Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008591.1 Hibiscus syriacus cultivar Beakdansim tig00111540_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: 1730314
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:169670 original size:112 final size:112
Alignment explanation
Indices: 168787--169640 Score: 1134
Period size: 112 Copynumber: 7.6 Consensus size: 112
168777 AAAATTATGT
** *
168787 AAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC-T--TCTTCAGATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* * * * *
168849 ATGAACTTT-TCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC
66 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGC
* *
168895 AAAAGGTTGAAAAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATGACGAGTTCTTCTC
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT---GAGTTCTTCTC
* * * * * *
168957 ATTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATAATGGATTTGAGC
63 ATTATGAACT-TTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGC
* *
169007 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCAT
*
169072 TATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTC-AGGC
65 TATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGA-GC
* * *
169120 AAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
169185 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGC
66 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGC
* * *
169232 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
169297 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGC
66 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGC
* * *
169344 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
*** * *
169409 ATGAACTTTCTCTGGAAAAAATAATTCATCAAGTGATGAATTC-AGGG
66 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGA-GC
* *
169456 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* ** * * * * ** **
169521 ATGAACTCTAACTGGCACTGTTGATCCACCGGGTGATGAATTTAAGC
66 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGC
* *
169568 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCAT
169633 TATGAACT
65 TATGAACT
169641 CGACCTGGAA
Statistics
Matches: 672, Mismatches: 56, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
105 3 0.00
106 2 0.00
108 36 0.05
111 22 0.03
112 473 0.70
113 121 0.18
114 1 0.00
115 6 0.01
116 8 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGC
Found at i:170102 original size:22 final size:22
Alignment explanation
Indices: 170077--170131 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
170067 GATAAAGCTT
*
170077 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
170099 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
170121 TCATCTTTGAA
1 TCATCTTTGAA
170132 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:172816 original size:83 final size:83
Alignment explanation
Indices: 172677--173318 Score: 993
Period size: 83 Copynumber: 7.7 Consensus size: 83
172667 GTAGTTCCTA
* * * * *
172677 CCAAACCAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAA
*
172742 ATTCAATGATTGGTTTTG
66 ATTCAATGATTGGTTCTG
*
172760 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAA
*
172825 ATTCAATGATTGATTCTG
66 ATTCAATGATTGGTTCTG
* * * *
172843 TCC-AACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCA
*
172907 AATTCAATGATTGGTTTTG
65 AATTCAATGATTGGTTCTG
*
172926 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAA
172991 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * * *
173009 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCC
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCA
173073 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* * *
173092 CTAAACCAGGTCAGATAACTCAAAGAACACTTTCAGAAGATGCTATTAACAAATTCATCTTACC-
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT-CCA
173156 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* * * *
173175 CTAAACCAGGTCAGATAACTCAAAGAACACTTTCAGAAGATGCTATTAACAAATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAA
173240 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
173258 CTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
173319 TCAGTTAATG
Statistics
Matches: 526, Mismatches: 27, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
82 5 0.01
83 515 0.98
84 6 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:175454 original size:7 final size:7
Alignment explanation
Indices: 175438--175478 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
175428 CTTGATTCAA
*
175438 TTTTCCT
1 TTTTCTT
175445 TTTTCTT
1 TTTTCTT
175452 TTTT-TT
1 TTTTCTT
175458 TTTT-TT
1 TTTTCTT
175464 TTTTCTT
1 TTTTCTT
*
175471 CTTTCTT
1 TTTTCTT
175478 T
1 T
175479 GCTGGATGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTCTT
Found at i:177450 original size:27 final size:27
Alignment explanation
Indices: 177420--177475 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
177410 GTAATTATGT
*
177420 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGCAAATACAAACGTA
* * *
177447 AAAAATGCAAATGCAAATTCAAATGTA
1 AAAAATGAAAATGCAAATACAAACGTA
177474 AA
1 AA
177476 TATGTGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGCAAATACAAACGTA
Found at i:177548 original size:14 final size:14
Alignment explanation
Indices: 177514--177566 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
177504 TTGTGCAATA
*
177514 CAAATGCAAAAATG
1 CAAATGTAAAAATG
*
177528 CCAAATGTAAATATG
1 -CAAATGTAAAAATG
177543 CAAATGTAAAAATG
1 CAAATGTAAAAATG
*
177557 TAAATGTAAA
1 CAAATGTAAA
177567 TTATTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (14 bp):
CAAATGTAAAAATG
Found at i:185299 original size:16 final size:16
Alignment explanation
Indices: 185278--185339 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
185268 TTACCCGACC
185278 TGTTTTCAACCTGACA
1 TGTTTTCAACCTGACA
*
185294 TGTTTTCAACCTGACC
1 TGTTTTCAACCTGACA
* **
185310 TGTTTTTAATATGACA
1 TGTTTTCAACCTGACA
*
185326 TGTTTTTAACCTGA
1 TGTTTTCAACCTGA
185340 TCTGATATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (16 bp):
TGTTTTCAACCTGACA
Found at i:185315 original size:32 final size:32
Alignment explanation
Indices: 185274--185339 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
185264 GGTATTACCC
*
185274 GACCTGTTTTCAACCTGACATGTTTTCAACCT
1 GACCTGTTTTCAACATGACATGTTTTCAACCT
* * *
185306 GACCTGTTTTTAATATGACATGTTTTTAACCT
1 GACCTGTTTTCAACATGACATGTTTTCAACCT
185338 GA
1 GA
185340 TCTGATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (32 bp):
GACCTGTTTTCAACATGACATGTTTTCAACCT
Found at i:185523 original size:13 final size:13
Alignment explanation
Indices: 185507--185533 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
185497 GACATATTAT
185507 ATAAAATTATTTA
1 ATAAAATTATTTA
185520 ATAAAATTATTTA
1 ATAAAATTATTTA
185533 A
1 A
185534 ATGTATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:185871 original size:13 final size:15
Alignment explanation
Indices: 185853--185887 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
185843 TAATTTACTT
185853 TATATA-GTT-TATA
1 TATATATGTTATATA
185866 TATATATGTTATATA
1 TATATATGTTATATA
185881 TATATAT
1 TATATAT
185888 ATATTACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 3 0.15
15 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (15 bp):
TATATATGTTATATA
Found at i:186354 original size:7 final size:7
Alignment explanation
Indices: 186342--186416 Score: 60
Period size: 7 Copynumber: 10.7 Consensus size: 7
186332 TCTATTTATA
186342 TTAGGGT
1 TTAGGGT
186349 TTAGGGT
1 TTAGGGT
**
186356 TTATAGT
1 TTAGGGT
*
186363 TTATGGT
1 TTAGGGT
**
186370 TTAAAGT
1 TTAGGGT
* *
186377 TAATGGT
1 TTAGGGT
186384 TTAGGGT
1 TTAGGGT
* *
186391 TTATGTT
1 TTAGGGT
*
186398 TTAAGGT
1 TTAGGGT
186405 TTAGGGT
1 TTAGGGT
186412 TTAGG
1 TTAGG
186417 TTTTTTTTAA
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (7 bp):
TTAGGGT
Found at i:186419 original size:21 final size:21
Alignment explanation
Indices: 186342--186420 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
186332 TCTATTTATA
*
186342 TTAGGGTTTAGGGTTTATA-GT
1 TTAGGGTTTAGGTTTTA-AGGT
* *
186363 TTATGGTTTAAAG--TTAATGGT
1 TTAGGGTTT-AGGTTTTAA-GGT
*
186384 TTAGGGTTTATGTTTTAAGGT
1 TTAGGGTTTAGGTTTTAAGGT
186405 TTAGGGTTTAGGTTTT
1 TTAGGGTTTAGGTTTT
186421 TTTTAATAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
19 1 0.02
20 5 0.10
21 36 0.75
22 6 0.12
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (21 bp):
TTAGGGTTTAGGTTTTAAGGT
Found at i:186484 original size:2 final size:2
Alignment explanation
Indices: 186473--186589 Score: 58
Period size: 2 Copynumber: 62.0 Consensus size: 2
186463 ATAGTGTTTC
*
186473 TA TA -A TA TA TA TA TA TA TA TA -A TA TA TA TA AA T- TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
186512 TA T- TA GT- TA GA CA TA CA TA TA TA TA TA TA TA CTA TA T- TA -A
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
186552 TA TA AA T- TA TA -A T- TA TA AA CTA TA TA TT 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
186590 GAAAATTAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 30
0.67 0.10 0.23
Matches are distributed among these distances:
1 11 0.13
2 71 0.82
3 5 0.06
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:186584 original size:49 final size:51
Alignment explanation
Indices: 186477--186589 Score: 128
Period size: 53 Copynumber: 2.3 Consensus size: 51
186467 TGTTTCTATA
*
186477 ATATATATATATATATAATATATATAAATTACTTATATTAGTTAGACATACAT
1 ATATATATATATATATAATATATATAAATTAC-TATATTAG-TAAACATACAT
* *
186530 ATATATATATATACTATATTA-ATATAAATTA-TA-ATTA-TAAAC-TATAT
1 ATATATATATATA-TATAATATATATAAATTACTATATTAGTAAACATACAT
*
186577 ATTTATATATATA
1 ATATATATATATA
186590 GAAAATTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
47 16 0.29
48 4 0.07
50 4 0.07
51 2 0.04
53 23 0.42
54 6 0.11
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (51 bp):
ATATATATATATATATAATATATATAAATTACTATATTAGTAAACATACAT
Found at i:186874 original size:17 final size:17
Alignment explanation
Indices: 186820--186870 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
186810 ATTTCCCAAT
*
186820 TTTCCTCTAAATTCTCAA
1 TTTCC-CTATATTCTCAA
186838 TTTCCCTATATTCTCAA
1 TTTCCCTATATTCTCAA
186855 TTTCCCTATA-TCTCAA
1 TTTCCCTATATTCTCAA
186871 ATTTTCTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 6 0.19
17 21 0.66
18 5 0.16
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTCCCTATATTCTCAA
Found at i:186877 original size:26 final size:26
Alignment explanation
Indices: 186848--186927 Score: 108
Period size: 26 Copynumber: 3.0 Consensus size: 26
186838 TTTCCCTATA
186848 TTCTCAATTTCCCTATA-TCTCAAATT
1 TTCTCAATTTCCCTATATTCTCAAA-T
186874 TTCTCAATTTCCCTATATTCTCAAAT
1 TTCTCAATTTCCCTATATTCTCAAAT
* *
186900 TTCTCAATTTTCCTCTAAATTCCCAAAT
1 TTCTCAA-TTTCC-CTATATTCTCAAAT
186928 AAAATCAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
26 25 0.51
27 12 0.24
28 12 0.24
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (26 bp):
TTCTCAATTTCCCTATATTCTCAAAT
Found at i:187185 original size:2 final size:2
Alignment explanation
Indices: 187175--187206 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
187165 TATATAAACT
187175 TA TA T- TA 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 TA TA TA TA T
187207 TTTTTTCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:192643 original size:19 final size:20
Alignment explanation
Indices: 192619--192656 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
192609 TAATAATTTT
*
192619 ATAATATT-ATTTTATTAAA
