Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008705.1 Hibiscus syriacus cultivar Beakdansim tig00111745_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: 1220187
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:428315 original size:12 final size:11
Alignment explanation
Indices: 428286--428371 Score: 55
Period size: 12 Copynumber: 7.3 Consensus size: 11
428276 ATATATCAAA
* *
428286 AATCAAAACAA
1 AATCAGAACAG
*
428297 AATTCAGATCAG
1 AA-TCAGAACAG
428309 ATATCAGAACAG
1 A-ATCAGAACAG
*
428321 AATCTAGATCAG
1 AATC-AGAACAG
428333 AAATCAGAACAG
1 -AATCAGAACAG
* *
428345 AATTAAGATCAG
1 AA-TCAGAACAG
*
428357 AAATCATAACAG
1 -AATCAGAACAG
428369 AAT
1 AAT
428372 TCAAATCGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
11 10 0.17
12 41 0.71
13 7 0.12
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.19
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:429685 original size:20 final size:20
Alignment explanation
Indices: 429653--429701 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
429643 AATTGGTTAC
*
429653 CTAG-ATTTTCTATGCAAAA
1 CTAGTATTTCCTATGCAAAA
* *
429672 CTAGTATTTCCTATGCACAT
1 CTAGTATTTCCTATGCAAAA
429692 C-AGTATTTCC
1 CTAGTATTTCC
429702 ATCAGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (20 bp):
CTAGTATTTCCTATGCAAAA
Found at i:430354 original size:16 final size:17
Alignment explanation
Indices: 430333--430365 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
430323 GTCGAAAAAC
430333 ATAAAA-TATGACTTTT
1 ATAAAATTATGACTTTT
*
430349 ATAAAATTTTGACTTTT
1 ATAAAATTATGACTTTT
430366 TGGTCAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (17 bp):
ATAAAATTATGACTTTT
Found at i:434186 original size:20 final size:20
Alignment explanation
Indices: 434163--434203 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
434153 GTATCAATAT
434163 TGAACTCTTGATATCGATAC
1 TGAACTCTTGATATCGATAC
*
434183 TGAACTCTTGGTATCGATAC
1 TGAACTCTTGATATCGATAC
434203 T
1 T
434204 CACCTGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
TGAACTCTTGATATCGATAC
Found at i:434213 original size:20 final size:20
Alignment explanation
Indices: 434165--434216 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
434155 ATCAATATTG
* *
434165 AACTCTTGATATCGATACTG
1 AACTCTTGGTATCGATACTC
434185 AACTCTTGGTATCGATACTC
1 AACTCTTGGTATCGATACTC
* *
434205 ACCTGTTGGTAT
1 AACTCTTGGTAT
434217 TTATACCCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (20 bp):
AACTCTTGGTATCGATACTC
Found at i:441175 original size:16 final size:16
Alignment explanation
Indices: 441149--441187 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
441139 TGAGGTTACT
441149 ATTTACGTGAATAGTGA
1 ATTT-CGTGAATAGTGA
441166 ATTTCGTGAATAGTGA
1 ATTTCGTGAATAGTGA
*
441182 AATTCG
1 ATTTCG
441188 GTCGGCGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (16 bp):
ATTTCGTGAATAGTGA
Found at i:441185 original size:17 final size:17
Alignment explanation
Indices: 441149--441182 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
441139 TGAGGTTACT
441149 ATTTACGTGAATAGTGA
1 ATTTACGTGAATAGTGA
441166 ATTT-CGTGAATAGTGA
1 ATTTACGTGAATAGTGA
441182 A
1 A
441183 ATTCGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATAGTGA
Found at i:449920 original size:13 final size:13
Alignment explanation
Indices: 449888--449954 Score: 57
Period size: 13 Copynumber: 5.0 Consensus size: 13
449878 ATTTTAAAAA
*
449888 TTATTAATTATAT
1 TTATTAAATATAT
449901 ATT-TTAAATATAT
1 -TTATTAAATATAT
*
449914 TTATTAAAAATTAT
1 TTATTAAATA-TAT
*
449928 TTAATT-ATTATAT
1 TT-ATTAAATATAT
449941 TATATTAAATATAT
1 T-TATTAAATATAT
449955 AAATAATCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
12 2 0.05
13 22 0.51
14 16 0.37
15 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATTAAATATAT
Found at i:450071 original size:26 final size:25
Alignment explanation
Indices: 450024--450109 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 25
450014 TTTTATTAAC
450024 ATAT-ATATATATTATTGAAATAAAA
1 ATATAATATATATTATT-AAATAAAA
*
450049 ATATAATATATATTATTACAATATAA
1 ATATAATATATATTATTA-AATAAAA
* *
450075 CT-TAGTATATTATTA-TAATATTAAAA
1 ATATAATATA-TATTATTAA-A-TAAAA
450101 ATATAATAT
1 ATATAATAT
450110 TAAAAATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
24 1 0.02
25 14 0.29
26 29 0.59
27 5 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
ATATAATATATATTATTAAATAAAA
Found at i:450073 original size:45 final size:48
Alignment explanation
Indices: 450000--450110 Score: 110
Period size: 52 Copynumber: 2.3 Consensus size: 48
449990 TATGAAATTC
450000 ATAAATAATATAA-ATTTTATTAACATAT-A-TA-TATATTATT-GAA-
1 ATAAA-AATATAATATTTTATTAACATATAACTAGTATATTATTAGAAT
*
450043 ATAAAAATATAATATATATTATT-ACAATATAACTTAGTATATTATTATAAT
1 ATAAAAATATAATAT-T-TTATTAAC-ATATAAC-TAGTATATTATTAGAAT
450094 ATTAAAAATATAATATT
1 A-TAAAAATATAATATT
450111 AAAAATATAA
Statistics
Matches: 56, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
42 7 0.12
43 7 0.12
44 3 0.05
45 9 0.16
46 1 0.02
48 2 0.04
49 9 0.16
50 2 0.04
51 2 0.04
52 14 0.25
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (48 bp):
ATAAAAATATAATATTTTATTAACATATAACTAGTATATTATTAGAAT
Found at i:450107 original size:14 final size:14
Alignment explanation
Indices: 450088--450125 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
450078 AGTATATTAT
450088 TATAATATTAAAAA
1 TATAATATTAAAAA
450102 TATAATATTAAAAA
1 TATAATATTAAAAA
450116 TATAATATTA
1 TATAATATTA
450126 TATTGTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATAATATTAAAAA
Found at i:450127 original size:22 final size:21
Alignment explanation
Indices: 450044--450150 Score: 83
Period size: 22 Copynumber: 4.9 Consensus size: 21
450034 ATTATTGAAA
450044 TAAAAATATAATATATATTAT
1 TAAAAATATAATATATATTAT
*
450065 T-ACAATATAACTTAGTATATTAT
1 TAAAAATATAA--TA-TATATTAT
* * *
450088 T-ATAATATTAAAAATATAATAT
1 TAAAAATA-T-AATATATATTAT
*
450110 TAAAAATATAATATTATATTGT
1 TAAAAATATAATA-TATATTAT
* *
450132 TAGAAATATAATAAATATT
1 TAAAAATATAATATATATT
450151 TAAATATTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
20 8 0.12
21 9 0.13
22 29 0.42
23 20 0.29
24 1 0.01
25 2 0.03
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAAAATATAATATATATTAT
Found at i:450205 original size:11 final size:12
Alignment explanation
Indices: 450150--450208 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
450140 TAATAAATAT
450150 TTAAATATTTAATA
1 TTAAATA-TT-ATA
* *
450164 ATAAATATTTTAA
1 TTAAATATTAT-A
*
450177 TTAAA-ATGATA
1 TTAAATATTATA
450188 TTAAATATTATA
1 TTAAATATTATA
450200 TT-AATATTA
1 TTAAATATTA
450209 AGTAAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
11 13 0.35
12 11 0.30
13 7 0.19
14 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
TTAAATATTATA
Found at i:454274 original size:17 final size:18
Alignment explanation
Indices: 454252--454286 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
454242 AACTTAAGGT
454252 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
454269 ATATTTTGTTAGTATTTA
1 ATATTTTATTAGTATTTA
454287 TGTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:456575 original size:13 final size:12
Alignment explanation
Indices: 456530--456582 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
456520 TTTAATACTA
456530 AATTTATTTTGTT
1 AATTT-TTTTGTT
*
456543 AATTTTGTTG--
1 AATTTTTTTGTT
456553 AA-TTTTTTGTT
1 AATTTTTTTGTT
456564 AATTTATTTTGTT
1 AATTT-TTTTGTT
456577 AATTTT
1 AATTTT
456583 GTTTATTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 6 0.18
10 2 0.06
11 2 0.06
12 7 0.21
13 17 0.50
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (12 bp):
AATTTTTTTGTT
Found at i:462746 original size:44 final size:41
Alignment explanation
Indices: 462669--462750 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
462659 GCAACGCGAT
* *
462669 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
462710 TTTGAAAAAAGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTG-AAAAA-TG-TGTTGCGATAGTGAAAAAGTGTTGCGA
462751 TAGTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 4 0.11
42 5 0.14
43 2 0.06
44 25 0.69
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:462760 original size:19 final size:20
