Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:496423 original size:29 final size:29
Alignment explanation
Indices: 496389--496471 Score: 112
Period size: 29 Copynumber: 2.9 Consensus size: 29
496379 TATCATATAT
**
496389 CATATTATATAGTTCATAGTCCATAATTG
1 CATATTATATAGTTCATAGTAAATAATTG
*
496418 CATATTATATAGTTCATATTAAATAATTG
1 CATATTATATAGTTCATAGTAAATAATTG
* * *
496447 CATATCATATAGTCCATATTAAATA
1 CATATTATATAGTTCATAGTAAATA
496472 GTACGTATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (29 bp):
CATATTATATAGTTCATAGTAAATAATTG
Found at i:498364 original size:20 final size:20
Alignment explanation
Indices: 498331--498369 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
498321 CTAATACTAA
*
498331 AATTAAACCTTTAGCTTTTT
1 AATTAAACCTTTAGATTTTT
498351 AATTAAAACC-TTAGATTTT
1 AATT-AAACCTTTAGATTTT
498370 ATTTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (20 bp):
AATTAAACCTTTAGATTTTT
Found at i:502623 original size:25 final size:26
Alignment explanation
Indices: 502594--502660 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 26
502584 ATTAAAAAAT
*
502594 AAAAAGGAGAAAAAAA-G-AAATTAA
1 AAAAAGGAGAAAAAAATGAAAATGAA
**
502618 AGAAAAAAAGAAGAAAAATGAAAAATGAA
1 A-AAAAGGAGAA-AAAAATG-AAAATGAA
502647 AAAAAGGAGAAAAA
1 AAAAAGGAGAAAAA
502661 GTAGAAAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
24 1 0.03
25 8 0.24
26 5 0.15
27 4 0.12
28 8 0.24
29 7 0.21
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (26 bp):
AAAAAGGAGAAAAAAATGAAAATGAA
Found at i:502672 original size:25 final size:24
Alignment explanation
Indices: 502616--502673 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 24
502606 AAAAGAAATT
502616 AAAGAAAAAAAGAAGAAAAATGAA
1 AAAGAAAAAAAGAAGAAAAATGAA
*
502640 AAATGAAAAAAAGGAGAAAAA-GTAGA
1 AAA-GAAAAAAAGAAGAAAAATG-A-A
502666 AAAGAAAA
1 AAAGAAAA
502674 TGGGGGTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 4 0.13
25 22 0.73
26 4 0.13
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (24 bp):
AAAGAAAAAAAGAAGAAAAATGAA
Found at i:504174 original size:6 final size:6
Alignment explanation
Indices: 504158--504220 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
504148 TAGGATATTT
* * ** *
504158 TTTTTA TTTTTTA TTTTAA CTTTTA TTTCCA TTTTT- TATTTA TTTTTA
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
504206 -TTTTA -TTTTA TTTTT
1 TTTTTA TTTTTA TTTTT
504221 TATTCACCTT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
5 14 0.32
6 24 0.55
7 6 0.14
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:504221 original size:12 final size:12
Alignment explanation
Indices: 504155--504224 Score: 67
Period size: 12 Copynumber: 6.0 Consensus size: 12
504145 GTCTAGGATA
504155 TTTT-TTTTATT
1 TTTTATTTTATT
**
504166 TTTTATTTTAAC
1 TTTTATTTTATT
*
504178 TTTTATTTCCATT
1 TTTTATTT-TATT
504191 TTTTA-TTTA-T
1 TTTTATTTTATT
504201 TTTTATTTTATT
1 TTTTATTTTATT
504213 TTATT-TTTTATT
1 TT-TTATTTTATT
504225 CACCTTTTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
10 6 0.12
11 9 0.19
12 25 0.52
13 8 0.17
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:520033 original size:20 final size:19
Alignment explanation
Indices: 520004--520043 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
519994 TGATTTTTGT
*
520004 ATAAGGAATAAATAAATAA
1 ATAAGGAATAAAGAAATAA
520023 ATAATGGAATAAAGAAATAA
1 ATAA-GGAATAAAGAAATAA
520043 A
1 A
520044 AGGGATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (19 bp):
ATAAGGAATAAAGAAATAA
Found at i:523171 original size:10 final size:10
Alignment explanation
Indices: 523158--523186 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
523148 TTAACTGTTA
523158 AAATTATTTT
1 AAATTATTTT
523168 AAATTATTTT
1 AAATTATTTT
523178 AAATTATTT
1 AAATTATTT
523187 CTTGTGTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
AAATTATTTT
Found at i:523395 original size:2 final size:2
Alignment explanation
Indices: 523388--523423 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
523378 TCAATCTACA
523388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
523424 TTACGAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:523599 original size:13 final size:13
Alignment explanation
Indices: 523583--523618 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
523573 GCTCAATGAA
523583 CGTCATAAATGCG
1 CGTCATAAATGCG
*
523596 CGTCATAAATGTG
1 CGTCATAAATGCG
*
523609 TGTCATAAAT
1 CGTCATAAAT
523619 TTATGACGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (13 bp):
CGTCATAAATGCG
Found at i:523601 original size:84 final size:85
Alignment explanation
Indices: 523441--523602 Score: 204
Period size: 84 Copynumber: 1.9 Consensus size: 85
523431 ATACAATCAC
* * * *
523441 GACACACGAATGTGTGTCATCTTTTTTAATGATGTGTGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTATTTAATGACGTGGGCTTCAATGACACGCAATGTAAGTCATA
* * *
523506 CATGTGTGTCATATATTTAT
66 AATGCGCGTCATATATTTAT
* *
523526 GACACACAAATGTGTGTCATCTTAATTT-ATGACG-GGGCTTCAATGACGCTCAATG-AACGTCA
1 GACACACAAATGTGTGTCATCTT-ATTTAATGACGTGGGCTTCAATGACACGCAATGTAA-GTCA
523588 TAAATGCGCGTCATA
64 TAAATGCGCGTCATA
523603 AATGTGTGTC
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
83 2 0.03
84 34 0.52
85 27 0.41
86 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTATTTAATGACGTGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCGCGTCATATATTTAT
Found at i:524030 original size:30 final size:30
Alignment explanation
Indices: 523996--524052 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
523986 AACAAGGTAA
* *
523996 TGTTCGCGTTCGTTTGTTTATTTTTTAAGG
1 TGTTCGCGTTCGTTTATTTATTGTTTAAGG
*
524026 TGTTCGTGTTCGTTTATTTATTGTTTA
1 TGTTCGCGTTCGTTTATTTATTGTTTA
524053 CGTACATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.11, C:0.09, G:0.21, T:0.60
Consensus pattern (30 bp):
TGTTCGCGTTCGTTTATTTATTGTTTAAGG
Found at i:524193 original size:22 final size:22
Alignment explanation
Indices: 524157--524204 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
524147 TTAGTCTTAA
*
524157 TTTAGTGTTCATTTAACGTTTG
1 TTTAGTGTTCATTTAACGTTCG
** *
524179 TTTAGTGTTTGTTTATCGTTCG
1 TTTAGTGTTCATTTAACGTTCG
524201 TTTA
1 TTTA
524205 TATGTTTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.15, C:0.08, G:0.19, T:0.58
Consensus pattern (22 bp):
TTTAGTGTTCATTTAACGTTCG
Found at i:529480 original size:22 final size:23
Alignment explanation
Indices: 529449--529492 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
529439 TTTTAATATC
529449 GTGTTCGTA-TTGTTTATTTATG
1 GTGTTCGTATTTGTTTATTTATG
*
529471 GTGTTTGTATTTGTTTATTTAT
1 GTGTTCGTATTTGTTTATTTAT
529493 TTTTTACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.14, C:0.02, G:0.20, T:0.64
Consensus pattern (23 bp):
GTGTTCGTATTTGTTTATTTATG
Found at i:532425 original size:20 final size:20
Alignment explanation
Indices: 532381--532507 Score: 75
Period size: 20 Copynumber: 6.4 Consensus size: 20
532371 GACCAACAAA
*
532381 TTCGCAACGCG-A-TCTCAAA
1 TTCGCAACGCGAATTC-CAAT
532400 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* * *
532420 TTCGCAAC-CCAGTTTCTAAT
1 TTCGCAACGCGA-ATTCCAAT
**
532440 TTCGCAACGCGAATATGTAA-
1 TTCGCAACGCGAAT-TCCAAT
* ** * *
532460 ATCGCATTGCGATTTTCCAAG
1 TTCGCAACGCGA-ATTCCAAT
*
532481 TTCGCAACGCGAATT-TAAT
1 TTCGCAACGCGAATTCCAAT
532500 TTCGCAAC
1 TTCGCAAC
532508 AGGTTTTAGT
Statistics
Matches: 82, Mismatches: 19, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
19 23 0.28
20 41 0.50
21 18 0.22
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:533442 original size:23 final size:24
Alignment explanation
Indices: 533412--533464 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
533402 GTATTCGAAA
533412 TTTGATCTTGGTCAATACTC-GAC
1 TTTGATCTTGGTCAATACTCGGAC
*
533435 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
533459 TTTGAT
1 TTTGAT
533465 GGTGTGATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:536354 original size:61 final size:63
Alignment explanation
Indices: 536223--536363 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 63
536213 TTTTAGAAAC
*
536223 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
536288 A
63 A
* * ** *
536289 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
536350 AACAAATCAACTTT
1 AACAAATCAACTTT
536364 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
60 4 0.06
61 35 0.51
62 3 0.04
66 26 0.38
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:540347 original size:21 final size:21
Alignment explanation
Indices: 540323--540363 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
540313 AGATAGACGG
*
540323 ATTTCGTTGGAAATGGGGACA
1 ATTTCGTCGGAAATGGGGACA
* *
540344 ATTTTGTCGGAGATGGGGAC
1 ATTTCGTCGGAAATGGGGAC
540364 GGATGTCGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.10, G:0.37, T:0.29
Consensus pattern (21 bp):
ATTTCGTCGGAAATGGGGACA
Found at i:540521 original size:20 final size:20
Alignment explanation
Indices: 540496--540622 Score: 173
Period size: 20 Copynumber: 6.2 Consensus size: 20
540486 ACGTAAAAAC
*
540496 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTCGCGA
* * *
540516 ATTTGACTTTCACGTTGCGA
1 ATTTGACTATCGCGTCGCGA
*
540536 ATTTAACTATCGCGTCGCGA
1 ATTTGACTATCGCGTCGCGA
540556 ATTTGACTATCGCGTCGCGA
1 ATTTGACTATCGCGTCGCGA
*
540576 ATTTGGAATATCGCGTCGCGA
1 ATTT-GACTATCGCGTCGCGA
*
540597 ATTTGGAATATCGCGTCGCGA
1 ATTT-GACTATCGCGTCGCGA
540618 ATTTG
1 ATTTG
540623 GAATATCGCA
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 58 0.59
21 40 0.41
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (20 bp):
ATTTGACTATCGCGTCGCGA
Found at i:540529 original size:41 final size:40
Alignment explanation
Indices: 540482--540563 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
540472 TAATATTGTG
* *
540482 TTTCACGTAAAAACATTTGACTATCGCGTTGCGAATTTGAC
1 TTTCACGTAAAAA-ATTTAACTATCGCGTCGCGAATTTGAC
****
540523 TTTCACGTTGCGAATTTAACTATCGCGTCGCGAATTTGAC
1 TTTCACGTAAAAAATTTAACTATCGCGTCGCGAATTTGAC
540563 T
1 T
540564 ATCGCGTCGC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
40 26 0.74
41 9 0.26
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (40 bp):
TTTCACGTAAAAAATTTAACTATCGCGTCGCGAATTTGAC
Found at i:540638 original size:21 final size:21
Alignment explanation
Indices: 540503--540631 Score: 167
Period size: 21 Copynumber: 6.3 Consensus size: 21
540493 AACATTTGAC
* *
540503 TATCGCGTTGCGAATTT-GAC
1 TATCGCGTCGCGAATTTGGAA
* * *
540523 TTTCACGTTGCGAATTT--AA
1 TATCGCGTCGCGAATTTGGAA
*
540542 CTATCGCGTCGCGAATTT-GAC
1 -TATCGCGTCGCGAATTTGGAA
540563 TATCGCGTCGCGAATTTGGAA
1 TATCGCGTCGCGAATTTGGAA
540584 TATCGCGTCGCGAATTTGGAA
1 TATCGCGTCGCGAATTTGGAA
540605 TATCGCGTCGCGAATTTGGAA
1 TATCGCGTCGCGAATTTGGAA
540626 TATCGC
1 TATCGC
540632 AATGCGATTT
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.01
20 46 0.47
21 51 0.52
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (21 bp):
TATCGCGTCGCGAATTTGGAA
Found at i:540652 original size:62 final size:61
Alignment explanation
Indices: 540543--540666 Score: 146
Period size: 62 Copynumber: 2.0 Consensus size: 61
540533 CGAATTTAAC
* * *
540543 TATCGCGTCGCGAATTTGACTATCGCGTCGCGAATTTGGAATATCGCGTCGCGAATTTGGAA
1 TATCGCGTCGCGAATTTGAATATCGCATCGCGAATTT-GAATATCGCGTCGCGAAATTGGAA
*
540605 TATCGCGTCGCGAATTTGGAATATCGCAAT-GCG-ATTT-ACATATTCGCGTTGCGAAATTGGAA
1 TATCGCGTCGCGAATTT-GAATATCGC-ATCGCGAATTTGA-ATA-TCGCGTCGCGAAATTGGAA
540667 ACTGGGTTGC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
60 1 0.02
61 3 0.06
62 38 0.70
63 11 0.20
64 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (61 bp):
