Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008051.1 Hibiscus syriacus cultivar Beakdansim tig00110546_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: 579609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:478973 original size:14 final size:14
Alignment explanation
Indices: 478953--479003 Score: 93
Period size: 14 Copynumber: 3.6 Consensus size: 14
478943 GATTGTTTAA
478953 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
478967 GTGATTTGTAAAAG
1 TTGATTTGTAAAAG
478981 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
478995 TTGATTTGT
1 TTGATTTGT
479004 TTAATTGATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:479226 original size:19 final size:19
Alignment explanation
Indices: 479108--479217 Score: 220
Period size: 19 Copynumber: 5.8 Consensus size: 19
479098 AAAAAGTACT
479108 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
479127 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
479146 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
479165 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
479184 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
479203 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
479218 TAAATTCGCG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 91 1.00
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:479244 original size:19 final size:19
Alignment explanation
Indices: 479222--479338 Score: 69
Period size: 19 Copynumber: 6.7 Consensus size: 19
479212 CGAAATTAAA
479222 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
479241 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
479256 --C-CGTTTGCGATTTTCAT
1 TTCGCG-TTGCGATTTTCAT
*
479273 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
479288 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
479306 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
479325 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
479339 AGACATTAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 27
0.66 0.10 0.24
Matches are distributed among these distances:
12 1 0.01
13 7 0.10
14 9 0.12
15 3 0.04
16 3 0.04
17 6 0.08
19 33 0.45
20 11 0.15
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:479269 original size:32 final size:33
Alignment explanation
Indices: 479226--479318 Score: 163
Period size: 32 Copynumber: 2.8 Consensus size: 33
479216 ATTAAATTCG
479226 CGTTGCGATTTTCATTTCGCATTGCGATTC-C-
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
479257 CGTTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CG-TTGCGATTTTCATTTCGCATTGCGATTCTCT
479291 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
479319 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.03
32 28 0.47
33 27 0.46
34 2 0.03
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:481955 original size:163 final size:161
Alignment explanation
Indices: 481771--482096 Score: 570
Period size: 164 Copynumber: 2.0 Consensus size: 161
481761 AGAGAAAGGT
481771 TGTGGGTTTGAGAAAACTTAG-TGATTACTACCCGCTACTGACCCAACAATACTACTTCTAGGTT
1 TGTGGGTTTGAGAAAACTTAGTTGATTACTACCCGCTACTGACCCAACAATACTACTTCTAGGTT
481835 CAACAAATACAATGTAACATCATC-C-TGAAACACTAATGTAAGCAATGAATCGTTCAACATCTT
66 CAAC--ATACAATGTAACATCATCACTTGAAACACTAATGTAAGCAATGAA--GTTCAACATCTT
481898 CATTGTCGGTTAACAAATAAACTTTA-CATTCCTC
127 CATTGTCGGTTAACAAATAAACTTTACCATTCCTC
481932 TGTGGGTTTTGAGAAAAACTTAGTTGATTACTACCCGCTACTGACCCAACAATACTACTTCTAGG
1 TGTGGG-TTTGAG-AAAACTTAGTTGATTACTACCCGCTACTGACCCAACAATACTACTTCTAGG
481997 TTCAACATACAATGTAACATCATCACTTGAAACACTAATGTAAGCAATGAAGTTCAACATCTTCA
64 TTCAACATACAATGTAACATCATCACTTGAAACACTAATGTAAGCAATGAAGTTCAACATCTTCA
482062 TTGTCGGTTAACAAATAAACTTTACCATTCCTC
129 TTGTCGGTTAACAAATAAACTTTACCATTCCTC
482095 TG
1 TG
482097 ATAAGATAGC
Statistics
Matches: 159, Mismatches: 0, Indels: 10
0.94 0.00 0.06
Matches are distributed among these distances:
161 6 0.04
162 62 0.39
163 20 0.13
164 71 0.45
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.30
Consensus pattern (161 bp):
TGTGGGTTTGAGAAAACTTAGTTGATTACTACCCGCTACTGACCCAACAATACTACTTCTAGGTT
CAACATACAATGTAACATCATCACTTGAAACACTAATGTAAGCAATGAAGTTCAACATCTTCATT
GTCGGTTAACAAATAAACTTTACCATTCCTC
Found at i:482615 original size:20 final size:21
Alignment explanation
Indices: 482590--482637 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
482580 CCTAATTCGT
*
482590 AATGCGAA-TAAGTAAATCGC
1 AATGCGAATTAAGAAAATCGC
**
482610 AATGCGAATTTGGAAAATCGC
1 AATGCGAATTAAGAAAATCGC
482631 AATGCGA
1 AATGCGA
482638 TACTGACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (21 bp):
AATGCGAATTAAGAAAATCGC
Found at i:482711 original size:20 final size:20
Alignment explanation
Indices: 482622--482713 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
482612 TGCGAATTTG
* *
482622 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
482642 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
482662 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
482683 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
482703 GAAAATCGCAA
1 GAAAATCGCAA
482714 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:482946 original size:20 final size:20
Alignment explanation
Indices: 482911--482948 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
482901 ATTCATTTGA
*
482911 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
482931 CTATCGCAACTAGAAAAT
1 CTATCGCAACGAGAAAAT
482949 CGCAATGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:483008 original size:19 final size:19
Alignment explanation
Indices: 482967--483034 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
482957 GAAATGAAAA
482967 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
482983 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
483000 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
483019 TTGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
483035 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:484950 original size:19 final size:18
Alignment explanation
Indices: 484886--485018 Score: 93
Period size: 20 Copynumber: 7.5 Consensus size: 18
484876 ACGAAACTTA
*
484886 AAATCGCAACGCGAAAATG
1 AAATCGCAATGCG-AAATG
* *
484905 ACTATCGCAACGCGAAAATGG
1 A-AATCGCAATGCG-AAAT-G
**
484926 CTATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
484944 CAAATCGCAA--CGACA--
1 -AAATCGCAATGCGAAATG
484959 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
484977 AAAATCGCAA--CGACA--
1 -AAATCGCAATGCGAAATG
484992 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
485010 AAATCGCAA
1 AAATCGCAA
485019 CTCGAAACAC
Statistics
Matches: 93, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
14 18 0.19
16 8 0.09
17 8 0.09
18 10 0.11
19 21 0.23
20 27 0.29
21 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.20, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Found at i:484964 original size:14 final size:14
Alignment explanation
Indices: 484945--485000 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
484935 TGCGAAATGC
484945 AAATCGCAACGACA
1 AAATCGCAACGACA
*
484959 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
484978 AAATCGCAACGACA
1 AAATCGCAACGACA
484992 AAATCGCAA
1 AAATCGCAA
485001 TGCGAAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:484970 original size:33 final size:32
Alignment explanation
Indices: 484928--485019 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 32
484918 GAAAATGGCT
484928 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
484961 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
484994 ATCGCAATGCGAAATGAAATCGCAAC
1 ATCGCAATGCGAAATGAAATCGCAAC
485020 TCGAAACACA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 10 0.17
33 48 0.83
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:485054 original size:19 final size:18
Alignment explanation
Indices: 485032--485095 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
485022 GAAACACAAA
485032 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
*
485051 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
