Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 2 of 18
Found at i:396123 original size:19 final size:20
Alignment explanation
Indices: 396075--396124 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
396065 AAAATTTTAT
396075 ATAAATATTTT-ATTAATTA
1 ATAAATATTTTAATTAATTA
396094 A-ATAATATTTTAATTAATTA
1 ATA-AATATTTTAATTAATTA
396114 ATAAAT-TTTTA
1 ATAAATATTTTA
396125 TGATTTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 14 0.50
20 12 0.43
21 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAAATATTTTAATTAATTA
Found at i:398282 original size:12 final size:12
Alignment explanation
Indices: 398262--398312 Score: 57
Period size: 12 Copynumber: 4.0 Consensus size: 12
398252 TATAAATATC
*
398262 GTATTAATTAAT
1 GTATAAATTAAT
398274 GTATAAATTAAT
1 GTATAAATTAAT
*
398286 AAAGTATTAATTAAT
1 ---GTATAAATTAAT
398301 GTATAAATTAAT
1 GTATAAATTAAT
398313 AAAGTATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 22 0.67
15 11 0.33
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (12 bp):
GTATAAATTAAT
Found at i:398286 original size:27 final size:27
Alignment explanation
Indices: 398262--398324 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
398252 TATAAATATC
398262 GTATTAATTAATGTATAAATTAATAAA
1 GTATTAATTAATGTATAAATTAATAAA
398289 GTATTAATTAATGTATAAATTAATAAA
1 GTATTAATTAATGTATAAATTAATAAA
398316 GTATTAATT
1 GTATTAATT
398325 TATCAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (27 bp):
GTATTAATTAATGTATAAATTAATAAA
Found at i:398339 original size:27 final size:27
Alignment explanation
Indices: 398262--398360 Score: 98
Period size: 27 Copynumber: 3.8 Consensus size: 27
398252 TATAAATATC
**
398262 GTATTAATTAATGTATAAATTAATAAA
1 GTATTAATTAATCAATAAATTAATAAA
**
398289 GTATTAATTAATGTATAAATTAATAAA
1 GTATTAATTAATCAATAAATTAATAAA
*
398316 GTATTAATTTATCAATTAAA-TAAT--A
1 GTATTAATTAATCAA-TAAATTAATAAA
* *
398341 -TTTTAATTAATTAATAAATT
1 GTATTAATTAATCAATAAATT
398361 TTTATGATCT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
23 4 0.06
24 12 0.19
25 1 0.02
27 43 0.67
28 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (27 bp):
GTATTAATTAATCAATAAATTAATAAA
Found at i:413863 original size:19 final size:18
Alignment explanation
Indices: 413849--413887 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
413839 GATTTTAAAT
413849 TTTAATTTATTTTTTATTAA
1 TTTAATTT-TTTTTTA-TAA
413869 TTTAATTTTTTTTTATAA
1 TTTAATTTTTTTTTATAA
413887 T
1 T
413888 ATACATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
20 8 0.42
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTAATTTTTTTTTATAA
Found at i:413870 original size:15 final size:16
Alignment explanation
Indices: 413850--413879 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
413840 ATTTTAAATT
413850 TTAATTT-ATTTTTTA
1 TTAATTTAATTTTTTA
413865 TTAATTTAATTTTTT
1 TTAATTTAATTTTTT
413880 TTTATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTAATTTAATTTTTTA
Found at i:424053 original size:14 final size:14
Alignment explanation
Indices: 424036--424062 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
424026 ATTCATGAAA
424036 TATCATATTATTAT
1 TATCATATTATTAT
424050 TATCATATTATTA
1 TATCATATTATTA
424063 AATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (14 bp):
TATCATATTATTAT
Found at i:424387 original size:25 final size:26
Alignment explanation
Indices: 424359--424456 Score: 86
Period size: 25 Copynumber: 4.0 Consensus size: 26
424349 AAGTATGTAA
*
424359 TTATATAATATAAAA-TATTAATATT
1 TTATATATTATAAAATTATTAATATT
424384 TTATAT-TTA-AAAATTAATTAATATT
1 TTATATATTATAAAATT-ATTAATATT
* *
424409 TT-TAATATTTTAATAA-TAATAATA-T
1 TTAT-ATATTATAA-AATTATTAATATT
424434 TTA-A-ATTATAAAATTATTAATAT
1 TTATATATTATAAAATTATTAATAT
424457 AAAATGTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
22 2 0.03
23 17 0.29
24 5 0.08
25 22 0.37
26 8 0.14
27 3 0.05
28 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTATATATTATAAAATTATTAATATT
Found at i:424444 original size:17 final size:17
Alignment explanation
Indices: 424411--424480 Score: 56
Period size: 17 Copynumber: 4.0 Consensus size: 17
424401 TTAATATTTT
*
424411 TAATATTTTAATAATAA
1 TAATATTTAAATAATAA
*
424428 TAATATTTAAATTATAA
1 TAATATTTAAATAATAA
424445 -AAT-TATTAATATAA-AA
1 TAATAT-TTAA-ATAATAA
424461 TGTTAATATTTAAATAATAA
1 ---TAATATTTAAATAATAA
424481 ATTATTAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
15 1 0.02
16 9 0.21
17 18 0.43
19 4 0.10
20 9 0.21
21 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (17 bp):
TAATATTTAAATAATAA
Found at i:424480 original size:22 final size:21
Alignment explanation
Indices: 424455--424502 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
424445 AATTATTAAT
*
424455 ATAAAATGTTAATATTTAAATA
1 ATAAAATATTAATATTTAAA-A
*
424477 ATAAATTATTAATATTTAAAA
1 ATAAAATATTAATATTTAAAA
424498 ATAAA
1 ATAAA
424503 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATAAAATATTAATATTTAAAA
Found at i:424503 original size:21 final size:22
Alignment explanation
Indices: 424463--424503 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
424453 ATATAAAATG
424463 TTAATATTTAAATAATAAATTA
1 TTAATATTTAAATAATAAATTA
424485 TTAATATTTAAA-AATAAAT
1 TTAATATTTAAATAATAAAT
424504 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAATATTTAAATAATAAATTA
Found at i:424666 original size:11 final size:11
Alignment explanation
Indices: 424652--424687 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
424642 CCATCATAAC
424652 TATTTTAATTT
1 TATTTTAATTT
*
424663 TATTTTGATTT
1 TATTTTAATTT
*
424674 AATTTTAATTT
1 TATTTTAATTT
424685 TAT
1 TAT
424688 AAAATAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
TATTTTAATTT
Found at i:424899 original size:9 final size:9
Alignment explanation
Indices: 424885--424911 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
424875 AAAAACATTA
424885 CTCACGTTC
1 CTCACGTTC
424894 CTCACGTTC
1 CTCACGTTC
424903 CTCACGTTC
1 CTCACGTTC
424912 TGCTATGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.44, G:0.11, T:0.33
Consensus pattern (9 bp):
CTCACGTTC
Found at i:432922 original size:28 final size:30
Alignment explanation
Indices: 432880--432935 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
432870 ATTCAAAAAA
432880 ATTTAAATAAAC-TTTTATACTTTTATTAT
1 ATTTAAATAAACTTTTTATACTTTTATTAT
* *
432909 ATTT-AATTAACTTTTTATATTTTTATT
1 ATTTAAATAAACTTTTTATACTTTTATT
432936 TTGAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTTAAATAAACTTTTTATACTTTTATTAT
Found at i:439360 original size:17 final size:17
Alignment explanation
Indices: 439338--439375 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
439328 ATACCATTTC
*
439338 AAAAAAGACT-AAATTA
1 AAAAAAAACTAAAATTA
*
439354 AAAAAAAATTAAAATTA
1 AAAAAAAACTAAAATTA
439371 AAAAA
1 AAAAA
439376 TTAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAAAAACTAAAATTA
Found at i:449170 original size:2 final size:2
Alignment explanation
Indices: 449163--449200 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
449153 CCCCTTGACA
449163 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