TATCGCGTCGCGAATTTGAATATCGCATCGCGAATTTGAATATCGCGTCGCGAAATTGGAA
Found at i:540695 original size:20 final size:21
Alignment explanation
Indices: 540503--540703 Score: 148
Period size: 20 Copynumber: 9.9 Consensus size: 21
540493 AACATTTGAC
*
540503 TATCGCGTTGCGAATTTG-AC
1 TATCGCGTTGCGAATTTGAAA
* * *
540523 TTTCACGTTGCGAATTT-AAC
1 TATCGCGTTGCGAATTTGAAA
* *
540543 TATCGCGTCGCGAATTTG-AC
1 TATCGCGTTGCGAATTTGAAA
* *
540563 TATCGCGTCGCGAATTTGGAA
1 TATCGCGTTGCGAATTTGAAA
* *
540584 TATCGCGTCGCGAATTTGGAA
1 TATCGCGTTGCGAATTTGAAA
* *
540605 TATCGCGTCGCGAATTTGGAA
1 TATCGCGTTGCGAATTTGAAA
** *
540626 TATCGCAATGCG-ATTT-ACA
1 TATCGCGTTGCGAATTTGAAA
* *
540645 TATTCGCGTTGCGAAATTGGAA
1 TA-TCGCGTTGCGAATTTGAAA
* *
540667 -A-CTGGGTTGCGAAATTGAAA
1 TATC-GCGTTGCGAATTTGAAA
*
540687 T-TCGCGTTGTGAATTTG
1 TATCGCGTTGCGAATTTG
540704 TTGGTCATTT
Statistics
Matches: 151, Mismatches: 21, Indels: 18
0.79 0.11 0.09
Matches are distributed among these distances:
19 4 0.03
20 89 0.59
21 57 0.38
22 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (21 bp):
TATCGCGTTGCGAATTTGAAA
Found at i:541358 original size:60 final size:60
Alignment explanation
Indices: 541260--541387 Score: 172
Period size: 60 Copynumber: 2.1 Consensus size: 60
541250 CACATGTCCT
* * *
541260 CAAATTATGATACTCATTGTAAATTAGTCCCTAAAC-TTTT-AAACATTTCAATACCATCCC
1 CAAACTATGATACTCATTCTAAATTAGTCCCCAAACTTTTTGAAA-ATTTCAATACCAT-CC
*
541320 CAAACTATGAT-CTTCATTCTAAATTAGTCCCCAAACTTTTTGAAAATTTCAATTCCATCC
1 CAAACTATGATAC-TCATTCTAAATTAGTCCCCAAACTTTTTGAAAATTTCAATACCATCC
541380 CAAACTAT
1 CAAACTAT
541388 ACGTACATAC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
59 1 0.02
60 41 0.67
61 16 0.26
62 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (60 bp):
CAAACTATGATACTCATTCTAAATTAGTCCCCAAACTTTTTGAAAATTTCAATACCATCC
Found at i:541582 original size:58 final size:59
Alignment explanation
Indices: 541509--541692 Score: 219
Period size: 60 Copynumber: 3.1 Consensus size: 59
541499 TTTGGATGAA
* * *
541509 TTTGAAGATAAAATTGGAAGATTCAAAAGTTTGGAGAACAATTTAAAATGAGGGTCAT-G
1 TTTGAGGATAAAATTGGAATATTCAAAAGTTT-AAGAACAATTTAAAATGAGGGTCATAG
* * * * * **
541568 -TTGGGGATAAAATTGGAATATTCAAAATTTTAAGTACTAATTTTAAATAAGACTCATAG
1 TTTGAGGATAAAATTGGAATATTCAAAAGTTTAAGAAC-AATTTAAAATGAGGGTCATAG
* *
541627 TTTGAGGATGAAATTTGAATATTCAAAAGTTTAAGAACCAATTTAAAATGAGGGTCATAG
1 TTTGAGGATAAAATTGGAATATTCAAAAGTTTAAGAA-CAATTTAAAATGAGGGTCATAG
541687 TTTGAG
1 TTTGAG
541693 AATGCAATTA
Statistics
Matches: 102, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
57 4 0.04
58 42 0.41
59 1 0.01
60 54 0.53
61 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (59 bp):
TTTGAGGATAAAATTGGAATATTCAAAAGTTTAAGAACAATTTAAAATGAGGGTCATAG
Found at i:542795 original size:6 final size:6
Alignment explanation
Indices: 542784--542809 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
542774 TTCAAGCTCG
542784 AACTCA AACTCA AACTCA AACTCA AA
1 AACTCA AACTCA AACTCA AACTCA AA
542810 TTTGAACCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (6 bp):
AACTCA
Found at i:548542 original size:42 final size:45
Alignment explanation
Indices: 548476--548573 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 45
548466 TTTAATTATA
*
548476 AAAATATAA-AAATTATTATAAAATATATTATTTTAA-CA-TTTT
1 AAAATATAATAAATGATTATAAAATATATTATTTTAATCATTTTT
*
548518 AAAATATAATAAATGATTAT-AAATATATTATTTTAATTATTTTT
1 AAAATATAATAAATGATTATAAAATATATTATTTTAATCATTTTT
548562 AAAATATTAATA
1 AAAATA-TAATA
548574 TATTCGGGTC
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
42 25 0.50
43 10 0.20
44 10 0.20
45 5 0.10
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (45 bp):
AAAATATAATAAATGATTATAAAATATATTATTTTAATCATTTTT
Found at i:555132 original size:55 final size:55
Alignment explanation
Indices: 555075--555535 Score: 531
Period size: 55 Copynumber: 8.5 Consensus size: 55
555065 TGACGAGCCT
* * *
555075 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCT
1 GCTCTCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGTGTCC
* * * *
555130 GCTCTCTATTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAAAAAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTC-ATAAAACGTGTCC
555186 GCTCTCTATTCCTTCAGAGAGTATAGAACTC-AGA-AATCTTCA-ATAAACAG-GTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGA-ACAATCTTCATA-AAAC-GTGTCC
* * * * *
555240 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTTA-ACAAACGTGTAC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGTGTCC
* * *
555291 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGAGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCC
555346 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGTGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGTGTCC
*
555401 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACAG-GTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAAC-GTGTCC
* * *
555456 GCTCTCTATTGCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACGAACTTGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGTGTCC
555511 GCTC-CTTATTCCTTCAGAGAGTATA
1 GCTCTC-TATTCCTTCAGAGAGTATA
555536 TGACTCAATC
Statistics
Matches: 358, Mismatches: 29, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
50 1 0.00
51 43 0.12
53 1 0.00
54 38 0.11
55 234 0.65
56 40 0.11
57 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (55 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCC
Found at i:555452 original size:216 final size:217
Alignment explanation
Indices: 555075--555541 Score: 644
Period size: 216 Copynumber: 2.1 Consensus size: 217
555065 TGACGAGCCT
* * *
555075 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTAT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCATAAAACGAGTCCGCTCTCTAT
*
555139 TCATTCAGAGAGTATAAGACTTGAACAATCTTCAAAAAAACGGGTCCGCTCTCTATTCCTTCAGA
65 TCATTCAGAGAGTATAAGACTCGAACAATCTTCAAAAAAACGGGTCCGCTCTCTATTCCTTCAGA
*
555204 GAGTATAGAACTCAGAAATCTTCAATAAACAGGTCCGCTCCCTATT-CTTTCAGAGAGTATAGGA
130 GAGTATAGAACTCAGAAATCTTCAATAAACAGGTCCGCTCCCTATTGC-TTCAGAGAGTATAGAA
*
555268 CT-CAATCTTTAACAAACGTGTAC
194 CTACAATCTTCAACAAACGTGTAC
*
555291 GCTCCCTATTCCTTCAGAGAGTAT-AGAACTCGAGCAATCTTCATAAAACGAGTCCGCTCTCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCATAAAACGAGTCCGCTCTCTAT
* * *
555355 TCCTTCAGAGAGTAT-AGAACTCGAACAATCTTC-AACAAACGTGTCCGCTCTCTATTCCTTCAG
65 TCATTCAGAGAGTATAAG-ACTCGAACAATCTTCAAAAAAACGGGTCCGCTCTCTATTCCTTCAG
*
555418 AGAGTATAGAACTC-GAACAATCTTC-ATGAAACAGGTCCGCTCTCTATTGCTTCAGAGAGTATA
129 AGAGTATAGAACTCAG-A-AATCTTCAAT-AAACAGGTCCGCTCCCTATTGCTTCAGAGAGTATA
* * *
555481 GAACTCGAACAATCTTCAACGAACTTGTCC
191 GAACT---ACAATCTTCAACAAACGTGTAC
* *
555511 GCTCCTTATTCCTTCAGAGAGTATATGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
555542 AATCTTCAAC
Statistics
Matches: 223, Mismatches: 16, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
214 1 0.00
215 49 0.22
216 126 0.57
217 2 0.01
220 44 0.20
221 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (217 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAACGAGTCCGCTCTCTATT
CATTCAGAGAGTATAAGACTCGAACAATCTTCAAAAAAACGGGTCCGCTCTCTATTCCTTCAGAG
AGTATAGAACTCAGAAATCTTCAATAAACAGGTCCGCTCCCTATTGCTTCAGAGAGTATAGAACT
ACAATCTTCAACAAACGTGTAC
Found at i:556923 original size:11 final size:11
Alignment explanation
Indices: 556909--556933 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
556899 TTTATTTCTC
556909 TTTTTTTCATT
1 TTTTTTTCATT
556920 TTTTTTTCATT
1 TTTTTTTCATT
556931 TTT
1 TTT
556934 CATTTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTCATT
Found at i:556934 original size:18 final size:17
Alignment explanation
Indices: 556911--556969 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
556901 TATTTCTCTT
556911 TTTTTCATTTTTTTTTC
1 TTTTTCATTTTTTTTTC
*
556928 ATTTTTCATTTTTTCTTCCC
1 -TTTTTCATTTTTT-TT-TC
* *
556948 TTTTCCATTTTTTCTTC
1 TTTTTCATTTTTTTTTC
556965 TTTTT
1 TTTTT
556970 TTTCTTTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 5 0.15
18 14 0.41
19 14 0.41
20 1 0.03
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCATTTTTTTTTC
Found at i:556970 original size:19 final size:19
Alignment explanation
Indices: 556903--557015 Score: 87
Period size: 19 Copynumber: 6.2 Consensus size: 19
556893 CCTCCTTTTA
*
556903 TTTC-TCTTTTTTTCATTT
1 TTTCTTCTTTTTTCCATTT
* *
556921 TTTTTTCATTTTT-CATTT
1 TTTCTTCTTTTTTCCATTT
**
556939 TTTCTTCCCTTTTCCATTT
1 TTTCTTCTTTTTTCCATTT
556958 TTTCTTCTTTTTT---TTCT
1 TTTCTTCTTTTTTCCATT-T
* **
556975 TTTCGT-TTTTTTCCATCA
1 TTTCTTCTTTTTTCCATTT
556993 TTT-TTCTTTTTTCTCATTT
1 TTTCTTCTTTTTTC-CATTT
557012 TTTC
1 TTTC
557016 ATTTTTTCTC
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
16 8 0.11
17 7 0.10
18 28 0.38
19 30 0.41
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.73
Consensus pattern (19 bp):
TTTCTTCTTTTTTCCATTT
Found at i:556976 original size:26 final size:27
Alignment explanation
Indices: 556929--557029 Score: 81
Period size: 28 Copynumber: 3.9 Consensus size: 27
556919 TTTTTTTTCA
556929 TTTTTCAT--TTTTTCTTCCCTTTTCCAT
1 TTTTTCATCATTTTTCTT--CTTTTCCAT
* * **
556956 TTTTTCTTC-TTTTTTTTCTTTTCGTT
1 TTTTTCATCATTTTTCTTCTTTTCCAT
556982 TTTTTCCATCATTTTTCTT-TTTTCTCAT
1 TTTTT-CATCATTTTTCTTCTTTTC-CAT
557010 TTTTTCAT--TTTTTC-TCTTTT
1 TTTTTCATCATTTTTCTTCTTTT
557030 ATTTCTTCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
24 1 0.02
25 10 0.16
26 12 0.20
27 18 0.30
28 20 0.33
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (27 bp):
TTTTTCATCATTTTTCTTCTTTTCCAT
Found at i:557024 original size:18 final size:18
Alignment explanation
Indices: 556903--557029 Score: 62
Period size: 19 Copynumber: 6.6 Consensus size: 18
556893 CCTCCTTTTA
*
556903 TTTCTCTTTTTTTCATTTT
1 TTTCTCATTTTTTCA-TTT
*
556922 TTTTTCA-TTTTTCATTT
1 TTTCTCATTTTTTCATTT
** *
556939 TTTCTTCCCTTTTCCATTT
1 TTTC-TCATTTTTTCATTT
* *
556958 TTTCTTCTTTTTTTTCTTTTCGTT
1 TTTC-TC-ATTTTTTC--AT--TT
*
556982 TTTTTCCATCATTTTTC-TTT
1 TTTCT-CAT--TTTTTCATTT
557002 TTTCTCATTTTTTCATTT
1 TTTCTCATTTTTTCATTT
557020 TTTCTC-TTTT
1 TTTCTCATTTT
557030 ATTTCTTCTT
Statistics
Matches: 85, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
17 16 0.19
18 18 0.21
19 24 0.28
20 11 0.13
22 2 0.02
23 2 0.02
24 6 0.07
25 6 0.07
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (18 bp):
TTTCTCATTTTTTCATTT
Found at i:557036 original size:9 final size:8
Alignment explanation
Indices: 556907--557036 Score: 57
Period size: 9 Copynumber: 14.5 Consensus size: 8
556897 CTTTTATTTC
556907 TCTTTTTT
1 TCTTTTTT
556915 TCATTTTTT
1 TC-TTTTTT
556924 T-TTCATTTT
1 TCTT--TTTT
*
556933 TCATTTTT
1 TCTTTTTT
556941 TCTTCCCTTTT
1 TCTT---TTTT
* *
556952 CCATTTTT
1 TCTTTTTT
556960 TCTTCTTTT
1 TCTT-TTTT
556969 T-TTTCTTT
1 TCTTT-TTT
556977 TCGTTTTTT
1 TC-TTTTTT
*
556986 TCCATCATTTT
1 T-C-T-TTTTT
556997 TCTTTTTT
1 TCTTTTTT
*
557005 CTCATTTTT
1 -TCTTTTTT
557014 TCATTTTTT
1 TC-TTTTTT
557023 CTCTTTTATT
1 -TCTTTT-TT
557033 TCTT
1 TCTT
557037 CTTCAAGCAA
Statistics
Matches: 94, Mismatches: 11, Indels: 33
0.68 0.08 0.24
Matches are distributed among these distances:
7 3 0.03
8 27 0.29
9 42 0.45
10 11 0.12
11 11 0.12
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (8 bp):
TCTTTTTT
Found at i:566350 original size:45 final size:46
Alignment explanation
Indices: 566283--566385 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 46
566273 TATTATCCAC
* *
566283 AAAAAGAAATCCTAACCTCATGATATCTAATTCGCATG-TTTATTC-
1 AAAAA-AAAACCTAACCGCATGATATCTAATTCGCATGATTTATTCG
