Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008413.1 Hibiscus syriacus cultivar Beakdansim tig00111191_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: 2772818
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:382535 original size:24 final size:23
Alignment explanation
Indices: 382508--382560 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
382498 TTTCCTTTTT
382508 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTT-GAGTGCTTTCAA
* *
382532 TTTCTTCTTTTGAGTGCTTTTAT
1 TTTCTTCTTTTGAGTGCTTTCAA
382555 TTTCTT
1 TTTCTT
382561 TGCTGTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (23 bp):
TTTCTTCTTTTGAGTGCTTTCAA
Found at i:383404 original size:90 final size:91
Alignment explanation
Indices: 383288--383459 Score: 274
Period size: 90 Copynumber: 1.9 Consensus size: 91
383278 GGGAAATGAT
* *
383288 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATG
*
383352 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * *
383378 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATG
*
383443 GGGGCTGGTCATATGCA
66 GGGGCTGGTCACATGCA
383460 GGGCACATGG
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 59 0.80
91 15 0.20
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.22
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:388178 original size:27 final size:26
Alignment explanation
Indices: 388121--388178 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
388111 AAGATTAGAA
388121 CAAAATAAATAAAAGATAAAAAAATT
1 CAAAATAAATAAAAGATAAAAAAATT
* * *
388147 GAAAATAAA-ATAAGATAATAAATATAT
1 CAAAATAAATAAAAGATAA-AAAAAT-T
388174 CAAAA
1 CAAAA
388179 GATCTCCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 8 0.31
26 13 0.50
27 5 0.19
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (26 bp):
CAAAATAAATAAAAGATAAAAAAATT
Found at i:389438 original size:18 final size:20
Alignment explanation
Indices: 389383--389431 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
389373 CATTCATGCA
389383 TCTAGTTCATTGAATAAAGT
1 TCTAGTTCATTGAATAAAGT
389403 TCTAGTTCATTGAATAAAG-
1 TCTAGTTCATTGAATAAAGT
389422 T-TAGTTCATT
1 TCTAGTTCATT
389432 AATTAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.31
19 1 0.03
20 19 0.66
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (20 bp):
TCTAGTTCATTGAATAAAGT
Found at i:389455 original size:16 final size:17
Alignment explanation
Indices: 389423--389474 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
389413 TGAATAAAGT
* *
389423 TAGTTCATTAATTAAAC
1 TAGTTCATTCATCAAAC
389440 TAG-TCATTCATCAAAC
1 TAGTTCATTCATCAAAC
* *
389456 TAGTTCATTGATTAAAC
1 TAGTTCATTCATCAAAC
389473 TA
1 TA
389475 ACTCTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (17 bp):
TAGTTCATTCATCAAAC
Found at i:391001 original size:19 final size:18
Alignment explanation
Indices: 390977--391019 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
390967 TGGGTTAGTG
390977 AAAAATAAAAAAAATCAAA
1 AAAAATAAAAAAAAT-AAA
390996 AAAAATAAAAAAAATAAA
1 AAAAATAAAAAAAATAAA
391014 ATAAAA
1 A-AAAA
391020 GAAATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.86, C:0.02, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAATAAAAAAAATAAA
Found at i:391024 original size:9 final size:9
Alignment explanation
Indices: 390977--391019 Score: 68
Period size: 9 Copynumber: 4.6 Consensus size: 9
390967 TGGGTTAGTG
390977 AAAAATAAA
1 AAAAATAAA
390986 AAAAATCAAA
1 AAAAAT-AAA
390996 AAAAATAAA
1 AAAAATAAA
391005 AAAAATAAA
1 AAAAATAAA
391014 ATAAAA
1 A-AAAA
391020 GAAATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 19 0.59
10 13 0.41
ACGTcount: A:0.86, C:0.02, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:392850 original size:23 final size:24
Alignment explanation
Indices: 392822--392875 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
392812 AAAATCAGCA
392822 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
392845 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
*
392869 AAAAAAA
1 AAGAAAA
392876 AAGTTAGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.65, C:0.11, G:0.15, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:397610 original size:21 final size:21
Alignment explanation
Indices: 397586--397630 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
397576 AAGAAGAAAC
*
397586 GAGAGTTGAAAA-AGACATTGA
1 GAGAATTGAAAAGAGA-ATTGA
397607 GAGAATTGAAAAGAGAATTGA
1 GAGAATTGAAAAGAGAATTGA
397628 GAG
1 GAG
397631 TGAAAATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.49, C:0.02, G:0.31, T:0.18
Consensus pattern (21 bp):
GAGAATTGAAAAGAGAATTGA
Found at i:399256 original size:17 final size:17
Alignment explanation
Indices: 399234--399286 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
399224 TGAATATAGT
399234 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
399251 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
399268 TAGTTTATTGATTAAAC
1 TAGTTCATTAATTAAAC
399285 TA
1 TA
399287 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:403662 original size:2 final size:2
Alignment explanation
Indices: 403655--403686 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
403645 CATGTTTTAA
403655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
403687 GTTTTAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:405615 original size:90 final size:91
Alignment explanation
Indices: 405462--405643 Score: 258
Period size: 90 Copynumber: 2.0 Consensus size: 91
405452 GGGAAATGAT
* *
405462 GCTTGGCCGAATAGGGAGATAGCTCTTCATCTTGGCACCTAAATAAACCACATACAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATACAAGGCACATG
*
405526 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * * * *
405552 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATACAAGGCACATG
* **
405617 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
405643 G
1 G
405644 GTGTTCTAGG
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 57 0.71
91 23 0.29
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATACAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:408977 original size:24 final size:23
Alignment explanation
Indices: 408942--408986 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
408932 TTCTTTCTTT
408942 ATTTTTCTTTTTCAAGTGCTTTCA
1 ATTTTTCTTTTTCAA-TGCTTTCA
*
408966 ATTTCTTC-TTTTGAATGCTTT
1 ATTT-TTCTTTTTCAATGCTTT
408987 TGTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 10 0.53
25 3 0.16
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.60
Consensus pattern (23 bp):
ATTTTTCTTTTTCAATGCTTTCA
Found at i:411619 original size:13 final size:13
Alignment explanation
Indices: 411601--411625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
411591 CTGTTAATCG
411601 TTGACTTTGACCA
1 TTGACTTTGACCA
411614 TTGACTTTGACC
1 TTGACTTTGACC
411626 GAAAAGTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGACTTTGACCA
Found at i:413499 original size:27 final size:27
Alignment explanation
Indices: 413468--413528 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
413458 GTTTCCTTAA
413468 GATCTATTCAGTGATGATTCCGAAGAT
1 GATCTATTCAGTGATGATTCCGAAGAT
*
413495 GATCTATTCAGTGATGATTCTGAAGAT
1 GATCTATTCAGTGATGATTCCGAAGAT
413522 GATCTAT
1 GATCTAT
413529 GGATAAGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (27 bp):
GATCTATTCAGTGATGATTCCGAAGAT
Found at i:413905 original size:48 final size:48
Alignment explanation
Indices: 413853--413957 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
413843 ATTATATTTA
* * * *
413853 ATTTCTGA-CTTGAATTCTGTTCTGATA-CATGACCTGAATTTTGTTCTG
1 ATTTCTGATCTAG-ATTCTGTTCGGATATC-TGACATGAATTATGTTCTG
* * *
413901 ATTTCTGATCTAGATTTTGTTCGGATATCTGATATGAATTATGTTTTG
1 ATTTCTGATCTAGATTCTGTTCGGATATCTGACATGAATTATGTTCTG
413949 ATTTCTGAT
1 ATTTCTGAT
413958 ATCTCCATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 44 0.92
49 4 0.08
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (48 bp):
ATTTCTGATCTAGATTCTGTTCGGATATCTGACATGAATTATGTTCTG
