Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007769.1 Hibiscus syriacus cultivar Beakdansim tig00110045_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: 634091
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 3 of 3
Found at i:467164 original size:27 final size:26
Alignment explanation
Indices: 467088--467170 Score: 86
Period size: 25 Copynumber: 3.3 Consensus size: 26
467078 TCATAATATT
* *
467088 TTTTATATATTAACTTAA-AAGATAT-
1 TTTTAT-TATTAACTTAATTAGAAATA
467113 TTTTA-TATTAACTT-ATTA-AATATA
1 TTTTATTATTAACTTAATTAGAA-ATA
467137 TTTTATTATTAACTTAATTTAGAAATA
1 TTTTATTATTAACTTAA-TTAGAAATA
467164 TTTTATT
1 TTTTATT
467171 TTCATTCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
22 2 0.04
23 12 0.24
24 5 0.10
25 14 0.29
26 1 0.02
27 13 0.27
28 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTTATTATTAACTTAATTAGAAATA
Found at i:470247 original size:22 final size:23
Alignment explanation
Indices: 470199--470247 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
470189 CTTAGCATTT
**
470199 TAAAAATAAACAAACTTGAAAAG
1 TAAAAATAAACAAAAGTGAAAAG
*
470222 -AAAAATAAAGAAAAGTG-AAAG
1 TAAAAATAAACAAAAGTGAAAAG
470243 TAAAA
1 TAAAA
470248 GAAAATTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.14
Consensus pattern (23 bp):
TAAAAATAAACAAAAGTGAAAAG
Found at i:470434 original size:19 final size:19
Alignment explanation
Indices: 470404--470451 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
470394 TATTCAAATT
*
470404 TAATCCTAAAAATAAAAGA
1 TAATCCTAAAAACAAAAGA
470423 TAATTCCTAAAAACAAAAGA
1 TAA-TCCTAAAAACAAAAGA
470443 TAATCCTAA
1 TAATCCTAA
470452 TTTCATATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.58, C:0.15, G:0.04, T:0.23
Consensus pattern (19 bp):
TAATCCTAAAAACAAAAGA
Found at i:478690 original size:23 final size:23
Alignment explanation
Indices: 478642--478684 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
478632 TTAGCATTTT
* *
478642 AAAAATAAAGAAAGCTTGAAAAC
1 AAAAATAAAGAAAGATCGAAAAC
478665 AAAAATAAAGAAA-ATCGAAA
1 AAAAATAAAGAAAGATCGAAA
478685 GTCAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.12
Consensus pattern (23 bp):
AAAAATAAAGAAAGATCGAAAAC
Found at i:478879 original size:19 final size:19
Alignment explanation
Indices: 478849--478896 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
478839 TATCCAAACT
*
478849 TAATCCTAAAAATAAAAGA
1 TAATCCTAAAAACAAAAGA
478868 TAATTCCTAAAAACAAAAGA
1 TAA-TCCTAAAAACAAAAGA
478888 TAATCCTAA
1 TAATCCTAA
478897 TTTCAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.58, C:0.15, G:0.04, T:0.23
Consensus pattern (19 bp):
TAATCCTAAAAACAAAAGA
Found at i:479901 original size:2 final size:2
Alignment explanation
Indices: 479892--480010 Score: 114
Period size: 2 Copynumber: 60.0 Consensus size: 2
479882 ATATCTTTAC
* * * *
479892 AT AT -T AT AT AT AT AT AT AT GT AT GT AT AT GT GT 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
* * *
479933 AT AT AT AT AT AT AT AT AT AT AT AT AT GT GT GT 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
* * * * * *
479975 AT AT GT AT AT GT GT AT AT GT AT AT GT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
480011 GAAATGACCA
Statistics
Matches: 100, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
1 1 0.01
2 99 0.99
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (2 bp):
AT
Found at i:482816 original size:25 final size:23
Alignment explanation
Indices: 482786--482866 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 23
482776 TATTAATAGT
* *
482786 ATTATATATAAAATATATCAATTAA
1 ATTATA-ATAAAA-ATATAAAATAA
482811 ATTATAATAAAAATATAAAATAA
1 ATTATAATAAAAATATAAAATAA
482834 ATTATTAAGTAATAAATTATTAAAATAA
1 ATTA-TAA-TAA-AAA-TA-TAAAATAA
482862 ATTAT
1 ATTAT
482867 TAAAATAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
23 13 0.27
24 9 0.18
25 9 0.18
26 3 0.06
27 3 0.06
28 12 0.24
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (23 bp):
ATTATAATAAAAATATAAAATAA
Found at i:482826 original size:23 final size:25
Alignment explanation
Indices: 482786--482866 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 25
482776 TATTAATAGT
* *
482786 ATTATATATAAAATATATCAATTAA
1 ATTATATATAAAATATATAAAATAA
482811 ATTATA-ATAAAA-ATATAAAATAA
1 ATTATATATAAAATATATAAAATAA
*
482834 ATTATTAAGTAATAAATTAT-TAAAATAA
1 ATTA-T-A-T-ATAAAATATATAAAATAA
482862 ATTAT
1 ATTAT
482867 TAAAATAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
23 13 0.28
24 7 0.15
25 7 0.15
27 1 0.02
28 17 0.36
29 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (25 bp):
