Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_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: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 16
Found at i:596031 original size:2 final size:2
Alignment explanation
Indices: 596024--596048 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
596014 ATTATATCAT
596024 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
596049 TAATGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:597799 original size:30 final size:30
Alignment explanation
Indices: 597765--597827 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
597755 GCATGCTGCT
*
597765 GGGATCTCTCGGCGTCTTCTTCAGCATGGG
1 GGGATCTCTCGACGTCTTCTTCAGCATGGG
*
597795 GGGATTTCTCGACGTCTTCTTCAGCATGGG
1 GGGATCTCTCGACGTCTTCTTCAGCATGGG
597825 GGG
1 GGG
597828 CCGAATGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.11, C:0.24, G:0.35, T:0.30
Consensus pattern (30 bp):
GGGATCTCTCGACGTCTTCTTCAGCATGGG
Found at i:600356 original size:39 final size:38
Alignment explanation
Indices: 600292--600371 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 38
600282 TGTACAATGA
* *
600292 AATTTATATTTAAATATTTAAATAAAAAT-TAAAAATTT
1 AATTTAAATTTAAATATTAAAAT-AAAATCTAAAAATTT
*
600330 AATTTAAATATTAAATA-TAAAGATAAAATCTAAATATTT
1 AATTTAAAT-TTAAATATTAAA-ATAAAATCTAAAAATTT
600369 AAT
1 AAT
600372 ATTATTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 16 0.44
39 20 0.56
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (38 bp):
AATTTAAATTTAAATATTAAAATAAAATCTAAAAATTT
Found at i:600388 original size:21 final size:22
Alignment explanation
Indices: 600364--600433 Score: 74
Period size: 21 Copynumber: 3.2 Consensus size: 22
600354 AAAATCTAAA
600364 TATTTAAT-ATTATTAAATTAT
1 TATTTAATAATTATTAAATTAT
*
600385 TATTAGTAATAATTATTAAATCAT
1 TATT--TAATAATTATTAAATTAT
*
600409 TA-TTAGTAATTATTATAATT-T
1 TATTTAATAATTATTA-AATTAT
600430 TATT
1 TATT
600434 ATTAGTAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
21 18 0.44
22 4 0.10
23 5 0.12
24 14 0.34
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (22 bp):
TATTTAATAATTATTAAATTAT
Found at i:600399 original size:24 final size:23
Alignment explanation
Indices: 600368--600458 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 23
600358 TCTAAATATT
*
600368 TAATATTATTAAATTATTATTAG
1 TAATATTATTAAATCATTATTAG
600391 TAATAATTATTAAATCATTATTAG
1 TAAT-ATTATTAAATCATTATTAG
* *
600415 TAATTATTA-TAATTTTATTATTAG
1 TAA-TATTATTAA-ATCATTATTAG
*
600439 TAATCATTACTAAATCATTA
1 TAAT-ATTATTAAATCATTA
600459 GTATCAAATC
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
23 8 0.14
24 46 0.79
25 4 0.07
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (23 bp):
TAATATTATTAAATCATTATTAG
Found at i:600477 original size:48 final size:48
Alignment explanation
Indices: 600381--600479 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 48
600371 TATTATTAAA
* * *
600381 TTATTATTAGTAATAATTATTAAATCATTATTAGTAATTATTATAATT
1 TTATTATTAGTAATAATTACTAAATCATTAGTAGTAATCATTATAATT
*
600429 TTATTATTAGTAATCATTACTAAATCATTAGTA-TCAAATCATTA-AATT
1 TTATTATTAGTAATAATTACTAAATCATTAGTAGT--AATCATTATAATT
600477 TTA
1 TTA
600480 ATAATAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
47 1 0.02
48 37 0.82
49 7 0.16
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.48
Consensus pattern (48 bp):
TTATTATTAGTAATAATTACTAAATCATTAGTAGTAATCATTATAATT
Found at i:600560 original size:14 final size:13
Alignment explanation
Indices: 600536--600605 Score: 59
Period size: 14 Copynumber: 5.0 Consensus size: 13
600526 ATCATTAAAT
* *
600536 TAATAATTATTAG
1 TAATCATTATTAA
600549 TAAATCATTATTAA
1 T-AATCATTATTAA
600563 TAATCATTATTACA
1 TAATCATTATTA-A
* *
600577 TATTATTATTCATTAG
1 TA--ATCATT-ATTAA
600593 TAATCATTATTAA
1 TAATCATTATTAA
600606 ATTATTAGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 16 0.35
14 19 0.41
16 7 0.15
17 4 0.09
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (13 bp):
TAATCATTATTAA
Found at i:600566 original size:24 final size:24
Alignment explanation
Indices: 600371--600615 Score: 86
Period size: 24 Copynumber: 10.3 Consensus size: 24
600361 AAATATTTAA
* * *
600371 TATTATTAAATTATTATTAGTAAT
1 TATTAGTAAATCATTATTAATAAT
* * *
600395 AATTATTAAATCATTATTAGTAAT
1 TATTAGTAAATCATTATTAATAAT
* * *
600419 TATTA-TAATTTTATTATTAGTAAT
1 TATTAGTAA-ATCATTATTAATAAT
* * *
600443 CATTACTAAATCATTAGT-ATCAA-
1 TATTAGTAAATCATTATTAAT-AAT
* * * *
600466 -ATCATTAAAT-TTTAATAATAAAATAT
1 TATTAGTAAATCATT-AT--TAATA-AT
* *
600492 TATTAGT-AATCATTACTAAATCAT
1 TATTAGTAAATCATTA-TTAATAAT
*
600516 TAAATA-TCAAATCATTAAATTAATAAT
1 T-ATTAGT-AAATCATT--ATTAATAAT
600543 TATTAGTAAATCATTATTAATAAT
1 TATTAGTAAATCATTATTAATAAT
* * *
600567 CATTATTACAT-ATTATT-AT--T
1 TATTAGTAAATCATTATTAATAAT
*
600587 CATTAGT-AATCATTATT-A-AAT
1 TATTAGTAAATCATTATTAATAAT
600608 TATTAGTA
1 TATTAGTA
600616 TTAAATTTAA
Statistics
Matches: 168, Mismatches: 31, Indels: 46
0.69 0.13 0.19
Matches are distributed among these distances:
19 2 0.01
20 14 0.08
21 9 0.05
22 11 0.07
23 10 0.06
24 74 0.44
25 10 0.06
26 22 0.13
27 15 0.09
28 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (24 bp):
TATTAGTAAATCATTATTAATAAT
Found at i:600589 original size:20 final size:20
Alignment explanation
Indices: 600544--600604 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
600534 ATTAATAATT
600544 ATTAGTAAATCATTATTAATAATC
1 ATTAGT-AATCATTATT-AT--TC
*
600568 ATTATTACAT-ATTATTATTC
1 ATTAGTA-ATCATTATTATTC
600588 ATTAGTAATCATTATTA
1 ATTAGTAATCATTATTA
600605 AATTATTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 2 0.06
20 15 0.45
22 2 0.06
23 7 0.21
24 7 0.21
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (20 bp):
ATTAGTAATCATTATTATTC
Found at i:600591 original size:10 final size:10
Alignment explanation
Indices: 600558--600605 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
600548 GTAAATCATT
*
600558 ATTAATAATC
1 ATTATTAATC
600568 ATTATTACAT-
1 ATTATTA-ATC
*
600578 ATTATTATTC
1 ATTATTAATC
*
600588 ATTAGTAATC
1 ATTATTAATC
600598 ATTATTAA
1 ATTATTAA
600606 ATTATTAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 1 0.03
10 28 0.90
11 2 0.06
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (10 bp):
ATTATTAATC
Found at i:600885 original size:22 final size:21
Alignment explanation
Indices: 600860--600946 Score: 99
Period size: 22 Copynumber: 4.1 Consensus size: 21
600850 AGTAATCATT
600860 ATTAAATCATTAGTATCAAATC
1 ATTAAATCATTAGTAT-AAATC
*
600882 ATTAAATCATTATTATTAAATC
1 ATTAAATCATTAGTA-TAAATC
600904 A-T--ATCATTAGTAGTAAATC
1 ATTAAATCATTAGTA-TAAATC
*
600923 ATTAAATCATTATTAATAAATC
1 ATTAAATCATTAGT-ATAAATC
600945 AT
1 AT
600947 ATCATTACTA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
19 16 0.29
20 1 0.02
21 1 0.02
22 36 0.64
23 2 0.04
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.40
Consensus pattern (21 bp):
ATTAAATCATTAGTATAAATC
Found at i:600911 original size:19 final size:19
Alignment explanation
Indices: 600887--600962 Score: 89
Period size: 19 Copynumber: 3.8 Consensus size: 19
600877 AAATCATTAA
600887 ATCATTATTATTAAATCAT
1 ATCATTATTATTAAATCAT
* *
600906 ATCATTAGTAGTAAATCATT
1 ATCATTATTATTAAATCA-T
*
600926 AAATCATTATTAATAAATCAT
1 --ATCATTATTATTAAATCAT
*
600947 ATCATTACTATTAAAT
1 ATCATTATTATTAAAT
600963 TGAGTTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 30 0.62
20 1 0.02
21 1 0.02
22 16 0.33
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (19 bp):
ATCATTATTATTAAATCAT
Found at i:600922 original size:41 final size:40
Alignment explanation
Indices: 600865--600962 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 40
600855 TCATTATTAA
*
600865 ATCATTAGTATCAAATCATTAAATCATTATTATTAAATCAT
1 ATCATTAGTAT-AAATCATTAAATCATTATTAATAAATCAT
600906 ATCATTAGTAGTAAATCATTAAATCATTATTAATAAATCAT
1 ATCATTAGTA-TAAATCATTAAATCATTATTAATAAATCAT
*
600947 ATCATTACTATTAAAT
1 ATCATTAGTA-TAAAT
600963 TGAGTTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
41 52 0.98
42 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (40 bp):
ATCATTAGTATAAATCATTAAATCATTATTAATAAATCAT
Found at i:601058 original size:2 final size:2
Alignment explanation
Indices: 601051--601110 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
601041 ACTTTAGGTA
601051 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
