Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000001.1 Hibiscus syriacus cultivar Beakdansim tig00000002_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: 2159989
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:476931 original size:27 final size:27
Alignment explanation
Indices: 476901--476971 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
476891 AAATCAGGTG
476901 AAGGCGACGGC-GACATCTGGTAATAAA
1 AAGGCGACGGCAG-CATCTGGTAATAAA
* *
476928 AAGGCGATGGCAGCATCTGGTAATGAA
1 AAGGCGACGGCAGCATCTGGTAATAAA
* *
476955 AAGGCGATGACAGCATC
1 AAGGCGACGGCAGCATC
476972 ATATATGGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.15
Consensus pattern (27 bp):
AAGGCGACGGCAGCATCTGGTAATAAA
Found at i:478697 original size:17 final size:18
Alignment explanation
Indices: 478654--478694 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
478644 GAATTATATT
478654 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
478671 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
478689 ATTAAA
1 AGTAAA
478695 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:478755 original size:10 final size:10
Alignment explanation
Indices: 478737--478776 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
478727 ATAAACAGAT
*
478737 AGAGTATTTG
1 AGAGAATTTG
478747 AGAGAATTTG
1 AGAGAATTTG
*
478757 AGAAAATTTG
1 AGAGAATTTG
478767 AGAGAATTTG
1 AGAGAATTTG
478777 GTGTGATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.33
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:479145 original size:38 final size:37
Alignment explanation
Indices: 479055--479159 Score: 120
Period size: 38 Copynumber: 2.8 Consensus size: 37
479045 CTTTTCGTCA
* *
479055 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATATGATAAAATTC
* * *
479092 TGCTAGGATTCAAACTCCTAAAAAATATGATAGAGTTC
1 TACTAGGATTCAAACTCCT-AAAAATATGATAAAATTC
* * * *
479130 TACTATGATTTAAACTCTTAAAGATATGAT
1 TACTAGGATTCAAACTCCTAAAAATATGAT
479160 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
37 28 0.49
38 29 0.51
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATATGATAAAATTC
Found at i:479552 original size:25 final size:26
Alignment explanation
Indices: 479522--479574 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
479512 TATTAGTCCT
* *
479522 TTTATTTATTGTATAGA-TATTTTTA
1 TTTATTTATTATATACATTATTTTTA
*
479547 TTTATTTATTATTTACATTATTTTTA
1 TTTATTTATTATATACATTATTTTTA
479573 TT
1 TT
479575 ATATAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTATTTATTATATACATTATTTTTA
Found at i:479688 original size:22 final size:21
Alignment explanation
Indices: 479632--479734 Score: 79
Period size: 22 Copynumber: 4.8 Consensus size: 21
479622 TTTTTTACAC
479632 TATATA-TTATTA-TTATCTATA
1 TATATATTTATTATTTAT-T-TA
* *
479653 CATATATTTTTTATTTATTTA
1 TATATATTTATTATTTATTTA
479674 TAT-TCATTTAGTTATTT-TTTAA
1 TATAT-ATTTA-TTATTTATTT-A
*
479696 TACTATATTTATTATTTATATA
1 TA-TATATTTATTATTTATTTA
*
479718 TATATATATATATATTT
1 TATATATTTAT-TATTT
479735 TAAATATTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.01
21 24 0.36
22 29 0.43
23 12 0.18
24 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (21 bp):
TATATATTTATTATTTATTTA
Found at i:479721 original size:19 final size:19
Alignment explanation
Indices: 479632--479722 Score: 69
Period size: 19 Copynumber: 4.6 Consensus size: 19
479622 TTTTTTACAC
*
479632 TATATAT-TA-TTATTATC
1 TATATATATATTTATTATT
* *
479649 TATACATATATTTTTTATT
1 TATATATATATTTATTATT
*
479668 TATTTATATTCATTTAGTTATTT
1 TATATATA-T-ATTTA-TTA-TT
*
479691 TTTAATACTATATTTATTATT
1 TAT-ATA-TATATTTATTATT
479712 TATATATATAT
1 TATATATATAT
479723 ATATATATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
17 6 0.11
18 2 0.04
19 17 0.30
20 4 0.07
21 8 0.14
22 6 0.11
23 9 0.16
24 3 0.05
25 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (19 bp):
TATATATATATTTATTATT
Found at i:480037 original size:12 final size:13
Alignment explanation
Indices: 480014--480092 Score: 51
Period size: 12 Copynumber: 6.4 Consensus size: 13
480004 ATATATATAA
480014 TATTTCATTTATT
1 TATTTCATTTATT
480027 TATTT-ATTTATT
1 TATTTCATTTATT
* *
480039 T-TTCCTTTTATT
1 TATTTCATTTATT
* *
480051 T-TTTTACTTATT
1 TATTTCATTTATT
* *
480063 TTTATTC-TTCATT
1 TAT-TTCATTTATT
480076 T-TTTCATTTATT
1 TATTTCATTTATT
*
480088 CATTT
1 TATTT
480093 TTTTCCTCTG
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
11 5 0.10
12 29 0.58
13 14 0.28
14 2 0.04
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTCATTTATT
Found at i:489755 original size:28 final size:27
Alignment explanation
Indices: 489703--489756 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
489693 GACATACAAA
* *
489703 AAAAAATCATATACACATATTTTAACT
1 AAAAAATCATAAACACATATATTAACT
489730 AAAAAATCATAAAC-CATGCATATTAAC
1 AAAAAATCATAAACACAT--ATATTAAC
489757 ATATTATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.13
27 13 0.57
28 7 0.30
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAAAATCATAAACACATATATTAACT
Found at i:496213 original size:21 final size:22
Alignment explanation
Indices: 496171--496223 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
496161 GGAATATATC
* *
496171 AATATTTTTTTATATTTAAAAT
1 AATATATTTTTATAATTAAAAT
*
496193 AATTTATTTTTATAATT-AAAT
1 AATATATTTTTATAATTAAAAT
496214 AATATATTTT
1 AATATATTTT
496224 AGTAGGTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATATATTTTTATAATTAAAAT
Found at i:496446 original size:9 final size:9
Alignment explanation
Indices: 496429--496460 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
496419 GACAATGACT
496429 ACCATACAA
1 ACCATACAA
*
496438 ACTATACAA
1 ACCATACAA
496447 ACCATACAA
1 ACCATACAA
496456 ACCAT
1 ACCAT
496461 TAAACTACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.53, C:0.31, G:0.00, T:0.16
Consensus pattern (9 bp):
ACCATACAA
Found at i:498564 original size:12 final size:13
Alignment explanation
Indices: 498527--498594 Score: 79
Period size: 12 Copynumber: 5.5 Consensus size: 13
498517 ATTTTTCTAA
498527 ATTTTATACAAAT
1 ATTTTATACAAAT
* *
498540 ATTTTTTATAAAT
1 ATTTTATACAAAT
498553 -TTTTATACAAAT
1 ATTTTATACAAAT
*
498565 ATTTT-TATAAAT
1 ATTTTATACAAAT
498577 -TTTTATACAAAT
1 ATTTTATACAAAT
*
498589 AATTTA
1 ATTTTA
498595 ATATATTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
11 4 0.09
12 22 0.49
13 19 0.42
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTTATACAAAT
Found at i:498602 original size:24 final size:24
Alignment explanation
Indices: 498515--498604 Score: 128
Period size: 24 Copynumber: 3.8 Consensus size: 24
498505 GTTGTGGAAT
*
498515 ATATTTTTCTAAA-TTTTATACAA
1 ATATTTTTATAAATTTTTATACAA
498538 ATATTTTTTATAAATTTTTATACAA
1 ATA-TTTTTATAAATTTTTATACAA
498563 ATATTTTTATAAATTTTTATACAA
1 ATATTTTTATAAATTTTTATACAA
* * *
498587 ATAATTTAATATATTTTT
1 ATATTTTTATAAATTTTT
498605 CTACCGCTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.05
24 45 0.74
25 13 0.21
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
ATATTTTTATAAATTTTTATACAA
Found at i:500327 original size:226 final size:221
Alignment explanation
Indices: 499938--500385 Score: 851
Period size: 226 Copynumber: 2.0 Consensus size: 221
499928 AATTTATTTT
499938 AAAATCAATGAGTAAGTGACGTGAACAATACAAAAATTACATTTGTGAAACTATAATTAAAATCC
1 AAAATCAATGAGTAAGTGACGTGAACAATACAAAAATTACATTTGTGAAACTATAATTAAAATCC
500003 TCAATATTATAACAAAACCATTTTCTTGACTATAATTCAAGATGCTTATAGCTTTTGCCATCTTA
66 TCAATATTATAACAAAACCATTTTCTTGACTATAATTCAAGATGCTTATAGCTTTTGCCATCTTA
500068 AATCTTGCCGGCATATTGTTGCAACTTCTAGCCACTTTTCTTGACTTTTCTACATAATTCCAAGA
131 AATCTTGCCGGCATATTGTTGCAACTTCTAGCCACTTTTCTTGACTTTTCTACATAATTCCAAGA
500133 GTTTGAATTCCAACACTCCCCCTCAA
196 GTTTGAATTCCAACACTCCCCCTCAA
500159 AAAATCAATGAGTAAGTGACGTGAACAATACAAAAATTACATTTGTGAAACTATAATTAAAATTC
1 AAAATCAATGAGTAAGTGACGTGAACAATACAAAAATTACATTTGTGAAACTATAATTAAAA-TC
500224 CTCAATATTATAAACAAAACACATTTTCTTGACTAAGTAATTCAAGATGCTTATAGCTTTTGCCA
65 CTCAATATTAT-AACAAAAC-CATTTTCTTGACT-A-TAATTCAAGATGCTTATAGCTTTTGCCA
500289 TCTTAAATCTTGCCGGCATATTGTTGCAACTTCTAGCCACTTTTCTTGACTTTTCTACATAATTC
126 TCTTAAATCTTGCCGGCATATTGTTGCAACTTCTAGCCACTTTTCTTGACTTTTCTACATAATTC
500354 CAAGAGTTTGAATTCCAACACTCCCCCTCAA
191 CAAGAGTTTGAATTCCAACACTCCCCCTCAA
500385 A
1 A
500386 CTCGACCTTC
Statistics
Matches: 222, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
221 62 0.28
222 13 0.06
223 8 0.04
224 13 0.06
225 1 0.00
226 125 0.56
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (221 bp):
AAAATCAATGAGTAAGTGACGTGAACAATACAAAAATTACATTTGTGAAACTATAATTAAAATCC
TCAATATTATAACAAAACCATTTTCTTGACTATAATTCAAGATGCTTATAGCTTTTGCCATCTTA
AATCTTGCCGGCATATTGTTGCAACTTCTAGCCACTTTTCTTGACTTTTCTACATAATTCCAAGA
GTTTGAATTCCAACACTCCCCCTCAA
Found at i:512817 original size:28 final size:28
Alignment explanation
Indices: 512783--512836 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
512773 AACTTAAGAT
512783 TTTAAGTTTAA-AATT-AAGATTTAAGTAA
1 TTTAAG-TTAAGAATTAAAGA-TTAAGTAA
512811 TTTAAGTTAAGAATTAAAGATTAAGT
1 TTTAAGTTAAGAATTAAAGATTAAGT
512837 TTCAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 4 0.17
28 16 0.67
29 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (28 bp):
TTTAAGTTAAGAATTAAAGATTAAGTAA
Found at i:512828 original size:34 final size:33
Alignment explanation
Indices: 512790--512867 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 33
512780 GATTTTAAGT
512790 TTAAAATTAAGATTT-AAGTAATTTAAGTTAAGAA
1 TTAAAATTAAG-TTTCAA-TAATTTAAGTTAAGAA
512824 TTAAAGATTAAGTTTCAATAATTTAAGTTAAGAA
1 TTAAA-ATTAAGTTTCAATAATTTAAGTTAAGAA
*
512858 TTAAATTTAA
1 TTAAAATTAA
512868 TTAGATTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
33 4 0.10
34 29 0.71
35 8 0.20
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.40
Consensus pattern (33 bp):
TTAAAATTAAGTTTCAATAATTTAAGTTAAGAA
Found at i:529112 original size:28 final size:28
Alignment explanation
Indices: 529069--529138 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
529059 CAAGAATTAG
*
529069 CTCGACGACATAATATTTTAAGCACTGA
1 CTCGACGACATAATATTTCAAGCACTGA
* * *
529097 CTCGATGACATCATATTTCAAGCACTGG
1 CTCGACGACATAATATTTCAAGCACTGA
* *
529125 CTCGAAGGCATAAT
1 CTCGACGACATAAT
529139 GTAAACATAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (28 bp):
CTCGACGACATAATATTTCAAGCACTGA
Found at i:535203 original size:21 final size:20
Alignment explanation
Indices: 535179--535225 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
535169 CGATATGTAG
535179 ATATGTATG-TTTATATAAAAA
1 ATAT-TATGCTTTA-ATAAAAA
*
535200 ATATTATAGCTTTAATAAATA
1 ATATTAT-GCTTTAATAAAAA
535221 ATATT
1 ATATT
535226 TATGAATCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.13
21 16 0.70
22 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (20 bp):
ATATTATGCTTTAATAAAAA
Found at i:538044 original size:8 final size:8
Alignment explanation
Indices: 538031--538057 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
538021 CCAATAAGTC
538031 ATTAAACT
1 ATTAAACT
538039 ATTAAACT
1 ATTAAACT
538047 ATTAAACT
1 ATTAAACT
538055 ATT
1 ATT
538058 TTACTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTAAACT
Found at i:538410 original size:2 final size:2
Alignment explanation
Indices: 538403--538431 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
538393 CCGCACTAAT
538403 TA 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 T
538432 TGAATAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:540504 original size:229 final size:227
Alignment explanation
Indices: 540204--540652 Score: 758
Period size: 229 Copynumber: 2.0 Consensus size: 227
540194 GTAAATTATC
* * * *
