Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008981.1 Hibiscus syriacus cultivar Beakdansim tig00112343_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: 1473337
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 6 of 7
Found at i:1182208 original size:20 final size:20
Alignment explanation
Indices: 1182183--1182236 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1182173 GATTTTGTAT
1182183 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1182203 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1182223 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1182237 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1182221 original size:61 final size:61
Alignment explanation
Indices: 1182123--1182239 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1182113 CGCTATGTAA
* * * * *
1182123 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1182184 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1182240 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1182255 original size:61 final size:61
Alignment explanation
Indices: 1182123--1182257 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1182113 CGCTATGTAA
* * * * * ** *
1182123 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1182184 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1182246 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1182258 TTACTTATTT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1182347 original size:21 final size:21
Alignment explanation
Indices: 1182307--1182347 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1182297 ACTGTATACC
**
1182307 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1182328 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1182348 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1189415 original size:2 final size:2
Alignment explanation
Indices: 1189408--1189432 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1189398 CTGAGGCAAA
1189408 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
1189433 AGAGAGAGAG
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:1189437 original size:2 final size:2
Alignment explanation
Indices: 1189432--1189478 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1189422 GTGTGTGTGT
1189432 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
1189474 GA GA G
1 GA GA G
1189479 GAGGACAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1193030 original size:60 final size:59
Alignment explanation
Indices: 1192893--1193047 Score: 154
Period size: 60 Copynumber: 2.6 Consensus size: 59
1192883 GTACATATGT
* * *
1192893 ATAGTTT-GGATAAAATTGAAATGTTCAAAAAGTTTGGAGACTAGCTTAGAATGAATGTC
1 ATAGTTTGGGATAAAATTGAAATGTTC-AAAAGTTTGGAGACTAACTTAGAATGAATATA
* * * *
1192952 ATAGTTTGAAGATGAAATTGAAATGTTCAAAAGTTT-GAGTACTAATTTAGGATG-ATAATA
1 ATAGTTTG-GGATAAAATTGAAATGTTCAAAAGTTTGGAG-ACTAACTTAGAATGAAT-ATA
* * *
1193012 ATAGTTTAGGGATAAAATTAAAATATTTAAAAGTTT
1 ATAGTTT-GGGATAAAATTGAAATGTTCAAAAGTTT
1193048 AGGGATCAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
59 12 0.15
60 49 0.62
61 18 0.23
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (59 bp):
ATAGTTTGGGATAAAATTGAAATGTTCAAAAGTTTGGAGACTAACTTAGAATGAATATA
Found at i:1196519 original size:24 final size:24
Alignment explanation
Indices: 1196470--1196520 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1196460 CTTCCTCTTA
* *
1196470 CTCCTCTTCTTCTACTGAGATTAC
1 CTCCTCTTCTTCTACTCAGATCAC
1196494 CTCCTCTTCTTCTACTCAG-TCCAC
1 CTCCTCTTCTTCTACTCAGAT-CAC
1196518 CTC
1 CTC
1196521 AGCTTCTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.14, C:0.41, G:0.06, T:0.39
Consensus pattern (24 bp):
CTCCTCTTCTTCTACTCAGATCAC
Found at i:1201657 original size:165 final size:157
Alignment explanation
Indices: 1201417--1201739 Score: 351
Period size: 159 Copynumber: 2.0 Consensus size: 157
1201407 ATACAGTTAG
* ** * ** *
1201417 ACAAATGACACTATCCTACGGACTGAAGCTTTGGCATGTGGAAACCTAATCAAATTTCCTATATG
1 ACAAATGACACTATCATACCAACTGAAGATTTGGCATGCAGAAACCTAATCAAATTTCCTACATG
* * * * * * *
1201482 TCAAGTTCAAGAATCAATTATGACTATTTCCTTTTAGGAATCTGAGCTAAGCTTAGTTTA-CTCC
66 TAAAGTTCAAGAAGCAATTAAGACAATTTCCTTTCAGG-----G-CCTAAGCTTAG-ATAGCTCC
*
1201546 CAAAAGTATTAGCTCAAGCCTCAAGGCAAAGCCA
124 CAAAAGTATTAGCTCAAGCCTCAAGACAAAGCCA
* * *
1201580 ACAAACTGACACTATCATACCAACTGGAGATTTGGCATGCAGAATCCTTATCAAAATTTCCTACA
1 ACAAA-TGACACTATCATACCAACTGAAGATTTGGCATGCAGAAACCTAATC-AAATTTCCTACA
* * * *
1201645 TTTAAAGTTCAAGCAGCAGTTAAGACAATTTTCTTTCAGGGCCTAAGCTTAGATAGCTCCCAAAA
64 TGTAAAGTTCAAGAAGCAATTAAGACAATTTCCTTTCAGGGCCTAAGCTTAGATAGCTCCCAAAA
*
1201710 GTATTAGCTCAAGCCTCAAGACAATGCCA
129 GTATTAGCTCAAGCCTCAAGACAAAGCCA
1201739 A
1 A
1201740 TAAAATTTAC
Statistics
Matches: 134, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
158 2 0.01
159 47 0.35
160 1 0.01
163 5 0.04
164 37 0.28
165 42 0.31
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (157 bp):
ACAAATGACACTATCATACCAACTGAAGATTTGGCATGCAGAAACCTAATCAAATTTCCTACATG
TAAAGTTCAAGAAGCAATTAAGACAATTTCCTTTCAGGGCCTAAGCTTAGATAGCTCCCAAAAGT
ATTAGCTCAAGCCTCAAGACAAAGCCA
Found at i:1214989 original size:23 final size:22
Alignment explanation
Indices: 1214963--1215006 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1214953 ATTCAAATTA
1214963 AAACAAATATATATAATTATATC
1 AAACAAATAT-TATAATTATATC
* *
1214986 AAACTAATATTTTAATTATAT
1 AAACAAATATTATAATTATAT
1215007 AACAACGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
AAACAAATATTATAATTATATC
Found at i:1217757 original size:179 final size:180
Alignment explanation
Indices: 1217455--1217816 Score: 654
Period size: 179 Copynumber: 2.0 Consensus size: 180
1217445 TTATAATTGT
* *
1217455 AGTTAAAGGGGTTAACGACATAATGTTATAATTGTAGTTAAATTTAAATGTTTGTATTAAAATTA
1 AGTTAAAGGGGTTAACGACATAATGTTATAATTGTAGTTAAATTTAAACGTTTATATTAAAATTA
*
1217520 ATAAAATTAAAACGTTAATGACATAAACGAATTTAAATTTAAAGGAGAGTGATATTTGAAGTAAT
66 ATAAAATTAAAACGTTAATGACATAAACGAATTTAAATTTAAAGGAAAGTGATATTTGAAGTAAT
*
1217585 TAACCT-AAAAAAAAATTGGCCGGTCCTCGCTAGTAATATAAGGGTTTTG
131 TAACCTAAAAAAAAAATTGGCCGGTCCTCGCTAGTAATATAAGGGTTTCG
*
1217634 AGTTAAAGGGGTTAACGATATAATGTTATAATTGTAGTTAAATTTAAACGTTTATATTAAAATTA
1 AGTTAAAGGGGTTAACGACATAATGTTATAATTGTAGTTAAATTTAAACGTTTATATTAAAATTA
*
1217699 ATAAAATTAAAACGTTAATGACATAAACGAATTTAAATTTAAAGGAAAGTGGTATTTGAAGTAAT
66 ATAAAATTAAAACGTTAATGACATAAACGAATTTAAATTTAAAGGAAAGTGATATTTGAAGTAAT
*
1217764 TAACCTAAAAAAAAAATTGGCCGGTCTTCGCTAGTAATATAAGGGTTTCG
131 TAACCTAAAAAAAAAATTGGCCGGTCCTCGCTAGTAATATAAGGGTTTCG
1217814 AGT
1 AGT
1217817 CTAACGAGGC
Statistics
Matches: 175, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
179 131 0.75
180 44 0.25
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.33
Consensus pattern (180 bp):
AGTTAAAGGGGTTAACGACATAATGTTATAATTGTAGTTAAATTTAAACGTTTATATTAAAATTA
ATAAAATTAAAACGTTAATGACATAAACGAATTTAAATTTAAAGGAAAGTGATATTTGAAGTAAT
TAACCTAAAAAAAAAATTGGCCGGTCCTCGCTAGTAATATAAGGGTTTCG
Found at i:1222989 original size:24 final size:22
Alignment explanation
Indices: 1222962--1223041 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 22
1222952 CCGGGTTTTA
1222962 TATTTATATTTTTATTGTATTATT
1 TATTT-TATTTTTATT-TATTATT
1222986 TA-TTTA--TTTATTTATTTATT
1 TATTTTATTTTTATTTA-TTATT
*
1223006 TATTTTATTATTATTATTATTATT
1 TATTTTATTTTTA-T-TTATTATT
*
1223030 TCTTTTATTTTT
1 TATTTTATTTTT
1223042 TTGCAAGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.04
20 13 0.28
21 4 0.09
22 2 0.04
23 5 0.11
24 18 0.38
25 3 0.06
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (22 bp):
TATTTTATTTTTATTTATTATT
Found at i:1222990 original size:4 final size:4
Alignment explanation
Indices: 1222962--1223010 Score: 66
Period size: 4 Copynumber: 12.2 Consensus size: 4
1222952 CCGGGTTTTA
1222962 TATT TATAT T-TT TATT GTA-T TATT TATT TATT TATT TATT TATT TATT
1 TATT TAT-T TATT TATT -TATT TATT TATT TATT TATT TATT TATT TATT
1223010 T
1 T
1223011 TATTATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 4 0.10
4 33 0.80
5 4 0.10
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1223016 original size:12 final size:12
Alignment explanation
Indices: 1222957--1223038 Score: 64
Period size: 12 Copynumber: 6.6 Consensus size: 12
1222947 TTTGACCGGG
1222957 TTTTA-TATTTA
1 TTTTATTATTTA
1222968 TATTT-TTATTGTA
1 T-TTTATTATT-TA
1222981 TTATTTATTTATTTA
1 -T-TTTA-TTATTTA
1222996 -TTTATTTATTTA
1 TTTTA-TTATTTA
1223008 TTTTATTA-TTA
1 TTTTATTATTTA
*
1223019 TTATTATTATTTC
1 TT-TTATTATTTA
1223032 TTTTATT
1 TTTTATT
1223039 TTTTTGCAAG
Statistics
Matches: 61, Mismatches: 1, Indels: 17
0.77 0.01 0.22
Matches are distributed among these distances:
11 6 0.10
12 33 0.54
13 10 0.16
14 5 0.08
15 2 0.03
16 5 0.08
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:1225742 original size:5 final size:5
Alignment explanation