*
566328 AAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAAA-AAACCTAACCGCATGATATCTAATTCGCATG-ATTTATTCG
566376 AAAAAAAAAC
1 AAAAAAAAAC
566386 GAAATAAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
44 1 0.02
45 33 0.65
47 11 0.22
48 6 0.12
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (46 bp):
AAAAAAAAACCTAACCGCATGATATCTAATTCGCATGATTTATTCG
Found at i:573261 original size:18 final size:17
Alignment explanation
Indices: 573234--573295 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 17
573224 ATTCTAAATG
573234 TTTACAATTATCAGATGA
1 TTTACAATTATCAGAT-A
*
573252 TTTTCAATTATCAGATA
1 TTTACAATTATCAGATA
*
573269 TTTACAA-TATCATAGT-
1 TTTACAATTATCAGA-TA
573285 TTTACAATTAT
1 TTTACAATTAT
573296 AAGACACAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
16 13 0.33
17 11 0.28
18 15 0.38
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.45
Consensus pattern (17 bp):
TTTACAATTATCAGATA
Found at i:579135 original size:13 final size:13
Alignment explanation
Indices: 579117--579150 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
579107 AATGGATAAT
579117 TTTGAAAACTAA-G
1 TTTGAAAAC-AAGG
579130 TTTGAAAACAAGG
1 TTTGAAAACAAGG
579143 TTTGAAAA
1 TTTGAAAA
579151 TCAATATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:579648 original size:22 final size:22
Alignment explanation
Indices: 579623--579677 Score: 92
Period size: 23 Copynumber: 2.5 Consensus size: 22
579613 TATCGGTTCC
579623 CTCAAGGGGGAATCGGTACCCA
1 CTCAAGGGGGAATCGGTACCCA
579645 CTCAAAGGGGGAATCGGTACCCA
1 CTC-AAGGGGGAATCGGTACCCA
*
579668 TTCAAGGGGG
1 CTCAAGGGGG
579678 GTATCGATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.27, C:0.24, G:0.35, T:0.15
Consensus pattern (22 bp):
CTCAAGGGGGAATCGGTACCCA
Found at i:579656 original size:23 final size:23
Alignment explanation
Indices: 579626--579683 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
579616 CGGTTCCCTC
579626 AAGGGGGAATCGGTACCCACTCA
1 AAGGGGGAATCGGTACCCACTCA
*
579649 AAGGGGGAATCGGTACCCATTCA
1 AAGGGGGAATCGGTACCCACTCA
* *
579672 AGGGGGGTATCG
1 AAGGGGGAATCG
579684 ATTCCTAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.36, T:0.16
Consensus pattern (23 bp):
AAGGGGGAATCGGTACCCACTCA
Found at i:585248 original size:21 final size:21
Alignment explanation
Indices: 585196--585248 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
585186 TAGAGCGTGG
*
585196 GGGGAATCGGAAACCCCTCAT
1 GGGGAATCGGTAACCCCTCAT
585217 GGGGAATCGGTAACCCCTCAAT
1 GGGGAATCGGTAACCCCTC-AT
585239 -GGGAATCGGT
1 GGGGAATCGGT
585249 TCCTGTAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.26, C:0.25, G:0.32, T:0.17
Consensus pattern (21 bp):
GGGGAATCGGTAACCCCTCAT
Found at i:587004 original size:15 final size:16
Alignment explanation
Indices: 586986--587015 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
586976 TTTTACTTTG
586986 AGATATTTT-AATGGA
1 AGATATTTTCAATGGA
587001 AGATATTTTCAATGG
1 AGATATTTTCAATGG
587016 CAAGTGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (16 bp):
AGATATTTTCAATGGA
Found at i:599161 original size:193 final size:193
Alignment explanation
Indices: 598832--599224 Score: 723
Period size: 193 Copynumber: 2.0 Consensus size: 193
598822 CAGGTACCAC
598832 TATGAATAATAACATTACTAGCTTTAATCAGCTGGTAACTGATCTGATGAATATGGACGTGACTT
1 TATGAATAATAACATTACTAGCTTTAATCAGCTGGTAACTGATCTGATGAATATGGACGTGACTT
*
598897 TTGAAGATGAAGATCTGGCTCTGATGTTGATGGGATCACTTCCTGATGAGTTTGAGTATCTTAAA
66 TTGAAGACGAAGATCTGGCTCTGATGTTGATGGGATCACTTCCTGATGAGTTTGAGTATCTTAAA
*
598962 ACTACTCTACTTCATGGGAAAGTTGATGTGTCTCTCAGTGAAGTAACTGCTGCCTTGTATAGT
131 ACTACTCTACTTCATGGGAAAGTTGATGTGTCTCTCAGTGAAGTAACTACTGCCTTGTATAGT
* *
599025 TATGAATGATCACATTACTAGCTTTAATCAGCTGGTAACTGATCTGATGAATATGGACGTGACTT
1 TATGAATAATAACATTACTAGCTTTAATCAGCTGGTAACTGATCTGATGAATATGGACGTGACTT
*
599090 TTGAAGACGAAGATCTGGCTCTGATGTTGATGGGATCACTTCCTGATGAGTTTGAGTATCTTGAA
66 TTGAAGACGAAGATCTGGCTCTGATGTTGATGGGATCACTTCCTGATGAGTTTGAGTATCTTAAA
* *
599155 ACTACTCTACTTCATGGGAAAGTTGATGTGTCTCTCAGTGAAGTGACTACTGCCTTGTATTGT
131 ACTACTCTACTTCATGGGAAAGTTGATGTGTCTCTCAGTGAAGTAACTACTGCCTTGTATAGT
599218 TATGAAT
1 TATGAAT
599225 TGAGAAATAA
Statistics
Matches: 193, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
193 193 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (193 bp):
TATGAATAATAACATTACTAGCTTTAATCAGCTGGTAACTGATCTGATGAATATGGACGTGACTT
TTGAAGACGAAGATCTGGCTCTGATGTTGATGGGATCACTTCCTGATGAGTTTGAGTATCTTAAA
ACTACTCTACTTCATGGGAAAGTTGATGTGTCTCTCAGTGAAGTAACTACTGCCTTGTATAGT
Found at i:616113 original size:18 final size:18
Alignment explanation
Indices: 616090--616132 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
616080 GTTGTTTTTA
* *
616090 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
616108 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
616126 AAATAAA
1 AAATAAA
616133 TAATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:618155 original size:62 final size:62
Alignment explanation
Indices: 618057--618179 Score: 219
Period size: 62 Copynumber: 2.0 Consensus size: 62
618047 GTAAATCAGA
*
618057 ATGAACAAAAAATAAAATTTTCTAACCCCCTGATTTCCTCATTGTAGTCTTCTAACTCCCTT
1 ATGAACAAAAAATAAAATTTTCTAACCCCCTAATTTCCTCATTGTAGTCTTCTAACTCCCTT
* *
618119 ATGAACAAAAAATTAAATTTTCTAACCCTCTAATTTCCTCATTGTAGTCTTCTAACTCCCT
1 ATGAACAAAAAATAAAATTTTCTAACCCCCTAATTTCCTCATTGTAGTCTTCTAACTCCCT
618180 GCATATATCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.37
Consensus pattern (62 bp):
ATGAACAAAAAATAAAATTTTCTAACCCCCTAATTTCCTCATTGTAGTCTTCTAACTCCCTT
Found at i:618808 original size:20 final size:20
Alignment explanation
Indices: 618783--618820 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
618773 TTTGGTTCAC
*
618783 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
618803 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
618821 GGAATAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:618823 original size:18 final size:19
Alignment explanation
Indices: 618783--618827 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
618773 TTTGGTTCAC
*
618783 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
618803 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
618821 GGAATAA
1 GGAATAA
618828 GATTACTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
20 16 0.67
ACGTcount: A:0.47, C:0.09, G:0.24, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:618840 original size:15 final size:16
Alignment explanation
Indices: 618788--618833 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 16
618778 TTCACGGAAT
618788 ATAAGATTACCAGTGGGA
1 ATAAGATTACCA--GGGA
618806 ATAAAAGATTACCAGGGA
1 AT--AAGATTACCAGGGA
618824 ATAAGATTAC
1 ATAAGATTAC
618834 TGGGAATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.31
18 8 0.31
20 10 0.38
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (16 bp):
ATAAGATTACCAGGGA
Found at i:621310 original size:22 final size:22
Alignment explanation
Indices: 621282--621357 Score: 134
Period size: 22 Copynumber: 3.5 Consensus size: 22
621272 TTTAGAAAAG
* *
621282 GATAAGATAAGGTAAATTTTTA
1 GATAAGATTAGGTAAAGTTTTA
621304 GATAAGATTAGGTAAAGTTTTA
1 GATAAGATTAGGTAAAGTTTTA
621326 GATAAGATTAGGTAAAGTTTTA
1 GATAAGATTAGGTAAAGTTTTA
621348 GATAAGATTA
1 GATAAGATTA
621358 AATAGGGGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (22 bp):
GATAAGATTAGGTAAAGTTTTA
Found at i:623528 original size:3 final size:3
Alignment explanation
Indices: 623520--623594 Score: 107
Period size: 3 Copynumber: 24.7 Consensus size: 3
623510 CTCCATTTTC
623520 TAT TAT TAT TATT TAT TAT TAT TAT TAT TA- TAT ATAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* *
623566 TAT TAT TAT TAT TAA AAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
623595 CAAACAGGCC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 2 0.03
3 57 0.88
4 6 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:625094 original size:15 final size:18
Alignment explanation
Indices: 625060--625098 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 18
625050 TGTTTTCTGA
625060 TATTTTTACTAAATATCC
1 TATTTTTACTAAATATCC
625078 TATTTTTA-T-AA-ATCC
1 TATTTTTACTAAATATCC
625093 TATTTT
1 TATTTT
625099 AAATAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 2 0.10
17 1 0.05
18 8 0.38
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTTACTAAATATCC
Found at i:625733 original size:26 final size:25
Alignment explanation
Indices: 625687--625750 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
625677 CATATATTTA
*
625687 ATTTATA-ATTCATTCTTTTCAAAAT
1 ATTTATATATT-ATTATTTTCAAAAT
* * *
625712 TTTTATATACTTATTATTTTCATAGT
1 ATTTATATA-TTATTATTTTCAAAAT
625738 ATTTATATATTAT
1 ATTTATATATTAT
625751 CTTATTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
25 10 0.31
26 20 0.62
27 2 0.06
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTATATATTATTATTTTCAAAAT
Found at i:627363 original size:14 final size:14
Alignment explanation
Indices: 627325--627378 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
627315 ATTTTAAATA
*
627325 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
627339 TTTTACATTTGCAT
1 ATTTACATTTGCAT
627353 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
627368 CTTTGCATTTG
1 ATTTACATTTG
627379 TATTTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:630698 original size:22 final size:22
Alignment explanation
Indices: 630670--630712 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
630660 TCCAGCAAAG
630670 AAAGAAGAAAAAAAAAGAAAAA
1 AAAGAAGAAAAAAAAAGAAAAA
* *
630692 AAAGAAGAAGAAAAAGGAAAA
1 AAAGAAGAAAAAAAAAGAAAA
630713 TTGAATCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAGAAGAAAAAAAAAGAAAAA
Found at i:633131 original size:115 final size:115
Alignment explanation
Indices: 632920--633138 Score: 357
Period size: 115 Copynumber: 1.9 Consensus size: 115
632910 CATTATCGTG
* * * * *
632920 GTAGGAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAATTATCTGATCTGGTTCGG
* * *
632985 TATGAACCCTAAAACCAATCATTGGATTTGAAAGATGAATATTGCTCATA
66 TAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATATTGCTCATA
633035 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAATTATCTGATCTGGTTCGG
1 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAATTATCTGATCTGGTTCGG
*
633100 TAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 TAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
633139 CTTCATGATC
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 95 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (115 bp):
GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAATTATCTGATCTGGTTCGG
TAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATATTGCTCATA
Found at i:634486 original size:191 final size:192
Alignment explanation
Indices: 634048--634475 Score: 786
Period size: 192 Copynumber: 2.2 Consensus size: 192
634038 AAGATCTATA
*
634048 TGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTAT
1 TGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTAT
*
634113 TAGCAAATGTTGGGGCATATCGAAAGCCCATTTCAGACAGAAATTATTCACGTGGGGCATTCTGA
66 TAGCAAATGTTGGGGCATATCGAAAGCCCATTTCAGACAGAAATGATTCACGTGGGGCATTCTGA
*
634178 GGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCATATCAACAATAAGCAAATGT
131 GGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCATATCAACAAGAAGCAAATGT
634240 TGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTAT
1 TGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTAT
*
634305 TAGCAAATGTTGGGGCATATCTAAAGCCCATTTCAGACAGAAATGATTCACGT-GGGCATTCTGA
