Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005466.1 Hibiscus syriacus cultivar Beakdansim tig00012523_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: 1151987
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 3 of 4
Found at i:517508 original size:20 final size:21
Alignment explanation
Indices: 517485--517525 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
517475 TTTAATATGT
517485 TAATAT-TTTTAATAAT-TAAA
1 TAATATATTTT-ATAATATAAA
517505 TAATATATTTTATAATATAAA
1 TAATATATTTTATAATATAAA
517526 ATAAAATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATATATTTTATAATATAAA
Found at i:517512 original size:22 final size:22
Alignment explanation
Indices: 517487--517529 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
517477 TAATATGTTA
*
517487 ATATTTT-TAATAATTAAATAAT
1 ATATTTTATAAT-ATAAAATAAT
517509 ATATTTTATAATATAAAATAA
1 ATATTTTATAATATAAAATAA
517530 AATTCTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTTTATAATATAAAATAAT
Found at i:517576 original size:21 final size:21
Alignment explanation
Indices: 517552--517592 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
517542 ATTATATATT
*
517552 ATATAGATATATATATAATAG
1 ATATAGATATATACATAATAG
* *
517573 ATATATATCTATACATAATA
1 ATATAGATATATACATAATA
517593 TAAATTAATC
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:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
ATATAGATATATACATAATAG
Found at i:517585 original size:17 final size:16
Alignment explanation
Indices: 517544--517599 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
517534 CTTAAAATAT
517544 TATATATTAT-ATAGA
1 TATATATTATAATAGA
517559 TATATA-TATAATAGA
1 TATATATTATAATAGA
517574 TATATATCTATACATA-A
1 TATATAT-TATA-ATAGA
*
517591 TATAAATTA
1 TATATATTA
517600 ATCTGATCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 3 0.08
15 17 0.47
16 2 0.06
17 11 0.31
18 3 0.08
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (16 bp):
TATATATTATAATAGA
Found at i:527847 original size:20 final size:20
Alignment explanation
Indices: 527824--527893 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
527814 AAACTCATAA
* * *
527824 TTTACTTTCAGATTTGTAGC
1 TTTACTTTCAGACTCGTAGT
527844 TTTACTTTCAGACTCGTAGT
1 TTTACTTTCAGACTCGTAGT
527864 TTTACTTTCAGACTCGTAGT
1 TTTACTTTCAGACTCGTAGT
527884 TTTACTTTCA
1 TTTACTTTCA
527894 TGATCATAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTACTTTCAGACTCGTAGT
Found at i:528309 original size:14 final size:14
Alignment explanation
Indices: 528272--528301 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
528262 TATCATTCTT
528272 AGAAATCATTTTGG
1 AGAAATCATTTTGG
528286 AGAAATCATTTTGG
1 AGAAATCATTTTGG
528300 AG
1 AG
528302 CATTCATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (14 bp):
AGAAATCATTTTGG
Found at i:534895 original size:35 final size:35
Alignment explanation
Indices: 534847--534958 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
534837 TCTAAACCTT
* * *
534847 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* ** *
534882 TAATTGAATTATTTTGGAATTTAAGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * *
534917 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
534952 AAATTGA
1 AAATTGA
534959 GGACTATTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
Found at i:537401 original size:78 final size:78
Alignment explanation
Indices: 537272--537425 Score: 299
Period size: 78 Copynumber: 2.0 Consensus size: 78
537262 AAAAGATCAT
537272 TTTCTTTTATATAATTACTAGTATCTGATCAATTAATTGACTAATCCGAATCAAGTATTACAGAG
1 TTTCTTTTATATAATTACTAGTATCTGATCAATTAATTGACTAATCCGAATCAAGTATTACAGAG
537337 ATAAATGTGACCC
66 ATAAATGTGACCC
*
537350 TTTCTTTTATATAATTACTAGTATCTGATCAATTAATTGACTAATCCGAATCAGGTATTACAGAG
1 TTTCTTTTATATAATTACTAGTATCTGATCAATTAATTGACTAATCCGAATCAAGTATTACAGAG
537415 ATAAATGTGAC
66 ATAAATGTGAC
537426 ACTCCCAACC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (78 bp):
TTTCTTTTATATAATTACTAGTATCTGATCAATTAATTGACTAATCCGAATCAAGTATTACAGAG
ATAAATGTGACCC
Found at i:539019 original size:31 final size:31
Alignment explanation
Indices: 538984--539059 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
538974 CAATTATTTG
538984 TTTAGTATTTAAACAATCAATTTT-GATCCGT
1 TTTAGTATTTAAACAATCAATTTTAG-TCCGT
* *
539015 TTTAGTATTTAAACAATCAGTTTTAGTTCGT
1 TTTAGTATTTAAACAATCAATTTTAGTCCGT
*
539046 TTTAGTATCTAAAC
1 TTTAGTATTTAAAC
539060 TTTTAATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (31 bp):
TTTAGTATTTAAACAATCAATTTTAGTCCGT
Found at i:541185 original size:15 final size:15
Alignment explanation
Indices: 541167--541212 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
541157 AATTACTGGA
541167 ACTGATAAATGAATT
1 ACTGATAAATGAATT
*
541182 ACTG-TAATTTGAATT
1 ACTGATAA-ATGAATT
*
541197 -CTGAAAAATGAATT
1 ACTGATAAATGAATT
541211 AC
1 AC
541213 ATTTCTGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (15 bp):
ACTGATAAATGAATT
Found at i:541586 original size:23 final size:23
Alignment explanation
Indices: 541537--541599 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
541527 AGTGTATATT
**
541537 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
541560 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
541583 ATATTATTAAAATATAT
1 ATATT-TTAAAA-ATAT
541600 AAATAATATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 23 0.74
24 5 0.16
25 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:541618 original size:29 final size:28
Alignment explanation
Indices: 541584--541674 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 28
541574 TTTATTAAAA
541584 TATTATTAAAATATATAAATAATATTAT
1 TATTATTAAAATATATAAATAATATTAT
*
541612 TCATTATT-AAATATATAAAAAATTATTAT
1 T-ATTATTAAAATATATAAATAA-TATTAT
*
541641 ATATTATTAAAATA-AAAATATAATA-TAT
1 -TATTATTAAAATATATAA-ATAATATTAT
541669 TATTAT
1 TATTAT
541675 ATAATTGATT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
27 6 0.11
28 17 0.31
29 23 0.42
30 9 0.16
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
TATTATTAAAATATATAAATAATATTAT
Found at i:541625 original size:26 final size:27
Alignment explanation
Indices: 541583--541741 Score: 100
Period size: 29 Copynumber: 5.9 Consensus size: 27
541573 CTTTATTAAA
541583 ATATTATTAAAATATATAAATAATATTAT
1 ATATTATT-AAATATATAAA-AATATTAT
541612 -TCATTATTAAATATATAAAAAATTATTAT
1 AT-ATTATTAAATATAT-AAAAA-TATTAT
*
541641 ATATTATT-AA-A-ATAAAAATATAAT
1 ATATTATTAAATATATAAAAATATTAT
* * ** *
541665 ATATTATTATATA-ATTGATTATTTTAT
1 ATATTATTAAATATA-TAAAAATATTAT
* * * *
541692 ATAATATTAAAAATAT-AATATAATAT
1 ATATTATTAAATATATAAAAATATTAT
*
541718 -TATTA-TAAATAAATAAATAATATT
1 ATATTATTAAATATATAAA-AATATT
541742 TTGATGAAAA
Statistics
Matches: 102, Mismatches: 18, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
24 20 0.20
25 12 0.12
26 15 0.15
27 19 0.19
28 14 0.14
29 21 0.21
30 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.45
Consensus pattern (27 bp):
ATATTATTAAATATATAAAAATATTAT
Found at i:541627 original size:19 final size:20
Alignment explanation
Indices: 541575--541651 Score: 65
Period size: 19 Copynumber: 4.0 Consensus size: 20
541565 TTAAATATCT
541575 TTATTAAA-ATATTATTAAA
1 TTATTAAATATATTATTAAA
* *
541594 ATATATAAATAATATTATT-CA
1 TTAT-TAAAT-ATATTATTAAA
**
541615 TTATTAAATATA-TAAAAAA
1 TTATTAAATATATTATTAAA
541634 TTATT--ATATATTATTAAA
1 TTATTAAATATATTATTAAA
541652 ATAAAAATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
17 5 0.11
18 7 0.16
19 12 0.27
20 9 0.20
21 4 0.09
22 8 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATTAAATATATTATTAAA
Found at i:541973 original size:42 final size:42
Alignment explanation
Indices: 541915--542033 Score: 168
Period size: 42 Copynumber: 2.9 Consensus size: 42
541905 ATGAATTACA
* *
541915 TTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGAAAAACAAATTACGTGAAACAAACACGGGAAAACATT
* *
541957 TTTCGAAAAACAAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGAAAAACAAATTACGTGAAACAAACACGGGAAAACATT
* * *
541999 TTCCGGAAAA-GAATTACGTGAAACAAACATGGGAA
1 TTCCGAAAAACAAATTACGTGAAACAAACACGGGAA
542034 TTCGGGGAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
41 23 0.33
42 46 0.67
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.18
Consensus pattern (42 bp):
TTCCGAAAAACAAATTACGTGAAACAAACACGGGAAAACATT
Found at i:544545 original size:16 final size:16
Alignment explanation
Indices: 544521--544554 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
544511 CTATAATAGA
544521 TTTAATTTATTATATT
1 TTTAATTTATTATATT
* *
544537 TTTATTTTATTTTATT
1 TTTAATTTATTATATT
544553 TT
1 TT
544555 CATATTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTAATTTATTATATT
Found at i:554052 original size:60 final size:60
Alignment explanation
Indices: 553875--554059 Score: 203
Period size: 60 Copynumber: 3.1 Consensus size: 60
553865 TAATTGTATG
* * * *
553875 TCCCCAAATTAT-AACTCTCATTTTAAATTAGTTCTTAAAATTTTAAACATTATAATTTTA
1 TCCCCAAACTATGAA-TCTCATTCTAAATTAGTCCTTAAAATTTTAAACATTCTAATTTTA
* * * * * * * *
553935 TTCTCAAACTATGACTCTCATTCTAGATTAGTCTTTAAATTTTTAAACATTCCAATTTCA
1 TCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAAAATTTTAAACATTCTAATTTTA
* * *
553995 TCCCCAAACTATGAATCTCATTCTAAATTAGTCCCTAAACTTTTAGATC-TTCTAATTTTA
1 TCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAAAATTTTA-AACATTCTAATTTTA
