Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008893.1 Hibiscus syriacus cultivar Beakdansim tig00112159_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: 2797279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1680337 original size:20 final size:20
Alignment explanation
Indices: 1680312--1680425 Score: 102
Period size: 20 Copynumber: 5.7 Consensus size: 20
1680302 AATTGGGAAA
*
1680312 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1680332 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1680353 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
1680373 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1680393 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1680413 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1680426 TTATTTAGCG
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 64 0.82
21 14 0.18
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1680386 original size:41 final size:41
Alignment explanation
Indices: 1680309--1680386 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1680299 GCGAATTGGG
* * **
1680309 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
1680350 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
1680387 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:1681022 original size:19 final size:19
Alignment explanation
Indices: 1681000--1681183 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
1680990 GAAACCAAAA
*
1681000 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1681019 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1681038 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
1681057 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1681077 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1681093 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1681110 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1681124 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1681143 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1681163 ATCTCGTTGCGA-TTTCATT
1 -TCGCGTTGCGATTTTCATT
1681182 TC
1 TC
1681184 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 15, Indels: 27
0.77 0.08 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 3 0.02
19 64 0.47
20 42 0.31
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1681077 original size:39 final size:38
Alignment explanation
Indices: 1681000--1681089 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
1680990 GAAACCAAAA
* *
1681000 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
1681038 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
1681077 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1681090 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:1681109 original size:33 final size:33
Alignment explanation
Indices: 1681072--1681159 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1681062 GTTGCGATTT
* *
1681072 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
1681105 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1681138 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1681160 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1681161 original size:20 final size:19
Alignment explanation
Indices: 1681127--1681183 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1681117 GCGATTCTCT
*
1681127 CGTTGCGATAGTCATTTCCG
1 CGTTGCGAT-TTCATTTCCG
*
1681147 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATT-TCATT-TCCG
1681167 CGTTGCGATTTCATTTC
1 CGTTGCGATTTCATTTC
1681184 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.03
19 5 0.16
20 25 0.78
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTCATTTCCG
Found at i:1684471 original size:14 final size:14
Alignment explanation
Indices: 1684452--1684484 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1684442 TGATGTTAAT
1684452 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1684466 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1684480 TGATT
1 TGATT
1684485 GTTTAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1684720 original size:32 final size:33
Alignment explanation
Indices: 1684664--1684755 Score: 152
Period size: 32 Copynumber: 2.8 Consensus size: 33
1684654 ATTAAATTCG
1684664 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
1684697 CGTTGCGATTTTCA-TTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1684729 CGTTGCGATTTTCATTTCGCA-TGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1684756 AGTAATTTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 35 0.64
33 20 0.36
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1686942 original size:12 final size:12
Alignment explanation
Indices: 1686925--1686949 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1686915 TCTTCGGGGA
1686925 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1686937 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1686949 C
1 C
1686950 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:1688439 original size:14 final size:14
Alignment explanation
Indices: 1688420--1688456 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1688410 CACCAATTAA
1688420 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1688434 ACAAATCATCTTTT
1 ACAAATCAACATTT
1688448 ACAAATCAA
1 ACAAATCAA
1688457 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1688850 original size:20 final size:20
Alignment explanation
Indices: 1688821--1688871 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1688811 ATTCATTTGA
* *
1688821 CTATCTCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
1688841 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1688861 TTATCGCAACG
1 CTATCGCAACG
1688872 AGAATATCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1688924 original size:14 final size:15
Alignment explanation
Indices: 1688901--1688973 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 15
1688891 TGATAATCGC
*
1688901 ATTGCAATTTTCTCG
1 ATTGCGATTTTCTCG
1688916 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
1688933 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
1688951 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
1688967 -TTGCGAT
1 ATTGCGAT
1688974 AGCCATTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
14 17 0.35
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.19
21 1 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:1688938 original size:19 final size:19
Alignment explanation
Indices: 1688916--1688963 Score: 89
Period size: 18 Copynumber: 2.6 Consensus size: 19
1688906 AATTTTCTCG
1688916 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1688935 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1688953 TTGCGATTTTC
1 TTGCGATTTTC
1688964 TCGTTGCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1689099 original size:14 final size:14
Alignment explanation
Indices: 1689080--1689116 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1689070 CATCAATTAA
1689080 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1689094 ACAAATCATCTTTT
1 ACAAATCAACATTT
1689108 ACAAATCAA
1 ACAAATCAA
1689117 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1691020 original size:20 final size:19
Alignment explanation
Indices: 1690985--1691051 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1690975 GAAACTTAAA
1690985 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1691004 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1691024 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1691043 ATCGCAACG
1 ATCGCAACG
1691052 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1691059 original size:14 final size:14
Alignment explanation
Indices: 1691040--1691097 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1691030 ATGCGAAATG
1691040 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1691054 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1691070 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1691086 AAAATCGCAACG
1 AAAATCGCAACG
1691098 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1691082 original size:32 final size:33
Alignment explanation
Indices: 1691024--1691102 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1691014 GGAAATGGCT
*
1691024 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1691057 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1691089 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1691103 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1691136 original size:19 final size:17
Alignment explanation
Indices: 1691114--1691204 Score: 68
Period size: 14 Copynumber: 5.4 Consensus size: 17
1691104 ACAAATCGCA
1691114 TTGCGATTTTCATTTCACG
1 TTGCGA-TTTCATTTC-CG
*
1691133 TTGCGATTT--TGT-CG
1 TTGCGATTTCATTTCCG
1691147 TTGCGATTTCATTTCGCG
1 TTGCGATTTCATTTC-CG
*
1691165 TTGCGATTT--TGT-CG
1 TTGCGATTTCATTTCCG
*
1691179 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTC-CG