66 TAGCAAATGTTGGGGCATATCGAAAGCCCATTTCAGACAGAAATGATTCACGTGGGGCATTCTGA
634369 GGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCATATCAACAAGAAGCAAATGT
131 GGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCATATCAACAAGAAGCAAATGT
* * *
634431 TGGGGTATGCTGAAAACCCATTTCAATCATAATCAGGAATATTGA
1 TGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTGA
634476 CGCGTTTTGA
Statistics
Matches: 229, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
191 114 0.50
192 115 0.50
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (192 bp):
TGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTAT
TAGCAAATGTTGGGGCATATCGAAAGCCCATTTCAGACAGAAATGATTCACGTGGGGCATTCTGA
GGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCATATCAACAAGAAGCAAATGT
Found at i:634505 original size:191 final size:192
Alignment explanation
Indices: 634048--634528 Score: 678
Period size: 191 Copynumber: 2.5 Consensus size: 192
634038 AAGATCTATA
* * * * * ***
634048 TGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTAT
1 TGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGGAATATTGACACATTTTGAACATTCACAT
* * * *
634113 TAGCAAATGTTGGGGCATATCGAAAGCCCATTTCAGACAGAAATTATTCACGTGGGGCATTCTGA
66 CAACAAATGTTGGGGCATATCTAAAGCCCATTTCAGACAGAAATGATTCACGTGGGGCATTCTGA
*
634178 GGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCATATCAACAATAAGCAAATGT
131 GGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCATATCAACAAGAAGCAAATGT
* * * * ***
634240 TGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTAT
1 TGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGGAATATTGACACATTTTGAACATTCACAT
* *
634305 TAGCAAATGTTGGGGCATATCTAAAGCCCATTTCAGACAGAAATGATTCACGT-GGGCATTCTGA
66 CAACAAATGTTGGGGCATATCTAAAGCCCATTTCAGACAGAAATGATTCACGTGGGGCATTCTGA
634369 GGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCATATCAACAAGAAGCAAATGT
131 GGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCATATCAACAAGAAGCAAATGT
* * * * * *
634431 TGGGGTATGCTGAAAACCCATTTCAATCATAATCAGGAATATTGACGCGTTTTGAATATTCACGT
1 TGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGGAATATTGACACATTTTGAACATTCACAT
*
634496 CAACAAATGTTGGGGCAT-GCTGAAAGCCCATTT
66 CAACAAATGTTGGGGCATATCT-AAAGCCCATTT
634529 TAATCAGAAA
Statistics
Matches: 268, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
190 2 0.01
191 151 0.56
192 115 0.43
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (192 bp):
TGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGGAATATTGACACATTTTGAACATTCACAT
CAACAAATGTTGGGGCATATCTAAAGCCCATTTCAGACAGAAATGATTCACGTGGGGCATTCTGA
GGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCATATCAACAAGAAGCAAATGT
Found at i:635503 original size:54 final size:54
Alignment explanation
Indices: 635411--635643 Score: 313
Period size: 54 Copynumber: 4.3 Consensus size: 54
635401 GTGACATCAT
* * * * * *
635411 TCAAAAGCTTTATGAACATCTGAGCAGAAGCCATAGAAAAGGATGAATATGTTG
1 TCAAACGCTTTACGAACATATGAGCAGAAACCACAGAAAAGGATGAATGTGTTG
* *
635465 TCAAACGCTTTACGAACATATGAGCAAAAACCACAGAAAATGATGAATGTGTTG
1 TCAAACGCTTTACGAACATATGAGCAGAAACCACAGAAAAGGATGAATGTGTTG
* *
635519 TCAAACGCTTTACGAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTG
1 TCAAACGCTTTACGAACATATGAGCAGAAACCACAGAAAAGGATGAATGTGTTG
* * * * *
635573 TCAAATGTTTTACGAACATATGAGCAGAAGCCACAGGAAAGGATGAATGTGCTG
1 TCAAACGCTTTACGAACATATGAGCAGAAACCACAGAAAAGGATGAATGTGTTG
* *
635627 TCAAATGTTTTACGAAC
1 TCAAACGCTTTACGAAC
635644 CTGCTATTCT
Statistics
Matches: 162, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 162 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (54 bp):
TCAAACGCTTTACGAACATATGAGCAGAAACCACAGAAAAGGATGAATGTGTTG
Found at i:636041 original size:22 final size:22
Alignment explanation
Indices: 636010--636064 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
636000 ATCTACACTC
*
636010 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
636032 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
636054 TTCAAAGATGA
1 TTCAAAGATGA
636065 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:636637 original size:101 final size:100
Alignment explanation
Indices: 636484--636791 Score: 422
Period size: 101 Copynumber: 3.0 Consensus size: 100
636474 CATTCAATGG
636484 ATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAGCATT-CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
636549 AATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
636585 ATCAGCAATTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAGC-ATTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
636650 AATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* *
636686 ATCATTCGATGGAT-CAGTGTTGCCAGAAGGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAG
1 ATCA-GC-AT---TCCAG-G-T--C-G-A-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
*
636749 AAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTGA
54 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
636792 CTCTATCACA
Statistics
Matches: 186, Mismatches: 9, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
101 98 0.53
102 6 0.03
104 3 0.02
105 2 0.01
106 1 0.01
108 1 0.01
109 1 0.01
110 47 0.25
111 27 0.15
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (100 bp):
ATCAGCATTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
Found at i:636884 original size:40 final size:40
Alignment explanation
Indices: 636839--636933 Score: 163
Period size: 40 Copynumber: 2.4 Consensus size: 40
636829 CCAGTTAGAG
*
636839 TTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAA
1 TTCATAATGAGAAGAACTCATCTAAAGAAAGAAGAAGAAA
* *
636879 TTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
1 TTCATAATGAGAAGAACTCATCTAAAGAAAGAAGAAGAAA
636919 TTCATAATGAGAAGA
1 TTCATAATGAGAAGA
636934 GCTTGTTCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (40 bp):
TTCATAATGAGAAGAACTCATCTAAAGAAAGAAGAAGAAA
Found at i:636935 original size:164 final size:162
Alignment explanation
Indices: 636715--637059 Score: 494
Period size: 164 Copynumber: 2.1 Consensus size: 162
636705 TTGCCAGAAG
* *
636715 GTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA
* * * * * * ** *
636780 CCTTTTGCTTGACTCTATCACATAAGAAGATAGATCAGCATTAACATTGCCAGTTAGAGTTCATA
66 CCTTTTGCATAACTCTATCACAAAAGAAGATAGATCAACATCAACATTGACAGAGAAAGTTCATA
*
636845 ATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAA
131 ATAAGAAGAACTCATCTAAAG-AGGAAGAA-AAA
636879 -TTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * * * *
636943 ACCTTTTGCATAACTCTATCATAAAAGGAGATAGATCAATATCAACTTTTACAGAGAAAGTTCAT
65 ACCTTTTGCATAACTCTATCACAAAAGAAGATAGATCAACATCAACATTGACAGAGAAAGTTCAT
*
637008 AATAAGAAGAACTCATCTGAAGAGGAAGAAAAA
130 AATAAGAAGAACTCATCTAAAGAGGAAGAAAAA
637041 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
637060 TGTTCAACCT
Statistics
Matches: 161, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
162 3 0.02
163 52 0.32
164 106 0.66
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (162 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA
CCTTTTGCATAACTCTATCACAAAAGAAGATAGATCAACATCAACATTGACAGAGAAAGTTCATA
ATAAGAAGAACTCATCTAAAGAGGAAGAAAAA
Found at i:637147 original size:123 final size:123
Alignment explanation
Indices: 636874--637119 Score: 311
Period size: 123 Copynumber: 2.0 Consensus size: 123
636864 AGAAGGAAGA
* * * *
636874 AGAAATTCATAATG-AGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTT
1 AGAAAGTCATAA-GAAGAAGAAATCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGAAGAACTT
* * * *
636938 GTTCAACCTTTTGCATAACTCTATCATAAAAGGAGATAGATCAATATCAACTTTTACAG
65 GTTCAACCTTTTGCATAACTCTATCACAAAAGAAGATAGATCAACATCAACATTTACAG
* * *
636997 AGAAAGTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGAAAAAGTTCATAATGAGAAGAACTT
1 AGAAAG-TCATAAGAAGAAGAAATCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGAAGAACTT
* * *
637061 GTTCAACC-TTTGCATAACTCTATCACAGAAA-AAGATAGGTCAGCATCAACATTTCCAG
65 GTTCAACCTTTTGCATAACTCTATCACA-AAAGAAGATAGATCAACATCAACATTTACAG
637119 A
1 A
637120 TTACATCACA
Statistics
Matches: 108, Mismatches: 12, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
122 40 0.37
123 44 0.41
124 24 0.22
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (123 bp):
AGAAAGTCATAAGAAGAAGAAATCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGCATAACTCTATCACAAAAGAAGATAGATCAACATCAACATTTACAG
Found at i:637347 original size:3 final size:3
Alignment explanation
Indices: 637341--637424 Score: 109
Period size: 3 Copynumber: 27.7 Consensus size: 3
637331 CTCCATTTTC
637341 TAT TAT TAT TATT TAT TAT TAT TAT TAT T-T TAT ATAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* *
637387 TAT TAT T-T TATT TAT TAT TAT TAA AAT TAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA
637425 CAAACAGGCC
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
2 4 0.06
3 59 0.82
4 9 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:638841 original size:15 final size:15
Alignment explanation
Indices: 638821--638859 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
638811 TTATTTTATT
638821 ATTATTATTGCTTTA
1 ATTATTATTGCTTTA
638836 ATTATTATTGCTTTA
1 ATTATTATTGCTTTA
638851 ATTATTATT
1 ATTATTATT
638860 TCATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (15 bp):
ATTATTATTGCTTTA
Found at i:638841 original size:18 final size:17
Alignment explanation
Indices: 638815--638871 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 17
638805 ACAATATTAT
638815 TTTATTATTATTATTGC
1 TTTATTATTATTATTGC
638832 TTTA--ATTATTATTGC
1 TTTATTATTATTATTGC
*
638847 TTTA--ATTATTATTTC
1 TTTATTATTATTATTGC
*
638862 ATTATTATTA
1 TTTATTATTA
638872 ATTTTATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
15 28 0.78
17 8 0.22
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTATTATTATTATTGC
Found at i:638843 original size:41 final size:43
Alignment explanation
Indices: 638791--638871 Score: 103
Period size: 44 Copynumber: 1.9 Consensus size: 43
638781 TTCCTTTTAT
*
638791 TTTAATCATTATT-TACAA-TATTATTTTATTATTATTATTGC
1 TTTAATCATTATTCTACAATTATTATTTCATTATTATTATTGC
* **
638832 TTTAATTATTATTGCTTTAATTATTATTTCATTATTATTA
1 TTTAATCATTATT-CTACAATTATTATTTCATTATTATTA
638872 ATTTTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 12 0.36
43 3 0.09
44 18 0.55
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (43 bp):
TTTAATCATTATTCTACAATTATTATTTCATTATTATTATTGC
Found at i:638880 original size:26 final size:27
Alignment explanation
Indices: 638810--638882 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
638800 TATTTACAAT
*
638810 ATTATT-TT-ATTATTATTATTGCTTTA
1 ATTATTATTAATT-TTATTATTGATTTA
** * *
638836 ATTATTATTGCTTTAATTATT-ATTTC
1 ATTATTATTAATTTTATTATTGATTTA
638862 ATTATTATTAATTTTATTATT
1 ATTATTATTAATTTTATTATT
638883 TATATAAGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 27 0.71
27 9 0.24
28 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (27 bp):
ATTATTATTAATTTTATTATTGATTTA
Found at i:638899 original size:2 final size:2
Alignment explanation
Indices: 638894--638919 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
638884 ATATAAGTAA
638894 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
638920 TTGTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:640227 original size:87 final size:87
Alignment explanation
Indices: 640079--640255 Score: 273
Period size: 87 Copynumber: 2.0 Consensus size: 87
640069 CATAAGGAAT
*
640079 GCATGCAACATTATAAGGAATTACAAATAAAAATATCCACCGGAGGCCACATGAAAGCCTCCAGG