554055 TCCCC
1 TCCCC
554060 CAGTTCATCC
Statistics
Matches: 101, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
60 98 0.97
61 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (60 bp):
TCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAAAATTTTAAACATTCTAATTTTA
Found at i:554337 original size:60 final size:60
Alignment explanation
Indices: 554213--554365 Score: 159
Period size: 60 Copynumber: 2.5 Consensus size: 60
554203 GAAATATCCA
* * ****
554213 AAAAGTTTGGGGACCAATTTAGAATGAAGATCATAGTTTGGGGATGAAAATGAAATTTTC
1 AAAAGTTTGAGGACTAATTTAGAATGAAGATCATAGTTTAAAAATGAAAATGAAATTTTC
*
554273 AAAAGTTTGAGGACTAATTTAGAATGATAG-TCATAGTTTAAAAAT-AAAATTGAACTGTTT-
1 AAAAGTTTGAGGACTAATTTAGAATGA-AGATCATAGTTTAAAAATGAAAA-TGAAAT-TTTC
* * * *
554333 AAAAGTTTAAGGATTAATTTAAAATGAGGATCA
1 AAAAGTTTGAGGACTAATTTAGAATGAAGATCA
554366 GATTGGGGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
59 5 0.06
60 68 0.87
61 5 0.06
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.32
Consensus pattern (60 bp):
AAAAGTTTGAGGACTAATTTAGAATGAAGATCATAGTTTAAAAATGAAAATGAAATTTTC
Found at i:554539 original size:11 final size:12
Alignment explanation
Indices: 554517--554549 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
554507 TGAGATGTTG
554517 ATAAATAAATTT
1 ATAAATAAATTT
*
554529 A-AAATATATTT
1 ATAAATAAATTT
554540 ATAAATAAAT
1 ATAAATAAAT
554550 AAAAAAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAAATAAATTT
Found at i:565000 original size:2 final size:2
Alignment explanation
Indices: 564993--565019 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
564983 GATAATCTTT
564993 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
565020 TAATAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:581356 original size:36 final size:36
Alignment explanation
Indices: 581316--581388 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
581306 AATGATGAGA
*
581316 TACTAAAATGAAATGAAAACTAAACGTTAGGTATGG
1 TACTAAAATGAAATGAAAAATAAACGTTAGGTATGG
*
581352 TACTAAAATGAAATGAAAAATAAACGTTATGTATGG
1 TACTAAAATGAAATGAAAAATAAACGTTAGGTATGG
581388 T
1 T
581389 GTTGGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (36 bp):
TACTAAAATGAAATGAAAAATAAACGTTAGGTATGG
Found at i:592812 original size:21 final size:21
Alignment explanation
Indices: 592788--592880 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
592778 CATATAATAT
592788 GTATATATTATAGTATATGTA
1 GTATATATTATAGTATATGTA
**
592809 GTATAATATT-TA--ATATACA
1 GTAT-ATATTATAGTATATGTA
592828 -T-TATATTATA-TATA-GTA
1 GTATATATTATAGTATATGTA
592845 TGTATAT-TATATAGTATATGGT-
1 -GTATATAT-TATAGTATAT-GTA
*
592867 CTATATATTATAGT
1 GTATATATTATAGT
592881 TATTAAGGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
16 5 0.09
17 4 0.07
18 4 0.07
19 7 0.12
20 7 0.12
21 21 0.38
22 6 0.11
23 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (21 bp):
GTATATATTATAGTATATGTA
Found at i:592840 original size:16 final size:18
Alignment explanation
Indices: 592821--592857 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
592811 ATAATATTTA
592821 ATATA-CAT-TATATTAT
1 ATATAGCATGTATATTAT
*
592837 ATATAGTATGTATATTAT
1 ATATAGCATGTATATTAT
592855 ATA
1 ATA
592858 GTATATGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 2 0.11
18 11 0.61
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (18 bp):
ATATAGCATGTATATTAT
Found at i:592853 original size:23 final size:23
Alignment explanation
Indices: 592821--592883 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
592811 ATAATATTTA
*
592821 ATATACATTATATTATATATAGT
1 ATATATATTATATTATATATAGT
* *
592844 ATGTATATTATA-TAGTATATGGT
1 ATATATATTATATTA-TATATAGT
*
592867 CTATATATTATAGTTAT
1 ATATATATTATA-TTAT
592884 TAAGGTTAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 2 0.06
23 27 0.84
24 1 0.03
25 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (23 bp):
ATATATATTATATTATATATAGT
Found at i:593096 original size:80 final size:81
Alignment explanation
Indices: 593004--593159 Score: 278
Period size: 81 Copynumber: 1.9 Consensus size: 81
592994 TTCTCACGAG
*
593004 ATTATATTAGAATTAGATTTAAAATATTTTAAA-TGAAAAAAAACTATACTATCCCCACAATAGG
1 ATTATATTAGAATTAGATTTAAAATATTTTAAATTAAAAAAAAACTATACTATCCCCACAATAGG
593068 GTTGTGGTTATCCGTA
66 GTTGTGGTTATCCGTA
* *
593084 ATTATATTAGAATTAGATTTAAAATCTTTTAAATTAAAAAAAAACTATACTATCCCCACAATAGT
1 ATTATATTAGAATTAGATTTAAAATATTTTAAATTAAAAAAAAACTATACTATCCCCACAATAGG
593149 GTTGTGGTTAT
66 GTTGTGGTTAT
593160 TGGTATCGGC
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 32 0.44
81 40 0.56
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (81 bp):
ATTATATTAGAATTAGATTTAAAATATTTTAAATTAAAAAAAAACTATACTATCCCCACAATAGG
GTTGTGGTTATCCGTA
Found at i:596972 original size:21 final size:20
Alignment explanation
Indices: 596948--597016 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
596938 ACGTAATGCG
596948 ATTTTTCAAATTCGCAACGCA
1 ATTTTTCAAA-TCGCAACGCA
* *
596969 ATTTTTAAAATCGCAACCCA
1 ATTTTTCAAATCGCAACGCA
** *
596989 ATTTTGGAAATCGCAACGTGA
1 ATTTTTCAAATCGCAACG-CA
597010 ATTTTTC
1 ATTTTTC
597017 TGCTGTGTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 24 0.62
21 15 0.38
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
ATTTTTCAAATCGCAACGCA
Found at i:597074 original size:97 final size:96
Alignment explanation
Indices: 596969--597268 Score: 255
Period size: 97 Copynumber: 3.1 Consensus size: 96
596959 TCGCAACGCA
596969 ATTTTTAAAATCGCAACCCAATTTTGGAAATCGCAACGTGAATTTTTCTGCTGTGTTTATCTATG
1 ATTTTTAAAATCGCAACCCAATTTTGGAAATCGCAACGTGAATTTTTCTGCTGTGTTTATCTATG
597034 TCGGTAATTAAGTTCGAAATTGGCAAATTTG
66 TCGGTAATTAAGTTCGAAATTGGCAAATTTG
* * * * * * ** * *
597065 ATTTGTTAAATTCG-----C---GTTGCGAAAACGAAATTCGCG--TTGTGATAGTTGTGTTTAC
1 ATTT-TTAAAATCGCAACCCAATTTTG-GAAATCGCAA--CGTGAATTTTTCT-GCTGTGTTTAT
* ** * ****
597120 CTATATCGGTAATTCGATTTTTC-AAATTCGC-AACGCA
61 CTATGTCGGTAATT--A-AGTTCGAAATTGGCAAATTTG
597157 ATTTTTAAAATCGCAACCCAATTTTGGAAATCGCAACGTGAATTTTTCTGCTGTGTTTATCTATG
1 ATTTTTAAAATCGCAACCCAATTTTGGAAATCGCAACGTGAATTTTTCTGCTGTGTTTATCTATG
597222 TCGGTAATTAAGTTGCGAAATTGGCAAATTTG
66 TCGGTAATTAAGTT-CGAAATTGGCAAATTTG
*
597254 ATTTGTTAAATTCGC
1 ATTT-TTAAAATCGC
597269 GTTGCGAAAA
Statistics
Matches: 145, Mismatches: 37, Indels: 42
0.65 0.17 0.19
Matches are distributed among these distances:
89 3 0.02
90 12 0.08
91 30 0.21
92 10 0.07
93 8 0.06
94 5 0.03
95 2 0.01
96 15 0.10
97 36 0.25
98 21 0.14
99 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (96 bp):
ATTTTTAAAATCGCAACCCAATTTTGGAAATCGCAACGTGAATTTTTCTGCTGTGTTTATCTATG
TCGGTAATTAAGTTCGAAATTGGCAAATTTG
Found at i:597129 original size:91 final size:91
Alignment explanation
Indices: 597020--597322 Score: 251
Period size: 91 Copynumber: 3.3 Consensus size: 91
597010 ATTTTTCTGC
* *
597020 TGTGTTTATCTATGTCGGTAATTAAGTTCGAAATTGGCAAATTTGATTTGTTAAATTCGCGTTGC
1 TGTGTTTACCTATATCGGTAATTAAGTTCGAAATTGGCAAATTTGATTTGTTAAATTCGCGTTGC
597085 GAAAACGAAATTCGCGTTGTGATAGT
66 GAAAACGAAATTCGCGTTGTGATAGT
** * **** *
597111 TGTGTTTACCTATATCGGTAATTCGATTTTTC-AAATTCGC-AACGCAATTT-TTAAAATCGCAA
1 TGTGTTTACCTATATCGGTAATT--A-AGTTCGAAATTGGCAAATTTGATTTGTTAAATTCG---
* * * * * ** *
597173 CCCAATTTTG-GAAATCGCAA--CGTGAATTTTTCT-GC
60 --C---GTTGCGAAAACGAAATTCGCG--TTGTGATAGT
* *
597208 TGTGTTTATCTATGTCGGTAATTAAGTTGCGAAATTGGCAAATTTGATTTGTTAAATTCGCGTTG
1 TGTGTTTACCTATATCGGTAATTAAGTT-CGAAATTGGCAAATTTGATTTGTTAAATTCGCGTTG
597273 CGAAAACGAAATTCGCGTTGTGATAGT
65 CGAAAACGAAATTCGCGTTGTGATAGT
597300 TGTGTTTACCTATATCGGTAATT
1 TGTGTTTACCTATATCGGTAATT
597323 CGCGTTGCGA
Statistics
Matches: 153, Mismatches: 38, Indels: 41
0.66 0.16 0.18
Matches are distributed among these distances:
90 3 0.02
91 41 0.27
92 28 0.18
93 12 0.08
94 5 0.03
95 2 0.01
96 11 0.07
97 28 0.18
98 20 0.13
99 3 0.02
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (91 bp):
TGTGTTTACCTATATCGGTAATTAAGTTCGAAATTGGCAAATTTGATTTGTTAAATTCGCGTTGC
GAAAACGAAATTCGCGTTGTGATAGT
Found at i:597162 original size:21 final size:20
Alignment explanation
Indices: 597136--597204 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
597126 CGGTAATTCG
597136 ATTTTTCAAATTCGCAACGCA
1 ATTTTTCAAA-TCGCAACGCA
* *
597157 ATTTTTAAAATCGCAACCCA
1 ATTTTTCAAATCGCAACGCA
** *
597177 ATTTTGGAAATCGCAACGTGA
1 ATTTTTCAAATCGCAACG-CA
597198 ATTTTTC
1 ATTTTTC
597205 TGCTGTGTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 24 0.62
21 15 0.38
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
ATTTTTCAAATCGCAACGCA
Found at i:597347 original size:20 final size:20
Alignment explanation
Indices: 597322--597372 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
597312 TATCGGTAAT
597322 TCGCGTTGCGAATTTGAAAA
1 TCGCGTTGCGAATTTGAAAA
*
597342 TCGCGTTACGAATTTGAAAA
1 TCGCGTTGCGAATTTGAAAA
597362 TCGCGTTGCGA
1 TCGCGTTGCGA
597373 TAGTACTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGAAAA
Found at i:597395 original size:77 final size:76
Alignment explanation
Indices: 597265--597508 Score: 245
Period size: 77 Copynumber: 3.1 Consensus size: 76
597255 TTTGTTAAAT
* * * **
597265 TCGCGTTGCGAAAACGAAATTCGCGTTGTGATAGTTGTGTTTACCTATATCGGTAATTCGCGTTG
1 TCGCGTTACGAAAATGAAAATCGCGTTGTGATAGTACTGTTTACCTATATCGGTAATT-GCGTTG
597330 CGAATTTGAAAA
65 CGAATTTGAAAA