540204 TATCCTTTTTATAAAAGTGTTCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
540269 TAATATTATTAAATTTAAAAT-CTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
66 TAATATTATTAAATTT-AAATGCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
540333 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAA-AAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAATAAA-T
540397 TGAAACATAAATTACATAACTTTCAAAAAAGTATA
194 TGAAACATAAATTACATAACTTT-AAAAAAGTATA
*
540432 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
540497 TTAATATTGTTAAATTTAAATGCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTATTAAATTTAAATGCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
540562 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAATAAATT
540627 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
540653 GCAGTTTTAA
Statistics
Matches: 208, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
228 43 0.21
229 162 0.78
230 3 0.01
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTATTAAATTTAAATGCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:540741 original size:20 final size:19
Alignment explanation
Indices: 540718--540763 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
540708 CGATATACCA
540718 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
540738 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
540758 GGTAAA
1 GGTAAA
540764 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:540905 original size:20 final size:19
Alignment explanation
Indices: 540882--540928 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
540872 CGATATAACA
*
540882 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
540902 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
540922 GGTAAAA
1 GGTAAAA
540929 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:543258 original size:32 final size:32
Alignment explanation
Indices: 543204--543264 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
543194 AAATAGATGG
*
543204 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
***
543236 AGTGGTGAAAGAAGTTTCGGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
543265 GTGATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.44, T:0.25
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:545095 original size:19 final size:19
Alignment explanation
Indices: 545051--545094 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
545041 AATGTCGAGT
545051 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
545070 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
545089 T-ATTTT
1 TAATTTT
545095 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:545530 original size:199 final size:199
Alignment explanation
Indices: 545175--546789 Score: 2992
Period size: 199 Copynumber: 8.1 Consensus size: 199
545165 TTAAGGGTCA
* *
545175 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
* *
545240 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATTGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
545305 GTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAA
545370 TAATG
195 TAATG
*
545375 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGGGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
545440 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
545505 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGG-TTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
545569 AATG
196 AATG
*
545573 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
545638 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
545703 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
545768 AATG
196 AATG
* *
545772 TGTCGACACTAATATAGTTTGCGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGGGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
545837 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
545902 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
545967 AATG
196 AATG
*
545971 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
546036 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
546101 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
546166 AATG
196 AATG
*
546170 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGGGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
546235 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
546300 TAATATGTAATTTTTCAACCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
546365 AATG
196 AATG
546369 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
546434 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
546499 TAATATGTAA-TTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
546563 AATG
196 AATG
546567 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
546631 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAA--ATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
546693 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
546758 AATG
196 AATG
546762 TGTCGACACTAATATA-TTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
546790 CTAATTTAAA
Statistics
Matches: 1382, Mismatches: 31, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
194 43 0.03
195 73 0.05
196 3 0.00
197 72 0.05
198 279 0.20
199 829 0.60
200 83 0.06
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
AATG
Found at i:547529 original size:18 final size:18
Alignment explanation
Indices: 547506--547573 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
547496 ATCGGTCGCA
547506 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
547524 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
547545 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
547566 GAAGATGA
1 GAAGATGA
547574 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:547530 original size:6 final size:6
Alignment explanation
Indices: 547506--547603 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
547496 ATCGGTCGCA
* * * * * *
547506 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
547554 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
547602 GA
1 GA
547604 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:547541 original size:3 final size:3
Alignment explanation
Indices: 547521--547607 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
547511 TGAAGCTGAC
* * * * * ** *
547521 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
547569 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
547608 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:547556 original size:42 final size:42
Alignment explanation
Indices: 547509--547599 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
547499 GGTCGCAGAA
*
547509 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
547551 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
547593 GATGAAG
1 GATGAAG
547600 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:547607 original size:18 final size:18
Alignment explanation
Indices: 547506--547603 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
547496 ATCGGTCGCA
* *
547506 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
547524 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
547542 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
547560 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
547578 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
547596 GAAGATGA
1 GAAGATGA
547604 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:549557 original size:181 final size:183
Alignment explanation
Indices: 549077--549727 Score: 1158
Period size: 181 Copynumber: 3.6 Consensus size: 183
549067 TTATAATAAA
*
549077 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGC-AATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAAC
549141 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTG-CGA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
549205 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATA---
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATATGT
* *
549255 AATAGATAATTTTGTAATATAACCGGTATAAATATA-CGGTTTTATGAGCCAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAAC
549319 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
* *
549384 TACAATTTAAAAAAGTGTCGAAATTTTACACATCGGAACCCATAATTATAATGT
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTAT-ATGT
*
549438 AATAGATAATTTTGTAATATAACCGGTAT-AA-ATACCGGTCTTATGCGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAAC
549501 C-ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
549565 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATATGT
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATATGT
*
549618 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAAC
*
549683 CTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
549728 CCATTTAAAA
Statistics
Matches: 451, Mismatches: 12, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
177 11 0.02
178 111 0.25
179 50 0.11
180 34 0.08
181 115 0.25
182 59 0.13
183 71 0.16
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAAC
CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATATGT
Found at i:551139 original size:23 final size:23
Alignment explanation
Indices: 551097--551141 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
551087 TAGCCCTTAT
*
551097 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTATCGGTTATATA
551120 ATGTAATAGGTAGT-GGTTATAT
1 ATGTAATAGGTA-TCGGTTATAT
551142 TGTAAAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.42
Consensus pattern (23 bp):
ATGTAATAGGTATCGGTTATATA
Found at i:551169 original size:20 final size:20
Alignment explanation
Indices: 551144--551182 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
551134 GGTTATATTG
* *
551144 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
551164 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
551183 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:551516 original size:23 final size:23
Alignment explanation
Indices: 551490--551552 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
551480 TATAGGTAAC
*
551490 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* * **
551513 ATATAATATAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
*
551536 AAATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
551553 ATGGTTATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:557581 original size:42 final size:42
Alignment explanation
Indices: 557533--557623 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
557523 AAGTAAATAA
* *
557533 ATAACACCATTAAGTCTCAGTAAGTCTAAAATAAATAACACC
1 ATAACACCATTAAGTCTCAATAAGTCTAAAATAAAAAACACC
557575 ATAACACCATTAAGTCTCAATAAGTCTAAAATAAAAAACACC
1 ATAACACCATTAAGTCTCAATAAGTCTAAAATAAAAAACACC
*
557617 GTAACAC
1 ATAACAC
557624 TAATAATAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.22
Consensus pattern (42 bp):
ATAACACCATTAAGTCTCAATAAGTCTAAAATAAAAAACACC
Found at i:560953 original size:21 final size:21
Alignment explanation
Indices: 560892--560959 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
560882 ACACTTTACA
* *
560892 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATT--ATT
*
560915 ATATAAACGATA-CTATTATT
1 ATATAAACGCTACCTATTATT
* *
560935 ATATAAGCGCTACCTATTATC
1 ATATAAACGCTACCTATTATT
560956 ATAT
1 ATAT
560960 TTTACCTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 13 0.34
21 11 0.29
22 5 0.13
23 9 0.24
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (21 bp):
ATATAAACGCTACCTATTATT
Found at i:561031 original size:410 final size:406
Alignment explanation
Indices: 560151--561151 Score: 1593
Period size: 408 Copynumber: 2.5 Consensus size: 406