485067 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
485084 TCGCATTGCGAT
1 TCGCATTGCGAT
485096 AGCCATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 4 0.11
19 17 0.45
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:485102 original size:19 final size:20
Alignment explanation
Indices: 485080--485123 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
485070 TTGCGATTTT
485080 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
485099 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
485119 CATTT
1 CATTT
485124 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:485131 original size:20 final size:20
Alignment explanation
Indices: 485089--485134 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
485079 TCATTTCGCA
*
485089 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
485109 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
485129 TTGCGA
1 TTGCGA
485135 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:486969 original size:20 final size:20
Alignment explanation
Indices: 486944--487017 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
486934 AATAGTTTCT
*
486944 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
486964 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
486984 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
487004 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
487018 GTTGCGATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:487256 original size:22 final size:22
Alignment explanation
Indices: 487229--487272 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
487219 GATGGAGATA
487229 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
487251 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
487273 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:487546 original size:20 final size:20
Alignment explanation
Indices: 487437--487571 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
487427 CGCTTTGAAA
*
487437 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
487458 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTAAGT
* * *
487478 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
487498 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
487519 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* *
487539 ATCTCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
487559 ATCGCATTGCGAT
1 ATCGCATTGCGAT
487572 TTTCTCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 64 0.68
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:487590 original size:61 final size:61
Alignment explanation
Indices: 487437--487592 Score: 188
Period size: 61 Copynumber: 2.6 Consensus size: 61
487427 CGCTTTGAAA
* * * *
487437 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
487498 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCTCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* *
487559 ATCGCATTGCGATTTTCTCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGAT
487593 TTACTTATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:487604 original size:20 final size:21
Alignment explanation
Indices: 487560--487611 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
487550 ATAGTCAGTA
*
487560 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACTCAAT
* *
487581 TCGCGTTGCGATTTACT-TAT
1 TCGCATTGCGATTTACTCAAT
487601 TCGCATTGCGA
1 TCGCATTGCGA
487612 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTACTCAAT
Found at i:487682 original size:21 final size:21
Alignment explanation
Indices: 487642--487682 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
487632 ACTGTAGACC
** *
487642 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
487663 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
487683 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:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:488720 original size:70 final size:71
Alignment explanation
Indices: 488596--488738 Score: 279
Period size: 70 Copynumber: 2.0 Consensus size: 71
488586 ACAGATCCAA
488596 GTTAAGGGGACAATATTTGTTGAAGGAAAGGCCATGAGGCGATTGTTGTGTCCATTGTTGCTGCC
1 GTTAAGGGGACAATATTTGTTGAAGGAAAGGCCATGAGGCGATTGTTGTGTCCATTGTTGCTGCC
488661 AACCAT
66 AACCAT
488667 GTTAAGGGGACAATATTTGTTGAAGG-AAGGCCATGAGGCGATTGTTGTGTCCATTGTTGCTGCC
1 GTTAAGGGGACAATATTTGTTGAAGGAAAGGCCATGAGGCGATTGTTGTGTCCATTGTTGCTGCC
488731 AACCAT
66 AACCAT
488737 GT
1 GT
488739 GCATTGTGCC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 46 0.64
71 26 0.36
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (71 bp):
GTTAAGGGGACAATATTTGTTGAAGGAAAGGCCATGAGGCGATTGTTGTGTCCATTGTTGCTGCC
AACCAT
Found at i:490283 original size:29 final size:29
Alignment explanation
Indices: 490241--490318 Score: 129
Period size: 29 Copynumber: 2.7 Consensus size: 29
490231 CCTAACTAAT
*
490241 TGATGTAAGCAATGACATCATTACTTAAA
1 TGATGTAAGCAATGACATCATTAATTAAA
*
490270 TGATGTAAGCAATGACATCTTTAATTAAA
1 TGATGTAAGCAATGACATCATTAATTAAA
*
490299 TGATGTAAGTAATGACATCA
1 TGATGTAAGCAATGACATCA
490319 ATTTAGATTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (29 bp):
TGATGTAAGCAATGACATCATTAATTAAA
Found at i:495013 original size:28 final size:28
Alignment explanation
Indices: 494972--495052 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 28
494962 ATCACCTAAC
*
494972 TAAATTGATGTAAGCATGACATCATTATT
1 TAAA-TGATGTAAGCATGACATCATTAAT
*
495001 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGC-ATGACATCATTAAT
**
495030 TAAATGATGTAATAATGACATCA
1 TAAATGATGTAAGCATGACATCA
495053 ATTTAGTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
28 18 0.39
29 28 0.61
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (28 bp):
TAAATGATGTAAGCATGACATCATTAAT
Found at i:496184 original size:15 final size:16
Alignment explanation
Indices: 496155--496184 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
496145 AACTCACGAC
496155 TCCATTAGAAGTGTAA
1 TCCATTAGAAGTGTAA
496171 TCCATTAG-AGTGTA
1 TCCATTAGAAGTGTA
496185 GTAGTGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (16 bp):
TCCATTAGAAGTGTAA
Found at i:503947 original size:22 final size:22
Alignment explanation
Indices: 503921--503973 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
503911 ACACATCATA
503921 TGTTTCAACATCCACTCATAAT
1 TGTTTCAACATCCACTCATAAT
503943 TGTTTCAACATCCACTCATAAT
1 TGTTTCAACATCCACTCATAAT
503965 TGTTTCAAC
1 TGTTTCAAC
503974 TCTTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (22 bp):
TGTTTCAACATCCACTCATAAT
Found at i:508301 original size:3 final size:3
Alignment explanation
Indices: 508293--508700 Score: 561
Period size: 3 Copynumber: 136.3 Consensus size: 3
508283 ATTTAAGTTT
508293 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
508341 GAA GAA GAA GAAA GAAA GAA GAA GAA GAA GAA GAA GAA -AG GAGA GAA
1 GAA GAA GAA G-AA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA
*
508388 GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA
*
508437 GAA GAA GAA GAA G-A GAA GGA GAA GAA GAA G-A GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
508483 GAA GAA G-A GAA G-A GAA GGA GAA GAA AAA GAA GAA GAA GAA G-A GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
508528 GAA GAA GAA GAGA GGA GAGA GAA GAA GGA GAA GAGA GAA GGA GAA GGAA
1 GAA GAA GAA GA-A GAA GA-A GAA GAA GAA GAA GA-A GAA GAA GAA -GAA
508577 GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GAGA GAA G-A GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA
508621 GAA G-A GAA G-A GAA GAA G-A GAA GAAA GAA GAA GAAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA G-AA GAA GAA GAA
508665 G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
508701 GGTAGCTAGG
Statistics
Matches: 367, Mismatches: 16, Indels: 44
0.86 0.04 0.10
Matches are distributed among these distances:
2 23 0.06
3 312 0.85
4 32 0.09
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:508724 original size:15 final size:15
Alignment explanation
Indices: 508704--508744 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