** * * **
597342 TCGCGTTACGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATGTCGGTAATTAAGTTGC
1 TCGCGTTACGAAAATGAAAATCGCGTTGTGATAGTACTGTTTACCTATATCGGTAATTGCGTTGC
* *
597407 GAAATTGGCGAATTCGAT
66 G-AATT--TGAA----AA
* * * * *
597425 TTGCGTTGCGAAAATGAAAATCGCGTTGTGATAGTACTGTTTACTTATATCGGTAATTAGCATTA
1 TCGCGTTACGAAAATGAAAATCGCGTTGTGATAGTACTGTTTACCTATATCGGTAATT-GCGTTG
597490 CGAATTTGAAAA
65 CGAATTTGAAAA
597502 TCGCGTT
1 TCGCGTT
597509 GCGATAGTAC
Statistics
Matches: 132, Mismatches: 27, Indels: 16
0.75 0.15 0.09
Matches are distributed among these distances:
76 6 0.05
77 60 0.45
79 3 0.02
81 3 0.02
83 56 0.42
84 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (76 bp):
TCGCGTTACGAAAATGAAAATCGCGTTGTGATAGTACTGTTTACCTATATCGGTAATTGCGTTGC
GAATTTGAAAA
Found at i:597468 original size:160 final size:163
Alignment explanation
Indices: 597210--597508 Score: 424
Period size: 160 Copynumber: 1.8 Consensus size: 163
597200 TTTTCTGCTG
* *
597210 TGTTTATCTATGTCGGTAATTAAGTTGCGAAATTGGCAAATTTGATTTGTTAAATTCGCGTTGCG
1 TGTTTACCTATGTCGGTAATTAAGTTGCGAAATTGGCAAATTCGA----TT--ATTCGCGTTGCG
* ** * * *
597275 AAAACGAAATTCGCGTTGTGATAGTTGTGTTTACCTATATCGGTAATTCGCGTTGCGAATTTGAA
60 AAAACGAAAATCGCGTTGTGATAGTACTGTTTACCTATATCGGTAATTAGCATTACGAATTTGAA
597340 AATCGCGTTACGAATTTGAAAATCGCGTTGCGATAGTAC
125 AATCGCGTTACGAATTTGAAAATCGCGTTGCGATAGTAC
* *
597379 TGTTTACCTATGTCGGTAATTAAGTTGCGAAATTGGCGAATTCGA-T-TT-GCGTTGCGAAAATG
1 TGTTTACCTATGTCGGTAATTAAGTTGCGAAATTGGCAAATTCGATTATTCGCGTTGCGAAAACG
*
597441 AAAATCGCGTTGTGATAGTACTGTTTACTTATATCGGTAATTAGCATTACGAATTTGAAAATCGC
66 AAAATCGCGTTGTGATAGTACTGTTTACCTATATCGGTAATTAGCATTACGAATTTGAAAATCGC
597506 GTT
131 GTT
597509 GCGATAGTAC
Statistics
Matches: 119, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
160 74 0.62
161 2 0.02
164 1 0.01
169 42 0.35
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (163 bp):
TGTTTACCTATGTCGGTAATTAAGTTGCGAAATTGGCAAATTCGATTATTCGCGTTGCGAAAACG
AAAATCGCGTTGTGATAGTACTGTTTACCTATATCGGTAATTAGCATTACGAATTTGAAAATCGC
GTTACGAATTTGAAAATCGCGTTGCGATAGTAC
Found at i:597531 original size:57 final size:57
Alignment explanation
Indices: 597439--597558 Score: 186
Period size: 57 Copynumber: 2.1 Consensus size: 57
597429 GTTGCGAAAA
* * *
597439 TGAAAATCGCGTTGTGATAGTACTGTTTACTTATATCGGTAATTAGCATTACGAATT
1 TGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATTAGCATTACGAATT
* *
597496 TGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATTAGCGTTACGATTT
1 TGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATTAGCATTACGAATT
597553 TCGAAA
1 T-GAAA
597559 CTGAGTTGCG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 53 0.93
58 4 0.07
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (57 bp):
TGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATTAGCATTACGAATT
Found at i:604807 original size:31 final size:31
Alignment explanation
Indices: 604769--604843 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
604759 TGATTTTGAA
604769 AAAATTGATAGTTTATGCATTAAAATAAATT
1 AAAATTGATAGTTTATGCATTAAAATAAATT
*
604800 AAAATTGATAGTTTATGTATTAAAATAAATT
1 AAAATTGATAGTTTATGCATTAAAATAAATT
604831 AAAATTGATAGTT
1 AAAATTGATAGTT
604844 CAGATACTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.48, C:0.01, G:0.11, T:0.40
Consensus pattern (31 bp):
AAAATTGATAGTTTATGCATTAAAATAAATT
Found at i:609457 original size:6 final size:6
Alignment explanation
Indices: 609446--609471 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
609436 ATAGAACCCA
609446 CATTGT CATTGT CATTGT CATTGT CA
1 CATTGT CATTGT CATTGT CATTGT CA
609472 ATCACTGCCG
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:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (6 bp):
CATTGT
Found at i:615566 original size:31 final size:31
Alignment explanation
Indices: 615524--615589 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
615514 GGGGAATAGT
615524 CTCTAACATTATCAATCCATTTGATTTTAGC
1 CTCTAACATTATCAATCCATTTGATTTTAGC
* * * *
615555 CTCTAATATTATCGATCCGTTTGATTTTAGT
1 CTCTAACATTATCAATCCATTTGATTTTAGC
615586 CTCT
1 CTCT
615590 CAGCCATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.45
Consensus pattern (31 bp):
CTCTAACATTATCAATCCATTTGATTTTAGC
Found at i:616657 original size:29 final size:30
Alignment explanation
Indices: 616590--616659 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
616580 TTATCGATAA
*
616590 AATGATTATAATAATAATAAATTAAAAGTTT
1 AATGATTA-AATAAAAATAAATTAAAAGTTT
** *
616621 AACAATTAAATTAAAAATAAA-T-AAATTTT
1 AATGATTAAA-TAAAAATAAATTAAAAGTTT
616650 AATGATTAAA
1 AATGATTAAA
616660 ATATGAATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 14 0.44
30 3 0.09
31 15 0.47
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (30 bp):
AATGATTAAATAAAAATAAATTAAAAGTTT
Found at i:617123 original size:60 final size:60
Alignment explanation
Indices: 617056--617168 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
617046 TCAGGTGACC
* * *
617056 ATTTTGTAACTTTTAATAGTCGAGGGACTTAA-AAAAGTAATATTCTATAGTTGAAGGCCT
1 ATTTTGTAAATTTTAATAGTCAAGAGACTTAATAAAA-TAATATTCTATAGTTGAAGGCCT
617116 ATTTTGTAAATTTTAATAGTCAAGAGACTTAATAAAATAATATTCTATAGTTG
1 ATTTTGTAAATTTTAATAGTCAAGAGACTTAATAAAATAATATTCTATAGTTG
617169 GGTACCATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
60 45 0.92
61 4 0.08
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (60 bp):
ATTTTGTAAATTTTAATAGTCAAGAGACTTAATAAAATAATATTCTATAGTTGAAGGCCT
Found at i:625823 original size:14 final size:14
Alignment explanation
Indices: 625783--625824 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
625773 GTTCATTTAT
* *
625783 GTTCATTTATATCC
1 GTTCATTTATGTTC
625797 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
625811 GTTCATTTGTGTTC
1 GTTCATTTATGTTC
625825 ATTTATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:625824 original size:24 final size:24
Alignment explanation
Indices: 625773--625830 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
625763 GTTTACGTTG
*
625773 GTTCATTTATGTTCATTTATATCC
1 GTTCATTTATGTTCATTCATATCC
* * **
625797 GTTCATTTATGTTCGTTCATTTGT
1 GTTCATTTATGTTCATTCATATCC
625821 GTTCATTTAT
1 GTTCATTTAT
625831 CATTTAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.57
Consensus pattern (24 bp):
GTTCATTTATGTTCATTCATATCC
Found at i:631080 original size:20 final size:20
Alignment explanation
Indices: 631055--631095 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
631045 CCTATCTCTC
631055 AGCTGCAATCAAATAGAGAA
1 AGCTGCAATCAAATAGAGAA
631075 AGCTGCAATCAAATAGAGAA
1 AGCTGCAATCAAATAGAGAA
631095 A
1 A
631096 CAAGAAGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.15, G:0.20, T:0.15
Consensus pattern (20 bp):
AGCTGCAATCAAATAGAGAA
Found at i:633308 original size:60 final size:60
Alignment explanation
Indices: 633240--633352 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
633230 AATGGTTTTA
** * *
633240 TGACTATAGGGTATTGTTTTATTAAG-T-CTATCGACTATTAAAAGTTATAAAATGATCATT
1 TGACTATAGAATATTATTTTATTAAGTTCCT-TAG-CTATTAAAAGTTATAAAATGATCATT
*
633300 TGACTATAGAATATTATTTTGTTAAGTTCCTTAGCTATTAAAAGTTATAAAAT
1 TGACTATAGAATATTATTTTATTAAGTTCCTTAGCTATTAAAAGTTATAAAAT
633353 TGTCACCCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 41 0.89
61 3 0.07
62 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (60 bp):
TGACTATAGAATATTATTTTATTAAGTTCCTTAGCTATTAAAAGTTATAAAATGATCATT
Found at i:637297 original size:31 final size:31
Alignment explanation
Indices: 637256--637326 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
637246 TTATTTTGAT
*
637256 TTTGCACCCTCATTTTCTATGGTTAATTATAC
1 TTTGC-CCCTCATTTTCTATGATTAATTATAC
*
637288 TTTGCCCCTCATTTTCTATGATTAATTATAT
1 TTTGCCCCTCATTTTCTATGATTAATTATAC
637319 TTTGCCCC
1 TTTGCCCC
637327 CTTAAGTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
31 32 0.86
32 5 0.14
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (31 bp):
TTTGCCCCTCATTTTCTATGATTAATTATAC
Found at i:643404 original size:28 final size:29
Alignment explanation
Indices: 643364--643438 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
643354 GAACAGTAAG
643364 TACCTATTTTGACATAAA-ATACTTTAGA
1 TACCTATTTTGACATAAATATACTTTAGA
*
643392 TACCTATTTTGACCA-AAATATACTTTAGG
1 TACCTATTTTGA-CATAAATATACTTTAGA
* *
643421 TACTTATTTGTGATATAA
1 TACCTATTT-TGACATAA
643439 GCCAAATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 15 0.38
29 20 0.50
30 5 0.12
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.41
Consensus pattern (29 bp):
TACCTATTTTGACATAAATATACTTTAGA
Found at i:644260 original size:60 final size:59
Alignment explanation
Indices: 644137--644250 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
644127 ATTGTCATGT
* * *
644137 GATCATTTTGTAACTTAAATAGACGAGGGACTTAACAAAGCAACATTCTATAGTCAAAA
1 GATCATTTTGTAACTTAAATAGACAAGAGACTTAACAAAGCAAAATTCTATAGTCAAAA
* * * ** *
644196 GATCATTTTGTAACTTTTAATCGTCAAGAGACTTATTAAAGCAAAATTCTTTAGT
1 GATCATTTTGTAAC-TTAAATAGACAAGAGACTTAACAAAGCAAAATTCTATAGT
644251 TAAGGGATCA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
59 14 0.31
60 31 0.69
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (59 bp):
GATCATTTTGTAACTTAAATAGACAAGAGACTTAACAAAGCAAAATTCTATAGTCAAAA
Found at i:648811 original size:60 final size:60
Alignment explanation