1691198 TTGCGAT
1 TTGCGAT
1691205 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
14 19 0.33
15 3 0.05
16 6 0.10
17 2 0.03
18 15 0.26
19 13 0.22
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (17 bp):
TTGCGATTTCATTTCCG
Found at i:1691150 original size:14 final size:14
Alignment explanation
Indices: 1691131--1691188 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1691121 TTTCATTTCA
1691131 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1691145 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1691161 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1691177 CGTTGCGATTTT
1 CGTTGCGATTTT
1691189 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1691195 original size:33 final size:33
Alignment explanation
Indices: 1691114--1691204 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1691104 ACAAATCGCA
*
1691114 TTGCGATTTTCATTTCACGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1691147 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
1691179 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
1691205 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:1691223 original size:20 final size:19
Alignment explanation
Indices: 1691189--1691243 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1691179 TTGCGATTTT
*
1691189 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1691208 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1691228 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1691244 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:1691742 original size:18 final size:18
Alignment explanation
Indices: 1691716--1691760 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1691706 GTCGATCAGA
*
1691716 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
1691734 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
1691752 TGATGGCTC
1 TGATGGCTC
1691761 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:1693403 original size:22 final size:22
Alignment explanation
Indices: 1693378--1693421 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1693368 GATTTAGATA
*
1693378 GACGGATTTCACCGGAGATGGG
1 GACGAATTTCACCGGAGATGGG
**
1693400 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCACCGGAGATGGG
1693422 TGAGAGAGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
GACGAATTTCACCGGAGATGGG
Found at i:1693634 original size:20 final size:20
Alignment explanation
Indices: 1693609--1693702 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1693599 GATTATGTAT
1693609 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1693629 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1693649 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1693670 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1693690 TATCGCATTGCGA
1 TATCGCGTTGCGA
1693703 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1693674 original size:41 final size:41
Alignment explanation
Indices: 1693629--1693706 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1693619 CGAAAGTCAG
* * *
1693629 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
1693670 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
1693707 CCCAATTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:1693703 original size:20 final size:20
Alignment explanation
Indices: 1693589--1693703 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1693579 CGCTTTGAAA
*
1693589 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1693610 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1693630 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1693650 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1693671 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1693691 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1693704 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1693722 original size:41 final size:41
Alignment explanation
Indices: 1693692--1693787 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
1693682 ATAGTCAGTA
* * * *
1693692 TCGCATTGCGATTTTCCCAATTTGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
1693733 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
1693774 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1693788 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:1693723 original size:21 final size:21
Alignment explanation
Indices: 1693692--1693767 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
1693682 ATAGTCAGTA
*
1693692 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* * **
1693713 TTGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
* *
1693733 TCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
1693754 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1693768 ACTTATTCGC
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:1693743 original size:20 final size:20
Alignment explanation
Indices: 1693718--1693784 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1693708 CCAATTTGCG
1693718 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
1693738 TTGCGAATTTCCCAATTCGCG
1 TTGCG-ATTTACTTATTCGCA
1693759 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
1693779 TTGCGA
1 TTGCGA
1693785 ATTGGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:1710125 original size:42 final size:42
Alignment explanation
Indices: 1710066--1710151 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
1710056 GTCTATGCCA
* *
1710066 AAGGACGAATTTCCGGGAAATGATATCAATAATGGAAGTAAC
1 AAGGACGAATTTCCGGGAAATGATATCAAGAATGGAACTAAC
* *
1710108 AAGGACGAATTTCCGGGAAGTGATATCACGAATGGAACTAAC
1 AAGGACGAATTTCCGGGAAATGATATCAAGAATGGAACTAAC
1710150 AA
1 AA
1710152 TGGTCCTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (42 bp):
AAGGACGAATTTCCGGGAAATGATATCAAGAATGGAACTAAC
Found at i:1711494 original size:18 final size:18
Alignment explanation
Indices: 1711471--1711513 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1711461 AAGACAACTA
*
1711471 AAGGATCTGCCAAATCTC
1 AAGGATCGGCCAAATCTC
*
1711489 AAGGATCGGCCAAGTCTC
1 AAGGATCGGCCAAATCTC
1711507 AAGGATC
1 AAGGATC
1711514 AGCTGAACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (18 bp):
AAGGATCGGCCAAATCTC
Found at i:1711542 original size:18 final size:18
Alignment explanation
Indices: 1711468--1711543 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 18
1711458 CAGAAGACAA
* **
1711468 CTAAAGGATCTGCCAAAT
1 CTAAAGGATCAGCCAAGC
* * *
1711486 CTCAAGGATCGGCCAAGT
1 CTAAAGGATCAGCCAAGC
* *
1711504 CTCAAGGATCAGCTGAA-C
1 CTAAAGGATCAGC-CAAGC
1711522 CTAAAGGATCAGCCAAGC
1 CTAAAGGATCAGCCAAGC
1711540 CTAA
1 CTAA
1711544 GCGACAAACT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 2 0.04
18 44 0.92
19 2 0.04
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (18 bp):
CTAAAGGATCAGCCAAGC
Found at i:1713751 original size:15 final size:15
Alignment explanation
Indices: 1713717--1713745 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1713707 GTTATATGAG
1713717 CTATGTGATAAGAAA
1 CTATGTGATAAGAAA
1713732 CTATGTGATAAGAA
1 CTATGTGATAAGAA
1713746 GTTATGAGCC
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:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (15 bp):
CTATGTGATAAGAAA
Found at i:1714715 original size:32 final size:32
Alignment explanation
Indices: 1714674--1714734 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1714664 CACCAAATTT
* *
1714674 TGTCCTTTAATGTTGTTGCATTATATAATATA
1 TGTCCTTTAATGTCGTTACATTATATAATATA
1714706 TGTCCTTTAATGTCGTTACATTATATAAT
1 TGTCCTTTAATGTCGTTACATTATATAAT
1714735 GTATTTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (32 bp):
TGTCCTTTAATGTCGTTACATTATATAATATA
Found at i:1715950 original size:14 final size:15
Alignment explanation
Indices: 1715928--1715965 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1715918 CAATTGACCC
*
1715928 TTATATTATTATT-T
1 TTATTTTATTATTAT
1715942 TTATTTTA-TATTAT
1 TTATTTTATTATTAT
1715956 TTATTTTATT
1 TTATTTTATT
1715966 GTATATGCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.19
14 16 0.76
15 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTATTATTAT
Found at i:1715952 original size:19 final size:19
Alignment explanation
Indices: 1715928--1715971 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1715918 CAATTGACCC
1715928 TTATATTA-TTATTTTTATT
1 TTATATTATTTA-TTTTATT
1715947 TTATATTATTTATTTTATT
1 TTATATTATTTATTTTATT
*
1715966 GTATAT
1 TTATAT
1715972 GCGTATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTATATTATTTATTTTATT
Found at i:1723941 original size:22 final size:22
Alignment explanation
Indices: 1723913--1723960 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1723903 CGCTGAATGT
1723913 TGAACGGTTCAGCATTCAACGC
1 TGAACGGTTCAGCATTCAACGC
*
1723935 TGAACGGTTCAGCATTTAACGC
1 TGAACGGTTCAGCATTCAACGC
1723957 TGAA
1 TGAA
1723961 TGATTTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (22 bp):