1 ATAATATTAATTATATTAAA
192638 ATAATATTAATTATATTAA
1 ATAATATTAATTATATTAA
192657 TATTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATATTAATTATATTAAA
Found at i:192701 original size:46 final size:44
Alignment explanation
Indices: 192567--192701 Score: 123
Period size: 45 Copynumber: 3.0 Consensus size: 44
192557 GTTTGTGCAG
* * *
192567 TATTATATTAATATTAAATATAAAAATAATATTAATCAT-TATTAA
1 TATTTTATTAATATTAAAT-TAAAAAT-ATAATATTCATATATTAA
** * *
192612 TAATTTTA-TAATATTATTTTATTAAA-ATAATATTAATTATATTAA
1 T-ATTTTATTAATATTAAATTA-AAAATATAATATTCA-TATATTAA
192657 TATTTTATTATATATTAAATTAAAAAGTATAATATTCATATATTA
1 TATTTTATTA-ATATTAAATTAAAAA-TATAATATTCATATATTA
192702 TTATAATAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
43 7 0.10
44 9 0.13
45 25 0.35
46 21 0.30
47 9 0.13
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (44 bp):
TATTTTATTAATATTAAATTAAAAATATAATATTCATATATTAA
Found at i:192767 original size:18 final size:19
Alignment explanation
Indices: 192722--192767 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
192712 CTTAGTATAT
*
192722 ATTA-ATATAATATTAAAA
1 ATTATATATATTATTAAAA
*
192740 AGTATA-ATATTATT-AAA
1 ATTATATATATTATTAAAA
192757 ATTATATATAT
1 ATTATATATAT
192768 ATATATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.35
18 14 0.61
19 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTATATATATTATTAAAA
Found at i:198539 original size:23 final size:23
Alignment explanation
Indices: 198512--198584 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
198502 ATACTTTATA
*
198512 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
198535 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
198558 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
198581 ATAT
1 ATAT
198585 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:198980 original size:23 final size:23
Alignment explanation
Indices: 198950--198999 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
198940 ATACTTTACA
*
198950 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATC
*
198973 ATATAAGCGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATC
198996 ATAT
1 ATAT
199000 TTTTACCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATC
Found at i:199314 original size:416 final size:415
Alignment explanation
Indices: 198535--200681 Score: 3992
Period size: 416 Copynumber: 5.2 Consensus size: 415
198525 CTATTACATT
* * *
198535 ATATAAACGCTACCTATTACATTATATAAGTGCTACCTATTACATCATATTTTTACCTATTATAT
1 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
* *
198600 TGAAAGTGTCCATACTTTTTATAAAAATGATCAATACTTTTTTTAAAGTTATGTAATTTATGTTT
66 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
198665 CAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
131 CAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
198730 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
196 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
198795 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATATC
261 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATATC
198860 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
326 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
*
198925 TTATAAAAATGATAGATACTTTACA
391 TTATAAAAAGGATAGATACTTTACA
198950 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
1 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
*
199015 TGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTTAAAGTTATGTAATTTATGTT
66 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTTAAAGTTATGTAATTTATGTT
199080 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
130 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
199145 CAAAAAATTATTTAATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
195 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
199210 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATAT
260 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATAT
199275 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
325 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
199340 TTTATAAAAAGGATAGATACTTTACA
390 TTTATAAAAAGGATAGATACTTTACA
*
199366 ATATAAGCACTACCTATTACATTATATAAGCGCTACATATTACATCATATTTTTACCTATTATAT
1 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
*
199431 TAAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTTAAAGTTATGTAATTTATGTT
66 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTTAAAGTTATGTAATTTATGTT
* *
199496 TCAATTTTTTTTAATAGTGTTTCATGTTTTCAACCTACAATATTAATTTAATAATTTCATTTGCA
130 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
199561 CAAAAAATTATTTGATTATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
195 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
199626 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATAT
260 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATAT
199691 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
325 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
*
199756 TTTATAAAAAGGATAAATACTTTACA
390 TTTATAAAAAGGATAGATACTTTACA
199782 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
1 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
*
199847 TGAAAGTGTGCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
66 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
* *
199912 C-AATTTTTTTAATAGTGTTTCTTGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGTAC
131 CAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
199976 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
196 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
200041 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATATC
261 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATATC
200106 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
326 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
*
200171 TTATAAAAAGGATATATACTTTACA
391 TTATAAAAAGGATAGATACTTTACA
* *
200196 ATATAAGTACTACCTATTACATTATATAAGCGCTATCTATTACATCATATTTTTACCTATTATAT
1 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
*
200261 TAAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
66 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
200326 C-AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
131 CAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
* *
200390 AAAAAATAATTTGATTGTTTTGATATTTTATAACATAATATTTAGAATTTAAATTTAACAATATT
196 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
*
200455 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAAATTAATATC
261 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATATC
* * *
200520 TTAAAACCCACTCAAAAGATAATCTTAAATTAATGTTTTCCACAGTAAAAAAAGTATGGACACTT
326 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
*
200585 TTATAAAAATGATAGATACTTTACA
391 TTATAAAAAGGATAGATACTTTACA
* *
200610 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATTATTTTTTTACCTATTATAT
1 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
200675 TGAAAGT
66 TGAAAGT
200682 TATGTAATTT
Statistics
Matches: 1687, Mismatches: 44, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
414 744 0.44
415 125 0.07
416 818 0.48
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (415 bp):
ATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
CAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
TTATAAAAAGGATAGATACTTTACA
Found at i:199396 original size:23 final size:23
Alignment explanation
Indices: 199366--199415 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
199356 ATACTTTACA
* *
199366 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACATATTACATC
*
199389 ATATAAGCGCTACATATTACATC
1 ATATAAGCACTACATATTACATC
199412 ATAT
1 ATAT
199416 TTTTACCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACATATTACATC
Found at i:199812 original size:23 final size:23
Alignment explanation
Indices: 199782--199831 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
199772 ATACTTTACA
*
199782 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATC
*
199805 ATATAAGCGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATC
199828 ATAT
1 ATAT
199832 TTTTACCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATC
Found at i:200640 original size:23 final size:23
Alignment explanation
Indices: 200610--200657 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
200600 ATACTTTACA
200610 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
200633 ATATAAGCGCTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
200656 AT
1 AT
200658 TTTTTTACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:203717 original size:183 final size:183
Alignment explanation
Indices: 203409--204170 Score: 1380
Period size: 183 Copynumber: 4.2 Consensus size: 183
203399 ACTCCTATTG
203409 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
*
203474 GTATATTTATACAGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
*
203539 AATGTCGACACTTTTTGACAAGGTATCGACATATTTTTCTTCCAATCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
203592 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
203657 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
*
203722 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCTAATCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
*
203775 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACTCATAAAACCG
1 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
* *
203840 GTATATTTATACCGGTTATATTACAAAATTATCTATTATATTACAATTCTGGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
*
203905 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
* *
203958 TAAAGTACAGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTG
1 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
* * *
204023 GTATATTTAAACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTATA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
* * *
204088 AATGTCGACACTTTTTGACATGGTATCGATACATTTTTCTTCCATTCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
*
204141 TAAAGTACAGACACAATATTAAAAAGTGTC
1 TAAAGTACCGACACAATATTAAAAAGTGTC
204171 AAAACTTTGT
Statistics
Matches: 561, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 561 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
Found at i:205369 original size:3 final size:3
Alignment explanation
Indices: 205361--205447 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
205351 ACTTGTTTGG
* * * * *
205361 ATC ATC ATC ATC ATC ATC ATC GTC GTC ATC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
205409 ATC GTC AGC TTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
205448 GTCAGCTTCA
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:205378 original size:12 final size:12
Alignment explanation
Indices: 205361--205464 Score: 109
Period size: 12 Copynumber: 8.7 Consensus size: 12
205351 ACTTGTTTGG
*
205361 ATCATCATCATC
1 ATCATCATCTTC
*
205373 ATCATCATCGTC
1 ATCATCATCTTC
*
205385 GTCATCATCTTC
1 ATCATCATCTTC
*
205397 ATCGTCATCTTC
1 ATCATCATCTTC
* *
205409 ATCGTCAGCTTC
1 ATCATCATCTTC
*
205421 ATCATCATCATC
1 ATCATCATCTTC
*
205433 ATCGTCATCTTC
1 ATCATCATCTTC
* *
205445 ATCGTCAGCTTC
1 ATCATCATCTTC
*
205457 ATCTTCAT
1 ATCATCAT
205465 TGACCGGTTG
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 78 1.00
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.38
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:205426 original size:36 final size:36
Alignment explanation
Indices: 205386--205464 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
205376 ATCATCGTCG
*
205386 TCATCATCTTCATCGTCATCTTCATCGTCAGCTTCA
