Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008627.1 Hibiscus syriacus cultivar Beakdansim tig00111594_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: 1073793
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 3 of 6
Found at i:438763 original size:24 final size:24
Alignment explanation
Indices: 438736--438784 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
438726 CGTTCATTTA
*
438736 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
438760 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
438784 C
1 C
438785 ATTTATGTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.10, C:0.16, G:0.27, T:0.47
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:438774 original size:14 final size:14
Alignment explanation
Indices: 438746--438784 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
438736 CGTTCGTGAA
438746 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
438760 CG-T---TTATGTT
1 CGTTCGGTTATGTT
438770 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
438784 C
1 C
438785 ATTTATGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
10 9 0.43
11 1 0.05
13 1 0.05
14 10 0.48
ACGTcount: A:0.08, C:0.15, G:0.26, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:438789 original size:24 final size:24
Alignment explanation
Indices: 438746--438807 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
438736 CGTTCGTGAA
* *
438746 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCATTTATGTG
438770 CGTTCGGTTATGTTCATTTATGTG
1 CGTTCGGTTATGTTCATTTATGTG
**
438794 CGTTCATTTATGTT
1 CGTTCGGTTATGTT
438808 TAACCCAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.11, C:0.13, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCATTTATGTG
Found at i:440391 original size:16 final size:16
Alignment explanation
Indices: 440370--440410 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
440360 GTCTCCAACG
*
440370 TTTATGTTTGTGTTCA
1 TTTATGTTCGTGTTCA
**
440386 TTTATGTTCGTGTTTG
1 TTTATGTTCGTGTTCA
440402 TTTATGTTC
1 TTTATGTTC
440411 ATTTATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.10, C:0.07, G:0.20, T:0.63
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:443651 original size:8 final size:8
Alignment explanation
Indices: 443638--443662 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
443628 CTGCAGCTAG
443638 TGTTGTAA
1 TGTTGTAA
443646 TGTTGTAA
1 TGTTGTAA
443654 TGTTGTAA
1 TGTTGTAA
443662 T
1 T
443663 ATTAAGGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (8 bp):
TGTTGTAA
Found at i:447026 original size:15 final size:15
Alignment explanation
Indices: 447006--447039 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
446996 TTTGGCTAAG
447006 CAAGGAGCTCAATTT
1 CAAGGAGCTCAATTT
447021 CAAGGAGCTCAATTT
1 CAAGGAGCTCAATTT
447036 CAAG
1 CAAG
447040 ATTCAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (15 bp):
CAAGGAGCTCAATTT
Found at i:449363 original size:25 final size:25
Alignment explanation
Indices: 449292--449371 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
449282 TCGTAGATAT
*
449292 ATTTGCACTCGAAAGTGCCTCGTAG
1 ATTTGCACTCGAAAGTGCCTTGTAG
* *
449317 AATTGCACTGGAAAGTGCCTTGTAG
1 ATTTGCACTCGAAAGTGCCTTGTAG
* *
449342 ATTTGCACTCGAAAGTGACTTGTGG
1 ATTTGCACTCGAAAGTGCCTTGTAG
449367 ATTTG
1 ATTTG
449372 TACCAGAGGT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (25 bp):
ATTTGCACTCGAAAGTGCCTTGTAG
Found at i:453090 original size:12 final size:12
Alignment explanation
Indices: 453036--453091 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
453026 TAAAAAATAT
453036 ATTAATTATAAA
1 ATTAATTATAAA
453048 A-T-ATTATAAAA
1 ATTAATTAT-AAA
* *
453059 ATGTATTTATAAC
1 AT-TAATTATAAA
*
453072 ATAAATTATAAA
1 ATTAATTATAAA
453084 ATTAATTA
1 ATTAATTA
453092 AAATATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
10 5 0.15
11 5 0.15
12 15 0.44
13 5 0.15
14 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (12 bp):
ATTAATTATAAA
Found at i:453576 original size:15 final size:15
Alignment explanation
Indices: 453556--453585 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
453546 GAATACCATT
*
453556 AATTTAATTTATAAA
1 AATTTAAATTATAAA
453571 AATTTAAATTATAAA
1 AATTTAAATTATAAA
453586 GGACTTACTG
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTAAATTATAAA
Found at i:456789 original size:47 final size:45
Alignment explanation
Indices: 456696--456827 Score: 142
Period size: 47 Copynumber: 2.9 Consensus size: 45
456686 GTAACCATGC
* * * * * *
456696 AAATAAGCTTATGAGCTTA-CGAAT-AATGGCAAGTATATAGGAA
1 AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGAA
*
456739 AAATAAACTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAACTTACGAGCTTATGGAA--TAAATGGTAAGTATTTTGGAA
* *
456786 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGATATTTT
1 AAATAAACTTACGAGCTTATGGAATAAATGGTAAG-TATTTT
456828 ATATTATTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
43 17 0.23
44 3 0.04
45 11 0.15
46 7 0.09
47 37 0.49
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (45 bp):
AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGAA
Found at i:459383 original size:17 final size:16
Alignment explanation
Indices: 459345--459424 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 16
459335 TATATATTAT
459345 AAGAAGAAGAAAAAAC-
1 AAGAAGAA-AAAAAACG
459361 -AGAAGAAAAAAAACAG
1 AAGAAGAAAAAAAAC-G
*
459377 AAGAAGAAAAAAAATAG
1 AAGAAGAAAAAAAA-CG
*
459394 AAAAAGAAAATGAAAACG
1 AAGAAGAAAA--AAAACG
459412 AAGAAGAAAAAAA
1 AAGAAGAAAAAAA
459425 TGAAAACGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.13
15 7 0.13
16 3 0.06
17 23 0.43
18 10 0.19
19 4 0.07
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.03
Consensus pattern (16 bp):
AAGAAGAAAAAAAACG
Found at i:459395 original size:14 final size:15
Alignment explanation
Indices: 459346--459388 Score: 79
Period size: 14 Copynumber: 2.9 Consensus size: 15
459336 ATATATTATA
459346 AGAAGAAGAAAAAAC
1 AGAAGAAGAAAAAAC
459361 AGAAGAA-AAAAAAC
1 AGAAGAAGAAAAAAC
459375 AGAAGAAGAAAAAA
1 AGAAGAAGAAAAAA
459389 AATAGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.77, C:0.05, G:0.19, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAAAAAC
Found at i:459415 original size:35 final size:34
Alignment explanation
Indices: 459363--459460 Score: 114
Period size: 34 Copynumber: 2.9 Consensus size: 34
459353 GAAAAAACAG
459363 AAGAAAA-AAAACAGAAGAAGAAAAAAAATAGAAA
1 AAGAAAAGAAAAC-GAAGAAGAAAAAAAATAGAAA
459397 AAGAAAATGAAAACGAAGAAG-AAAAAAAT-GAAA
1 AAGAAAA-GAAAACGAAGAAGAAAAAAAATAGAAA
* *
459430 ACGAGAAAGAAAAC-AAAAAGAGAAAAAAATA
1 AAGA-AAAGAAAACGAAGAAGA-AAAAAAATA
459461 TTTCACTTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
32 5 0.09
33 13 0.23
34 26 0.46
35 7 0.12
36 5 0.09
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (34 bp):
AAGAAAAGAAAACGAAGAAGAAAAAAAATAGAAA
Found at i:459436 original size:20 final size:22
Alignment explanation
Indices: 459392--459442 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
459382 GAAAAAAAAT
*
459392 AGAAA-AAGAAAATGAAAACGA
1 AGAAAGAAAAAAATGAAAACGA
459413 AG-AAGAAAAAAATGAAAACG-
1 AGAAAGAAAAAAATGAAAACGA
459433 AGAAAGAAAA
1 AGAAAGAAAA
459443 CAAAAAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.73, C:0.04, G:0.20, T:0.04
Consensus pattern (22 bp):
AGAAAGAAAAAAATGAAAACGA
Found at i:459447 original size:17 final size:16
Alignment explanation
Indices: 459354--459458 Score: 56
Period size: 17 Copynumber: 6.4 Consensus size: 16
459344 TAAGAAGAAG
*
459354 AAAAAAC-AGAAGA-A
1 AAAAAACAAAAAGAGA
*
459368 AAAAAACAGAAGAAGAAA
1 AAAAAACA-AA-AAGAGA
*
459386 AAAAATAGAAAAAGA-A
1 AAAAA-ACAAAAAGAGA
*
459402 AATGAAAACGAAGAAGA-A
1 AA--AAAAC-AAAAAGAGA
** *
459420 AAAAATGAAAACGAGA
1 AAAAAACAAAAAGAGA
459436 AAGAAAACAAAAAGAGA
1 AA-AAAACAAAAAGAGA
459453 AAAAAA
1 AAAAAA
459459 TATTTCACTT
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
14 7 0.10
15 5 0.07
16 14 0.20
17 22 0.31
18 20 0.29
19 2 0.03
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAAACAAAAAGAGA
Found at i:462596 original size:126 final size:126
Alignment explanation
Indices: 462444--462679 Score: 463
Period size: 126 Copynumber: 1.9 Consensus size: 126
462434 GAAGATTGAA
462444 ATGATTGGTGATTTAAGTACAATAATTGCATAGTTGGGGTACTTAAATGTATTTATGCTTTTGTA
1 ATGATTGGTGATTTAAGTACAATAATTGCATAGTTGGGGTACTTAAATGTATTTATGCTTTTGTA
*
462509 AAAGCATTTGAATGGAAATAATTTTAATGTTGGAATTATTGGCATTAAGAATTTAAGTGGT
66 AAAGCATTTGAATGGAAATAATTTCAATGTTGGAATTATTGGCATTAAGAATTTAAGTGGT
462570 ATGATTGGTGATTTAAGTACAATAATTGCATAGTTGGGGTACTTAAATGTATTTATGCTTTTGTA
1 ATGATTGGTGATTTAAGTACAATAATTGCATAGTTGGGGTACTTAAATGTATTTATGCTTTTGTA
462635 AAAGCATTTGAATGGAAATAATTTCAATGTTGGAATTATTGGCAT
66 AAAGCATTTGAATGGAAATAATTTCAATGTTGGAATTATTGGCAT
462680 AAAAATGGTG
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 109 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (126 bp):
ATGATTGGTGATTTAAGTACAATAATTGCATAGTTGGGGTACTTAAATGTATTTATGCTTTTGTA
AAAGCATTTGAATGGAAATAATTTCAATGTTGGAATTATTGGCATTAAGAATTTAAGTGGT
Found at i:463669 original size:47 final size:45
Alignment explanation
Indices: 463575--463700 Score: 137
Period size: 47 Copynumber: 2.8 Consensus size: 45
463565 GTAACCATGC
* * * *
463575 AAATAAGCTTATGAGCTTACGAAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * * * *
463619 AAATAAGTTTGCGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
463666 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
463701 AGATTTTATA
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
44 19 0.28
45 11 0.16
46 1 0.01
47 36 0.54
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:464461 original size:19 final size:20
Alignment explanation
Indices: 464407--464463 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
464397 GTGTTACATA
464407 GGTA-CCCCT-GGGGGAATC
1 GGTACCCCCTGGGGGGAATC
* *
464425 TGTTCCCCCTGGGGGGGAAT-
1 GGTACCCCCT-GGGGGGAATC
464445 GGTACCCCCTGGGGGGAAT
1 GGTACCCCCTGGGGGGAAT
464464 ATGTACCCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.06
19 14 0.44
20 8 0.25
21 8 0.25
ACGTcount: A:0.14, C:0.26, G:0.40, T:0.19
Consensus pattern (20 bp):
GGTACCCCCTGGGGGGAATC
Found at i:464469 original size:20 final size:19
Alignment explanation
Indices: 464411--464472 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
464401 TACATAGGTA
*
464411 CCCCT-GGGGGAATCTGTTC
1 CCCCTGGGGGGAAT-TGTAC
*
464430 CCCCTGGGGGGGAATGGTAC
1 CCCCT-GGGGGGAATTGTAC
464450 CCCCTGGGGGGAATATGTAC
1 CCCCTGGGGGGAAT-TGTAC
464470 CCC
1 CCC
464473 ATGGACAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 14 0.38
20 15 0.41
21 8 0.22
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.19
Consensus pattern (19 bp):
CCCCTGGGGGGAATTGTAC
Found at i:464472 original size:19 final size:18
Alignment explanation
Indices: 464408--464472 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
464398 TGTTACATAG
464408 GTACCCCT-GGGGGAATCT
1 GTACCCCTGGGGGGAAT-T
* *
464426 GTTCCCCCTGGGGGGGAATG
1 G-TACCCCT-GGGGGGAATT
464446 GTACCCCCTGGGGGGAATAT
1 GTA-CCCCTGGGGGGAAT-T
464466 GTACCCC
1 GTACCCC
464473 ATGGACAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
18 1 0.03