Indices: 1225729--1225765 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
1225719 CTTTTCATTT
* *
1225729 TTTTG TTTTA TTTTA TTTTA TTTTA TTTTA TTATA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1225766 CATTCGCATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1226731 original size:19 final size:19
Alignment explanation
Indices: 1226720--1226769 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1226710 CCGAGCCGTT
1226720 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
1226739 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
1226758 TGAGCCGAGCCG
1 TGAGCCGAGCCG
1226770 AGCCGCCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.16, C:0.28, G:0.38, T:0.18
Consensus pattern (19 bp):
TGAGCCGAGCCGTTTGAGC
Found at i:1226764 original size:14 final size:14
Alignment explanation
Indices: 1226698--1226745 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
1226688 GAAGCATGAG
1226698 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
1226712 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
*
1226726 GAGCCGTTTGAGCT
1 GAGCCGTTTGAGCC
1226740 GAGCCG
1 GAGCCG
1226746 AGCCGTTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.15, C:0.27, G:0.38, T:0.21
Consensus pattern (14 bp):
GAGCCGTTTGAGCC
Found at i:1228125 original size:18 final size:18
Alignment explanation
Indices: 1228099--1228133 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1228089 TCGAAAGGAC
*
1228099 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1228117 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1228134 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1231818 original size:19 final size:19
Alignment explanation
Indices: 1231807--1231856 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1231797 CCGAGCCGTT
1231807 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
1231826 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
1231845 TGAGCCGAGCCG
1 TGAGCCGAGCCG
1231857 AGCCGCCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.16, C:0.28, G:0.38, T:0.18
Consensus pattern (19 bp):
TGAGCCGAGCCGTTTGAGC
Found at i:1231851 original size:14 final size:14
Alignment explanation
Indices: 1231785--1231832 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
1231775 GAAGCATGAG
1231785 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
1231799 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
*
1231813 GAGCCGTTTGAGCT
1 GAGCCGTTTGAGCC
1231827 GAGCCG
1 GAGCCG
1231833 AGCCGTTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.15, C:0.27, G:0.38, T:0.21
Consensus pattern (14 bp):
GAGCCGTTTGAGCC
Found at i:1233214 original size:18 final size:18
Alignment explanation
Indices: 1233188--1233222 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1233178 TCGAAAGGAC
*
1233188 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1233206 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1233223 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1238733 original size:43 final size:43
Alignment explanation
Indices: 1238672--1238827 Score: 127
Period size: 43 Copynumber: 3.4 Consensus size: 43
1238662 CAGAGCCAAT
1238672 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
* * * * * *
1238715 TTCAACTTCACGACGAAGGGACCGCTGATTGTCAAT--AAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA----T-ATTG-GACTCCAGACAA---CACAAG
* *
1238766 TTCAACTTAACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
*
1238809 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
1238828 GACCGCTGGT
Statistics
Matches: 86, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
43 37 0.43
44 5 0.06
45 4 0.05
46 6 0.07
48 6 0.07
49 4 0.05
50 5 0.06
51 19 0.22
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
Found at i:1238734 original size:106 final size:106
Alignment explanation
Indices: 1238546--1239006 Score: 721
Period size: 106 Copynumber: 4.5 Consensus size: 106
1238536 ACGAAGGGGC
* * *
1238546 TTCCCAATTTCAGGGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
1238611 CAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACAAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
*
1238652 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
1238717 CAACTTCACGACGAAGGGACCGCTGATTGTCAATAAACAAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
1238758 TTCCCAATTTCA-A--C---TT--A----ACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
1238811 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
1238852 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
* *
1238917 CAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
* * * * *
1238958 TTCTCAGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1239007 TGGAACAATA
Statistics
Matches: 328, Mismatches: 15, Indels: 24
0.89 0.04 0.07
Matches are distributed among these distances:
94 87 0.27
95 1 0.00
97 1 0.00
98 1 0.00
100 4 0.01
102 1 0.00
103 1 0.00
105 1 0.00
106 231 0.70
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
Found at i:1238905 original size:200 final size:200
Alignment explanation
Indices: 1238562--1238960 Score: 735
Period size: 200 Copynumber: 2.0 Consensus size: 200
1238552 ATTTCAGGGT
* *
1238562 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAG
1 CAATTTCAACTTAACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAG
1238627 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
66 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
*
1238692 TATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAATAAACAA
131 TATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAACAAACAA
1238757 TTTCC
196 TTTCC
*
1238762 CAATTTCAACTTAACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTAACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAG
1238827 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
66 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
* * *
1238892 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAA
131 TATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAACAAACAA
1238957 TTTC
196 TTTC
1238961 TCAGTTCCAG
Statistics
Matches: 192, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 192 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (200 bp):
CAATTTCAACTTAACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAG
GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
TATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAACAAACAA
TTTCC
Found at i:1239618 original size:36 final size:36
Alignment explanation
Indices: 1239528--1239640 Score: 156
Period size: 36 Copynumber: 3.1 Consensus size: 36
1239518 AAAATCTTTG
* * * * *
1239528 AACAAATTTCGTCTCCCTTGAGACAATTT-CTTTTA
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
1239563 GAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGA
1 -AACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGA
1239601 AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
1239637 AACA
1 AACA
1239641 CCAATCTTTG
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
36 40 0.57
37 26 0.37
38 4 0.06
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.37
Consensus pattern (36 bp):
AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
Found at i:1240094 original size:24 final size:22
Alignment explanation
Indices: 1240067--1240146 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 22
1240057 CCGGGTTTTA
1240067 TATTTATATTTTTATTGTATTATT
1 TATTT-TATTTTTATT-TATTATT
1240091 TA-TTTA--TTTATTTATTTATT
1 TATTTTATTTTTATTTA-TTATT
*
1240111 TATTTTATTATTATTATTATTATT
1 TATTTTATTTTTA-T-TTATTATT
*
1240135 TCTTTTATTTTT
1 TATTTTATTTTT
1240147 TTGCAGGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.04
20 13 0.28
21 4 0.09
22 2 0.04
23 5 0.11
24 18 0.38
25 3 0.06
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (22 bp):
TATTTTATTTTTATTTATTATT
Found at i:1240095 original size:4 final size:4
Alignment explanation
Indices: 1240067--1240115 Score: 66
Period size: 4 Copynumber: 12.2 Consensus size: 4
1240057 CCGGGTTTTA
1240067 TATT TATAT T-TT TATT GTA-T TATT TATT TATT TATT TATT TATT TATT
1 TATT TAT-T TATT TATT -TATT TATT TATT TATT TATT TATT TATT TATT
1240115 T
1 T
1240116 TATTATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 4 0.10
4 33 0.80
5 4 0.10
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1240121 original size:12 final size:12
Alignment explanation
Indices: 1240062--1240143 Score: 64
Period size: 12 Copynumber: 6.6 Consensus size: 12
1240052 TTTGACCGGG
1240062 TTTTA-TATTTA
1 TTTTATTATTTA
1240073 TATTT-TTATTGTA
1 T-TTTATTATT-TA
1240086 TTATTTATTTATTTA
1 -T-TTTA-TTATTTA
1240101 -TTTATTTATTTA
1 TTTTA-TTATTTA
1240113 TTTTATTA-TTA
1 TTTTATTATTTA
*
1240124 TTATTATTATTTC
1 TT-TTATTATTTA
1240137 TTTTATT
1 TTTTATT
1240144 TTTTTGCAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 17
0.77 0.01 0.22