1 TCATCATCATCATCGTCATCTTCATCGTCAGCTTCA
205422 TCATCATCATCATCGTCATCTTCATCGTCAGCTTCA
1 TCATCATCATCATCGTCATCTTCATCGTCAGCTTCA
*
205458 TCTTCAT
1 TCATCAT
205465 TGACCGGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.20, C:0.33, G:0.08, T:0.39
Consensus pattern (36 bp):
TCATCATCATCATCGTCATCTTCATCGTCAGCTTCA
Found at i:205458 original size:18 final size:18
Alignment explanation
Indices: 205401--205464 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
205391 ATCTTCATCG
205401 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
* * * *
205419 TCATCATCATCATCATCG
1 TCATCTTCATCGTCAGCT
205437 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
205455 TCATCTTCAT
1 TCATCTTCAT
205465 TGACCGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.20, C:0.33, G:0.08, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:205462 original size:6 final size:6
Alignment explanation
Indices: 205365--205464 Score: 83
Period size: 6 Copynumber: 16.7 Consensus size: 6
205355 GTTTGGATCA
* * * * * * *
205365 TCATCA TCATCA TCATCG TCGTCA TCATCT TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * * *
205413 TCAGCT TCATCA TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
205461 TCAT
1 TCAT
205465 TGACCGGTTG
Statistics
Matches: 76, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 76 1.00
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:207285 original size:200 final size:200
Alignment explanation
Indices: 206923--208092 Score: 2091
Period size: 200 Copynumber: 5.9 Consensus size: 200
206913 TTTAAATTAG
*
206923 TATCGACACAAACTAAAAAAGTGTCGACACATT-TTTAGACCTA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
206985 CTTGTACCGGTTAGATTGAAAAATTACATATTAC---ATAC-TTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
207046 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTATGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACC
207111 AAAAA
196 AAAAA
* * *
207116 TATCGACACAAACTACAAAAGTTTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* * **
207181 TTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTACGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
207246 TCGACACTTTTTATATATGGATCGACACTTTACGGTTGCACCCTGTTTGCCATTAATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACC
207311 AAAAA
196 AAAAA
207316 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
207381 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATG-TTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
207445 TCGACACTTTTTATATA-GGATCGACACTTTATGGTT-CACCCTGTTTGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACC
207508 AAAAA
196 AAAAA
*
207513 TATCGACACAAACTAAAAAAGTGTCGACAC-TTATTTAGACACATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
207577 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
207642 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACC
207707 AAAAA
196 AAAAA
*
207712 TATCGACACAAACTAAAAAAGTGCCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
207777 CTTTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGG
66 C-TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGG
207842 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTGCCATTCATTCTGGA
130 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTG-TTTGCCATTCATTCTGGA
207907 CC-AAAA
194 CCAAAAA
207913 TATCGACACAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
207977 CTTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
208041 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCA-CCTGTTTGCCAT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
208093 ATTGTAATTT
Statistics
Matches: 940, Mismatches: 24, Indels: 23
0.95 0.02 0.02
Matches are distributed among these distances:
193 31 0.03
194 10 0.01
195 1 0.00
196 148 0.16
197 90 0.10
198 111 0.12
199 116 0.12
200 287 0.31
201 126 0.13
202 20 0.02
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACC
AAAAA
Found at i:207703 original size:396 final size:400
Alignment explanation
Indices: 206923--208092 Score: 2084
Period size: 396 Copynumber: 3.0 Consensus size: 400
206913 TTTAAATTAG
*
206923 TATCGACACAAACTAAAAAAGTGTCGACACATT-TTTAGACCTA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
206985 CTTGTACCGGTTAGATTGAAAAATTACATATTAC---ATAC-TTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
207046 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTATGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACC
* *
207111 AAAAATATCGACACAAACTACAAAAGTTTCGACACATTATTTAGAC-CTATTCTCTCATAAAACC
196 AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACAC-ATTCTCTCATAAAACC
* *
207175 GGTATATTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTT
260 GGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTT
** *
207240 ACGGGATCGACACTTTTTATATATGGATCGACACTTTACGGTTGCACCCTGTTTGCCATTAATTC
325 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTAATTC
207305 TGGACCAAAAA
390 TGGACCAAAAA
207316 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
207381 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATG-TTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
207445 TCGACACTTTTTATATA-GGATCGACACTTTATGGTT-CACCCTGTTTGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACC
207508 AAAAATATCGACACAAACTAAAAAAGTGTCGACAC-TTATTTAGACACATTCTCTCATAAAACCG
196 AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACACATTCTCTCATAAAACCG
207572 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
261 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
*
207637 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
326 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTAATTCT
207702 GGACCAAAAA
391 GGACCAAAAA
*
207712 TATCGACACAAACTAAAAAAGTGCCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
207777 CTTTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGG
66 C-TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGG
207842 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTGCCATTCATTCTGGA
130 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTG-TTTGCCATTCATTCTGGA
*
207907 CC-AAAATATCGACACAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAAC
194 CCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACACATTCTCTCATAAAAC
207970 CGGTATACTTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGTTTTCGATGTT
259 CGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTT
208034 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCA-CCTGTTTGCCAT
324 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
208093 ATTGTAATTT
Statistics
Matches: 750, Mismatches: 13, Indels: 23
0.95 0.02 0.03
Matches are distributed among these distances:
393 33 0.04
394 9 0.01
395 1 0.00
396 278 0.37
397 114 0.15
398 56 0.07
399 137 0.18
400 102 0.14
401 20 0.03
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (400 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACC
AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACACATTCTCTCATAAAACCG
GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTAATTCT
GGACCAAAAA
Found at i:208214 original size:18 final size:18
Alignment explanation
Indices: 208191--208251 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
208181 TCTCATTCAT
*
208191 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
208209 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
208228 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
208247 AATTA
1 AATTA
208252 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:208227 original size:19 final size:19
Alignment explanation
Indices: 208203--208251 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
208193 TTATATTCAC
208203 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
208222 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
208241 ATACAAAATTA
1 ATACAAAATTA
208252 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:210069 original size:33 final size:33
Alignment explanation
Indices: 210032--210097 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
210022 CATCTTAATA
*
210032 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* * *
210065 TCACCCCTCAACATCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
210098 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:210156 original size:21 final size:21
Alignment explanation
Indices: 210131--210174 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
210121 CCCCTTATGC
210131 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
210152 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
210173 CT
1 CT
210175 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:212623 original size:20 final size:19
Alignment explanation
Indices: 212577--212637 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
212567 TCCGGTAACG
212577 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
212596 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
*
212617 TTTTACCTGG-TATATCATT
1 TTTTACC-GGTTTTATCATT
212636 TT
1 TT
212638 GGATCGATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:212691 original size:180 final size:182
Alignment explanation
Indices: 212364--212834 Score: 696
Period size: 180 Copynumber: 2.6 Consensus size: 182
212354 CGTACTTACG
* * *
212364 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCAGTTTTATCATTTTGATACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
212429 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
212493 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCTTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
212544 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
212609 TATCATATTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
212674 AGGATTTAAAA-TGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * ** *
212725 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATTATTTCAATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
212790 TATCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
212835 AATTTGGATC
Statistics
Matches: 262, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
180 133 0.51
181 129 0.49
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:213681 original size:2 final size:2
Alignment explanation
Indices: 213674--213722 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
213664 TAGCTATGTC
213674 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
213716 TA TA TA T
1 TA TA TA T
213723 TTGAGGCTGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:219265 original size:12 final size:12
Alignment explanation
Indices: 219248--219272 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
219238 AAAAGTTGAT
219248 AAGTTAAATTGG
1 AAGTTAAATTGG
219260 AAGTTAAATTGG
1 AAGTTAAATTGG
219272 A
1 A
219273 CTTGCCAATG
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:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
AAGTTAAATTGG
Found at i:221146 original size:2 final size:2
Alignment explanation
Indices: 221135--221167 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
221125 CTAAGGAAAA
221135 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
221168 TTATTTAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:221665 original size:17 final size:16
Alignment explanation
Indices: 221643--221693 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
221633 CATTTCTTTG
221643 ATATTAAAAATAAATAA
1 ATATTAAAAAT-AATAA
* *
221660 ATATTAAGAAGAATATA
1 ATATTAAAAATAATA-A
*
221677 ATAATAAAAATAATAA
1 ATATTAAAAATAATAA
221693 A
1 A
221694 AAAGAAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (16 bp):