ATTATATATAAAATATATAAAATAA
Found at i:482846 original size:28 final size:28
Alignment explanation
Indices: 482815--482869 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
482805 AATTAAATTA
482815 TAATAAAA-ATATAAAATAAATTATTAAG
1 TAATAAAATAT-TAAAATAAATTATTAAG
*
482843 TAATAAATTATTAAAATAAATTATTAA
1 TAATAAAATATTAAAATAAATTATTAA
482870 AATAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
TAATAAAATATTAAAATAAATTATTAAG
Found at i:482849 original size:15 final size:14
Alignment explanation
Indices: 482808--482921 Score: 93
Period size: 13 Copynumber: 8.6 Consensus size: 14
482798 ATATATCAAT
482808 TAAATTA-TAATAA
1 TAAATTATTAATAA
482821 -AAA-TA-TAA-AA
1 TAAATTATTAATAA
482831 TAAATTATTAAGTAA
1 TAAATTATTAA-TAA
482846 TAAATTATTAA-AA
1 TAAATTATTAATAA
482859 TAAATTATTAA-AA
1 TAAATTATTAATAA
**
482872 TAAATTATT--TTT
1 TAAATTATTAATAA
* * *
482884 TAAAGATGTTAATAT
1 TAAA-TTATTAATAA
482899 TAAATTATTAAGTAA
1 TAAATTATTAA-TAA
482914 TAAATTAT
1 TAAATTAT
482922 ATTAAATATA
Statistics
Matches: 83, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
10 2 0.02
11 8 0.10
12 9 0.11
13 30 0.36
14 5 0.06
15 29 0.35
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (14 bp):
TAAATTATTAATAA
Found at i:482911 original size:68 final size:67
Alignment explanation
Indices: 482826--482990 Score: 217
Period size: 68 Copynumber: 2.4 Consensus size: 67
482816 AATAAAAATA
*
482826 TAAAATAAATTATTAAGTAATAAATTATTAAAATAAATTA-TTAAAATAAA-TTATTTTTTAAAG
1 TAAAATAAATTATTAAGTAATAAATTATTAAAATAAATCATTTAAAATAAATTTA-TTTTTAAAG
482889 ATGT
65 AT-T
* * * * *
482893 TAATATTAAATTATTAAGTAATAAATTATATTAAATATATCATTTAAATTATATTTATTTTTAAA
1 TAA-AATAAATTATTAAGTAATAAATTAT-TAAAATAAATCATTTAAAATAAATTTATTTTTAAA
*
482958 TATT
64 GATT
482962 TAAAATAAATTATTAAGTAATAAATTATT
1 TAAAATAAATTATTAAGTAATAAATTATT
482991 TTTTAAGGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
67 4 0.05
68 48 0.56
69 13 0.15
70 18 0.21
71 3 0.03
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (67 bp):
TAAAATAAATTATTAAGTAATAAATTATTAAAATAAATCATTTAAAATAAATTTATTTTTAAAGA
TT
Found at i:487376 original size:94 final size:95
Alignment explanation
Indices: 487214--487398 Score: 309
Period size: 94 Copynumber: 2.0 Consensus size: 95
487204 GTGGCTTCGC
* *
487214 CCACCTTCTATTTTTATTTTATAGTTGGGTGAATAAAATAGGAGCGAGAGTAAAGTTAAATGAGG
1 CCACCTTCTATTTTTATTTTATAGTTGGGTGAACAAAATAGGAGCGAGAGTAAAGTTAAATGAAG
487279 AACAATGTAATATACCCATTATATTTATGG
66 AACAATGTAATATACCCATTATATTTATGG
* *
487309 CCACCTTCTGTTTTTATTTTATAG-TGGGTGAACAAAATAGGAGCGAGAGTAAAGTTCAATGAAG
1 CCACCTTCTATTTTTATTTTATAGTTGGGTGAACAAAATAGGAGCGAGAGTAAAGTTAAATGAAG
* *
487373 AACAATGTAATTTACCCTTTATATTT
66 AACAATGTAATATACCCATTATATTT
487399 TCAATTTTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
94 61 0.73
95 23 0.27
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (95 bp):
CCACCTTCTATTTTTATTTTATAGTTGGGTGAACAAAATAGGAGCGAGAGTAAAGTTAAATGAAG
AACAATGTAATATACCCATTATATTTATGG
Found at i:489958 original size:49 final size:49
Alignment explanation
Indices: 489847--489946 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
489837 ATTTTTATAA
* * *
489847 TTTTATAAATTAAACTAATGTCAATCGACTTATAAATCATTACACCAAT
1 TTTTATAAATTAAATTAATATCAATCGACTTATAAATCATTAAACCAAT
* *
489896 TTTTATAAATTAAATTAATATCAATTGGCTTATAAATCATTAAACCAAT
1 TTTTATAAATTAAATTAATATCAATCGACTTATAAATCATTAAACCAAT
489945 TT
1 TT
489947 CTTTTTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (49 bp):
TTTTATAAATTAAATTAATATCAATCGACTTATAAATCATTAAACCAAT
Found at i:493043 original size:2 final size:2
Alignment explanation
Indices: 493036--493060 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
493026 TTTGTTATTA
493036 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 A
493061 GATAAATACT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:496282 original size:45 final size:45
Alignment explanation
Indices: 496221--496342 Score: 148
Period size: 45 Copynumber: 2.8 Consensus size: 45
496211 ATATATTTAT
*
496221 TAATATTTATAATAATATAATATTATATTTTTATTT-ATAATATAA
1 TAATAATTATAATAATA-AATATTATATTTTTATTTAATAATATAA
*
496266 TAATAATTATAATAATAAAGATATATATTTTTATTTAATAATATAA
1 TAATAATTATAATAATAAATAT-TATATTTTTATTTAATAATATAA
496312 T-A-AATTAT--TAATAAA-ATTTATATTATTTATT
1 TAATAATTATAATAATAAATA-TTATATT-TTTATT
496343 AATTTCATAG
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
41 7 0.10
42 14 0.20
44 10 0.14
45 30 0.42
46 10 0.14
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (45 bp):
