size:27
Alignment explanation
Indices: 27712990--27713042 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
27712980 TTTGGAGTAT
*
27712990 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
27713018 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
27713043 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:27713048 original size:28 final size:28
Alignment explanation
Indices: 27712990--27713048 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
27712980 TTTGGAGTAT
* *
27712990 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
27713018 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
27713046 AGG
1 AGG
27713049 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:27715607 original size:24 final size:25
Alignment explanation
Indices: 27715575--27715622 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
27715565 GATTAATGAC
27715575 TCAATTAATTAAT-ATAAATTTCAA
1 TCAATTAATTAATAATAAATTTCAA
* *
27715599 TCAATTAATTTATAATCAATTTCA
1 TCAATTAATTAATAATAAATTTCA
27715623 TAGACCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (25 bp):
TCAATTAATTAATAATAAATTTCAA
Found at i:27734260 original size:33 final size:31
Alignment explanation
Indices: 27734222--27734294 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 31
27734212 TTGTAAGACA
*
27734222 TTTAGAAAAATGATAACA-TATGTTTGTATGTT
1 TTTAGAAAAATCATAA-AGTATGTTTGTATG-T
*
27734254 TATTAGATAAATCATAAAGTATGTTTGTATGT
1 T-TTAGAAAAATCATAAAGTATGTTTGTATGT
27734286 TTTAGAAAA
1 TTTAGAAAA
27734295 TGCTTCTAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 7 0.19
32 4 0.11
33 25 0.69
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (31 bp):
TTTAGAAAAATCATAAAGTATGTTTGTATGT
Found at i:27741558 original size:22 final size:22
Alignment explanation
Indices: 27741533--27741586 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
27741523 TGGTACCTCA
*
27741533 CTCAAGTGTCTACACAATACTT
1 CTCATGTGTCTACACAATACTT
*
27741555 CTCATGTGTCTATACAATACTT
1 CTCATGTGTCTACACAATACTT
27741577 CTCATGTGTC
1 CTCATGTGTC
27741587 AATTGTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (22 bp):
CTCATGTGTCTACACAATACTT
Found at i:27760984 original size:42 final size:42
Alignment explanation
Indices: 27760925--27761058 Score: 160
Period size: 42 Copynumber: 3.2 Consensus size: 42
27760915 TCACATGAGT
*
27760925 TGATGATGACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGT
1 TGATGATGACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGC
** * * *
27760967 TGATGATGACCTAGCTATGTGAGAGTAGGAATACGCATAAGC
1 TGATGATGACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGC
** * * *
27761009 CAATGATGACCCGGCTATGTGCAAGTAGCAAGTGTGCATAAGC
1 TGATGATGACCCGGCTATGTGCGAGTAG-GAGTGCGCATAAGC
27761052 TGATGAT
1 TGATGAT
27761059 AATGACTCGG
Statistics
Matches: 73, Mismatches: 18, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
42 58 0.79
43 15 0.21
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (42 bp):
TGATGATGACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGC
Found at i:27794290 original size:2 final size:2
Alignment explanation
Indices: 27794283--27794313 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27794273 ATAGCTTAAA
27794283 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 T
27794314 ATTATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:27794321 original size:3 final size:3
Alignment explanation
Indices: 27794313--27794419 Score: 169
Period size: 3 Copynumber: 34.7 Consensus size: 3
27794303 TGTGTGTGTG
27794313 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* *
27794359 TAT TAGT TAG NAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27794405 TAT TAT TAT GTAT TA
1 TAT TAT TAT -TAT TA
27794420 GTGGCATGCA
Statistics
Matches: 97, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
3 88 0.91
4 9 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:27794533 original size:29 final size:31
Alignment explanation
Indices: 27794476--27794534 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
27794466 AAAAAAAAGA
* *
27794476 TAATTGAAGTAAAGAGAATGGTTGAAGGACC
1 TAATTGAAATAAAGAGAATAGTTGAAGGACC
*
27794507 TAATTGAAATAAAGA-AA-AGTTGGAGGAC
1 TAATTGAAATAAAGAGAATAGTTGAAGGAC
27794535 TTAAGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 2 0.08