Alignment explanation
Indices: 462671--462761 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
462661 AACGCGATTT
462671 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
462691 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
462710 TTTGAAAAAAGTGTTGTTGCGATAG
1 --TG-AAAAA-TG-TGTTGCGATAG
462735 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
462754 TGAAAAAT
1 TGAAAAAT
462762 CCAAAATAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 34 0.57
20 2 0.03
21 1 0.02
22 5 0.08
23 6 0.10
24 2 0.03
25 10 0.17
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:463065 original size:6 final size:6
Alignment explanation
Indices: 463054--463080 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
463044 TCTCGTCCCG
463054 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
463081 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:463176 original size:19 final size:20
Alignment explanation
Indices: 463138--463178 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
463128 TTCTTAAGAA
463138 ATCGCAACGTGAACTTGGACT
1 ATCGCAACG-GAACTTGGACT
*
463159 ATCGCAAC-GAATTTGGACT
1 ATCGCAACGGAACTTGGACT
463178 A
1 A
463179 ACTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAACGGAACTTGGACT
Found at i:464540 original size:25 final size:25
Alignment explanation
Indices: 464502--464565 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
464492 AATAGTCTTT
464502 TAAATATAATTAAATGA-AAACATTAAA
1 TAAATA-AA-TAAATGACAAA-ATTAAA
*
464529 TAAATAAATAAATGACCAAATTAAA
1 TAAATAAATAAATGACAAAATTAAA
464554 -AAATGAAATAAA
1 TAAAT-AAATAAA
464566 ATGTGGGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 4 0.12
25 20 0.59
26 4 0.12
27 6 0.18
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (25 bp):
TAAATAAATAAATGACAAAATTAAA
Found at i:465576 original size:2 final size:2
Alignment explanation
Indices: 465571--465668 Score: 70
Period size: 2 Copynumber: 52.0 Consensus size: 2
465561 CAATAGAATA
* *
465571 AT AT AT A- AT A- AC AT AT A- AT AA AT A- 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
*
465609 A- AT GAT AT A- AT AT AT AT AC AT AT ACT AT AT A- AT AT AT A- AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
465649 AT AA AT AT CAT AT AT A- AT AT
1 AT AT AT AT -AT AT AT AT AT AT
465669 GCGTGAATAC
Statistics
Matches: 77, Mismatches: 7, Indels: 24
0.71 0.06 0.22
Matches are distributed among these distances:
1 9 0.12
2 62 0.81
3 6 0.08
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:465580 original size:7 final size:7
Alignment explanation
Indices: 465568--465668 Score: 91
Period size: 7 Copynumber: 14.0 Consensus size: 7
465558 GTACAATAGA
465568 ATAATAT
1 ATAATAT
465575 ATAATAACAT
1 ATAAT---AT
*
465585 ATAATAA
1 ATAATAT
465592 ATAATAT
1 ATAATAT
465599 ATATATAT
1 ATA-ATAT
465607 ATAATGAT
1 ATAAT-AT
465615 ATAATAT
1 ATAATAT
*
465622 ATATACAT
1 ATA-ATAT
*
465630 ATACTAT
1 ATAATAT
465637 ATAATAT
1 ATAATAT
465644 AT-A-AT
1 ATAATAT
465649 ATAA-AT
1 ATAATAT
*
465655 ATCATAT
1 ATAATAT
465662 ATAATAT
1 ATAATAT
465669 GCGTGAATAC
Statistics
Matches: 78, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
5 4 0.05
6 7 0.09
7 40 0.51
8 20 0.26
10 7 0.09
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:465601 original size:45 final size:45
Alignment explanation
Indices: 465568--465668 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
465558 GTACAATAGA
*
465568 ATAATATATAATAACATATAATAAATAATATATATATATATAATGAT
1 ATAATATAT-AT-ACATATAATAAATAATATATATATAAATAATGAT
* *
465615 ATAATATATATACATATACTATATAATATATAATATAAATATCAT-AT
1 ATAATATATATACATATAATAAATAATATAT-ATATAAATA--ATGAT
465662 ATAATAT
1 ATAATAT
465669 GCGTGAATAC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
45 18 0.38
46 10 0.21
47 18 0.38
48 2 0.04
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (45 bp):
ATAATATATATACATATAATAAATAATATATATATAAATAATGAT
Found at i:465604 original size:47 final size:45
Alignment explanation
Indices: 465551--465651 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 45
465541 ATGATAAATG
*
465551 TATATATGTACAATAGA-ATAATATATAATAACATATAATAAATAATA
1 TATATATATACAAT-GATATAATATAT-AT-ACATATAATAAATAATA
* * *
465598 TATATATATATAATGATATAATATATATACATATACTATATAATA
1 TATATATATACAATGATATAATATATATACATATAATAAATAATA
465643 TATA-ATATA
1 TATATATATA
465652 AATATCATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
44 5 0.10
45 19 0.39
46 4 0.08
47 21 0.43
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (45 bp):
TATATATATACAATGATATAATATATATACATATAATAAATAATA
Found at i:465618 original size:27 final size:27
Alignment explanation
Indices: 465562--465668 Score: 98
Period size: 29 Copynumber: 3.9 Consensus size: 27
465552 ATATATGTAC
*
465562 AATAGAATA-ATATATAATA-ACATATAAT
1 AATATAATATATATAT-ATATA-ATAT-AT
465590 AA-ATAATATATATATATATAATGATAT
1 AATATAATATATATATATATAAT-ATAT
*
465617 AATATATATACATATACTATATAATATAT
1 AATATA-ATATATATA-TATATAATATAT
*
465646 AATATAA-ATAT-CATATATAATAT
1 AATATAATATATATATATATAATAT
465669 GCGTGAATAC
Statistics
Matches: 69, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
25 10 0.14
26 1 0.01
27 17 0.25
28 15 0.22
29 18 0.26
30 8 0.12
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (27 bp):
AATATAATATATATATATATAATATAT
Found at i:465650 original size:25 final size:25
Alignment explanation
Indices: 465568--465668 Score: 93
Period size: 25 Copynumber: 4.0 Consensus size: 25
465558 GTACAATAGA
*
465568 ATAATATATAATA-AC-ATATAATAA
1 ATAATATA-AATATACTATATAATAT
* *
465592 ATAATATATATATA-TATAATGATAT
1 ATAATATAAATATACTAT-ATAATAT
*
465617 AATATATATACATATACTATATAATAT
1 -ATA-ATATAAATATACTATATAATAT
465644 ATAATATAAATAT-CATATATAATAT
1 ATAATATAAATATAC-TATATAATAT
465669 GCGTGAATAC
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
23 3 0.05
24 12 0.19
25 24 0.38
26 6 0.09
27 16 0.25
28 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (25 bp):
ATAATATAAATATACTATATAATAT
Found at i:466785 original size:2 final size:2
Alignment explanation
Indices: 466778--466908 Score: 93
Period size: 2 Copynumber: 68.5 Consensus size: 2
466768 GTTATTCCAC
466778 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
* * * *
466820 ACT AT AC A- AT AT AA AT AT AT -T AT AC A- AT AT A- AT AA AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
466859 AGT CAT AT A- AT AT GT -T TT ACT AT A- AT AT AT -T AT AT AA AT
1 A-T -AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
466898 AT A- AT A- AT AT A
1 AT AT AT AT AT AT A
466909 CTAAATAAGT
Statistics
Matches: 105, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
1 10 0.10
2 88 0.84
3 6 0.06
4 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:468754 original size:3 final size:3
Alignment explanation
Indices: 468734--468776 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
468724 TTATTTTAGT
* * *
468734 TTA TTA TAA TCA TCA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
468777 TACATTACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:471021 original size:29 final size:29
Alignment explanation
Indices: 470987--471045 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
470977 CCTAAATTAA
470987 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
471016 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
471045 T
1 T
471046 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:475692 original size:29 final size:29
Alignment explanation
Indices: 475658--475716 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
475648 CCTAAATTAA
475658 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
475687 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
475716 T
1 T
475717 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:482409 original size:14 final size:14
Alignment explanation
Indices: 482390--482446 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
482380 AATCCGTTTG
*
482390 TTTATGTTTGTTCA
1 TTTATGTTCGTTCA
*
482404 TTTATG---G-TCG
1 TTTATGTTCGTTCA
*
482414 TTTATGTTCATTCA
1 TTTATGTTCGTTCA
*
482428 TTTATATTCGTTCA
1 TTTATGTTCGTTCA
482442 TTTAT
1 TTTAT
482447 ATTCAGCCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