Matches are distributed among these distances:
11 6 0.10
12 33 0.54
13 10 0.16
14 5 0.08
15 2 0.03
16 5 0.08
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:1241701 original size:23 final size:22
Alignment explanation
Indices: 1241631--1241715 Score: 68
Period size: 23 Copynumber: 3.8 Consensus size: 22
1241621 ATGGGTTCCT
1241631 TTTTTATATTTATTTCATTT-A-G
1 TTTTTAT-TTTATTT-ATTTAATG
* * *
1241653 TTTATTACTTT-TTTATTTCATT
1 TTT-TTATTTTATTTATTTAATG
*
1241675 TTTTTCTTTTGATTTATTTAATG
1 TTTTTATTTT-ATTTATTTAATG
*
1241698 TTTTTATTTTCTTTATTT
1 TTTTTATTTTATTTATTT
1241716 TCTTATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
20 4 0.08
21 9 0.18
22 16 0.32
23 21 0.42
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTTATTTTATTTATTTAATG
Found at i:1241786 original size:14 final size:13
Alignment explanation
Indices: 1241756--1241797 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
1241746 CTTCTTTTCA
1241756 TTTATTTAATA--
1 TTTATTTAATATT
*
1241767 TTTATTTATTATT
1 TTTATTTAATATT
1241780 CTTTATTTAATATT
1 -TTTATTTAATATT
1241794 TTTA
1 TTTA
1241798 ACTTTTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 10 0.38
13 4 0.15
14 12 0.46
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTTAATATT
Found at i:1250136 original size:3 final size:3
Alignment explanation
Indices: 1250128--1250152 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1250118 AGTTCAATGA
1250128 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
1250153 GTCGGAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1254524 original size:3 final size:3
Alignment explanation
Indices: 1254516--1254561 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1254506 TGAATGGTTG
1254516 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1254562 TATTATTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1254566 original size:3 final size:3
Alignment explanation
Indices: 1254560--1254592 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1254550 AATAATAATA
1254560 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1254593 TAAGGAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1254719 original size:20 final size:20
Alignment explanation
Indices: 1254696--1254811 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 20
1254686 CAATGCGAAC
1254696 TCCAATTTCGCAACACAATT
1 TCCAATTTCGCAACACAATT
* * * *
1254716 TCCAAATTCGAAACTCAGTT
1 TCCAATTTCGCAACACAATT
*
1254736 TCTGCAA-TT-GCAACGCGAATT
1 TC--CAATTTCGCAACAC-AATT
* *
1254757 T-C-TTTCTCGCAACACGATTT
1 TCCAATT-TCGCAACAC-AATT
*
1254777 TCCAAATTCGCAACACAAGTT
1 TCCAATTTCGCAACACAA-TT
*
1254798 TCC-TTTTCGCAACA
1 TCCAATTTCGCAACA
1254812 AGATTTTTTA
Statistics
Matches: 72, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
18 2 0.03
19 1 0.01
20 44 0.61
21 21 0.29
22 4 0.06
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.31
Consensus pattern (20 bp):
TCCAATTTCGCAACACAATT
Found at i:1254789 original size:21 final size:21
Alignment explanation
Indices: 1254763--1254839 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
1254753 AATTTCTTTC
1254763 TCGCAACACGATTTTCCAAAT
1 TCGCAACACGATTTTCCAAAT
* * **
1254784 TCGCAACACAAGTTTCC-TTT
1 TCGCAACACGATTTTCCAAAT
* **
1254804 TCGCAACAAGATTTTTTAAA-
1 TCGCAACACGATTTTCCAAAT
1254824 TCGCAACACGAATTTT
1 TCGCAACACG-ATTTT
1254840 TTTTAACTCG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 22 0.52
21 20 0.48
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.32
Consensus pattern (21 bp):
TCGCAACACGATTTTCCAAAT
Found at i:1254790 original size:41 final size:41
Alignment explanation
Indices: 1254741--1254838 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
1254731 CAGTTTCTGC
* *
1254741 AATT-GCAACGCGAATTT-CTTTCTCGCAACACGATTTTCCA
1 AATTCGCAACACGAATTTCCTTT-TCGCAACAAGATTTTCCA
**
1254781 AATTCGCAACAC-AAGTTTCCTTTTCGCAACAAGATTTTTTA
1 AATTCGCAACACGAA-TTTCCTTTTCGCAACAAGATTTTCCA
1254822 AA-TCGCAACACGAATTT
1 AATTCGCAACACGAATTT
1254839 TTTTTAACTC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
40 18 0.36
41 28 0.56
42 4 0.08
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (41 bp):
AATTCGCAACACGAATTTCCTTTTCGCAACAAGATTTTCCA
Found at i:1260599 original size:17 final size:17
Alignment explanation
Indices: 1260577--1260611 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1260567 TTAGGGCATG
1260577 ATTGAAATCTAACACAT
1 ATTGAAATCTAACACAT
*
1260594 ATTGAAATCTAGCACAT
1 ATTGAAATCTAACACAT
1260611 A
1 A
1260612 AGCAAACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (17 bp):
ATTGAAATCTAACACAT
Found at i:1263611 original size:22 final size:21
Alignment explanation
Indices: 1263569--1263608 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1263559 GAGTTTATTT
*
1263569 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1263590 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1263609 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:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1266971 original size:21 final size:21
Alignment explanation
Indices: 1266947--1267002 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
1266937 GTGAATCGGG
* **
1266947 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAAAGGGGC
1266968 CTCTTGAACGATGAAAGGGGC
1 CTCTTGAACGATGAAAGGGGC
1266989 CTCTTGAACGATGA
1 CTCTTGAACGATGA
1267003 CAGGTGAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAAAGGGGC
Found at i:1267165 original size:12 final size:12
Alignment explanation
Indices: 1267146--1267187 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1267136 GGTCCGCTAA
1267146 AAATAAATTAAT
1 AAATAAATTAAT
* *
1267158 ACATAAATTATT
1 AAATAAATTAAT
1267170 AAATAAA-TAATT
1 AAATAAATTAA-T
1267182 AAATAA
1 AAATAA
1267188 TGCCAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 2 0.08
12 23 0.92
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:1267439 original size:21 final size:21
Alignment explanation
Indices: 1267415--1267454 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1267405 GTCGTCATGT
*
1267415 AAAGTACCGACCTCATCACAC
1 AAAGCACCGACCTCATCACAC
*
1267436 AAAGCACTGACCTCATCAC
1 AAAGCACCGACCTCATCAC
1267455 GTAACTCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAGCACCGACCTCATCACAC
Found at i:1267673 original size:42 final size:42
Alignment explanation
Indices: 1267573--1267712 Score: 210
Period size: 42 Copynumber: 3.4 Consensus size: 42
1267563 GTGATGAAAT
* * * *
1267573 AGGTGATGACTCTCGGTGTGGAGGTGTATAATCGACTCGATC
1 AGGTGATGACTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
* *
1267615 -GGTGATGGCTCTCGGTGTCGAGTTGTAGAATCGGCTCGATC
1 AGGTGATGACTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
*
1267656 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGACTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
1267698 AGGTGATGACTCTCG
1 AGGTGATGACTCTCG
1267713 AATTGGGGGG
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
41 36 0.40
42 54 0.60
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.28
Consensus pattern (42 bp):
AGGTGATGACTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
Found at i:1272824 original size:29 final size:29
Alignment explanation
Indices: 1272779--1272835 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1272769 AGTGTTGGTC
* *
1272779 GTAGATCGCCATGCACTCCGTGCGACCTT
1 GTAGATCGCCATACACTCCGGGCGACCTT
*
1272808 GTAGGTCGCCATACACTCCGGGCGACCT
1 GTAGATCGCCATACACTCCGGGCGACCT
1272836 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (29 bp):
GTAGATCGCCATACACTCCGGGCGACCTT
Found at i:1276533 original size:50 final size:51
Alignment explanation
Indices: 1276476--1276591 Score: 130
Period size: 50 Copynumber: 2.3 Consensus size: 51
1276466 GACGAGTTCT
* * *
1276476 AATAAAAAATATTTTTTTATT-GAAACTCGTCA-TTCGACTTGACAAAATCA
1 AATAAAAAATATTATTTTATTAG-AACTCGTCACCTCGACGTGACAAAATCA
* * ** *
1276526 AATAAAAATTA-TATTTTATTAGAACTCGTCACCTCGACGTGACGAGTTTA
1 AATAAAAAATATTATTTTATTAGAACTCGTCACCTCGACGTGACAAAATCA
1276576 AATAAAAAATATTATT
1 AATAAAAAATATTATT
1276592 CGGGCAAATG
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
49 17 0.31
50 33 0.61
51 4 0.07
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.35
Consensus pattern (51 bp):
AATAAAAAATATTATTTTATTAGAACTCGTCACCTCGACGTGACAAAATCA
Found at i:1279869 original size:2 final size:2
Alignment explanation
Indices: 1279862--1279886 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1279852 AACGACCGAC
1279862 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1279887 GCATTTCTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1295462 original size:94 final size:93
Alignment explanation
Indices: 1295356--1295532 Score: 284
Period size: 94 Copynumber: 1.9 Consensus size: 93
1295346 GCGACATCAT
* * * *
1295356 ATATTTTATTTTGAAAATTAAGATATTTAT-TTTAATGATTTGAAACTCGTTATAATATATTTTT
1 ATATTTTATTTTGAAAATTAAGATATTT-TCTATAATGATTTAAAACTCGTTACAATAT-GTTTT
