Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 21
Found at i:1368342 original size:23 final size:23
Alignment explanation
Indices: 1368316--1368362 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1368306 GAATTGAAAG
1368316 ATAATTTTATCCGCAGAATACCC
1 ATAATTTTATCCGCAGAATACCC
1368339 ATAATTTTATCCGCAGAATACCC
1 ATAATTTTATCCGCAGAATACCC
1368362 A
1 A
1368363 CTAACTCTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.30
Consensus pattern (23 bp):
ATAATTTTATCCGCAGAATACCC
Found at i:1371464 original size:3 final size:3
Alignment explanation
Indices: 1371458--1371505 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
1371448 TTTTTTTATT
* *
1371458 TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1371506 AACAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1371789 original size:76 final size:76
Alignment explanation
Indices: 1371663--1372121 Score: 823
Period size: 76 Copynumber: 6.0 Consensus size: 76
1371653 GGTCTTATGA
* * *
1371663 ATGACCCCG-AGGGTTTAAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGA-CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1371727 AAGGACTTACAG
65 AAGGACTTACAG
*
1371739 ATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1371804 AGGACTTACAG
66 AGGACTTACAG
*
1371815 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAATGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1371880 AGGACTTACAG
66 AGGACTTACAG
1371891 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1371956 AGGACTTACAG
66 AGGACTTACAG
1371967 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1372032 AGGACTTACAG
66 AGGACTTACAG
* *
1372043 ATGACCCTG-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTCTTGAAAACATCATGCACTG
1 ATGACCC-GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1372107 AAGGACTTACAG
65 AAGGACTTACAG
1372119 ATG
1 ATG
1372122 TGGGAAACAG
Statistics
Matches: 372, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
75 3 0.01
76 368 0.99
77 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (76 bp):
ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:1372822 original size:22 final size:22
Alignment explanation
Indices: 1372797--1372851 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1372787 TATAAAGTTT
*
1372797 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
1372819 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1372841 TCATCTTTGAA
1 TCATCTTTGAA
1372852 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1373323 original size:52 final size:54
Alignment explanation
Indices: 1373213--1373333 Score: 167
Period size: 54 Copynumber: 2.3 Consensus size: 54
1373203 TCAGAATAAC
***
1373213 ATGTTCGTAAAACATTTGACAGTGCATTCATCTTTTCCTGTGGCTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAG
* *
1373267 ATGTTCGTAAAACATTTGACAACACATTTAT-TTTT-TTGTGGCTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAG
*
1373319 ATGTTC-TCAAACATT
1 ATGTTCGTAAAACATT
1373334 GAAGCTCTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
51 8 0.13
52 22 0.36
53 4 0.07
54 27 0.44
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (54 bp):
ATGTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAG
Found at i:1375683 original size:114 final size:114
Alignment explanation
Indices: 1375472--1375697 Score: 389
Period size: 114 Copynumber: 2.0 Consensus size: 114
1375462 GATCATGCAG
*
1375472 TTCACCTTTCAATTCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCACCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1375537 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
1375586 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCACCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
1375651 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTATTATGAGCA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
1375698 CATGACACTT
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCACCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1378033 original size:26 final size:27
Alignment explanation
Indices: 1377996--1378049 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
1377986 TTCTTATTTT
1377996 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1378023 TTTTTCTTTTTT-CTTTCTTTGCTGGA
1 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1378049 T
1 T
1378050 GAGTACAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.04, C:0.17, G:0.11, T:0.69
Consensus pattern (27 bp):
TTTTTCTTTTTTCCTTTCTTTGCTGGA
Found at i:1382743 original size:20 final size:22
Alignment explanation
Indices: 1382691--1382743 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
1382681 TTAATATAAT
1382691 AATAAAT-AA-TAAAAATTTAA
1 AATAAATGAATTAAAAATTTAA
* *
1382711 AAGAAAAGAATTAAAAA-TT-A
1 AATAAATGAATTAAAAATTTAA
1382731 AATAAATGAATTA
1 AATAAATGAATTA
1382744 TTAATTTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 17 0.63
21 4 0.15
22 6 0.22
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (22 bp):
AATAAATGAATTAAAAATTTAA
Found at i:1384817 original size:3 final size:3
Alignment explanation
Indices: 1384811--1384858 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
1384801 TTTTTTTATT
* *
1384811 TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1384859 AACAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1388744 original size:23 final size:23
Alignment explanation
Indices: 1388718--1388792 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
1388708 TCAATAATAT
1388718 ATTTAGTATATAATTGAAAATGA
1 ATTTAGTATATAATTGAAAATGA
*
1388741 ATTTA--ACTCA-AAATGCAATAAT-A
1 ATTTAGTA-T-ATAATTG-AA-AATGA
1388764 TATTTAGTATATAATTGAAAATGA
1 -ATTTAGTATATAATTGAAAATGA
1388788 ATTTA
1 ATTTA
1388793 ACTCAAAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 18
0.67 0.03 0.30
Matches are distributed among these distances:
21 1 0.02
22 5 0.12
23 17 0.41
24 12 0.29
25 5 0.12
26 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (23 bp):
ATTTAGTATATAATTGAAAATGA
Found at i:1388811 original size:47 final size:47
Alignment explanation
Indices: 1388709--1388802 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
1388699 AACATATTTT
1388709 CAATAATATATTTAGTATATAATTGAAAATGAATTTAACTCAAAATG
1 CAATAATATATTTAGTATATAATTGAAAATGAATTTAACTCAAAATG
1388756 CAATAATATATTTAGTATATAATTGAAAATGAATTTAACTCAAAATG
1 CAATAATATATTTAGTATATAATTGAAAATGAATTTAACTCAAAATG
1388803 TTTGAATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (47 bp):
CAATAATATATTTAGTATATAATTGAAAATGAATTTAACTCAAAATG
Found at i:1389019 original size:37 final size:37
Alignment explanation
Indices: 1388966--1389038 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
1388956 ATTACTATTA
* *
1388966 TTTATTTGTTGTTTAAGACTTCTAGTATTTAATTTTT
1 TTTATTTGTTGCTTAAGACTTCTAATATTTAATTTTT
1389003 TTTATTTGTTGCTTAAGACTTCTAATATTTAATTTT
1 TTTATTTGTTGCTTAAGACTTCTAATATTTAATTTT
1389039 CTATTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.23, C:0.07, G:0.10, T:0.60
Consensus pattern (37 bp):
TTTATTTGTTGCTTAAGACTTCTAATATTTAATTTTT
Found at i:1389649 original size:31 final size:31
Alignment explanation
Indices: 1389611--1389703 Score: 120
Period size: 30 Copynumber: 3.0 Consensus size: 31
1389601 ATTAAGGGTA
*
1389611 TATGGTTCCTAACGTTATCGATCTGTTTGAT
1 TATGGTTCCTAACGTTATCGATCCGTTTGAT
* *
1389642 TATGGTTCC-AACATTATAGATCCGTTTGAT
1 TATGGTTCCTAACGTTATCGATCCGTTTGAT
1389672 TATGG-TCTCTAACGTTATCGATCC-TTTCGAT
1 TATGGTTC-CTAACGTTATCGATCCGTTT-GAT
1389703 T
1 T
1389704 TTAGTTTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
29 2 0.04
30 27 0.50
31 25 0.46
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (31 bp):
TATGGTTCCTAACGTTATCGATCCGTTTGAT
Found at i:1391096 original size:18 final size:18
Alignment explanation
Indices: 1391073--1391116 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1391063 TTAGGATTAT
*
1391073 CTTTAGGTGTTATATTTC
1 CTTTAGGTATTATATTTC
*
1391091 CTTTAGGTATTTTATTTC
1 CTTTAGGTATTATATTTC
1391109 CTTTAGGT
1 CTTTAGGT
1391117 TGTCTCAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (18 bp):
CTTTAGGTATTATATTTC
Found at i:1396546 original size:21 final size:20
Alignment explanation
Indices: 1396503--1396546 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1396493 CTGTAAAAAA
* *
1396503 TTACCTAAAATATTATTTTT
1 TTACCTAAAACATTATGTTT
1396523 TTACCTAAAACATTAATGTTT
1 TTACCTAAAACATT-ATGTTT
1396544 TTA
1 TTA
1396547 ATATTTCCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.50
Consensus pattern (20 bp):
TTACCTAAAACATTATGTTT
Found at i:1398466 original size:7 final size:6
Alignment explanation
Indices: 1398438--1398463 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1398428 TATTTTTATT
1398438 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
1398464 ATATAACGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:1398602 original size:17 final size:16
Alignment explanation
Indices: 1398572--1398604 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1398562 TTTAGGAGTC
1398572 TAAAAGTTTATTTTTT
1 TAAAAGTTTATTTTTT
1398588 TAAATAGTTT-TTTTTT
1 TAAA-AGTTTATTTTTT
1398604 T
1 T
1398605 GAATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TAAAAGTTTATTTTTT
Found at i:1400064 original size:10 final size:10
Alignment explanation
Indices: 1400051--1400083 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1400041 GAAAGGAAGG
1400051 AAAAGAAAAT
1 AAAAGAAAAT
*
1400061 AAAA-ATAAT
1 AAAAGAAAAT
1400070 AAAAGAAAAT
1 AAAAGAAAAT
1400080 AAAA
1 AAAA
1400084 ATATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:1400101 original size:18 final size:19
Alignment explanation
Indices: 1400051--1400091 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1400041 GAAAGGAAGG