14 25 0.74
ACGTcount: A:0.18, C:0.11, G:0.12, T:0.60
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:482438 original size:24 final size:24
Alignment explanation
Indices: 482389--482439 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
482379 TAATCCGTTT
** *
482389 GTTTATGTTTGTTCATTTATGGTC
1 GTTTATGTTCATTCATTTATAGTC
*
482413 GTTTATGTTCATTCATTTATATTC
1 GTTTATGTTCATTCATTTATAGTC
482437 GTT
1 GTT
482440 CATTTATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.59
Consensus pattern (24 bp):
GTTTATGTTCATTCATTTATAGTC
Found at i:482447 original size:14 final size:14
Alignment explanation
Indices: 482414--482451 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
482404 TTTATGGTCG
*
482414 TTTATGTTCATTCA
1 TTTATATTCATTCA
*
482428 TTTATATTCGTTCA
1 TTTATATTCATTCA
482442 TTTATATTCA
1 TTTATATTCA
482452 GCCCATCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (14 bp):
TTTATATTCATTCA
Found at i:482628 original size:20 final size:20
Alignment explanation
Indices: 482599--482646 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
482589 TTTATGTTCA
*
482599 TTCGTTTATGTTTGTTTACG
1 TTCGTTTATGTTAGTTTACG
* *
482619 TTCTTTTATGTTAGTTTATG
1 TTCGTTTATGTTAGTTTACG
482639 TTCGTTTA
1 TTCGTTTA
482647 CATTCATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.12, C:0.08, G:0.17, T:0.62
Consensus pattern (20 bp):
TTCGTTTATGTTAGTTTACG
Found at i:482636 original size:10 final size:10
Alignment explanation
Indices: 482599--482646 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
482589 TTTATGTTCA
482599 TTCGTTTATG
1 TTCGTTTATG
* *
482609 TTTGTTTACG
1 TTCGTTTATG
*
482619 TTCTTTTATG
1 TTCGTTTATG
*
482629 TTAGTTTATG
1 TTCGTTTATG
482639 TTCGTTTA
1 TTCGTTTA
482647 CATTCATTCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.12, C:0.08, G:0.17, T:0.62
Consensus pattern (10 bp):
TTCGTTTATG
Found at i:484450 original size:15 final size:15
Alignment explanation
Indices: 484430--484497 Score: 75
Period size: 15 Copynumber: 4.5 Consensus size: 15
484420 ATATTTAACT
*
484430 GGGCGGGAGGATGTG
1 GGGCGGGAGGATGCG
*
484445 GGGCGGGAGGATGTGG
1 GGGCGGGAGGATG-CG
* *
484461 GGGCAGGCGGATGCG
1 GGGCGGGAGGATGCG
484476 GGGC-GGATGGATGCG
1 GGGCGGGA-GGATGCG
484491 GGGCGGG
1 GGGCGGG
484498 TAATGTCTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
14 2 0.04
15 29 0.64
16 14 0.31
ACGTcount: A:0.12, C:0.12, G:0.66, T:0.10
Consensus pattern (15 bp):
GGGCGGGAGGATGCG
Found at i:484472 original size:16 final size:16
Alignment explanation
Indices: 484430--484478 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
484420 ATATTTAACT
*
484430 GGGCGGGAGGATGT-G
1 GGGCAGGAGGATGTGG
*
484445 GGGCGGGAGGATGTGG
1 GGGCAGGAGGATGTGG
* *
484461 GGGCAGGCGGATGCGG
1 GGGCAGGAGGATGTGG
484477 GG
1 GG
484479 CGGATGGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 14 0.47
16 16 0.53
ACGTcount: A:0.12, C:0.10, G:0.67, T:0.10
Consensus pattern (16 bp):
GGGCAGGAGGATGTGG
Found at i:491219 original size:30 final size:30
Alignment explanation
Indices: 491185--491245 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
491175 TGACGATGTG
491185 ACATATAACACATGTATAAAATGATGACAT
1 ACATATAACACATGTATAAAATGATGACAT
* * * * *
491215 ACATATATCACGTGTTTAAAGTGATGTCAT
1 ACATATAACACATGTATAAAATGATGACAT
491245 A
1 A
491246 ACACGTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (30 bp):
ACATATAACACATGTATAAAATGATGACAT
Found at i:497041 original size:16 final size:17
Alignment explanation
Indices: 497011--497042 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
497001 ATATTTATTT
497011 ATATAAAATATAATATA
1 ATATAAAATATAATATA
497028 ATATAAAA-ATAATAT
1 ATATAAAATATAATAT
497043 TATGGTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:497089 original size:18 final size:17
Alignment explanation
Indices: 497056--497099 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
497046 GGTTGTAAAA
497056 TATTATTTTAAATAATTAC
1 TATT-TTTTAAATAA-TAC
497075 -ATTTTTTACAATAATAC
1 TATTTTTTA-AATAATAC
497092 TATTTTTT
1 TATTTTTT
497100 CATCCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTTTTTAAATAATAC
Found at i:506689 original size:16 final size:17
Alignment explanation
Indices: 506668--506708 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
506658 CATAAAATTA
*
506668 TAAATAATT-AATATAT
1 TAAATAATTAAAAATAT
506684 TAAAT-ATTAAAAATAT
1 TAAATAATTAAAAATAT
*
506700 AAAATAATT
1 TAAATAATT
506709 TTAATTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 15 0.71
17 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAATTAAAAATAT
Found at i:509625 original size:15 final size:15
Alignment explanation
Indices: 509579--509625 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
509569 CGCCCCGCAT
*
509579 CCGCCCCGCATCCAC
1 CCGCCCCGCATCCGC
* *
509594 CCGCCCCGTATCTGC
1 CCGCCCCGCATCCGC
*
509609 CCGCCCCACATCCGC
1 CCGCCCCGCATCCGC
509624 CC
1 CC
509626 ACCCAGCTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.11, C:0.64, G:0.15, T:0.11
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:512230 original size:15 final size:15
Alignment explanation
Indices: 512183--512231 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
512173 AAAAAACCGC
512183 TTTTC-GCCTTTTTG
1 TTTTCAGCCTTTTTG
*
512197 TTTCCAGCCTTTTTG
1 TTTTCAGCCTTTTTG
512212 TTTTCAG-CTTTTTAG
1 TTTTCAGCCTTTTT-G
512227 TTTTC
1 TTTTC
512232 TTTATTCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.06, C:0.20, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTTCAGCCTTTTTG
Found at i:512410 original size:23 final size:22
Alignment explanation
Indices: 512375--512423 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
512365 TGTGGGGATA
*
512375 TTTTTAGTTTTTTTATTAAATAT
1 TTTTTAGTATTTTTATTAAAT-T
* *
512398 TTTTTGGTATTTTTATTTAATT
1 TTTTTAGTATTTTTATTAAATT
512420 TTTT
1 TTTT
512424 AAATAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.73
Consensus pattern (22 bp):
TTTTTAGTATTTTTATTAAATT
Found at i:513980 original size:24 final size:24
Alignment explanation
Indices: 513953--514020 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
513943 AGCTCGTATA
513953 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
* *
513977 AATTTGTC-CCAAAG-GACCGCGTAG
1 AATTTG-CACCGAAGTG-CCACGTAG
*
514001 AATTTTGCACCGTAGTGCCA
1 AA-TTTGCACCGAAGTGCCA
514021 TATAATATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
23 1 0.03
24 21 0.62
25 11 0.32
26 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:514050 original size:48 final size:48
Alignment explanation
Indices: 513955--514050 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
513945 CTCGTATAAA
* *
513955 TTTGCACCGAAGTGCCACGTAGAATTTGTCCCAAAGGACCGCGTAGAAT
1 TTTGCACCGAAGTGCCAC-TAGAATTTGTCCCAAAGGACCACATAGAAT
* *
514004 TTTGCACCGTAGTGCCA-TATAATATTGT-CCATAAGGACCACATAGAA
1 TTTGCACCGAAGTGCCACTAGAAT-TTGTCCCA-AAGGACCACATAGAA
514051 ATTCCTTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
47 8 0.20
48 17 0.41
49 16 0.39
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (48 bp):
TTTGCACCGAAGTGCCACTAGAATTTGTCCCAAAGGACCACATAGAAT
Found at i:514311 original size:30 final size:30
Alignment explanation
Indices: 514266--514324 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
514256 ATCGCGTAGA
* *
514266 CATATTATTTCCATACCTTTATCACATAGG
1 CATATCATTTACATACCTTTATCACATAGG
514296 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
514325 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGG
Found at i:514425 original size:34 final size:29
Alignment explanation
Indices: 514346--514417 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
514336 TTTTCTGCAT
514346 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
514375 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
514404 ATTCATGTCATGTA
1 ATTCATGTCATGTA
514418 TCATAATATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATGA
Found at i:521279 original size:2 final size:2
Alignment explanation
Indices: 521272--521317 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
521262 TTTCCAAATA
*
521272 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
521313 -T AT AT
1 AT AT AT