19 20 0.53
20 9 0.24
21 8 0.21
ACGTcount: A:0.15, C:0.29, G:0.35, T:0.20
Consensus pattern (18 bp):
GTACCCCTGGGGGGAATT
Found at i:465984 original size:18 final size:17
Alignment explanation
Indices: 465963--466022 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 17
465953 AATTATATCT
465963 ATATTTATATTTATAAAA
1 ATATTTA-ATTTATAAAA
*
465981 ATATATTAATTATAATATAA
1 ATAT-TTAATT-T-ATAAAA
466001 AT-TTTAAATATTATAAAA
1 ATATTT-AAT-TTATAAAA
466019 ATAT
1 ATAT
466023 ATTTGTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
18 16 0.47
19 10 0.29
20 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTTAATTTATAAAA
Found at i:466384 original size:30 final size:30
Alignment explanation
Indices: 466348--466407 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
466338 ATTCTTCCAA
466348 AGTTTCATATCTTTCGGTTGAGTACAATCT
1 AGTTTCATATCTTTCGGTTGAGTACAATCT
466378 AGTTTCATATCTTTCGGTTGAGTACAATCT
1 AGTTTCATATCTTTCGGTTGAGTACAATCT
466408 CTTGAGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (30 bp):
AGTTTCATATCTTTCGGTTGAGTACAATCT
Found at i:467478 original size:39 final size:39
Alignment explanation
Indices: 467434--467528 Score: 122
Period size: 39 Copynumber: 2.5 Consensus size: 39
467424 AAGTTAAAAG
* *
467434 AATAATTTAAGAAATTAACAATTTAGAA-GATTATGGTGA
1 AATAATTTAAGAAATTAACAATTTAGAATG-TTAGGGTCA
* *
467473 AATAATTTAAGAAAATAAGAATTTAGAATGTTAGGGTCA
1 AATAATTTAAGAAATTAACAATTTAGAATGTTAGGGTCA
*
467512 AATAATTTGAG-AATTAA
1 AATAATTTAAGAAATTAA
467529 GAATAAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
38 5 0.10
39 43 0.88
40 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (39 bp):
AATAATTTAAGAAATTAACAATTTAGAATGTTAGGGTCA
Found at i:468426 original size:29 final size:29
Alignment explanation
Indices: 468383--468440 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
468373 ACTTAAACGA
468383 GATTTTTCATAGTAAAAGTTAGCAATTTG
1 GATTTTTCATAGTAAAAGTTAGCAATTTG
*
468412 GATTTTTCATTGTAAAAGTTAGCAATTTG
1 GATTTTTCATAGTAAAAGTTAGCAATTTG
468441 AGCTTTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (29 bp):
GATTTTTCATAGTAAAAGTTAGCAATTTG
Found at i:469596 original size:24 final size:25
Alignment explanation
Indices: 469569--469622 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
469559 TTTTATCCAT
* *
469569 TATTTTTTGTTATCA-TTAATTTCA
1 TATTATTTGTTATCATTTAATTTAA
469593 TATTATTTGTTATCATTTAATTTAA
1 TATTATTTGTTATCATTTAATTTAA
469618 TATTA
1 TATTA
469623 AATTCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.61
Consensus pattern (25 bp):
TATTATTTGTTATCATTTAATTTAA
Found at i:469679 original size:19 final size:18
Alignment explanation
Indices: 469655--469721 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 18
469645 GAATAGCAAG
469655 TTAAAATTAAGCATCAAAA
1 TTAAAATTAAG-ATCAAAA
*
469674 TTAAAATTAATGATCAATA
1 TTAAAATTAA-GATCAAAA
*
469693 TTAAAATTTACGTATCAAAA
1 TTAAAA-TTAAG-ATCAAAA
*
469713 TTAATATTA
1 TTAAAATTA
469722 TCATGATTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 26 0.63
20 15 0.37
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.36
Consensus pattern (18 bp):
TTAAAATTAAGATCAAAA
Found at i:472240 original size:78 final size:81
Alignment explanation
Indices: 472157--472304 Score: 205
Period size: 82 Copynumber: 1.9 Consensus size: 81
472147 AAGTAAAAGA
* *
472157 TATTTATTATATTTTTAAA-TT-AATATT-AAATATA-TTAAAAGAATATCAATATATTTTTGAA
1 TATTTATTATATTTTTAAATTTAAATATTAAAAGATATTTAAAA-AATATCAATATATTTTTAAA
472218 TATTTTAAATTAGTAGG
65 TATTTTAAATTAGTAGG
* * *
472235 TATTTATTATCTTTTTAAATTTAAATATTAAAAAGATATTTAAAATATATCAATATCTTTTTAAA
1 TATTTATTATATTTTTAAATTTAAATATT-AAAAGATATTTAAAAAATATCAATATATTTTTAAA
472300 TATTT
65 TATTT
472305 AATTAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
78 18 0.30
79 2 0.03
80 6 0.10
82 28 0.47
83 6 0.10
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (81 bp):
TATTTATTATATTTTTAAATTTAAATATTAAAAGATATTTAAAAAATATCAATATATTTTTAAAT
ATTTTAAATTAGTAGG
Found at i:476075 original size:29 final size:29
Alignment explanation
Indices: 476042--476129 Score: 149
Period size: 29 Copynumber: 3.0 Consensus size: 29
476032 AGTCCATTAT
476042 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
476071 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
* * *
476100 TCATTTACTCAATAGTGTTTAACCATTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
476129 T
1 T
476130 TAACGGCATA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (29 bp):
TCTTTTACTCAACAGTGTTTAACCGTTCA
Found at i:476239 original size:81 final size:80
Alignment explanation
Indices: 476103--476423 Score: 434
Period size: 81 Copynumber: 4.0 Consensus size: 80
476093 CCGTTCATCA
* * *
476103 TTTACTCAATAGTGTTTAACCATTCATTAAC-GGCATAATTGGCACCTTTCTGCCAAATGCACAG
1 TTTACTCAATAGTATTTAACCATTCATTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAA
476167 CTAGGCCATTATTCT
66 CTAGGCCATTATTCT
* ** *
476182 TTTACTCAACAGTATTTAATTATTCATATAACTGGCATAATTGACACATTTCTGCCAAATGCACA
1 TTTACTCAATAGTATTTAACCATTCAT-TAACTGGCATAATTGACACCTTTCTGCCAAATGCACA
* *
476247 GCTAGGCCTTTATTCT
65 ACTAGGCCATTATTCT
* *
476263 TTTACTCAATGGTATTTAACCGTTCATTTAACTGGCATAATTGACACCTTTCAT-CCAAATGCAC
1 TTTACTCAATAGTATTTAACCATTCA-TTAACTGGCATAATTGACACCTTTC-TGCCAAATGCAC
476327 AACTAGGCCATTATTCT
64 AACTAGGCCATTATTCT
* * * *
476344 TTTACTCAATGGTATTTAACCGTT-ATCTAACTGGCGTAATTGACACCTTTCTG-CAAATGCAAA
1 TTTACTCAATAGTATTTAACCATTCAT-TAACTGGCATAATTGACACCTTTCTGCCAAATGCACA
*
476407 ACTAGGTCATTATTCT
65 ACTAGGCCATTATTCT
476423 T
1 T
476424 GTTGAAAACA
Statistics
Matches: 218, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
79 50 0.23
80 28 0.13
81 138 0.63
82 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (80 bp):
TTTACTCAATAGTATTTAACCATTCATTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAA
CTAGGCCATTATTCT
Found at i:476759 original size:19 final size:19
Alignment explanation
Indices: 476735--476773 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
476725 TCGAATGCAT
476735 TCCATGCACCAATGCACTC
1 TCCATGCACCAATGCACTC
* *
476754 TCCATGCATCGATGCACTC
1 TCCATGCACCAATGCACTC
476773 T
1 T
476774 GAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (19 bp):
TCCATGCACCAATGCACTC
Found at i:476870 original size:63 final size:65
Alignment explanation
Indices: 476721--476878 Score: 187
Period size: 65 Copynumber: 2.5 Consensus size: 65
476711 GAATTAATTG
* * * *** *
476721 AACATCGAATGCATTCCATGCACCAATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
476786 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATC-ATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
476848 A
65 A
*
476849 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
476879 TCCTTAGTGC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
63 34 0.42
64 11 0.14
65 36 0.44
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:478410 original size:117 final size:118
Alignment explanation
Indices: 478199--478412 Score: 265
Period size: 117 Copynumber: 1.8 Consensus size: 118
478189 ATCTTATTTT
*
478199 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGGAGTTAGAGCTTTCAAAAA
1 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGAAGTTAGAGCTTTCAAAAA
*
478264 TAAAATCGGAAAACTTTGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
66 TAAAATCGGAAAACTTGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
* * * * *
478317 GAAA-CTAAAATGGATTTTGAAAA-ACAAAATGAAAT-TTCGAAGAAGAATTTAGAGCTTTCAAA
1 GAAAGCTAAAAAGGACTTGGAAAATA-AAAATGAAATGTT-GAAAAAGAAGTTAGAGCTTTCAAA
* ** * *
478379 GATAAAATTTG-AAAGTATGGAAAAGGAAATTTTC
64 AATAAAATCGGAAAACT-TGGAAAAAGAAATTTTC
478413 GATTTAGAAG
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
116 7 0.09
117 70 0.86
118 4 0.05
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (118 bp):
GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGAAGTTAGAGCTTTCAAAAA
TAAAATCGGAAAACTTGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
Found at i:483429 original size:31 final size:31
Alignment explanation
Indices: 483358--483437 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
483348 ATTTAACAAA
* * **
483358 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
483389 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
483420 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
483438 CAAAATCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:483853 original size:19 final size:19
Alignment explanation
Indices: 483829--483867 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
483819 TCGAATGTAT
483829 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
483848 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
483867 T
1 T
483868 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:483884 original size:65 final size:64
Alignment explanation
Indices: 483766--483973 Score: 183
Period size: 65 Copynumber: 3.2 Consensus size: 64
483756 TATTCAAAGG
* * *
483766 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGT
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
483827 ATTC
61 ATTT
*
483831 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATTGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
483896 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
* *
483960 TATGCATCGATGCA
1 CATGCACCGATGCA
483974 TCCTTAGTGT
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
63 7 0.06
64 50 0.41
65 63 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:483970 original size:64 final size:65
Alignment explanation
Indices: 483815--483973 Score: 187
Period size: 65 Copynumber: 2.5 Consensus size: 65
483805 GAATTAATTG
* * * *** *
483815 AACATCGAATGTATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* * **
483880 AACATTGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
483943 A
65 A
*
483944 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
483974 TCCTTAGTGT
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 33 0.41
65 47 0.59
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:484999 original size:81 final size:81
Alignment explanation
Indices: 484679--484991 Score: 473
Period size: 81 Copynumber: 3.9 Consensus size: 81
484669 TAACTCAACA
*
484679 ATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTCTGCCAAAT
1 ATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAAT
* *
484744 GCATAGCTAGACCATT
66 GCACAGCTAGGCCATT
* * *
484760 ATTCTTTTAATCAACGGTATTTAACCGTTCAACTAACTAGCATAATTGACACCTTTCTGCCAAAT
1 ATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAAT
484825 GCACAGCTAGGCCATT
66 GCACAGCTAGGCCATT
* * * *
484841 ATTCTTTTACTCAACGGTATTTAACCATTAATCTAACTGGCGTAATTGACACCTTTCTTCCAAAT
1 ATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAAT
*
484906 GCATAGCTAGGCCATT
66 GCACAGCTAGGCCATT
** * * * *
484922 ATTCTTTTACTCAACTATATTTAACCGTTCATCTAACTGGCATAATTTACACCTGTCTGTCAATT
1 ATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAAT
484987 GCACA
66 GCACA
484992 ATTAGGCCTC
Statistics
Matches: 207, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 207 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (81 bp):
ATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAAT
GCACAGCTAGGCCATT