508694 GAAGAAGGGT
508704 AGCTAGGGGAATGAA
1 AGCTAGGGGAATGAA
508719 AGCTAGGGGAATGAA
1 AGCTAGGGGAATGAA
508734 AGCTAGGGGAA
1 AGCTAGGGGAA
508745 GGGTGGCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.41, T:0.12
Consensus pattern (15 bp):
AGCTAGGGGAATGAA
Found at i:508874 original size:113 final size:114
Alignment explanation
Indices: 508757--509018 Score: 467
Period size: 113 Copynumber: 2.3 Consensus size: 114
508747 GTGGCTACGG
* * * *
508757 GAAGAAGCAGAAGAAGAAGAAAAAGGGCAGCTAGGGGGGAGGGTGGCTACGGGTGTATATTTGAT
1 GAAGAAGAAGAAGAAGAAGAAGAAGGGCAGCTAGGGGGAAGGGTGGCTAAGGGTGTATATTTGAT
508822 TTAGTATAGTTAAAATTTTTCTTTATA-TTTTTTCATATGCAATACGTT
66 TTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTT
508870 GAAGAAGAAGAAGAAGAAGAAGAAGGGCAGCTAGGGGGAAGGGTGGCTAAGGGTGTATATTTGAT
1 GAAGAAGAAGAAGAAGAAGAAGAAGGGCAGCTAGGGGGAAGGGTGGCTAAGGGTGTATATTTGAT
508935 TTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTT
66 TTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTT
508984 GAAGAAGAAGAAG-A-AAGAAGAAGGGCAGCTAGGGG
1 GAAGAAGAAGAAGAAGAAGAAGAAGGGCAGCTAGGGG
509019 AATGAAAGCT
Statistics
Matches: 144, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
112 21 0.15
113 89 0.62
114 34 0.24
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.28
Consensus pattern (114 bp):
GAAGAAGAAGAAGAAGAAGAAGAAGGGCAGCTAGGGGGAAGGGTGGCTAAGGGTGTATATTTGAT
TTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTT
Found at i:508878 original size:3 final size:3
Alignment explanation
Indices: 508870--508894 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
508860 GCAATACGTT
508870 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
508895 GGCAGCTAGG
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:509055 original size:179 final size:175
Alignment explanation
Indices: 508870--509370 Score: 754
Period size: 179 Copynumber: 2.9 Consensus size: 175
508860 GCAATACGTT
* * *
508870 GAAGAAGAAGAAGAAGAAGAAGAAGGGCAGCTAGGGGGAAGGGTGGCTAAGGGTGTATATTTGAT
1 GAAGAAGAAGAAGAAGAAGAAAAAGGGCAGCTAGGGGGGAGGGTGGCTACGGGTGTATATTTGAT
508935 TTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTGAAGAAGAAGAAGAAA
66 TTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTGAAGAAGAAGAAGAAA
*
509000 GAAGAAGGGCAGCTAGGGGAATGAAAGCTAGGGGGAAGGGTGGCTACGG-
131 GAAGAAGGGCAGCTAGGGG---G-AAGCTA-AGGGAAGGGTGGCTACGGA
* * *
509049 GAAGAAGCAGAAGAAGAAGAAAAAGGGAAGCTAGGGGGGAGGGTGGCTACGAGTGTATATTTGAT
1 GAAGAAGAAGAAGAAGAAGAAAAAGGGCAGCTAGGGGGGAGGGTGGCTACGGGTGTATATTTGAT
509114 TTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTGAAGAAGAAGAAG-AA
66 TTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTGAAGAAGAAGAAGAAA
*
509178 GAAGAA--G-A---A--GGGCAGCTAAGGGAAGGGTGGCTACGGAAA
131 GAAGAAGGGCAGCTAGGGGGAAGCTAAGGGAAGGGTGGCTACGG--A
*
509217 GAAGCAGAAGAAGAAGAAGAAAAAGGGCAGCTAGGGGGGAGGGTGGCTACGGGTGTATATTTGAT
1 GAAGAAGAAGAAGAAGAAGAAAAAGGGCAGCTAGGGGGGAGGGTGGCTACGGGTGTATATTTGAT
*
509282 TTAGTATAGTTAAAATTTTTCTTTATA-TTTTTTCATATGCAATACGTTAAAGAAGAAGAAGAAG
66 TTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTGAAGAAGAAGAAG-A-
509346 AAGAAGAAGGGCAGCTAGGGGGAAG
129 AAGAAGAAGGGCAGCTAGGGGGAAG
509371 GGTGGCTACG
Statistics
Matches: 294, Mismatches: 14, Indels: 29
0.87 0.04 0.09
Matches are distributed among these distances:
165 17 0.06
166 5 0.02
167 34 0.12
168 88 0.30
170 10 0.03
172 2 0.01
173 1 0.00
175 1 0.00
176 2 0.01
178 13 0.04
179 121 0.41
ACGTcount: A:0.37, C:0.07, G:0.32, T:0.24
Consensus pattern (175 bp):
GAAGAAGAAGAAGAAGAAGAAAAAGGGCAGCTAGGGGGGAGGGTGGCTACGGGTGTATATTTGAT
TTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTGAAGAAGAAGAAGAAA
GAAGAAGGGCAGCTAGGGGGAAGCTAAGGGAAGGGTGGCTACGGA
Found at i:509171 original size:3 final size:3
Alignment explanation
Indices: 509163--509187 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
509153 GCAATACGTT
509163 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
509188 GGCAGCTAAG
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:509244 original size:54 final size:55
Alignment explanation
Indices: 509163--509268 Score: 169
Period size: 54 Copynumber: 1.9 Consensus size: 55
509153 GCAATACGTT
*
509163 GAAGAAGAAGAAGAAGAAGAAGAAGGGCAGCTA-AGGGAAGGGTGGCTACGGAAA
1 GAAGAAGAAGAAGAAGAAGAAAAAGGGCAGCTAGAGGGAAGGGTGGCTACGGAAA
* * *
509217 GAAGCAGAAGAAGAAGAAGAAAAAGGGCAGCTAGGGGGGAGGGTGGCTACGG
1 GAAGAAGAAGAAGAAGAAGAAAAAGGGCAGCTAGAGGGAAGGGTGGCTACGG
509269 GTGTATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 31 0.66
55 16 0.34
ACGTcount: A:0.42, C:0.08, G:0.43, T:0.06
Consensus pattern (55 bp):
GAAGAAGAAGAAGAAGAAGAAAAAGGGCAGCTAGAGGGAAGGGTGGCTACGGAAA
Found at i:509307 original size:168 final size:165
Alignment explanation
Indices: 509025--509381 Score: 617
Period size: 168 Copynumber: 2.1 Consensus size: 165
509015 GGGGAATGAA
* *
509025 AGCTAGGGGGAAGGGTGGCTACGGGAAGAAGCAGAAGAAGAAGAAAAAGGGAAGCTAGGGGGGAG
1 AGCTAGAGGGAAGGGTGGCTACGGAAAGAAGCAGAAGAAGAAGAAAAAGGGAAGCTAGGGGGGAG
509090 GGTGGCTACGAGTGTATATTTGATTTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGC
66 GGTGGCTACGAGTGTATATTTGATTTAGTATAGTTAAAATTTTTCTTTATA-TTTTTTCATATGC
*
509155 AATACGTTGAAGAAGAAGAAGAAGAAGAAGAAGGGC
130 AATACGTTAAAGAAGAAGAAGAAGAAGAAGAAGGGC
*
509191 AGCTA-AGGGAAGGGTGGCTACGGAAAGAAGCAGAAGAAGAAGAAGAAAAAGGGCAGCTAGGGGG
1 AGCTAGAGGGAAGGGTGGCTACGGAAAGAAGC---AGAAGAAGAAGAAAAAGGGAAGCTAGGGGG
*
509255 GAGGGTGGCTACGGGTGTATATTTGATTTAGTATAGTTAAAATTTTTCTTTATATTTTTTCATAT
63 GAGGGTGGCTACGAGTGTATATTTGATTTAGTATAGTTAAAATTTTTCTTTATATTTTTTCATAT
509320 GCAATACGTTAAAGAAGAAGAAGAAGAAGAAGAAGGGC
128 GCAATACGTTAAAGAAGAAGAAGAAGAAGAAGAAGGGC
*
509358 AGCTAGGGGGAAGGGTGGCTACGG
1 AGCTAGAGGGAAGGGTGGCTACGG
509382 GTGTATATTT
Statistics
Matches: 181, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
165 24 0.13
166 5 0.03
167 53 0.29
168 99 0.55
ACGTcount: A:0.36, C:0.08, G:0.33, T:0.23
Consensus pattern (165 bp):
AGCTAGAGGGAAGGGTGGCTACGGAAAGAAGCAGAAGAAGAAGAAAAAGGGAAGCTAGGGGGGAG
GGTGGCTACGAGTGTATATTTGATTTAGTATAGTTAAAATTTTTCTTTATATTTTTTCATATGCA
ATACGTTAAAGAAGAAGAAGAAGAAGAAGAAGGGC
Found at i:509415 original size:113 final size:114
Alignment explanation
Indices: 509222--509468 Score: 460
Period size: 113 Copynumber: 2.2 Consensus size: 114
509212 GGAAAGAAGC
* *
509222 AGAAGAAGAAGAAGAAAAAGGGCAGCTAGGGGGGAGGGTGGCTACGGGTGTATATTTGATTTAGT
1 AGAAGAAGAAGAAGAAGAAGGGCAGCTAGGGGGAAGGGTGGCTACGGGTGTATATTTGATTTAGT
509287 ATAGTTAAAATTTTTCTTTATA-TTTTTTCATATGCAATACGTTAAAGA
66 ATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTAAAGA
509335 AGAAGAAGAAGAAGAAGAAGGGCAGCTAGGGGGAAGGGTGGCTACGGGTGTATATTTGATTTAGT
1 AGAAGAAGAAGAAGAAGAAGGGCAGCTAGGGGGAAGGGTGGCTACGGGTGTATATTTGATTTAGT
*
509400 ATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTGAAGA
66 ATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTAAAGA
509449 AGAAGAAGAAGAAGAAGAAG
1 AGAAGAAGAAGAAGAAGAAG
509469 AAGAAGGCGA
Statistics
Matches: 130, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
113 85 0.65
114 45 0.35
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (114 bp):
AGAAGAAGAAGAAGAAGAAGGGCAGCTAGGGGGAAGGGTGGCTACGGGTGTATATTTGATTTAGT
ATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTAAAGA
Found at i:509452 original size:3 final size:3
Alignment explanation
Indices: 509444--509474 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
509434 GCAATACGTT
509444 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
509475 GCGAGTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:509565 original size:96 final size:97
Alignment explanation
Indices: 509382--509566 Score: 318
Period size: 97 Copynumber: 1.9 Consensus size: 97
509372 GTGGCTACGG
* *
509382 GTGTATATTTGATTTAGTATAGTTAAAATTTTTCTTTATATTTTTTTCATATGCAATACGTTGAA
1 GTGTATATTTGATTTAGTATAGTTAAAAATTTTCTTTATATTTTTTTCATATGCAATACGTTAAA
*
509447 GAAGAAGAAGAAGAAGAAGAAGAAGAAGGCGA
66 GAAGAAAAAGAAGAAGAAGAAGAAGAAGGCGA
*
509479 GTGTTTATTTGATTTAGTATAGTTAAAAATTTTCTTTATATTTTTTT-ATATGCAATACGTTAAA
1 GTGTATATTTGATTTAGTATAGTTAAAAATTTTCTTTATATTTTTTTCATATGCAATACGTTAAA
