Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007872.1 Hibiscus syriacus cultivar Beakdansim tig00110247_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: 853105
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:467382 original size:35 final size:35
Alignment explanation
Indices: 467332--467407 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
467322 AATTGAATTT
* *
467332 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
467367 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
467402 AATTGA
1 AATTGA
467408 GGATTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:468097 original size:21 final size:20
Alignment explanation
Indices: 468073--468116 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
468063 AAAATATTTT
468073 TTAATTCAAAAAAAATTATAA
1 TTAATTCAAAAAAAA-TATAA
* * *
468094 TTAATTTAAATAATATATAA
1 TTAATTCAAAAAAAATATAA
468114 TTA
1 TTA
468117 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATTCAAAAAAAATATAA
Found at i:468361 original size:185 final size:181
Alignment explanation
Indices: 468052--468438 Score: 596
Period size: 185 Copynumber: 2.1 Consensus size: 181
468042 TTTTCTAATT
* * * *
468052 TATATAA-AAATAAAATATTTTTTAATTCAAAAAAAATTATAATTAATTTAAATAATATATAATT
1 TATATAATATATATAATA-TTTTTAATTAAAAAAAAATTACAATTAATTTAAATAATATATAATT
** ** * *
468116 ATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTG
65 ATAAAATAAAAAAATTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTA
*
468181 GATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGATAAGCTCATATGTTA
130 GATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGATAAGC-CATATGTTA
468234 TATATAATATATATAATATTTTTAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATATAATATTTTTAATTAAAAAAAA-A--TTACAATTAATTTAAATAATATATAA
468299 TTATAAAATAAAAAAATTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
63 TTATAAAATAAAAAAATTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* *
468364 TAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCCATATGTTA
128 TAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGATAAGCCATATGTTA
*
468418 TATATAATATATTTAATATTT
1 TATATAATATATATAATATTT
468439 AAAATTTAAT
Statistics
Matches: 187, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
182 23 0.12
183 9 0.05
184 29 0.16
185 126 0.67
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (181 bp):
TATATAATATATATAATATTTTTAATTAAAAAAAAATTACAATTAATTTAAATAATATATAATTA
TAAAATAAAAAAATTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTAG
ATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGATAAGCCATATGTTA
Found at i:470231 original size:34 final size:34
Alignment explanation
Indices: 470188--470255 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
470178 TCCGCCCAAG
*
470188 TTCGCTTCATCACGACAAGATTGCATTTCAGCTC
1 TTCGCTTCATCACGACAAGATTGCATTGCAGCTC
*
470222 TTCGCTTCATCACGATAAGATTGCATTGCAGCTC
1 TTCGCTTCATCACGACAAGATTGCATTGCAGCTC
470256 ATTCAGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (34 bp):
TTCGCTTCATCACGACAAGATTGCATTGCAGCTC
Found at i:475691 original size:2 final size:2
Alignment explanation
Indices: 475684--475747 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
475674 AAATATTTTG
475684 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
475726 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
475748 CAAATGCAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:476486 original size:22 final size:22
Alignment explanation
Indices: 476429--476487 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
476419 ACGCGATTCT
*
476429 GACTATCGCATTGCAATTTTTC
1 GACTATCGCATTGCGATTTTTC
* * *
476451 AAAT-TCGCGTTGCGATTTTTC
1 GACTATCGCATTGCGATTTTTC
*
476472 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
476488 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTTC
Found at i:476520 original size:20 final size:20
Alignment explanation
Indices: 476497--476578 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
476487 AATATGTAAA
*
476497 TCGCAATGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTG
476517 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTG
476537 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTG
476557 TCGCAACGCGATTCT-ACTG
1 TCGCAACGCGATTCTGACTG
476576 TCG
1 TCG
476579 TAACACTGAA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
19 7 0.11
20 54 0.89
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTG
Found at i:477435 original size:24 final size:24
Alignment explanation
Indices: 477403--477456 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
477393 GTATTCGAAA
477403 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
477427 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