521318 TATTTGGCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:521880 original size:22 final size:21
Alignment explanation
Indices: 521846--521886 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
521836 ATAATTATTT
521846 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
521867 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
521887 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:528376 original size:32 final size:29
Alignment explanation
Indices: 528329--528394 Score: 78
Period size: 32 Copynumber: 2.2 Consensus size: 29
528319 TATGTAAAAC
528329 ATTTTTTTATCAAAATAAATACCTAAAGTT
1 ATTTTTTTATCAAAATAAATACCTAAAG-T
** *
528359 ATTTTTTTATTCAAAAATAGGTACGTAAAGT
1 ATTTTTTTA-TC-AAAATAAATACCTAAAGT
528390 ATTTT
1 ATTTT
528395 ATGTCAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 9 0.29
31 8 0.26
32 14 0.45
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (29 bp):
ATTTTTTTATCAAAATAAATACCTAAAGT
Found at i:528394 original size:28 final size:28
Alignment explanation
Indices: 528363--528420 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
528353 AAAGTTATTT
*
528363 TTTTAT-TCAAAAATAGGTACGTAAAGTA
1 TTTTATGTC-AAAATAGGTACGTAAACTA
*
528391 TTTTATGTCAAAATAGGTACTTAAACTA
1 TTTTATGTCAAAATAGGTACGTAAACTA
528419 TT
1 TT
528421 CAAACTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (28 bp):
TTTTATGTCAAAATAGGTACGTAAACTA
Found at i:528546 original size:31 final size:29
Alignment explanation
Indices: 528508--528576 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 29
528498 AATTGATTAT
528508 TTTAGGTACCTATTTTGACCAAAAATATAAC
1 TTTAGGTACCTATTTTGACCAAAAA-AT-AC
* * *
528539 TTTAGGTACTTCTTTTGACCAAAAAATTC
1 TTTAGGTACCTATTTTGACCAAAAAATAC
528568 TTTAGGTAC
1 TTTAGGTAC
528577 TTAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 10 0.29
30 2 0.06
31 23 0.66
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (29 bp):
TTTAGGTACCTATTTTGACCAAAAAATAC
Found at i:532849 original size:31 final size:30
Alignment explanation
Indices: 532793--532850 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
532783 GGGGTAAACT
532793 GTCCCTTTAGTACCTAAACTATCATTTTTA
1 GTCCCTTTAGTACCTAAACTATCATTTTTA
* * *
532823 GTCCGTTTGAGTATCTAAACTTTCATTT
1 GTCCCTTT-AGTACCTAAACTATCATTT
532851 GTTTCAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (30 bp):
GTCCCTTTAGTACCTAAACTATCATTTTTA
Found at i:544103 original size:15 final size:15
Alignment explanation
Indices: 544075--544108 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
544065 CCGTAGGACC
544075 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
* *
544090 ACTACGTCCTGAAGG
1 ACTACATCCCGAAGG
544105 ACTA
1 ACTA
544109 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:544657 original size:64 final size:63
Alignment explanation
Indices: 544588--544744 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 63
544578 TAACGAAGGT
* **
544588 ATGCATCGATGCACACCTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCACACCTTGTGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAA-AA
544651 G
63 G
** * *
544652 ATGCATCGATGCATGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACACCTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
*
544715 AGTGCATTGATGCACTACC-TGTGCATCGAT
1 A-TGCATCGATGCAC-ACCTTGTGCATCGAT
544745 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
63 2 0.03
64 66 0.85
65 10 0.13
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACACCTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
Found at i:547292 original size:19 final size:19
Alignment explanation
Indices: 547270--547333 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
547260 AATTATTTAA
547270 ATATATTTAAATTAAATAT
1 ATATATTTAAATTAAATAT
* *
547289 ATATTTTTAATTTAAAT-T
1 ATATATTTAAATTAAATAT
* * *
547307 AAATTTATTAATATTATATAT
1 ATATAT-TTAA-ATTAAATAT
547328 ATATAT
1 ATATAT
547334 ATATATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.17
19 19 0.54
20 5 0.14
21 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATTTAAATTAAATAT
Found at i:549320 original size:20 final size:20
Alignment explanation
Indices: 549295--549366 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
549285 CAATCGTAAA
549295 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
* ** *
549315 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
*
549336 ATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
549356 TTCGCGTTGCG
1 TTCGCGTTGCG
549367 GTAGTCTACA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:549418 original size:22 final size:22
Alignment explanation
Indices: 549360--549412 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
549350 TTCCATTTCG
*
549360 CGTTGCGGTAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
549382 CGTTGTGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
549404 CGTTGCGAT
1 CGTTGCGAT
549413 TTTCTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.15, C:0.17, G:0.30, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:549564 original size:5 final size:6
Alignment explanation
Indices: 549513--549561 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
549503 GACACGTATT
**
549513 ACCACG ACCATT ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
549559 ACC
1 ACC
549562 CGATTGGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.31, C:0.51, G:0.14, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:549862 original size:22 final size:22
Alignment explanation
Indices: 549836--549885 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
549826 TTGAAAAATT
549836 GCAACGACAACTGTAGACTATC
1 GCAACGACAACTGTAGACTATC
*
549858 GCAACAACAACTGTAGACTATC
1 GCAACGACAACTGTAGACTATC
549880 GCAACG
1 GCAACG
549886 CGAATTTGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (22 bp):
GCAACGACAACTGTAGACTATC
Found at i:550047 original size:22 final size:22
Alignment explanation
Indices: 550020--550072 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
550010 AATTTGGAAA
550020 ATCGCAACGACAACTGTAAACT
1 ATCGCAACGACAACTGTAAACT
* *
550042 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAAACT
550064 ATCGCAACG
1 ATCGCAACG
550073 CGAAATGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAAACT
Found at i:553550 original size:18 final size:18
Alignment explanation
Indices: 553527--553571 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
553517 TCTGCTACTT
*
553527 AAGGTTTCTATGATGATA
1 AAGGTTTCTATGATGAAA
553545 AAGGTTTCTATGATGAAA
1 AAGGTTTCTATGATGAAA
553563 AAGGTTTCT
1 AAGGTTTCT
553572 CATTTTGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (18 bp):
AAGGTTTCTATGATGAAA
Found at i:554787 original size:27 final size:25
Alignment explanation
Indices: 554735--554787 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
554725 ATACATCTTT
* *
554735 TTTATTTTATTTTTAAAATTAAATA
1 TTTATTTTATTTTGAAAATGAAATA
*
554760 TTTATTTTATCTATTGAAAATGGAATA
1 TTTATTTTAT-T-TTGAAAATGAAATA
554787 T
1 T
554788 ATATATAGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 10 0.43
26 1 0.04
27 12 0.52
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (25 bp):
TTTATTTTATTTTGAAAATGAAATA
Found at i:563784 original size:20 final size:20
Alignment explanation
Indices: 563759--563799 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
563749 AGAGCCCATT
563759 TAGGAGCATATAGTTGCATG
1 TAGGAGCATATAGTTGCATG
563779 TAGGAGCATATAGTTGCATG
1 TAGGAGCATATAGTTGCATG
563799 T
1 T
563800 GGTGAAATAT
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:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (20 bp):
TAGGAGCATATAGTTGCATG
Found at i:566876 original size:22 final size:23
Alignment explanation
Indices: 566844--566888 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
566834 TGATATGATG
*
566844 AAATTTTAGGGTGGGCAC-CATA
1 AAATTTGAGGGTGGGCACACATA
566866 AAATTTGAGGGTGGGCACACATA
1 AAATTTGAGGGTGGGCACACATA
566889 TATTAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.24
Consensus pattern (23 bp):
AAATTTGAGGGTGGGCACACATA
Found at i:568678 original size:134 final size:137
Alignment explanation
Indices: 568417--568688 Score: 297
Period size: 134 Copynumber: 2.0 Consensus size: 137