ATATTAAAAATAATAA
Found at i:223166 original size:3 final size:3
Alignment explanation
Indices: 223160--223207 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
223150 TTTTTTTATT
223160 TAA TAA TAA TAA T-A TAA T-A TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
223205 TAA
1 TAA
223208 GATGAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.14
3 36 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:223809 original size:22 final size:22
Alignment explanation
Indices: 223783--223824 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
223773 CATATTGCTC
223783 AGAGGGAACCGATTCCCCCCCA
1 AGAGGGAACCGATTCCCCCCCA
* *
223805 AGAGGGTACCGATTTCCCCC
1 AGAGGGAACCGATTCCCCCC
223825 TGAATGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.38, G:0.24, T:0.14
Consensus pattern (22 bp):
AGAGGGAACCGATTCCCCCCCA
Found at i:229661 original size:22 final size:22
Alignment explanation
Indices: 229633--229717 Score: 59
Period size: 22 Copynumber: 3.9 Consensus size: 22
229623 TTTTGGTGCA
*
229633 GAGGGAATCGATCCCCCCTCAT
1 GAGGGAACCGATCCCCCCTCAT
* * *
229655 GAGGGAACCAATTCCCCCT-TT
1 GAGGGAACCGATCCCCCCTCAT
*
229676 GAAGGGGAACCGATTCCCCCCACA-
1 G-A-GGGAACCGA-TCCCCCCTCAT
* *
229700 G-GGGAATCGATACCCCCT
1 GAGGGAACCGATCCCCCCT
229718 GGGGTTCTGT
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
20 6 0.12
21 10 0.21
22 17 0.35
23 8 0.17
24 7 0.15
ACGTcount: A:0.25, C:0.35, G:0.24, T:0.16
Consensus pattern (22 bp):
GAGGGAACCGATCCCCCCTCAT
Found at i:233295 original size:32 final size:31
Alignment explanation
Indices: 233254--233374 Score: 93
Period size: 31 Copynumber: 3.9 Consensus size: 31
233244 AGTCGAGGGT
233254 TTACCTATGTTCTACGGAACATATGGATAGAA
1 TTACCTATGTTCTACGGAACATATGGATAG-A
*** *
233286 TTACCTATG-TCTTTTGAGACATATGGACAG-
1 TTACCTATGTTCTACGGA-ACATATGGATAGA
* * * *
233316 TATACCTATGTTTTAAGGAGCATATGGATAGT
1 T-TACCTATGTTCTACGGAACATATGGATAGA
* * * *
233348 TTACCTAGGTTCTTCGGGACCTATGGA
1 TTACCTATGTTCTACGGAACATATGGA
233375 CAGTTGTCGA
Statistics
Matches: 68, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
30 1 0.01
31 42 0.62
32 25 0.37
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGATAGA
Found at i:233340 original size:31 final size:30
Alignment explanation
Indices: 233255--233354 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 30
233245 GTCGAGGGTT
* * *
233255 TACCTATGTTCTACGGAACATATGGATAGAA
1 TACCTATGTTTTA-GGAGCATATGGATAGTA
* *
233286 TTACCTATGTCTTT-TGAGACATATGGACAGTA
1 -TACCTATGT-TTTAGGAG-CATATGGATAGTA
*
233318 TACCTATGTTTTAAGGAGCATATGGATAGTT
1 TACCTATGTTTT-AGGAGCATATGGATAGTA
233349 TACCTA
1 TACCTA
233355 GGTTCTTCGG
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
30 3 0.05
31 28 0.50
32 23 0.41
33 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (30 bp):
TACCTATGTTTTAGGAGCATATGGATAGTA
Found at i:239717 original size:16 final size:17
Alignment explanation
Indices: 239691--239730 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
239681 ATTCATTACT
239691 ATTTACGTGAATAGTG-A
1 ATTT-CGTGAATAGTGAA
239708 ATTTCGTGAATAGTGAA
1 ATTTCGTGAATAGTGAA
239725 ATTTCG
1 ATTTCG
239731 GTCAGCGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.38
Consensus pattern (17 bp):
ATTTCGTGAATAGTGAA
Found at i:245404 original size:835 final size:834
Alignment explanation
Indices: 243787--245457 Score: 3227
Period size: 835 Copynumber: 2.0 Consensus size: 834
243777 AGCAGTCGGC
243787 TGCTACCATTTTTGTCAAAGTTTGGCAAGGATTTTGAATTTAAGTAATGACTAATTACATTTTAG
1 TGCTACCATTTTTGTCAAAGTTTGGCAAGGATTTTGAATTTAAGTAATGACTAATTACATTTTAG
*
243852 TCATTGCACTTTAGGGTATTTTCAATGATTAGTCCCTAAGTTTTAACTATAAATACCCTAGTTCA
66 TCATTGCACTTTAGGGTATTTTCAAAGATTAGTCCCTAAGTTTTAACTATAAATACCCTAGTTCA
243917 TTTAGCTTCAAAATCATCCCAAAAATCATTTCTTTCTCCCAATACTAGAGAGCTTTCTTGTGAGT
131 TTTAGCTTCAAAATCATCCCAAAAATCATTTCTTTCTCCCAATACTAGAGAGCTTTCTTGTGAGT
*
243982 AGTGAGTGTTTTGTAAACACCTGTAAAATTTCTCTCTTAGTAAAAGATTTGCAGTAGTCCGGAGA
196 AGTGAGTGTTTTGTAAACACCTGTAAAATTTCTCTCTTAGTAAAAGATCTGCAGTAGTCCGGAGA
244047 CGTAAGCAAAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTCCGCTTTTATTTCGCA
261 CGTAAGCAAAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTCCGCTTTTATTTCGCA
*
244112 TTCTCACTAATCTGGTTATAGGGAAATTACTTCTACTCGGTTTATTTCCTAACATGGTTTCCATC
326 TTCTCACTAATCTGGTTATAGGAAAATTACTTCTACTCGGTTTATTTCCTAACATGGTTTCCATC
* *
244177 GGAGATGTTGTTCGTGTTGTGCTGAGTGAGCATCGTGCAGAGCTGGACCGCTTGAACGCTTTCAT
391 GGAGATGTTGTTCGTGCTGTGCTGAGTGAGCATCATGCAGAGCTGGACCGCTTGAACGCTTTCAT
244242 GTAGGGAGGATATTAGATGATGATGATGATAAAATATTGTATGTTTAACCCATTGGACTTAAGCA
456 GTAGGGAGGATATTAGATGATGATGATGATAAAATATTGTATGTTTAACCCATTGGACTTAAGCA
244307 AGCAAGCGGAGAGTTTGCAAATGTGCTGTGTTTTTTTAGATTCTTCTCAAGTTCTTCTGTGAATG
521 AGCAAGCGGAGAGTTTGCAAATGTGCTGTGTTTTTTTAGATTCTTCTCAAGTTCTTCTGTGAATG
244372 TGCAAGTGATGTTGGAATAATTCCCGTGTGGACCAAGTGTTCAATAGTAAACATTCTCATGTTGC
586 TGCAAGTGATGTTGGAATAATTCCCGTGTGGACCAAGTGTTCAATAGTAAACATTCTCATGTTGC
*
244437 TTCTTCCTATTTTTCTAGGCAAATGGCAAGGGCAAAATAAATTAAATTATCCCCTTTTATAATAA
651 TTCTTCCTATTTTTCTAGGCAAATGGCAAAGGCAAAATAAATTAAATTATCCCCTTTTATAATAA
244502 ATCGTGAAGAATAATTAATTAATTTTACAGAATCCTTTTCTCCGCCCCCAGCATGTTACCGAAAA
716 ATCGTGAAGAATAATTAATTAATTTTACAGAATCCTTTTCTCCGCCCCCAGCATGTTACCG-AAA
244567 AAAAAGAGCATACCAACGAAAGCGTCGTGCACAGCTTTCTTCTTCCCTTAACAGA
780 AAAAAGAGCATACCAACGAAAGCGTCGTGCACAGCTTTCTTCTTCCCTTAACAGA
244622 TGCTACCATTTTTGTCAAAGTTTGGCAAGGATTTTGAATTTAAGTAATGACTAATTACATTTTAG
1 TGCTACCATTTTTGTCAAAGTTTGGCAAGGATTTTGAATTTAAGTAATGACTAATTACATTTTAG
244687 TCATTGCACTTTAGGGTATTTTCAAAGATTAGTCCCTAAGTTTTAACTATAAATACCCTAGTTCA
66 TCATTGCACTTTAGGGTATTTTCAAAGATTAGTCCCTAAGTTTTAACTATAAATACCCTAGTTCA
*
244752 TTTAGCTTCAAAATCATCCCAAAAATCATTTTTTTCTCCCAATACTAGAGAGCTTTCTTGTGAGT
131 TTTAGCTTCAAAATCATCCCAAAAATCATTTCTTTCTCCCAATACTAGAGAGCTTTCTTGTGAGT
244817 AGTGAGTGTTTTGTAAACACCTGTAAAATTTCTCTCTTAGTAAAAGATCTGCAGTAGTCCGGAGA
196 AGTGAGTGTTTTGTAAACACCTGTAAAATTTCTCTCTTAGTAAAAGATCTGCAGTAGTCCGGAGA
*
244882 CGTAAGCAAAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTCCTCTTTTATTTCGCA
261 CGTAAGCAAAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTCCGCTTTTATTTCGCA
*
244947 TTCTCACTAATCTGGTTATAGGAAAATTACTTCTACTCGGTTTATTTCCTAGCATGGTTTCCATC
326 TTCTCACTAATCTGGTTATAGGAAAATTACTTCTACTCGGTTTATTTCCTAACATGGTTTCCATC
245012 GGAGATGTTGTTCGTGCTGTGCTGAGTGAGCATCATGCAGAGCTGGACCGCTTGAACGCTTTCAT
391 GGAGATGTTGTTCGTGCTGTGCTGAGTGAGCATCATGCAGAGCTGGACCGCTTGAACGCTTTCAT
*
245077 GTAGGGAGGATATTAGATGATGATGATGATAAAATATTGTATGTTTAACCCGTTGGACTTAAGCA
456 GTAGGGAGGATATTAGATGATGATGATGATAAAATATTGTATGTTTAACCCATTGGACTTAAGCA
245142 AGCAAGCGGAGAGTTTGCAAATGTGCTGTG-TTTTTTAGATTCTTCTCAAGTTCTTCTGTGAATG
521 AGCAAGCGGAGAGTTTGCAAATGTGCTGTGTTTTTTTAGATTCTTCTCAAGTTCTTCTGTGAATG
245206 TGCAAGTGATGTTGGAATAATTCCCGTGTGGACCAAGTGTTCAATAGTAAACATTCTCATGTTGC
586 TGCAAGTGATGTTGGAATAATTCCCGTGTGGACCAAGTGTTCAATAGTAAACATTCTCATGTTGC
245271 TTCTTCCTATTTTTCTAGGCAAATGGCAAAGGCAAAATAAATTAAATTATCCCCTTTTATAATAA
651 TTCTTCCTATTTTTCTAGGCAAATGGCAAAGGCAAAATAAATTAAATTATCCCCTTTTATAATAA
*
245336 ATCGTGAAGAATAATTAATTAATTTTACAGAATCCTTTTCTCCGCCCCCAGCATGTTATCGAAAA
716 ATCGTGAAGAATAATTAATTAATTTTACAGAATCCTTTTCTCCGCCCCCAGCATGTTACCGAAAA
245401 AAAAGAGCATACCAACGAAAGCGTCGTGCACAGCTTTCTTCTTCCCTTAACAGA
781 AAAAGAGCATACCAACGAAAGCGTCGTGCACAGCTTTCTTCTTCCCTTAACAGA
245455 TGC
1 TGC
245458 ACAATGTTGA
Statistics
Matches: 825, Mismatches: 11, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
833 61 0.07
834 223 0.27
835 541 0.66
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (834 bp):
TGCTACCATTTTTGTCAAAGTTTGGCAAGGATTTTGAATTTAAGTAATGACTAATTACATTTTAG
TCATTGCACTTTAGGGTATTTTCAAAGATTAGTCCCTAAGTTTTAACTATAAATACCCTAGTTCA
TTTAGCTTCAAAATCATCCCAAAAATCATTTCTTTCTCCCAATACTAGAGAGCTTTCTTGTGAGT
AGTGAGTGTTTTGTAAACACCTGTAAAATTTCTCTCTTAGTAAAAGATCTGCAGTAGTCCGGAGA
CGTAAGCAAAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTCCGCTTTTATTTCGCA
TTCTCACTAATCTGGTTATAGGAAAATTACTTCTACTCGGTTTATTTCCTAACATGGTTTCCATC
GGAGATGTTGTTCGTGCTGTGCTGAGTGAGCATCATGCAGAGCTGGACCGCTTGAACGCTTTCAT
GTAGGGAGGATATTAGATGATGATGATGATAAAATATTGTATGTTTAACCCATTGGACTTAAGCA
AGCAAGCGGAGAGTTTGCAAATGTGCTGTGTTTTTTTAGATTCTTCTCAAGTTCTTCTGTGAATG
TGCAAGTGATGTTGGAATAATTCCCGTGTGGACCAAGTGTTCAATAGTAAACATTCTCATGTTGC
TTCTTCCTATTTTTCTAGGCAAATGGCAAAGGCAAAATAAATTAAATTATCCCCTTTTATAATAA
ATCGTGAAGAATAATTAATTAATTTTACAGAATCCTTTTCTCCGCCCCCAGCATGTTACCGAAAA
AAAAGAGCATACCAACGAAAGCGTCGTGCACAGCTTTCTTCTTCCCTTAACAGA
Found at i:246982 original size:9 final size:9
Alignment explanation
Indices: 246965--247058 Score: 64
Period size: 10 Copynumber: 9.8 Consensus size: 9
246955 GGCTGCTGGA
246965 AACCGGTTT
1 AACCGGTTT
*
246974 AACCTGTTTT
1 AACC-GGTTT
246984 CAACCGGTTCT
1 -AACCGGTT-T
*
246995 GACCGGTTT
1 AACCGGTTT
247004 -ACCGGTTT
1 AACCGGTTT
*
247012 CAACCGGTTCG
1 -AACCGGTT-T
247023 AACCGGTTTT
1 AACCGG-TTT
* *
247033 GACCGGTCTG
1 AACCGGT-TT
247043 AACCGGTTT
1 AACCGGTTT
*
247052 GACCGGT
1 AACCGGT
247059 CTGACCCGAC
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
8 8 0.12
9 13 0.19
10 39 0.58
11 7 0.10
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:247009 original size:8 final size:9
Alignment explanation
Indices: 246986--247064 Score: 70
Period size: 10 Copynumber: 8.3 Consensus size: 9
246976 CCTGTTTTCA
246986 ACCGGTTCTG
1 ACCGGTT-TG
246996 ACCGGTTT-
1 ACCGGTTTG
*
247004 ACCGGTTTCA
1 ACCGGTTT-G
*
247014 ACCGGTTCG
1 ACCGGTTTG
247023 AACCGGTTTTG
1 -ACCGG-TTTG
*
247034 ACCGGTCTG
1 ACCGGTTTG
247043 AACCGGTTTG
1 -ACCGGTTTG
*
247053 ACCGGTCTG
1 ACCGGTTTG
247062 ACC
1 ACC
247065 CGACCCGACC
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
8 8 0.14
9 15 0.26
10 32 0.55
11 3 0.05
ACGTcount: A:0.15, C:0.29, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:247085 original size:22 final size:22
Alignment explanation
Indices: 247059--247113 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
247049 TTTGACCGGT
247059 CTGACCCGACCCGACCGTTAAC
1 CTGACCCGACCCGACCGTTAAC
*
247081 CTGACCCGACCCGACCGTTGAC
1 CTGACCCGACCCGACCGTTAAC
*
247103 CCGACCCGACC
1 CTGACCCGACC
247114 GTTGACCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.11
Consensus pattern (22 bp):
CTGACCCGACCCGACCGTTAAC
Found at i:247102 original size:17 final size:17
Alignment explanation
Indices: 247082--247120 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
247072 ACCGTTAACC
247082 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
247099 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
247116 TGACC
1 TGACC
247121 GTTGACCGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:247120 original size:7 final size:7
Alignment explanation
Indices: 247110--247155 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
247100 GACCCGACCC
247110 GACCGTT
1 GACCGTT
247117 GACCGTT
1 GACCGTT
247124 GACCGCTT
1 GACCG-TT
*
247132 -ATCGTT
1 GACCGTT
247138 GACCCGTT
1 GA-CCGTT
247146 GACCGTT
1 GACCGTT
247153 GAC
1 GAC
247156 TTACTTTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 2 0.06
7 24 0.71
8 8 0.24
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.28
Consensus pattern (7 bp):
GACCGTT
Found at i:253583 original size:11 final size:10
Alignment explanation
Indices: 253558--253645 Score: 63
Period size: 10 Copynumber: 8.9 Consensus size: 10
253548 GGCTGCTGGA
253558 AACCGG-TTT
1 AACCGGTTTT
253567 AACCGGTTTT
1 AACCGGTTTT
*
253577 CAACCGGTTCT
1 -AACCGGTTTT
*
253588 GACCGG-TTT
1 AACCGGTTTT
* *
253597 GACCGGTTTC
1 AACCGGTTTT
* **
253607 AATCGGTTCG
1 AACCGGTTTT