TGAACGGTTCAGCATTCAACGC
Found at i:1724131 original size:20 final size:22
Alignment explanation
Indices: 1724106--1724146 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
1724096 TAAAAATTAT
1724106 CTAAAATATT-AT-TTTTTTTC
1 CTAAAATATTAATGTTTTTTTC
1724126 CTAAAATATTAATGTTTTTTT
1 CTAAAATATTAATGTTTTTTT
1724147 TAATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (22 bp):
CTAAAATATTAATGTTTTTTTC
Found at i:1724248 original size:21 final size:21
Alignment explanation
Indices: 1724222--1724262 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1724212 TAAAACGTCT
*
1724222 AATAATAATATTTTCAGTAAA
1 AATAATAATATTTTAAGTAAA
1724243 AATAATAATATTTTAAGTAA
1 AATAATAATATTTTAAGTAA
1724263 TTTTTATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
AATAATAATATTTTAAGTAAA
Found at i:1725463 original size:200 final size:201
Alignment explanation
Indices: 1725105--1725479 Score: 583
Period size: 200 Copynumber: 1.9 Consensus size: 201
1725095 AAAGTTATGA
1725105 GAATTGTCTGTCCAGCTCAGTTGGTTAGAGCGCAAAGCTCTTAACCTTGTGGTCATGAGATCGAG
1 GAATTGTCTGTCCAGCTCAGTTGGTTAGAGCGCAAAGCTCTTAACCTTGTGGTCATGAGATCGAG
* **
1725170 TCTCACGGTGGGCAATTCAAAATTTTGACTGTCGGAGGTCTCCCACGGAAGTTGCTCTCAACCTG
66 TCCCACGGTGGGCAATTCAAAATTTTGACTGTCGGAGGTCTCCCACGGAAACTGCTCTCAACCTG
* * * * *
1725235 GCGTTAGGGGCATCCTACTGTCCTACCTCCCCTTATCCCATTACACATGGGAATAGGGTCATCTA
131 GCGTTAGAGGCAACCTACTCTCCTACCTCCCCTCACCCCATTACACATGGGAATAGGGTCATCTA
1725300 ATTTAT
196 ATTTAT
* * * * *
1725306 GAATTGTTTGTCCAGCTCAGTTGG-TAGAGCGCAAGGCTCTTAATCTTGTGGTCGTGGGATCGAG
1 GAATTGTCTGTCCAGCTCAGTTGGTTAGAGCGCAAAGCTCTTAACCTTGTGGTCATGAGATCGAG
* * *
1725370 TCCCACGGTGGGCAATTCATAATTTTGATTGTCGGAGGTCTTCCACGGAAACTGCTCTCAACCTG
66 TCCCACGGTGGGCAATTCAAAATTTTGACTGTCGGAGGTCTCCCACGGAAACTGCTCTCAACCTG
1725435 GCGTTAGAGGCAACCTACTACT-CTACCTCCCCTCACCCCATTACA
131 GCGTTAGAGGCAACCTACT-CTCCTACCTCCCCTCACCCCATTACA
1725480 TATAAGAATA
Statistics
Matches: 157, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
200 133 0.85
201 24 0.15
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (201 bp):
GAATTGTCTGTCCAGCTCAGTTGGTTAGAGCGCAAAGCTCTTAACCTTGTGGTCATGAGATCGAG
TCCCACGGTGGGCAATTCAAAATTTTGACTGTCGGAGGTCTCCCACGGAAACTGCTCTCAACCTG
GCGTTAGAGGCAACCTACTCTCCTACCTCCCCTCACCCCATTACACATGGGAATAGGGTCATCTA
ATTTAT
Found at i:1726205 original size:29 final size:30
Alignment explanation
Indices: 1726171--1726228 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1726161 ATTATCAGTT
1726171 TTGG-TTAGTTTTAATACCTAAA-TTTAAAA
1 TTGGTTTA-TTTTAATACCTAAACTTTAAAA
*
1726200 TTGGTTTATTTTAGTACCTAAACTTTAAA
1 TTGGTTTATTTTAATACCTAAACTTTAAA
1726229 TTATTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (30 bp):
TTGGTTTATTTTAATACCTAAACTTTAAAA
Found at i:1726210 original size:234 final size:234
Alignment explanation
Indices: 1725751--1726210 Score: 665
Period size: 234 Copynumber: 2.0 Consensus size: 234
1725741 TAACGCGTTT
*
1725751 CCAAAAAACAGGATATAAGTTTCATTATAGGGTAAAATTTACTTTTAGTACTTAAATTATCAGTT
1 CCAAAAAACAGGATATAAGTTTCATTATAGGGTAAAATTTACTTTTAGTACCTAAATTATCAGTT
* * * *
1725816 TTGATTTGTTTTAGTACTTAAATGTTCAATTTTTTTAAATCATGTCTAACGTTTAGTTTTTTTTT
66 TTGATATGTTTTAGTACTTAAATGTTCAATTTTTTTAAATCATGCCTAACGTTTAATTTTTGTTT
** * *
1725881 TGTTTTAGTACCTCACCGTAAAAAGCTTAACGCGTTTCGTACTTAAACTATCAATTTTTGTTCGT
131 TGTTTTAGTACCTCACCGTAAAAAGCTTAACGCGTTTCGTAAGTAAACTATCAATTTTGGTTAGT
** ** **
1725946 TTAATTTCTGGTTTCATTATGGGTTTTATTTATATCTTA
196 TTAATACCTAATTTCAAAATGGGTTTTATTTATATCTTA
** *
1725985 CCAAAAAACAGGATATGGGTTTCATTATAGGGT-AAATTCTACTTTTAGTACCTAAATTATCATT
1 CCAAAAAACAGGATATAAGTTTCATTATAGGGTAAAATT-TACTTTTAGTACCTAAATTATCAGT
*
1726049 TTTGATATGTTTTAGTACTTAAATGTTCAATTTTTTTAAATCATGCCTAATGTTTAATTTTTGTT
65 TTTGATATGTTTTAGTACTTAAATGTTCAATTTTTTTAAATCATGCCTAACGTTTAATTTTTGTT
* * *
1726114 TTGTTTTAGTACCTCACCGTAAAAAGCTTAACTCGTTTCGTAAGTAAATTATCAGTTTTGGTTAG
130 TTGTTTTAGTACCTCACCGTAAAAAGCTTAACGCGTTTCGTAAGTAAACTATCAATTTTGGTTAG
*
1726179 TTTTAATACCTAAATTT-AAAATTGG-TTTATTT
195 -TTTAATACCT-AATTTCAAAATGGGTTTTATTT
1726211 TAGTACCTAA
Statistics
Matches: 200, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
233 5 0.03
234 179 0.89
235 13 0.06
236 3 0.01
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (234 bp):
CCAAAAAACAGGATATAAGTTTCATTATAGGGTAAAATTTACTTTTAGTACCTAAATTATCAGTT
TTGATATGTTTTAGTACTTAAATGTTCAATTTTTTTAAATCATGCCTAACGTTTAATTTTTGTTT
TGTTTTAGTACCTCACCGTAAAAAGCTTAACGCGTTTCGTAAGTAAACTATCAATTTTGGTTAGT
TTAATACCTAATTTCAAAATGGGTTTTATTTATATCTTA
Found at i:1726838 original size:23 final size:21
Alignment explanation
Indices: 1726804--1726845 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
1726794 AAAAAAAATA
1726804 TGGTTTTGTAGAATGTCTGGT
1 TGGTTTTGTAGAATGTCTGGT
1726825 TGGTGTTTGATAGAATGTCTG
1 TGGT-TTTG-TAGAATGTCTG
1726846 ATCGAGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 11 0.58
ACGTcount: A:0.17, C:0.05, G:0.33, T:0.45
Consensus pattern (21 bp):
TGGTTTTGTAGAATGTCTGGT
Found at i:1730538 original size:19 final size:19
Alignment explanation
Indices: 1730514--1730565 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1730504 GAATGTAATT
*
1730514 AGTGCACCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
1730533 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
1730552 AGTGCATCGATGCA
1 AGTGCATCGATGCA
1730566 CCCCCTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:1733323 original size:15 final size:15
Alignment explanation
Indices: 1733303--1733341 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1733293 GAGAAGCAGT
1733303 ATGATATGTTAGAGC
1 ATGATATGTTAGAGC
1733318 ATGATATGTTAGAGC
1 ATGATATGTTAGAGC
*
1733333 ATGTTATGT
1 ATGATATGT
1733342 AAAATCTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (15 bp):
ATGATATGTTAGAGC
Found at i:1735862 original size:15 final size:15
Alignment explanation
Indices: 1735838--1735868 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1735828 AGATTTTCTC
1735838 AAATTATAAAACCCT
1 AAATTATAAAACCCT
*
1735853 AAATTTTAAAACCCT
1 AAATTATAAAACCCT
1735868 A
1 A
1735869 TAACGTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTATAAAACCCT
Found at i:1740612 original size:28 final size:31
Alignment explanation
Indices: 1740569--1740664 Score: 107
Period size: 29 Copynumber: 3.3 Consensus size: 31
1740559 AGTCAGGACA
1740569 AGGATATAATTC-CATGCAAAATCAAGA-CG
1 AGGATATAATTCTCATGCAAAATCAAGAGCG
* *
1740598 A-GATA-AATTCTCATGTAAAAT-TAGAGCG
1 AGGATATAATTCTCATGCAAAATCAAGAGCG
* *
1740626 AGGATATAATTCT-ATGCAGAATCAAGA-TG
1 AGGATATAATTCTCATGCAAAATCAAGAGCG
1740655 AGGATATAAT
1 AGGATATAAT
1740665 CCCATGAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
27 8 0.14
28 16 0.29
29 23 0.41
30 9 0.16
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (31 bp):
AGGATATAATTCTCATGCAAAATCAAGAGCG
Found at i:1740657 original size:29 final size:30
Alignment explanation
Indices: 1740542--1740664 Score: 105
Period size: 29 Copynumber: 4.3 Consensus size: 30
1740532 ACAAGATTGA
* * * *
1740542 GATATAA-TCTAATGCAGAGTCAGGACAAG
1 GATATAATTCTAATGCAAAATCAAGACGAG
*
1740571 GATATAATTC-CATGCAAAATCAAGACGA-
1 GATATAATTCTAATGCAAAATCAAGACGAG
* * *
1740599 GATA-AATTCTCATGTAAAAT-TAGAGCGAG
1 GATATAATTCTAATGCAAAATCAAGA-CGAG
* *
1740628 GATATAATTCT-ATGCAGAATCAAGATGAG
1 GATATAATTCTAATGCAAAATCAAGACGAG
1740657 GATATAAT
1 GATATAAT
1740665 CCCATGAAGA
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
27 8 0.10
28 16 0.21
29 42 0.55
30 11 0.14
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (30 bp):
GATATAATTCTAATGCAAAATCAAGACGAG
Found at i:1740675 original size:29 final size:29
Alignment explanation
Indices: 1740625--1740707 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
1740615 AAATTAGAGC
* * *
1740625 GAGGATATAATTCTATGCAGAATCAAGAT
1 GAGGATATAATCCCATGAAGAATCAAGAT
* *
1740654 GAGGATATAATCCCATGAAGAATTAGGAT
1 GAGGATATAATCCCATGAAGAATCAAGAT
*
1740683 G-GGAACATAATCCCATGCAA-AATCA
1 GAGG-ATATAATCCCATG-AAGAATCA
1740708 GGACAAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
28 2 0.04
29 41 0.91
30 2 0.04
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.23
Consensus pattern (29 bp):
GAGGATATAATCCCATGAAGAATCAAGAT
Found at i:1742852 original size:30 final size:32
Alignment explanation
Indices: 1742792--1742859 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
1742782 TCATTAAAAG
*
1742792 TAGGTGTCTAATATTTTTTTCGGTTACACTTT
1 TAGGTGTCTAATAGTTTTTTCGGTTACACTTT
* *
1742824 TAGGTGTCTAA-CGTTTTTTC-GTTGCACTTT
1 TAGGTGTCTAATAGTTTTTTCGGTTACACTTT
1742854 TAGGTG
1 TAGGTG
1742860 CCTATGTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 15 0.45
31 7 0.21
32 11 0.33
ACGTcount: A:0.16, C:0.13, G:0.21, T:0.50
Consensus pattern (32 bp):
TAGGTGTCTAATAGTTTTTTCGGTTACACTTT
Found at i:1743775 original size:31 final size:31
Alignment explanation
Indices: 1743738--1743867 Score: 165
Period size: 31 Copynumber: 4.2 Consensus size: 31
