Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009586.1 Hibiscus syriacus cultivar Beakdansim tig00116964_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: 3773412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 19
Found at i:988789 original size:14 final size:14
Alignment explanation
Indices: 988770--988818 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
988760 TGATATGAGA
988770 ACATGACATGAGCT
1 ACATGACATGAGCT
* **
988784 ACATGATCATAAGAG
1 ACATGA-CATGAGCT
*
988799 AAATGACATGAGCT
1 ACATGACATGAGCT
988813 ACATGA
1 ACATGA
988819 TCACAAGAGA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (14 bp):
ACATGACATGAGCT
Found at i:988805 original size:29 final size:29
Alignment explanation
Indices: 988766--988862 Score: 167
Period size: 29 Copynumber: 3.3 Consensus size: 29
988756 TATGTGATAT
*
988766 GAGAACATGACATGAGCTACATGATCATAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
988796 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
988825 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
988854 GAGAAATGA
1 GAGAAATGA
988863 GTCCTTCGGG
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 60 0.92
30 5 0.08
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:988880 original size:15 final size:15
Alignment explanation
Indices: 988862--988894 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
988852 AAGAGAAATG
988862 AGTCCTTCGGGACGT
1 AGTCCTTCGGGACGT
*
988877 AGTCCTTCGGGATGT
1 AGTCCTTCGGGACGT
988892 AGT
1 AGT
988895 GGTCCTACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
AGTCCTTCGGGACGT
Found at i:990836 original size:24 final size:23
Alignment explanation
Indices: 990805--990869 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 23
990795 AGCTCGTATA
990805 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* *
990828 AATTTGCACCGAAGTGCCGCGTAG
1 AA-TTGCACCGAAGTGCCACATAG
* *
990852 AAATGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
990870 TATAAGATTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 15 0.42
24 21 0.58
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:991120 original size:16 final size:17
Alignment explanation
Indices: 991096--991128 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
991086 ATCTTTTATA
*
991096 ATTATCACATA-TTCAC
1 ATTAGCACATAGTTCAC
991112 ATTAGCACATAGTTCAC
1 ATTAGCACATAGTTCAC
991129 TTACACGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (17 bp):
ATTAGCACATAGTTCAC
Found at i:993776 original size:30 final size:30
Alignment explanation
Indices: 993726--993794 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
993716 TAATATATTA
**
993726 AACTAATAAATTATTCTTTAA-TATAACTTT
1 AACTAATAAACGATTCTTTAATTATAA-TTT
*
993756 AACTAATAAACGATTTTTTAATTATAATTT
1 AACTAATAAACGATTCTTTAATTATAATTT
*
993786 -ACTACTAAA
1 AACTAATAAA
993795 AAAACTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.24
30 21 0.62
31 5 0.15
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.43
Consensus pattern (30 bp):
AACTAATAAACGATTCTTTAATTATAATTT
Found at i:994065 original size:18 final size:18
Alignment explanation
Indices: 994044--994098 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
994034 TTGTTTTACC
994044 CTAATTTATAATAATAAA
1 CTAATTTATAATAATAAA
*
994062 CTAA--T-T-A-ACT-AA
1 CTAATTTATAATAATAAA
994074 -TAATTTATAATAATAAA
1 CTAATTTATAATAATAAA
994091 CTAATTTA
1 CTAATTTA
994099 AATCTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
11 3 0.11
12 2 0.07
13 3 0.11
14 2 0.07
15 2 0.07
16 3 0.11
17 2 0.07
18 11 0.39
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (18 bp):
CTAATTTATAATAATAAA
Found at i:994106 original size:29 final size:29
Alignment explanation
Indices: 994044--994106 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
994034 TTGTTTTACC
*
994044 CTAATTTATAATAATAAACTAATTAACTA
1 CTAATTTATAATAATAAACTAATTAAATA
*
994073 ATAATTTATAATAATAAACTAATTTAAAT-
1 CTAATTTATAATAATAAACTAA-TTAAATA
994102 CTAAT
1 CTAAT
994107 AAATTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (29 bp):
CTAATTTATAATAATAAACTAATTAAATA
Found at i:994348 original size:352 final size:343
Alignment explanation
Indices: 993786--994447 Score: 967
Period size: 352 Copynumber: 1.9 Consensus size: 343
993776 ATTATAATTT
993786 ACTACTAAAAAAACTAATTAACTAATTTTTTATATAATATAAATTCAACAAACAAATATAACTTA
1 ACTACTAAAAAAACTAATTAACTAATTTTTTATATAATATAAATTCAACAAACAAATATAACTTA
*
993851 ACTATTTAACTAACACAAACTAATTACATATTTTTTTATATATAACTAACTACTAACAACAAACT
66 ACTATTTAACTAACACAAAC-AATTACATATATTTTTATATATAACTAACTACTAACAACAAACT
* * *
993916 AATTATTTTTATAATATTAACTATCAAACATACTAATTAAATAATTTTTTTATTTCTATATGAAT
130 AATTATTTTTATAATATTAACTATCAAACAAACTAATTAAATAATTTTTATATTTATATATGAAT
* **
993981 AACTTAAAGTAACAATAATATAACTTAAACTAACAAACTAATTAACTAATTTTTTGTTTTACCCT
195 AACTTAAACTAACAATAATATAACTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTA-CC-
* ** *
994046 AATTTATAATAATAAACTAATTAACTAATAATTTATAATAATAAACTAATTTAAATCTAATAAAT
258 ---TTA-AACAATAAACTAACAAACTAATAATTTAAAATAATAAACTAATTTAAATCTAATAAAT
994111 TATTTTTTATTATAATAAAACTTAA
319 TATTTTTTATTATAATAAAACTTAA
* *
994136 ACTACT-AATAAACTAATTAACTAAATTTTTTATATAATATAAATTCAACAACCAAAGTATAACT
1 ACTACTAAAAAAACTAATTAACT-AATTTTTTATATAATATAAATTCAACAAACAAA-TATAACT
*
994200 TAACTATTTAACTAAC-TAAA-AATTA-A-ATATTTTTATATATAACTAACGACTAACTAACACA
64 TAACTATTTAACTAACACAAACAATTACATATATTTTTATATATAACT-A--ACT-ACTAACA-A
* * *
994261 CTAATTAATTATTTTTTTAATATATAACTATCAAACAAACTAATTAAATAA-TTTTATATTTATA
124 CAAACTAATTATTTTTATAATAT-TAACTATCAAACAAACTAATTAAATAATTTTTATATTTATA
*
994325 TATGATATAACTTAAACTAACAATAATATAACTTAAATTAACAAACTAATTAACTAAAATTTTGT
188 TATGA-ATAACTTAAACTAACAATAATATAACTTAAACTAACAAACTAATTAACTAAAATTTTGT
*
994390 TTTACCTTAAACCATAAACTAACAAACTAATAATTTAAAATAATAAACTAATTTAAAT
252 TTTACCTTAAACAATAAACTAACAAACTAATAATTTAAAATAATAAACTAATTTAAAT
994448 AATTAAAAAC
Statistics
Matches: 284, Mismatches: 19, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
346 61 0.21
347 5 0.02
348 5 0.02
349 18 0.06
350 48 0.17
351 62 0.22
352 85 0.30
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (343 bp):
ACTACTAAAAAAACTAATTAACTAATTTTTTATATAATATAAATTCAACAAACAAATATAACTTA
ACTATTTAACTAACACAAACAATTACATATATTTTTATATATAACTAACTACTAACAACAAACTA
ATTATTTTTATAATATTAACTATCAAACAAACTAATTAAATAATTTTTATATTTATATATGAATA
ACTTAAACTAACAATAATATAACTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTACCTTA
AACAATAAACTAACAAACTAATAATTTAAAATAATAAACTAATTTAAATCTAATAAATTATTTTT
TATTATAATAAAACTTAA
Found at i:994353 original size:21 final size:21
Alignment explanation
Indices: 994329--994368 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
994319 TTTATATATG
994329 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
*
994350 ATATAACTTAAATTAACAA
1 ATATAACTTAAACTAACAA
994369 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:994657 original size:23 final size:22
Alignment explanation
Indices: 994629--994689 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
994619 GCTGTTGAAG
994629 GGCTGCAATAATGCAACAATAAA
1 GGCTGCAATAATGCAACAAT-AA
*
994652 GGCTGCAATAATGCATCAATAA
1 GGCTGCAATAATGCAACAATAA
*
994674 GTGATGCAATAATGCA
1 G-GCTGCAATAATGCA
994690 GCTGAATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 3 0.09
23 32 0.91
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (22 bp):
GGCTGCAATAATGCAACAATAA
Found at i:994685 original size:12 final size:12
Alignment explanation
Indices: 994632--994689 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 12
994622 GTTGAAGGGC
994632 TGCAATAATGCA
1 TGCAATAATGCA
* *
994644 -ACAATAAAGGC-
1 TGCAAT-AATGCA
994655 TGCAATAATGCA
1 TGCAATAATGCA
994667 T-CAATAAGTG-A
1 TGCAATAA-TGCA
994678 TGCAATAATGCA
1 TGCAATAATGCA
994690 GCTGAATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
11 18 0.50
12 18 0.50
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (12 bp):
TGCAATAATGCA
Found at i:1008986 original size:63 final size:64
Alignment explanation
Indices: 1008832--1008987 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 64
1008822 TAATGAAGGT
* ** * * * * *
1008832 ATGCATCAATGCACTAATTGTGCATCGGTGTATAAAATGCATTCGATGTTTTATTATTAATGGG
1 ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTTTATTATAAAAGAG
* * *
1008896 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTTTATT-TAAAAG
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTTTATTATAAAAG
1008958 AG
63 AG
1008960 -TGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACCTGTGCATCGAT
1008988 ACACCTTCAA
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
63 23 0.31
64 44 0.59
65 8 0.11
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTTTATTATAAAAGAG
Found at i:1021208 original size:23 final size:21
Alignment explanation
Indices: 1021156--1021217 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
1021146 TTTTGGTGCA
*
1021156 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
1021176 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
