Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001174.1 Hibiscus syriacus cultivar Beakdansim tig00002338_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: 2182627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1509459 original size:6 final size:6
Alignment explanation
Indices: 1509448--1509490 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1509438 ATGAATAGTG
** * *
1509448 AATGAT AATGAT AATGAT AATGAT GTTGAT GATGAT GATGAT A
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT A
1509491 TATATATAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (6 bp):
AATGAT
Found at i:1513175 original size:22 final size:23
Alignment explanation
Indices: 1513142--1513184 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1513132 AGTAATTTTT
*
1513142 TTTTCATTCTAATATTTAAATTC
1 TTTTCATTCTAACATTTAAATTC
1513165 TTTT-ATTCTAACATTTAAAT
1 TTTTCATTCTAACATTTAAAT
1513185 ATTTGAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTCATTCTAACATTTAAATTC
Found at i:1529715 original size:35 final size:34
Alignment explanation
Indices: 1529625--1529732 Score: 103
Period size: 35 Copynumber: 3.1 Consensus size: 34
1529615 AGACATTTTC
**
1529625 TTTCAAAACAAAATTTTTTATCACACTTGAGGCAGT
1 TTTCAAAACAAAA--TTTTATCACACTTGAGATAGT
*
1529661 TTCTCTAGAAA-AAAA-TTTATCACACTTGAGATGGT
1 TT-TC-A-AAACAAAATTTTATCACACTTGAGATAGT
* *
1529696 GTTTCAAAACAAAATTTTATCTCACTTGAGATTGT
1 -TTTCAAAACAAAATTTTATCACACTTGAGATAGT
1529731 TT
1 TT
1529733 CTCCCAAAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
33 3 0.05
34 7 0.11
35 37 0.61
36 4 0.07
37 2 0.03
38 5 0.08
39 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (34 bp):
TTTCAAAACAAAATTTTATCACACTTGAGATAGT
Found at i:1531512 original size:65 final size:66
Alignment explanation
Indices: 1531384--1531513 Score: 190
Period size: 65 Copynumber: 2.0 Consensus size: 66
1531374 GGGGGAAGTG
* * *
1531384 GGTGGAAAAATAGATGGAGTGGTAAAAGAAGTTGTGGAATTGATGGGTGAACTTAAGATGGTGAT
1 GGTGGAAAAATAGATGGAGTGGTAAAAGAAGTTGTGGAATTGAGGGGTGAACTAAAGAGGGTGAT
1531449 A
66 A
* * * *
1531450 GGTGG-AAAATTGATGGAGTGGTGAAGGAAGTTGTGGAATTGAGGGGTGAACTAAAGGGGGTGAT
1 GGTGGAAAAATAGATGGAGTGGTAAAAGAAGTTGTGGAATTGAGGGGTGAACTAAAGAGGGTGAT
1531514 GGGAGTGATT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
65 52 0.91
66 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.41, T:0.25
Consensus pattern (66 bp):
GGTGGAAAAATAGATGGAGTGGTAAAAGAAGTTGTGGAATTGAGGGGTGAACTAAAGAGGGTGAT
A
Found at i:1536231 original size:2 final size:2
Alignment explanation
Indices: 1536226--1536251 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1536216 AAATGAATCG
1536226 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
1536252 TCCATACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1536518 original size:2 final size:2
Alignment explanation
Indices: 1536513--1536553 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1536503 CACAAACACT
1536513 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1536554 CCATACTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1537112 original size:225 final size:225
Alignment explanation
Indices: 1536686--1537164 Score: 719
Period size: 225 Copynumber: 2.1 Consensus size: 225
1536676 AAATCAAGTG
* * * * *
1536686 ATTAACCGATTATGTTATTGTCGGATTCCTAAGGCTCCATCAGCTTAAATTTTGTTAACATTTAG
1 ATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTTAAAATTTGGTAACATTTAG
* *
1536751 GCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCATCG
66 GCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTTTGTTATCATCG
* * *
1536816 GATTTCTAAGGCCCCATCAGCTTTAATAATACGCAACCTATTACGTTACATAAGCTCTACCTAAT
131 GATTTCTAAAGCCCCATCAGCTTTAATAATACGCAACATATTACGTTACATAAGCACTACCTAAT
*
1536881 ATGTTATTATGCTTCGTAATGTTTCCAGTA
196 ATGTTATTATGCTTCATAATGTTTCCAGTA
* * *
1536911 ATTAACCGGTTATGTTATCATCGGATTTCTAAGGCTCTATCAACTTAAAATTTGGTAACATTTTA
1 ATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTTAAAATTTGGTAACA-TTTA
* *
1536976 GGTGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTTTGTTATCGTC
65 GGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTTTGTTATCATC
* * **
1537041 GGATTTCTAAAGCCCCATCAGC-TTAA-AATGGCGCTACATATTACGTTATTTAAGCACTACCTA
130 GGATTTCTAAAGCCCCATCAGCTTTAATAAT-ACGCAACATATTACGTTACATAAGCACTACCTA
*
1537104 ATATGTTATTATGCTTCATAATGTTTCCATTA
194 ATATGTTATTATGCTTCATAATGTTTCCAGTA
* *
1537136 ATTAACCAATTATGTTATCGTCGAATTTC
1 ATTAACCGATTATGTTATCGTCGGATTTC
1537165 CAAAGCCCTA
Statistics
Matches: 227, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
224 3 0.01
225 138 0.61
226 86 0.38
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (225 bp):
ATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTTAAAATTTGGTAACATTTAG
GCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTTTGTTATCATCG
GATTTCTAAAGCCCCATCAGCTTTAATAATACGCAACATATTACGTTACATAAGCACTACCTAAT
ATGTTATTATGCTTCATAATGTTTCCAGTA
Found at i:1537237 original size:118 final size:117
Alignment explanation
Indices: 1537015--1537272 Score: 347
Period size: 118 Copynumber: 2.2 Consensus size: 117
1537005 TAACAAATTA
* * * * *
1537015 AGTAATTAA-CATATTTTGTTATCGTCGGATTTCTAAAGCCCCATCAGCTTAAAATGGCGCTACA
1 AGTAATTAACCA-ATTATGTTATCGTCGAATTTCCAAAGCCCCATCAGCTTAAAAAGACGCTACA
*
1537079 TATTACGTTATTTAAGCACTACCTAATATGTTATTATGCTTCATAATGTTTCC
65 TATTACGTTATGTAAGCACTACCTAATATGTTATTATGCTTCATAATGTTTCC
* * * *
1537132 ATTAATTAACCAATTATGTTATCGTCGAATTTCCAAAGCCCTATCAGCTTTAAAAAGACTCTACC
1 AGTAATTAACCAATTATGTTATCGTCGAATTTCCAAAGCCCCATCAGC-TTAAAAAGACGCTACA
** * *
1537197 TATTACGTTATGTAAGCGTTACCTAATATGTTATTGTGCTTGATAATGTTTCC
65 TATTACGTTATGTAAGCACTACCTAATATGTTATTATGCTTCATAATGTTTCC
**
1537250 AGTAATTAACCGGTTATGTTATC
1 AGTAATTAACCAATTATGTTATC
1537273 TTCTATATTT
Statistics
Matches: 122, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
117 40 0.33
118 82 0.67
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (117 bp):
AGTAATTAACCAATTATGTTATCGTCGAATTTCCAAAGCCCCATCAGCTTAAAAAGACGCTACAT
ATTACGTTATGTAAGCACTACCTAATATGTTATTATGCTTCATAATGTTTCC
Found at i:1539463 original size:14 final size:14
Alignment explanation
Indices: 1539444--1539471 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1539434 TCCTTACTTA
1539444 AGTGTAAAATTGTG
1 AGTGTAAAATTGTG
1539458 AGTGTAAAATTGTG
1 AGTGTAAAATTGTG
1539472 TTTTAGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (14 bp):
AGTGTAAAATTGTG
Found at i:1546044 original size:12 final size:13
Alignment explanation
Indices: 1546015--1546047 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1546005 GTATTATGGT
*
1546015 TTTTCAAACATTG
1 TTTTCAAACATAG
1546028 TTTTCAAA-ATAG
1 TTTTCAAACATAG
1546040 TTTTCAAA
1 TTTTCAAA
1546048 TTTTGCCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:1547803 original size:13 final size:13
Alignment explanation
Indices: 1547781--1547814 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1547771 AAGGGGAGTA
*
1547781 ATTTTCAAAACTG
1 ATTTTCAAAAATG
1547794 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1547806 ATTTTCAAA
1 ATTTTCAAA
1547815 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1550601 original size:20 final size:21
Alignment explanation
Indices: 1550563--1550601 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1550553 AAAAAAATTA
**
1550563 TATATAAATTTTATTATAAAG
1 TATATAAATTTTAAAATAAAG
1550584 TATATAAA-TTTAAAATAA
1 TATATAAATTTTAAAATAA
1550602 TAAAACAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
TATATAAATTTTAAAATAAAG
Found at i:1558837 original size:15 final size:15
Alignment explanation
Indices: 1558819--1558849 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1558809 AATAAAATAT
*
1558819 TTTTTAATATTCTAA
1 TTTTTAATATTATAA
1558834 TTTTTAATATTATAA
1 TTTTTAATATTATAA
1558849 T
1 T
1558850 AATATTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTAATATTATAA
Found at i:1558877 original size:25 final size:26
Alignment explanation
Indices: 1558822--1558879 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
1558812 AAAATATTTT
1558822 TTAATATTCTAATTTTTAATATTATAA
1 TTAATATTCTAATTTTTAATA-TATAA
*
1558849 -TAATATTCTTA-TTTTAATA-AGTAA
1 TTAATATTCTAATTTTTAATATA-TAA
1558873 TTAATAT
1 TTAATAT
1558880 AATTAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 1 0.04
24 3 0.11
25 14 0.50
26 10 0.36
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (26 bp):
TTAATATTCTAATTTTTAATATATAA
Found at i:1558909 original size:41 final size:40
Alignment explanation
Indices: 1558845--1558921 Score: 127
Period size: 41 Copynumber: 1.9 Consensus size: 40
1558835 TTTTAATATT
* *
1558845 ATAATAATATTCTTATTTTAATAAGTAATTAATATAATTA
1 ATAATAATATTCTTATTTCAATAAATAATTAATATAATTA
1558885 ATAATATATATTCTTATTTCAATAAATAATTAATATA
1 ATAATA-ATATTCTTATTTCAATAAATAATTAATATA
1558922 GTTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 6 0.18
41 28 0.82
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (40 bp):