1743728 ACGGCGTAGG
* *
1743738 CACCTAAAAGTGTAACGT-AGAAAACGTTACG
1 CACCTAAAAGTATAACGTCA-AAAACGTTACA
*
1743769 CACCTAAAAGTGTAACGT-AGAAAACGTTACA
1 CACCTAAAAGTATAACGTCA-AAAACGTTACA
* *
1743800 CACCTAAAAGTATAACATCAAAAATGTTACA
1 CACCTAAAAGTATAACGTCAAAAACGTTACA
*
1743831 CACCTAAAAATATAACGTCAAAAACGTTACA
1 CACCTAAAAGTATAACGTCAAAAACGTTACA
*
1743862 TACCTA
1 CACCTA
1743868 TTTTTAGAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (31 bp):
CACCTAAAAGTATAACGTCAAAAACGTTACA
Found at i:1746869 original size:29 final size:29
Alignment explanation
Indices: 1746829--1746934 Score: 122
Period size: 30 Copynumber: 3.6 Consensus size: 29
1746819 TGAAAAATTG
1746829 AATACTTTAGGTACTTATTTTGACAAAAA
1 AATACTTTAGGTACTTATTTTGACAAAAA
* **
1746858 AATACTTTAGGTATTTATTGCGATCAAAAA
1 AATACTTTAGGTACTTATTTTGA-CAAAAA
* * * *
1746888 GATAAATTTAAGTACTTATTTTGATAAAAA
1 AAT-ACTTTAGGTACTTATTTTGACAAAAA
1746918 AACTACTTTAGGTACTT
1 AA-TACTTTAGGTACTT
1746935 CGATAAGAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
29 20 0.33
30 25 0.41
31 16 0.26
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (29 bp):
AATACTTTAGGTACTTATTTTGACAAAAA
Found at i:1746948 original size:61 final size:60
Alignment explanation
Indices: 1746834--1746950 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
1746824 AATTGAATAC
* * ** *
1746834 TTTAGGTACTTATTTTGACAAAAAAATACTTTAGGTATTTATTGCGATCAAAAAGATAAA
1 TTTAAGTACTTATTTTGACAAAAAAATACTTTAGGTATTGATTAAGATAAAAAAGATAAA
* *
1746894 TTTAAGTACTTATTTTGATAAAAAAACTACTTTAGGTACTTCGA-TAAGAAAAAAAAG
1 TTTAAGTACTTATTTTGACAAAAAAA-TACTTTAGGTA-TT-GATTAAGATAAAAAAG
1746951 TATACTTTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 24 0.51
61 11 0.23
62 11 0.23
63 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (60 bp):
TTTAAGTACTTATTTTGACAAAAAAATACTTTAGGTATTGATTAAGATAAAAAAGATAAA
Found at i:1749106 original size:37 final size:37
Alignment explanation
Indices: 1749063--1749139 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
1749053 CATTAATGTC
1749063 AAATTTT-AGTATT-AAGATAATTTCATACAATATATGA
1 AAATTTTGA-TATTCAA-ATAATTTCATACAATATATGA
* *
1749100 AAATTTTGATATTCAAATAATTTCTTGCAATATATGA
1 AAATTTTGATATTCAAATAATTTCATACAATATATGA
1749137 AAA
1 AAA
1749140 AAAACTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
37 33 0.92
38 3 0.08
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (37 bp):
AAATTTTGATATTCAAATAATTTCATACAATATATGA
Found at i:1749778 original size:23 final size:23
Alignment explanation
Indices: 1749737--1749802 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
1749727 CAAAAGGCAG
* *
1749737 ATATAAACGTGCCACAAAGATAA
1 ATATAAACGTGTCATAAAGATAA
* * *
1749760 ATATAAATGTGTCATAAAGGTAG
1 ATATAAACGTGTCATAAAGATAA
* *
1749783 AGATAAACATGTCATAAAGA
1 ATATAAACGTGTCATAAAGA
1749803 CATAAATTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.23
Consensus pattern (23 bp):
ATATAAACGTGTCATAAAGATAA
Found at i:1750287 original size:3 final size:3
Alignment explanation
Indices: 1750279--1750361 Score: 159
Period size: 3 Copynumber: 28.0 Consensus size: 3
1750269 TTTACATCTG
1750279 TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1750326 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1750362 ACGATTTAAT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.03
3 77 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1750626 original size:51 final size:52
Alignment explanation
Indices: 1750566--1750675 Score: 179
Period size: 53 Copynumber: 2.1 Consensus size: 52
1750556 TCATCTGTAA
1750566 ATTTT-AAATTTATATATAATTTAAGCA-TTTTTATGTTTTTAATATTATTT
1 ATTTTCAAATTTATATATAATTTAAGCATTTTTTATGTTTTTAATATTATTT
*
1750616 ATTTTCAAATTTATATATAATTTAAGTATTTTTTTATGTTTTTAATATTATTT
1 ATTTTCAAATTTATATATAATTTAAGCA-TTTTTTATGTTTTTAATATTATTT
*
1750669 AATTTCA
1 ATTTTCA
1750676 TATCTTTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
50 5 0.09
51 21 0.38
53 29 0.53
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.60
Consensus pattern (52 bp):
ATTTTCAAATTTATATATAATTTAAGCATTTTTTATGTTTTTAATATTATTT
Found at i:1753498 original size:157 final size:158
Alignment explanation
Indices: 1753212--1753523 Score: 617
Period size: 157 Copynumber: 2.0 Consensus size: 158
1753202 ACGCAAATGC
1753212 CTTTATTGAGTTTTTGGAAGGCCATAAATCTTTAGTGTGCTCCAAGAACTTGTCTTCTTATTTAT
1 CTTTATTGAGTTTTTGGAAGGCCATAAATCTTTAGTGTGCTCCAAGAACTTGTCTTCTTATTTAT
1753277 TAAGGAAAATGAAAGCTTTGTTAGCGTCATCAAATATGTTATGTGGTATAAATTCAAAAATTAGT
66 TAAGGAAAATGAAAGCTTTGTTAGCGTCATCAAATATGTTATGTGGTATAAATTCAAAAATTAGT
1753342 ACACTATTTAGAGGGG-TTGAATAACAA
131 ACACTATTTAGAGGGGTTTGAATAACAA
1753369 CTTTATTGAGTTTTTGGAAGGCCATAAATCTTTAGTGTGCTCCAAGAACTTGTCTTCTTATTTAT
1 CTTTATTGAGTTTTTGGAAGGCCATAAATCTTTAGTGTGCTCCAAGAACTTGTCTTCTTATTTAT
1753434 TAAGGAAAATGAAAGCTTTGTTAGCGTCATCAAATATGTTATGTGGTATAAATTCAAAAATTAGT
66 TAAGGAAAATGAAAGCTTTGTTAGCGTCATCAAATATGTTATGTGGTATAAATTCAAAAATTAGT
1753499 ACACTATTTAGAGGGGTTTGAATAA
131 ACACTATTTAGAGGGGTTTGAATAA
1753524 AAATATTATA
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
157 146 0.95
158 8 0.05
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (158 bp):
CTTTATTGAGTTTTTGGAAGGCCATAAATCTTTAGTGTGCTCCAAGAACTTGTCTTCTTATTTAT
TAAGGAAAATGAAAGCTTTGTTAGCGTCATCAAATATGTTATGTGGTATAAATTCAAAAATTAGT
ACACTATTTAGAGGGGTTTGAATAACAA
Found at i:1754123 original size:16 final size:15
Alignment explanation
Indices: 1754082--1754122 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1754072 TAGATTTAAT
*
1754082 TTATCATTTTTACCC
1 TTATAATTTTTACCC
1754097 TTATAATTTTTACCC
1 TTATAATTTTTACCC
*
1754112 TTATGATTTTT
1 TTATAATTTTT
1754123 TCGTATCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.02, T:0.59
Consensus pattern (15 bp):
TTATAATTTTTACCC
Found at i:1757631 original size:27 final size:27
Alignment explanation
Indices: 1757601--1757689 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
1757591 AAATTTAAAC
1757601 CCTTAATTTTATTTAAAGAACTTAATA
1 CCTTAATTTTATTTAAAGAACTTAATA
* *
1757628 CCTT-ATTTTA-GTAAACCAACTATTTTAATA
1 CCTTAATTTTATTTAAA-GAAC----TTAATA
* *
1757658 CCTTAATTTTATTTAAGGAATTTAATA
1 CCTTAATTTTATTTAAAGAACTTAATA
1757685 CCTTA
1 CCTTA
1757690 TTTCAGTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
25 4 0.08
26 9 0.18
27 15 0.31
30 10 0.20
31 8 0.16
32 3 0.06
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.45
Consensus pattern (27 bp):
CCTTAATTTTATTTAAAGAACTTAATA
Found at i:1757656 original size:30 final size:29
Alignment explanation
Indices: 1757622--1757709 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
1757612 TTTAAAGAAC
1757622 TTAATACCTTATTTTAGTAAACCAACTATT
1 TTAATACCTTATTTTAGTAAACCAAC-ATT
* * **
1757652 TTAATACCTTAATTTTATTTAA-GGA-A-T
1 TTAATACCTT-ATTTTAGTAAACCAACATT
*
1757679 TTAATACCTTATTTCAGTAAACCAACCATT
1 TTAATACCTTATTTTAGTAAACCAA-CATT
1757709 T
1 T
1757710 AATCACGGGC
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
26 8 0.18
27 12 0.27
28 1 0.02
29 1 0.02
30 13 0.30
31 9 0.20
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (29 bp):
TTAATACCTTATTTTAGTAAACCAACATT
Found at i:1757664 original size:57 final size:57
Alignment explanation
Indices: 1757601--1757709 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
1757591 AAATTTAAAC
* *
1757601 CCTTAATTTTATTTAAAGAACTTAATACCTTATTTTAGTAAACCAACTATTTTAATA
1 CCTTAATTTTATTTAAAGAACTTAATACCTTATTTCAGTAAACCAACCATTTTAATA
* *
1757658 CCTTAATTTTATTTAAGGAATTTAATACCTTATTTCAGTAAACCAACCATTT
1 CCTTAATTTTATTTAAAGAACTTAATACCTTATTTCAGTAAACCAACCATTT
1757710 AATCACGGGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.43
Consensus pattern (57 bp):
CCTTAATTTTATTTAAAGAACTTAATACCTTATTTCAGTAAACCAACCATTTTAATA
Found at i:1765028 original size:39 final size:38
Alignment explanation
Indices: 1764877--1765028 Score: 155
Period size: 39 Copynumber: 3.9 Consensus size: 38
1764867 TCATTTCAAC
* * *
1764877 CCAATATATAGTCTTATCAAAACTTC-TTGGAAAGATAA
1 CCAATATCTAGTCTTGTCAAAAC-TCGTTGGAAAGACAA
* *
1764915 CCTAATATCTAGTCTTGTCAAAACTCTTTGGGAAGACAA
1 CC-AATATCTAGTCTTGTCAAAACTCGTTGGAAAGACAA
* * * * *
1764954 CAAAAATCTAATCTTGTCAAAACTCGTTGGGAAGACAG
1 CCAATATCTAGTCTTGTCAAAACTCGTTGGAAAGACAA
*
1764992 CTCAATATCTTGTCTTGTCAAAACTTC-TTGGAAAGAC
1 C-CAATATCTAGTCTTGTCAAAAC-TCGTTGGAAAGAC
1765029 CATCTGATAT
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
38 37 0.39
39 57 0.59
40 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (38 bp):
CCAATATCTAGTCTTGTCAAAACTCGTTGGAAAGACAA
Found at i:1765039 original size:39 final size:38
Alignment explanation
Indices: 1764879--1765052 Score: 154
Period size: 39 Copynumber: 4.5 Consensus size: 38
1764869 ATTTCAACCC
* * *
1764879 AATATATAGTCTTATCAAAACTTC-TTGGAAAGATAACCT
1 AATATCTAGTCTTGTCAAAAC-TCGTTGGAAAGACAA-CT
* * *
1764918 AATATCTAGTCTTGTCAAAACTCTTTGGGAAGACAACA
1 AATATCTAGTCTTGTCAAAACTCGTTGGAAAGACAACT
* * * *
1764956 AAAATCTAATCTTGTCAAAACTCGTTGGGAAGACAGCT
1 AATATCTAGTCTTGTCAAAACTCGTTGGAAAGACAACT