1400051 AAAAGAAAATAAAAATAAT
1 AAAAGAAAATAAAAATAAT
*
1400070 AAAAGAAAATAAAAATATT
1 AAAAGAAAATAAAAATAAT
1400089 AAA
1 AAA
1400092 TAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (19 bp):
AAAAGAAAATAAAAATAAT
Found at i:1401669 original size:20 final size:21
Alignment explanation
Indices: 1401627--1401673 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
1401617 TCCTACAAAA
1401627 AATAA-AATAAAGAAATTATT
1 AATAATAATAAAGAAATTATT
*
1401647 AATAATAATAAATAAATTA-T
1 AATAATAATAAAGAAATTATT
1401667 AATAATA
1 AATAATA
1401674 GAAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AATAATAATAAAGAAATTATT
Found at i:1402119 original size:36 final size:36
Alignment explanation
Indices: 1402072--1402177 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
1402062 CAAAGATTGG
1402072 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
1402108 TGTTTCAAGGGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
1402144 TGTTTCAAGAGAAACCGTCTCAAGAGAGGCAAAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1402178 CTTAGTTTTG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.23
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1402153 original size:21 final size:21
Alignment explanation
Indices: 1402091--1402154 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
1402081 GGAAACTGTC
*
1402091 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGGGACAAAATTTGTT
* *
1402112 TC-A-AGGG---AAA-CTGTC
1 TCAAGAGGGACAAAATTTGTT
1402127 TCAAGAGGGACAAAATTTGTT
1 TCAAGAGGGACAAAATTTGTT
1402148 TCAAGAG
1 TCAAGAG
1402155 AAACCGTCTC
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
15 5 0.16
16 4 0.12
17 4 0.12
19 3 0.09
20 4 0.12
21 12 0.38
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (21 bp):
TCAAGAGGGACAAAATTTGTT
Found at i:1402925 original size:105 final size:105
Alignment explanation
Indices: 1402319--1403833 Score: 2654
Period size: 105 Copynumber: 14.4 Consensus size: 105
1402309 AGTTGAAAGT
* * *
1402319 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
1402384 CCTTTGCTATGAAGTTGAAATTGACTCTGAAATT-AGGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGA-GAAA
* * *
1402424 TTGTTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATA
1 -TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* * *
1402489 TCCTTCGTTGTGAAGTTGAAATTGGCTCAGAAATTGAGAAGT
65 TCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAA-A
1402531 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
1402596 CCTTCGTTGTGAAGTTGAAATTGGCTCAGAAATTGAGAAGT
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAA-A
*
1402637 TGTTTGTTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
1402702 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAA-A
1402743 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1402808 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
* *
1402848 TGTTTGTTGACAATCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
**
1402913 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCAAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
*
1402953 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
1403018 CCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
1403058 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1403123 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
1403163 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1403228 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
*
1403268 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
1403333 CCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
1403373 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1403438 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
1403478 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1403543 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
1403583 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1403648 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
*
1403688 TGTTTGTTGACAACCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
1403753 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
1403793 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
1403834 ATCCGCTCTC
Statistics
Matches: 1361, Mismatches: 46, Indels: 5
0.96 0.03 0.00
Matches are distributed among these distances:
105 957 0.70
106 403 0.30
107 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
CCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
Found at i:1407538 original size:20 final size:20
Alignment explanation
Indices: 1407515--1407556 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1407505 GAAAGGAAGG
1407515 AAAAGAAAATAAAAATAATA
1 AAAAGAAAATAAAAATAATA
*
1407535 AAAAGAAAATAAAAATATTA
1 AAAAGAAAATAAAAATAATA
1407555 AA
1 AA
1407557 TAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (20 bp):
AAAAGAAAATAAAAATAATA
Found at i:1407565 original size:29 final size:28
Alignment explanation
Indices: 1407476--1407588 Score: 72
Period size: 29 Copynumber: 3.9 Consensus size: 28
1407466 AATGTTAGAT
*
1407476 AAAAGATAAAAGATAAATATTAAATAAATGA
1 AAAAGA-AAAA-A-AAATATTAAATAAATTA
* *
1407507 AAGGAAGGAAAAGAAAATA-AAAAT-AA-TA
1 AA--AA-GAAAAAAAAATATTAAATAAATTA
1407535 AAAAGAAAATAAAAATATTAAATAAATTA
1 AAAAGAAAA-AAAAATATTAAATAAATTA
* * *
1407564 AAAGGGAAAGAAAAATAAT-AATAAA
1 AAA-AGAAAAAAAAATATTAAATAAA
1407589 AAGAAGTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
25 5 0.08
26 8 0.12
27 4 0.06
28 11 0.17
29 15 0.23
30 8 0.12
31 7 0.11
32 1 0.02
33 5 0.08
34 2 0.03
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (28 bp):
AAAAGAAAAAAAAATATTAAATAAATTA
Found at i:1409133 original size:20 final size:21
Alignment explanation
Indices: 1409091--1409137 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
1409081 TCCTACAAAA
1409091 AATAA-AATAAAGAAATTATT
1 AATAATAATAAAGAAATTATT
*
1409111 AATAATAATAAATAAATTA-T
1 AATAATAATAAAGAAATTATT
1409131 AATAATA
1 AATAATA
1409138 GAAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AATAATAATAAAGAAATTATT
Found at i:1411953 original size:120 final size:119
Alignment explanation
Indices: 1411726--1411964 Score: 419
Period size: 120 Copynumber: 2.0 Consensus size: 119
1411716 AGGAGAAAAC
* *
1411726 AATGATAATTCTCTCTAGATAAAAAAGGAGAAACCAACTCTCAAGAAACTCTCTAAAATCTCTCT
1 AATGATAATTCTCTCTAGATAAAAAAAGAGAAAACAACTCTCAAGAAACTCTCTAAAATCTCTCT
1411791 AGTATTGGAAGAAAGCTAGAATGCTTTGGGATGATTTTGAAGCTAAATGAGCTA
66 AGTATTGGAAGAAAGCTAGAATGCTTTGGGATGATTTTGAAGCTAAATGAGCTA
1411845 AATGATAATTCTCTCTAGATAAAAAAAAAGAGAAAACAACTCTCAAGAAACTCTCT-AAAT-TCT
1 AATGATAATTCTCTCTAGAT--AAAAAAAGAGAAAACAACTCTCAAGAAACTCTCTAAAATCTCT
1411908 CTAGTATTTGGAAGAAAGCTAGAATGCTTTGGGATGATTTTGAAGCTAAATGAGCTA
64 CTAGTA-TTGGAAGAAAGCTAGAATGCTTTGGGATGATTTTGAAGCTAAATGAGCTA
1411965 GGGTATTTAT
Statistics
Matches: 115, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
119 29 0.25
120 54 0.47
121 32 0.28
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (119 bp):
AATGATAATTCTCTCTAGATAAAAAAAGAGAAAACAACTCTCAAGAAACTCTCTAAAATCTCTCT
AGTATTGGAAGAAAGCTAGAATGCTTTGGGATGATTTTGAAGCTAAATGAGCTA
Found at i:1416700 original size:118 final size:119
Alignment explanation
Indices: 1416471--1416707 Score: 417
Period size: 118 Copynumber: 2.0 Consensus size: 119
1416461 AAGGAGAAAC
*
1416471 AATGATAATTCTCTCTAGATAAAAAAAGAGAAAACAACTCTCAAGAAACTCTCTAAAATCTCTCT
1 AATGATAATTCTCTCTAAATAAAAAAAGAGAAAACAACTCTCAAGAAACTCTCTAAAATCTCTCT
*
1416536 AGTATTGGAAGAAATCTAGAATGTTTTGGGATGATTTTGAAGCTAAATGAGCTA
66 AGTATTGGAAGAAAGCTAGAATGTTTTGGGATGATTTTGAAGCTAAATGAGCTA
1416590 AATGATAATTCTCTCTAAAT-AAAAAAGAAGAAAACAACTCTCAAGAAACTCTCT-AAAT-TCTC
1 AATGATAATTCTCTCTAAATAAAAAAAG-AGAAAACAACTCTCAAGAAACTCTCTAAAATCTCTC
1416652 TAGTATTTGGAAGAAAGCTAGAATGTTTTGGGATGATTTTGAAGCTAAATGAGCTA
65 TAGTA-TTGGAAGAAAGCTAGAATGTTTTGGGATGATTTTGAAGCTAAATGAGCTA
1416708 GGGTATTTAT
Statistics
Matches: 114, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
117 9 0.08
118 60 0.53
119 45 0.39
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (119 bp):
AATGATAATTCTCTCTAAATAAAAAAAGAGAAAACAACTCTCAAGAAACTCTCTAAAATCTCTCT
AGTATTGGAAGAAAGCTAGAATGTTTTGGGATGATTTTGAAGCTAAATGAGCTA
Found at i:1416854 original size:12 final size:12
Alignment explanation
Indices: 1416837--1416861 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1416827 ACAAAGCACC
1416837 ATTTGGTGCCTA
1 ATTTGGTGCCTA
1416849 ATTTGGTGCCTA
1 ATTTGGTGCCTA
1416861 A
1 A
1416862 ATTATTTGAC
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:1423206 original size:21 final size:21
Alignment explanation
Indices: 1423089--1423206 Score: 71
Period size: 21 Copynumber: 5.7 Consensus size: 21
1423079 ACGCGAAATA
**
1423089 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
1423109 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
1423129 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
1423150 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
1423171 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
*
1423192 AGAATCGCAACGCGA
1 AAAATCGCAACGCGA
1423207 ACACATAAAT
Statistics
Matches: 71, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.34
21 44 0.62
22 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:1423235 original size:20 final size:20
Alignment explanation
Indices: 1423194--1423402 Score: 226
Period size: 20 Copynumber: 10.4 Consensus size: 20
1423184 GATTTTCCAG
* *
1423194 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1423214 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1423234 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1423254 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1423274 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1423294 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1423314 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