560141 TATTACATTA
*
560151 TATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAATTATGTAATTTA
1 TATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTA
560216 --TTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCA-CTACAATATTAATTAATAATTTCATTT
65 TGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATT-ATAATTTCATTT
*
560278 GCACAAAAAATTATTTGATTATTTGATATTTTAT-AAATATTATTTAGAATTTTTATTAATAATA
129 GCACAAAAAATTATTTGATT-TTTGATATTTTATAAAATATTA-TTAGAATTTTAATTAATAATA
* *
560342 ATATATATCGTAACGTAAAAAATAAATCATTATCGCCTATAATTACTAATTATATCTTAAAACTC
192 ATATATATCGTAACGTAAAAAATAAATCATTAACGCCTATAATTACTAA-TATATCTAAAAACTC
*
560407 ACTCAAAAGATAACCTTAATTAATATTTTCCATAGTGAAAAAGTATGAACACTTTATAAAAGGAT
256 ACTCAAAAGATAACCTTAATTAATATTTTCCACAGTGAAAAAGTATGAACACTTTATAAAAGGAT
560472 AGACACTTTACAAATAACCATACTATTACATTATATAACGATACCTTTATTATATAAGCGCTACC
321 AGACACTTTACAAATAACCATACTATTACATTATATAACGATACCTTTATTATATAAGCGCTACC
560537 TATTACATCATATTTTTACTAT
386 TATTA-ATCATATTTTTACTAT
* *
560559 TATATTGAAAGTGTCCATACTTTTTTAAAAAAGGATCGAGACTTCTTTT-AAGTTATGTAATTTA
1 TATATTGAAAGTGTCCATAC-TTTTTATAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTA
560623 TGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATT-TAATTTCATTTG
65 TGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTATAATTTCATTTG
560687 CACAAAAAA-TATTTGATTTTTGATATTTTATAAAATATTATTAGAATTTTAAATTAATAATAAT
130 CACAAAAAATTATTTGATTTTTGATATTTTATAAAATATTATTAGAATTTT-AATTAATAATAAT
560751 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAA-ATATCTAAAAACTCAC
194 ATATATCGTAACGTAAAAAATAAATCATTA-ACGCCTATAATTACTAATATATCTAAAAACTCAC
* * *
560815 TC-AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTTTGGACACTTTTATAAAAGGA
258 TCAAAAGATAACCTT-AATTAATATTTTCCACAGTG-AAAAAGTATGAACAC-TTTATAAAAGGA
560879 TAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATA-CTATTATTATATAAGC
320 TAGACACTTTACAA-ATAACCA-TA-CTATTACATTATAT-AACGATACCT-TTATTATATAAGC
560943 GCTACCTATT-ATCATA-TTTTACCTAT
380 GCTACCTATTAATCATATTTTTA-CTAT
560969 TATATTGAAAAGTGTCCATACTTTTTATAAAAGGATCGATACTTCTTTTAAAGTTA-GTAATTTA
1 TATATTG-AAAGTGTCCATACTTTTTATAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTA
*
561033 TGTTTCAA-TTTTTTTAATAGTGTTTCATG-TTTCCACCTACAATAGTAATTAATAATTTCA-TT
65 TGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATT-ATAATTTCATTT
*
561095 GCACAAAAAATTATTTGATTATTGATATTTTATAAAATATTATTAGAATTTTTAATT
129 GCACAAAAAATTATTTGATTTTTGATATTTTATAAAATATTATTAGAA-TTTTAATT
561152 TAACAACATT
Statistics
Matches: 557, Mismatches: 14, Indels: 42
0.91 0.02 0.07
Matches are distributed among these distances:
405 12 0.02
406 58 0.10
407 86 0.15
408 123 0.22
409 86 0.15
410 123 0.22
411 39 0.07
412 30 0.05
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.42
Consensus pattern (406 bp):
TATATTGAAAGTGTCCATACTTTTTATAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTAT
GTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTATAATTTCATTTGC
ACAAAAAATTATTTGATTTTTGATATTTTATAAAATATTATTAGAATTTTAATTAATAATAATAT
ATATCGTAACGTAAAAAATAAATCATTAACGCCTATAATTACTAATATATCTAAAAACTCACTCA
AAAGATAACCTTAATTAATATTTTCCACAGTGAAAAAGTATGAACACTTTATAAAAGGATAGACA
CTTTACAAATAACCATACTATTACATTATATAACGATACCTTTATTATATAAGCGCTACCTATTA
ATCATATTTTTACTAT
Found at i:561416 original size:39 final size:39
Alignment explanation
Indices: 561362--561441 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
561352 AAGTTGTAGA
*
561362 TTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGAAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGAAT
* *
561401 TTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGGAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGAAT
561440 TT
1 TT
561442 GATGAGCATC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.49
Consensus pattern (39 bp):
TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGAAT
Found at i:561724 original size:18 final size:18
Alignment explanation
Indices: 561701--561735 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
561691 CCGAAATATA
561701 TGAAATTCAAACTCAAAT
1 TGAAATTCAAACTCAAAT
* *
561719 TGAAATTTAAATTCAAA
1 TGAAATTCAAACTCAAA
561736 CTCCAATTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (18 bp):
TGAAATTCAAACTCAAAT
Found at i:561754 original size:24 final size:25
Alignment explanation
Indices: 561698--561754 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
561688 GAGCCGAAAT
561698 ATATGAAATTCAAACTCAAATTGAA
1 ATATGAAATTCAAACTCAAATTGAA
* * *
561723 AT-TTAAATTCAAACTCCAATT-AC
1 ATATGAAATTCAAACTCAAATTGAA
561746 ATATGAAAT
1 ATATGAAAT
561755 GAATTTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 3 0.11
24 22 0.81
25 2 0.07
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (25 bp):
ATATGAAATTCAAACTCAAATTGAA
Found at i:562064 original size:176 final size:172
Alignment explanation
Indices: 561764--562114 Score: 625
Period size: 176 Copynumber: 2.0 Consensus size: 172
561754 TGAATTTGAA
561764 ATGCAGTGTTAATTGAACATGAAAATGCATAATTGATTCATACTGTTCAAGTACATGCTTTATGA
1 ATGCAGTGTTAATTGAACATGAAAATGCATAATTGATTCATACTGTTCAAGTACATGCTTTATGA
561829 ACCATCAAGCTAAAAGATAATTGATTGAGTTCAAAGCTGAGTTGTGAGTGATGGGAGTTGTCACA
66 ACCATCAAGCTAAAAGATAATTGATTGAGTTCAAAGCTGAGTTGTGAGTGATGGGAGTTGTCACA
561894 CTTGTCAC-AGTTGGAATAAAGTAATTTGATTTAATAATTTT
131 CTTGTCACAAGTTGGAATAAAGTAATTTGATTTAATAATTTT
561935 ATGCAGTGTTAAATTGAACATGAAAATTGCATAATTGATTCATACTGTTCAAGTAACATGCTTTA
1 ATGCAGTGTT-AATTGAACATGAAAA-TGCATAATTGATTCATACTGTTCAAGT-ACATGCTTTA
562000 TGAACCATCAAGCTAAAAGATAATATTGATTGAGTTCAAAGCTGAGTTGTGAGTTGAT-GGAGTT
63 TGAACCATCAAGCTAAAAGAT-A-ATTGATTGAGTTCAAAGCTGAGTTGTGAG-TGATGGGAGTT
562064 GTCACACTTGTCACATAGTTGGAATAAAGTAATTTGATTTAATAATTTT
125 GTCACACTTGTCACA-AGTTGGAATAAAGTAATTTGATTTAATAATTTT
562113 AT
1 AT
562115 TTGCACAAAA
Statistics
Matches: 172, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
171 10 0.06
172 15 0.09
173 27 0.16
174 31 0.18
175 1 0.01
176 49 0.28
177 4 0.02
178 35 0.20
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (172 bp):
ATGCAGTGTTAATTGAACATGAAAATGCATAATTGATTCATACTGTTCAAGTACATGCTTTATGA
ACCATCAAGCTAAAAGATAATTGATTGAGTTCAAAGCTGAGTTGTGAGTGATGGGAGTTGTCACA
CTTGTCACAAGTTGGAATAAAGTAATTTGATTTAATAATTTT
Found at i:562366 original size:23 final size:23
Alignment explanation
Indices: 562339--562406 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
562329 ACACTTTATA
562339 ATATAACCACTACCTATTACATT
1 ATATAACCACTACCTATTACATT
* *
562362 ATATAAACGA-TACGTATTACATT
1 ATAT-AACCACTACCTATTACATT
* *
562385 ATATAAGCGCTACCTATTACAT
1 ATATAACCACTACCTATTACAT
562407 ATGTTTACCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
22 2 0.05
23 31 0.84
24 4 0.11
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATT
Found at i:562803 original size:25 final size:25
Alignment explanation
Indices: 562746--562811 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
562736 CACTCAAAAG
*
562746 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
562771 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
562796 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
562812 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:564893 original size:183 final size:183
Alignment explanation
Indices: 564368--564860 Score: 817
Period size: 183 Copynumber: 2.7 Consensus size: 183
564358 TTAAAATTAC
* *
564368 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACAGAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* * *
564433 ATTATAAAGTGTCAATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * *
564498 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATATGTAAATGT
131 ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATATGTAAATGT
* * *
564551 CGATACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
564616 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACTGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
564681 ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATATGTAAATGT
* * *
564734 CGACACTTTTTAACAAT-GTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACATAA
1 CGACACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
564798 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
564861 ATAGCATTGC
Statistics
Matches: 288, Mismatches: 21, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
183 285 0.99
184 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATATGTAAATGT
Found at i:566079 original size:3 final size:3
Alignment explanation
Indices: 566062--566104 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
566052 TACTTGTTGG
* *
566062 ATC ATC -TC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC -TC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
566105 GCCAGCTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.26, C:0.35, G:0.02, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:566115 original size:12 final size:12
Alignment explanation
Indices: 566086--566136 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
566076 ATCATCATCA
*
566086 TCATCGTCATCAT
1 TCATCGTCAGC-T
*
566099 CTCATCGCCAGCT
1 -TCATCGTCAGCT
*
566112 TCATCGTCATCT
1 TCATCGTCAGCT
566124 TCATCGTCAGCT
1 TCATCGTCAGCT
566136 T
1 T
566137 TATCTTCTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 22 0.69
13 1 0.03
14 9 0.28
ACGTcount: A:0.18, C:0.35, G:0.12, T:0.35
Consensus pattern (12 bp):
TCATCGTCAGCT
Found at i:566115 original size:26 final size:24
Alignment explanation
Indices: 566086--566136 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 24
566076 ATCATCATCA
566086 TCATCGTCATCATCTCATCGCCAGCT
1 TCATCGTCATC-T-TCATCGCCAGCT
*
566112 TCATCGTCATCTTCATCGTCAGCT
1 TCATCGTCATCTTCATCGCCAGCT
566136 T
1 T
566137 TATCTTCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 12 0.50
25 1 0.04
26 11 0.46
ACGTcount: A:0.18, C:0.35, G:0.12, T:0.35
Consensus pattern (24 bp):
TCATCGTCATCTTCATCGCCAGCT
Found at i:567924 original size:199 final size:200
Alignment explanation
Indices: 567565--569496 Score: 3450
Period size: 199 Copynumber: 9.7 Consensus size: 200
567555 TTTAAATTAG
*
567565 TATCGACACAAACTAAA--ACGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1 TATCGACACAAACTAAATTA-GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAA
* *
567628 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTGGGG
65 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGG
*
567692 ATCGAGACTTTTTATATATGGATCGACACTTTATAGG-TGCACCCTGTTTTCCATTCATTCTGGA
130 ATCGACACTTTTTATATATGGATCGACACTTTAT-GGTTGCACCCTGTTTTCCATTCATTCTGGA
567756 ACAAAAA
194 ACAAAAA
*
567763 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTAATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
567828 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
* *
567892 TCGACACTTTTTATATGTGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTATGGAAC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
567957 AAAAA
196 AAAAA
*
567962 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACAAATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
568027 CTTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
* *
568091 TCGACACTTTTTATATATGGATTGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
568156 AAAAA
196 AAAAA
*
568161 TATCGATACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
* *
568226 CTTGTACTGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-ATTCGATGATTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
* * *
568290 TCGATACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGTAAC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
568355 AAAAA
196 AAAAA