1295420 TATTGAAATTTATTATTTCGGTGAAACAAG
64 TATTGAAATTTATTATTTCGGTGAAACAAG
*
1295450 ATATTTTATTTTGAAAATTACGATATTTTCTATAATGATTTAAAACTCGTTACAATATGTTTTTA
1 ATATTTTATTTTGAAAATTAAGATATTTTCTATAATGATTTAAAACTCGTTACAATATGTTTTTA
1295515 TTGAAATTTATTATTTCG
66 TTGAAATTTATTATTTCG
1295533 ATAAAATAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
93 25 0.32
94 52 0.68
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.50
Consensus pattern (93 bp):
ATATTTTATTTTGAAAATTAAGATATTTTCTATAATGATTTAAAACTCGTTACAATATGTTTTTA
TTGAAATTTATTATTTCGGTGAAACAAG
Found at i:1298379 original size:34 final size:34
Alignment explanation
Indices: 1298336--1298403 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1298326 TTGGGCATGC
1298336 TCTTCCACTCCCAAAGTTGCAACTCTCCATCAAA
1 TCTTCCACTCCCAAAGTTGCAACTCTCCATCAAA
1298370 TCTTCCACTCCCAAAGTTGCAACTCTCCATCAAA
1 TCTTCCACTCCCAAAGTTGCAACTCTCCATCAAA
1298404 AATATATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.38, G:0.06, T:0.26
Consensus pattern (34 bp):
TCTTCCACTCCCAAAGTTGCAACTCTCCATCAAA
Found at i:1303015 original size:67 final size:67
Alignment explanation
Indices: 1302907--1303038 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
1302897 AGTATTTTTT
*
1302907 CTAACACATGTATGTTGCAATAATAGGAGAATGATCATGCAACACAACATGTAAAAGGTCCAACA
1 CTAACACATGTATGTTGCAATAATAGGAGAATGATCATGCAACACAACATGTAAAAGCTCCAACA
1302972 TA
66 TA
* * *
1302974 CTAACACATGTATGTTGCAGTAGTAGGAGAATGATCATGCAACATAACATGTAAAAGCTCCAACA
1 CTAACACATGTATGTTGCAATAATAGGAGAATGATCATGCAACACAACATGTAAAAGCTCCAACA
1303039 CAACAATTGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (67 bp):
CTAACACATGTATGTTGCAATAATAGGAGAATGATCATGCAACACAACATGTAAAAGCTCCAACA
TA
Found at i:1308865 original size:16 final size:15
Alignment explanation
Indices: 1308822--1308865 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 15
1308812 CGGTATCAGC
1308822 TTCTCCTCAACTAAA
1 TTCTCCTCAACTAAA
*
1308837 TT-TCATC-ACTAAA
1 TTCTCCTCAACTAAA
1308850 TTTCTCCTCAACTAAA
1 -TTCTCCTCAACTAAA
1308866 GATTAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 6 0.25
16 6 0.25
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (15 bp):
TTCTCCTCAACTAAA
Found at i:1310130 original size:21 final size:21
Alignment explanation
Indices: 1310086--1310147 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
1310076 TATTTTGTAT
*
1310086 ATATATTATAATTAA-TATTTTA
1 ATATATTAT--TTAATTATTATA
*
1310108 ATA-ATTTTTTATATTATTATA
1 ATATATTATTTA-ATTATTATA
1310129 ATATATTATTTAATTATTA
1 ATATATTATTTAATTATTA
1310148 AAAATATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.09
20 1 0.03
21 20 0.59
22 10 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATTATTTAATTATTATA
Found at i:1310160 original size:29 final size:31
Alignment explanation
Indices: 1310128--1310226 Score: 116
Period size: 32 Copynumber: 3.3 Consensus size: 31
1310118 ATATTATTAT
1310128 AATATATTA-TTTAATTA-TTAAAAATATAA
1 AATATATTATTTTAATTATTTAAAAATATAA
* *
1310157 AATATATTATTTTAA-CAGTTTAAATATAATAA
1 AATATATTATTTTAATTA-TTTAAAAAT-ATAA
* *
1310189 AATATATTATTTTAATTATTTTAAAATAT-T
1 AATATATTATTTTAATTATTTAAAAATATAA
1310219 AATATATT
1 AATATATT
1310227 CAGATTGGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
29 10 0.17
30 13 0.22
31 9 0.15
32 26 0.44
33 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (31 bp):
AATATATTATTTTAATTATTTAAAAATATAA
Found at i:1310924 original size:14 final size:14
Alignment explanation
Indices: 1310905--1310931 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1310895 ATTAAAAATT
1310905 TATATTTTAGAAAA
1 TATATTTTAGAAAA
1310919 TATATTTTAGAAA
1 TATATTTTAGAAA
1310932 TCTTTAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
TATATTTTAGAAAA
Found at i:1310983 original size:14 final size:16
Alignment explanation
Indices: 1310947--1310987 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
1310937 AATCAATTAG
1310947 TTTTAAAATATATATT
1 TTTTAAAATATATATT
**
1310963 TAATAAAAT-T-TATT
1 TTTTAAAATATATATT
1310977 TTTTAAAATAT
1 TTTTAAAATAT
1310988 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 11 0.55
15 2 0.10
16 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTAAAATATATATT
Found at i:1311236 original size:2 final size:2
Alignment explanation
Indices: 1311231--1311271 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
1311221 AAGGATAGAA
*
1311231 AT AT AT -T AT -T A- AT AT AT AT AT AT AT GT 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
1311270 AT
1 AT
1311272 CTAAATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1312921 original size:8 final size:8
Alignment explanation
Indices: 1312886--1312923 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1312876 TTATTTCACT
1312886 TATATGT-
1 TATATGTA
1312893 TATAT-TA
1 TATATGTA
*
1312900 TATATATA
1 TATATGTA
1312908 TATATGTA
1 TATATGTA
1312916 TATATGTA
1 TATATGTA
1312924 CACATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:1313033 original size:13 final size:14
Alignment explanation
Indices: 1313015--1313046 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1313005 TATATATATA
1313015 TATTTTC-TTATTT
1 TATTTTCATTATTT
1313028 TATTTTCATTATTT
1 TATTTTCATTATTT
1313042 T-TTTT
1 TATTTT
1313047 TATTTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTTTCATTATTT
Found at i:1314178 original size:10 final size:10
Alignment explanation
Indices: 1314163--1314196 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1314153 TTCATTTACC
1314163 ATTTATTTTT
1 ATTTATTTTT
1314173 ATTTATTTTT
1 ATTTATTTTT
* *
1314183 ATCTATTTCT
1 ATTTATTTTT
1314193 ATTT
1 ATTT
1314197 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:1324591 original size:105 final size:105
Alignment explanation
Indices: 1324409--1325078 Score: 1223
Period size: 105 Copynumber: 6.4 Consensus size: 105
1324399 AGGTTTTACC
*
1324409 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1324474 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
1324514 CAGAGCCAATTCCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1324579 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
1324619 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1324684 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
1324724 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCACACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
1324789 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
* *
1324829 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACTACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
1324894 ACGAAGGGACCGCTGGTTGTCAACGAGCATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
** * * *
1324934 CAGAGCCAATTTCTGCTTCCCAACGAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
1324999 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
1325039 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1325079 GAAACGATGC
Statistics
Matches: 544, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 544 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
Found at i:1326545 original size:8 final size:8
Alignment explanation
Indices: 1326510--1326547 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1326500 TTATTTCACT
1326510 TATATGT-
1 TATATGTA
1326517 TATAT-TA
1 TATATGTA
*
1326524 TATATATA
1 TATATGTA
1326532 TATATGTA
1 TATATGTA
1326540 TATATGTA
1 TATATGTA
1326548 CACATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:1326656 original size:13 final size:14
Alignment explanation
Indices: 1326638--1326669 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1326628 TATATATATA
1326638 TATTTTC-TTATTT
1 TATTTTCATTATTT
1326651 TATTTTCATTATTT
1 TATTTTCATTATTT
1326665 T-TTTT
1 TATTTT
1326670 ATTTTACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTTTCATTATTT
Found at i:1328654 original size:21 final size:22
Alignment explanation
Indices: 1328600--1328656 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
1328590 AAAACCTTCA
1328600 AAAAAATTAAATATAAATAACT
1 AAAAAATTAAATATAAATAACT
*
1328622 AAGAATAA--AAAT-TAAATTACT
1 AA-AA-AATTAAATATAAATAACT
1328643 AAAAAATTAAATAT
1 AAAAAATTAAATAT
1328657 TTTTTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
19 2 0.07
20 2 0.07
21 14 0.48
22 7 0.24
23 2 0.07
24 2 0.07
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAAATTAAATATAAATAACT
Found at i:1329085 original size:20 final size:20
Alignment explanation
Indices: 1329060--1329115 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1329050 TGGTTTACGT
1329060 AATATAAGATTACCAGTGGG
1 AATATAAGATTACCAGTGGG
1329080 AATATAAGATTACCAGTGGG
1 AATATAAGATTACCAGTGGG
* *
1329100 AATAAAAGATTGCCAG
1 AATATAAGATTACCAG
1329116 GGAATAGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (20 bp):
AATATAAGATTACCAGTGGG
Found at i:1331690 original size:25 final size:25
Alignment explanation