1 GCATGCAACATTATAAGGAATTACAAATAAAAATATCCACCGGAGGCCACATGAAAACCTCCAGG
*
640144 GATGAAGCTACCACCGCACACA
66 GATGAAACTACCACCGCACACA
* * * * * *
640166 GCATGTAACATTGTTAGGAATTACAAATAAAAGTCTCCACCGGAGGCCACATGAAAACCTCCCGG
1 GCATGCAACATTATAAGGAATTACAAATAAAAATATCCACCGGAGGCCACATGAAAACCTCCAGG
*
640231 GATGAAACTACCACCGCACCCA
66 GATGAAACTACCACCGCACACA
640253 GCA
1 GCA
640256 CTTGGGTTCG
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.16
Consensus pattern (87 bp):
GCATGCAACATTATAAGGAATTACAAATAAAAATATCCACCGGAGGCCACATGAAAACCTCCAGG
GATGAAACTACCACCGCACACA
Found at i:647620 original size:267 final size:267
Alignment explanation
Indices: 647091--647625 Score: 1009
Period size: 268 Copynumber: 2.0 Consensus size: 267
647081 CACAATAAAT
647091 GCACCAAAATTAGCTGGAAATTTGGCACCGAAAGTAGCTGGAAAATGTTGAATTTTGGACAATAG
1 GCACCAAAATTAGCTGGAAATTTGGCACCGAAAGTAGCTGGAAAATGTTGAATTTTGGACAATAG
*
647156 TAGAATCATATTTTATTCATTGTAATTTAGGATATTTACAAATTAGTCCTTAAGTTTCAACTATA
66 TAGAATCATATTTTAGTCATTGTAATTTAGGATATTTACAAATTAGTCCTTAAGTTTCAACTATA
647221 AATACCCTAGCTCATTTAGCTTCAAAACCATCCCAAAGCATTCTAGCTTTCTTCCAATGCTAGAG
131 AATACCCTAGCTCATTTAGCTTCAAAACCATCCCAAAGCATTCTAGCTTTCTTCCAATGCTAGAG
647286 AGAATTTAGAGAGCTTCTTGAGAGTTGTTTTCTCCTTTTTATCAAGAGAAAATTATCATTGTTTT
196 AGAATTTAGAGAGCTTCTTGAGAGTTGTTTTCTCCTTTTTATCAAGAGAAAATTATCATTGTTTT
647351 CTCCTTG
261 CTCCTTG
* *
647358 GCACCAAAATTAGCTGGAAATTTGGCACCGAAAGTAGCTGTAAAATGTTGAATTTTGGACAATGG
1 GCACCAAAATTAGCTGGAAATTTGGCACCGAAAGTAGCTGGAAAATGTTGAATTTTGGACAATAG
*
647423 TAGAATCATATTTTTAGTCATTGTAATTTAGGGTATTTACAAATTAGTCCTTAAGTTTCAACTAT
66 TAGAATCATA-TTTTAGTCATTGTAATTTAGGATATTTACAAATTAGTCCTTAAGTTTCAACTAT
*
647488 AAATACCCTAGCTCATTTAGCTTCAAAACCATCCCAAAGCATTCTAGCTTTCTTTCAATGCTAGA
130 AAATACCCTAGCTCATTTAGCTTCAAAACCATCCCAAAGCATTCTAGCTTTCTTCCAATGCTAGA
647553 GAGAATTTAGAGAGCTTCTTGAGAGTTGTTTTCTCCTTTTTATCAAGAGAAAATTATCATT-TTT
195 GAGAATTTAGAGAGCTTCTTGAGAGTTGTTTTCTCCTTTTTATCAAGAGAAAATTATCATTGTTT
647617 TCTCCTTG
260 TCTCCTTG
647625 G
1 G
647626 TAGATCGAGA
Statistics
Matches: 262, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
267 85 0.32
268 177 0.68
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (267 bp):
GCACCAAAATTAGCTGGAAATTTGGCACCGAAAGTAGCTGGAAAATGTTGAATTTTGGACAATAG
TAGAATCATATTTTAGTCATTGTAATTTAGGATATTTACAAATTAGTCCTTAAGTTTCAACTATA
AATACCCTAGCTCATTTAGCTTCAAAACCATCCCAAAGCATTCTAGCTTTCTTCCAATGCTAGAG
AGAATTTAGAGAGCTTCTTGAGAGTTGTTTTCTCCTTTTTATCAAGAGAAAATTATCATTGTTTT
CTCCTTG
Found at i:654640 original size:15 final size:15
Alignment explanation
Indices: 654620--654650 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
654610 AAACAATATT
654620 GTGTAAAATGAATGG
1 GTGTAAAATGAATGG
654635 GTGTAAAATGAATGG
1 GTGTAAAATGAATGG
654650 G
1 G
654651 AAGTTCTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (15 bp):
GTGTAAAATGAATGG
Found at i:654780 original size:21 final size:21
Alignment explanation
Indices: 654739--654780 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
654729 GGTAAAAAAA
* *
654739 TACCTAAAATATTATTATTTT
1 TACCTAAAAAATAATTATTTT
654760 TACCTAAAAAATCAATT-TTTT
1 TACCTAAAAAAT-AATTATTTT
654781 AACATTTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (21 bp):
TACCTAAAAAATAATTATTTT
Found at i:654908 original size:39 final size:39
Alignment explanation
Indices: 654854--654937 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
654844 ATTTTTACCA
*
654854 ATTTTATTATTTAAACAATAATAAAACCGGT-AGCACCTT
1 ATTTTATTATTTAAACAATAACAAAACCGGTGA-CACCTT
* *
654893 ATTTTGTTATTTAAACAATAACAAAATCGGTGACACCTT
1 ATTTTATTATTTAAACAATAACAAAACCGGTGACACCTT
654932 ATTTTA
1 ATTTTA
654938 GCCTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 39 0.98
40 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.38
Consensus pattern (39 bp):
ATTTTATTATTTAAACAATAACAAAACCGGTGACACCTT
Found at i:661877 original size:15 final size:15
Alignment explanation
Indices: 661857--661887 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
661847 CTCCCCCTTA
661857 CTATAACACTTCTCC
1 CTATAACACTTCTCC
*
661872 CTATAACCCTTCTCC
1 CTATAACACTTCTCC
661887 C
1 C
661888 CCTTTTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (15 bp):
CTATAACACTTCTCC
Found at i:662215 original size:21 final size:21
Alignment explanation
Indices: 662176--662217 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
662166 AATATAAATC
* * *
662176 CAAACAAATTCAAACATCCAA
1 CAAACAAAGTAAAAAATCCAA
662197 CAAACAAAGTAAAAAATCCAA
1 CAAACAAAGTAAAAAATCCAA
662218 AAGTATTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.24, G:0.02, T:0.12
Consensus pattern (21 bp):
CAAACAAAGTAAAAAATCCAA
Found at i:664249 original size:21 final size:22
Alignment explanation
Indices: 664187--664268 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 22
664177 GCATGGCCTT
664187 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTC-AGGA
* * * *
664210 GTGCATTGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGA
*
664231 GTGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC--AGGA
664254 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
664269 TGTTAAGTGG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 18 0.39
24 12 0.26
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:670165 original size:64 final size:63
Alignment explanation
Indices: 670084--670242 Score: 230
Period size: 64 Copynumber: 2.5 Consensus size: 63
670074 TGCACTAAGA
* *
670084 GTGCACCGATGCATGAAGTGCATTCGATGTTTCA-AACAAGCCCGAGTGCATCGATGCATGGTCT
1 GTGCATCGATGCATGAAGTGCATTCGATGTTTCATAA-AA-CCCGAGTGCATCGATGCATGGTAT
*
670148 GTGCATCGATGCATGAAGTGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCATAAAACCCGAGTGCATCGATGCATGGTAT
* * *
670212 GTGCATCGATGCATAAAATGCATTCAATGTT
1 GTGCATCGATGCATGAAGTGCATTCGATGTT
670243 CAATTTATTC
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
63 2 0.02
64 76 0.87
65 7 0.08
66 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (63 bp):
GTGCATCGATGCATGAAGTGCATTCGATGTTTCATAAAACCCGAGTGCATCGATGCATGGTAT
Found at i:671570 original size:299 final size:299
Alignment explanation
Indices: 671032--671632 Score: 1157
Period size: 299 Copynumber: 2.0 Consensus size: 299
671022 CATAGAGATG
671032 TCAGAATTGATACATGATTATATTGTTAGAGAACAATATATTGGATTGACCCATCATGAGCATAT
1 TCAGAATTGATACATGATTATATTGTTAGAGAACAATATATTGGATTGACCCATCATGAGCATAT
* *
671097 GTTTTGGATTATTATGTAACAGTCATAACATTGCTCATGGTGATGACTATATGTATGATCCTCGG
66 ATTTTGGATTATTATGTAACAGTCATAACATTGCTCATGGTGATGACTATATGTATGATCCTCAG
*
671162 ACTTGAGATCAATGTCATCCCAACATATATTGTTGTATGTTTTGATATAATTAAACATGCTCCGT
131 ACTTGAGATCAATGTCATCCCAACATATATTGTTGTATGTTTTGATACAATTAAACATGCTCCGT
671227 AATTGGTTGCATTATAAAGACTGTTATTAAATAAATCTCGATATATGTAGTAGGGTGTATATGGT
196 AATTGGTTGCATTATAAAGACTGTTATTAAATAAATCTCGATATATGTAGTAGGGTGTATATGGT
671292 TAAGATAGGATTTGTCCTGCCTACATAATAGGAAATATA
261 TAAGATAGGATTTGTCCTGCCTACATAATAGGAAATATA
671331 TCAGAATTGATACATGATTATATTGTTAGAGAACAATATATTGGATTGACCCATCATGAGCATAT
1 TCAGAATTGATACATGATTATATTGTTAGAGAACAATATATTGGATTGACCCATCATGAGCATAT
671396 ATTTTGGATTATTATGTAACAGTCATAACATTGCTCATGGTGATGACTATATGTATGATCCTCAG
66 ATTTTGGATTATTATGTAACAGTCATAACATTGCTCATGGTGATGACTATATGTATGATCCTCAG
*
671461 ACTTGAGATCAATGTCATCCTAACATATATTGTTGTATGTTTTGATACAATTAAACATGCTCCGT
131 ACTTGAGATCAATGTCATCCCAACATATATTGTTGTATGTTTTGATACAATTAAACATGCTCCGT
*
671526 AATTGGTTGCATTATAAAGACTGTTATTGAATAAATCTCGATATATGTAGTAGGGTGTATATGGT
196 AATTGGTTGCATTATAAAGACTGTTATTAAATAAATCTCGATATATGTAGTAGGGTGTATATGGT
671591 TAAGATAGGATTTGTCCTGCCTACATAATAGGAAATATA
261 TAAGATAGGATTTGTCCTGCCTACATAATAGGAAATATA
671630 TCA
1 TCA
671633 CAGGCCACTT
Statistics
Matches: 297, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
299 297 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (299 bp):
TCAGAATTGATACATGATTATATTGTTAGAGAACAATATATTGGATTGACCCATCATGAGCATAT
ATTTTGGATTATTATGTAACAGTCATAACATTGCTCATGGTGATGACTATATGTATGATCCTCAG
ACTTGAGATCAATGTCATCCCAACATATATTGTTGTATGTTTTGATACAATTAAACATGCTCCGT
AATTGGTTGCATTATAAAGACTGTTATTAAATAAATCTCGATATATGTAGTAGGGTGTATATGGT
TAAGATAGGATTTGTCCTGCCTACATAATAGGAAATATA
Found at i:677775 original size:31 final size:29
Alignment explanation
Indices: 677712--677803 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 29
677702 TAATTTTTTA
* * *
677712 AAATTGTCTAAAAAAATTAAATAAATCATC
1 AAATT-TCTAAAAAAATCAATTATATCATC
*
677742 AAACTTTCTATAAAAAATCAATTATATCCTC
1 AAA-TTTCTA-AAAAAATCAATTATATCATC
*
677773 AAATTTAAC-CAAAAAATCAATTATAGTCATC
1 AAATTT--CTAAAAAAATCAATTATA-TCATC
677804 TATTCCATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
30 25 0.49
31 25 0.49
32 1 0.02
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (29 bp):
AAATTTCTAAAAAAATCAATTATATCATC
Found at i:678422 original size:21 final size:20
Alignment explanation
Indices: 678397--678435 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
678387 ATAGTTTTTA
678397 ATTTTCAAAAAAATAAAAACT
1 ATTTTC-AAAAAATAAAAACT
*
678418 ATTTTCTAAAAATAAAAA
1 ATTTTCAAAAAATAAAAA
678436 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (20 bp):
ATTTTCAAAAAATAAAAACT
Found at i:679335 original size:23 final size:25
Alignment explanation
Indices: 679309--679359 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
679299 AACTATTAAA
679309 TAATTATAAAAATATT-AAT-GAAT
1 TAATTATAAAAATATTAAATCGAAT
* **
679332 TAATTGTAAACTTATTAAATCGAAT
1 TAATTATAAAAATATTAAATCGAAT
679357 TAA
1 TAA
679360 ATTTTGATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 13 0.57
24 3 0.13
25 7 0.30
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (25 bp):
TAATTATAAAAATATTAAATCGAAT
Found at i:708118 original size:2 final size:2
Alignment explanation
Indices: 708111--708151 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
708101 TAAGTTTACA
708111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
708152 CGACATGACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:714127 original size:12 final size:12
Alignment explanation
Indices: 714078--714119 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
714068 GAGGATGAGT
* *
714078 GTTAAGAAGCTA
1 GTTAGGAAGTTA
*
714090 GTTAGCAAGTTA
1 GTTAGGAAGTTA
714102 GTTAGGAAGTTA
1 GTTAGGAAGTTA
714114 GTTAGG
1 GTTAGG
714120 TTGTTAGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (12 bp):
GTTAGGAAGTTA
Found at i:715348 original size:9 final size:9
Alignment explanation
Indices: 715321--715354 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
715311 GTTTAATATC
715321 AAATAAAATT
1 AAATAAAA-T
*
715331 AAGTAAAAT
1 AAATAAAAT
715340 AAATAAAAT
1 AAATAAAAT
715349 AAATAA
1 AAATAA
715355 GAACGATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (9 bp):
AAATAAAAT
Found at i:715812 original size:6 final size:6
Alignment explanation
Indices: 715801--715835 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
715791 TAGAAACTTA
*
715801 AATTAT AATTAT AATTAT AATTTAA AATTAT AATT
1 AATTAT AATTAT AATTAT AA-TTAT AATTAT AATT
715836 TTATTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AATTAT
Found at i:715828 original size:25 final size:23
Alignment explanation
Indices: 715800--715853 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
715790 ATAGAAACTT
*
715800 AAATTATAATTATAATTATAATTTA
1 AAATTATAATT-TAATT-TAATTAA
*
715825 AAATTATAATTTTATTTAATTAA
1 AAATTATAATTTAATTTAATTAA
715848 AAATTA
1 AAATTA
715854 AGTAAAGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 12 0.44
24 4 0.15
25 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATTATAATTTAATTTAATTAA
Found at i:715831 original size:13 final size:13