** * *
1423334 AATCGCAACTAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1423354 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1423374 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1423394 AATCACAAC
1 AATCGCAAC
1423403 ACTGAAATTT
Statistics
Matches: 161, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.01
20 158 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1423943 original size:20 final size:20
Alignment explanation
Indices: 1423918--1424103 Score: 232
Period size: 20 Copynumber: 9.3 Consensus size: 20
1423908 AGAAGTAGTA
*
1423918 CGCAACGCGTATCCGTAAAC
1 CGCAACGCGTATCCGTAAAT
*
1423938 CGCAACGTGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
1423958 CGCAACGCGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
*
1423978 CGCAATGCGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
*
1423998 CGCAACGTGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
*
1424018 CGCAACG-ATAATCCGTAAAT
1 CGCAACGCGT-ATCCGTAAAT
* * *
1424038 CGCAACGAGAATCTGTAAAT
1 CGCAACGCGTATCCGTAAAT
*
1424058 CGCAACG-ATAATCCGTAAAT
1 CGCAACGCGT-ATCCGTAAAT
* * *
1424078 CGCAACGAGAATCTGTAAAT
1 CGCAACGCGTATCCGTAAAT
1424098 CGCAAC
1 CGCAAC
1424104 ACTGAAATTT
Statistics
Matches: 146, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 145 0.99
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
CGCAACGCGTATCCGTAAAT
Found at i:1424560 original size:701 final size:701
Alignment explanation
Indices: 1423217--1424618 Score: 2723
Period size: 701 Copynumber: 2.0 Consensus size: 701
1423207 ACACATAAAT
1423217 CGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTAAATAGCAACGCGTATCCGTAAATCGCAA
1 CGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTAAATAGCAACGCGTATCCGTAAATCGCAA
*
1423282 TGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACTAGA
66 TGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGA
1423347 ATCTGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCACAACACTGAAATT
131 ATCTGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCACAACACTGAAATT
*
1423412 TTGGGTATATAACTACGCAACAGCAGCAAATCATAAACTAAATCCCTAAATCGTAACTCATTCCA
196 TTGGGTATATAACTACGCAACAGCAGCAAATCATAAACTAAATCCCTAAATCGCAACTCATTCCA
1423477 TCTCCATCTATCACTCTCTCCGGCGACATCCGTTCCTATATCCAACGACATCCTTCCCAATCCGG
261 TCTCCATCTATCACTCTCTCCGGCGACATCCGTTCCTATATCCAACGACATCCTTCCCAATCCGG
1423542 CAACAGGTTTTAGTTTCGCAGCTCGTCTGTTTAGTAAATTAATTTACAACCATGAAATCATCTAA
326 CAACAGGTTTTAGTTTCGCAGCTCGTCTGTTTAGTAAATTAATTTACAACCATGAAATCATCTAA
1423607 TGTTGATCATGTTTGGATAGATTTGTGTTTTGGAGGGTCATGGGAGAATGTTCATGGTGTTTTAC
391 TGTTGATCATGTTTGGATAGATTTGTGTTTTGGAGGGTCATGGGAGAATGTTCATGGTGTTTTAC
*
1423672 AATATATGCCTTTACCCATGAATCTTCAACTAAAATTGTCTTTACAAACGTTAACTTATGAAACT
456 AATATATGCCTTTACCCATGAATCTTCAACTAAAATTGTCTTTACAAAAGTTAACTTATGAAACT
1423737 CTAATGCTACGTGTTTCAAAGAAATTGAATTTAGAGCCCCTAAGTGGATTTAGGCTATCTTATCA
521 CTAATGCTACGTGTTTCAAAGAAATTGAATTTAGAGCCCCTAAGTGGATTTAGGCTATCTTATCA
*
1423802 GAGAAATGGTAAAGTTTATTTGTTAACCGACAATGAAGATGTTGAACGATTCATTGCTTACATTA
586 GAGAAATGATAAAGTTTATTTGTTAACCGACAATGAAGATGTTGAACGATTCATTGCTTACATTA
1423867 GTGTTTCACAAGATGATGTTACATTGTATGTTGTTGAACCTAGAAGTAGTA
651 GTGTTTCACAAGATGATGTTACATTGTATGTTGTTGAACCTAGAAGTAGTA
*
1423918 CGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAA
1 CGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTAAATAGCAACGCGTATCCGTAAATCGCAA
*
1423983 TGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGA
66 TGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGA
*
1424048 ATCTGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACACTGAAATT
131 ATCTGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCACAACACTGAAATT
*
1424113 TTGGGTATATAACTACGCAACAGCAGCAAATCATAAACTAAATCCCTAAATCGCAACTCATTCTA
196 TTGGGTATATAACTACGCAACAGCAGCAAATCATAAACTAAATCCCTAAATCGCAACTCATTCCA
1424178 TCTCCATCTATCACTCTCTCCGGCGACATCCGTTCCTATATCCAACGACATCCTTCCCAATCCGG
261 TCTCCATCTATCACTCTCTCCGGCGACATCCGTTCCTATATCCAACGACATCCTTCCCAATCCGG
1424243 CAACAGGTTTTAGTTTCGCAGCTCGTCTGTTTAGTAAATTAATTTACAACCATGAAATCATCTAA
326 CAACAGGTTTTAGTTTCGCAGCTCGTCTGTTTAGTAAATTAATTTACAACCATGAAATCATCTAA
*
1424308 TGTTGATCATGTTTGGATAGATTTGTGTTTTGGAGGGTCATGGGATAATGTTCATGGTGTTTTAC
391 TGTTGATCATGTTTGGATAGATTTGTGTTTTGGAGGGTCATGGGAGAATGTTCATGGTGTTTTAC
1424373 AATATATGCCTTTACCCATGAATCTTCAACTAAAATTGTCTTTACAAAAGTTAACTTATGAAACT
456 AATATATGCCTTTACCCATGAATCTTCAACTAAAATTGTCTTTACAAAAGTTAACTTATGAAACT
1424438 CTAATGCTACGTGTTTCAAAGAAATTGAATTTAGAGCCCCTAAGTGGATTTAGGCTATCTTATCA
521 CTAATGCTACGTGTTTCAAAGAAATTGAATTTAGAGCCCCTAAGTGGATTTAGGCTATCTTATCA
1424503 GAGAAATGATAAAGTTTATTTGTTAACCGACAATGAAGATGTTGAACGATTCATTGCTTACATTA
586 GAGAAATGATAAAGTTTATTTGTTAACCGACAATGAAGATGTTGAACGATTCATTGCTTACATTA
1424568 GTGTTTCACAAGATGATGTTACATTGTATGTTGTTGAACCTAGAAGTAGTA
651 GTGTTTCACAAGATGATGTTACATTGTATGTTGTTGAACCTAGAAGTAGTA
1424619 TTGTTGGGTC
Statistics
Matches: 692, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
701 692 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (701 bp):
CGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTAAATAGCAACGCGTATCCGTAAATCGCAA
TGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGA
ATCTGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCACAACACTGAAATT
TTGGGTATATAACTACGCAACAGCAGCAAATCATAAACTAAATCCCTAAATCGCAACTCATTCCA
TCTCCATCTATCACTCTCTCCGGCGACATCCGTTCCTATATCCAACGACATCCTTCCCAATCCGG
CAACAGGTTTTAGTTTCGCAGCTCGTCTGTTTAGTAAATTAATTTACAACCATGAAATCATCTAA
TGTTGATCATGTTTGGATAGATTTGTGTTTTGGAGGGTCATGGGAGAATGTTCATGGTGTTTTAC
AATATATGCCTTTACCCATGAATCTTCAACTAAAATTGTCTTTACAAAAGTTAACTTATGAAACT
CTAATGCTACGTGTTTCAAAGAAATTGAATTTAGAGCCCCTAAGTGGATTTAGGCTATCTTATCA
GAGAAATGATAAAGTTTATTTGTTAACCGACAATGAAGATGTTGAACGATTCATTGCTTACATTA
GTGTTTCACAAGATGATGTTACATTGTATGTTGTTGAACCTAGAAGTAGTA
Found at i:1424835 original size:24 final size:24
Alignment explanation
Indices: 1424796--1424842 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1424786 AAATTTGGTC
1424796 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1424820 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1424843 GACGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1425034 original size:12 final size:12
Alignment explanation
Indices: 1425017--1425041 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1425007 ATATAATCCT
1425017 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1425029 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1425041 G
1 G
1425042 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1427412 original size:19 final size:19
Alignment explanation
Indices: 1427344--1427533 Score: 187
Period size: 19 Copynumber: 10.7 Consensus size: 19
1427334 GCAACGAGAG
1427344 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
1427362 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1427376 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1427396 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1427415 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1427429 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1427449 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1427468 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1427482 AATCACAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1427502 AATCGCATTGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1427521 AATCGCATTGCGA
1 AATCGCAATGCGA
1427534 TTCTCTCGTT
Statistics
Matches: 144, Mismatches: 9, Indels: 37
0.76 0.05 0.19
Matches are distributed among these distances:
13 3 0.02
14 27 0.19
15 2 0.01
16 4 0.03
17 6 0.04
18 7 0.05
19 55 0.38
20 40 0.28
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1427441 original size:53 final size:53
Alignment explanation
Indices: 1427344--1427527 Score: 309
Period size: 53 Copynumber: 3.5 Consensus size: 53
1427334 GCAACGAGAG
* *
1427344 AATCGCAATGCGAAATG-AAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
1427396 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
1427449 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
1427502 AATCGCATTGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
1427528 TTGCGATTCT
Statistics
Matches: 126, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
52 17 0.13
53 108 0.86
54 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:1427564 original size:53 final size:52
Alignment explanation
Indices: 1427507--1427619 Score: 154
Period size: 53 Copynumber: 2.2 Consensus size: 52
1427497 ATGAAAATCG
1427507 CATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCA
1 CATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CA
** ** ** *
1427560 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 CATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCA
1427612 CATTGCGA
1 CATTGCGA
1427620 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
52 9 0.17
53 44 0.83
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (52 bp):
CATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCA
Found at i:1427634 original size:53 final size:53
Alignment explanation
Indices: 1427523--1427640 Score: 211
Period size: 53 Copynumber: 2.2 Consensus size: 53
1427513 GAAATGAAAA
1427523 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCACATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCACATTGCGATTTTCATT
*
1427576 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCACATTGCGATTTTCATT
1427628 TCCGCATTGCGAT
1 T-CGCATTGCGAT
1427641 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 18 0.29
53 45 0.71