568360 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
568425 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
*
568490 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
568555 AAAAA
196 AAAAA
*
568560 TATTGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
568625 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
568689 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
568754 --AAA
196 AAAAA
568757 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
568822 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
*
568887 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
568952 AAAAA
196 AAAAA
568957 TATCGACACAAACTAAATTAGTGTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
* *
569020 CTTGTACCGGTTAGATTGAAACATTAC--ATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
*
569082 TCGACACTTTTTATATATGGATCTACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
569147 AAAAA
196 AAAAA
569152 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
569217 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
569282 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
*
569347 AACAA
196 AAAAA
569352 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
569415 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATG-TTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
*
569479 TTGACACTTTTTATATAT
131 TCGACACTTTTTATATAT
569497 ACACTTTATG
Statistics
Matches: 1669, Mismatches: 51, Indels: 29
0.95 0.03 0.02
Matches are distributed among these distances:
195 109 0.07
196 18 0.01
197 202 0.12
198 263 0.16
199 700 0.42
200 377 0.23
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
AAAAA
Found at i:569680 original size:19 final size:19
Alignment explanation
Indices: 569634--569682 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
569624 ATTATTTCAC
*
569634 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
569653 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
569672 ATACAAAATTA
1 ATACAAAATTA
569683 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:571519 original size:32 final size:33
Alignment explanation
Indices: 571460--571524 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
571450 CATCTTAATA
*
571460 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
*
571493 TCACCCCTCAACA-CCCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
571525 CCATCTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.23, C:0.49, G:0.00, T:0.28
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:571583 original size:21 final size:21
Alignment explanation
Indices: 571558--571601 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
571548 CCCCTTATGC
571558 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
571579 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
571600 CT
1 CT
571602 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:573818 original size:17 final size:18
Alignment explanation
Indices: 573796--573838 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
573786 ATATATCCGG
573796 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
573813 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
573833 TATCAT
1 TATCAT
573839 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:573856 original size:20 final size:19
Alignment explanation
Indices: 573801--573847 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
573791 TCCGGTATCA
573801 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
573820 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
573841 TTTTACC
1 TTTTACC
573848 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:574758 original size:228 final size:228
Alignment explanation
Indices: 574074--574788 Score: 1305
Period size: 228 Copynumber: 3.1 Consensus size: 228
574064 ACTTTTATAC
*
574074 GTATAGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
574139 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
574204 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
131 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
574269 GATAATAATAAATATGTTTTCCACAGTGAAATAA
196 GATAATAATAAATATGTTTT-CACAGTGAAATAA
574303 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
574368 TTTTT-A-A-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
574430 TTATTTGATTATTTGATA-TTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
131 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
574494 GATAATAATAAATATGTTTTCACAGTGAAATAA
196 GATAATAATAAATATGTTTTCACAGTGAAATAA
* *
574527 GTATGGACTCTTTTATAAAAATGATATATA-TATTTTTTAAATTTATGTAATTTATGTTTCAATT
1 GTATGGACACTTTTATAAAAATGATATATACT-TTTTTTAAAGTTATGTAATTTATGTTTCAATT
* *
574591 TTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTACACACAAA
65 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAA
574656 ATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
130 ATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
*
574721 AGATAATAATAAATATATTTTCACAGTGAAATAA
195 AGATAATAATAAATATGTTTTCACAGTGAAATAA
* *
574755 GTATGGACACTTTTATAAAAAGGATAGATACTTT
1 GTATGGACACTTTTATAAAAATGATATATACTTT
574789 ACAATATAAC
Statistics
Matches: 471, Mismatches: 9, Indels: 13
0.96 0.02 0.03
Matches are distributed among these distances:
223 1 0.00
224 79 0.17
225 67 0.14
226 74 0.16
227 72 0.15
228 108 0.23
229 70 0.15
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (228 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
GATAATAATAAATATGTTTTCACAGTGAAATAA
Found at i:578024 original size:21 final size:22
Alignment explanation
Indices: 578000--578044 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
577990 AAAAGATATA
*
578000 AAATAGTCATTAAA-ATTATTG
1 AAATAGTCACTAAATATTATTG
*
578021 AAATAGTCACTAAATTTTATTG
1 AAATAGTCACTAAATATTATTG
578043 AA
1 AA
578045 TTATTGCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.38
Consensus pattern (22 bp):
AAATAGTCACTAAATATTATTG
Found at i:588507 original size:28 final size:28
Alignment explanation
Indices: 588466--588519 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
588456 TGGCCAGATC
*
588466 CCCATCCTTTGTTGTAAACAAGGCTCTT
1 CCCATCCTTAGTTGTAAACAAGGCTCTT
588494 CCCATCCTTAGTTGTAAACAAGGCTC
1 CCCATCCTTAGTTGTAAACAAGGCTC
588520 ATGGACCGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (28 bp):
CCCATCCTTAGTTGTAAACAAGGCTCTT
Found at i:595459 original size:161 final size:164
Alignment explanation
Indices: 595284--595607 Score: 627
Period size: 161 Copynumber: 2.0 Consensus size: 164
595274 TTTAGCATTG
595284 TATATTATATATAAGTTATAAATCTAGTCTGTAGAAATGACCATCCAGTTCAATTGGTAGAGCAC
1 TATATTATATATAAGTTATAAATCTAGTCTGTAGAAATGACCATCCAGTTCAATTGGTAGAGCAC
595349 AAGGTTTTTAACCTTGAGGTCGTGGGATTGAGTCCCACAGAGGGCATTTTATAATTCGGAGGTCT
66 AAGGTTTTTAACCTTGAGGTCGTGGGATTGAGTCCCACAGAGGGCATTTTATAATTCGGAGGTCT
595414 TATAC-GAAGTTGCTCTCAA-TTGGTATTGGGGT
131 TATACGGAAGTTGCTCTCAACTTGGTATTGGGGT
595446 TATA-TATATATAAGTTATAAATCTAGTCTGTAGAAATGACCATCCAGTTCAATTGGTAGAGCAC
1 TATATTATATATAAGTTATAAATCTAGTCTGTAGAAATGACCATCCAGTTCAATTGGTAGAGCAC
595510 AAGGTTTTTAACCTTGAGGTCGTGGGATTGAGTCCCACAGAGGGCATTTTATAATTCGGAGGTCT
66 AAGGTTTTTAACCTTGAGGTCGTGGGATTGAGTCCCACAGAGGGCATTTTATAATTCGGAGGTCT
595575 TATACGGAAGTTGCTCTCAACTTGGTATTGGGG
131 TATACGGAAGTTGCTCTCAACTTGGTATTGGGG
595608 GCAGCCTACT
Statistics
Matches: 160, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
161 130 0.81
162 18 0.11
163 12 0.08
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (164 bp):
TATATTATATATAAGTTATAAATCTAGTCTGTAGAAATGACCATCCAGTTCAATTGGTAGAGCAC
AAGGTTTTTAACCTTGAGGTCGTGGGATTGAGTCCCACAGAGGGCATTTTATAATTCGGAGGTCT
TATACGGAAGTTGCTCTCAACTTGGTATTGGGGT
Found at i:598427 original size:267 final size:271
Alignment explanation
Indices: 598143--598674 Score: 1018
Period size: 267 Copynumber: 2.0 Consensus size: 271
598133 CGCTTTTCCT
*
598143 TTCAGAGAGAGAGAGAGAGAAATCCATGATATTAAAGCATTAATTTTTTTCTCTGTTTGGAAGAA
1 TTCAGAGAGAGAGAGAGAGAAATCCATGATATTAAAGCATTAATTTTTTTCTCTGTTTGAAAGAA
598208 AAGTTAATTTTCTTTCGTTCTTTCATTGTTCAATTACTTTTCCATAATACGCTAGATA-TTAGTT
66 AAGTTAATTTTCTTTCGTTCTTTCATTGTTCAATTACTTTTCCATAATACGCTAGATATTTAGTT
598272 GGCTGATACAATGAA-TTTCCATAATACGCTTGATATTAAGTTGTTATAGATATATATCATGTTA
131 GGCTGATACAATGAATTTTCCATAATACGCTTGATATTAAGTTGTTATAGATATATATCATGTTA
598336 TATTCTCTTGTGTGTTGCCCATGATCTTTTTCATTG-TTTTGTCTCTTATTGTTCTTTA-TTTTG
196 TATTCTCTTGTGTGTTGCCCATGATCTTTTTCATTGTTTTTGTCTCTTATTGTTCTTTATTTTTG
598399 TTTTATCGTGA
261 TTTTATCGTGA
598410 TTCAGAGAGAGAGAGAGAGAAATCCATGATATTAAAGCATTAATTTTTTTCTCTGTTTGAAAGAA
1 TTCAGAGAGAGAGAGAGAGAAATCCATGATATTAAAGCATTAATTTTTTTCTCTGTTTGAAAGAA
598475 AAGTTAATTTTCTTTCGTTCTTTCATTGTTCAATTACTTTTCCATAATACGCTAGATATTTAGTT
66 AAGTTAATTTTCTTTCGTTCTTTCATTGTTCAATTACTTTTCCATAATACGCTAGATATTTAGTT
598540 GGCTGATACAATGAATTTTTCCATAATACGCTTGATATTAAGTTGTTATAGATATATATCATGTT
131 GGCTGATACAATGAA-TTTTCCATAATACGCTTGATATTAAGTTGTTATAGATATATATCATGTT
598605 ATATTCTCTTGTGTGTTGCCCATGATCTTTTTCATTGTTTTTGTCTCTTATTGTTCTTTATTTTT
195 ATATTCTCTTGTGTGTTGCCCATGATCTTTTTCATTGTTTTTGTCTCTTATTGTTCTTTATTTTT
598670 GTTTT
260 GTTTT
598675 CAGGGACAAA
Statistics
Matches: 259, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
267 122 0.47
268 21 0.08
270 85 0.33
271 22 0.08
272 9 0.03
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (271 bp):
TTCAGAGAGAGAGAGAGAGAAATCCATGATATTAAAGCATTAATTTTTTTCTCTGTTTGAAAGAA
AAGTTAATTTTCTTTCGTTCTTTCATTGTTCAATTACTTTTCCATAATACGCTAGATATTTAGTT
GGCTGATACAATGAATTTTCCATAATACGCTTGATATTAAGTTGTTATAGATATATATCATGTTA
TATTCTCTTGTGTGTTGCCCATGATCTTTTTCATTGTTTTTGTCTCTTATTGTTCTTTATTTTTG
TTTTATCGTGA
Found at i:598793 original size:20 final size:20
Alignment explanation
Indices: 598765--598876 Score: 161
Period size: 20 Copynumber: 5.5 Consensus size: 20
598755 AAGATGCTTG
*
598765 TTAATTTATTCTTAATTAAA
1 TTAATTTATTCTTAATTATA
* * *
598785 TTTATTTATTCTTAGTTTAAA
1 TTAATTTATTCTTA-ATTATA
*
598806 TTAATATATTCTTAATTTATA
1 TTAATTTATTCTTAA-TTATA
598827 TTAATTTATTCTTAATTATA
1 TTAATTTATTCTTAATTATA
598847 TTAATTTATTCTTAATTATA
1 TTAATTTATTCTTAATTATA
598867 TTAATTTATT
1 TTAATTTATT
598877 GTTGGTATTG
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
20 48 0.58
21 35 0.42
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (20 bp):
TTAATTTATTCTTAATTATA
Found at i:598810 original size:41 final size:40
Alignment explanation
Indices: 598765--598876 Score: 161
Period size: 41 Copynumber: 2.8 Consensus size: 40
598755 AAGATGCTTG
* * *
598765 TTAATTTATTCTTAATTAAATTTATTTATTCTTAGTTTAAA
1 TTAATTTATTCTTAATTATATTAATTTATTCTTA-ATTAAA
* *
598806 TTAATATATTCTTAATTTATATTAATTTATTCTTAATTATA
1 TTAATTTATTCTTAA-TTATATTAATTTATTCTTAATTAAA
598847 TTAATTTATTCTTAATTATATTAATTTATT
1 TTAATTTATTCTTAATTATATTAATTTATT
598877 GTTGGTATTG
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
40 15 0.23
41 32 0.50
42 17 0.27
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (40 bp):
TTAATTTATTCTTAATTATATTAATTTATTCTTAATTAAA
Found at i:598832 original size:10 final size:10
Alignment explanation
Indices: 598817--598875 Score: 68
Period size: 10 Copynumber: 5.9 Consensus size: 10
598807 TAATATATTC
598817 TTAATTTATA
1 TTAATTTATA
*
598827 TTAATTTATTC
1 TTAATTTA-TA
598838 TTAA-TTATA
1 TTAATTTATA
*
598847 TTAATTTATTC
1 TTAATTTA-TA
598858 TTAA-TTATA
1 TTAATTTATA
598867 TTAATTTAT
1 TTAATTTAT
598876 TGTTGGTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 10 0.24
10 21 0.51
11 10 0.24
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (10 bp):
TTAATTTATA
Found at i:599042 original size:21 final size:21
Alignment explanation
Indices: 599016--599074 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