449201 TTTCCTTTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:450076 original size:30 final size:30
Alignment explanation
Indices: 450040--450096 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
450030 ATCATAAAAG
*
450040 CTTATTTTACTCAAAATAAAAATATAATAA
1 CTTATTTGACTCAAAATAAAAATATAATAA
* *
450070 CTTATTTGACTTAAAGTAAAAATATAA
1 CTTATTTGACTCAAAATAAAAATATAA
450097 AGATTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (30 bp):
CTTATTTGACTCAAAATAAAAATATAATAA
Found at i:451446 original size:3 final size:3
Alignment explanation
Indices: 451438--451478 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
451428 TGTATATATG
451438 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
451479 ATGTATTTAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:452378 original size:6 final size:6
Alignment explanation
Indices: 452367--452394 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
452357 TCCATAATTA
452367 ATATTT ATATTT ATATTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT ATAT
452395 ATACATACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:457882 original size:2 final size:2
Alignment explanation
Indices: 457875--457921 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
457865 AATTACATTC
457875 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
457917 AT AT A
1 AT AT A
457922 GATGAATGAA
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:459809 original size:56 final size:56
Alignment explanation
Indices: 459654--459811 Score: 163
Period size: 56 Copynumber: 2.7 Consensus size: 56
459644 CGTTGTTACT
* * * ** *
459654 AATAAAGGAGCTGGTGTACCTATGCTTTGTCTTTGATTCTTTAAGAGTTTTACTTTA
1 AATAAAGGAGCAGGTGTATCTATGTTTTGTCTTTGATTC-TTAAGAGTACTACTCTA
* ** * *
459711 AATAAAGGAGAAATTATACCTATATATGTTTTGTCTTTGATTCTTAAGAGTACTACTCTA
1 AATAAAGGAG-CA-GGT--GTATCTATGTTTTGTCTTTGATTCTTAAGAGTACTACTCTA
*
459771 AATGAAGGAGCAGGTGTATCTATGTTTTGTCTTTGATTCTT
1 AATAAAGGAGCAGGTGTATCTATGTTTTGTCTTTGATTCTT
459812 CCAGCGCTTT
Statistics
Matches: 80, Mismatches: 17, Indels: 9
0.75 0.16 0.08
Matches are distributed among these distances:
56 24 0.30
57 10 0.12
58 1 0.01
59 2 0.03
60 23 0.29
61 20 0.25
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (56 bp):
AATAAAGGAGCAGGTGTATCTATGTTTTGTCTTTGATTCTTAAGAGTACTACTCTA
Found at i:462360 original size:22 final size:22
Alignment explanation
Indices: 462335--462389 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
462325 TGTTATTGAG
*
462335 TTTTAGGTATTGTGAAACTGAT
1 TTTTAGATATTGTGAAACTGAT
* **
462357 TTTTAGACATTGTGTGACTGAT
1 TTTTAGATATTGTGAAACTGAT
462379 TTTTAGATATT
1 TTTTAGATATT
462390 ACATGAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.49
Consensus pattern (22 bp):
TTTTAGATATTGTGAAACTGAT
Found at i:462472 original size:22 final size:23
Alignment explanation
Indices: 462447--462495 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
462437 TAAGAACTAA
462447 TCACACAATGC-ATATCAATCAG
1 TCACACAATGCTATATCAATCAG
*
462469 TCACATAATGCTATATCAATCAG
1 TCACACAATGCTATATCAATCAG
462492 TCAC
1 TCAC
462496 GTAATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.27
Consensus pattern (23 bp):
TCACACAATGCTATATCAATCAG
Found at i:462529 original size:22 final size:22
Alignment explanation
Indices: 462490--462531 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
462480 TATATCAATC
* **
462490 AGTCACGTAATATTTAAAAATT
1 AGTCACATAATACCTAAAAATT
462512 AGTCACATAATACCTAAAAA
1 AGTCACATAATACCTAAAAA
462532 CAAGTTATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (22 bp):
AGTCACATAATACCTAAAAATT
Found at i:464685 original size:2 final size:2
Alignment explanation
Indices: 464678--464710 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
464668 ACTTGGGGTT
464678 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
464711 CTCTCATGGT
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:479598 original size:4 final size:4
Alignment explanation
Indices: 479589--479617 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
479579 ATTGAATCAC
479589 AGAA AGAA AGAA AGAA AGAA AGAA A-AA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
479618 GTACTACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:488007 original size:22 final size:22
Alignment explanation
Indices: 487946--488015 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
487936 AAAATATATA
*
487946 AAATAAATAATATTATTGATAATT
1 AAATATATAATATTA-T-ATAATT
*
487970 AAAT-TATTAATTTTATATAATT
1 AAATATA-TAATATTATATAATT
*
487992 AAATATATAAAATTAT-TAAATT
1 AAATATATAATATTATAT-AATT
488014 AA
1 AA
488016 TTAAAATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 1 0.03
22 23 0.59
23 4 0.10
24 11 0.28
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (22 bp):
AAATATATAATATTATATAATT
Found at i:488012 original size:8 final size:8
Alignment explanation
Indices: 487967--488026 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
487957 ATTATTGATA
487967 ATTAAATT
1 ATTAAATT
487975 ATT-AATT
1 ATTAAATT
* *
487982 -TTATATA
1 ATTAAATT
487989 ATTAAATAT
1 ATTAAAT-T
*
487998 ATAAAATT
1 ATTAAATT
488006 ATTAAATT
1 ATTAAATT
488014 AATTAAAATT
1 -ATT-AAATT
488024 ATT
1 ATT
488027 TTTTTCTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
6 2 0.05
7 6 0.15
8 16 0.39
9 12 0.29
10 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTAAATT
Found at i:491484 original size:15 final size:15
Alignment explanation
Indices: 491450--491493 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
491440 TTATAAATAT
*
491450 TTTTATCATGATTAAA
1 TTTTATTAT-ATTAAA
*
491466 ATTTATTGATATTAAA
1 TTTTATT-ATATTAAA
491482 TTTTATTATATT
1 TTTTATTATATT
491494 TGATAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.21
16 17 0.71
17 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (15 bp):
TTTTATTATATTAAA
Found at i:491500 original size:19 final size:18
Alignment explanation
Indices: 491478--491529 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
491468 TTATTGATAT
491478 TAAATTTTATTATATTTGA
1 TAAATTTTATTATATTT-A
* *
491497 TAAATATTATAATATTTA
1 TAAATTTTATTATATTTA
*
491515 TAATTTTTTATTATA
1 TAA-ATTTTATTATA
491530 AATTTAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TAAATTTTATTATATTTA
Found at i:503698 original size:7 final size:7
Alignment explanation
Indices: 503686--503711 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
503676 ATATGACTCC
503686 CAAACCT
1 CAAACCT
503693 CAAACCT
1 CAAACCT
503700 CAAACCT
1 CAAACCT
503707 CAAAC
1 CAAAC
503712 AAAGTTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.42, G:0.00, T:0.12
Consensus pattern (7 bp):
CAAACCT
Found at i:504531 original size:2 final size:2
Alignment explanation
Indices: 504524--504567 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
504514 AAGCATGCAC
504524 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
504566 AT
1 AT
504568 CTGCTTTCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:507018 original size:24 final size:24
Alignment explanation
Indices: 506973--507019 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
506963 TATCAATTGG
* *
506973 AAAAAATAAATATTATTTTTTTTA
1 AAAAAATAAATACTATTATTTTTA
506997 AAAAAATAAA-ACTATATATTTTT