ACGTcount: A:0.14, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCACATTGCGATTTTCATT
Found at i:1427648 original size:20 final size:19
Alignment explanation
Indices: 1427542--1427640 Score: 127
Period size: 20 Copynumber: 5.4 Consensus size: 19
1427532 GATTCTCTCG
*
1427542 TTGCGATTTTCATTTCCACA
1 TTGCGATTTTCATTT-CGCA
1427562 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1427581 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1427595 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1427614 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1427634 TTGCGAT
1 TTGCGAT
1427641 AGTCATTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 24 0.34
20 26 0.37
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1427766 original size:14 final size:14
Alignment explanation
Indices: 1427747--1427783 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1427737 CATCAATTAA
1427747 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1427761 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1427775 ACAAATCAA
1 ACAAATCAA
1427784 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1427863 original size:11 final size:11
Alignment explanation
Indices: 1427847--1427880 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1427837 ATCAACTTTT
1427847 ACAATCAATTA
1 ACAATCAATTA
**
1427858 ACAATCAAAAA
1 ACAATCAATTA
1427869 ACAATCAATTA
1 ACAATCAATTA
1427880 A
1 A
1427881 ACTATTGAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAATCAATTA
Found at i:1429742 original size:19 final size:19
Alignment explanation
Indices: 1429700--1429871 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
1429690 TAGTTTACTT
* *
1429700 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
1429720 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
1429739 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
1429758 TCGCAACGCGAAA-CCAAA
1 TCGCAACGCGAAATGAAAA
1429776 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1429795 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1429809 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1429828 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
1429842 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1429861 TCGCAATGCGA
1 TCGCAACGCGA
1429872 TTTTGGTTTC
Statistics
Matches: 125, Mismatches: 16, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.06
17 7 0.06
18 18 0.14
19 62 0.50
20 12 0.10
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1429812 original size:14 final size:14
Alignment explanation
Indices: 1429793--1429849 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1429783 GCGAAATGAA
*
1429793 AATCGCAACGACAG
1 AATCGCAACGAAAG
1429807 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
1429824 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
1429840 AATCGCAACG
1 AATCGCAACG
1429850 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1429820 original size:33 final size:33
Alignment explanation
Indices: 1429774--1429866 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1429764 CGCGAAACCA
1429774 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
1429807 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1429840 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1429867 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:1429902 original size:14 final size:14
Alignment explanation
Indices: 1429883--1429941 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1429873 TTTGGTTTCG
1429883 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1429897 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
1429914 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
1429930 CGTTGCGATTTT
1 CGTTGCGATTTT
1429942 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1429909 original size:33 final size:33
Alignment explanation
Indices: 1429867--1429990 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
1429857 AAAATCGCAA
*
1429867 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1429900 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
1429933 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
1429966 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
1429991 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1429921 original size:19 final size:18
Alignment explanation
Indices: 1429867--1429958 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
1429857 AAAATCGCAA
1429867 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1429886 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
1429900 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
1429919 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
1429933 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1429952 TGCGATT
1 TGCGATT
1429959 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1429968 original size:14 final size:14
Alignment explanation
Indices: 1429916--1429972 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1429906 TTTGGTTTCG
*
1429916 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
1429930 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1429949 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1429963 CGTTGCGATT
1 CGTTGCGATT
1429973 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1431939 original size:20 final size:20
Alignment explanation
Indices: 1431909--1432015 Score: 104
Period size: 19 Copynumber: 5.7 Consensus size: 20
1431899 CTTTGGTTGA
1431909 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
**
1431929 AATGACTATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1431949 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
1431968 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
* *
1431983 AATGAAAATCGTAACGCGA-
1 AATGAAAATCGCAACGAGAG
1432002 AATGAAAATCGCAA
1 AATGAAAATCGCAA
1432016 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 28 0.38
20 18 0.24
21 13 0.18
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1431960 original size:21 final size:21
Alignment explanation
Indices: 1431907--1431971 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
1431897 GTCTTTGGTT
1431907 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
**
1431928 G-AATGACTATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1431948 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1431969 GAA
1 GAA
1431972 TCGCAACGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 18 0.46
21 21 0.54
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1432053 original size:14 final size:14
Alignment explanation
Indices: 1432034--1432088 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1432024 TGGTTTCGCA
1432034 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1432048 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
1432067 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
1432081 TTGCGATT
1 TTGCGATT
1432089 TTCATTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1432064 original size:33 final size:33
Alignment explanation
Indices: 1432016--1432095 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1432006 AAAATCGCAA
**
1432016 TGCGATTTTGGTTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1432049 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1432082 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1432096 TTCTCGTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1432101 original size:21 final size:21
Alignment explanation
Indices: 1432076--1432149 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1432066 GTTGCGATTC
1432076 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
1432097 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
1432118 TCGCGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
1432139 TCTCGTTGCGA
1 TCTCGTTGCGA
1432150 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:1432271 original size:33 final size:33
Alignment explanation
Indices: 1432229--1432299 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
1432219 AATACTAACT
1432229 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
*
1432262 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1432295 TGAAA
1 TGAAA
1432300 TCTAAGTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1432275 original size:19 final size:19
Alignment explanation
Indices: 1432251--1432299 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 19
1432241 CGAGAGAATA
1432251 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
1432270 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
1432284 GCAACGCGAAATGAAA
1 GCAACGCGAAATGAAA
1432300 TCTAAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 10
0.66 0.06 0.29
Matches are distributed among these distances:
14 10 0.43
15 1 0.04
16 2 0.09
17 2 0.09
18 1 0.04
19 7 0.30
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.08
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:1432285 original size:14 final size:14
Alignment explanation
Indices: 1432233--1432289 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1432223 CTAACTTGAA
1432233 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
1432247 AATAGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1432266 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1432280 AATCGCAACG
1 AATCGCAACG
1432290 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.21, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1432696 original size:20 final size:20
Alignment explanation
Indices: 1432671--1432863 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
1432661 CTTTAAAAAT
1432671 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1432691 CGCGTTGCGATTTTACGCAT-