599006 TTCAAAAAAA
599016 GAATTATATTAATTTATTCTT
1 GAATTATATTAATTTATTCTT
*
599037 GAATTAAATTAATTTATTCTT
1 GAATTATATTAATTTATTCTT
*
599058 -AGTTATATTAATTTATT
1 GAATTATATTAATTTATT
599075 GTTGGTATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 15 0.43
21 20 0.57
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (21 bp):
GAATTATATTAATTTATTCTT
Found at i:599163 original size:198 final size:197
Alignment explanation
Indices: 598822--599207 Score: 675
Period size: 198 Copynumber: 2.0 Consensus size: 197
598812 TATTCTTAAT
*
598822 TTATATTAATTTATTCTTAATTATATTAATTTATTCTTAATTATATTAATTTATTGTTGGTATTG
1 TTATATTAATTTATTCTTAATTAAATTAATTTATTCTTAATTATATTAATTTATTGTTGGTATTG
* * *
598887 TAATGTCATCGTTTCGGTGCACTTTTTTTCCCTCCGATTAGTTGTAGGGAGGTTTTTTAACAGGC
66 TAATGTCATCGTTTCGGTGCACTTTTTTTCCCTCCAATTAGGTGTAGGGAGGTTTTGTAACAGGC
*
598952 CCGATTCGATGTTTTGTTTTGTATGTTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAAG
131 CCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAAG
599017 AA
196 AA
*
599019 TTATATTAATTTATTCTTGAATTAAATTAATTTATTCTTAGTTATATTAATTTATTGTTGGTATT
1 TTATATTAATTTATTCTT-AATTAAATTAATTTATTCTTAATTATATTAATTTATTGTTGGTATT
*
599084 GTAATGTCATCGTTTCGGTGCACTTTTTTT-CCTCCAATTAGGTGTAGGGAGGTTTTGTAACGTG
65 GTAATGTCATCGTTTCGGTGCACTTTTTTTCCCTCCAATTAGGTGTAGGGAGGTTTTGTAAC-AG
*
599148 GCCCGATTTGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCCCTTTCA
129 GCCCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCCCTTTCA
599208 TTTTTTCTTA
Statistics
Matches: 179, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
197 46 0.26
198 133 0.74
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (197 bp):
TTATATTAATTTATTCTTAATTAAATTAATTTATTCTTAATTATATTAATTTATTGTTGGTATTG
TAATGTCATCGTTTCGGTGCACTTTTTTTCCCTCCAATTAGGTGTAGGGAGGTTTTGTAACAGGC
CCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAAG
AA
Found at i:599276 original size:21 final size:21
Alignment explanation
Indices: 599212--599270 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
599202 CTTTCATTTT
*
599212 TTCTTAATTTATATTAAGTTA
1 TTCTTAATTTATATTAACTTA
* *
599233 TTCATAATTTATGTTAACTTA
1 TTCTTAATTTATATTAACTTA
599254 TTCTTAATTTATATTAA
1 TTCTTAATTTATATTAA
599271 TATATTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (21 bp):
TTCTTAATTTATATTAACTTA
Found at i:601006 original size:19 final size:21
Alignment explanation
Indices: 600982--601023 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
600972 ATTGTTAATT
600982 TTCTTGAATTAT-T-AATTTA
1 TTCTTGAATTATATAAATTTA
601001 TTCTTGAATTATATAAATTTA
1 TTCTTGAATTATATAAATTTA
601022 TT
1 TT
601024 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.57
20 1 0.05
21 8 0.38
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TTCTTGAATTATATAAATTTA
Found at i:606780 original size:91 final size:87
Alignment explanation
Indices: 606661--606836 Score: 273
Period size: 91 Copynumber: 2.0 Consensus size: 87
606651 GTTAAAAAGG
* *
606661 ATCACGATGTGCAATATCTGATAATGACCTTGCTCTGTCACTTCATCACGGATATTCATGCATTA
1 ATCACGATGTGCAATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATA-TCATGCATTA
606726 G-TTATTCATCATTTTTTTCTCAGA
65 GTTTATTCATC--TTTTTTCTCAGA
*
606750 ATCATGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATCATGCATT
1 ATCACGATGTGC-A-ATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATCATGCATT
606815 AGTTTATTCATCTTTTTTCTCA
64 AGTTTATTCATCTTTTTTCTCA
606837 TTACATGTCA
Statistics
Matches: 81, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
89 21 0.26
90 12 0.15
91 48 0.59
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (87 bp):
ATCACGATGTGCAATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATCATGCATTAG
TTTATTCATCTTTTTTCTCAGA
Found at i:607073 original size:27 final size:27
Alignment explanation
Indices: 607042--607119 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
607032 ATTCTCCAAA
607042 TTGTAATTAGTAATTCTTAGCTTATCT
1 TTGTAATTAGTAATTCTTAGCTTATCT
*
607069 TTGTAATTAGTAATTCTTAGCGTATCT
1 TTGTAATTAGTAATTCTTAGCTTATCT
607096 TTGTAATTAGT-ATTCTTAGCTTAT
1 TTGTAATTAGTAATTCTTAGCTTAT
607120 TTGTAACTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 12 0.24
27 37 0.76
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (27 bp):
TTGTAATTAGTAATTCTTAGCTTATCT
Found at i:608504 original size:28 final size:28
Alignment explanation
Indices: 608472--608529 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
608462 TATACCAAAG
*
608472 TTAATCTATTTAGTGTGGTGCTCACTGT
1 TTAATCTATTTAATGTGGTGCTCACTGT
*
608500 TTAATCTATTTAATGTGGTGCTCATTGT
1 TTAATCTATTTAATGTGGTGCTCACTGT
608528 TT
1 TT
608530 CATACATCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (28 bp):
TTAATCTATTTAATGTGGTGCTCACTGT
Found at i:609864 original size:94 final size:92
Alignment explanation
Indices: 609675--609865 Score: 303
Period size: 94 Copynumber: 2.0 Consensus size: 92
609665 AAGTTTTATG
609675 TTTTCCAGGCATTTCTTTAGTGAAGTTTCTTTGGTTTTCACGGTTCTTAAGATGAAATGTATCTA
1 TTTTCCAGGCATTTCTTTAGTGAAGTTTCTTTGGTTTTCACGG-T-TTAAGATGAAATGTATCTA
***
609740 CTTTATAAGGCTTAGGCGAGTTTTATTGA
64 CTTTATAAGGCTTAGGCGAACATTATTGA
609769 TTTTCCAGGCATTTCTTTAGTGAAGTTTCTTTTGGTTTTCACGG-TTAAGATGAAAATGTATCTA
1 TTTTCCAGGCATTTCTTTAGTGAAGTTTC-TTTGGTTTTCACGGTTTAAGATG-AAATGTATCTA
609833 CTTTATAAGGCTTAGGCGAACATTATCTGA
64 CTTTATAAGGCTTAGGCGAACATTAT-TGA
609863 TTT
1 TTT
609866 ATTGGGTTGA
Statistics
Matches: 91, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
92 8 0.09
93 34 0.37
94 35 0.38
95 14 0.15
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (92 bp):
TTTTCCAGGCATTTCTTTAGTGAAGTTTCTTTGGTTTTCACGGTTTAAGATGAAATGTATCTACT
TTATAAGGCTTAGGCGAACATTATTGA
Found at i:611984 original size:6 final size:6
Alignment explanation
Indices: 611953--612011 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
611943 CGCCGTCTCG
611953 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
611997 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
612012 AATACGTGTC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.38
6 33 0.62
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:612139 original size:20 final size:20
Alignment explanation
Indices: 612114--612441 Score: 341
Period size: 20 Copynumber: 15.8 Consensus size: 20
612104 CTCATTTTCT
612114 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
612134 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
612155 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
612174 GAAGATCGCGTTGCGATT-TTCT
1 G-A-ATCGCGTTGCGATTCTT-G
612196 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
612216 GAAGATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCTTG
612238 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
612259 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
612278 GAAGATCGCGTTGCGATT-TTCT
1 G-A-ATCGCGTTGCGATTCTT-G
*
612300 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
612320 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
612340 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
612360 GAAGATCGCGTTGCGATTTTTG
1 G-A-ATCGCGTTGCGATTCTTG
*
612382 GAAGATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTT-G
*
612404 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
612424 GAAGATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
612442 TTCTTTTCAA
Statistics
Matches: 275, Mismatches: 9, Indels: 46
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.04
20 136 0.49
21 21 0.08
22 108 0.39
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.37
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:612195 original size:42 final size:41
Alignment explanation
Indices: 612107--612500 Score: 391
Period size: 42 Copynumber: 9.6 Consensus size: 41
612097 GAATTTACTC
612107 ATTTTCTGAATCGCGTTGCGATTCTTGG-AATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCG
*
612147 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG
612189 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG
* ***
612231 ATTCTT-GGAATCGCGTTGCGATT-TTCTTAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCG
* *
612271 ATTCTT-GGAAGATCGCGTTGCGATT-TTCTG-AATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTT-GGAAATCGCGTTGCG
*
612313 ATTTTCTGAATCGCGTTGCGATT-TTCTG-AATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTT-GGAAATCGCGTTGCG
* *
612353 ATTCTT-GGAAGATCGCGTTGCGATTTTTGGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG
* *
612397 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG
** * * **
612439 ATTTTCT-TTTCAACGTTGCGCTT-TTCTAAATCGCGTTGCG
1 ATTTTCTGAATC-GCGTTGCGATTCTTGGAAATCGCGTTGCG
*
612479 -GTTT-TGATATCGCGTTGCGATT
1 ATTTTCTGA-ATCGCGTTGCGATT
612501 TGTTGGTCAT
Statistics
Matches: 310, Mismatches: 27, Indels: 35
0.83 0.07 0.09
Matches are distributed among these distances:
38 1 0.00
39 12 0.04
40 94 0.30
41 17 0.05
42 163 0.53
43 8 0.03
44 15 0.05
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.38
Consensus pattern (41 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCG
Found at i:612296 original size:104 final size:103
Alignment explanation
Indices: 612116--612501 Score: 514
Period size: 104 Copynumber: 3.7 Consensus size: 103
612106 CATTTTCTGA
*
612116 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAGATC
1 ATCGCGTTGCGATT-TTGGAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAGATC
612181 GCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
65 GCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
*
612220 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAGATC
1 ATCGCGTTGCGATT-TTGGAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAGATC
*
612285 GCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTCTG-A-
65 GCGTTGCGATTTTCTGAATCGCGTTGCGATTCTT-GGAAG
* ** *
612322 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTTGGAAGA
1 ATCGCGTTGCGATTTT-GGAATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTCTTGGAAGA
* *
612387 TCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAG
63 TCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
**** * * * *
612428 ATCGCGTTGCGATTTTCTTTTCAACGTTGCGCTTTTCTAAATCGCGTTGCGGTT-TT-G-ATATC
1 ATCGCGTTGCGATTTTGGAATC-GCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAGATC
612490 GCGTTGCGATTT
65 GCGTTGCGATTT
612502 GTTGGTCATT
Statistics
Matches: 255, Mismatches: 19, Indels: 19
0.87 0.06 0.06
Matches are distributed among these distances:
101 18 0.07
102 31 0.12
103 8 0.03
104 164 0.64
105 9 0.04
106 25 0.10
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.38
Consensus pattern (103 bp):
ATCGCGTTGCGATTTTGGAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAGATCG
CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
Found at i:612475 original size:20 final size:20
Alignment explanation
Indices: 612107--612501 Score: 332
Period size: 20 Copynumber: 19.2 Consensus size: 20
612097 GAATTTACTC
*
612107 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
612127 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
612147 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
612167 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
612189 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
612209 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
612231 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
612251 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
612271 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
612293 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
*
612313 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
*