601093 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
601111 TCGAATAATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:605377 original size:19 final size:19
Alignment explanation
Indices: 605355--605393 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
605345 GCAAATGCAT
605355 TCTCTCTCCTCCTAATTGC
1 TCTCTCTCCTCCTAATTGC
605374 TCTCTCTCCTCCTAATTGC
1 TCTCTCTCCTCCTAATTGC
605393 T
1 T
605394 AAATTCAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.41, G:0.05, T:0.44
Consensus pattern (19 bp):
TCTCTCTCCTCCTAATTGC
Found at i:613012 original size:2 final size:2
Alignment explanation
Indices: 613005--613030 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
612995 ACTTATGCTC
613005 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
613031 CACACAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:614009 original size:3 final size:3
Alignment explanation
Indices: 614001--614035 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
613991 TCTCTTGTAT
614001 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
614036 TGATGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:621424 original size:13 final size:13
Alignment explanation
Indices: 621406--621432 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
621396 ATTACAGATG
621406 TGCATATGAAGAC
1 TGCATATGAAGAC
621419 TGCATATGAAGAC
1 TGCATATGAAGAC
621432 T
1 T
621433 TTTCAACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (13 bp):
TGCATATGAAGAC
Found at i:621606 original size:3 final size:3
Alignment explanation
Indices: 621598--621623 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
621588 GAATAGGGTT
621598 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
621624 TATATGATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:622321 original size:137 final size:140
Alignment explanation
Indices: 622078--622352 Score: 412
Period size: 137 Copynumber: 2.0 Consensus size: 140
622068 AAATTTGAAC
* **
622078 CACATGCTCCTAAAACATAATAGAATACATGTGCACTTTCAATTCCTCTTTTTGATAACAATTTT
1 CACATGCTCCTAAAACATAATAGAATACATGTGAACTTAAAATTCCTCTTTTTGATAACAATTTT
* * *
622143 TTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTATTTCTTTAATTCGTCATTTATT
66 TTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATATCCTTATTTATTCAATTCGTCATTTATT
622208 TTAAGTCCGA
131 TTAAGTCCGA
* * *
622218 CACATGCTCCTAAATCATAGTAGAATACATGTGAACTTAAAATT-CTCTTTTTGAT-A-ATTTTT
1 CACATGCTCCTAAAACATAATAGAATACATGTGAACTTAAAATTCCTCTTTTTGATAACAATTTT
* * * *
622280 TTTATTTTTTAATTTAGTCCTTCGATTTTTCATAATATCCTTATTTATTCAATTTGTGATTTATT
66 TTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATATCCTTATTTATTCAATTCGTCATTTATT
622345 TTAAGTCC
131 TTAAGTCC
622353 CCTTTTCACC
Statistics
Matches: 122, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
137 71 0.58
138 1 0.01
139 11 0.09
140 39 0.32
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (140 bp):
CACATGCTCCTAAAACATAATAGAATACATGTGAACTTAAAATTCCTCTTTTTGATAACAATTTT
TTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATATCCTTATTTATTCAATTCGTCATTTATT
TTAAGTCCGA
Found at i:622989 original size:48 final size:48
Alignment explanation
Indices: 622917--623015 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
622907 CAGTTATCAC
*
622917 TGAAATAGAGAGATGTCATAATAAATGTTAAAAATAAAATTGATATAA
1 TGAAATAGAGAGATGTCATAATAAATGTTAAAAATAAAATTGACATAA
* *
622965 TGAAATAGAGAGATGTCATGATAAATTTTAAAAATAAAATTGACATAA
1 TGAAATAGAGAGATGTCATAATAAATGTTAAAAATAAAATTGACATAA
623013 TGA
1 TGA
623016 TTAATGAGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.29
Consensus pattern (48 bp):
TGAAATAGAGAGATGTCATAATAAATGTTAAAAATAAAATTGACATAA
Found at i:624076 original size:13 final size:13
Alignment explanation
Indices: 624058--624085 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
624048 GTACCTCCTC
624058 AATTTCTAAATCT
1 AATTTCTAAATCT
624071 AATTTCTAAATCT
1 AATTTCTAAATCT
624084 AA
1 AA
624086 AAGAATTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTTCTAAATCT
Found at i:642977 original size:12 final size:12
Alignment explanation
Indices: 642960--642984 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
642950 AAGAGTTGAT
642960 AAGTTGAATTTG
1 AAGTTGAATTTG
642972 AAGTTGAATTTG
1 AAGTTGAATTTG
642984 A
1 A
642985 CTTGTCATCT
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:645165 original size:23 final size:23
Alignment explanation
Indices: 645133--645183 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
645123 ATGATAGATG
*
645133 ATATGTGAACATATGA-AAATGAC
1 ATATGCGAACATAT-ACAAATGAC
645156 ATATGCGAACATATACAAATGAC
1 ATATGCGAACATATACAAATGAC
645179 ATATG
1 ATATG
645184 TTATATGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (23 bp):
ATATGCGAACATATACAAATGAC
Found at i:647507 original size:12 final size:12
Alignment explanation
Indices: 647490--647514 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
647480 AAGAGTTGAT
647490 AAGTTGAATTTG
1 AAGTTGAATTTG
647502 AAGTTGAATTTG
1 AAGTTGAATTTG
647514 A
1 A
647515 CTTGTCATCT
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:649267 original size:19 final size:19
Alignment explanation
Indices: 649243--649292 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
649233 CTGTTCACGG
649243 TACTGTTCATAACAAATTT
1 TACTGTTCATAACAAATTT
* * **
649262 TACTGTTTATACCGTATTT
1 TACTGTTCATAACAAATTT
649281 TACTGTTCATAA
1 TACTGTTCATAA
649293 ATACATTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (19 bp):
TACTGTTCATAACAAATTT
Found at i:652666 original size:62 final size:63
Alignment explanation
Indices: 652592--652718 Score: 247
Period size: 62 Copynumber: 2.0 Consensus size: 63
652582 TAATATGGAT
652592 ATGAAATGCATTATTTTTATTATATGTTTTATATGCCTCACTAA-TCATAGACTTAGCGTGTG
1 ATGAAATGCATTATTTTTATTATATGTTTTATATGCCTCACTAAGTCATAGACTTAGCGTGTG
652654 ATGAAATGCATTATTTTTATTATATGTTTTATATGCCTCACTAAGTCATAGACTTAGCGTGTG
1 ATGAAATGCATTATTTTTATTATATGTTTTATATGCCTCACTAAGTCATAGACTTAGCGTGTG
652717 AT
1 AT
652719 TGGTTCACAC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 44 0.69
63 20 0.31
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (63 bp):
ATGAAATGCATTATTTTTATTATATGTTTTATATGCCTCACTAAGTCATAGACTTAGCGTGTG
Found at i:653055 original size:21 final size:21
Alignment explanation
Indices: 653031--653070 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
653021 AATTTTTGAC
653031 GCATCGATGCACTGTAGTAAT
1 GCATCGATGCACTGTAGTAAT
653052 GCATCGATGCACTGTAGTA
1 GCATCGATGCACTGTAGTA
653071 CTGTTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (21 bp):
GCATCGATGCACTGTAGTAAT
Found at i:653576 original size:20 final size:19
Alignment explanation
Indices: 653551--653598 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
653541 ACTTAATATT
653551 ATTATTTTTAAAATATTAAA
1 ATTATTTTT-AAATATTAAA
* *
653571 ATTATTTATTTATTATTAAA
1 ATTATTT-TTAAATATTAAA
653591 A-TATTTTT
1 ATTATTTTT
653599 TTTATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 2 0.08
19 5 0.20
20 16 0.64
21 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATTTTTAAATATTAAA
Found at i:653749 original size:23 final size:23
Alignment explanation
Indices: 653700--653750 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
653690 ATGTTATATT
**
653700 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
653723 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
653746 ATATT
1 ATATT
653751 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:653921 original size:29 final size:30
Alignment explanation
Indices: 653850--653922 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
653840 ATATAAATTT
*
653850 TATTAAT-AATTTATTATATATTATTAAAA
1 TATTAATAAATATATTATATATTATTAAAA
** *
653879 TAAAAATATA-ATATTATAT-TT-TTAGAAA
1 TATTAATAAATATATTATATATTATTA-AAA
653907 TATTAATAAATATATT
1 TATTAATAAATATATT
653923 TTCAATATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
27 3 0.09
28 12 0.35
29 18 0.53
30 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
TATTAATAAATATATTATATATTATTAAAA
Found at i:655979 original size:246 final size:246
Alignment explanation
Indices: 655523--656060 Score: 729
Period size: 246 Copynumber: 2.2 Consensus size: 246
655513 GATGATAAAG
* * *
655523 AGGCATTGTCCCAACACCTAAAGATTCCGAATACTGTGGGAGCACAACTGAACCATTTTCCAACA
1 AGGCATTGTCCCAACACCAAAAGATTCTGAATACTGTGGGAGCACAAATGAACCATTTTCCAACA