ATAATAATATTCTTATTTCAATAAATAATTAATATAATTA
Found at i:1558937 original size:41 final size:41
Alignment explanation
Indices: 1558850--1558937 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
1558840 ATATTATAAT
* * *
1558850 AATATTCTTATTTTAATAAGTAATTAATATAATTAATAATA
1 AATATTCTTATTTCAATAAATAATTAATATAATTAATAAAA
* * *
1558891 TATATTCTTATTTCAATAAATAATTAATATAGTTTATAAAA
1 AATATTCTTATTTCAATAAATAATTAATATAATTAATAAAA
1558932 AATATT
1 AATATT
1558938 TTAATAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (41 bp):
AATATTCTTATTTCAATAAATAATTAATATAATTAATAAAA
Found at i:1559739 original size:28 final size:29
Alignment explanation
Indices: 1559691--1559746 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
1559681 GATTTTTCTC
*
1559691 AAATCCGATTTCGGATATTTTT-TGCACA
1 AAATCAGATTTCGGATATTTTTGTGCACA
1559719 AAATCAGATATTCGGAT-TTTTTGTGCAC
1 AAATCAGAT-TTCGGATATTTTTGTGCAC
1559747 CTCTAATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (29 bp):
AAATCAGATTTCGGATATTTTTGTGCACA
Found at i:1559740 original size:29 final size:28
Alignment explanation
Indices: 1559691--1559746 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
1559681 GATTTTTCTC
* *
1559691 AAATCCGATTTCGGATATTTTTTGCACA
1 AAATCAGATTTCGGATATTTTGTGCACA
*
1559719 AAATCAGATATTCGGATTTTTTGTGCAC
1 AAATCAGAT-TTCGGATATTTTGTGCAC
1559747 CTCTAATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (28 bp):
AAATCAGATTTCGGATATTTTGTGCACA
Found at i:1565337 original size:21 final size:22
Alignment explanation
Indices: 1565312--1565353 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1565302 TATTATAAGT
**
1565312 ATATTTATGAATAT-ATAAAAA
1 ATATTTAACAATATAATAAAAA
1565333 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
1565354 TAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATTTAACAATATAATAAAAA
Found at i:1567652 original size:123 final size:120
Alignment explanation
Indices: 1567509--1568473 Score: 400
Period size: 112 Copynumber: 8.4 Consensus size: 120
1567499 GTTGAACAAA
* * *
1567509 TTCTCTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTATGGAAATGCTGATACTGATCT
1 TTCT-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATCT
*
1567574 ATCT-CATTCTGTGATAGAATCA-AACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
65 ATCTGC-TTCTGTGATAAAATCAGAA-AAAGGTTGAACAAGCTCTTCTCATTATGAA---C
* * * *
1567633 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAATGTTGATGCTAATCTA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATCTA
* * * *
1567698 TTTGCTTCTGTGATAAAATTATGTAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC
66 TCTGCTTCTGTGATAAAATCA-GAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* *
1567754 TTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTTCTGGAAAAGCTGAT-C-CATC-A
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATCTA
* ** * * * * ** *
1567814 --AG-TGATG-GAT---TTGAGCAAAAGGTTGAAAAAATTCTTCTCATTATGAAT
66 TCTGCTTCTGTGATAAAATCAGAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* ** *
1567862 TTCTT-CTTCTTCAGATGACAAGTTCTTCTCATTATGAACTCTACCTGGCAA---TG-T--TAAT
1 TTCTTCCTTCTTCAGATG---AGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAAT
* *** ** * * * **
1567920 CCATCAAATAATG-GAT---TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
63 CTATCTGCTTCTGTGATAAAATCAGAAAAAGGTTGAACAAGCTCTTCTCATTATGAA---C
* * * *
1567977 TTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA---AG-T--TAATCCA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATCTA
** * * * * **
1568036 --T-C--AAGTGATGAATTCAGGCAAAAGGTTAAACAAATTCTTCTCATTATGAATTTC
66 TCTGCTTCTGTGATAAAATCA-GAAAAAGGTTGAACAAGCTCTTCTCATTATGAA---C
* * *
1568090 TTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA---TG-T--TAATCCA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATCTA
** * * * * *
1568148 --T-C--AAGTGATGAATTCGAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
66 TCTGCTTCTGTGATAAAATC-AGAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* * * *
1568199 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA-----A-AATAA--
1 TTCTTC--CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATC
** * * * **
1568256 T-TCAT-C--AAGTGATGAATTCAGGGAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
64 TATC-TGCTTCTGTGATAAAATCA-GAAAAAGGTTGAACAAGCTCTTCTCATTATGAA---C
* * *
1568314 TTCTTCC-TCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA---TG-T--TAATCCA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATCTA
** * * * * *
1568372 --T-C--AAGTGATGAATTCGAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
66 TCTGCTTCTGTGATAAAATC-AGAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* * **
1568423 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTCCTCTGGAAA
1 TTCTTC--CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAA
1568474 AAATAATTCA
Statistics
Matches: 731, Mismatches: 65, Indels: 102
0.81 0.07 0.11
Matches are distributed among these distances:
108 51 0.07
109 22 0.03
111 23 0.03
112 365 0.50
113 85 0.12
114 1 0.00
115 12 0.02
116 12 0.02
117 3 0.00
118 1 0.00
119 14 0.02
120 31 0.04
121 6 0.01
123 70 0.10
124 34 0.05
125 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (120 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAATGCTGATACTAATCTA
TCTGCTTCTGTGATAAAATCAGAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
Found at i:1567994 original size:24 final size:23
Alignment explanation
Indices: 1567959--1568003 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1567949 TGAACAAATT
*
1567959 CTTCTCATTATGAATTTCTTCTTC
1 CTTCTCATTATG-AGTTCTTCTTC
1567983 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGAGTTCTTCT
1568004 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.24, G:0.07, T:0.53
Consensus pattern (23 bp):
CTTCTCATTATGAGTTCTTCTTC
Found at i:1568606 original size:336 final size:335
Alignment explanation
Indices: 1567599--1568779 Score: 1301
Period size: 336 Copynumber: 3.5 Consensus size: 335
1567589 AGAATCAAAC
** * *
1567599 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
* * ** * * *
1567664 ATGAACTTTCTCTGAAAATGTTGATGCTAATCTATTTGCTTCTGTGATAAAATT-ATGTAAAAGG
66 ATGAACTTTCTCTGGAAA---TG-T--TAATCCA--T-C--AAGTGAT-GAATTCAGGCAAAAGG
* * * *
1567728 TTGAACAAGCTCTTCTCATTGTGAACTTCTTC-T--TCTTCAGATGAGTTCTTCTCATTATGAAC
119 TTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC
* * * * * *
1567790 TTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAAAAAATTCTTCTCAT
184 TTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAATTCTTCTCAT
* * *
1567855 TATGAATTTCTTC-T--TCTTCAGATGACAAGTTCTTCTCATTATGAACTCTACCTGGCAATGTT
249 TATGAATTTCTTCTTCCTCTTCAGATG---AGTTCTTCTCATTATGAACTCTAACTGACAATGAT
* * * *
1567917 AATCCATCAAATAATGGATTTGAGCA
311 AATCCATCAAGTGATGAATTAG-GCA
*
1567943 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
* *
1568008 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTAAACAAATTC
66 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTAAACAAGTTC
*
1568073 TTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
131 TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
* * * * *
1568138 TGTTAATCCATCAAGTGATGAATTCGAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCT
195 AGATAATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCT
* * ** ** *
1568203 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGA-AAAAATAATTCATCAAGTG
260 TCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT-GACAATGATAATCCATCAAGTG
*
1568267 ATGAATTCAGGGA
324 ATGAATT-AGGCA
1568280 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAAATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
1568344 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTC-GAGCAAAAGGTTAAACAAGTT
66 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCAG-GCAAAAGGTTAAACAAGTT
1568408 CTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTCCTCTGGAA
130 CTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT-CTCTGGAA
* * * *
1568473 AAAATAATTCATCAAGTAATGAATTC-AGGGAAAAGGTTGAACAAATTCTTCTCATTATGAATTT
194 AAGATAATCCATCAAGTGATGAATTCGA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTT
* * * * **
1568537 CTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGACACTGCTGATCCACCGGGT
258 CTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGACAATGATAATCCATCAAGT
*
1568602 GATGAATTTAAGCA
323 GATGAA-TTAGGCA
*
1568616 AAAAGTTG----AA-------CA--A-G------TTCTT-CTTCTTCAAATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
* ** * * * * * * * *
1568660 ATGAACTCTAACTGGTAATGATGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAGTTC
66 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTAAACAAGTTC
*
1568725 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
131 TTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT
1568780 CGACCTGGAA
Statistics
Matches: 736, Mismatches: 83, Indels: 63
0.83 0.09 0.07