1 AAAAAATAAATACTAT-TATTTTT
507020 CCCTCTCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAAAAATAAATACTATTATTTTTA
Found at i:508849 original size:21 final size:19
Alignment explanation
Indices: 508805--508841 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
508795 GAAATATAAG
*
508805 AGAAAGTATTTAGAGGGAA
1 AGAAAGTATTTAGAGAGAA
*
508824 AGAAAGTATTTTGAGAGA
1 AGAAAGTATTTAGAGAGA
508842 GTAAGAAAAT
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:0.46, C:0.00, G:0.30, T:0.24
Consensus pattern (19 bp):
AGAAAGTATTTAGAGAGAA
Found at i:509128 original size:15 final size:16
Alignment explanation
Indices: 509096--509130 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
509086 ATACTTCGTT
509096 AAAACCTTACAAGAAA
1 AAAACCTTACAAGAAA
**
509112 AAAACCTTATGAGAAA
1 AAAACCTTACAAGAAA
509128 AAA
1 AAA
509131 TCCGAGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (16 bp):
AAAACCTTACAAGAAA
Found at i:510750 original size:17 final size:17
Alignment explanation
Indices: 510710--510744 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
510700 ATAATAAGCA
510710 TACATGTGATCATCTAG
1 TACATGTGATCATCTAG
510727 TACATGTGATCATCTAG
1 TACATGTGATCATCTAG
510744 T
1 T
510745 CGATGTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (17 bp):
TACATGTGATCATCTAG
Found at i:511860 original size:16 final size:15
Alignment explanation
Indices: 511839--511879 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
511829 ACAATAAGTT
511839 TTTTATATTCTTTTTA
1 TTTT-TATTCTTTTTA
511855 -TTTTATT-TTTTTA
1 TTTTTATTCTTTTTA
511868 TTTTTA-TCTTTT
1 TTTTTATTCTTTT
511880 CATTATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.30
14 13 0.57
15 3 0.13
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTATTCTTTTTA
Found at i:517853 original size:18 final size:19
Alignment explanation
Indices: 517809--517853 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
517799 ACGATTTAAG
517809 GTTAATATT-AAAATTTTA
1 GTTAATATTAAAAATTTTA
* *
517827 ATTTA-ATTAAAAATTTT-
1 GTTAATATTAAAAATTTTA
517844 GTTAATATTA
1 GTTAATATTA
517854 TTATAATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
GTTAATATTAAAAATTTTA
Found at i:518579 original size:2 final size:2
Alignment explanation
Indices: 518572--518601 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
518562 TATATCCAAG
518572 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
518602 GGATAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:520005 original size:96 final size:96
Alignment explanation
Indices: 519840--520021 Score: 287
Period size: 96 Copynumber: 1.9 Consensus size: 96
519830 TAATATTTAG
519840 ATAAGAAATATTGATAATTTTAAAAGAGAATACATATATGTGTGTGTTTTATATGTATATGAAGA
1 ATAAGAAATATTGATAATTTTAAAAGAGAATA-ATATATGTGTGTGTTTTATATG-ATATGAAGA
519905 TGGATCAACATATTAAAATTATAAAATAGATAA
64 TGGATCAACATATTAAAATTATAAAATAGATAA
*
519938 ATAAGAAATATTGGTAATTTTAAAAGAGAAT-ATATATGTGTGTGTTTTATGCATG-TATGAAGA
1 ATAAGAAATATTGATAATTTTAAAAGAGAATAATATATGTGTGTGTTTTAT--ATGATATGAAGA
* *
520001 TGGATCAACTTATTAAGATTA
64 TGGATCAACATATTAAAATTA
520022 ATTCCAATTA
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
96 46 0.58
98 33 0.42
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.37
Consensus pattern (96 bp):
ATAAGAAATATTGATAATTTTAAAAGAGAATAATATATGTGTGTGTTTTATATGATATGAAGATG
GATCAACATATTAAAATTATAAAATAGATAA
Found at i:530007 original size:4 final size:4
Alignment explanation
Indices: 530000--530033 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
529990 TAAATAAGTC
530000 TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
530034 TAATGTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:530309 original size:56 final size:56
Alignment explanation
Indices: 530223--530328 Score: 176
Period size: 56 Copynumber: 1.9 Consensus size: 56
530213 CAGTTGTTTG
* *
530223 ATTTACAACAATGAGCTGGTGATAAACAATTGATCTTGTTTTTGGATATACCTTGA
1 ATTTACAACAATGAGCTGGTAATAAACAATTGATCTTGTTTTCGGATATACCTTGA
* *
530279 ATTTAGAACAATGAGTTGGTAATAAACAATTGATCTTGTTTTCGGATATA
1 ATTTACAACAATGAGCTGGTAATAAACAATTGATCTTGTTTTCGGATATA
530329 TATCTAAGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (56 bp):
ATTTACAACAATGAGCTGGTAATAAACAATTGATCTTGTTTTCGGATATACCTTGA
Found at i:543367 original size:12 final size:12
Alignment explanation
Indices: 543352--543378 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
543342 AATATTCCTC
543352 TATATATATCAT
1 TATATATATCAT
543364 TATATATATCAT
1 TATATATATCAT
543376 TAT
1 TAT
543379 TATTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATATCAT
Found at i:545270 original size:17 final size:17
Alignment explanation
Indices: 545240--545273 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
545230 TATATTTTAA
545240 TTTTAAATTAAATAATT
1 TTTTAAATTAAATAATT
545257 TTTTATAATT-AATAATT
1 TTTTA-AATTAAATAATT
545274 AATTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAATTAAATAATT
Found at i:545279 original size:18 final size:20
Alignment explanation
Indices: 545236--545280 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
545226 CATTTATATT
545236 TTAATTT-TAAATTAAATAA
1 TTAATTTATAAATTAAATAA
*
545255 TT-TTTTAT-AATT-AATAA
1 TTAATTTATAAATTAAATAA
545272 TTAATTTAT
1 TTAATTTAT
545281 TATCATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTTATAAATTAAATAA
Found at i:565888 original size:33 final size:33
Alignment explanation
Indices: 565846--565914 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
565836 TTTTCCTTCT
565846 TGTGCTTAGCATGAACAATGAAATTCTTTACAA
1 TGTGCTTAGCATGAACAATGAAATTCTTTACAA
565879 TGTGCTTAGCATGAACAATGAAATTCTTTACAA
1 TGTGCTTAGCATGAACAATGAAATTCTTTACAA
565912 TGT
1 TGT
565915 TAATGACTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (33 bp):
TGTGCTTAGCATGAACAATGAAATTCTTTACAA
Found at i:568505 original size:24 final size:24
Alignment explanation
Indices: 568473--568518 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
568463 TCAAATAAAA
**
568473 TTTTATAAAAAATTTTTAAAAATT
1 TTTTATAAAAAAGGTTTAAAAATT
*
568497 TTTTTTAAAAAAGGTTTAAAAA
1 TTTTATAAAAAAGGTTTAAAAA
568519 AAAACTCCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TTTTATAAAAAAGGTTTAAAAATT
Found at i:568761 original size:23 final size:23
Alignment explanation
Indices: 568711--568757 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
568701 TGCATTTTGA
568711 TATTTTTTTTCTATTGAGTTTTT
1 TATTTTTTTTCTATTGAGTTTTT
*
568734 TATTTTATTTTTTATT-A-TTTTT
1 TATTTT-TTTTCTATTGAGTTTTT
568756 TA
1 TA
568758 ATTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 7 0.32
24 8 0.36
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (23 bp):
TATTTTTTTTCTATTGAGTTTTT
Found at i:571674 original size:2 final size:2
Alignment explanation
Indices: 571667--571716 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
571657 TATAAAAGAT
571667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
571707 TA TA TA TA TA
1 TA TA TA TA TA
571717 GGAATTAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:582851 original size:30 final size:30
Alignment explanation
Indices: 582817--582873 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
