Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000914.1 Hibiscus syriacus cultivar Beakdansim tig00001825_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: 1342319
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 6 of 6
Found at i:1195747 original size:12 final size:12
Alignment explanation
Indices: 1195730--1195754 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1195720 TCTTCGGGGA
1195730 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1195742 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1195754 C
1 C
1195755 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:1195963 original size:24 final size:24
Alignment explanation
Indices: 1195929--1195982 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1195919 CTGAAACATC
*
1195929 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1195953 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1195977 ATCAAA
1 ATCAAA
1195983 TTTCGAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1196793 original size:20 final size:21
Alignment explanation
Indices: 1196768--1196819 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1196758 TTTTCCTAAT
*
1196768 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1196788 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1196809 TCGCAATGCGA
1 TCGCAATGCGA
1196820 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1196841 original size:20 final size:20
Alignment explanation
Indices: 1196808--1196886 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
1196798 AATTTGGAAA
* *
1196808 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
1196828 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
1196849 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* * *
1196869 TTCGTAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
1196887 AAATCGCAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
19 2 0.04
20 29 0.62
21 14 0.30
22 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:1197164 original size:20 final size:20
Alignment explanation
Indices: 1197109--1197156 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1197099 CAACGGGGAA
*
1197109 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATAGCT
1197129 ATCGCAACGCGAAAATAGCT
1 ATCGCAACGCGAAAATAGCT
1197149 ATCGCAAC
1 ATCGCAAC
1197157 TAGAAAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAGCT
Found at i:1197207 original size:14 final size:14
Alignment explanation
Indices: 1197188--1197241 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1197178 GAAAATCGCA
1197188 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1197202 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1197219 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1197235 TTGCGAT
1 TTGCGAT
1197242 AGTCAGTTTC
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:1197207 original size:33 final size:33
Alignment explanation
Indices: 1197170--1197240 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1197160 AAAATCGCAA
1197170 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
1197203 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1197236 TGCGA
1 TGCGA
1197241 TAGTCAGTTT
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:1198860 original size:44 final size:42
Alignment explanation
Indices: 1198812--1198904 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1198802 CCTCTTCAAC
* * *
1198812 GATGACAGTGGCCTCTTGAACGGTGGGGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAT--GGGAGGGGACTCTTGAGG
* *
1198856 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
*
1198898 AATGACA
1 GATGACA
1198905 AGTGAGTCAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 21 0.50
44 21 0.50
ACGTcount: A:0.22, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:1198932 original size:20 final size:20
Alignment explanation
Indices: 1198907--1198952 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1198897 GAATGACAAG
1198907 TGAGTCAGGCTTCTTCTTGC
1 TGAGTCAGGCTTCTTCTTGC
*
1198927 TGAGTCGGGCTTCTTCTTGC
1 TGAGTCAGGCTTCTTCTTGC
*
1198947 GGAGTC
1 TGAGTC
1198953 TTCGCGCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.09, C:0.24, G:0.30, T:0.37
Consensus pattern (20 bp):
TGAGTCAGGCTTCTTCTTGC
Found at i:1199312 original size:20 final size:20
Alignment explanation
Indices: 1199289--1199354 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
1199279 AAACTTACTT
*
1199289 TCGCAACGAGAAAATGATTA
1 TCGCAACGAGGAAATGATTA
* *
1199309 TCGCAACGCGGAAATGACTA
1 TCGCAACGAGGAAATGATTA
*
1199329 TCGCAAC-ATGGAAATGGTTA
1 TCGCAACGA-GGAAATGATTA
1199349 TCGCAA
1 TCGCAA
1199355 TGCGAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (20 bp):
TCGCAACGAGGAAATGATTA
Found at i:1199313 original size:40 final size:40
Alignment explanation
Indices: 1199269--1199354 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 40
1199259 TAGTTTACTT
* *
1199269 TCGCAACAC-GAAACTTACTTTCGCAACGA-GAAAATGATTA
1 TCGCAACACGGAAA-TGACTATCGCAAC-ATGAAAATGATTA
* * *
1199309 TCGCAACGCGGAAATGACTATCGCAACATGGAAATGGTTA
1 TCGCAACACGGAAATGACTATCGCAACATGAAAATGATTA
1199349 TCGCAA
1 TCGCAA
1199355 TGCGAAATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
39 1 0.03
40 34 0.87
41 4 0.10
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACATGAAAATGATTA
Found at i:1199423 original size:19 final size:19
Alignment explanation
Indices: 1199401--1199464 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
1199391 GAAACACAAA
1199401 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1199420 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1199436 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1199453 TCGCATTGCGAT
1 TCGCATTGCGAT
1199465 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 17 0.46
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1199483 original size:20 final size:19
Alignment explanation
Indices: 1199449--1199503 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1199439 TTGCGATTTT
*
1199449 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1199468 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1199488 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1199504 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:1200069 original size:18 final size:18
Alignment explanation
Indices: 1200046--1200085 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1200036 TCAGGCGATG
1200046 GCTCTGAGTGAGGTGATA
1 GCTCTGAGTGAGGTGATA
* *
1200064 GCTCTGGGTGAGGTGATG
1 GCTCTGAGTGAGGTGATA
1200082 GCTC
1 GCTC
1200086 CCGAAGTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.42, T:0.28
Consensus pattern (18 bp):
GCTCTGAGTGAGGTGATA
Found at i:1201447 original size:20 final size:20
Alignment explanation
Indices: 1201405--1201447 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1201395 AATAGTTTCT
*
1201405 GAAAATGAAAATCGTAACAC
1 GAAAATGAAAATCGCAACAC
*
1201425 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
1201445 GAA
1 GAA
1201448 TTTGACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1201753 original size:22 final size:22
Alignment explanation
Indices: 1201726--1201769 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1201716 GATGGAGATA
1201726 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1201748 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1201770 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:1202055 original size:41 final size:40
Alignment explanation
Indices: 1201936--1202114 Score: 173
Period size: 41 Copynumber: 4.4 Consensus size: 40
1201926 CGCTTTGAAA
* *
1201936 ATCGCATTGCGATTATGT-ATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATT-T-TAATTATCGCGTTGCGAAAGTCAGT
* * ** * *
1201977 ATTGAGTTGCGAAATTAAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTAATTATCGCGTTGCGAAAGTCAGT
*
1202017 ATCGCGTTGCGATTTTATATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTA-ATTATCGCGTTGCGAAAGTCAGT
* * * *
1202058 ACCGCGTTGCGATTTTCCAAAT-TCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATTTT--AATTATCGCGTTGCGAAAGTCAGT
*
1202099 ATCGCATTGCGATTTT
1 ATCGCGTTGCGATTTT
1202115 CCAAATTCGC
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 34 0.30
41 76 0.67
42 2 0.02
43 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (40 bp):
ATCGCGTTGCGATTTTAATTATCGCGTTGCGAAAGTCAGT