* *
1764994 CAATATCTTGTCTTGTCAAAACTTC-TTGGAAAGACCATCT
1 -AATATCTAGTCTTGTCAAAAC-TCGTTGGAAAGA-CAACT
* * *
1765034 GATATCTATTCTGGTCAAA
1 AATATCTAGTCTTGTCAAA
1765053 TCTCCTTGTT
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
38 36 0.32
39 70 0.62
40 6 0.05
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (38 bp):
AATATCTAGTCTTGTCAAAACTCGTTGGAAAGACAACT
Found at i:1768090 original size:30 final size:30
Alignment explanation
Indices: 1768051--1768110 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1768041 AGTAATGAAT
1768051 GAATAAAAATAAAACGAGTTTGACAATCGA
1 GAATAAAAATAAAACGAGTTTGACAATCGA
*
1768081 GAATGAAAATAAAACGAGTTTGACAATCGA
1 GAATAAAAATAAAACGAGTTTGACAATCGA
1768111 TTACGTGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.10, G:0.18, T:0.20
Consensus pattern (30 bp):
GAATAAAAATAAAACGAGTTTGACAATCGA
Found at i:1769117 original size:20 final size:20
Alignment explanation
Indices: 1769089--1769129 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1769079 AGCGCCTCAA
* *
1769089 TATCGATATTGACCTCTGGG
1 TATCAATATTAACCTCTGGG
1769109 TATCAATATTAACCTCTGGG
1 TATCAATATTAACCTCTGGG
1769129 T
1 T
1769130 GGTATCGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
TATCAATATTAACCTCTGGG
Found at i:1769532 original size:12 final size:13
Alignment explanation
Indices: 1769502--1769530 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1769492 TTTAAAACAT
1769502 AAAATTGAAAAAA
1 AAAATTGAAAAAA
1769515 AAAATTGAAAAAA
1 AAAATTGAAAAAA
1769528 AAA
1 AAA
1769531 TTTATTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAATTGAAAAAA
Found at i:1770355 original size:22 final size:21
Alignment explanation
Indices: 1770310--1770351 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1770300 ATAGTATAAC
1770310 AAGTGTATTGTAATATTTTTT
1 AAGTGTATTGTAATATTTTTT
1770331 AAGTGTATTGTAATATTTTTT
1 AAGTGTATTGTAATATTTTTT
1770352 TAAGGTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (21 bp):
AAGTGTATTGTAATATTTTTT
Found at i:1780363 original size:164 final size:164
Alignment explanation
Indices: 1780092--1780420 Score: 658
Period size: 164 Copynumber: 2.0 Consensus size: 164
1780082 TAATTTCTGG
1780092 ACAACCTCCTCGGATACTACATTCTCACAACTACCGCTGTCAATGATCATTTTGCAGACTTTATC
1 ACAACCTCCTCGGATACTACATTCTCACAACTACCGCTGTCAATGATCATTTTGCAGACTTTATC
1780157 TGCAACTGTGCAGGTCGTGTGGAAAATATTGGTTCTCAACCAATCGTCCCCTGAATCGCCTTTGG
66 TGCAACTGTGCAGGTCGTGTGGAAAATATTGGTTCTCAACCAATCGTCCCCTGAATCGCCTTTGG
1780222 GAGTAAGTAGACTCTTGCGAATGACCAGAGTCTC
131 GAGTAAGTAGACTCTTGCGAATGACCAGAGTCTC
1780256 ACAACCTCCTCGGATACTACATTCTCACAACTACCGCTGTCAATGATCATTTTGCAGACTTTATC
1 ACAACCTCCTCGGATACTACATTCTCACAACTACCGCTGTCAATGATCATTTTGCAGACTTTATC
1780321 TGCAACTGTGCAGGTCGTGTGGAAAATATTGGTTCTCAACCAATCGTCCCCTGAATCGCCTTTGG
66 TGCAACTGTGCAGGTCGTGTGGAAAATATTGGTTCTCAACCAATCGTCCCCTGAATCGCCTTTGG
1780386 GAGTAAGTAGACTCTTGCGAATGACCAGAGTCTC
131 GAGTAAGTAGACTCTTGCGAATGACCAGAGTCTC
1780420 A
1 A
1780421 TGACCATCTC
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 165 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (164 bp):
ACAACCTCCTCGGATACTACATTCTCACAACTACCGCTGTCAATGATCATTTTGCAGACTTTATC
TGCAACTGTGCAGGTCGTGTGGAAAATATTGGTTCTCAACCAATCGTCCCCTGAATCGCCTTTGG
GAGTAAGTAGACTCTTGCGAATGACCAGAGTCTC
Found at i:1784814 original size:82 final size:84
Alignment explanation
Indices: 1784521--1784889 Score: 532
Period size: 83 Copynumber: 4.4 Consensus size: 84
1784511 ATTTTTTTAA
* * * *
1784521 ATATATGGAATAATTATACTATTTGTTT-TCCACTTGTTTCCTTAATTTAAGCTATAGTGGTTTG
1 ATATATGAAATTATTATAATATTTGTTTCTCCACTTGTTTCCTTAATTTAAGCTATAGTGGTTTA
1784585 GTTTTTTATTGATTATAAT
66 GTTTTTTATTGATTATAAT
* * **
1784604 ATATAT-AGAATTATTATACTATTTGTTTC-CCACTTGTTTTCTTAATTTAAATTATAGTGGTTT
1 ATATATGA-AATTATTATAATATTTGTTTCTCCACTTGTTTCCTTAATTTAAGCTATAGTGGTTT
*
1784667 GGTTTTTTATTGATTATAAT
65 AGTTTTTTATTGATTATAAT
* *
1784687 ATATATATATAATTATTATAATATTTGTTTCCCCACTTGTTTCCTTAATTTAAGCTATAGTGGTT
1 ATATAT-GA-AATTATTATAATATTTGTTTCTCCACTTGTTTCCTTAATTTAAGCTATAGTGGTT
*
1784752 TAG-TTTTT-TTAATTATAAT
64 TAGTTTTTTATTGATTATAAT
*
1784771 ATATATGAAATTATTATAATATTTGTTTCTCCACTTATTTCCTTAATTTAAGCTATAGTGGTTTA
1 ATATATGAAATTATTATAATATTTGTTTCTCCACTTGTTTCCTTAATTTAAGCTATAGTGGTTTA
1784836 GTTTTTTATTGATTATAAT
66 GTTTTTTATTGATTATAAT
* * *
1784855 ATATATGGAATTATTGTAATATTTGTTTCTTCACT
1 ATATATGAAATTATTATAATATTTGTTTCTCCACT
1784890 CTCCCTAATG
Statistics
Matches: 260, Mismatches: 19, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
82 56 0.22
83 88 0.34
84 58 0.22
85 26 0.10
86 32 0.12
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (84 bp):
ATATATGAAATTATTATAATATTTGTTTCTCCACTTGTTTCCTTAATTTAAGCTATAGTGGTTTA
GTTTTTTATTGATTATAAT
Found at i:1785586 original size:15 final size:15
Alignment explanation
Indices: 1785566--1785598 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1785556 CGTAGGACCC
1785566 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
1785581 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
1785596 CTA
1 CTA
1785599 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:1785747 original size:23 final size:26
Alignment explanation
Indices: 1785710--1785778 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
1785700 TTCTCTTGTG
1785710 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
1785734 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
1785759 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
1785779 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:1785760 original size:12 final size:12
Alignment explanation
Indices: 1785743--1785778 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1785733 TATCATGTTC
1785743 TCATATCACATG
1 TCATATCACATG
*
1785755 TCATATCACATA
1 TCATATCACATG
1785767 TCATATCACATG
1 TCATATCACATG
1785779 AACATATATA
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:1786194 original size:64 final size:64
Alignment explanation
Indices: 1786086--1786207 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
1786076 TAATAAAGGT
* * *
1786086 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGT-TTCATTATTGCTGGG
* * * **
1786150 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATT
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTTTCATTATT
1786208 AAAAGAGTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 2 0.04
64 47 0.96
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTTTCATTATTGCTGGG
Found at i:1792130 original size:15 final size:15
Alignment explanation
Indices: 1792110--1792142 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1792100 CGTAAGACCC
1792110 CTACATCCCGAAAGA
1 CTACATCCCGAAAGA
*
1792125 CTACATCCCGAAGGA
1 CTACATCCCGAAAGA
1792140 CTA
1 CTA
1792143 TTATACCCTC
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:0.36, C:0.33, G:0.15, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAAGA
Found at i:1792306 original size:12 final size:12
Alignment explanation
Indices: 1792289--1792322 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1792279 TCATGTTCTT
1792289 ATATCACATGTC
1 ATATCACATGTC
*
1792301 ATATCACATATC
1 ATATCACATGTC
1792313 ATATCACATG
1 ATATCACATG
1792323 GACATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (12 bp):
ATATCACATGTC
Found at i:1792738 original size:64 final size:64
Alignment explanation
Indices: 1792630--1792751 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
1792620 TAATGAAGGT
* * *
1792630 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGT-TTCATTATTGCTGGG
* * * **
1792694 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATT
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTTTCATTATT
1792752 AAAAGAGTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 2 0.04
64 47 0.96
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTTTCATTATTGCTGGG
Found at i:1796097 original size:18 final size:19
Alignment explanation
Indices: 1796065--1796107 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1796055 ATTTTTAATA
1796065 AAAATATATAAAATAAATTT
1 AAAATATAT-AAATAAATTT
*
1796085 AAAATATAT-AATAATTTT
1 AAAATATATAAATAAATTT
1796103 AAAAT
1 AAAAT
1796108 TTTAGGAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.59
20 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATATATAAATAAATTT
Found at i:1798580 original size:2 final size:2
Alignment explanation
Indices: 1798573--1798597 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1798563 CGGAATTGTC
1798573 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1798598 ACTGCATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1801966 original size:18 final size:18
Alignment explanation
Indices: 1801914--1801958 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1801904 AACCCCATCT
*
1801914 GGAGTAATCGCTAGGTCG
1 GGAGTAATCGCTAGGCCG
*
1801932 GGAGTAGTCGCTAGGCCG
1 GGAGTAATCGCTAGGCCG
1801950 GGAGTAATC
1 GGAGTAATC
1801959 ACTCGGCCTA