612333 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
612353 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
612375 ATTTT-TGGAAGATCGCGTTGCG
1 ATTTTCT--AA-ATCGCGTTGCG
* * *
612397 ATTTTATGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
612417 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
** *
612439 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
612459 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
612479 GTTTT-GATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
612498 ATTT
1 ATTT
612502 GTTGGTCATT
Statistics
Matches: 313, Mismatches: 44, Indels: 37
0.79 0.11 0.09
Matches are distributed among these distances:
19 21 0.07
20 168 0.54
21 32 0.10
22 91 0.29
23 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:634755 original size:63 final size:63
Alignment explanation
Indices: 634656--634781 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
634646 TGTTTTAAGC
634656 TTGATATCTGCTGTTTAATATTGCTCTAGCATAAATCTAAAATCTTAAGTGTTGGAATCATCG
1 TTGATATCTGCTGTTTAATATTGCTCTAGCATAAATCTAAAATCTTAAGTGTTGGAATCATCG
634719 TTGATATCTGCTGTTT-ATATTGCTCTAGCATAAAATCTAAAATCTTAAGTGTTGGAATCATCG
1 TTGATATCTGCTGTTTAATATTGCTCTAGCAT-AAATCTAAAATCTTAAGTGTTGGAATCATCG
634782 AGAGTGCAAG
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 15 0.24
63 47 0.76
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (63 bp):
TTGATATCTGCTGTTTAATATTGCTCTAGCATAAATCTAAAATCTTAAGTGTTGGAATCATCG
Found at i:636569 original size:161 final size:157
Alignment explanation
Indices: 636317--636622 Score: 526
Period size: 161 Copynumber: 1.9 Consensus size: 157
636307 TTTGACATGC
636317 TTGCTTAACATTCCATTTTATTTTATTTATTTTCATGTGATAGGTTTAGTGTATTTTCTGTATGT
1 TTGCTTAACATTCCATTTTATTTTATTTATTTTCATGTGATAGGTTTAGTGTATTTTCTGTATGT
636382 AAACACATGTTCTTTGCCGAATGATTAGACATTTAAATGAGGACATTACTTTTGGGATCTCAGCC
66 AAACACATGTTCTTTGCCGAATGATTAGACATTTAAATGAGGACATTACTTTTGGGATCTCAGCC
636447 TTTTGTTGTTAGTTATTGACATGCTCTG
131 -TTTGTTGTTAGTTATTGACATGCTCTG
*
636475 TTGCTTCACATTCCATTTTATTTTTATTTATTTTTCATGTGATAGGTTTTAGTGTATTTTCTGTA
1 TTGCTTAACATTCCATTTTA-TTTTATTTA-TTTTCATGTGATAGG-TTTAGTGTATTTTCTGTA
*
636540 TGTAAATTACATGTT-TCTTGCCG-ATGATTAGACATTTAAATGAGGACATTACTTTTGGGATCT
63 TGTAAA-CACATGTTCT-TTGCCGAATGATTAGACATTTAAATGAGGACATTACTTTTGGGATCT
636603 CAGCCTTTGTTGTTAGTTAT
126 CAGCCTTTGTTGTTAGTTAT
636623 ACATCCTCTT
Statistics
Matches: 141, Mismatches: 2, Indels: 8
0.93 0.01 0.05
Matches are distributed among these distances:
158 19 0.13
159 9 0.06
160 30 0.21
161 70 0.50
162 13 0.09
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.48
Consensus pattern (157 bp):
TTGCTTAACATTCCATTTTATTTTATTTATTTTCATGTGATAGGTTTAGTGTATTTTCTGTATGT
AAACACATGTTCTTTGCCGAATGATTAGACATTTAAATGAGGACATTACTTTTGGGATCTCAGCC
TTTGTTGTTAGTTATTGACATGCTCTG
Found at i:637785 original size:54 final size:53
Alignment explanation
Indices: 637641--637839 Score: 159
Period size: 54 Copynumber: 3.7 Consensus size: 53
637631 TAATGTAAGT
* * * * * *
637641 GGTTAAAAATAACAA-ACACAACTGTTAACGTTACTCCTACTTATAAGGTAACC
1 GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCATATTTAT-AGGTAACA
* * * * * * * *
637694 GATACAAAACAAAACAAGACTCAACCGTAAACATTACTCATATTTAATAAGGTAACC
1 GGT-TAAAA-ATAACAAGGCGCAACCGTTAACGTTACTCATATTT-AT-AGGTAACA
* * * * *
637751 GGTTAAAAATGA-AAGGTGCAACCGTTAACGTTACTCCTGTTTGTAGGTAACA
1 GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCATATTTATAGGTAACA
*
637803 TGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTC
1 GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTC
637840 TTATAAGTTG
Statistics
Matches: 116, Mismatches: 25, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
52 17 0.15
53 26 0.22
54 27 0.23
55 8 0.07
56 25 0.22
57 13 0.11
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.25
Consensus pattern (53 bp):
GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCATATTTATAGGTAACA
Found at i:639478 original size:2 final size:2
Alignment explanation
Indices: 639473--639501 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
639463 GGTCATTTTT
639473 TA TA TA TA T- 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
639502 ATAATATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:642577 original size:27 final size:27
Alignment explanation
Indices: 642539--642604 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
642529 AACCAACGGC
642539 TCATATGTAACGGCTCATAGGAGCCTA
1 TCATATGTAACGGCTCATAGGAGCCTA
642566 TCATATGTAACGGCTCATAGGAGCCTA
1 TCATATGTAACGGCTCATAGGAGCCTA
642593 TCATATGTAACG
1 TCATATGTAACG
642605 AGCCTATCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (27 bp):
TCATATGTAACGGCTCATAGGAGCCTA
Found at i:642609 original size:18 final size:18
Alignment explanation
Indices: 642586--642622 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
642576 CGGCTCATAG
642586 GAGCCTATCATATGTAAC
1 GAGCCTATCATATGTAAC
642604 GAGCCTATCATATGTAAC
1 GAGCCTATCATATGTAAC
642622 G
1 G
642623 GCTCATATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (18 bp):
GAGCCTATCATATGTAAC
Found at i:643366 original size:2 final size:2
Alignment explanation
Indices: 643359--643385 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
643349 CGTGATTCAT
643359 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
643386 AATCCATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:643741 original size:20 final size:21
Alignment explanation
Indices: 643716--643760 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
643706 ATGCTTGTTA
*
643716 ATTTATTCTTAATTTAAAT-T
1 ATTTATTCGTAATTTAAATAT
643736 ATTTATTCGTAATTTAAATAT
1 ATTTATTCGTAATTTAAATAT
643757 ATTT
1 ATTT
643761 TTAATTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTATTCGTAATTTAAATAT
Found at i:643954 original size:20 final size:20
Alignment explanation
Indices: 643929--643986 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
643919 TTTCAAAAAA
*
643929 GAATTATATTAATCTATTCT
1 GAATTATATTAATTTATTCT
*
643949 GAATTAAATTAATTTATTCT
1 GAATTATATTAATTTATTCT
* *
643969 TAGTTATATTAATTTATT
1 GAATTATATTAATTTATT
643987 GTTGGTATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
GAATTATATTAATTTATTCT
Found at i:644149 original size:21 final size:21
Alignment explanation
Indices: 644123--644172 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
644113 CATTTTTTCT
*
644123 TAATTTATATTAAGTTATTCA
1 TAATTTATATTAACTTATTCA
* *
644144 TAATTTATGTTAACTTATTCT
1 TAATTTATATTAACTTATTCA
644165 TAATTTAT
1 TAATTTAT
644173 TCTTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (21 bp):
TAATTTATATTAACTTATTCA
Found at i:644179 original size:11 final size:11
Alignment explanation
Indices: 644114--644181 Score: 68
Period size: 11 Copynumber: 6.4 Consensus size: 11
644104 ACACCCTTTC
*
644114 ATTTTTTCTTA
1 ATTTATTCTTA
*
644125 ATTTA-TATTA
1 ATTTATTCTTA
* *
644135 AGTTATTCATA
1 ATTTATTCTTA
*
644146 ATTTA-TGTTA
1 ATTTATTCTTA
*
644156 ACTTATTCTTA
1 ATTTATTCTTA
644167 ATTTATTCTTA
1 ATTTATTCTTA
644178 ATTT
1 ATTT
644182 TTATAATATA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
10 15 0.34
11 29 0.66
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.60
Consensus pattern (11 bp):
ATTTATTCTTA
Found at i:644217 original size:21 final size:20
Alignment explanation
Indices: 644181--644219 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
644171 ATTCTTAATT
*
644181 TTTATAATATATTAATATAG
1 TTTATAATATAATAATATAG
644201 TTTATAAGTATAATAATAT
1 TTTATAA-TATAATAATAT
644220 TCATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTATAATATAATAATATAG
Found at i:645915 original size:21 final size:21
Alignment explanation
Indices: 645882--645932 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
645872 AAAAGCATTG
645882 TTAATTT-TTCTTGAATTATA
1 TTAATTTATTCTTGAATTATA
645902 TTAATTTATTCTTGAATTATA
1 TTAATTTATTCTTGAATTATA
*
645923 TAAATTTATT
1 TTAATTTATT
645933 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (21 bp):
TTAATTTATTCTTGAATTATA
Found at i:656755 original size:196 final size:196
Alignment explanation
Indices: 656421--656812 Score: 784
Period size: 196 Copynumber: 2.0 Consensus size: 196
656411 ACCATAAGCT
656421 CTGATACCACTAAATGTAACCCCCTCAAACTGATACGGATATCCCGATCCGATCTGGGGTGTCAC
1 CTGATACCACTAAATGTAACCCCCTCAAACTGATACGGATATCCCGATCCGATCTGGGGTGTCAC
656486 ATTAGGGCCACCGGAGCGACCCACTGTAAAAATGGTGGAAAATTTAAAACTTTTATTAAAATATG
66 ATTAGGGCCACCGGAGCGACCCACTGTAAAAATGGTGGAAAATTTAAAACTTTTATTAAAATATG
656551 TAACTTATAAAATGATTTATCAATATGCAGAAATAAAACAGATTTCCAGACTCGTATATAAATCA
131 TAACTTATAAAATGATTTATCAATATGCAGAAATAAAACAGATTTCCAGACTCGTATATAAATCA
656616 A
196 A
656617 CTGATACCACTAAATGTAACCCCCTCAAACTGATACGGATATCCCGATCCGATCTGGGGTGTCAC
1 CTGATACCACTAAATGTAACCCCCTCAAACTGATACGGATATCCCGATCCGATCTGGGGTGTCAC
656682 ATTAGGGCCACCGGAGCGACCCACTGTAAAAATGGTGGAAAATTTAAAACTTTTATTAAAATATG
66 ATTAGGGCCACCGGAGCGACCCACTGTAAAAATGGTGGAAAATTTAAAACTTTTATTAAAATATG
656747 TAACTTATAAAATGATTTATCAATATGCAGAAATAAAACAGATTTCCAGACTCGTATATAAATCA
131 TAACTTATAAAATGATTTATCAATATGCAGAAATAAAACAGATTTCCAGACTCGTATATAAATCA
656812 A
196 A
656813 AATACAATTA
Statistics
Matches: 196, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
196 196 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (196 bp):
CTGATACCACTAAATGTAACCCCCTCAAACTGATACGGATATCCCGATCCGATCTGGGGTGTCAC
ATTAGGGCCACCGGAGCGACCCACTGTAAAAATGGTGGAAAATTTAAAACTTTTATTAAAATATG
TAACTTATAAAATGATTTATCAATATGCAGAAATAAAACAGATTTCCAGACTCGTATATAAATCA
A
Found at i:661483 original size:92 final size:91
Alignment explanation
Indices: 661321--661503 Score: 321
Period size: 92 Copynumber: 2.0 Consensus size: 91
661311 GTTAAAAAGG
* *
661321 ATCACGATGTGCAATATATCTGATAATGACCTTGCTCTGTCACTTCATCACGGATATTCATGCAT
1 ATCACGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
*
661386 TAGTTTATTCATCATTTTTTTCTCAGA
66 TAGTTTATTCATC-TTTTTCTCTCAGA
*
661413 ATCATGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
1 ATCACGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
661478 TAGTTTATTCATCTTTTTCTCTCAGA
66 TAGTTTATTCATCTTTTTCTCTCAGA
661504 TTACATGTCA
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 12 0.14
92 75 0.86
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.40
Consensus pattern (91 bp):
ATCACGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
TAGTTTATTCATCTTTTTCTCTCAGA
Found at i:661757 original size:27 final size:27
Alignment explanation
Indices: 661719--661797 Score: 158
Period size: 27 Copynumber: 2.9 Consensus size: 27
661709 ATTCTCCAAA
661719 TTGTAATTAGTAATTCTTAGCTTATCT
1 TTGTAATTAGTAATTCTTAGCTTATCT
661746 TTGTAATTAGTAATTCTTAGCTTATCT
1 TTGTAATTAGTAATTCTTAGCTTATCT
661773 TTGTAATTAGTAATTCTTAGCTTAT
1 TTGTAATTAGTAATTCTTAGCTTAT
661798 TTGTAACTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.52
Consensus pattern (27 bp):
TTGTAATTAGTAATTCTTAGCTTATCT
Found at i:663385 original size:27 final size:27
Alignment explanation
Indices: 663355--663410 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
663345 TATAACCAAG
*
663355 TTAATCTA-TTAGTGTGGTGCTCACTGT
1 TTAATCTATTTAATGTGGTGCTCA-TGT
663382 TTAATCTATTTAATGTGGTGCTCATGT
1 TTAATCTATTTAATGTGGTGCTCATGT
663409 TT
1 TT
663411 CATACATCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (27 bp):
TTAATCTATTTAATGTGGTGCTCATGT
Found at i:668234 original size:18 final size:18
Alignment explanation
Indices: 668211--668247 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
668201 CTGTTTTTAA
668211 TTCCGAAAGATTAGAAAC
1 TTCCGAAAGATTAGAAAC
668229 TTCCGAAAGATTAGAAAC
1 TTCCGAAAGATTAGAAAC
668247 T
1 T
668248 AATTGCCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (18 bp):
TTCCGAAAGATTAGAAAC