655588 CTTGGCCTTCATTCTGAGATACATTAACTGCACCATTGTCGAAGTCCTCTTGTTGTACATCTAAG
66 CTTGGCCTTCATTCTGAGATACATTAACTGCACCATTGTCGAAGTCCTCTTGTTGTACATCTAAG
** * * * *
655653 ATGGGCCCATCAGACACTGTGAAATTCAAATTGCTAGGTCCGACACGGGAGAAATGCTGCAACGG
131 ATGAACCCATAAGACACTGTGAAATTCAAATTGATAGGTCCGACACCGGAGAAATGATGCAACGG
** *
655718 TGGCACTTCCGGTTGAAAATGATGATAAAGAGGCATTGATACCAATGGAGC
196 CAGAACTTCCGGTTGAAAATGATGATAAAGAGGCATTGATACCAATGGAGC
* * * * *
655769 AGGCATTGTCCCAACACCGAAAGATTCTGAATTCTGTTGGAGCACAAATGAACCATTTTTCAGCA
1 AGGCATTGTCCCAACACCAAAAGATTCTGAATACTGTGGGAGCACAAATGAACCATTTTCCAACA
* * *
655834 CTTGGCCTTTATTCTGAGCTACATTAACTGCACCATTGTCGACGTCCTCTTGTTGTACATCTACA
66 CTTGGCCTTCATTCTGAGATACATTAACTGCACCATTGTCGAAGTCCTCTTGTTGTACATCTA-A
* * ** * *
655899 -ATGAACTCATAAGGCGTTGTGAAATTCAAATTGATAGGTCCGGCACCGGA-AAACTGATGCGAC
130 GATGAACCCATAAGACACTGTGAAATTCAAATTGATAGGTCCGACACCGGAGAAA-TGATGCAAC
* * * *
655962 GGCAGAACTTTCGGTTGAAACTGATGATAAGGAGGCATTGATGCCAATGGAGC
194 GGCAGAACTTCCGGTTGAAAATGATGATAAAGAGGCATTGATACCAATGGAGC
* * * * *
656015 AGGCATTGTACCAGCACCAAAAGATTCTGTATACCGTGGGAACACA
1 AGGCATTGTCCCAACACCAAAAGATTCTGAATACTGTGGGAGCACA
656061 TAATCATTAT
Statistics
Matches: 253, Mismatches: 37, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
245 3 0.01
246 249 0.98
247 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (246 bp):
AGGCATTGTCCCAACACCAAAAGATTCTGAATACTGTGGGAGCACAAATGAACCATTTTCCAACA
CTTGGCCTTCATTCTGAGATACATTAACTGCACCATTGTCGAAGTCCTCTTGTTGTACATCTAAG
ATGAACCCATAAGACACTGTGAAATTCAAATTGATAGGTCCGACACCGGAGAAATGATGCAACGG
CAGAACTTCCGGTTGAAAATGATGATAAAGAGGCATTGATACCAATGGAGC
Found at i:657191 original size:21 final size:21
Alignment explanation
Indices: 657138--657198 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
657128 ATATTCTCCC
657138 TATAAATAAAAAATAAAATAA
1 TATAAATAAAAAATAAAATAA
* ** * * *
657159 AATTTATTAAAAATGACATAA
1 TATAAATAAAAAATAAAATAA
657180 TATAAATAAAAATATAAAA
1 TATAAATAAAAA-ATAAAA
657199 AACTACATTA
Statistics
Matches: 27, Mismatches: 12, Indels: 1
0.68 0.30 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
TATAAATAAAAAATAAAATAA
Found at i:657710 original size:20 final size:20
Alignment explanation
Indices: 657673--657710 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
657663 AATGGAATTA
*
657673 TAATTTTAAAATATTATAAT
1 TAATTTTAAAATAATATAAT
657693 TAATCTTTAAAA-AATATA
1 TAAT-TTTAAAATAATATA
657711 TTTATGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATTTTAAAATAATATAAT
Found at i:657727 original size:26 final size:26
Alignment explanation
Indices: 657698--657755 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
657688 ATAATTAATC
*
657698 TTTAAAAAATATATTTATGTATTATT
1 TTTAAAAAATATATTTATATATTATT
*
657724 TTTATAAAATATATTTATATATTATT
1 TTTAAAAAATATATTTATATATTATT
*
657750 TATAAA
1 TTTAAA
657756 TAATCAAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTAAAAAATATATTTATATATTATT
Found at i:657858 original size:12 final size:12
Alignment explanation
Indices: 657841--657865 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
657831 TATATTTTTA
657841 AAATTAATATAT
1 AAATTAATATAT
657853 AAATTAATATAT
1 AAATTAATATAT
657865 A
1 A
657866 TTATAAATAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTAATATAT
Found at i:657863 original size:29 final size:28
Alignment explanation
Indices: 657808--657876 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
657798 TATTTATTAA
657808 TTTTATAAATAATTATAAAATAATATAT
1 TTTTATAAATAATTATAAAATAATATAT
*
657836 TTTTA-AAATTAATATATAAATTAATATA-
1 TTTTATAAA-TAAT-TATAAAATAATATAT
*
657864 TATTATAAATAAT
1 TTTTATAAATAAT
657877 CTTTAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 3 0.08
28 17 0.47
29 16 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TTTTATAAATAATTATAAAATAATATAT
Found at i:657883 original size:28 final size:26
Alignment explanation
Indices: 657809--657885 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 26
657799 ATTTATTAAT
*
657809 TTTATAAATAATTATAAAATAATATA
1 TTTATAAATAATTATAAATTAATATA
*
657835 TTTTTAAAATTAATATATAAATTAATATA
1 TTTAT-AAA-TAAT-TATAAATTAATATA
*
657864 TATTATAAATAATCTTTAAATT
1 T-TTATAAATAAT-TATAAATT
657886 TTATAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
26 4 0.10
27 3 0.07
28 15 0.36
29 17 0.40
30 3 0.07
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
TTTATAAATAATTATAAATTAATATA
Found at i:659999 original size:291 final size:293
Alignment explanation
Indices: 659456--660039 Score: 1145
Period size: 291 Copynumber: 2.0 Consensus size: 293
659446 CACTTTTTGA
659456 CTTGAAACAAACTCGGTTTAGGCTTAGAATCGATTAAACTTGTAGCTCTGATACTAAAAAATGTA
1 CTTGAAACAAACTCGGTTTAGGCTTAGAATCGATTAAACTTGTAGCTCTGATACTAAAAAATGTA
659521 ACACCCTTAACACGTATACGTACTCGAATACGAGTAAAAGATATCACATAGCTTTATATACATTA
66 ACACCCTTAACACGTATACGTACTCGAATACGAGTAAAAGATATCACATAGCTTTATATACATTA
659586 TAAGGTTGAAATCTAGCAAAATTTTGAACTTTTAAAATCCATCCAATTTAACCCTTTCAATAAAT
131 TAAGGTTGAAATCTAGCAAAATTTTGAACTTTTAAAATCCATCCAATTTAACCCTTTCAATAAAT
659651 AATGCAATCACGTAAAATCATATTATAGTATTTAAGCCTCTAAATCAATAGCAGTTTCAAGTAAC
196 AATGCAATCACGTAAAATCATATTATAGTATTTAAGCCTCTAAATCAATAGCAGTTTCAAGTAAC
659716 AACTAGACAATTCTATA-TGTTTTATATCATAC
261 AACTAGACAATTCTATATTGTTTTATATCATAC
659748 CTTGAAACAAACTC-GTTTAGGCTTAGAATCGATTAAACTTGTAGCTCTGATACTAAAAAATGTA
1 CTTGAAACAAACTCGGTTTAGGCTTAGAATCGATTAAACTTGTAGCTCTGATACTAAAAAATGTA
659812 ACACCCTTAACACGTATACGTACTCGAATACGAGTAAAAGATATCACATAGCTTTATATACATTA
66 ACACCCTTAACACGTATACGTACTCGAATACGAGTAAAAGATATCACATAGCTTTATATACATTA
659877 TAAGGTTGAAATCTAGCAAAATTTTGAACTTTTAAAATCCATCCAATTTAACCCTTTCAATAAAT
131 TAAGGTTGAAATCTAGCAAAATTTTGAACTTTTAAAATCCATCCAATTTAACCCTTTCAATAAAT
*
659942 AATGCAATCACGTAAAATCATATTATAGTATTTAAGCCTCTAAATCAATATCAGTTTCAAGTAAC
196 AATGCAATCACGTAAAATCATATTATAGTATTTAAGCCTCTAAATCAATAGCAGTTTCAAGTAAC
660007 AACTAGACAATTCTATATTGTTTTATATCATAC
261 AACTAGACAATTCTATATTGTTTTATATCATAC
660040 GATACACTAT
Statistics
Matches: 290, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
291 261 0.90
292 29 0.10
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (293 bp):
CTTGAAACAAACTCGGTTTAGGCTTAGAATCGATTAAACTTGTAGCTCTGATACTAAAAAATGTA
ACACCCTTAACACGTATACGTACTCGAATACGAGTAAAAGATATCACATAGCTTTATATACATTA
TAAGGTTGAAATCTAGCAAAATTTTGAACTTTTAAAATCCATCCAATTTAACCCTTTCAATAAAT
AATGCAATCACGTAAAATCATATTATAGTATTTAAGCCTCTAAATCAATAGCAGTTTCAAGTAAC
AACTAGACAATTCTATATTGTTTTATATCATAC
Found at i:660571 original size:39 final size:39
Alignment explanation
Indices: 660528--660610 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 39
660518 CTCATGATTT
*
660528 TATCAAAACCATGATAAAAAATA-TCATATATAATAGTCA
1 TATCAAAACCATGATAAAAAATAGT-ATACATAATAGTCA
* *
660567 TATCAAAGCCATGATAAACAATAGTATACATAATAGTCA
1 TATCAAAACCATGATAAAAAATAGTATACATAATAGTCA
660606 TATCA
1 TATCA
660611 CAATAGTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 39 0.98
40 1 0.03
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (39 bp):
TATCAAAACCATGATAAAAAATAGTATACATAATAGTCA
Found at i:660617 original size:14 final size:14
Alignment explanation
Indices: 660584--660624 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
660574 GCCATGATAA
660584 ACAATAGT-ATA-C
1 ACAATAGTCATATC
*
660596 ATAATAGTCATATC
1 ACAATAGTCATATC
660610 ACAATAGTCATATC
1 ACAATAGTCATATC
660624 A
1 A
660625 TATTCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 7 0.28
13 3 0.12
14 15 0.60
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (14 bp):
ACAATAGTCATATC
Found at i:662130 original size:35 final size:35
Alignment explanation
Indices: 662090--662159 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
662080 TTTTCAAAAC
*
662090 TTTATTTATATTTAAGTGGTGAAACCCTTAATTCA
1 TTTATTTATATTCAAGTGGTGAAACCCTTAATTCA
662125 TTTATTTATATTCAAGTGGTGAAACCCTTAATTCA
1 TTTATTTATATTCAAGTGGTGAAACCCTTAATTCA
662160 AATTTACTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (35 bp):
TTTATTTATATTCAAGTGGTGAAACCCTTAATTCA
Found at i:662697 original size:24 final size:24
Alignment explanation
Indices: 662662--662763 Score: 120
Period size: 23 Copynumber: 4.3 Consensus size: 24
662652 ATAAATTGCA
*
662662 CCGAAGTG-CCACATAGAATTTATC
1 CCGAAG-GACCACATAGAATTTGTC
* * *
662686 CCAAAGGACCACGTATAATTTGTC
1 CCGAAGGACCACATAGAATTTGTC
*
662710 CCGAAGGACCACAAAGAA-TTGTC
1 CCGAAGGACCACATAGAATTTGTC
*