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:0.22, C:0.18, G:0.40, T:0.20
Consensus pattern (18 bp):
GGAGTAATCGCTAGGCCG
Found at i:1802001 original size:39 final size:39
Alignment explanation
Indices: 1801957--1802045 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
1801947 CCGGGAGTAA
** *
1801957 TCACTCGGCCTATTACCCCATCTATGGCTGGAGTCATAG
1 TCACTCGGCCTATTACCCCATCTATAACTGGACTCATAG
*
1801996 TCACTCGGCCTATTACCCCATCTATAACTGGACTCGTAG
1 TCACTCGGCCTATTACCCCATCTATAACTGGACTCATAG
1802035 TCACTCGGCCT
1 TCACTCGGCCT
1802046 GTGACCAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (39 bp):
TCACTCGGCCTATTACCCCATCTATAACTGGACTCATAG
Found at i:1810834 original size:24 final size:23
Alignment explanation
Indices: 1810805--1810853 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
1810795 AAAAATTCAA
*
1810805 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTCAAGCTCGAG-CTC
1810829 GAGCTCGATTCAAGCTCGAGCTC
1 GAGCTCGATTCAAGCTCGAGCTC
1810852 GA
1 GA
1810854 TTAAAGCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGAGCTC
Found at i:1810848 original size:17 final size:17
Alignment explanation
Indices: 1810826--1810864 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1810816 AAGCTCGAGA
*
1810826 CTCGAGCTCGATTCAAG
1 CTCGAGCTCGATTAAAG
1810843 CTCGAGCTCGATTAAAG
1 CTCGAGCTCGATTAAAG
1810860 CTCGA
1 CTCGA
1810865 ACTCAAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (17 bp):
CTCGAGCTCGATTAAAG
Found at i:1811261 original size:26 final size:26
Alignment explanation
Indices: 1811225--1811311 Score: 138
Period size: 26 Copynumber: 3.3 Consensus size: 26
1811215 CCTGCAGACA
1811225 CACAAAACAAGGGACAGAGCACCAAG
1 CACAAAACAAGGGACAGAGCACCAAG
1811251 CACAAAACAAGGGACAGAGCACCAAG
1 CACAAAACAAGGGACAGAGCACCAAG
* * *
1811277 CAAAAAACAAGGGACAGAGAACCAAA
1 CACAAAACAAGGGACAGAGCACCAAG
1811303 CACCAAAAC
1 CA-CAAAAC
1811312 CAATACTAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
26 51 0.91
27 5 0.09
ACGTcount: A:0.54, C:0.26, G:0.20, T:0.00
Consensus pattern (26 bp):
CACAAAACAAGGGACAGAGCACCAAG
Found at i:1813014 original size:21 final size:21
Alignment explanation
Indices: 1812989--1813055 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1812979 TGGCATAACT
1812989 TAAACCCTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
* * *
1813010 TAAACTCTAA-ACTTTAAACCT
1 TAAACCCTAACAC-ATAAACCC
* * *
1813031 TAAATCCTATCACATAAACTC
1 TAAACCCTAACACATAAACCC
1813052 TAAA
1 TAAA
1813056 TCCCAAACCC
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCTAACACATAAACCC
Found at i:1813070 original size:42 final size:42
Alignment explanation
Indices: 1812987--1813074 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1812977 CATGGCATAA
* **
1812987 CTTAAACCCTAACACATAAACCCTAAACTCTAAACTTTAAAC
1 CTTAAACCCTAACACATAAACCCTAAACTCCAAACCCTAAAC
* * *
1813029 CTTAAATCCTATCACATAAACTCTAAA-TCCCAAACCCTAAAC
1 CTTAAACCCTAACACATAAACCCTAAACT-CCAAACCCTAAAC
1813071 CTTA
1 CTTA
1813075 TCACATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (42 bp):
CTTAAACCCTAACACATAAACCCTAAACTCCAAACCCTAAAC
Found at i:1813353 original size:14 final size:14
Alignment explanation
Indices: 1813336--1813376 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1813326 TTTATTCATC
1813336 AATAATGTATTTTT
1 AATAATGTATTTTT
1813350 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
1813361 AATAATGTAATTTT
1 AATAATGTATTTTT
1813375 AA
1 AA
1813377 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:1814134 original size:17 final size:18
Alignment explanation
Indices: 1814104--1814137 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1814094 TACCAAAAAA
1814104 AAAAAGCTCAAAATCCCT
1 AAAAAGCTCAAAATCCCT
*
1814122 AAAAATCTC-AAATCCC
1 AAAAAGCTCAAAATCCC
1814138 CAACCATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.29, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAAGCTCAAAATCCCT
Found at i:1814872 original size:2 final size:2
Alignment explanation
Indices: 1814865--1814950 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
1814855 TTAACTCTAC
1814865 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1814907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1814949 AT
1 AT
1814951 TTTTTTACGT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1815627 original size:19 final size:21
Alignment explanation
Indices: 1815603--1815648 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
1815593 GTTTCCAATT
*
1815603 TCGCAACGTGAA-GTA-AAAA
1 TCGCAACGCGAATGTAGAAAA
*
1815622 TCGCAACGCGAATTTAGAAAA
1 TCGCAACGCGAATGTAGAAAA
1815643 TCGCAA
1 TCGCAA
1815649 AATCGCGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 2 0.09
21 10 0.43
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAATGTAGAAAA
Found at i:1816023 original size:20 final size:20
Alignment explanation
Indices: 1815998--1816043 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1815988 CATATAGATT
* *
1815998 CGTTGCGATTTTACTATTTA
1 CGTTGCAATTTTACTATTCA
1816018 CGTTGCAATTTTACTATTCA
1 CGTTGCAATTTTACTATTCA
1816038 CGTTGC
1 CGTTGC
1816044 CAAATTGACT
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:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (20 bp):
CGTTGCAATTTTACTATTCA
Found at i:1816061 original size:20 final size:20
Alignment explanation
Indices: 1816018--1816248 Score: 138
Period size: 20 Copynumber: 11.8 Consensus size: 20
1816008 TTACTATTTA
* *
1816018 CGTTGC-AATTTTACTATTCA
1 CGTTGCGAATTTGACT-TTCG
* *
1816038 CGTTGCCAAATTGACTTTCG
1 CGTTGCGAATTTGACTTTCG
*
1816058 CGTTGCGAATTTGACTTTTG
1 CGTTGCGAATTTGACTTTCG
* * *
1816078 TGTTGCGAGTTTGACTATCG
1 CGTTGCGAATTTGACTTTCG
*
1816098 CGTTGCGAATTTGACTTTTG
1 CGTTGCGAATTTGACTTTCG
* * * *
1816118 TGTTACAAATTTGACTATCG
1 CGTTGCGAATTTGACTTTCG
*
1816138 CGTTGGGAATTTGACTTAT-G
1 CGTTGCGAATTTGACTT-TCG
* *
1816158 TGTTGC-AATTT-AC-AT-G
1 CGTTGCGAATTTGACTTTCG
** * *
1816174 -AAT-C-AGTTTTGACTATCG
1 CGTTGCGA-ATTTGACTTTCG
*
1816192 CGTTGCGAATTTGACTTTTG
1 CGTTGCGAATTTGACTTTCG
* * * *
1816212 TGTTACAAATTTGACTATCG
1 CGTTGCGAATTTGACTTTCG
*
1816232 CGTTGGGAATTTGACTT
1 CGTTGCGAATTTGACTT
1816249 CTGTGTTGCG
Statistics
Matches: 157, Mismatches: 45, Indels: 18
0.71 0.20 0.08
Matches are distributed among these distances:
14 2 0.01
15 4 0.03
16 4 0.03
17 2 0.01
18 3 0.02
19 6 0.04
20 127 0.81
21 9 0.06
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGAATTTGACTTTCG
Found at i:1816083 original size:40 final size:40
Alignment explanation
Indices: 1816039--1816163 Score: 171
Period size: 40 Copynumber: 3.1 Consensus size: 40
1816029 TACTATTCAC
*
1816039 GTTGCCAAATTGACTTTCGCGTTGCGAATTTGACTTTTGT
1 GTTGCCAAATTGACTATCGCGTTGCGAATTTGACTTTTGT
* **
1816079 GTTGCGAGTTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCCAAATTGACTATCGCGTTGCGAATTTGACTTTTGT
* * *
1816119 GTT-ACAAATTTGACTATCGCGTTGGGAATTTGACTTATGT
1 GTTGCCAAA-TTGACTATCGCGTTGCGAATTTGACTTTTGT
1816159 GTTGC
1 GTTGC
1816164 AATTTACATG
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.42
Consensus pattern (40 bp):
GTTGCCAAATTGACTATCGCGTTGCGAATTTGACTTTTGT
Found at i:1816205 original size:94 final size:94
Alignment explanation
Indices: 1816087--1816277 Score: 355
Period size: 94 Copynumber: 2.0 Consensus size: 94
1816077 GTGTTGCGAG
1816087 TTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTACAAATTTGACTATCGCGTTGGGAATTTGA
1 TTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTACAAATTTGACTATCGCGTTGGGAATTTGA
*
1816152 CTTATGTGTTGCAATTTACATGAATCAGT
66 CTTATGTGTTGCAATTTACAGGAATCAGT
1816181 TTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTACAAATTTGACTATCGCGTTGGGAATTTGA
1 TTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTACAAATTTGACTATCGCGTTGGGAATTTGA
* *
1816246 CTTCTGTGTTGCGATTTACAGGAATCAGT
66 CTTATGTGTTGCAATTTACAGGAATCAGT
1816275 TTT
1 TTT
1816278 TTCTTAATAT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (94 bp):
TTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTACAAATTTGACTATCGCGTTGGGAATTTGA
CTTATGTGTTGCAATTTACAGGAATCAGT
Found at i:1816564 original size:20 final size:21
Alignment explanation
Indices: 1816535--1816603 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
1816525 CATATAGATT
*
1816535 CGTTGCGA-TTTTACTATTTA
1 CGTTGCGATTTTTACTATTCA
*
1816555 CGTTGTGATTTTTACTATTCA
1 CGTTGCGATTTTTACTATTCA
* * *
1816576 CGTTGCGAATTTGACTA-TCG
1 CGTTGCGATTTTTACTATTCA
1816596 CGTTGCGA
1 CGTTGCGA
1816604 ATTTGACTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (21 bp):
CGTTGCGATTTTTACTATTCA
Found at i:1816624 original size:40 final size:40
Alignment explanation
Indices: 1816577--1816667 Score: 148
Period size: 40 Copynumber: 2.3 Consensus size: 40
1816567 TACTATTCAC
* *
1816577 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTAACTATCGCGTTGCGAATTTGACTTATGT
1816617 GTTGCGAATTTAACTATCGCGTTGCGAATTTGACTTATGT
1 GTTGCGAATTTAACTATCGCGTTGCGAATTTGACTTATGT
*
1816657 ATTGCG-ATTTA
1 GTTGCGAATTTA