1 CGCGTTGCGA-TTTACGGATA
*
1432711 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1432732 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1432752 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1432772 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1432792 CACGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
1432812 CGCGTTGTGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1432832 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1432852 CGCGTTGCGATT
1 CGCGTTGCGATT
1432864 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1445515 original size:14 final size:14
Alignment explanation
Indices: 1445493--1445537 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1445483 CTGGGCATCT
*
1445493 GAGGCCATCCGACC
1 GAGGGCATCCGACC
1445507 GAGGGCATCCGACC
1 GAGGGCATCCGACC
*
1445521 GA-GGCTATCCGAGC
1 GAGGGC-ATCCGACC
1445535 GAG
1 GAG
1445538 CTATGCGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 3 0.11
14 24 0.89
ACGTcount: A:0.22, C:0.33, G:0.36, T:0.09
Consensus pattern (14 bp):
GAGGGCATCCGACC
Found at i:1446868 original size:22 final size:21
Alignment explanation
Indices: 1446829--1446886 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
1446819 ATATATATAT
* *
1446829 TTCATATATATATTAAAATTAAA
1 TTCA-ATAT-TATAAAAATAAAA
1446852 TTCAATATGTATAAAAATAAAA
1 TTCAATAT-TATAAAAATAAAA
*
1446874 TTTAATATTATAA
1 TTCAATATTATAA
1446887 TAGATTCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 5 0.16
22 22 0.71
23 4 0.13
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (21 bp):
TTCAATATTATAAAAATAAAA
Found at i:1446899 original size:17 final size:17
Alignment explanation
Indices: 1446871--1447019 Score: 117
Period size: 17 Copynumber: 8.4 Consensus size: 17
1446861 TATAAAAATA
1446871 AAATTTAATATTATAAT
1 AAATTTAATATTATAAT
* * *
1446888 AGATTCAATATTTTGAAATT
1 AAATTTAATATTAT--AA-T
1446908 AAATTTAATATTATAAT
1 AAATTTAATATTATAAT
1446925 AAATTTAATATGTATAAAAAT
1 AAATTTAATAT-TAT---AAT
*
1446946 ATATTTAATATTATAAT
1 AAATTTAATATTATAAT
* *
1446963 AATTTTAATTATTTTTAAATT
1 AAATTTAA-TA-TTAT-AA-T
1446984 AAATTTAATATTATAAT
1 AAATTTAATATTATAAT
1447001 --ATTT-ATATTA-AAT
1 AAATTTAATATTATAAT
1447014 AAATTT
1 AAATTT
1447020 TATTTTAAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 28
0.73 0.08 0.19
Matches are distributed among these distances:
13 3 0.03
14 6 0.06
15 8 0.07
17 33 0.31
18 9 0.08
19 8 0.07
20 19 0.18
21 21 0.20
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATTTAATATTATAAT
Found at i:1446935 original size:76 final size:76
Alignment explanation
Indices: 1446838--1447001 Score: 242
Period size: 76 Copynumber: 2.1 Consensus size: 76
1446828 TTTCATATAT
*
1446838 ATATTAAAATTAAATTCAATATGTATAAAAATAAAATTTAATATTATAATAGA-TTCAA-TATTT
1 ATATTATAA-TAAATTCAATATGTATAAAAAT-AAATTTAATATTATAATA-ATTTCAATTATTT
1446901 TGAAATTAAATTTA
63 TGAAATTAAATTTA
* * * *
1446915 ATATTATAATAAATTTAATATGTATAAAAATATATTTAATATTATAATAATTTTAATTATTTTTA
1 ATATTATAATAAATTCAATATGTATAAAAATAAATTTAATATTATAATAATTTCAATTATTTTGA
1446980 AATTAAATTTA
66 AATTAAATTTA
1446991 ATATTATAATA
1 ATATTATAATA
1447002 TTTATATTAA
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
74 1 0.01
75 21 0.26
76 50 0.62
77 8 0.10
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (76 bp):
ATATTATAATAAATTCAATATGTATAAAAATAAATTTAATATTATAATAATTTCAATTATTTTGA
AATTAAATTTA
Found at i:1446961 original size:38 final size:37
Alignment explanation
Indices: 1446838--1447001 Score: 175
Period size: 38 Copynumber: 4.3 Consensus size: 37
1446828 TTTCATATAT
*
1446838 ATATTAAAATTAAATTCAATATGTATAAAAATAAAATTTA
1 ATATTATAA-TAAATTCAATAT-TATAAAAAT-AAATTTA
* * * *
1446878 ATATTATAATAGATTCAATATTTTGAAATTAAATTTA
1 ATATTATAATAAATTCAATATTATAAAAATAAATTTA
* *
1446915 ATATTATAATAAATTTAATATGTATAAAAATATATTTA
1 ATATTATAATAAATTCAATAT-TATAAAAATAAATTTA
* * * * *
1446953 ATATTATAATAATTTTAATTATTTTTAAATTAAATTTA
1 ATATTATAATAAATTCAA-TATTATAAAAATAAATTTA
1446991 ATATTATAATA
1 ATATTATAATA
1447002 TTTATATTAA
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
37 26 0.25
38 58 0.55
39 14 0.13
40 8 0.08
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (37 bp):
ATATTATAATAAATTCAATATTATAAAAATAAATTTA
Found at i:1448807 original size:17 final size:17
Alignment explanation
Indices: 1448754--1448815 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 17
1448744 GAAATATAAG
*
1448754 TTCAAAC-ATCCATAAA
1 TTCAAACAATCCACAAA
*
1448770 TTCAAACAAAT--TCAAA
1 TTCAAAC-AATCCACAAA
*
1448786 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
1448803 TTCAAACATTCCA
1 TTCAAACAATCCA
1448816 AATATCCAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
15 3 0.08
16 16 0.44
17 15 0.42
18 2 0.06
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:1450699 original size:22 final size:22
Alignment explanation
Indices: 1450619--1450700 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
1450609 GAACCCCAGA
* *
1450619 GGGGTATCGATTCCCCTACAGG
1 GGGGTATCGATTCCCCTTCAAG
* * * * *
1450641 GGGGGATCGGTTACTCTTCAAAA
1 GGGGTATCGATTCCCCTTC-AAG
* * *
1450664 GGGGAATTGGTTCCCCTTCAAG
1 GGGGTATCGATTCCCCTTCAAG
1450686 GGGGTATCGATTCCC
1 GGGGTATCGATTCCC
1450701 TCTGCACCGA
Statistics
Matches: 44, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
22 28 0.64
23 16 0.36
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.26
Consensus pattern (22 bp):
GGGGTATCGATTCCCCTTCAAG
Found at i:1455461 original size:20 final size:19
Alignment explanation
Indices: 1455438--1455497 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 19
1455428 AGAACCCCAG
*
1455438 GGGGGTATCGATTCCCCTA
1 GGGGGAATCGATTCCCCTA
*
1455457 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-T---A
*
1455480 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
1455498 TCAAGGGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 15 0.43
20 1 0.03
22 1 0.03
23 18 0.51
ACGTcount: A:0.17, C:0.27, G:0.33, T:0.23
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCTA
Found at i:1455503 original size:22 final size:23
Alignment explanation
Indices: 1455456--1455505 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1455446 CGATTCCCCT
1455456 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
1455479 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
1455501 AGGGG
1 AGGGG
1455506 TGTCGATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.20, C:0.24, G:0.36, T:0.20
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:1455515 original size:21 final size:22
Alignment explanation
Indices: 1455456--1455516 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
1455446 CGATTCCCCT
*
1455456 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGG-ATCGATTCCCCTTCAA
*
1455479 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGG-ATCGATTCCCCTTCAA
1455501 AGGGGTG-TCGATTCCC
1 AGGGG-GATCGATTCCC
1455517 TCTGCCCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 8 0.22
22 6 0.17
23 22 0.61
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (22 bp):
AGGGGGATCGATTCCCCTTCAA
Found at i:1464129 original size:22 final size:21
Alignment explanation
Indices: 1464088--1464127 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1464078 GTGCTTATTT
*
1464088 TCATTTTTCAATTTTGAAACG
1 TCATTTTTCAATTTTAAAACG
1464109 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1464128 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACG
Found at i:1472616 original size:21 final size:21
Alignment explanation
Indices: 1472590--1472646 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
1472580 CATGTACATA
*
1472590 TATCATCTACT-TTCTTAGCAT
1 TATCATCTA-TATTATTAGCAT
* *
1472611 TATCATATATATTATTATCAT
1 TATCATCTATATTATTAGCAT
*
1472632 TATCATC-ACATTATT
1 TATCATCTATATTATT
1472647 TATCACATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.49
Consensus pattern (21 bp):
TATCATCTATATTATTAGCAT
Found at i:1472904 original size:23 final size:23
Alignment explanation
Indices: 1472873--1472917 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1472863 CACCACATCT
*
1472873 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
*
1472896 CGTAGAAATGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1472918 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1477167 original size:21 final size:21
Alignment explanation
Indices: 1477142--1477197 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
1477132 TACATATATC
*
1477142 ATCATCTACT-TTCTTAGCATT
1 ATCATCTA-TATTATTAGCATT
* *
1477163 ATCATATATATTATTATCATT
1 ATCATCTATATTATTAGCATT
*
1477184 ATCATC-ACATTATT
1 ATCATCTATATTATT
1477198 TATCACATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.48
Consensus pattern (21 bp):
ATCATCTATATTATTAGCATT
Found at i:1477458 original size:23 final size:23
Alignment explanation
Indices: 1477427--1477517 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
1477417 CACCACAGCT
*
1477427 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1477450 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCG
* *
1477473 CGTAGAATTGCACCAAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
*
1477496 CGTAGAAATGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1477518 ATATAATAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1477909 original size:18 final size:20
Alignment explanation
Indices: 1477886--1477924 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1477876 CTTATACCAT
*
1477886 TACAT-AAT-TCATTTAACA
1 TACATAAATATCATGTAACA
1477904 TACATAAATATCATGTAACA
1 TACATAAATATCATGTAACA
1477924 T
1 T
1477925 TATAATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 10 0.56
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (20 bp):