1021197 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
1021218 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:1035095 original size:16 final size:17
Alignment explanation
Indices: 1035065--1035096 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1035055 GTTAAAATAA
1035065 TATATTTTATAATAATT
1 TATATTTTATAATAATT
1035082 TATATTTT-TAATAAT
1 TATATTTTATAATAAT
1035097 ATAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTTTATAATAATT
Found at i:1038474 original size:20 final size:22
Alignment explanation
Indices: 1038442--1038496 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
1038432 ATTTTTTATT
1038442 TTTATTT-TTATTATT-AT-AA
1 TTTATTTATTATTATTAATAAA
1038461 TTTATTTATTATTATTAATAAA
1 TTTATTTATTATTATTAATAAA
1038483 TTT-TTTATT-TTATT
1 TTTATTTATTATTATT
1038497 TTTTATAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.21
20 13 0.39
21 8 0.24
22 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATTTATTATTATTAATAAA
Found at i:1038475 original size:23 final size:20
Alignment explanation
Indices: 1038440--1038496 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 20
1038430 AGATTTTTTA
*
1038440 TTTTTATTTTTATTATTATAAT
1 TTTTTA-TTTTATTAATA-AAT
1038462 TTATTTATTATTATTAATAAAT
1 TT-TTTATT-TTATTAATAAAT
1038484 TTTTTATTTTATT
1 TTTTTATTTTATT
1038497 TTTTATAGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.16
21 6 0.19
22 9 0.28
23 12 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTATTTTATTAATAAAT
Found at i:1038701 original size:38 final size:38
Alignment explanation
Indices: 1038651--1038735 Score: 127
Period size: 38 Copynumber: 2.3 Consensus size: 38
1038641 TGCAAGCCAT
* * * *
1038651 GAAA-GGGGGATTTTTTTTATTGGTTTTGATCCTATGA
1 GAAAGGGGGGATTTTATTGATTGGTTCTGATCCCATGA
1038688 GAAAGGGGGGATTTTATTGATTGGTTCTGATCCCATGA
1 GAAAGGGGGGATTTTATTGATTGGTTCTGATCCCATGA
1038726 GAAAGGGGGG
1 GAAAGGGGGG
1038736 CACCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 4 0.09
38 39 0.91
ACGTcount: A:0.24, C:0.07, G:0.34, T:0.35
Consensus pattern (38 bp):
GAAAGGGGGGATTTTATTGATTGGTTCTGATCCCATGA
Found at i:1039829 original size:22 final size:22
Alignment explanation
Indices: 1039815--1039863 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1039805 TTGTACTAAC
1039815 TTTTATTTATCTTTGTTATCTA
1 TTTTATTTATCTTTGTTATCTA
*
1039837 TTTTATTTAT-TTTATTAT-TA
1 TTTTATTTATCTTTGTTATCTA
1039857 TTATTAT
1 TT-TTAT
1039864 ATTAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 10 0.40
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATTTATCTTTGTTATCTA
Found at i:1043679 original size:16 final size:16
Alignment explanation
Indices: 1043658--1043688 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1043648 GGTTCGAGAA
1043658 CCAGTTCAAAACAAAT
1 CCAGTTCAAAACAAAT
*
1043674 CCAGTTCAACACAAA
1 CCAGTTCAAAACAAA
1043689 CTCAACCATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.29, G:0.06, T:0.16
Consensus pattern (16 bp):
CCAGTTCAAAACAAAT
Found at i:1044028 original size:106 final size:105
Alignment explanation
Indices: 1043864--1044753 Score: 1286
Period size: 106 Copynumber: 8.4 Consensus size: 105
1043854 TTCCAATTTC
* * * * *
1043864 ATTCAGAGTCTATTTCAACTTCGCAGCGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTC
1 ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
*
1043929 ACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCCA
* *
1043969 CTTCTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
1 ATTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* * * * *
1044034 CACGACGAAGGTACCGCTGGTTGTCAATAAATAACTTCCCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCCA
* * *
1044075 ATTTCAGAGCCAATTTCAATTTCACAGCGAATGATATTGGACTCCAGACAACGCATGTTCAACTT
1 A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
*
1044140 CACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTT--A
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TT-TTCCA
*
1044181 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
1 A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
1044246 CACGATGAAGGGACCGCTGGTTGTCAACAAACAA-CTTCTCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTC-CA
*
1044287 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
1 A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* * * *
1044352 TACGATGAAGGGACCGTTGGTTGTCAATAAAC-ATTTTCCCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTT-CCA
*
1044393 ATATCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
1 AT-TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
1044458 CACGACGAAGGGACCGCTGGTTGTCAATAAACAA-CTTCTCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTC-CA
*
1044499 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
1 A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
1044564 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCCA
*
1044605 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
1 A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
1044670 CACGACGAAGAGACCGCTGGTTGTCAACAAACAATTTCCCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCCA
* ** *
1044711 GTTCTAGAGCCAATTTCAACTTCATGGCGGAGGATATTGGACT
1 ATTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
1044754 TGGAACAATA
Statistics
Matches: 721, Mismatches: 49, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
103 2 0.00
105 9 0.01
106 700 0.97
107 9 0.01
108 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
ACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCCA
Found at i:1044442 original size:318 final size:317
Alignment explanation
Indices: 1043839--1044753 Score: 1456
Period size: 318 Copynumber: 2.9 Consensus size: 317
1043829 AAAAGTTGTC
* * * * *
1043839 TGTCAACAAACAACTT-TCCAATTTCATTCAGAGTCTATTTCAACTTCGCAGCGAAGAAAATTGG
1 TGTCAACAAACAACTTCT-CAA--T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1043903 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTTC
61 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
1043967 CACTTCTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
126 AATTTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* * * *
1044032 TTCACGACGAAGGTACCGCTGGTTGTCAATAAATAACTTCCCAATTTCAGAGCCAATTTCAATTT
190 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAA-TTCAGAGCCAATTTCAACTT
*
1044097 CACAGCGAATGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGT
254 CACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
1044161 TGTCAACAAATAACTTCTTAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
1044226 AGACAACGCATGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
1044291 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACG
131 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1044356 ATGAAGGGACCGTTGGTTGTCAATAAACATTTTCCCAATATCAGAGCCAATTTCAACTTCACAGC
196 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT-TCAGAGCCAATTTCAACTTCACAGC
1044421 GAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGT
260 GAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
1044479 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
1044544 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1044609 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
131 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * **
1044674 ACGAAGAGACCGCTGGTTGTCAACAAACAATTTCCCAGTTCTAGAGCCAATTTCAACTTCATGGC
196 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTC-AGAGCCAATTTCAACTTCACAGC
*
1044739 GGAGGATATTGGACT
260 GAAGGATATTGGACT
1044754 TGGAACAATA
Statistics
Matches: 550, Mismatches: 39, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
317 3 0.01
318 520 0.95
319 8 0.01
320 1 0.00
322 17 0.03
323 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (317 bp):
TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTCAGAGCCAATTTCAACTTCACAGCG
AAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:1045318 original size:18 final size:17
Alignment explanation
Indices: 1045281--1045324 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1045271 ATTTTTTATT
**
1045281 TTTATTATTATAATTTA
1 TTTATTATTATAATAAA
1045298 TTTATTATTAATAATAAA
1 TTTATTATT-ATAATAAA
*
1045316 TTTTTTATT
1 TTTATTATT
1045325 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATTATTATAATAAA
Found at i:1045534 original size:38 final size:38
Alignment explanation
Indices: 1045484--1045568 Score: 127
Period size: 38 Copynumber: 2.3 Consensus size: 38
1045474 TGCAAGCCAT
* * * *
1045484 GAAA-GGGGGATTTTTTTTATTGGTTTTGATCCTATGA
1 GAAAGGGGGGATTTTATTGATTGGTTCTGATCCCATGA
1045521 GAAAGGGGGGATTTTATTGATTGGTTCTGATCCCATGA
1 GAAAGGGGGGATTTTATTGATTGGTTCTGATCCCATGA
1045559 GAAAGGGGGG
1 GAAAGGGGGG
1045569 CACCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 4 0.09
38 39 0.91
ACGTcount: A:0.24, C:0.07, G:0.34, T:0.35
Consensus pattern (38 bp):
GAAAGGGGGGATTTTATTGATTGGTTCTGATCCCATGA
Found at i:1046657 original size:22 final size:22
Alignment explanation
Indices: 1046643--1046691 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1046633 TTGTACTAAC