Found at i:413917 original size:24 final size:24
Alignment explanation
Indices: 413853--413959 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
413843 ATTATATTTA
*
413853 ATTTCTGACT-TGAATTCTGTTCTG
1 ATTTCTGA-TATGAATTTTGTTCTG
* **
413877 A-TACATGACCTGAATTTTGTTCTG
1 ATTTC-TGATATGAATTTTGTTCTG
* *
413901 ATTTCTGATCT-AGATTTTGTTCGG
1 ATTTCTGATATGA-ATTTTGTTCTG
* * *
413925 ATATCTGATATGAATTATGTTTTG
1 ATTTCTGATATGAATTTTGTTCTG
413949 ATTTCTGATAT
1 ATTTCTGATAT
413960 CTCCATTTAC
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
23 3 0.05
24 60 0.91
25 3 0.05
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (24 bp):
ATTTCTGATATGAATTTTGTTCTG
Found at i:414146 original size:19 final size:20
Alignment explanation
Indices: 414122--414167 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
414112 GGTAGTGTTC
414122 ATGTTTTAAAA-ATATATAT
1 ATGTTTTAAAAGATATATAT
*
414141 ATGTTTTAAAAGATATGTAT
1 ATGTTTTAAAAGATATATAT
414161 AT-TTTTA
1 ATGTTTTA
414168 CTGGTTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (20 bp):
ATGTTTTAAAAGATATATAT
Found at i:416114 original size:13 final size:13
Alignment explanation
Indices: 416096--416127 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
416086 ATGTTGATCG
*
416096 TTGACCGTTGACT
1 TTGACCGTTAACT
416109 TTGACCGTTAACT
1 TTGACCGTTAACT
416122 TTGACC
1 TTGACC
416128 AAAAAAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (13 bp):
TTGACCGTTAACT
Found at i:418012 original size:27 final size:27
Alignment explanation
Indices: 417981--418041 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
417971 GTTTCCTTAA
*
417981 GATCTATTCCGTGATGATTCCGAAGAT
1 GATCTATTCAGTGATGATTCCGAAGAT
418008 GATCTATTCAGTGATGATTCCGAAGAT
1 GATCTATTCAGTGATGATTCCGAAGAT
418035 GATCTAT
1 GATCTAT
418042 GGATAAGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (27 bp):
GATCTATTCAGTGATGATTCCGAAGAT
Found at i:418400 original size:24 final size:24
Alignment explanation
Indices: 418377--418472 Score: 77
Period size: 24 Copynumber: 4.0 Consensus size: 24
418367 ATTTCCGACT
* *
418377 TGAATTCTGTTATGATACATGA-C
1 TGAATTCTGTTATGATATATGATA
* * * *
418400 TGGATTCTGTTCTGATTTATGATC
1 TGAATTCTGTTATGATATATGATA
* *
418424 TGGATTTTGTTATGATATATGATA
1 TGAATTCTGTTATGATATATGATA
* * * *
418448 TGAATTTTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGATATATGATA
418472 T
1 T
418473 CTCTGTTTAC
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
23 18 0.30
24 42 0.70
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTATGATATATGATA
Found at i:418406 original size:23 final size:24
Alignment explanation
Indices: 418380--418446 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
418370 TCCGACTTGA
*
418380 ATTCTGTTATGATACATGA-CTGG
1 ATTCTGTTATGATATATGATCTGG
* *
418403 ATTCTGTTCTGATTTATGATCTGG
1 ATTCTGTTATGATATATGATCTGG
*
418427 ATTTTGTTATGATATATGAT
1 ATTCTGTTATGATATATGAT
418447 ATGAATTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 16 0.43
24 21 0.57
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.48
Consensus pattern (24 bp):
ATTCTGTTATGATATATGATCTGG
Found at i:425068 original size:11 final size:11
Alignment explanation
Indices: 425052--425092 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
425042 AACCCCACAT
425052 AAAAAGAAAAA
1 AAAAAGAAAAA
425063 AAAAAG--AAA
1 AAAAAGAAAAA
*
425072 AAAAGGAAAAA
1 AAAAAGAAAAA
425083 AAAGAAGAAA
1 AAA-AAGAAA
425093 TAGAAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
9 8 0.32
11 12 0.48
12 5 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:425073 original size:18 final size:21
Alignment explanation
Indices: 425052--425092 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
425042 AACCCCACAT
425052 AAAAA-GAAAAAAAA-AAGAA
1 AAAAAGGAAAAAAAAGAAGAA
425071 AAAAAGGAAAAAAAAGAAGAA
1 AAAAAGGAAAAAAAAGAAGAA
425092 A
1 A
425093 TAGAAGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 9 0.45
21 6 0.30
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAGGAAAAAAAAGAAGAA
Found at i:428201 original size:23 final size:24
Alignment explanation
Indices: 428173--428226 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
428163 AAAATCAGCA
428173 AAGAAAATAAAACCACTC-AAAAG
1 AAGAAAATAAAACCACTCGAAAAG
* * * *
428196 AAGAAATTGAAAGCTCTCGAAAAG
1 AAGAAAATAAAACCACTCGAAAAG
428220 AAGAAAA
1 AAGAAAA
428227 AGAAAGAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.61, C:0.13, G:0.15, T:0.11
Consensus pattern (24 bp):
AAGAAAATAAAACCACTCGAAAAG
Found at i:460646 original size:24 final size:24
Alignment explanation
Indices: 460600--460647 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
460590 CTTTGCTTTG
* *
460600 TCTTCTTTTTGAGTGCTGGAATTT
1 TCTTCTTTTGGAGTGCTGCAATTT
*
460624 TCTTCTTTTGGAGTGCTTCAATTT
1 TCTTCTTTTGGAGTGCTGCAATTT
460648 GTTTGCTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.12, C:0.15, G:0.19, T:0.54
Consensus pattern (24 bp):
TCTTCTTTTGGAGTGCTGCAATTT
Found at i:466756 original size:32 final size:32
Alignment explanation
Indices: 466720--466791 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
466710 AATGGCCTTC
466720 ATTTCTTCCCACGAAGTGATGGGGCGTTCACA
1 ATTTCTTCCCACGAAGTGATGGGGCGTTCACA
* *
466752 ATTTCTTCCCACGTAGTGATGGGGCGTTCACC
1 ATTTCTTCCCACGAAGTGATGGGGCGTTCACA
466784 ATTTCTTC
1 ATTTCTTC
466792 TTCTTGAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.33
Consensus pattern (32 bp):
ATTTCTTCCCACGAAGTGATGGGGCGTTCACA
Found at i:467415 original size:22 final size:23
Alignment explanation
Indices: 467371--467416 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
467361 TTGGTGCTGG
467371 AAACAAGATAAGAAATAAGATTA
1 AAACAAGATAAGAAATAAGATTA
467394 AAACAAGATAA-AGAA-AAGATTA
1 AAACAAGATAAGA-AATAAGATTA
467416 A
1 A
467417 GGAATTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.67, C:0.04, G:0.13, T:0.15
Consensus pattern (23 bp):
AAACAAGATAAGAAATAAGATTA
Found at i:470812 original size:25 final size:24
Alignment explanation
Indices: 470770--470817 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
470760 TTCTTTGCTT
* *
470770 TTTTGTAGTGCTGGAATTTTCTTTC
1 TTTTGGAGTGCTGCAA-TTTCTTTC
*
470795 TTTTGGAGTGCTTCAATTTCTTT
1 TTTTGGAGTGCTGCAATTTCTTT
470818 TCTGATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.56
Consensus pattern (24 bp):
TTTTGGAGTGCTGCAATTTCTTTC
Found at i:471603 original size:367 final size:370
Alignment explanation
Indices: 470954--471643 Score: 1140
Period size: 367 Copynumber: 1.9 Consensus size: 370
470944 GTACCTCTTC
* *
470954 AATTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCACAACTATATGGCTCAAAAGAGATAG
1 AATTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCACAACTATATGGCTCAAAACAAATAG
* * *
471019 TTAAGGGTGGTAAACGTAAGGGTGAATAGGTGGGTTGTTTAATAAATGAGAGATGGAAGCTGTAG
66 TTAAGGGTGGTAAACGTAAGGGTGAATAGGTGGGCTGCTTAAT--ATGAGAGATGGAAGCTGAAG
471084 ATGATTGATATGGCTATGGGTTATGGTTAATGAAACAAAGGGATGGTTGTAAGGATAGTATCTTA
129 ATGATTGATATGGCTATGGGTTATGGTTAATGAAACAAAGGGATGGTTGTAAGGATAGTATCTTA
471149 AAGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTA
194 AAGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTA
*
471214 AGGGGTGATATGAAGGACTTTGACCCACTAGTTATA-AGAATTAGAAACCAAAAGTATCAAGGGG
259 AGGGGTGATATGAAGGACTTTGACCCACTAGTTATAGAGAACTAGAAACCAAAAGTATCAAGGGG
471278 AAAGGGGTTGATACCACATGATGTAAGGCTCTTCTGATGCCTTAACA
324 AAAGGGGTTGATACCACATGATGTAAGGCTCTTCTGATGCCTTAACA
*
471325 AATTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCA-AAGTGA-ATGGCTCAAAACATAAT
1 AATTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCACAACT-ATATGGCTCAAAACA-AAT
* * *
471388 GGTTAAGGGTGGTAAACGTATGGGTGATTAGGTGGGCTGCTTAAT-TGAGAGATGGAAG-TGGAA
64 AGTTAAGGGTGGTAAACGTAAGGGTGAATAGGTGGGCTGCTTAATATGAGAGATGGAAGCT-GAA
* * *
471451 GATGTTTGATATGGCTAT-GGTTATGGTTTATGAAACAAAGGGATGGTTGTGAGGATAGTATCTT
128 GATGATTGATATGGCTATGGGTTATGGTTAATGAAACAAAGGGATGGTTGTAAGGATAGTATCTT
*
471515 AAAGAAGACTCAAAGAAGAACCAATGCTATATAGAGCAAAGACCCAGACTTTATATTGCTTCTTT
193 AAAGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTT
* * *
471580 AAGGGGTGATATGAAGTACTTTGACCCACTAGTTATAGAGAACTAGGAACCAGAAGTATCAAGG
258 AAGGGGTGATATGAAGGACTTTGACCCACTAGTTATAGAGAACTAGAAACCAAAAGTATCAAGG
471644 TAAAAAGAGA
Statistics
Matches: 298, Mismatches: 17, Indels: 11
0.91 0.05 0.03
Matches are distributed among these distances:
367 145 0.49
368 55 0.18
370 15 0.05
371 83 0.28
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.26
Consensus pattern (370 bp):
AATTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCACAACTATATGGCTCAAAACAAATAG
TTAAGGGTGGTAAACGTAAGGGTGAATAGGTGGGCTGCTTAATATGAGAGATGGAAGCTGAAGAT
GATTGATATGGCTATGGGTTATGGTTAATGAAACAAAGGGATGGTTGTAAGGATAGTATCTTAAA
GAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTAAG
GGGTGATATGAAGGACTTTGACCCACTAGTTATAGAGAACTAGAAACCAAAAGTATCAAGGGGAA
AGGGGTTGATACCACATGATGTAAGGCTCTTCTGATGCCTTAACA
Found at i:486354 original size:17 final size:16
Alignment explanation
Indices: 486326--486380 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
486316 AATTGGACTG
486326 CAAAAAGAAAAGAAAAGA
1 CAAAAAG-AAAGAAAA-A
*
486344 CAAAAAGAAAGAAAAT
1 CAAAAAGAAAGAAAAA
*
486360 CAGAAAGAAAGAAAAA
1 CAAAAAGAAAGAAAAA
*
486376 GAAAA
1 CAAAA
486381 TTCAAAAGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 17 0.53
17 8 0.25
18 7 0.22
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.02
Consensus pattern (16 bp):
CAAAAAGAAAGAAAAA
Found at i:488237 original size:17 final size:18
Alignment explanation
Indices: 488208--488241 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
488198 CCAAATTGAT
488208 CAAATCAAGATAAAACAA
1 CAAATCAAGATAAAACAA
488226 CAAATC-AGATAAAACA
1 CAAATCAAGATAAAACA
488242 GTGTTGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.65, C:0.18, G:0.06, T:0.12
Consensus pattern (18 bp):
CAAATCAAGATAAAACAA
Found at i:496715 original size:19 final size:20
Alignment explanation
Indices: 496691--496730 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
496681 TATCCTTTCT
*
496691 TTATTTCTTTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
*
496710 TTATTTATTTTTATTACTTA
1 TTATTTATTTTCATTACTTA
496730 T
1 T
496731 ATTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:508782 original size:16 final size:16
Alignment explanation
Indices: 508763--508793 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
508753 CATGCCTTGC
508763 ACATGGAAGCTTTGGT
1 ACATGGAAGCTTTGGT
508779 ACATGGAAGCTTTGG
1 ACATGGAAGCTTTGG
508794 CGCCAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.29
Consensus pattern (16 bp):
ACATGGAAGCTTTGGT
Found at i:511678 original size:30 final size:31
Alignment explanation
Indices: 511626--511685 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
511616 CTTAGCTTTA
**
511626 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
511656 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
511686 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:512597 original size:19 final size:20
Alignment explanation
Indices: 512573--512623 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
512563 CGGCCAAGAG
* *
512573 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
512592 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
512612 CATGTATTTTCA
1 CATGTATTTTCA
512624 AATGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:513060 original size:19 final size:20
Alignment explanation
Indices: 513036--513075 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
513026 TATCCTTTCT
513036 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
* *
513055 TTATTTCTTTTGATTACTTA
1 TTATTTCATTTCATTACTTA
513075 T
1 T
513076 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:514315 original size:19 final size:20
Alignment explanation
Indices: 514291--514336 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
514281 CGTCCAAGAG
**
514291 CATGTATCTTCAT-TTAAAT
1 CATGTATCTTCATCAAAAAT
*
514310 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
514330 CATGTAT
1 CATGTAT
514337 TTTGAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:517719 original size:22 final size:20
Alignment explanation
Indices: 517694--517733 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
517684 ATGTTTGTTT
517694 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
517716 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
517734 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:523160 original size:30 final size:31
Alignment explanation
Indices: 523108--523167 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
523098 CTTAGCTTTA
**
523108 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
523138 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
523168 GGAAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:524101 original size:19 final size:20
Alignment explanation
Indices: 524077--524122 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
524067 CGTCCAACAG
*
524077 CATGTATCATCAT-TAAAAT
1 CATGTATCATCATCAAAAAT
**
524096 CATGTATTTTCATCAAAAAT
1 CATGTATCATCATCAAAAAT
524116 CATGTAT
1 CATGTAT
524123 TTTCAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (20 bp):
CATGTATCATCATCAAAAAT
Found at i:524564 original size:19 final size:20
Alignment explanation
Indices: 524540--524579 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
524530 TATCCTTTAT
524540 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
524559 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
524579 T
1 T
524580 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:527148 original size:24 final size:23
Alignment explanation
Indices: 527113--527161 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
527103 AAGAAAATCA
**
527113 AACTAAAAAGAAGAAATTGAAAG
1 AACTAAAAAGAAGAAAAAGAAAG
527136 AACTCAAAAAGAAGAAAAAGAAAG
1 AACT-AAAAAGAAGAAAAAGAAAG
527160 AA
1 AA
527162 AGAAAAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.69, C:0.06, G:0.16, T:0.08
Consensus pattern (23 bp):
AACTAAAAAGAAGAAAAAGAAAG
Found at i:528408 original size:24 final size:21
Alignment explanation
Indices: 528374--528416 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
528364 TCCACAAGAT
*
528374 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
528396 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
528417 ATAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:530275 original size:91 final size:91
Alignment explanation
Indices: 530120--530300 Score: 272
Period size: 91 Copynumber: 2.0 Consensus size: 91
530110 CCTAGAACAC
* *
530120 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
*
530185 AAGAGTTCTCTCCCTATTCGGCCAAT
66 AAGAGTTCTCTCCCTATTCGACCAAT
** * * * *
530211 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTGATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
*
530276 AAGAGTTCTCTCCTTATTCGACCAA
66 AAGAGTTCTCTCCCTATTCGACCAA
530301 GCATCAACTA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
AAGAGTTCTCTCCCTATTCGACCAAT
Found at i:545444 original size:91 final size:91
Alignment explanation
Indices: 545281--545454 Score: 258
Period size: 91 Copynumber: 1.9 Consensus size: 91
545271 TGCTTGGTCA
* *
545281 AATAGGGATAGAACTCTTCATCTTGGCACCTAAATGAACCATATGCAAGGCACATAGGGGCTGAT
1 AATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATAGGGGCTGAT
545346 CACATGCAAAACACATGGCTTAGCCG
66 CACATGCAAAACACATGGCTTAGCCG
* * * * *
545372 AATAGGGAGAGAATTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATGGGGGCTGGT
1 AATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATAGGGGCTGAT
* **
545437 CATATGCAAGGCACATGG
66 CACATGCAAAACACATGG
545455 GTGTTCTAGG
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 73 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (91 bp):
AATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATAGGGGCTGAT
CACATGCAAAACACATGGCTTAGCCG
Found at i:554568 original size:13 final size:13
Alignment explanation
Indices: 554550--554575 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