TACATAAATATCATGTAACA
Found at i:1480300 original size:23 final size:23
Alignment explanation
Indices: 1480256--1480300 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1480246 AATTACTATT
* *
1480256 ATTCTTTAATTTCTTTTAATTTG
1 ATTCTTAAATTTCTTTAAATTTG
1480279 ATTCTTAAATTT-TTTAATATTT
1 ATTCTTAAATTTCTTTAA-ATTT
1480301 TTAACAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTCTTAAATTTCTTTAAATTTG
Found at i:1481347 original size:11 final size:11
Alignment explanation
Indices: 1481333--1481365 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1481323 ATTGGTTGCT
1481333 GATAGAATTGA
1 GATAGAATTGA
1481344 GATAGAATTGA
1 GATAGAATTGA
*
1481355 GATAAAATTGA
1 GATAGAATTGA
1481366 ATTGCTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.27
Consensus pattern (11 bp):
GATAGAATTGA
Found at i:1487690 original size:9 final size:9
Alignment explanation
Indices: 1487676--1487732 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
1487666 TTCAGATGAT
1487676 ACAGCAGCA
1 ACAGCAGCA
1487685 ACAGCAGCA
1 ACAGCAGCA
*
1487694 GCAGCAATTGCA
1 ACAGC-A--GCA
* *
1487706 ACAACAACA
1 ACAGCAGCA
1487715 ACAGCAGCA
1 ACAGCAGCA
*
1487724 GCAGCAGCA
1 ACAGCAGCA
1487733 GCCATCGCAG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
9 30 0.79
10 1 0.03
11 1 0.03
12 6 0.16
ACGTcount: A:0.44, C:0.32, G:0.21, T:0.04
Consensus pattern (9 bp):
ACAGCAGCA
Found at i:1488247 original size:15 final size:15
Alignment explanation
Indices: 1488229--1488257 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1488219 TTACATGAAC
1488229 CAGCAGCAGCAACAA
1 CAGCAGCAGCAACAA
1488244 CAGCAGCAGCAACA
1 CAGCAGCAGCAACA
1488258 GTTGCAATTG
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:0.34, G:0.21, T:0.00
Consensus pattern (15 bp):
CAGCAGCAGCAACAA
Found at i:1488270 original size:18 final size:18
Alignment explanation
Indices: 1488249--1488305 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
1488239 AACAACAGCA
1488249 GCAGCAACAGTTGCAATT
1 GCAGCAACAGTTGCAATT
*
1488267 GCAGCAACA---AC-A--
1 GCAGCAACAGTTGCAATT
1488279 GCAGCAACAGTTGCAATT
1 GCAGCAACAGTTGCAATT
1488297 GCAGCAACA
1 GCAGCAACA
1488306 ACAGCAACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
12 9 0.29
14 1 0.03
15 2 0.06
16 1 0.03
18 18 0.58
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (18 bp):
GCAGCAACAGTTGCAATT
Found at i:1488281 original size:30 final size:30
Alignment explanation
Indices: 1488241--1488329 Score: 148
Period size: 30 Copynumber: 3.1 Consensus size: 30
1488231 GCAGCAGCAA
*
1488241 CAACAGCAGCAGCAACAGTTGCAATTGCAG
1 CAACAACAGCAGCAACAGTTGCAATTGCAG
1488271 CAACAACAGCAGCAACAGTTGCAATTGCAG
1 CAACAACAGCAGCAACAGTTGCAATTGCAG
1488301 CAAC-A-A-CAGCAACAGTTGCAATTGCAG
1 CAACAACAGCAGCAACAGTTGCAATTGCAG
1488328 CA
1 CA
1488330 GCAGCTGCAT
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
27 23 0.40
28 1 0.02
29 1 0.02
30 33 0.57
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.13
Consensus pattern (30 bp):
CAACAACAGCAGCAACAGTTGCAATTGCAG
Found at i:1488285 original size:21 final size:21
Alignment explanation
Indices: 1488246--1488285 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1488236 AGCAACAACA
* **
1488246 GCAGCAGCAACAGTTGCAATT
1 GCAGCAACAACAGCAGCAATT
1488267 GCAGCAACAACAGCAGCAA
1 GCAGCAACAACAGCAGCAA
1488286 CAGTTGCAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.28, G:0.23, T:0.10
Consensus pattern (21 bp):
GCAGCAACAACAGCAGCAATT
Found at i:1488304 original size:27 final size:27
Alignment explanation
Indices: 1488247--1488334 Score: 131
Period size: 27 Copynumber: 3.1 Consensus size: 27
1488237 GCAACAACAG
1488247 CAGCAGCAACAGTTGCAATTGCAGCAACAA
1 CAGCAGCAACAGTTGCAATTGCAG---CAA
1488277 CAGCAGCAACAGTTGCAATTGCAGCAA
1 CAGCAGCAACAGTTGCAATTGCAGCAA
* *
1488304 CAACAGCAACAGTTGCAATTGCAGCAG
1 CAGCAGCAACAGTTGCAATTGCAGCAA
1488331 CAGC
1 CAGC
1488335 TGCATCAACG
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
27 31 0.56
30 24 0.44
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.14
Consensus pattern (27 bp):
CAGCAGCAACAGTTGCAATTGCAGCAA
Found at i:1488372 original size:24 final size:24
Alignment explanation
Indices: 1488331--1488404 Score: 58
Period size: 27 Copynumber: 2.9 Consensus size: 24
1488321 ATTGCAGCAG
* * *
1488331 CAGCTGCATCAACGGCAACAACAA
1 CAGCTGCAGCAGCAGCAACAACAA
1488355 CAGCTGCAGCAGCAGCAATTACAACAA
1 CAGCTGCAGCAGCAGC-A--ACAACAA
* * *
1488382 CAACCGCAGCAGCAAGAAACAAC
1 CAGCTGCAGCAGC-AGCAACAAC
1488405 CTCACCACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
24 13 0.32
25 6 0.15
27 19 0.47
28 2 0.05
ACGTcount: A:0.43, C:0.32, G:0.18, T:0.07
Consensus pattern (24 bp):
CAGCTGCAGCAGCAGCAACAACAA
Found at i:1494142 original size:52 final size:52
Alignment explanation
Indices: 1494085--1494184 Score: 191
Period size: 52 Copynumber: 1.9 Consensus size: 52
1494075 CGGCTCTGGG
1494085 TATTTTTTGGCCCAGGGCGAAATAAAAGAAATGGGCCTCTATTTATGTTCTT
1 TATTTTTTGGCCCAGGGCGAAATAAAAGAAATGGGCCTCTATTTATGTTCTT
*
1494137 TATTTTTTGGCTCAGGGCGAAATAAAAGAAATGGGCCTCTATTTATGT
1 TATTTTTTGGCCCAGGGCGAAATAAAAGAAATGGGCCTCTATTTATGT
1494185 GATATTAACA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (52 bp):
TATTTTTTGGCCCAGGGCGAAATAAAAGAAATGGGCCTCTATTTATGTTCTT
Found at i:1499483 original size:7 final size:7
Alignment explanation
Indices: 1499471--1499508 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1499461 GTCAAAGAAA
1499471 GTCAACG
1 GTCAACG
1499478 GTCAACG
1 GTCAACG
1499485 GTCAACG
1 GTCAACG
1499492 GTCAACG
1 GTCAACG
1499499 GTCAACG
1 GTCAACG
1499506 GTC
1 GTC
1499509 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1499520 original size:17 final size:17
Alignment explanation
Indices: 1499498--1499538 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1499488 AACGGTCAAC
*
1499498 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1499515 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1499532 GGTCAAC
1 GGTCAAC
1499539 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1499556 original size:19 final size:19
Alignment explanation
Indices: 1499532--1499621 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
1499522 AGTCGGGTCG
*
1499532 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1499551 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1499570 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* * *
1499589 GGTCAAACTGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
1499609 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1499622 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 48 0.76
20 14 0.22
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1499570 original size:10 final size:10
Alignment explanation
Indices: 1499534--1499621 Score: 85
Period size: 9 Copynumber: 9.1 Consensus size: 10
1499524 TCGGGTCGGG
*
1499534 TCAACCCGGT
1 TCAAACCGGT
*
1499544 TCAGACCGG-
1 TCAAACCGGT
1499553 TCAAACCGGT
1 TCAAACCGGT
*
1499563 TCAGACCGG-
1 TCAAACCGGT
1499572 TCAAACCGGT
1 TCAAACCGGT
*
1499582 TCGAACCGG-
1 TCAAACCGGT
*
1499591 TCAAACTGGT
1 TCAAACCGGT
*
1499601 TCAAAACTGG-
1 TC-AAACCGGT
1499611 TCAAACCGGT
1 TCAAACCGGT
1499621 T
1 T
1499622 TTCCAGCAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 29 0.45
10 28 0.44
11 7 0.11
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1499588 original size:29 final size:30
Alignment explanation
Indices: 1499540--1499621 Score: 57
Period size: 29 Copynumber: 2.8 Consensus size: 30
1499530 CGGGTCAACC
*
1499540 CGGTTCAGACCGGTC-AAACCGGTTCAGAC
1 CGGTTCAGACCGGTCAAAACCGGTTCAAAC
* *
1499569 CGG-TCAAACCGGTTC-GAACCGG-TCAAAC
1 CGGTTCAGACCGG-TCAAAACCGGTTCAAAC
* * *
1499597 TGGTTCAAAACTGGTC-AAACCGGTT
1 CGGTTC-AGACCGGTCAAAACCGGTT
1499622 TTCCAGCAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 15 0.35
29 21 0.49
30 7 0.16
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.20
Consensus pattern (30 bp):
CGGTTCAGACCGGTCAAAACCGGTTCAAAC
Found at i:1500661 original size:18 final size:19
Alignment explanation
Indices: 1500624--1500662 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1500614 CAATGCTCTC
*
1500624 AAACAAAGTATTCAAAAGA
1 AAACAAAGTAATCAAAAGA
*
1500643 AAACAAA-TAATCAAGAGA
1 AAACAAAGTAATCAAAAGA
1500661 AA
1 AA
1500663 TTTGACTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.13
Consensus pattern (19 bp):
AAACAAAGTAATCAAAAGA
Found at i:1500859 original size:224 final size:224
Alignment explanation
Indices: 1500469--1500918 Score: 891
Period size: 224 Copynumber: 2.0 Consensus size: 224
1500459 TATCAGACTG
1500469 CTTGTGAAGATATTGATAGAAACTTGACCAACCCTTTTTAACATGAGGGGCCCGATACAAGAGTG
1 CTTGTGAAGATATTGATAGAAACTTGACCAACCCTTTTTAACATGAGGGGCCCGATACAAGAGTG
1500534 TCATCTTTTAACAATTCAATCACTTTCAGTCCTTCACCCGAGTAGGGTTTTCACAAAATAATCCA
66 TCATCTTTTAACAATTCAATCACTTTCAGTCCTTCACCCGAGTAGGGTTTTCACAAAATAATCCA
1500599 CTTGTAAAGGAAACTCAATGCTCTCAAACAAAGTATTCAAAAGAAAACAAATAATCAAGAGAAAT
131 CTTGTAAAGGAAACTCAATGCTCTCAAACAAAGTATTCAAAAGAAAACAAATAATCAAGAGAAAT
1500664 TTGACTAAATCTCTAAGTCTCAACGGTGA
196 TTGACTAAATCTCTAAGTCTCAACGGTGA
*
1500693 CTTGTGAAGATATTGATAGAAACTTGACCAGCCCTTTTTAACATGAGGGGCCCGATACAAGAGTG
1 CTTGTGAAGATATTGATAGAAACTTGACCAACCCTTTTTAACATGAGGGGCCCGATACAAGAGTG
1500758 TCATCTTTTAACAATTCAATCACTTTCAGTCCTTCACCCGAGTAGGGTTTTCACAAAATAATCCA
66 TCATCTTTTAACAATTCAATCACTTTCAGTCCTTCACCCGAGTAGGGTTTTCACAAAATAATCCA
1500823 CTTGTAAAGGAAACTCAATGCTCTCAAACAAAGTATTCAAAAGAAAACAAATAATCAAGAGAAAT
131 CTTGTAAAGGAAACTCAATGCTCTCAAACAAAGTATTCAAAAGAAAACAAATAATCAAGAGAAAT
1500888 TTGACTAAATCTCTAAGTCTCAACGGTGA
196 TTGACTAAATCTCTAAGTCTCAACGGTGA
1500917 CT
1 CT
1500919 ACGGACAAAC
Statistics