568407 ATCCTGTTGC
568417 TGCTAAAGTGGCTGAGTTGCTAATGAGGGGTCTGGTGAGTTCAGTTGGTTGACTTCATCTTTGAT
1 TGCTAAAGTGGCTGAGTTGCTAATGAGGGGTCTGGT-AGTT-A-TTGGTTGACTTCATCTTTGAT
* * * * *
568482 TAAACCATACCGACTACCCGTTGGTCTAGCGAGATGAGATGTTAGGTTCCTCGATGTCCAGGGTT
63 TAAACCATACAGACTACCAGTTGGTATAACGAGATGAGATGTTAGGTTCCTCAATGTCCAGGGTT
568547 CGAATCCTGT
128 CGAATCCTGT
* * * *
568557 TGCTAAAGTGTCTGAGTTGCTAATGATGGGTGTGGT-G-T-TTGGTTGGCTTCAT-TGTTGATTA
1 TGCTAAAGTGGCTGAGTTGCTAATGAGGGGTCTGGTAGTTATTGGTTGACTTCATCT-TTGATTA
* * * * *
568618 AACTATATCAG-CTACCAGTTGGTATAATGGGATGAGAT-TCTAGG-TCTCTTAATGTTCAGGGT
65 AACCATA-CAGACTACCAGTTGGTATAACGAGATGAGATGT-TAGGTTC-CTCAATGTCCAGGGT
*
568680 TGGAATCCT
127 TCGAATCCT
568689 AAAGTTGTGA
Statistics
Matches: 113, Mismatches: 15, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
133 4 0.04
134 72 0.64
135 2 0.02
137 1 0.01
138 1 0.01
140 33 0.29
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.35
Consensus pattern (137 bp):
TGCTAAAGTGGCTGAGTTGCTAATGAGGGGTCTGGTAGTTATTGGTTGACTTCATCTTTGATTAA
ACCATACAGACTACCAGTTGGTATAACGAGATGAGATGTTAGGTTCCTCAATGTCCAGGGTTCGA
ATCCTGT
Found at i:569225 original size:4 final size:4
Alignment explanation
Indices: 569216--569243 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
569206 TTCAAACTGA
569216 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
569244 ATTGTATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:572171 original size:3 final size:3
Alignment explanation
Indices: 572163--572192 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
572153 AATTATCTTA
572163 ATT ATT ATT ATT ATT ATTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT AT
572193 GTATCATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:578551 original size:23 final size:22
Alignment explanation
Indices: 578517--578559 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
578507 TGGTCTTTTC
*
578517 AAATATTTTTATTATTATAATGG
1 AAATATTATTATTA-TATAATGG
578540 AAATATTATTATTATATAAT
1 AAATATTATTATTATATAAT
578560 TCATAGACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
AAATATTATTATTATATAATGG
Found at i:580698 original size:12 final size:12
Alignment explanation
Indices: 580676--580718 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
580666 CCCCGATTAT
*
580676 CCGATTACCCGCC
1 CCGA-TACCCGAC
580689 CCGATACCCGAC
1 CCGATACCCGAC
*
580701 CCGATACCCAAC
1 CCGATACCCGAC
580713 CCGATA
1 CCGATA
580719 AATATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 24 0.86
13 4 0.14
ACGTcount: A:0.26, C:0.49, G:0.14, T:0.12
Consensus pattern (12 bp):
CCGATACCCGAC
Found at i:580774 original size:37 final size:36
Alignment explanation
Indices: 580719--580825 Score: 117
Period size: 37 Copynumber: 2.9 Consensus size: 36
580709 CAACCCGATA
*
580719 AATATTAA-AAATAATAATTATATATATATATATATAT
1 AATATTAATAAAT-TTAATT-TATATATATATATATAT
* * * *
580756 AATATTAATAAATTTAATTTAAATTAAAAAAATATAT
1 AATATTAATAAATTTAATTTATA-TATATATATATAT
* *
580793 AATATTTATATATTTAATTTATATATATATATA
1 AATATTAATAAATTTAATTTATATATATATATA
580826 CCCGGCCCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
36 10 0.18
37 43 0.75
38 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
AATATTAATAAATTTAATTTATATATATATATATAT
Found at i:586288 original size:192 final size:193
Alignment explanation
Indices: 585941--586529 Score: 602
Period size: 194 Copynumber: 3.0 Consensus size: 193
585931 ACAACAAGCC
* * * * ** *
585941 AACATACACACCTCTTCTAACTAATTTCAACACTAAATACTGAGATCATTC---AAGTT-ACTGC
1 AACATAC-C-CCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGCTCAAGAAGTTCA-TGA
* * * *
586002 TAATTGAAGTAATCAATGCACCAACAACAAAAACAGGACTTAAATTGAATGATTGGATCAACTCA
63 TAATTGGAGTAACCAACGCACCAACAACAAAAACAAGACTTAAA-T--A-GA----ATCAACTCA
* *
586067 AATAAGACCCTAATAAGTGAAACAATTCAAGCAAGTAACCTTGGGGGCTATAAATCTCTATATTC
120 AATAAGACCCTAATAAGTGAAACAATTCAAGCATGTAAACTTGGGGGCTATAAATCTCTATATTC
586132 TGCATCATA
185 TGCATCATA
* * *
586141 AACAT-CTCCTCTTCTGACTAGTTCCAGCACTAAATACTGAAATCGCTCAAGAAGTTCCTGATAA
1 AACATACCCCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGCTCAAGAAGTTCATGATAA
* * * *
586205 TTGGAGTAACCAATGCATCAACAACAAAAACAATACTTAAATAGAATCAACTTAAATAAGACTCC
66 TTGGAGTAACCAACGCACCAACAACAAAAACAAGACTTAAATAGAATCAACTCAAATAAGAC-CC
* * * * * *
586270 -AATAATTGAAACAATTCAAGCATGTAAACTT-GAGGCTTTTAAATGTCTATAATCTACATCA-A
130 TAATAAGTGAAACAATTCAAGCATGTAAACTTGGGGGC-TATAAATCTCTATATTCTGCATCATA
* * *
586332 AAGCATACCCCCTTTTCTGACTAATTCCAGCACTAAATACTGAAATCGTTCTAGAAGTTCATGAT
1 AA-CATA-CCCCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGCTCAAGAAGTTCATGAT
* * * * * * *
586397 AATTGGAGTAATCAACGCACCACCAACAAAAAGAGGACTTAAATTGAATCAACGCAAATAAGGCC
64 AATTGGAGTAACCAACGCACCAACAACAAAAACAAGACTTAAATAGAATCAACTCAAATAAGACC
* * * * *
586462 CTACTAAGTGAAACAATTCAAGCATGTAAACTTGAGGGCTATAAATGC-CAATATTTTGCATCCT
129 CTAATAAGTGAAACAATTCAAGCATGTAAACTTGGGGGCTATAAAT-CTCTATATTCTGCATCAT
586526 A
193 A
586527 AAC
1 AAC
586530 TATAAGTGCT
Statistics
Matches: 324, Mismatches: 52, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
191 7 0.02
192 67 0.21
193 4 0.01
194 150 0.46
195 6 0.02
196 2 0.01
197 35 0.11
199 2 0.01
200 51 0.16
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (193 bp):
AACATACCCCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGCTCAAGAAGTTCATGATAA
TTGGAGTAACCAACGCACCAACAACAAAAACAAGACTTAAATAGAATCAACTCAAATAAGACCCT
AATAAGTGAAACAATTCAAGCATGTAAACTTGGGGGCTATAAATCTCTATATTCTGCATCATA
Found at i:589833 original size:32 final size:31
Alignment explanation
Indices: 589792--589979 Score: 148
Period size: 32 Copynumber: 5.9 Consensus size: 31
589782 AGTCGAGGGT
*
589792 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATG-TCTTCGGAACATATGGACAGAA
*
589824 TTACCTATGTCTTTCGGGACATATGGACAGAA
1 TTACCTATGTC-TTCGGAACATATGGACAGAA
* *
589856 TTACCTATGTCTTTC-AAGACATATGGGCAGAA
1 TTACCTATGTC-TTCGGA-ACATATGGACAGAA
** * *
589888 TTACCTATGTCTTTTGAGACATATGGTCAGTA
1 TTACCTATGTCTTCGGA-ACATATGGACAGAA
** * * *
589920 -TACCTATGTTCTAAGGAATATATGAACA-AT
1 TTACCTATG-TCTTCGGAACATATGGACAGAA
* * *
589950 TTACCTAGGTTCTTCGGGACCTATGGACAG
1 TTACCTATG-TCTTCGGAACATATGGACAG
589980 TTGTCGAGGT
Statistics
Matches: 126, Mismatches: 24, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
31 41 0.33
32 85 0.67
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (31 bp):
TTACCTATGTCTTCGGAACATATGGACAGAA
Found at i:589879 original size:64 final size:63
Alignment explanation
Indices: 589810--589928 Score: 184
Period size: 64 Copynumber: 1.9 Consensus size: 63
589800 GTTCTACGGA
*
589810 ACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGTCTTTCAAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAGAA-TACCTATGTCTTTCAAG
* * * *
589874 ACATATGGGCAGAATTACCTATGTCTTTTGAGACATATGGTCAGTATACCTATGT
1 ACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAGAATACCTATGT
589929 TCTAAGGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
63 9 0.18
64 41 0.82
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (63 bp):
ACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAGAATACCTATGTCTTTCAAG
Found at i:596068 original size:115 final size:115
Alignment explanation
Indices: 595929--596160 Score: 464
Period size: 115 Copynumber: 2.0 Consensus size: 115
595919 ACTGTTAATC
595929 TTACCCTTTAATTGATTTTATTTATTATTATTTACCTTATTTAATTCAAATTCTTATACATTTAA
1 TTACCCTTTAATTGATTTTATTTATTATTATTTACCTTATTTAATTCAAATTCTTATACATTTAA
595994 CGAGTTATAAAATATCAATGACAAATTAGTTTCATAATATGAAGTTGTGA
66 CGAGTTATAAAATATCAATGACAAATTAGTTTCATAATATGAAGTTGTGA
596044 TTACCCTTTAATTGATTTTATTTATTATTATTTACCTTATTTAATTCAAATTCTTATACATTTAA
1 TTACCCTTTAATTGATTTTATTTATTATTATTTACCTTATTTAATTCAAATTCTTATACATTTAA
596109 CGAGTTATAAAATATCAATGACAAATTAGTTTCATAATATGAAGTTGTGA
66 CGAGTTATAAAATATCAATGACAAATTAGTTTCATAATATGAAGTTGTGA
596159 TT
1 TT
596161 TCAAAACGTA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 117 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (115 bp):
TTACCCTTTAATTGATTTTATTTATTATTATTTACCTTATTTAATTCAAATTCTTATACATTTAA
CGAGTTATAAAATATCAATGACAAATTAGTTTCATAATATGAAGTTGTGA
Found at i:596558 original size:32 final size:32
Alignment explanation