Found at i:673903 original size:21 final size:21
Alignment explanation
Indices: 673877--673916 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
673867 CAGAACCCCA
*
673877 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
673898 GGGGGGAATCGATTCCCCT
1 GGGGGGAATCGATTCCCCT
673917 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:688331 original size:107 final size:108
Alignment explanation
Indices: 688122--688369 Score: 242
Period size: 107 Copynumber: 2.3 Consensus size: 108
688112 ACCATTAACG
* * *
688122 TTACTCCTATTTGT-AGGTAACAGGTTAAAA-TAACAAGGCGCAACCGTTAACGTTACTCTTACT
1 TTACTCCTATCTGTAAGGTAACA-GTTAAAATTAAAAAGGCACAACCGTTAACGTTACTC-T-CT
* * **
688185 TATAAGGTAACAGGTAAAAAAACAAAACATTGTGCAATCGTAAACA
63 TATAAGGTAACAGATAAAAAAACAAAACATAGCACAATCGTAAACA
*
688231 TTACTCCTATCTGTAAGGTAACATGTTAAAATTAAAAAGGCACAACC-TATTACGTTACTC-CTT
1 TTACTCCTATCTGTAAGGTAACA-GTTAAAATTAAAAAGGCACAACCGT-TAACGTTACTCTCTT
* **
688294 ATAAGTTAATC-GAT-AAAAAACAAAACA-AGACACAATCGTAAATG
64 ATAAGGTAA-CAGATAAAAAAACAAAACATAG-CACAATCGTAAACA
* *
688338 TCACTCCTA-CTTATAAGGTAACCAGTTAAAAT
1 TTACTCCTATC-TGTAAGGTAA-CAGTTAAAAT
688370 AACAAGAAGT
Statistics
Matches: 118, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
106 2 0.02
107 48 0.41
108 15 0.13
109 14 0.12
110 16 0.14
111 23 0.19
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (108 bp):
TTACTCCTATCTGTAAGGTAACAGTTAAAATTAAAAAGGCACAACCGTTAACGTTACTCTCTTAT
AAGGTAACAGATAAAAAAACAAAACATAGCACAATCGTAAACA
Found at i:688506 original size:54 final size:53
Alignment explanation
Indices: 688340--688507 Score: 142
Period size: 56 Copynumber: 3.1 Consensus size: 53
688330 CGTAAATGTC
* * ** * *
688340 ACTCCTACTTATAAGGTAACCAGTT-AAAATAACAAGAAGTAGCCTATAATATT
1 ACTCATACTTATAAGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAA-ATT
* * * * * *
688393 ACTCTTACTTATAAGCTAACTGGTAAAAAACAAAACCAGGTGCAACC-ATAAATGTT
1 ACTCATACTTATAAGGTAACCGGT-TAAAA-ATAACAAGGTGCAACCTATAAA--TT
* *
688449 ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAACATT
1 ACTCATACTTATAAGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAA-ATT
688503 ACTCA
1 ACTCA
688508 AGAATGTTAA
Statistics
Matches: 89, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
53 20 0.22
54 22 0.25
55 15 0.17
56 32 0.36
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (53 bp):
ACTCATACTTATAAGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAAATT
Found at i:698420 original size:53 final size:54
Alignment explanation
Indices: 698275--698538 Score: 221
Period size: 56 Copynumber: 4.8 Consensus size: 54
698265 ATAACAATCA
* * * * *
698275 CAACTGTTAACGTTACTCCTACTTATAAGGTAACCGATACAAAACAAAACAAGACT
1 CAACCGTTAACGTTACTTCTACTTATAAGGTAACCGGTA-AAAA-AAAACAAGGCG
* * * * **
698331 CAACCGTAAACATTAC-TCATATTTAATAAGGTAACCGGTCAAAAATGA-AAGGCG
1 CAACCGTTAACGTTACTTC-TACTT-ATAAGGTAACCGGTAAAAAAAAACAAGGCG
* * *
698385 CAACCGTTAACGTTACTTCTACTTATAAGGTAACCGATAAAAAACAAAACAATGTG
1 CAACCGTTAACGTTACTTCTACTTATAAGGTAACCGGT-AAAAA-AAAACAAGGCG
* * ** * ** * *
698441 CAACCGTAAACGTTACTCCTGTTTGT-AGGTAACATGTTAAAAATAACAAGGCG
1 CAACCGTTAACGTTACTTCTACTTATAAGGTAACCGGTAAAAAAAAACAAGGCG
*
698494 CAACCGTTAACGTTAC-TCTTACTTATAAGGTAACAGGTAAAAAAA
1 CAACCGTTAACGTTACTTC-TACTTATAAGGTAACCGGTAAAAAAA
698539 CAAAACATTG
Statistics
Matches: 160, Mismatches: 40, Indels: 18
0.73 0.18 0.08
Matches are distributed among these distances:
52 1 0.01
53 40 0.25
54 45 0.28
55 15 0.09
56 46 0.29
57 13 0.08
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (54 bp):
CAACCGTTAACGTTACTTCTACTTATAAGGTAACCGGTAAAAAAAAACAAGGCG
Found at i:698535 original size:109 final size:110
Alignment explanation
Indices: 698258--698603 Score: 425
Period size: 110 Copynumber: 3.2 Consensus size: 110
698248 AATGTAAGTG
* * * * *
698258 GTTAAAAATAACAA-TCACAACTGTTAACGTTACTCCTACTTATAAGGTAACCGATACAAAACAA
1 GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCTTACTTATAAGGTAACCGATAAAAAACAA
* * **
698322 AACAA-GACT-CAACCGTAAACATTACTCATATTTAATAAGGTAACCG
66 AACAATG--TGCAACCGTAAACATTACTCCTATTT-GTAAGGTAACAT
* *
698368 GTCAAAAATGA-AAGGCGCAACCGTTAACGTTACT-TCTACTTATAAGGTAACCGATAAAAAACA
1 GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCT-TACTTATAAGGTAACCGATAAAAAACA
* *
698431 AAACAATGTGCAACCGTAAACGTTACTCCTGTTTGT-AGGTAACAT
65 AAACAATGTGCAACCGTAAACATTACTCCTATTTGTAAGGTAACAT
* *
698476 GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCTTACTTATAAGGTAACAGGTAAAAAAACA
1 GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCTTACTTATAAGGTAACCGAT-AAAAAACA
* * *
698541 AAACATTGTGCAATCGTAAACATTACTCCTATCTGTAAGGTAACAT
65 AAACAATGTGCAACCGTAAACATTACTCCTATTTGTAAGGTAACAT
* *
698587 GTTAAAATTAAAAAGGC
1 GTTAAAAATAACAAGGC
698604 ACAAGTTAAT
Statistics
Matches: 204, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
108 16 0.08
109 44 0.22
110 119 0.58
111 25 0.12
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (110 bp):
GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCTTACTTATAAGGTAACCGATAAAAAACAA
AACAATGTGCAACCGTAAACATTACTCCTATTTGTAAGGTAACAT
Found at i:698580 original size:57 final size:56
Alignment explanation
Indices: 698384--698585 Score: 180
Period size: 57 Copynumber: 3.6 Consensus size: 56
698374 AATGAAAGGC
* * * * *
698384 GCAACCGTTAACGTTACTTCTA-CTTATAAGGTAACCGATAAAAAACAAAACAATGT
1 GCAACCGTAAACGTTACTCCTATC-TGTAAGGTAACAGGTAAAAAACAAAACAATGT
* * * * * * *
698440 GCAACCGTAAACGTTACTCCTGTTTGT-AGGTAACATGT-TAAAA-ATAACAAGGC
1 GCAACCGTAAACGTTACTCCTATCTGTAAGGTAACAGGTAAAAAACAAAACAATGT
* * * *
698493 GCAACCGTTAACGTTACTCTTA-CTTATAAGGTAACAGGTAAAAAAACAAAACATTGT
1 GCAACCGTAAACGTTACTCCTATC-TGTAAGGTAACAGGT-AAAAAACAAAACAATGT
* *
698550 GCAATCGTAAACATTACTCCTATCTGTAAGGTAACA
1 GCAACCGTAAACGTTACTCCTATCTGTAAGGTAACA
698586 TGTTAAAATT
Statistics
Matches: 111, Mismatches: 28, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
53 28 0.25
54 14 0.13
55 8 0.07
56 25 0.23
57 35 0.32
58 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (56 bp):
GCAACCGTAAACGTTACTCCTATCTGTAAGGTAACAGGTAAAAAACAAAACAATGT
Found at i:698819 original size:54 final size:53
Alignment explanation
Indices: 698642--698819 Score: 121
Period size: 54 Copynumber: 3.2 Consensus size: 53
698632 AGACACAATC
* * * * ** * *
698642 ATAAATGTCACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGAAGTAGCCT
1 ATAAAT-T-ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCT
* * * *
698697 ATAATATTACTCTTAC--TTATGAGCTAACTGGTAAAAAACAA-AACTTGGTGCAACC-
1 ATAA-ATTACTCATACTTTTATG-G-TAACCGGTTAAAAATAACAA---GGTGCAACCT
698752 ATAAATGTTACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCT
1 ATAAA--TTACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCT
698807 ATAACATTACTCA
1 ATAA-ATTACTCA
698820 ATAATGTTAA
Statistics
Matches: 95, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
52 3 0.03
53 3 0.03
54 37 0.39
55 13 0.14
56 31 0.33
57 3 0.03
58 5 0.05
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (53 bp):
ATAAATTACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCT
Found at i:702591 original size:27 final size:27
Alignment explanation
Indices: 702561--702621 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
702551 AAAATAAAAA
*
702561 AAATTTATCAAAA-GTAAAAATCTAATC
1 AAATTTAT-AAAATATAAAAATCTAATC
* *
702588 AAATTCATAAAATATAAAAATTTAATC
1 AAATTTATAAAATATAAAAATCTAATC
*
702615 GAATTTA
1 AAATTTA
702622 AAATAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (27 bp):
AAATTTATAAAATATAAAAATCTAATC
Found at i:702634 original size:25 final size:26
Alignment explanation
Indices: 702575--702632 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
702565 TTATCAAAAG
*
702575 TAAAAATCTAATCAAATTCATAAAATA
1 TAAAAATTTAATCAAATT-ATAAAATA
*
702602 TAAAAATTTAATCGAATT-TAAAATAA
1 TAAAAATTTAATCAAATTATAAAAT-A
702628 TAAAA
1 TAAAA
702633 TTAAGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 6 0.21
26 6 0.21
27 16 0.57
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (26 bp):
TAAAAATTTAATCAAATTATAAAATA
Found at i:702888 original size:25 final size:24
Alignment explanation
Indices: 702841--702888 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
702831 TCTATGAGTA
702841 TTCAAATAATAAATAAATGATATT
1 TTCAAATAATAAATAAATGATATT
*
702865 TTCAAATTAA-AATATAAATTATAT
1 TTCAAA-TAATAA-ATAAATGATAT
702889 ATTTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TTCAAATAATAAATAAATGATATT
Found at i:702996 original size:13 final size:13
Alignment explanation
Indices: 702978--703006 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
702968 AATATGTATT
702978 TTTTTTCAAATTG
1 TTTTTTCAAATTG
702991 TTTTTTCAAATTG
1 TTTTTTCAAATTG
703004 TTT
1 TTT
703007 AAAAGAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TTTTTTCAAATTG
Found at i:703417 original size:26 final size:27
Alignment explanation
Indices: 703381--703488 Score: 128
Period size: 26 Copynumber: 3.7 Consensus size: 27
703371 CAACAACGGC
703381 TCATATGTAACGGCTCATAGGAG-CTA
1 TCATATGTAACGGCTCATAGGAGCCTA
703407 TCATATGTAACGGCTCATAGGAGCCTA
1 TCATATGTAACGGCTCATAGGAGCCTA
703434 TCATATGTAACGAGCCTATCATATGTAACGAGCCTA
1 TCATATGTAACG-G-C--TCATA-G----GAGCCTA
703470 TCATATGTAACGGCTCATA
1 TCATATGTAACGGCTCATA
703489 TTCAACCAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 14
0.84 0.00 0.16
Matches are distributed among these distances:
26 23 0.32
27 15 0.21
28 1 0.01
29 1 0.01
31 5 0.07
32 6 0.08
34 1 0.01
35 1 0.01
36 19 0.26
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (27 bp):
TCATATGTAACGGCTCATAGGAGCCTA
Found at i:703450 original size:18 final size:18
Alignment explanation
Indices: 703427--703481 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
703417 CGGCTCATAG
703427 GAGCCTATCATATGTAAC
1 GAGCCTATCATATGTAAC
703445 GAGCCTATCATATGTAAC
1 GAGCCTATCATATGTAAC
703463 GAGCCTATCATATGTAAC
1 GAGCCTATCATATGTAAC
703481 G
1 G
703482 GCTCATATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (18 bp):
GAGCCTATCATATGTAAC
Found at i:704604 original size:21 final size:21
Alignment explanation
Indices: 704577--704669 Score: 134
Period size: 21 Copynumber: 4.5 Consensus size: 21
704567 AAGATGCTTG
704577 TTAATTTATTCTTAATTTAAA
1 TTAATTTATTCTTAATTTAAA
* *
704598 TTTATTTATTCTTAGTTTAAA
1 TTAATTTATTCTTAATTTAAA
* *
704619 TTAATATATTCTTAATTTATA
1 TTAATTTATTCTTAATTTAAA
*
704640 TTAATTTATTCTTAA-TTATA
1 TTAATTTATTCTTAATTTAAA
704660 TTAATTTATT
1 TTAATTTATT
704670 GTTGGTATTG
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
20 15 0.23
21 50 0.77
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (21 bp):
TTAATTTATTCTTAATTTAAA
Found at i:704835 original size:21 final size:21
Alignment explanation
Indices: 704809--704867 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
704799 TTCAAAAAAA
704809 GAATTATATTAATTTATTCTT
1 GAATTATATTAATTTATTCTT
*
704830 GAATTAAATTAATTTATTCTT
1 GAATTATATTAATTTATTCTT
*
704851 -AGTTATATTAATTTATT
1 GAATTATATTAATTTATT
704868 GTTGGTATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 15 0.43
21 20 0.57
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (21 bp):
GAATTATATTAATTTATTCTT
Found at i:704963 original size:198 final size:198
Alignment explanation
Indices: 704618--705000 Score: 628
Period size: 198 Copynumber: 1.9 Consensus size: 198
704608 CTTAGTTTAA
*
704618 ATTAATATATTCTTAATTTATATTAATTTATTCTTAATTATATTAATTTATTGTTGGTATTGTAA
1 ATTAATATATTCTTAATTTAAATTAATTTATTCTTAATTATATTAATTTATTGTTGGTATTGTAA
* * *
704683 TGTCATCGTTTCGGTGCACTTTTTTCCCCTCCGATTAGTTGTAGGGAGGTTTTTTAACAGGCCCG
66 TGTCATCGTTTCGGTGCACTTTTTTCCCCTCCAATTAGGTGTAGGGAGGTTTTGTAACAGGCCCG
*