*
509543 GAATAAAAAGAAGAAGAAGAAGAA
66 GAAGAAAAAGAAGAAGAAGAAGAA
509567 TGAGGAGGAA
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
96 38 0.46
97 45 0.54
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (97 bp):
GTGTATATTTGATTTAGTATAGTTAAAAATTTTCTTTATATTTTTTTCATATGCAATACGTTAAA
GAAGAAAAAGAAGAAGAAGAAGAAGAAGGCGA
Found at i:509742 original size:6 final size:6
Alignment explanation
Indices: 509581--509786 Score: 172
Period size: 6 Copynumber: 35.3 Consensus size: 6
509571 GAGGAAGAGG
* * * * * * *
509581 AGGAGG AGGAGA ATGAGA ATGAGA ATGAGA AGGAGG AGGAGG AGGAGG
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* * * * * * *
509629 AGGAGG ATGAGG ATGAGG ATGAGA AGGAGA AGGAGA ATGAGA AGGAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
*
509677 AGGAGA AGGAGA AGAAGA AGGAGA AGGAG- A--AGA AGGAGA AGGAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
** ** *
509722 AGGAG- A--AGA AGGAGA AGGAGA AAAAGA AGGAGA AAAAGA AGAAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* *
509767 AGGAGA AGAAGA AGAAGA AG
1 AGGAGA AGGAGA AGGAGA AG
509787 AAAAAGAAGA
Statistics
Matches: 174, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
3 4 0.02
4 2 0.01
5 2 0.01
6 166 0.95
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (6 bp):
AGGAGA
Found at i:509787 original size:6 final size:6
Alignment explanation
Indices: 509650--509802 Score: 137
Period size: 6 Copynumber: 25.5 Consensus size: 6
509640 GATGAGGATG
* * * * * *
509650 AGAAGG AGAAGG AGAATG- AGAAGG AGAAGG AGAAGG AGAAGA AGAAGG
1 AGAAGA AGAAGA AGAA-GA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
509698 AGAAGG AGAAGA AGGAGA AGGAGA AGGAGA AGAAGG AGAAGG AGAAAA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * *
509746 AGAAGG AGAAAA AGAAGA AGAAGG AGAAGA AGAAGA AGAAGA AAAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
509794 AGAAGA AGA
1 AGAAGA AGA
509803 CGGGTGTATA
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
5 1 0.01
6 126 0.98
7 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.01
Consensus pattern (6 bp):
AGAAGA
Found at i:509799 original size:15 final size:15
Alignment explanation
Indices: 509650--509802 Score: 137
Period size: 15 Copynumber: 10.2 Consensus size: 15
509640 GATGAGGATG
* *
509650 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* *
509665 ATG-AGAAGGAGAAGG
1 A-GAAGAAGAAGAAGA
*
509680 AGAAGGAGAAGAAGA
1 AGAAGAAGAAGAAGA
* *
509695 AGGAGAAGGAGAAGA
1 AGAAGAAGAAGAAGA
* * *
509710 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* *
509725 AGAAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* *
509740 AGAAAAAGAAGGAGA
1 AGAAGAAGAAGAAGA
* *
509755 AAAAGAAGAAGAAGG
1 AGAAGAAGAAGAAGA
509770 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
*
509785 AGAAAAAGAAGAAGA
1 AGAAGAAGAAGAAGA
509800 AGA
1 AGA
509803 CGGGTGTATA
Statistics
Matches: 113, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
14 1 0.01
15 111 0.98
16 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.01
Consensus pattern (15 bp):
AGAAGAAGAAGAAGA
Found at i:509865 original size:3 final size:3
Alignment explanation
Indices: 509850--509884 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
509840 TGGCTACGGT
* *
509850 AAG AAG AAT AAG AAG AAG AAG AAA AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
509885 AAAGGGCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:509882 original size:12 final size:12
Alignment explanation
Indices: 509850--509888 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
509840 TGGCTACGGT
* *
509850 AAGAAGAATAAG
1 AAGAAGAAGAAA
509862 AAGAAGAAGAAA
1 AAGAAGAAGAAA
509874 AAGAAGAAGAAA
1 AAGAAGAAGAAA
509886 AAG
1 AAG
509889 GGCAAATAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:513461 original size:31 final size:31
Alignment explanation
Indices: 513426--513521 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
513416 CAGGTCAATA
*
513426 TTGGGTCGGGTCAATACCGGATCGATTGATT
1 TTGGGTCGGGTCAATACCGGATCGGTTGATT
* * **
513457 TTGGGTTGGGTTAATACTAGATCGGTTAGATT
1 TTGGGTCGGGTCAATACCGGATCGGTT-GATT
** * *
513489 TCAGGTCGGGTCAATATCGAATCGGTTGATT
1 TTGGGTCGGGTCAATACCGGATCGGTTGATT
513520 TT
1 TT
513522 CGGTTTAGGT
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
31 27 0.54
32 23 0.46
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.36
Consensus pattern (31 bp):
TTGGGTCGGGTCAATACCGGATCGGTTGATT
Found at i:513513 original size:32 final size:30
Alignment explanation
Indices: 513429--513520 Score: 85
Period size: 32 Copynumber: 2.9 Consensus size: 30
513419 GTCAATATTG
* * **
513429 GGTCGGGTCAATACCGGATCGATTGATTTTG
1 GGTCGGGTCAATA-CGAATCGGTTGATTTCA
* * *
513460 GGTTGGGTTAATACTAGATCGGTTAGATTTCA
1 GGTCGGGTCAATACGA-ATCGGTT-GATTTCA
513492 GGTCGGGTCAATATCGAATCGGTTGATTT
1 GGTCGGGTCAATA-CGAATCGGTTGATTT
513521 TCGGTTTAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
30 1 0.02
31 22 0.46
32 23 0.48
33 2 0.04
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (30 bp):
GGTCGGGTCAATACGAATCGGTTGATTTCA
Found at i:514311 original size:49 final size:48
Alignment explanation
Indices: 514239--514354 Score: 117
Period size: 49 Copynumber: 2.4 Consensus size: 48
514229 TTCGGGTCGG
* * * *
514239 GTTAAATTCGGTTAGGGTTGCTTTTGA-ATCGGGTTAAAATTTGGTTCAA
1 GTTAATTTCGGTTCGGTTTGCTTTCGATA-CGGGTT-AAATTTGGTTCAA
*** **
514288 GTTAATTTCGGTTCGGTTTGCTTTCGATACGGGTTGCTTTTGGTTCGG
1 GTTAATTTCGGTTCGGTTTGCTTTCGATACGGGTTAAATTTGGTTCAA
514336 GTTAATTTCGGTTTCGGTT
1 GTTAATTTCGG-TTCGGTT
514355 CGGGTTGATT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 19 0.34
49 36 0.64
50 1 0.02
ACGTcount: A:0.16, C:0.11, G:0.28, T:0.45
Consensus pattern (48 bp):
GTTAATTTCGGTTCGGTTTGCTTTCGATACGGGTTAAATTTGGTTCAA
Found at i:514312 original size:16 final size:16
Alignment explanation
Indices: 514293--514348 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
514283 TTCAAGTTAA
*
514293 TTTCGGTTCGGTTTGC
1 TTTCGGTTCGGGTTGC
* *
514309 TTTCGATACGGGTTGC
1 TTTCGGTTCGGGTTGC
* **
514325 TTTTGGTTCGGGTTAA
1 TTTCGGTTCGGGTTGC
514341 TTTCGGTT
1 TTTCGGTT
514349 TCGGTTCGGG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.07, C:0.14, G:0.30, T:0.48
Consensus pattern (16 bp):
TTTCGGTTCGGGTTGC
Found at i:514354 original size:22 final size:22
Alignment explanation
Indices: 514329--514373 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
514319 GGTTGCTTTT
*
514329 GGTTCGGGTTAATTTCGGTTTC
1 GGTTCGGGTTAATTTCAGTTTC
*
514351 GGTTCGGGTTGATTTCAGTTTC
1 GGTTCGGGTTAATTTCAGTTTC
514373 G
1 G
514374 CTAAATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.13, G:0.33, T:0.44
Consensus pattern (22 bp):
GGTTCGGGTTAATTTCAGTTTC
Found at i:517818 original size:2 final size:2
Alignment explanation
Indices: 517811--517861 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
517801 ATATTAAAAT
517811 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
517853 TA TA TA TA T
1 TA TA TA TA T
517862 TTTGATATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:534161 original size:20 final size:20
Alignment explanation
Indices: 534138--534180 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
534128 AATCCACCAC
*
534138 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
534158 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
534178 ATG
1 ATG
534181 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:534654 original size:17 final size:16
Alignment explanation
Indices: 534632--534684 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
534622 ATTTAAGAGT
534632 TAGTTTGATTAATGAAC
1 TAGTTT-ATTAATGAAC
*
534649 TAGTTTAATCAATGAAC
1 TAGTTT-ATTAATGAAC
*
534666 CAGCTTTATTCAATGAAC
1 TAG-TTTATT-AATGAAC
534684 T
1 T
534685 TAATGCATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (16 bp):
TAGTTTATTAATGAAC
Found at i:534678 original size:18 final size:17
Alignment explanation
Indices: 534642--534683 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
534632 TAGTTTGATT
*
534642 AATGAACTAGTTTAATC
1 AATGAACCAGTTTAATC
*