Found at i:1202070 original size:20 final size:20
Alignment explanation
Indices: 1201956--1202069 Score: 102
Period size: 20 Copynumber: 5.7 Consensus size: 20
1201946 GATTATGTAT
*
1201956 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
1201976 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
1201996 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*** * *
1202016 TATCGCGTTGCGATTTTATAT
1 TATCGCGTTGCGAAAGT-CAG
*
1202037 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1202057 TACCGCGTTGCGA
1 TATCGCGTTGCGA
1202070 TTTTCCAAAT
Statistics
Matches: 74, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
20 58 0.78
21 16 0.22
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1202090 original size:21 final size:21
Alignment explanation
Indices: 1202064--1202151 Score: 92
Period size: 20 Copynumber: 4.3 Consensus size: 21
1202054 CAGTACCGCG
1202064 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
** *
1202085 TTGCGATAGT-C-AGTATCGCA
1 TTGCGATTTTCCAAAT-TCGCA
1202105 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* **
1202126 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCAAATTCGCA
1202146 TTGCGA
1 TTGCGA
1202152 ATTGGGAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 31 0.56
21 20 0.36
22 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:1202105 original size:20 final size:20
Alignment explanation
Indices: 1201936--1202111 Score: 81
Period size: 20 Copynumber: 8.7 Consensus size: 20
1201926 CGCTTTGAAA
*
1201936 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1201957 ATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1201977 ATTG-AGTTGCGAAATTAAGT
1 ATCGCA-TTGCGATAGTCAGT
*
1201997 ATCG-AGTTGCGAAAGTCAGT
1 ATCGCA-TTGCGATAGTCAGT
* ** * *
1202017 ATCGCGTTGCGATTTTATATT
1 ATCGCATTGCGATAGT-CAGT
*
1202038 ATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * ** *
1202058 ACCGCGTTGCGATTTTCCA-A
1 ATCGCATTGCGATAGT-CAGT
1202078 ATTCGCATTGCGATAGTCAGT
1 A-TCGCATTGCGATAGTCAGT
1202099 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1202112 TTTCCAAATT
Statistics
Matches: 117, Mismatches: 31, Indels: 15
0.72 0.19 0.09
Matches are distributed among these distances:
19 2 0.02
20 75 0.64
21 40 0.34
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1202115 original size:41 final size:41
Alignment explanation
Indices: 1202003--1202132 Score: 183
Period size: 41 Copynumber: 3.2 Consensus size: 41
1201993 AAGTATCGAG
* * *
1202003 TTGCGAAAGTCAGTATCGCGTTGCGATTTT--ATATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCA-AAT-TCGCA
*
1202044 TTGCGATAGTCAGTACCGCGTTGCGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
*
1202085 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
1202126 TTGCGAT
1 TTGCGAT
1202133 TTACTTATTC
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
41 78 0.96
42 2 0.02
43 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
Found at i:1202167 original size:21 final size:21
Alignment explanation
Indices: 1202141--1202181 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1202131 ATTTACTTAT
1202141 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATTGGGAAAA
1202162 TCGCATTGCGAATTGGGAAA
1 TCGCATTGCGAATTGGGAAA
1202182 GTCATAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (21 bp):
TCGCATTGCGAATTGGGAAAA
Found at i:1213909 original size:21 final size:21
Alignment explanation
Indices: 1213892--1213964 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
1213882 CACCGAATTC
1213892 CCACATAATTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
*
1213913 CCACATAGGTT-TGCACCGAAGTG-
1 CCACATA-ATTGT-C-CCGAAG-GA
*
1213936 CCACATAATTGTCCCGAATGA
1 CCACATAATTGTCCCGAAGGA
1213957 CCACATAA
1 CCACATAA
1213965 AACCCTCGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 1 0.02
21 21 0.49
22 6 0.14
23 14 0.33
24 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.21
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAGGA
Found at i:1213929 original size:44 final size:44
Alignment explanation
Indices: 1213878--1213963 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
1213868 CAACTCGTAA
*
1213878 TTTGCACCGAATTCCCACATAATTGTCCCGAAGGACCACATAGG
1 TTTGCACCGAAGTCCCACATAATTGTCCCGAAGGACCACATAGG
* *
1213922 TTTGCACCGAAGTGCCACATAATTGTCCCGAATGACCACATA
1 TTTGCACCGAAGTCCCACATAATTGTCCCGAAGGACCACATA
1213964 AAACCCTCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (44 bp):
TTTGCACCGAAGTCCCACATAATTGTCCCGAAGGACCACATAGG
Found at i:1214152 original size:21 final size:21
Alignment explanation
Indices: 1214128--1214168 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1214118 ATCACATTTC
1214128 CATAA-TCATATAATCATAAAA
1 CATAACTCATATAAT-ATAAAA
*
1214149 CATAACTTATATAATATAAA
1 CATAACTCATATAATATAAA
1214169 TTGAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (21 bp):
CATAACTCATATAATATAAAA
Found at i:1236989 original size:17 final size:17
Alignment explanation
Indices: 1236967--1237011 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
1236957 GTAAAAACAC
1236967 AAGCAAAATCAAGATCA
1 AAGCAAAATCAAGATCA
1236984 AAGCAAAATCAAGATCA
1 AAGCAAAATCAAGATCA
*
1237001 AATCAAAATCA
1 AAGCAAAATCA
1237012 TGTTGTCGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.60, C:0.18, G:0.09, T:0.13
Consensus pattern (17 bp):
AAGCAAAATCAAGATCA
Found at i:1237536 original size:46 final size:46
Alignment explanation
Indices: 1237428--1237533 Score: 110
Period size: 46 Copynumber: 2.3 Consensus size: 46
1237418 AGATAAGAAA
* * * * * *
1237428 AAAATAGTAAAGTAATA-ATTATATATAGTAATATTATATTATAAGT
1 AAAATAATAAAGAAATATA-TATATATAATAATAATAAAATATAAGT
*
1237474 AAAATATTAAAGAAATATATATATATAATAATAATAAAATAT-AGT
1 AAAATAATAAAGAAATATATATATATAATAATAATAAAATATAAGT
1237519 AAAA-AATAAATGAAA
1 AAAATAATAAA-GAAA
1237534 ATAATTTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
44 5 0.10
45 11 0.22
46 34 0.67
47 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (46 bp):
AAAATAATAAAGAAATATATATATATAATAATAATAAAATATAAGT
Found at i:1237580 original size:54 final size:53
Alignment explanation
Indices: 1237487--1237590 Score: 126
Period size: 54 Copynumber: 1.9 Consensus size: 53
1237477 ATATTAAAGA
*
1237487 AATATATATATATAATAATAATAAAATATAGTAAAAAATAAATGAAAATAATTT
1 AATATATATATATAATAATAATAAAATATAGTAAAAAAT-AATAAAAATAATTT
1237541 AATATATATATAT-ATACAT-ATAATAATA-A-TAACATAAATAATAAAAATAA
1 AATATATATATATAATA-ATAATAA-AATATAGTAA-A-AAATAATAAAAATAA
1237591 ATGAATAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
52 3 0.07
53 19 0.42
54 23 0.51
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (53 bp):
AATATATATATATAATAATAATAAAATATAGTAAAAAATAATAAAAATAATTT
Found at i:1237583 original size:18 final size:17
Alignment explanation
Indices: 1237560--1237602 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1237550 ATATATACAT
1237560 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
1237578 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
1237595 ATAA-AATA
1 ATAATAATA
1237603 TTCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:1237599 original size:14 final size:13
Alignment explanation
Indices: 1237562--1237600 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1237552 ATATACATAT
1237562 AATAATAATAACATA
1 AATAATAA-AA-ATA
1237577 AATAATAAAAATA
1 AATAATAAAAATA
1237590 AATGAATAAAA
1 AAT-AATAAAA
1237601 TATTCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:1238035 original size:37 final size:37
Alignment explanation
Indices: 1237953--1238056 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 37
1237943 GTACTTGTGG
* * * * * *
1237953 ATCCTATCTTTAAGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* * * *
1237990 ATCTTATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
1238027 ATCCTATTTTTAGAAGTTTGAATCATAGTA
1 ATCCTATTTTTAGGAGTTTGAATCATAGTA
1238057 GGACGAAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:1238904 original size:105 final size:105
Alignment explanation
Indices: 1238600--1239222 Score: 932
Period size: 105 Copynumber: 6.0 Consensus size: 105
1238590 ACATTGTTCC
** * * ** *
1238600 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAA
* * * * *
1238665 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1238706 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAATT-TTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