Indices: 1331643--1331690 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1331633 TTCAGTGACA
* *
1331643 CGTGGAACTCTTATATCGATCCCGT
1 CGTGGAACTCCTATATCCATCCCGT
* *
1331668 CGTGGAACTCCTATCTCCCTCCC
1 CGTGGAACTCCTATATCCATCCC
1331691 TATCTCCCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.17, C:0.38, G:0.17, T:0.29
Consensus pattern (25 bp):
CGTGGAACTCCTATATCCATCCCGT
Found at i:1331694 original size:12 final size:12
Alignment explanation
Indices: 1331677--1331717 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
1331667 TCGTGGAACT
1331677 CCTATCTCCCTC
1 CCTATCTCCCTC
1331689 CCTATCTCCCTC
1 CCTATCTCCCTC
1331701 CC--TCTCCCTC
1 CCTATCTCCCTC
1331711 TCCTATC
1 -CCTATC
1331718 AAGTTCAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 14 0.54
13 2 0.08
ACGTcount: A:0.07, C:0.59, G:0.00, T:0.34
Consensus pattern (12 bp):
CCTATCTCCCTC
Found at i:1331802 original size:6 final size:6
Alignment explanation
Indices: 1331791--1331825 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
1331781 ACCTATCTCC
1331791 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCC
1331826 CCTCTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CTCCCT
Found at i:1337211 original size:28 final size:29
Alignment explanation
Indices: 1337180--1337243 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1337170 TAAAGGTTAT
1337180 AAATACAAAAT-TATTA-AAAAAAATAAAA
1 AAATA-AAAATATATTATAAAAAAATAAAA
* *
1337208 AAATAAAGATATATTATAATAAAATAAAA
1 AAATAAAAATATATTATAAAAAAATAAAA
1337237 ATAATAA
1 A-AATAA
1337244 TAAACACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 4 0.13
28 10 0.32
29 12 0.39
30 5 0.16
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (29 bp):
AAATAAAAATATATTATAAAAAAATAAAA
Found at i:1344666 original size:60 final size:60
Alignment explanation
Indices: 1344553--1344669 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
1344543 AATAGTCAGG
* * **
1344553 TGACCATTTTGTAACTTTTAATAGTCGATGGACTTAACAAAGCAACATTCTATAGTCGAA
1 TGACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAACAACAACCTATAGTCGAA
* * * *
1344613 TGACTATTTTGTAACTTTTAATAGTCGATAGACTTAATAAAATAATAACCTATAGTC
1 TGACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAACAACAACCTATAGTC
1344670 AAGGGACCGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (60 bp):
TGACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAACAACAACCTATAGTCGAA
Found at i:1344690 original size:60 final size:60
Alignment explanation
Indices: 1344544--1344690 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 60
1344534 AACATAATGA
* * **
1344544 ATAGTC-AGGTGACCATTTTGTAACTTTTAATAGTCGATGGACTTAACAAAGCAACATTCT
1 ATAGTCAAGG-GACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAACAACAACCT
* * * * *
1344604 ATAGTCGAA-TGACTATTTTGTAACTTTTAATAGTCGATAGACTTAATAAAATAATAACCT
1 ATAGTC-AAGGGACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAACAACAACCT
*
1344664 ATAGTCAAGGGACCGTTTGTGT-ACTTT
1 ATAGTCAAGGGACCATTT-TGTAACTTT
1344691 ACCCTGAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
59 2 0.03
60 65 0.92
61 3 0.04
62 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (60 bp):
ATAGTCAAGGGACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAACAACAACCT
Found at i:1347595 original size:51 final size:50
Alignment explanation
Indices: 1347511--1347616 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 50
1347501 AGCGCACTCT
** *
1347511 TTGCACCGCGCTATACGATGATTTGGCACCACGTAGGGTATAGCGCTCCCC
1 TTGCACCGCGCTATACGATGAACTGGCACCACGT-GGGTATAGCGCGCCCC
** * *
1347562 TTGCACCGCGCTATAC-AGTGAACTGGCGTCACGTGGTTATAGCGCGGCCC
1 TTGCACCGCGCTATACGA-TGAACTGGCACCACGTGGGTATAGCGCGCCCC
1347612 TTGCA
1 TTGCA
1347617 GCGAGTTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
50 19 0.40
51 28 0.60
ACGTcount: A:0.19, C:0.30, G:0.27, T:0.24
Consensus pattern (50 bp):
TTGCACCGCGCTATACGATGAACTGGCACCACGTGGGTATAGCGCGCCCC
Found at i:1353543 original size:110 final size:111
Alignment explanation
Indices: 1353349--1353569 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 111
1353339 ATTACAAAAA
* * * *
1353349 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
1353414 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
1353460 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
1353524 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
1353570 ATGATTTTCA
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 33 0.32
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:1353707 original size:12 final size:10
Alignment explanation
Indices: 1353693--1353733 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1353683 ACCTTAAAAA
*
1353693 GAGAGTATTT
1 GAGAGAATTT
1353703 GAGAGAAATTT
1 GAGAG-AATTT
1353714 -AGAGAATTT
1 GAGAGAATTT
1353723 GAGAGAATTT
1 GAGAGAATTT
1353733 G
1 G
1353734 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:1353960 original size:51 final size:48
Alignment explanation
Indices: 1353856--1353979 Score: 131
Period size: 51 Copynumber: 2.5 Consensus size: 48
1353846 AGATATACAG
* * * **
1353856 GTATAGCACGCTGCAGGGGCCGCGCTATACCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGG--GCACTATACCCACGTGGCGCCAAATCACC
* *
1353906 GTATAGCGCGGTGCAAGGGGTGCACTATACCCCATGTGGCGCCAAATCATC
1 GTATAGCGCGGTGC-AGGGG-GCACTATA-CCCACGTGGCGCCAAATCACC
*
1353957 GTATAGCGTGGTGCAGGGGGCAC
1 GTATAGCGCGGTGCAGGGGGCAC
1353980 GCTTTACTGC
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
49 4 0.06
50 24 0.38
51 35 0.56
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (48 bp):
GTATAGCGCGGTGCAGGGGGCACTATACCCACGTGGCGCCAAATCACC
Found at i:1358054 original size:20 final size:20
Alignment explanation
Indices: 1358022--1358077 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1358012 ACGCGATTTT
*
1358022 AAATTCGCTACACGAACTCC
1 AAATTCGCAACACGAACTCC
* **
1358042 AATTTCGCAACAC-AGTTTCC
1 AAATTCGCAACACGA-ACTCC
1358062 AAATTCGCAACACGAA
1 AAATTCGCAACACGAA
1358078 TTTAACAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.38, C:0.30, G:0.11, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACACGAACTCC
Found at i:1358814 original size:20 final size:20
Alignment explanation
Indices: 1358768--1358825 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1358758 CTTGAAACTT
* *
1358768 AAATTCACAACACGAAAATG
1 AAATTCGCAACGCGAAAATG
1358788 AAATTCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
*
1358808 AAATTCGCAATGCGAAAA
1 AAATTCGCAACGCGAAAA
1358826 CAAAAATCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATG
Found at i:1358835 original size:20 final size:20
Alignment explanation
Indices: 1358792--1358845 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
1358782 AAAATGAAAT
** *
1358792 TCGCAACGCGAAAATGAAAT
1 TCGCAACGCGAAAACAAAAA
*
1358812 TCGCAATGCGAAAACAAAAA
1 TCGCAACGCGAAAACAAAAA
* *
1358832 TCGCCACACGAAAA
1 TCGCAACGCGAAAA
1358846 ATAAATTCGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAACAAAAA
Found at i:1358871 original size:20 final size:20
Alignment explanation
Indices: 1358848--1358885 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1358838 CACGAAAAAT
1358848 AAATTCG-AGTTGCGAATTCA
1 AAATTCGTA-TTGCGAATTCA
1358868 AAATTCGTATTGCGAATT
1 AAATTCGTATTGCGAATT
1358886 TCATTTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (20 bp):
AAATTCGTATTGCGAATTCA
Found at i:1358894 original size:20 final size:20
Alignment explanation
Indices: 1358871--1358961 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
1358861 GAATTCAAAA
1358871 TTCGTATTGCGAATTTCATT
1 TTCGTATTGCGAATTTCATT
1358891 TTCG-AGTTGCG------ATT
1 TTCGTA-TTGCGAATTTCATT
* *
1358905 TTCGTTTTACGAATTTCATT
1 TTCGTATTGCGAATTTCATT
* * *
1358925 TTCATGTTGTGAATTTCATT
1 TTCGTATTGCGAATTTCATT
* *
1358945 TTCGTGTTGCGATTTTC
1 TTCGTATTGCGAATTTC
1358962 GTGTTGCGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
14 11 0.20
19 1 0.02
20 42 0.78
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTCGTATTGCGAATTTCATT
Found at i:1358959 original size:14 final size:14
Alignment explanation
Indices: 1358942--1358970 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1358932 TGTGAATTTC
1358942 ATTTTCGTGTTGCG
1 ATTTTCGTGTTGCG
1358956 ATTTTCGTGTTGCG
1 ATTTTCGTGTTGCG
1358970 A
1 A
1358971 ATTTAAGTTT
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:0.10, C:0.14, G:0.28, T:0.48
Consensus pattern (14 bp):
ATTTTCGTGTTGCG
Found at i:1360543 original size:42 final size:42
Alignment explanation
Indices: 1360497--1360599 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 42
1360487 ATTCTCTACT
*
1360497 TCGACA-TCGAGATCCATCACCTGATCGAGCCGATTATACACC
1 TCGACACT-GAGATCCATCACCTGATCGAGCCGACTATACACC
* * * * *
1360539 TCGACACTGAGAGCCATCA---GCTCTAGCCGACTCTATACC
1 TCGACACTGAGATCCATCACCTGATCGAGCCGACTATACACC
1360578 TCGACACTGAGATCCATCACCT
1 TCGACACTGAGATCCATCACCT
1360600 ATTCTATCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