Matches: 225, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 225 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (224 bp):
CTTGTGAAGATATTGATAGAAACTTGACCAACCCTTTTTAACATGAGGGGCCCGATACAAGAGTG
TCATCTTTTAACAATTCAATCACTTTCAGTCCTTCACCCGAGTAGGGTTTTCACAAAATAATCCA
CTTGTAAAGGAAACTCAATGCTCTCAAACAAAGTATTCAAAAGAAAACAAATAATCAAGAGAAAT
TTGACTAAATCTCTAAGTCTCAACGGTGA
Found at i:1500885 original size:18 final size:19
Alignment explanation
Indices: 1500848--1500886 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1500838 CAATGCTCTC
*
1500848 AAACAAAGTATTCAAAAGA
1 AAACAAAGTAATCAAAAGA
*
1500867 AAACAAA-TAATCAAGAGA
1 AAACAAAGTAATCAAAAGA
1500885 AA
1 AA
1500887 TTTGACTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.13
Consensus pattern (19 bp):
AAACAAAGTAATCAAAAGA
Found at i:1504183 original size:65 final size:64
Alignment explanation
Indices: 1504084--1504219 Score: 184
Period size: 65 Copynumber: 2.1 Consensus size: 64
1504074 CGCACCCATT
* * * * *
1504084 TCGAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGGTGCACTCTTGAATATTTTGAAACA
1 TCGAATGCATTTTGTATACCGATACACAAGCCATGCATCGATGCACTCTCGAAT-CTTTGAAACA
* *
1504149 TCGAATGCATTTTGTATACTGATACAC-AGACCATGCATCGATGCACTCTCGACTCTTTGAAACA
1 TCGAATGCATTTTGTATACCGATACACAAG-CCATGCATCGATGCACTCTCGAATCTTTGAAACA
1504213 TCGAATG
1 TCGAATG
1504220 TAATTAGTGT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 18 0.29
65 45 0.71
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (64 bp):
TCGAATGCATTTTGTATACCGATACACAAGCCATGCATCGATGCACTCTCGAATCTTTGAAACA
Found at i:1505099 original size:39 final size:39
Alignment explanation
Indices: 1505000--1505103 Score: 154
Period size: 39 Copynumber: 2.7 Consensus size: 39
1504990 CTTGGCAACC
* ** *
1505000 AATTTCAACAAAAGATGCACCAACAAGTTTGACCAACAA
1 AATTTCAACAAATGATGCACCTGCAAGTTTAACCAACAA
* *
1505039 AATTTCAACAAATAATGCACCTGCAAGTTTAACGAACAA
1 AATTTCAACAAATGATGCACCTGCAAGTTTAACCAACAA
1505078 AATTTCAACAAATGATGCACCTGCAA
1 AATTTCAACAAATGATGCACCTGCAA
1505104 TTTTGGCCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.21
Consensus pattern (39 bp):
AATTTCAACAAATGATGCACCTGCAAGTTTAACCAACAA
Found at i:1506724 original size:118 final size:114
Alignment explanation
Indices: 1506529--1506764 Score: 330
Period size: 118 Copynumber: 2.0 Consensus size: 114
1506519 GGGCCTCTAA
* * *
1506529 TTTTTATATTTAAAATTAAGGCCCTAATTTTTATAATTTCATGAAATTTTAATTTTTAACTCTTT
1 TTTTTATATTTAAAATTAAGGCCCTAATTTTTATAAATTCATAAAATTTTAATTTTTAACTCCTT
*
1506594 TTTCCATTTCTCTTACTAATTCATCCAATTTTGAATTAAATTTAACCAAT
66 TTTCAATTTCTCTTACTAATTCATCCAATTTTGAATTAAATTTAACC-AT
* *
1506644 TTTTTATATTTATAAA-TAAGGCCCCTACTTTTTATAAATTCATAAAATGTTTAATTTTTTACCT
1 TTTTTATATTTA-AAATTAAGG-CCCTAATTTTTATAAATTCATAAAAT-TTTAA-TTTTTAACT
* * * *
1506708 CCTTTTTCAATTTCTCTTATTTATTCATTCAATTTTGAATTAAATTTAATCAT
62 CCTTTTTCAATTTCTCTTACTAATTCATCCAATTTTGAATTAAATTTAACCAT
1506761 TTTT
1 TTTT
1506765 CTTTTCTTTT
Statistics
Matches: 107, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
115 17 0.16
116 26 0.24
117 11 0.10
118 53 0.50
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.52
Consensus pattern (114 bp):
TTTTTATATTTAAAATTAAGGCCCTAATTTTTATAAATTCATAAAATTTTAATTTTTAACTCCTT
TTTCAATTTCTCTTACTAATTCATCCAATTTTGAATTAAATTTAACCAT
Found at i:1510006 original size:20 final size:20
Alignment explanation
Indices: 1509958--1510006 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1509948 TGAGCATCGG
* *
1509958 TACTGTTCACACAGTAATGA
1 TACTGTTCACACAATAACGA
*
1509978 TACTATTCACACAATAACGA
1 TACTGTTCACACAATAACGA
*
1509998 TATTGTTCA
1 TACTGTTCA
1510007 TTAAAAACAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (20 bp):
TACTGTTCACACAATAACGA
Found at i:1519290 original size:24 final size:25
Alignment explanation
Indices: 1519243--1519294 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
1519233 ATTGTTTTTC
1519243 TAAGTTAAAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
*
1519268 TAAGTTAGAGATTA-TTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
1519292 TAA
1 TAA
1519295 TAAATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.50
Consensus pattern (25 bp):
TAAGTTAAAGATTATTTTTTTCTCA
Found at i:1520776 original size:15 final size:16
Alignment explanation
Indices: 1520748--1520780 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1520738 ACATTTATCA
1520748 TATATTTTAATTTTTT
1 TATATTTTAATTTTTT
1520764 TATA-TTT-ATTTTTT
1 TATATTTTAATTTTTT
1520778 TAT
1 TAT
1520781 TAAAAAGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 10 0.59
15 3 0.18
16 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TATATTTTAATTTTTT
Found at i:1524866 original size:23 final size:22
Alignment explanation
Indices: 1524826--1524868 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1524816 ATTTTCATAT
* *
1524826 ATTATTTTTTATTGAATAAATA
1 ATTATTTTTTACTAAATAAATA
1524848 ATTATTCTTTTACTAAATAAA
1 ATTATT-TTTTACTAAATAAA
1524869 CAAAGAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTATTTTTTACTAAATAAATA
Found at i:1533350 original size:18 final size:19
Alignment explanation
Indices: 1533327--1533366 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1533317 TAAAAATAAT
1533327 AAAAT-AATATATGTTTTA
1 AAAATAAATATATGTTTTA
* *
1533345 AAAATAAATATTTTTTTTA
1 AAAATAAATATATGTTTTA
1533364 AAA
1 AAA
1533367 TTTAACAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
AAAATAAATATATGTTTTA
Found at i:1533367 original size:18 final size:18
Alignment explanation
Indices: 1533326--1533367 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1533316 TTAAAAATAA
1533326 TAAAATAATATATGTTTT
1 TAAAATAATATATGTTTT
* *
1533344 AAAAATAA-ATATTTTTTT
1 TAAAATAATATA-TGTTTT
1533362 TAAAAT
1 TAAAAT
1533368 TTAACAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TAAAATAATATATGTTTT
Found at i:1536446 original size:44 final size:43
Alignment explanation
Indices: 1536306--1536514 Score: 217
Period size: 43 Copynumber: 4.9 Consensus size: 43
1536296 CAAAACAAAG
* * * * *
1536306 AACGCCGCAATAGGTATTAATATTTAGCGGTGTTTGTGTGACA
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTATGACA
* *
1536349 AACGCCGCAATAAGTGTTGATATTTAACGGCGTTTTTATGACA
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTATGACA
* *
1536392 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTTAGATA
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTAT-GACA
* * *
1536436 AACGCTGCAATAGGT-TATGAT-TTTAGCGGCGTTTTTCTCTA-A
1 AACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTTTAT-GACA
* * * * *
1536478 AACGCCGCAGTATGTGCTGATGTTTTGCGGCGTTTTT
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT
1536515 GCTAAAAACG
Statistics
Matches: 142, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
42 17 0.12
43 104 0.73
44 21 0.15
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (43 bp):
AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTATGACA
Found at i:1536615 original size:43 final size:42
Alignment explanation
Indices: 1536502--1536619 Score: 112
Period size: 43 Copynumber: 2.8 Consensus size: 42
1536492 TGCTGATGTT
* * * * *
1536502 TTGCGGCG-TTTTTGCTAAAAACGCCGATAAAGGTCTGTATA
1 TTGCGGCGTTTTTTGATACAAACGCCGCTAAATGTATGTATA
* * ** *
1536543 TAGCGGCATTTCTAAGATACAAACACCGCTAAATGTATGGTATA
1 TTGCGGCGTTT-TTTGATACAAACGCCGCTAAATGTAT-GTATA
*
1536587 TTGCGGCGTTTTTTGTTACAAACGCCGCTAAAT
1 TTGCGGCGTTTTTTGATACAAACGCCGCTAAAT
1536620 AACACAGAAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
41 6 0.10
42 2 0.03
43 36 0.62
44 14 0.24
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (42 bp):
TTGCGGCGTTTTTTGATACAAACGCCGCTAAATGTATGTATA
Found at i:1536948 original size:21 final size:21
Alignment explanation
Indices: 1536924--1537012 Score: 92
Period size: 21 Copynumber: 4.3 Consensus size: 21
1536914 GCTGATATGT
*
1536924 TGCTTCTCTCTCTGCTTCCAC
1 TGCTTCTCTCTCTGCTTCCGC
*
1536945 TGCTTCTCTCTCTGCTTTCGC
1 TGCTTCTCTCTCTGCTTCCGC
* ** *
1536966 TGCTGCTCTGGCTGCTTCTGC
1 TGCTTCTCTCTCTGCTTCCGC
*
1536987 TGCTGC-CTCTCTGCTTCC-C
1 TGCTTCTCTCTCTGCTTCCGC
1537006 TTGCTTC
1 -TGCTTC
1537013 ATTTTCCGCT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
19 1 0.02
20 14 0.25
21 41 0.73
ACGTcount: A:0.01, C:0.39, G:0.17, T:0.43
Consensus pattern (21 bp):
TGCTTCTCTCTCTGCTTCCGC
Found at i:1538501 original size:17 final size:15
Alignment explanation
Indices: 1538479--1538512 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
1538469 CATAATATCT
1538479 ATAATAAACAAACATGA
1 ATAATAAA-AAA-ATGA
1538496 ATAATAAAAAAATGA
1 ATAATAAAAAAATGA
1538511 AT
1 AT
1538513 TAATTAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (15 bp):
ATAATAAAAAAATGA
Found at i:1544478 original size:25 final size:22
Alignment explanation
Indices: 1544427--1544481 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1544417 TAACTGTCTA
* *
1544427 AAACAATATTCCCTTAATTATG
1 AAACAACATTCCCTTAATTACG
1544449 AAACAACATTCCCTTAATTACG
1 AAACAACATTCCCTTAATTACG
1544471 AAACAACATTC
1 AAACAACATTC
1544482 GTGTTCAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.29
Consensus pattern (22 bp):
AAACAACATTCCCTTAATTACG
Found at i:1544504 original size:21 final size:22
Alignment explanation
Indices: 1544478--1544523 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
1544468 ACGAAACAAC
*
1544478 ATTCGTGTTCAGTAAAAAAC-A
1 ATTCGTGTTCACTAAAAAACTA
1544499 ATTCGTGTTCACTAAAAAACTA
1 ATTCGTGTTCACTAAAAAACTA
1544521 ATT
1 ATT
1544524 GCTCGTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (22 bp):
ATTCGTGTTCACTAAAAAACTA
Found at i:1545299 original size:42 final size:42
Alignment explanation
Indices: 1545170--1545299 Score: 94
Period size: 42 Copynumber: 3.1 Consensus size: 42
1545160 ATTGCTACGT
* *
1545170 TTTTTTTATGAAAATGCCACTAAGGA-ATTATTCTATT-GC-GCG