TAATAATTATAATAATAAATATTATATTTTTATTTAATAATATAA
Found at i:496411 original size:27 final size:26
Alignment explanation
Indices: 496315--496416 Score: 75
Period size: 27 Copynumber: 3.8 Consensus size: 26
496305 AATATAATAA
*
496315 ATTA-TTAATA-AAATTTATATTATTT
1 ATTATTTAATATAAA-TAATATTATTT
* * *
496340 ATTAATTTCATAGAAATAATATTATTAA
1 ATT-ATTTAATATAAATAATATTATT-T
*
496368 ATTA-TTAATAATGAATAATATTATTT
1 ATTATTTAAT-ATAAATAATATTATTT
496394 ATGTATTTAATATTAATATAATA
1 AT-TATTTAATA-TAA-ATAATA
496417 ATCTAATAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
25 3 0.05
26 7 0.12
27 31 0.52
28 13 0.22
29 6 0.10
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (26 bp):
ATTATTTAATATAAATAATATTATTT
Found at i:496428 original size:22 final size:23
Alignment explanation
Indices: 496354--496491 Score: 83
Period size: 24 Copynumber: 6.0 Consensus size: 23
496344 ATTTCATAGA
*
496354 AATAATATTATTA-AAT-TA-TT
1 AATAATATTAATATAATATATTT
* * * *
496374 AATAATGAATAATATTATTTATGT
1 AATAAT-ATTAATATAATATATTT
* *
496398 ATTTAATATTAATATAATA-ATCT
1 A-ATAATATTAATATAATATATTT
496421 AATAATATTTTAATA-AATATATTTT
1 AATAATA--TTAATATAATATA-TTT
* *
496446 AA-AATA-TAATATACTATTTTT
1 AATAATATTAATATAATATATTT
496467 AATAATATTAATATATATAATATTT
1 AATAATATTAATATA-AT-ATATTT
496492 TTATTTCAAT
Statistics
Matches: 89, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
20 6 0.07
21 15 0.17
22 15 0.17
23 17 0.19
24 23 0.26
25 13 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
AATAATATTAATATAATATATTT
Found at i:496465 original size:20 final size:23
Alignment explanation
Indices: 496401--496481 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 23
496391 TTTATGTATT
* * *
496401 TAATATTAATATAATA-ATCTAA
1 TAATATTAATATACTATTTTTAA
*
496423 TAATATTTTAATA-AATATATTTTAA
1 TAATA--TTAATATACTAT-TTTTAA
496448 -AATA-TAATATACTATTTTTAA
1 TAATATTAATATACTATTTTTAA
496469 TAATATTAATATA
1 TAATATTAATATA
496482 TATAATATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
21 11 0.22
22 13 0.27
23 11 0.22
24 10 0.20
25 4 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATATTAATATACTATTTTTAA
Found at i:496537 original size:28 final size:31
Alignment explanation
Indices: 496467--496537 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
496457 TACTATTTTT
*
496467 AATAATATTAATATATATAATATTTTTATTTC
1 AATAAAATT-ATATATATAATATTTTTATTTC
496499 AATAAAA-TATATAT-TAATATTTTTA-TT-
1 AATAAAATTATATATATAATATTTTTATTTC
*
496526 GATAAAATTATA
1 AATAAAATTATA
496538 AAAAAATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 6 0.17
28 6 0.17
29 11 0.31
30 6 0.17
31 1 0.03
32 6 0.17
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
AATAAAATTATATATATAATATTTTTATTTC
Found at i:496563 original size:19 final size:20
Alignment explanation
Indices: 496535--496572 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
496525 TGATAAAATT
496535 ATAAAAAAA-TATTTTAATA
1 ATAAAAAAATTATTTTAATA
*
496554 ATAAATAAATTATTTTAAT
1 ATAAAAAAATTATTTTAAT
496573 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:496616 original size:25 final size:23
Alignment explanation
Indices: 496554--496616 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
496544 TATTTTAATA
*
496554 ATAAATAA-ATTATTTTAATTTTT
1 ATAAATAATATTA-TTGAATTTTT
* *
496577 AAAAATAATAATATTGAATTTTGT
1 ATAAATAATATTATTGAATTTT-T
496601 GATAAATAATATTATT
1 -ATAAATAATATTATT
496617 TATTGTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 15 0.47
24 4 0.12
25 13 0.41
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATAAATAATATTATTGAATTTTT
Found at i:496719 original size:12 final size:14
Alignment explanation
Indices: 496698--496730 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
496688 CAAACATTGT
496698 AAAATATTTTTT-A
1 AAAATATTTTTTCA
496711 AAAAT-TTTTTTCA
1 AAAATATTTTTTCA
496724 AAAATAT
1 AAAATAT
496731 AATTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 11 0.61
14 1 0.06
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATTTTTTCA
Found at i:497610 original size:14 final size:14
Alignment explanation
Indices: 497591--497617 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
497581 GAGTACAATA
497591 AATTACTAGTGTAT
1 AATTACTAGTGTAT
497605 AATTACTAGTGTA
1 AATTACTAGTGTA
497618 AATATAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
AATTACTAGTGTAT
Found at i:500671 original size:19 final size:19
Alignment explanation
Indices: 500644--500682 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
500634 AAAAGTTATA
500644 AAATAATTATTAAAAT-ATT
1 AAATAATTA-TAAAATCATT