704748 ATTCGATGTTTTGTTTTGTATGTTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAAGAAT
131 ATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAAGAAT
704813 TAT
196 TAT
* *
704816 ATTAATTTATTCTTGAA-TTAAATTAATTTATTCTTAGTTATATTAATTTATTGTTGGTATTGTA
1 ATTAATATATTCTT-AATTTAAATTAATTTATTCTTAATTATATTAATTTATTGTTGGTATTGTA
*
704880 ATGTCATCGTTTCGGTGCACTTTTTT-TCCTCCAATTAGGTGTAGGGAGGTTTTGTAAC-GTGAC
65 ATGTCATCGTTTCGGTGCACTTTTTTCCCCTCCAATTAGGTGTAGGGAGGTTTTGTAACAG-G-C
* *
704943 CCGATTTGATGTTTTGTTTTGTATGGTTTTTCTCTATTTATACAAAACACCCCTTTCA
128 CCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCCCTTTCA
705001 TTTTTTCTTA
Statistics
Matches: 172, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
196 1 0.01
197 29 0.17
198 140 0.81
199 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (198 bp):
ATTAATATATTCTTAATTTAAATTAATTTATTCTTAATTATATTAATTTATTGTTGGTATTGTAA
TGTCATCGTTTCGGTGCACTTTTTTCCCCTCCAATTAGGTGTAGGGAGGTTTTGTAACAGGCCCG
ATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAAGAAT
TAT
Found at i:705727 original size:21 final size:21
Alignment explanation
Indices: 705700--705792 Score: 125
Period size: 21 Copynumber: 4.5 Consensus size: 21
705690 AAGATGCTTG
705700 TTAATTTATTCTTAATTTAAA
1 TTAATTTATTCTTAATTTAAA
* *
705721 TTTATTTATTCGTAATTTAAA
1 TTAATTTATTCTTAATTTAAA
* * *
705742 TTAATATATTTTTAATTTATA
1 TTAATTTATTCTTAATTTAAA
*
705763 TTAATTTATTCTTAA-TTATA
1 TTAATTTATTCTTAATTTAAA
705783 TTAATTTATT
1 TTAATTTATT
705793 GTTGGTATTG
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
20 15 0.24
21 48 0.76
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
TTAATTTATTCTTAATTTAAA
Found at i:705957 original size:21 final size:21
Alignment explanation
Indices: 705931--706010 Score: 126
Period size: 21 Copynumber: 3.9 Consensus size: 21
705921 TTCAAAAAAA
*
705931 GAATTATATTAATTTATTCTT
1 GAATTAAATTAATTTATTCTT
705952 GAATTAAATTAATTTATTCTT
1 GAATTAAATTAATTTATTCTT
*
705973 GATTTAAATTAATTTATTC-T
1 GAATTAAATTAATTTATTCTT
*
705993 GAATTATATTAATTTATT
1 GAATTAAATTAATTTATT
706011 GTTGGTATTG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
20 17 0.31
21 38 0.69
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (21 bp):
GAATTAAATTAATTTATTCTT
Found at i:706118 original size:218 final size:215
Alignment explanation
Indices: 705724--706226 Score: 715
Period size: 218 Copynumber: 2.3 Consensus size: 215
705714 ATTTAAATTT
* * * *
705724 ATTTATTCGTAATTTAAATTAATATATTTTTAATTTATATTAATTTATTCTTAATTATATTAATT
1 ATTTATTCTTAATTTAAATTAATTTATTCTT-ATTTATATTAATTTATTCTAAATTATATTAATT
* * *
705789 TATTGTTGGTATTGTAATGTCATTGTTTCGGTGCACTTTTTTCCCTCCGATTAGGTGTAGGGAGG
65 TATTGTTGGTATTGTAATGTCATCGTTTCAGTGCACTTTTTTCCCTCCAATTAGGTGTAGGGAGG
* * * *
705854 TTTTTTAACATGCTCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATTTATACAAAACACCC
130 TGTTTTAACAGGCCCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCC
705919 CTTTCAAAAAAAGAATTATATTA
195 CTTTC-AAAAAA-AATTATATTA
* *
705942 ATTTATTCTTGAA-TTAAATTAATTTATTCTTGATTTAAATTAATTTATTCTGAATTATATTAAT
1 ATTTATTCTT-AATTTAAATTAATTTATTCTT-ATTTATATTAATTTATTCTAAATTATATTAAT
706006 TTATTGTTGGTATTGTAATGTCATCGTTTCAGTGCACTTTTTTTCCCTCCAATTAGGTGTAGGGA
64 TTATTGTTGGTATTGTAATGTCATCGTTTCAGTGCAC-TTTTTTCCCTCCAATTAGGTGTAGGGA
*
706071 GG-GTTTTAATGAGGCCCGATTCGATGTTTTGTTTTGTATGG-TTTTCTCTATCTATACAAAACA
128 GGTGTTTTAA-CAGGCCCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACA
* *
706134 CTCCTTTCAAAACAAATTATATTA
192 CCCCTTTCAAAAAAAATTATATTA
** * * * *
706158 ATTTATTCTTAATTTATGTTAATTTAATCTTAATTATATTAGTTTATTCTTAAATTAAATTAATT
1 ATTTATTCTTAATTTAAATTAATTTATTCTTATTTATATTAATTTATTC-TAAATTATATTAATT
706223 TATT
65 TATT
706227 CTTAATTTAA
Statistics
Matches: 256, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
215 17 0.07
216 52 0.20
217 5 0.02
218 124 0.48
219 58 0.23
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (215 bp):
ATTTATTCTTAATTTAAATTAATTTATTCTTATTTATATTAATTTATTCTAAATTATATTAATTT
ATTGTTGGTATTGTAATGTCATCGTTTCAGTGCACTTTTTTCCCTCCAATTAGGTGTAGGGAGGT
GTTTTAACAGGCCCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCCC
TTTCAAAAAAAATTATATTA
Found at i:706174 original size:21 final size:21
Alignment explanation
Indices: 706150--706289 Score: 192
Period size: 21 Copynumber: 6.7 Consensus size: 21
706140 TCAAAACAAA
706150 TTATATTAATTTATTCTTAAT
1 TTATATTAATTTATTCTTAAT
* *
706171 TTATGTTAATTTAATCTTAA-
1 TTATATTAATTTATTCTTAAT
* *
706191 TTATATTAGTTTATTCTTAAA
1 TTATATTAATTTATTCTTAAT
*
706212 TTAAATTAATTTATTCTTAAT
1 TTATATTAATTTATTCTTAAT
* *
706233 TTAAATTAATTTATTCATAAT
1 TTATATTAATTTATTCTTAAT
*
706254 TTATATTAACTTATTCTTAAT
1 TTATATTAATTTATTCTTAAT
*
706275 TTATATTAATATATT
1 TTATATTAATTTATT
706290 AATAGTTTAT
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
20 17 0.16
21 87 0.84
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.57
Consensus pattern (21 bp):
TTATATTAATTTATTCTTAAT
Found at i:706244 original size:62 final size:63
Alignment explanation
Indices: 706147--706289 Score: 198
Period size: 62 Copynumber: 2.3 Consensus size: 63
706137 CTTTCAAAAC
** * **
706147 AAATTATATTAATTTATTCTTAATTTATGTTAATTTAATCTTAA-TTATATTAGTTTATTCTT
1 AAATTATATTAATTTATTCTTAATTTAAATTAATTTAATCATAATTTATATTAACTTATTCTT
* *
706209 AAATTAAATTAATTTATTCTTAATTTAAATTAATTTATTCATAATTTATATTAACTTATTCTT
1 AAATTATATTAATTTATTCTTAATTTAAATTAATTTAATCATAATTTATATTAACTTATTCTT
* *
706272 AATTTATATTAATATATT
1 AAATTATATTAATTTATT
706290 AATAGTTTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
62 39 0.56
63 31 0.44
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (63 bp):
AAATTATATTAATTTATTCTTAATTTAAATTAATTTAATCATAATTTATATTAACTTATTCTT
Found at i:708018 original size:18 final size:19
Alignment explanation
Indices: 707997--708052 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
707987 AATTAAAAAG
*
707997 GAATTGTTAATTT-TTCTT
1 GAATTATTAATTTATTCTT
708015 GAATTATATTAATTTATTCTT
1 GAA-T-TATTAATTTATTCTT
708036 GAATTAAATTAATTTAT
1 GAATT--ATTAATTTAT
708053 ATTCATTGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 9 0.28
21 18 0.56
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (19 bp):
GAATTATTAATTTATTCTT
Found at i:708036 original size:21 final size:21
Alignment explanation
Indices: 708003--708052 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
707993 AAAGGAATTG
*
708003 TTAATTT-TTCTTGAATTATA
1 TTAATTTATTCTTGAATTAAA
708023 TTAATTTATTCTTGAATTAAA
1 TTAATTTATTCTTGAATTAAA
708044 TTAATTTAT
1 TTAATTTAT
708053 ATTCATTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (21 bp):
TTAATTTATTCTTGAATTAAA
Found at i:725195 original size:427 final size:422
Alignment explanation
Indices: 724384--725215 Score: 1128
Period size: 427 Copynumber: 1.9 Consensus size: 422
724374 AATACTTTTT
* * * *
724384 TGTTGTGCTTTACATGGGGAATGAAATAAGCTTTATCATATTCTCTTCCAGGGGAAGTAGTGCTA
1 TGTTGTGCTTGACATGGGGAATCAAATAAGCTTGATCATATTCTCTTCCAGGGGAAGTAGCGCTA
*
724449 AAGCTAATGATCACTCTCAGGATGGAAGGTAATCATGAAATAAGCTTGATCATCTTCCATCCAGG
66 AAGCTAATGATCACTCTCAGGATGGAAGGTAACCATGAAATAAGCTTGATCATCTTCCATCCAGG
*
724514 CGAAGCTTACAAGTGTTGAAATTTAAAGCCTAGACTTGTTGCATCCACTCTTAAGTGTGCATCTT
131 CGAAGCTTACAAGTGTTGAAATTTAAAGCCTAGACTTGTTGCATCCACTCTTAAGTGTGCATCTA
*
724579 AACCATCTAGGCTAAACTTCAATTGTAGTTGATCAATCTTTATTAGACAATAATTGTTGGTTTCT
196 AACCATATAGGCTAAACTTCAATTGTAGTTGATCAATCTTTATT----AAT-ATTGTTGGTTTCT
* * * *
724644 TGTTTCTTGAATTTTCTAAAGGAAAAAAATATCTTTTTGCAGGTAGCATGAGCGCAAGCATTCTC
256 TGTTTCTTGAACTTTCTAAAGAAAAAAAATATCTTTTTGCAGGTAACATGAGCACAAGCATTCTC
*
724709 ACCAAAATGTCGGTACTCCTCGCAGTTATGTAGAAGCAGTAAGTGAGATTCAGATTCCTTCTTAT
321 ACCAAAATGTCAGTACTCCTCGCAGTTATGTAGAAGCAGTAAGTGAGATTCAGATTCCTTCTTAT
*
724774 AGCGCAAGGTATTTCAGCGACATGTTACTTTTAATTG
386 AGCGAAAGGTATTTCAGCGACATGTTACTTTTAATTG
* * * * *
724811 TGTTTTGCTTGACA-GGGGAATCTAATTAGCTTGATCATCTTCTCTGT-CAGGGGAAG-CGCGCT
1 TGTTGTGCTTGACATGGGGAATCAAATAAGCTTGATCATATTCTCT-TCCAGGGGAAGTAGCGCT
* * *
724873 AGAGCTAATGATCACTCTCAGGAT-GAAGGTAACCATGAAATAAGCTTGATCATTTTCTCTTCCA
65 AAAGCTAATGATCACTCTCAGGATGGAAGGTAACCATGAAATAAGCTTGATCATCTTC-CATCCA
* *
724937 GGGGAAGCTTGATGCTTTACAAGTGTTGAAATTTAAAGTCTAGACTTGTTGCATCCCACCTCTTA
129 ---G--GC--GAAGC-TTACAAGTGTTGAAATTTAAAGCCTAGACTTGTTGCAT-CCA-CTCTTA
*
725002 AGTGTGTATTCTGAAACCATATAGGCTAAACTTCAATTGTAGTTGATCAATC-TT-TT-AT-TTG
184 AGTGTGCA-TCT-AAACCATATAGGCTAAACTTCAATTGTAGTTGATCAATCTTTATTAATATTG
* *
725063 TTGGTTTCTTGTTTC-TGAACTTTCTGAAGAAAAAAAAATGTCTTTGTT-CAGGTAACA-GAGCA
247 TTGGTTTCTTGTTTCTTGAACTTTCTAAAG-AAAAAAAATATCTTT-TTGCAGGTAACATGAGCA
* * *
725125 CAAGCATTCTCACCAAAATGTCAGTGCTCCTTGCAGTTATGTAGAAGCAGTAAGTGAGATTCATA
310 CAAGCATTCTCACCAAAATGTCAGTACTCCTCGCAGTTATGTAGAAGCAGTAAGTGAGATTCAGA
*
725190 TTCCTTCTTATAGTGAAAGGTATTTC
375 TTCCTTCTTATAGCGAAAGGTATTTC
725216 TTTCAAAACA
Statistics
Matches: 359, Mismatches: 30, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
424 31 0.09
425 32 0.09
426 35 0.10
427 114 0.32
428 40 0.11
429 2 0.01
430 4 0.01
432 4 0.01
433 37 0.10
434 3 0.01
435 15 0.04
436 5 0.01
437 37 0.10
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (422 bp):
TGTTGTGCTTGACATGGGGAATCAAATAAGCTTGATCATATTCTCTTCCAGGGGAAGTAGCGCTA
AAGCTAATGATCACTCTCAGGATGGAAGGTAACCATGAAATAAGCTTGATCATCTTCCATCCAGG
CGAAGCTTACAAGTGTTGAAATTTAAAGCCTAGACTTGTTGCATCCACTCTTAAGTGTGCATCTA
AACCATATAGGCTAAACTTCAATTGTAGTTGATCAATCTTTATTAATATTGTTGGTTTCTTGTTT
CTTGAACTTTCTAAAGAAAAAAAATATCTTTTTGCAGGTAACATGAGCACAAGCATTCTCACCAA
AATGTCAGTACTCCTCGCAGTTATGTAGAAGCAGTAAGTGAGATTCAGATTCCTTCTTATAGCGA
AAGGTATTTCAGCGACATGTTACTTTTAATTG
Found at i:726373 original size:15 final size:15
Alignment explanation
Indices: 726334--726374 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
726324 ACCTTCATTA
*
726334 CACAACC-CAATAAC
1 CACAACCTCAAAAAC
*
726348 C-CAAACTCAAAAAC
1 CACAACCTCAAAAAC
726362 CACAACCTCAAAA
1 CACAACCTCAAAA
726375 CACTCATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 4 0.18
14 8 0.36
15 10 0.45
ACGTcount: A:0.54, C:0.39, G:0.00, T:0.07
Consensus pattern (15 bp):
CACAACCTCAAAAAC
Found at i:744184 original size:107 final size:105
Alignment explanation
Indices: 744021--744238 Score: 418
Period size: 107 Copynumber: 2.1 Consensus size: 105
744011 TAGGTATTTT
744021 ATAATTATTAATTAATGACTTAATATATATATATAGAAAGGTAACTTATCAATATGGTTTCGTGC
1 ATAATTATTAATTAATGACTTAATATATATATATAGAAAGGTAACTTATCAATATGGTTTCGTGC
744086 ATATAGGTTTAGACACAACATCATTTTTGCATAAAACTTC
66 ATATAGGTTTAGACACAACATCATTTTTGCATAAAACTTC
744126 ATAATTATTAATTAATGACTTAATATATATATATATAGAAAGGTAACTTATCAATATGGTTTCGT
1 ATAATTATTAATTAATGACTT-A-ATATATATATATAGAAAGGTAACTTATCAATATGGTTTCGT
744191 GCATATAGGTTTAGACACAACATCATTTTTGCATAAAACTTC
64 GCATATAGGTTTAGACACAACATCATTTTTGCATAAAACTTC
744233 ATAATT
1 ATAATT
744239 TGACTAGGGT
Statistics
Matches: 111, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
105 21 0.19
106 1 0.01
107 89 0.80
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (105 bp):
ATAATTATTAATTAATGACTTAATATATATATATAGAAAGGTAACTTATCAATATGGTTTCGTGC
ATATAGGTTTAGACACAACATCATTTTTGCATAAAACTTC
Found at i:745091 original size:41 final size:39
Alignment explanation
Indices: 745012--745108 Score: 140
Period size: 39 Copynumber: 2.4 Consensus size: 39
745002 TTCGGTTTGC
* *
745012 AAAAAACCAGTTTTTAAAAAAAACCGGATTTTTTCGGAT
1 AAAAAACCAGTTTTTTAAAAAAACCGGATTTTTCCGGAT
*
745051 AAAAAATCAGTTTTTTAAAAAAACCGGTATTTTATCCGGAT
1 AAAAAACCAGTTTTTTAAAAAAACCGG-ATTTT-TCCGGAT
*
745092 AAAAAACCGGTTTTTTA
1 AAAAAACCAGTTTTTTA
745109 TCCGGATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 25 0.49
40 5 0.10
41 21 0.41
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (39 bp):
AAAAAACCAGTTTTTTAAAAAAACCGGATTTTTCCGGAT
Done.