39 33 0.66
42 16 0.32
43 1 0.02
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.21
Consensus pattern (42 bp):
TCGACACTGAGATCCATCACCTGATCGAGCCGACTATACACC
Found at i:1360725 original size:21 final size:21
Alignment explanation
Indices: 1360699--1360868 Score: 112
Period size: 21 Copynumber: 8.1 Consensus size: 21
1360689 ACCTCCACGA
*
1360699 GATGAGTTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
1360720 GATGAGGTCA-ATACTTTACGT
1 GATGAGGT-AGGTGCTTTACGT
*
1360741 GATGAGGTCGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
*** * **
1360762 GAT-AACAATGGTGCATGGCGT
1 GATGAGGTA-GGTGCTTTACGT
**
1360783 GATGAGGTAGG-GTCTTTAATT
1 GATGAGGTAGGTG-CTTTACGT
* * *
1360804 GGTGATGTAGCTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* * *
1360825 GGTGAAGTAGCTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
1360846 GATGAGGTCGGTGCTCTACGT
1 GATGAGGTAGGTGCTTTACGT
1360867 GA
1 GA
1360869 GATTGTTTCA
Statistics
Matches: 111, Mismatches: 32, Indels: 12
0.72 0.21 0.08
Matches are distributed among these distances:
20 2 0.02
21 105 0.95
22 4 0.04
ACGTcount: A:0.21, C:0.13, G:0.34, T:0.33
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:1361177 original size:21 final size:20
Alignment explanation
Indices: 1361151--1361262 Score: 100
Period size: 21 Copynumber: 5.3 Consensus size: 20
1361141 GAAGAAGCTT
*
1361151 GATCCACCTACCATTGTTCAG
1 GATCCACCT-CCATCGTTCAG
*
1361172 GATCCACCTCCTATTGTTCAG
1 GATCCACCTCC-ATCGTTCAG
* *
1361193 GATTCACCTCTCATCGTTCAA
1 GATCCACCTC-CATCGTTCAG
* *
1361214 GATGCC-CCTCCTATCATTTAG
1 GAT-CCACCTCC-ATCGTTCAG
*
1361235 GATCCACCTCCCATCGTTCAA
1 GATCCACCT-CCATCGTTCAG
1361256 GATCCAC
1 GATCCAC
1361263 ATTCCATACC
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
20 5 0.07
21 66 0.88
22 4 0.05
ACGTcount: A:0.22, C:0.36, G:0.12, T:0.29
Consensus pattern (20 bp):
GATCCACCTCCATCGTTCAG
Found at i:1361224 original size:42 final size:42
Alignment explanation
Indices: 1361151--1361258 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
1361141 GAAGAAGCTT
* * * **
1361151 GATCCACCTACCATTGTTCAGGAT-CCACCTCCTATTGTTCAG
1 GATCCACCTCCCATCGTTCAAGATGCC-CCTCCTATCATTCAG
* * *
1361193 GATTCACCTCTCATCGTTCAAGATGCCCCTCCTATCATTTAG
1 GATCCACCTCCCATCGTTCAAGATGCCCCTCCTATCATTCAG
1361235 GATCCACCTCCCATCGTTCAAGAT
1 GATCCACCTCCCATCGTTCAAGAT
1361259 CCACATTCCA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 53 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.34, G:0.13, T:0.31
Consensus pattern (42 bp):
GATCCACCTCCCATCGTTCAAGATGCCCCTCCTATCATTCAG
Found at i:1363536 original size:12 final size:12
Alignment explanation
Indices: 1363515--1363548 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1363505 AGTTGTGGAT
*
1363515 TTTGAGATTGTG
1 TTTGATATTGTG
1363527 TTTGATATTGTG
1 TTTGATATTGTG
*
1363539 TTTGGTATTG
1 TTTGATATTG
1363549 GAAATGTGGT
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:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1364460 original size:39 final size:40
Alignment explanation
Indices: 1364354--1364481 Score: 120
Period size: 39 Copynumber: 3.2 Consensus size: 40
1364344 CAAAAATCGA
** ** * *
1364354 GTTGCGAAAAATAAAATTCGCGTTGCGAAATTGAAACGTGCT
1 GTTGCGAATTATAAAATT-GCGTTGCGAAAAAGAATCTTG-T
* *
1364396 -TTGCGAATTATAAAATCT-TGTTGCGAAAACGAATCTTGT
1 GTTGCGAATTATAAAAT-TGCGTTGCGAAAAAGAATCTTGT
1364435 GTTGCGAATT-TAAAATTGCGTTGCGAAAAAGAAAT-TTGT
1 GTTGCGAATTATAAAATTGCGTTGCGAAAAAG-AATCTTGT
1364474 GTTGCGAA
1 GTTGCGAA
1364482 ATTGTCAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
38 1 0.01
39 30 0.41
40 27 0.37
41 14 0.19
42 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (40 bp):
GTTGCGAATTATAAAATTGCGTTGCGAAAAAGAATCTTGT
Found at i:1364479 original size:20 final size:20
Alignment explanation
Indices: 1364414--1364482 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1364404 TATAAAATCT
*
1364414 TGTTGCGAAAACG-AATCTTG
1 TGTTGCGAAAAAGAAAT-TTG
**
1364434 TGTTGCGAATTTA-AAA-TTG
1 TGTTGCGAA-AAAGAAATTTG
*
1364453 CGTTGCGAAAAAGAAATTTG
1 TGTTGCGAAAAAGAAATTTG
1364473 TGTTGCGAAA
1 TGTTGCGAAA
1364483 TTGTCAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.03
19 14 0.37
20 21 0.55
21 2 0.05
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (20 bp):
TGTTGCGAAAAAGAAATTTG
Found at i:1368649 original size:21 final size:21
Alignment explanation
Indices: 1368623--1368697 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
1368613 GTTTCCAGAT
**
1368623 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1368644 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1368665 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
1368686 TCGTAATGCGAA
1 TCGCAATGCGAA
1368698 TATGTAAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1368747 original size:21 final size:21
Alignment explanation
Indices: 1368721--1368762 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1368711 ATGCGATAGT
1368721 TTGCGATAGTCCAAAATCGCA
1 TTGCGATAGTCCAAAATCGCA
1368742 TTGCGATAGTCCAAAATCGCA
1 TTGCGATAGTCCAAAATCGCA
1368763 ACGACTGGTG
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:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
TTGCGATAGTCCAAAATCGCA
Found at i:1369340 original size:5 final size:5
Alignment explanation
Indices: 1369330--1369362 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1369320 GCCGTCCGTC
*
1369330 TCGGG TCGGG TCGTG TCGGG TCGGG TCGGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG
1369363 TGGTAATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.21, G:0.55, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:1370133 original size:13 final size:12
Alignment explanation
Indices: 1370115--1370249 Score: 80
Period size: 13 Copynumber: 10.8 Consensus size: 12
1370105 AATAGTAAGT
1370115 AAAATAAATATAA
1 AAAATAAATA-AA
*
1370128 AAAATAAAGAAA
1 AAAATAAATAAA
*
1370140 AAGAAGAAA-AAGA
1 AA-AATAAATAA-A
* *
1370153 AAAAAAAGAAAAA
1 AAAATAA-ATAAA
1370166 AAATATAGAAATAAA
1 AAA-AT--AAATAAA
1370181 ACAAATAAATAAA
1 A-AAATAAATAAA
*
1370194 ATAAT-AATAAA
1 AAAATAAATAAA
* *
1370205 AAAGTAAA-AAT
1 AAAATAAATAAA
* *
1370216 AATATATATAAA
1 AAAATAAATAAA
1370228 AAAA-AAATAAA
1 AAAATAAATAAA
1370239 AAAAGTAAATA
1 AAAA-TAAATA
1370250 TATATATATA
Statistics
Matches: 95, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
11 26 0.27
12 20 0.21
13 35 0.37
14 3 0.03
15 7 0.07
16 4 0.04
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.16
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:1370153 original size:15 final size:15
Alignment explanation
Indices: 1370133--1370165 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1370123 TATAAAAAAT
*
1370133 AAAGAAAAAGAAGAA
1 AAAGAAAAAAAAGAA
1370148 AAAGAAAAAAAAGAA
1 AAAGAAAAAAAAGAA
1370163 AAA
1 AAA
1370166 AAATATAGAA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAGAA
Found at i:1370216 original size:20 final size:20
Alignment explanation
Indices: 1370191--1370237 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1370181 ACAAATAAAT
1370191 AAAATAATA-ATA-AAAAAGTA
1 AAAATAATATATATAAAAA--A
1370211 AAAATAATATATATAAAAAA
1 AAAATAATATATATAAAAAA
1370231 AAAATAA
1 AAAATAA
1370238 AAAAAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 17 0.68
21 3 0.12
22 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAATAATATATATAAAAAA
Found at i:1370239 original size:9 final size:9
Alignment explanation
Indices: 1370114--1370247 Score: 74
Period size: 9 Copynumber: 14.4 Consensus size: 9
1370104 AAATAGTAAG
*
1370114 TAAAATAAA
1 TAAAAAAAA
*
1370123 TATAAAAAA
1 TAAAAAAAA
1370132 TAAAGAAAAA
1 TAAA-AAAAA
* *
1370142 GAAGAAAAA
1 TAAAAAAAA
*
1370151 GAAAAAAAA
1 TAAAAAAAA
*
1370160 GAAAAAAAA
1 TAAAAAAAA
* *
1370169 T-ATAGAAA
1 TAAAAAAAA
*
1370177 TAAAACAAA
1 TAAAAAAAA
1370186 TAAATAAAATAA
1 T-AA-AAAA-AA
1370198 TAATAAAAAA
1 TAA-AAAAAA
*
1370208 GTAAAAATAA
1 -TAAAAAAAA
* * *
1370218 TATATATAA
1 TAAAAAAAA
1370227 -AAAAAAAA
1 TAAAAAAAA
*
1370235 TAAAAAAAG
1 TAAAAAAAA
1370244 TAAA
1 TAAA
1370248 TATATATATA
Statistics
Matches: 99, Mismatches: 19, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
8 11 0.11
9 56 0.57
10 16 0.16
11 13 0.13
12 3 0.03
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.16
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1370354 original size:21 final size:20
Alignment explanation
Indices: 1370326--1370370 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 20
1370316 ATAAAAATAT
1370326 ATACTAAAA-TAAAAAAGAAA
1 ATACTAAAAGTAAAAAA-AAA
1370346 ATACATAAAATGTAAAAAAAAA
1 ATAC-TAAAA-GTAAAAAAAAA
1370368 ATA
1 ATA
1370371 TTACATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 5 0.23
22 6 0.27
23 7 0.32
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (20 bp):
ATACTAAAAGTAAAAAAAAA
Found at i:1370696 original size:37 final size:37
Alignment explanation