Found at i:485154 original size:67 final size:68
Alignment explanation
Indices: 484949--485338 Score: 536
Period size: 68 Copynumber: 5.8 Consensus size: 68
484939 TATTTAACCG
* * * * * * *
484949 TTCATCTAACTGGCATAATTTACACCTGTCTGTCAATTGCACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGACATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
485014 CCT
66 CCT
* * * * *
485017 TTAATCTAACTTG-CATAAATGACACATTTATATCAAATGCATAGTTAGTCCTCAAAGGCACTTA
1 TTCATCTAAC-TGACATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
485081 GCCT
65 GCCT
* * *
485085 TTCATCTAACTGACATAAATGATAC-TTTTTGTCAAATGCACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGACATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
485149 CCT
66 CCT
485152 TTCATCTAACTGACATAAATGACAC-TTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGACATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
485216 CCT
66 CCT
* * * *
485219 TTCATCTAACTGGCATGAATGACACCATTT-TTTAAAATGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGACATAAATGACA-CATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
485283 GCCT
65 GCCT
* * *
485287 TTCATTTAACTGGCATAAATGACACATTTCTATCAAATGCACAGTTAGGCCT
1 TTCATCTAACTGACATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCT
485339 ATTAATATTT
Statistics
Matches: 288, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
67 130 0.45
68 153 0.53
69 5 0.02
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGACATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:485174 original size:135 final size:136
Alignment explanation
Indices: 484949--485338 Score: 556
Period size: 135 Copynumber: 2.9 Consensus size: 136
484939 TATTTAACCG
* * * * * * *
484949 TTCATCTAACTGGCATAATTTACACC-TGTCTGTCAATTGCACAATTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGACATAAATGACACCATTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
* * * *
485013 GCCTTTAATCTAACTTGCATAAATGACACATTTATATCAAATGCATAGTTAGTCCTCAAAGGCAC
66 GCCTTTCATCTAAC-TGCATAAATGACACATTTCTATCAAATGCACAGTTAGGCCTCAAAGGCAC
485078 TTAGCCT
130 TTAGCCT
* *
485085 TTCATCTAACTGACATAAATGATA-C-TTTTTGTCAAATGCACAGTTAGGCCTCAAAGACACTTA
1 TTCATCTAACTGACATAAATGACACCATTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
*
485148 GCCTTTCATCTAACTGACATAAATGACAC-TTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCAC
66 GCCTTTCATCTAACTG-CATAAATGACACATTTCTATCAAATGCACAGTTAGGCCTCAAAGGCAC
485212 TTAGCCT
130 TTAGCCT
* * *
485219 TTCATCTAACTGGCATGAATGACACCATTTTT-TAAAATGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGACATAAATGACACCATTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
*
485283 GCCTTTCATTTAACTGGCATAAATGACACATTTCTATCAAATGCACAGTTAGGCCT
66 GCCTTTCATCTAACT-GCATAAATGACACATTTCTATCAAATGCACAGTTAGGCCT
485339 ATTAATATTT
Statistics
Matches: 228, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
134 61 0.27
135 116 0.51
136 51 0.22
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (136 bp):
TTCATCTAACTGACATAAATGACACCATTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
GCCTTTCATCTAACTGCATAAATGACACATTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACT
TAGCCT
Found at i:485615 original size:54 final size:55
Alignment explanation
Indices: 485549--485695 Score: 192
Period size: 55 Copynumber: 2.7 Consensus size: 55
485539 ACATATATTT
* *
485549 CCCATACGGAAATTCATACAATTGGTATGAATTTCTTAG-TTTGCACACATAA-TG
1 CCCATACAGAAATTCATACACTTGGTATGAATTTCTTAGTTTTGCACACA-AAGTG
* *
485603 CCCATACAGAAATTCATACACTTAGG-ATGAATTTCTTAGTTTTTCACACAAAGTT
1 CCCATACAGAAATTCATACACTT-GGTATGAATTTCTTAGTTTTGCACACAAAGTG
* * *
485658 CCCATATAGAAAATCATACACTTAGTATGAATTTCTTA
1 CCCATACAGAAATTCATACACTTGGTATGAATTTCTTA
485696 AGTATTTTCA
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
54 37 0.45
55 45 0.55
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (55 bp):
CCCATACAGAAATTCATACACTTGGTATGAATTTCTTAGTTTTGCACACAAAGTG
Found at i:485676 original size:55 final size:55
Alignment explanation
Indices: 485535--485708 Score: 210
Period size: 54 Copynumber: 3.1 Consensus size: 55
485525 CTTCTGAATA
* * * *
485535 TTTCACATATATTTCCCATACGGAAATTCATACAATT-GGTATGAATTTCTTAG-T
1 TTTCACACATAATTCCCATACAGAAATTCATACACTTAGG-ATGAATTTCTTAGTT
* *
485589 TTGCACACATAATGCCCATACAGAAATTCATACACTTAGGATGAATTTCTTAGTT
1 TTTCACACATAATTCCCATACAGAAATTCATACACTTAGGATGAATTTCTTAGTT
* * *
485644 TTTCACACA-AAGTTCCCATATAGAAAATCATACACTTAGTATGAATTTCTTAAGTAT
1 TTTCACACATAA-TTCCCATACAGAAATTCATACACTTAGGATGAATTTCTT-AGT-T
485701 TTTCACAC
1 TTTCACAC
485709 TTAGTGCCAT
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
54 46 0.44
55 46 0.44
56 3 0.03
57 9 0.09
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (55 bp):
TTTCACACATAATTCCCATACAGAAATTCATACACTTAGGATGAATTTCTTAGTT
Found at i:489598 original size:29 final size:29
Alignment explanation
Indices: 489561--489621 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
489551 AGTCCATTAT
*
489561 TCTTTTACTCAACAGTGTTTAACAATTCA
1 TCTTTTACTCAACAGTATTTAACAATTCA
* *
489590 TCTTTTACTCAACGGTATTTAACCATTCA
1 TCTTTTACTCAACAGTATTTAACAATTCA
489619 TCT
1 TCT
489622 AACTAGCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.43
Consensus pattern (29 bp):
TCTTTTACTCAACAGTATTTAACAATTCA
Found at i:489673 original size:110 final size:110
Alignment explanation
Indices: 489480--489702 Score: 279
Period size: 110 Copynumber: 2.0 Consensus size: 110
489470 ATTCTTTTAT
* * * * **
489480 TCTTTTACCCAAAGGTATTTAGCCTTTCATCTAACTTGCATATTTAACACTTTTATGTCAAATGC
1 TCTTTTACCCAAAGGTATTTAACCATTCATCTAACTAGCATATTAAACACTTTTATACCAAATGC
* * *
489545 ATAACTAGTCCATTATTCTTTTACTCAACAGTGTTTAACAATTCA
66 ACAACTAGGCCATTATTCTTTTACTCAACAGTATTTAACAATTCA
* *
489590 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGAAAC-CTTTT-TACCAAAT
1 TCTTTTACCCAAAGGTATTTAACCATTCATCTAACTAGCAT-ATT-AAACACTTTTATACCAAAT
* * **
489653 GCACAGCTAGGCCATTATTCTTTTACTCAACTGTATTTAACCGTTCA
64 GCACAACTAGGCCATTATTCTTTTACTCAACAGTATTTAACAATTCA
489700 TCT
1 TCT
489703 AACTTCCATA
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
110 85 0.89
111 8 0.08
112 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (110 bp):
TCTTTTACCCAAAGGTATTTAACCATTCATCTAACTAGCATATTAAACACTTTTATACCAAATGC
ACAACTAGGCCATTATTCTTTTACTCAACAGTATTTAACAATTCA
Found at i:489679 original size:81 final size:81
Alignment explanation
Indices: 489590--489978 Score: 521
Period size: 81 Copynumber: 4.8 Consensus size: 81
489580 TAACAATTCA
* *
489590 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGAAACCTTTTTACCAAATGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGC
489655 ACAGCTAGGCCATTAT
66 ACAGCTAGGCCATTAT
* * ** **
489671 TCTTTTACTCAACTGTATTTAACCGTTCATCTAACTTCCATAATTGACACCTTT-TGTCAAATGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGC
* *
489735 ATAACTAGGCCATTAT
66 ACAGCTAGGCCATTAT
* * * * *
489751 TATTTTACTCAATGGTATTTAACCATTCATCTAACTAGCATAATTGACACATTTATGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGC
*
489816 ACAGCTAGGGCATTAT
66 ACAGCTAGGCCATTAT
* **
489832 TCTTTTACTCTAACGGTATTTAACCGTTCATCTAACT-GCATAATTGACACCTTTCTGGCAAATG
1 TCTTTTACTC-AACGGTATTTAACCATTCATCTAACTAGCATAATTGACACCTTTCTACCAAATG
* *
489896 CACAGTTAGACCATTAT
65 CACAGCTAGGCCATTAT
* * * * *
489913 TCTTTTACTCAACGATATTAAACCATTCATCTAACTGGCATAATTGACACATTTCTATCAAATGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGC
489978 A
66 A
489979 TAATTAGGCC
Statistics
Matches: 270, Mismatches: 35, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
80 92 0.34
81 154 0.57
82 24 0.09
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGC
ACAGCTAGGCCATTAT
Found at i:489956 original size:162 final size:161
Alignment explanation
Indices: 489590--489978 Score: 582
Period size: 162 Copynumber: 2.4 Consensus size: 161
489580 TAACAATTCA
* * *
489590 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGAAACCTTTTTACCAAATGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGACACATTTATACCAAATGC
*
489655 ACAGCTAGGCCATTATTCTTTTACTCAACTGTATTTAACCGTTCATCTAACTTCCATAATTGACA
66 ACAGCTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTTCCATAATTGACA
* * *
489720 CCTTTTGTCAAATGCATAACTAGGCCATTAT
131 CCTTTTGGCAAATGCACAACTAGACCATTAT
* * *
489751 TATTTTACTCAATGGTATTTAACCATTCATCTAACTAGCATAATTGACACATTTATGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGACACATTTATACCAAATGC
* *
489816 ACAGCTAGGGCATTATTCTTTTACTCTAACGGTATTTAACCGTTCATCTAAC-TGCATAATTGAC
66 ACAGCTAGGCCATTATTCTTTTACTC-AACGGTATTTAACCGTTCATCTAACTTCCATAATTGAC
**
489880 ACCTTTCTGGCAAATGCACAGTTAGACCATTAT
130 ACCTTT-TGGCAAATGCACAACTAGACCATTAT
* * * * *
489913 TCTTTTACTCAACGATATTAAACCATTCATCTAACTGGCATAATTGACACATTTCTATCAAATGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGACACATTTATACCAAATGC
489978 A
66 A
489979 TAATTAGGCC
Statistics
Matches: 204, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
161 101 0.50
162 103 0.50
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (161 bp):
TCTTTTACTCAACGGTATTTAACCATTCATCTAACTAGCATAATTGACACATTTATACCAAATGC
ACAGCTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTTCCATAATTGACA
CCTTTTGGCAAATGCACAACTAGACCATTAT
Found at i:490029 original size:68 final size:68
Alignment explanation
Indices: 489938--490260 Score: 513
Period size: 68 Copynumber: 4.8 Consensus size: 68
489928 TATTAAACCA
* * * * *
489938 TTCATCTAACTGGCATAATTGACACATTTCTATCAAATGCATAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
490003 CCT
66 CCT
*
490006 TTCATCTAACTGGCATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTC-AAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
490070 CCT
66 CCT
* *
490073 TTCATCTAATTGGCATAAATGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
490138 CCT
66 CCT
* * *
490141 TTCATATAACTGGCATAAATGACACCTTTTTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
490206 CCT
66 CCT
* * *
490209 TTCACCTAACTGGCATAAATGACACCTTTCTGTCAACTGCACATTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCT
490261 ATTAATCTTT
Statistics
Matches: 234, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
67 64 0.27
68 170 0.73
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:490180 original size:135 final size:136
Alignment explanation
Indices: 489938--490260 Score: 531
Period size: 135 Copynumber: 2.4 Consensus size: 136
489928 TATTAAACCA
* * *
489938 TTCATCTAACTGGCATAATTGACACATTTCTATCAAATGCATAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAG
*
490003 CCTTTCATCTAACTGGCATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTC-AAGGCACT
66 CCTTTCATATAACTGGCATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACT
490067 TAGCCT
131 TAGCCT
* *
490073 TTCATCTAATTGGCATAAATGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAG
* *
490138 CCTTTCATATAACTGGCATAAATGACACCTTTTTGTCAAATGCATAGTTAGGCCTCAAAGGCACT
66 CCTTTCATATAACTGGCATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACT
490203 TAGCCT
131 TAGCCT
* * * *
490209 TTCACCTAACTGGCATAAATGACACCTTTCTGTCAACTGCACATTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACAATTAGGCCT
490261 ATTAATCTTT
Statistics
Matches: 174, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
135 113 0.65
136 61 0.35