Indices: 648675--648812 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 60
648665 TTAAATACAC
*
648675 AAATGGTCCTCCGACTATAGGGTACTACTTTATTAAGTCTCTCGACTATTAAAAGTTAGA
1 AAATGGTCCTCCGACTATAGAGTACTACTTTATTAAGTCTCTCGACTATTAAAAGTTAGA
* * ** ** * *
648735 AAACGATCCTTTGACTATAGAGTGTTACTTTGTTGAGTCTCTCGACTATTAAAAGTTAGA
1 AAATGGTCCTCCGACTATAGAGTACTACTTTATTAAGTCTCTCGACTATTAAAAGTTAGA
648795 AAATGGTCAC-CCGACTAT
1 AAATGGTC-CTCCGACTAT
648813 TCATTATGTA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 63 0.98
61 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (60 bp):
AAATGGTCCTCCGACTATAGAGTACTACTTTATTAAGTCTCTCGACTATTAAAAGTTAGA
Found at i:649083 original size:60 final size:60
Alignment explanation
Indices: 649009--649147 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
648999 AGCATAATGA
* * ** * *
649009 ATAGTCA-AGTGACTATTTTGTAACTTTTAATAGTTGAGGGACTTAATAAAGCAACAT-TCT
1 ATAGTCAGAG-GACTATTTTATAACTATTAATAGTCAACGGACTTAATAAAACAACATCT-T
* * *
649069 ATAGTCAGAGGACTATTTTATAACTATTAATAGTCAACTGACTTAATAAAATAATATCTT
1 ATAGTCAGAGGACTATTTTATAACTATTAATAGTCAACGGACTTAATAAAACAACATCTT
*
649129 ATAGTCAGGGGACTATTTT
1 ATAGTCAGAGGACTATTTT
649148 TGCACTTTAC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 64 0.96
61 3 0.04
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (60 bp):
ATAGTCAGAGGACTATTTTATAACTATTAATAGTCAACGGACTTAATAAAACAACATCTT
Found at i:650622 original size:21 final size:21
Alignment explanation
Indices: 650568--650623 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
650558 TTTACTGATA
* *
650568 ATGTCTACCTTAAAAATTTTC
1 ATGTCTAACTTGAAAATTTTC
* *
650589 ATGTCT-ACATGAAAATTTTT
1 ATGTCTAACTTGAAAATTTTC
650609 ATGTCTAACTTGAAA
1 ATGTCTAACTTGAAA
650624 TCTGAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (21 bp):
ATGTCTAACTTGAAAATTTTC
Found at i:661344 original size:2 final size:2
Alignment explanation
Indices: 661337--661380 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
661327 CCATGGTTTC
661337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
661379 AT
1 AT
661381 TCTTTGCACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:673829 original size:10 final size:10
Alignment explanation
Indices: 673816--673840 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
673806 ATATGATAGG
673816 CCATGGCATT
1 CCATGGCATT
673826 CCATGGCATT
1 CCATGGCATT
673836 CCATG
1 CCATG
673841 TCCATGCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.28
Consensus pattern (10 bp):
CCATGGCATT
Found at i:676292 original size:18 final size:18
Alignment explanation
Indices: 676255--676294 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
676245 TTCTTCTTCC
*
676255 TTCTTTTCTCCCCCTTCT
1 TTCTTTTCTCCCCCTCCT
*
676273 TTCTTTTCTCCTCCTCCT
1 TTCTTTTCTCCCCCTCCT
676291 TTCT
1 TTCT
676295 GCTGCTCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.57
Consensus pattern (18 bp):
TTCTTTTCTCCCCCTCCT
Found at i:676312 original size:33 final size:33
Alignment explanation
Indices: 676270--676376 Score: 146
Period size: 33 Copynumber: 3.2 Consensus size: 33
676260 TTCTCCCCCT
* *
676270 TCTTTCTTTTCTCC-TCCTCCTT-TCTGCTGCTCC
1 TCTTTCTTTTCACCTTCCTCCTTCTTTG--GCTCC
*
676303 TCTTTCTTTTCACCTTCGTCCTTCTTTGGCTCC
1 TCTTTCTTTTCACCTTCCTCCTTCTTTGGCTCC
*
676336 TCTTTCTTTTCACCTTCTTCCTTCTTTGGCTCC
1 TCTTTCTTTTCACCTTCCTCCTTCTTTGGCTCC
676369 TCTTTCTT
1 TCTTTCTT
676377 CTCCGGTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
33 58 0.85
34 7 0.10
35 3 0.04
ACGTcount: A:0.02, C:0.37, G:0.07, T:0.54
Consensus pattern (33 bp):
TCTTTCTTTTCACCTTCCTCCTTCTTTGGCTCC
Found at i:676372 original size:18 final size:18
Alignment explanation
Indices: 676321--676378 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
676311 TTCACCTTCG
676321 TCCTTCTTTGGCTCCTC-
1 TCCTTCTTTGGCTCCTCT
* *
676338 T--TTCTTT-TCACCTTCT
1 TCCTTCTTTGGCTCC-TCT
676354 TCCTTCTTTGGCTCCTCT
1 TCCTTCTTTGGCTCCTCT
*
676372 TTCTTCT
1 TCCTTCT
676379 CCGGTTCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
14 3 0.10
15 8 0.26
16 1 0.03
17 1 0.03
18 15 0.48
19 3 0.10
ACGTcount: A:0.02, C:0.36, G:0.07, T:0.55
Consensus pattern (18 bp):
TCCTTCTTTGGCTCCTCT
Found at i:685987 original size:37 final size:37
Alignment explanation
Indices: 685914--685988 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
685904 GTTGAAAAAT
* * *
685914 ATTTATATATTTTCTTTAAAAAATTTATATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
685951 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
685988 A
1 A
685989 AGATTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:689558 original size:17 final size:17
Alignment explanation
Indices: 689536--689569 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
689526 TTTTGAGCTT
*
689536 GATTCAAACTCGAACTC
1 GATTCAAACTAGAACTC
*
689553 GATTCAAGCTAGAACTC
1 GATTCAAACTAGAACTC
689570 AAACTCGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (17 bp):
GATTCAAACTAGAACTC
Found at i:692607 original size:7 final size:7
Alignment explanation
Indices: 692595--692646 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
692585 CATAATTGAA
692595 TTTAGGG
1 TTTAGGG
692602 TTTAGGG
1 TTTAGGG
* *
692609 TTTAAGA
1 TTTAGGG
*
692616 TTTATGGT
1 TTTA-GGG
*
692624 TTTAGGA
1 TTTAGGG
*
692631 TTTATGG
1 TTTAGGG
692638 TTTAGGG
1 TTTAGGG
692645 TT
1 TT
692647 CATTACAAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
7 31 0.86
8 5 0.14
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:692632 original size:15 final size:15
Alignment explanation
Indices: 692595--692640 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
692585 CATAATTGAA
* *
692595 TTTAGGGTTTA-GGG
1 TTTAGGATTTATGGT
*
692609 TTTAAGATTTATGGT
1 TTTAGGATTTATGGT
692624 TTTAGGATTTATGGT
1 TTTAGGATTTATGGT
692639 TT
1 TT
692641 AGGGTTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
TTTAGGATTTATGGT
Found at i:692642 original size:14 final size:14
Alignment explanation
Indices: 692595--692643 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
692585 CATAATTGAA
* *
692595 TTTAGGGTTTAGGG
1 TTTAGGATTTATGG
*
692609 TTTAAGATTTATGG
1 TTTAGGATTTATGG
692623 TTTTAGGATTTATGG
1 -TTTAGGATTTATGG
692638 TTTAGG
1 TTTAGG
692644 GTTCATTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
TTTAGGATTTATGG
Found at i:695065 original size:309 final size:308
Alignment explanation
Indices: 694508--695123 Score: 1207
Period size: 309 Copynumber: 2.0 Consensus size: 308
694498 GTTTTGAAGA
694508 AAAAAATTAAGTCTATGTACTAAAATAGGCCAAAACTGATAGTTTATGTATTAAATGCGTTAAGT
1 AAAAAATTAAGTCTATGTACTAAAATAGGCCAAAACTGATAGTTTATGTATTAAATGCGTTAAGT
694573 TTTTAACGCATGTACTAAAATGAAACAAAAATTAAATGTTAAGTATGATTTTAGAAAAATTAAAA
66 TTTTAACGCATGTACTAAAATGAAACAAAAATTAAATGTTAAGTATGATTTTAGAAAAATTAAAA
694638 GTTTAGGTACTAAAACGGATCAAATATGATAGTTAGATACTAAATGCATAGTTTATCCTAGTTAA
131 GTTTAGGTACTAAAACGGATCAAATATGATAGTTAGATACTAAATGCATAGTTTATCCTAGTTAA
694703 AATCATATGTATAAACCCACGGGGATCTAAAATGTAATTTAACTAATTTTTAAAAAATAATGTAC
196 AATCATATGTATAAACCCACGGGGATCTAAAATGTAATTTAACTAATTTTTAAAAAATAATGTAC
694768 CCTACCGAAGTGCATCGTCACTTTCACGTGGACAGATTTTCTCAATGAG
261 CCTACCGAAGTGCATCGTCACTTTCACGTGGACAGA-TTTCTCAATGAG
694817 AAAAAATTAAGTCTATGTACTAAAATAGGCCAAAACTGATAGTTTATGTATTAAATGCGTTAAGT
1 AAAAAATTAAGTCTATGTACTAAAATAGGCCAAAACTGATAGTTTATGTATTAAATGCGTTAAGT
694882 TTTTAACGCATGTACTAAAATGAAACAAAAATTAAATGTTAAGTATGATTTTAGAAAAATTAAAA
66 TTTTAACGCATGTACTAAAATGAAACAAAAATTAAATGTTAAGTATGATTTTAGAAAAATTAAAA
694947 GTTTAGGTACTAAAACGGATCAAATATGATAGTTTAGATACTAAATGCATAGTTTATCCTAGTTA
131 GTTTAGGTACTAAAACGGATCAAATATGATAG-TTAGATACTAAATGCATAGTTTATCCTAGTTA
695012 AAATCATATGTATAAACCCACGGGGATCTAAAATGTAATTTAACTAA-TTTTAAAAAATAATGTA
195 AAATCATATGTATAAACCCACGGGGATCTAAAATGTAATTTAACTAATTTTTAAAAAATAATGTA
695076 CCCTACCGAAGTGCATCGTCACTTTCACGTGGACAGATTTCTCAATGA
260 CCCTACCGAAGTGCATCGTCACTTTCACGTGGACAGATTTCTCAATGA
695124 ATGATTGTTA
Statistics
Matches: 306, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
308 11 0.04
309 216 0.71
310 79 0.26
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (308 bp):
AAAAAATTAAGTCTATGTACTAAAATAGGCCAAAACTGATAGTTTATGTATTAAATGCGTTAAGT
TTTTAACGCATGTACTAAAATGAAACAAAAATTAAATGTTAAGTATGATTTTAGAAAAATTAAAA
GTTTAGGTACTAAAACGGATCAAATATGATAGTTAGATACTAAATGCATAGTTTATCCTAGTTAA
AATCATATGTATAAACCCACGGGGATCTAAAATGTAATTTAACTAATTTTTAAAAAATAATGTAC
CCTACCGAAGTGCATCGTCACTTTCACGTGGACAGATTTCTCAATGAG
Found at i:696243 original size:17 final size:18
Alignment explanation
Indices: 696207--696249 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
696197 CAAGTCAGAA
*
696207 TAGAAAAATATATTATTT
1 TAGAAAAATATATTAATT
*
696225 TAGATAAAT-TATTAATT
1 TAGAAAAATATATTAATT
*
696242 TATAAAAA
1 TAGAAAAA
696250 ATCTAGTGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TAGAAAAATATATTAATT
Found at i:697969 original size:21 final size:21
Alignment explanation
Indices: 697943--697987 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
697933 CAAAATTTTA
697943 AATCATCATTTTAACATAAGT
1 AATCATCATTTTAACATAAGT
697964 AATCATCATTTTAACATAAGT
1 AATCATCATTTTAACATAAGT
697985 AAT
1 AAT
697988 TAACGATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38
Consensus pattern (21 bp):
AATCATCATTTTAACATAAGT
Found at i:707014 original size:6 final size:6
Alignment explanation