554540 TAAACACCTC
554550 ACATACCTTTTCA
1 ACATACCTTTTCA
554563 ACATACCTTTTCA
1 ACATACCTTTTCA
554576 TCTTTGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:559818 original size:19 final size:20
Alignment explanation
Indices: 559794--559833 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
559784 TATCCTTTCT
559794 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
559813 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
559833 T
1 T
559834 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:563420 original size:24 final size:23
Alignment explanation
Indices: 563361--563421 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
563351 AAAATCCAGT
*
563361 AAAGAAAATCAAAGCACTCAAAA
1 AAAGAAAATGAAAGCACTCAAAA
*
563384 AAAGAAATTGAAAGCACTCGAAAA
1 AAAGAAAATGAAAGCACTC-AAAA
* *
563408 GAAGAAAAAGAAAG
1 AAAGAAAATGAAAG
563422 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 17 0.53
24 15 0.47
ACGTcount: A:0.64, C:0.11, G:0.16, T:0.08
Consensus pattern (23 bp):
AAAGAAAATGAAAGCACTCAAAA
Found at i:567833 original size:13 final size:13
Alignment explanation
Indices: 567815--567840 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
567805 AACACCTCTC
567815 ACATACCTTTTCA
1 ACATACCTTTTCA
567828 ACATACCTTTTCA
1 ACATACCTTTTCA
567841 TATTTGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:568993 original size:19 final size:21
Alignment explanation
Indices: 568963--569014 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
568953 CGGCGAAGAG
*
568963 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
*
568982 CATGTCTTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
569003 CATGTATTTTCA
1 CATGTATTTTCA
569015 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:570092 original size:19 final size:19
Alignment explanation
Indices: 570068--570117 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
570058 GAAACCCCTT
*
570068 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
570087 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
570106 TGAAGATACATG
1 TGAAAATACATG
570118 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:573492 original size:11 final size:11
Alignment explanation
Indices: 573478--573533 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
573468 TTCTTTTGAA
573478 TTCTTTTTCTT
1 TTCTTTTTCTT
573489 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
573502 TTCTTCTTCTTT
1 TTCTTTTTC-TT
573514 ATGTCTTTTTC-T
1 -T-TCTTTTTCTT
573526 TTCTTTTT
1 TTCTTTTT
573534 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 7 0.18
12 8 0.21
13 9 0.24
14 7 0.18
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:573500 original size:19 final size:18
Alignment explanation
Indices: 573478--573533 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
573468 TTCTTTTGAA
573478 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
573496 CTTC-TTTTCTTCTTCTTTAT
1 -TTCTTTTTCTT-TTCTTT-T
*
573516 GTCTTTTTC-TTTCTTTT
1 TTCTTTTTCTTTTCTTTT
573533 T
1 T
573534 GCACTCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 1 0.03
18 13 0.41
19 12 0.38
20 6 0.19
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:574304 original size:19 final size:20
Alignment explanation
Indices: 574263--574313 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
574253 GAAACCCCTT
*
574263 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
574283 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
574302 TGAAGATACATG
1 TGAAAATACATG
574314 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:579496 original size:949 final size:952
Alignment explanation
Indices: 577384--579849 Score: 4884
Period size: 949 Copynumber: 2.6 Consensus size: 952
577374 CAGCTGAAAT
577384 GAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTGACAAC
1 GAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTGACAAC
577449 TTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATGAAAGTTTTCCTAGCTCCTTATCA
66 TTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATGAAAGTTTTCCTAGCTCCTTATCA
577514 TTAGTTAAGCTCAAATGTAGCTCCCAAGTGTTGGCCGAATATGCCTACATGCATAACATAAAGAA
131 TTAGTTAAGCTCAAATGTAGCTCCCAAGTGTTGGCCGAATATGCCTACATGCATAACATAAAGAA
*
577579 ATAAACTAAGTATATAAACTATATAATGCATATAATATAATGATGTGCATATTATAAAGATGTGA
196 ATAAACTAAGTATATAAACTATATAATGCATATAATATAATGATGTGCATATTATAAAGATATGA
577644 ACTATAGGTTATAATAATAATTCATGCATCATATGATAATGAATGAATATTAATATTATAACTAT
261 ACTATAGGTTATAATAATAATTCATGCATCATATGATAATGAATGAATATTAATATTATAACTAT
577709 AGATTATATACATGAATATTAATCAATGATGCAAACCATAGGATATAATGAATGAATGCACATAC
326 AGATTATATACATGAATATTAATCAATGATGCAAACCATAGGATATAATGAATGAATGCACATAC
577774 TATGAGAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATAATAATATATATAGTGCATAAA
391 TATGAGAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATAATAATATATATAGTGCATAAA
577839 TAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATATTGAGTTTGATGGTTCTTCAATGAT
456 TAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATATTGAGTTTGATGGTTCTTCAATGAT
577904 GTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACATCATCCTCCCCTTCTTTTGGGCG
521 GTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACATCATCCTCCCCTTCTTTTGGGCG
577969 ATTTGTCCTCAAATCGAAAGATGACTTCTCCAAATTGTACGCCCATTCAATCGTTGCTGGTTTGC
586 ATTTGTCCTCAAATCGAAAGATGACTTCTCCAAATTGTACGCCCATTCAATCGTTGCTGGTTTGC
578034 TTCCATAGATCCTCTTTATGAAAGGATTCTTATCAAGATTCATATCCCTTGAATAGGTTCCTTGA
651 TTCCATAGATCCTCTTTATGAAAGGATTCTTATCAAGATTCATATCCCTTGAATAGGTTCCTTGA
578099 ATGTCCATGACCTGAAAAGATAAGAAACTTTCATAAGTAAGAGAATTGTTAATTATGAACAAGTT
716 ATGTCCATGACCTGAAAAGATAAGAAACTTTCATAAGTAAGAGAATTGTTAATTATGAACAAGTT
578164 AAAAATGTACTCCCTGTTCTCATGTTTTGAATAGCCAAAAGTTATGTCATTTGAATCACAAGACA
781 AAAAATGTACTCCCTGTTCTCATGTTTTGAATAGCCAAAAGTTATGTCATTTGAATCACAAGACA
578229 TGTTGTTTTGAATGATCACTTCTTTTCGCACTCTAAAAGACATATTCTTTGGTTTCCCAAAGATC
846 TGTTGTTTTGAATGATCACTTCTTTTCGCACTCTAAAAGACATATTCTTTGGTTTCCCAAAGATC
578294 ACATCCTTTAAATGAAAAGTCATATCTTCTAGTACTTGAGAA
911 ACATCCTTTAAATGAAAAGTCATATCTTCTAGTACTTGAGAA
578336 GAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTGACAAC
1 GAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTGACAAC
578401 TTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATGAAAGTTTTCCTAGCTCCTTATCA
66 TTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATGAAAGTTTTCCTAGCTCCTTATCA
578466 TTAGTTAAGCTCAAATGTAGCTCCCAAGTGTTGGCCGAATATGCCTACATGCATAACATAAAGAA
131 TTAGTTAAGCTCAAATGTAGCTCCCAAGTGTTGGCCGAATATGCCTACATGCATAACATAAAGAA
578531 ATAAACTAAGTATATAAACTATATAATGCATATAATATAATGATGTGCATATTATAAAGATATGA
196 ATAAACTAAGTATATAAACTATATAATGCATATAATATAATGATGTGCATATTATAAAGATATGA
578596 ACTATAGGTTATAATAATAATTCATGCATCATATGATAATGAATGAATATTAATATTATAACTAT
261 ACTATAGGTTATAATAATAATTCATGCATCATATGATAATGAATGAATATTAATATTATAACTAT
*
578661 AGATTATATACATGAATATTAATCAATGATGCAAACCATATGATATAATGAATGAATGCACATAC
326 AGATTATATACATGAATATTAATCAATGATGCAAACCATAGGATATAATGAATGAATGCACATAC
578726 TATGAGAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATAATAATATATATAGTGCATAAA
391 TATGAGAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATAATAATATATATAGTGCATAAA
578791 TAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATATTGAGTTTGATGGTTCTTCAATGAT
456 TAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATATTGAGTTTGATGGTTCTTCAATGAT
578856 GTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACATCATCCTCCCCTTC-TTTGGGCG
521 GTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACATCATCCTCCCCTTCTTTTGGGCG
578920 ATTTGTCCTCAAATCGAAAGATGACTTCTCCAAATTGTACGCCCATTCAATCGTTGCTGGTTTGC
586 ATTTGTCCTCAAATCGAAAGATGACTTCTCCAAATTGTACGCCCATTCAATCGTTGCTGGTTTGC
*
578985 TTCCATAGATCCTCTTTATGAAAGGATTCTTATCAATATTCATATCCC-TGAATAGGTTCCTTGA
651 TTCCATAGATCCTCTTTATGAAAGGATTCTTATCAAGATTCATATCCCTTGAATAGGTTCCTTGA
579049 ATGTCCATGACCTGAAAAGATAAG-AACTTTCATAAGTAAGAGAATTGTTAATTATGAACAAGTT
716 ATGTCCATGACCTGAAAAGATAAGAAACTTTCATAAGTAAGAGAATTGTTAATTATGAACAAGTT