1046643 TTTTATTTATCTTTGTTATATA
1 TTTTATTTATCTTTGTTATATA
*
1046665 TTTTATTTAT-TTTATTAT-TA
1 TTTTATTTATCTTTGTTATATA
1046685 TTATTAT
1 TT-TTAT
1046692 ATTAATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 10 0.40
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATTTATCTTTGTTATATA
Found at i:1053256 original size:15 final size:15
Alignment explanation
Indices: 1053236--1053264 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1053226 GTAAGAGCAG
1053236 AGCAAGGAAAGCAAA
1 AGCAAGGAAAGCAAA
1053251 AGCAAGGAAAGCAA
1 AGCAAGGAAAGCAA
1053265 CTTATCAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.14, G:0.28, T:0.00
Consensus pattern (15 bp):
AGCAAGGAAAGCAAA
Found at i:1057816 original size:17 final size:17
Alignment explanation
Indices: 1057794--1057832 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1057784 TGAATCAAAT
1057794 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1057811 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1057828 -AATTA
1 TAATTA
1057833 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1065374 original size:23 final size:23
Alignment explanation
Indices: 1065319--1065386 Score: 100
Period size: 24 Copynumber: 2.9 Consensus size: 23
1065309 CAATCTTATA
*
1065319 TGGCACTACGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTATG
1065342 TGGGCACTTCGGTGCAATTCTATG
1 T-GGCACTTCGGTGCAATTCTATG
* *
1065366 TGGCACTTCGATGCATTTCTA
1 TGGCACTTCGGTGCAATTCTA
1065387 CGCGGTCCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.46
24 22 0.54
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTATG
Found at i:1066634 original size:18 final size:18
Alignment explanation
Indices: 1066611--1066655 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1066601 AGAGAAGGTT
1066611 TTATGATGTTAAATGATA
1 TTATGATGTTAAATGATA
1066629 TTATGATGTTAAATGATA
1 TTATGATGTTAAATGATA
1066647 TTATGATGT
1 TTATGATGT
1066656 GTTTTCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.47
Consensus pattern (18 bp):
TTATGATGTTAAATGATA
Found at i:1070911 original size:21 final size:21
Alignment explanation
Indices: 1070885--1070924 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1070875 AGATTGAGCA
1070885 GGGGGTA-CAGATTCCCCCTGG
1 GGGGGTATC-GATTCCCCCTGG
1070906 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
1070925 AAATGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.12, C:0.30, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCTGG
Found at i:1072065 original size:24 final size:23
Alignment explanation
Indices: 1071972--1072065 Score: 84
Period size: 23 Copynumber: 4.0 Consensus size: 23
1071962 CAATCTTATA
* * * *
1071972 TGGCACTACGGTGCAATTCTATG
1 TGGCACTTCGGTGTATTTCTACG
1071995 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTTCGGTGTATTTCTACG
*
1072018 TGGTC-CTTCGG-GACAATTTCTACG
1 TGG-CACTTCGGTG--TATTTCTACG
*
1072042 TGGCACTTCGGTGTAGTTTATACG
1 TGGCACTTCGGTGTA-TTTCTACG
1072066 AGCTGTGGTG
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
22 1 0.02
23 30 0.52
24 26 0.45
25 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (23 bp):
TGGCACTTCGGTGTATTTCTACG
Found at i:1072802 original size:21 final size:22
Alignment explanation
Indices: 1072776--1072817 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1072766 TAGCAGTACC
*
1072776 GTAGCA-GGGTATCGGTTCCCT
1 GTAGCAGGGGAATCGGTTCCCT
1072797 GTAGCAGGGGAATCGGTTCCC
1 GTAGCAGGGGAATCGGTTCCC
1072818 CTCTTTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.17, C:0.24, G:0.36, T:0.24
Consensus pattern (22 bp):
GTAGCAGGGGAATCGGTTCCCT
Found at i:1073958 original size:12 final size:12
Alignment explanation
Indices: 1073916--1073970 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 12
1073906 AAATGTAAAT
1073916 ATACTAATAATA
1 ATACTAATAATA
*
1073928 ATAATAATAATTCTA
1 ATACTAATAA---TA
1073943 ATACTAATAATA
1 ATACTAATAATA
*
1073955 ATACTTAATTATA
1 ATAC-TAATAATA
1073968 ATA
1 ATA
1073971 TTTTTTGACC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 15 0.42
13 10 0.28
15 11 0.31
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (12 bp):
ATACTAATAATA
Found at i:1074472 original size:111 final size:111
Alignment explanation
Indices: 1074285--1074490 Score: 254
Period size: 111 Copynumber: 1.9 Consensus size: 111
1074275 ACGAGGACGG
* * * *
1074285 TTGGTTATCTAGGGGTGACACTACTCTTACGTGATGAAGAGGTCTGGTCAGTGGATGACAAGGTT
1 TTGGTTATCTAGAGGTGACACTACTCCTACATGATGAAGAGGTCTGGTCAGTGGATGACAAGGAT
* * * *
1074350 TCTACGTGATGAGGATGATATACCATCTTTAGGGATGATAACAAAA
66 TCTACGCGATGAAGACGACATACCATCTTTAGGGATGATAACAAAA
* * * *
1074396 TTGGTTATGTAGAGGTGACAC-AGCTCCTACATGATGAGGAGGTCTGGTCGGTGGATGA-AATGA
1 TTGGTTATCTAGAGGTGACACTA-CTCCTACATGATGAAGAGGTCTGGTCAGTGGATGACAAGGA
* *
1074459 TTCATATGCGATGAAGACGACATGCCATCTTT
65 TTC-TACGCGATGAAGACGACATACCATCTTT
1074491 CAGGATAATG
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
110 7 0.09
111 72 0.91
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (111 bp):
TTGGTTATCTAGAGGTGACACTACTCCTACATGATGAAGAGGTCTGGTCAGTGGATGACAAGGAT
TCTACGCGATGAAGACGACATACCATCTTTAGGGATGATAACAAAA
Found at i:1074624 original size:66 final size:63
Alignment explanation
Indices: 1074501--1074711 Score: 226
Period size: 66 Copynumber: 3.2 Consensus size: 63
1074491 CAGGATAATG
* * *
1074501 GTTTCAAGGGAAACCGACTCAAAGATGTCTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTT
1 GTTTCAAGGGAAA-CGTCTCAAAGATGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
1074565 GTTTCAAGGGAAACGTTCTCAAAGATGGGTGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAACT
1 GTTTCAAGGGAAACG-TCTCAAAGAT--GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1074630 T
63 T
* * * * * *
1074631 GTTTAAAGGGAAACACTCTCAAAGGTTAGTGTTTCAAGGGAAA-TAATCTCAAGGGTGACAAAAC
1 GTTTCAAGGGAAAC-GTCTCAAA-GAT-GTGTTTCAAGAGAAACT-GTCTCAAGGGAGACAAAA-
1074695 TTT
61 TTT
*
1074698 GTTTCAAGAGAAAC
1 GTTTCAAGGGAAAC
1074712 AAACTCAAAG
Statistics
Matches: 124, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
63 2 0.02
64 22 0.18
65 1 0.01
66 83 0.67
67 16 0.13
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (63 bp):
GTTTCAAGGGAAACGTCTCAAAGATGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:1079025 original size:16 final size:17
Alignment explanation
Indices: 1079004--1079036 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1078994 TTTTTAAAAC
1079004 AATTTTAAGA-AAAATA
1 AATTTTAAGACAAAATA
*
1079020 AATTTTTAGACAAAATA
1 AATTTTAAGACAAAATA
1079037 CGGTTTACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (17 bp):
AATTTTAAGACAAAATA
Found at i:1079460 original size:15 final size:17
Alignment explanation
Indices: 1079440--1079488 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
1079430 GCATAGGCTT
1079440 AAAATGAAATAA-TAA-
1 AAAATGAAATAATTAAC
*
1079455 AAAATGAATTAATTAAC
1 AAAATGAAATAATTAAC
*
1079472 AAAATAAAATCAATTAA
1 AAAATGAAAT-AATTAA
1079489 TTTATATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
17 8 0.29
18 6 0.21
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (17 bp):
AAAATGAAATAATTAAC
Found at i:1082582 original size:21 final size:21
Alignment explanation
Indices: 1082519--1082576 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1082509 TTTCTGGGCT
1082519 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGGTACCCATTCA
1082540 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGGTACCCATTCA
*
1082561 AGGGGAATCGATACCC
1 AGGGGAATCGGTACCC
1082577 CCTCAAACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.17
Consensus pattern (21 bp):
AGGGGAATCGGTACCCATTCA
Found at i:1082801 original size:75 final size:75
Alignment explanation
Indices: 1082711--1082863 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
1082701 TTAATTTCAA
1082711 GACTTAGGCATTTGATAATCATATTGAAAATTATGTTTATGTAGATATTGAGCCTAATCGAGTTC
1 GACTTAGGCATTTGATAATCATATTGAAAATTATGTTTATGTAGATATTGAGCCTAATCGAGTTC
1082776 TGGAACAATC
66 TGGAACAATC
1082786 GACTTAGGCATTTGATAATCATATTGAAAATTATGTTTATGTAGATATTGAGCCTAATCGAGTTC
1 GACTTAGGCATTTGATAATCATATTGAAAATTATGTTTATGTAGATATTGAGCCTAATCGAGTTC
1082851 TGGAACAATC
66 TGGAACAATC
1082861 GAC
1 GAC
1082864 AATGAATATA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (75 bp):
GACTTAGGCATTTGATAATCATATTGAAAATTATGTTTATGTAGATATTGAGCCTAATCGAGTTC
TGGAACAATC
Found at i:1083079 original size:29 final size:31
Alignment explanation
Indices: 1083016--1083079 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
1083006 TGAATTATGT
* **
1083016 GATAAAGGTATGTAAAATGAAATGTTTATGT
1 GATAAAGGTATGTAAAATGAAATGTCTATCC
*
1083047 GATAAAGGTATG-GAAATG-AATGTCTATCC
1 GATAAAGGTATGTAAAATGAAATGTCTATCC
1083076 GATA
1 GATA
1083080 TAAATTATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.41
30 5 0.17
31 12 0.41
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (31 bp):
GATAAAGGTATGTAAAATGAAATGTCTATCC
Found at i:1083295 original size:24 final size:24
Alignment explanation
Indices: 1083268--1083338 Score: 115
Period size: 24 Copynumber: 2.9 Consensus size: 24