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (136 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAG
CCTTTCATATAACTGGCATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACT
TAGCCT
Found at i:490593 original size:55 final size:55
Alignment explanation
Indices: 490476--490626 Score: 200
Period size: 55 Copynumber: 2.7 Consensus size: 55
490466 TCCCAAACGA
* *
490476 AAATTCATACACTTGGTATGAATTTCTTAG-TTCGCACACATAATGCCCATAAGG
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAATGCCCATAAGG
*
490530 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACA-AGGTGCCCATACA-G
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATA-ATGCCCATA-AGG
* *
490585 AAATTCATACACATAGTAAGAATTTCTTAAGTATTTGCACAC
1 AAATTCATACACTTAGTATGAATTTCTT-AGT-TTTGCACAC
490627 GTAGTGCCAT
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
54 30 0.34
55 44 0.51
56 4 0.05
57 9 0.10
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (55 bp):
AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAATGCCCATAAGG
Found at i:492890 original size:21 final size:21
Alignment explanation
Indices: 492833--492890 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
492823 ATTTACCGTG
*
492833 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGACGCT
* * *
492854 ATTGTGGCTGTTGCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
*
492875 ATTGCAGCCGTCGCGG
1 ATTGCGGCCGTCGCGG
492891 GTAACTCGGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.09, C:0.28, G:0.40, T:0.24
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:494750 original size:14 final size:14
Alignment explanation
Indices: 494724--494766 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
494714 AAAACGCTAG
494724 AAAACAGAAAAAGAT
1 AAAACA-AAAAAGAT
494739 AAAACAAAAAAGA-
1 AAAACAAAAAAGAT
*
494752 AAAAAAAAATAAGAT
1 AAAACAAAA-AAGAT
494767 GAAATAGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
14 11 0.44
15 6 0.24
ACGTcount: A:0.79, C:0.05, G:0.09, T:0.07
Consensus pattern (14 bp):
AAAACAAAAAAGAT
Found at i:497145 original size:23 final size:23
Alignment explanation
Indices: 497100--497181 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
497090 GTATGAATCT
* *
497100 TTTTGAACACATTGTTCTTGAAAG
1 TTTTGAA-ACTTTGATCTTGAAAG
497124 TTTTGAAACTTTGATCTTGAAAG
1 TTTTGAAACTTTGATCTTGAAAG
497147 TTTTGAAACTTTGA---TGAAAG
1 TTTTGAAACTTTGATCTTGAAAG
497167 TTTTGAAACTTTGAT
1 TTTTGAAACTTTGAT
497182 GAGTGAAACT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
20 20 0.36
23 28 0.51
24 7 0.13
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (23 bp):
TTTTGAAACTTTGATCTTGAAAG
Found at i:497166 original size:20 final size:20
Alignment explanation
Indices: 497118--497183 Score: 105
Period size: 20 Copynumber: 3.1 Consensus size: 20
497108 ACATTGTTCT
497118 TGAAAGTTTTGAAACTTTGA
1 TGAAAGTTTTGAAACTTTGA
497138 TCTTGAAAGTTTTGAAACTTTGA
1 ---TGAAAGTTTTGAAACTTTGA
497161 TGAAAGTTTTGAAACTTTGA
1 TGAAAGTTTTGAAACTTTGA
497181 TGA
1 TGA
497184 GTGAAACTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
20 23 0.53
23 20 0.47
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (20 bp):
TGAAAGTTTTGAAACTTTGA
Found at i:498193 original size:17 final size:17
Alignment explanation
Indices: 498173--498222 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
498163 TTTAGGGAAG
498173 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
498190 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
498207 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
498223 TTAACTCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:499670 original size:13 final size:13
Alignment explanation
Indices: 499652--499690 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
499642 CCGGGTTAGT
499652 AAAAAAATCAAAA
1 AAAAAAATCAAAA
*
499665 AAAAAATTCAAAA
1 AAAAAAATCAAAA
*
499678 AAAAAAATTAAAA
1 AAAAAAATCAAAA
499691 GAAAGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAAATCAAAA
Found at i:499678 original size:14 final size:14
Alignment explanation
Indices: 499652--499690 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
499642 CCGGGTTAGT
499652 AAAAAAA-TC-AAA
1 AAAAAAATTCAAAA
499664 AAAAAAATTCAAAA
1 AAAAAAATTCAAAA
499678 AAAAAAATT-AAAA
1 AAAAAAATTCAAAA
499691 GAAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 12 0.48
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAAAATTCAAAA
Found at i:526634 original size:21 final size:21
Alignment explanation
Indices: 526609--526664 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
526599 TACATATATC
* *
526609 ATCATCTATTTTCTTAGCATT
1 ATCATCTATATTATTAGCATT
* *
526630 ATCATATATATTATTATCATT
1 ATCATCTATATTATTAGCATT
526651 ATC-TCTATCATTAT
1 ATCATCTAT-ATTAT
526665 CATCAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (21 bp):
ATCATCTATATTATTAGCATT
Found at i:526669 original size:21 final size:21
Alignment explanation
Indices: 526626--526669 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
526616 ATTTTCTTAG
*
526626 CATTATCATATATATTATTAT
1 CATTATCATATATATTATCAT
*
526647 CATTATC-TCTATCATTATCAT
1 CATTATCATATAT-ATTATCAT
526668 CA
1 CA
526670 AATTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
CATTATCATATATATTATCAT
Found at i:527258 original size:151 final size:148
Alignment explanation
Indices: 526881--527334 Score: 730
Period size: 149 Copynumber: 3.0 Consensus size: 148
526871 CCGAAGTGCA
* *
526881 CGTAGAATTACACCGTAGTGCCATATAATAATGTTCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTG-CATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
526946 CATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
65 CATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
527011 TATATATCCCCAAGGACCG
130 TATATATCCCGAAGGACCG
527030 CGTAGAATTGCACCGTAGTGCGATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGC-ATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
*
527095 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
65 CATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAG-A-ATA
527160 TATATATATCCCGAAGGACCG
128 TATATATATCCCGAAGGACCG
*
527181 CGTAGAATTGCACCGTAGTGTCATATAATAATGTCCATAAGAACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTG-CATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
* * * * * * *
527246 CATATACATATACTAAGGACCAAGTATGTGCCTCA-AAGACCTCATAAATGTTCCAAAGAATATA
65 CATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
* *
527310 CATATGTCCCGAAGGACCG
130 TATATATCCCGAAGGACCG
527329 CGTAGA
1 CGTAGA
527335 CCCTCGACTC
Statistics
Matches: 286, Mismatches: 15, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
148 29 0.10
149 120 0.42
150 20 0.07
151 116 0.41
152 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (148 bp):
CGTAGAATTGCACCGTAGTGCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATC
ATATACATATACTAAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATAT
ATATATCCCGAAGGACCG
Found at i:528815 original size:64 final size:62
Alignment explanation
Indices: 528682--528842 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 62
528672 TAATGAAGGT
* * *
528682 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * *
528747 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGTTGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
528811 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
528843 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:532261 original size:18 final size:18
Alignment explanation
Indices: 532238--532279 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
532228 AGTATATTTA
532238 TTTATTTAAAA-ATAATAT
1 TTTATTTAAAATATAAT-T
*
532256 TTTA-TTAAAATTTAATT
1 TTTATTTAAAATATAATT
532273 TTTATTT
1 TTTATTT
532280 TTAATAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATTTAAAATATAATT
Found at i:532311 original size:29 final size:30
Alignment explanation
Indices: 532259--532331 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
532249 ATAATATTTT
* * *
532259 ATTAAAATTTAATT-TTTATTTTTAATAGA
1 ATTATAATTTATTTATTTATTTTTAATAAA
*
532288 ATTATAATTTATTTATTTA-TTTTATTAAA
1 ATTATAATTTATTTATTTATTTTTAATAAA
* *
532317 ATAATAATTAATTTA
1 ATTATAATTTATTTA
532332 AGTAGTCTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 33 0.89
30 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (30 bp):
ATTATAATTTATTTATTTATTTTTAATAAA
Found at i:533137 original size:20 final size:20
Alignment explanation
Indices: 533095--533137 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
533085 ATAATATTTT
* *
533095 ATTTGTATTAATTTTATATC
1 ATTTGTATTAATTGTATACC
533115 ATTTGATATTAATTGT-TACC
1 ATTTG-TATTAATTGTATACC
533135 ATT
1 ATT
533138 AATTTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (20 bp):
ATTTGTATTAATTGTATACC
Found at i:533981 original size:16 final size:17
Alignment explanation
Indices: 533960--534026 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
533950 TGAACTAACA
* *
533960 ATTAATTTTTA-TTAGT
1 ATTAATTTTAATTTAAT
533976 ATTAATTTTAATTTAAT
1 ATTAATTTTAATTTAAT
*
533993 ATTAATTGTGATAATTTATT
1 ATTAATT-T--TAATTTAAT
*
534013 ATTAATTTTGATTT
1 ATTAATTTTAATTT
534027 TATTAATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
16 10 0.23
17 16 0.37
18 1 0.02
19 1 0.02
20 15 0.35
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
ATTAATTTTAATTTAAT
Found at i:534007 original size:20 final size:20
Alignment explanation
Indices: 533984--534024 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
533974 GTATTAATTT
533984 TAATTTAATATTAATTGTGA
1 TAATTTAATATTAATTGTGA
* *
534004 TAATTTATTATTAATTTTGA
1 TAATTTAATATTAATTGTGA
534024 T
1 T
534025 TTTATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
TAATTTAATATTAATTGTGA
Found at i:543200 original size:14 final size:14
Alignment explanation
Indices: 543181--543207 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
543171 ATTTTACAAG
543181 AGAATGGAAAACTA
1 AGAATGGAAAACTA
543195 AGAATGGAAAACT
1 AGAATGGAAAACT
543208 CTTATCTTGT
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:0.56, C:0.07, G:0.22, T:0.15
Consensus pattern (14 bp):
AGAATGGAAAACTA
Found at i:543481 original size:20 final size:20
Alignment explanation
Indices: 543456--543494 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
543446 TTACTGTAGC
* *
543456 AGTATCGGTACTATTCATAT
1 AGTATCAGTACTATACATAT
543476 AGTATCAGTACTATACATA
1 AGTATCAGTACTATACATA
543495 CAATACAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
AGTATCAGTACTATACATAT
Found at i:547863 original size:21 final size:23
Alignment explanation
Indices: 547823--547864 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
547813 GAGCATTGAA
*
547823 TTGAATTTGCAACTTGAATTTCT
1 TTGAATGTGCAACTTGAATTTCT
547846 TTGAATGT-CAAC-TGAATTT
1 TTGAATGTGCAACTTGAATTT
547865 AAAACTCTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (23 bp):
TTGAATGTGCAACTTGAATTTCT
Found at i:550881 original size:37 final size:37
Alignment explanation
Indices: 550822--550918 Score: 108
Period size: 37 Copynumber: 2.6 Consensus size: 37
550812 TTGAAATAAG
* * *
550822 TCAATATTAAGCATTCACGAAAGAATAATGAAGCAAGA
1 TCAATATTAAGCCTTCAAGAAAGAATAATAAAGCAA-A
* * *
550860 -CAATTTTAAGCCTTCAAGAAAGAGTAGTAAAGCAAA