477451 TTTGAT
1 TTTGAT
477457 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:478926 original size:20 final size:20
Alignment explanation
Indices: 478903--478970 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
478893 TCTGAAACTT
*
478903 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
* **
478923 AAAATCACAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
** *
478943 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
478962 AAAATCGCA
1 AAAATCGCA
478971 TTGCGATTCT
Statistics
Matches: 37, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
19 7 0.19
20 30 0.81
ACGTcount: A:0.47, C:0.24, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:479588 original size:20 final size:20
Alignment explanation
Indices: 479561--479664 Score: 136
Period size: 20 Copynumber: 5.2 Consensus size: 20
479551 AATCGTATTA
*
479561 CGATAGTCAGCATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
*
479581 CGACAGTCAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
* *
479601 CGATAGTCAGAATCTCGTTA
1 CGATAGTCAGAATCGCGTTG
479621 CGATAGTCAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
* * * *
479641 CGATTGTCATACTCGCATTG
1 CGATAGTCAGAATCGCGTTG
479661 CGAT
1 CGAT
479665 TTACATATTC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (20 bp):
CGATAGTCAGAATCGCGTTG
Found at i:479665 original size:20 final size:20
Alignment explanation
Indices: 479633--479684 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
479623 ATAGTCAGAA
*
479633 TCGCGTTGCGATTGT-CATAC
1 TCGCATTGCGATT-TACATAC
*
479653 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAC
479673 TCGCATTGCGAT
1 TCGCATTGCGAT
479685 AGTCGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAC
Found at i:481518 original size:31 final size:31
Alignment explanation
Indices: 481461--481524 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
481451 CAGTTACTTC
* *
481461 GGGGACCATATTACAAACATACTAAATTTTG
1 GGGGACCATATTACAAACAGACTAAATGTTG
* * *
481492 GGGGACCATATTGCAAACGGATTAAATGTTG
1 GGGGACCATATTACAAACAGACTAAATGTTG
481523 GG
1 GG
481525 AGACTGTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (31 bp):
GGGGACCATATTACAAACAGACTAAATGTTG
Found at i:482901 original size:17 final size:18
Alignment explanation
Indices: 482874--482911 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
482864 TATGTAGTTA
482874 ACCCTTTAAATTAATTTT
1 ACCCTTTAAATTAATTTT
482892 ACCC-TTAAATTAATTTT
1 ACCCTTTAAATTAATTTT
482909 ACC
1 ACC
482912 AAAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (18 bp):
ACCCTTTAAATTAATTTT
Found at i:488432 original size:2 final size:2
Alignment explanation
Indices: 488427--488460 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
488417 TGTGTGTATG
488427 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
488461 AAAGGACGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:491837 original size:21 final size:21
Alignment explanation
Indices: 491807--491851 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
491797 TCAAATTTTA
*
491807 AAAAAATTATTTTGTGGTGTC
1 AAAAAATTATTTTGGGGTGTC
*
491828 AAAAATTTATTTTGGGGTGTC
1 AAAAAATTATTTTGGGGTGTC
491849 AAA
1 AAA
491852 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (21 bp):
AAAAAATTATTTTGGGGTGTC
Found at i:491854 original size:19 final size:20
Alignment explanation
Indices: 491808--491856 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
491798 CAAATTTTAA
* *
491808 AAAAATTATTTTGTGGTGTC
1 AAAATTTATTTTGGGGTGTC
491828 AAAAATTTATTTTGGGGTGTC
1 -AAAATTTATTTTGGGGTGTC
*
491849 AAATTTTA
1 AAAATTTA
491857 AAAAATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (20 bp):
AAAATTTATTTTGGGGTGTC
Found at i:501918 original size:27 final size:27
Alignment explanation
Indices: 501880--501933 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
501870 GACGTGAATG
501880 GTAGCAATGAAATGTTGCTTAGTAAAA
1 GTAGCAATGAAATGTTGCTTAGTAAAA
501907 GTAGCAATGAAATGTTGCTTAGTAAAA
1 GTAGCAATGAAATGTTGCTTAGTAAAA
501934 CCTTTTCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (27 bp):
GTAGCAATGAAATGTTGCTTAGTAAAA
Found at i:504145 original size:2 final size:2
Alignment explanation
Indices: 504134--504162 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
504124 TTATGTAAAT
504134 TA TA -A 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
504163 ATGTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:505915 original size:2 final size:2
Alignment explanation
Indices: 505910--505938 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
505900 AAAACAATGG
505910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
505939 CTCCTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:507083 original size:23 final size:23