Alignment explanation
Indices: 715800--715836 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
715790 ATAGAAACTT
715800 AAATTATAA-TTA
1 AAATTATAATTTA
*
715812 TAATTATAATTTA
1 AAATTATAATTTA
715825 AAATTATAATTT
1 AAATTATAATTT
715837 TATTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AAATTATAATTTA
Found at i:718709 original size:42 final size:42
Alignment explanation
Indices: 718584--718823 Score: 320
Period size: 42 Copynumber: 5.6 Consensus size: 42
718574 CTGCTATGTG
* ** * * * *
718584 CAAGGGTAAGTCCTTACCGTTATCGTAGGCTCCCTTGCTGTGTG
1 CAAGGGTAAG-CCTTACAGTT-TCCCAGGTTCCTTTGTTGTGTA
718628 CAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTA
1 CAAGGGTAAGCCTTACAGTTT-CCCAGGTTCCTTTGTTGTGTA
718671 CAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTA
1 CAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTA
* * * *
718713 CGAGGGTAAGCCTTACAG-GTCCCTAGGTTCCTTTGCTGTGTG
1 CAAGGGTAAGCCTTACAGTTTCCC-AGGTTCCTTTGTTGTGTA
*
718755 TAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTA
1 CAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTA
*
718797 CAAGGGTAAGCCTTACATTTTCCCAGG
1 CAAGGGTAAGCCTTACAGTTTCCCAGG
718824 CTCTTTTGCT
Statistics
Matches: 175, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
41 4 0.02
42 112 0.64
43 49 0.28
44 10 0.06
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.33
Consensus pattern (42 bp):
CAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTA
Found at i:718760 original size:84 final size:85
Alignment explanation
Indices: 718565--718854 Score: 341
Period size: 84 Copynumber: 3.4 Consensus size: 85
718555 GGAAGTATTT
* * * * ** * * * *
718565 CAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTATCGTAGGCTCCCTTGCTGTGTGCA
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTT-TCCCAGGTTCCTTTGTTGTGTACA
*
718630 AGGGTAAGCCTTACAGTTTCCC
64 AGGGTAAGCCTTACAGTGTCCC
* * *
718652 CAGGTTCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTACGAG
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTACAAG
718717 GGTAAGCCTTACAG-GTCCC
66 GGTAAGCCTTACAGTGTCCC
* *
718736 TAGGTTCCTTTGCTGTGTGTAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTACAAG
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTACAAG
* *
718801 GGTAAGCCTTACA-TTTTCC
66 GGTAAGCCTTACAGTGTCCC
* * * *
718820 CAGGCTCTTTTGCTATGTGCAAGGATAAGACCTTA
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTA
718855 TCGTTTTTGC
Statistics
Matches: 174, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
84 103 0.59
85 38 0.22
86 9 0.05
87 24 0.14
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (85 bp):
CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTACAAG
GGTAAGCCTTACAGTGTCCC
Found at i:718843 original size:42 final size:42
Alignment explanation
Indices: 718565--718854 Score: 294
Period size: 42 Copynumber: 6.8 Consensus size: 42
718555 GGAAGTATTT
* * * * * *
718565 CAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTATCG
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTA-CATTTTCC
* * * *
718609 TAGGCTCCCTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACA-TTTTCC
* * *
718652 CAGGTTCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTTCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACATTTTCC
* * * **
718694 CAGGTTCCTTTGTTGTGTACGAGGGTAAGCCTTACA-GGTCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACATTTTCC
* *
718735 CTAGGTTCCTTTGCTGTGTGTAAGGGTAAGCCTTACAGTTTCC
1 C-AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACATTTTCC
* *
718778 CAGGTTCCTTTGTTGTGTACAAGGGTAAGCCTTACATTTTCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACATTTTCC
* * * *
718820 CAGGCTCTTTTGCTATGTGCAAGGATAAGACCTTA
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTA
718855 TCGTTTTTGC
Statistics
Matches: 208, Mismatches: 34, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
41 4 0.02
42 131 0.63
43 48 0.23
44 25 0.12
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (42 bp):
CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACATTTTCC
Found at i:723648 original size:42 final size:42
Alignment explanation
Indices: 723524--723835 Score: 426
Period size: 42 Copynumber: 7.3 Consensus size: 42
723514 TACTATGTGA
* ** * * * *
723524 AAGGGTAAGTCCTTACAGTTACCGCAGACTCCCTTGCTGTATGC
1 AAGGGTAAG-CCTTACAGTTTCC-CAGGTTCCTTTGTTGTGTAC
*
723568 AAGGGTAAGCCTTAAAGTTTCCCCAGGTTCCTTTGTTGTGTAC
1 AAGGGTAAGCCTTACAGTTT-CCCAGGTTCCTTTGTTGTGTAC
723611 AAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
1 AAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
* * * *
723653 GAGGGTAAGCCTTACAGTTCCCCAGGTTCCTTTGCTGTGTGC
1 AAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
723695 AAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
1 AAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
723737 AAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
1 AAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
* * * * *
723779 AAGGGTAAGCCTTACAATTTCCCAGGCTCTTTTGCTATGTAC
1 AAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
*
723821 AAGGATAAGACCTTA
1 AAGGGTAAG-CCTTA
723836 TCGTTTTTGC
Statistics
Matches: 243, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
42 185 0.76
43 47 0.19
44 11 0.05
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (42 bp):
AAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
Found at i:723784 original size:126 final size:127
Alignment explanation
Indices: 723524--723835 Score: 473
Period size: 126 Copynumber: 2.4 Consensus size: 127
723514 TACTATGTGA
* * * *
723524 AAGGGTAAGTCCTTACAGTTACCGCAGACTCCCTTGCTGTATGCAAGGGTAAGCCTTAAAGTTTC
1 AAGGGTAAG-CCTTACAGTT-CCCCAGGCTCCTTTGCTGTGTGCAAGGGTAAGCCTTAAAGTTTC
723589 CCCAGGTTCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
64 CCCAGGTTCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
* * *
723653 GAGGGTAAGCCTTACAGTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CC
1 AAGGGTAAGCCTTACAGTTCCCCAGGCTCCTTTGCTGTGTGCAAGGGTAAGCCTTAAAGTTTCCC
723717 CAGGTTCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
66 CAGGTTCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
* * * * * *
723779 AAGGGTAAGCCTTACAATTTCCCAGGCTCTTTTGCTATGTACAAGGATAAGACCTTA
1 AAGGGTAAGCCTTACAGTTCCCCAGGCTCCTTTGCTGTGTGCAAGGGTAAG-CCTTA
723836 TCGTTTTTGC
Statistics
Matches: 167, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
126 107 0.64
127 42 0.25
128 10 0.06
129 8 0.05
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (127 bp):
AAGGGTAAGCCTTACAGTTCCCCAGGCTCCTTTGCTGTGTGCAAGGGTAAGCCTTAAAGTTTCCC
CAGGTTCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTAC
Found at i:728376 original size:136 final size:136
Alignment explanation
Indices: 728184--728961 Score: 884
Period size: 136 Copynumber: 5.7 Consensus size: 136
728174 CAAGGCGTTA
* * * * * *
728184 CTGATTTGAAATGTTATGAATCGAGCAATAGGTCAAATAAGTTATTCTCATTATGAACTTCTTCT
1 CTGATTTGAAGTGTTGTGAATAGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * *
728249 CCCTTTGTCGGATGAGTTCTTCTTATTATGAACTCTCTATTAGAAATGTTAATCCCTAAAGTGAG
66 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCTATTAGAAATATTAATCCCTAAAGTGAG
*
728314 GCATTA
131 GCATTG
* * * ** *
728320 CTGATTTGAAGTGTTGTGAAAAAAGTAATAGGTAAAACAAGTTCTTCTCATTATGAA-TTTTTCT
1 CTGATTTGAAGTGTTGTGAATAGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * * * ** *
728384 -CCTCTGTCGGATAAGTTCTCCTCATTATGAACCCT-TAATTAGAAATATCAATCCCTCGAGCGA
66 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCT-ATTAGAAATATTAATCCCTAAAGTGA
728447 GGCATTG
130 GGCATTG
* *
728454 CTGATTTGAAGTGTTGTGAATAAAGCAATAGGTCGAACAAGTTCTTCTTATTATGAACTTCTTCT
1 CTGATTTGAAGTGTTGTGAATAGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
** * * * * * * *
728519 CCCTCTGTTAGATGAATTCTTCTCATTATAAACTCTCTAAT-GTAAATCTTAATCCTTCAACTGA
66 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCTATTAG-AAATATTAATCCCTAAAGTGA
728583 GGCATTG
130 GGCATTG
** * *
728590 CTGATTCAAAGTGTTGTGAATAGAGCAATAGATCGAACAAGTTCTTCTCATTATGAACTTGTTCT
1 CTGATTTGAAGTGTTGTGAATAGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * * * * *
728655 CCCT-TTTCGAATGAGTTCTTCTCATTATGAACTCTCAATTGGAAATGTTAATCCCTTAAGTGAG
66 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCTATTAGAAATATTAATCCCTAAAGTGAG
**
728719 GTGTTG
131 GCATTG
* * * * *
728725 CTGATTTTAAGTGTTGTGAATCGAGCAACAGGTAGAACAAGTTCTTCTCATTATGAACTTTTTCT
1 CTGATTTGAAGTGTTGTGAATAGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
* ** * * * *
728790 CTCTCTGTTAGATGAGTTATTCTCATTATGAACTCTCCATTGGAAATATTAATCTCTAAAGTGAG
66 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCTATTAGAAATATTAATCCCTAAAGTGAG
728855 GCATTG
131 GCATTG
* * * * * *
728861 CTGATTCGAAGTGTTGTGAATCGAGCAACAGATTGAACAAGTTCATCTCATTATGAACTT-TTGC
1 CTGATTTGAAGTGTTGTGAATAGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTT-C
* * *
728925 TCCCTCTGTTGAATGAGTTCTTCTTATTATGAACTCT
65 TCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCT
728962 ACAATGGAAA
Statistics
Matches: 544, Mismatches: 90, Indels: 16
0.84 0.14 0.02
Matches are distributed among these distances:
133 1 0.00
134 109 0.20
135 126 0.23
136 307 0.56
137 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (136 bp):
CTGATTTGAAGTGTTGTGAATAGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCTATTAGAAATATTAATCCCTAAAGTGAG
GCATTG
Found at i:728798 original size:271 final size:270
Alignment explanation
Indices: 728164--728974 Score: 977
Period size: 271 Copynumber: 3.0 Consensus size: 270
728154 GGAAAGGCTG
* * * * * * *
728164 ATCCCTCAAGCAAGGCGTTACTGATTTGAAATGTTATGAATCGAGCAATAGGTCA-AATAAGTTA
1 ATCCCTCAAGCGAGGCATTGCTGATTTGAAGTGTTGTGAATCGAGCAATAGGT-AGAACAAGTTC
* ** *
728228 TTCTCATTATGAACTTCTTCTCCCTTTGTCGGATGAGTTCTTCTTATTATGAACTCTCTATTAGA
65 TTCTCATTATGAACTTCTTCTCCCTCTGTTAGATGAGTTCTTCTCATTATGAACTCTCTATT-GA
* * * * * * * * *
728293 AATGTTAATCCCTAAAGTGAGGCATTACTGATTTGAAGTGTTGTGAAAAAAGTAATAGGTAAAAC
129 AATATTAATCCTTAAAGTGAGGCATTGCTGATTCGAAGTGTTGTGAATAGAGCAATAGATAGAAC
* * * * * * *
728358 AAGTTCTTCTCATTATGAATTTTTCT-CCTCTGTCGGATAAGTTCTCCTCATTATGAACCCTTAA
194 AAGTTCTTCTCATTATGAACTTTTCTCCCTCTTTCGAATGAGTTCTTCTCATTATGAACTCTCAA
*
728422 TTAGAAATATCA
259 TTGGAAATATCA
* ** *
728434 ATCCCTCGAGCGAGGCATTGCTGATTTGAAGTGTTGTGAATAAAGCAATAGGTCGAACAAGTTCT
1 ATCCCTCAAGCGAGGCATTGCTGATTTGAAGTGTTGTGAATCGAGCAATAGGTAGAACAAGTTCT
* * * *
728499 TCTTATTATGAACTTCTTCTCCCTCTGTTAGATGAATTCTTCTCATTATAAACTCTCTAATGTAA
66 TCTCATTATGAACTTCTTCTCCCTCTGTTAGATGAGTTCTTCTCATTATGAACTCTCTATTG-AA
* * * * *
728564 ATCTTAATCCTTCAACTGAGGCATTGCTGATTCAAAGTGTTGTGAATAGAGCAATAGATCGAACA
130 ATATTAATCCTTAAAGTGAGGCATTGCTGATTCGAAGTGTTGTGAATAGAGCAATAGATAGAACA
728629 AGTTCTTCTCATTATGAACTTGTTCTCCCT-TTTCGAATGAGTTCTTCTCATTATGAACTCTCAA
195 AGTTCTTCTCATTATGAACTT-TTCTCCCTCTTTCGAATGAGTTCTTCTCATTATGAACTCTCAA
* *
728693 TTGGAAATGTTA
259 TTGGAAATATCA
* * ** * *
728705 ATCCCTTAAGTGAGGTGTTGCTGATTTTAAGTGTTGTGAATCGAGCAACAGGTAGAACAAGTTCT
1 ATCCCTCAAGCGAGGCATTGCTGATTTGAAGTGTTGTGAATCGAGCAATAGGTAGAACAAGTTCT
* * * *
728770 TCTCATTATGAACTTTTTCTCTCTCTGTTAGATGAGTTATTCTCATTATGAACTCTCCATTGGAA
66 TCTCATTATGAACTTCTTCTCCCTCTGTTAGATGAGTTCTTCTCATTATGAACTCTCTATT-GAA
* * *
728835 ATATTAAT-CTCTAAAGTGAGGCATTGCTGATTCGAAGTGTTGTGAATCGAGCAACAGATTGAAC
130 ATATTAATCCT-TAAAGTGAGGCATTGCTGATTCGAAGTGTTGTGAATAGAGCAATAGATAGAAC
* *
728899 AAGTTCATCTCATTATGAACTTTTGCTCCCTCTGTT-GAATGAGTTCTTCTTATTATGAACTCTA
194 AAGTTCTTCTCATTATGAACTTTT-CTCCCTCT-TTCGAATGAGTTCTTCTCATTATGAACTCT-
728963 CAA-TGGAAATAT
256 CAATTGGAAATAT