662733 CCGAAGGACAACATAG-ATTTGTC
1 CCGAAGGACCACATAGAATTTGTC
662756 CCGAAGGA
1 CCGAAGGA
662764 GTGCGTAGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
22 1 0.02
23 33 0.50
24 32 0.48
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.20
Consensus pattern (24 bp):
CCGAAGGACCACATAGAATTTGTC
Found at i:663352 original size:20 final size:21
Alignment explanation
Indices: 663327--663367 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
663317 CAGGCTGAAG
*
663327 AGTATCGGTAC-CTCTTCTAC
1 AGTATCGATACTCTCTTCTAC
663347 AGTATCGATACTTCTCTTCTA
1 AGTATCGATAC-TCTCTTCTA
663368 TGGTACCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (21 bp):
AGTATCGATACTCTCTTCTAC
Found at i:667535 original size:117 final size:117
Alignment explanation
Indices: 667344--667577 Score: 468
Period size: 117 Copynumber: 2.0 Consensus size: 117
667334 CAGTTAGAAA
667344 TACGTCTAAAAATTCTATGACCATTAAAATATCCTCCGGTCTTCTATCATTGACTCGAGTATCGA
1 TACGTCTAAAAATTCTATGACCATTAAAATATCCTCCGGTCTTCTATCATTGACTCGAGTATCGA
667409 TTACATTGCCTATGAAAGCTTGACATCCTTGCAACATTAACTTCTTAACCGG
66 TTACATTGCCTATGAAAGCTTGACATCCTTGCAACATTAACTTCTTAACCGG
667461 TACGTCTAAAAATTCTATGACCATTAAAATATCCTCCGGTCTTCTATCATTGACTCGAGTATCGA
1 TACGTCTAAAAATTCTATGACCATTAAAATATCCTCCGGTCTTCTATCATTGACTCGAGTATCGA
667526 TTACATTGCCTATGAAAGCTTGACATCCTTGCAACATTAACTTCTTAACCGG
66 TTACATTGCCTATGAAAGCTTGACATCCTTGCAACATTAACTTCTTAACCGG
667578 CATCACCGAT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (117 bp):
TACGTCTAAAAATTCTATGACCATTAAAATATCCTCCGGTCTTCTATCATTGACTCGAGTATCGA
TTACATTGCCTATGAAAGCTTGACATCCTTGCAACATTAACTTCTTAACCGG
Found at i:669883 original size:23 final size:23
Alignment explanation
Indices: 669850--669902 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
669840 ATTTGTCACA
669850 AAGGACCACATAGAATTATCCCG
1 AAGGACCACATAGAATTATCCCG
* * * *
669873 AAGGACTACATAGATTTGTCTCG
1 AAGGACCACATAGAATTATCCCG
669896 AAGGACC
1 AAGGACC
669903 GCGTAGAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (23 bp):
AAGGACCACATAGAATTATCCCG
Found at i:672849 original size:103 final size:103
Alignment explanation
Indices: 672669--672970 Score: 315
Period size: 103 Copynumber: 2.9 Consensus size: 103
672659 TAAGACCCAA
* * * * ** *
672669 TAGAAGCTAAGTTGTATTGGTACACAACCAA-TATCGATACTAGCATATAACACTAAATTGCGGG
1 TAGAAGCTAAGATGTACTGGTACACAA-CAAGTATCGATACTGGCATATAACAATGTATTACGGG
* *
672733 TTACATTCAATGTA-ATGATACCTTTAAAGTATCGATACC
65 TTACATCCAATGTATA-GATACCTTTAATGTATCGATACC
* * * *
672772 TAGAAGCTAAGATATACTGGTACATAATAAGTATCGATACTGGCATATAACATTGTATTACGGGT
1 TAGAAGCTAAGATGTACTGGTACACAACAAGTATCGATACTGGCATATAACAATGTATTACGGGT
* * * *
672837 TACATCCGATGTATCGATA-CTAGTAATGTATTGATACC
66 TACATCCAATGTATAGATACCT-TTAATGTATCGATACC
* * * * * * *
672875 TAGAAGCTAA-ACTGTACCGGTACACCAGAAGTATCAACACTGACATATAACAATGTATTACGAG
1 TAGAAGCTAAGA-TGTACTGGTACACAACAAGTATCGATACTGGCATATAACAATGTATTACGGG
*
672939 TTACATCCAATGTATACATACCTTTAATGTAT
65 TTACATCCAATGTATAGATACCTTTAATGTAT
672971 TCACTGTTAC
Statistics
Matches: 164, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
102 5 0.03
103 157 0.96
104 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (103 bp):
TAGAAGCTAAGATGTACTGGTACACAACAAGTATCGATACTGGCATATAACAATGTATTACGGGT
TACATCCAATGTATAGATACCTTTAATGTATCGATACC
Found at i:673274 original size:21 final size:19
Alignment explanation
Indices: 673248--673294 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 19
673238 TAACACATGA
673248 AAATTTGTATCTAATTAA-AAT
1 AAATTT-TAT-TAA-TAAGAAT
673269 AAATTTTATTAATAAGAAT
1 AAATTTTATTAATAAGAAT
673288 ATAATTT
1 A-AATTT
673295 CAATCAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.12
19 7 0.29
20 8 0.33
21 6 0.25
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (19 bp):
AAATTTTATTAATAAGAAT
Found at i:678726 original size:15 final size:14
Alignment explanation
Indices: 678708--678746 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
678698 TTTTTCCATT
*
678708 TTTTTCTTTCATGTC
1 TTTTTCTTTC-TCTC
*
678723 TTTTTTTTTCTCTC
1 TTTTTCTTTCTCTC
678737 TTTTTCTTTC
1 TTTTTCTTTC
678747 GAACAACTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTCTTTCTCTC
Found at i:690610 original size:16 final size:16
Alignment explanation
Indices: 690589--690620 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
690579 ACAATTTAAT
*
690589 TTATTGATGTTCGTCG
1 TTATTGACGTTCGTCG
690605 TTATTGACGTTCGTCG
1 TTATTGACGTTCGTCG
690621 CTACTCATCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (16 bp):
TTATTGACGTTCGTCG
Found at i:691689 original size:2 final size:2
Alignment explanation
Indices: 691678--691712 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
691668 CTAACATTAT
691678 TA TA TA -A 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
691713 ACTGGGTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:692615 original size:31 final size:31
Alignment explanation
Indices: 692573--692649 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
692563 AATAAATTAA
*
692573 AGTTTAGATACTAAAACGAAATAAAACTGAT
1 AGTTTAGATACTAAAACGAAACAAAACTGAT
* *
692604 AGTTTAAATACTAAAATGAAACAAAACTGAT
1 AGTTTAGATACTAAAACGAAACAAAACTGAT
*
692635 AGTTTAGATAGTAAA
1 AGTTTAGATACTAAA
692650 TATATAGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (31 bp):
AGTTTAGATACTAAAACGAAACAAAACTGAT
Found at i:703011 original size:32 final size:33
Alignment explanation
Indices: 702966--703047 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 33
702956 CTTTTTGTAT
*
702966 TCGGGTCCA-ATTTTTTTTAAAA-AAATTCGAGA
1 TCGGGT-CAGATTTTTTTAAAAAGAAATTCGAGA
* *
702998 TCGGGTCAGA--TTTTTAAAAAGAAATTCGGGT
1 TCGGGTCAGATTTTTTTAAAAAGAAATTCGAGA
703029 TCGGGTCAGATTTTTTTAA
1 TCGGGTCAGATTTTTTTAA
703048 GTTTGATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 9 0.21
31 20 0.47
32 7 0.16
33 7 0.16
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (33 bp):
TCGGGTCAGATTTTTTTAAAAAGAAATTCGAGA
Found at i:703667 original size:22 final size:22
Alignment explanation
Indices: 703633--703692 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
703623 GAAAACAGGT
*
703633 TTCAGATTCAGATTCCAATTCC
1 TTCAGATTTAGATTCCAATTCC
* *
703655 TTCAAATTTAGATTCCAATTCT
1 TTCAGATTTAGATTCCAATTCC
*
703677 TTCAGATTTAAATTCC
1 TTCAGATTTAGATTCC
703693 TTCACAGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.42
Consensus pattern (22 bp):
TTCAGATTTAGATTCCAATTCC
Found at i:704699 original size:30 final size:30
Alignment explanation
Indices: 704665--704729 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
704655 AGGAAAGAGA
704665 ATGTTGGTGTAAGTTTTAAGCCAAGATCCG
1 ATGTTGGTGTAAGTTTTAAGCCAAGATCCG
704695 ATGTTGGTGTAAGTTTTAAGCCAAGATCCG
1 ATGTTGGTGTAAGTTTTAAGCCAAGATCCG
704725 ATGTT
1 ATGTT
704730 AACTTCAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (30 bp):
ATGTTGGTGTAAGTTTTAAGCCAAGATCCG
Found at i:712115 original size:14 final size:15
Alignment explanation
Indices: 712104--712138 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
712094 TAAAATTATA
712104 AAATTTAAATTACAG
1 AAATTTAAATTACAG
* *
712119 AAATTTAGATTACTG
1 AAATTTAAATTACAG
712134 AAATT
1 AAATT
712139 AAGACTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (15 bp):
AAATTTAAATTACAG
Found at i:714470 original size:22 final size:22
Alignment explanation
Indices: 714439--714487 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
714429 AAATAAAACA
714439 AGAAAA-T-AAAGAAGATTAAAG
1 AGAAAAGTAAAAGAAGATT-AAG
714460 AGAAAAGTAAAAGAAGATTAAG
1 AGAAAAGTAAAAGAAGATTAAG
714482 A-AAAAG
1 AGAAAAG
714488 ATTTAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.42
22 5 0.19
23 10 0.38
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.12
Consensus pattern (22 bp):
AGAAAAGTAAAAGAAGATTAAG
Found at i:717642 original size:42 final size:42
Alignment explanation
Indices: 717583--717666 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
717573 GGCAGCAAAT
717583 TCATTGAAGCTCCAACGAATGATGCAAGATTTTATGTTGAGG
1 TCATTGAAGCTCCAACGAATGATGCAAGATTTTATGTTGAGG
717625 TCATTGAAGCTCCAACGAATGATGCAAGATTTTATGTTGAGG
1 TCATTGAAGCTCCAACGAATGATGCAAGATTTTATGTTGAGG
717667 GCGAACTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (42 bp):
TCATTGAAGCTCCAACGAATGATGCAAGATTTTATGTTGAGG
Found at i:718065 original size:2 final size:2
Alignment explanation
Indices: 718058--718097 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