*
500663 AAATTATTATAAAATCATT
1 AAATAATTATAAAATCATT
500682 A
1 A
500683 TTGCAACTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATAATTATAAAATCATT
Found at i:506073 original size:13 final size:14
Alignment explanation
Indices: 506055--506084 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
506045 TTGTCTTCTC
506055 AAGGGTGAAAAA-A
1 AAGGGTGAAAAATA
506068 AAGGGTGAAAAATA
1 AAGGGTGAAAAATA
506082 AAG
1 AAG
506085 AGACTTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.10
Consensus pattern (14 bp):
AAGGGTGAAAAATA
Found at i:514641 original size:14 final size:15
Alignment explanation
Indices: 514617--514649 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
514607 ATTTTTTTGA
514617 TTTGTTTGTGAATTT
1 TTTGTTTGTGAATTT
514632 TTTG-TTGTGAATTT
1 TTTGTTTGTGAATTT
514646 TTTG
1 TTTG
514650 AGCCGAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.12, C:0.00, G:0.21, T:0.67
Consensus pattern (15 bp):
TTTGTTTGTGAATTT
Found at i:517670 original size:29 final size:29
Alignment explanation
Indices: 517628--517711 Score: 159
Period size: 29 Copynumber: 2.9 Consensus size: 29
517618 AAACTAAATT
517628 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
517657 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
517686 GATGTCATTGCTTACATCATTTAAGT
1 GATGTCATTGCTTACATCATTTAAGT
517712 TAGGTGAGAG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:522380 original size:29 final size:28
Alignment explanation
Indices: 522338--522448 Score: 168
Period size: 29 Copynumber: 3.8 Consensus size: 28
522328 AAACTAAATT
* *
522338 GATGGCATTGCTTACCTCATTTAAGTACA
1 GATGTCATTGCTTACATCATTTAAGTA-A
522367 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGT-AA
522396 GATGTCATTGCTTACATCATTTAAGTAA
1 GATGTCATTGCTTACATCATTTAAGTAA
522424 TGATGTCATTGCTTACATCAATTTA
1 -GATGTCATTGCTTACATC-ATTTA
522449 GTTAGGTGAG
Statistics
Matches: 77, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
28 2 0.03
29 69 0.90
30 6 0.08
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (28 bp):
GATGTCATTGCTTACATCATTTAAGTAA
Found at i:527744 original size:20 final size:21
Alignment explanation
Indices: 527721--527773 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
527711 ACACAGGTTC
*
527721 CAAAATCGCAACGCGAA-AGT
1 CAAAATCGCAACGCAAATAGT
* *
527741 CAAATTCACAACGCAAATAGT
1 CAAAATCGCAACGCAAATAGT
*
527762 -TAAATCGCAACG
1 CAAAATCGCAACG
527774 ATAATATGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (21 bp):
CAAAATCGCAACGCAAATAGT
Found at i:527833 original size:20 final size:20
Alignment explanation
Indices: 527805--527842 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
527795 GAATGTTGCG
*
527805 AATAGGTAAATCGCAACGAT
1 AATAGGTAAATCACAACGAT
*
527825 AATATGTAAATCACAACG
1 AATAGGTAAATCACAACG
527843 CAAATTCTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (20 bp):
AATAGGTAAATCACAACGAT
Found at i:527961 original size:41 final size:41
Alignment explanation
Indices: 527897--528016 Score: 204
Period size: 41 Copynumber: 2.9 Consensus size: 41
527887 CGATATAGAT
*
527897 AATTAGCGTTGCGAAAACAAAATTCGCGTTGCGATTTTGGAG
1 AATT-GCGTTGCGAAAACGAAATTCGCGTTGCGATTTTGGAG
*
527939 AATTGCGTTGCGAAAACGAAATTCGCGTTGCAATTTTGGAG
1 AATTGCGTTGCGAAAACGAAATTCGCGTTGCGATTTTGGAG
*
527980 AATCGCGTTGCGAAAACGAAATTCGCGTTGCGATTTT
1 AATTGCGTTGCGAAAACGAAATTCGCGTTGCGATTTT
528017 CCAAATTCGC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 70 0.95
42 4 0.05
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (41 bp):
AATTGCGTTGCGAAAACGAAATTCGCGTTGCGATTTTGGAG
Found at i:527968 original size:20 final size:20
Alignment explanation
Indices: 527897--528012 Score: 85
Period size: 20 Copynumber: 5.7 Consensus size: 20
527887 CGATATAGAT
* *
527897 AATTAGCGTTGCGAAAACAA
1 AATTCGCGTTGCGAAAACGA
****
527917 AATTCGCGTTGCGATTTTGGA
1 AATTCGCGTTGCGA-AAACGA
527938 GAATT-GCGTTGCGAAAACGA
1 -AATTCGCGTTGCGAAAACGA
***
527958 AATTCGCGTTGC-AATTTTGGA
1 AATTCGCGTTGCGAA--AACGA
527979 GAA-TCGCGTTGCGAAAACGA
1 -AATTCGCGTTGCGAAAACGA
527999 AATTCGCGTTGCGA
1 AATTCGCGTTGCGA
528013 TTTTCCAAAT
Statistics
Matches: 72, Mismatches: 16, Indels: 16
0.69 0.15 0.15
Matches are distributed among these distances:
19 8 0.11
20 35 0.49
21 21 0.29
22 8 0.11
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (20 bp):
AATTCGCGTTGCGAAAACGA
Found at i:528024 original size:21 final size:21
Alignment explanation
Indices: 527916--528026 Score: 86
Period size: 21 Copynumber: 5.4 Consensus size: 21
527906 TGCGAAAACA
*
527916 AAATTCGCGTTGCGATTTTGG