31 14 0.56
ACGTcount: A:0.46, C:0.05, G:0.27, T:0.22
Consensus pattern (31 bp):
TAATTGAAATAAAGAGAATAGTTGAAGGACC
Found at i:27795642 original size:39 final size:39
Alignment explanation
Indices: 27795586--27795671 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
27795576 ATGTTTGGTG
*
27795586 TCACCTTTTGCCAGAAAGTGGAAATACGTTGATATAGTA
1 TCACCTTTTGCCAGAAAGTGAAAATACGTTGATATAGTA
* * *
27795625 TCACCTTTTGTCGGAAAGTGAAAATACGTTGGTATAGTA
1 TCACCTTTTGCCAGAAAGTGAAAATACGTTGATATAGTA
27795664 TCACCTTT
1 TCACCTTT
27795672 GATGGGGAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (39 bp):
TCACCTTTTGCCAGAAAGTGAAAATACGTTGATATAGTA
Found at i:27795873 original size:57 final size:57
Alignment explanation
Indices: 27795812--27795919 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
27795802 ATTCTATTCG
* * *
27795812 ATGAGTATATTTTGGATGATGATGTTAACACTGTATGTGTTTCTGGGAGTTTGCCCA
1 ATGAGTACATTTCGGATGATGATGTTAACACTATATGTGTTTCTGGGAGTTTGCCCA
* * *
27795869 ATGAGTGCATTTCGGGTGATGATGTTAACACTATATGTGTTTTTGGGAGTT
1 ATGAGTACATTTCGGATGATGATGTTAACACTATATGTGTTTCTGGGAGTT
27795920 CACCTGATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (57 bp):
ATGAGTACATTTCGGATGATGATGTTAACACTATATGTGTTTCTGGGAGTTTGCCCA
Found at i:27799506 original size:39 final size:40
Alignment explanation
Indices: 27799414--27799506 Score: 129
Period size: 39 Copynumber: 2.4 Consensus size: 40
27799404 GCTTTAGACA
*
27799414 ATGACATGAGTATT-TCGTCAGTGGCTATGACACTGGACG
1 ATGACATGAGTATTCTCGTCAGTGGCTATGACACTGAACG
* *
27799453 ATGACATGAGTATTCT-GTTAGTGGCTACTG-CACTGAATG
1 ATGACATGAGTATTCTCGTCAGTGGCTA-TGACACTGAACG
27799492 ATGACATGAGTATTC
1 ATGACATGAGTATTC
27799507 CATCGATGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
39 46 0.94
40 3 0.06
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (40 bp):
ATGACATGAGTATTCTCGTCAGTGGCTATGACACTGAACG
Found at i:27833769 original size:6 final size:6
Alignment explanation
Indices: 27833758--27833783 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27833748 AATCATATCT
27833758 GGAGTA GGAGTA GGAGTA GGAGTA GG
1 GGAGTA GGAGTA GGAGTA GGAGTA GG
27833784 GCAGGGACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (6 bp):
GGAGTA
Found at i:27841576 original size:34 final size:32
Alignment explanation
Indices: 27841514--27841576 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 32
27841504 ATGGTAAGTT
* *
27841514 ACAAGAAAAGAAAAATAAAAATAAAAAGACAC
1 ACAAGAAAAGAAAAAGAAAAAGAAAAAGACAC
*
27841546 ACAAGAGAAGAGAAAAAGAAAAAGAGAAAGA
1 ACAAGA-AA-AGAAAAAGAAAAAGAAAAAGA
27841577 GGTGTAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 6 0.23
33 2 0.08
34 18 0.69
ACGTcount: A:0.73, C:0.06, G:0.17, T:0.03
Consensus pattern (32 bp):
ACAAGAAAAGAAAAAGAAAAAGAAAAAGACAC
Found at i:27842072 original size:1 final size:1
Alignment explanation
Indices: 27842066--27842090 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
27842056 TTGAAATTGA
27842066 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
27842091 ACTTTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27843928 original size:33 final size:32
Alignment explanation
Indices: 27843823--27843951 Score: 105
Period size: 33 Copynumber: 3.9 Consensus size: 32
27843813 AGTGAATGAC
* * *
27843823 AACAAGTTTAAGTTGAGGGTGAGCTTGAACCAT
1 AACAAGTTGAAGTTGAGGG-GAACCTGAACCAT
* * * * * * *
27843856 AGCAAGCTAAAGTTGAAGGGGAGCCTAAATCAC
1 AACAAGTTGAAGTTG-AGGGGAACCTGAACCAT
*
27843889 AGCAAGTTGAAGTTGAGGGGAAACCTGAACCAT
1 AACAAGTTGAAGTTGAGGGG-AACCTGAACCAT
* *
27843922 AACAAGTTGAGGCTGAGGGGGAACCTGAAC
1 AACAAGTTGAAGTTGA-GGGGAACCTGAAC
27843952 TAGAGCAAGT
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
32 5 0.06
33 64 0.83
34 8 0.10
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.19
Consensus pattern (32 bp):
AACAAGTTGAAGTTGAGGGGAACCTGAACCAT
Found at i:27843961 original size:33 final size:33
Alignment explanation
Indices: 27843889--27843968 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
27843879 CCTAAATCAC
* *
27843889 AGCAAGTTGAAGTTGAGGGGAAACCTGAACCAT
1 AGCAAGTTGAAGCTGAGGGGAAACCTGAACCAG
* * * *
27843922 AACAAGTTGAGGCTGAGGGGGAACCTGAACTAG
1 AGCAAGTTGAAGCTGAGGGGAAACCTGAACCAG
*
27843955 AGCAAGTTAAAGCT
1 AGCAAGTTGAAGCT