Indices: 596521--596600 Score: 160
Period size: 32 Copynumber: 2.5 Consensus size: 32
596511 ACTTTTAAGA
596521 GTTATAAAATAGACATTTAAACTTTGAATTTT
1 GTTATAAAATAGACATTTAAACTTTGAATTTT
596553 GTTATAAAATAGACATTTAAACTTTGAATTTT
1 GTTATAAAATAGACATTTAAACTTTGAATTTT
596585 GTTATAAAATAGACAT
1 GTTATAAAATAGACAT
596601 CGCACCGTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.41
Consensus pattern (32 bp):
GTTATAAAATAGACATTTAAACTTTGAATTTT
Found at i:600457 original size:21 final size:22
Alignment explanation
Indices: 600431--600474 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
600421 TGTAGCAGTA
600431 CTGTAGCA-GAGAATCGGTTCC
1 CTGTAGCAGGAGAATCGGTTCC
*
600452 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGAGAATCGGTTCC
600474 C
1 C
600475 CTCAAGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (22 bp):
CTGTAGCAGGAGAATCGGTTCC
Found at i:609849 original size:31 final size:31
Alignment explanation
Indices: 609800--609873 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
609790 GTAGAAAATA
* * *
609800 ATTAAATATTTAGCTGATGTTTTATTTATATT
1 ATTAAAT-TTTAGATGATGTGTGATTTATATT
609832 ATTAAATTTTAGATGATGTGTGATTTATATT
1 ATTAAATTTTAGATGATGTGTGATTTATATT
*
609863 ATTGAATTTTA
1 ATTAAATTTTA
609874 CTTTTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
31 31 0.82
32 7 0.18
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (31 bp):
ATTAAATTTTAGATGATGTGTGATTTATATT
Found at i:612084 original size:3 final size:3
Alignment explanation
Indices: 612076--612116 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
612066 TCGGTTTCAA
612076 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
612117 AAAATTGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:624957 original size:2 final size:2
Alignment explanation
Indices: 624950--624996 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
624940 TCATTGTTTG
624950 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
624992 AT AT A
1 AT AT A
624997 GAGAGAGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:625001 original size:2 final size:2
Alignment explanation
Indices: 624996--625024 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
624986 ATATATATAT
624996 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
625025 CAGACCAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:625282 original size:53 final size:53
Alignment explanation
Indices: 625202--625319 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
625192 GAATTGAGGA
*
625202 GAATTGGAATCCAATTCCATCACTTTCCCATGTTTGGTTCAAGTTTTCCAAGG
1 GAATTGGAATCCAATTCCACCACTTTCCCATGTTTGGTTCAAGTTTTCCAAGG
*
625255 GAATTGGAATCTAATTCCACCACTTTCCCATGTTTGGTTCAAGTTTTCCAAGG
1 GAATTGGAATCCAATTCCACCACTTTCCCATGTTTGGTTCAAGTTTTCCAAGG
625308 GAATTGGAATCC
1 GAATTGGAATCC
625320 CTCATGGCTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (53 bp):
GAATTGGAATCCAATTCCACCACTTTCCCATGTTTGGTTCAAGTTTTCCAAGG
Found at i:625855 original size:226 final size:222
Alignment explanation
Indices: 625480--625932 Score: 613
Period size: 226 Copynumber: 2.0 Consensus size: 222
625470 AATTCATATA
* * *
625480 TTCGGGTCGGGTTAGGTGAAATTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATT
1 TTCGGGTCGGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATT
* * * *
625545 CGGGTTGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCTACCCGAAAATATATATAATTTTACC
66 C--G--GGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCCGAAAAAAAATATAATTTTACC
* * *
625610 TTATATATTTAGAAATAATTACAATAATACCCATCTCTCTAT-ATATTTTTCAATTAAGTCACTG
127 TTATATATTTAGAAATAATTACAATAATACCCATCTATATATAATATTTTTCAATTAAGTCAATG
625674 TTTTTATTAAATAAAAACAATTTTTTATTAT
192 TTTTTATTAAATAAAAACAATTTTTTATTAT
* * *
625705 TTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTTGGGTCGGGTTTTTTAAGTGTGAGATA
1 TTCGGGTCGGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGGTTTTTTAAGTGT--GATA
* * *
625770 TTC-GGGTCGGGTTCGGGTTTATGGTGAAAAAAATCGGATCGACCCGAAAAAAAATATAATTTTA
64 TTCGGGGTCGAGTTCGGGTTTAGGGTGAAAAAAA-C---CCGACCCGAAAAAAAATATAATTTTA
* * *
625834 CCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAA
125 CCTTATATATTTAGAAATAATTACAATAATACCCATCTATATATAATATTTTTCAATTAAGTCAA
* *
625899 TGTTTTTATTGAATAAAAATAATTTTTTATTAT
190 TGTTTTTATTAAATAAAAACAATTTTTTATTAT
625932 T
1 T
625933 GTGTCGTGCC
Statistics
Matches: 200, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
222 27 0.14
223 1 0.00
225 53 0.26
226 62 0.31
227 57 0.28
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (222 bp):
TTCGGGTCGGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATT
CGGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCCGAAAAAAAATATAATTTTACCTTAT
ATATTTAGAAATAATTACAATAATACCCATCTATATATAATATTTTTCAATTAAGTCAATGTTTT
TATTAAATAAAAACAATTTTTTATTAT
Found at i:626400 original size:18 final size:17
Alignment explanation
Indices: 626357--626403 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
626347 TATGGAATTG
*
626357 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
626374 GATAT-CAATTCATTCACA
1 GAT-TCCAATTC-CTCACA
626392 GATTCCAATTCC
1 GATTCCAATTCC
626404 CTCATAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.32
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:627261 original size:29 final size:28
Alignment explanation
Indices: 627216--627274 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
627206 ATAAGTTATT
* *
627216 ACTTGGTAATGATCTTTTCCGTGAACCAA
1 ACTTGGTAATGAGCTTTTCC-CGAACCAA
627245 ACTTGGTAATGAGCTTTTCCCGAACCAA
1 ACTTGGTAATGAGCTTTTCCCGAACCAA
627273 AC
1 AC
627275 GCCCCCTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (28 bp):
ACTTGGTAATGAGCTTTTCCCGAACCAA
Found at i:629145 original size:22 final size:22
Alignment explanation
Indices: 629120--629162 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
629110 GTCGCAACAT
629120 TGATACAAAAGTGCATTCGCAC
1 TGATACAAAAGTGCATTCGCAC
*
629142 TGATACTAAAGTGCATTCGCA
1 TGATACAAAAGTGCATTCGCA
629163 TTGGGGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (22 bp):
TGATACAAAAGTGCATTCGCAC
Found at i:629453 original size:18 final size:18
Alignment explanation
Indices: 629407--629458 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
629397 ACTAAGCATG
629407 TTAGTATCGATACCGACC
1 TTAGTATCGATACCGACC
** *
629425 TTAGGGTATCGATATTGGCC
1 TTA--GTATCGATACCGACC
629445 TTAGTATCGATACC
1 TTAGTATCGATACC
629459 ACTTTGAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 12 0.44
20 15 0.56
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (18 bp):
TTAGTATCGATACCGACC
Found at i:641446 original size:12 final size:12
Alignment explanation
Indices: 641410--641446 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
641400 CTTTTATACA
641410 TTTTTATCAATT
1 TTTTTATCAATT
*
641422 ATTTTATCAATT
1 TTTTTATCAATT
641434 TTTTTATCAATT
1 TTTTTATCAATT
641446 T
1 T
641447 AGCTATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTTTATCAATT
Found at i:641670 original size:23 final size:24
Alignment explanation
Indices: 641644--641689 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
641634 AAATAAAAAT
*
641644 TAAAAGAGAAT-TAAAATTTTAAA
1 TAAAAAAGAATATAAAATTTTAAA
*
641667 TAAAAAATAATATAAAATTTTAA
1 TAAAAAAGAATATAAAATTTTAA
641690 TGTAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
TAAAAAAGAATATAAAATTTTAAA
Found at i:641707 original size:26 final size:24
Alignment explanation
Indices: 641655--641709 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
641645 AAAAGAGAAT
*
641655 TAAAATTTTAAATAAAAAATAATA
1 TAAAATTTTAAATAAAAAATAAAA
*
641679 TAAAATTTTAATGTAATAAAATAAAA
1 TAAAATTTTAA-ATAA-AAAATAAAA
641705 TAAAA
1 TAAAA
641710 GTAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 11 0.41
25 3 0.11
26 13 0.48
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAATTTTAAATAAAAAATAAAA
Found at i:642277 original size:188 final size:189
Alignment explanation
Indices: 641962--642356 Score: 584
Period size: 188 Copynumber: 2.1 Consensus size: 189
641952 ATAAAATTTT
* * *
641962 AAATATTAAATATA-T-TATATATAACATGTGGGTTAAACCCAAACCATTTAATACTCAATTAAT
1 AAATATTAAATATATTATATATATAACATATGGGCTAAACCCAAACCATTTAAAACTCAATTAAT