*
1238766 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1238806 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
1238871 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1238911 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGATATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
*
1238976 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1239016 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
*
1239081 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1239121 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAA
* * * *
1239186 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1239223 ACTCGAGTGT
Statistics
Matches: 483, Mismatches: 28, Indels: 12
0.92 0.05 0.02
Matches are distributed among these distances:
100 82 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 305 0.63
106 83 0.17
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1239490 original size:36 final size:36
Alignment explanation
Indices: 1239434--1239504 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
1239424 TGGAGAGAAA
* *
1239434 CTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAG
1 CTGTCTCAAGCGAGACAAAATTCATTTCAAGGGAAG
*
1239470 CTGTCTCAAGCGAGATAAAATTCATTTCAAGGGAA
1 CTGTCTCAAGCGAGACAAAATTCATTTCAAGGGAA
1239505 ATGTTTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (36 bp):
CTGTCTCAAGCGAGACAAAATTCATTTCAAGGGAAG
Found at i:1239724 original size:15 final size:15
Alignment explanation
Indices: 1239704--1239758 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
1239694 AAAAAATTAA
1239704 TTTCAAGGGAAATGT
1 TTTCAAGGGAAATGT
1239719 TTTCAAGGGAAATGT
1 TTTCAAGGGAAATGT
*
1239734 TTTCAAGAGAAACTG-
1 TTTCAAGGGAAA-TGT
*
1239749 TCTCAAGGGA
1 TTTCAAGGGA
1239759 GACAAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 34 0.94
16 2 0.06
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (15 bp):
TTTCAAGGGAAATGT
Found at i:1239805 original size:105 final size:105
Alignment explanation
Indices: 1239405--1239805 Score: 589
Period size: 106 Copynumber: 3.9 Consensus size: 105
1239395 TTCATTAAAT
* ** *
1239405 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * *
1239467 AAGCTGTCTCAAGC-GAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGCAGAGAAAAAATTCATTTCAAGGGAAA
1239506 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
1239571 AAACTATCTCAAGAGAGAGAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAG-CAGAGAAAAAATTCATTTCAAGGGAAA
1239612 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
1239677 AAACTATCTC-AGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGCAGAGAAAAAATTCATTTCAAGGGAAA
* *** *
1239716 TGTTTTCAAGGGAAATGTTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTTGAGG
1 TGTTTTCAATGTTTATG-TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGG
*
1239781 GAAACTATCTCAAGCA-AGATAAAAT
65 GAAACTATCTCAAGCAGAGAAAAAAT
1239806 CTTCTTAAAA
Statistics
Matches: 275, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
101 46 0.17
103 3 0.01
104 58 0.21
105 67 0.24
106 101 0.37
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (105 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGCAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:1239957 original size:72 final size:76
Alignment explanation
Indices: 1239823--1239979 Score: 193
Period size: 72 Copynumber: 2.1 Consensus size: 76
1239813 AAAAAACAGC
* *
1239823 CTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGATATCAAGCGAGACAAATCTTGTTTTA
1 CTTGAGTGAAATGAAAT-CCTTCTTTCGAGTAAAAACGATATCAAGCGAGACAAATCATGTTTTA
*
1239888 AGAAAAA-TAAT
65 AGAAAAACAAAT
* *
1239899 CTTGAGTGAAATG-AAT-CTTCTTTCGAG-AAAAAC-AGTCTCAAGTGAGACAAAGT-ATGTTTT
1 CTTGAGTGAAATGAAATCCTTCTTTCGAGTAAAAACGA-TATCAAGCGAGACAAA-TCATGTTTT
1239959 AAGAAAAACAAAT
64 AAGAAAAACAAAT
1239972 -TTGAGTGA
1 CTTGAGTGA
1239980 GATAATCATC
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
71 1 0.01
72 41 0.56
73 15 0.21
75 3 0.04
76 13 0.18
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (76 bp):
CTTGAGTGAAATGAAATCCTTCTTTCGAGTAAAAACGATATCAAGCGAGACAAATCATGTTTTAA
GAAAAACAAAT
Found at i:1241440 original size:183 final size:183
Alignment explanation
Indices: 1241126--1241662 Score: 961
Period size: 183 Copynumber: 2.9 Consensus size: 183
1241116 ATCAGGTTTA
*
1241126 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACTGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACTGAATT
* ** *
1241191 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTTGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
1241255 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTGGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
1241309 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGTAAACACTGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACTGAATT
*
1241374 GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
1241439 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
1241492 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACA-TCGAAT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACT-GAAT
1241556 TGCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
65 TGCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
1241621 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
1241663 CGGATTTAAT
Statistics
Matches: 340, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
182 1 0.00
183 338 0.99
184 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACTGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:1245730 original size:20 final size:21
Alignment explanation
Indices: 1245691--1245730 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1245681 GGGAAAAAAT
* *
1245691 AAAATAAATAAGTAAGATAAG
1 AAAAAAAATAAGTAAAATAAG
1245712 AAAAAAAAT-AGTAAAATAA
1 AAAAAAAATAAGTAAAATAA
1245731 TAATTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAAAAAATAAGTAAAATAAG
Found at i:1245864 original size:12 final size:11
Alignment explanation
Indices: 1245849--1245899 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 11
1245839 TACATATAAT
1245849 AATAATAACATA
1 AATAATAA-ATA
1245861 AATAATAAATA
1 AATAATAAATA
1245872 AATGAATAAATA
1 AAT-AATAAATA
1245884 TACATATATAAATA
1 -A-ATA-ATAAATA
1245898 AA
1 AA
1245900 GGGACTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.17
12 17 0.49
13 3 0.09
14 9 0.26
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (11 bp):
AATAATAAATA
Found at i:1245872 original size:16 final size:16
Alignment explanation
Indices: 1245781--1245868 Score: 57
Period size: 16 Copynumber: 5.8 Consensus size: 16
1245771 AAAGAAATAT
*
1245781 ATATAATAATAATAAA
1 ATATAATAATAATAAC
*
1245797 ATATAGTAA-AA-AA-
1 ATATAATAATAATAAC
1245810 ATA-AATGAA-AAT-A-
1 ATATAAT-AATAATAAC
*
1245823 ATTTAATATATATATATAC
1 ATATAATA-ATA-ATA-AC
1245842 ATATAATAATAATAAC
1 ATATAATAATAATAAC
1245858 ATA-AATAATAA
1 ATATAATAATAA
1245869 ATAAATGAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
12 2 0.03
13 11 0.19
14 6 0.10
15 11 0.19
16 15 0.25
17 3 0.05
18 4 0.07
19 7 0.12
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (16 bp):
ATATAATAATAATAAC
Found at i:1245891 original size:55 final size:60
Alignment explanation
Indices: 1245781--1245893 Score: 137
Period size: 61 Copynumber: 1.9 Consensus size: 60
1245771 AAAGAAATAT
* * *
1245781 ATATAATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTAATATATATATATAC
1 ATATAATAATAATAAAATATAATAAAAAAATAAATG-AAATAATATAATACATATATATAC
* *
1245842 ATATAATAATAATAACATA-AAT-AATAAATAAATG-AATAA-AT-ATACATATATA
1 ATATAATAATAATAAAATATAATAAAAAAATAAATGAAATAATATAATACATATATA
1245894 AATAAAGGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
55 10 0.21
56 1 0.02
57 5 0.11
59 11 0.23
60 2 0.04
61 18 0.38
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (60 bp):
ATATAATAATAATAAAATATAATAAAAAAATAAATGAAATAATATAATACATATATATAC
Found at i:1246298 original size:37 final size:37
Alignment explanation
Indices: 1246252--1246336 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
1246242 TAAGAATTTA
* * *
1246252 AATCTTAGTAGAACTCTATCCTATTTTTAGGAGTTGG
1 AATCCTAGTAGAACTCTATCCTAATTTTAGAAGTTGG
* * * *
1246289 AATCCTAGTAAAATTTTATCCTAATTTTAGAAGTTTG
1 AATCCTAGTAGAACTCTATCCTAATTTTAGAAGTTGG
1246326 AATCCTAGTAG