Indices: 1370655--1370735 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
1370645 GGATCATATC
* * *
1370655 TTTAGGAATTTAAATAATAGTAGAACTCTATTCTATT
1 TTTAGGAATTTAAATAATAGCAAAACTCTATCCTATT
* * * * *
1370692 TTTAGGAGTTTGAATCATAGCAAAATTTTATCCTATT
1 TTTAGGAATTTAAATAATAGCAAAACTCTATCCTATT
1370729 TTTAGGA
1 TTTAGGA
1370736 GTTTGAATCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.43
Consensus pattern (37 bp):
TTTAGGAATTTAAATAATAGCAAAACTCTATCCTATT
Found at i:1370763 original size:34 final size:34
Alignment explanation
Indices: 1370688--1370781 Score: 134
Period size: 34 Copynumber: 2.7 Consensus size: 34
1370678 AACTCTATTC
* * *
1370688 TATTTTTAGGAGTTTGAATCATAGCAAAATTTTATCC
1 TATTTTTAGGAGTTTGAATCCT---AAAATTCTATCA
1370725 TATTTTTAGGAGTTTGAATCCTAAAATTCTATCA
1 TATTTTTAGGAGTTTGAATCCTAAAATTCTATCA
1370759 TATTTTTAGGAGTTTGAATCCTA
1 TATTTTTAGGAGTTTGAATCCTA
1370782 GTAGGACGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
34 33 0.61
37 21 0.39
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (34 bp):
TATTTTTAGGAGTTTGAATCCTAAAATTCTATCA
Found at i:1371637 original size:105 final size:105
Alignment explanation
Indices: 1371330--1372266 Score: 1436
Period size: 105 Copynumber: 9.0 Consensus size: 105
1371320 CATTGTTCCA
* * * ** * * *
1371330 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
1371395 CAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * **
1371436 AGTCCAATATCATTCGTTATGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1371496 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1371536 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1371601 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1371641 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTATTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * *
1371706 AGCGGTCCATTCGTCGTGAAGTTGAACTTGCATTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1371746 AGTCCAATATCCTTCGTTGTGAAATTGAAATTAGCTCTGAAATTGAGAAGTTGTTGTTGACAAGA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1371811 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1371851 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1371916 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1371956 AGTCCAATATCCTTCATTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1372021 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1372061 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1372126 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1372166 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
1372231 CAGTC-GTCCATTCGTTGTGAAGTTGAACTTGTGTTG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1372267 CCTCGAGTGC
Statistics
Matches: 774, Mismatches: 50, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
100 82 0.11
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 606 0.78
106 73 0.09
107 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1373044 original size:67 final size:66
Alignment explanation
Indices: 1372909--1373066 Score: 201
Period size: 68 Copynumber: 2.4 Consensus size: 66
1372899 AAGATATCTG
* * **
1372909 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
1372974 TT
65 TT
* * * * *
1372976 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATT-TGTTTTAGGGGAAATAAATTCAAAGG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
1373040 TT
65 TT
*
1373042 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
1373067 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 31 0.39
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:1373082 original size:65 final size:67
Alignment explanation
Indices: 1372910--1373092 Score: 183
Period size: 65 Copynumber: 2.7 Consensus size: 67
1372900 AGATATCTGT
* * * * * ** *
1372910 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
1372975 TTG
65 TTG
* * * *
1372978 TGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
1373042 T-
66 TG
* * * *
1373043 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-GAAAATTTGTTTTAAGGGAAA
1373093 CTGTCTCAAG
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
65 37 0.38
66 7 0.07
67 22 0.23
68 31 0.32
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:1373093 original size:36 final size:35
Alignment explanation
Indices: 1373042--1373248 Score: 160
Period size: 36 Copynumber: 5.9 Consensus size: 35
1373032 TTCAAAGGTT
* *
1373042 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1373078 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1373113 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
1373151 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
1373180 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1373215 TTTATTTCAAGGGAAACTGTCTCAAGATAGACAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1373249 TGGTGAGCAC
Statistics
Matches: 138, Mismatches: 19, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.01
29 17 0.12
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 7 0.05
36 74 0.54
37 30 0.22
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1373138 original size:37 final size:36
Alignment explanation
Indices: 1373053--1373164 Score: 129
Period size: 37 Copynumber: 3.1 Consensus size: 36
1373043 TGTTTCAAGG
* * *
1373053 GAAACTGTCTCAAGATAGACGAAAATTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACGAAAATTGTTCCAAAA
1373089 GAAACTGTCTCAAGAGAGAC-AAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACGAAAA-TT-GTTCCAAAA
* * * *
1373126 GAAACTGTCTCAAGGGAGACGGAATTTGTTTC-AAA
1 GAAACTGTCTCAAGAGAGACGAAAATTGTTCCAAAA
1373161 GAAA
1 GAAA
1373165 ACATATTCAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
35 11 0.17
36 25 0.38
37 28 0.42
38 2 0.03
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACGAAAATTGTTCCAAAA
Found at i:1373152 original size:138 final size:138
Alignment explanation
Indices: 1372990--1373248 Score: 367
Period size: 138 Copynumber: 1.9 Consensus size: 138
1372980 TTTCAAGAGT
* * ** * * *
1372990 AACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
1373055 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
1373119 TCCAAAAGA
130 TCCAAAAGA
** * *
1373128 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
1373193 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACAA
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAA
1373249 TGGTGAGCAC
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
137 4 0.04
138 101 0.96
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (138 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
CCAAAAGA
Found at i:1373710 original size:18 final size:18
Alignment explanation
Indices: 1373683--1373718 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1373673 TGTTGAATCC
* *
1373683 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
1373701 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1373719 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1374211 original size:22 final size:22
Alignment explanation
Indices: 1374134--1374204 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
1374124 TTGTGTTTGG
*
1374134 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
1374156 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
1374178 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
1374200 TCAAA
1 TCAAA
1374205 AGATTGATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:1374856 original size:23 final size:24
Alignment explanation
Indices: 1374830--1374882 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
1374820 TTTGCATGTG
*
1374830 CTTTTTGTCCCTTTTT-CTTTTTT
1 CTTTTTGTCCCTTTTTGCTTTTGT
* *
1374853 CTTTTTGTTCTTTTTTGCTTTTGT
1 CTTTTTGTCCCTTTTTGCTTTTGT
1374877 -TTTTTG
1 CTTTTTG
1374883 CTTCTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.75
Consensus pattern (24 bp):
CTTTTTGTCCCTTTTTGCTTTTGT
Found at i:1377873 original size:15 final size:15
Alignment explanation
Indices: 1377855--1377884 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1377845 AAAACCATGT
1377855 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1377870 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1377885 GAAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1377891 original size:15 final size:15
Alignment explanation
Indices: 1377858--1377892 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1377848 ACCATGTTAG
* *
1377858 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
1377873 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
1377888 ATAAA
1 ATAAA
1377893 TTAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:1378037 original size:25 final size:25
Alignment explanation
Indices: 1377971--1378086 Score: 78
Period size: 25 Copynumber: 4.6 Consensus size: 25
1377961 AAATAGTAAG
*
1377971 TAAAATAAATATAAAAAATAAAGAAA
1 TAAAATAAATA-AAAAAATATAGAAA
* * *
1377997 AAGAAGAAAAAGAAAAAAATATAGAAA