Indices: 707003--707033 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
706993 GGATAGTATT
707003 GTTGCA GTTGCA GTTGCA GTTGCA GTTGCA G
1 GTTGCA GTTGCA GTTGCA GTTGCA GTTGCA G
707034 CTTGTAGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.35, T:0.32
Consensus pattern (6 bp):
GTTGCA
Found at i:707775 original size:41 final size:42
Alignment explanation
Indices: 707705--707785 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
707695 TTAAGATTCA
* *
707705 AATTTTTGATCTTACTTAAGAGATTTAAT-ATTTATCTCATT
1 AATTTTTGATCTTACTTAAGAAATCTAATAATTTATCTCATT
*
707746 AATTTTT-ATCTTACTTAAAGAAATCTAATAATTTTTCTCA
1 AATTTTTGATCTTACTT-AAGAAATCTAATAATTTATCTCA
707786 CTAAACTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 9 0.26
41 17 0.49
42 9 0.26
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (42 bp):
AATTTTTGATCTTACTTAAGAAATCTAATAATTTATCTCATT
Found at i:712108 original size:13 final size:13
Alignment explanation
Indices: 712090--712118 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
712080 AATTTATTAA
712090 TATATATATATAT
1 TATATATATATAT
712103 TATATATATATAT
1 TATATATATATAT
712116 TAT
1 TAT
712119 TAAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATATATATATAT
Found at i:716008 original size:48 final size:48
Alignment explanation
Indices: 715936--716032 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
715926 CATATGTAAT
715936 GGGGTAAAGGGGAGGTAGGGTAGTAGGCTGGCCCCCAACGCCAGGTTGA
1 GGGGTAAAGGGGAGGTAGGGTAGTAGGCTGGCCCCCAAC-CCAGGTTGA
715985 GGGGTAAA-GGGAGGTAGGGTAGTAGGCTGGCCCCCAACCCAGGTTGA
1 GGGGTAAAGGGGAGGTAGGGTAGTAGGCTGGCCCCCAACCCAGGTTGA
716032 G
1 G
716033 AGTCCCCCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 10 0.21
48 30 0.62
49 8 0.17
ACGTcount: A:0.23, C:0.19, G:0.44, T:0.14
Consensus pattern (48 bp):
GGGGTAAAGGGGAGGTAGGGTAGTAGGCTGGCCCCCAACCCAGGTTGA
Found at i:716041 original size:21 final size:22
Alignment explanation
Indices: 716015--716056 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
716005 AGTAGGCTGG
716015 CCCCCAAC-CCAGGTTGAGAGT
1 CCCCCAACACCAGGTTGAGAGT
716036 CCCCCAACACCAGGTTGAGAG
1 CCCCCAACACCAGGTTGAGAG
716057 CAGCTTCCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.26, C:0.38, G:0.24, T:0.12
Consensus pattern (22 bp):
CCCCCAACACCAGGTTGAGAGT
Found at i:720072 original size:145 final size:146
Alignment explanation
Indices: 719872--720162 Score: 530
Period size: 145 Copynumber: 2.0 Consensus size: 146
719862 GTATTACTAT
719872 GCTTTTATTTACTATTTAAGGTGTGTGAAAGATGTGTCATATTTCTAACTCGTTGGTTTGGTATT
1 GCTTTTATTTACTATTTAAGGTGTGTGAAAGATGTGTCATATTTCTAACTCGTTGGTTTGGTATT
* *
719937 CTTAATGTCATGATTAATAGTTTGTTGTTTATTGTAATG-TCATGGTTTGTTGTTTTTATAGTCC
66 CTTAATGTCATGATTAATAGTTTGTTGTTTAATATAATGTTCATGGTTTGTTGTTTTTATAGTCC
720001 AAATCTATAACAAATG
131 AAATCTATAACAAATG
* * *
720017 GCTTTTATTTACTATTTAAGGTTTGTGAAAGATGTGTCGTATTTCTAACTTGTTGGTTTGGTATT
1 GCTTTTATTTACTATTTAAGGTGTGTGAAAGATGTGTCATATTTCTAACTCGTTGGTTTGGTATT
720082 CTTAATGTCATGATTAATAGTTTGTTGTTTAATATAATGTTCATGGTTTGTTGTTTTTATAGTCC
66 CTTAATGTCATGATTAATAGTTTGTTGTTTAATATAATGTTCATGGTTTGTTGTTTTTATAGTCC
720147 AAATCTATAACAAATG
131 AAATCTATAACAAATG
720163 TCGTATTGAA
Statistics
Matches: 140, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
145 99 0.71
146 41 0.29
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.48
Consensus pattern (146 bp):
GCTTTTATTTACTATTTAAGGTGTGTGAAAGATGTGTCATATTTCTAACTCGTTGGTTTGGTATT
CTTAATGTCATGATTAATAGTTTGTTGTTTAATATAATGTTCATGGTTTGTTGTTTTTATAGTCC
AAATCTATAACAAATG
Found at i:734433 original size:59 final size:60
Alignment explanation
Indices: 734276--734443 Score: 198
Period size: 60 Copynumber: 2.8 Consensus size: 60
734266 TACGATCCCT
* * * *
734276 ATTCTAAATTGGTCCCTAAACTTTTGATTATTTTAATTTCATCCTCAAACTATGATACTC
1 ATTCTAAATTGGTCCCTAAACTTTTGAATCTTCTAATTTCATCCTCAAACTACGATACTC
* * *
734336 ATTCTAAATTAGG-CCTTAAACTTTTGAA-CATTCTAATTTTATCCTCAAACTACGA-CCTC
1 ATTCTAAATT-GGTCCCTAAACTTTTGAATC-TTCTAATTTCATCCTCAAACTACGATACTC
* * * *
734395 ATTCTAAATTGGTCCCCAAACTTTTAAATCTTCCAATTTCATCCCCAAA
1 ATTCTAAATTGGTCCCTAAACTTTTGAATCTTCTAATTTCATCCTCAAA
734444 GTCATCCAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 41 0.45
60 46 0.51
61 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.39
Consensus pattern (60 bp):
ATTCTAAATTGGTCCCTAAACTTTTGAATCTTCTAATTTCATCCTCAAACTACGATACTC
Found at i:738304 original size:2 final size:2
Alignment explanation
Indices: 738297--738341 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
738287 TACAAACACT
738297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
738339 TA T
1 TA T
738342 TAAGTTTACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:745392 original size:37 final size:36
Alignment explanation
Indices: 745308--745439 Score: 171
Period size: 37 Copynumber: 3.7 Consensus size: 36
745298 GTCCTACTAG
*
745308 GATTCAAACTCCTAAAAATAGGATAGAA-TTT-TAG
1 GATTCAAACTCCTAAAAATAGGATAGAATTTTCTAT
745342 GATTCAAACTCCTAAAAATAGGATA-ACATTTTGCTAT
1 GATTCAAACTCCTAAAAATAGGATAGA-ATTTT-CTAT
* *
745379 GATTCAAACTCCTAAAAATAGGATAGAGTTCTACTAT
1 GATTCAAACTCCTAAAAATAGGATAGAATT-TTCTAT
* *
745416 GATTTAAACTCCTAAAGATAGGAT
1 GATTCAAACTCCTAAAAATAGGAT
745440 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
33 1 0.01
34 26 0.30
35 3 0.03
37 55 0.63
38 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (36 bp):
GATTCAAACTCCTAAAAATAGGATAGAATTTTCTAT
Found at i:745901 original size:2 final size:2
Alignment explanation
Indices: 745850--745882 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
745840 TTAGTGTTAT
745850 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
745883 TTTATTTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:748925 original size:16 final size:16
Alignment explanation
Indices: 748899--748944 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
748889 AGATCCAATC
748899 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
748914 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
748931 AA-AA-AAAAAA-CAA
1 AAGAACAAAAAAGCAA
748944 A
1 A
748945 GAAAAAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 5 0.17
16 10 0.34
17 4 0.14
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:749656 original size:22 final size:22
Alignment explanation
Indices: 749628--749671 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
749618 AGCTACCCCA
749628 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
749650 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
749672 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:750666 original size:36 final size:36
Alignment explanation
Indices: 750623--750901 Score: 290
Period size: 36 Copynumber: 7.9 Consensus size: 36
750613 ACTAGAAGAG
*
750623 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACATA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
750659 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
750695 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
750731 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
750767 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * * * *
750796 TTCCGTCTCCCTTGAGACAGTTT-CTTGTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCT-TGAAAC-AAA
*
750833 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
750868 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAAC
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAAC
750902 GAAACCTTTG
Statistics
Matches: 201, Mismatches: 29, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 9 0.04
36 139 0.69
37 29 0.14
38 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:750862 original size:102 final size:102
Alignment explanation
Indices: 750679--750867 Score: 283
Period size: 102 Copynumber: 1.9 Consensus size: 102
750669 CTTGAGACAG
* *
750679 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
750744 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* * * *
750781 TTTCT-TTGAAACAAATTCCGTCTCCCTTGAGACAGTTT-CTTGTGGAACTAAGTTTTGTCTCTC
1 TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCT-T-GAAATAAATTTTGTCTCTC
*
750844 TTGAGACAGTTTCTCTTGAAACAA
64 TTGAGACAGTTTCCCTTGAAACAA
750868 TTTTCGTCTA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
100 2 0.03
101 31 0.40
102 45 0.58
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:750896 original size:138 final size:137
Alignment explanation
Indices: 750643--750967 Score: 411
Period size: 138 Copynumber: 2.4 Consensus size: 137
750633 CTTGAGACAG
* *
750643 TTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* *
750708 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
750773 GAATATG
131 GAATATA
* * ** * * * *
750780 TTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCT-TGTGGAACTAAGTTTTGTCTCTC
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCT-TGAAAC-AAATTTCGTCTATC
* * * *
750844 TTGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACGAAACC
64 TTGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACA
*
750908 TTTGAATTTA
128 TTTGAATATA
* * * *
750918 TTTCCCCTAAAATAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
750968 CAAAATCTTC
Statistics
Matches: 157, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
136 1 0.01
137 47 0.30
138 108 0.69