728975 TGATCGGTTC
Statistics
Matches: 461, Mismatches: 70, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
269 1 0.00
270 184 0.40
271 232 0.50
272 39 0.08
273 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (270 bp):
ATCCCTCAAGCGAGGCATTGCTGATTTGAAGTGTTGTGAATCGAGCAATAGGTAGAACAAGTTCT
TCTCATTATGAACTTCTTCTCCCTCTGTTAGATGAGTTCTTCTCATTATGAACTCTCTATTGAAA
TATTAATCCTTAAAGTGAGGCATTGCTGATTCGAAGTGTTGTGAATAGAGCAATAGATAGAACAA
GTTCTTCTCATTATGAACTTTTCTCCCTCTTTCGAATGAGTTCTTCTCATTATGAACTCTCAATT
GGAAATATCA
Found at i:730011 original size:26 final size:26
Alignment explanation
Indices: 729981--730040 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
729971 GAACATCTCC
*
729981 TATTCTTTTCTTTTCCTT-TTTATTTT
1 TATTCTTTT-TATTCCTTCTTTATTTT
*
730007 TATTCTTCTTTATTCTTTCTTTATTTT
1 TATTCTT-TTTATTCCTTCTTTATTTT
730034 T-TTCTTT
1 TATTCTTT
730041 CTTAGGCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 18 0.60
27 11 0.37
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (26 bp):
TATTCTTTTTATTCCTTCTTTATTTT
Found at i:750418 original size:13 final size:12
Alignment explanation
Indices: 750391--750442 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
750381 AAATATTAAA
*
750391 ATAATAAAAAAC
1 ATAAAAAAAAAC
750403 ATAAAAAAACAAC
1 ATAAAAAAA-AAC
*
750416 ATAAAAATAAA-
1 ATAAAAAAAAAC
*
750427 AT-AAAATAAAC
1 ATAAAAAAAAAC
750438 ATAAA
1 ATAAA
750443 TACAAAGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 8 0.23
11 4 0.11
12 12 0.34
13 11 0.31
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
ATAAAAAAAAAC
Found at i:758257 original size:16 final size:16
Alignment explanation
Indices: 758236--758271 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
758226 ACTAACCCAT
*
758236 TTTTATTATGTTTTTA
1 TTTTATTATGATTTTA
*
758252 TTTTATTTTGATTTTA
1 TTTTATTATGATTTTA
758268 TTTT
1 TTTT
758272 CTAGCATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (16 bp):
TTTTATTATGATTTTA
Found at i:760293 original size:12 final size:11
Alignment explanation
Indices: 760269--760320 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
760259 AAAGGGCAAT
760269 ATTTTTTTAAA
1 ATTTTTTTAAA
*
760280 ATTTTTTATTAA
1 ATTTTTT-TAAA
*
760292 ATATTTTTCAAA
1 AT-TTTTTTAAA
*
760304 ATTCTTTTTCAA
1 ATT-TTTTTAAA
760316 ATTTT
1 ATTTT
760321 GAAAATAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
11 10 0.30
12 18 0.55
13 5 0.15
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTTTTTAAA
Found at i:762139 original size:45 final size:45
Alignment explanation
Indices: 762011--762568 Score: 360
Period size: 45 Copynumber: 12.6 Consensus size: 45
762001 GAAGCTTCAA
* * *
762011 CTTGACTCTCTCATGAAGAGGAA-TCAATCTTTTAATG-T-T-ATC
1 CTTGACTTTCTCATGAAGA-GAAGTCAATCTTTTAGTGTTGTCATT
* ** * * *
762053 CTTGACTTTCTCATTAAGAGAA-TCTTTC-ATTACT-AT-T-ATT
1 CTTGACTTTCTCATGAAGAGAAGTCAATCTTTTAGTGTTGTCATT
* *
762093 CTTGACTTTCTCATGAAGAGAAGTCAATCTTTCAGTATTGTCATT
1 CTTGACTTTCTCATGAAGAGAAGTCAATCTTTTAGTGTTGTCATT
* * * *
762138 CTTGACTTTCTCATTAAAAGGAGTCAATCTTTTAGTGTTTTC-TT
1 CTTGACTTTCTCATGAAGAGAAGTCAATCTTTTAGTGTTGTCATT
* * * * *
762182 ACTTGACTTTCTCGTGAAGAGAAATTAACCTTTTAGTGTTGTTATT
1 -CTTGACTTTCTCATGAAGAGAAGTCAATCTTTTAGTGTTGTCATT
* * * * * * * *
762228 CTTGACTTTCACGTAAAGAGAATTCAATCTTTCAGTATTATGATT
1 CTTGACTTTCTCATGAAGAGAAGTCAATCTTTTAGTGTTGTCATT
* ** * * *
762273 CTTTACTTTCTTGTGAAGAGGAGTTAGTCTTTTAGTGTTGT-ATT
1 CTTGACTTTCTCATGAAGAGAAGTCAATCTTTTAGTGTTGTCATT
* * * * * *
762317 CCTTTACTTTATCGTGAAGAGGAGTCAATCTTTCTTTGGTGTTGTCCTT
1 -CTTGACTTTCTCATGAAGAGAAGTCAATC--T-TTTAGTGTTGTCATT
* * * *
762366 CTTGACTTTCTCGTGAAGAGAATTCAA-CATTTTAGTGATGTTATT
1 CTTGACTTTCTCATGAAGAGAAGTCAATC-TTTTAGTGTTGTCATT
* *
762411 -TATGACTTTCTC--GCTAG-G-AGTCAATCTTTTAATGTTGTCATT
1 CT-TGACTTTCTCATG-AAGAGAAGTCAATCTTTTAGTGTTGTCATT
** * * *
762453 CTTGACTTTCTCGCGAAGAGAAATCTATCTTTTAGTGTTGTCCTT
1 CTTGACTTTCTCATGAAGAGAAGTCAATCTTTTAGTGTTGTCATT
* * * * * * *
762498 CATGACTTTGTCATGAAGA-AGAGTCAACCTTTTAGCGGTGTTATA
1 CTTGACTTTCTCATGAAGAGA-AGTCAATCTTTTAGTGTTGTCATT
* *
762543 CTTGACTTTCTCATGAAAAGGAGTCA
1 CTTGACTTTCTCATGAAGAGAAGTCA
762569 TTTTTTCAGT
Statistics
Matches: 403, Mismatches: 90, Indels: 43
0.75 0.17 0.08
Matches are distributed among these distances:
40 29 0.07
41 11 0.03
42 48 0.12
43 7 0.02
44 12 0.03
45 256 0.64
46 3 0.01
47 2 0.00
48 33 0.08
49 2 0.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (45 bp):
CTTGACTTTCTCATGAAGAGAAGTCAATCTTTTAGTGTTGTCATT
Found at i:762255 original size:135 final size:133
Alignment explanation
Indices: 762088--762516 Score: 402
Period size: 135 Copynumber: 3.2 Consensus size: 133
762078 TTCATTACTA
* * *
762088 TTATTCTTGACTTTCTCATGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCATT
1 TTATTCTTGACTTTCTCGTGAAGAGAATTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTT
*
762153 AAAAGGAGTCAATCTTTTAGTGTTTTCTTACTTGACTTTCTCGTGAAGAGAAATTAACCTTTTAG
66 -AAAGGAGTCAATCTTTTAGTGTTGTCTT-CTTGACTTTCTCGTGAAGAGAAATTAACCTTTTAG
762218 TGTTG
129 TGTTG
* * * * * * *
762223 TTATTCTTGACTTTCACGTAAAGAGAATTCAATCTTTCAGTATTATGATTCTTTACTTTCTTGTG
1 TTATTCTTGACTTTCTCGTGAAGAGAATTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTT
* * * * * * * * *
762288 AAGAGGAGTTAGTCTTTTAGTGTTGTATTCCTTTACTTTATCGTGAAGAGGAGTCAATCTTTCTT
66 AA-AGGAGTCAATCTTTTAGTGTTGTCTT-CTTGACTTTCTCGTGAAGAGAAATTAA-C-CT-TT
*
762353 TGGTGTTG
126 TAGTGTTG
** * *
762361 TCCTTCTTGACTTTCTCGTGAAGAGAATTCAA-CATTTTAGTGA-TGTTATT-TATGACTTTCTC
1 TTATTCTTGACTTTCTCGTGAAGAGAATTCAATC-TTTCAGT-ATTGTCATTCT-TGACTTTCTC
* * * *
762423 GCT--AGGAGTCAATCTTTTAATGTTGTCATTCTTGACTTTCTCGCGAAGAGAAATCT-ATCTTT
63 GTTAAAGGAGTCAATCTTTTAGTGTTGTC-TTCTTGACTTTCTCGTGAAGAGAAAT-TAACCTTT
762485 TAGTGTTG
126 TAGTGTTG
** * * *
762493 TCCTTCATGACTTTGTCATGAAGA
1 TTATTCTTGACTTTCTCGTGAAGA
762517 AGAGTCAACC
Statistics
Matches: 236, Mismatches: 49, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
132 30 0.13
133 1 0.00
134 2 0.01
135 139 0.59
136 3 0.01
137 3 0.01
138 57 0.24
139 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (133 bp):
TTATTCTTGACTTTCTCGTGAAGAGAATTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTT
AAAGGAGTCAATCTTTTAGTGTTGTCTTCTTGACTTTCTCGTGAAGAGAAATTAACCTTTTAGTG
TTG
Found at i:775624 original size:2 final size:2
Alignment explanation
Indices: 775617--775641 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
775607 TCGTTTGGTT
775617 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
775642 GGTCATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:775849 original size:26 final size:26
Alignment explanation
Indices: 775813--775869 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
775803 CTAACCAAAA
*
775813 CCCAATTAGCAGCCCAAAACAAGAGG
1 CCCAATTAGCAGCCAAAAACAAGAGG
* *
775839 CCCAATTAGCAGCCAAAAATAGGAGG
1 CCCAATTAGCAGCCAAAAACAAGAGG
775865 CCCAA
1 CCCAA
775870 ACCTGGTAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.42, C:0.30, G:0.19, T:0.09
Consensus pattern (26 bp):
CCCAATTAGCAGCCAAAAACAAGAGG
Found at i:777343 original size:4 final size:4
Alignment explanation
Indices: 777336--777382 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
777326 TATATATATA
777336 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
777383 ATGTATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:779800 original size:33 final size:33
Alignment explanation
Indices: 779748--779844 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
779738 ATATAGATAT
*
779748 TATTA-TAAATAAAAATCACTCCAATGTGGGTG
1 TATTACTAAATAAAAGTCACTCCAATGTGGGTG
*
779780 TATTGCTAAACT-AAAGTCACTCCAATGTGGGTG
1 TATTACTAAA-TAAAAGTCACTCCAATGTGGGTG
*
779813 TATTACTAAATAAAAGCCACTCCAATGTGGGT
1 TATTACTAAATAAAAGTCACTCCAATGTGGGT
779845 ACAACTTTGA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
32 5 0.09
33 52 0.90
34 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (33 bp):
TATTACTAAATAAAAGTCACTCCAATGTGGGTG
Found at i:780038 original size:2 final size:2
Alignment explanation
Indices: 780031--780063 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
780021 TTGGTACTAA
*
780031 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
780064 GTAGCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:782625 original size:6 final size:6
Alignment explanation
Indices: 782614--782676 Score: 63
Period size: 6 Copynumber: 10.5 Consensus size: 6
782604 ACAAAATCAT
* * ** * *
782614 TAACAA TAACAA TAATAA TATCAA TGTCAA TAACAA TAATAA TATCAA
1 TAACAA TAACAA TAACAA TAACAA TAACAA TAACAA TAACAA TAACAA
*
782662 TGACAA TAACAA TAA
1 TAACAA TAACAA TAA
782677 TTTTAATAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25
Consensus pattern (6 bp):
TAACAA
Found at i:782644 original size:24 final size:24
Alignment explanation
Indices: 782616--782677 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
782606 AAAATCATTA
782616 ACAATAACAATAATAATATCAATG
1 ACAATAACAATAATAATATCAATG
*
782640 TCAATAACAATAATAATATCAATG
1 ACAATAACAATAATAATATCAATG
782664 ACAATAACAATAAT
1 ACAATAACAATAAT
782678 TTTAATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (24 bp):
ACAATAACAATAATAATATCAATG
Found at i:783029 original size:8 final size:8
Alignment explanation
Indices: 783016--783078 Score: 90
Period size: 8 Copynumber: 7.8 Consensus size: 8
783006 ATACATACAT
783016 ATACATGC
1 ATACATGC
783024 ATACATGC
1 ATACATGC
783032 ATACATGC
1 ATACATGC
783040 ATACATGC
1 ATACATGC
783048 ATACCATGC
1 ATA-CATGC
* *
783057 ATGCATGT
1 ATACATGC
*
783065 ATGCATGC
1 ATACATGC
783073 ATACAT
1 ATACAT
783079 AATAGGGGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
8 43 0.86
9 7 0.14
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (8 bp):
ATACATGC
Found at i:783061 original size:4 final size:4
Alignment explanation
Indices: 783019--783074 Score: 58
Period size: 4 Copynumber: 13.8 Consensus size: 4
783009 CATACATATA
* * * * *
783019 CATG CATA CATG CATA CATG CATA CATG CATAC CATG CATG CATG TATG
1 CATG CATG CATG CATG CATG CATG CATG CAT-G CATG CATG CATG CATG
783068 CATG CAT
1 CATG CAT
783075 ACATAATAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
4 38 0.93
5 3 0.07
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (4 bp):
CATG
Found at i:783430 original size:18 final size:17
Alignment explanation
Indices: 783390--783432 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
783380 ATCTCAAATT
783390 ATTTTAAATTTAGTTTA
1 ATTTTAAATTTAGTTTA
* *
783407 ACTTTATAATTTATTTTA
1 ATTTTA-AATTTAGTTTA
*
783425 TTTTTAAA
1 ATTTTAAA
783433 AAAATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTTAAATTTAGTTTA
Found at i:785210 original size:60 final size:59
Alignment explanation
Indices: 785123--785234 Score: 170
Period size: 60 Copynumber: 1.9 Consensus size: 59
785113 ATAGTCCCCC
785123 GACTATAGGAAACTCTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGATCCTCT
1 GACTATAGGAAACTCTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGATCCTCT
* * ** *
785182 GACTATAGGGAATTACTTTGTTGAGTCTCTTGACTATTAAAAGTTAGAAAATG
1 GACTATAGGAAACT-CTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATG
785235 GTCACCAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 12 0.26
60 35 0.74
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (59 bp):
GACTATAGGAAACTCTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGATCCTCT
Found at i:785247 original size:60 final size:59
Alignment explanation
Indices: 785124--785247 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 59
785114 TAGTCCCCCG