253617 AACCGGTTTT
1 AACCGGTTTT
* * *
253627 GACCGGTCTG
1 AACCGGTTTT
253637 AACCGGTTT
1 AACCGGTTT
253646 GACCGGTCTG
Statistics
Matches: 60, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
9 14 0.23
10 37 0.62
11 9 0.15
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (10 bp):
AACCGGTTTT
Found at i:253583 original size:20 final size:21
Alignment explanation
Indices: 253558--253596 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
253548 GGCTGCTGGA
253558 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
253578 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
253597 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:253594 original size:10 final size:10
Alignment explanation
Indices: 253579--253658 Score: 64
Period size: 10 Copynumber: 8.3 Consensus size: 10
253569 CCGGTTTTCA
253579 ACCGGTTCTG
1 ACCGGTTCTG
253589 ACCGGTT-TG
1 ACCGGTTCTG
*
253598 ACCGGTT-TCA
1 ACCGGTTCT-G
*
253608 ATCGGTTC-G
1 ACCGGTTCTG
*
253617 AACCGGTTTTG
1 -ACCGGTTCTG
253628 ACCGG-TCTG
1 ACCGGTTCTG
253637 AACCGGTT-TG
1 -ACCGGTTCTG
253647 ACCGG-TCTG
1 ACCGGTTCTG
253656 ACC
1 ACC
253659 CTACCCGACC
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
8 1 0.02
9 23 0.40
10 31 0.54
11 2 0.04
ACGTcount: A:0.15, C:0.28, G:0.29, T:0.29
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:253595 original size:30 final size:29
Alignment explanation
Indices: 253559--253658 Score: 114
Period size: 30 Copynumber: 3.4 Consensus size: 29
253549 GCTGCTGGAA
*
253559 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
*
253589 ACCGGTTTGACCGGTTTCAATCGGTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* *
253617 AACCGGTTTTGACCGGTCTGAACCGGTT-TG
1 -ACCGG-TTTGACCGGTTTCAACCGGTTCTG
*
253647 ACCGGTCTGACC
1 ACCGGTTTGACC
253659 CTACCCGACC
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
28 7 0.11
29 22 0.36
30 32 0.52
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:253678 original size:12 final size:12
Alignment explanation
Indices: 253661--253709 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
253651 GTCTGACCCT
253661 ACCCGACCGTTG
1 ACCCGACCGTTG
*
253673 ACCCGACC--CG
1 ACCCGACCGTTG
*
253683 ACCCGACGGTTG
1 ACCCGACCGTTG
253695 ACCCGACCGTTG
1 ACCCGACCGTTG
253707 ACC
1 ACC
253710 GTTGACCGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 8 0.26
12 23 0.74
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.12
Consensus pattern (12 bp):
ACCCGACCGTTG
Found at i:253681 original size:22 final size:22
Alignment explanation
Indices: 253655--253702 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
253645 TGACCGGTCT
*
253655 GACCCTACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
253677 GACCCGACCCGACGGTTGACCC
1 GACCCGACCCGACCGTTGACCC
253699 GACC
1 GACC
253703 GTTGACCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.48, G:0.23, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:253711 original size:7 final size:7
Alignment explanation
Indices: 253699--253750 Score: 95
Period size: 7 Copynumber: 7.4 Consensus size: 7
253689 CGGTTGACCC
253699 GACCGTT
1 GACCGTT
253706 GACCGTT
1 GACCGTT
253713 GACCGTT
1 GACCGTT
*
253720 GATCGTT
1 GACCGTT
253727 GACCGTT
1 GACCGTT
253734 GACCGTT
1 GACCGTT
253741 GACCGTT
1 GACCGTT
253748 GAC
1 GAC
253751 TTTCTTTGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:258451 original size:18 final size:18
Alignment explanation
Indices: 258418--258453 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
258408 ATCAGTTGTT
*
258418 GGAGTAAAAATGGCAAAC
1 GGAGTAAAAATCGCAAAC
*
258436 GGAGTAAAATTCGCAAAC
1 GGAGTAAAAATCGCAAAC
258454 AACCTTCGAA
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:0.47, C:0.14, G:0.25, T:0.14
Consensus pattern (18 bp):
GGAGTAAAAATCGCAAAC
Found at i:266788 original size:28 final size:29
Alignment explanation
Indices: 266734--266828 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 29
266724 TTAACTTGTT
266734 AAATATATTTTATTATTAACTTAATTTAA
1 AAATATATTTTATTATTAACTTAATTTAA
* * *
266763 AAATAT-TTTTATTTTTATCTTCATTTAAAA
1 AAATATATTTTATTATTAACTTAATTT--AA
* *
266793 AAATATATTTT-TATATTGAAATTTATTTAA
1 AAATATATTTTAT-TATT-AACTTAATTTAA
266823 AAATAT
1 AAATAT
266829 GACTAAATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
28 17 0.31
29 6 0.11
30 17 0.31
31 7 0.13
32 7 0.13
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (29 bp):
AAATATATTTTATTATTAACTTAATTTAA
Found at i:277974 original size:205 final size:206
Alignment explanation
Indices: 277671--278090 Score: 648
Period size: 205 Copynumber: 2.0 Consensus size: 206
277661 AAATGCCGCG
* * *
277671 TAGAGTGGTTTATAGTGGGCGTTTTCCAACAAACGCCGCAATGAAGAACACTTTTGCTTCGTTTT
1 TAGAGTGGTTTATAGTGGGCGTTTTCCAACAAACGCCACAATGAAGAACACGTTTGCGTCGTTTT
* *
277736 TAGACAAATGCCACAGAAGGGTTAATCAATAGCGGCGTTTATAGTAAAAATGCCGCAATAGAGTA
66 TAGACAAACGCCACAAAAGGGTTAATCAATAGCGGCGTTTATAGTAAAAATGCCGCAATAGAGTA
* *
277801 GCCATTTAGCGGCGTTTTAGCCCAAACACTGTAATAGAGTGGTAATTTAGCGACGTTTATACCTA
131 GACATTTAGCGGCGTTTTAGCCCAAACACGGTAATAGAGTGGTAATTTAGCGACGTTTATACC-A
* *
277866 -AAATGCCGTAA
195 CAAACGCCGCAA
* * *
277877 TAGGGTGGTTTATAGT-GGCGTTTTTCCAACAAATGCCACAATGAAGAATACGTTTGCGTCG-TT
1 TAGAGTGGTTTATAGTGGGCG-TTTTCCAACAAACGCCACAATGAAGAACACGTTTGCGTCGTTT
* *
277940 TTAGATAAACGCCACAAAAGGGTTAATCAATAGCGGCGTTTATAGTACAAATGCCGCAATAGAGT
65 TTAGACAAACGCCACAAAAGGGTTAATCAATAGCGGCGTTTATAGTAAAAATGCCGCAATAGAGT
** *
278005 AGACATTTAGCGGCGTTTTAGCCCAAATGCGGTAATAGAGTGGTAATTTAGCGGCGTTTATACCA
130 AGACATTTAGCGGCGTTTTAGCCCAAACACGGTAATAGAGTGGTAATTTAGCGACGTTTATACCA
278070 CAAACGCCGCAA
195 CAAACGCCGCAA
278082 TAGAGTGGT
1 TAGAGTGGT
278091 AAATTAGCGG
Statistics
Matches: 194, Mismatches: 18, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
204 1 0.01
205 143 0.74
206 50 0.26
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (206 bp):
TAGAGTGGTTTATAGTGGGCGTTTTCCAACAAACGCCACAATGAAGAACACGTTTGCGTCGTTTT
TAGACAAACGCCACAAAAGGGTTAATCAATAGCGGCGTTTATAGTAAAAATGCCGCAATAGAGTA
GACATTTAGCGGCGTTTTAGCCCAAACACGGTAATAGAGTGGTAATTTAGCGACGTTTATACCAC
AAACGCCGCAA
Found at i:278042 original size:41 final size:42
Alignment explanation
Indices: 277765--278108 Score: 176
Period size: 41 Copynumber: 8.3 Consensus size: 42
277755 GGTTAATCAA
* * **
277765 TAGCGGCGTTTATAGTAAAAATGCCGCAATAGAGTAGCCATT
1 TAGCGGCGTTTATAGCACAAATGCCGCAATAGAGTAGTAATT
* ** * * *
277807 TAGCGGCGTTT-TAGCCCAAACACTGTAATAGAGTGGTAATT
1 TAGCGGCGTTTATAGCACAAATGCCGCAATAGAGTAGTAATT
* * * * *
277848 TAGCGACGTTTATACCTA-AAATGCCGTAATAGGGTGGT--TT
1 TAGCGGCGTTTATAGC-ACAAATGCCGCAATAGAGTAGTAATT
* ** * * *
277888 ATAGTGGCGTTT-TTCCAACAAATGCCACAAT-GAAG-AATACGTT
1 -TAGCGGCGTTTATAGC-ACAAATGCCGCAATAG-AGTAGTA-ATT
* * * * * * *
277931 T-GCGTCGTTT-TAG-ATAAACGCCACAAAAGGGT--TAATCAA
1 TAGCGGCGTTTATAGCACAAATGCCGCAATAGAGTAGTAAT--T
*
277970 TAGCGGCGTTTATAGTACAAATGCCGCAATAGAGTAG-ACATT
1 TAGCGGCGTTTATAGCACAAATGCCGCAATAGAGTAGTA-ATT
* * * *
278012 TAGCGGCGTTT-TAGCCCAAATGCGGTAATAGAGTGGTAATT
1 TAGCGGCGTTTATAGCACAAATGCCGCAATAGAGTAGTAATT
* * * *
278053 TAGCGGCGTTTATACCACAAACGCCGCAATAGAGTGGTAAAT
1 TAGCGGCGTTTATAGCACAAATGCCGCAATAGAGTAGTAATT
*
278095 TAGCGGCATTTATA
1 TAGCGGCGTTTATA
278109 CCTAAAACGC
Statistics
Matches: 227, Mismatches: 55, Indels: 40
0.70 0.17 0.12
Matches are distributed among these distances:
37 1 0.00
38 2 0.01
39 13 0.06
40 17 0.07
41 95 0.42
42 94 0.41
43 3 0.01
44 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (42 bp):
TAGCGGCGTTTATAGCACAAATGCCGCAATAGAGTAGTAATT
Found at i:278098 original size:42 final size:42
Alignment explanation
Indices: 277970--278132 Score: 172
Period size: 42 Copynumber: 3.9 Consensus size: 42
277960 GGTTAATCAA
** * *
277970 TAGCGGCGTTTATAGTACAAATGCCGCAATAGAGTAG-ACATT
1 TAGCGGCGTTTATACCACAAACGCCGCAATAGAGTGGTA-ATT
* * *
278012 TAGCGGCGTTT-TAGCC-CAAATGCGGTAATAGAGTGGTAATT
1 TAGCGGCGTTTATA-CCACAAACGCCGCAATAGAGTGGTAATT
*
278053 TAGCGGCGTTTATACCACAAACGCCGCAATAGAGTGGTAAAT
1 TAGCGGCGTTTATACCACAAACGCCGCAATAGAGTGGTAATT
* * *
278095 TAGCGGCATTTATACCTA-AAACGCCGTAATAGGGTGGT
1 TAGCGGCGTTTATACC-ACAAACGCCGCAATAGAGTGGT
278133 TTATAGTGGC
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
41 35 0.34
42 68 0.65
43 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (42 bp):
TAGCGGCGTTTATACCACAAACGCCGCAATAGAGTGGTAATT
Found at i:285285 original size:21 final size:21
Alignment explanation
Indices: 285261--285312 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
285251 TGAAGCAAGG
*
285261 GAAGCAGAGAGAGCAACAGTA
1 GAAGCAGAGAGAGCAACAGCA
** * *
285282 GAAGCAGCTAGAGCAGCAGCG
1 GAAGCAGAGAGAGCAACAGCA
285303 GAAGCAGAGA
1 GAAGCAGAGA
285313 AAGAAGCAAC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.37, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGAGAGCAACAGCA
Found at i:285320 original size:21 final size:21
Alignment explanation
Indices: 285296--285343 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
285286 CAGCTAGAGC
*
285296 AGCAGCGGAAGCAGAGAAAGA
1 AGCAGCGGAAGCACAGAAAGA
* * *
285317 AGCAACGGCAGCACAGAGAGA
1 AGCAGCGGAAGCACAGAAAGA
285338 AGCAGC
1 AGCAGC
285344 ATATCAGCAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.21, G:0.35, T:0.00
Consensus pattern (21 bp):
AGCAGCGGAAGCACAGAAAGA
Found at i:285818 original size:43 final size:43
Alignment explanation
Indices: 285755--285937 Score: 163
Period size: 43 Copynumber: 4.3 Consensus size: 43
285745 CATTTTTAGC
* *
285755 AAAAACACCGCAAAACATCAACACCTACTGCAGTGTTTGTGAG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGTGTTTGTGAG
* * *
285798 AAAAATGCCGCAAAATATCAACACCTACTGCGGAGTTT-TAGAG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGTGTTTGT-GAG
* * * ** **
285841 AAAAACGTCGCTAAACATCATA-ACCTATTGCGACGTTTGTCTG
1 AAAAACGCCGCAAAACATCA-ACACCTACTGCGGTGTTTGTGAG
* * * * * **
285884 AAAAACACCGCTAAATATCAACACCTATTGCGGTGTTTTTCTG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGTGTTTGTGAG
285927 AAAAACGCCGC
1 AAAAACGCCGC
285938 GAACTTTAGC
Statistics
Matches: 115, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
42 2 0.02
43 111 0.97
44 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCAAAACATCAACACCTACTGCGGTGTTTGTGAG
Found at i:292034 original size:2 final size:2
Alignment explanation
Indices: 292023--292087 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
292013 TAAATATTTA
292023 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
292064 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
292088 TATTTAGCTT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:294526 original size:35 final size:36
Alignment explanation
Indices: 294480--294567 Score: 155
Period size: 35 Copynumber: 2.5 Consensus size: 36
294470 GCCCCGATTA
294480 TATATATATATAATATTTTATAT-TTTTATATTAAT
1 TATATATATATAATATTTTATATATTTTATATTAAT
294515 TATATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATATAATATTTTATATATTTTATATTAAT
294551 TATATATA-A-AATATTTT
1 TATATATATATAATATTTT
294568 TGGGTTCGGG
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
34 8 0.15
35 24 0.46
36 20 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (36 bp):
TATATATATATAATATTTTATATATTTTATATTAAT
Found at i:295661 original size:3 final size:3
Alignment explanation
Indices: 295653--295680 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
295643 TAAAGGATAT
295653 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
295681 CATCATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:299523 original size:3 final size:3
Alignment explanation
Indices: 299515--299542 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