27843969 AAGAATGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.36, C:0.15, G:0.31, T:0.17
Consensus pattern (33 bp):
AGCAAGTTGAAGCTGAGGGGAAACCTGAACCAG
Found at i:27845057 original size:27 final size:27
Alignment explanation
Indices: 27845019--27845073 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
27845009 ACAAAATCCA
*
27845019 ACTTATAACACATGTA-ATTGCTTAATT
1 ACTTATAACACAT-TACATTACTTAATT
27845046 ACTTATAACACATTACATTACTTAATT
1 ACTTATAACACATTACATTACTTAATT
27845073 A
1 A
27845074 GATAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (27 bp):
ACTTATAACACATTACATTACTTAATT
Found at i:27846066 original size:23 final size:23
Alignment explanation
Indices: 27846040--27846083 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
27846030 AAACAACATT
* *
27846040 CAAATAATAACAATAATTTCACA
1 CAAATAACAACAACAATTTCACA
*
27846063 CAAATAACAACCACAATTTCA
1 CAAATAACAACAACAATTTCA
27846084 TATATGAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (23 bp):
CAAATAACAACAACAATTTCACA
Found at i:27854695 original size:92 final size:91
Alignment explanation
Indices: 27854545--27854802 Score: 325
Period size: 78 Copynumber: 3.0 Consensus size: 91
27854535 TTAACCACCT
* *
27854545 CCAAGTAAAGTATAAGTTT-C--CAAGACAAATTATCATTCAGATACCAGAACAGACAAATTCAT
1 CCAAGTAAACTATAAGTTTCCAGCAAGACAAATTATCATTCAGATACCAGAACAGACAAATTTAT
27854607 CCTCATAAAGGGCATTAACCACCCCC
66 CCTCATAAAGGGCATTAACCACCCCC
*
27854633 CCAAGTGAACTATAAGTTTCCAGGACAAGACAAATTATCA-TCAGATACCAGAACAGACAAATTT
1 CCAAGTAAACTATAAGTTTCCA-G-CAAGACAAATTATCATTCAGATACCAGAACAGACAAATTT
27854697 AT-C-C-T------CATTAACCA-CCCC
64 ATCCTCATAAAGGGCATTAACCACCCCC
*
27854715 CCAAGTAAACTATAAGTTTCCAG---GACAAATTATCATTCAGATATCAGAACAGACAAATTTAT
1 CCAAGTAAACTATAAGTTTCCAGCAAGACAAATTATCATTCAGATACCAGAACAGACAAATTTAT
* *
27854777 CCTTATAAAGGGAATTAACCACCCCC
66 CCTCATAAAGGGCATTAACCACCCCC
27854803 AGTAATTTAT
Statistics
Matches: 147, Mismatches: 7, Indels: 32
0.79 0.04 0.17
Matches are distributed among these distances:
77 12 0.08
78 25 0.17
79 1 0.01
81 2 0.01
82 25 0.17
83 9 0.06
87 8 0.05
88 21 0.14
89 2 0.01
90 1 0.01
91 1 0.01
92 25 0.17
93 15 0.10
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (91 bp):
CCAAGTAAACTATAAGTTTCCAGCAAGACAAATTATCATTCAGATACCAGAACAGACAAATTTAT
CCTCATAAAGGGCATTAACCACCCCC
Found at i:27859318 original size:3 final size:3
Alignment explanation
Indices: 27859310--27859342 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
27859300 AGATTGATAG
27859310 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27859343 CACAGTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:27868891 original size:21 final size:21
Alignment explanation
Indices: 27868867--27868944 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
27868857 AAGATAAGAT
*
27868867 ATTACATTTAAATTTAAACAA
1 ATTAAATTTAAATTTAAACAA
* **
27868888 ATTAAATTTAAATGTAATTAA
1 ATTAAATTTAAATTTAAACAA
*
27868909 TCATT--ATTTAAATTTATACAA
1 --ATTAAATTTAAATTTAAACAA
27868930 ATTAAATTTAAATTT
1 ATTAAATTTAAATTT
27868945 CTATCCTATC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
19 3 0.07
21 39 0.87
23 3 0.07
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (21 bp):
ATTAAATTTAAATTTAAACAA
Found at i:27870828 original size:45 final size:46
Alignment explanation
Indices: 27870773--27870883 Score: 120
Period size: 45 Copynumber: 2.5 Consensus size: 46
27870763 ATTTTTATTT
* * * *
27870773 AACATAGCGTGTAACAAATTTT-GAACTTG-CATGTAACATGTTGTG
1 AACATGGCGTGTAAC-AATTTTCGAACATGACATGTAACATGTTCTA
* *
27870818 AACATGGCGTGTAAC-ATTTTCGAACATGACGTGTAACATTTTCTA
1 AACATGGCGTGTAACAATTTTCGAACATGACATGTAACATGTTCTA
* *
27870863 AACATGGTGTGTAACATTTTT
1 AACATGGCGTGTAACAATTTT
27870884 TAAAAATGGC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
43 5 0.09
44 6 0.11
45 40 0.73
46 4 0.07
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (46 bp):
AACATGGCGTGTAACAATTTTCGAACATGACATGTAACATGTTCTA
Found at i:27870832 original size:23 final size:23
Alignment explanation
Indices: 27870749--27870901 Score: 139
Period size: 23 Copynumber: 6.7 Consensus size: 23
27870739 ATGTGTTAGC
*
27870749 ACATGGCGTGTAACATTTTTATTTA
1 ACATGGCGTGTAACA-TTTT-TTGA
* **
27870774 ACATAGCGTGTAACAAATTTTGA
1 ACATGGCGTGTAACATTTTTTGA
* * * *
27870797 AC-TTGCATGTAACATGTTGTGA