642025 AATTTAAGATCCAATAACTTTTAAACCCAAATCAATATTAAAAAATTAAAAAAATTATATAAAAT
66 AATTTAAGATCCAATAACTTTTAAACCCAAATCAATATTAAAAAATTAAAAAAATTATATAAAAT
* *
642090 TTTTATTTTATAATTATATATTATTTACATTAATTGTAAA-T-TATTTTTCTGAATTAAA
131 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGT-TTTTTCTGAATTAAA
* **
642148 AAATATTAAATATATTATATATATAACATATGGGCTCAGTCCAAACCATTTAAAACTCAATTAAT
1 AAATATTAAATATATTATATATATAACATATGGGCTAAACCCAAACCATTTAAAACTCAATTAAT
* * ** **
642213 AATTTAAGATCCAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAACTTTATATAAAAT
66 AATTTAAGATCCAATAACTTTTAAACCCAAATCAATATTAAAAAATTAAAAAAATTATATAAAAT
* *
642278 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTTGAATTATA
131 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTCTGAATTAAA
* *
642337 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
642357 AATTAGAAAA
Statistics
Matches: 187, Mismatches: 18, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
186 14 0.07
187 1 0.01
188 147 0.79
189 24 0.13
190 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (189 bp):
AAATATTAAATATATTATATATATAACATATGGGCTAAACCCAAACCATTTAAAACTCAATTAAT
AATTTAAGATCCAATAACTTTTAAACCCAAATCAATATTAAAAAATTAAAAAAATTATATAAAAT
TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTCTGAATTAAA
Found at i:645877 original size:19 final size:19
Alignment explanation
Indices: 645855--645907 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
645845 TGCAATAACT
*
645855 ATTTGACATTGGTGATTTA
1 ATTTGACACTGGTGATTTA
* *
645874 ATTTTATACTGGTGATTTA
1 ATTTGACACTGGTGATTTA
* *
645893 ATTTTATACTGGTGA
1 ATTTGACACTGGTGA
645908 AATAATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (19 bp):
ATTTGACACTGGTGATTTA
Found at i:645913 original size:19 final size:19
Alignment explanation
Indices: 645872--645913 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
645862 ATTGGTGATT
**
645872 TAATTTTATACTGGTGATT
1 TAATTTTATACTGGTGAAA
645891 TAATTTTATACTGGTGAAA
1 TAATTTTATACTGGTGAAA
645910 TAAT
1 TAAT
645914 AAGTTTTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (19 bp):
TAATTTTATACTGGTGAAA
Found at i:646846 original size:18 final size:19
Alignment explanation
Indices: 646823--646859 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
646813 CCAGTAATCC
646823 TATT-CACTGGTAATCTTT
1 TATTACACTGGTAATCTTT
646841 TATTCACACTGGTAATCTT
1 TATT-ACACTGGTAATCTT
646860 ACATTCTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (19 bp):
TATTACACTGGTAATCTTT
Found at i:646865 original size:20 final size:20
Alignment explanation
Indices: 646827--646865 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
646817 TAATCCTATT
**
646827 CACTGGTAATCTTTTATTCA
1 CACTGGTAATCTTACATTCA
646847 CACTGGTAATCTTACATTC
1 CACTGGTAATCTTACATTC
646866 TGTTAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (20 bp):
CACTGGTAATCTTACATTCA
Found at i:648173 original size:19 final size:17
Alignment explanation
Indices: 648125--648175 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
648115 TTTTTTAGAA
648125 ATTATTTAT-TAAAAAT
1 ATTATTTATATAAAAAT
**
648141 ATTAAATATAATAAAAATT
1 ATTATTTAT-ATAAAAA-T
648160 ATTATTTATCATAAAA
1 ATTATTTAT-ATAAAA
648176 TTCAATATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 7 0.26
18 6 0.22
19 14 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTATTTATATAAAAAT
Found at i:654560 original size:24 final size:25
Alignment explanation
Indices: 654514--654562 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
654504 AGAATTTTCC
654514 AAAAAAATTTAAATTTTCGAAATTA
1 AAAAAAATTTAAATTTTCGAAATTA
654539 AAAAAAATGTT-AATTTTC-AAATTA
1 AAAAAAAT-TTAAATTTTCGAAATTA
654563 TTGTGTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 15 0.65
26 2 0.09
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
AAAAAAATTTAAATTTTCGAAATTA
Found at i:656724 original size:20 final size:20
Alignment explanation
Indices: 656699--656746 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
656689 CAAAATAATC
656699 TTTCAAAGTATTTCGAACCA
1 TTTCAAAGTATTTCGAACCA
*
656719 TTTCAAAGTATTTTGAACCA
1 TTTCAAAGTATTTCGAACCA
656739 TTTCAAAG
1 TTTCAAAG
656747 CCAAAAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
TTTCAAAGTATTTCGAACCA
Found at i:657760 original size:20 final size:23
Alignment explanation
Indices: 657715--657787 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
657705 AATATCTAAT
*
657715 TATAATATAATT-GAATATATTAG
1 TATAATATCATTAGAA-ATATTAG
*
657738 TATAATATTA-TA-AAATA-TAG
1 TATAATATCATTAGAAATATTAG
*
657758 TATTATATCATTAGAAATATTAG
1 TATAATATCATTAGAAATATTAG
657781 TA-AATAT
1 TATAATAT
657788 ATTTATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
20 11 0.26
21 5 0.12
22 12 0.29
23 14 0.33
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (23 bp):
TATAATATCATTAGAAATATTAG
Found at i:660640 original size:62 final size:62
Alignment explanation
Indices: 660521--660640 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
660511 TAGTATCCAA
* * ** *
660521 ACTATTAATTTTGGTCAATTTTAATACTTAAAGTTTTTTAAATCATATTTAATGTTTAATTT
1 ACTATTAATTTTGGTCAATCTTAATACTTAAACTTTTTTAAATCATACATAACGTTTAATTT
* * *
660583 ACTATTAGTTTTGGTCAATCTTAGTACTTAAACTTTTTTAAATCATACATACCGTTTA
1 ACTATTAATTTTGGTCAATCTTAATACTTAAACTTTTTTAAATCATACATAACGTTTA
660641 GTTTTTGATT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (62 bp):
ACTATTAATTTTGGTCAATCTTAATACTTAAACTTTTTTAAATCATACATAACGTTTAATTT
Found at i:661833 original size:23 final size:25
Alignment explanation
Indices: 661805--661859 Score: 96
Period size: 23 Copynumber: 2.3 Consensus size: 25
661795 ATCACTTAAT
661805 TTTAAAATAATTTTTTAAA-AA-TA
1 TTTAAAATAATTTTTTAAATAATTA
661828 TTTAAAATAATTTTTTAAATAATTA
1 TTTAAAATAATTTTTTAAATAATTA
661853 TTTAAAA
1 TTTAAAA
661860 AAAATGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 19 0.63
24 2 0.07
25 9 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAAAATAATTTTTTAAATAATTA
Found at i:661849 original size:12 final size:12
Alignment explanation
Indices: 661804--661858 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
661794 AATCACTTAA
*
661804 TTTTAAAATAAT
1 TTTTTAAATAAT
661816 TTTTTAAA-AAT
1 TTTTTAAATAAT
* *
661827 ATTTAAAATAAT
1 TTTTTAAATAAT
661839 TTTTTAAATAAT
1 TTTTTAAATAAT
*
661851 TATTTAAA
1 TTTTTAAA
661859 AAAAATGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
11 9 0.25
12 27 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTTTAAATAAT
Found at i:674892 original size:29 final size:29
Alignment explanation
Indices: 674850--674908 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
674840 GCAAGGCAGT
674850 CATTAGGGGCTTTTGTTCTATAATGTGGG
1 CATTAGGGGCTTTTGTTCTATAATGTGGG
674879 CATTAGGGGCTTTTGTTCTATAATGTGGG
1 CATTAGGGGCTTTTGTTCTATAATGTGGG
674908 C
1 C
674909 TCTTTTAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.12, G:0.31, T:0.41
Consensus pattern (29 bp):
CATTAGGGGCTTTTGTTCTATAATGTGGG
Found at i:675925 original size:21 final size:21
Alignment explanation
Indices: 675899--675957 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
675889 ATTTACCGTG
675899 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
* *
675920 ATTGCGGCCATCGCGGACGCT
1 ATTGCGGCCGTCGCGGGCGCT
*
675941 ATTGCGGCCGTCACGGG
1 ATTGCGGCCGTCGCGGG
675958 TAACTCGGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.10, C:0.32, G:0.39, T:0.19
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGCGCT
Found at i:678695 original size:7 final size:7
Alignment explanation
Indices: 678683--678709 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
678673 GCACATAGAC
678683 TAAAGAT
1 TAAAGAT
678690 TAAAGAT
1 TAAAGAT
678697 TAAAGAT
1 TAAAGAT
678704 TAAAGA
1 TAAAGA
678710 AGAAGAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (7 bp):
TAAAGAT
Found at i:686372 original size:69 final size:69
Alignment explanation
Indices: 686261--686393 Score: 232
Period size: 69 Copynumber: 1.9 Consensus size: 69
686251 CTAATGAACT
*
686261 TTGATTTATACCGAAAACTATATGGAGGATGAGCTGATCATGCTCATCTGTTGGACGGTAAACAT
1 TTGATGTATACCGAAAACTATATGGAGGATGAGCTGATCATGCTCATCTGTTGGACGGTAAACAT
686326 GATA
66 GATA
*
686330 TTGATGTATACCGAAAA-TGATATGGAGGATGAGCTGATCATGCTCATCTGTTGGATGGTAAACA