534659 AATGAACCAGCTTTATTC
1 AATGAACCAG-TTTAATC
534677 AATGAAC
1 AATGAAC
534684 TTAATGCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (17 bp):
AATGAACCAGTTTAATC
Found at i:534709 original size:46 final size:46
Alignment explanation
Indices: 534659--534747 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
534649 TAGTTTAATC
* * * *
534659 AATGAACCAGCTTTATTCAATGAACTTA-ATGCATGAATGAACTATG
1 AATGAACCAG-TTTATTAAATGAACTAATATACATGAATAAACTATG
**
534705 AATGAAGTAGTTTATTAAATGAACTAATATACATGAATAAACT
1 AATGAACCAGTTTATTAAATGAACTAATATACATGAATAAACT
534748 TGTTGAGTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
45 15 0.42
46 21 0.58
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (46 bp):
AATGAACCAGTTTATTAAATGAACTAATATACATGAATAAACTATG
Found at i:535540 original size:64 final size:63
Alignment explanation
Indices: 535468--535623 Score: 192
Period size: 64 Copynumber: 2.5 Consensus size: 63
535458 GTGCACCAAG
* * **
535468 AGTGCATCGATACATTAAATGCATTCGATG-TTTCA-AACAAGTTTGAGTGCATCGATGCATGGT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CCTGAGTGCATCGATGCATGG-
535531 CT
63 -T
* *
535533 A-TGCATCGATGCATAAAATGTATTCGATGTTTTCATAAAACCTGAGTGTATCGATGCATGGT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
*
535595 AGTGCATCGATGCATAAAATACATTCGAT
1 AGTGCATCGATGCATAAAATGCATTCGAT
535624 ATGGTTAGTG
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
62 2 0.03
63 25 0.31
64 43 0.54
65 8 0.10
66 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
Found at i:544185 original size:45 final size:45
Alignment explanation
Indices: 544134--544239 Score: 153
Period size: 45 Copynumber: 2.4 Consensus size: 45
544124 GGTGCACTAA
* *
544134 GAGTGCATCGATGCATTAAATGCATTCTATG-TTTCA-AACAAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CCT
544179 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCT
*
544224 GAGTGTATCGATGCAT
1 GAGTGCATCGATGCAT
544240 GGTAGTGTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
45 47 0.84
46 7 0.12
47 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCT
Found at i:550398 original size:20 final size:20
Alignment explanation
Indices: 550375--550426 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
550365 AACGCGATCC
550375 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
550395 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
550415 CCAAAATCGCAA
1 CCAGAATCGCAA
550427 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:550443 original size:21 final size:20
Alignment explanation
Indices: 550417--550514 Score: 70
Period size: 21 Copynumber: 4.8 Consensus size: 20
550407 ATCAGTTTCC
550417 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * * *
550438 AAAATCGCGATGCGATAGTAG
1 AAAATCGCAACGCGAT-TTTG
* ** *
550459 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-G
* * *
550480 ATAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
550500 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
550515 ACACATAAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 5
0.71 0.22 0.06
Matches are distributed among these distances:
20 15 0.26
21 42 0.74
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:550507 original size:20 final size:20
Alignment explanation
Indices: 550482--550675 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
550472 GATTTTCCAT
* *
550482 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
550502 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
550522 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
550542 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
550562 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
550582 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
550602 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
550622 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
550643 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
550663 AATCGCAACGCGA
1 AATCGCAACGCGA
550676 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:550527 original size:40 final size:39
Alignment explanation
Indices: 550478--550675 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
550468 TTGCGATTTT
* ** *
550478 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
550516 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
550557 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
550597 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
550636 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
550676 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:550565 original size:60 final size:60
Alignment explanation
Indices: 550482--550674 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
550472 GATTTTCCAT
* ** * *
550482 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
550542 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
550602 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
550663 AATCGCAACGCG
1 AATCGCAACGCG
550675 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:551094 original size:33 final size:33
Alignment explanation
Indices: 551055--551125 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
551045 TTCACTTAGA
*
551055 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
551088 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
551121 TTTCA
1 TTTCA
551126 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:551265 original size:14 final size:14
Alignment explanation
Indices: 551246--551300 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
551236 AGAATGACTG
551246 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
551260 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
551279 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
551293 TCGCAACG
1 TCGCAACG
551301 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:551283 original size:33 final size:33
Alignment explanation
Indices: 551246--551316 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
551236 AGAATGACTG
**
551246 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
551279 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
551312 TCGCA
1 TCGCA
551317 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:551334 original size:19 final size:19
Alignment explanation
Indices: 551312--551409 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
551302 GAAACCAAAA
*
551312 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
551331 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
551345 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
551364 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
551378 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
551397 TCGCGTTGCGATT
1 TCGCGTTGCGATT
551410 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:551353 original size:14 final size:14
Alignment explanation
Indices: 551334--551423 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
551324 TTTCATTTCG
551334 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
551348 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
551367 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
551381 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
551398 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
551414 CGTTGCGATT
1 CGTTGCGATT
551424 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:551359 original size:33 final size:33
Alignment explanation
Indices: 551317--551431 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
551307 CAAAATCGCA
551317 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
551350 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
551383 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
551416 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
551432 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:553359 original size:185 final size:186
Alignment explanation
Indices: 553129--553693 Score: 1107
Period size: 185 Copynumber: 3.0 Consensus size: 186
553119 TAGATTGCTT
*
553129 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