Matches are distributed among these distances:
315 1 0.00
316 105 0.14
317 29 0.04
322 1 0.00
323 1 0.00
325 2 0.00
332 6 0.01
333 40 0.05
334 1 0.00
335 7 0.01
336 290 0.39
337 155 0.21
338 9 0.01
340 10 0.01
341 1 0.00
344 78 0.11
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (335 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTAAACAAGTTC
TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTCTCTGGAAAA
GATAATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTT
CTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGACAATGATAATCCATCAAGTGAT
GAATTAGGCA
Found at i:1568609 original size:112 final size:113
Alignment explanation
Indices: 1567722--1568574 Score: 1196
Period size: 112 Copynumber: 7.6 Consensus size: 113
1567712 AAAATTATGT
** * *
1567722 AAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* * * *
1567784 ATGAACTTT-TCTGGAAAAGCTGATCCATCAAGTGATGGATT-TGAGC
66 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGC
*
1567830 AAAAGGTTGAAAAAATTCTTCTCATTATGAATTTCTTC-T--TCTTCAGATGACAAGTTCTTCTC
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATG---AGTTCTTCTC
* * * * * * *
1567892 ATTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATAATGGATT-TGAGC
63 ATTATGAACT-TTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGC
*
1567942 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCAT
1568007 TATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAG-GC
65 TATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGC
* *
1568055 AAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
*
1568120 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTC-GAGC
66 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGC
* * * *
1568167 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
** * *
1568232 ATGAACTTTCTCTGGAAAAAATAATTCATCAAGTGATGAATTCAG-GG
66 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGC
*
1568279 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
*
1568344 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTC-GAGC
66 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGC
* * * *
1568391 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* ** * * *
1568456 ATGAACTTCCTCTGGAAAAAATAATTCATCAAGTAATGAATTCAG-GG
66 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGC
1568503 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
1568568 ATGAACT
66 ATGAACT
1568575 CTAACTGACA
Statistics
Matches: 670, Mismatches: 57, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
108 37 0.06
110 1 0.00
111 26 0.04
112 504 0.75
113 92 0.14
114 1 0.00
116 9 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGC
Found at i:1568697 original size:92 final size:92
Alignment explanation
Indices: 1568538--1568728 Score: 292
Period size: 92 Copynumber: 2.1 Consensus size: 92
1568528 TATGAATTTC
* * * * ***
1568538 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGACACTGCTGATCCACCGGGTG
1 TTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGACAATGATGATCCACCAAATG
1568603 ATGAATTTAAGCAAAAAGTTGAACAAG
66 ATGAATTTAAGCAAAAAGTTGAACAAG
** *
1568630 TTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGTAATGATGATCCATCAAATG
1 TTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGACAATGATGATCCACCAAATG
1568695 ATGAATTTAAGCAAAAAGTTGAACAAG
66 ATGAATTTAAGCAAAAAGTTGAACAAG
1568722 TTCTTCT
1 TTCTTCT
1568729 CATTATGAAC
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (92 bp):
TTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGACAATGATGATCCACCAAATG
ATGAATTTAAGCAAAAAGTTGAACAAG
Found at i:1569255 original size:22 final size:22
Alignment explanation
Indices: 1569216--1569269 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1569206 GATAAAGCTT
* *
1569216 TCATCTTT-GAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
1569237 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
1569259 TCATCTTTAAA
1 TCATCTTTAAA
1569270 GAATGTAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 8 0.28
22 21 0.72
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:1571853 original size:103 final size:105
Alignment explanation
Indices: 1571649--1571896 Score: 473
Period size: 103 Copynumber: 2.4 Consensus size: 105
1571639 CCTACCGAAT
*
1571649 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAG
1 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAG
1571714 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAAC
66 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAAC
1571754 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCC-TA-TTCTACTATGAG
1 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAG
1571817 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAAC
66 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAAC
1571857 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1571897 GAACAAATTC
Statistics
Matches: 142, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
103 92 0.65
104 2 0.01
105 48 0.34
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (105 bp):
CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAG
CAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAAC
Found at i:1571950 original size:83 final size:83
Alignment explanation
Indices: 1571810--1572074 Score: 460
Period size: 83 Copynumber: 3.2 Consensus size: 83
1571800 TCCTATTCTA
* *
1571810 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATTAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTG-CCAAACCAGATCAGATAACTCAA
1571874 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
1571893 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1571958 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
1571976 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1572041 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
1572059 CTATGAGCACATTCAT
1 CTATGAGCAAATTCAT
1572075 TTGTTCCATT
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 2 0.01
83 172 0.99
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:1574312 original size:9 final size:9
Alignment explanation
Indices: 1574287--1574316 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1574277 CTTTATTCGA
1574287 TTTTTTTTC
1 TTTTTTTTC
1574296 TTTCTTTTTC
1 TTT-TTTTTC
1574306 TTTTTTTTC
1 TTTTTTTTC
1574315 TT
1 TT
1574317 CTTTCTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1576275 original size:28 final size:28
Alignment explanation
Indices: 1576244--1576301 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
1576234 TGTAATATGT
*
1576244 AAAAAATGAAAATGTAAATACAAACGTA
1 AAAAAATGAAAATGCAAATACAAACGTA
* * *
1576272 AAAAAATGCAAATGCAAATTCAAATGTA
1 AAAAAATGAAAATGCAAATACAAACGTA
1576300 AA
1 AA
1576302 TATGTGAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.62, C:0.09, G:0.10, T:0.19
Consensus pattern (28 bp):
AAAAAATGAAAATGCAAATACAAACGTA
Found at i:1576371 original size:29 final size:27
Alignment explanation
Indices: 1576339--1576393 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
1576329 TTGTGCAATA
1576339 CAAATGCAAAAATGCCAAATGTAAATATG
1 CAAATGCAAAAATG--AAATGTAAATATG
* *
1576368 CAAATGTAAAAATGTAATGTAAATAT
1 CAAATGCAAAAATGAAATGTAAATAT
1576394 TTAAAATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.46
29 13 0.54
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (27 bp):
CAAATGCAAAAATGAAATGTAAATATG
Found at i:1576373 original size:14 final size:14
Alignment explanation
Indices: 1576339--1576390 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
1576329 TTGTGCAATA
*
1576339 CAAATGCAAAAATG
1 CAAATGTAAAAATG
*
1576353 CCAAATGTAAATATG
1 -CAAATGTAAAAATG
1576368 CAAATGTAAAAATG
1 CAAATGTAAAAATG
*
1576382 -TAATGTAAA
1 CAAATGTAAA
1576391 TATTTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 8 0.24
14 13 0.39
15 12 0.36
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (14 bp):
CAAATGTAAAAATG
Found at i:1582612 original size:34 final size:32
Alignment explanation
Indices: 1582567--1582648 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 32
1582557 CCAGTAGTAT
*
1582567 GGTATCGATACTAGAGGAGTAGCATCCATACC-AG
1 GGTATCTATACTAGAGGA--AGCAT-CATACCAAG
* *
1582601 GGTATCTATACTAGAGTAAGTATCATACCAAG
1 GGTATCTATACTAGAGGAAGCATCATACCAAG
1582633 GGTATCTATACTAGAG
1 GGTATCTATACTAGAG
1582649 TAAAGGTATC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 6 0.14
32 22 0.50
34 16 0.36
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (32 bp):
GGTATCTATACTAGAGGAAGCATCATACCAAG
Found at i:1582640 original size:32 final size:34
Alignment explanation
Indices: 1582593--1582666 Score: 118
Period size: 32 Copynumber: 2.2 Consensus size: 34
1582583 GAGTAGCATC
1582593 CATACC-AGGGTATCTATACTAGAGT-AA-GTAT
1 CATACCAAGGGTATCTATACTAGAGTAAAGGTAT
1582624 CATACCAAGGGTATCTATACTAGAGTAAAGGTAT
1 CATACCAAGGGTATCTATACTAGAGTAAAGGTAT
1582658 CAGTACCAA
1 CA-TACCAA
1582667 TTTCAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