1 AAATTCGCGTTGCGATTTTCG
***
527937 AGAATT-GCGTTGCGA-AAACG
1 A-AATTCGCGTTGCGATTTTCG
* *
527957 AAATTCGCGTTGCAATTTTGG
1 AAATTCGCGTTGCGATTTTCG
***
527978 AGAA-TCGCGTTGCGA-AAACG
1 A-AATTCGCGTTGCGATTTTCG
*
527998 AAATTCGCGTTGCGATTTTCC
1 AAATTCGCGTTGCGATTTTCG
528019 AAATTCGC
1 AAATTCGC
528027 AACGATGATA
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
19 6 0.09
20 23 0.35
21 31 0.47
22 6 0.09
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (21 bp):
AAATTCGCGTTGCGATTTTCG
Found at i:528357 original size:20 final size:20
Alignment explanation
Indices: 528334--528444 Score: 95
Period size: 20 Copynumber: 5.5 Consensus size: 20
528324 TTCCAAATTT
528334 GCAACGCGAA-AGTCAAAATC
1 GCAACGCGAATAGT-AAAATC
*
528354 GCAACGCGAATAGTTAAATC
1 GCAACGCGAATAGTAAAATC
** *
528374 GCAACGATAATATGT-AATTC
1 GCAACGCGAATA-GTAAAATC
*
528394 ACAACGCGAATAG-ATAAATC
1 GCAACGCGAATAGTA-AAATC
**
528414 GCAACGATAATATGT-AAATC
1 GCAACGCGAATA-GTAAAATC
528434 GCAACGCGAAT
1 GCAACGCGAAT
528445 TCTCCAAATT
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
19 1 0.01
20 65 0.90
21 6 0.08
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (20 bp):
GCAACGCGAATAGTAAAATC
Found at i:528379 original size:40 final size:40
Alignment explanation
Indices: 528349--528444 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
528339 GCGAAAGTCA
*
528349 AAATCGCAACGCGAATAGTTAAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATAGATAAATCGCAACGATAATATGT
* *
528389 AATTCACAACGCGAATAGATAAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATAGATAAATCGCAACGATAATATGT
528429 AAATCGCAACGCGAAT
1 AAATCGCAACGCGAAT
528445 TCTCCAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGCGAATAGATAAATCGCAACGATAATATGT
Found at i:528611 original size:20 final size:20
Alignment explanation
Indices: 528585--528654 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
528575 TGACTTCTGT
*
528585 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACCTATTCGC
*
528605 ATTGCGATTTACCTATTCGC
1 GTTGCGATTTACCTATTCGC
528625 GTTGCGATTTACCTATTCGC
1 GTTGCGATTTACCTATTCGC
528645 GTTGCGATTT
1 GTTGCGATTT
528655 TGGAACTTGT
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:0.17, C:0.21, G:0.20, T:0.41
Consensus pattern (20 bp):
GTTGCGATTTACCTATTCGC
Found at i:529179 original size:30 final size:28
Alignment explanation
Indices: 529116--529179 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
529106 GAAAATTAAA
* *
529116 TTAAACGAGACAGGAAAAATCGTTTATG
1 TTAAACGAGACAGGAAAAAACGTTTACG
*
529144 ATAAACGGAGAC-GGAAAAAAACTGTTTACG
1 TTAAAC-GAGACAGG-AAAAAAC-GTTTACG
529174 TTAAAC
1 TTAAAC
529180 AGGGACGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 7 0.24
29 11 0.38
30 11 0.38
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.22
Consensus pattern (28 bp):
TTAAACGAGACAGGAAAAAACGTTTACG
Found at i:532765 original size:20 final size:19
Alignment explanation
Indices: 532742--532807 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 19
532732 AACTTTATAT
532742 TATTTTTATTATAAATATAA
1 TATTTTTATTATAAAT-TAA
*
532762 TATTTTTA--ATAAATTAT
1 TATTTTTATTATAAATTAA
*
532779 TAATTTTATT-TAAATTAA
1 TATTTTTATTATAAATTAA
*
532797 T-TTATTATTAT
1 TATTTTTATTAT
532808 CATTTAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
17 15 0.39
18 15 0.39
20 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTTTATTATAAATTAA
Found at i:532773 original size:18 final size:19
Alignment explanation
Indices: 532737--532797 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
532727 AAGTAAACTT
*
532737 TATATTATTTTTATTATAAA
1 TATAATATTTTTA-TATAAA
532757 TATAATATTTTTA-ATAAA
1 TATAATATTTTTATATAAA
* * *
532775 T-TATTAATTTTATTTAAA
1 TATAATATTTTTATATAAA
532793 T-TAAT
1 TATAAT
532798 TTATTATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.26
18 14 0.40
20 12 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAATATTTTTATATAAA
Found at i:533041 original size:16 final size:16
Alignment explanation
Indices: 533022--533070 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
533012 TGCTTTTAAA
*
533022 TCGGGTTAAATTTGGT
1 TCGGGTTAATTTTGGT
*
533038 TCGGATTAATTTTGGT
1 TCGGGTTAATTTTGGT
533054 TCGGGTTAATTTTGGT
1 TCGGGTTAATTTTGGT
533070 T
1 T
533071 TTGGTTCAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.16, C:0.06, G:0.29, T:0.49
Consensus pattern (16 bp):
TCGGGTTAATTTTGGT
Found at i:533072 original size:22 final size:22
Alignment explanation
Indices: 533047--533095 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
533037 TTCGGATTAA