718048 GCATTTCTTA
718058 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
718098 TGTTGGAAAA
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):
AT
Found at i:720220 original size:34 final size:35
Alignment explanation
Indices: 720160--720227 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
720150 TTCTTTTATA
* *
720160 GTTGTTTTCTCCTTTTTAACAAGAGAGAA-TTGTC
1 GTTGTTTTCTCATTGTTAACAAGAGAGAAGTTGTC
*
720194 GTTGTTTTCTCATTGTTAA-ATTGAGAGAAGTTGT
1 GTTGTTTTCTCATTGTTAACA-AGAGAGAAGTTGT
720228 AATTCTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.03
34 24 0.83
35 4 0.14
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.46
Consensus pattern (35 bp):
GTTGTTTTCTCATTGTTAACAAGAGAGAAGTTGTC
Found at i:723235 original size:169 final size:169
Alignment explanation
Indices: 722969--723274 Score: 456
Period size: 169 Copynumber: 1.8 Consensus size: 169
722959 AAATATCTCA
*
722969 GATGCTTCACAGTGGATGACAGTGATGTAAGAAGAAATTGAAGCCCTTTATAAAAATAACATATG
1 GATGCTTCACAGTGGATGACAGTGATGTAAGAAGAAATTGAAGCCCTTTATAAAAATAACACATG
* ** *
723034 GGACATTATGCCACTACCGTAAAGAAGGAAGCCAACTGGTAACAAAT-GAGTCTTTAAAATCAAG
66 GGACATCATGCCACTACCACAAAGAAGGAAGCCAACTGGTAACAAATGGA-TCTTCAAAATCAAG
723098 CGAAATGGCAACGATCTAATTAAAGGAAATAAATAGCCCC
130 CGAAATGGCAACGATCTAATTAAAGGAAATAAATAGCCCC
* * *
723138 GATGCTTCACAGTGGATGA-TG-GCATTGTAAGAAGAAATTGAAGCCTTTTATAAAAATAATACA
1 GATGCTTCACAGTGGATGACAGTG-A-TGTAAGAAGAAATTGAAGCCCTTTATAAAAATAACACA
* * * *
723201 TGTGACGTCATGCCACTACCACAAGGAAGGAAGCCAATTGGTAACAAATGGATCTTCAAAATCAA
64 TGGGACATCATGCCACTACCACAAAGAAGGAAGCCAACTGGTAACAAATGGATCTTCAAAATCAA
723266 GCGAAATGG
129 GCGAAATGG
723275 TGACGATCAA
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
167 1 0.01
168 2 0.02
169 117 0.96
170 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (169 bp):
GATGCTTCACAGTGGATGACAGTGATGTAAGAAGAAATTGAAGCCCTTTATAAAAATAACACATG
GGACATCATGCCACTACCACAAAGAAGGAAGCCAACTGGTAACAAATGGATCTTCAAAATCAAGC
GAAATGGCAACGATCTAATTAAAGGAAATAAATAGCCCC
Found at i:726080 original size:205 final size:207
Alignment explanation
Indices: 725728--726140 Score: 812
Period size: 205 Copynumber: 2.0 Consensus size: 207
725718 AGCTATCATT
725728 TTTTTGTGATATCACGATACATAAAACTATCATGAAATGATTTTCTTTCTTTCTCCTTTGCCCTT
1 TTTTTGTGATATCACGATACATAAAACTATCATGAAATGATTTTCTTTCTTTCTCCTTTGCCCTT
725793 ATTTTAGGTAGTGTAGTGTCATTTTAGCATATCTCTGTTGCAAATTTTTCCAGTGAAGTAGGTAG
66 ATTTTAGGTAGTGTAGTGTCATTTTAGCATATCTCTGTTGCAAATTTTTCCAGTGAAGTAGGTAG
725858 CTTTGATGATTTGTTGGGATATTTAACTGATTTCTTGTTTGTAAT-AAAGTTT-CCTTGAACTAT
131 CTTTGATGATTTGTTGGGATATTTAACTGATTTCTTGTTTGTAATAAAAGTTTCCCTTGAACTAT
725921 TTTTATTTATGA
196 TTTTATTTATGA
725933 TTTTTGTGATATCACGATACATAAAACTATCATGAAATGATTTTCTTTCTTTCTCCTTTGCCCTT
1 TTTTTGTGATATCACGATACATAAAACTATCATGAAATGATTTTCTTTCTTTCTCCTTTGCCCTT
725998 ATTTTAGGTAGTGTAGTGTCATTTTAGCATATCTCTGTTGCAAATTTTTCCAGTGAAGTAGGTAG
66 ATTTTAGGTAGTGTAGTGTCATTTTAGCATATCTCTGTTGCAAATTTTTCCAGTGAAGTAGGTAG
726063 CTTTGATGATTTGTTGGGATATTTAACTGATTTCTTGTTTGTAATAAAAGTTTCCCTTGAACTAT
131 CTTTGATGATTTGTTGGGATATTTAACTGATTTCTTGTTTGTAATAAAAGTTTCCCTTGAACTAT
726128 TTTTATTTATGA
196 TTTTATTTATGA
726140 T
1 T
726141 GATCCAAGTA
Statistics
Matches: 206, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
205 175 0.85
206 7 0.03
207 24 0.12
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (207 bp):
TTTTTGTGATATCACGATACATAAAACTATCATGAAATGATTTTCTTTCTTTCTCCTTTGCCCTT
ATTTTAGGTAGTGTAGTGTCATTTTAGCATATCTCTGTTGCAAATTTTTCCAGTGAAGTAGGTAG
CTTTGATGATTTGTTGGGATATTTAACTGATTTCTTGTTTGTAATAAAAGTTTCCCTTGAACTAT
TTTTATTTATGA
Found at i:728515 original size:85 final size:85
Alignment explanation
Indices: 728414--728579 Score: 219
Period size: 85 Copynumber: 2.0 Consensus size: 85
728404 ATACAATCAC
* * *
728414 GACACACGAATGTGTGTCATCTT-TTTTAATGACGCGTGCTTCAATGACACGCAATGCAA-GTCA
1 GACACACAAATGTGTGTCATCTTAATTT-ATGACGCGGGCTTCAATGACACGCAATG-AACGTCA
* *
728477 TACATGCGTGTTATAAATTTAT
64 TAAATGCGTGTCATAAATTTAT
* * *
728499 GACACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACGCTCAATGAACGTCATA
1 GACACACAAATGTGTGTCATCTTAATTTATGACGCGGGCTTCAATGACACGCAATGAACGTCATA
*
728564 AATGTGTGTCATAAAT
66 AATGCGTGTCATAAAT
728580 GCACGTCATA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 2 0.03
85 65 0.93
86 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTAATTTATGACGCGGGCTTCAATGACACGCAATGAACGTCATA
AATGCGTGTCATAAATTTAT
Found at i:731999 original size:21 final size:21
Alignment explanation
Indices: 731975--732017 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
731965 TCTTTAGTTG
* *
731975 ATCATTTTACTTTTATA-AATA
1 ATCATATTAATTTT-TACAATA
731996 ATCATATTAATTTTTACAATA
1 ATCATATTAATTTTTACAATA
732017 A
1 A
732018 AAAAGTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (21 bp):
ATCATATTAATTTTTACAATA
Found at i:733896 original size:21 final size:19
Alignment explanation
Indices: 733856--733892 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
733846 GAGTGTTTTG
733856 ATATATACCGGATTTTGAT
1 ATATATACCGGATTTTGAT
* *
733875 ATATATATCGGGTTTTGA
1 ATATATACCGGATTTTGA
733893 GATACATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (19 bp):
ATATATACCGGATTTTGAT
Found at i:735567 original size:16 final size:16
Alignment explanation
Indices: 735543--735573 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
735533 TCCCTGCATA
735543 TATTCATGGTTTGTAC
1 TATTCATGGTTTGTAC
*
735559 TATTTATGGTTTGTA
1 TATTCATGGTTTGTA
735574 GTGTTGGGAG
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:0.19, C:0.06, G:0.19, T:0.55
Consensus pattern (16 bp):
TATTCATGGTTTGTAC
Found at i:740442 original size:93 final size:94
Alignment explanation
Indices: 740283--740469 Score: 367
Period size: 93 Copynumber: 2.0 Consensus size: 94
740273 CAATGGAGCT
740283 GAAGTGCTGGAAAATGGGATTCCACCTCCGGCTCGATGTCAACAGTTTGATGCTGCTGCCATGAA
1 GAAGTGCTGGAAAATGGGATTCCACCTCCGGCTCGATGTCAACAGTTTGATGCTGCTGCCATGAA
740348 CATGGAGACGCCACAGAAAAC-AGATTAA
66 CATGGAGACGCCACAGAAAACAAGATTAA
740376 GAAGTGCTGGAAAATGGGATTCCACCTCCGGCTCGATGTCAACAGTTTGATGCTGCTGCCATGAA
1 GAAGTGCTGGAAAATGGGATTCCACCTCCGGCTCGATGTCAACAGTTTGATGCTGCTGCCATGAA
740441 CATGGAGACGCCACAGAAAACAAGATTAA
66 CATGGAGACGCCACAGAAAACAAGATTAA
740470 ACAAGTCTTG
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 86 0.92
94 7 0.08
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (94 bp):
GAAGTGCTGGAAAATGGGATTCCACCTCCGGCTCGATGTCAACAGTTTGATGCTGCTGCCATGAA
CATGGAGACGCCACAGAAAACAAGATTAA
Found at i:741088 original size:2 final size:2
Alignment explanation
Indices: 741077--741134 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
741067 AAAATACTTT
741077 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
741118 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
741135 TGAAAGTAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:744063 original size:18 final size:18
Alignment explanation
Indices: 744040--744075 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
744030 TGCCTTTATT
* *
744040 TATTTAATCTCTTTTTAC
1 TATTTAATATCATTTTAC
744058 TATTTAATATCATTTTAC
1 TATTTAATATCATTTTAC
744076 CAAAATCCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTAATATCATTTTAC
Found at i:755764 original size:43 final size:43
Alignment explanation
Indices: 755671--755765 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
755661 TAAACTTGTG
* * * *
755671 ACGTTTGTAAACACAAACGCCACTAAAGTATAAGTCTATGGCG
1 ACGTTTGTAAACACAAACGACACTAAAGTACAAGTCTATAGCA
* * *
755714 GCATTTGTAAACACAAACGACACTAAAGTACGAGTCTATAGCA
1 ACGTTTGTAAACACAAACGACACTAAAGTACAAGTCTATAGCA
755757 ACGTTTGTA
1 ACGTTTGTA
755766 TACAAACGCC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (43 bp):
ACGTTTGTAAACACAAACGACACTAAAGTACAAGTCTATAGCA
Found at i:760058 original size:51 final size:51
Alignment explanation
Indices: 759998--760101 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
759988 TGGTGACTAC
759998 AAAATGCCTCTGATAAATATTGGGATTTCTCTAGTATGTTCCTTATATTTT
1 AAAATGCCTCTGATAAATATTGGGATTTCTCTAGTATGTTCCTTATATTTT
*
760049 AAAATGCCTCTGATAAATATTGGGATTTCTCTAGTGTGTTCCTTATATTTT
1 AAAATGCCTCTGATAAATATTGGGATTTCTCTAGTATGTTCCTTATATTTT
760100 AA
1 AA
760102 TAAATTGTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.44
Consensus pattern (51 bp):
AAAATGCCTCTGATAAATATTGGGATTTCTCTAGTATGTTCCTTATATTTT