31 6 0.15
32 19 0.49
33 2 0.05
34 6 0.15
35 6 0.15
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.26
Consensus pattern (34 bp):
CATACCAAGGGTATCTATACTAGAGTAAAGGTAT
Found at i:1583420 original size:23 final size:23
Alignment explanation
Indices: 1583377--1583439 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1583367 GAGTCAAGGG
* **
1583377 TTCTACGCGGTCATTTGGGATAA
1 TTCTACGCGGTCCTTCAGGATAA
* *
1583400 TTCTACGTGGTCCTTCAGGATAT
1 TTCTACGCGGTCCTTCAGGATAA
*
1583423 TTCTATGCGGTCCTTCA
1 TTCTACGCGGTCCTTCA
1583440 AGACATCTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCAGGATAA
Found at i:1592116 original size:223 final size:225
Alignment explanation
Indices: 1591713--1592161 Score: 884
Period size: 223 Copynumber: 2.0 Consensus size: 225
1591703 ACACTTCAAT
1591713 AATTTAAGCCATGAAAACAATGAAATAATTATACCAACTTGTAGATAATTTAATGGGGATTATTT
1 AATTTAAGCCATGAAAACAATGAAATAATTATACCAACTTGTAGATAATTTAATGGGGATTATTT
1591778 TCTCATTTCACCCTTTAGTTCAAAATCCTAATAAATTGGACCAAAATTGAAGAAAAAACAAACTT
66 TCTCATTTCACCCTTTAGTTCAAAATCCTAATAAATTGGACCAAAATTGAAGAAAAAACAAACTT
1591843 ACTCACTTTGGTAATGGAGTCACGACAGAATGGAGAAGATGAGCTGAACTTCTTGAAATTTCTCA
131 ACTCACTTTGGTAATGGAGTCACGACAGAATGGAGAAGATGAGCTGAACTTCTTGAAATTTCTCA
1591908 CAAAATATCTCTTTAAAAATCCAATTTAAA
196 CAAAATATCTCTTTAAAAATCCAATTTAAA
1591938 AATTTAAGCCATG-AAACAATGAAATAATTATACCAACTTGTAGATAATTTAATGGGGATTATTT
1 AATTTAAGCCATGAAAACAATGAAATAATTATACCAACTTGTAGATAATTTAATGGGGATTATTT
1592002 T-TCATTTCACCCTTTAGTTCAAAATCCTAATAAATTGGACCAAAATTGAAGAAAAAACAAACTT
66 TCTCATTTCACCCTTTAGTTCAAAATCCTAATAAATTGGACCAAAATTGAAGAAAAAACAAACTT
1592066 ACTCACTTTGGTAATGGAGTCACGACAGAATGGAGAAGATGAGCTGAACTTCTTGAAATTTCTCA
131 ACTCACTTTGGTAATGGAGTCACGACAGAATGGAGAAGATGAGCTGAACTTCTTGAAATTTCTCA
1592131 CAAAATATCTCTTTAAAAATCCAATTTAAA
196 CAAAATATCTCTTTAAAAATCCAATTTAAA
1592161 A
1 A
1592162 TGAATTAAAA
Statistics
Matches: 224, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
223 159 0.71
224 52 0.23
225 13 0.06
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (225 bp):
AATTTAAGCCATGAAAACAATGAAATAATTATACCAACTTGTAGATAATTTAATGGGGATTATTT
TCTCATTTCACCCTTTAGTTCAAAATCCTAATAAATTGGACCAAAATTGAAGAAAAAACAAACTT
ACTCACTTTGGTAATGGAGTCACGACAGAATGGAGAAGATGAGCTGAACTTCTTGAAATTTCTCA
CAAAATATCTCTTTAAAAATCCAATTTAAA
Found at i:1593418 original size:23 final size:23
Alignment explanation
Indices: 1593350--1593412 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1593340 GAGTCGAGGG
* * *
1593350 TTCTACACAGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAT
*
1593373 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
1593396 TTCTACGCGGTCCTTCG
1 TTCTACGCGGTCCTTCG
1593413 AAACATCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.16, C:0.30, G:0.22, T:0.32
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAT
Found at i:1593931 original size:20 final size:20
Alignment explanation
Indices: 1593906--1593947 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1593896 TTGTAAACCT
1593906 TTTGATTTAAATAATGTAAA
1 TTTGATTTAAATAATGTAAA
1593926 TTTGATTTAAATAATGTAAA
1 TTTGATTTAAATAATGTAAA
1593946 TT
1 TT
1593948 ATTCAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (20 bp):
TTTGATTTAAATAATGTAAA
Found at i:1595525 original size:20 final size:21
Alignment explanation
Indices: 1595500--1595551 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1595490 TTTTCCCAAT
*
1595500 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1595520 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1595541 TCGCAATGCGA
1 TCGCAATGCGA
1595552 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1595565 original size:20 final size:20
Alignment explanation
Indices: 1595540--1595684 Score: 96
Period size: 20 Copynumber: 7.7 Consensus size: 20
1595530 AATTGGGAAA
1595540 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
1595560 ATCGCAAT--G---C-GA--
1 ATCGCAATGCGATACTGACT
*
1595572 -TCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1595591 ATCGCAATGCGATAAT-ACAA
1 ATCGCAATGCGATACTGAC-T
* *
1595611 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1595631 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
1595651 TTCGCAATGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1595671 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1595685 TTTCAAAGCG
Statistics
Matches: 98, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
11 7 0.07
13 1 0.01
14 2 0.02
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 4 0.04
20 66 0.67
21 14 0.14
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1595578 original size:31 final size:31
Alignment explanation
Indices: 1595540--1595603 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1595530 AATTGGGAAA
1595540 ATCGCAATGCGATACTGACTATCGCAATGCG
1 ATCGCAATGCGATACTGACTATCGCAATGCG
*
1595571 ATCGCAATGCGATACTTACTATCGCAATGCG
1 ATCGCAATGCGATACTGACTATCGCAATGCG
1595602 AT
1 AT
1595604 AATACAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (31 bp):
ATCGCAATGCGATACTGACTATCGCAATGCG
Found at i:1595885 original size:21 final size:22
Alignment explanation
Indices: 1595845--1595887 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1595835 CACTCTCTCA
1595845 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1595867 CCCATCTCCGGCG-AATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1595888 TATCTCCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.19, C:0.47, G:0.16, T:0.19
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1596201 original size:21 final size:21
Alignment explanation
Indices: 1596139--1596193 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
1596129 TCGGGTGCGA
* *
1596139 TTTCTCGTTGCGATAGTCA-A
1 TTTCGCGTTGCGATAGTCATT
*
1596159 ATTCGCGTTGCGATAGTCATT
1 TTTCGCGTTGCGATAGTCATT
*
1596180 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
1596194 TTTCATTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (21 bp):
TTTCGCGTTGCGATAGTCATT
Found at i:1597530 original size:17 final size:18
Alignment explanation
Indices: 1597493--1597536 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1597483 TCCACTTCGG
*
1597493 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCGACCA
*
1597511 GAGCTATCACCTC-ACCA
1 GAGCCATCACCTCGACCA
1597528 GAGCCATCA
1 GAGCCATCA
1597537 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.27, C:0.43, G:0.16, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCGACCA
Found at i:1598067 original size:19 final size:20
Alignment explanation
Indices: 1598013--1598078 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1598003 TAGTTTACTT
* *
1598013 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1598033 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* *
1598053 TCGCAATGC-GAAATGA-AA
1 TCGCAACGCGGAAATGACTA
1598071 TCGCAACG
1 TCGCAACG
1598079 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.21
19 6 0.15
20 25 0.64
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1598087 original size:14 final size:14
Alignment explanation
Indices: 1598068--1598123 Score: 76
Period size: 14 Copynumber: 3.8 Consensus size: 14
1598058 ATGCGAAATG
1598068 AAATCGCAACGACA
1 AAATCGCAACGACA
*
1598082 AAATCGCAAGCGAAA
1 AAATCGCAA-CGACA
1598097 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
1598113 AAATCGCAACG
1 AAATCGCAACG
1598124 CGAATGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
14 20 0.54
15 4 0.11
16 4 0.11
17 9 0.24
ACGTcount: A:0.48, C:0.25, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:1598097 original size:31 final size:32
Alignment explanation
Indices: 1598052--1598138 Score: 151
Period size: 31 Copynumber: 2.8 Consensus size: 32
1598042 GGAAATGGCT
*
1598052 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1598084 ATCGCAA-GCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1598115 ATCGCAACGCG-AATGAAATCGCAA
1 ATCGCAACGCGAAATGAAATCGCAA
1598139 TGCGATTGTG
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
31 44 0.81
32 10 0.19
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:1598104 original size:17 final size:18
Alignment explanation
Indices: 1598052--1598143 Score: 87
Period size: 17 Copynumber: 5.7 Consensus size: 18
1598042 GGAAATGGCT
1598052 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
1598070 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
1598084 ATCGCAA-GCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
1598101 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
*
1598115 ATCGCAACGCG-AATGAA
1 ATCGCAATGCGAAATGAA
1598132 ATCGCAATGCGA
1 ATCGCAATGCGA
1598144 TTGTGTTTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
14 18 0.30
15 5 0.08
16 10 0.16
17 21 0.34
18 7 0.11
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.12
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:1598191 original size:12 final size:13