299505 ATAATTCAGT
299515 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
299543 AAAACCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:304840 original size:17 final size:17
Alignment explanation
Indices: 304818--304859 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
304808 ATATATACAT
*
304818 ATAATAATAATACATGA
1 ATAATAATAATAAATGA
*
304835 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
304852 ATAA-AATA
1 ATAATAATA
304860 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:306155 original size:105 final size:105
Alignment explanation
Indices: 305855--306901 Score: 1594
Period size: 105 Copynumber: 10.0 Consensus size: 105
305845 CATTGTTCCA
* * * ** *
305855 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTAGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * *
305919 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * *
305961 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
306021 AGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
306061 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
306126 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
306166 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
306226 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
306266 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* *
306331 AACGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
306371 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
306436 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
306476 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
306541 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
306581 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
306646 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
306686 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTTG-TTGTTGACAA
306751 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
306793 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAC
** * * *
306858 CAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
306899 AGT
1 AGT
306902 GCCACGATAT
Statistics
Matches: 870, Mismatches: 58, Indels: 26
0.91 0.06 0.03
Matches are distributed among these distances:
100 170 0.20
101 7 0.01
102 8 0.01
103 1 0.00
104 10 0.01
105 484 0.56
106 94 0.11
107 96 0.11
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:307717 original size:67 final size:68
Alignment explanation
Indices: 307645--307785 Score: 216
Period size: 67 Copynumber: 2.1 Consensus size: 68
307635 GAAACGAAAT
* *
307645 TTTGTTTTAAGAGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATAGGAGAC
1 TTTGTTTT-AGAGAGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGAC
307708 AAAA
65 AAAA
* *
307712 TTTG-TTTCGAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACA
1 TTTGTTTTAGAGAGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACA
307776 AAA
66 AAA
307779 TTTGTTT
1 TTTGTTT
307786 CAAGGGAAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
65 6 0.09
66 6 0.09
67 53 0.79
68 2 0.03
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (68 bp):
TTTGTTTTAGAGAGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACA
AAA
Found at i:307728 original size:36 final size:35
Alignment explanation
Indices: 307678--307950 Score: 196
Period size: 36 Copynumber: 7.9 Consensus size: 35
307668 AAAGATTTTG
*
307678 TGTTTCAAGAGAAACTGTCTCATAGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCA-AGGAGACAAAATT
* ** **
307714 TGTTTCGAGGGAAACAATCTCAA--AG---ATTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
*
307744 GTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTC-AAGGAGACAAAATT
* * *
307781 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
** * * *
307817 CATTTCAAGGGAAA-TGTTTTCAA--TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGAGACAAAATT
307845 ATGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGG-GAAACTGTCTCAA-GGAGACAAAA-TT
* *
307883 TGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
307919 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAA
307951 TGGTGAGCAC
Statistics
Matches: 184, Mismatches: 30, Indels: 46
0.71 0.12 0.18
Matches are distributed among these distances:
28 5 0.03
29 13 0.07
30 5 0.03
31 17 0.09
32 3 0.02
33 3 0.02
34 2 0.01
35 5 0.03
36 97 0.53
37 30 0.16
38 4 0.02
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
Found at i:307786 original size:67 final size:67
Alignment explanation
Indices: 307666--307803 Score: 240
Period size: 67 Copynumber: 2.1 Consensus size: 67
307656 AGAGATAAAT
* *
307666 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATAGGAGACAAAATTTGTTTCGAGGGAAACAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAACAA
307731 TC
66 TC
**
307733 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAATTA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAACAA
307798 TC
66 TC
307800 TCAA
1 TCAA
307804 GAGAGACGAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAACAA
TC
Found at i:307816 original size:103 final size:101
Alignment explanation
Indices: 307678--307933 Score: 309
Period size: 103 Copynumber: 2.5 Consensus size: 101
307668 AAAGATTTTG
* *
307678 TGTTTCAAGAGAAACTGTCTCATAG-GAGACAAAATTTGTTTCGAGGGAAACAATCTCAAAGATT
1 TGTTTCAAGGGAAACTGTCTCA-AGAGAGAC-AAATTTGTTTCAAGGGAAACAATCTCAAAG--T
*
307742 TTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAA-TT
62 TTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTT
* * ** *** * *
307781 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATTTGTTTCAAGGGAAACAATCTCAAAGTTTA
* *
307846 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTT
65 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTT
*
307883 TGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA-TTTGTTTCAAGGGAAAC
307934 TGTCTCAAGA
Statistics
Matches: 129, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
101 38 0.29
102 45 0.35
103 46 0.36
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (101 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTGTTTCAAGGGAAACAATCTCAAAGTTTAT
GTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTT
Found at i:308421 original size:18 final size:18
Alignment explanation
Indices: 308394--308429 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
308384 TGATGAATCC
* *
308394 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
308412 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
308430 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:308922 original size:22 final size:22
Alignment explanation
Indices: 308845--308915 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
308835 TTGTGTTTGG
*
308845 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
308867 TCAAAGGTTTAACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
* *
308889 TTAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
308911 TCAAA
1 TCAAA
308916 AGATTGATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:309585 original size:8 final size:7
Alignment explanation
Indices: 309573--309643 Score: 61
Period size: 8 Copynumber: 9.1 Consensus size: 7
309563 TGATTTTTGC
309573 TCTTTTT
1 TCTTTTT
309580 TCCTTTTGT
1 T-CTTTT-T
*
309589 TCTTGTT
1 TCTTTTT
309596 TCTCTTTT
1 TCT-TTTT
309604 TCTTTGTT
1 TCTTT-TT
*
309612 TTTTTTT
1 TCTTTTT
309619 TGCTTTTT
1 T-CTTTTT
309627 TGCTTCTTT
1 T-CTT-TTT
309636 TCTTTTT
1 TCTTTTT
309643 T
1 T
309644 GTTCTTGATT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
7 14 0.26
8 34 0.63
9 6 0.11
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:309586 original size:16 final size:17
Alignment explanation
Indices: 309567--309622 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
309557 TCTTTTTGAT
*
309567 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
309583 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* * *
309600 TTTTTCT-TTGTTTTTT
1 TTTTGCTCTTGTTTCTC
309616 TTTTGCT
1 TTTTGCT
309623 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 26 0.81
17 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:309640 original size:16 final size:16
Alignment explanation
Indices: 309598--309649 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
309588 TTCTTGTTTC
*
309598 TCTTTTTCTTTGTTT-T
1 TCTTTTGCTTT-TTTGT
*
309614 TTTTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
309631 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
309646 TCTT
1 TCTT
309650 GATTAGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.26
16 17 0.55
17 6 0.19
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:313326 original size:16 final size:17
Alignment explanation
Indices: 313294--313330 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
313284 ATATATACAT
*
313294 ATAATAATAATACATGA
1 ATAATAATAATAAATGA
313311 ATAATAA-AATAAATGA
1 ATAATAATAATAAATGA
313327 ATAA
1 ATAA
313331 ATATCCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:315742 original size:2 final size:2
Alignment explanation
Indices: 315735--315816 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
315725 ATTAGGGCAC
315735 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
315777 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
315817 TATTGCAAAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:319837 original size:20 final size:20
Alignment explanation
Indices: 319809--319870 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
319799 AGTCAACATG
*
319809 TCAGATCGGTTTGAGTTGAC
1 TCAGATCGGTTCGAGTTGAC
* *
319829 TCAGGTCGGTTCGGGTTGAC
1 TCAGATCGGTTCGAGTTGAC
* * * *
319849 TCAAACCAGTTCGAGTTAAC
1 TCAGATCGGTTCGAGTTGAC
319869 TC
1 TC
319871 GAACCAGTTC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (20 bp):
TCAGATCGGTTCGAGTTGAC
Found at i:319875 original size:20 final size:20
Alignment explanation
Indices: 319837--319880 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
319827 ACTCAGGTCG
* *
319837 GTTCGGGTTGACTCAAACCA
1 GTTCGAGTTAACTCAAACCA
*
319857 GTTCGAGTTAACTCGAACCA
1 GTTCGAGTTAACTCAAACCA
319877 GTTC
1 GTTC
319881 CAGGAAGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (20 bp):
GTTCGAGTTAACTCAAACCA
Found at i:321098 original size:22 final size:21
Alignment explanation
Indices: 321047--321103 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
321037 TTAATAAAGA
*
321047 TTTAATTATAATATACATTAT
1 TTTAATTATATTATACATTAT
*
321068 TTTATTTATATTATA-ATTAAAT
1 TTTAATTATATTATACATT--AT
321090 TTTAATTATATTAT
1 TTTAATTATATTAT
321104 GTTCATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 13 0.42
22 15 0.48
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAATTATATTATACATTAT
Found at i:328854 original size:24 final size:23
Alignment explanation
Indices: 328821--328869 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
328811 TTTATTAGTT
*
328821 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTA-TAA
*
328845 TAATTAAATATATAATATTATAA
1 TAATTAAATATATAAAATTATAA
328868 TA
1 TA
328870 TATAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATTAAATATATAAAATTATAA
Found at i:328860 original size:15 final size:15
Alignment explanation
Indices: 328842--328874 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
328832 ATAAAATTAT
328842 TAATAATTA-AATATA
1 TAAT-ATTATAATATA
328857 TAATATTATAATATA
1 TAATATTATAATATA
328872 TAA
1 TAA
328875 AAAATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATATTATAATATA
Found at i:332210 original size:20 final size:20
Alignment explanation
Indices: 332187--332241 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