**
785124 ACTATAGGAAACTCTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGATCCTCTG
1 ACTATAGGAAACTCTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGATCCTCAA
* * ** * *
785183 ACTATAGGGAATTACTTTGTTGAGTCTCTTGACTATTAAAAGTTAGAAAATGGTCAC-CAA
1 ACTATAGGAAACT-CTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGATC-CTCAA
785243 ACTAT
1 ACTAT
785248 TCATTATGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 11 0.20
60 43 0.78
61 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (59 bp):
ACTATAGGAAACTCTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGATCCTCAA
Found at i:786951 original size:23 final size:20
Alignment explanation
Indices: 786925--786969 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
786915 ATTAACATAT
786925 TCTTCAAAAAAAAATACTGACAC
1 TCTT-AAAAAAAAAT--TGACAC
*
786948 TCTTAAAAATAAATTGACAC
1 TCTTAAAAAAAAATTGACAC
786968 TC
1 TC
786970 ATTATTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
22 9 0.43
23 4 0.19
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (20 bp):
TCTTAAAAAAAAATTGACAC
Found at i:789217 original size:29 final size:29
Alignment explanation
Indices: 789168--789228 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
789158 AGTGGTTATC
* * *
789168 TTTTTTGGTCAATATAGGTACTTAGAGTA
1 TTTTTTGGTCAAAATAGGTACCTAAAGTA
*
789197 TTTTTTGGTCAAAATATGTACCTAAAGTA
1 TTTTTTGGTCAAAATAGGTACCTAAAGTA
789226 TTT
1 TTT
789229 AATTTTCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (29 bp):
TTTTTTGGTCAAAATAGGTACCTAAAGTA
Found at i:794211 original size:654 final size:660
Alignment explanation
Indices: 791841--794470 Score: 5063
Period size: 661 Copynumber: 4.0 Consensus size: 660
791831 GGAGAGATTG
**
791841 ATCCCAGGGCATCCCGTCTTACTTTTTGGATTTGATCAGATATGTTTGCCTCACTTGGTGACTAC
1 ATCCCAGTACATCCCGTCTTACTTTTTGGATTTGATCAGATATGTTTGCCTCACTTGGTGACTAC
791906 ACTCTTCCAAATTAACCCACCCCCCTCAACTATACAGCATCATATGCTTTGTTAGGGTGGAGCCG
66 ACTCTTCCAAATTAACCCACCCCCCTCAACTATACAGCATCATATGCTTTGTTAGGGTGGAGCCG
791971 AGCAAGAAATCTAAGTAACAAGACCAAAACTAGTTGAGAAACCAAAAATGTTGGGAGAATAAGAC
131 AGCAAGAAATCTAAGTAACAAGACCAAAACTAGTTGAGAAACC-AAAATGTTGGGAGAATAAGAC
792036 TTCACTACATTTTGATATAGCTCTATAATCTTCTGTTTACGTTGTTACTATAGTGAAATTATGTC
195 TTCACTACATTTTGATATAGCTCTATAATCTTCTGTTTACGTTGTTACTATAGTGAAATTATGTC
792101 TTATAATCAATTATTAAAGCAAGAGAAAAAGATCTTTTTAGCAATTTCATGTTGCAGATTAGGGG
260 TTATAATCAATTATTAAAGCAAGAGAAAAAGATCTTTTTAGCAATTTCATGTTGCAGATTAGGGG
792166 TGTGCAAAAAAATCTAATCGATACTATGTAACCCTTCCCTACTTATCCATACTAATTCTCTTTCA
325 TGTGCAAAAAAATCTAATCGATACTATGTAACCCTTCCCTACTTATCCATACTAATTCTCTTTCA
792231 TTTGGATACTTAAAATATCTAGTATCTCTCAAATGCATTTGATTCTAAGAATCATACCAAAATTT
390 TTTGGATACTTAAAATATCTAGTATCTCTCAAATGCATTTGATTCTAAGAATCATACCAAAATTT
*
792296 CCAACTTGCTTTGAAGCTCATTATATGCTTCTAATCTTTCATTTACCTCATTGACAAGTCAATTC
455 CCAACTTGTTTTGAAGCTCATTATATGCTTCTAATCTTTCATTTACCTCATTGACAAGTCAATTC
*
792361 TACCAATAAACATTACTAAAAACATCTTATATTAACATATCATTATAACACCCATTTTTTAAAAT
520 TACCAATAAACATTACTAAAAACATCTTATATTAACATATCATTATAACACCCATTTTCTAAAAT
792426 CTCTTTTATTTTCCTTATCTCATCGTTTTAATCTCATCTAAACCTTCCTTAAGCTTTCATCATAT
585 CTCTTTTATTTTCCTTATCTCATCGTTTTAATCTCATCTAAACCTTCCTTAAGCTTTCATCATAT
792491 ACAAGGCTTTA
650 ACAAGGCTTTA
792502 ATCCCAGTACATCCCGTCTTACTTTTTGGATTTGATCAGATATGTTTGCCTCACTTGGTGACTAC
1 ATCCCAGTACATCCCGTCTTACTTTTTGGATTTGATCAGATATGTTTGCCTCACTTGGTGACTAC
792567 ACTCTTCCAAATTAACCCACCCCCCTCAACTATACAGCATCATATGCTTTGTTAGGGTGGAGCCG
66 ACTCTTCCAAATTAACCCACCCCCCTCAACTATACAGCATCATATGCTTTGTTAGGGTGGAGCCG
792632 AGCAAGAAATCTAAGTAACAAGACCAAAACTAGTTGAGAAACCAAAATGTTGGGAGAATAAGACT
131 AGCAAGAAATCTAAGTAACAAGACCAAAACTAGTTGAGAAACCAAAATGTTGGGAGAATAAGACT
792697 TCACTACATTTTGATATAGCTCTATAATCTTCTGTTTACGTTGTTACTATAGTGAAATTATGTCT
196 TCACTACATTTTGATATAGCTCTATAATCTTCTGTTTACGTTGTTACTATAGTGAAATTATGTCT
792762 TATAATCAATTATTAAAGCAAGAGAAAAAGATCTTTTTAGCAATTTCATGTTGCAGATTAGGGGT
261 TATAATCAATTATTAAAGCAAGAGAAAAAGATCTTTTTAGCAATTTCATGTTGCAGATTAGGGGT
792827 GTGCAAAAAAATCTAATCGATACTATGTAACCCTTCCCTACTTATCCATACTAATTCTCTTTCAT
326 GTGCAAAAAAATCTAATCGATACTATGTAACCCTTCCCTACTTATCCATACTAATTCTCTTTCAT
792892 TTGGATACTTAAAATATCTAGTATCTCTCAAAATGCATTTGATTCTAAGAATCATACCAAAATTT
391 TTGGATACTTAAAATATCTAGTATCTCTC-AAATGCATTTGATTCTAAGAATCATACCAAAATTT
792957 CCAACTTGTTTTGAAGCTCATTATATGCTTCTAATCTTTCATTTACCTCATTGACAAGTCAATTC
455 CCAACTTGTTTTGAAGCTCATTATATGCTTCTAATCTTTCATTTACCTCATTGACAAGTCAATTC
793022 TACCAATAAACATTACTAAAAACATCTTATATTAACATATCATTATAACACCCATTTTCTAAAAT
520 TACCAATAAACATTACTAAAAACATCTTATATTAACATATCATTATAACACCCATTTTCTAAAAT
793087 CTCTTTTATTTTCCTTATCTCATCGTTTTAATCTCATCTAAACCTTCCTTAAGCTTTCATCATAT
585 CTCTTTTATTTTCCTTATCTCATCGTTTTAATCTCATCTAAACCTTCCTTAAGCTTTCATCATAT
793152 ACAAGGCTTTA
650 ACAAGGCTTTA
793163 ATCCCAGTACAT-CCGTCTTAC-TTTTGGATTTGATCAGATATGTTTGCCTCACTTGGTGACTAC
1 ATCCCAGTACATCCCGTCTTACTTTTTGGATTTGATCAGATATGTTTGCCTCACTTGGTGACTAC
* *
793226 ACTCTTCTAAATTAACCCA-CCCCCTCAACTATATAGCATCATATGCTTTGTTAGGGTGGAG-CG
66 ACTCTTCCAAATTAACCCACCCCCCTCAACTATACAGCATCATATGCTTTGTTAGGGTGGAGCCG
793289 AGCAAGAAATCTAAGTAACAAGACC-AAACTAGTTGAGAAACCAAAATGTTGGGAGAATAAGACT
131 AGCAAGAAATCTAAGTAACAAGACCAAAACTAGTTGAGAAACCAAAATGTTGGGAGAATAAGACT
793353 TCA-TACA-TTTGATATAGCTCTATAATCTTCTGTTTACGTTGTTACTATAGTGAAATTATGTCT
196 TCACTACATTTTGATATAGCTCTATAATCTTCTGTTTACGTTGTTACTATAGTGAAATTATGTCT
793416 TATAATCAATTA-TAAAGCAAGAGAAAAAGATCTTTTTAGCAATTTCATGTTGCAGATTAGGGGT
261 TATAATCAATTATTAAAGCAAGAGAAAAAGATCTTTTTAGCAATTTCATGTTGCAGATTAGGGGT
*
793480 GTGCAAAAAAATCTAATCGATACTATGTAACCCTTCTCTACTTATCCATACTAATTCTCTTTCAT
326 GTGCAAAAAAATCTAATCGATACTATGTAACCCTTCCCTACTTATCCATACTAATTCTCTTTCAT
793545 TTGGATACTTAAAATATCTAGTATCTCTCAAATGCA-TTGATTCTAAGAATCATACCAAAATTTC
391 TTGGATACTTAAAATATCTAGTATCTCTCAAATGCATTTGATTCTAAGAATCATACCAAAATTTC
793609 CAACTTG-TTTGAAGCTCATTATATG-TTCTAATCTTTCATTTACCTCATTGACAAGTCAATTCT
456 CAACTTGTTTTGAAGCTCATTATATGCTTCTAATCTTTCATTTACCTCATTGACAAGTCAATTCT
793672 ACCAAT-AACATTACT-AAAACATC-TATATTAACATATCATTATAACACCCATTTTCTAAAATC
521 ACCAATAAACATTACTAAAAACATCTTATATTAACATATCATTATAACACCCATTTTCTAAAATC
793734 TCTTTTATTTTCCTTATCTCATCGTTTTAATCTCATCTAAACCTTCCTTAAGCTTTCATCATATA
586 TCTTTTATTTTCCTTATCTCATCGTTTTAATCTCATCTAAACCTTCCTTAAGCTTTCATCATATA
793799 CAAGGCTTTA
651 CAAGGCTTTA
793809 ATCCCAGTACATCCCGTCTTACTTTTTGGATTTGATCAGATATGTTTGCCTCACTTGGTGACTAC
1 ATCCCAGTACATCCCGTCTTACTTTTTGGATTTGATCAGATATGTTTGCCTCACTTGGTGACTAC
793874 ACTCTTCCAAATTAACCCACCCCCCTCAACTATACAGCATCATATGCTTTGTTAGGGTGGAGCCG
66 ACTCTTCCAAATTAACCCACCCCCCTCAACTATACAGCATCATATGCTTTGTTAGGGTGGAGCCG
793939 AGCAAGAAATCTAAGTAACAAGACCAAAACTAGTTGAGAAACCAAAATGTTGGGAGAATAAGACT
131 AGCAAGAAATCTAAGTAACAAGACCAAAACTAGTTGAGAAACCAAAATGTTGGGAGAATAAGACT
794004 TCACTACATTTTGATATAGCTCTATAATCTTCTGTTTACGTTGTTACTATAGTGAAATTATGTCT
196 TCACTACATTTTGATATAGCTCTATAATCTTCTGTTTACGTTGTTACTATAGTGAAATTATGTCT
794069 TATAATCAATTATTAAAGCAAGAGAAAAAGATCTTTTTAGCAATTTCATGTTGCAGATTAGGGGT
261 TATAATCAATTATTAAAGCAAGAGAAAAAGATCTTTTTAGCAATTTCATGTTGCAGATTAGGGGT
794134 GTGCAAAAAAATCTAATCGATACTATGTAACCCTTCCCTACTTATCCATACTAATTCTCTTTCAT
326 GTGCAAAAAAATCTAATCGATACTATGTAACCCTTCCCTACTTATCCATACTAATTCTCTTTCAT
794199 TTGGATACTTAAAATATCTAGTATCTCTCAAATGCATTTGATTCTAAGAATCATACCAAAATTTC
391 TTGGATACTTAAAATATCTAGTATCTCTCAAATGCATTTGATTCTAAGAATCATACCAAAATTTC
794264 CAACTTGTTTTGAAGCTCATTATATGCTTCTAATCTTTCATTTACCTCATTGACAAGTCAATTCT
456 CAACTTGTTTTGAAGCTCATTATATGCTTCTAATCTTTCATTTACCTCATTGACAAGTCAATTCT
*
794329 ACCAATAAACATTACTAAAAACATCTTATATTAACATATCATTATAACACCCATTTTTTAAAATC
521 ACCAATAAACATTACTAAAAACATCTTATATTAACATATCATTATAACACCCATTTTCTAAAATC
794394 TCTTTTATTTTCCTTATCTCATCGTTTTAATCTCATCTAAACCTTCCTTAAGCTTTCATCATATA
586 TCTTTTATTTTCCTTATCTCATCGTTTTAATCTCATCTAAACCTTCCTTAAGCTTTCATCATATA
*
794459 CAGGGCTTTA
651 CAAGGCTTTA
794469 AT
1 AT
794471 AACCAACAAA
Statistics
Matches: 1942, Mismatches: 12, Indels: 31
0.98 0.01 0.02
Matches are distributed among these distances:
646 126 0.06
647 17 0.01
648 69 0.04
649 85 0.04
650 45 0.02
651 77 0.04
652 11 0.01
653 213 0.11
654 220 0.11
655 39 0.02
656 60 0.03
657 71 0.04
658 50 0.03
659 68 0.04
660 369 0.19
661 422 0.22
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (660 bp):
ATCCCAGTACATCCCGTCTTACTTTTTGGATTTGATCAGATATGTTTGCCTCACTTGGTGACTAC
ACTCTTCCAAATTAACCCACCCCCCTCAACTATACAGCATCATATGCTTTGTTAGGGTGGAGCCG
AGCAAGAAATCTAAGTAACAAGACCAAAACTAGTTGAGAAACCAAAATGTTGGGAGAATAAGACT
TCACTACATTTTGATATAGCTCTATAATCTTCTGTTTACGTTGTTACTATAGTGAAATTATGTCT
TATAATCAATTATTAAAGCAAGAGAAAAAGATCTTTTTAGCAATTTCATGTTGCAGATTAGGGGT
GTGCAAAAAAATCTAATCGATACTATGTAACCCTTCCCTACTTATCCATACTAATTCTCTTTCAT
TTGGATACTTAAAATATCTAGTATCTCTCAAATGCATTTGATTCTAAGAATCATACCAAAATTTC
CAACTTGTTTTGAAGCTCATTATATGCTTCTAATCTTTCATTTACCTCATTGACAAGTCAATTCT
ACCAATAAACATTACTAAAAACATCTTATATTAACATATCATTATAACACCCATTTTCTAAAATC
TCTTTTATTTTCCTTATCTCATCGTTTTAATCTCATCTAAACCTTCCTTAAGCTTTCATCATATA
CAAGGCTTTA
Found at i:800510 original size:59 final size:59
Alignment explanation
Indices: 800089--800483 Score: 598
Period size: 59 Copynumber: 6.7 Consensus size: 59
800079 TTTATCAACC
* * * * *
800089 ATTCATACACTTAGTATGAATTGCTAAACATTTTAGCAC-CCGAAGTGCCATATACT-AAA
1 ATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACC-AAGTGCCCTATA-TGGAA
* * * *
800148 ATTCATACACATAATATGAATTTCTTATCATTTTAGCATACCAAGTGCCCTATACGGAA
1 ATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACCAAGTGCCCTATATGGAA
* *
800207 ATTCATACACTTAGTATGAATTTTTTATCATTTTAGCACACCAAGTGCCCTATACGGAA
1 ATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACCAAGTGCCCTATATGGAA
800266 ATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACCAAGTGCCCTATATGGAA
1 ATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACCAAGTGCCCTATATGGAA
* *
800325 ATTTATACACTTAGTATGAATTTCTTATCATTTTAGCATACCAAGTGCCCTATATGGAA
1 ATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACCAAGTGCCCTATATGGAA
* * *
800384 ATTCATAAACTTAGTATGAATTTCTTATCATTTTAGTACACGAAGTGCCCTATATGGAA
1 ATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACCAAGTGCCCTATATGGAA
800443 ATTCATACACTTAGTAT-AATCTTCTTATCATTTTAGCACAC
1 ATTCATACACTTAGTATGAAT-TTCTTATCATTTTAGCACAC
800484 TTAATGCCAT
Statistics
Matches: 309, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
58 3 0.01
59 304 0.98
60 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (59 bp):
ATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACCAAGTGCCCTATATGGAA
Found at i:801868 original size:15 final size:16
Alignment explanation
Indices: 801850--801886 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
801840 AATATTGTAC
801850 AAAATTAT-AAAATAT
1 AAAATTATAAAAATAT
*
801865 AAAAATATAAAAATAT
1 AAAATTATAAAAATAT
801881 AAAATT
1 AAAATT
801887 GAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTATAAAAATAT
Found at i:801869 original size:8 final size:8
Alignment explanation
Indices: 801858--801884 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
801848 ACAAAATTAT
801858 AAAATATA
1 AAAATATA
801866 AAAATATA
1 AAAATATA
801874 AAAATATA
1 AAAATATA
801882 AAA
1 AAA
801885 TTGAAATTTA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAATATA
Found at i:802583 original size:21 final size:21
Alignment explanation
Indices: 802559--802616 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
802549 AACAATTCTC
*
802559 TTCATGAAATGATTAAATCCT
1 TTCATGAAAAGATTAAATCCT
* *
802580 TTCATGAAAAGGTTAAGTCCT
1 TTCATGAAAAGATTAAATCCT
*
802601 TTAATTGAAAAG-TTAA
1 TTCA-TGAAAAGATTAA
802617 TATTGAGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TTCATGAAAAGATTAAATCCT
Done.