Alignment explanation
Indices: 1598176--1598204 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1598166 TTGCGATTTC
1598176 ATTTG-CGTTGCG
1 ATTTGTCGTTGCG
1598188 ATTTGTCGTTGCG
1 ATTTGTCGTTGCG
1598201 ATTT
1 ATTT
1598205 CATTTCGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.10, C:0.14, G:0.28, T:0.48
Consensus pattern (13 bp):
ATTTGTCGTTGCG
Found at i:1600094 original size:14 final size:14
Alignment explanation
Indices: 1600075--1600110 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1600065 ATTGTTTAAT
1600075 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1600089 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1600103 TGATTTGT
1 TGATTTGT
1600111 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1600218 original size:20 final size:20
Alignment explanation
Indices: 1600193--1600231 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1600183 ATGTTGAAGT
1600193 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
1600213 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
1600232 GAGAGAATCG
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:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:1600347 original size:20 final size:20
Alignment explanation
Indices: 1600289--1600397 Score: 177
Period size: 20 Copynumber: 5.5 Consensus size: 20
1600279 GCGATTTTGT
1600289 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
1600308 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
* *
1600327 CATTGCGATAGCTATTTTCG
1 CGTTGCGATAGCCATTTTCG
*
1600347 CGTTACGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1600367 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1600387 CGTTGCGATAG
1 CGTTGCGATAG
1600398 TCAAATGAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
19 31 0.37
20 52 0.63
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:1600630 original size:20 final size:20
Alignment explanation
Indices: 1600605--1600675 Score: 142
Period size: 20 Copynumber: 3.5 Consensus size: 20
1600595 AAATGATTGC
1600605 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
1600625 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
1600645 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
1600665 CTTTCGCAACG
1 CTTTCGCAACG
1600676 AGATAATACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.30
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:1600862 original size:20 final size:21
Alignment explanation
Indices: 1600823--1600862 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1600813 ACTCTCTCCG
*
1600823 ACGACATCCGTTCCTAATCCA
1 ACGACATCCGTTCCCAATCCA
*
1600844 ACGACATCC-TTCCCCATCC
1 ACGACATCCGTTCCCAATCC
1600863 GCAACAGGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.45, G:0.07, T:0.23
Consensus pattern (21 bp):
ACGACATCCGTTCCCAATCCA
Found at i:1601433 original size:24 final size:24
Alignment explanation
Indices: 1601406--1601459 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1601396 GTATTCGAAA
*
1601406 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1601430 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1601454 TTTGAT
1 TTTGAT
1601460 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1601651 original size:12 final size:12
Alignment explanation
Indices: 1601634--1601658 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1601624 ATATAATCCT
1601634 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1601646 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1601658 G
1 G
1601659 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1603962 original size:33 final size:33
Alignment explanation
Indices: 1603920--1604046 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
1603910 GGAAATTACT
1603920 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1603953 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1603985 TTTCGCAATGTGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1604019 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1604047 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1604027 original size:66 final size:66
Alignment explanation
Indices: 1603921--1604053 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1603911 GAAATTACTA
*
1603921 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1603986 T
66 T
* *
1603987 TCGCAATGTGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1604052 T
66 T
1604053 T
1 T
1604054 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1604078 original size:14 final size:14
Alignment explanation
Indices: 1604061--1604117 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1604051 TTTAATTTCG
1604061 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1604075 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1604094 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1604108 CGTTGCGATT
1 CGTTGCGATT
1604118 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1604097 original size:33 final size:33
Alignment explanation
Indices: 1604046--1604127 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
1604036 AAATCGCAAC
* *
1604046 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1604079 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1604112 GCGATTTTCATTTCGC
1 GCGATTTTCATTTCGC
1604128 ATTGTGATAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:1604099 original size:19 final size:19
Alignment explanation
Indices: 1604075--1604127 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
1604065 GCGATTCTCT
1604075 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1604094 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
1604108 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1604127 C
1 C
1604128 ATTGTGATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 10 0.37
16 3 0.11
17 3 0.11
19 11 0.41
ACGTcount: A:0.09, C:0.25, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1604260 original size:14 final size:14
Alignment explanation
Indices: 1604241--1604277 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1604231 CATCAATTAA
1604241 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1604255 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1604269 ACAAATCAA
1 ACAAATCAA
1604278 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1605692 original size:21 final size:21
Alignment explanation
Indices: 1605626--1605692 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1605616 GTGAATCGGG
*
1605626 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1605646 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1605668 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1605689 CTCT
1 CTCT
1605693 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1605711 original size:42 final size:41
Alignment explanation
Indices: 1605626--1605748 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1605616 GTGAATCGGG
* * * *
1605626 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1605668 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1605710 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1605749 TGAGTCAGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1606142 original size:91 final size:93
Alignment explanation
Indices: 1605966--1606150 Score: 297
Period size: 91 Copynumber: 2.0 Consensus size: 93
1605956 ATTTCAAACT
*
1605966 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGTATACACAGTTTAGC
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGTATACACAGTTTAGC
1606031 AGAATTGGCAGCAACCGAATAAATTTAC
66 AGAATTGGCAGCAACCGAATAAATTTAC
1606059 TTCAACCAAAAGACAAAAAAAAAAGACAAATACTAACTTCACAGTGTT-AA-TA-A-ACAGTTTA
1 TTCAACCAAAAGAC--AAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGTATACACAGTTTA
**
1606120 GCAGTTTTGGCAGCAACCGAATAAATTTAC
64 GCAGAATTGGCAGCAACCGAATAAATTTAC
1606150 T
1 T
1606151 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 37 0.43
92 1 0.01
93 16 0.18
94 2 0.02
95 31 0.36
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.23
Consensus pattern (93 bp):
TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGTATACACAGTTTAGC
AGAATTGGCAGCAACCGAATAAATTTAC
Found at i:1607883 original size:20 final size:19
Alignment explanation
Indices: 1607838--1607992 Score: 61
Period size: 19 Copynumber: 8.8 Consensus size: 19
1607828 TCTTTTGGTT
*
1607838 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGA
* *
1607857 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1607878 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1607897 G--A-G--AATCGCAACGT
1 GAAATGAAAATCGCAACGA
** *
1607911 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
1607930 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
1607944 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
1607963 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1607977 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1607993 TGCGATTTTT