579113 AAAAATGTACTCCCTGTTCTCATGTTTTGAATAGCCAAAAGTTATGTCATTTGAATCACAAGACA
781 AAAAATGTACTCCCTGTTCTCATGTTTTGAATAGCCAAAAGTTATGTCATTTGAATCACAAGACA
579178 TGTTGTTTTGAATGATCACTTCTTTTCGCACTCTAAAAGACATATTCTTTGGTTTCCCAAAGATC
846 TGTTGTTTTGAATGATCACTTCTTTTCGCACTCTAAAAGACATATTCTTTGGTTTCCCAAAGATC
579243 ACATCCTTTAAATGAAAAGTCATATCTTCTAGTACTTGAGAA
911 ACATCCTTTAAATGAAAAGTCATATCTTCTAGTACTTGAGAA
579285 GAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTGACAAC
1 GAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTGACAAC
579350 TTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATGAAAGTTTTCCTAGCTCCTTATCA
66 TTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATGAAAGTTTTCCTAGCTCCTTATCA
579415 TTAGTTAAGCTCAAATGTAGCTCCCAAGTGTTGGCCGAATATGCCTACATGCATAACATAAAGAA
131 TTAGTTAAGCTCAAATGTAGCTCCCAAGTGTTGGCCGAATATGCCTACATGCATAACATAAAGAA
579480 ATAAACTAAGTATATAAACTATATAATGCATATAATATAATGATGTGCATATTATAAAGATATGA
196 ATAAACTAAGTATATAAACTATATAATGCATATAATATAATGATGTGCATATTATAAAGATATGA
579545 ACTATAGGTTATAATAATAATTCATGCATCATATGATAATGAATGAATATTAATATTATAACTAT
261 ACTATAGGTTATAATAATAATTCATGCATCATATGATAATGAATGAATATTAATATTATAACTAT
579610 AGATTATATACATGAATATTAATCAATGATGCAAACCATAGGATATAATGAATGAATGCACATAC
326 AGATTATATACATGAATATTAATCAATGATGCAAACCATAGGATATAATGAATGAATGCACATAC
579675 TATGAGAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATAATAATATATATAGTGCATAAA
391 TATGAGAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATAATAATATATATAGTGCATAAA
579740 TAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATATTGAGTTTGATGGTTCTTCAATGAT
456 TAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATATTGAGTTTGATGGTTCTTCAATGAT
579805 GTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACATCA
521 GTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACATCA
579850 CCATGGAAAC
Statistics
Matches: 1510, Mismatches: 4, Indels: 3
1.00 0.00 0.00
Matches are distributed among these distances:
949 776 0.51
950 40 0.03
951 120 0.08
952 574 0.38
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (952 bp):
GAGGTCTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTGACAAC
TTTTCATCATTTGTTCTTCATGATCTCCCGAGTCATCCTATGAAAGTTTTCCTAGCTCCTTATCA
TTAGTTAAGCTCAAATGTAGCTCCCAAGTGTTGGCCGAATATGCCTACATGCATAACATAAAGAA
ATAAACTAAGTATATAAACTATATAATGCATATAATATAATGATGTGCATATTATAAAGATATGA
ACTATAGGTTATAATAATAATTCATGCATCATATGATAATGAATGAATATTAATATTATAACTAT
AGATTATATACATGAATATTAATCAATGATGCAAACCATAGGATATAATGAATGAATGCACATAC
TATGAGAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATAATAATATATATAGTGCATAAA
TAAGTAAATATAATATAAAGTATGGTAGAACTCCCTTATATTGAGTTTGATGGTTCTTCAATGAT
GTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACATCATCCTCCCCTTCTTTTGGGCG
ATTTGTCCTCAAATCGAAAGATGACTTCTCCAAATTGTACGCCCATTCAATCGTTGCTGGTTTGC
TTCCATAGATCCTCTTTATGAAAGGATTCTTATCAAGATTCATATCCCTTGAATAGGTTCCTTGA
ATGTCCATGACCTGAAAAGATAAGAAACTTTCATAAGTAAGAGAATTGTTAATTATGAACAAGTT
AAAAATGTACTCCCTGTTCTCATGTTTTGAATAGCCAAAAGTTATGTCATTTGAATCACAAGACA
TGTTGTTTTGAATGATCACTTCTTTTCGCACTCTAAAAGACATATTCTTTGGTTTCCCAAAGATC
ACATCCTTTAAATGAAAAGTCATATCTTCTAGTACTTGAGAA
Found at i:580949 original size:16 final size:16
Alignment explanation
Indices: 580928--580960 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
580918 TAGTTAGCTC
580928 ATTTGCATTATAACAT
1 ATTTGCATTATAACAT
*
580944 ATTTGCATTCTAACAT
1 ATTTGCATTATAACAT
580960 A
1 A
580961 GGTGGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTATAACAT
Found at i:581984 original size:23 final size:22
Alignment explanation
Indices: 581930--581987 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
581920 CTTTTCTTTA
*
581930 TTTCTTTTTCTTTTTCAAGTGC
1 TTTCATTTTCTTTTTCAAGTGC
* *
581952 TTTCAATTTCTTCTTTTAAGTGC
1 TTTCATTTTCTT-TTTCAAGTGC
**
581975 TTTTGTTTTCTTT
1 TTTCATTTTCTTT
581988 GCTGAATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.10, C:0.16, G:0.09, T:0.66
Consensus pattern (22 bp):
TTTCATTTTCTTTTTCAAGTGC
Found at i:584778 original size:19 final size:20
Alignment explanation
Indices: 584758--584793 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
584748 CTTTCTTTAT
584758 TTTA-TTTCATT-CTTATTA
1 TTTATTTTCATTACTTATTA
584776 TTTATTTTCATTACTTAT
1 TTTATTTTCATTACTTAT
584794 ATTATTATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 7 0.44
20 5 0.31
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTTCATTACTTATTA
Found at i:584796 original size:19 final size:17
Alignment explanation
Indices: 584754--584796 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
584744 TATCCTTTCT
584754 TTAT-TTTATTTCATTC
1 TTATATTTATTTCATTC
584770 TTATTATTTATTTTCATTAC
1 TTA-TATTTA-TTTCATT-C
584790 TTATATT
1 TTATATT
584797 ATTATCCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 1 0.04
18 4 0.17
19 11 0.48
20 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTTATTTCATTC
Found at i:585092 original size:19 final size:18
Alignment explanation
Indices: 585062--585147 Score: 68
Period size: 19 Copynumber: 4.6 Consensus size: 18
585052 ATTGGAGTGC
*
585062 AAAAAGAAAGAAAAAGAG
1 AAAAAGAAAGAAAAAAAG
*
585080 AAAAAGAAGAGAAAAATCAG
1 AAAAAGAA-AGAAAAA-AAG
585100 -AAAAGAATA-AAAGAAAAG
1 AAAAAGAA-AGAAA-AAAAG
**
585118 AAAAAGAATTCAAAAAAAG
1 AAAAAGAA-AGAAAAAAAG
585137 AAGAAAGAAAG
1 AA-AAAGAAAG
585148 CAAGCCAAGG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
18 13 0.23
19 32 0.57
20 11 0.20
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAGAAAAAAAG
Found at i:586155 original size:22 final size:22
Alignment explanation
Indices: 586113--586156 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
586103 AAAATACCTT
* *
586113 AAAGAAGAACATTGAAGCAATG
1 AAAGAACAACATTAAAGCAATG
586135 AAAGAACAAC-TTAAAGACAATG
1 AAAGAACAACATTAAAG-CAATG
586157 CAACTGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.57, C:0.11, G:0.18, T:0.14
Consensus pattern (22 bp):
AAAGAACAACATTAAAGCAATG
Found at i:587478 original size:23 final size:23
Alignment explanation
Indices: 587433--587478 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
587423 TTATACCTAT
*
587433 AGATGTTTATTTCATATGTTATA
1 AGATGTTTATTTCATATGATATA
*
587456 AGATAGTTTTTTTCATAT-ATATA
1 AGAT-GTTTATTTCATATGATATA
587479 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (23 bp):
AGATGTTTATTTCATATGATATA
Found at i:590037 original size:24 final size:21
Alignment explanation
Indices: 590003--590045 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
589993 TGCACAAGAT
*
590003 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
590025 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
590046 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:597037 original size:22 final size:21
Alignment explanation
Indices: 596998--597038 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
596988 CCATCTCTAT
*
596998 TTCATCATCAACATCATCAAC
1 TTCATCATCAACACCATCAAC
*
597019 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
597039 TTTCCACAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.37, C:0.34, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:599639 original size:18 final size:18
Alignment explanation
Indices: 599616--599653 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
599606 TTACATCATT
599616 AATGAAATAACATTATTC
1 AATGAAATAACATTATTC
* *
599634 AATGAAATCACTTTATTC
1 AATGAAATAACATTATTC
599652 AA
1 AA
599654 CGAACTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (18 bp):
AATGAAATAACATTATTC
Found at i:599737 original size:17 final size:18
Alignment explanation
Indices: 599717--599754 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
599707 ACTACTTCCC
599717 TAAATGAAATACATG-TT
1 TAAATGAAATACATGCTT
* *
599734 TAAATGCAATGCATGCTT
1 TAAATGAAATACATGCTT
599752 TAA
1 TAA
599755 TAAACAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (18 bp):
TAAATGAAATACATGCTT
Found at i:602078 original size:19 final size:20
Alignment explanation
Indices: 602043--602092 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