1816668 CAGATTCGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 5 0.10
40 43 0.90
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (40 bp):
GTTGCGAATTTAACTATCGCGTTGCGAATTTGACTTATGT
Found at i:1816663 original size:20 final size:20
Alignment explanation
Indices: 1816576--1816651 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1816566 TTACTATTCA
1816576 CGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
* *
1816596 CGTTGCGAATTTGACTTTTG
1 CGTTGCGAATTTGACTATCG
* *
1816616 TGTTGCGAATTTAACTATCG
1 CGTTGCGAATTTGACTATCG
1816636 CGTTGCGAATTTGACT
1 CGTTGCGAATTTGACT
1816652 TATGTATTGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGAATTTGACTATCG
Found at i:1816725 original size:21 final size:21
Alignment explanation
Indices: 1816673--1816729 Score: 96
Period size: 22 Copynumber: 2.7 Consensus size: 21
1816663 ATTTACAGAT
1816673 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAATTTGGAAAA
*
1816694 TCACAAACGCGAATTTGGAAAA
1 TCGC-AACGCGAATTTGGAAAA
1816716 TCGCAACGCGAATT
1 TCGCAACGCGAATT
1816730 ACATATTCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 13 0.39
22 20 0.61
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAATTTGGAAAA
Found at i:1817222 original size:20 final size:20
Alignment explanation
Indices: 1817164--1817213 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
1817154 AATGGTCTGA
* * *
1817164 TGAATATCTGTCATGATCCGA
1 TGAATATCTGTCAT-TTTCGG
1817185 TGAATATCTGTCATTTTCGG
1 TGAATATCTGTCATTTTCGG
1817205 TGAATATCT
1 TGAATATCT
1817214 TCTTATTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (20 bp):
TGAATATCTGTCATTTTCGG
Found at i:1818287 original size:18 final size:19
Alignment explanation
Indices: 1818252--1818288 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1818242 CACGGAATGT
1818252 AAGATTATCAGTGAGAATAA
1 AAGATTATCAG-GAGAATAA
1818272 AAGATTATCA-GAGAATA
1 AAGATTATCAGGAGAATA
1818289 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGAGAATAA
Found at i:1820984 original size:15 final size:15
Alignment explanation
Indices: 1820966--1821008 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
1820956 TATGGATTTT
1820966 ATATCATAATTATCG
1 ATATCATAATTATCG
*
1820981 ATATCCA-AATTA-CT
1 ATAT-CATAATTATCG
1820995 ATATCATAATTATC
1 ATATCATAATTATC
1821009 TGATCTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 10 0.42
16 2 0.08
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (15 bp):
ATATCATAATTATCG
Found at i:1821005 original size:14 final size:15
Alignment explanation
Indices: 1820965--1821009 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1820955 TTATGGATTT
1820965 TATATCATAATTATC
1 TATATCATAATTATC
*
1820980 GATATCCA-AATTA-C
1 TATAT-CATAATTATC
1820994 TATATCATAATTATC
1 TATATCATAATTATC
1821009 T
1 T
1821010 GATCTATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
15 11 0.44
16 2 0.08
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (15 bp):
TATATCATAATTATC
Found at i:1831550 original size:39 final size:39
Alignment explanation
Indices: 1831485--1831615 Score: 115
Period size: 39 Copynumber: 3.4 Consensus size: 39
1831475 ACAGGTGTTC
* * *
1831485 CACGG-GTCTTCAAGTCAAATA-TGAAGACTCCGCGACTG
1 CACGGCGTCTTC-AGGCAAATAGAGAAGACCCCGCGACTG
* * * *
1831523 CATGGCGTCTTCAGGCTAATAGAGAAGACCCCACAACTG
1 CACGGCGTCTTCAGGCAAATAGAGAAGACCCCGCGACTG
** * * *
1831562 CACGATGTCTTCAGACAAATGGAGAAGACCCCAG-GAGTG
1 CACGGCGTCTTCAGGCAAATAGAGAAGACCCC-GCGACTG
1831601 CACGGCGTCTTCAGG
1 CACGGCGTCTTCAGG
1831616 TCAATAAGAA
Statistics
Matches: 71, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
38 11 0.15
39 60 0.85
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (39 bp):
CACGGCGTCTTCAGGCAAATAGAGAAGACCCCGCGACTG
Found at i:1834974 original size:14 final size:15
Alignment explanation
Indices: 1834955--1834993 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1834945 CCTTACAACA
1834955 AAATATTATTT-GTT
1 AAATATTATTTCGTT
* *
1834969 AAATATCATTTCTTT
1 AAATATTATTTCGTT
1834984 AAATATTATT
1 AAATATTATT
1834994 GATTTAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (15 bp):
AAATATTATTTCGTT
Found at i:1836986 original size:4 final size:4
Alignment explanation
Indices: 1836965--1837002 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
1836955 AAATTTGGTC
*
1836965 AAAT AATT AAAT --AT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1837003 TTACCTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:1837748 original size:2 final size:2
Alignment explanation
Indices: 1837683--1837731 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1837673 ACATTTGAGG
1837683 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
1837725 GA GA GA G
1 GA GA GA G
1837732 TTGAAGTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1851345 original size:253 final size:258
Alignment explanation
Indices: 1850860--1851358 Score: 617
Period size: 261 Copynumber: 1.9 Consensus size: 258
1850850 TTAAAATTTT
* * * * *
1850860 AAAAGGAAATGATAATTCAGCACTTTCAACACACAAATAACATTAGGGCCATGCAAAATAGACTG
1 AAAAGAAAATGATAATACAGCACTTTCAACACACAAATAACATCAGGGCCATACAAAACAGACTG
* * *
1850925 CAATATCAGCATGGCTCAGCTAAAACTTGCAATACCATTTAAACAAATAAAACAAAAAATAACAC
66 CAATATAAGCATGGCTCAGCTAAAACTTGCAATACCATTCAAACAAACAAAACAAAAAATAACAC
* * * * * *
1850990 AAATATATATATATATATATAACATTAAACTCTCGTTTATATTCTAGTAAAAGTTAAAGAGGGTC
131 -AACACATATATATATATAT-ACATTAAACTCTCGTTAATATCCCAGTAAAAGCTAAAGAGGGTC
* *
1851055 CAAGCTTAAGTTAGGTAAAGAAACTACAAAGAATAATCTGAAAGATGCCCAGAAATTCTACACAA
194 CAAGCTTAAGCTAGGTAAAGAAACTACAAAGAATAATCTGAAAGATACCCAGAAATTCTACACAA
*
1851120 AAAAGAAAATGATAATACAGCAC-TTCAACACACAAAAATAACATCATGGCCATACAAAACA-AC
1 AAAAGAAAATGATAATACAGCACTTTCAACACAC--AAATAACATCAGGGCCATACAAAACAGA-
* * *
1851183 CTGCAATATAAGCATGGCTGAGCTACAAC-TGCAATTACCATTCAATACAAACAAAAC-AAGAA-
63 CTGCAATATAAGCATGGCTCAGCTAAAACTTGCAA-TACCATTCAA-ACAAACAAAACAAAAAAT
* * * *
1851245 AGCAC-ACGCATATATATATCTAT-CATTAAATTCTCGTTAATATCCCAGTAAAAGCT-AA-A-G
126 AACACAACACATATATATATATATACATTAAACTCTCGTTAATATCCCAGTAAAAGCTAAAGAGG
1851305 G-CCTAAGCTTAAGCTAGGTAAAGAAA-TAACAAAGAATAATCTGAAAGATACCCA
191 GTCC-AAGCTTAAGCTAGGTAAAGAAACT-ACAAAGAATAATCTGAAAGATACCCA
1851359 ATATCCTATC
Statistics
Matches: 208, Mismatches: 24, Indels: 21
0.82 0.09 0.08
Matches are distributed among these distances:
252 3 0.01
253 48 0.23
254 1 0.00
255 2 0.01
256 28 0.13
258 14 0.07
259 10 0.05
260 31 0.15
261 61 0.29
262 10 0.05
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (258 bp):
AAAAGAAAATGATAATACAGCACTTTCAACACACAAATAACATCAGGGCCATACAAAACAGACTG
CAATATAAGCATGGCTCAGCTAAAACTTGCAATACCATTCAAACAAACAAAACAAAAAATAACAC
AACACATATATATATATATACATTAAACTCTCGTTAATATCCCAGTAAAAGCTAAAGAGGGTCCA
AGCTTAAGCTAGGTAAAGAAACTACAAAGAATAATCTGAAAGATACCCAGAAATTCTACACAA
Found at i:1859869 original size:15 final size:15
Alignment explanation
Indices: 1859834--1859868 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1859824 AAATAGAATG
1859834 ATAAAATAAACAAAA
1 ATAAAATAAACAAAA
*
1859849 ATAAAATAAA-AAAT
1 ATAAAATAAACAAAA
1859863 ATAAAA
1 ATAAAA
1859869 AAGGACCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (15 bp):
ATAAAATAAACAAAA
Found at i:1861067 original size:38 final size:38
Alignment explanation
Indices: 1860940--1861183 Score: 240
Period size: 38 Copynumber: 6.9 Consensus size: 38
1860930 ATACATATAT
* *
1860940 TTCAAAAATATTTTTTAAACTATATATTATAT---TTA
1 TTCAAAAATGTTTTTAAAACTATATATTATATAAGTTA
*
1860975 ---AAAAA-GTTTTCAAAAC--TATATTATAT-AGTT-
1 TTCAAAAATGTTTTTAAAACTATATATTATATAAGTTA
1861005 TTC-AAAATG-TTTT-AAA--A-ATATTATATAAGTT-
1 TTCAAAAATGTTTTTAAAACTATATATTATATAAGTTA
* * *
1861036 TTAAAAAACGTTTTTTAAAACTATATATTATATAATTTA
1 TTCAAAAATG-TTTTTAAAACTATATATTATATAAGTTA
*
1861075 TTCAAAAATGTTTTTAAAACTATATATTATATAATTTA
1 TTCAAAAATGTTTTTAAAACTATATATTATATAAGTTA
1861113 TTCAAAAATGTTTTTAAAACTATATATTATATAAGTT-
1 TTCAAAAATGTTTTTAAAACTATATATTATATAAGTTA
* *
1861150 TT-TAAAATGATTTTAAAACTATATGATATATATA
1 TTCAAAAATGTTTTTAAAACTATAT-AT-TATATA
1861184 TTTTCAAAAA
Statistics
Matches: 179, Mismatches: 12, Indels: 33
0.80 0.05 0.15
Matches are distributed among these distances:
29 10 0.06
30 9 0.05
31 19 0.11
32 17 0.09
33 1 0.01
34 4 0.02
35 3 0.02
36 20 0.11
37 5 0.03
38 83 0.46
39 8 0.04
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (38 bp):
TTCAAAAATGTTTTTAAAACTATATATTATATAAGTTA
Found at i:1864933 original size:165 final size:164
Alignment explanation
Indices: 1864519--1865336 Score: 1203
Period size: 164 Copynumber: 5.0 Consensus size: 164
1864509 ACCTGCCACC
*
1864519 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
**
1864584 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCGTAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAG
*
1864649 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTTACCA
*
1864683 AAGACCTTTGAGTTCGACTACGCTCAGCTCCTAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