Statistics
Matches: 99, Mismatches: 20, Indels: 34
0.65 0.13 0.22
Matches are distributed among these distances:
14 28 0.28
16 6 0.06
17 6 0.06
19 29 0.29
20 28 0.28
21 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1607906 original size:14 final size:14
Alignment explanation
Indices: 1607887--1607975 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
1607877 GGAAATGACT
1607887 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1607901 ATCGCAACGTGAAATGA
1 ATCGCAAC--GAGA-GA
*
1607918 CTATCGCGACGAGAGA
1 --ATCGCAACGAGAGA
*
1607934 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
*
1607951 CTATCGCGACGAGAGA
1 --ATCGCAACGAGAGA
1607967 ATCGCAACG
1 ATCGCAACG
1607976 CGAAATGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
14 22 0.39
16 11 0.19
17 11 0.19
19 13 0.23
ACGTcount: A:0.37, C:0.24, G:0.27, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1607920 original size:33 final size:33
Alignment explanation
Indices: 1607863--1607992 Score: 206
Period size: 33 Copynumber: 3.9 Consensus size: 33
1607853 ATGAGATAAT
1607863 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
* *
1607897 GAGAATCGCAACGTGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
*
1607930 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
1607963 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
1607993 TGCGATTTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
33 77 0.86
34 13 0.14
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1607956 original size:19 final size:19
Alignment explanation
Indices: 1607867--1607957 Score: 67
Period size: 14 Copynumber: 5.3 Consensus size: 19
1607857 GATAATGAGA
1607867 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
1607887 ATCGCAA--CGAGA-GA--
1 ATCGCAACGCGAAATGACT
*
1607901 ATCGCAACGTGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
1607920 ATCGCGA--CGAGA-GA--
1 ATCGCAACGCGAAATGACT
1607934 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
1607953 ATCGC
1 ATCGC
1607958 GACGAGAGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 21
0.65 0.10 0.26
Matches are distributed among these distances:
14 13 0.25
16 11 0.21
17 10 0.19
18 1 0.02
19 11 0.21
20 7 0.13
ACGTcount: A:0.36, C:0.24, G:0.25, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1608029 original size:19 final size:19
Alignment explanation
Indices: 1607993--1608037 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1607983 AAAATCGCAA
*
1607993 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1608012 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
1608031 TGCGATT
1 TGCGATT
1608038 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1608638 original size:20 final size:20
Alignment explanation
Indices: 1608590--1608629 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1608580 GCGCTATGTA
1608590 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1608610 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1608630 TATCTCGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1608676 original size:20 final size:20
Alignment explanation
Indices: 1608651--1608704 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1608641 GATTTTGTAT
1608651 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1608671 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1608691 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1608705 TTTACCAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1608705 original size:61 final size:61
Alignment explanation
Indices: 1608591--1608707 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1608581 CGCTATGTAA
* * * * *
1608591 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTACGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTTGTATT
* * * *
1608652 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTT
1608708 ACCAATCTGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTTGTATT
Found at i:1608815 original size:21 final size:21
Alignment explanation
Indices: 1608775--1608815 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1608765 ACTGTAGACC
**
1608775 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1608796 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1608816 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1609894 original size:18 final size:19
Alignment explanation
Indices: 1609860--1609899 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1609850 GCGCGGGATT
*
1609860 AATTTAATTTAATTAAT-A
1 AATTTAATTTAACTAATCA
*
1609878 AATTTAATTTCACTAATCA
1 AATTTAATTTAACTAATCA
1609897 AAT
1 AAT
1609900 GATTTAGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTAATTTAACTAATCA
Found at i:1610277 original size:22 final size:24
Alignment explanation
Indices: 1610240--1610283 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1610230 AAAAATAGAG
1610240 ATTTAAAAGATTAG-AATGAAATA
1 ATTTAAAAGATTAGAAATGAAATA
*
1610263 ATTTTAAA-ATTAGAAATGAAA
1 ATTTAAAAGATTAGAAATGAAA
1610284 AATCTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (24 bp):
ATTTAAAAGATTAGAAATGAAATA
Found at i:1610762 original size:2 final size:2
Alignment explanation
Indices: 1610752--1610804 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1610742 TTTTTTCTCC
*
1610752 AT AT TT 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
1610794 AT AT AT AT AT A
1 AT AT AT AT AT A
1610805 CAAGATTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1613687 original size:21 final size:21
Alignment explanation
Indices: 1613661--1613702 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1613651 CCAGAATGGG
*
1613661 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1613682 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1613703 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1613860 original size:21 final size:20
Alignment explanation
Indices: 1613816--1613895 Score: 124
Period size: 21 Copynumber: 3.9 Consensus size: 20
1613806 AACCATTCAA
1613816 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCTGTTCCCCCTGG
1613836 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCTGTTCCCCCTGG
* *
1613856 AGGGGAATCTGTACCCCATGG
1 -GGGGAATCTGTTCCCCCTGG
1613877 GGGGTAATCTGTTCCCCCT
1 GGGG-AATCTGTTCCCCCT
1613896 AGGCAATCTG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
20 24 0.44
21 30 0.56
ACGTcount: A:0.14, C:0.29, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGAATCTGTTCCCCCTGG
Found at i:1613878 original size:41 final size:42
Alignment explanation
Indices: 1613815--1613895 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 42
1613805 AAACCATTCA
* *
1613815 AGGGGAATCTGTTCCCCCTGGGGGG-AATCTGTTCCCCCTGG
1 AGGGGAATCTGTACCCCATGGGGGGTAATCTGTTCCCCCTGG
1613856 AGGGGAATCTGTACCCCATGGGGGGTAATCTGTTCCCCCT
1 AGGGGAATCTGTACCCCATGGGGGGTAATCTGTTCCCCCT
1613896 AGGCAATCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
41 23 0.62
42 14 0.38
ACGTcount: A:0.15, C:0.28, G:0.32, T:0.25
Consensus pattern (42 bp):
AGGGGAATCTGTACCCCATGGGGGGTAATCTGTTCCCCCTGG
Found at i:1615387 original size:19 final size:20
Alignment explanation
Indices: 1615344--1615391 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1615334 TTCTAAATCC
*
1615344 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1615364 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1615383 TTTTCAAAA
1 TTTTCAAAA
1615392 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1616628 original size:21 final size:21
Alignment explanation
Indices: 1616602--1616643 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1616592 CCAGAATGGG
*
1616602 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1616623 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1616644 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1616707 original size:21 final size:21
Alignment explanation
Indices: 1616683--1616734 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1616673 TGAACAGTGA
1616683 GGGAATCGGTACCCCCTTAGG
1 GGGAATCGGTACCCCCTTAGG
*
1616704 GGGAATCGGTACCCCCTTAGT
1 GGGAATCGGTACCCCCTTAGG
1616725 GGGAATCGGT
1 GGGAATCGGT
1616735 TCCCTCCGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTTAGG
Found at i:1616802 original size:20 final size:20
Alignment explanation
Indices: 1616777--1616893 Score: 129
Period size: 21 Copynumber: 6.0 Consensus size: 20
1616767 AAACCATTCA
1616777 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
**
1616797 GGGGGGAATC--TATTCCC-
1 GGGGGGAATCTGTACCCCCT
1616814 --GGGGAATC-GATACCCCCT
1 GGGGGGAATCTG-TACCCCCT
*
1616832 GGGGGGGAATCTGTTCCCCCT
1 -GGGGGGAATCTGTACCCCCT
1616853 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
*
1616873 GGGGGGGAATCTGTTCCCCCT
1 -GGGGGGAATCTGTACCCCCT
1616894 AGACAATCTG
Statistics
Matches: 82, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.10
17 5 0.06
18 5 0.06
20 29 0.35