602033 CCTTGGCTTG
602043 TTTTC-TCTTTT-TCTTTTA
1 TTTTCTTCTTTTCTCTTTTA
*
602061 TTTTCTTCTTTTCT-TTTTC
1 TTTTCTTCTTTTCTCTTTTA
602080 TTTT-TTGCTTTTC
1 TTTTCTT-CTTTTC
602093 GTCTATTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.25
19 20 0.71
20 1 0.04
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTCTTCTTTTCTCTTTTA
Found at i:602384 original size:21 final size:21
Alignment explanation
Indices: 602345--602384 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
602335 AAGGAAGATT
*
602345 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
602366 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
602385 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:603796 original size:91 final size:91
Alignment explanation
Indices: 603639--603821 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 91
603629 CCTAGAACAC
* *
603639 CCATGTGCCTTGCATATGACCAGCCCCCGTGTGCCTTGCATGTGGATCATTTAGGCACCAACATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCACCAACATG
603704 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * * * * *
603730 CCATGTGTTTTGCATTTGATCAGCCCCTATGTGCCTTGCATATGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCACCAACATG
603795 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
603821 C
1 C
603822 AACAACTACC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCACCAACATG
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:609445 original size:91 final size:91
Alignment explanation
Indices: 609290--609472 Score: 285
Period size: 91 Copynumber: 2.0 Consensus size: 91
609280 CCTAGAACAT
* *
609290 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCATTGCATATGGATAATTTAGGCACCAAGATG
* *
609355 AAGAGTTCTCTCCTTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTAGGCCAAG
** * * *
609381 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCATTGCATATGGTTAATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCATTGCATATGGATAATTTAGGCACCAAGATG
609446 AAGAGTTCTCTCCCTATTAGGCCAAG
66 AAGAGTTCTCTCCCTATTAGGCCAAG
609472 C
1 C
609473 ATCAACTACC
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCATTGCATATGGATAATTTAGGCACCAAGATG
AAGAGTTCTCTCCCTATTAGGCCAAG
Found at i:611110 original size:34 final size:36
Alignment explanation
Indices: 611041--611112 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
611031 AGACTATAGG
611041 TTATTATAATAACTCATGCATTATATGATAATGAATA
1 TTATTATAATAACTCATGCATTATATGAT-ATGAATA
* *
611078 TTATTATTATAACT-ATAG-ATTATATGCT-TGAATA
1 TTATTATAATAACTCAT-GCATTATATGATATGAATA
611112 T
1 T
611113 CAATCAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 7 0.22
36 11 0.34
37 14 0.44
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (36 bp):
TTATTATAATAACTCATGCATTATATGATATGAATA
Found at i:611413 original size:19 final size:20
Alignment explanation
Indices: 611376--611415 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
611366 GGATAATAAT
611376 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
611396 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
611415 A
1 A
611416 AGAAATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:616167 original size:21 final size:21
Alignment explanation
Indices: 616143--616185 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
616133 TCATTCAAAG
616143 AACGTATCTTTGGGAGAACCA
1 AACGTATCTTTGGGAGAACCA
616164 AACGTATCTTTGGGAGAACCA
1 AACGTATCTTTGGGAGAACCA
616185 A
1 A
616186 TGGACGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (21 bp):
AACGTATCTTTGGGAGAACCA
Found at i:617500 original size:19 final size:21
Alignment explanation
Indices: 617457--617508 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
617447 GAAACCCCTT
617457 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
617478 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
617497 TGAACATACATG
1 TGAAAATACATG
617509 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:620492 original size:19 final size:21
Alignment explanation
Indices: 620468--620519 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
620458 CGGCCAAGAG
*
620468 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
620487 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
620508 CATGTATTTTCA
1 CATGTATTTTCA
620520 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:620910 original size:9 final size:9
Alignment explanation
Indices: 620898--620928 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
620888 CATCCATCTC
620898 TTCCATCAA
1 TTCCATCAA
620907 TTCCATCAA
1 TTCCATCAA
620916 TTCCATCAA
1 TTCCATCAA
620925 TTCC
1 TTCC
620929 GCAACCATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (9 bp):
TTCCATCAA
Found at i:620974 original size:19 final size:20
Alignment explanation
Indices: 620950--620989 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
620940 TATCCTTTCT
620950 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
620969 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
620989 T
1 T
620990 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:628894 original size:19 final size:20
Alignment explanation
Indices: 628870--628921 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
628860 GGCCAAGAGA
*
628870 ATGTATCTTCAAT-AAAATC
1 ATGTATTTTCAATAAAAATC
*
628889 ATGTATTTTCATTTAAAAATC
1 ATGTATTTTCA-ATAAAAATC
628910 ATGTATTTTCAA
1 ATGTATTTTCAA
628922 AGGGGTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.36
20 1 0.04
21 17 0.61
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (20 bp):
ATGTATTTTCAATAAAAATC
Found at i:629148 original size:15 final size:15
Alignment explanation
Indices: 629130--629165 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
629120 CTTTCCATCT
629130 TGATTCCAAAATTCC
1 TGATTCCAAAATTCC
629145 TGATTCCAAAATTCC
1 TGATTCCAAAATTCC
629160 TAGATT
1 T-GATT
629166 GATATCTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.36
Consensus pattern (15 bp):
TGATTCCAAAATTCC
Found at i:632729 original size:19 final size:19
Alignment explanation
Indices: 632697--632742 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
632687 GGTCAAGAGC
632697 TGTATCTTCATT-AAAATCA
1 TGTAT-TTCATTAAAAATCA
632716 TGTATTTCATTTAAAAATCA
1 TGTATTTCA-TTAAAAATCA
632736 TGTATTT
1 TGTATTT
632743 TCAATGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.16
19 7 0.28
20 14 0.56
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.48
Consensus pattern (19 bp):
TGTATTTCATTAAAAATCA
Found at i:641703 original size:11 final size:11
Alignment explanation
Indices: 641687--641713 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
641677 TTACAAGAAA
641687 ATTCATGATGG
1 ATTCATGATGG
641698 ATTCATGATGG
1 ATTCATGATGG
641709 ATTCA
1 ATTCA
641714 CAAATCGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (11 bp):
ATTCATGATGG
Found at i:643984 original size:21 final size:19
Alignment explanation
Indices: 643944--643995 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
643934 CGGCCAAGAG
*
643944 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
643963 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
*
643984 CATTTATTTTCA
1 CATGTATTTTCA
643996 AAAGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.48
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:644452 original size:19 final size:19
Alignment explanation
Indices: 644412--644449 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
644402 TCTTTATTTC
644412 ATTTCATTTTATTCTTATT
1 ATTTCATTTTATTCTTATT
644431 ATTT-ATTTTCATTACTTAT
1 ATTTCATTTT-ATT-CTTAT
644450 ATTATTATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTCATTTTATTCTTATT
Found at i:644452 original size:28 final size:28
Alignment explanation
Indices: 644404--644457 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
644394 CTATCCTTTC
* * *
644404 TTTATTTCATTTCATTTTATTCTTATTA
1 TTTATTTCATTACATTATATTATTATTA
644432 TTTATTTTCATTAC-TTATATTATTAT
1 TTTA-TTTCATTACATTATATTATTAT
644458 CCCCTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 14 0.64