1 TTTTTTTA-AAAAATGCCACTAA-AATATTATTCT-TTAGCGGCG
* ** **
1545212 -TTTTTTAATAAATGCCAC-AAAATTAAGAGTAT-TTTA-CGGTA
1 TTTTTTTAAAAAATGCCACTAAAA-TATTA-T-TCTTTAGCGGCG
1545253 TTTTTTTAAAAAATGCCACTAAAATATTATTCTTTAGCGGCG
1 TTTTTTTAAAAAATGCCACTAAAATATTATTCTTTAGCGGCG
1545295 TTTTT
1 TTTTT
1545300 GGATACAAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 20
0.67 0.12 0.20
Matches are distributed among these distances:
38 1 0.02
39 2 0.03
40 15 0.23
41 15 0.23
42 29 0.44
43 4 0.06
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.42
Consensus pattern (42 bp):
TTTTTTTAAAAAATGCCACTAAAATATTATTCTTTAGCGGCG
Found at i:1546706 original size:41 final size:41
Alignment explanation
Indices: 1546579--1546729 Score: 180
Period size: 41 Copynumber: 3.7 Consensus size: 41
1546569 GTTTATACAA
*
1546579 AAAAATGCCACTATTGATT-ACACTATTGTGGCGTTTGT-T
1 AAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
** * * *
1546618 AAAAAACACCACTATTGATTAATACTATTGCGACGATTGTCT
1 -AAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
* *
1546660 AAAAATGCCACCATTGATTAACACTATCGCGGCGTTTGTCT
1 AAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
* * *
1546701 AAAAATGTCACTATTAATTATCACTATTG
1 AAAAATGCCACTATTGATTAACACTATTG
1546730 ATTATCACTA
Statistics
Matches: 91, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
40 17 0.19
41 73 0.80
42 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (41 bp):
AAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
Found at i:1546742 original size:13 final size:13
Alignment explanation
Indices: 1546708--1546742 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1546698 TCTAAAAATG
*
1546708 TCACTATTAATTA
1 TCACTATTGATTA
1546721 TCACTATTGATTA
1 TCACTATTGATTA
1546734 TCACTATTG
1 TCACTATTG
1546743 CCGCTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (13 bp):
TCACTATTGATTA
Found at i:1549223 original size:57 final size:55
Alignment explanation
Indices: 1549152--1549371 Score: 246
Period size: 55 Copynumber: 4.0 Consensus size: 55
1549142 ATTACCAAAT
* * *
1549152 GGCACTAAGCGTGCAAAAACTTAAGAGATTCATACTAAGTGTATGAATTTTCGTATG
1 GGCACTATGTGTGC-AAAAC-TAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * * * * *
1549209 AGCACTATGTGTGCAAAGCTAATAAATTGATACTAAGTGTATGAATTTCCATATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * * * *
1549264 GGAACTATGTGTTCAAAACTAAGATATTCATATTAAGTGTATGAATTTTTGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * *
1549319 GGCACTATGTGTGC-AAACTAAGAAA-TCGTTACTAAGTGTATTAATTTCCGTAT
1 GGCACTATGTGTGCAAAACTAAGAAATTC-ATACTAAGTGTATGAATTTTCGTAT
1549372 AGGAAATATA
Statistics
Matches: 134, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
53 2 0.01
54 30 0.22
55 87 0.65
56 4 0.03
57 11 0.08
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (55 bp):
GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
Found at i:1549923 original size:68 final size:68
Alignment explanation
Indices: 1549583--1549905 Score: 511
Period size: 68 Copynumber: 4.8 Consensus size: 68
1549573 AAGATTACAT
* *
1549583 GGCCTAACTGTGCATTTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGATAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1549648 TGA
66 TGA
* * *
1549651 GGCCTAACTGTGCATTTGACAGAAATGTGCCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1549716 TGA
66 TGA
* * * *
1549719 GGCCTAACTGTGCATTTGATAGAAATGTGTCAATTATTCCAGTTAGATGAAAGGCTAAGTACCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1549784 TGA
66 TGA
* * * *
1549787 GGCATAATTGTGCTTTTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1549852 TGA
66 TGA
* *
1549855 GGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAA
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1549906 CTGTTAAAGA
Statistics
Matches: 231, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 231 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:1550237 original size:81 final size:81
Alignment explanation
Indices: 1549855--1550196 Score: 544
Period size: 81 Copynumber: 4.2 Consensus size: 81
1549845 GTGCCTTTGA
* *
1549855 GGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACTG-TTAAAGACCG
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAC-GATTAAAGACCG
*
1549919 TTGAGTAAGAA-ATATAT
65 TTGAGTAA-AAGATACAT
*
1549936 GGCCTAGCTGTGTATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGT
1550001 TGAGTAAAAGATACAT
66 TGAGTAAAAGATACAT
*
1550017 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGT
1550082 TGAGTAAAAGATACAT
66 TGAGTAAAAGATACAT
* * * * *
1550098 GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGACAATTAGATGAACGGTTAAAGACCTT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGT
*
1550163 TCAGTAAAAGATACAT
66 TGAGTAAAAGATACAT
*
1550179 GACCTAGCTGTGCATTTG
1 GGCCTAGCTGTGCATTTG
1550197 AAAGAAGAGT
Statistics
Matches: 245, Mismatches: 14, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
80 3 0.01
81 242 0.99
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGT
TGAGTAAAAGATACAT
Found at i:1550279 original size:162 final size:161
Alignment explanation
Indices: 1549857--1550237 Score: 417
Period size: 162 Copynumber: 2.4 Consensus size: 161
1549847 GCCTTTGAGG
* ** * ***
1549857 CCTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGTC-AGTTAGATGAACTGTTAAAGACCGTT
1 CCTAGCTGTGCATTTGAAAGAAAGGTGTCAATCATG-CAAGTTAGATGAAAAATTAAAGACCGTT
* * * * * * *
1549921 GAGTAAGAA-ATATATGGCCTAGCTGTGTATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATG
65 GAGTAA-AAGATACAAGGACTA-CTATGTATTTGGTAGAAAGGTGTCAATTATGACAATTAGATG
* *
1549985 AACGATTAAAGACCGTTGAGTAAAAGATACATGG
128 AACGATTAAAGACCGTTCAGTAAAAGATACATGA
* ** * * **
1550019 CCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTG
1 CCTAGCTGTGCATTTGAAAGAAAGGTGTCAATCATGCAAGTTAGATGAAAAATTAAAGACCGTTG
* * * *
1550084 AGTAAAAGATACATGGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGACAATTAGATGAA
66 AGTAAAAGATACAAGGACTA-CTATGTATTTGGTAGAAAGGTGTCAATTATGACAATTAGATGAA
* *
1550149 CGGTTAAAGACCTTTCAGTAAAAGATACATGA
130 CGATTAAAGACCGTTCAGTAAAAGATACATGA
**
1550181 CCTAGCTGTGCATTTGAAAG-AAGAGTGTCAATCATTTAAGTTAGATGAAAAATTAAA
1 CCTAGCTGTGCATTTGAAAGAAAG-GTGTCAATCATGCAAGTTAGATGAAAAATTAAA
1550238 TGCCTTTGGG
Statistics
Matches: 194, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
161 6 0.03
162 188 0.97
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (161 bp):
CCTAGCTGTGCATTTGAAAGAAAGGTGTCAATCATGCAAGTTAGATGAAAAATTAAAGACCGTTG
AGTAAAAGATACAAGGACTACTATGTATTTGGTAGAAAGGTGTCAATTATGACAATTAGATGAAC
GATTAAAGACCGTTCAGTAAAAGATACATGA
Found at i:1554083 original size:29 final size:30
Alignment explanation
Indices: 1554050--1554122 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
1554040 CAAACCCGTC
1554050 CCCGTCCCCGTTTAGCATAAACGA-TTTTT
1 CCCGTCCCCGTTTAGCATAAACGATTTTTT
1554079 CCCGTCCCCGTTTAGCATAAACGATTTTTT
1 CCCGTCCCCGTTTAGCATAAACGATTTTTT
* *
1554109 CCCGCCCCCATTTA
1 CCCGTCCCCGTTTA
1554123 ATTCGATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 24 0.59
30 17 0.41
ACGTcount: A:0.19, C:0.36, G:0.12, T:0.33
Consensus pattern (30 bp):
CCCGTCCCCGTTTAGCATAAACGATTTTTT
Found at i:1558772 original size:19 final size:20
Alignment explanation
Indices: 1558748--1558789 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
1558738 TAACAATAAC
1558748 ATAATTT-AAACAAAAC-ACA
1 ATAATTTGAAA-AAAACAACA
1558767 ATAATTTGAAAAAAACAACA
1 ATAATTTGAAAAAAACAACA
1558787 ATA
1 ATA
1558790 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.21
Consensus pattern (20 bp):
ATAATTTGAAAAAAACAACA
Found at i:1567282 original size:27 final size:26
Alignment explanation
Indices: 1567208--1567283 Score: 64
Period size: 28 Copynumber: 2.8 Consensus size: 26
1567198 TCCTATTACA
**
1567208 TGAGGGTATTTAT-GTCATTTTGGAGC
1 TGAGGGTATTT-TGGTCATTTTAAAGC
* * *
1567234 TCGAGGGTAATTTGAATAATTTTAAAGCC
1 T-GAGGGTATTTTG-GTCATTTTAAAG-C
1567263 TGAGGGTATTTTGGTCATTTT
1 TGAGGGTATTTTGGTCATTTT
1567284 GAAAAATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
26 2 0.05
27 15 0.39
28 19 0.50
29 2 0.05
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (26 bp):
TGAGGGTATTTTGGTCATTTTAAAGC
Found at i:1568689 original size:73 final size:73
Alignment explanation
Indices: 1568565--1568708 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 73
1568555 ACTATAGATT
* * *
1568565 TAGGATTTTTAGTTTGATTATTTTACTATTATTTTATTTAAGAATTAGTTATTTTATTTATTTAG
1 TAGGATTTTTAGTTTGATTATATCACTATTATTTTATTTAAGAATTAGTTATTTTATTTACTTAG
1568630 AACTTCTAG
66 AA-TTCTAG
*
1568639 TAGGATTTTTAGTTTGATTATATCATTATT-TTTTATTTAAGAATTAGTTATTTTATTTACTTAG
1 TAGGATTTTTAGTTTGATTATATCACTATTATTTTATTTAAGAATTAGTTATTTTATTTACTTAG
1568703 AATTCT
66 AATTCT
1568709 CGGGTTATAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
72 4 0.06
73 35 0.53
74 27 0.41
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.57
Consensus pattern (73 bp):
TAGGATTTTTAGTTTGATTATATCACTATTATTTTATTTAAGAATTAGTTATTTTATTTACTTAG
AATTCTAG
Found at i:1568828 original size:13 final size:13
Alignment explanation
Indices: 1568810--1568841 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1568800 ATTTCCACCC
1568810 TTCTTTCTTTATT
1 TTCTTTCTTTATT
1568823 TTCTTTCTTTATT
1 TTCTTTCTTTATT
1568836 TTCTTT
1 TTCTTT
1568842 TCACAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTCTTTATT
Found at i:1569451 original size:19 final size:18
Alignment explanation
Indices: 1569429--1569479 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
1569419 ATTCTTCTAC
1569429 TTTTTTTATTTTCTAATTA
1 TTTTTTTATTTT-TAATTA
* *
1569448 TTTTTTCATTTATTATTTA
1 TTTTTTTATTT-TTAATTA
1569467 TTTTTATTATTTT
1 TTTTT-TTATTTT
1569480 ATTACTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTTATTTTTAATTA
Done.