1083258 ATTTATATGT
1083268 GGTCCTTCGGGACAAATTCTACAC
1 GGTCCTTCGGGACAAATTCTACAC
*
1083292 GGTCCTTCGGGACAAATTCTACGC
1 GGTCCTTCGGGACAAATTCTACAC
*
1083316 AGTCCTTCGGGACAAATTTCTAC
1 GGTCCTTCGGGACAAA-TTCTAC
1083339 GCGGCACTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 38 0.86
25 6 0.14
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTACAC
Found at i:1083348 original size:25 final size:23
Alignment explanation
Indices: 1083271--1083350 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 23
1083261 TATATGTGGT
*
1083271 CCTTCGGGACAAATTCTACACGG
1 CCTTCGGGACAAATTCTACGCGG
*
1083294 TCCTTCGGGACAAATTCTACGCAGT
1 -CCTTCGGGACAAATTCTACGC-GG
1083319 CCTTCGGGACAAATTTCTACGCGG
1 CCTTCGGGACAAA-TTCTACGCGG
1083343 CACTTCGG
1 C-CTTCGG
1083351 TGCAATTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
24 35 0.70
25 15 0.30
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (23 bp):
CCTTCGGGACAAATTCTACGCGG
Found at i:1084513 original size:3 final size:3
Alignment explanation
Indices: 1084505--1084606 Score: 181
Period size: 3 Copynumber: 34.7 Consensus size: 3
1084495 ATCCCAACAG
1084505 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1084551 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1084599 TTA TAA TA
1 TAA TAA TA
1084607 TTTTTTGATC
Statistics
Matches: 95, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 4 0.04
3 91 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1089912 original size:25 final size:27
Alignment explanation
Indices: 1089856--1089913 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
1089846 GAGGATCTTC
*
1089856 AATT-ATAAAATAAAATAATTAATTAT
1 AATTAATAAAACAAAATAATTAATTAT
1089882 AA--AATAAAACAAAATAATT-ATT-T
1 AATTAATAAAACAAAATAATTAATTAT
1089905 AATTAATAA
1 AATTAATAA
1089914 TATATTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 3 0.11
24 3 0.11
25 20 0.71
26 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
AATTAATAAAACAAAATAATTAATTAT
Found at i:1091135 original size:21 final size:21
Alignment explanation
Indices: 1091063--1091135 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 21
1091053 ATACAAAATT
* *
1091063 TTTAATAAAATTTATTTTATAA
1 TTTATTAAAATTTAATTT-TAA
*
1091085 TTTATAAAAAATGTTTAATATTTAGA
1 TTTAT-TAAAA--TTTAAT-TTTA-A
1091111 -TTATTAAAATTTAATTTTAA
1 TTTATTAAAATTTAATTTTAA
1091131 TTTAT
1 TTTAT
1091136 ATATATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
20 1 0.02
21 8 0.20
22 10 0.24
23 4 0.10
24 4 0.10
25 11 0.27
26 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTATTAAAATTTAATTTTAA
Found at i:1091871 original size:18 final size:18
Alignment explanation
Indices: 1091848--1091888 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1091838 TAAAAGTTTC
1091848 TTTTCTTGATATTTTTAG
1 TTTTCTTGATATTTTTAG
1091866 TTTTCTTGATATTTTTAG
1 TTTTCTTGATATTTTTAG
1091884 TTTTC
1 TTTTC
1091889 AATCAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (18 bp):
TTTTCTTGATATTTTTAG
Found at i:1095117 original size:34 final size:34
Alignment explanation
Indices: 1095079--1095145 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
1095069 AGTTGACTAT
* * *
1095079 TATAATATTTATATGGTATTTTATAGTGTTAATC
1 TATAATATTAATATGATAATTTATAGTGTTAATC
*
1095113 TATAATATTAATGTGATAATTTATAGTGTTAAT
1 TATAATATTAATATGATAATTTATAGTGTTAAT
1095146 GATATAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (34 bp):
TATAATATTAATATGATAATTTATAGTGTTAATC
Found at i:1095550 original size:2 final size:2
Alignment explanation
Indices: 1095536--1095592 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
1095526 ATTGTGAAAC
*
1095536 TA TA TA -A TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1095576 TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1095593 ATAATCATAC
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1095778 original size:19 final size:20
Alignment explanation
Indices: 1095754--1095793 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1095744 AAAACATATT
1095754 ATTTTTAGTAATT-AATTTA
1 ATTTTTAGTAATTAAATTTA
*
1095773 ATTTTTAGTATTTAAATTTA
1 ATTTTTAGTAATTAAATTTA
1095793 A
1 A
1095794 AATATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTTAGTAATTAAATTTA
Found at i:1096087 original size:2 final size:2
Alignment explanation
Indices: 1096075--1096168 Score: 160
Period size: 2 Copynumber: 49.0 Consensus size: 2
1096065 TTTTGCCTAT
1096075 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1096115 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1096156 TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA
1096169 AGCAACTTAG
Statistics
Matches: 88, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
1 4 0.05
2 84 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1098353 original size:15 final size:15
Alignment explanation
Indices: 1098329--1098366 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1098319 GATATTTAGT
1098329 TGGG-CGGGCGGATG
1 TGGGACGGGCGGATG
1098343 TGGGACGGGCGGATG
1 TGGGACGGGCGGATG
*
1098358 CGGGACGGG
1 TGGGACGGG
1098367 TAATGTCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.11, C:0.16, G:0.63, T:0.11
Consensus pattern (15 bp):
TGGGACGGGCGGATG
Found at i:1103823 original size:14 final size:14
Alignment explanation
Indices: 1103804--1103852 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1103794 TGATATGAGA
1103804 ACATGACATGAGCT
1 ACATGACATGAGCT
* **
1103818 ACATGATCATAAGAG
1 ACATGA-CATGAGCT
*
1103833 AAATGACATGAGCT
1 ACATGACATGAGCT
1103847 ACATGA
1 ACATGA
1103853 TCACAAGAGA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (14 bp):
ACATGACATGAGCT
Found at i:1103839 original size:29 final size:29
Alignment explanation
Indices: 1103800--1103909 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
1103790 ATATTGATAT
*
1103800 GAGAACATGACATGAGCTACATGATCATAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
1103830 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
1103859 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1103888 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1103910 ACATATAAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.09
29 65 0.84
30 5 0.06
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.18
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1106862 original size:12 final size:12
Alignment explanation
Indices: 1106847--1106882 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1106837 TATCATGTTC
1106847 TCATATCACATG
1 TCATATCACATG
*
1106859 TCATATCACATA
1 TCATATCACATG
1106871 TCATATCACATG
1 TCATATCACATG
1106883 AACATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:1107334 original size:69 final size:69
Alignment explanation
Indices: 1107241--1107369 Score: 199
Period size: 69 Copynumber: 1.9 Consensus size: 69
1107231 TTATTGCTGG
1107241 GATGCATCGATGCACTCCTATGCATCGATGCACCAATTGCATTCGATG-TTTTATTATTAATGGA
1 GATGCATCGATGCACTCCTATGCATCGATGCACCAATTGCATTCGATGTTTTTATT-TTAATGGA
1107305 TGGAT
65 TGGAT
* **
1107310 GATGCATC-ATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATTTTAA
1 GATGCATCGATGCACT-CCTATGCATCGATGCACCAATTGCATTCGATGTTTTTATTTTAA
1107370 AAGAGTGCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
68 7 0.13
69 41 0.75
70 7 0.13
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (69 bp):
GATGCATCGATGCACTCCTATGCATCGATGCACCAATTGCATTCGATGTTTTTATTTTAATGGAT
GGAT
Found at i:1109155 original size:13 final size:13
Alignment explanation
Indices: 1109137--1109162 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1109127 ATGGAAATAG
1109137 GTACACCATGTAA
1 GTACACCATGTAA
1109150 GTACACCATGTAA
1 GTACACCATGTAA
1109163 CCGTATAATC
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:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
GTACACCATGTAA
Found at i:1113631 original size:15 final size:15
Alignment explanation
Indices: 1113611--1113643 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1113601 CGTAGGACCC
1113611 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
1113626 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
1113641 CTA
1 CTA
1113644 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:1114224 original size:61 final size:59
Alignment explanation
Indices: 1114156--1114286 Score: 156
Period size: 61 Copynumber: 2.2 Consensus size: 59
1114146 CATAAAAGGT
**
1114156 ATTCGATGT-ATTATTGCTGGGATACATCGATGCACTCCTTATGCAGCGATGCACCAATTGC
1 ATTCGATGTCATTATTAATGGGATACATCGATGCA---CTTATGCAGCGATGCACCAATTGC
* * **
1114217 ATTCGATGTTTCATTATTAATGGGATGCATCGATGCACTTATGCATCGATGCATGAATTGC
1 ATTCGATG--TCATTATTAATGGGATACATCGATGCACTTATGCAGCGATGCACCAATTGC
1114278 ATTCGATGT
1 ATTCGATGT
1114287 TTTTATTTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
59 1 0.02
61 37 0.61
63 1 0.02
64 22 0.36
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (59 bp):
ATTCGATGTCATTATTAATGGGATACATCGATGCACTTATGCAGCGATGCACCAATTGC
Found at i:1114307 original size:61 final size:61
Alignment explanation