Found at i:776468 original size:57 final size:57
Alignment explanation
Indices: 776356--776470 Score: 135
Period size: 57 Copynumber: 2.0 Consensus size: 57
776346 TTTAAAAAAT
* * * ** *
776356 TAAATAATTATTTTATAATTTTTAATAATTAGAGGATCAATAAAACATATCTTATAA
1 TAAAAAATTATTTTATAACTTTTAATAATTAAAAAATCAATAAAAAATATCTTATAA
*
776413 TAAAAAATTATTTTATAACTTTTAATAA-TAAAAAA-CTAATAAAATAATATTTTATAA
1 TAAAAAATTATTTTATAACTTTTAATAATTAAAAAATC-AATAAAA-AATATCTTATAA
776470 T
1 T
776471 TAATAATCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
55 1 0.02
56 11 0.22
57 37 0.76
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (57 bp):
TAAAAAATTATTTTATAACTTTTAATAATTAAAAAATCAATAAAAAATATCTTATAA
Found at i:784104 original size:18 final size:18
Alignment explanation
Indices: 784081--784131 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
784071 GGATTATCAA
784081 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
* *
784099 TGGTCCTTTGGGATATAG
1 TGGTCCTTCGGGACATAG
*
784117 TGGTCCTACGGGACA
1 TGGTCCTTCGGGACA
784132 AATTCTACGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.33, T:0.29
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:789247 original size:13 final size:13
Alignment explanation
Indices: 789229--789256 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
789219 AACGTGAAAA
789229 TCCCTTGATTTTC
1 TCCCTTGATTTTC
789242 TCCCTTGATTTTC
1 TCCCTTGATTTTC
789255 TC
1 TC
789257 AACTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.32, G:0.07, T:0.54
Consensus pattern (13 bp):
TCCCTTGATTTTC
Found at i:789264 original size:14 final size:13
Alignment explanation
Indices: 789232--789265 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
789222 GTGAAAATCC
*
789232 CTTGATTTTCTCC
1 CTTGATTTTCTCA
789245 CTTGATTTTCTCAA
1 CTTGATTTTCTC-A
789259 CTTGATT
1 CTTGATT
789266 GTATATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.15, C:0.24, G:0.09, T:0.53
Consensus pattern (13 bp):
CTTGATTTTCTCA
Found at i:791962 original size:2 final size:2
Alignment explanation
Indices: 791957--791989 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
791947 CCATGAAAGT
791957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
791990 GAAATTCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:811288 original size:12 final size:12
Alignment explanation
Indices: 811271--811342 Score: 50
Period size: 12 Copynumber: 6.4 Consensus size: 12
811261 AGAATTGGAC
811271 AAATGAAAAGAA
1 AAATGAAAAGAA
811283 AAATGAAAA-AA
1 AAATGAAAAGAA
*
811294 AAA--AGAAG-A
1 AAATGAAAAGAA
811303 AAA-G-AAAGAA
1 AAATGAAAAGAA
*
811313 AGAAAG-AAAGAA
1 A-AATGAAAAGAA
*
811325 AGAAAGAAAAGAA
1 A-AATGAAAAGAA
811338 AAATG
1 AAATG
811343 GGAAATTGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
9 10 0.20
10 2 0.04
11 7 0.14
12 25 0.49
13 7 0.14
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (12 bp):
AAATGAAAAGAA
Found at i:811310 original size:4 final size:4
Alignment explanation
Indices: 811277--811338 Score: 67
Period size: 4 Copynumber: 15.8 Consensus size: 4
811267 GGACAAATGA
* *
811277 AAAG AAA- AATG AAA- AAAA AAAG -AAG AAAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG
811323 AAAG AAAG AAAAG AAA
1 AAAG AAAG -AAAG AAA
811339 AATGGGAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
3 8 0.16
4 35 0.70
5 7 0.14
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:812311 original size:2 final size:2
Alignment explanation
Indices: 812304--812339 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
812294 AAATATTTTA
812304 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
812340 TTGATTATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:817550 original size:2 final size:2
Alignment explanation
Indices: 817543--817580 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
817533 ATTAAAAACC
817543 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
817581 CTCACTAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:819384 original size:21 final size:21
Alignment explanation
Indices: 819358--819413 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
819348 GTAGAATTTG
819358 TCCCGAAGGACCACGTAGATA
1 TCCCGAAGGACCACGTAGATA
*
819379 TCCCGAAGGACCACGTAGATG
1 TCCCGAAGGACCACGTAGATA
819400 TCCCGAAGGACCAC
1 TCCCGAAGGACCAC
819414 ATATAACACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.32, G:0.25, T:0.12
Consensus pattern (21 bp):
TCCCGAAGGACCACGTAGATA
Found at i:820297 original size:20 final size:20
Alignment explanation
Indices: 820272--820348 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
820262 TTCCCATTGA
*
820272 AGTGCATCGGTGCATTCTCC
1 AGTGCATCGATGCATTCTCC
*
820292 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-CC
*
820315 ATGTGCATCGATGCACTC-CTC
1 A-GTGCATCGATGCATTCTC-C
820336 A-TGCATCGATGCA
1 AGTGCATCGATGCA
820349 CCAACTGTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
19 12 0.25
20 16 0.33
21 2 0.04
22 1 0.02
23 2 0.04
24 15 0.31
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTCC
Found at i:821382 original size:2 final size:2
Alignment explanation
Indices: 821375--821409 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
821365 TACTTGTATC
821375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
821410 AATAAAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:823375 original size:31 final size:30
Alignment explanation
Indices: 823299--823379 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
823289 CAACAGTTAC
*
823299 GTTGGGGACCATATTGCAAACGAACTAAAT
1 GTTGGGGACCATATTGTAAACGAACTAAAT
*
823329 GTTGAGGGACCATATTGTAAACGGACTAAAT
1 GTTG-GGGACCATATTGTAAACGAACTAAAT
* **
823360 ATTTGGGGATTATATTGTAA
1 -GTTGGGGACCATATTGTAA
823380 GTTTTAAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 4 0.09
31 37 0.84
32 3 0.07
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.30
Consensus pattern (30 bp):
GTTGGGGACCATATTGTAAACGAACTAAAT
Found at i:826907 original size:31 final size:31
Alignment explanation
Indices: 826836--826913 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
826826 CTTTTAAAAC
** * *
826836 TTGCAATATAATCCCTCAAAATTTTGTCTAT
1 TTGCAATATGGTCCCTCAAAATTTAGTCCAT
* *
826867 TTGCAATATGGTCCCTCAACATTTAGTCCGT
1 TTGCAATATGGTCCCTCAAAATTTAGTCCAT
826898 TTGCAATATGGTCCCT
1 TTGCAATATGGTCCCT
826914 GCCGTAACTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (31 bp):
TTGCAATATGGTCCCTCAAAATTTAGTCCAT
Found at i:827416 original size:27 final size:28
Alignment explanation
Indices: 827384--827437 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
827374 TTTTTTTTAT
*
827384 CATTTTTCAAA-TTAATTATCAAAATAA
1 CATTTTTCAAAGATAATTATCAAAATAA
* *
827411 CATTTTTTAAAGATATTTATCAAAATA
1 CATTTTTCAAAGATAATTATCAAAATA
827438 GTATTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (28 bp):
CATTTTTCAAAGATAATTATCAAAATAA
Found at i:827736 original size:29 final size:29
Alignment explanation
Indices: 827682--827759 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
827672 CTATAATTAT
*
827682 CATTCTAAATTTATCCTCAAACTTTTGAA
1 CATTCTAAATTTATCCTCAAACTTTTCAA
827711 CATTCTAAA-TTAGTCCTC-AACTTTTTCAA
1 CATTCTAAATTTA-TCCTCAAAC-TTTTCAA
*
827740 CATT-TCAATTTCATCC-CAAA
1 CATTCTAAATTT-ATCCTCAAA
827760 TTATATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
28 10 0.24
29 31 0.74
30 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (29 bp):
CATTCTAAATTTATCCTCAAACTTTTCAA
Found at i:827977 original size:29 final size:30
Alignment explanation
Indices: 827941--828027 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 30
827931 ACAATATGGG
*
827941 TCATAGTTTGAAGATAAAATTGAAAT-GT-
1 TCATAGTTTGAAGATAAAATTAAAATAGTA
* *
827969 TCAATAGTTTAAAGA-ATAATTTAAAATAAGTA
1 TC-ATAGTTTGAAGATA-AAATTAAAAT-AGTA
*
828001 TCATAGTTTGAGGATAAAATTAAAATA
1 TCATAGTTTGAAGATAAAATTAAAATA
828028 TTTAAAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
28 3 0.06
29 19 0.40
30 1 0.02
31 21 0.45
32 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.34
Consensus pattern (30 bp):
TCATAGTTTGAAGATAAAATTAAAATAGTA
Found at i:828052 original size:60 final size:59
Alignment explanation
Indices: 827892--828070 Score: 151
Period size: 60 Copynumber: 3.0 Consensus size: 59
827882 AAGAATTTAG
** ** * * * *
827892 GGATAAAATTAAAGGATTTAAAAGTTTGGGGACCAATTTACAATATGGGTCATAGTTTGA