553194 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
553259 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
553314 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
553378 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
553443 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
553499 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
553564 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
553629 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
553685 AGTAAATTT
1 AGTAAATTT
553694 ATCCATTCAA
Statistics
Matches: 377, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 92 0.24
185 153 0.41
186 132 0.35
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:553535 original size:93 final size:93
Alignment explanation
Indices: 553129--553693 Score: 1107
Period size: 93 Copynumber: 6.1 Consensus size: 93
553119 TAGATTGCTT
*
553129 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
553194 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
553222 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
553286 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
553314 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
553378 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
553406 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
553471 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
553499 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
553564 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
553592 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
553657 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
553685 AGTAAATTT
1 AGTAAATTT
553694 ATCCATTCAA
Statistics
Matches: 470, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 184 0.39
93 286 0.61
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:553777 original size:19 final size:19
Alignment explanation
Indices: 553737--553865 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
553727 TAGTTTACTT
* *
553737 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
553757 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
553776 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
553795 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
553809 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
553828 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
553842 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
553861 TCGCA
1 TCGCA
553866 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:553816 original size:33 final size:32
Alignment explanation
Indices: 553773--553865 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
553763 CGCGAAACCA
**
553773 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
553805 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
553838 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
553866 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:553863 original size:52 final size:52
Alignment explanation
Indices: 553737--553865 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
553727 TAGTTTACTT
**
553737 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
553789 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
553842 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
553866 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:553883 original size:19 final size:19
Alignment explanation
Indices: 553861--553995 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
553851 GAAACCAAAA
*
553861 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
553880 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
553896 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
553913 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
553929 T--CGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
553946 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
553965 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
553985 TCGTGTTGCGA
1 TCGCGTTGCGA
553996 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 11 0.12
19 46 0.49
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:553902 original size:14 final size:14
Alignment explanation
Indices: 553883--553939 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
553873 TTTCATTTCG
553883 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
553897 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
553914 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
553930 CGTTGCGATT
1 CGTTGCGATT
553940 TTAATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:553908 original size:33 final size:33
Alignment explanation
Indices: 553866--553958 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
553856 CAAAATCGCA
*
553866 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
553899 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
553932 TTGCGATTTTAATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
553959 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:555938 original size:14 final size:14
Alignment explanation
Indices: 555919--555954 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
555909 ATTGTTTAAT
555919 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
555933 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
555947 TGATTTGT
1 TGATTTGT
555955 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:556077 original size:19 final size:19
Alignment explanation
Indices: 556061--556181 Score: 189
Period size: 19 Copynumber: 6.6 Consensus size: 19
556051 AAAAATGACT
556061 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
556080 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
556099 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
556118 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
556132 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
556151 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
556171 ATCGCAATGCG
1 ATCGCAATGCG
556182 TTTATAATTT
Statistics
Matches: 94, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 59 0.63
20 19 0.20
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:556140 original size:33 final size:36
Alignment explanation
Indices: 556061--556181 Score: 167
Period size: 33 Copynumber: 3.3 Consensus size: 36
556051 AAAAATGACT
556061 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
*
556099 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
556132 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GC-G-AATGAAA
556171 ATCGCAATGCG
1 ATCGCAATGCG
556182 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
33 29 0.39
34 1 0.01
35 1 0.01
36 3 0.04
38 27 0.36
39 14 0.19
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:556234 original size:19 final size:19
Alignment explanation
Indices: 556210--556516 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
556200 GATTATCTCG
556210 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
556229 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
556248 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
556262 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
556281 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
556300 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
556319 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
556338 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
556352 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
556371 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
556390 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
556404 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
556423 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
556442 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
556456 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
556476 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
556490 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
556509 TTGCGATT