139 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:752010 original size:105 final size:104
Alignment explanation
Indices: 751640--752712 Score: 1549
Period size: 105 Copynumber: 10.3 Consensus size: 104
751630 GCCATCCGCG
* * * * * *
751640 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
751705 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAA-TTCAGAGCCA
751749 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
751814 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAA-CAACAA-CTTCCCAA-TTCAGAGCCA
*
751856 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
751921 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
751961 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
752026 ACCGCTGCTTGTCAACAACAACTTTCCAGTCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
752066 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
752131 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* *
752166 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
752231 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
752271 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
752336 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* *
752371 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
752436 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
* *
752476 ATTTCAACTTTACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
752541 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* * * *
752576 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGGCAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
752641 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATT-CAGAGCCA
* *
752682 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
752713 TGGAACAATG
Statistics
Matches: 888, Mismatches: 57, Indels: 41
0.90 0.06 0.04
Matches are distributed among these distances:
100 257 0.29
101 11 0.01
102 9 0.01
103 10 0.01
104 12 0.01
105 375 0.42
106 93 0.10
107 99 0.11
109 22 0.02
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
Found at i:752246 original size:205 final size:205
Alignment explanation
Indices: 751640--752712 Score: 1619
Period size: 205 Copynumber: 5.2 Consensus size: 205
751630 GCCATCCGCG
* * * * * *
751640 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
751705 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAAC-AA-AA-TT-TC-A-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* * *
751770 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
122 ATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
* *
751835 ATTTTCCCAATTTCAGAGCCA
186 ACTTT-CCAATCTCAGAGCCA
*
751856 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
751921 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
751986 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
126 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
*
752051 CCAGTCTCAGAGCCA
191 CCAATCTCAGAGCCA
*
752066 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
752131 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
752196 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
752261 CTCAGAGCCA
196 CTCAGAGCCA
752271 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
752336 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
752401 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
*
752466 CCCAGAGCCA
196 CTCAGAGCCA
* *
752476 ATTTCAACTTTACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
752541 ACCGCTGCTTGTCAACAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* * ** * * * *
752606 TCGAGGCAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCCG
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTT-CCA
*
752670 GT-TCCAGAGCCA
194 ATCT-CAGAGCCA
* *
752682 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
752713 TGGAACAATG
Statistics
Matches: 808, Mismatches: 45, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
205 484 0.60
206 45 0.06
207 1 0.00
208 2 0.00
209 2 0.00
210 93 0.12
211 9 0.01
212 99 0.12
213 49 0.06
214 3 0.00
216 21 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (205 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
CTCAGAGCCA
Found at i:752254 original size:310 final size:311
Alignment explanation
Indices: 751640--752712 Score: 1576
Period size: 310 Copynumber: 3.4 Consensus size: 311
751630 GCCATCCGCG
* * * *
751640 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACACAAGTTCAACTTCACAACGAA
* * * *
751705 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAACAAACAA-TT-TCCAGTTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
751770 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
126 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
*
751835 ATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
190 ACTTT--CAA-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
*
751900 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
252 GTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-CCAATCTCAGAGCCA
** *
751961 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
752026 ACCGCTGCTTGTCAAC-AACAACTTTCCAGTCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
66 ACCGCTGCTTGTCAACAAACAA-TTTCCAGT-TCAGAGCCAATTTCAACTTCACAACGAAGGATA
*
752090 TTGGACTCCAGACGACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT
129 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT
*
752153 TC-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAAC
194 TCAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
752217 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
259 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAAC-TTCCAATCTCAGAGCCA
* *
752271 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
*
752336 ACCGCTGCTTGTCAAC-AA-AATTT-CA-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
66 ACCGCTGCTTGTCAACAAACAATTTCCAGTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
* * *
752397 GGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-T
* * * *
752462 CAATCCCAGAGCCAATTTCAACTTTACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAAC
195 CAAT-TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* **
752527 TTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTTC-AT-TCAGATTCA
259 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGAGCCA
* *
752576 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGGCAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
752641 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATA
66 ACCGCTGCTTGTCAACAAACAATTT-CCAGTT-CAGAGCCAATTTCAACTTCACAACGAAGGATA
752706 TTGGACT
129 TTGGACT
752713 TGGAACAATG
Statistics
Matches: 699, Mismatches: 40, Indels: 36
0.90 0.05 0.05
Matches are distributed among these distances:
305 170 0.24
306 7 0.01
307 12 0.02
308 4 0.01
309 7 0.01
310 281 0.40
311 39 0.06
312 1 0.00
314 3 0.00
315 2 0.00
316 6 0.01
317 95 0.14
318 47 0.07
319 3 0.00
321 22 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (311 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
ACCGCTGCTTGTCAACAAACAATTTCCAGTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
AATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGAGCCA
Found at i:753342 original size:37 final size:36
Alignment explanation
Indices: 753258--753389 Score: 171
Period size: 37 Copynumber: 3.7 Consensus size: 36
753248 GTCCTACTAG
*
753258 GATTCAAACTCCTAAAAATAGGATAGAA-TTT-TAG
1 GATTCAAACTCCTAAAAATAGGATAGAATTTTCTAT
753292 GATTCAAACTCCTAAAAATAGGATA-ACATTTTGCTAT
1 GATTCAAACTCCTAAAAATAGGATAGA-ATTTT-CTAT
* *
753329 GATTCAAACTCCTAAAAATAGGATAGAGTTCTACTAT
1 GATTCAAACTCCTAAAAATAGGATAGAATT-TTCTAT
* *
753366 GATTTAAACTCCTAAAGATAGGAT
1 GATTCAAACTCCTAAAAATAGGAT
753390 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
33 1 0.01
34 26 0.30
35 3 0.03
37 55 0.63
38 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (36 bp):
GATTCAAACTCCTAAAAATAGGATAGAATTTTCTAT
Found at i:758451 original size:25 final size:25
Alignment explanation
Indices: 758423--758472 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
758413 GGTAAATTAC
* *
758423 ATTGTTCCTCATTGTACTTTACTCT
1 ATTGTTCCTCACTGAACTTTACTCT
758448 ATTGTTCCTCACTGAACTTTACTCT
1 ATTGTTCCTCACTGAACTTTACTCT
758473 CTCTCCTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.18, C:0.26, G:0.08, T:0.48
Consensus pattern (25 bp):
ATTGTTCCTCACTGAACTTTACTCT
Found at i:765562 original size:40 final size:40
Alignment explanation
Indices: 765518--765593 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
765508 GGGCTGGGCA
765518 TGGGTTTGTTGTTCGGCTCAATTGAGGGATTTTTCGAGCT
1 TGGGTTTGTTGTTCGGCTCAATTGAGGGATTTTTCGAGCT
765558 TGGGTTTGTTGTTCGGCTCAATTGAGGGATTTTTCG
1 TGGGTTTGTTGTTCGGCTCAATTGAGGGATTTTTCG
765594 TTAACTGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.12, C:0.12, G:0.33, T:0.43
Consensus pattern (40 bp):
TGGGTTTGTTGTTCGGCTCAATTGAGGGATTTTTCGAGCT
Found at i:766184 original size:156 final size:153
Alignment explanation
Indices: 765941--766245 Score: 475
Period size: 156 Copynumber: 2.0 Consensus size: 153
765931 GTTGAGACTA
*
765941 CAGTTAAGGAATGGTTGAATTTTCATTCATCCACTTTAGATATTTAGGTTTCTTCCTCTATGTTC
1 CAGTTAAGGAATGGTTGAATTTTCATTCATCCACTTTAGATATTTAGGTTTCTTCCTCTATATTC
** * *
766006 AATGTTTGGGAATGTTGGAGTAATCGATCTTTATATGACATTGCTTCAACCGTTCACACTCTTAT