1 GGATAAAATTAAAATATTTAAAA-TTTAAGGAACAATTTAAAATAAGGATCATAGTTTGA
* * * * * * * *
827952 AGATAAAATTGAAATGTTCAATAGTTTAAAGAATAATTTAAAATAAGTATCATAGTTTGA
1 GGATAAAATTAAAATATTTAA-AATTTAAGGAACAATTTAAAATAAGGATCATAGTTTGA
* ** *
828012 GGATAAAATTAAAATATTTAAAATTTTAGGAACAAGTTTAAAATGTGGATCGTAGTTTG
1 GGATAAAATTAAAATATTTAAAATTTAAGGAACAA-TTTAAAATAAGGATCATAGTTTG
828071 GTTGTCCTGG
Statistics
Matches: 89, Mismatches: 28, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
59 10 0.11
60 78 0.88
61 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.34
Consensus pattern (59 bp):
GGATAAAATTAAAATATTTAAAATTTAAGGAACAATTTAAAATAAGGATCATAGTTTGA
Found at i:833422 original size:37 final size:38
Alignment explanation
Indices: 833290--833464 Score: 141
Period size: 35 Copynumber: 4.6 Consensus size: 38
833280 ATATATATAT
* *
833290 ATATATTAATATAGTATAATTTTTGAAAATATTTTTG-AAA
1 ATATA-TAATATA-TAT-AGTTTTGAAAACATTTTTGAAAA
* *
833330 A-ATATAATATAGA-ATTTTTATAGAAAACGATTTTTGAAAA
1 ATATATAATATATATA-GTTT-T-GAAAAC-ATTTTTGAAAA
*
833370 AAATATATATAATATATAGTTTTGAAAACA-TTTTGAAAA
1 ATATATA-AT-ATATATAGTTTTGAAAACATTTTTGAAAA
*
833409 ATATAT-A-ATATATAGTTTTGAAAATA-TTTTGAAAA
1 ATATATAATATATATAGTTTTGAAAACATTTTTGAAAA
*
833444 ACATAT-ATAATATATAGTTTT
1 ATATATAAT-ATATATAGTTTT
833465 TTAAAAACAT
Statistics
Matches: 117, Mismatches: 7, Indels: 25
0.79 0.05 0.17
Matches are distributed among these distances:
35 34 0.29
36 4 0.03
37 15 0.13
38 12 0.10
39 24 0.21
40 6 0.05
41 11 0.09
42 3 0.03
43 7 0.06
44 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (38 bp):
ATATATAATATATATAGTTTTGAAAACATTTTTGAAAA
Found at i:833471 original size:27 final size:29
Alignment explanation
Indices: 833435--833488 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
833425 TTTGAAAATA
833435 TTTTGAAAAACA-TATATA-ATATATAGT
1 TTTTGAAAAACATTATATATATATATAGT
*
833462 TTTTTAAAAACATTATATATATATATA
1 TTTTGAAAAACATTATATATATATATA
833489 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 11 0.46
28 6 0.25
29 7 0.29
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (29 bp):
TTTTGAAAAACATTATATATATATATAGT
Found at i:833480 original size:2 final size:2
Alignment explanation
Indices: 833475--833522 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
833465 TTAAAAACAT
833475 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
833517 TA TA TA
1 TA TA TA
833523 GTTTTTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:833548 original size:36 final size:37
Alignment explanation
Indices: 833508--833593 Score: 122
Period size: 38 Copynumber: 2.4 Consensus size: 37
833498 ATATATATAT
* *
833508 ATATATATATATATAGTTTTTAAAA-ATATTTTGAAA
1 ATATATATATATATAGTTTTGAAAATATATTTTAAAA
*
833544 ATATATATACTATATAGTTTTGAAAATATTTTTTAAAA
1 ATATATATA-TATATAGTTTTGAAAATATATTTTAAAA
833582 ATATATAT-TATA
1 ATATATATATATA
833594 AAAACAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
36 13 0.29
37 15 0.33
38 17 0.38
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.48
Consensus pattern (37 bp):
ATATATATATATATAGTTTTGAAAATATATTTTAAAA
Found at i:833586 original size:100 final size:98
Alignment explanation
Indices: 833409--833593 Score: 239
Period size: 100 Copynumber: 1.9 Consensus size: 98
833399 ATTTTGAAAA
* *
833409 ATATATAATATATAGTTTTGAAAATATTTTGAAAAACATATATAATATATAGTTTTTTAAAAACA
1 ATATATAATATATAGTTTTAAAAATATTTTGAAAAACATATATAATATATAGTTTTTGAAAAACA
* *
833474 TTATATATATATATATATATATATATATATATAT
66 TTATAAAAATATATAT-TATATATATATATATAT
* *
833508 ATATATATATATATAGTTTTTAAAAATATTTTG-AAAATATATATACTATATAG-TTTTGAAAAT
1 ATATATA-ATATATAG-TTTTAAAAATATTTTGAAAAACATATATAATATATAGTTTTTGAAAA-
** *
833571 ATTTTTTAAAAATATATATTATA
63 ACATTATAAAAATATATATTATA
833594 AAAACAATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
99 19 0.26
100 40 0.54
101 15 0.20
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (98 bp):
ATATATAATATATAGTTTTAAAAATATTTTGAAAAACATATATAATATATAGTTTTTGAAAAACA
TTATAAAAATATATATTATATATATATATATAT
Found at i:833716 original size:28 final size:29
Alignment explanation
Indices: 833679--833733 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
833669 TAAAAAAATG
833679 ATTATATATAT-TATTTTATTTATTATTTT
1 ATTATATATATATA-TTTATTTATTATTTT
*
833708 ATTA-ATATATATATTTATTTTTTATT
1 ATTATATATATATATTTATTTATTATT
833734 ATTCATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
ATTATATATATATATTTATTTATTATTTT
Found at i:833746 original size:11 final size:11
Alignment explanation
Indices: 833687--833751 Score: 62
Period size: 12 Copynumber: 5.7 Consensus size: 11
833677 TGATTATATA
833687 TATTATTTTATT
1 TATTATTTTA-T
833699 TATTATTTTAT
1 TATTATTTTAT
* *
833710 TAATATATATATT
1 TATTAT-TTTA-T
833723 TATT-TTTTAT
1 TATTATTTTAT
833733 TATTCATTTT-T
1 TATT-ATTTTAT
833744 TATTATTT
1 TATTATTT
833752 CCATTTTAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
10 9 0.20
11 14 0.31
12 18 0.40
13 4 0.09
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:833758 original size:15 final size:14
Alignment explanation
Indices: 833719--833750 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
833709 TTAATATATA
*
833719 TATTTATTTTTTAT
1 TATTCATTTTTTAT
833733 TATTCATTTTTTAT
1 TATTCATTTTTTAT
833747 TATT
1 TATT
833751 TCCATTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TATTCATTTTTTAT
Found at i:834909 original size:3 final size:3
Alignment explanation
Indices: 834901--834937 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
834891 TCTACTTTAT
*
834901 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
834938 TTTTTCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:846870 original size:3 final size:3
Alignment explanation
Indices: 846858--846918 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
846848 GTGGTGGTGG
* * * *
846858 TGA TGG TGA TGA TGT TGA TGA GGG TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* *
846906 TGG TGA TGT TGA T
1 TGA TGA TGA TGA T
846919 AGATTGATTC
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:846870 original size:9 final size:9
Alignment explanation
Indices: 846837--846913 Score: 82
Period size: 9 Copynumber: 8.6 Consensus size: 9
846827 TAGATGACGA
*
846837 TGATGGTGG
1 TGATGATGG
* *
846846 TGGTGGTGG
1 TGATGATGG
*
846855 TGGTGATGG
1 TGATGATGG
*
846864 TGATGATGT
1 TGATGATGG
*
846873 TGATGAGGG
1 TGATGATGG
*
846882 TGATGATGA
1 TGATGATGG
*
846891 TGATGATGA
1 TGATGATGG
846900 TGATGATGG
1 TGATGATGG
846909 TGATG
1 TGATG
846914 TTGATAGATT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.34
Consensus pattern (9 bp):
TGATGATGG
Found at i:848513 original size:116 final size:116
Alignment explanation
Indices: 848309--848528 Score: 275
Period size: 116 Copynumber: 1.9 Consensus size: 116
848299 CAATACTTAG
* ** *
848309 AATGTCTCATATATGCTGATAGTAGCCTCAATTGAAACATAAGTATCAATACTATGCCTTTAATC
1 AATGTCTCATATATGCTAATAGTAGCCTCAATTGAAACATAAGTATCAATACTACACCTCTAATC
848374 TTATAAATGACAAAAAAATTTAGATTAACCT-CTCGAAAATACTCCCTGAAC
66 TTATAAATGACAAAAAAATTTAGATTAA-CTACTCGAAAATACTCCCTGAAC
* * *
848425 AATGTCTCATATGTGCTAATATTA-CTCTCAATTGAAAGATAAGT-TACAATACTACACCTCTAA
1 AATGTCTCATATATGCTAATAGTAGC-CTCAATTGAAACATAAGTAT-CAATACTACACCTCTAA
* ** ***
848488 TCTTATAAATTATGAAATTTTTTAGATTAACTACTCGAAAA
64 TCTTATAAATGACAAAAAAATTTAGATTAACTACTCGAAAA
848529 AAAATCCCTC
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
115 4 0.05
116 84 0.95
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.34
Consensus pattern (116 bp):
AATGTCTCATATATGCTAATAGTAGCCTCAATTGAAACATAAGTATCAATACTACACCTCTAATC
TTATAAATGACAAAAAAATTTAGATTAACTACTCGAAAATACTCCCTGAAC
Found at i:850031 original size:16 final size:17
Alignment explanation
Indices: 850010--850041 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
850000 CGAGATCACA
850010 ATATTAT-TTTTATATT
1 ATATTATATTTTATATT
850026 ATATTATATTTTATAT
1 ATATTATATTTTATAT
850042 AAATAAATAT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:852596 original size:20 final size:21
Alignment explanation
Indices: 852584--852631 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
852574 CGATTTTGAC
852584 TATCGCGTTGCGATTTTCCAA
1 TATCGCGTTGCGATTTTCCAA
*
852605 TTTCGCGTTGCGATTTTCCCAA
1 TATCGCGTTGCGATTTT-CCAA
852627 T-TCGC
1 TATCGC
852632 AATGCGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.15, C:0.27, G:0.19, T:0.40
Consensus pattern (21 bp):