1 TTGCGATT
556517 GTATTTTCCG
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 35 0.14
16 31 0.12
17 27 0.11
18 3 0.01
19 144 0.57
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:556285 original size:71 final size:71
Alignment explanation
Indices: 556210--556449 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
556200 GATTATCTCG
556210 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
556275 TTCGCA
66 TTCGCA
*
556281 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
*
556344 TTC-TGTCG--
61 TTCATTTCGCA
*
556352 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
556417 TTCGCA
66 TTCGCA
556423 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
556450 CTCTCGTTGC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 6 0.04
68 7 0.05
69 6 0.04
71 115 0.75
73 6 0.04
74 8 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:556360 original size:142 final size:137
Alignment explanation
Indices: 556172--556516 Score: 516
Period size: 142 Copynumber: 2.5 Consensus size: 137
556162 GAAATGAAAA
*
556172 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTT-TAATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGAT
*
556236 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
63 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
*
556301 TGCGATTTTCATT
128 TGCGA--TTC-TC
556314 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGATT
556379 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
64 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
556444 GCGATTCTC
129 GCGATTCTC
* * *
556453 TCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTAATTT-CGCATTGCGATTTTC--GTTGCGATTTTCATTTCGCATTGCGAT
556516 T
63 T
556517 GTATTTTCCG
Statistics
Matches: 191, Mismatches: 8, Indels: 12
0.91 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 15 0.08
138 38 0.20
139 4 0.02
140 3 0.02
142 126 0.66
143 3 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (137 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCGTTGCGATTTTCATTTCGCATTGCGATTTT
CATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTC
Found at i:556455 original size:52 final size:52
Alignment explanation
Indices: 556210--556488 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
556200 GATTATCTCG
*
556210 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
*
556262 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
556319 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
556371 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
556423 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
556476 TTGCGATTTTCAT
1 TTGCGATTTTCAT
556489 GTTGGGATTT
Statistics
Matches: 217, Mismatches: 4, Indels: 11
0.94 0.02 0.05
Matches are distributed among these distances:
52 161 0.74
53 17 0.08
54 7 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:558816 original size:12 final size:12
Alignment explanation
Indices: 558799--558823 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
558789 TCTTCGGGGA
558799 CTTTTTCTTCTT
1 CTTTTTCTTCTT
558811 CTTTTTCTTCTT
1 CTTTTTCTTCTT
558823 C
1 C
558824 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:559031 original size:24 final size:24
Alignment explanation
Indices: 558997--559043 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
558987 TCTGAACATC
558997 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
559021 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
559044 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:559753 original size:20 final size:20
Alignment explanation
Indices: 559725--560074 Score: 456
Period size: 20 Copynumber: 17.5 Consensus size: 20
559715 AAATTTCAGT
* * * *
559725 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
559745 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
559765 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
559785 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
559805 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
559825 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
559845 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
559865 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
559885 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
559905 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
559925 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
559945 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
559965 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
559985 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
560005 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
560025 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
560045 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
560065 GTTGCGATTT
1 GTTGCGATTT
560075 TCATATTCGC
Statistics
Matches: 295, Mismatches: 28, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.02
20 285 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:560083 original size:20 final size:20
Alignment explanation
Indices: 560042--560093 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
560032 TTTACGGATA
* *
560042 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTTATATATT
560062 CGCGTTGCGATTT-TCATATT
1 CGCGTTGCGATTTAT-ATATT
*
560082 CGCGTTACGATT
1 CGCGTTGCGATT
560094 ATGGAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.42
Consensus pattern (20 bp):
CGCGTTGCGATTTATATATT
Found at i:560819 original size:2 final size:2
Alignment explanation
Indices: 560812--560845 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
560802 ATTTTTGTCC
560812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
560846 GATTGAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:560995 original size:39 final size:38
Alignment explanation
Indices: 560938--561249 Score: 347
Period size: 37 Copynumber: 8.2 Consensus size: 38
560928 ATTTTTGAAA
* *
560938 ATATATATTATATCGTTTTGAAATT-TTTTTTAAAAATAT
1 ATATATATTATATAGTTTTGAAATTAGTTTTT-AAAA-AT
** *
560977 ATATATATTATATAGTTTTGAAATTTTTTTTTGAAAAAC
1 ATATATATTATATAGTTTTGAAATTAGTTTTT-AAAAAT
561016 ATATATATTATATAGTTTTGAAAATTAGTTTTT--AAAT
1 ATATATATTATATAGTTTTG-AAATTAGTTTTTAAAAAT
**
561053 ATATATATTATATAGTTTTGAAAACA-TTTTTGAAAAAT
1 ATATATATTATATAGTTTTGAAATTAGTTTTT-AAAAAT
561091 ATATATATTATATAGTTTTGAAAATTAGTTTTT--AAAT
1 ATATATATTATATAGTTTTG-AAATTAGTTTTTAAAAAT
* *
561128 ATATATATTATATAGTTTTAAAAATTAGCTTTTAAAAATAT
1 ATATATATTATATAGTTTT-GAAATTAG-TTTTTAAAA-AT
561169 ATATATATTATATAGTTTTGAAAGTTAGTTTTT--AAA-
1 ATATATATTATATAGTTTTGAAA-TTAGTTTTTAAAAAT
* *
561205 ATATATATTATAT-GATTTTGAAAATTATTTTTTAAAAAC
1 ATATATATTATATAG-TTTTG-AAATTAGTTTTTAAAAAT
561244 ATATAT
1 ATATAT
561250 TGTATAGTTT
Statistics
Matches: 240, Mismatches: 15, Indels: 36
0.82 0.05 0.12
Matches are distributed among these distances:
35 6 0.03
36 30 0.12
37 57 0.24
38 33 0.14
39 55 0.23
40 34 0.14
41 25 0.10
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (38 bp):
ATATATATTATATAGTTTTGAAATTAGTTTTTAAAAAT
Found at i:561020 original size:114 final size:113
Alignment explanation
Indices: 560902--561276 Score: 387
Period size: 114 Copynumber: 3.3 Consensus size: 113
560892 TGTTTTGAAA
* *
560902 ATATATGATATATAATTTTTAAAAATA-TTTTTGAAA-ATATATATTATATCGTTTTGAAATTTT
1 ATATAT-ATATATAATTTTTAAAAATAGTTTTT-AAATATATATATTATATAGTTTTGAAATTAT
*
560965 TTTTAAAAATATATATATATTATATAGTTTTG-AAATTTTTTTTTGAAAAAC
64 TTTT-AAAATATATATATATTATATAGTTTTGAAAATTATTTTTT-AAAAAC
* * * **
561016 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAATATATATATTATATAGTTTTGAAAACATT
1 ATATATA-TATATAATTTTTAAAAATAGTTTTTAAATATATATATTATATAGTTTTGAAATTATT
* * *
561081 TTTGAAAA-ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAATAT
65 TTT-AAAATATATATATATTATATAGTTTTGAAAATTATTTTTTAAAAAC
* *
561130 ATATAT-TATAT-AGTTTTAAAAATTAGCTTTTAAAAATATATATATATTATATAGTTTTGAAAG
1 ATATATATATATAATTTTTAAAAA-TAG-TTTT--TAA-ATATATATATTATATAGTTTTGAAA-
*
561193 TTAGTTTTTAAAATATATAT-TA-TAT-GA-TTTTGAAAATTATTTTTTAAAAAC
60 TTA-TTTTTAAAATATATATATATTATATAGTTTTGAAAATTATTTTTTAAAAAC