1 AATCCTAGTAG
1246337 GACGAAAATG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (37 bp):
AATCCTAGTAGAACTCTATCCTAATTTTAGAAGTTGG
Found at i:1253220 original size:28 final size:28
Alignment explanation
Indices: 1253182--1253239 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
1253172 TCATGTCAAT
* **
1253182 AAAAGATTAGTTTTTGATTTAATTTATA
1 AAAAGAATAGTTTTCAATTTAATTTATA
1253210 AAAAGAATAGTTTTCAATTTAATTTATA
1 AAAAGAATAGTTTTCAATTTAATTTATA
1253238 AA
1 AA
1253240 TTTTAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (28 bp):
AAAAGAATAGTTTTCAATTTAATTTATA
Found at i:1253336 original size:31 final size:30
Alignment explanation
Indices: 1253226--1253338 Score: 91
Period size: 31 Copynumber: 3.5 Consensus size: 30
1253216 ATAGTTTTCA
*
1253226 ATTTAATTTATAAATTTTAAATAAAATATTT
1 ATTTAATTTTTAAATTTTAAATAAAATA-TT
* * *
1253257 ATTTAATCAACTTTTAAATATTAAATAATATATCA
1 ATTTAAT----TTTTAAATTTTAAATAAAATAT-T
* ** *
1253292 ATTTGATCCTTAAATTTTAAATAAAACATT
1 ATTTAATTTTTAAATTTTAAATAAAATATT
1253322 AGTTTAATTTTTAAATT
1 A-TTTAATTTTTAAATT
1253339 CGAACAAAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
30 1 0.02
31 36 0.58
34 1 0.02
35 24 0.39
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (30 bp):
ATTTAATTTTTAAATTTTAAATAAAATATT
Found at i:1254378 original size:36 final size:36
Alignment explanation
Indices: 1254331--1254402 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1254321 TGCAAACTCA
1254331 ACAGATGAGAGGTGCTTATATAACTGCTTATCATTT
1 ACAGATGAGAGGTGCTTATATAACTGCTTATCATTT
1254367 ACAGATGAGAGGTGCTTATATAACTGCTTATCATTT
1 ACAGATGAGAGGTGCTTATATAACTGCTTATCATTT
1254403 TTTTAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (36 bp):
ACAGATGAGAGGTGCTTATATAACTGCTTATCATTT
Found at i:1266399 original size:19 final size:19
Alignment explanation
Indices: 1266375--1266414 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1266365 ATTTGCAACC
* *
1266375 TTTAAATGCAATGTTTGAA
1 TTTAAATACAATGTTTAAA
1266394 TTTAAATACAATGTTTAAA
1 TTTAAATACAATGTTTAAA
1266413 TT
1 TT
1266415 AATCTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (19 bp):
TTTAAATACAATGTTTAAA
Found at i:1270971 original size:2 final size:2
Alignment explanation
Indices: 1270964--1271000 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1270954 CCAAGCACAT
* *
1270964 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1271001 CACTGACGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1276163 original size:28 final size:27
Alignment explanation
Indices: 1276104--1276230 Score: 200
Period size: 28 Copynumber: 4.6 Consensus size: 27
1276094 ACAAAGTAAA
1276104 AAAAAAAAGAGACCACCAACAGAGATT
1 AAAAAAAAGAGACCACCAACAGAGATT
1276131 AAAAAAAAGAGACCACCAACAGAGATT
1 AAAAAAAAGAGACCACCAACAGAGATT
*
1276158 AGAAAAAAAAAGACCACCAACAGAGATT
1 A-AAAAAAAGAGACCACCAACAGAGATT
1276186 AGAAAAAAAGGAGACCACCAACAGAGATT
1 A-AAAAAAA-GAGACCACCAACAGAGATT
*
1276215 AAAAAAGAGGAGACCA
1 AAAAAA-AAGAGACCA
1276231 ACGAAAAATT
Statistics
Matches: 94, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
27 28 0.30
28 46 0.49
29 20 0.21
ACGTcount: A:0.59, C:0.17, G:0.17, T:0.06
Consensus pattern (27 bp):
AAAAAAAAGAGACCACCAACAGAGATT
Found at i:1276194 original size:57 final size:55
Alignment explanation
Indices: 1276103--1276230 Score: 204
Period size: 57 Copynumber: 2.3 Consensus size: 55
1276093 TACAAAGTAA
1276103 AAAAAAAAAGAGACCACCAACAGAGATTAAAAAAAAGAGACCACCAACAGAGATT
1 AAAAAAAAAGAGACCACCAACAGAGATTAAAAAAAAGAGACCACCAACAGAGATT
1276158 AGAAAAAAAA-AGACCACCAACAGAGATTAGAAAAAAAGGAGACCACCAACAGAGATT
1 A-AAAAAAAAGAGACCACCAACAGAGATTA-AAAAAAA-GAGACCACCAACAGAGATT
* *
1276215 AAAAAAGAGGAGACCA
1 AAAAAAAAAGAGACCA
1276231 ACGAAAAATT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
55 20 0.30
56 21 0.31
57 26 0.39
ACGTcount: A:0.59, C:0.17, G:0.17, T:0.06
Consensus pattern (55 bp):
AAAAAAAAAGAGACCACCAACAGAGATTAAAAAAAAGAGACCACCAACAGAGATT
Found at i:1279602 original size:6 final size:6
Alignment explanation
Indices: 1279593--1279622 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1279583 TAACACCTTG
*
1279593 TGCATG TGCATT TGCATT TGCATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT
1279623 CTTATTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.47
Consensus pattern (6 bp):
TGCATT
Found at i:1285727 original size:80 final size:80
Alignment explanation
Indices: 1285594--1285925 Score: 574
Period size: 80 Copynumber: 4.2 Consensus size: 80
1285584 GTCTTTCGGG
* *
1285594 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTAATTTTTAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
1285659 AGTAGTGAAGCAAAC
66 AGTAGTGAAGCAAAC
* * * * *
1285674 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTAATTTGTAAGCCTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
*
1285739 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAC
1285754 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
1285819 AGTAGTGAAGCAAAC
66 AGTAGTGAAGCAAAC
1285834 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
*
1285899 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAC
*
1285914 CCGTCAGTAAGT
1 CCATCAGTAAGT
1285926 GTCATCAATA
Statistics
Matches: 240, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 240 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
AGTAGTGAAGCAAAC
Found at i:1285966 original size:22 final size:21
Alignment explanation
Indices: 1285933--1286008 Score: 75
Period size: 22 Copynumber: 3.6 Consensus size: 21
1285923 AGTGTCATCA
*
1285933 ATAAGTCTTTCGAGCATGATG
1 ATAAATCTTTCGAGCATGATG
* *
1285954 ATGAAATCTTTCGGGTCATCA-G
1 AT-AAATCTTTCGAG-CATGATG
*
1285976 -TAAGTCTTTCGAGCATGATG
1 ATAAATCTTTCGAGCATGATG
1285996 ATTAAATCTTTCG
1 A-TAAATCTTTCG
1286009 GTTCATTTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 4 0.09
20 11 0.26
21 3 0.07
22 21 0.49
23 4 0.09
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (21 bp):
ATAAATCTTTCGAGCATGATG
Found at i:1285985 original size:42 final size:42
Alignment explanation
Indices: 1285926--1286014 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
1285916 GTCAGTAAGT
1285926 GTCATCAATAAGTCTTTCGAGCATGATGATGAAATCTTTCGG
1 GTCATCAATAAGTCTTTCGAGCATGATGATGAAATCTTTCGG
* *
1285968 GTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGG
1 GTCATCAATAAGTCTTTCGAGCATGATGATGAAATCTTTCGG
*
1286010 TTCAT
1 GTCAT
1286015 TTGTGAGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (42 bp):
GTCATCAATAAGTCTTTCGAGCATGATGATGAAATCTTTCGG
Found at i:1286038 original size:42 final size:42
Alignment explanation
Indices: 1285926--1286056 Score: 131
Period size: 42 Copynumber: 3.1 Consensus size: 42
1285916 GTCAGTAAGT
* * * *
1285926 GTCATCAATAAGTCTTTCGAGCATGATGATGAAATCTTTCGG
1 GTCATCAGTAAGTCTTTCGAACAAGATGATTAAATCTTTCGG
* *
1285968 GTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGG
1 GTCATCAGTAAGTCTTTCGAACAAGATGATTAAATCTTTCGG
* ** * * *
1286010 TTCATTTGTGAGT-TTCTCGAACAAGATGA-TAAATCCTTCAG
1 GTCATCAGTAAGTCTT-TCGAACAAGATGATTAAATCTTTCGG
1286051 GTCATC
1 GTCATC
1286057 CATAAGACCT
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 16 0.21
42 60 0.79
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (42 bp):
GTCATCAGTAAGTCTTTCGAACAAGATGATTAAATCTTTCGG
Found at i:1286565 original size:53 final size:53
Alignment explanation
Indices: 1286485--1286738 Score: 375
Period size: 53 Copynumber: 4.8 Consensus size: 53
1286475 GAATCACACT
* *
1286485 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
1286538 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
* *
1286591 AGAAGATTGTTCGAGTTCTACTCTCTGAAGCAAGAGGGAGCGAACCCGTAAAC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
* * ****
1286644 AGAAGAGTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTTTTT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
* *
1286697 AGAAGATTGTTCAAGTTTCTTAATCCCTGAA-CAAGAGGGAGC
1 AGAAGATTGTTCGAG-TTC-TACTCCCTGAAGCAAGAGGGAGC
1286739 AGACCTGTCA
Statistics
Matches: 184, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
53 161 0.88
54 13 0.07
55 10 0.05
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (53 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
Found at i:1287188 original size:54 final size:55
Alignment explanation
Indices: 1287101--1287226 Score: 193
Period size: 57 Copynumber: 2.3 Consensus size: 55