TATCGCGTTGCGATTTTCCAA
Found at i:852612 original size:21 final size:22
Alignment explanation
Indices: 852586--852628 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
852576 ATTTTGACTA
852586 TCGCGTTGCGATTTT-CCAATT
1 TCGCGTTGCGATTTTCCCAATT
852607 TCGCGTTGCGATTTTCCCAATT
1 TCGCGTTGCGATTTTCCCAATT
852629 CGCAATGCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.42
Consensus pattern (22 bp):
TCGCGTTGCGATTTTCCCAATT
Found at i:852637 original size:21 final size:21
Alignment explanation
Indices: 852592--852638 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
852582 ACTATCGCGT
**
852592 TGCGATTTTCCAATTTCGCGT
1 TGCGATTTTCCAATTTCGCAA
852613 TGCGATTTTCCCAA-TTCGCAA
1 TGCGATTTT-CCAATTTCGCAA
852634 TGCGA
1 TGCGA
852639 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
TGCGATTTTCCAATTTCGCAA
Found at i:852653 original size:20 final size:21
Alignment explanation
Indices: 852628--852679 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
852618 TTTTCCCAAT
*
852628 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
852648 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
852669 TCGCAATGCGA
1 TCGCAATGCGA
852680 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:852692 original size:41 final size:42
Alignment explanation
Indices: 852647--852740 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 42
852637 GAATAAGTAA
* ** *
852647 ATCGCAACGCGAAT-TTGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATAATACAAAATCGCAACGCGATACTGACT
852688 ATCGCAACGCG-ATAATACAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCGAATAATACAAAATCGCAACGCGATACTGACT
*
852729 TTCGCAACGCGA
1 ATCGCAACGCGA
852741 TTCTGACTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 2 0.04
41 44 0.96
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (42 bp):
ATCGCAACGCGAATAATACAAAATCGCAACGCGATACTGACT
Found at i:852693 original size:20 final size:20
Alignment explanation
Indices: 852668--852802 Score: 137
Period size: 20 Copynumber: 6.7 Consensus size: 20
852658 AATTTGGAAA
*
852668 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
852688 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
852709 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
852729 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
852749 TTCGCAACGTGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
852769 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
852789 ATCGCAACGAGATA
1 ATCGCAACGCGATA
852803 ATACAGAATC
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 82 0.81
21 15 0.15
22 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:853566 original size:24 final size:24
Alignment explanation
Indices: 853539--853585 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
853529 AGTCAGTATT
*
853539 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACC
*
853563 CGAACTTTGATATTGGTCAATAC
1 CGAAATTTGATATTGGTCAATAC
853586 TCAGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACC
Found at i:853597 original size:24 final size:24
Alignment explanation
Indices: 853544--853590 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
853534 GTATTCGAAA
* *
853544 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATATTGGTCAATACCAGAAC
853568 TTTGATATTGGTCAATACTCAGA
1 TTTGATATTGGTCAATAC-CAGA
853591 TTTTGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCAGAAC
Found at i:856093 original size:20 final size:20
Alignment explanation
Indices: 856065--856120 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
856055 CAACGGGGAA
856065 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
856085 ATCGTAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
856105 ATCGCAACGCGAAAAT
1 ATCGCAACGCGAAAAT
856121 CGCATTGCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:857775 original size:41 final size:42
Alignment explanation
Indices: 857721--857812 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
857711 CCTCTTCAAC
* *
857721 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
857762 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
857804 GATGACAGG
1 GATGACAGG
857813 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:857777 original size:21 final size:21
Alignment explanation
Indices: 857748--857808 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
857738 GAACGGTGGG
*
857748 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
857769 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
857790 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
857809 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:858198 original size:20 final size:20
Alignment explanation
Indices: 858175--858227 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
858165 AAACTTACTT
*
858175 TCGCAACGTGAAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
*
858195 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
858215 TCGCAACGCGAAA
1 TCGCAACGCGAAA
858228 TGAAAATCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGGCTA
Found at i:858229 original size:19 final size:19
Alignment explanation
Indices: 858175--858248 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 19
858165 AAACTTACTT
*
858175 TCGCAACGTGAAAATGGCTA
1 TCGCAACGCG-AAATGGCTA
858195 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGGCTA
***
858215 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGGCTA
*
858234 TCGCAATGCGAAATG
1 TCGCAACGCGAAATG
858249 AAAATCGCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 21 0.44
20 26 0.54
21 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (19 bp):
TCGCAACGCGAAATGGCTA
Found at i:858249 original size:19 final size:19
Alignment explanation
Indices: 858214--858291 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
858204 GGAAATGGCT
*
858214 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
858233 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
858252 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
858266 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
858285 ATCGCAA
1 ATCGCAA
858292 CGAAAAAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 35 0.69
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:858272 original size:33 final size:33
Alignment explanation
Indices: 858230--858323 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
858220 ACGCGAAATG
* *
858230 AAAATCGCAATGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAATGCGAAATAAAAATCGCAACGAA
858263 AAAATCGCAATGCGAAATAAAAATCGCAACGAA
1 AAAATCGCAATGCGAAATAAAAATCGCAACGAA
* * * *
858296 AAAATCACAACGCGAAACACAAATCGCA
1 AAAATCGCAATGCGAAATAAAAATCGCA
858324 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.52, C:0.22, G:0.15, T:0.11
Consensus pattern (33 bp):
AAAATCGCAATGCGAAATAAAAATCGCAACGAA
Found at i:858300 original size:14 final size:14
Alignment explanation
Indices: 858249--858307 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
858239 ATGCGAAATG
*
858249 AAAATCGCAACGAC
1 AAAATCGCAACGAA
858263 AAAATCGCAATGCGAAATA
1 AAAATCGCAA--CG--A-A
858282 AAAATCGCAACGAA
1 AAAATCGCAACGAA
*
858296 AAAATCACAACG
1 AAAATCGCAACG
858308 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.54, C:0.22, G:0.14, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:858341 original size:19 final size:19
Alignment explanation
Indices: 858319--858385 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
858309 GAAACACAAA
858319 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
858338 TCGCGTTGAGA-TTT--TG
1 TCGCATTGCGATTTTCATT
858354 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
858371 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
858386 GTCGTTGCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 5 0.13
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 19 0.50
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:858364 original size:14 final size:14
Alignment explanation
Indices: 858341--858399 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
858331 TTTCATTTCG
*
858341 CGTTGAGATTTTGT
1 CGTTGCGATTTTGT
*
858355 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
858372 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
858388 CGTTGCGATTTT
1 CGTTGCGATTTT
858400 ATTTCTCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Done.