1 ACATGGCGTGTAACATTTTTTGA
*
27870819 ACATGGCGTGTAACA-TTTTCGA
1 ACATGGCGTGTAACATTTTTTGA
* * *
27870841 ACATGACGTGTAACATTTTCTAA
1 ACATGGCGTGTAACATTTTTTGA
* *
27870864 ACATGGTGTGTAACATTTTTTAA
1 ACATGGCGTGTAACATTTTTTGA
*
27870887 AAATGGCGTGTAACA
1 ACATGGCGTGTAACA
27870902 ACATGACTGA
Statistics
Matches: 103, Mismatches: 23, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
22 35 0.34
23 52 0.50
24 2 0.02
25 14 0.14
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (23 bp):
ACATGGCGTGTAACATTTTTTGA
Found at i:27874772 original size:31 final size:30
Alignment explanation
Indices: 27874737--27874865 Score: 83
Period size: 31 Copynumber: 4.4 Consensus size: 30
27874727 CCCAATTGTG
27874737 GTGACACGCTGAGTGCATGCAGACTTCTGGT
1 GTGACACGCTGAGTGCATGCAGA-TTCTGGT
* * * * *
27874768 GTGACACGCTGACTTG-TTGTAGTATTGTGGG
1 GTGACACGCTGA-GTGCATGCAG-ATTCTGGT
* ** *
27874799 GTGACACGC-CA-TGC-CCCA-ATTGT-G-
1 GTGACACGCTGAGTGCATGCAGATTCTGGT
*
27874823 GTGACACGCTGAGTGCATGCAGACTTCTAGT
1 GTGACACGCTGAGTGCATGCAGA-TTCTGGT
27874854 GTGACACGCTGA
1 GTGACACGCTGA
27874866 CTTGTTGCAG
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
24 9 0.12
25 2 0.03
26 8 0.11
27 2 0.03
28 4 0.05
29 3 0.04
30 2 0.03
31 42 0.56
32 3 0.04
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.26
Consensus pattern (30 bp):
GTGACACGCTGAGTGCATGCAGATTCTGGT
Found at i:27874869 original size:172 final size:172
Alignment explanation
Indices: 27874560--27875174 Score: 802
Period size: 172 Copynumber: 3.6 Consensus size: 172
27874550 CAATGACATC
* * * *
27874560 TTGTGGTGACACGCTGAGTGCATGCAGACTTTTTGCATGACACGTTGACTTGTTGTAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCGTGACACGCTGACTTGTTGTAGTATTGTG
* * * * *
27874625 GGGTGACATGGCAC-CTGCCAATTGTGGTGACACGCTGAGTGCATGCAAACTTTTAGTTTGACAC
66 GGGTGACACGCCACGC-CCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTTTAGTATGACAC
** *
27874689 ATTGACTTGTTGCAGTATTGTGGGGTGACACGCCATGCCCCAA
130 GCTGACTTGTTGCAGTATTGTGGGGTGACACGCCACGCCCCAA
*
27874732 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGTGTGACACGCTGACTTGTTGTAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCGTGACACGCTGACTTGTTGTAGTATTGTG
* * *
27874797 GGGTGACACGCCATGCCCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTCTAGTGTGACACG
66 GGGTGACACGCCACGCCCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTTTAGTATGACACG
* **
27874862 CTGACTTGTTGCAGTATTGTGGGGTGACACGGCACGGGCCAA
131 CTGACTTGTTGCAGTATTGTGGGGTGACACGCCACGCCCCAA
*** ** * * * *
27874904 TTGTGGTGACATAATGAGTATATGTAGACTTCAGGTGTGACACACTGACTTGTTGTAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCGTGACACGCTGACTTGTTGTAGTATTGTG
* * ** * * * * *
27874969 AGGTGACACGGCACGGGCCAATTGTGGTGACACGTTGAGTGCATGTAGACTTTTTGCATGACGCG
66 GGGTGACACGCCACGCCCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTTTAGTATGACACG
* *
27875034 CTGACTTGTTGCAGTATTGTGGGGTGACACGTCACGCCTCAA
131 CTGACTTGTTGCAGTATTGTGGGGTGACACGCCACGCCCCAA
* * *
27875076 TTGTGGTGACACGCTGAGTGCATGCAGATTTCTAGCGTGACACGCTGACTTGTTGCAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCGTGACACGCTGACTTGTTGTAGTATTGTG
** *
27875141 GGGTGACAATCCACGCCCCAATAG-GGTGACACGC
66 GGGTGACACGCCACGCCCCAATTGTGGTGACACGC
27875175 CACGTGGTTG
Statistics
Matches: 380, Mismatches: 62, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
171 9 0.02
172 370 0.97
173 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (172 bp):
TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCGTGACACGCTGACTTGTTGTAGTATTGTG
GGGTGACACGCCACGCCCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTTTAGTATGACACG
CTGACTTGTTGCAGTATTGTGGGGTGACACGCCACGCCCCAA
Found at i:27875038 original size:258 final size:258
Alignment explanation
Indices: 27874560--27875148 Score: 829
Period size: 258 Copynumber: 2.3 Consensus size: 258
27874550 CAATGACATC
* * * * *
27874560 TTGTGGTGACACGCTGAGTGCATGCAGACTTTTTGCATGACACGTTGACTTGTTGTAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTAGCGTGACACGCTGACTTGTTGCAGTATTGTG
* * ** * * *
27874625 GGGTGACATGGCACCTGCCAATTGTGGTGACACGCTGAGTGCATGCAAACTTTTAGTTTGACACA
66 GGGTGACACGGCACCGGCCAATTGTGGTGACACAATGAGTACATGCAAACTTTCAGTGTGACACA
* * *
27874690 TTGACTTGTTGCAGTATTGTGGGGTGACACGCCATGCCCCAATTGTGGTGACACGCTGAGTGCAT