1 TCAATATTAAGCCTTCAAGAAAGAATAATAAAGCAAA
*
550896 TCAATCTT-AGCCTTCAAGAAAGA
1 TCAATATTAAGCCTTCAAGAAAGA
550919 GTAGCGAAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
36 16 0.31
37 35 0.69
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (37 bp):
TCAATATTAAGCCTTCAAGAAAGAATAATAAAGCAAA
Found at i:550915 original size:36 final size:36
Alignment explanation
Indices: 550868--550938 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
550858 GACAATTTTA
*
550868 AGCCTTCAAGAAAGAGTAG-TAAAGCAAATCAATCTT
1 AGCCTTCAAGAAAGAGTAGCGAAA-CAAATCAATCTT
550904 AGCCTTCAAGAAAGAGTAGCGAAACAAATCAATCT
1 AGCCTTCAAGAAAGAGTAGCGAAACAAATCAATCT
550939 CGAGTCTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 30 0.91
37 3 0.09
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (36 bp):
AGCCTTCAAGAAAGAGTAGCGAAACAAATCAATCTT
Found at i:551035 original size:55 final size:55
Alignment explanation
Indices: 550975--551416 Score: 457
Period size: 55 Copynumber: 8.0 Consensus size: 55
550965 GTGGAGCATG
*
550975 CCCATTTTCTGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
1 CCCATTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
551030 CCCATTTTCTGAAGATAT-TTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
1 CCCATTTTCTGAAGAT-TGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
* * ** **
551085 CCTATTTTCCGAAGATTGTTTAAGTCCTATACTCCCTGAAAGAAGAGGGAGTTGA
1 CCCATTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
** * * * * * * *
551140 CCTGTTTTTTCGAAGATTGTTCAAATACTATACTCCTTAAAAGAAGAGGGAGCAGA
1 CCCATTTTCT-GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
* *
551196 TCCAATTTTC-GAAGATTGTTCGAGTCCTATACT-CCTGAAAGAAGAGGGAGTGGA
1 -CCCATTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
* * * *
551250 ACCATTTT-TCAAAGATTGCTT-GAGTCCTATACTCCCTGAAAGAATAGGGAGTGGA
1 CCCATTTTCT-GAAGATTG-TTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
* * * * *
551305 CCCATCTTTC-GAAGATTTTTTGAGTCTTAT-CTCCCTGAAAGAAGAATGGAGCAGA
1 CCCAT-TTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAG-AGGGAGCGGA
* * * * * * *
551360 CGCATTTTATCAAGTTTTTTTCGAGTCCTATACTCCCTGAAAGAAGAGTGAGTGGA
1 CCCATTTTCTGAAG-ATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
551416 C
1 C
551417 ACGTCTTCCA
Statistics
Matches: 323, Mismatches: 49, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
53 6 0.02
54 55 0.17
55 180 0.56
56 62 0.19
57 20 0.06
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (55 bp):
CCCATTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
Found at i:551393 original size:220 final size:222
Alignment explanation
Indices: 550978--551407 Score: 536
Period size: 220 Copynumber: 1.9 Consensus size: 222
550968 GAGCATGCCC
* *
550978 ATTTTCTGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAA
1 ATTTTCTGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGAACCATTTTCTAAA
*
551043 GATATTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCTATTTTCCGAAGATTGTTTAA
66 GATATTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCCGAAGATTGTTTAA
** * *
551108 GTCCTATACTCCCTGAAAGAAGAGGGAGTTGACCTGTTTTTTCGAAGATTGTTCAAATACTATAC
131 GTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCTATTTTATCGAAGATTGTTCAAATACTATAC
*
551173 TCCTTAAAAGAAGAGGGAGCAGATCCA
196 TCCCTAAAAGAAGAGGGAGCAGATCCA
* *
551200 ATTTTC-GAAGATTGTTCGAGTCCTATACT-CCTGAAAGAAGAGGGAGTGGAACCATTTT-TCAA
1 ATTTTCTGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGAACCATTTTCT-AA
* * *
551262 AGAT-TGCTT-GAGTCCTATACTCCCTGAAAGAATAGGGAGTGGACCCATCTTT-CGAAGATTTT
65 AGATAT--TTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCAT-TTTCCGAAGATTGT
* * * * * * *
551324 TTGAGTCTTAT-CTCCCTGAAAGAAGAATGGAGCAGACGC-ATTTTATC-AAGTTTTTTTCGAGT
127 TTAAGTCCTATACTCCCTGAAAGAAG-AGGGAGCAGAC-CTATTTTATCGAAG-ATTGTTCAAAT
* *
551386 CCTATACTCCCTGAAAGAAGAG
189 ACTATACTCCCTAAAAGAAGAG
551408 TGAGTGGACA
Statistics
Matches: 179, Mismatches: 22, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
219 19 0.11
220 126 0.70
221 28 0.16
222 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (222 bp):
ATTTTCTGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGAACCATTTTCTAAA
GATATTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCCGAAGATTGTTTAA
GTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCTATTTTATCGAAGATTGTTCAAATACTATAC
TCCCTAAAAGAAGAGGGAGCAGATCCA
Found at i:551413 original size:111 final size:108
Alignment explanation
Indices: 550975--551416 Score: 453
Period size: 111 Copynumber: 4.0 Consensus size: 108
550965 GTGGAGCATG
550975 CCCATTTTCTGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCA-TTTTC
1 CCCATTTTC-GAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA-CCATTTTTC
* *
551039 TGAAGATATTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
64 -AAAGATTTTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
* * ** *
551085 CCTATTTTCCGAAGATTGTTTAAGTCCTATACTCCCTGAAAGAAGAGGGAGTTGACCTGTTTTTT
1 CCCATTTT-CGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACC--ATTTTT
* * * * * * * *
551150 CGAAGATTGTTCAAATACTATACTCCTTAAAAGAAGAGGGAGCAGA
63 CAAAGATTTTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
* * *
551196 TCCAATTTTCGAAGATTGTTCGAGTCCTATACT-CCTGAAAGAAGAGGGAGTGGAACCATTTTTC
1 -CCCATTTTCGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGG-ACCATTTTTC
* * *
551260 AAAGATTGCTT-GAGTCCTATACTCCCTGAAAGAATAGGGAGTGGA
64 AAAGATT-TTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
* ** * * *
551305 CCCATCTTTCGAAGATTTTTTGAGTCTTAT-CTCCCTGAAAGAAGAATGGAGCAGACGCATTTTA
1 CCCAT-TTTCGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAG-AGGGAGCGGAC-CATTTT-
* * *
551369 TC-AAGTTTTTTTCGAGTCCTATACTCCCTGAAAGAAGAGTGAGTGGA
62 TCAAAG-ATTTTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
551416 C
1 C
551417 ACGTCTTCCA
Statistics
Matches: 279, Mismatches: 39, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
108 6 0.02
109 74 0.27
110 87 0.31
111 100 0.36
112 12 0.04
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (108 bp):
CCCATTTTCGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCATTTTTCAA
AGATTTTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGA
Found at i:551617 original size:81 final size:81
Alignment explanation
Indices: 551414--551713 Score: 352
Period size: 81 Copynumber: 3.7 Consensus size: 81
551404 AGAGTGAGTG
* * * *
551414 GACACGTCTTCCAAAATAGATCTATCTACCTGAAAAGAGGCACATATCAAGTTTGATTTCCCCTG
1 GACACGTCTTCCAAAATAGATCTGTCTACCCGAAAAAAGGCACATATCAAGTCTGATTTCCCCTG
* * *
551479 AAAGAAGAG-GGAACA
66 AATGAACAGTGGAGCA
* * * * * * *
551494 AACACGTCTTCCAAAATATATTTGTCTACTCGAAGAAGAGGCACAGATCAAGTCTGATTCCCCCT
1 GACACGTCTTCCAAAATAGATCTGTCTACCCGAA-AAAAGGCACATATCAAGTCTGATTTCCCCT
* *
551559 GAATGAATAGTCGAGCA
65 GAATGAACAGTGGAGCA
* *
551576 GACACATCTTCCAAAATAGATCTGTCTACCCGAAAAAAGGCACATATCAAGTTTGATTTCCCCTG
1 GACACGTCTTCCAAAATAGATCTGTCTACCCGAAAAAAGGCACATATCAAGTCTGATTTCCCCTG
*
551641 AATGAACAGTGGAGTA
66 AATGAACAGTGGAGCA
* * * *
551657 GACACGTCTTCTAAAATAGATTTGTCTACCC-AAAAAAGTGGAACAAATCAAGTCTGA
1 GACACGTCTTCCAAAATAGATCTGTCTACCCGAAAAAA--GGCACATATCAAGTCTGA
551714 CCACCATGAA
Statistics
Matches: 185, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
80 34 0.18
81 103 0.56
82 48 0.26
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.24
Consensus pattern (81 bp):
GACACGTCTTCCAAAATAGATCTGTCTACCCGAAAAAAGGCACATATCAAGTCTGATTTCCCCTG
AATGAACAGTGGAGCA
Found at i:556775 original size:3 final size:3
Alignment explanation
Indices: 556761--556793 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
556751 TGCAACAAAT
556761 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
556794 GGTGTCGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:557006 original size:39 final size:39
Alignment explanation
Indices: 556949--557044 Score: 138
Period size: 39 Copynumber: 2.5 Consensus size: 39
556939 CATTAACTAA
* *
556949 GCATCAAAATTAAAATTAATGATCAATATTCAAACTTGT
1 GCATCAAAATTAATATTAATGATCAATATTCAAACTTGC
* *
556988 GCATCAAAATTAATATTAATGATCAATATTCTAATTTGC
1 GCATCAAAATTAATATTAATGATCAATATTCAAACTTGC
* *
557027 GTATTAAAATTAATATTA
1 GCATCAAAATTAATATTA
557045 TCGTGACTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (39 bp):
GCATCAAAATTAATATTAATGATCAATATTCAAACTTGC
Found at i:557612 original size:2 final size:2
Alignment explanation
Indices: 557599--557634 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
557589 AGTCCTTCAT
*
557599 TA TA TG 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
557635 ATGAAGCATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:558939 original size:3 final size:3
Alignment explanation
Indices: 558926--559002 Score: 61
Period size: 3 Copynumber: 25.0 Consensus size: 3
558916 AGTTTTTGTC
* *
558926 TAT TTT TAT TAT TAAT TA- TAT TAT TAT TAT TAT TAT TA- TAT TACA
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
*
558971 TATT TAT TAT ATAT AAT ATAT TAT TA- TAT TAT
1 TA-T TAT TAT -TAT TAT -TAT TAT TAT TAT TAT
559003 ATTTGCATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
2 6 0.10
3 42 0.70
4 12 0.20
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:558952 original size:18 final size:19
Alignment explanation
Indices: 558926--559005 Score: 85
Period size: 18 Copynumber: 4.2 Consensus size: 19
558916 AGTTTTTGTC
*
558926 TATTTTTATTATTA-ATTA
1 TATTATTATTATTATATTA
558944 TATTATTATTATTATTATTA
1 TATTATTATTATTA-TATTA
*
558964 TATTACATATTTATTATA-TA
1 TATTA-TTA-TTATTATATTA
*
558984 TAATA-TATTATTATATTA
1 TATTATTATTATTATATTA
559002 TATT
1 TATT
559006 TGCATTTACA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
17 8 0.15
18 20 0.38
20 15 0.28
21 4 0.08
22 6 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTATTATTATTATATTA
Found at i:558979 original size:16 final size:16
Alignment explanation
Indices: 558935--559001 Score: 72
Period size: 16 Copynumber: 4.3 Consensus size: 16
558925 CTATTTTTAT
558935 TATTAAT-TA-TATTA
1 TATTAATATATTATTA
558949 TTATT-AT-TATTATTA
1 -TATTAATATATTATTA
558964 TATTACATAT-TTATTA
1 TATTA-ATATATTATTA
558980 TATATAATATATTATTA
1 TAT-TAATATATTATTA
558997 TATTA
1 TATTA
559002 TATTTGCATT
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.17
15 9 0.20
16 17 0.37
17 12 0.26
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAATATATTATTA
Found at i:558982 original size:36 final size:38
Alignment explanation
Indices: 558935--559005 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 38
558925 CTATTTTTAT
558935 TATTAATTATAT-T-AT-TATTATTATTATTATATTACA
1 TATTAATTATATATAATATATTATTA-TATTATATTACA
*
558971 TATTTATTATATATAATATATTATTATATTATATT
1 TATTAATTATATATAATATATTATTATATTATATT
559006 TGCATTTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 11 0.35
37 1 0.03
38 11 0.35
39 8 0.26
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (38 bp):
TATTAATTATATATAATATATTATTATATTATATTACA
Found at i:559806 original size:21 final size:22
Alignment explanation
Indices: 559759--559825 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
559749 TTTTCGGCCA
*
559759 CCAGAATAGTGACCGGCGATTG
1 CCAGAATAGTGACCGGCGATGG
* *
559781 CCAGAATAGTGA-CTGCGGTGG
1 CCAGAATAGTGACCGGCGATGG