582807 GTCTAGGCCA
* *
582817 AGCACAGACAATAGAGAGAAAGCAAGAGCC
1 AGCACAGACAAAAAAGAGAAAGCAAGAGCC
* *
582847 AGCACTGACAAAAAAGAGAAATCAAGA
1 AGCACAGACAAAAAAGAGAAAGCAAGA
582874 AAGAGCATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.54, C:0.18, G:0.23, T:0.05
Consensus pattern (30 bp):
AGCACAGACAAAAAAGAGAAAGCAAGAGCC
Found at i:587030 original size:24 final size:24
Alignment explanation
Indices: 587003--587074 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
586993 TCTTAAGGTA
587003 ATCTCTTTAGTATTTGTAAAAACT
1 ATCTCTTTAGTATTTGTAAAAACT
* *
587027 ATCTATTCTA--A---GAAAAAACT
1 ATCTCTT-TAGTATTTGTAAAAACT
587047 ATCTCTTTAGTATTTGTAAAAACT
1 ATCTCTTTAGTATTTGTAAAAACT
587071 ATCT
1 ATCT
587075 GTTCTAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
19 2 0.05
20 14 0.37
21 1 0.03
23 1 0.03
24 18 0.47
25 2 0.05
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.42
Consensus pattern (24 bp):
ATCTCTTTAGTATTTGTAAAAACT
Found at i:587066 original size:44 final size:44
Alignment explanation
Indices: 587003--587089 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
586993 TCTTAAGGTA
587003 ATCTCTTTAGTATTTGTAAAAACTATCTATTCTAAGAAAAAACT
1 ATCTCTTTAGTATTTGTAAAAACTATCTATTCTAAGAAAAAACT
*
587047 ATCTCTTTAGTATTTGTAAAAACTATCTGTTCTAAGAAAAAAC
1 ATCTCTTTAGTATTTGTAAAAACTATCTATTCTAAGAAAAAAC
587090 ACTACTGTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (44 bp):
ATCTCTTTAGTATTTGTAAAAACTATCTATTCTAAGAAAAAACT
Found at i:592680 original size:20 final size:19
Alignment explanation
Indices: 592626--592686 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
592616 CCACCCTTCC
*
592626 TCCATCACCCCCCTCATCT
1 TCCATCACCCCCCTCACCT
* ** **
592645 TCCCTTTCCCTTCTCACCCT
1 TCCATCACCCCCCTCA-CCT
*
592665 TCCATCACCCCCCTCATCT
1 TCCATCACCCCCCTCACCT
592684 TCC
1 TCC
592687 CTTTCCTCCG
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.11, C:0.57, G:0.00, T:0.31
Consensus pattern (19 bp):
TCCATCACCCCCCTCACCT
Found at i:595129 original size:29 final size:29
Alignment explanation
Indices: 595086--595143 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
595076 AATTATTTTT
*
595086 TATAAAAAATGAAAAAA-AGATAAAAAAAA
1 TATAAAAAAT-AAAAAATAAATAAAAAAAA
* *
595115 TATATAAAATAAAAAATAAATAACAAAAA
1 TATAAAAAATAAAAAATAAATAAAAAAAA
595144 CATCAACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (29 bp):
TATAAAAAATAAAAAATAAATAAAAAAAA
Found at i:601388 original size:2 final size:2
Alignment explanation
Indices: 601376--601405 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
601366 TATTTATTTG
601376 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
601406 ACTTTTCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:605316 original size:190 final size:191
Alignment explanation
Indices: 604987--605368 Score: 642
Period size: 190 Copynumber: 2.0 Consensus size: 191
604977 TTTGCTTATT
* *
604987 TTGCTTGATTAGATAAATGTTTTACCATGTTTCCTCAAACTTGTATAAAAACCATGTTGGAATTT
1 TTGCTTGATTAGATAAATGTTTTACCATGTTTCCTCAAACTTGCATAAAAACCATCTTGGAATTT
*
605052 TGAGTTTACCAAAGCAATATTCTCTCATGGAGTTATCTATATCAATTTGCTATTCCGGTGCAGAG
66 TGAGTTTACCAAAGCAATATTCTCTCATAGAGTTATCTATATCAATTTGCTATTCCGGTGCAGAG
605117 TTCTTGATATTATGAGGAGAGATGCAGAG-AAAATCCTGCAACAAACCCTCATGCATTACA
131 TTCTTGATATTATGAGGAGAGATGCAGAGCAAAATCCTGCAACAAACCCTCATGCATTACA
* *
605177 TTGCTTGATTAGATGAATGTTTTA-CATTGTTTCCTCAAACTTGCATAAAAATCATCTTGGAATT
1 TTGCTTGATTAGATAAATGTTTTACCA-TGTTTCCTCAAACTTGCATAAAAACCATCTTGGAATT
* *
605241 TTGAGTTTACCAAAGCTATATTCTCTCATAGAGTTATCTATATCAATTTGCTATTCTGGTGCAGA
65 TTGAGTTTACCAAAGCAATATTCTCTCATAGAGTTATCTATATCAATTTGCTATTCCGGTGCAGA
* * * *
605306 GTTGTTGATATTATGAGGCGAGATGCAGAGCAAGATCCTGCAACAAATCCTCATGCATTACA
130 GTTCTTGATATTATGAGGAGAGATGCAGAGCAAAATCCTGCAACAAACCCTCATGCATTACA
605368 T
1 T
605369 GCTCGGCTTC
Statistics
Matches: 179, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
189 2 0.01
190 147 0.82
191 30 0.17
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (191 bp):
TTGCTTGATTAGATAAATGTTTTACCATGTTTCCTCAAACTTGCATAAAAACCATCTTGGAATTT
TGAGTTTACCAAAGCAATATTCTCTCATAGAGTTATCTATATCAATTTGCTATTCCGGTGCAGAG
TTCTTGATATTATGAGGAGAGATGCAGAGCAAAATCCTGCAACAAACCCTCATGCATTACA
Found at i:606489 original size:2 final size:2
Alignment explanation
Indices: 606482--606508 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
606472 TTAACATGCA
606482 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
606509 AGTTTTAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:619652 original size:66 final size:66
Alignment explanation
Indices: 619544--619675 Score: 210
Period size: 66 Copynumber: 2.0 Consensus size: 66
619534 ATCTTGTGTG
* *
619544 CGTAAGTGATCTTTCTGCCGAGATAGAGACTTATTATCAAGAATTTTCCAGCATTACTGCTCTTG
1 CGTAAGTGATCTTTCTGCCGAGATAGAAACTTATTATCAAGAATTTTCCAACATTACTGCTCTTG
619609 T
66 T
* * * *
619610 CGTATGTGATCTTTCTGCTGAGTTAGAAACTTATTATTAAGAATTTTCCAACATTACTGCTCTTG
1 CGTAAGTGATCTTTCTGCCGAGATAGAAACTTATTATCAAGAATTTTCCAACATTACTGCTCTTG
619675 T
66 T
619676 GAGTGTGTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (66 bp):
CGTAAGTGATCTTTCTGCCGAGATAGAAACTTATTATCAAGAATTTTCCAACATTACTGCTCTTG
T
Found at i:646501 original size:20 final size:21
Alignment explanation
Indices: 646476--646522 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
646466 GGACACAATA
*
646476 TGAAAAGATA-ATTTTTCA-TT
1 TGAAAAGACATATTTTT-ATTT
646496 TGAAAAGACATATTTTTATTT
1 TGAAAAGACATATTTTTATTT
646517 TGAAAA
1 TGAAAA
646523 TATGACGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (21 bp):
TGAAAAGACATATTTTTATTT
Found at i:648530 original size:22 final size:21
Alignment explanation
Indices: 648499--648539 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
648489 CCTTTTTTTT
648499 TTAACCCTAAACCCTAAACCAA
1 TTAACCCTAAA-CCTAAACCAA
*
648521 TTAACTCTAAACCTAAACC
1 TTAACCCTAAACCTAAACC
648540 CTATCATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (21 bp):
TTAACCCTAAACCTAAACCAA
Found at i:652829 original size:23 final size:23
Alignment explanation
Indices: 652801--652859 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
652791 CATTTTTCAC
* *
652801 TCTATAAGAAAATTTGGGTTTAC
1 TCTATAAGAAAATTTGGATTTAA
* *
652824 TTTATAAGGAAATTTGGATTTAA
1 TCTATAAGAAAATTTGGATTTAA
652847 TCTATAAAGAAAA
1 TCTAT-AAGAAAA
652860 AAGAAAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.37
Consensus pattern (23 bp):
TCTATAAGAAAATTTGGATTTAA
Found at i:669172 original size:17 final size:18
Alignment explanation
Indices: 669146--669184 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
669136 TTAAGTTTAA
*
669146 TGAAAGTGAT-CTTATGG
1 TGAAAATGATGCTTATGG
*
669163 TGAAAATGATGTTTATGG
1 TGAAAATGATGCTTATGG
669181 TGAA
1 TGAA
669185 TAGGTCTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (18 bp):
TGAAAATGATGCTTATGG
Found at i:669262 original size:62 final size:61
Alignment explanation
Indices: 669148--669264 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 61
669138 AAGTTTAATG
* * ** * *
669148 AAAGTGATCTTATGGTGAAAATGATGTTTATGGTGAATAGGTCTGATGTTAAGTTTGCGCA
1 AAAGTGATCTTATGGTGAAAATGATATTTATAGTGAATAAATCCGATATTAAGTTTGCGCA
* *