66 AATGTTTGGGAATGTTGGAGTAATCGATCTCCATATGACATTGATTCAAACGTTCACACTCTTAT
*
766071 TTATTAGATTATCATTGTGATTG
131 TTATTAGACTATCATTGTGATTG
* * * *
766094 CAGTTAAGGGATGGTTGATTTTTCATTCGTCCACTTTGGATATTCTTTAGGTTTCTTCCTCTATA
1 CAGTTAAGGAATGGTTGAATTTTCATTCATCCACTTTAGATA---TTTAGGTTTCTTCCTCTATA
* *
766159 TTCAATGTTTGGGAATGTTGGAGTAATCGATCTCCATATGACGTTGATTCAAACGTTCATACTCT
63 TTCAATGTTTGGGAATGTTGGAGTAATCGATCTCCATATGACATTGATTCAAACGTTCACACTCT
766224 TATTTATTAGACTATCATTGTG
128 TATTTATTAGACTATCATTGTG
766246 TGTGAACTCT
Statistics
Matches: 137, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
153 38 0.28
156 99 0.72
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (153 bp):
CAGTTAAGGAATGGTTGAATTTTCATTCATCCACTTTAGATATTTAGGTTTCTTCCTCTATATTC
AATGTTTGGGAATGTTGGAGTAATCGATCTCCATATGACATTGATTCAAACGTTCACACTCTTAT
TTATTAGACTATCATTGTGATTG
Found at i:778390 original size:67 final size:67
Alignment explanation
Indices: 778282--778418 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
778272 GCTGTCATGT
778282 ACTCAAAGTTTTCCTTCTATCTATTTATTTAATTCTATGTTAATCGAGTATTCTTGTATGTTGCA
1 ACTCAAAGTTTTCCTTCTATCTATTTATTTAATTCTATGTTAATCGAGTATTCTTGTATGTTGCA
778347 GA
66 GA
778349 ACTCAAAGTTTTCCTTCTATCTATTTATTTAATTCTATGTTAATCGAGTATTCTTGTATGTTGCA
1 ACTCAAAGTTTTCCTTCTATCTATTTATTTAATTCTATGTTAATCGAGTATTCTTGTATGTTGCA
778414 GA
66 GA
778416 ACT
1 ACT
778419 TGAAGTATGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (67 bp):
ACTCAAAGTTTTCCTTCTATCTATTTATTTAATTCTATGTTAATCGAGTATTCTTGTATGTTGCA
GA
Found at i:781041 original size:35 final size:35
Alignment explanation
Indices: 780999--781069 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
780989 TGTTAAAAAA
780999 TTCAAAATACTTCAATTACATTCTAAAACCC-AAAT
1 TTCAAAATACTTCAATTACATTCT-AAACCCTAAAT
* *
781034 TTCAAAATACTTTAATTATATTCTAAACCCTAAAT
1 TTCAAAATACTTCAATTACATTCTAAACCCTAAAT
781069 T
1 T
781070 GAAGTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 6 0.18
35 27 0.82
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (35 bp):
TTCAAAATACTTCAATTACATTCTAAACCCTAAAT
Found at i:781113 original size:35 final size:35
Alignment explanation
Indices: 781065--781141 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
781055 TCTAAACCCT
781065 AAATTGAAGTATTTT-AGAATTTGAGGTTTAAAATG
1 AAATTGAAGTATTTTGA-AATTTGAGGTTTAAAATG
* * * *
781100 TAATTGAATTATTTTGAAATTTGGGGTTTAGAATG
1 AAATTGAAGTATTTTGAAATTTGAGGTTTAAAATG
781135 AAATTGA
1 AAATTGA
781142 GAAACCTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.42
Consensus pattern (35 bp):
AAATTGAAGTATTTTGAAATTTGAGGTTTAAAATG
Found at i:786517 original size:24 final size:24
Alignment explanation
Indices: 786490--786535 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
786480 TACTTTATTG
*
786490 TAATTTATCCTGTAATATTTGAAT
1 TAATTTATCCTCTAATATTTGAAT
*
786514 TAATTTATCTTCTAATATTTGA
1 TAATTTATCCTCTAATATTTGA
786536 CTGATGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.52
Consensus pattern (24 bp):
TAATTTATCCTCTAATATTTGAAT
Found at i:790382 original size:36 final size:36
Alignment explanation
Indices: 790342--790434 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
790332 TTTTACTCAC
*
790342 CAAAATGATGTCGTTTTGGAGTATATTTAAATTTTT
1 CAAAATGACGTCGTTTTGGAGTATATTTAAATTTTT
790378 CAAAATGACGTCGTTTTGGAGTATATTTAAATTTTT
1 CAAAATGACGTCGTTTTGGAGTATATTTAAATTTTT
*
790414 CAAAATGACGTCGTTTCGGAG
1 CAAAATGACGTCGTTTTGGAG
790435 GTCGATGCTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (36 bp):
CAAAATGACGTCGTTTTGGAGTATATTTAAATTTTT
Found at i:790690 original size:31 final size:29
Alignment explanation
Indices: 790652--790710 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
790642 TTAATGGCAG
*
790652 AGTGAGCAAAATGATTCAATTTGTAAAGTTT
1 AGTGAGCAAAATGA-TCAAATTG-AAAGTTT
*
790683 AGTGAGCAAATTGATCAAATTGAAAGTT
1 AGTGAGCAAAATGATCAAATTGAAAGTT
790711 GGGTGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 7 0.27
31 13 0.50
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (29 bp):
AGTGAGCAAAATGATCAAATTGAAAGTTT
Found at i:790716 original size:29 final size:31
Alignment explanation
Indices: 790651--790723 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
790641 GTTAATGGCA
*
790651 GAGTGAGCAAAATGATTCAATTTGTAAAGTT
1 GAGTGAGCAAAATGATTCAAATTGTAAAGTT
* *
790682 TAGTGAGCAAATTGA-TCAAATTG-AAAGTT
1 GAGTGAGCAAAATGATTCAAATTGTAAAGTT
* *
790711 GGGTGAGAAAAAT
1 GAGTGAGCAAAAT
790724 AGGAGAGAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 15 0.43
30 7 0.20
31 13 0.37
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.29
Consensus pattern (31 bp):
GAGTGAGCAAAATGATTCAAATTGTAAAGTT
Found at i:795181 original size:15 final size:17
Alignment explanation
Indices: 795163--795218 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 17
795153 ATTATTTAGG
795163 TTATAATTTAATTAATTA
1 TTATAATTTAATTAA-TA
795181 TTAATAATTTAATTAATTA
1 TT-ATAATTTAATTAA-TA
*
795200 TTAATAATTTAATGAATA
1 TT-ATAATTTAATTAATA
795218 T
1 T
795219 AATGTGATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 5 0.14
19 31 0.86
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTATAATTTAATTAATA
Found at i:795189 original size:19 final size:19
Alignment explanation
Indices: 795165--795212 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
795155 TATTTAGGTT
795165 ATAATTTAATTAATTATTA
1 ATAATTTAATTAATTATTA
795184 ATAATTTAATTAATTATTA
1 ATAATTTAATTAATTATTA
795203 ATAATTTAAT
1 ATAATTTAAT
795213 GAATATAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAATTTAATTAATTATTA
Found at i:797203 original size:2 final size:2
Alignment explanation
Indices: 797196--797230 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
797186 GAACATTTAA
797196 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 A
797231 GAACGCGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:806477 original size:29 final size:29
Alignment explanation
Indices: 806442--806523 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
806432 AAACTAAATT
*
806442 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
806471 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
806500 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
806524 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:811039 original size:29 final size:29
Alignment explanation
Indices: 811004--811085 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
810994 AAACTAAATT
*
811004 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
811033 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
811062 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
811086 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:830742 original size:23 final size:23
Alignment explanation
Indices: 830712--830765 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
830702 AAAAAACAGC
830712 TTGCCTTGAGTTACAAGAAGTAG
1 TTGCCTTGAGTTACAAGAAGTAG
830735 TTGCCTTGAGTTACAAGAAGTAG
1 TTGCCTTGAGTTACAAGAAGTAG
*
830758 TAGCCTTG
1 TTGCCTTG
830766 GTTTTCATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (23 bp):
TTGCCTTGAGTTACAAGAAGTAG
Found at i:834326 original size:16 final size:17
Alignment explanation
Indices: 834290--834324 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
834280 ATTAAAAACA
834290 TTAAAAAAATAATATTT
1 TTAAAAAAATAATATTT
* *
834307 TTAATAAAATATTATTT
1 TTAAAAAAATAATATTT
834324 T
1 T
834325 AACCGTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAAAAAATAATATTT
Found at i:837851 original size:12 final size:12
Alignment explanation
Indices: 837830--837859 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
837820 TAGAGTCTTA
*
837830 TTCTTTAGCTTC
1 TTCTTCAGCTTC
837842 TTCTTCAGCTTC
1 TTCTTCAGCTTC
837854 TTCTTC
1 TTCTTC
837860 TCCCCATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.07, T:0.57
Consensus pattern (12 bp):
TTCTTCAGCTTC
Found at i:838474 original size:19 final size:19
Alignment explanation
Indices: 838450--838515 Score: 132
Period size: 19 Copynumber: 3.5 Consensus size: 19
838440 TGATTGGTGT
838450 ATCGATGCATGGGTAGTGC
1 ATCGATGCATGGGTAGTGC
838469 ATCGATGCATGGGTAGTGC
1 ATCGATGCATGGGTAGTGC
838488 ATCGATGCATGGGTAGTGC
1 ATCGATGCATGGGTAGTGC
838507 ATCGATGCA
1 ATCGATGCA
838516 CATGTTAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.26
Consensus pattern (19 bp):
ATCGATGCATGGGTAGTGC
Found at i:838549 original size:20 final size:22
Alignment explanation
Indices: 838504--838561 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
838494 GCATGGGTAG
838504 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
838528 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
838548 TGTATCGATGCACT
1 TGCATCGATGCACT
838562 TCAAAGGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:839282 original size:2 final size:2
Alignment explanation
Indices: 839275--839312 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
839265 GTGCTATGTG
839275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
839313 GAACATATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:839569 original size:31 final size:31
Alignment explanation
Indices: 839469--839576 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 31
839459 GAGTCGAGGG
* *
839469 TTTACCTATGTTCTACGGAACATATGTACAT
1 TTTACCTATGTTCTAAGGAACATATGGACAT