332177 AGGTAAAAAT
*
332187 ATGACAAAACCGGTATCGAA
1 ATGATAAAACCGGTATCGAA
332207 ATGATAAAACCGGTATCGAA
1 ATGATAAAACCGGTATCGAA
*
332227 ATGATAAAACTGGTA
1 ATGATAAAACCGGTA
332242 AAGAGCTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (20 bp):
ATGATAAAACCGGTATCGAA
Found at i:332353 original size:202 final size:202
Alignment explanation
Indices: 332046--332420 Score: 644
Period size: 202 Copynumber: 1.9 Consensus size: 202
332036 TGTAAATCCT
* **
332046 TACCGGATATATTGAACGTGTCGATATTTTAATATAATGATCGACACTTTGTGAATTTAAAAGAG
1 TACCGGATATATTGAAAGTGTCGATACATTAATATAATGATCGACACTTTGTGAATTTAAAAGAG
*
332111 AAGCATTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAA
66 AAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAA
*
332176 CAGGTAAAAATATGACAAAACCGGTATCGAAATGATAAAACCGGTATCGAAATGATAAAACTGGT
131 CAGGTAAAAATATGACAAAACCGGTATCAAAATGATAAAACCGGTATCGAAATGATAAAACTGGT
332241 AAAGAGC
196 AAAGAGC
* *
332248 TACCGGATATATTTAAAGTGTCGGTACATTAATATAA-GTATCGACACTTTGTGAATTTAAAAGA
1 TACCGGATATATTGAAAGTGTCGATACATTAATATAATG-ATCGACACTTTGTGAATTTAAAAGA
* *
332312 GAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGTTCCACAACGATATA
65 GAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACGATATA
*
332377 ACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCG
130 ACAGGTAAAAATATGACAAAACCGGTATCAAAATGATAAAACCG
332421 ATAAAGCGCT
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
201 1 0.01
202 161 0.99
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (202 bp):
TACCGGATATATTGAAAGTGTCGATACATTAATATAATGATCGACACTTTGTGAATTTAAAAGAG
AAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAA
CAGGTAAAAATATGACAAAACCGGTATCAAAATGATAAAACCGGTATCGAAATGATAAAACTGGT
AAAGAGC
Found at i:332403 original size:20 final size:19
Alignment explanation
Indices: 332380--332425 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
332370 CGATATAACA
332380 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
332400 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
332420 GATAAA
1 GGTAAA
332426 GCGCTACCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:334586 original size:15 final size:15
Alignment explanation
Indices: 334566--334613 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
334556 TGGTTGTATT
334566 GGGGGATGACGATGA
1 GGGGGATGACGATGA
334581 GGGGGATGACGATGA
1 GGGGGATGACGATGA
*
334596 GGGGGATGACGGTGA
1 GGGGGATGACGATGA
334611 GGG
1 GGG
334614 AAAACAGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.23, C:0.06, G:0.58, T:0.12
Consensus pattern (15 bp):
GGGGGATGACGATGA
Found at i:334720 original size:21 final size:21
Alignment explanation
Indices: 334696--334739 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
334686 AAGACAATCA
334696 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
334717 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
334738 AG
1 AG
334740 GCATAAGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:334815 original size:33 final size:33
Alignment explanation
Indices: 334773--334838 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
334763 AAATAGATGG
*
334773 AGTGATGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
334806 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
334839 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:337223 original size:180 final size:180
Alignment explanation
Indices: 336921--337486 Score: 776
Period size: 180 Copynumber: 3.0 Consensus size: 180
336911 GTAAAATTTA
** * * *
336921 TCGATCCCAGAAACAT-ATGCATCCATAAGTATAATATAATAGGTAAATTTTCAATGTAACCGGT
1 TCGATCCCAGAAACATCA-AAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAACCGGT
336985 ATAAATATACC-AGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGT
65 ATAAATATACCGA-TTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGT
337049 GTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTG
129 GTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTG
* *
337101 TCGATCCCAGAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCAGTA
1 TCGATCCCAGAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAACCGGTA
*
337166 TAAATATACCGATTTTATGAGAGAATAGGTCTACAATATGTATCGACACTTTTTTAATTTTGTGT
66 TAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGT
* *
337231 CGATACTTTTGGTCCAGGATGGATGCCAAAAAGGGTGAACGCATAAAATG
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTG
* *
337281 TCGATACATTTTCAAAAAATGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
1 TCG----A---TC---------C-----CAGAAACATCAAAACCCATAATTATAATGTAATAGGT
* *
337346 AAATTTTCAATGTAACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACAACATGTATC
45 AAATTTTCAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATC
*
337411 GACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGGGTGCCAAAAAGGGTGAACGCAT
110 GACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCAT
337476 AAAGTG
175 AAAGTG
337482 TCGAT
1 TCGAT
337487 ATATTTTCAA
Statistics
Matches: 343, Mismatches: 20, Indels: 32
0.87 0.05 0.08
Matches are distributed among these distances:
180 169 0.49
181 2 0.01
184 1 0.00
187 2 0.01
194 1 0.00
196 1 0.00
197 1 0.00
201 166 0.48
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (180 bp):
TCGATCCCAGAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAACCGGTA
TAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGT
CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTG
Found at i:337729 original size:200 final size:201
Alignment explanation
Indices: 337095--337839 Score: 1181
Period size: 201 Copynumber: 3.7 Consensus size: 201
337085 GTGAACGCAT
* * *
337095 AAAGTGTCGATCCCAGAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
1 AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAA
* * *
337160 CCAGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAATATGTATCGACACTTTTTTAATT
66 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATT
* *
337225 TTGTGTCGATACTTTTGGTCCAGGATGGATGCCAAAAAGGGTGAACGCATAAAATGTCGATACAT
131 TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
337290 TTTCAA
196 TTTCAA
* *
337296 AAAATGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAA
1 AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAA
*
337361 CCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATT
66 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATT
* *
337426 TTGTGTCGATACTTTTGGTCCAGAATGGGTGCCAAAAAGGGTGAACGCATAAAGTGTCGATATAT
131 TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
337491 TTTCAA
196 TTTCAA
* *
337497 AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT-AATTTTGTAATATA
1 AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTT-CAATGTA
* * * * * *
337561 ACTGGTATACATATATCGGTTTTATGAGAGAATAGGTCTATAATATGTATCGACAC-TTATTAAT
65 ACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAAT
* * * * *
337625 ATTGCGTCGATAAGTTTT-GTACATAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATAC
130 TTTGTGTCGAT-ACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATAC
337689 ATTTTCAA
194 ATTTTCAA
*
337697 AAAGTGTTGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAA
1 AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAA
* * *
337762 CCGGTATAAATATACCAGTTTTATGAGATAATAGGTCTACAACATGTATCGACACGTTTTTAATT
66 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATT
337827 TTGTGTCGATACT
131 TTGTGTCGATACT
337840 AATTTAAATA
Statistics
Matches: 495, Mismatches: 45, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
200 177 0.36
201 318 0.64
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (201 bp):
AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAA
CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATT
TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
TTTCAA
Found at i:337839 original size:401 final size:402
Alignment explanation
Indices: 337095--337839 Score: 1224
Period size: 401 Copynumber: 1.9 Consensus size: 402
337085 GTGAACGCAT
* *
337095 AAAGTGTCGATCCCAGAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
1 AAAGTGTCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATATAA
* *
337160 CCAGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAATATGTATCGACACTTTTTTAATT
66 CCAGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAATATGTATCGACACTTTATTAATA
* * *
337225 TTGTGTCGATACTTTTGGTCCAGGATGGATGCCAAAAAGGGTGAACGCATAAAATGTCGATACAT
131 TTGCGTCGATACTTTTGGTACAGAATGGATGCCAAAAAGGGTGAACGCATAAAATGTCGATACAT
337290 TTTCAAAAAATGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCA
196 TTTCAAAAAATGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCA
** *
337355 ATGTAACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTT
261 ATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTT
337420 TTAATTTTGTGTCGATACTTTTGGTCCAGAATGGGTGCCAAAAAGGGTGAACGCATAAAGTGTCG
326 TTAATTTTGTGTCGATACTTTTGGTCCAGAATGGGTGCCAAAAAGGGTGAACGCATAAAGTGTCG
337485 ATATATTTTCAA
391 ATATATTTTCAA
* * **
337497 AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAA
1 AAAGTGTCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATATAA
** * * * *
337562 CTGGTATACATATATCGGTTTTATGAGAGAATAGGTCTATAATATGTATCGACAC-TTATTAATA
66 CCAGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAATATGTATCGACACTTTATTAATA
* * *
337626 TTGCGTCGATAAGTTTT-GTACATAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACA
131 TTGCGTCGAT-ACTTTTGGTACAGAATGGATGCCAAAAAGGGTGAACGCATAAAATGTCGATACA
* **
337690 TTTTCAAAAAGTGTTGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTC
195 TTTTCAAAAAATGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTC
*
337755 AATGTAACCGGTATAAATATACCAGTTTTATGAGATAATAGGTCTACAACATGTATCGACACGTT
260 AATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTT
337820 TTTAATTTTGTGTCGATACT
325 TTTAATTTTGTGTCGATACT
337840 AATTTAAATA
Statistics
Matches: 315, Mismatches: 27, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
401 202 0.64
402 113 0.36
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (402 bp):
AAAGTGTCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATATAA
CCAGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAATATGTATCGACACTTTATTAATA
TTGCGTCGATACTTTTGGTACAGAATGGATGCCAAAAAGGGTGAACGCATAAAATGTCGATACAT
TTTCAAAAAATGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCA
ATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTT
TTAATTTTGTGTCGATACTTTTGGTCCAGAATGGGTGCCAAAAAGGGTGAACGCATAAAGTGTCG
ATATATTTTCAA
Found at i:341053 original size:251 final size:251
Alignment explanation
Indices: 340648--341101 Score: 730
Period size: 251 Copynumber: 1.8 Consensus size: 251
340638 TAACGACCCA
* * *
340648 AAAAACATCGAAACTCATAATTATAATATAATGGGTAATTTTTTAATATAACCGGTATAAATATA
1 AAAAACATCGAAACCCATAATTATAATATAATAGGTAATTTTGTAATATAACCGGTATAAATATA
* * * *
340713 CCGGTTTTATGAAAAATATATCTATAACATTTATCGACACTTATTAGTATTGTGTCGATACTTTT
66 CCGGTTTTATGAAAAATAGATCTATAACATGTATCGACACTTATTAATATTGTGTCGATAATTTT
** * *
340778 TGTCCAGAATGGATGCCAAAAAGGGTGAACTTACAAAGTGTCGATACATTTTCATAGAGTGTCGA
131 TGTCCAGAATGGATGCCAAAAAGGGTGAACACACAAAGTGTCGATACATTTTCAAAAAGTGTCGA
340843 -TCCAAAAGGGTTGCACGCATAAAGTGTTGATACAATTATTAAAAGTGTCGATCCC
196 TTCCAAAAGGGTTGCACGCATAAAGTGTTGATACAATTATTAAAAGTGTCGATCCC
* *
340898 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATACATATA
1 AAAAACATCGAAACCCATAATTATAATATAATAGGTAATTTTGTAATATAACCGGTATAAATATA
* *
340963 CCGGTTTTATGAAAGAATAGGTCTATAATATGTATCGACACTTATTAATATTGTGTCGATAATTT
66 CCGGTTTTATGAAA-AATAGATCTATAACATGTATCGACACTTATTAATATTGTGTCGATAATTT
* * *
341028 TTGTCCATAATGGATGTCAAAAAGGGTGAACACATAAAGTGTCGATACATTTTCAAAAAGTGTCG