1287091 TATAAAGTAA
1287101 AAAAAAAAGAGACCACCAACAGAGATT-AAAAAAAA-AGACCACCAACAGAGATT
1 AAAAAAAAGAGACCACCAACAGAGATTAAAAAAAAAGAGACCACCAACAGAGATT
*
1287154 AGAAAAAAAGAGACCACCAACAGAGATTAGAAAAAAAGGAGACCACCAACAGAGATT
1 A-AAAAAAAGAGACCACCAACAGAGATTA-AAAAAAAAGAGACCACCAACAGAGATT
*
1287211 AAAAAAGAGGAGACCA
1 AAAAAA-AAGAGACCA
1287227 ACGAAAAATT
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
53 1 0.02
54 26 0.39
56 12 0.18
57 27 0.41
ACGTcount: A:0.59, C:0.17, G:0.17, T:0.06
Consensus pattern (55 bp):
AAAAAAAAGAGACCACCAACAGAGATTAAAAAAAAAGAGACCACCAACAGAGATT
Found at i:1287224 original size:28 final size:27
Alignment explanation
Indices: 1287101--1287226 Score: 200
Period size: 28 Copynumber: 4.6 Consensus size: 27
1287091 TATAAAGTAA
1287101 AAAAAAAAGAGACCACCAACAGAGATT
1 AAAAAAAAGAGACCACCAACAGAGATT
1287128 AAAAAAAA-AGACCACCAACAGAGATT
1 AAAAAAAAGAGACCACCAACAGAGATT
1287154 AGAAAAAAAGAGACCACCAACAGAGATT
1 A-AAAAAAAGAGACCACCAACAGAGATT
1287182 AGAAAAAAAGGAGACCACCAACAGAGATT
1 A-AAAAAAA-GAGACCACCAACAGAGATT
*
1287211 AAAAAAGAGGAGACCA
1 AAAAAA-AAGAGACCA
1287227 ACGAAAAATT
Statistics
Matches: 94, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
26 19 0.20
27 15 0.16
28 39 0.41
29 21 0.22
ACGTcount: A:0.59, C:0.17, G:0.17, T:0.06
Consensus pattern (27 bp):
AAAAAAAAGAGACCACCAACAGAGATT
Found at i:1287228 original size:54 final size:54
Alignment explanation
Indices: 1287102--1287226 Score: 198
Period size: 54 Copynumber: 2.3 Consensus size: 54
1287092 ATAAAGTAAA
1287102 AAAAAAAGAGACCACCAACAGAGATTAAAAAAAAAGACCACCAACAGAGATTAG
1 AAAAAAAGAGACCACCAACAGAGATTAAAAAAAAAGACCACCAACAGAGATTAG
1287156 AAAAAAAGAGACCACCAACAGAGATTAGAAAAAAAGGAGACCACCAACAGAGATTA-
1 AAAAAAAGAGACCACCAACAGAGATTA-AAAAAAA--AGACCACCAACAGAGATTAG
*
1287212 AAAAAGAGGAGACCA
1 AAAAA-AAGAGACCA
1287227 ACGAAAAATT
Statistics
Matches: 66, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
54 27 0.41
55 7 0.11
56 5 0.08
57 27 0.41
ACGTcount: A:0.58, C:0.18, G:0.18, T:0.06
Consensus pattern (54 bp):
AAAAAAAGAGACCACCAACAGAGATTAAAAAAAAAGACCACCAACAGAGATTAG
Found at i:1295070 original size:39 final size:39
Alignment explanation
Indices: 1295014--1295120 Score: 112
Period size: 39 Copynumber: 2.7 Consensus size: 39
1295004 ACAAAAAATG
* *
1295014 GTTTCTGAAAATATATATA-ATATATTTTTTTTTAAAAAC
1 GTTTTTGAAAAT-TATATACATATATTTTGTTTTAAAAAC
**
1295053 GTTTTTGAAAACTTATATACA-ATATATAAGTTTTAAAAAC
1 GTTTTTGAAAA-TTATATACATATAT-TTTGTTTTAAAAAC
* *
1295093 -ATTTTGAAAATTATAAACATATATTTTG
1 GTTTTTGAAAATTATATACATATATTTTG
1295121 AAATCATTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
38 10 0.18
39 33 0.59
40 13 0.23
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.45
Consensus pattern (39 bp):
GTTTTTGAAAATTATATACATATATTTTGTTTTAAAAAC
Found at i:1295087 original size:40 final size:37
Alignment explanation
Indices: 1295043--1295116 Score: 103
Period size: 40 Copynumber: 1.9 Consensus size: 37
1295033 ATATATTTTT
* *
1295043 TTTTAAAAACGTTTTTGAAAACTTATATACAATATATAAG
1 TTTTAAAAAC-ATTTTGAAAA-TTATAAAC-ATATATAAG
1295083 TTTTAAAAACATTTTGAAAATTATAAACATATAT
1 TTTTAAAAACATTTTGAAAATTATAAACATATAT
1295117 TTTGAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 6 0.19
38 7 0.22
39 9 0.28
40 10 0.31
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (37 bp):
TTTTAAAAACATTTTGAAAATTATAAACATATATAAG
Found at i:1295138 original size:24 final size:22
Alignment explanation
Indices: 1295093--1295139 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
1295083 TTTTAAAAAC
*
1295093 ATTTTGAAAATTATAAACATAT
1 ATTTTGAAAATTATAAAAATAT
*
1295115 ATTTTGAAATCATTTTAAAAATAT
1 ATTTTGAAA--ATTATAAAAATAT
1295139 A
1 A
1295140 ATGTATAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
24 12 0.57
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
ATTTTGAAAATTATAAAAATAT
Found at i:1295232 original size:33 final size:32
Alignment explanation
Indices: 1295182--1295250 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
1295172 ATTTTATATA
1295182 ATATATAGTTTTAAAAAT-ATTTTGGAAAACT
1 ATATATAGTTTTAAAAATCATTTTGGAAAACT
* *
1295213 CATATAATATTTTTAAAAATCATTTTTGAAAACT
1 -ATAT-ATAGTTTTAAAAATCATTTTGGAAAACT
1295247 ATAT
1 ATAT
1295251 GGTATATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 4 0.12
33 17 0.52
34 12 0.36
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (32 bp):
ATATATAGTTTTAAAAATCATTTTGGAAAACT
Found at i:1295235 original size:20 final size:21
Alignment explanation
Indices: 1295197--1295235 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1295187 TAGTTTTAAA
*
1295197 AATATTTTGGAAAACTCATAT
1 AATATTTTGGAAAAATCATAT
*
1295218 AATATTTT-TAAAAATCAT
1 AATATTTTGGAAAAATCAT
1295236 TTTTGAAAAC
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:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (21 bp):
AATATTTTGGAAAAATCATAT
Found at i:1295269 original size:108 final size:102
Alignment explanation
Indices: 1295043--1295305 Score: 238
Period size: 108 Copynumber: 2.5 Consensus size: 102
1295033 ATATATTTTT
* * * *
1295043 TTTTAAAAACGTTTTTGAAAACTTATATACAATATATAAGTTTTAAAAACATTTTGAAAATTATA
1 TTTTAAAAACATTTTTGAAAA-TT-TATATAATATAT-AGTTTTAAAAATATTTTGAAAATCATA
*
1295108 AACATATATTTTGAAATCATTTTAAAAATATAATGTATAG
63 AACATATATTTTAAAATCATTTTAAAAATATAATGTATAG
1295148 TTTAAAATAAAAACATTTTTGAAAATTTTATATAATATATAGTTTTAAAAATATTTTGGAAAACT
1 TTT----TAAAAACATTTTTGAAAA-TTTATATAATATATAGTTTTAAAAATATTTT-GAAAA-T
* *
1295213 CATATA-ATAT-TTTTAAAAATCATTTTTGAAAACTAT-ATGGTATATAG
59 CATAAACATATATTTT-AAAATCA-TTTT-AAAAATATAAT-G--TATAG
* *
1295260 TTTTGAAAACATTTTT---AA---ATATAATATATAGTTTAAAAAATATTTT
1 TTTTAAAAACATTTTTGAAAATTTATATAATATATAGTTTTAAAAATATTTT
1295306 TTGGGATATA
Statistics
Matches: 136, Mismatches: 10, Indels: 28
0.78 0.06 0.16
Matches are distributed among these distances:
101 27 0.20
105 5 0.04
107 20 0.15
108 38 0.28
109 30 0.22
110 8 0.06
112 8 0.06
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (102 bp):
TTTTAAAAACATTTTTGAAAATTTATATAATATATAGTTTTAAAAATATTTTGAAAATCATAAAC
ATATATTTTAAAATCATTTTAAAAATATAATGTATAG
Found at i:1295376 original size:18 final size:18
Alignment explanation
Indices: 1295355--1295393 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1295345 ATTATTTCTT
*
1295355 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
1295373 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
1295391 TTC
1 TTC
1295394 TGTTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:1302711 original size:26 final size:27
Alignment explanation
Indices: 1302660--1302711 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
1302650 CATTTTTAAA
*
1302660 ATTAATATTATATTATTATTTTTACTGC
1 ATTAATATTATATTATTA-TTATACTGC
1302688 ATTAATTATTATATTA-TA-TATACT
1 ATTAA-TATTATATTATTATTATACT
1302712 ATATTTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 5 0.23
28 7 0.32
29 10 0.45
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (27 bp):
ATTAATATTATATTATTATTATACTGC
Found at i:1303171 original size:7 final size:7
Alignment explanation
Indices: 1303163--1303211 Score: 80
Period size: 7 Copynumber: 7.0 Consensus size: 7
1303153 CTAGAGTTCT
*
1303163 CCTTTCT
1 CCTTTCC
*
1303170 CCTTTCT
1 CCTTTCC
1303177 CCTTTCC
1 CCTTTCC
1303184 CCTTTCC
1 CCTTTCC
1303191 CCTTTCC
1 CCTTTCC
1303198 CCTTTCC
1 CCTTTCC
1303205 CCTTTCC
1 CCTTTCC
1303212 TACACATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (7 bp):
CCTTTCC
Found at i:1305661 original size:15 final size:15
Alignment explanation
Indices: 1305641--1305788 Score: 190
Period size: 15 Copynumber: 9.5 Consensus size: 15
1305631 TAATAAGGTT
1305641 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1305656 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1305671 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1305686 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1305701 ATTTATTGTAAAATA
1 ATTTATTTTAAAATA
1305716 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1305731 ATTTATTATAAAATATAGA
1 ATTTATT-TTAAA-AT--A
1305750 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
1305768 ATTTA-TTTAAAATA
1 ATTTATTTTAAAATA
1305782 ATTTATT
1 ATTTATT
1305789 AGTATGAATT
Statistics
Matches: 119, Mismatches: 6, Indels: 16
0.84 0.04 0.11
Matches are distributed among these distances:
14 14 0.12
15 84 0.71