1 TTGATGTATACCGAAAACT-ATATGGAGGATGAGCTGATCATGCTCATCTGTTGGACGGTAAACA
686394 CAATAAGAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 1 0.02
69 60 0.98
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (69 bp):
TTGATGTATACCGAAAACTATATGGAGGATGAGCTGATCATGCTCATCTGTTGGACGGTAAACAT
GATA
Found at i:689535 original size:31 final size:31
Alignment explanation
Indices: 689491--689597 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
689481 GGACTGTATT
*
689491 ATATTTTTCAAAAGTTGAATAATCAAAATATA
1 ATATTCTT-AAAAGTTGAATAATCAAAATATA
* ** *** *
689523 ATATTCCTAAAAGTTTG-AGGATTGTATTATA
1 ATATTCTTAAAAG-TTGAATAATCAAAATATA
*
689554 AT-TT-TTAAAAGTTGAATAACCAAAATATA
1 ATATTCTTAAAAGTTGAATAATCAAAATATA
689583 ATATTCTTAAAAGTT
1 ATATTCTTAAAAGTT
689598 TGGGGACTAT
Statistics
Matches: 55, Mismatches: 16, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
28 3 0.05
29 15 0.27
30 4 0.07
31 24 0.44
32 9 0.16
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (31 bp):
ATATTCTTAAAAGTTGAATAATCAAAATATA
Found at i:689564 original size:60 final size:60
Alignment explanation
Indices: 689471--689613 Score: 200
Period size: 60 Copynumber: 2.4 Consensus size: 60
689461 AACTAATGGC
* * *
689471 AAAAATTTAAGGACTGTATTATATTTTTCAAAAGTTGAATAATCAAAATATAATATTCCT
1 AAAAGTTTGAGGACTGTATTATATTTTTCAAAAGTTGAATAACCAAAATATAATATTCCT
* *
689531 AAAAGTTTGAGGATTGTATTATAATTTTT-AAAAGTTGAATAACCAAAATATAATATTCTT
1 AAAAGTTTGAGGACTGTATTAT-ATTTTTCAAAAGTTGAATAACCAAAATATAATATTCCT
* *
689591 AAAAGTTTGGGGACTAT-TTATAT
1 AAAAGTTTGAGGACTGTATTATAT
689614 ACTTTACCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
58 2 0.03
59 4 0.05
60 62 0.84
61 6 0.08
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (60 bp):
AAAAGTTTGAGGACTGTATTATATTTTTCAAAAGTTGAATAACCAAAATATAATATTCCT
Found at i:693602 original size:6 final size:6
Alignment explanation
Indices: 693587--693618 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
693577 TTAATGCCGC
*
693587 CTGCTG CTGCTA CTGCTA CTGCTA CTGCTA CT
1 CTGCTA CTGCTA CTGCTA CTGCTA CTGCTA CT
693619 AGTAGAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.12, C:0.34, G:0.19, T:0.34
Consensus pattern (6 bp):
CTGCTA
Found at i:695499 original size:2 final size:2
Alignment explanation
Indices: 695492--695531 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
695482 GCGAAACTCG
695492 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
695532 GAGGCTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:695921 original size:30 final size:27
Alignment explanation
Indices: 695864--695921 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
695854 CTCAAAACAT
**
695864 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATAAAAATA
695891 TATTATTTTAGTATCATTTTAATAAAAATA
1 TATTATTTTA-TAT-A-TTTAATAAAAATA
695921 T
1 T
695922 TAATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 3 0.12
29 1 0.04
30 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAATA
Found at i:697298 original size:12 final size:12
Alignment explanation
Indices: 697281--697305 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
697271 GTCTTTGGCA
697281 TGCTTTTCAACT
1 TGCTTTTCAACT
697293 TGCTTTTCAACT
1 TGCTTTTCAACT
697305 T
1 T
697306 TCTTCTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TGCTTTTCAACT
Found at i:698156 original size:13 final size:13
Alignment explanation
Indices: 698138--698167 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
698128 CGCACCCTTA
698138 ATATAATTAAAGG
1 ATATAATTAAAGG
698151 ATATAATTAAAGG
1 ATATAATTAAAGG
698164 ATAT
1 ATAT
698168 GTGATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (13 bp):
ATATAATTAAAGG
Found at i:700775 original size:20 final size:20
Alignment explanation
Indices: 700752--700802 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
700742 TTTTAGTCCT
700752 TTGACCAACGTTTTCCGTCG
1 TTGACCAACGTTTTCCGTCG
*
700772 TTGACCAGCGTTTTCCGTCG
1 TTGACCAACGTTTTCCGTCG
700792 TTGACCAACGT
1 TTGACCAACGT
700803 CTCCTTTATT
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:0.16, C:0.29, G:0.22, T:0.33
Consensus pattern (20 bp):
TTGACCAACGTTTTCCGTCG
Found at i:704278 original size:16 final size:18
Alignment explanation
Indices: 704259--704295 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
704249 GTTAAATAAT
704259 AAAAAAT-CAAAGAAA-A
1 AAAAAATACAAAGAAATA
*
704275 AAAAAATACAATGAAATA
1 AAAAAATACAAAGAAATA
704293 AAA
1 AAA
704296 TAAGATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.11
Consensus pattern (18 bp):
AAAAAATACAAAGAAATA
Found at i:706928 original size:84 final size:83
Alignment explanation
Indices: 706698--706984 Score: 301
Period size: 84 Copynumber: 3.4 Consensus size: 83
706688 CTGAATGAAA
* * * * * * *
706698 TCGAACTCGTCAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTTTAAATGATG
1 TCGAACTCG-AAGGTCTTTGG-TGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATG
* * * *
706763 TGCCCTCGAAGCTGAGTGTAA
64 TGCCTTAG-AGCTGAGCGTAG
* * * * * *
706784 TCGAACTCGAGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATGTG
706846 CCTTAGAGCTGAGCGTAG
66 CCTTAGAGCTGAGCGTAG
* * * *
706864 TCGAACTCAAAGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGTGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATGT
*
706929 GCCTTGGAGCTGAGCGTAG
65 GCCTTAGAGCTGAGCGTAG
* *
706948 TCGAACTCGAAGGTCTTTGTTGACAAATAATCCTTCT
1 TCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCT
706985 TTGAGTTGGA
Statistics
Matches: 173, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
80 23 0.13
81 45 0.26
82 2 0.01
83 20 0.12
84 67 0.39
85 7 0.04
86 9 0.05
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATGTG
CCTTAGAGCTGAGCGTAG
Found at i:707332 original size:106 final size:106
Alignment explanation
Indices: 707147--707814 Score: 973
Period size: 106 Copynumber: 6.3 Consensus size: 106
707137 GCATTGTTCC
* ** * * * * * *
707147 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTAGGAAATTATTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
707212 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
707253 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATCGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
707318 CCAGCGGTCCCTTCGTCATGAAGTTGGACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
707359 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTCTCTGAAATTGGGAAATTATTTATCGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
707424 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
707465 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
707530 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
707571 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
707636 CCAGCGGTCCCTTCG-CTGTGAAGTTGAACTTACGTTGTTTG
66 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTG
* * *
707677 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * * * * *
707741 TCAGCCGCCCCTTCGTCATAAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
707783 GA-TTCGAGATCCTTCGTTGAGAAGTTGAAATT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
707815 TACTCTCGAG
Statistics
Matches: 515, Mismatches: 44, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
105 66 0.13
106 449 0.87
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:711517 original size:19 final size:18
Alignment explanation
Indices: 711475--711520 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
711465 AATGTTAAAT
711475 AATAAAA-AAATCAAAGA
1 AATAAAATAAATCAAAGA
* *
711492 AAAAAAATAAATACAATGA
1 AATAAAATAAAT-CAAAGA
711511 AATAAAATAA
1 AATAAAATAA
711521 GATAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 14 0.58
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (18 bp):
AATAAAATAAATCAAAGA
Found at i:714876 original size:12 final size:11
Alignment explanation
Indices: 714846--714885 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
714836 CATAATCAAA
714846 AAAATATTTTT
1 AAAATATTTTT
*
714857 AAACTATTTTT
1 AAAATATTTTT
714868 AAATATATTTTT
1 AAA-ATATTTTT
714880 ATAAAT
1 A-AAAT
714886 GTATATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 13 0.52
12 10 0.40
13 2 0.08
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
AAAATATTTTT
Done.