21 34 0.41
22 1 0.01
ACGTcount: A:0.15, C:0.29, G:0.35, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:1616859 original size:41 final size:41
Alignment explanation
Indices: 1616777--1616893 Score: 167
Period size: 41 Copynumber: 3.0 Consensus size: 41
1616767 AAACCATTCA
*
1616777 GGGGGGAATCTGTACCCCCT-GGGGGGAATCTATT--CCC-
1 GGGGGGAATCTGTACCCCCTGGGGGGGAATCTGTTCCCCCT
1616814 --GGGGAATC-GATACCCCCTGGGGGGGAATCTGTTCCCCCT
1 GGGGGGAATCTG-TACCCCCTGGGGGGGAATCTGTTCCCCCT
1616853 GGGGGGAATCTGTACCCCCTGGGGGGGAATCTGTTCCCCCT
1 GGGGGGAATCTGTACCCCCTGGGGGGGAATCTGTTCCCCCT
1616894 AGACAATCTG
Statistics
Matches: 71, Mismatches: 1, Indels: 12
0.85 0.01 0.14
Matches are distributed among these distances:
34 1 0.01
35 16 0.23
36 13 0.18
38 3 0.04
41 37 0.52
42 1 0.01
ACGTcount: A:0.15, C:0.29, G:0.35, T:0.21
Consensus pattern (41 bp):
GGGGGGAATCTGTACCCCCTGGGGGGGAATCTGTTCCCCCT
Found at i:1618671 original size:2 final size:2
Alignment explanation
Indices: 1618664--1618692 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1618654 TAATTATAGT
1618664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1618693 CCAATCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1619759 original size:26 final size:25
Alignment explanation
Indices: 1619718--1619768 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
1619708 TTTTAATTTA
*
1619718 AATTAATATCAAATTAAAATATAAT
1 AATTAATATCAAATTAAAAAATAAT
*
1619743 AATTAAATTTCAAATTAAAAAATAAT
1 AATT-AATATCAAATTAAAAAATAAT
1619769 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTAATATCAAATTAAAAAATAAT
Found at i:1619776 original size:26 final size:26
Alignment explanation
Indices: 1619726--1619776 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1619716 TAAATTAATA
* *
1619726 TCAAATTAAAATATAATAATTAAATT
1 TCAAATTAAAAAATAATAATAAAATT
1619752 TCAAATTAAAAAATAATTAA-AAAAT
1 TCAAATTAAAAAATAA-TAATAAAAT
1619777 ATAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (26 bp):
TCAAATTAAAAAATAATAATAAAATT
Found at i:1620734 original size:2 final size:2
Alignment explanation
Indices: 1620727--1620754 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1620717 GGTAATTCCT
1620727 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1620755 GTGCCGTTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1622614 original size:2 final size:2
Alignment explanation
Indices: 1622607--1622636 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1622597 CAATGCTTCT
1622607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1622637 CATTTAAATA
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):
TA
Found at i:1628565 original size:39 final size:39
Alignment explanation
Indices: 1628488--1628633 Score: 166
Period size: 39 Copynumber: 3.7 Consensus size: 39
1628478 CAGACTCATT
* ** * *
1628488 GGCTTTGTGCTCAGGGTAAGTCCTTACCGCAAGTTCCTC
1 GGCTTTGTGCACAGGGTAAGTCCTTACTACAGGCTCCTC
*
1628527 GGCTTTGTGCTCAGGGTAAGTCCTTACTACAGGCTCCTC
1 GGCTTTGTGCACAGGGTAAGTCCTTACTACAGGCTCCTC
* * * * *
1628566 TGCTTTGTGCACATGATAAGACCTTACTACAGACTCCTC
1 GGCTTTGTGCACAGGGTAAGTCCTTACTACAGGCTCCTC
** *
1628605 TTCTTTATGCACAGGGTAAGTCCTTACTA
1 GGCTTTGTGCACAGGGTAAGTCCTTACTA
1628634 GGTGTACAGG
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 92 1.00
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (39 bp):
GGCTTTGTGCACAGGGTAAGTCCTTACTACAGGCTCCTC
Found at i:1632902 original size:18 final size:18
Alignment explanation
Indices: 1632879--1632967 Score: 133
Period size: 18 Copynumber: 4.9 Consensus size: 18
1632869 AGGGATTATC
*
1632879 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
*
1632897 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
*
1632915 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
*
1632933 AGTGGTCCTTCTGGACAT
1 AGTGGTCCTTCGGGACAT
*
1632951 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
1632968 AATATTCAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1639054 original size:18 final size:18
Alignment explanation
Indices: 1639031--1639081 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
1639021 AGGGATTATC
1639031 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1639049 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1639067 AGTGGTCCTTTGGGA
1 AGTGGTCCTTCGGGA
1639082 AAAATATTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.16, C:0.20, G:0.35, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1643145 original size:2 final size:2
Alignment explanation
Indices: 1643140--1643166 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1643130 AACACAACAC
1643140 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1643167 CGCCCATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1643358 original size:24 final size:24
Alignment explanation
Indices: 1643324--1643395 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
1643314 AAACTGAGAT
* * *
1643324 ATCATAAATCAAAATAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
1643348 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
1643372 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
1643396 GTAATGTATC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1643395 original size:12 final size:12
Alignment explanation
Indices: 1643339--1643395 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
1643329 AAATCAAAAT
*
1643339 AGAATTCAGATC
1 AGAATTCAGAAC
1643351 AG-ATATCAGAAC
1 AGAAT-TCAGAAC
* *
1643363 AGAATCCAGATC
1 AGAATTCAGAAC
*
1643375 AGAAATCAGAAC
1 AGAATTCAGAAC
1643387 AGAATTCAG
1 AGAATTCAG
1643396 GTAATGTATC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (12 bp):
AGAATTCAGAAC
Found at i:1643694 original size:27 final size:27
Alignment explanation
Indices: 1643664--1643720 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1643654 ATTCTTATCC
1643664 ATAGATCATCTTCGAAATCATCACTGA
1 ATAGATCATCTTCGAAATCATCACTGA
* *
1643691 ATAGATCATCTTCGGATTCATCACTGA
1 ATAGATCATCTTCGAAATCATCACTGA
1643718 ATA
1 ATA
1643721 TCTTAAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (27 bp):
ATAGATCATCTTCGAAATCATCACTGA
Found at i:1652012 original size:44 final size:44
Alignment explanation
Indices: 1651962--1652047 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
1651952 GATGCTGGTA
* *
1651962 GCTCGGGCGTGCTTGGCGGGGGAACGAACGGTGGAGTCCTCGTG
1 GCTCGGGAGTGCTTGACGGGGGAACGAACGGTGGAGTCCTCGTG
1652006 GCTCGGGAGTGCTTGACGGGGGAACGAACGGTGGAGTCCTCG
1 GCTCGGGAGTGCTTGACGGGGGAACGAACGGTGGAGTCCTCG
1652048 CGCCAATGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.14, C:0.22, G:0.47, T:0.17
Consensus pattern (44 bp):
GCTCGGGAGTGCTTGACGGGGGAACGAACGGTGGAGTCCTCGTG
Found at i:1652537 original size:21 final size:21
Alignment explanation
Indices: 1652511--1652586 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1652501 GCAAATAAGT
1652511 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1652532 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1652552 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
1652573 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1652587 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1652565 original size:20 final size:20
Alignment explanation
Indices: 1652494--1652567 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
1652484 TTTTTCCAAT
* *
1652494 TCGCAATGCAAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
1652514 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
1652535 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
1652555 TCGCAACGCGAAT
1 TCGCAACGCGAAT
1652568 TGGGAAAATC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:1652585 original size:41 final size:41
Alignment explanation
Indices: 1652494--1652586 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1652484 TTTTTCCAAT
*
1652494 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1652535 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1652576 TCGCAATGCGA
1 TCGCAATGCGA
1652587 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1652599 original size:41 final size:41
Alignment explanation
Indices: 1652513--1652647 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
1652503 AAATAAGTAA
* *
1652513 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1652554 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
1652595 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1652636 TTCGCAACGCGA
1 ATCGCAACGCGA
1652648 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1652600 original size:20 final size:20
Alignment explanation
Indices: 1652575--1652669 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1652565 AATTGGGAAA
*
1652575 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1652595 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1652616 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1652636 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1652656 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1652670 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1652884 original size:22 final size:22