Indices: 1114193--1114316 Score: 162
Period size: 61 Copynumber: 2.0 Consensus size: 61
1114183 CGATGCACTC
* *
1114193 CTTATGCAGCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGATGCATCGATGCA
1 CTTATGCAGCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATGCATCGATGCA
* ** *
1114254 CTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AGAGTGCATCGATGCA
1 CTTATGCAGCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAGA-TGCATCGATGCA
1114315 CT
1 CT
1114317 ACCAATGCAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 2 0.04
61 47 0.85
62 6 0.11
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (61 bp):
CTTATGCAGCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATGCATCGATGCA
Found at i:1118510 original size:29 final size:28
Alignment explanation
Indices: 1118471--1118567 Score: 140
Period size: 29 Copynumber: 3.3 Consensus size: 28
1118461 TATGTGATAT
1118471 GAGAACATGACATGAGTTACATGATCACAA
1 GAGAA-ATGACATGA-TTACATGATCACAA
1118501 GAGAAATGACATGATCTACATGATCACAA
1 GAGAAATGACATGAT-TACATGATCACAA
* *
1118530 GAGAAATGACATGAACTACATGATCATAA
1 GAGAAATGACATG-ATTACATGATCACAA
1118559 GAGAAATGA
1 GAGAAATGA
1118568 GAACATATAA
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.02
29 56 0.89
30 6 0.10
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (28 bp):
GAGAAATGACATGATTACATGATCACAA
Found at i:1121155 original size:24 final size:24
Alignment explanation
Indices: 1121128--1121177 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1121118 TGGTGGTTAA
1121128 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
1121152 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
1121176 TT
1 TT
1121178 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:1128029 original size:25 final size:24
Alignment explanation
Indices: 1127968--1128041 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 24
1127958 CCTCTTAAAT
*
1127968 TTTTAACTTTTTCTTTTCTCTTTC
1 TTTTAACTTTTACTTTTCTCTTTC
* *
1127992 -TTT-A--TTAATTTTTCTCTTTC
1 TTTTAACTTTTACTTTTCTCTTTC
*
1128012 ATTTTAACTTTTACTTTTCTATTTC
1 -TTTTAACTTTTACTTTTCTCTTTC
1128037 TTTTA
1 TTTTA
1128042 CTCATCTTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
20 13 0.33
22 4 0.10
23 4 0.10
24 5 0.13
25 13 0.33
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTAACTTTTACTTTTCTCTTTC
Found at i:1131309 original size:24 final size:24
Alignment explanation
Indices: 1131282--1131331 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1131272 TGGTGGTTGA
1131282 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
1131306 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
1131330 TT
1 TT
1131332 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:1133294 original size:139 final size:139
Alignment explanation
Indices: 1133067--1133327 Score: 405
Period size: 139 Copynumber: 1.9 Consensus size: 139
1133057 TGCATGGATA
* * * * *
1133067 AAATGAGATGATATTGTCAACATATGTGTAGTGGGCGAAATGATAAGGTTGTCAATTCCATCCAA
1 AAATGAGATGATATTATCAAAATATGTGTAGTGGACGAAATGATAAGATTGTCAACTCCATCCAA
* * *
1133132 AATAAGCTTTCAAACCGCCATCCTTTCTGAAACTACGTCGTCAGAGAGAGAGAGAGATTGCATGG
66 AATAAGCTTTCAAACAGCAATCCTTTCTGAAACTACGTCGACAGAGAGAGAGAGAGATTGCATGG
1133197 ATAAACCTC
131 ATAAACCTC
*
1133206 AAATGAGATGATATTATCAAAATATGTGTAGTGGACGAAATGATAAGATTGTCAGCTCCATCCAA
1 AAATGAGATGATATTATCAAAATATGTGTAGTGGACGAAATGATAAGATTGTCAACTCCATCCAA
* * * *
1133271 AATAGGCTTTCAAACAGTAATCCTTTCTGAAACTGCGTCGAGAGAGAGAGAGAGAGA
66 AATAAGCTTTCAAACAGCAATCCTTTCTGAAACTACGTCGACAGAGAGAGAGAGAGA
1133328 GAGAGAGAGA
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
139 109 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (139 bp):
AAATGAGATGATATTATCAAAATATGTGTAGTGGACGAAATGATAAGATTGTCAACTCCATCCAA
AATAAGCTTTCAAACAGCAATCCTTTCTGAAACTACGTCGACAGAGAGAGAGAGAGATTGCATGG
ATAAACCTC
Found at i:1133317 original size:2 final size:2
Alignment explanation
Indices: 1133310--1133387 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
1133300 AAACTGCGTC
1133310 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1133352 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1133388 TTGCATGGAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1133521 original size:133 final size:133
Alignment explanation
Indices: 1133378--1133636 Score: 446
Period size: 133 Copynumber: 1.9 Consensus size: 133
1133368 GAGAGAGAGA
* *
1133378 GAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATTAAAATATGTGTAGTCGATGA
1 GAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTCGACGA
* * *
1133443 AATGATAGGGTTGTCAACTCCATCCAGAATAAGCTTTCAAACAATCATCCTTTCTGAAACCGTGT
66 AATGATAAGGTTGTCAACTCCATCCAAAATAAGCTTTCAAACAACCATCCTTTCTGAAACCGTGT
1133508 CGT
131 CGT
* *
1133511 GAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTGTCAAAATATGTGTAGTGGACGA
1 GAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTCGACGA
*
1133576 AATGATAAGGTTGTCAGCTCCATCCAAAATAAGCTTTCAAACAACCATCCTTTCTGAAACC
66 AATGATAAGGTTGTCAACTCCATCCAAAATAAGCTTTCAAACAACCATCCTTTCTGAAACC
1133637 ACGTCATGTA
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 118 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (133 bp):
GAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTCGACGA
AATGATAAGGTTGTCAACTCCATCCAAAATAAGCTTTCAAACAACCATCCTTTCTGAAACCGTGT
CGT
Found at i:1136002 original size:52 final size:53
Alignment explanation
Indices: 1135945--1136053 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 53
1135935 ACATGAGCAA
1135945 GTTGGTTGTGCGCTGCAGCTAAACAAGTTAAAGCAGTTAGTTT-TTGAAGTTT
1 GTTGGTTGTGCGCTGCAGCTAAACAAGTTAAAGCAGTTAGTTTGTTGAAGTTT
1135997 GTTGGTTGTGCGCTGCAGCTAAACAAGTTAAAGCAGTTAGTTTGTTGAAGTTT
1 GTTGGTTGTGCGCTGCAGCTAAACAAGTTAAAGCAGTTAGTTTGTTGAAGTTT
1136050 GTTG
1 GTTG
1136054 AAGATCAGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 43 0.77
53 13 0.23
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (53 bp):
GTTGGTTGTGCGCTGCAGCTAAACAAGTTAAAGCAGTTAGTTTGTTGAAGTTT
Found at i:1145005 original size:60 final size:60
Alignment explanation
Indices: 1144880--1144995 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
1144870 ATCATTTTTA
* * * *
1144880 AACTTTTAATAATCAGAAGATTCAATAAAGCAACATCTTATAGTTGAGAGATCATTATGT
1 AACTTTTAATAATCAGAAGACTCAATAAAGCAACATCCTATAGTCGAGAGACCATTATGT
* *
1144940 AACTTTTAATAGTC-GAAAGACTCAATAAAGCATCATCCTATAGTCGAG-GAACCATT
1 AACTTTTAATAATCAG-AAGACTCAATAAAGCAACATCCTATAGTCGAGAG-ACCATT
1144996 TGTGTACTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 46 0.96
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (60 bp):
AACTTTTAATAATCAGAAGACTCAATAAAGCAACATCCTATAGTCGAGAGACCATTATGT
Found at i:1146030 original size:54 final size:54
Alignment explanation
Indices: 1145938--1146516 Score: 578
Period size: 54 Copynumber: 10.8 Consensus size: 54
1145928 ATGTCCACCG
* * * ** *
1145938 CCACTGGAACTTGGACCTGAGTTGGTCACAGCATCAACGAATGCATTACCATGT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* * * * *
1145992 CCTCCGGAGCTTGGACCCGAGTTGGTGACGGCAACAACGAGTGCATGGCC-TGT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
*** * * * * *
1146045 CCTTTGGAACTAGGAACCGAGTCGGTGACAGCATCAACGAATGTATGGCCTTTT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* * * *
1146099 CCACCGAAACTTGGACCTGAGTTGGTGACAGCATCAATGAATGCATGGCCTTTT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* * ** ** *
1146153 CCACCAGAGCTTGGACTTGAGTTGGTGACCA-CATCAACGAATGCATTACCATGT
1 CCACCGGAACTTGGACCCGAGTTGGTGA-CAGCATCAACGAATGCATGGCCTTGT
* * * * **
1146207 CCTCTGGAACTTGGACCTGAGTTTGTGACAGCATCAACGAATGCATTACCTTGT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* * * * * * * *
1146261 CCTCCGGAGCTTGGACCCGAGTTGCTGACTGCAACAAACTAGTGCATGGCCATGT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATC-AACGAATGCATGGCCTTGT
* * * * *
1146316 CCTCTGGAACTAGGAACCG-GTTGGTGACAGCATCAACGAATGCATGGCCTTTT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* *
1146369 CCACCGGAACTTGGACCTGAGTTGGTGACAGCATCAAAGAATGCATGGCCTT-T
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
** *
1146422 ACCACCGGAACTTGGACCCGAG-ACGTGACAGCATCAACGAATGCATGGCCTTTT
1 -CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
*
1146476 CCACCGGAGCTTGGACCCG-GTTGGTGACCA-CATCAACGAAT
1 CCACCGGAACTTGGACCCGAGTTGGTGA-CAGCATCAACGAAT
1146517 CCTCTGGAAC
Statistics
Matches: 433, Mismatches: 83, Indels: 19
0.81 0.16 0.04
Matches are distributed among these distances:
52 1 0.00
53 135 0.31
54 266 0.61
55 31 0.07
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (54 bp):
CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
Found at i:1146222 original size:108 final size:108
Alignment explanation
Indices: 1145938--1146640 Score: 618
Period size: 107 Copynumber: 6.7 Consensus size: 108
1145928 ATGTCCACCG
* * * * ** *
1145938 CCACTGGAACTTGGACCTGAGTTGGTCACAGCATCAACGAATGCATTACCATGTCCTCCGGAGCT
1 CCACCGGAGCTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCATGTCCTCCGGAACT
* * * *
1146003 TGGACCCGAGTTGGTGACGGCAACAACGAGTGCATGGCC-TGT