131 CTGACTTGTTGCAGTATTGTGAGGTGACACGCCACGCCCCAATTGTGGTGACACGCTGAGTGCAT
** * *
27874755 GCAGACTTCTGGTGTGACACGCTGACTTGTTGTAGTATTGTGGGGTGACACGCCATGCCCCAA
196 GCAGACTTCTGGCATGACACGCTGACTTGTTGCAGTATTGTGGGGTGACACGCCACGCCCCAA
*
27874818 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTAGTGTGACACGCTGACTTGTTGCAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTAGCGTGACACGCTGACTTGTTGCAGTATTGTG
* * * * *
27874883 GGGTGACACGGCACGGGCCAATTGTGGTGACATAATGAGTATATGTAGAC-TTCAGGTGTGACAC
66 GGGTGACACGGCACCGGCCAATTGTGGTGACACAATGAGTACATGCAAACTTTCA-GTGTGACAC
* * ** *
27874947 ACTGACTTGTTGTAGTATTGTGAGGTGACACGGCACGGGCCAATTGTGGTGACACGTTGAGTGCA
130 ACTGACTTGTTGCAGTATTGTGAGGTGACACGCCACGCCCCAATTGTGGTGACACGCTGAGTGCA
* * * * * *
27875012 TGTAGACTTTTTGCATGACGCGCTGACTTGTTGCAGTATTGTGGGGTGACACGTCACGCCTCAA
195 TGCAGACTTCTGGCATGACACGCTGACTTGTTGCAGTATTGTGGGGTGACACGCCACGCCCCAA
*
27875076 TTGTGGTGACACGCTGAGTGCATGCAGATTTCTAGCGTGACACGCTGACTTGTTGCAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTAGCGTGACACGCTGACTTGTTGCAGTATTGTG
27875141 GGGTGACA
66 GGGTGACA
27875149 ATCCACGCCC
Statistics
Matches: 292, Mismatches: 38, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
257 3 0.01
258 289 0.99
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (258 bp):
TTGTGGTGACACGCTGAGTGCATGCAGACTTCTAGCGTGACACGCTGACTTGTTGCAGTATTGTG
GGGTGACACGGCACCGGCCAATTGTGGTGACACAATGAGTACATGCAAACTTTCAGTGTGACACA
CTGACTTGTTGCAGTATTGTGAGGTGACACGCCACGCCCCAATTGTGGTGACACGCTGAGTGCAT
GCAGACTTCTGGCATGACACGCTGACTTGTTGCAGTATTGTGGGGTGACACGCCACGCCCCAA
Found at i:27875156 original size:86 final size:86
Alignment explanation
Indices: 27874560--27875174 Score: 729
Period size: 86 Copynumber: 7.2 Consensus size: 86
27874550 CAATGACATC
* ** * *
27874560 TTGTGGTGACACGCTGAGTGCATGCAGACTTT-TTGCATGACACGTTGACTTGTTGTAGTATTGT
1 TTGTGGTGACACGCTGAGTGCATGCAGA-TTTCTAGTGTGACACGCTGACTTGTTGCAGTATTGT
* * *
27874624 GGGGTGACATGGCAC-CTGCCAA
65 GGGGTGACACGCCACGC-CCCAA
* * **
27874646 TTGTGGTGACACGCTGAGTGCATGCAAACTTT-TAGTTTGACACATTGACTTGTTGCAGTATTGT
1 TTGTGGTGACACGCTGAGTGCATGCAGA-TTTCTAGTGTGACACGCTGACTTGTTGCAGTATTGT
*
27874710 GGGGTGACACGCCATGCCCCAA
65 GGGGTGACACGCCACGCCCCAA
* * *
27874732 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGTGTGACACGCTGACTTGTTGTAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGATTTCTAGTGTGACACGCTGACTTGTTGCAGTATTGTG
*
27874797 GGGTGACACGCCATGCCCCAA
66 GGGTGACACGCCACGCCCCAA
*
27874818 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTAGTGTGACACGCTGACTTGTTGCAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGATTTCTAGTGTGACACGCTGACTTGTTGCAGTATTGTG
* **
27874883 GGGTGACACGGCACGGGCCAA
66 GGGTGACACGCCACGCCCCAA
*** ** * * * *
27874904 TTGTGGTGACATAATGAGTATATGTAGACTTC-AGGTGTGACACACTGACTTGTTGTAGTATTGT
1 TTGTGGTGACACGCTGAGTGCATGCAGATTTCTA-GTGTGACACGCTGACTTGTTGCAGTATTGT
* * **
27874968 GAGGTGACACGGCACGGGCCAA
65 GGGGTGACACGCCACGCCCCAA
* * * ** *
27874990 TTGTGGTGACACGTTGAGTGCATGTAGACTTT-TTGCATGACGCGCTGACTTGTTGCAGTATTGT
1 TTGTGGTGACACGCTGAGTGCATGCAGA-TTTCTAGTGTGACACGCTGACTTGTTGCAGTATTGT
* *
27875054 GGGGTGACACGTCACGCCTCAA
65 GGGGTGACACGCCACGCCCCAA
*
27875076 TTGTGGTGACACGCTGAGTGCATGCAGATTTCTAGCGTGACACGCTGACTTGTTGCAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGATTTCTAGTGTGACACGCTGACTTGTTGCAGTATTGTG
**
27875141 GGGTGACAATCCACGCCCCAA
66 GGGTGACACGCCACGCCCCAA
*
27875162 TAG-GGTGACACGC
1 TTGTGGTGACACGC
27875175 CACGTGGTTG
Statistics
Matches: 464, Mismatches: 59, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
85 16 0.03
86 445 0.96
87 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (86 bp):
TTGTGGTGACACGCTGAGTGCATGCAGATTTCTAGTGTGACACGCTGACTTGTTGCAGTATTGTG
GGGTGACACGCCACGCCCCAA
Found at i:27876736 original size:81 final size:81
Alignment explanation
Indices: 27876566--27876737 Score: 215
Period size: 81 Copynumber: 2.1 Consensus size: 81
27876556 GAAAGATGCT
* *
27876566 CTCCTTCAACCACAAGCGAGTGAAGGTCCCCCTCTCCTCTCGCAAATTCATCGATAACTAAATCA
1 CTCCTTCAGCCACAAGCGAGTGAAGGTCCCCCTCTCCTCTCCCAAATTCATCGATAACTAAATCA
*
27876631 ACCTCAGGAACATGGA
66 ACCTCAAGAACATGGA
* * * * *
27876647 CTCCTTCAGCCACGAGCGAGTGAAGGTCCCTCTC-CCT-TCCCTCAGTTACATCGATAA-TGGAA
1 CTCCTTCAGCCACAAGCGAGTGAAGGTCCCCCTCTCCTCTCCC-AAATT-CATCGATAACT-AAA
*
27876709 TCAGCCTCAAGAACATGGA
63 TCAACCTCAAGAACATGGA