669209 AAAGTGACTTTTATGGTGAAAATGATATTTGTAGTGAATAAATCCGATATTAAGTT
1 AAAGTGA-TCTTATGGTGAAAATGATATTTATAGTGAATAAATCCGATATTAAGTT
669265 ATTACGGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
61 7 0.15
62 40 0.85
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (61 bp):
AAAGTGATCTTATGGTGAAAATGATATTTATAGTGAATAAATCCGATATTAAGTTTGCGCA
Found at i:674145 original size:37 final size:38
Alignment explanation
Indices: 674095--674171 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 38
674085 ACTTTGTAGG
674095 TTAATTTCATACTGAAATCTAAT-AAAAAAATTTATGA
1 TTAATTTCATACTGAAATCTAATAAAAAAAATTTATGA
674132 TTAATTTCATACTGAAATCTAATAAAAAAAATTTATGA
1 TTAATTTCATACTGAAATCTAATAAAAAAAATTTATGA
674170 TT
1 TT
674172 TAAAGAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
37 23 0.59
38 16 0.41
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (38 bp):
TTAATTTCATACTGAAATCTAATAAAAAAAATTTATGA
Found at i:687623 original size:164 final size:164
Alignment explanation
Indices: 687352--687684 Score: 603
Period size: 164 Copynumber: 2.0 Consensus size: 164
687342 AGCAAAGAAA
* * *
687352 CTATTAAAGCAATTGCAAGAGAGAAGTGTACATAACAAGCCAAAGAAAAAGGGAGACCCCAAGAA
1 CTATTAAAGCAACTGAAAGAGAGAAGCGTACATAACAAGCCAAAGAAAAAGGGAGACCCCAAGAA
*
687417 ATTTATTTGCTTAGCTTGCTTATAATACAAAGTTCACTTTTACCCATTATTTCTTTGAATTTTAA
66 ATTTATTTGCTTAGCTTGCTTATAACACAAAGTTCACTTTTACCCATTATTTCTTTGAATTTTAA
687482 CAAGCTTTAGATTTTAGTATTCATTTTTACCTTT
131 CAAGCTTTAGATTTTAGTATTCATTTTTACCTTT
687516 CTATTAAAGCAACTGAAAGAGAGAAGCGTACATAACAAGCCAAAGAAAAAGGGAGACCCCAAGAA
1 CTATTAAAGCAACTGAAAGAGAGAAGCGTACATAACAAGCCAAAGAAAAAGGGAGACCCCAAGAA
*
687581 ATTTATTTGCTTAGCTTGCTTATGACACAAAGTTCACTTTTACCCATTATTTCTTTGAATTTTAA
66 ATTTATTTGCTTAGCTTGCTTATAACACAAAGTTCACTTTTACCCATTATTTCTTTGAATTTTAA
* *
687646 GATGCTTTAGATTTTAGTATTCATTTTTACCTTT
131 CAAGCTTTAGATTTTAGTATTCATTTTTACCTTT
687680 CTATT
1 CTATT
687685 TCCTTCTGGT
Statistics
Matches: 162, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
164 162 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (164 bp):
CTATTAAAGCAACTGAAAGAGAGAAGCGTACATAACAAGCCAAAGAAAAAGGGAGACCCCAAGAA
ATTTATTTGCTTAGCTTGCTTATAACACAAAGTTCACTTTTACCCATTATTTCTTTGAATTTTAA
CAAGCTTTAGATTTTAGTATTCATTTTTACCTTT
Found at i:690738 original size:88 final size:88
Alignment explanation
Indices: 690573--690743 Score: 236
Period size: 88 Copynumber: 1.9 Consensus size: 88
690563 TGTTATTCAC
* * *
690573 AAATAAGAAAATGGATATATATGTATAATGTAAGATATCAAGAGTATAATCAGTTGCGATACAAG
1 AAATAAGAAAATGGATATATATGTATAATGTAAGATATCAACAGTATAAACAGTTACGATACAAG
690638 CAAAAAACAAAATAAATTCTAAT
66 CAAAAAACAAAATAAATTCTAAT
** * * * *
690661 AAATAAGACTATGGATGTTTATGTATAAATGTAAGATATTAACAGTATAAACAGTTACGGTACAA
1 AAATAAGAAAATGGATATATATGTAT-AATGTAAGATATCAACAGTATAAACAGTTACGATACAA
*
690726 G-AAAATACAAAATAAATT
65 GCAAAAAACAAAATAAATT
690744 TTAAAAGATG
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 38 0.53
89 34 0.47
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (88 bp):
AAATAAGAAAATGGATATATATGTATAATGTAAGATATCAACAGTATAAACAGTTACGATACAAG
CAAAAAACAAAATAAATTCTAAT
Found at i:703473 original size:52 final size:53
Alignment explanation
Indices: 703390--703492 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 53
703380 GGCATTACTG
*
703390 CTAATTGGTATAGACTCCATGACAGGTCAGTGCTGTGAAGGATTA-AATTCTT
1 CTAATTGCTATAGACTCCATGACAGGTCAGTGCTGTGAAGGATTAGAATTCTT
* * *
703442 CTAATTGCTATGGACTGCATGGA-AGGTCAGTGTTGTGAAGGATTAGAATTC
1 CTAATTGCTATAGACTCCAT-GACAGGTCAGTGCTGTGAAGGATTAGAATTC
703493 CAGGCCATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
52 38 0.84
53 7 0.16
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (53 bp):
CTAATTGCTATAGACTCCATGACAGGTCAGTGCTGTGAAGGATTAGAATTCTT
Found at i:706117 original size:20 final size:20
Alignment explanation
Indices: 706092--706129 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
706082 ACCTGATCTC
* *
706092 ATGCATGCATATATACATCA
1 ATGCATACATACATACATCA
706112 ATGCATACATACATACAT
1 ATGCATACATACATACAT
706130 ACATACACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (20 bp):
ATGCATACATACATACATCA
Found at i:711340 original size:2 final size:2
Alignment explanation
Indices: 711333--711366 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
711323 CCGTATCACA
711333 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
711367 TTCTTTGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:712680 original size:25 final size:24
Alignment explanation
Indices: 712637--712688 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
712627 ATAAGTAGTA
*
712637 TTTTAATTAATAAAGTTTAATTAAT
1 TTTTAATTAATAAAATTT-ATTAAT
*
712662 TTTTAATT-ATAAAAATTTATTTAT
1 TTTTAATTAAT-AAAATTTATTAAT
712686 TTT
1 TTT
712689 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTAATTAATAAAATTTATTAAT
Found at i:725624 original size:16 final size:17
Alignment explanation
Indices: 725591--725625 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
725581 CTCTTTCCAC
*
725591 TTTTCTTTTTTTGTCCT
1 TTTTCTCTTTTTGTCCT
725608 TTTTCTCTTTTTG-CCT
1 TTTTCTCTTTTTGTCCT
725624 TT
1 TT
725626 GCCCTTCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTCTCTTTTTGTCCT
Found at i:725756 original size:15 final size:15
Alignment explanation
Indices: 725710--725757 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
725700 ATTTATTCAC
*
725710 TTTTTATATTTTTAA
1 TTTTTATATTTATAA
*
725725 ATTTTAT-TTTATTTAA
1 TTTTTATATTTA--TAA
725741 TTTTTATATTTATAA
1 TTTTTATATTTATAA
725756 TT
1 TT
725758 AAAATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 3 0.11
15 11 0.41
16 9 0.33
17 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTATATTTATAA
Found at i:726681 original size:15 final size:15
Alignment explanation
Indices: 726661--726690 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
726651 TGATGTAGTC
726661 TTTAATCTAAAAAAT
1 TTTAATCTAAAAAAT
*
726676 TTTAATTTAAAAAAT
1 TTTAATCTAAAAAAT
726691 ATAACTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTAATCTAAAAAAT
Found at i:726730 original size:4 final size:4
Alignment explanation
Indices: 726706--726744 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
726696 TTGAAATATC
726706 AAAT AAAAT AAA- AATAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT -AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AA
726745 TTCAAAGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
3 2 0.06
4 24 0.75
5 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:727204 original size:17 final size:18
Alignment explanation
Indices: 727159--727204 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
727149 AAAAAAATAT
727159 TTATATATATTTTTTAACA
1 TTATA-ATATTTTTTAACA
*
727178 TTATAA-ATTTTTTACCA
1 TTATAATATTTTTTAACA
727195 TTA-AATATTT
1 TTATAATATTT
727205 AGCTTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 17 0.68
18 1 0.04
19 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATAATATTTTTTAACA
Found at i:746393 original size:22 final size:23
Alignment explanation
Indices: 746351--746401 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
746341 TTCTAACAAC
746351 TATTTTTATTATATCATAAATTT
1 TATTTTTATTATATCATAAATTT
*