66 TGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTTT
*** * * * * * * * * *
1146045 CCTTTGGAACTAGGAACCGAGTCGGTGACAGCATCAACGAATGTATGGCCTTTTCCACCGAAACT
1 CCACCGGAGCTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCATGTCCTCCGGAACT
* *
1146110 TGGACCTGAGTTGGTGACAGCATCAATGAATGCATGGCCTTTT
66 TGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTTT
* ** ** *
1146153 CCACCAGAGCTTGGACTTGAGTTGGTGACCA-CATCAACGAATGCATTACCATGTCCTCTGGAAC
1 CCACCGGAGCTTGGACCCGAGTTGGTGA-CAGCATCAACGAATGCATGGCCATGTCCTCCGGAAC
* * ** *
1146217 TTGGACCTGAGTTTGTGACAGCATCAACGAATGCATTACCTTGT
65 TTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTTT
* * * * * * *
1146261 CCTCCGGAGCTTGGACCCGAGTTGCTGACTGCAACAAACTAGTGCATGGCCATGTCCTCTGGAAC
1 CCACCGGAGCTTGGACCCGAGTTGGTGACAGCATC-AACGAATGCATGGCCATGTCCTCCGGAAC
* *
1146326 TAGGAACCG-GTTGGTGACAGCATCAACGAATGCATGGCCTTTT
65 TTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTTT
* * * * *
1146369 CCACCGGAACTTGGACCTGAGTTGGTGACAGCATCAAAGAATGCATGGCC-TTTACCACCGGAAC
1 CCACCGGAGCTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCATGT-CCTCCGGAAC
**
1146433 TTGGACCCGAG-ACGTGACAGCATCAACGAATGCATGGCCTTTT
65 TTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTTT
1146476 CCACCGGAGCTTGGACCCG-GTTGGTGACCA-CATCAACG-A---AT--CC---T-CT--GGAAC
1 CCACCGGAGCTTGGACCCGAGTTGGTGA-CAGCATCAACGAATGCATGGCCATGTCCTCCGGAAC
* * * * ** * *
1146527 TTGGACCTGAG-TGTTGACAGCATCAAAGAAAGCATTCCCCTGT
65 TTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTTT
** * * * * * *
1146570 CCTTCGGAGCATGGACCAGAGTTGGCGACAGCATCAACGAATGCATGGCCTTTTCCACCGGAACT
1 CCACCGGAGCTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCATGTCCTCCGGAACT
1146635 TGGACC
66 TGGACC
1146641 ACCGGTCTTG
Statistics
Matches: 477, Mismatches: 98, Indels: 42
0.77 0.16 0.07
Matches are distributed among these distances:
94 55 0.12
95 15 0.03
96 2 0.00
98 1 0.00
99 2 0.00
100 2 0.00
101 2 0.00
102 2 0.00
104 1 0.00
105 2 0.00
106 17 0.04
107 173 0.36
108 170 0.36
109 33 0.07
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (108 bp):
CCACCGGAGCTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCATGTCCTCCGGAACT
TGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTTT
Found at i:1149517 original size:190 final size:191
Alignment explanation
Indices: 1149194--1149574 Score: 739
Period size: 190 Copynumber: 2.0 Consensus size: 191
1149184 GCAACACAAA
1149194 TGACAAACTATCATAACACTAGGCTAAGTCGTGTCATAAAAGCATACAACACTAGGTTAAATCAA
1 TGACAAACTATCATAACACTAGGCTAAGTCGTGTCATAAAAGCATACAACACTAGGTTAAATCAA
1149259 CCAACCAACACCATATACTTATGTCTCACGTTTTTAAATGTTTATAAAAAAATTGTAGTATTAAT
66 CCAACCAACACCATATACTTATGTCTCACGTTTTTAAATGTTTATAAAAAAATTGTAGTATTAAT
1149324 ATTTGATACACTAATCAACCAATCATA-TTGAATATTACGCAAATTCATGATAATTTTCCT
131 ATTTGATACACTAATCAACCAATCATATTTGAATATTACGCAAATTCATGATAATTTTCCT
1149384 TGACAAACTATCATAACACTAGGCTAAGTCGTGTCATAAAAGCATACAACACTAGGTTAAATCAA
1 TGACAAACTATCATAACACTAGGCTAAGTCGTGTCATAAAAGCATACAACACTAGGTTAAATCAA
1149449 CCAACCAACACCATATACTTATGTCTCACGTTTTTAAATG-TTATAAAAAAATTGTAGTCATTAA
66 CCAACCAACACCATATACTTATGTCTCACGTTTTTAAATGTTTATAAAAAAATTGTAGT-ATTAA
1149513 TATTTGATACACTAATCAACCAATCATATTTGAATATTACGCAAATTCATGATAATTTTCCT
130 TATTTGATACACTAATCAACCAATCATATTTGAATATTACGCAAATTCATGATAATTTTCCT
1149575 AATCTAATTT
Statistics
Matches: 189, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
189 18 0.10
190 138 0.73
191 33 0.17
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (191 bp):
TGACAAACTATCATAACACTAGGCTAAGTCGTGTCATAAAAGCATACAACACTAGGTTAAATCAA
CCAACCAACACCATATACTTATGTCTCACGTTTTTAAATGTTTATAAAAAAATTGTAGTATTAAT
ATTTGATACACTAATCAACCAATCATATTTGAATATTACGCAAATTCATGATAATTTTCCT
Found at i:1150394 original size:52 final size:51
Alignment explanation
Indices: 1150300--1150403 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 51
1150290 TTAGGCTTAT
1150300 CTTCCCAAATCGAATCCTATCATACCCTGGTTGGCCCTTTCCTTTTTCCGA
1 CTTCCCAAATCGAATCCTATCATACCCTGGTTGGCCCTTTCCTTTTTCCGA
1150351 CTTCCCAAATCGAATCCTATCAATACCCTGGTTGGCCCTTTCCTTTTTCCGA
1 CTTCCCAAATCGAATCCTATC-ATACCCTGGTTGGCCCTTTCCTTTTTCCGA
1150403 C
1 C
1150404 CGAAAATGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 21 0.40
52 31 0.60
ACGTcount: A:0.18, C:0.36, G:0.12, T:0.35
Consensus pattern (51 bp):
CTTCCCAAATCGAATCCTATCATACCCTGGTTGGCCCTTTCCTTTTTCCGA
Found at i:1150665 original size:2 final size:2
Alignment explanation
Indices: 1150658--1150687 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1150648 ATTCATTATT
1150658 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
1150688 GAGAGAGAGA
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:1150692 original size:2 final size:2
Alignment explanation
Indices: 1150687--1150723 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1150677 ATATATATAT
1150687 AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1150724 TAGGTTAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1150712 original size:17 final size:17
Alignment explanation
Indices: 1150690--1150723 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1150680 TATATATAGA
1150690 GAGAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAGAG
1150707 GAGAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAGAG
1150724 TAGGTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (17 bp):
GAGAGAGAGAGAGAGAG
Found at i:1151569 original size:27 final size:27
Alignment explanation
Indices: 1151539--1151604 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 27
1151529 CACTAAGATT
* *
1151539 ATAATTATAAATATAAAAGA-ATTAAAG
1 ATAA-TATAAATATAAAAAATATTAAAA
*
1151566 ATAA-ATAAAAATAAAAAATATTAAAA
1 ATAATATAAATATAAAAAATATTAAAA
1151592 ATAAACTATAAAT
1 AT-AA-TATAAAT
1151605 TTAATCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
25 12 0.39
26 8 0.26
27 6 0.19
29 5 0.16
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (27 bp):
ATAATATAAATATAAAAAATATTAAAA
Found at i:1151589 original size:26 final size:25
Alignment explanation
Indices: 1151545--1151596 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1151535 GATTATAATT
* * *
1151545 ATAAATATAAAAGAATTAAAGATAA
1 ATAAAAATAAAAAAATTAAAAATAA
1151570 ATAAAAATAAAAAATATTAAAAATAA
1 ATAAAAATAAAAAA-ATTAAAAATAA
1151596 A
1 A
1151597 CTATAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (25 bp):
ATAAAAATAAAAAAATTAAAAATAA
Found at i:1154561 original size:27 final size:28
Alignment explanation
Indices: 1154525--1154592 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
1154515 AAATAAATCA
*
1154525 TTTTATATAAATATTTTA-AAAAATAGAT
1 TTTTA-ATAAATATTGTATAAAAATAGAT
* **
1154553 TTTTAATAAATCTTGTATAAAAATATTT
1 TTTTAATAAATATTGTATAAAAATAGAT
1154581 TTTTAA-AAATAT
1 TTTTAATAAATAT
1154593 AAATAATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (28 bp):
TTTTAATAAATATTGTATAAAAATAGAT
Found at i:1161324 original size:21 final size:21
Alignment explanation
Indices: 1161295--1161339 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1161285 CGGATAAAAA
* * *
1161295 TTATTTAAAATATTATTATTT
1 TTATCTAAAACATTAATATTT
*
1161316 TTATCTAAAACATTAATGTTT
1 TTATCTAAAACATTAATATTT
1161337 TTA
1 TTA
1161340 ATATTTTCGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
TTATCTAAAACATTAATATTT
Found at i:1163074 original size:30 final size:30
Alignment explanation
Indices: 1163038--1163105 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
1163028 TTAGTCTTTA
1163038 AGCTTCAACTATAAATACCCTAGCTCATTT
1 AGCTTCAACTATAAATACCCTAGCTCATTT
1163068 AGCTTCAACTATAAATACCCTAGCTCATTT
1 AGCTTCAACTATAAATACCCTAGCTCATTT
1163098 AGCTTCAA
1 AGCTTCAA
1163106 AACCATCCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.32
Consensus pattern (30 bp):
AGCTTCAACTATAAATACCCTAGCTCATTT
Found at i:1175121 original size:20 final size:21
Alignment explanation
Indices: 1175096--1175147 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1175086 TTTTCCCAAT
*
1175096 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1175116 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1175137 TCGCAATGCGA
1 TCGCAATGCGA
1175148 TACTTACTAT
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:1175226 original size:20 final size:20
Alignment explanation
Indices: 1175178--1175230 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1175168 TAATACAAAA
* *
1175178 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
1175198 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
1175218 TCGCAACGCGATT
1 TCGCAACGCGATT
1175231 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:1175806 original size:19 final size:19
Alignment explanation
Indices: 1175746--1175826 Score: 82
Period size: 19 Copynumber: 4.5 Consensus size: 19
1175736 TTCGAGAATG
1175746 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1175766 ACTATCGCAA--CGAAAT-
1 AAAATCGCAACGCGAAATA
1175782 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1175799 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1175818 AAAATCGCA
1 AAAATCGCA