27876728 CTCCTTCAGC
1 CTCCTTCAGC
27876738 GTCATCTGAT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
79 3 0.04
80 7 0.09
81 69 0.87
ACGTcount: A:0.27, C:0.34, G:0.17, T:0.22
Consensus pattern (81 bp):
CTCCTTCAGCCACAAGCGAGTGAAGGTCCCCCTCTCCTCTCCCAAATTCATCGATAACTAAATCA
ACCTCAAGAACATGGA
Found at i:27879042 original size:31 final size:31
Alignment explanation
Indices: 27879017--27879095 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
27879007 AAATGTTATT
27879017 ACACGCCATGCATATCAAGTAAAATGTCGTG
1 ACACGCCATGCATATCAAGTAAAATGTCGTG
*
27879048 ACACGCCATGCATATCAAGTCAAATGTCGTG
1 ACACGCCATGCATATCAAGTAAAATGTCGTG
*
27879079 ACACACCATGCATATCA
1 ACACGCCATGCATATCA
27879096 GTGTCGTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (31 bp):
ACACGCCATGCATATCAAGTAAAATGTCGTG
Found at i:27879132 original size:25 final size:25
Alignment explanation
Indices: 27879072--27879133 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
27879062 TCAAGTCAAA
**
27879072 TGTCGTGACACACCATGCATATCAG
1 TGTCGTGACATGCCATGCATATCAG
*
27879097 TGTCGTGACATGCCATGCGTATCAG
1 TGTCGTGACATGCCATGCATATCAG
27879122 TGTCGTGACATG
1 TGTCGTGACATG
27879134 TCAATCACTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (25 bp):
TGTCGTGACATGCCATGCATATCAG
Found at i:27879256 original size:55 final size:55
Alignment explanation
Indices: 27879172--27879542 Score: 456
Period size: 55 Copynumber: 6.8 Consensus size: 55
27879162 ACCAATAGTA
* * *
27879172 GTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCTAGGAACAGTC
1 GTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAAGAACAGCC
* *** * * *
27879227 GTGACATGCTAAAAATTTAAAAAACCAGTTAACCCACAACACGCCAAAAACAACA
1 GTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAAGAACAGCC
* *
27879282 GTGACACGCTAAAAATCCAAAAAACCAGTTAACCCACAACATGCCAAGAACAGCC
1 GTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAAGAACAGCC
* * * * *
27879337 GTGACACGCCAAAAACTCAAAAAACCAGTTAACCCATAACACACCAAGAACATCC
1 GTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAAGAACAGCC
* * * * * * *
27879392 GTGACACGCCAAAAACCTAAAAAATCAATTAACCCACAACATGCCAGGAGCAGCC
1 GTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAAGAACAGCC
* * * * *
27879447 TTGACATGCCAAAAACCCAAAAAATCAGTTAACCCACAACACGCCAAGAACAACC
1 GTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAAGAACAGCC
* *
27879502 GTGACATGCTAAAAACCC-AAAAACCAGTTAACCCATAACAC
1 GTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACAC
27879543 CCCATATGTA
Statistics
Matches: 270, Mismatches: 46, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
54 21 0.08
55 249 0.92
ACGTcount: A:0.46, C:0.30, G:0.11, T:0.12
Consensus pattern (55 bp):
GTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAAGAACAGCC
Found at i:27879328 original size:27 final size:27
Alignment explanation
Indices: 27879245--27879328 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
27879235 CTAAAAATTT
*
27879245 AAAAAACCAGTTAACCCACAACACGCC
1 AAAAAACCAGTTAACCCACAACATGCC
* * * *
27879272 AAAAACAACAGTGACACGCTA-AAAAT-CC
1 AAAAA-ACCAGTTA-AC-CCACAACATGCC
27879300 AAAAAACCAGTTAACCCACAACATGCC
1 AAAAAACCAGTTAACCCACAACATGCC
27879327 AA
1 AA
27879329 GAACAGCCGT
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
25 2 0.05
26 6 0.14
27 15 0.35
28 13 0.30
29 5 0.12
30 2 0.05
ACGTcount: A:0.51, C:0.31, G:0.08, T:0.10
Consensus pattern (27 bp):
AAAAAACCAGTTAACCCACAACATGCC
Found at i:27880148 original size:104 final size:103
Alignment explanation
Indices: 27880010--27880360 Score: 337
Period size: 104 Copynumber: 3.4 Consensus size: 103
27880000 ACATGTTTGA
* * * * * *
27880010 CCATGGTGTGTCGCACACTCTAAACCCTGTCGTGTCACACCCGTCTCACATATTCTCACCATGCC
1 CCATGGCGTGTCACACACTCTAAACTCTGCCGTGTCACACCCGTGTCACATATTCTCACCATGTC
27880075 GTCTCACACATTATCACACTAG-CGTGTCACAAATTCCCT
66 GTCTCACACATTATCAC-CT-GCCGTGTCACAAATTCCCT
* * * * * *
27880114 CCATGACGTGTCACACACTCTAAACTCTACCGTGTTACACCCGTGTCACACATTATCACCGTGTC
1 CCATGGCGTGTCACACACTCTAAACTCTGCCGTGTCACACCCGTGTCACATATTCTCACCATGTC
* * * *** ***
27880179 ATTTCACACATTATGACCTTGCCGTGTCACACGCTCTGA
66 GTCTCACACATTATCACC-TGCCGTGTCACAAATTCCCT
* * * * * *
27880218 CCACGGCATGTCACACATTTTAAACGT-TGCCATGTCACACCCGTGTCACATATTCTCACCTTGT
1 CCATGGCGTGTCACACACTCTAAAC-TCTGCCGTGTCACACCCGTGTCACATATTCTCACCATGT