746374 TATTTTTCATTTTAT-A-AAATTT
1 TATTTTT-ATTATATCATAAATTT
*
746396 AATTTT
1 TATTTT
746402 AAATTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 8 0.32
24 6 0.24
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTTTATTATATCATAAATTT
Found at i:747618 original size:28 final size:28
Alignment explanation
Indices: 747583--747650 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
747573 GGGCAGTTTG
747583 GACTAAATGTAGTCCCGTTCCCTAGGAT
1 GACTAAATGTAGTCCCGTTCCCTAGGAT
* * *
747611 GAGTAAATGTAGTCTCGTTCCCTAGGGT
1 GACTAAATGTAGTCCCGTTCCCTAGGAT
747639 GACTAAATGTAG
1 GACTAAATGTAG
747651 GTCTTTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (28 bp):
GACTAAATGTAGTCCCGTTCCCTAGGAT
Found at i:757346 original size:2 final size:2
Alignment explanation
Indices: 757339--757363 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
757329 AAATAAATAA
757339 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
757364 CTTGTCGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:773834 original size:24 final size:24
Alignment explanation
Indices: 773772--773837 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
773762 AATCAATAAG
* * *
773772 AGATAAGAGAAATTATTTTTGACA
1 AGATAAAATAAATTATTTTTAACA
* * *
773796 AGATAAGATAGATTATTTTTAATA
1 AGATAAAATAAATTATTTTTAACA
*
773820 AGGTAAAATAAATTATTT
1 AGATAAAATAAATTATTT
773838 GACATATAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.38
Consensus pattern (24 bp):
AGATAAAATAAATTATTTTTAACA
Found at i:774745 original size:28 final size:29
Alignment explanation
Indices: 774693--774748 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
774683 CGGAGAGAAG
* * *
774693 AAAATTATTATTTTATGTATTTTTTTTAA
1 AAAATTAATATTTAATGTATATTTTTTAA
774722 AAAATTAATATTTAAT-TATATTTTTTA
1 AAAATTAATATTTAATGTATATTTTTTA
774749 TATATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
AAAATTAATATTTAATGTATATTTTTTAA
Found at i:774754 original size:21 final size:21
Alignment explanation
Indices: 774729--774769 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
774719 TAAAAAATTA
* *
774729 ATATTTAATTATATTTTTTAT
1 ATATTTAAATAAATTTTTTAT
774750 ATATTTAAATAAATTTTTTA
1 ATATTTAAATAAATTTTTTA
774770 ATGTTTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTAAATAAATTTTTTAT
Found at i:775277 original size:43 final size:43
Alignment explanation
Indices: 775230--775330 Score: 193
Period size: 43 Copynumber: 2.3 Consensus size: 43
775220 TGGATTAGGG
775230 TAAGGCTTTTAAAAGTCAACACTGATTATGAGACGAATTAAGA
1 TAAGGCTTTTAAAAGTCAACACTGATTATGAGACGAATTAAGA
775273 TAAGGCTTTTAAAAGTCAACACTGATTATGAGACGAATTAAGA
1 TAAGGCTTTTAAAAGTCAACACTGATTATGAGACGAATTAAGA
*
775316 TAAGGTTTTTAAAAG
1 TAAGGCTTTTAAAAG
775331 CCAAGACGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.30
Consensus pattern (43 bp):
TAAGGCTTTTAAAAGTCAACACTGATTATGAGACGAATTAAGA
Found at i:778775 original size:28 final size:29
Alignment explanation
Indices: 778730--778793 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
778720 ACTTGAATTG
*
778730 TTATGTAAGTCTTAACAATTACATTCACA
1 TTATATAAGTCTTAACAATTACATTCACA
* *
778759 -TATATAAGTCTTAACAATTATATTCATA
1 TTATATAAGTCTTAACAATTACATTCACA
778787 TTATATA
1 TTATATA
778794 GTAATGATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 25 0.81
29 6 0.19
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (29 bp):
TTATATAAGTCTTAACAATTACATTCACA
Found at i:778823 original size:84 final size:84
Alignment explanation
Indices: 778675--778843 Score: 257
Period size: 84 Copynumber: 2.0 Consensus size: 84
778665 CTTAAATTGT
* * * *
778675 TATATAAGTTTTAACAATTATATTCACATTAGATAGTAGTGATAGACTTGAATTGTTATGTAAGT
1 TATATAAGTCTTAACAATTATATTCACATTAGATAGTAATGATAGACTTGAATTGCTATATAAGT
*
778740 CTTAACAATTACATTCACA
66 CTTAACAATCACATTCACA
* * *
778759 TATATAAGTCTTAACAATTATATTCATATTATATAGTAATGATAGACTTGGATTGCTATATAAGT
1 TATATAAGTCTTAACAATTATATTCACATTAGATAGTAATGATAGACTTGAATTGCTATATAAGT
*
778824 CTTAACAATCACATTTACA
66 CTTAACAATCACATTCACA
778843 T
1 T
778844 CAAATGTAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (84 bp):
TATATAAGTCTTAACAATTATATTCACATTAGATAGTAATGATAGACTTGAATTGCTATATAAGT
CTTAACAATCACATTCACA
Found at i:779145 original size:93 final size:93
Alignment explanation
Indices: 778986--779158 Score: 285
Period size: 93 Copynumber: 1.9 Consensus size: 93
778976 CACGTGGTTC
* * * *
778986 TAAAAAGCTTAAACTCAAGTTGTTAGTAGCAATGGACTTGAATTGTTATATAAGTCTTAACAATC
1 TAAAAAGCTCAAACTCAAGTTATTAGTAGCAATGGACTTGAATTGTTATATAAATATTAACAATC
779051 ATAATCATATTAAATAACTACATGGTCT
66 ATAATCATATTAAATAACTACATGGTCT
*
779079 TAAAAAGCTCAAACTCAAGTTATTCGTA-CTAATGGACTTGAATTGTTATATAAATATTAACAAT
1 TAAAAAGCTCAAACTCAAGTTATTAGTAGC-AATGGACTTGAATTGTTATATAAATATTAACAAT
779143 CATAATCATATTAAAT
65 CATAATCATATTAAAT
779159 GTGGAATGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
92 1 0.01
93 73 0.99
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35
Consensus pattern (93 bp):
TAAAAAGCTCAAACTCAAGTTATTAGTAGCAATGGACTTGAATTGTTATATAAATATTAACAATC
ATAATCATATTAAATAACTACATGGTCT
Found at i:794721 original size:2 final size:2
Alignment explanation
Indices: 794714--794752 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
794704 GAAGGAAAAC
794714 TA TA TA 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 TA TA TA T
794753 TCATTCATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:800827 original size:14 final size:14
Alignment explanation
Indices: 800808--800840 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
800798 CTCACATTGC
*
800808 ATTAATTTTCATTA
1 ATTAATTTTAATTA
800822 ATTAATTTTAATTA
1 ATTAATTTTAATTA
800836 ATTAA
1 ATTAA
800841 GAGTTAAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTAATTTTAATTA
Found at i:801662 original size:18 final size:19
Alignment explanation
Indices: 801634--801672 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
801624 TAATATAAAA
801634 TAATAAATAA-TATTTTAAT
1 TAATAAATAATTA-TTTAAT
801653 TAAT-AATAATTATTTAAT
1 TAATAAATAATTATTTAAT
801671 TA
1 TA
801673 TTATATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAAATAATTATTTAAT
Found at i:803360 original size:28 final size:28
Alignment explanation
Indices: 803328--803421 Score: 127
Period size: 28 Copynumber: 3.4 Consensus size: 28
803318 AAATGTAATG
*
803328 TTATATGTCATGTTTTAAAATTTAGTTA
1 TTATATGTCATGTTTAAAAATTTAGTTA
803356 TTATATGTCATG-TTAAAAATTTAGTTA
1 TTATATGTCATGTTTAAAAATTTAGTTA
** * *
803383 TTATATGTCATGTAGAAAAATGTAGTTG
1 TTATATGTCATGTTTAAAAATTTAGTTA
*
803411 TTACATGTCAT
1 TTATATGTCAT
803422 ATTTGCTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 26 0.44
28 33 0.56
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (28 bp):
TTATATGTCATGTTTAAAAATTTAGTTA
Found at i:814494 original size:21 final size:21
Alignment explanation
Indices: 814441--814495 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
814431 AAATTGCTTC
814441 AATGATCTTTGAACTTGTTAG
1 AATGATCTTTGAACTTGTTAG
* *
814462 AGTGATCCTTGAACTTGTTAG
1 AATGATCTTTGAACTTGTTAG
*
814483 AATGATTTTTGAA
1 AATGATCTTTGAA
814496 GTTGCTTAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (21 bp):
AATGATCTTTGAACTTGTTAG