* * *
561244 ATATAT-TGTAT-AGTTTTAAAAAAATGTTTTTAA
1 ATATATATATATAATTTTTAAAAATA-GTTTTTAA
561277 TTTATTTATC
Statistics
Matches: 222, Mismatches: 26, Indels: 29
0.80 0.09 0.10
Matches are distributed among these distances:
111 9 0.04
112 8 0.04
113 10 0.05
114 100 0.45
115 49 0.22
116 28 0.13
117 7 0.03
118 11 0.05
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (113 bp):
ATATATATATATAATTTTTAAAAATAGTTTTTAAATATATATATTATATAGTTTTGAAATTATTT
TTAAAATATATATATATTATATAGTTTTGAAAATTATTTTTTAAAAAC
Found at i:561276 original size:37 final size:37
Alignment explanation
Indices: 560894--561265 Score: 323
Period size: 37 Copynumber: 9.9 Consensus size: 37
560884 TTTTTAAATG
* *
560894 TTTTGAAAATATATGA-TATATAATTTTTAAAAA-TA-T
1 TTTTAAAAATATAT-ATTATAT-AGTTTTAAAAATTAGT
* * * *
560930 TTTTGAAAATATATATTATATCGTTTT-GAAATT-TT
1 TTTTAAAAATATATATTATATAGTTTTAAAAATTAGT
* **
560965 TTTTAAAAATATATATATATTATATAGTTTT-GAAATTTTT
1 TTTT--AAA-A-ATATATATTATATAGTTTTAAAAATTAGT
*
561005 TTTTGAAAAACATATATATTATATAGTTTTGAAAATTAGT
1 TTTT--AAAA-ATATATATTATATAGTTTTAAAAATTAGT
*
561045 TTTTAAATATATATATTATATAGTTTTGAAAACATT--T
1 TTTTAAAAATATATATTATATAGTTTT-AAAA-ATTAGT
** *
561082 TTGAAAAATATATATATTATATAGTTTTGAAAATTAGT
1 TTTTAAAA-ATATATATTATATAGTTTTAAAAATTAGT
*
561120 TTTTAAATATATATATTATATAGTTTTAAAAATTAGCT
1 TTTTAAAAATATATATTATATAGTTTTAAAAATTAG-T
* * *
561158 TTTAAAAATATATATATATTATATAGTTTTGAAAGTTAGT
1 TTT-TAAA-A-ATATATATTATATAGTTTTAAAAATTAGT
* *
561198 TTTT-AAAATATATATTATAT-GATTTTGAAAATTATT
1 TTTTAAAAATATATATTATATAG-TTTTAAAAATTAGT
* *
561234 TTTTAAAAACATATATTGTATAGTTTTAAAAA
1 TTTTAAAAATATATATTATATAGTTTTAAAAA
561266 AATGTTTTTA
Statistics
Matches: 285, Mismatches: 30, Indels: 41
0.80 0.08 0.12
Matches are distributed among these distances:
34 3 0.01
35 12 0.04
36 51 0.18
37 80 0.28
38 39 0.14
39 50 0.18
40 24 0.08
41 26 0.09
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (37 bp):
TTTTAAAAATATATATTATATAGTTTTAAAAATTAGT
Found at i:561285 original size:4 final size:4
Alignment explanation
Indices: 561276--561356 Score: 60
Period size: 4 Copynumber: 20.0 Consensus size: 4
561266 AATGTTTTTA
* * *
561276 ATTT ATTT ATCT ATTT -TTT ATTT ATTTT ATTT CATTT ATTT TTTT ATCT
1 ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT -ATTT ATTT ATTT ATTT
* *
561325 ATTTT CTTT CATTT ATTT -TTT -TTT ATCT ATTT
1 A-TTT ATTT -ATTT ATTT ATTT ATTT ATTT ATTT
561357 TGGGTCCAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
3 9 0.15
4 39 0.64
5 13 0.21
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:561314 original size:14 final size:13
Alignment explanation
Indices: 561289--561346 Score: 75
Period size: 14 Copynumber: 4.5 Consensus size: 13
561279 TATTTATCTA
561289 TTTTTT-ATTTAT
1 TTTTTTCATTTAT
561301 TTTATTTCATTTAT
1 TTT-TTTCATTTAT
*
561315 TTTTTT-ATCTAT
1 TTTTTTCATTTAT
561327 TTTCTTTCATTTAT
1 TTT-TTTCATTTAT
561341 TTTTTT
1 TTTTTT
561347 TTATCTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 11 0.28
13 12 0.30
14 17 0.43
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTCATTTAT
Found at i:561327 original size:26 final size:26
Alignment explanation
Indices: 561277--561357 Score: 103
Period size: 26 Copynumber: 3.1 Consensus size: 26
561267 ATGTTTTTAA
* *
561277 TTTATTT-ATCTA-TTTTTTATTTAT
1 TTTATTTCATTTATTTTTTTATCTAT
561301 TTTATTTCATTTATTTTTTTATCTAT
1 TTTATTTCATTTATTTTTTTATCTAT
*
561327 TTTCTTTCATTTATTTTTTTTTATCTAT
1 TTTATTTCATTTA--TTTTTTTATCTAT
561355 TTT
1 TTT
561358 GGGTCCAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
24 7 0.14
25 4 0.08
26 23 0.46
28 16 0.32
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTATTTCATTTATTTTTTTATCTAT
Found at i:561355 original size:14 final size:14
Alignment explanation
Indices: 561314--561357 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
561304 ATTTCATTTA
561314 TTTTTTTATCTATT
1 TTTTTTTATCTATT
* * *
561328 TTCTTTCATTTATT
1 TTTTTTTATCTATT
561342 TTTTTTTATCTATT
1 TTTTTTTATCTATT
561356 TT
1 TT
561358 GGGTCCAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTATCTATT
Found at i:562628 original size:4 final size:4
Alignment explanation
Indices: 562621--562674 Score: 56
Period size: 4 Copynumber: 13.0 Consensus size: 4
562611 TATATATATA
* *
562621 TATT TATT TATT TATT TATT TATT TAATT TCGTT TATT CTA-T TATA TATT
1 TATT TATT TATT TATT TATT TATT T-ATT T-ATT TATT -TATT TATT TATT
562671 TATT
1 TATT
562675 ATTATTATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
3 2 0.05
4 31 0.74
5 9 0.21
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:565520 original size:16 final size:16
Alignment explanation
Indices: 565499--565531 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
565489 TTCTAAGAGT
565499 ATGAGTGTTCAATATC
1 ATGAGTGTTCAATATC
565515 ATGAGTGTTCAATATC
1 ATGAGTGTTCAATATC
565531 A
1 A
565532 AAATGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (16 bp):
ATGAGTGTTCAATATC
Found at i:567505 original size:92 final size:91
Alignment explanation
Indices: 567321--567505 Score: 259
Period size: 95 Copynumber: 2.0 Consensus size: 91
567311 TCAAAATGAA
567321 ACAAAAACATATGATTTCATAAAAACGTATCAAAAGTGAAACTTTAGGTACTAAATGTGTCATTT
1 ACAAAAACATATGATTTCATAAAAACGTATCAAAAGTGAAACTTTAGGTACTAAATGTGTCATTT
567386 ATCCAAAATAAATAATTTATAACTAT
66 ATCCAAAATAAATAATTTATAACTAT
* *
567412 ACAAAAACGTATGTTTTCATAAAAAAGAACGTATCAAAAGTGAAACTTTAGGTACTAAAT-T-T-
1 ACAAAAACATATGATTTCAT---AAA-AACGTATCAAAAGTGAAACTTTAGGTACTAAATGTGTC
** * *
567474 ATTTATCTTAAATAATTAATTTATAATTAT
62 ATTTATCCAAAATAAATAATTTATAACTAT
567504 AC
1 AC
567506 GTTGAGTAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
91 18 0.21
92 28 0.33
93 1 0.01
94 4 0.05
95 33 0.39
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (91 bp):
ACAAAAACATATGATTTCATAAAAACGTATCAAAAGTGAAACTTTAGGTACTAAATGTGTCATTT
ATCCAAAATAAATAATTTATAACTAT
Found at i:575009 original size:27 final size:29
Alignment explanation
Indices: 574946--575147 Score: 258
Period size: 27 Copynumber: 7.2 Consensus size: 29
574936 ATAAATTTAT
* *
574946 TTACGAAATTAACACCCTTTTAAAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAA
* * *
574975 TTAGGAAAATAGCA-TCTTTT-AAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
*
575002 TTACG-AAATAGCACCC-TTTAAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
*
575029 TTA-TAAAATAACACCCTTTT-AAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
*
575056 TTAC-AAAATAGCACCCTTTTAAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
*
575084 TTACAAAAATAACACCCTTTTAAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
*
575113 TTAC-AAAATAACACCCTTTTGAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
575141 TTACGAA
1 TTACGAA
575148 TATGTCACCG
Statistics
Matches: 153, Mismatches: 12, Indels: 16
0.85 0.07 0.09
Matches are distributed among these distances:
26 11 0.07
27 56 0.37
28 46 0.30
29 40 0.26
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (29 bp):
TTACGAAAATAACACCCTTTTAAAAATAA
Found at i:579511 original size:29 final size:29
Alignment explanation
Indices: 579294--579498 Score: 279
Period size: 29 Copynumber: 7.1 Consensus size: 29
579284 ATAAATTTAT
* *
579294 TTACGAAATTAACACCCTTTTAAAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAA
* * **
579323 TTAGGAAAATAGC-GTCTTTTAAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
*
579351 TTACGAAAATATCACCC-TTTAAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
*
579379 TTATGAAAATAACACCCTTTTTAAAAATAA
1 TTACGAAAATAACACCC-TTTTAAAAATAA
*
579409 TTACGAAAATAACACCCTTTTGAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
579438 TTACGAAAATAACACCCTTTTAAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
* * *
579467 TTACAAAAATAGCACCCTTTTGAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
579496 TTA
1 TTA
579499 TGAATATGTC
Statistics
Matches: 155, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
28 49 0.32
29 79 0.51
30 27 0.17
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (29 bp):
TTACGAAAATAACACCCTTTTAAAAATAA
Done.