* * *
533047 TTTTGGTTCGGGTTAATTTTGG
1 TTTTGGTTCAGGCTAATTTCGG
533069 TTTTGGTTCAGGCTAATTTCGG
1 TTTTGGTTCAGGCTAATTTCGG
533091 TTTTG
1 TTTTG
533096 CTAAATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.10, C:0.08, G:0.29, T:0.53
Consensus pattern (22 bp):
TTTTGGTTCAGGCTAATTTCGG
Found at i:533076 original size:16 final size:16
Alignment explanation
Indices: 533025--533076 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
533015 TTTTAAATCG
*
533025 GGTTAAATTTGG-TTC
1 GGTTAATTTTGGTTTC
533040 GGATTAATTTTGG-TTC
1 GG-TTAATTTTGGTTTC
*
533056 GGGTTAATTTTGGTTTT
1 -GGTTAATTTTGGTTTC
533073 GGTT
1 GGTT
533077 CAGGCTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 2 0.06
16 26 0.81
17 4 0.12
ACGTcount: A:0.15, C:0.04, G:0.29, T:0.52
Consensus pattern (16 bp):
GGTTAATTTTGGTTTC
Found at i:536590 original size:20 final size:21
Alignment explanation
Indices: 536544--536604 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
536534 TTCCCCTGTG
536544 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
536567 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
536587 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
536605 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:544079 original size:22 final size:22
Alignment explanation
Indices: 544045--544144 Score: 146
Period size: 22 Copynumber: 4.5 Consensus size: 22
544035 TGACTCCTAT
* *
544045 GTCCCAAATGACCACTAGATAC
1 GTCCCGAAGGACCACTAGATAC
*
544067 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTAGATAC
* *
544089 GTCTCAAAGGACCACTAGATAC
1 GTCCCGAAGGACCACTAGATAC
*
544111 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTAGATAC
544133 GTCCCGAAGGAC
1 GTCCCGAAGGAC
544145 TAATATACCC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 69 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (22 bp):
GTCCCGAAGGACCACTAGATAC
Found at i:544106 original size:44 final size:44
Alignment explanation
Indices: 544045--544144 Score: 173
Period size: 44 Copynumber: 2.3 Consensus size: 44
544035 TGACTCCTAT
*
544045 GTCCCAAATGACCACTAGATACGTCCCGAAGGACCACTGGATAC
1 GTCCCAAAGGACCACTAGATACGTCCCGAAGGACCACTGGATAC
*
544089 GTCTCAAAGGACCACTAGATACGTCCCGAAGGACCACTGGATAC
1 GTCCCAAAGGACCACTAGATACGTCCCGAAGGACCACTGGATAC
*
544133 GTCCCGAAGGAC
1 GTCCCAAAGGAC
544145 TAATATACCC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (44 bp):
GTCCCAAAGGACCACTAGATACGTCCCGAAGGACCACTGGATAC
Found at i:548978 original size:22 final size:22
Alignment explanation
Indices: 548935--549035 Score: 139
Period size: 22 Copynumber: 4.6 Consensus size: 22
548925 GTTCAGTATT
* *
548935 CGTCCCGAAGGACCACTAGATA
1 CGTCCCAAAGGACCACTGGATA
* * *
548957 TGACCCAAAGAACCACTGGATA
1 CGTCCCAAAGGACCACTGGATA
548979 CGTCCCAAAGGACCACTGGATA
1 CGTCCCAAAGGACCACTGGATA
*
549001 CGTCCCGAAGGACCACTGGATA
1 CGTCCCAAAGGACCACTGGATA
*
549023 CGTCCCGAAGGAC
1 CGTCCCAAAGGAC
549036 TAATATACCC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.13
Consensus pattern (22 bp):
CGTCCCAAAGGACCACTGGATA
Found at i:552706 original size:26 final size:25
Alignment explanation
Indices: 552651--552706 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
552641 TAGGACTAAA
552651 TTAAATGAAAATTAAACTTTACAAT
1 TTAAATGAAAATTAAACTTTACAAT
* * *
552676 CTAAATTAAGAATTAAA-TTATAGAAT
1 TTAAATGAA-AATTAAACTT-TACAAT
552702 TTAAA
1 TTAAA
552707 AAGGTGAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (25 bp):
TTAAATGAAAATTAAACTTTACAAT
Found at i:553032 original size:17 final size:17
Alignment explanation
Indices: 553010--553042 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
553000 CTTTCTTCCT
553010 TTTTACTTTCTTCTTCA
1 TTTTACTTTCTTCTTCA
553027 TTTTACTTTCTTCTTC
1 TTTTACTTTCTTCTTC
553043 CTCTTTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTACTTTCTTCTTCA
Found at i:554182 original size:2 final size:2
Alignment explanation
Indices: 554125--554165 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
554115 CCACCAAACA
554125 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
554166 AAAGGATAAA
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:570002 original size:2 final size:2
Alignment explanation
Indices: 569995--570036 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
569985 TATCATGTTA
569995 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
570037 TAAATTAGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:574389 original size:14 final size:14
Alignment explanation
Indices: 574370--574400 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