16 4 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.03
22 7 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1305766 original size:37 final size:37
Alignment explanation
Indices: 1305716--1305843 Score: 142
Period size: 37 Copynumber: 3.6 Consensus size: 37
1305706 TTGTAAAATA
1305716 ATTTATTTTAAAATAATTTATTATAAAATATAGATTG
1 ATTTATTTTAAAATAATTTATTATAAAATATAGATTG
*
1305753 ATTTATTTTAAAATAATTTATT-T-AAA-ATA-ATTT
1 ATTTATTTTAAAATAATTTATTATAAAATATAGATTG
* * * * * * *
1305786 A-TTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTATAAAATATAGATTG
1305822 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
1305844 GTATGAATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 11
0.75 0.13 0.11
Matches are distributed among these distances:
32 15 0.21
33 5 0.07
34 6 0.08
35 5 0.07
36 15 0.21
37 27 0.37
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (37 bp):
ATTTATTTTAAAATAATTTATTATAAAATATAGATTG
Found at i:1305805 original size:18 final size:18
Alignment explanation
Indices: 1305782--1305860 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 18
1305772 ATTTAAAATA
1305782 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
1305800 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AGTATGAATTG
* *
1305822 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
1305836 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
1305854 ATTTATT
1 ATTTATT
1305861 TTAAAATATG
Statistics
Matches: 46, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.04
17 1 0.02
18 15 0.33
20 4 0.09
22 14 0.30
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:1305807 original size:22 final size:22
Alignment explanation
Indices: 1305791--1305833 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1305781 AATTTATTAG
1305791 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
1305813 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1305834 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1305823 original size:69 final size:67
Alignment explanation
Indices: 1305686--1305868 Score: 235
Period size: 69 Copynumber: 2.7 Consensus size: 67
1305676 TTATAAAATA
1305686 ATTTATTTTAAAATAATTTATTGTAAAATAATTTATTTTAAAATAATTTATTATAAAATATAGAT
1 ATTTATTTTAAAATAATTTATTGTAAAATAATTTATTTTAAAATAATTTATTATAAAATATAGAT
1305751 TG
66 TG
* * * * *
1305753 ATTTATTTTAAAATAATTTATT-TAAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTGTAAAATAATTTATT--T-TAAAATAATTTATTATAAAATATA
1305817 GATTG
63 GATTG
* *
1305822 ATTTATTTT-AAATAATTTATTAGTATGAATTGATTTATTTTAAAATA
1 ATTTATTTTAAAATAATTTATT-GTA--AAATAATTTATTTTAAAATA
1305869 TGGATTGATT
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
66 14 0.14
67 22 0.22
68 13 0.13
69 37 0.37
70 3 0.03
72 10 0.10
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.51
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTGTAAAATAATTTATTTTAAAATAATTTATTATAAAATATAGAT
TG
Found at i:1305839 original size:54 final size:54
Alignment explanation
Indices: 1305768--1306496 Score: 709
Period size: 54 Copynumber: 13.4 Consensus size: 54
1305758 TTTTAAAATA
* *
1305768 ATTTATTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1305822 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1305876 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* **
1305930 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * ***
1305979 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATATAGTTGTATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT-T-TA-AAATATGGATTG
*
1306035 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
**
1306089 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATAATTTATT-
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATTG
* * ** * * * *** *
1306142 AGTATGAATTTATTTATTTTA-AAATATGGATTGATTTATTATTGTATTTGTATAGATTG
1 A-T-TTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
*
1306201 ATTTATTTTAAATAGTTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1306255 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1306309 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * ** * * * * * ***
1306359 ATTTGTATGGATTGATTTATTTTAAAATATGGATTTATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGA--T-TTATTTTA-AAATATGGATTG
* *
1306421 ATTTATTTTAAATAATTTATTAGTACGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1306475 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
1306497 TTGTAGTCGT
Statistics
Matches: 554, Mismatches: 83, Indels: 76
0.78 0.12 0.11
Matches are distributed among these distances:
47 4 0.01
48 27 0.05
49 3 0.01
50 21 0.04
51 1 0.00
52 4 0.01
53 11 0.02
54 340 0.61
55 31 0.06
56 18 0.03
57 42 0.08
58 30 0.05
59 4 0.01
60 2 0.00
62 16 0.03
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1305856 original size:32 final size:32
Alignment explanation
Indices: 1305813--1305919 Score: 135
Period size: 32 Copynumber: 3.7 Consensus size: 32
1305803 TATTTTAAAA
1305813 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
1305845 TATGAATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
1305867 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
1305899 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1305920 ATATGGATTG
Statistics
Matches: 63, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
22 13 0.21
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 34 0.54
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:1305870 original size:22 final size:22
Alignment explanation
Indices: 1305845--1305887 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1305835 AATTTATTAG
1305845 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
1305867 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1305888 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1305913 original size:18 final size:18
Alignment explanation
Indices: 1305890--1305937 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1305880 ATTTTAAATA
*
1305890 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1305908 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1305930 ATTTATTA
1 ATTTATTA
1305938 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1305967 original size:80 final size:80
Alignment explanation
Indices: 1305867--1306261 Score: 641
Period size: 80 Copynumber: 4.9 Consensus size: 80
1305857 TATTTTAAAA
1305867 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1305932 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
1305947 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
1306012 TTATTA-TATAGTTG
66 TTATTATTGTAGTTG
*
1306026 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
1306091 TTATTTTAAATAATTTA-TTAG
66 TTA--TT--AT--TGTAGTT-G
* *
1306112 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTTATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
1306177 TTATTATTGTATTTG
66 TTATTATTGTAGTTG
* *
1306192 TATAGATTGATTTATTTTAAATAGTTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1306257 TTATT
66 TTATT
1306262 TTAAATAATT
Statistics
Matches: 295, Mismatches: 11, Indels: 18
0.91 0.03 0.06
Matches are distributed among these distances:
79 74 0.25
80 141 0.48
81 4 0.01
82 2 0.01
83 1 0.00
84 2 0.01
85 2 0.01
86 69 0.23
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:1305993 original size:18 final size:18
Alignment explanation
Indices: 1305970--1306017 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1305960 ATTTTAAATA
*
1305970 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1305988 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1306010 ATTTATTA
1 ATTTATTA
1306018 TATAGTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1305995 original size:220 final size:214
Alignment explanation
Indices: 1305768--1306496 Score: 883
Period size: 220 Copynumber: 3.4 Consensus size: 214
1305758 TTTTAAAATA
1305768 ATTTATTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
*
1305833 ATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
* *
1305898 GTATGGATTGATTTATTTTAAAATA-TGGATTG-ATTTATTATTGTAGTTGTATGGATTGATTTA
131 GTATGGATTGATTTATTTTAAAATATTAG-TTGAATTTATTATT-TA-TTATATGGATTGATTTA
1305961 TTTTAAATAATTTATTAGTATGGATTG
193 -TTT--AT-ATTTATT-GTATGGATTG
** ** * * *
1305988 ATTTATTTTAAAAT-ATGGATT-G-ATTTATT-ATATA-GTT---GTATGGATTGATTTATTTTA
1 ATTTA-TTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTA
*
1306045 AATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTGATTTATTTTAAATAATTTATT
65 AATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATT
**
1306110 AGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTTATTTATTTTAAAATATGGATTG
130 AGTATGGATTGATTTATTTT-AA-AA--TATTAGT-TGAATTTA-TTA-TTTATTATATGGATTG
* *
1306175 ATTTA-TTAT-TGTATTTGTATAGATTG
188 ATTTATTTATATTTA-TTGTATGGATTG
* * *
1306201 ATTTATTTTAAATAGTTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
*
1306266 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTA
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
* * * ** *
1306331 GTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTTA
131 GTATGGATTGATTTATTTT-AA-AA--TATTAGT-TGAATTTA-TTA-TTTATTATATGGATTGA
*
1306396 TTTA-TTAT-TGTAGTTGTATGGATTG
189 TTTATTTATATTTA-TTGTATGGATTG
* *
1306421 ATTTATTTTAAATAATTTATTAGTACGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1306486 ATAATTTATTA
66 ATAATTTATTA
1306497 TTGTAGTCGT
Statistics
Matches: 455, Mismatches: 35, Indels: 38
0.86 0.07 0.07
Matches are distributed among these distances:
212 7 0.02
213 123 0.27
214 5 0.01
215 9 0.02
216 6 0.01
217 11 0.02
218 9 0.02
219 20 0.04
220 255 0.56
221 10 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (214 bp):
ATTTATTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
GTATGGATTGATTTATTTTAAAATATTAGTTGAATTTATTATTTATTATATGGATTGATTTATTT
ATATTTATTGTATGGATTG
Found at i:1306064 original size:32 final size:32
Alignment explanation
Indices: 1306025--1306384 Score: 263
Period size: 32 Copynumber: 11.7 Consensus size: 32
1306015 TTATATAGTT
1306025 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1306057 GTATGGATTGATTTATTTT--A-AA---A-TA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1306082 -T-T-GATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1306111 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* * **
1306143 GTATGAATTTATTTATTTTAAA-ATATGGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** *
1306174 G-ATTTATT-ATTGTATTTGTATAGATTGATTTATT-
1 GTATGGATTGATT-TATTT-TA-A-A-TAATTTATTA
** * * * *
1306208 -T-TAAATAG-TTTATTAGTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
1306245 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1306277 GTATGGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1306303 G-A---ATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1306331 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1306363 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
1306385 ATATGGATTT
Statistics
Matches: 265, Mismatches: 23, Indels: 80
0.72 0.06 0.22
Matches are distributed among these distances:
22 27 0.10
23 3 0.01
24 4 0.02
25 5 0.02
26 4 0.02
27 2 0.01
28 4 0.02
29 8 0.03
30 14 0.05
31 7 0.03
32 149 0.56
33 6 0.02
34 12 0.05
36 7 0.03
37 1 0.00
38 2 0.01
39 4 0.02
40 6 0.02
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1306249 original size:22 final size:22
Alignment explanation
Indices: 1306224--1306266 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1306214 AGTTTATTAG
1306224 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1306246 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1306267 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1306303 original size:22 final size:22
Alignment explanation
Indices: 1306278--1306320 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1306268 AATTTATTAG
*
1306278 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
1306300 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1306321 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1306562 original size:31 final size:31
Alignment explanation
Indices: 1306511--1306569 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1306501 AGTCGTATGG
* * *
1306511 ATTATTTAAATTTTAATATTGTAAAACTAAA
1 ATTATTTAAATCTCAATATTGCAAAACTAAA
*
1306542 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAATATTGCAAAACT
1306570 CTTTTAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTCAATATTGCAAAACTAAA
Found at i:1308409 original size:31 final size:30
Alignment explanation
Indices: 1308369--1308458 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
1308359 CTAAGGGAGT
*
1308369 ATCTTGGGGCCTAAGAGCCTACCCAAGAAAA
1 ATCTCGGGGCC-AAGAGCCTACCCAAGAAAA
* * *
1308400 TTCTCGGGGCCATGGAGACTTACCCAAGAAAA
1 ATCTCGGGGCCA-AGAG-CCTACCCAAGAAAA
*
1308432 ATCTCAGGG-CAGCAGAGCCTACCCAAG
1 ATCTCGGGGCCA--AGAGCCTACCCAAG
1308459 GGCCGCCTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
30 1 0.02
31 23 0.49
32 23 0.49
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (30 bp):
ATCTCGGGGCCAAGAGCCTACCCAAGAAAA
Found at i:1310068 original size:31 final size:30
Alignment explanation
Indices: 1310033--1310110 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
1310023 GTCAACTCGG
*
1310033 CTCGGTCTGCTCGGTCGGCTCTGTCAGACAA
1 CTCGGTC-GCTCGGTCGGCTCGGTCAGACAA
* * **
1310064 CTCGGTCGACTCGATCGGTTCGGTCAGACGG
1 CTCGGTCG-CTCGGTCGGCTCGGTCAGACAA
*
1310095 CTTGGTCGGCTCGGTC
1 CTCGGTC-GCTCGGTC
1310111 AGGCGTCTCG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 1 0.03
31 36 0.95
32 1 0.03
ACGTcount: A:0.10, C:0.31, G:0.33, T:0.26
Consensus pattern (30 bp):
CTCGGTCGCTCGGTCGGCTCGGTCAGACAA
Found at i:1310108 original size:22 final size:22
Alignment explanation
Indices: 1310073--1310126 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1310063 ACTCGGTCGA
* *
1310073 CTCGATCGGTTCGGTCAGACGG
1 CTCGGTCGGCTCGGTCAGACGG
* * *
1310095 CTTGGTCGGCTCGGTCAGGCGT
1 CTCGGTCGGCTCGGTCAGACGG
1310117 CTCGGTCGGC
1 CTCGGTCGGC
1310127 ACAGCTCGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.07, C:0.30, G:0.39, T:0.24
Consensus pattern (22 bp):
CTCGGTCGGCTCGGTCAGACGG
Found at i:1313121 original size:26 final size:25
Alignment explanation
Indices: 1313092--1313225 Score: 86
Period size: 26 Copynumber: 5.4 Consensus size: 25
1313082 ATTATGAATT
1313092 TAATGATTTGATATT-TAATGATTTAG
1 TAATGATTTGAT-TTATAATGA-TTAG
*
1313118 TAATGATATGATTTAGTAATGATTAG
1 TAATGATTTGATTTA-TAATGATTAG
* * *
1313144 TAATGATTT-ACTAATAATGA-TAC
1 TAATGATTTGATTTATAATGATTAG
* *
1313167 TAATAATTT-TTATTATTAAT-ATT--
1 TAATGATTTGAT-TTA-TAATGATTAG
**
1313190 TAATGATTTGATACA-AATGATTTAG
1 TAATGATTTGATTTATAATGA-TTAG
1313215 TAATGATTTGA
1 TAATGATTTGA
1313226 AATAATGAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
21 3 0.04
22 1 0.01
23 21 0.25
24 10 0.12
25 21 0.25
26 23 0.27
27 6 0.07
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (25 bp):
TAATGATTTGATTTATAATGATTAG
Found at i:1313130 original size:16 final size:16
Alignment explanation
Indices: 1313109--1313140 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1313099 TTGATATTTA
1313109 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
1313125 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
1313141 TAGTAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
ATGATTTAGTAATGAT
Found at i:1313253 original size:24 final size:24
Alignment explanation
Indices: 1313226--1313279 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1313216 AATGATTTGA
*
1313226 AATAATGAAATT-GTAATAATTACT
1 AATAATG-AATTAATAATAATTACT
* *
1313250 AATAATGATTTAATAATTATTACT
1 AATAATGAATTAATAATAATTACT
1313274 AATAAT
1 AATAAT
1313280 TATTTAGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.41
Consensus pattern (24 bp):
AATAATGAATTAATAATAATTACT
Found at i:1313284 original size:24 final size:24
Alignment explanation
Indices: 1313239--1313285 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1313229 AATGAAATTG
1313239 TAATAATTACTAATAATGATTTAA
1 TAATAATTACTAATAATGATTTAA
* *
1313263 TAATTATTACTAATAATTATTTA
1 TAATAATTACTAATAATGATTTA
1313286 GTAGTAAAAA
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:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
TAATAATTACTAATAATGATTTAA
Found at i:1313867 original size:13 final size:13
Alignment explanation
Indices: 1313837--1313877 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
1313827 AGGGTTCAGA
1313837 GTTTAGAGTTTAAG
1 GTTTAGAGTTT-AG
1313851 GTTTAGAGTTTAG
1 GTTTAGAGTTTAG
*
1313864 GTTTAGGGTTTAG
1 GTTTAGAGTTTAG
1313877 G
1 G
1313878 GTAATCCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (13 bp):
GTTTAGAGTTTAG