29 8 0.36
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTATTTCATTACATTATATTATTATTA
Found at i:644753 original size:19 final size:19
Alignment explanation
Indices: 644714--644753 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
644704 AACAAAATTG
*
644714 AAGTGCAAAAAGAAAAGAA
1 AAGTGCAAAAAGAAAAAAA
644733 AAGT-CAAAAAGAATAAAAA
1 AAGTGCAAAAAGAA-AAAAA
644752 AA
1 AA
644754 ATTTAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.07
Consensus pattern (19 bp):
AAGTGCAAAAAGAAAAAAA
Found at i:647874 original size:18 final size:19
Alignment explanation
Indices: 647851--647899 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
647841 CGGCCAAGAG
647851 CATGTATCTTCA-TT-AAAT
1 CATGTAT-TTCATTTAAAAT
647869 CATGTATTGTCATTTAAAAT
1 CATGTATT-TCATTTAAAAT
647889 CATGTATTTCA
1 CATGTATTTCA
647900 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.04
18 10 0.36
19 5 0.18
20 12 0.43
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (19 bp):
CATGTATTTCATTTAAAAT
Found at i:651863 original size:19 final size:20
Alignment explanation
Indices: 651822--651872 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
651812 GAAACCCCTT
*
651822 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
651842 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
651861 TGAAGATACATG
1 TGAAAATACATG
651873 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:654933 original size:13 final size:12
Alignment explanation
Indices: 654915--654956 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
654905 GCTTGCTTTC
654915 TCTTTTTGAATTT
1 TCTTTTTG-ATTT
*
654928 TCTTTTT-CTTT
1 TCTTTTTGATTT
654939 TCTTTTCTGATTT
1 TCTTTT-TGATTT
654952 TCTTT
1 TCTTT
654957 CTTTTTGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (12 bp):
TCTTTTTGATTT
Found at i:654959 original size:17 final size:18
Alignment explanation
Indices: 654931--654981 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
654921 TGAATTTTCT
654931 TTTTCTTTTCTTTTCTG-A
1 TTTTCTTTTCTTTT-TGTA
*
654949 TTTTC-TTTCTTTTTGTC
1 TTTTCTTTTCTTTTTGTA
654966 TTTTCTTTTCTTTTTG
1 TTTTCTTTTCTTTTTG
654982 CACTCTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 2 0.07
17 13 0.43
18 15 0.50
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTGTA
Found at i:655684 original size:19 final size:21
Alignment explanation
Indices: 655641--655692 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
655631 GAAACCCCTT
655641 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
655662 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
655681 TGAACATACATG
1 TGAAAATACATG
655693 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:658168 original size:20 final size:20
Alignment explanation
Indices: 658143--658198 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
658133 TTCTTCATTT
658143 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
658163 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
658183 AAATCATGTATTTTCA
1 AAATCATGTATTTTCA
658199 AAGGTGATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.41
Consensus pattern (20 bp):
AAATCATGTATTTTCATCAA
Found at i:664762 original size:24 final size:25
Alignment explanation
Indices: 664735--664786 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
664725 AAGAAAAATC
* *
664735 AGAAAAG-AAAGTGAAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
*
664759 AG-AAAGAAAAATCCAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
664783 AGAA
1 AGAA
664787 GAAAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 4 0.17
24 18 0.78
25 1 0.04
ACGTcount: A:0.60, C:0.15, G:0.17, T:0.08
Consensus pattern (25 bp):
AGAAAAGAAAAATCAAGCACTCAAA
Found at i:664797 original size:14 final size:14
Alignment explanation
Indices: 664780--664812 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
664770 TCCAGCACTC
664780 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
664794 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
664808 AAAAG
1 AAAAG
664813 TAGTTGAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:668731 original size:24 final size:25
Alignment explanation
Indices: 668704--668755 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
668694 AAGAAAAATC
* *
668704 AGAAAAG-AAAGTGAAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
*
668728 AG-AAAGAAAAATCCAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
668752 AGAA
1 AGAA
668756 GAAAAAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 4 0.17
24 18 0.78
25 1 0.04
ACGTcount: A:0.60, C:0.15, G:0.17, T:0.08
Consensus pattern (25 bp):
AGAAAAGAAAAATCAAGCACTCAAA
Found at i:671996 original size:20 final size:20
Alignment explanation
Indices: 671971--672026 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
671961 ATCTTCATTT
671971 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
671991 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
672011 AAATCATGTATTTTCA
1 AAATCATGTATTTTCA
672027 AAGGGGTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.41
Consensus pattern (20 bp):
AAATCATGTATTTTCATCAA
Found at i:674453 original size:24 final size:24
Alignment explanation
Indices: 674426--674480 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
674416 CAAAGGAAAG
*
674426 CTCACCTTAGCTAGAGGAGCTAAA
1 CTCAACTTAGCTAGAGGAGCTAAA
674450 CTCAACTTAGCTAGAGGAGCTAAA
1 CTCAACTTAGCTAGAGGAGCTAAA
674474 CTCAACT
1 CTCAACT
674481 GAAGATACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (24 bp):
CTCAACTTAGCTAGAGGAGCTAAA
Found at i:676803 original size:21 final size:21
Alignment explanation
Indices: 676779--676819 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
676769 TGAAAGCACT
*
676779 TAAAAAGGAAGAA-AAAGAAAA
1 TAAAAA-GAAAAAGAAAGAAAA
676800 TAAAAAGAAAAAGAAAGAAA
1 TAAAAAGAAAAAGAAAGAAA
676820 GTTGAAGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (21 bp):
TAAAAAGAAAAAGAAAGAAAA
Found at i:682705 original size:11 final size:12
Alignment explanation
Indices: 682675--682720 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
682665 TTGGTGCTAG
682675 AAACAAGATAAA
1 AAACAAGATAAA
* *
682687 AAATAAGAT-TA
1 AAACAAGATAAA
682698 AAACAAGATAAA
1 AAACAAGATAAA
*
682710 GAA-AAGATAAA
1 AAACAAGATAAA
682721 GGAATTGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:682705 original size:23 final size:22
Alignment explanation
Indices: 682675--682717 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
682665 TTGGTGCTAG
682675 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
682698 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
682718 AAAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:685036 original size:11 final size:13
Alignment explanation
Indices: 685004--685033 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
684994 TGGCCAAAGA
685004 TGAAAAGGTATGT
1 TGAAAAGGTATGT
685017 TGAAAAGGTATG-
1 TGAAAAGGTATGT
685029 TGAAA
1 TGAAA
685034 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:690053 original size:22 final size:22
Alignment explanation
Indices: 690022--690064 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
690012 AAATAACTTC
* *
690022 CATGTCGGCTATCATGTGCATT
1 CATGTAGGCTACCATGTGCATT
*
690044 CATGTAGGCTGCCATGTGCAT
1 CATGTAGGCTACCATGTGCAT
690065 CATTCAAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (22 bp):
CATGTAGGCTACCATGTGCATT
Found at i:692273 original size:24 final size:21
Alignment explanation
Indices: 692239--692281 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
692229 TGCACAAGAT
*
692239 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
692261 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
692282 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:699382 original size:19 final size:19
Alignment explanation
Indices: 699358--699404 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
699348 ATGTTGCCAT
699358 AACATATGAATG-ATATAAA
1 AACATATGAATGAATAT-AA
**
699377 AACATAACAAATGAATATAA