1 TA-AA-ATAAATAAAAAAATATAGAAA
*
1378024 TAAAACAAATAAAATAAA-ATA-ATAA
1 TAAAATAAATAAAA-AAATATAGA-AA
* * *
1378049 TAAAA-AAGTAAAAATAATATATATA
1 TAAAATAAATAAAAA-AATATAGAAA
1378074 TAAAATAAA-AAAA
1 TAAAATAAATAAAA
1378087 TAAAAAAAGT
Statistics
Matches: 72, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
23 1 0.01
24 10 0.14
25 31 0.43
26 9 0.12
27 16 0.22
28 5 0.07
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (25 bp):
TAAAATAAATAAAAAAATATAGAAA
Found at i:1378081 original size:30 final size:31
Alignment explanation
Indices: 1378042--1378105 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
1378032 ATAAAATAAA
* *
1378042 ATAATAATAAAAAAGTAAAAATAA-TATATAT
1 ATAATAATAAAAAAATAAAAA-AAGTAAATAT
1378073 ATAA-AATAAAAAAATAAAAAAAGTAAATAT
1 ATAATAATAAAAAAATAAAAAAAGTAAATAT
1378103 ATA
1 ATA
1378106 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 24 0.80
31 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (31 bp):
ATAATAATAAAAAAATAAAAAAAGTAAATAT
Found at i:1378094 original size:9 final size:9
Alignment explanation
Indices: 1377971--1378099 Score: 64
Period size: 9 Copynumber: 13.4 Consensus size: 9
1377961 AAATAGTAAG
*
1377971 TAAAATAAA
1 TAAAAAAAA
*
1377980 TATAAAAAA
1 TAAAAAAAA
1377989 TAAAGAAAAA
1 TAAA-AAAAA
* *
1377999 GAAGAAAAA
1 TAAAAAAAA
*
1378008 GAAAAAAATA
1 TAAAAAAA-A
1378018 TAGAAATAAAA
1 TA-AAA-AAAA
* *
1378029 CAAATAAAA
1 TAAAAAAAA
1378038 TAAAATAATAA
1 TAAAA-AA-AA
*
1378049 T-AAAAAAG
1 TAAAAAAAA
1378057 TAAAAATAATA
1 TAAAAA-AA-A
*
1378068 TATATATAAAA
1 TA-A-AAAAAA
1378079 T-AAAAAAA
1 TAAAAAAAA
*
1378087 TAAAAAAAG
1 TAAAAAAAA
1378096 TAAA
1 TAAA
1378100 TATATATATA
Statistics
Matches: 92, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
8 8 0.09
9 46 0.50
10 18 0.20
11 12 0.13
12 6 0.07
13 2 0.02
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1378105 original size:36 final size:40
Alignment explanation
Indices: 1378032--1378177 Score: 118
Period size: 41 Copynumber: 3.4 Consensus size: 40
1378022 AATAAAACAA
*
1378032 ATAAAATAAAATAATAATAAAAAAGTAAAAATAATATATAT
1 ATAAAATAAAAAAATAATAAAAAAGT-AAAATAATATATAT
1378073 ATAAAATAAAAAAAT-A-AAAAAAGTAAATATATATATATATAT
1 ATAAAATAAAAAAATAATAAAAAAGT-AA-A-ATA-ATATATAT
* *
1378115 ATATAAATTAATAAAACTGATAATAAAAAA-TAATATATTTATATAT
1 ATA-AAA-TAA-AAAA---ATAATAAAAAAGTAAAATA-ATATATAT
**
1378161 ATAATCTAAAAAAATAA
1 ATAAAATAAAAAAATAA
1378178 AAATATATAC
Statistics
Matches: 89, Mismatches: 5, Indels: 23
0.76 0.04 0.20
Matches are distributed among these distances:
39 11 0.12
40 6 0.07
41 17 0.19
42 11 0.12
43 7 0.08
44 6 0.07
45 5 0.06
46 14 0.16
48 4 0.04
49 2 0.02
50 6 0.07
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (40 bp):
ATAAAATAAAAAAATAATAAAAAAGTAAAATAATATATAT
Found at i:1378113 original size:44 final size:45
Alignment explanation
Indices: 1378032--1378177 Score: 146
Period size: 44 Copynumber: 3.4 Consensus size: 45
1378022 AATAAAACAA
*
1378032 ATAAAATAAAATAATAATAAAAAAGT-AA-AA-ATA-ATATATAT
1 ATAAAATAAAAAAATAATAAAAAAGTAAATAATATATATATATAT
1378073 ATAAAATAAAAAAAT-A-AAAAAAGTAAATATATATATATATATAT
1 ATAAAATAAAAAAATAATAAAAAAGTAAATA-ATATATATATATAT
* * * * *
1378117 ATAAATTAATAAAACTGATAATAAA--AAATAATATATTTATATAT
1 ATAAAATAA-AAAAATAATAAAAAAGTAAATAATATATATATATAT
**
1378161 ATAATCTAAAAAAATAA
1 ATAAAATAAAAAAATAA
1378178 AAATATATAC
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
39 8 0.09
40 3 0.03
41 15 0.17
42 1 0.01
43 9 0.10
44 36 0.41
45 10 0.11
46 1 0.01
47 5 0.06
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (45 bp):
ATAAAATAAAAAAATAATAAAAAAGTAAATAATATATATATATAT
Found at i:1378318 original size:14 final size:15
Alignment explanation
Indices: 1378299--1378337 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1378289 AAATGTGCTT
*
1378299 ATAAATAAAATTA-A
1 ATAAATAAAATAATA
1378313 ATAAATAAAATAATA
1 ATAAATAAAATAATA
*
1378328 ATAATTAAAA
1 ATAAATAAAA
1378338 CGTAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAAATAAAATAATA
Found at i:1378555 original size:37 final size:37
Alignment explanation
Indices: 1378514--1378594 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
1378504 GGATCATATC
* *
1378514 TTTAGGAATTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAATTTAAATAATAGCAAAACTCTATCCTATT
* * * * * *
1378551 TTTAGGAGTTTGAATCATAGCAAAATTTTATTCTATT
1 TTTAGGAATTTAAATAATAGCAAAACTCTATCCTATT
1378588 TTTAGGA
1 TTTAGGA
1378595 GTTTGAATCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.43
Consensus pattern (37 bp):
TTTAGGAATTTAAATAATAGCAAAACTCTATCCTATT
Found at i:1378622 original size:34 final size:33
Alignment explanation
Indices: 1378540--1378640 Score: 130
Period size: 34 Copynumber: 2.9 Consensus size: 33
1378530 ATAGTAGAAC
*
1378540 TCTATCCTATTTTTAGGAGTTTGAATCATAGCAAAAT
1 TCTAT-CTATTTTTAGGAGTTTGAATCCT---AAAAT
*
1378577 TTTATTCTATTTTTAGGAGTTTGAATCCTAAAAT
1 TCTA-TCTATTTTTAGGAGTTTGAATCCTAAAAT
1378611 TCTATCATATTTTTAGGAGTTTGAATCCTA
1 TCTATC-TATTTTTAGGAGTTTGAATCCTA
1378641 GTAGGACGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
33 2 0.03
34 31 0.53
37 25 0.42
38 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.46
Consensus pattern (33 bp):
TCTATCTATTTTTAGGAGTTTGAATCCTAAAAT
Found at i:1378842 original size:19 final size:19
Alignment explanation
Indices: 1378818--1378862 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1378808 TATAAAATAT
*
1378818 TTTAAAACTTAAGAAC-TAA
1 TTTAAAA-TAAAGAACATAA
*
1378837 TTTAAAATAAAGATCATAA
1 TTTAAAATAAAGAACATAA
1378856 TTTAAAA
1 TTTAAAA
1378863 ACATAGTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (19 bp):
TTTAAAATAAAGAACATAA
Found at i:1380020 original size:18 final size:18
Alignment explanation
Indices: 1379970--1380020 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1379960 TATGAAATTG
* *
1379970 GATTCCAATTCC-TGACA
1 GATTTCAATTCCTTCACA
*
1379987 GA-TTCTAATTCATTCACA
1 GATTTC-AATTCCTTCACA
1380005 GATTTCAATTCCTTCA
1 GATTTCAATTCCTTCA
1380021 GAAATATTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 2 0.07
17 7 0.26
18 15 0.56
19 3 0.11
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:1380570 original size:18 final size:18
Alignment explanation
Indices: 1380547--1380582 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1380537 CCTATTTTTA
1380547 TTAATAAAAATAATATTT
1 TTAATAAAAATAATATTT
* *
1380565 TTAATAAATATATTATTT
1 TTAATAAAAATAATATTT
1380583 CAGATCGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATAAAAATAATATTT
Found at i:1386089 original size:185 final size:184
Alignment explanation
Indices: 1385737--1386104 Score: 587
Period size: 185 Copynumber: 2.0 Consensus size: 184
1385727 TTTAAATGTT
* *
1385737 TTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGA
1 TTTTAATTCAAAAAAAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGA
*
1385802 TAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTG
66 TAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTA
* * *
1385867 GGTTTTAAATGGTTTGGACTGAGCTTATATGTTATATATAATATATTTAATATA
131 AGTTTTAAATGGTTTGGACTGAGCTCATATATTATATATAATATATTTAATATA
* * *
1385921 TTTTAATTTAAAAAACAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTAT
1 TTTTAATTCAAAAAA-AATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
*
1385986 ATACATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTATAA-TATTAAT
65 ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTA-AATTATTAAT
* *
1386050 TAAGTTTTAAATGGTTTGGGCT-AGGTCCATATATTATATATAATATATTTAATAT
129 TAAGTTTTAAATGGTTTGGACTGAGCT-CATATATTATATATAATATATTTAATAT
1386105 TTAAAATTTA
Statistics
Matches: 169, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
184 17 0.10
185 150 0.89
186 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (184 bp):
TTTTAATTCAAAAAAAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGA
TAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTA
AGTTTTAAATGGTTTGGACTGAGCTCATATATTATATATAATATATTTAATATA
Found at i:1388401 original size:20 final size:19
Alignment explanation
Indices: 1388352--1388403 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
1388342 ATCTTACAAC
*
1388352 TATATATTTTATTTAAATA
1 TATATATTTAATTTAAATA
1388371 -ATAATTAATTTAATTATAAATA
1 TAT-A-T-ATTTAATT-TAAATA
1388393 TATATATTTAA
1 TATATATTTAA
1388404 ATATTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
18 2 0.07
19 1 0.04
20 7 0.26
21 8 0.30
22 7 0.26
23 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATATATTTAATTTAAATA
Found at i:1399517 original size:16 final size:16
Alignment explanation
Indices: 1399492--1399532 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1399482 ATAAAGCATC
*
1399492 TGAATTATTCAGTATT
1 TGAATCATTCAGTATT
1399508 TGAATCATTCAGTATT
1 TGAATCATTCAGTATT
*
1399524 TAAATCATT
1 TGAATCATT
1399533 TAACGCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (16 bp):
TGAATCATTCAGTATT
Done.