*** * * *
1864748 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
66 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAG
* * * **
1864813 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
131 CATAACTCAAGGCTAGAAGGGTTATCTG-TTACCA
1864848 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* **
1864913 AAGGGCTATCTGCCAAAGACCCATAAGTTCGATTACACTCAGCTTCAAGGGCGTAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAG
*
1864978 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTTACCA
*
1865012 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACAACATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* *
1865077 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAG
*
1865142 CATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTTACC-A
* * * *
1865177 AAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * * * * * *
1865242 AAGGGTTATCTGCTAAA-AACCTGTGAGTTCGATTATATTCAACTT--AGAGGCA-AATCAAGTT
66 AAGGGCTATCTGCCAAAGACCCT-TAAGTTCGATTACACTCAGCTTCAAG-GGCACAA-C-A-TT
* * *
1865303 TACAGAATAGCTCAAGGCAAGAAGGGTTATCTGT
126 TACAGCATAACTCAAGGCTAGAAGGGTTATCTGT
1865337 CAATAAAATT
Statistics
Matches: 592, Mismatches: 55, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
163 3 0.01
164 312 0.53
165 244 0.41
166 33 0.06
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (164 bp):
AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAG
CATAACTCAAGGCTAGAAGGGTTATCTGTTACCA
Found at i:1865117 original size:329 final size:327
Alignment explanation
Indices: 1864478--1865254 Score: 1322
Period size: 329 Copynumber: 2.4 Consensus size: 327
1864468 TAAACAAACT
* * * *
1864478 ATTTGCAGCTTAGCTCAAGGTCAGAAGGGCTACCTGCCACC-AAGACCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAACTCAA-GTCAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGC
*
1864542 TCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCT
65 TCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCA
1864607 TAAGTTCGATTACACTCAGCTTCAAGGGCGTAACATTTACAGCATAACTCAAGGCTAGAAGGGTT
130 TAAGTTCGATTACACTCAGCTTCAAGGGCGTAACATTTACAGCATAACTCAAGGCTAGAAGGGTT
* *
1864672 ATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCTAGGCACATCATTTGCAGAATAG
195 ATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACAACATTTGCAGAATAG
*
1864737 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
260 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCAC
1864802 ATC
325 ATC
* *
1864805 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGTC-AGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACG
1864870 CTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
64 CTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
1864935 ATAAGTTCGATTACACTCAGCTTCAAGGGCGTAACATTTACAGCATAACTCAAGGCTAGAAGGGT
129 ATAAGTTCGATTACACTCAGCTTCAAGGGCGTAACATTTACAGCATAACTCAAGGCTAGAAGGGT
1865000 TATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACAACATTTGCAGAATA
194 TATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACAACATTTGCAGAATA
**
1865065 GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCGAGGGCA
259 GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCA
1865130 CATC
324 CATC
* * ** *
1865134 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCG
1 ATTTGCAGCATAACTCAAGTC-AGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACG
* * *
1865199 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGC
64 CTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGC
1865255 TAAAAACCTG
Statistics
Matches: 423, Mismatches: 23, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
326 3 0.01
327 29 0.07
328 6 0.01
329 385 0.91
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.24
Consensus pattern (327 bp):
ATTTGCAGCATAACTCAAGTCAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCT
CAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCAT
AAGTTCGATTACACTCAGCTTCAAGGGCGTAACATTTACAGCATAACTCAAGGCTAGAAGGGTTA
TCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACAACATTTGCAGAATAGC
TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACA
TC
Found at i:1866023 original size:38 final size:37
Alignment explanation
Indices: 1865934--1866188 Score: 242
Period size: 38 Copynumber: 7.2 Consensus size: 37
1865924 TTGCAAACGG
*
1865934 TTTTTG-AAAA-TATATATATCATATAGTTTTAAAATCA
1 TTTTTGAAAAATTATATA-AT-ATATAGTTTTAAAAACA
1865971 -TTTT-AAAAACTTATATAATATATAGTTTTAAAAACA
1 TTTTTGAAAAA-TTATATAATATATAGTTTTAAAAACA
1866007 TTTTTGAATAAATTATATAATATATAGTTTTAAAAACA
1 TTTTTGAA-AAATTATATAATATATAGTTTTAAAAACA
*
1866045 TTTTTGAATAAATTATATAATATATAGTTTTAAAAAACG
1 TTTTTGAA-AAATTATATAATATATAGTTTT-AAAAACA
* *
1866084 TTTTTTAAAACTTATAT-A-ATAT--TTTT-AAAACA
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
* *
1866116 -TTTTG-AAAACTATAT-A-ATATAGTTTTGAAAAC-
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
* * *
1866148 TTTTT---TAA--ATATAATATATAGTTTAAAAAATA
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
1866180 TTTTTGAAA
1 TTTTTGAAA
1866189 TATATGTATT
Statistics
Matches: 188, Mismatches: 13, Indels: 36
0.79 0.05 0.15
Matches are distributed among these distances:
29 4 0.02
30 14 0.07
31 19 0.10
32 14 0.07
33 9 0.05
34 4 0.02
36 28 0.15
37 7 0.04
38 73 0.39
39 16 0.09
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
Found at i:1866267 original size:15 final size:14
Alignment explanation
Indices: 1866232--1866260 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1866222 TTATTATTAT
1866232 TTATTTTCTTTTTA
1 TTATTTTCTTTTTA
1866246 TTATTTTCTTTTTA
1 TTATTTTCTTTTTA
1866260 T
1 T
1866261 GTTTTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTTCTTTTTA
Found at i:1869886 original size:22 final size:22
Alignment explanation
Indices: 1869854--1869917 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
1869844 CACACTGAAT
*
1869854 GCTGAACGGTTCAGCATTCAAC
1 GCTGAATGGTTCAGCATTCAAC
*
1869876 GCTGAATGGTTTAGCATTCAAC
1 GCTGAATGGTTCAGCATTCAAC
*
1869898 GCTGAATGGTTCAACATTCA
1 GCTGAATGGTTCAGCATTCA
1869918 GAGCTAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (22 bp):
GCTGAATGGTTCAGCATTCAAC
Found at i:1870623 original size:15 final size:15
Alignment explanation
Indices: 1870603--1870631 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1870593 AATAATCTAG
1870603 AAAAACCCTAAACCA
1 AAAAACCCTAAACCA
1870618 AAAAACCCTAAACC
1 AAAAACCCTAAACC
1870632 TAATTGACTC
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:0.34, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAAACCCTAAACCA
Found at i:1871162 original size:42 final size:44
Alignment explanation
Indices: 1871106--1871225 Score: 162
Period size: 43 Copynumber: 2.8 Consensus size: 44
1871096 GATCCGGATA
* *
1871106 TATTA-ATATTTTAAAATAATTAAA-AATATATTTTATAATCATT
1 TATTATAT-TTTTAAAATAATTAAATAATATATTTTATAATAACT
1871149 TATTAT-TTTTTAAAAT-ATTAAAATAATATATTTTATAATAACT
1 TATTATATTTTTAAAATAATT-AAATAATATATTTTATAATAACT
1871192 TATTATATTTTT--AATAATTAAATAATATATTTTA
1 TATTATATTTTTAAAATAATTAAATAATATATTTTA
1871226 ACATTATAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
41 3 0.04
42 30 0.43
43 32 0.46
44 5 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (44 bp):
TATTATATTTTTAAAATAATTAAATAATATATTTTATAATAACT
Found at i:1871266 original size:2 final size:2
Alignment explanation
Indices: 1871259--1871285 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1871249 AAAATCTTAA
1871259 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1871286 AAACCGGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1871574 original size:4 final size:4
Alignment explanation
Indices: 1871565--1871595 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1871555 GCAACATTTT
*
1871565 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1871596 ATAGTCGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:1871585 original size:16 final size:16
Alignment explanation
Indices: 1871564--1871595 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1871554 TGCAACATTT
1871564 TATACATACATACATA
1 TATACATACATACATA
1871580 TATACATACATACATA
1 TATACATACATACATA
1871596 ATAGTCGACA
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:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (16 bp):
TATACATACATACATA
Found at i:1876244 original size:31 final size:31
Alignment explanation
Indices: 1876209--1876312 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
1876199 TGATAAATTA
1876209 CACATGTCCAAAATGATGATATAACATATGT
1 CACATGTCCAAAATGATGATATAACATATGT
* *
1876240 CACATGTCTAAAATGATGACA-AAGCAT-TGT
1 CACATGTCCAAAATGATGATATAA-CATATGT
* ** * ** *
1876270 TATGTGT-CTAAGGGATGATATATCATATGT
1 CACATGTCCAAAATGATGATATAACATATGT
1876300 CACATGTCCAAAA
1 CACATGTCCAAAA
1876313 AACTATGTCA
Statistics
Matches: 53, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
29 11 0.21
30 17 0.32
31 25 0.47
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (31 bp):
CACATGTCCAAAATGATGATATAACATATGT
Done.