130 TTGTCCAGAATGGATGCCAAAAAGGGTGAACACACAAAGTGTCGATACATTTTCAAAAAGTGTCG
341093 ATTCCAAAA
195 ATTCCAAAA
341102 ACATCGAAAC
Statistics
Matches: 184, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
250 74 0.40
251 103 0.56
252 7 0.04
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (251 bp):
AAAAACATCGAAACCCATAATTATAATATAATAGGTAATTTTGTAATATAACCGGTATAAATATA
CCGGTTTTATGAAAAATAGATCTATAACATGTATCGACACTTATTAATATTGTGTCGATAATTTT
TGTCCAGAATGGATGCCAAAAAGGGTGAACACACAAAGTGTCGATACATTTTCAAAAAGTGTCGA
TTCCAAAAGGGTTGCACGCATAAAGTGTTGATACAATTATTAAAAGTGTCGATCCC
Found at i:342783 original size:23 final size:23
Alignment explanation
Indices: 342753--342799 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
342743 CGTTGTGTCG
342753 AACGCAATTACATCACCGAACAA
1 AACGCAATTACATCACCGAACAA
342776 AACGCAATTACATCACCGAACAA
1 AACGCAATTACATCACCGAACAA
342799 A
1 A
342800 TTATGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.30, G:0.09, T:0.13
Consensus pattern (23 bp):
AACGCAATTACATCACCGAACAA
Found at i:344227 original size:200 final size:196
Alignment explanation
Indices: 343827--344532 Score: 703
Period size: 200 Copynumber: 3.5 Consensus size: 196
343817 ACCTAAATAT
* * * *
343827 GTGTCGATACATTT-TATACAAGTATCGA-CCCAAAAAACATCAAAATCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAA
* * * * * * *
343890 TAGATAAATTAACAATGTAACCGGTATAAATATACC-GATTAATTAGAAAACATGTCAACATAAT
64 TAGGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATAGGTC-ACATAAT
* * * * *
343954 GTATTGACACTTGTGTAATTTGTGTTGATACTTATTGTCCAGGATGAATGCACAAACGAGGTGC-
128 GTATCGACACTTGT-TAATTTGTGTCGATACTT-TTGTCCAGAATGAATCCA-AAAAG-GGTGCA
344018 ACGCATAAA
189 AC-CATAAA
* *
344027 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATTGAAACCGATAATTATAATGTATTA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * *
344092 GGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGATAAAATAGGTCAGCATAAAGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATAGGTCA-CATAATGT
* *
344157 ATCGACACTTAATAAATTTGTGTCGATACTTTTGGTCCAGAATGAATACCAAAAAGGGTGCAACC
130 ATCGACACTT-GTTAATTTGTGTCGATACTTTT-GTCCAGAATGAAT-CCAAAAAGGGTGCAACC
344222 ATAAA
192 ATAAA
* ** * * *
344227 GTGTCGATACATTTATAAAAAGTATCGATCCCGGAAATATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * ** * *
344292 GGTAAATTTTCAATGTAACCGGTTTAAATATACTTGTTTTATGAGAGAATAGGTCTAAATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATAGGTC-ACATAATGT
* * **
344357 ATCGACACGTTGTTAGTTTGTGTCGATACTTTTTTCCAAAATGAAATATGAATGTCCAACCA-GG
130 ATCGACAC-TTGTTAATTTGTGTCGATACTTTTGTCC---A-G--A-ATGAA--TCCAAAAAGGG
*
344421 TGCAAACATAAA
185 TGCAACCATAAA
* * * *
344433 GTGTCGATACATTTA--AAATTGTATCGAT-CTAAAAACATCGTAACCGATAATAATAATGTAAT
1 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* * *
344495 AGGTAAATTT--AATGTTATCGGTATAAATATACTAGTTT
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCAGTTT
344533 ACTTCGAAAA
Statistics
Matches: 426, Mismatches: 60, Indels: 38
0.81 0.11 0.07
Matches are distributed among these distances:
199 3 0.01
200 236 0.55
201 71 0.17
202 28 0.07
203 1 0.00
204 39 0.09
205 9 0.02
206 33 0.08
207 5 0.01
208 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATAGGTCACATAATGTA
TCGACACTTGTTAATTTGTGTCGATACTTTTGTCCAGAATGAATCCAAAAAGGGTGCAACCATAA
A
Found at i:344663 original size:86 final size:87
Alignment explanation
Indices: 344547--344711 Score: 260
Period size: 86 Copynumber: 1.9 Consensus size: 87
344537 CGAAAATAGG
* * * *
344547 TTAATATAAGCGCTACATATTACATTATATAAGAGTTATCTAATATGTTATTGTACTTGATAATA
1 TTAATATAAACGCTACATATTACATTATATAAGAGCTACCTAATATGTTATTATACTTGATAATA
344612 TTTCCGGTTAAATGTTATTTTA
66 TTTCCGGTTAAATGTTATTTTA
* *
344634 TTAA-ATAAACGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTGATAATA
1 TTAATATAAACGCTACATATTACATTATATAAGAGCTACCTAATATGTTATTATACTTGATAATA
*
344698 TTTCTGGTTAAATG
66 TTTCCGGTTAAATG
344712 ATATAACATT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 67 0.94
87 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (87 bp):
TTAATATAAACGCTACATATTACATTATATAAGAGCTACCTAATATGTTATTATACTTGATAATA
TTTCCGGTTAAATGTTATTTTA
Found at i:344683 original size:23 final size:23
Alignment explanation
Indices: 344633--344677 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
344623 ATGTTATTTT
* *
344633 ATTAAATAAACGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
*
344656 ATTATATAAGCGCTACCTAATA
1 ATTATATAAACGCTACCTAATA
344678 TGTTATTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:352644 original size:21 final size:21
Alignment explanation
Indices: 352618--352660 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
352608 CCTCCCTCTT
*
352618 AGTTGGCTCTTGAAAAGAGGC
1 AGTTGGCTCTTAAAAAGAGGC
352639 AGTTGGCTCTTAAAAAGAGGC
1 AGTTGGCTCTTAAAAAGAGGC
352660 A
1 A
352661 ACTAGCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (21 bp):
AGTTGGCTCTTAAAAAGAGGC
Found at i:379321 original size:3 final size:3
Alignment explanation
Indices: 379309--379356 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
379299 TTTAGTTTTA
379309 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
379356 T
1 T
379357 TAATATGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:383598 original size:21 final size:20
Alignment explanation
Indices: 383566--383605 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
383556 GATCAACATT
*
383566 TTTGCATTTGCATTTGCATC
1 TTTGCATTTGCATATGCATC
383586 TTTGCATTTTGCATATGCAT
1 TTTGCA-TTTGCATATGCAT
383606 TTCATTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.50
Consensus pattern (20 bp):
TTTGCATTTGCATATGCATC
Found at i:384564 original size:6 final size:6
Alignment explanation
Indices: 384549--384582 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
384539 GAGCAAGAAG
384549 CAAAAA -AAAAA CAAAAA CAAAAA CAAAAA CAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAA
384583 TTAATTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:386185 original size:4 final size:4
Alignment explanation
Indices: 386144--386178 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
386134 ATACATCAAC
*
386144 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
386179 CATACATGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.26, G:0.03, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:386545 original size:38 final size:36
Alignment explanation
Indices: 386489--386630 Score: 146
Period size: 35 Copynumber: 3.9 Consensus size: 36
386479 TGTTTCTCTC
* *
386489 AAAACAAAATGTTGTCTCGCTAGAGACAGCTTCTTTTGA
1 AAAAC-AAATCTTGTCTCGCTTGAGACAG-TT-TTTTGA
*
386528 AAAACAAATCTTGTCTCGCTTGAGACAGTTTTCT-A
1 AAAACAAATCTTGTCTCGCTTGAGACAGTTTTTTGA
* * * * *
386563 AAATCAAATCTTGTATCGTTTGAGACAATTTCTTGA
1 AAAACAAATCTTGTCTCGCTTGAGACAGTTTTTTGA
*
386599 AAAAAAAAT-TTCGTCTCGCTTGAGACA-TTTTT
1 AAAACAAATCTT-GTCTCGCTTGAGACAGTTTTT
386631 CCTTTGAAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
35 35 0.40
36 24 0.28
37 2 0.02
38 21 0.24
39 5 0.06
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (36 bp):
AAAACAAATCTTGTCTCGCTTGAGACAGTTTTTTGA
Found at i:386730 original size:21 final size:21
Alignment explanation
Indices: 386706--386749 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
386696 TCTCATAAAT
*
386706 AAATTTTGTCTCGCATGAGAC
1 AAATTTTGTCTCACATGAGAC
*
386727 AAATTTTGTCTCACTTGAGAC
1 AAATTTTGTCTCACATGAGAC
386748 AA
1 AA
386750 TTTCCTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (21 bp):
AAATTTTGTCTCACATGAGAC
Found at i:386765 original size:36 final size:33
Alignment explanation
Indices: 386725--386822 Score: 126
Period size: 32 Copynumber: 2.9 Consensus size: 33
386715 CTCGCATGAG
386725 ACAAATTTTGTCTCACTTGAGACAATTTCCTTAAAA
1 ACAAATTTTGTCTCACTTGAGACAATTTCC---AAA
**
386761 ACAAATTTTGTCTCGTTTGAGACAATTT-CAAA
1 ACAAATTTTGTCTCACTTGAGACAATTTCCAAA
* *
386793 ACAAATTTCGTCTCACTTGAGACATTTTCC
1 ACAAATTTTGTCTCACTTGAGACAATTTCC
386823 CTCATAATAC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
32 27 0.49
33 1 0.02
35 1 0.02
36 26 0.47
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (33 bp):
ACAAATTTTGTCTCACTTGAGACAATTTCCAAA
Found at i:387120 original size:29 final size:29
Alignment explanation
Indices: 387062--387120 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
387052 CTCTTGAAAC
** *
387062 AAATCTTTGAGTCTGTTCTTTTTTAGTAA
1 AAATCTTTGAGTCTGTTCTTTTGAAATAA
387091 AAATCTTTGAG-CTGTTTCTTTTGAAATAA
1 AAATCTTTGAGTCTG-TTCTTTTGAAATAA
387120 A
1 A
387121 GTTTTGTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
AAATCTTTGAGTCTGTTCTTTTGAAATAA
Found at i:387242 original size:61 final size:60
Alignment explanation
Indices: 387083--387236 Score: 226
Period size: 59 Copynumber: 2.6 Consensus size: 60
387073 TCTGTTCTTT
*
387083 TTTAGT-AAAAATCTTTGAG-CTGTTTCTTTTGAAATAAAGTTTTGTCTCTCTTAAGACAA
1 TTTAGTGAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTG-CTCTCTTAAGACAA
* *
387142 TTTAGTGAAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTG-TCTCTTGAGACAA
1 TTTAGTGAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTGCTCTCTTAAGACAA
*
387201 TTTCGTGAAAAAATCTTTGAGTC-GTTTCTTTTGAAA
1 TTTAGTG-AAAAATCTTTGAGTCTGTTTCTTTTGAAA
387237 AACAAATCTT
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
59 36 0.41
60 28 0.32
61 23 0.26
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.44
Consensus pattern (60 bp):
TTTAGTGAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTGCTCTCTTAAGACAA
Found at i:387272 original size:29 final size:28
Alignment explanation
Indices: 387208--387276 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
387198 CAATTTCGTG
*
387208 AAAAAATCTTTGAGTCGTTTCTTTTGAA
1 AAAAAATCTTTGAGTCGTTTCTTTGGAA
*
387236 AAACAAATCTTTGAGTATGTTTCTTTGGAA
1 AAA-AAATCTTTGAGT-CGTTTCTTTGGAA
*
387266 ACAAAAT-TTTG
1 AAAAAATCTTTG
387277 TCTATCTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 7 0.19
29 16 0.44
30 13 0.36
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (28 bp):
AAAAAATCTTTGAGTCGTTTCTTTGGAA
Found at i:387311 original size:67 final size:64
Alignment explanation
Indices: 387225--387391 Score: 187
Period size: 67 Copynumber: 2.6 Consensus size: 64
387215 CTTTGAGTCG
* *
387225 TTTCTTTTGA-AAAACAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTATCTTGAGA
1 TTTCTTTTGAGAAAA-AAATCTTTGAGTCTG-TTCTTT-AAAAC-AAATTTTGTCTATCTTGAGA
*
387289 GAA
62 CAA
* * *
387292 TTTCTTTTGAGAAAAAAATCTTTGAGCCTGCTTCTCTTAAAACAATTTTTGTCTCTCTTGAGACA
1 TTTCTTTTGAGAAAAAAATCTTTGAGTCTG-TTCT-TTAAAACAAATTTTGTCTATCTTGAGACA
*
387357 G
64 A
*
387358 TTTCTTTT--GAAACAAATCTTTGAGTCTGTTCTTT
1 TTTCTTTTGAGAAAAAAATCTTTGAGTCTGTTCTTT
387392 TTAAAAAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
62 2 0.02
63 4 0.05
64 18 0.20
66 27 0.31
67 31 0.35
68 6 0.07
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (64 bp):
TTTCTTTTGAGAAAAAAATCTTTGAGTCTGTTCTTTAAAACAAATTTTGTCTATCTTGAGACAA
Found at i:387423 original size:28 final size:28
Alignment explanation
Indices: 387357--387449 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
387347 TCTTGAGACA
* * *
387357 GTTTCTTTTGAAACAAATCTTTGAGTCT
1 GTTTCTTTTAAAAAAAACCTTTGAGTCT
*
387385 G-TTCTTTTTAAAAAAAACCTTTGAGTTT
1 GTTTC-TTTTAAAAAAAACCTTTGAGTCT
* * *
387413 GTTTCTCTTAACAAAATCATCTTTGAGTCT
1 GTTTCTTTTAA-AAAA-AACCTTTGAGTCT
*
387443 ATTTCTT
1 GTTTCTT
387450 CAAAAACAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
27 3 0.06
28 26 0.51
29 7 0.14
30 15 0.29
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (28 bp):
GTTTCTTTTAAAAAAAACCTTTGAGTCT
Done.