1 AACAT-ATGAATGAATATAA
699397 AACATATG
1 AACATATG
699405 CAAAACATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
19 6 0.27
20 12 0.55
21 4 0.18
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (19 bp):
AACATATGAATGAATATAA
Found at i:703960 original size:24 final size:23
Alignment explanation
Indices: 703933--703987 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
703923 AGAATAATGG
*
703933 CTTTTGGAGGACTAAAATA-TGTGA
1 CTTTTGGAGAAC--AAATAGTGTGA
*
703957 CTTTTGAAGAACAAATAGTTGTGA
1 CTTTTGGAGAACAAATAG-TGTGA
703981 CTTTTGG
1 CTTTTGG
703988 TGATCCACGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.19
24 21 0.81
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (23 bp):
CTTTTGGAGAACAAATAGTGTGA
Found at i:723474 original size:31 final size:30
Alignment explanation
Indices: 723416--723474 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
723406 TTGGTTCTTC
* *
723416 AAAAGACATGTTTCTTGAATTTTCTACTTG
1 AAAAGACATGTTTCTTGAATATCCTACTTG
* *
723446 AAAAGATATGTCTTTTTGAATATCCTACT
1 AAAAGACATGT-TTCTTGAATATCCTACT
723475 AGGAAAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (30 bp):
AAAAGACATGTTTCTTGAATATCCTACTTG
Found at i:724699 original size:23 final size:23
Alignment explanation
Indices: 724650--724702 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
724640 TTTCTTTGCT
* *
724650 TTTCTTCTTTTTGAGTGCTGGAAA
1 TTTCTTCTTTTGGAGTGCTCG-AA
724674 TTTCTTCTTTTGGAGTGCTTCG-A
1 TTTCTTCTTTTGGAGTGC-TCGAA
724697 TTTCTT
1 TTTCTT
724703 TTCTGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 17 0.65
25 2 0.08
ACGTcount: A:0.11, C:0.15, G:0.19, T:0.55
Consensus pattern (23 bp):
TTTCTTCTTTTGGAGTGCTCGAA
Found at i:732548 original size:24 final size:22
Alignment explanation
Indices: 732497--732551 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
732487 AAAATTCAGC
732497 AAAGAAAACAAAAGCACTCAAA
1 AAAGAAAACAAAAGCACTCAAA
* *
732519 AGAAGAAATTCAAAAGCACTTGAAA
1 A-AAGAAA-ACAAAAGCAC-TCAAA
732544 AAAGAAAA
1 AAAGAAAA
732552 AGAAAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.04
23 6 0.22
24 15 0.56
25 5 0.19
ACGTcount: A:0.65, C:0.13, G:0.13, T:0.09
Consensus pattern (22 bp):
AAAGAAAACAAAAGCACTCAAA
Found at i:747203 original size:24 final size:21
Alignment explanation
Indices: 747170--747225 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 21
747160 CTTGGCTTGC
*
747170 TTTCTCTTTTTGAACTTCTTTTCT
1 TTTCTTTTTTTGAA-TT-TTTT-T
747194 TTTCTTTTTTTTGAATTTTTTT
1 TTTC-TTTTTTTGAATTTTTTT
747216 TCTTCTTTTT
1 T-TTCTTTTT
747226 GTCTTCTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 7 0.24
23 7 0.24
24 6 0.21
25 9 0.31
ACGTcount: A:0.07, C:0.14, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTCTTTTTTTGAATTTTTTT
Found at i:747218 original size:20 final size:21
Alignment explanation
Indices: 747188--747244 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
747178 TTTGAACTTC
*
747188 TTTTCTTTTCTTTTTTTTGAA
1 TTTTCTTTTCTTCTTTTTGAA
**
747209 TTTT-TTTTCTTCTTTTTGTC
1 TTTTCTTTTCTTCTTTTTGAA
*
747229 TTCTCTTTTCTT-TTTT
1 TTTTCTTTTCTTCTTTT
747245 GCACTCCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.79
Consensus pattern (21 bp):
TTTTCTTTTCTTCTTTTTGAA
Found at i:749658 original size:13 final size:13
Alignment explanation
Indices: 749636--749665 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
749626 ACTAGACACC
749636 TTTC-ACATACCT
1 TTTCAACATACCT
749648 TTTCAACATACCT
1 TTTCAACATACCT
749661 TTTCA
1 TTTCA
749666 GTTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:752247 original size:21 final size:22
Alignment explanation
Indices: 752178--752259 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
752168 TTGGTGTAGC
*
752178 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
752200 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
752223 GGGAACCGATTCCCCC-TGTAG
1 GGGAACCGATACCCCCTTGAAG
*
752244 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
752260 ATGGGGTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 18 0.33
22 14 0.26
23 22 0.41
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:754152 original size:17 final size:16
Alignment explanation
Indices: 754123--754188 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
754113 CTTTTTGGAT
*
754123 ATTTTGGAATGTTTGA
1 ATTTTGGATTGTTTGA
754139 ATTTGTGGATTGTTTG-
1 ATTT-TGGATTGTTTGA
* *
754155 ACTTTGAATTTGTTTGA
1 ATTTTGGA-TTGTTTGA
754172 ATTTATGGA-TGTTTGA
1 ATTT-TGGATTGTTTGA
754188 A
1 A
754189 CTTATATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.07
16 22 0.54
17 13 0.32
18 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (16 bp):
ATTTTGGATTGTTTGA
Found at i:757187 original size:25 final size:26
Alignment explanation
Indices: 757155--757204 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
757145 TTTCTTTTTC
*
757155 TTTTTCTTC-CTTTTTGAGTGCTTGA
1 TTTTTCTTCTCTTTTGGAGTGCTTGA
757180 TTTTTCTTCTTCTTTTGGAGTGCTT
1 TTTTTCTTC-TCTTTTGGAGTGCTT
757205 CAATTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
27 13 0.59
ACGTcount: A:0.06, C:0.16, G:0.16, T:0.62
Consensus pattern (26 bp):
TTTTTCTTCTCTTTTGGAGTGCTTGA
Found at i:757211 original size:26 final size:28
Alignment explanation
Indices: 757158--757213 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
757148 CTTTTTCTTT
* * *
757158 TTCTTCCTTTTTGAGTGCTTGATTTTTC
1 TTCTTCCTTTTGGAGTGCTTCATATTTC
757186 TTCTT-CTTTTGGAGTGCTTCA-ATTTC
1 TTCTTCCTTTTGGAGTGCTTCATATTTC
757212 TT
1 TT
757214 TTACTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 14 0.56
28 5 0.20
ACGTcount: A:0.09, C:0.18, G:0.14, T:0.59
Consensus pattern (28 bp):
TTCTTCCTTTTGGAGTGCTTCATATTTC
Found at i:758980 original size:24 final size:24
Alignment explanation
Indices: 758931--758981 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
758921 ATTCTTTGCT
* *
758931 TTTTCTTCTTTTTGAGTGCTGGAA
1 TTTTCTTCTTTTGGAGTGCTGCAA
*
758955 TTTTCTTCTTTTGGAGTGCTTCAA
1 TTTTCTTCTTTTGGAGTGCTGCAA
758979 TTT
1 TTT
758982 GTTTGCTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.57
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTGCAA
Found at i:765756 original size:24 final size:23
Alignment explanation
Indices: 765708--765757 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
765698 TTTCTATTCT
* *
765708 TTTTCTTTTTTTGAGTGCTGGAA
1 TTTTCTTTTTTGGAGTGCTGCAA
*
765731 TTTTCTTCTTTTGGAGTGCTTCAA
1 TTTTCTT-TTTTGGAGTGCTGCAA
765755 TTT
1 TTT
765758 GTTTGCTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (23 bp):
TTTTCTTTTTTGGAGTGCTGCAA
Found at i:774378 original size:24 final size:25
Alignment explanation
Indices: 774321--774378 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
774311 TATTTAAATA
774321 AATATTTATAAAATATTTAATAACAC
1 AATATTT-TAAAATATTTAATAACAC
*
774347 CATATTTTAAAAT-TTATAA-AACAC
1 AATATTTTAAAATATT-TAATAACAC
*
774371 AATTTTTT
1 AATATTTT
774379 TAGAAATCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 13 0.46
25 9 0.32
26 6 0.21
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (25 bp):
AATATTTTAAAATATTTAATAACAC
Found at i:774533 original size:19 final size:19
Alignment explanation
Indices: 774509--774555 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
774499 TCAAAATCAT
* *
774509 TTTTCAAAACTT-CATTTTG
1 TTTTCAAAA-TTAAATTTTC
774528 TTTTCAAAATTAAATTTTC
1 TTTTCAAAATTAAATTTTC
774547 TTTTCAAAA
1 TTTTCAAAA
774556 GAAATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTCAAAATTAAATTTTC
Found at i:777193 original size:33 final size:33
Alignment explanation
Indices: 777156--777223 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
777146 TGAAATGAAA
777156 GAAACAATTCAGGCA-TTGCAACAAGAAACAAAG
1 GAAACAATTCAGGCACTT-CAACAAGAAACAAAG
* *
777189 GAAACAATTCATGCACTTCGACAAGAAACAAAG
1 GAAACAATTCAGGCACTTCAACAAGAAACAAAG
777222 GA
1 GA
777224 GATAAGAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.50, C:0.19, G:0.18, T:0.13
Consensus pattern (33 bp):
GAAACAATTCAGGCACTTCAACAAGAAACAAAG
Done.