* *
559802 CCAGAATACTGATCGGCGATGG
1 CCAGAATAGTGACCGGCGATGG
559824 CC
1 CC
559826 GAGGAGGGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 17 0.45
22 21 0.55
ACGTcount: A:0.25, C:0.24, G:0.33, T:0.18
Consensus pattern (22 bp):
CCAGAATAGTGACCGGCGATGG
Found at i:560389 original size:26 final size:27
Alignment explanation
Indices: 560340--560390 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
560330 TTAATAACCT
* *
560340 ATTATTTTGATATTTTTATTTTTAATC
1 ATTATTTTGATATATTTATATTTAATC
*
560367 ATTATTTT-ATATATTTGTATTTAA
1 ATTATTTTGATATATTTATATTTAA
560391 GTTATATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
ATTATTTTGATATATTTATATTTAATC
Found at i:567590 original size:249 final size:249
Alignment explanation
Indices: 567143--567605 Score: 730
Period size: 249 Copynumber: 1.9 Consensus size: 249
567133 GAAAAATGAG
* * * **
567143 AAAGTTTCTCATTTAATTTTCTAAAAAATGAAATTCTTGAAAAGTAAGAAGGTTTTTTACCCAGT
1 AAAGTTTCTCATTTAATGTTCTAAAAAATCAAATTCTTGAAAAGTAAGAAGGTCTCATACCCAGT
*
567208 AAAATATTTTCACGAATTTCTAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCATGATGCTTAA
66 AAAATATTTTCACGAATTTATAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCATGATGCTTAA
* *
567273 AACCATCGGGTCATCTGTTAGCCTTTCGAGCAAGATGATAAGTCATTAGGGCCATCCATCAAACC
131 AACCATAGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCATTAGGGCCATCCATCAAACC
*
567338 TTTGGGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGATAGAGATTTTC
196 TTTGGGCAGGATGTTTACATATGATTTTCGCATGAAAATGAGATAGAGATTTTC
* *
567392 AAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAA-GTCTCATACCCAGT
1 AAAGTTTCTCATTTAATGTTCTAAAAAATCAAATTCTTGAAAAGTAAGAAGGTCTCATACCCAGT
* * *
567456 AAAATATTTCTCACGAATTTATAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGTATGATGTTTA
66 AAAATATTT-TCACGAATTTATAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCATGATGCTTA
* * * * * *
567521 AACCCTTAGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAGAC
130 AAACCATAGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCATTAGGGCCATCCATCAAAC
567586 CTTTGGGCAGGATGTTTACA
195 CTTTGGGCAGGATGTTTACA
567606 CTTTTTAATT
Statistics
Matches: 193, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
248 20 0.10
249 173 0.90
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (249 bp):
AAAGTTTCTCATTTAATGTTCTAAAAAATCAAATTCTTGAAAAGTAAGAAGGTCTCATACCCAGT
AAAATATTTTCACGAATTTATAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCATGATGCTTAA
AACCATAGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCATTAGGGCCATCCATCAAACC
TTTGGGCAGGATGTTTACATATGATTTTCGCATGAAAATGAGATAGAGATTTTC
Found at i:568505 original size:22 final size:22
Alignment explanation
Indices: 568477--568538 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
568467 TTTTCCACCG
* *
568477 GAATAGTGACCGGCGGTTGCCA
1 GAATAGTGACCGACGGTGGCCA
*
568499 GAATAGTGACCGATGGTGGCCA
1 GAATAGTGACCGACGGTGGCCA
*
568521 GAATAGTGATCGACGGTG
1 GAATAGTGACCGACGGTG
568539 AGTGAGCGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.37, T:0.19
Consensus pattern (22 bp):
GAATAGTGACCGACGGTGGCCA
Found at i:568627 original size:30 final size:30
Alignment explanation
Indices: 568592--568657 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
568582 GGAGTTTAGA
* *
568592 GAGAAGGGAGAGTTTTTCTCTCCTTAGAGG
1 GAGAAGGGAAAGCTTTTCTCTCCTTAGAGG
568622 GAGAAGGGAAAGCTTTTCTCTCCTTAGAGG
1 GAGAAGGGAAAGCTTTTCTCTCCTTAGAGG
568652 GAGAAG
1 GAGAAG
568658 TAAATTGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.26
Consensus pattern (30 bp):
GAGAAGGGAAAGCTTTTCTCTCCTTAGAGG
Found at i:569176 original size:13 final size:13
Alignment explanation
Indices: 569158--569205 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
569148 TTTGATATTT
569158 TTATTTTTAATCA
1 TTATTTTTAATCA
**
569171 TTATTTTGTATATTT
1 TTATTTT-TA-ATCA
*
569186 TTATTTTTATTCA
1 TTATTTTTAATCA
569199 TTATTTT
1 TTATTTT
569206 ATATATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 15 0.54
14 4 0.14
15 9 0.32
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (13 bp):
TTATTTTTAATCA
Found at i:569192 original size:28 final size:28
Alignment explanation
Indices: 569143--569219 Score: 129
Period size: 28 Copynumber: 2.8 Consensus size: 28
569133 TTAATAAACT
569143 ATTATTTTG-ATATTTTTATTTTTAATC
1 ATTATTTTGTATATTTTTATTTTTAATC
*
569170 ATTATTTTGTATATTTTTATTTTTATTC
1 ATTATTTTGTATATTTTTATTTTTAATC
*
569198 ATTATTTTATATATTTTTATTT
1 ATTATTTTGTATATTTTTATTT
569220 AAGTTATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 9 0.19
28 38 0.81
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (28 bp):
ATTATTTTGTATATTTTTATTTTTAATC
Found at i:571741 original size:29 final size:30
Alignment explanation
Indices: 571707--571779 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
571697 AAAAAAATTA
571707 ATTAAATAAAATATAAA-AAAAT-TTAAAT
1 ATTAAATAAAATATAAACAAAATATTAAAT
* *
571735 ACTTAAATAAATTAAAAAACAAAATATTAAAT
1 A-TTAAATAAAAT-ATAAACAAAATATTAAAT
571767 A-T-AATAAAATATA
1 ATTAAATAAAATATA
571780 CCTTAAACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 3 0.08
29 17 0.46
30 5 0.14
31 5 0.14
32 7 0.19
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (30 bp):
ATTAAATAAAATATAAACAAAATATTAAAT
Found at i:574592 original size:44 final size:44
Alignment explanation
Indices: 574538--574791 Score: 400
Period size: 44 Copynumber: 5.8 Consensus size: 44
574528 GACACCTTTT
* * *
574538 TGCCAATAATGTACCATTATGCATTTTCATTTATGGTACATTTC
1 TGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACATTTC
* *
574582 TGCTAATAATGCACCGTTATGCATTTTCATTTATGACACATTTC
1 TGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACATTTC
* *
574626 TGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTA
1 TGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACATTTC
* * * *
574670 TACCAATAATGCAACGTTATGCATTTTCATTTATGACACCTTTC
1 TGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACATTTC
574714 TGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACATTTC
1 TGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACATTTC
*
574758 TGCCAATAATGCATCGTTATGCATTTTCATTTAT
1 TGCCAATAATGCACCGTTATGCATTTTCATTTAT
574792 TTCAGTAACA
Statistics
Matches: 192, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 192 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
TGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACATTTC
Found at i:575352 original size:18 final size:18
Alignment explanation
Indices: 575325--575384 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
575315 CCTTTTTCTT
*
575325 AGTATAGATACCCACATC
1 AGTATCGATACCCACATC
575343 AGTATCGATA--C-C--C
1 AGTATCGATACCCACATC
575356 AGTATCGATACCCACATC
1 AGTATCGATACCCACATC
575374 AGTATCGATAC
1 AGTATCGATAC
575385 GAATTGCATC
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 11 0.31
15 2 0.06
16 2 0.06
18 21 0.58
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.23
Consensus pattern (18 bp):
AGTATCGATACCCACATC
Found at i:575360 original size:13 final size:13
Alignment explanation
Indices: 575342--575369 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
575332 ATACCCACAT
575342 CAGTATCGATACC
1 CAGTATCGATACC
575355 CAGTATCGATACC
1 CAGTATCGATACC
575368 CA
1 CA
575370 CATCAGTATC
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:0.32, C:0.32, G:0.14, T:0.21
Consensus pattern (13 bp):
CAGTATCGATACC
Found at i:575366 original size:31 final size:31
Alignment explanation
Indices: 575325--575384 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
575315 CCTTTTTCTT
575325 AGTATAGATACCCACATCAGTATCGATACCC
1 AGTATAGATACCCACATCAGTATCGATACCC
*
575356 AGTATCGATACCCACATCAGTATCGATAC
1 AGTATAGATACCCACATCAGTATCGATAC
575385 GAATTGCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.23
Consensus pattern (31 bp):
AGTATAGATACCCACATCAGTATCGATACCC
Found at i:580239 original size:14 final size:14
Alignment explanation
Indices: 580210--580250 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
580200 CTTGAAAAAA
*
580210 AATAAAAAATATAAT
1 AATAATAAA-ATAAT
580225 AATAATAAAATAAT
1 AATAATAAAATAAT
*
580239 AAAAATAAAATA
1 AATAATAAAATA
580251 TCAGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:580500 original size:20 final size:20
Alignment explanation
Indices: 580472--580516 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
580462 TAGGTAAGAA
*
580472 ACTTAGGGAATCATTTTCTT
1 ACTTTGGGAATCATTTTCTT
580492 ACTTTGGGAATCATTTTCTT
1 ACTTTGGGAATCATTTTCTT
580512 ACTTT
1 ACTTT
580517 TCAAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (20 bp):
ACTTTGGGAATCATTTTCTT
Found at i:580817 original size:244 final size:244
Alignment explanation
Indices: 580492--581111 Score: 832
Period size: 244 Copynumber: 2.5 Consensus size: 244
580482 TCATTTTCTT
* * *
580492 ACTTTGGGAATCATTTTCTTACTTTTCAAAAATTTCAATTTTTACTTTTAAATGAGAAACTTTTC
1 ACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTCAATTTTAACATTTAAATGAGAAACTTTTC
* * * * *
580557 TAATTTTTCAAGAAACATGTGAAAACATCATGCTCGAAGGTCTTGTGGATGGCCTGAAGGATTTA
66 TAATTTTTCGAGAAACATGTGAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAGGACTTA
** *
580622 TCATCTT-ATTCGAAAGGCTTGCAAATAACCCGAAAGATTTAATCATCATGCTTGAAATACTTAC
131 TCATCTTGATT-GAAAGGCTTGCAAATAACCCGAAAGATTTAATCATCATGCTCAAAAAACTTAC
*
580686 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACT-AGATAAGAA
195 TGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAAG-TAAGAA
** * * * *
580736 ACTTTGGAAATTGTTTTCTTACTTTTCAATATTTTCAATTTTAAGATTTAAATGAGAAAGTTTTC
1 ACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTCAATTTTAACATTTAAATGAGAAACTTTTC
* * * *
580801 TCATTTTTCGAGAAACATGTAAAAACATCCTACCCGAAGGTCTTGTGGATGGCCCGAAGAACTTA
66 TAATTTTTCGAGAAACATGTGAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAGGACTTA
* * * * * *
580866 TCATCTTGCTTGAAAGGCTTGTAGATGACCTGAAGGATTTAATCATCATGCTCAAAAAACTTACT
131 TCATCTTGATTGAAAGGCTTGCAAATAACCCGAAAGATTTAATCATCATGCTCAAAAAACTTACT
**
580931 GATGGCCCGAAGGACTTACCGATTTTGGAAATAGTTTACTAAGTAAGAA
196 GATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAAGTAAGAA
* * *
580980 ACTTTGGAAATCATTTTTTTAACTTTTCAAAAAATTT-AATTTTAATATTTAAATGTGAAACTTT
1 ACTTTGGAAATCATTTTCTT-ACTTTTC-AAAAATTTCAATTTTAACATTTAAATGAGAAACTTT
* * * * * *
581044 TCTTATTTTTCGAGAAATATGTGAAAAAATCCTGCCCGAAAGTCTTATGAATGGCCCGAAGGACT
64 TCTAATTTTTCGAGAAACATGTGAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAGGACT
581109 TAT
129 TAT
581112 TAGCTTGCTC
Statistics
Matches: 325, Mismatches: 47, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
244 225 0.69
245 94 0.29
246 6 0.02
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (244 bp):
ACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTCAATTTTAACATTTAAATGAGAAACTTTTC
TAATTTTTCGAGAAACATGTGAAAACATCCTGCCCGAAGGTCTTGTGGATGGCCCGAAGGACTTA
TCATCTTGATTGAAAGGCTTGCAAATAACCCGAAAGATTTAATCATCATGCTCAAAAAACTTACT
GATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAAGTAAGAA
Found at i:589065 original size:127 final size:130
Alignment explanation
Indices: 588836--589088 Score: 406
Period size: 127 Copynumber: 2.0 Consensus size: 130
588826 TTTTAAGAAT
* *
588836 GAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGTAGTCA
1 GAAAACAATAATATCTAATTATTTTCAATCGAGAATAAATAACCTCTCATGCCTTAAAGTAGTCA
*
588901 TTATTACTCCAACCGAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGATTCGAGA
66 TTATTACTCCAACCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATTCGAGA
* * *
588966 GAAAACAATAATATCTAATTA-TTTCCATTGAGAATAAATAACCTCTCATGTCTTAAAGTA-T-A
1 GAAAACAATAATATCTAATTATTTTCAATCGAGAATAAATAACCTCTCATGCCTTAAAGTAGTCA
*
589028 -TATTTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATTC
66 TTA-TTACTCCAACCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATTC
589089 AAGTGTTATT
Statistics
Matches: 115, Mismatches: 7, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
126 2 0.02
127 57 0.50
128 1 0.01
129 35 0.30
130 20 0.17
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.34
Consensus pattern (130 bp):
GAAAACAATAATATCTAATTATTTTCAATCGAGAATAAATAACCTCTCATGCCTTAAAGTAGTCA
TTATTACTCCAACCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATTCGAGA
Found at i:597054 original size:81 final size:81
Alignment explanation
Indices: 596947--597452 Score: 728
Period size: 81 Copynumber: 6.2 Consensus size: 81
596937 AAAATACAAT
* * * *
596947 ATTAAGCATTTAGTC-TTTCCTCTAAAGGCATTTAGCCTTTCATCCAACTTGAATGATTGGCACC
1 ATTAGGCATTTAATCTTTTACTC-AAAGGCATTTAGCCTTTCATCCAACTTGCATGATTGGCACC
*
597011 TTTCTGGCAAATGCACA
65 TTTCTGCCAAATGCACA
* * * * *
597028 ATTAGGCATTTAATCTTTTACTTAAAGGTATTTATCCTTTCATCCAACTTGCATGATTAGCACAT
1 ATTAGGCATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCCAACTTGCATGATTGGCACCT
*
597093 TTCTGCAAAATGCACA
66 TTCTGCCAAATGCACA
* *
597109 TTTAGGCATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCGAACTTGCATGATTGGCACCT
1 ATTAGGCATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCCAACTTGCATGATTGGCACCT
597174 TTCTGCCAAATGCACA
66 TTCTGCCAAATGCACA
* * ** *
597190 GTTAGGCATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCGAACTTGCATGATTGTTACGT
1 ATTAGGCATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCCAACTTGCATGATTGGCACCT
597255 TTCTGCCAAATGCACA
66 TTCTGCCAAATGCACA
* * * **
597271 GTTAGGTATTTAATCTTTTACTCACAGGCATTTAGCCTTTCATCCAACTTGCACAATTGGCACCT
1 ATTAGGCATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCCAACTTGCATGATTGGCACCT
597336 TAT-TGCCAAATGCACA
66 T-TCTGCCAAATGCACA
* * *
597352 ATTAGGCATTTAATATTTTACTCAAAGGCATTTAGCTTTTCATCCAACTTGCATGATTGGCACAT
1 ATTAGGCATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCCAACTTGCATGATTGGCACCT
*
597417 TTCTGCCTAATGCACA
66 TTCTGCCAAATGCACA
*
597433 ATTAAGCATTTAATCTTTTA
1 ATTAGGCATTTAATCTTTTA
597453 TTTTAAAACA
Statistics
Matches: 380, Mismatches: 42, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
80 1 0.00
81 373 0.98
82 6 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (81 bp):
ATTAGGCATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCCAACTTGCATGATTGGCACCT
TTCTGCCAAATGCACA
Found at i:599593 original size:77 final size:77
Alignment explanation
Indices: 599479--599621 Score: 175
Period size: 77 Copynumber: 1.9 Consensus size: 77
599469 TTAATAAATA
*
599479 AAATATTATTTAATTAATTCAAATTAAATATACATTAAA-GACTTATAATCTGAATTACAATCTT
1 AAATATTATTTAATTAATTCAAATTAAATATACATTAAATGACTTATAATCTAAATTACAATCTT
599543 TAATGTTTATTT
66 TAATGTTTATTT
* * * * * *
599555 AAATACTTATTTAATT-ATTCTGAGTTATATAT-CAATTAAATGAGTTGTAATCTAAATTACATT
1 AAATA-TTATTTAATTAATTC-AAATTAAATATAC-ATTAAATGACTTATAATCTAAATTACAAT
599618 CTTT
63 CTTT
599622 TGATGCTTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
76 10 0.18
77 24 0.43
78 22 0.39
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (77 bp):
AAATATTATTTAATTAATTCAAATTAAATATACATTAAATGACTTATAATCTAAATTACAATCTT
TAATGTTTATTT
Found at i:608175 original size:15 final size:15
Alignment explanation
Indices: 608155--608183 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
608145 ACACTTTTAT
608155 ATATTTAATAAATAC
1 ATATTTAATAAATAC
608170 ATATTTAATAAATA
1 ATATTTAATAAATA
608184 TATTTATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATTTAATAAATAC
Found at i:612117 original size:6 final size:6
Alignment explanation
Indices: 612106--612180 Score: 123
Period size: 6 Copynumber: 12.5 Consensus size: 6
612096 AAAATACCAT
* * *
612106 TGTATA TGTATA TGTACA TGTACA TGTACA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
612154 TGTATA TGTATA TGTATA TGTATA TGT
1 TGTATA TGTATA TGTATA TGTATA TGT
612181 CATTCAAATG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (6 bp):
TGTATA
Found at i:612579 original size:52 final size:53
Alignment explanation
Indices: 612518--612626 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 53
612508 TCATTGTTTA
612518 AATTTCATTTCTGCAATTAGACTTGATGGGCATGGGTTTTTGTTTTTACATT-
1 AATTTCATTTCTGCAATTAGACTTGATGGGCATGGGTTTTTGTTTTTACATTG
612570 AATTTCATTTCTGCAATTAGACTTGATGGGCATGGGTTTTTGTTTTTACATTG
1 AATTTCATTTCTGCAATTAGACTTGATGGGCATGGGTTTTTGTTTTTACATTG
612623 AATT
1 AATT
612627 CAATTTTTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 52 0.93
53 4 0.07
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (53 bp):
AATTTCATTTCTGCAATTAGACTTGATGGGCATGGGTTTTTGTTTTTACATTG
Found at i:612999 original size:29 final size:30
Alignment explanation
Indices: 612966--613030 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
612956 AAATCAATTT
*
612966 GACCACCGAAC-TTTCAATTGAATT-AATCA
1 GACCACCAAACATTTCAATTG-ATTCAATCA
*
612995 GACCACCAAACATTTTAATTGATTCAATCA
1 GACCACCAAACATTTCAATTGATTCAATCA
*
613025 AACCAC
1 GACCAC
613031 TCTCCGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (30 bp):
GACCACCAAACATTTCAATTGATTCAATCA
Found at i:613661 original size:13 final size:13
Alignment explanation
Indices: 613643--613733 Score: 58
Period size: 13 Copynumber: 7.6 Consensus size: 13
613633 TAAAATGCTA
613643 TATATATGTTTAG
1 TATATATGTTTAG
*
613656 TATATATG---GG
1 TATATATGTTTAG
*
613666 T-T-TACTGTTAAG
1 TATATA-TGTTTAG
613678 TATATATGTTTAG
1 TATATATGTTTAG
*
613691 TATATATG---GG
1 TATATATGTTTAG
*
613701 T-T-TACTGTTAAG
1 TATATA-TGTTTAG
613713 TATATATGTTTAG
1 TATATATGTTTAG
613726 TATATATG
1 TATATATG
613734 GGTTTCCTGT
Statistics
Matches: 60, Mismatches: 6, Indels: 24
0.67 0.07 0.27
Matches are distributed among these distances:
8 4 0.07
9 6 0.10
10 4 0.07
12 4 0.07
13 38 0.63
14 4 0.07
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (13 bp):
TATATATGTTTAG
Found at i:613684 original size:35 final size:35
Alignment explanation
Indices: 613643--613743 Score: 193
Period size: 35 Copynumber: 2.9 Consensus size: 35
613633 TAAAATGCTA
613643 TATATATGTTTAGTATATATGGGTTTACTGTTAAG
1 TATATATGTTTAGTATATATGGGTTTACTGTTAAG
613678 TATATATGTTTAGTATATATGGGTTTACTGTTAAG
1 TATATATGTTTAGTATATATGGGTTTACTGTTAAG
*
613713 TATATATGTTTAGTATATATGGGTTTCCTGT
1 TATATATGTTTAGTATATATGGGTTTACTGT
613744 GTTTACTATT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.50
Consensus pattern (35 bp):
TATATATGTTTAGTATATATGGGTTTACTGTTAAG
Found at i:614028 original size:15 final size:15
Alignment explanation
Indices: 614010--614043 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
614000 AATAATGATA
*
614010 TGTTTACTGATTATT
1 TGTTTACTGATTATG
*
614025 TGTTTACTGGTTATG
1 TGTTTACTGATTATG
614040 TGTT
1 TGTT
614044 CTGATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.21, T:0.59
Consensus pattern (15 bp):
TGTTTACTGATTATG
Found at i:614074 original size:34 final size:34
Alignment explanation
Indices: 614036--614115 Score: 78
Period size: 34 Copynumber: 2.4 Consensus size: 34
614026 GTTTACTGGT
614036 TATGTGTTCTGATAATATGTTTATTAATA-AATTA
1 TATGTGTTCTGATAATATGTTTATTAATAGAA-TA
* * * *
614070 TATGT-TTATTAATGATATGTTTATTGATAGAATA
1 TATGTGTT-CTGATAATATGTTTATTAATAGAATA
614104 TA--TGTTCTGATA
1 TATGTGTTCTGATA
614116 GAATTATTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
32 4 0.11
33 4 0.11
34 26 0.72
35 2 0.06
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.50
Consensus pattern (34 bp):
TATGTGTTCTGATAATATGTTTATTAATAGAATA
Found at i:614108 original size:19 final size:19
Alignment explanation
Indices: 614050--614143 Score: 73
Period size: 19 Copynumber: 5.4 Consensus size: 19
614040 TGTTCTGATA
*
614050 ATATGTTTATTAATA-AATT
1 ATATGTTTATTGATAGAA-T
*
614069 ATATGTTTATTAAT-G---
1 ATATGTTTATTGATAGAAT
614084 ATATGTTTATTGATAGAAT
1 ATATGTTTATTGATAGAAT
*
614103 ATATG-TT-CTGATAGAAT
1 ATATGTTTATTGATAGAAT
614120 -TAT-TTGT-TTGATAGAAT
1 ATATGTT-TATTGATAGAAT
614137 ATATGTT
1 ATATGTT
614144 CTGATATGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
15 13 0.21
16 5 0.08
17 19 0.30
18 5 0.08
19 21 0.33
ACGTcount: A:0.35, C:0.01, G:0.14, T:0.50
Consensus pattern (19 bp):
ATATGTTTATTGATAGAAT
Found at i:614114 original size:17 final size:17
Alignment explanation
Indices: 614094--614149 Score: 87
Period size: 17 Copynumber: 3.3 Consensus size: 17
614084 ATATGTTTAT
614094 TGATAGAATATATGTTC
1 TGATAGAATATATGTTC
*
614111 TGATAGAATTATTTGTT-
1 TGATAGAA-TATATGTTC
614128 TGATAGAATATATGTTC
1 TGATAGAATATATGTTC
614145 TGATA
1 TGATA
614150 TGTTTATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 7 0.20
17 21 0.60
18 7 0.20
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.45
Consensus pattern (17 bp):
TGATAGAATATATGTTC
Found at i:614279 original size:17 final size:17
Alignment explanation
Indices: 614239--614279 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
614229 CATGAAATCA
614239 ATGAATATATGTACTAC
1 ATGAATATATGTACTAC
* *
614256 ATG--TATATGTTCTGC
1 ATGAATATATGTACTAC
614271 ATGAATATA
1 ATGAATATA
614280 CATGTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 13 0.65
17 7 0.35
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (17 bp):
ATGAATATATGTACTAC
Found at i:615060 original size:30 final size:30
Alignment explanation
Indices: 614950--615060 Score: 100
Period size: 30 Copynumber: 3.7 Consensus size: 30
614940 TAATGAACCT
* * **
614950 GAAATTGATGAACCAGAACTAGCTGAGCCA
1 GAAATTAATGAACCAGAACCAATTGAGCCA
* ** *
614980 TG-AATTAATGAACTAGAATAAATTGGGCCA
1 -GAAATTAATGAACCAGAACCAATTGAGCCA
* *
615010 AAAATTAATGAA-CTGAAACCAATTGAGCCA
1 GAAATTAATGAACCAG-AACCAATTGAGCCA
615040 GAAATTAATGAACCAGAACCA
1 GAAATTAATGAACCAGAACCA
615061 GCTGAGGTGA
Statistics
Matches: 62, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
29 1 0.02
30 58 0.94
31 3 0.05
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (30 bp):
GAAATTAATGAACCAGAACCAATTGAGCCA
Found at i:617145 original size:10 final size:9
Alignment explanation
Indices: 617130--617304 Score: 83
Period size: 9 Copynumber: 19.2 Consensus size: 9
617120 TAGAAGGAAA
617130 AAAATAAAT
1 AAAATAAAT
617139 GAAAATAAAT
1 -AAAATAAAT
*
617149 AAGAT-AA-
1 AAAATAAAT
* *
617156 AAAACAATT
1 AAAATAAAT
617165 AAAAATAAAT
1 -AAAATAAAT
*
617175 GAAATAAAT
1 AAAATAAAT
*
617184 AAGATAAGAT
1 AAAATAA-AT
617194 AAAA-AAAT
1 AAAATAAAT
*
617202 AAAAAAAAT
1 AAAATAAAT
*
617211 GAAGATAAAT
1 -AAAATAAAT
**
617221 AGGATAAAT
1 AAAATAAAT
*
617230 ATAATAAAT
1 AAAATAAAT
617239 AATAA-ATAAT
1 AA-AATA-AAT
617249 AAAA-AAAT
1 AAAATAAAT
** *
617257 AAAGGAAAA
1 AAAATAAAT
* **
617266 AGAAACAAGG
1 A-AAATAAAT
617276 AAAA-AAAT
1 AAAATAAAT
*
617284 AAAATATAT
1 AAAATAAAT
617293 AATAATAAAT
1 AA-AATAAAT
617303 AA
1 AA