* *
27880282 CGTCTCACACATTATCACCCTGCCATGTCACAAATTTCCT
65 CGTCTCACACATTATCA-CCTGCCGTGTCACAAATTCCCT
* * * **
27880322 CCATGGTGTGCCACACACTCTAAACCCTGCATTGTCACA
1 CCATGGCGTGTCACACACTCTAAACTCTGCCGTGTCACA
27880361 TATTATCACA
Statistics
Matches: 190, Mismatches: 52, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
103 2 0.01
104 185 0.97
105 3 0.02
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.28
Consensus pattern (103 bp):
CCATGGCGTGTCACACACTCTAAACTCTGCCGTGTCACACCCGTGTCACATATTCTCACCATGTC
GTCTCACACATTATCACCTGCCGTGTCACAAATTCCCT
Found at i:27880208 original size:23 final size:23
Alignment explanation
Indices: 27880154--27880210 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
27880144 CGTGTTACAC
27880154 CCGTGTCACACATTATCACCGTG
1 CCGTGTCACACATTATCACCGTG
* * * * *
27880177 TCATTTCACACATTATGACCTTG
1 CCGTGTCACACATTATCACCGTG
27880200 CCGTGTCACAC
1 CCGTGTCACAC
27880211 GCTCTGACCA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30
Consensus pattern (23 bp):
CCGTGTCACACATTATCACCGTG
Found at i:27880313 original size:208 final size:195
Alignment explanation
Indices: 27879991--27880451 Score: 519
Period size: 208 Copynumber: 2.3 Consensus size: 195
27879981 GTTCAAGCCA
* * * ** * * * *
27879991 TGCCGTGTCACATGTTTGACCATGGTGTGTCGCACACTCTAAACCCTGTCGTGTCACACCCGTCT
1 TGCCGTGTCACACGTCTGACCACGGCATGTCACACACTCTAAACCTTGCCATGTCACACCCGTCT
*
27880056 CACATATTCTCACCATGCCGTCTCACACATTATCACACTAGCGTGTCACAAATTCCCTCCATGAC
66 CACATATTCTCACCATGCCGTCTCACACATTATCACACTAGCATGTCACAAATTCCCTCCATGAC
* *
27880121 GTGTCACACACTCTAAACTCTACCGTGTTACACCCGTGTCACACATTATCACCGTGTCATTTCAC
131 GTGCCACACACTCTAAA--C--CC-TG---CA---GTGTCACACATTATCA-CATGTCATTTCAC
* *
27880186 ACATTATGACCT
184 ACATTATAACCC
* * * *
27880198 TGCCGTGTCACACGCTCTGACCACGGCATGTCACACATTTTAAACGTTGCCATGTCACACCCGTG
1 TGCCGTGTCACACG-TCTGACCACGGCATGTCACACACTCTAAACCTTGCCATGTCACACCCGTC
* * * *
27880263 TCACATATTCTCACCTTGTCGTCTCACACATTATCACCCT-GCCATGTCACAAATTTCCTCCATG
65 TCACATATTCTCACCATGCCGTCTCACACATTATCACACTAG-CATGTCACAAATTCCCTCCATG
** * * *
27880327 GTGTGCCACACACTCTAAACCCTGCATTGTCACATATTATCACATGTCGTTTCACACATTATAAC
129 ACGTGCCACACACTCTAAACCCTGCAGTGTCACACATTATCACATGTCATTTCACACATTATAAC
27880392 CC
194 CC
* * *
27880394 TGTCGTGTCACACGTCTGACCATGGCATGTCACACACTCTAAACCTTGCCGTGTCACA
1 TGCCGTGTCACACGTCTGACCACGGCATGTCACACACTCTAAACCTTGCCATGTCACA
27880452 TATTCTCACC
Statistics
Matches: 219, Mismatches: 33, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
195 39 0.18
196 34 0.16
197 14 0.06
200 2 0.01
203 2 0.01
204 2 0.01
206 1 0.00
207 14 0.06
208 111 0.51
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (195 bp):
TGCCGTGTCACACGTCTGACCACGGCATGTCACACACTCTAAACCTTGCCATGTCACACCCGTCT
CACATATTCTCACCATGCCGTCTCACACATTATCACACTAGCATGTCACAAATTCCCTCCATGAC
GTGCCACACACTCTAAACCCTGCAGTGTCACACATTATCACATGTCATTTCACACATTATAACCC
Found at i:27880404 original size:23 final size:22
Alignment explanation
Indices: 27880354--27880406 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
27880344 AACCCTGCAT
* *
27880354 TGTCACATATTATCACATGTCG
1 TGTCACACATTATAACATGTCG
* *
27880376 TTTCACACATTATAACCCTGTCG
1 TGTCACACATTATAA-CATGTCG
27880399 TGTCACAC
1 TGTCACAC
27880407 GTCTGACCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.34
Consensus pattern (22 bp):
TGTCACACATTATAACATGTCG
Found at i:27880453 original size:91 final size:92
Alignment explanation
Indices: 27880258--27880460 Score: 237
Period size: 91 Copynumber: 2.2 Consensus size: 92
27880248 CATGTCACAC
* * * *
27880258 CCGTGTCACATATTCTCACCTTGTCGTCTCACACATTATCACCCTGCCATGTCACAAATTTCCTC
1 CCGTGTCACATATTCTCA-CATGTCGTCTCACACATTATAACCCTGCCATGTCACAAATCTCCAC
**
27880323 CATGGTGTGCCACACACTCTAAACCCTG
65 CATGGCATGCCACACACTCTAAACCCTG
** * * * * ** *
27880351 CATTGTCACATATTATCACATGTCGTTTCACACATTATAACCCTGTCGTGTCACACGTCT-GACC
1 CCGTGTCACATATTCTCACATGTCGTCTCACACATTATAACCCTGCCATGTCACAAATCTCCACC
* *
27880415 ATGGCATGTCACACACTCTAAACCTTG
66 ATGGCATGCCACACACTCTAAACCCTG
27880442 CCGTGTCACATATTCTCAC
1 CCGTGTCACATATTCTCAC
27880461 CGTGTCACAC
Statistics
Matches: 90, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
91 41 0.46
92 34 0.38
93 15 0.17
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.30