Found at i:1313877 original size:7 final size:7
Alignment explanation
Indices: 1313800--1313879 Score: 72
Period size: 7 Copynumber: 11.6 Consensus size: 7
1313790 TTGGTTTCTC
1313800 GGGTTTA
1 GGGTTTA
* *
1313807 TGGTTCA
1 GGGTTTA
*
1313814 GGGTTCA
1 GGGTTTA
*
1313821 GGGTTCA
1 GGGTTTA
*
1313828 GGGTTCA
1 GGGTTTA
*
1313835 GAGTTTA
1 GGGTTTA
*
1313842 GAGTTTA
1 GGGTTTA
*
1313849 AGGTTTA
1 GGGTTTA
*
1313856 GAGTTTA
1 GGGTTTA
1313863 -GGTTTA
1 GGGTTTA
1313869 GGGTTTA
1 GGGTTTA
1313876 GGGT
1 GGGT
1313880 AATCCGAACT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
6 5 0.08
7 57 0.92
ACGTcount: A:0.19, C:0.05, G:0.38, T:0.39
Consensus pattern (7 bp):
GGGTTTA
Found at i:1314437 original size:13 final size:13
Alignment explanation
Indices: 1314419--1314464 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
1314409 TTTACTACTA
1314419 AATAATTATTAGT
1 AATAATTATTAGT
1314432 AATAATTATTA--
1 AATAATTATTAGT
*
1314443 AATCATTATTAGT
1 AATAATTATTAGT
*
1314456 AATTATTAT
1 AATAATTAT
1314465 AATTTCATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.34
13 19 0.66
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (13 bp):
AATAATTATTAGT
Found at i:1314472 original size:24 final size:24
Alignment explanation
Indices: 1314417--1314568 Score: 82
Period size: 24 Copynumber: 6.4 Consensus size: 24
1314407 TTTTTACTAC
*
1314417 TAAATAATTATTAGTAATAATTAT
1 TAAATCATTATTAGTAATAATTAT
*
1314441 TAAATCATTATTAGTAATTATTA-
1 TAAATCATTATTAGTAATAATTAT
* *** * *
1314464 TAATTTCATTATTTCAAATCATTAC
1 TAA-ATCATTATTAGTAATAATTAT
* *
1314489 TAAATCATT-TGTA-TCA-AATCAT
1 TAAATCATTAT-TAGTAATAATTAT
* * *
1314511 TAAAT-ATTAATAATAAAAATTAT
1 TAAATCATTATTAGTAATAATTAT
* * *
1314534 TAGTATCATTATTAGTAAATCATTAC
1 TA-AATCATTATTAGT-AATAATTAT
1314560 T-AATCATTA
1 TAAATCATTA
1314569 CTAAATCATA
Statistics
Matches: 95, Mismatches: 24, Indels: 18
0.69 0.18 0.13
Matches are distributed among these distances:
21 5 0.05
22 10 0.11
23 12 0.13
24 51 0.54
25 10 0.11
26 7 0.07
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (24 bp):
TAAATCATTATTAGTAATAATTAT
Found at i:1314583 original size:16 final size:16
Alignment explanation
Indices: 1314562--1314593 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1314552 ATCATTACTA
1314562 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
1314578 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
1314594 TAAATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:1314595 original size:11 final size:11
Alignment explanation
Indices: 1314544--1314577 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1314534 TAGTATCATT
*
1314544 ATTAGTAAATC
1 ATTACTAAATC
1314555 ATTACT-AATC
1 ATTACTAAATC
1314565 ATTACTAAATC
1 ATTACTAAATC
1314576 AT
1 AT
1314578 ATCATTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:1314602 original size:26 final size:25
Alignment explanation
Indices: 1314550--1314610 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
1314540 CATTATTAGT
1314550 AAATCATTACTAATCATTACTAAATC
1 AAATCATTACTAATCATTAC-AAATC
*
1314576 ATATCATTACTAAATCATTA-AATATC
1 AAATCATTACT-AATCATTACAA-ATC
1314602 AAATCATTA
1 AAATCATTA
1314611 AATTCATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 21 0.68
27 8 0.26
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATCATTACTAATCATTACAAATC
Found at i:1314663 original size:98 final size:93
Alignment explanation
Indices: 1314477--1314681 Score: 211
Period size: 98 Copynumber: 2.1 Consensus size: 93
1314467 TTTCATTATT
**
1314477 TCAAATCATTACTAAATCATTTGTATCAAATCATTAAATATTAATAATAAAAATTATTAGTATCA
1 TCAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAAAATTATTAGTATCA
* *
1314542 TTATTAGTAAATCATTACTAATCATTACTAAA
66 TAATTA-TAAATCAGTAC-AATCATT--TAAA
* *
1314574 TCATATCATTACTAAATCATTAAATATCAAATCATTAAAT-TCATAATTAATAAATCATTATTAG
1 TCAAATCATTACTAAATCATT-AATATCAAATCATTAAATAT--TAA-TAATAAA-AATTATTAG
* *
1314638 TAATCATGAATT-T-AATTAGTA-AATCATTTATA
61 T-ATCAT-AATTATAAATCAGTACAATCATTTAAA
1314670 TCAAATCATTAC
1 TCAAATCATTAC
1314682 ATTATTATTA
Statistics
Matches: 92, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
96 14 0.15
97 21 0.23
98 23 0.25
99 3 0.03
100 13 0.14
101 10 0.11
102 5 0.05
103 3 0.03
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.40
Consensus pattern (93 bp):
TCAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAAAATTATTAGTATCA
TAATTATAAATCAGTACAATCATTTAAA
Found at i:1316313 original size:74 final size:72
Alignment explanation
Indices: 1316185--1316324 Score: 237
Period size: 74 Copynumber: 1.9 Consensus size: 72
1316175 TCTATAAGGC
1316185 TAAAACTTGACACATTGAACAATGATACAAATATTTGTATTTGGTCAAAAGAAAAACTACCCTAA
1 TAAAACTTGACACATTGAACAATGATACAAATATTTGTATTTGGTCAAAAGAAAAACTACCCTAA
1316250 AAAGGGA
66 AAAGGGA
*
1316257 TAAAAGTTGACACATTGAACAATGAT-CAATATATATTTGTATTTGGTCAAAAGAAAAACTACCC
1 TAAAACTTGACACATTGAACAATGATAC-A-A-ATATTTGTATTTGGTCAAAAGAAAAACTACCC
1316321 TAAA
63 TAAA
1316325 GGCTACAATT
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
71 1 0.02
72 26 0.41
73 1 0.02
74 36 0.56
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (72 bp):
TAAAACTTGACACATTGAACAATGATACAAATATTTGTATTTGGTCAAAAGAAAAACTACCCTAA
AAAGGGA
Found at i:1323081 original size:2 final size:2
Alignment explanation
Indices: 1323070--1323110 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1323060 GGTACCTATT
1323070 TC TC -C TC TC TC TC 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 TC TC TC TC TC TC TC
1323111 AGTTTGTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1328397 original size:14 final size:14
Alignment explanation
Indices: 1328378--1328411 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1328368 AAACAACAAA
1328378 GCACCACCACGAGC
1 GCACCACCACGAGC
1328392 GCACCACCACGAGC
1 GCACCACCACGAGC
1328406 GCACCA
1 GCACCA
1328412 TCCAACTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.50, G:0.21, T:0.00
Consensus pattern (14 bp):
GCACCACCACGAGC
Found at i:1329348 original size:18 final size:18
Alignment explanation
Indices: 1329325--1329361 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1329315 AATCCGGGAA
1329325 TTTATTGAATGATTTCAG
1 TTTATTGAATGATTTCAG
1329343 TTTATTGAATGATTTCAG
1 TTTATTGAATGATTTCAG
1329361 T
1 T
1329362 GTTAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.51
Consensus pattern (18 bp):
TTTATTGAATGATTTCAG
Found at i:1334770 original size:30 final size:30
Alignment explanation
Indices: 1334736--1334795 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1334726 ATTTAGGTGT
1334736 TTTTAGATTGAACCTAATATTGAGATTAAA
1 TTTTAGATTGAACCTAATATTGAGATTAAA
1334766 TTTTAGATTGAACCTAATATTGAGATTAAA
1 TTTTAGATTGAACCTAATATTGAGATTAAA
1334796 AATAAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (30 bp):
TTTTAGATTGAACCTAATATTGAGATTAAA
Found at i:1334791 original size:18 final size:18
Alignment explanation
Indices: 1334740--1334792 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
1334730 AGGTGTTTTT
1334740 AGATTGAACCTAATATTG
1 AGATTGAACCTAATATTG
*
1334758 AGATT--A---AAT-TTT
1 AGATTGAACCTAATATTG
1334770 AGATTGAACCTAATATTG
1 AGATTGAACCTAATATTG
1334788 AGATT
1 AGATT
1334793 AAAAATAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 7 0.26
13 3 0.11
14 1 0.04
16 1 0.04
17 3 0.11
18 12 0.44
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (18 bp):
AGATTGAACCTAATATTG
Found at i:1336997 original size:3 final size:3
Alignment explanation
Indices: 1336991--1337055 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
1336981 CTCCATTTTC
1336991 TAT TAT TATT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TA-T TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
1337036 TTT TAT TAA AAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1337056 CAAACGGGCC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 45 0.87
4 4 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1337562 original size:16 final size:16
Alignment explanation
Indices: 1337525--1337563 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1337515 GGAGCAACCA
1337525 ACAGCAAACCCAAAGC
1 ACAGCAAACCCAAAGC
*
1337541 AGAGCAAACCCACAA-C
1 ACAGCAAACCCA-AAGC
1337557 ACAGCAA
1 ACAGCAA
1337564 CCAAAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.51, C:0.36, G:0.13, T:0.00
Consensus pattern (16 bp):
ACAGCAAACCCAAAGC
Done.