1175827 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
14 7 0.14
16 6 0.12
17 5 0.10
18 1 0.02
19 24 0.47
20 8 0.16
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1175844 original size:19 final size:19
Alignment explanation
Indices: 1175822--1176006 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
1175812 GAAACCAAAA
*
1175822 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1175841 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1175860 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1175879 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1175899 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1175915 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1175932 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1175946 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
1175965 TCCGTGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1175985 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1176005 TC
1 TC
1176007 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.44
20 47 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1175899 original size:39 final size:38
Alignment explanation
Indices: 1175822--1176006 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
1175812 GAAACCAAAA
*
1175822 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
1175860 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
1175899 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
1175932 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
1175965 TCCGTGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
1176005 TC
1 TC
1176007 AACCAAAAGA
Statistics
Matches: 123, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 9 0.07
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1175983 original size:20 final size:20
Alignment explanation
Indices: 1175947--1176006 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1175937 TTGCGATTCT
**
1175947 CTCGTTGCGATAGTCATTTC
1 CTCGTTGCGATTCTCATTTC
1175967 CGT-GTTGCGATTCTCATTAT-
1 C-TCGTTGCGATTCTCATT-TC
*
1175987 CTCGTTGCGATTTTCATTTC
1 CTCGTTGCGATTCTCATTTC
1176007 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (20 bp):
CTCGTTGCGATTCTCATTTC
Found at i:1178066 original size:21 final size:21
Alignment explanation
Indices: 1178042--1178108 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1178032 TCATTCCTCG
1178042 AGAGTCCCCTCTCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
* * * * *
1178063 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCTCACCGTTCA
* *
1178084 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCTCACCGTTCA
1178105 AGAG
1 AGAG
1178109 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCTCACCGTTCA
Found at i:1178066 original size:42 final size:42
Alignment explanation
Indices: 1177987--1178078 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
1177977 CCCGACTCGT
* *
1177987 CTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTATCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCCC
* * * *
1178029 CTATCATTCCTCGAGAGTCCCCT-CTCACCGTTCAAGAGGCCA
1 CTATCATCCCTCAAGAGTCCACTCCT-ACCGTTCAAGAGGCCC
*
1178071 CTGTCATC
1 CTATCATC
1178079 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.05
42 39 0.95
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.25
Consensus pattern (42 bp):
CTATCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCCC
Found at i:1179425 original size:14 final size:14
Alignment explanation
Indices: 1179406--1179441 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1179396 ATTGTTTAAT
1179406 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1179420 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1179434 TGATTTGT
1 TGATTTGT
1179442 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1179584 original size:20 final size:20
Alignment explanation
Indices: 1179548--1179600 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1179538 AAAAAGTACT
*
1179548 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGAAA
1179567 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCGAAAATGAAA
*
1179587 ATCGTAACGCGAAA
1 ATCGCAACGCGAAA
1179601 TTAAATTCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGAAA
Found at i:1179628 original size:19 final size:19
Alignment explanation
Indices: 1179606--1179756 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1179596 CGAAATTAAA
1179606 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1179625 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
1179640 -CCTCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1179658 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1179672 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1179691 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1179706 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1179724 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1179743 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1179757 GGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1179654 original size:33 final size:32
Alignment explanation
Indices: 1179610--1179736 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1179600 ATTAAATTCG
1179610 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
1179643 CGTTGCAATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1179676 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1179709 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1179737 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1179711 original size:66 final size:66
Alignment explanation
Indices: 1179603--1179735 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1179593 ACGCGAAATT
*
1179603 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
1179668 G
66 G
* *
1179669 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
1179734 G
66 G
1179735 A
1 A
1179736 TAGTAATTTC
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:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
G
Found at i:1182040 original size:12 final size:12
Alignment explanation
Indices: 1182023--1182047 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1182013 TCTTCGGGGA
1182023 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1182035 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1182047 C
1 C
1182048 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1182261 original size:24 final size:24
Alignment explanation
Indices: 1182234--1182280 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1182224 CAAAATCCGT
*
1182234 GTATTGACCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1182258 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1182281 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1182289 original size:24 final size:24
Alignment explanation
Indices: 1182238--1182289 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1182228 ATCCGTGTAT
* ** *
1182238 TGACCAATATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
1182262 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
1182286 TGAC
1 TGAC
1182290 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:1183361 original size:20 final size:20
Alignment explanation
Indices: 1183333--1183390 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1183323 ATTCATTTGA
1183333 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1183353 CTATTGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1183373 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1183391 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1183433 original size:14 final size:14
Alignment explanation
Indices: 1183414--1183467 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1183404 GAAAATCGCA
1183414 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1183428 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1183445 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1183461 TTGCGAT
1 TTGCGAT
1183468 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1183433 original size:33 final size:33
Alignment explanation
Indices: 1183396--1183466 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1183386 AAAATCGCAA
1183396 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
1183429 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1183462 TGCGA
1 TGCGA
1183467 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:1183467 original size:33 final size:33
Alignment explanation
Indices: 1183409--1183486 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
1183399 GAAATGAAAA
***
1183409 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1183442 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
1183475 TCGCGTTGCGAT
1 TCGCATTGCGAT
1183487 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:1185507 original size:20 final size:19
Alignment explanation
Indices: 1185472--1185538 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1185462 GAAACTTAAA
*