Consensus pattern (92 bp):
CCGTGTCACATATTCTCACATGTCGTCTCACACATTATAACCCTGCCATGTCACAAATCTCCACC
ATGGCATGCCACACACTCTAAACCCTG
Found at i:27880614 original size:23 final size:23
Alignment explanation
Indices: 27880567--27880615 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27880557 CCCTGTCGTA
* * *
27880567 TCACATATTCTCACCATTACGTG
1 TCACACATTCCCACCATTACATG
*
27880590 TCACACATTCCCACCATTCCATG
1 TCACACATTCCCACCATTACATG
27880613 TCA
1 TCA
27880616 TAAACTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.37, G:0.06, T:0.31
Consensus pattern (23 bp):
TCACACATTCCCACCATTACATG
Found at i:27880670 original size:23 final size:23
Alignment explanation
Indices: 27880644--27880699 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
27880634 GTGTCACAGC
* *
27880644 CGTGTCACATATTCTCACCATGA
1 CGTGTCACACATTCCCACCATGA
*
27880667 CGTGTCACACATTCCCACCATGT
1 CGTGTCACACATTCCCACCATGA
27880690 CGTGTCACAC
1 CGTGTCACAC
27880700 CCCACCATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.36, G:0.14, T:0.27
Consensus pattern (23 bp):
CGTGTCACACATTCCCACCATGA
Found at i:27880705 original size:20 final size:21
Alignment explanation
Indices: 27880659--27880708 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 21
27880649 CACATATTCT
27880659 CACCATGACGTGTCACACATTCC
1 CACCATGACGTGTCACAC--TCC
*
27880682 CACCATGTCGTGTCACAC-CC
1 CACCATGACGTGTCACACTCC
27880702 CACCATG
1 CACCATG
27880709 CCTTTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.35
23 17 0.65
ACGTcount: A:0.24, C:0.42, G:0.14, T:0.20
Consensus pattern (21 bp):
CACCATGACGTGTCACACTCC
Found at i:27880748 original size:100 final size:102
Alignment explanation
Indices: 27880567--27880755 Score: 240
Period size: 100 Copynumber: 1.9 Consensus size: 102
27880557 CCCTGTCGTA
* * * *
27880567 TCACATATTCTCACCATTACGTGTCACACATTCCCACCATTCCATGTCATAAACTCTATACCCTA
1 TCACACATTCCCACCATTACGTGTCACAC--TCCCACCATGCCATGTCATAAACTCTAAACCCTA
** **
27880632 TCGTGTCACAGCCGTGTCACATATTCTCACCATGACGTG
64 TCGTCACACAAACGTGTCACATATTCTCACCATGACGTG
* *
27880671 TCACACATTCCCACCATGT-CGTGTCACAC-CCCACCATGCC-TTTCATAAACTTTAAACCCTAT
1 TCACACATTCCCACCAT-TACGTGTCACACTCCCACCATGCCATGTCATAAACTCTAAACCCTAT
27880733 CGTCACACAAACGTGTCACATAT
65 CGTCACACAAACGTGTCACATAT
27880756 GGCCTGCTGT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
100 38 0.51
101 10 0.14
104 25 0.34
105 1 0.01
ACGTcount: A:0.28, C:0.35, G:0.10, T:0.28
Consensus pattern (102 bp):
TCACACATTCCCACCATTACGTGTCACACTCCCACCATGCCATGTCATAAACTCTAAACCCTATC
GTCACACAAACGTGTCACATATTCTCACCATGACGTG
Found at i:27885396 original size:20 final size:20
Alignment explanation
Indices: 27885367--27885406 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27885357 GGGAGTGCGC
*
27885367 ATGAGCTGGTGATG-ATGATG
1 ATGAGATGGTG-TGCATGATG
27885387 ATGAGATGGTGTGCATGATG
1 ATGAGATGGTGTGCATGATG
27885407 GTGATGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.25, C:0.05, G:0.40, T:0.30
Consensus pattern (20 bp):
ATGAGATGGTGTGCATGATG
Found at i:27885846 original size:39 final size:39
Alignment explanation
Indices: 27885792--27885877 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
27885782 AGAAAGAATC
*
27885792 TCGCTGCAGCAAGAAACCTTCTGTTTCTGGGTTACAATT
1 TCGCTGCAGCAAGAAACCTTATGTTTCTGGGTTACAATT
27885831 TCGCTGCAGCAAGAAACCTTATGTTTCTGGGTTACAATT
1 TCGCTGCAGCAAGAAACCTTATGTTTCTGGGTTACAATT
27885870 TCGCTGCA
1 TCGCTGCA
27885878 ACAAAAAAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (39 bp):
TCGCTGCAGCAAGAAACCTTATGTTTCTGGGTTACAATT
Found at i:27885846 original size:60 final size:60
Alignment explanation
Indices: 27885713--27885846 Score: 141
Period size: 60 Copynumber: 2.2 Consensus size: 60
27885703 GTAGCTTCTT
* *
27885713 GCTGCAGCGAA-AAGGAATCTCGTTGCAGCGAAAAACTCTCTGTTTCATCAGTTAAATTTC
1 GCTGCAGC-AAGAAAGAATCTCGCTGCAGCGAAAAACTCTCTGTTTCATCAGTTAAATTTC
* * * **
27885773 GTTGTAGCGAGAAAGAATCTCGCTGCAGC-AAGAAAC-CTTCTGTTTC-TGGGTTACAATTTC
1 GCTGCAGCAAGAAAGAATCTCGCTGCAGCGAA-AAACTC-TCTGTTTCATCAGTTA-AATTTC
27885833 GCTGCAGCAAGAAA
1 GCTGCAGCAAGAAA
27885847 CCTTATGTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
59 9 0.15
60 51 0.85
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (60 bp):
GCTGCAGCAAGAAAGAATCTCGCTGCAGCGAAAAACTCTCTGTTTCATCAGTTAAATTTC
Done.