574360 ATGTGACCTA
574370 TAAATTATAAACCC
1 TAAATTATAAACCC
574384 TAAATTATAAACCC
1 TAAATTATAAACCC
574398 TAA
1 TAA
574401 TTAAAGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAATTATAAACCC
Found at i:576455 original size:20 final size:20
Alignment explanation
Indices: 576407--576557 Score: 82
Period size: 20 Copynumber: 7.6 Consensus size: 20
576397 AAATGACCAA
576407 CAAATTCGCAACGCG-A-TC
1 CAAATTCGCAACGCGAATTC
576425 TCAAATTCGCAACGCGAATTC
1 -CAAATTCGCAACGCGAATTC
* * *
576446 CAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACGCGA-ATTC
* *
576466 CAAGTTCGCAACGCGAATATG
1 CAAATTCGCAACGCGAAT-TC
* * ** *
576487 TAAA-TCGTATTGCGATTTTC
1 CAAATTCGCAACGCGA-ATTC
576507 CAAATTCGCAACGCG-ATGGT-
1 CAAATTCGCAACGCGAAT--TC
* * *
576527 CAAATTCACAAC-TGAATTT
1 CAAATTCGCAACGCGAATTC
576546 CAAATTCGCAAC
1 CAAATTCGCAAC
576558 AGGTTTTAGT
Statistics
Matches: 99, Mismatches: 22, Indels: 22
0.69 0.15 0.15
Matches are distributed among these distances:
18 1 0.01
19 29 0.29
20 54 0.55
21 15 0.15
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTC
Found at i:577472 original size:24 final size:24
Alignment explanation
Indices: 577445--577503 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
577435 AGTCAGTATT
577445 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
* *
577469 CGAACTTTGATCTTGGTCAATACT
1 CGAAATTTGATCTTGGTCAATACC
*
577493 CGAATTTTGAT
1 CGAAATTTGAT
577504 GATGTGATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:596038 original size:44 final size:44
Alignment explanation
Indices: 595973--596056 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
595963 ATGTGAAAAT
* *
595973 GAAAGGTTGAGAATAGGGAGATTTGGACTTAGAGATAATTTACA
1 GAAAGGTTGAGAATAGAGAGATTTGGACTTAGAGAGAATTTACA
* *
596017 GAAAGGTTGAGAATTGAGAGATTTGGACTTGGAGAGAATT
1 GAAAGGTTGAGAATAGAGAGATTTGGACTTAGAGAGAATT
596057 AAACGATGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.37, C:0.04, G:0.32, T:0.27
Consensus pattern (44 bp):
GAAAGGTTGAGAATAGAGAGATTTGGACTTAGAGAGAATTTACA
Found at i:603213 original size:110 final size:110
Alignment explanation
Indices: 603014--603239 Score: 398
Period size: 110 Copynumber: 2.1 Consensus size: 110
603004 TTTGTTTCTG
* * *
603014 ACATAAGATCAGTATCTTGACTTCCCCTCATGTTCTTATCTCTATTCTCTCTCTCTCCTCTTTCC
1 ACATAAAATCAGTATCTCGACTTCCCCTCATGTTCTTATCTCTATTCTCACTCTCTCCTCTTTCC
603079 ACCCTTCCGCACCAACATTATCTTATTACAGCTTGGTATCAAGAT
66 ACCCTTCCGCACCAACATTATCTTATTACAGCTTGGTATCAAGAT
*
603124 GCATAAAATCAGTATCTCGACTTCCCCTCATGTTCTTATCTCTATTCTCACTCTCTCCTCTTTCC
1 ACATAAAATCAGTATCTCGACTTCCCCTCATGTTCTTATCTCTATTCTCACTCTCTCCTCTTTCC
* *
603189 ACCCTTCCGCATCAACATTCTCTTATTACAGCTTGGTATCAAGAT
66 ACCCTTCCGCACCAACATTATCTTATTACAGCTTGGTATCAAGAT
603234 ACATAA
1 ACATAA
603240 CTCACTCTCC
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.23, C:0.32, G:0.08, T:0.37
Consensus pattern (110 bp):
ACATAAAATCAGTATCTCGACTTCCCCTCATGTTCTTATCTCTATTCTCACTCTCTCCTCTTTCC
ACCCTTCCGCACCAACATTATCTTATTACAGCTTGGTATCAAGAT
Found at i:608308 original size:15 final size:15
Alignment explanation
Indices: 608261--608309 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
608251 TTTTATAACT
608261 TTATTAATA-ATTATA
1 TTATTAATATATTA-A
* *
608276 TTTTTAATATTTTTAA
1 TTATTAATA-TATTAA
608292 TTATTAATATATTAA
1 TTATTAATATATTAA
608307 TTA
1 TTA
608310 AAACTAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 16 0.57
16 9 0.32
17 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTAATATATTAA
Found at i:608592 original size:46 final size:44
Alignment explanation
Indices: 608541--608627 Score: 104
Period size: 46 Copynumber: 1.9 Consensus size: 44
608531 AATACTATAT
*
608541 TAATATTAAATGTAT-AAAGTAATATTACTCATTACTAATAATTTAA
1 TAATATT-AATGTATAAAAATAATATTA-TCATTA-TAATAATTTAA
* * *
608587 TAATATTATTTTATAAAAATAATATTATTATTATAATAATT
1 TAATATTAATGTATAAAAATAATATTATCATTATAATAATT
608628 CATTATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 8 0.22
45 10 0.28
46 18 0.50
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (44 bp):
TAATATTAATGTATAAAAATAATATTATCATTATAATAATTTAA
Found at i:608609 original size:19 final size:20
Alignment explanation
Indices: 608585--608622 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
608575 CTAATAATTT
608585 AATAATATTATT-TTATAAA
1 AATAATATTATTATTATAAA
608604 AATAATATTATTATTATAA
1 AATAATATTATTATTATAA
608623 TAATTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATATTATTATTATAAA
Found at i:608926 original size:21 final size:22
Alignment explanation