* *** * * *
839500 AATTACCTATG-TCTTTCGAGAGATATGGATAG
1 -TTTACCTATGTTCTAAGGA-ACATATGGACAT
*
839532 TATACCTATGTTCTAAGGAACATATGGACAT
1 TTTACCTATGTTCTAAGGAACATATGGACAT
*
839563 TTTACCTAGGTTCT
1 TTTACCTATGTTCT
839577 TCGGGACCTA
Statistics
Matches: 56, Mismatches: 18, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
31 34 0.61
32 22 0.39
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (31 bp):
TTTACCTATGTTCTAAGGAACATATGGACAT
Found at i:847516 original size:115 final size:116
Alignment explanation
Indices: 847280--847517 Score: 317
Period size: 115 Copynumber: 2.1 Consensus size: 116
847270 AAAGGGAGAG
* *
847280 AAAAACATGACTAAATTTAATTTAAAAATGAATGAATAAATAAGAAAATTGCAAAAAGAGGATAA
1 AAAAA-ATGACTAAATTTAATTCAAAAATGAATGAATAAATAAGAAAATTGAAAAAAGAGGATAA
*
847345 AAAATTAAACATTTTATGAATTTATAAAAATTAGGGCCCATATTATAAATAT
65 AAAATTAAACATTTTATGAAATTATAAAAATTAGGGCCCATATTATAAATAT
* * *
847397 -AAAAATGATTAAATTTAATTCAAAATTGAATGAATTAATAAGAGAAA-TGAAAAAAGATGG-TA
1 AAAAAATGACTAAATTTAATTCAAAAATGAATGAATAAATAAGA-AAATTGAAAAAAGA-GGATA
* *
847459 AAGACTT-AA-ATTTTATGAAATTATAAAAATTAGGAGCCC-TAATTATAAATAT
64 AAAAATTAAACATTTTATGAAATTATAAAAATTAGG-GCCCAT-ATTATAAATAT
847511 AAAAAAT
1 AAAAAAT
847518 TAGAAGTTCT
Statistics
Matches: 108, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
113 25 0.23
114 17 0.16
115 57 0.53
116 9 0.08
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (116 bp):
AAAAAATGACTAAATTTAATTCAAAAATGAATGAATAAATAAGAAAATTGAAAAAAGAGGATAAA
AAATTAAACATTTTATGAAATTATAAAAATTAGGGCCCATATTATAAATAT
Found at i:847518 original size:29 final size:29
Alignment explanation
Indices: 847483--847545 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
847473 ATGAAATTAT
* * *
847483 AAAAATTAGGAGCCCTAATTATAAATATA
1 AAAAATTAGAAGCCCTAATTATAAACACA
**
847512 AAAAATTAGAAGTTCTAATTATAAACACA
1 AAAAATTAGAAGCCCTAATTATAAACACA
847541 AAAAA
1 AAAAA
847546 AATTGGGGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.25
Consensus pattern (29 bp):
AAAAATTAGAAGCCCTAATTATAAACACA
Found at i:852075 original size:22 final size:19
Alignment explanation
Indices: 852026--852075 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 19
852016 GTTCCAGAAC
852026 TCTCTCATTTCTTCTTCCT
1 TCTCTCATTTCTTCTTCCT
852045 TCTTCCTCATTTTCTTCTCTTCCT
1 TC-T-CTCA-TTTC-T-TCTTCCT
852069 TCTCTCA
1 TCTCTCA
852076 ACGTGTGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 4 0.15
22 8 0.31
23 2 0.08
24 9 0.35
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (19 bp):
TCTCTCATTTCTTCTTCCT
Found at i:852555 original size:21 final size:21
Alignment explanation
Indices: 852529--852571 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
852519 TTTCTGGGTT
* *
852529 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
852550 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
852571 A
1 A
852572 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:852672 original size:68 final size:67
Alignment explanation
Indices: 852551--852702 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 67
852541 ACCCATTCAA
* *
852551 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCAG
852616 GG
66 GG
* * * **
852618 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCA
852683 GGG
65 GGG
* *
852686 GAGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
852703 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 21 0.28
68 54 0.72
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCAG
GG
Found at i:853040 original size:29 final size:29
Alignment explanation
Indices: 853006--853077 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
852996 CATATTATGA
**
853006 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
853035 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
853064 TACATGACATGAAT
1 TACATGACATGAAT
853078 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:853134 original size:30 final size:31
Alignment explanation
Indices: 853092--853151 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
853082 AGAAAAAGTT
*
853092 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
853123 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
853152 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:853399 original size:22 final size:22
Alignment explanation
Indices: 853371--853415 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
853361 TTATGGACAT
853371 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
853393 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
853415 A
1 A
853416 TTTATACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:853423 original size:22 final size:22
Alignment explanation
Indices: 853371--853423 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
853361 TTATGGACAT
*
853371 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
853393 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
853415 ATTTATACG
1 AATTATACG
853424 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (22 bp):
AATTATACGGGCACTTCGGTGC
Found at i:859477 original size:21 final size:21
Alignment explanation
Indices: 859451--859493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
859441 TTTCTGTGTT
* *
859451 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
859472 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
859493 A
1 A
859494 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:859594 original size:68 final size:67
Alignment explanation
Indices: 859472--859624 Score: 207
Period size: 68 Copynumber: 2.3 Consensus size: 67
859462 TACCCATTCA
* *
859472 AGGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCCA
1 AGGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCA
859537 GG
66 GG
* * * * **
859539 GGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCC
859604 AGG
65 AGG
* *
859607 AGAGGAACCGATTCCCCC
1 AGGGGAACCGATACCCCC
859625 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
67 21 0.28
68 53 0.72
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.17
Consensus pattern (67 bp):
AGGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCA
GG
Found at i:859613 original size:21 final size:21
Alignment explanation
Indices: 859589--859630 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
859579 TTGCTTGAGG
*
859589 GGAATCGATACCCCCAGGAGA
1 GGAACCGATACCCCCAGGAGA
* *
859610 GGAACCGATTCCCCCATGAGA
1 GGAACCGATACCCCCAGGAGA
859631 AAAAGAAGAA
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:0.31, C:0.31, G:0.26, T:0.12
Consensus pattern (21 bp):
GGAACCGATACCCCCAGGAGA
Found at i:859962 original size:29 final size:29
Alignment explanation
Indices: 859928--859999 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
859918 CATATTATGA
**
859928 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
859957 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
859986 TACATGACATGAAT
1 TACATGACATGAAT
860000 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:860056 original size:30 final size:31
Alignment explanation
Indices: 860014--860073 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
860004 AGAAAAAGTT
*
860014 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
860045 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
860074 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:860367 original size:22 final size:22
Alignment explanation
Indices: 860293--860359 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
860283 TTATGGACAT
860293 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
860315 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
860337 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
860359 A
1 A
860360 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:863575 original size:18 final size:18
Alignment explanation
Indices: 863554--863588 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
863544 ATAGTTGCAA
863554 ATAACTTTCATTCACTCG
1 ATAACTTTCATTCACTCG
*
863572 ATAAGTTTCATTCACTC
1 ATAACTTTCATTCACTC
863589 CTCTGGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.40
Consensus pattern (18 bp):
ATAACTTTCATTCACTCG
Found at i:869507 original size:8 final size:8
Alignment explanation
Indices: 869494--869534 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
869484 CTCATTTTCA
869494 GAGAATTT
1 GAGAATTT
869502 GAGAATTT
1 GAGAATTT
*
869510 -AGAGTTT
1 GAGAATTT
*
869517 GGGAATTT
1 GAGAATTT
869525 GAGAATTT
1 GAGAATTT
869533 GA
1 GA
869535 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:869833 original size:128 final size:128
Alignment explanation
Indices: 869605--869949 Score: 602
Period size: 128 Copynumber: 2.7 Consensus size: 128
869595 TAATCGGAGT
**
869605 ACTATTCACATGAAGGCGCGTTCCCGGGGATGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
869670 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
869733 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
869798 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* ***
869861 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
869925 TCATTGCCCTATTATGTCACTCATG
65 TCATTGCCCTATTATGTCACTCATG
869950 ATATATCAGT
Statistics
Matches: 207, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
127 1 0.00
128 206 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Done.