617305 GTAAAAACTA
Statistics
Matches: 127, Mismatches: 26, Indels: 24
0.72 0.15 0.14
Matches are distributed among these distances:
7 3 0.02
8 21 0.17
9 55 0.43
10 48 0.38
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:617148 original size:4 final size:4
Alignment explanation
Indices: 617131--617259 Score: 70
Period size: 4 Copynumber: 30.8 Consensus size: 4
617121 AGAAGGAAAA
* *
617131 AAAT AAAT GAAAAT AAAT AAGAT AAA- AAA- CAAT TAA- AAAT AAAT GAAAT
1 AAAT AAAT --AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT
* * *
617180 AAAT AAGAT AAGAT AAAA AAAT AAAAA AAAT GAAGAT AAAT AGGAT AAAT
1 AAAT AA-AT AA-AT AAAT AAAT -AAAT AAAT -AA-AT AAAT A-AAT AAAT
*
617230 ATAAT AAAT -AAT AAAT -AAT AAAA AAAT AAA
1 A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
617260 GGAAAAAGAA
Statistics
Matches: 100, Mismatches: 11, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
3 13 0.13
4 50 0.50
5 31 0.31
6 6 0.06
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:617176 original size:36 final size:37
Alignment explanation
Indices: 617129--617258 Score: 146
Period size: 37 Copynumber: 3.6 Consensus size: 37
617119 TTAGAAGGAA
* *
617129 AAAAATAAATGAAAATAAATAAGATAAA-AAACAATT
1 AAAAATAAATGAAAATAAATAAGATAAATAAAAAAAT
617165 AAAAATAAATG-AAATAAATAAGATAAGATAAAAAAAT
1 AAAAATAAATGAAAATAAATAAGATAA-ATAAAAAAAT
* * *
617202 AAAAA-AAATGAAGATAAATAGGATAAATATAATAAAT
1 AAAAATAAATGAAAATAAATAAGATAAATA-AAAAAAT
617239 AATAAAT-AAT-AAAA-AAATAA
1 AA-AAATAAATGAAAATAAATAA
617259 AGGAAAAAGA
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
35 15 0.19
36 25 0.31
37 35 0.43
38 6 0.07
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (37 bp):
AAAAATAAATGAAAATAAATAAGATAAATAAAAAAAT
Found at i:617266 original size:14 final size:13
Alignment explanation
Indices: 617249--617286 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
617239 AATAAATAAT
617249 AAAAAAATAAAGG
1 AAAAAAATAAAGG
617262 AAAAAGAA-ACAAGG
1 AAAAA-AATA-AAGG
617276 AAAAAAATAAA
1 AAAAAAATAAA
617287 ATATATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (13 bp):
AAAAAAATAAAGG
Found at i:617361 original size:10 final size:10
Alignment explanation
Indices: 617346--617371 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
617336 ATAAAGATAA
617346 AAAATACAAT
1 AAAATACAAT
617356 AAAATACAAT
1 AAAATACAAT
617366 AAAATA
1 AAAATA
617372 ATATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATACAAT
Found at i:617361 original size:23 final size:21
Alignment explanation
Indices: 617322--617374 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
617312 CTAGAAAGGA
*
617322 AAAAAATAAACACAATAAAGAT
1 AAAAAATAAACAAAATAAA-AT
* *
617344 AAAAAATACAATAAAATACAAT
1 AAAAAATA-AACAAAATAAAAT
617366 AAAATAATA
1 AAAA-AATA
617375 TATATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.74, C:0.08, G:0.02, T:0.17
Consensus pattern (21 bp):
AAAAAATAAACAAAATAAAAT
Found at i:617589 original size:11 final size:11
Alignment explanation
Indices: 617583--617615 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
617573 GTATAAATAA
617583 AAAATAAGAAAT
1 AAAATAA-AAAT
617595 AAAATAAAAAT
1 AAAATAAAAAT
617606 AAAATAAAAA
1 AAAATAAAAA
617616 AGATAAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:618025 original size:15 final size:16
Alignment explanation
Indices: 618001--618030 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
617991 AAATATTTTC
618001 TTTTCTTTTTTCGAAT
1 TTTTCTTTTTTCGAAT
618017 TTTTC-TTTTTCGAA
1 TTTTCTTTTTTCGAA
618031 ACTCCCCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTTCTTTTTTCGAAT
Found at i:619229 original size:84 final size:84
Alignment explanation
Indices: 618840--620049 Score: 1228
Period size: 84 Copynumber: 14.4 Consensus size: 84
618830 ATTTTTTCGA
* * * * * * * ** *
618840 CAGATATCCCTTCTTGCCTTGAGCTATGTTGTAAATTTGATTTGTCTCT-GAGTTGAATGTAATC
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAA--TGATGTGCCT-TGGAGCTGAGCGTAGTC
* *
618904 GAACTCGAAGGTC-TTTGATGA
63 GAACTCGAAGGTCTTTTGTTGG
* * * * * * * * * *
618925 CAGATAACCTTTCTCGCCTTGAGTTATGTTGTAAATGATGTGCCTTTGAGCTTAGTGTAATCAAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
618990 CTCGAAGGTC-TTTGTTGA
66 CTCGAAGGTCTTTTGTTGG
* * ** * * *
619008 CAGATAACCCTTCTAGCCTTTAGTTATGCTATAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
619073 CTCGAAGGTC-TTTGTTGA
66 CTCGAAGGTCTTTTGTTGG
* * * * ** *
619091 CAGATAACCCTTATAGCCTTGAGTTATGTTGTAAATGATGTGCC-TGAGAGCTGAGTTTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTG-GAGCTGAGCGTAGTCGA
*
619155 ACTCGAAGGTCTTTGGTTGG
65 ACTCGAAGGTCTTTTGTTGG
* * * * * * * * * * *
619175 CAGATATCCCTTTTCGACTTAAGCTATACAGCAAATTATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
619240 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * *
619259 CAGATAACCCTTCTAGCCTTGAGTTATGCTACAAACGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
619324 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * * **
619343 CAAATAACCCTTCTTGCCTTGAGCTATG-TAGCAAATAATATGCCTTGGAGCTGAGCGTAGTATA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCT-GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
*
619407 ACTCGAAGGTCTTTTGATGG
65 ACTCGAAGGTCTTTTGTTGG
* * * * *
619427 CAGATAGCCCTTCTAACCTTTTAGCTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCC-TTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* * *
619492 ACTTGAAGATCTTTTGATGG
65 ACTCGAAGGTCTTTTGTTGG
* * * * *
619512 CAGATAGCCCTTCTAGCTTTTGAGCTATGCTGCAAATAATGTGCTTTGGAGTTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGC-CTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
*
619577 ACTCGAAGGTCTTTGGTTGG
65 ACTCGAAGGTCTTTTGTTGG
* * * * ** * *
619597 CAGATAACCCTTCTAGCCTTAAGTTATGTTGTAAATGATACGCCTTTGAGCTGAGCGTAGTAGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
619662 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * ** * * *
619681 CAAATATCCCTTCTTGCCTTGAGCTATATTGCAAATAATGTGCCTTGGAGCTGAGTGTAGTCAAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
619746 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * * *
619765 CAAATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTGGAACTGAGTGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
619830 CTTGAAGGTCTTTTGATGG
66 CTCGAAGGTCTTTTGTTGG
* * * * * * *
619849 AAGATAGCCCTTCTAGCCTTGAGGTATGCTGCAAATGATATGGCTTGGAGCTGAGCGTAATCAAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
619914 CTTGAAGGTCTTTGGTTGGG
66 CTCGAAGGTCTTTTGTT-GG
* * * ** *
619934 AAGATAACCCTTCTCGCCTTGA-CTTATGATGCAAATGATACGCCTTAGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGC-TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* *
619998 ACTAGAAGGTCTTTGGTTGG
65 ACTCGAAGGTCTTTTGTTGG
* *
620018 CAGATAATCCTTCTCGCCTTGAGCTATGCTGC
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGC
620050 CGATAGTTTC
Statistics
Matches: 962, Mismatches: 152, Indels: 23
0.85 0.13 0.02
Matches are distributed among these distances:
82 2 0.00
83 183 0.19
84 525 0.55
85 251 0.26
86 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (84 bp):
CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTTGTTGG
Found at i:619665 original size:506 final size:503
Alignment explanation
Indices: 618898--620049 Score: 1440
Period size: 506 Copynumber: 2.3 Consensus size: 503
618888 TGAGTTGAAT
* * * * * *
618898 GTAATCGAACTCGAAGGTC-TTTGATGACAGATAACCTTTCTCGCCTTGAGTTATGTTGTAAATG
1 GTAATCAAACTCGAAGGTCTTTTGATGGCAGATAACCCTTCTCGCCTTGAGCTATGATGCAAATG
* * * * * * * *
618962 ATGTGCCTTTGAGCTTAGTGTAATCAAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCC
66 ATATGCCTTAGAGCTGAGCGTAGTCGAACTAGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG-C
* ** * *
619026 TTT-AGTTATGCTATAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTG
130 TTTGAGCTATGCTGCAAATAATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTG
* ** ** *
619090 ACAGATAACCCTTATAGCCTTGAGTTATGTTGTAAATGATGTGCCTGAGAGCTGAGTTTAATCGA
195 ACAGATAACCCTTATAGCCTTAAGTTATGTTGTAAATGATACGCCTGAGAGCTGAGCGTAATAGA
* *
619155 ACTCGAAGGTCTTTGGTTGGCAGATATCCCTT-TTCGACTTAAGCTATACAGCAAATTATGTGCC
260 ACTCGAAGGTCTTTGGTTGGCAAATATCCCTTCTT-GACTTAAGCTATACAGCAAATAATGTGCC
* * * *
619219 TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTT
324 TTGGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTAGCCTTGAGTT
* * *
619284 ATGCTACAAACGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAA-AT
389 ATACTACAAACGATATGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGG-AAGAT
*
619348 AACCCTTCTTGCCTTGAGCTATG-TAGCAAATAATATGCCTTGGAGCTGAGC
453 AACCCTTCTAGCCTTGAGCTATGCT-GCAAATAATATGCCTTGGAGCTGAGC
* * ** * * *
619399 GTAGT-ATAACTCGAAGGTCTTTTGATGGCAGATAGCCCTTCTAACCTTTTAGCTATGCTACAAA
1 GTAATCA-AACTCGAAGGTCTTTTGATGGCAGATAACCCTTCTCGCC-TTGAGCTATGATGCAAA
* * * * *
619463 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGATCTTTTGATGGCAGATAGCCCTTCTAG
64 TGATATGCCTTAGAGCTGAGCGTAGTCGAACTAGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* *
619528 CTTTTGAGCTATGCTGCAAATAATGTG-CTTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTG
129 C-TTTGAGCTATGCTGCAAATAATGTGCCTTT-GAGCTGAGCGTAATCGAACTCGAAGGTCTTT-
* * ** *
619592 GTTGGCAGATAACCCTTCTAGCCTTAAGTTATGTTGTAAATGATACGCCTTTGAGCTGAGCGTAG
191 GTTGACAGATAACCCTTATAGCCTTAAGTTATGTTGTAAATGATACGCCTGAGAGCTGAGCGTAA
* * * **
619657 TAGAACTCGAAGGTCTTTTGTTGGCAAATATCCCTTCTTGCCTTGAGCTATATTGCAAATAATGT
256 TAGAACTCGAAGGTCTTTGGTTGGCAAATATCCCTTCTTGACTTAAGCTATACAGCAAATAATGT
*
619722 GCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTAGCCTTGA
321 GCCTTGGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTAGCCTTGA
* * * * *
619787 GTTATACTGCAAATGATGTGCCTTGGAACTGAGTGTAGTCGAACTTGAAGGTCTTTTGATGGAAG
386 GTTATACTACAAACGATATGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGGAAG
* * * *
619852 ATAGCCCTTCTAGCCTTGAGGTATGCTGCAAATGATATGGCTTGGAGCTGAGC
451 ATAACCCTTCTAGCCTTGAGCTATGCTGCAAATAATATGCCTTGGAGCTGAGC
* * * *
619905 GTAATCAAACTTGAAGGTCTTTGGTTGGGAAGATAACCCTTCTCGCCTTGA-CTTATGATGCAAA
1 GTAATCAAACTCGAAGGTCTTTTGAT-GGCAGATAACCCTTCTCGCCTTGAGC-TATGATGCAAA
* * * *
619969 TGATACGCCTTAGAGCTGAGCGTAGTCGAACTAGAAGGTCTTTGGTTGGCAGATAATCCTTCTCG
64 TGATATGCCTTAGAGCTGAGCGTAGTCGAACTAGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
*
620034 CCTTGAGCTATGCTGC
129 CTTTGAGCTATGCTGC
620050 CGATAGTTTC
Statistics
Matches: 550, Mismatches: 87, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
501 16 0.03
502 21 0.04
503 45 0.08
504 28 0.05
505 62 0.11
506 358 0.65
507 20 0.04
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (503 bp):
GTAATCAAACTCGAAGGTCTTTTGATGGCAGATAACCCTTCTCGCCTTGAGCTATGATGCAAATG
ATATGCCTTAGAGCTGAGCGTAGTCGAACTAGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCT
TTGAGCTATGCTGCAAATAATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGA
CAGATAACCCTTATAGCCTTAAGTTATGTTGTAAATGATACGCCTGAGAGCTGAGCGTAATAGAA
CTCGAAGGTCTTTGGTTGGCAAATATCCCTTCTTGACTTAAGCTATACAGCAAATAATGTGCCTT
GGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTAGCCTTGAGTTAT
ACTACAAACGATATGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGGAAGATAAC
CCTTCTAGCCTTGAGCTATGCTGCAAATAATATGCCTTGGAGCTGAGC
Done.