Alignment explanation
Indices: 1652856--1652898 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1652846 CACTCTCTCA
*
1652856 CCATCTCCGATGAAATCCGTCC
1 CCATCTCCGACGAAATCCGTCC
*
1652878 CCATCTCCGGCGAAATCCGTC
1 CCATCTCCGACGAAATCCGTC
1652899 TATCTCCATC
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:0.21, C:0.42, G:0.16, T:0.21
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCC
Found at i:1653179 original size:20 final size:20
Alignment explanation
Indices: 1653154--1653191 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1653144 GTTGCGATTC
1653154 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1653174 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1653192 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1654834 original size:18 final size:18
Alignment explanation
Indices: 1654813--1654857 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1654803 TCCACTTTGG
*
1654813 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1654831 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1654849 GAGCCATCA
1 GAGCCATCA
1654858 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1655397 original size:19 final size:20
Alignment explanation
Indices: 1655343--1655409 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1655333 TAGTTTACTT
* *
1655343 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1655363 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1655383 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1655402 TCGCAACG
1 TCGCAACG
1655410 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1655417 original size:14 final size:14
Alignment explanation
Indices: 1655398--1655455 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1655388 ATGCGAAATG
1655398 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1655412 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1655428 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1655444 AAAATCGTAACG
1 AAAATCGCAACG
1655456 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1655440 original size:32 final size:33
Alignment explanation
Indices: 1655382--1655472 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1655372 GGAAATGGCT
1655382 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1655415 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1655447 ATCGTAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1655473 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1655508 original size:14 final size:14
Alignment explanation
Indices: 1655489--1655546 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1655479 TTGTGTTTCG
1655489 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1655503 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
1655519 CGCATTGCAATTTTGT
1 CG--TTGCGATTTTGT
1655535 CGTTGCGATTTT
1 CGTTGCGATTTT
1655547 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1655532 original size:32 final size:33
Alignment explanation
Indices: 1655484--1655557 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 33
1655474 GCGATTTGTG
* *
1655484 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
1655516 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
1655549 TTTCGCATT
1 TTTCGCATT
1655558 ACGATAGCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 25 0.64
33 14 0.36
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
Found at i:1655589 original size:20 final size:19
Alignment explanation
Indices: 1655560--1655597 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1655550 TTCGCATTAC
1655560 GATAGCCATTTCCGCGTTGT
1 GATAGCCATTT-CGCGTTGT
*
1655580 GATAGTCATTTCGCGTTG
1 GATAGCCATTTCGCGTTG
1655598 CGATTTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (19 bp):
GATAGCCATTTCGCGTTGT
Found at i:1655596 original size:19 final size:19
Alignment explanation
Indices: 1655535--1655601 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
1655525 GCAATTTTGT
**
1655535 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
1655554 CATTACGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
1655574 CGTTGTGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
1655593 CGTTGCGAT
1 CGTTGCGAT
1655602 TTAAGTTTCG
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 22 0.59
20 15 0.41
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1657968 original size:24 final size:24
Alignment explanation
Indices: 1657941--1657994 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1657931 GTATTCGAAA
* *
1657941 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
* *
1657965 TTTGATATTTGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1657989 TTTGAT
1 TTTGAT
1657995 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1658183 original size:12 final size:12
Alignment explanation
Indices: 1658166--1658190 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1658156 ATATAATCCT
1658166 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1658178 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1658190 G
1 G
1658191 TCCCGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1660472 original size:38 final size:37
Alignment explanation
Indices: 1660429--1660578 Score: 128
Period size: 33 Copynumber: 4.4 Consensus size: 37
1660419 CTTAATGTCC
1660429 ATCGCAACGCGGAAATTACTATCGCAAT-CGAAATGAAA
1 ATCGCAACGC-GAAATTA-TATCGCAATGCGAAATGAAA
* *
1660467 ATCGCAA--CGAGA-GA-ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATTATATCGCAATGCGAAATGAAA
*
1660500 ATCGCAACGC-TAATT-T-T-GCAATGCGAAATGAAA
1 ATCGCAACGCGAAATTATATCGCAATGCGAAATGAAA
*** *
1660533 ATCGCAA--CG-AGGGA-ATCGTAATGCGAAATGAAA
1 ATCGCAACGCGAAATTATATCGCAATGCGAAATGAAA
1660566 ATCGCAACGCGAA
1 ATCGCAACGCGAA
1660579 TTTAATTTCG
Statistics
Matches: 91, Mismatches: 9, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
31 2 0.02
32 9 0.10
33 62 0.68
34 3 0.03
35 6 0.07
36 2 0.02
38 7 0.08
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (37 bp):
ATCGCAACGCGAAATTATATCGCAATGCGAAATGAAA
Found at i:1660497 original size:33 final size:33
Alignment explanation
Indices: 1660449--1660574 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
1660439 GGAAATTACT
1660449 ATCGCAAT-CGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1660481 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1660513 TTTTGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1660547 ATCGTAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1660575 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
32 9 0.11
33 71 0.88
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1660540 original size:66 final size:65
Alignment explanation
Indices: 1660452--1660581 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 65
1660442 AATTACTATC
*
1660452 GCAATCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTT
1 GCAATCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTT
* *
1660517 GCAATGCGAAATGAAAATCGCAACGAGGGAATCGTAATGCGAAATGAAAATCGCAACGCGAATTT
1 GCAAT-CGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1660582 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 5 0.08
66 56 0.92
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (65 bp):
GCAATCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTT
Found at i:1660596 original size:19 final size:19
Alignment explanation
Indices: 1660574--1660636 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
1660564 AAATCGCAAC
*
1660574 GCGAATTTAATTTCGCGTT
1 GCGATTTTAATTTCGCGTT
*
1660593 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AATTTCGCGTT
* *
1660613 GCGATTTTCATTTCGCATT
1 GCGATTTTAATTTCGCGTT
1660632 GCGAT
1 GCGAT
1660637 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 20 0.53
20 18 0.47
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (19 bp):
GCGATTTTAATTTCGCGTT
Found at i:1660609 original size:20 final size:19
Alignment explanation
Indices: 1660583--1660636 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
1660573 CGCGAATTTA
1660583 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1660602 ATTTTCGCGTTGCGATTTTC
1 A-TTTCGCGTTGCGATTTTC
*
1660622 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
1660637 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:1660777 original size:13 final size:14
Alignment explanation
Indices: 1660743--1660791 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
1660733 CATCAATTAA
*
1660743 ACAAATCAACTTTT
1 ACAAATCACCTTTT
1660757 ACAAATCACCTTTT
1 ACAAATCACCTTTT
1660771 A-AAATCACCTTTT
1 ACAAATCACCTTTT
1660784 ACAAATCA
1 ACAAATCA
1660792 ATTAAACAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 13 0.39
14 20 0.61
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCACCTTTT
Done.