Found at i:814654 original size:21 final size:22
Alignment explanation
Indices: 814610--814665 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
814600 TTTAATGATC
814610 TTTGAAGTTT-TTTGAATGAGTT
1 TTTGAA-TTTGTTTGAATGAGTT
814632 TTTGAATTTGTTTGAAT-AGTT
1 TTTGAATTTGTTTGAATGAGTT
* *
814653 TTTAAACTTGTTT
1 TTTGAATTTGTTT
814666 AAAGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.23, C:0.02, G:0.18, T:0.57
Consensus pattern (22 bp):
TTTGAATTTGTTTGAATGAGTT
Found at i:814796 original size:21 final size:21
Alignment explanation
Indices: 814703--814796 Score: 89
Period size: 21 Copynumber: 4.5 Consensus size: 21
814693 CTATGTCAAA
* * *
814703 AGTTTTAAAATTGCTTGAATT
1 AGTTTTAAACTTGTTTAAATT
* * *
814724 AGTTTTAAAATTGCTTAAACT
1 AGTTTTAAACTTGTTTAAATT
* * *
814745 ATTTTTAAACTTGTTTTAATA
1 AGTTTTAAACTTGTTTAAATT
*
814766 ATTTTTAAACTTGTTTAAATT
1 AGTTTTAAACTTGTTTAAATT
*
814787 AGTGTTAAAC
1 AGTTTTAAAC
814797 CTCCCTTGCA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (21 bp):
AGTTTTAAACTTGTTTAAATT
Found at i:814960 original size:20 final size:20
Alignment explanation
Indices: 814935--815027 Score: 89
Period size: 20 Copynumber: 4.6 Consensus size: 20
814925 AATGATTATG
*
814935 TCCAAAATGTATGGATATAT
1 TCCAAAATGTATGAATATAT
* *
814955 TCCAAAATGTATGGATACATT
1 TCCAAAATGTATGAATATA-T
* *
814976 TCCAAAATCTATTAATATAT
1 TCCAAAATGTATGAATATAT
** *
814996 TTTAAAATGTATCAATGA-AT
1 TCCAAAATGTATGAAT-ATAT
815016 TCCAAAATGTAT
1 TCCAAAATGTAT
815028 TAAAATGCAT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
20 43 0.72
21 17 0.28
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (20 bp):
TCCAAAATGTATGAATATAT
Found at i:815583 original size:28 final size:28
Alignment explanation
Indices: 815543--815619 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
815533 TTAAAGGTTG
815543 TGCTTGAACTTTGAAAAGGCAATAGTTA
1 TGCTTGAACTTTGAAAAGGCAATAGTTA
* * *
815571 TGCTTGATCTTTGAAAAGGTAATGGTTA
1 TGCTTGAACTTTGAAAAGGCAATAGTTA
*
815599 TGCTTAAACCTTT-AAAAGGCA
1 TGCTTGAA-CTTTGAAAAGGCA
815620 TTGTATTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 38 0.90
29 4 0.10
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34
Consensus pattern (28 bp):
TGCTTGAACTTTGAAAAGGCAATAGTTA
Found at i:816155 original size:14 final size:14
Alignment explanation
Indices: 816136--816164 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
816126 GCTTTGTCCT
816136 TCATCTTTGGACTA
1 TCATCTTTGGACTA
816150 TCATCTTTGGACTA
1 TCATCTTTGGACTA
816164 T
1 T
816165 TAATATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (14 bp):
TCATCTTTGGACTA
Found at i:822901 original size:8 final size:8
Alignment explanation
Indices: 822888--822934 Score: 76
Period size: 8 Copynumber: 5.9 Consensus size: 8
822878 ATAAGGGGTC
822888 AAATTATA
1 AAATTATA
*
822896 AAATTAGA
1 AAATTATA
822904 AAATTATA
1 AAATTATA
*
822912 AAATTAGA
1 AAATTATA
822920 AAATTATA
1 AAATTATA
822928 AAATTAT
1 AAATTAT
822935 TGTAGGGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (8 bp):
AAATTATA
Found at i:822909 original size:16 final size:16
Alignment explanation
Indices: 822888--822933 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
822878 ATAAGGGGTC
822888 AAATTATAAAATTAGA
1 AAATTATAAAATTAGA
822904 AAATTATAAAATTAGA
1 AAATTATAAAATTAGA
822920 AAATTATAAAATTA
1 AAATTATAAAATTA
822934 TTGTAGGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (16 bp):
AAATTATAAAATTAGA
Found at i:841372 original size:41 final size:41
Alignment explanation
Indices: 841315--841398 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
841305 TTAATGATGC
841315 ACTGCAGATTATTGTCAACTTGATCCTGGTTAGTGCAATTG
1 ACTGCAGATTATTGTCAACTTGATCCTGGTTAGTGCAATTG
* * * *
841356 ACTGCAGGTTCTTGTCAACTTGATTCTGGTTAGTGCCATTG
1 ACTGCAGATTATTGTCAACTTGATCCTGGTTAGTGCAATTG
841397 AC
1 AC
841399 CCCGGAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (41 bp):
ACTGCAGATTATTGTCAACTTGATCCTGGTTAGTGCAATTG
Found at i:842450 original size:4 final size:4
Alignment explanation
Indices: 842441--842475 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
842431 CTTTCAACTA
* *
842441 TATG TATG TATT TATG CATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
842476 TCACCCTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:845363 original size:19 final size:18
Alignment explanation
Indices: 845339--845377 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
845329 AAGTTGATGC
*
845339 TTATTTTCTATTTATTTCA
1 TTATTTTCTATCT-TTTCA
*
845358 TTATTTTTTATCTTTTCA
1 TTATTTTCTATCTTTTCA
845376 TT
1 TT
845378 TTTGAACAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTTTCTATCTTTTCA
Found at i:846306 original size:35 final size:35
Alignment explanation
Indices: 846256--846322 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
846246 GCAGGAGGTG
846256 GTATGGATTTAGTAAAATGACAAACTTTTGAACAA
1 GTATGGATTTAGTAAAATGACAAACTTTTGAACAA
* * * *
846291 GTATGGTTTTGGTAAAATGATAAAGTTTTGAA
1 GTATGGATTTAGTAAAATGACAAACTTTTGAA
846323 TCAGTTCCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (35 bp):
GTATGGATTTAGTAAAATGACAAACTTTTGAACAA
Found at i:849456 original size:3 final size:3
Alignment explanation
Indices: 849448--849475 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
849438 TTCATTCACC
849448 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
849476 ATTGGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:856260 original size:2 final size:2
Alignment explanation
Indices: 856243--856292 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
856233 GCGGATGTAT
* *
856243 GA GA AA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
856285 GA GA GA GA
1 GA GA GA GA
856293 CCCCAAAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:858415 original size:15 final size:15
Alignment explanation
Indices: 858395--858430 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
858385 GGATATTATT
*
858395 GTTTTATTATAATTA
1 GTTTTATGATAATTA
*
858410 GTTTTATGATTATTA
1 GTTTTATGATAATTA
858425 GTTTTA
1 GTTTTA
858431 AATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
GTTTTATGATAATTA
Found at i:858470 original size:17 final size:16
Alignment explanation
Indices: 858445--858481 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
858435 TAAATAATAA
858445 AATTATATTTCATTTGT
1 AATTATATTTCATTT-T
*
858462 AATTGTATTTCATTTT
1 AATTATATTTCATTTT
858478 AATT
1 AATT
858482 TAATTATGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (16 bp):
AATTATATTTCATTTT
Found at i:862572 original size:81 final size:81
Alignment explanation
Indices: 862432--862586 Score: 208
Period size: 81 Copynumber: 1.9 Consensus size: 81
862422 TTATATTGAT
*
862432 AAAAAAAAAATTATTATTACACGTTATATACAAAATCATGTTATAAATCATGGTTAAAAAAAAT-
1 AAAAAAAAAATTATTATTACACGTTATATACAAAAACATGTTATAAATCATGGTTAAAAAAAATA
862496 TGTTACACGTCATGTC
66 TGTTACACGTCATGTC
* * * *
862512 AAAAAAAAATATTATTATTACACGTTATGTATAAAAACATGTTA-CATTCAAT-GTTGAAAAAAA
1 AAAAAAAAA-ATTATTATTACACGTTATATACAAAAACATGTTATAAATC-ATGGTT-AAAAAAA
862575 ATACTGTTACAC
63 ATA-TGTTACAC
862587 TACGTTGAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
80 15 0.23
81 42 0.65
83 8 0.12