Indices: 608881--608927 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
608871 TTTAATAATT
* *
608881 AATATTTTATTAAAATTACTAA
1 AATATTGTATTAAAAATACTAA
608903 AATATTGTATTAAAAATA-TAA
1 AATATTGTATTAAAAATACTAA
608924 AATA
1 AATA
608928 AATAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AATATTGTATTAAAAATACTAA
Found at i:610192 original size:13 final size:13
Alignment explanation
Indices: 610183--610220 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
610173 TTTTTATTTT
610183 TTATTATT-ATTAA
1 TTATTATTAATT-A
*
610196 TTATTATTAACTA
1 TTATTATTAATTA
610209 TTATTATTAATT
1 TTATTATTAATT
610221 TTACATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTATTAATTA
Found at i:610198 original size:10 final size:10
Alignment explanation
Indices: 610185--610214 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
610175 TTTATTTTTT
610185 ATTATTATTA
1 ATTATTATTA
610195 ATTATTATTA
1 ATTATTATTA
*
610205 ACTATTATTA
1 ATTATTATTA
610215 TTAATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTATTATTA
Found at i:610756 original size:15 final size:16
Alignment explanation
Indices: 610736--610765 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
610726 GAACGAAACC
610736 AGAAAA-AAAAAGAAG
1 AGAAAACAAAAAGAAG
610751 AGAAAACAAAAAGAA
1 AGAAAACAAAAAGAA
610766 AAAGACAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AGAAAACAAAAAGAAG
Found at i:612852 original size:23 final size:23
Alignment explanation
Indices: 612814--612857 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
612804 ATTAAAGTCA
*
612814 TAATTGTTTTTAAAAATAATATT
1 TAATTGTTTTTAAAAAAAATATT
612837 TAATTG-TTTTACAAAAAAATA
1 TAATTGTTTTTA-AAAAAAATA
612858 GTTATGACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (23 bp):
TAATTGTTTTTAAAAAAAATATT
Found at i:624881 original size:135 final size:129
Alignment explanation
Indices: 624594--624902 Score: 354
Period size: 135 Copynumber: 2.3 Consensus size: 129
624584 TCAACATCAG
* ** * * *
624594 CTGACCAGATCTCCTCATCACGTAGGAGCAACGTCAACATTAGATAACCAGCCGTCCTCATTACG
1 CTGACCAGATATCCTCATCACGTAGGAGC-GTGTCACCCTTAGATAACCAGCCGTCCTCATCACG
* *
624659 TAGGAACTATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGTAGGAGCAGTGTCATCCC
65 TAGGAACGATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGCAGGAGCAGTGTCATCCC
* *
624724 CTGACTAGATATCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGCCGTCCTCATCGCG
1 CTGACCAGATATCCTCATCACGTAGGAG-CGTGTCACCCTTAGATAACCAGCCGTCCTCATCACG
* *
624789 TAGGAACCGA-GTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGCATGAGTC-GTG
65 TAGGAA-CGATGTTATCA--C-T-ATAAA-ATGGCCAAGAACTCTTCATCACGCAGGAG-CAGTG
624852 TCAT-CC
123 TCATCCC
* * * *
624858 TTCGACCAGATTTCCTCATCACGTATGAACCGTGTCACCCTTAGA
1 CT-GACCAGATATCCTCATCACGTA-GGAGCGTGTCACCCTTAGA
624903 CGACCCGAAC
Statistics
Matches: 152, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
130 68 0.45
131 3 0.02
132 1 0.01
133 1 0.01
134 7 0.05
135 69 0.45
136 3 0.02
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (129 bp):
CTGACCAGATATCCTCATCACGTAGGAGCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGT
AGGAACGATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGCAGGAGCAGTGTCATCCC
Found at i:624920 original size:43 final size:40
Alignment explanation
Indices: 624825--624928 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
624815 AAGATGGCCA
* ** *
624825 AGAACTCTTCATCACGCATGAGTCGTGTCATCCTTCGACC
1 AGAACTCTTCATCACGTATGAACCGTGTCACCCTTCGACC
** *
624865 AGATTTCCTCATCACGTATGAACCGTGTCACCCTTAGACGACC
1 AGAACTCTTCATCACGTATGAACCGTGTCACCCTT---CGACC
*
624908 CGAACTCTTCATCACGTATGA
1 AGAACTCTTCATCACGTATGA
624929 GCAGTGTCGT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
40 28 0.56
43 22 0.44
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAACCGTGTCACCCTTCGACC
Found at i:625679 original size:16 final size:16
Alignment explanation
Indices: 625658--625688 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
625648 GAACGAAACC
625658 AGAAAAAAAAAAGAAG
1 AGAAAAAAAAAAGAAG
*
625674 AGAAAACAAAAAGAA
1 AGAAAAAAAAAAGAA
625689 AAAGACAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAAAGAAG
Found at i:627776 original size:23 final size:23
Alignment explanation
Indices: 627738--627781 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
627728 ATTAAAGTCA
*
627738 TAATTGTTTTTAAAAATAATATT
1 TAATTGTTTTTAAAAAAAATATT
627761 TAATTG-TTTTACAAAAAAATA
1 TAATTGTTTTTA-AAAAAAATA
627782 GTTATGACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (23 bp):
TAATTGTTTTTAAAAAAAATATT
Done.