1185472 ATCGCAATGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1185491 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1185511 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1185530 ATCGCAACG
1 ATCGCAACG
1185539 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1185533 original size:19 final size:19
Alignment explanation
Indices: 1185453--1185570 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
1185443 TAGTTTACTT
* *
1185453 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
1185473 TCGCAATGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
1185492 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1185512 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1185531 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1185545 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
1185563 TCGCAACG
1 TCGCAACG
1185571 ACAAAATCGT
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.15
19 24 0.30
20 28 0.35
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1185546 original size:14 final size:14
Alignment explanation
Indices: 1185527--1185584 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1185517 ATGCGAAATG
1185527 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1185541 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1185557 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1185573 AAAATCGTAACG
1 AAAATCGCAACG
1185585 CGAAACACAA
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:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1185569 original size:32 final size:33
Alignment explanation
Indices: 1185511--1185589 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1185501 GGAAATGGCT
*
1185511 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1185544 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
1185576 ATCGTAACGCGAAA
1 ATCGCAACGCGAAA
1185590 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1185637 original size:14 final size:14
Alignment explanation
Indices: 1185618--1185675 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1185608 TTTCATTTCG
1185618 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
1185632 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
*
1185648 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTTT
1185664 CGTTGCGATTTT
1 CGTTGCGATTTT
1185676 CATTTCGCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:1185682 original size:33 final size:33
Alignment explanation
Indices: 1185601--1185691 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1185591 ACAAATCGCA
* *
1185601 TTGCGATTTTCATTTCGCGTTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1185634 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1185666 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1185692 AGCCATTTCC
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:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1185710 original size:20 final size:19
Alignment explanation
Indices: 1185676--1185730 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1185666 TTGCGATTTT
*
1185676 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1185695 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1185715 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1185731 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1186238 original size:18 final size:18
Alignment explanation
Indices: 1186212--1186256 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1186202 GTCGATCAGA
*
1186212 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1186230 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1186248 TGATGGCTC
1 TGATGGCTC
1186257 CCGAAGTGGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1187599 original size:20 final size:20
Alignment explanation
Indices: 1187574--1187611 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1187564 AATAGTTTCT
1187574 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1187594 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1187612 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1187900 original size:22 final size:22
Alignment explanation
Indices: 1187875--1187918 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1187865 GATTTAGATA
1187875 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1187897 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1187919 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1188131 original size:20 final size:20
Alignment explanation
Indices: 1188106--1188158 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1188096 GATTATGTAT
*
1188106 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
1188126 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
1188146 TATCTCGTTGCGA
1 TATCGCGTTGCGA
1188159 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:1188219 original size:41 final size:41
Alignment explanation
Indices: 1188128--1188262 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
1188118 AAAGTCAGTA
* * * ** *
1188128 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
* *
1188168 ATCGCATTGCGATAGTCAGTATCACATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
* ** *
1188210 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCACATTGCGATTTTCCCAAT
1188251 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1188263 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
Found at i:1188220 original size:21 final size:21
Alignment explanation
Indices: 1188194--1188264 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
1188184 CAGTATCACA
1188194 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
1188215 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
1188235 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
1188256 TTGCGATTT
1 TTGCGATTT
1188265 ACTTATTCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:1188233 original size:20 final size:20
Alignment explanation
Indices: 1188208--1188281 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1188198 GATTTTCCCA
*
1188208 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
1188228 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
1188249 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
1188269 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1188282 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:1188263 original size:41 final size:41
Alignment explanation
Indices: 1188192--1188281 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
1188182 GTCAGTATCA
1188192 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1188233 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1188274 CATTGCGA
1 CATTGCGA
1188282 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
Found at i:1192470 original size:17 final size:17
Alignment explanation
Indices: 1192448--1192482 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1192438 CTATCATCTA
1192448 TTTTATTCTT-TGATTTT
1 TTTTATT-TTCTGATTTT
1192465 TTTTATTTTCTGATTTT
1 TTTTATTTTCTGATTTT
1192482 T
1 T
1192483 GATATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTATTTTCTGATTTT
Found at i:1193493 original size:21 final size:20
Alignment explanation
Indices: 1193453--1193494 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1193443 CCAACTTACA
*
1193453 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
1193473 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
1193494 A
1 A
1193495 GTTGCATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:1200341 original size:22 final size:22
Alignment explanation
Indices: 1200310--1200381 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
1200300 CTGAGTGGCA
1200310 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
1200333 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
1200355 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
1200376 TATGAA
1 TATGAA
1200382 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.44
22 22 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:1200366 original size:21 final size:21
Alignment explanation
Indices: 1200318--1200380 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1200308 CATATGAAAT
* *
1200318 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
1200340 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
1200361 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
1200381 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:1201852 original size:64 final size:64
Alignment explanation
Indices: 1201752--1201912 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 64
1201742 TAATGAAGGT
* * *
1201752 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
1201815 GG
63 GC
* *
1201817 ATGCATCGATGCACTACTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
1201881 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
1201913 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 57 0.67
65 25 0.29
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Done.