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.32
Consensus pattern (81 bp):
AAAAAAAAAATTATTATTACACGTTATATACAAAAACATGTTATAAATCATGGTTAAAAAAAATA
TGTTACACGTCATGTC
Found at i:863292 original size:14 final size:13
Alignment explanation
Indices: 863246--863295 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
863236 ATATTAAAAC
863246 TTTATTTATGTAA
1 TTTATTTATGTAA
*
863259 TTTATTTACT-TAT
1 TTTATTTA-TGTAA
863272 TTATATTTAGTGTAA
1 TT-TATTTA-TGTAA
863287 TTTATTTAT
1 TTTATTTAT
863296 TTATAACATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 13 0.42
14 14 0.45
15 4 0.13
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (13 bp):
TTTATTTATGTAA
Found at i:866310 original size:17 final size:17
Alignment explanation
Indices: 866290--866364 Score: 77
Period size: 17 Copynumber: 4.6 Consensus size: 17
866280 AGGTTTTATT
866290 TATTTATATTATTTAAC
1 TATTTATATTATTTAAC
866307 TATTTATA-TATTTAAC
1 TATTTATATTATTTAAC
**
866323 TATTTAATAAAATTT---
1 TATTT-ATATTATTTAAC
* *
866338 TATATATTTTATTTAAC
1 TATTTATATTATTTAAC
866355 TATTTATATT
1 TATTTATATT
866365 TTATGTATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.13
15 4 0.09
16 13 0.28
17 19 0.41
18 4 0.09
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTATATTATTTAAC
Found at i:866318 original size:19 final size:18
Alignment explanation
Indices: 866290--866326 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
866280 AGGTTTTATT
866290 TATT-TATATTATTTAAC
1 TATTATATATTATTTAAC
866307 TATT-TATA-TATTTAAC
1 TATTATATATTATTTAAC
866323 TATT
1 TATT
866327 TAATAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATATATTATTTAAC
Found at i:866366 original size:28 final size:30
Alignment explanation
Indices: 866315--866390 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 30
866305 ACTATTTATA
866315 TATTTAACTATTTAATAAAATTTTATATATTT
1 TATTTAACTATTTAAT--AATTTTATATATTT
* *
866347 TATTTAACTATTT-AT-ATTTTATGTATTA
1 TATTTAACTATTTAATAATTTTATATATTT
*
866375 TAGTTTTA-TATTTAAT
1 TA-TTTAACTATTTAAT
866391 GTTTTAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 18 0.46
29 6 0.15
31 2 0.05
32 13 0.33
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (30 bp):
TATTTAACTATTTAATAATTTTATATATTT
Found at i:866385 original size:22 final size:21
Alignment explanation
Indices: 866357--866401 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
866347 TATTTAACTA
*
866357 TTTATATTTTATGTATTATAGT
1 TTTATATTTAATGTATTA-AGT
*
866379 TTTATATTTAATGTTTTAAGT
1 TTTATATTTAATGTATTAAGT
866400 TT
1 TT
866402 AAACATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTATATTTAATGTATTAAGT
Found at i:867507 original size:15 final size:17
Alignment explanation
Indices: 867477--867514 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
867467 TTTCGTGCTC
*
867477 ATTTGACTTGATTTA-T
1 ATTTAACTTGATTTATT
867493 ATTTAACTT-ATTTATT
1 ATTTAACTTGATTTATT
867509 ATTTAA
1 ATTTAA
867515 AAGTAGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (17 bp):
ATTTAACTTGATTTATT
Found at i:867562 original size:13 final size:14
Alignment explanation
Indices: 867544--867577 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
867534 TAAGATTTCG
867544 TAAAAAGT-TTTTT
1 TAAAAAGTATTTTT
*
867557 TAAAAAATATTTTT
1 TAAAAAGTATTTTT
867571 TAAAAAG
1 TAAAAAG
867578 AATAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
TAAAAAGTATTTTT
Found at i:867854 original size:12 final size:12
Alignment explanation
Indices: 867837--867866 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
867827 TTATTTATTT
867837 TTTTTAATTTTA
1 TTTTTAATTTTA
867849 TTTTTAATTTTA
1 TTTTTAATTTTA
867861 TTTTTA
1 TTTTTA
867867 TCTATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTAATTTTA
Found at i:875951 original size:2 final size:2
Alignment explanation
Indices: 875944--875974 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
875934 TCAACACTTT
875944 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 T
875975 GGGTGTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:876305 original size:20 final size:20
Alignment explanation
Indices: 876260--876305 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
876250 AAATTTAATT
* *
876260 ATAAATGATATGATCTTTTG
1 ATAAATAATATGATCTTTCG
876280 AT-AATAATGATGA-CTTTCG
1 ATAAATAAT-ATGATCTTTCG
876299 ATAAATA
1 ATAAATA
876306 GTCATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (20 bp):
ATAAATAATATGATCTTTCG
Found at i:877067 original size:44 final size:45
Alignment explanation
Indices: 877017--877113 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
877007 CACGTTATGA
* * * * *
877017 TGTTACACACTACGTACAGAAACATGT-ATACACCATGGTTAGGT
1 TGTTACACACCACATACAAAAACATGTGACACACCATGGTTAGAT
* * * *
877061 TGTTACACGCCATATATAAAAACGTGTGACACACCATGGTTAGAT
1 TGTTACACACCACATACAAAAACATGTGACACACCATGGTTAGAT
877106 TGTTACAC
1 TGTTACAC
877114 GCCATGCACA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
44 20 0.47
45 23 0.53
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (45 bp):
TGTTACACACCACATACAAAAACATGTGACACACCATGGTTAGAT
Found at i:877143 original size:45 final size:45
Alignment explanation
Indices: 877036--877143 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
877026 CTACGTACAG
* * * *
877036 AAACATGT-ATACACCATGGTTAGGTTGTTACACGCCATATATAA
1 AAACATGTGACACACCATGGTTAGATTGTTACACGCCATACACAA
* *
877080 AAACGTGTGACACACCATGGTTAGATTGTTACACGCCATGCACAA
1 AAACATGTGACACACCATGGTTAGATTGTTACACGCCATACACAA
* * *
877125 AAATATGTTACACTCCATG
1 AAACATGTGACACACCATG
877144 ATTAAGTTGT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
44 7 0.13
45 46 0.87
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (45 bp):
AAACATGTGACACACCATGGTTAGATTGTTACACGCCATACACAA
Found at i:877332 original size:81 final size:81
Alignment explanation
Indices: 877164--877332 Score: 243
Period size: 81 Copynumber: 2.1 Consensus size: 81
877154 TAAATGCATG
877164 TTAAAAAAAATACTGTTGTTACACGTCATGTATCAAAATATGTTACACACCATGGTTAAAAAAAA
1 TTAAAAAAAATACTGTTGTTACACGTCATGTATCAAAATATGTTACACACCATGGTTAAAAAAAA
* * *
877229 TTGTTGCATGCCAAGT
66 TTATTACACGCCAAGT
* *
877245 TGAAAAAAAATACTGTTGTTACACGTCATGTA-CAAAAATATGTTACACGCCATGGTTAAAAAAA
1 TTAAAAAAAATACTGTTGTTACACGTCATGTATC-AAAATATGTTACACACCATGGTTAAAAAAA
* *
877309 GTTATTACACGTCATA-T
65 ATTATTACACGCCA-AGT
877326 TTAAAAA
1 TTAAAAA
877333 CATTTTGATA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
80 1 0.01
81 76 0.97
82 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (81 bp):
TTAAAAAAAATACTGTTGTTACACGTCATGTATCAAAATATGTTACACACCATGGTTAAAAAAAA
TTATTACACGCCAAGT
Found at i:878908 original size:30 final size:30
Alignment explanation
Indices: 878849--878916 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
878839 AATCATTAAC
* *
878849 TATAAAAATTTATTTGACTCCAAACAAAAA
1 TATAAAAATTTATTTAACTCAAAACAAAAA
* *
878879 TA-AAAATATTTATTTAACTTAAAATAAAAA
1 TATAAAA-ATTTATTTAACTCAAAACAAAAA
878909 TATAAAAA
1 TATAAAAA
878917 CTTGATTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.12
30 24 0.75
31 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.32
Consensus pattern (30 bp):
TATAAAAATTTATTTAACTCAAAACAAAAA
Done.