Alignment explanation
Indices: 507057--507106 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
507047 AGACTTTTCT
*
507057 CGAACGATCGCATAGAAATATCC
1 CGAACGATCACATAGAAATATCC
* * * *
507080 CGAAGGATCACGTAGAATTGTCC
1 CGAACGATCACATAGAAATATCC
507103 CGAA
1 CGAA
507107 AGATTGTGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (23 bp):
CGAACGATCACATAGAAATATCC
Found at i:507282 original size:31 final size:31
Alignment explanation
Indices: 507246--507347 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
507236 TTTTCACATT
507246 TCACATATTCATATAATCACGTAGTTCAATA
1 TCACATATTCATATAATCACGTAGTTCAATA
** * * * * *
507277 TCACATAGACATAAAATCACATAGATCCTTATT
1 TCACATATTCATATAATCACGTAG-TTC-AATA
507310 TCACATATTCATATAATCACGTAGTTCAATA
1 TCACATATTCATATAATCACGTAGTTCAATA
507341 TCACATA
1 TCACATA
507348 GACATAAAAT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
31 29 0.53
32 4 0.07
33 22 0.40
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (31 bp):
TCACATATTCATATAATCACGTAGTTCAATA
Found at i:507297 original size:16 final size:16
Alignment explanation
Indices: 507276--507365 Score: 58
Period size: 16 Copynumber: 5.6 Consensus size: 16
507266 GTAGTTCAAT
507276 ATCACATAGACATAAA
1 ATCACATAGACATAAA
* * *
507292 ATCACATAGATCCTTAT
1 ATCACATAGA-CATAAA
* ** *
507309 TTCACATATTCATATA
1 ATCACATAGACATAAA
* * *
507325 ATCACGTAG--TTCAAT
1 ATCACATAGACAT-AAA
507340 ATCACATAGACATAAA
1 ATCACATAGACATAAA
507356 ATCACATAGA
1 ATCACATAGA
507366 TCCTTATCAC
Statistics
Matches: 51, Mismatches: 19, Indels: 8
0.65 0.24 0.10
Matches are distributed among these distances:
14 1 0.02
15 9 0.18
16 30 0.59
17 11 0.22
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (16 bp):
ATCACATAGACATAAA
Found at i:507315 original size:33 final size:33
Alignment explanation
Indices: 507274--507372 Score: 121
Period size: 33 Copynumber: 3.1 Consensus size: 33
507264 ACGTAGTTCA
507274 ATATCACATAGACATAAAATCACATAGATCCTT
1 ATATCACATAGACATAAAATCACATAGATCCTT
* ** * * * *
507307 ATTTCACATATTCATATAATCACGTAG-TTC-A
1 ATATCACATAGACATAAAATCACATAGATCCTT
507338 ATATCACATAGACATAAAATCACATAGATCCTT
1 ATATCACATAGACATAAAATCACATAGATCCTT
507371 AT
1 AT
507373 CACATTGCTT
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
31 22 0.44
32 4 0.08
33 24 0.48
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.31
Consensus pattern (33 bp):
ATATCACATAGACATAAAATCACATAGATCCTT
Found at i:507318 original size:64 final size:64
Alignment explanation
Indices: 507243--507372 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
507233 CCATTTTCAC
507243 ATTTCACATATTCATATAATCACGTAGTTCAATATCACATAGACATAAAATCACATAGATCCTT
1 ATTTCACATATTCATATAATCACGTAGTTCAATATCACATAGACATAAAATCACATAGATCCTT
507307 ATTTCACATATTCATATAATCACGTAGTTCAATATCACATAGACATAAAATCACATAGATCCTT
1 ATTTCACATATTCATATAATCACGTAGTTCAATATCACATAGACATAAAATCACATAGATCCTT
507371 AT
1 AT
507373 CACATTGCTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (64 bp):
ATTTCACATATTCATATAATCACGTAGTTCAATATCACATAGACATAAAATCACATAGATCCTT
Found at i:507359 original size:31 final size:31
Alignment explanation
Indices: 507246--507360 Score: 122
Period size: 31 Copynumber: 3.6 Consensus size: 31
507236 TTTTCACATT
** *
507246 TCACATATTCATATAATCACGTAGTTCAATA
1 TCACATAGACATAAAATCACGTAGTTCAATA
* * * *
507277 TCACATAGACATAAAATCACATAGATCCTTATT
1 TCACATAGACATAAAATCACGTAG-TTC-AATA
** *
507310 TCACATATTCATATAATCACGTAGTTCAATA
1 TCACATAGACATAAAATCACGTAGTTCAATA
507341 TCACATAGACATAAAATCAC
1 TCACATAGACATAAAATCAC
507361 ATAGATCCTT
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
31 39 0.60
32 4 0.06
33 22 0.34
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (31 bp):
TCACATAGACATAAAATCACGTAGTTCAATA
Found at i:507374 original size:31 final size:31
Alignment explanation
Indices: 507275--507377 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 31
507265 CGTAGTTCAA
507275 TATCACATAGACATAAAATCACATAGATCCT
1 TATCACATAGACATAAAATCACATAGATCCT
** * * * **
507306 TATTTCACATATTCATATAATCACGTAGTTCAA
1 TA--TCACATAGACATAAAATCACATAGATCCT
507339 TATCACATAGACATAAAATCACATAGATCCT
1 TATCACATAGACATAAAATCACATAGATCCT
507370 TATCACAT
1 TATCACAT
507378 TGCTTATATC
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
31 32 0.57
33 24 0.43
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (31 bp):
TATCACATAGACATAAAATCACATAGATCCT
Found at i:508560 original size:32 final size:32
Alignment explanation
Indices: 508519--508580 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
508509 AATCACTTAA
508519 AAAACCCTTTTTATTCAATCTCCCGTAACTTG
1 AAAACCCTTTTTATTCAATCTCCCGTAACTTG
508551 AAAACCCTTTTTATTCAATCTCCCGTAACT
1 AAAACCCTTTTTATTCAATCTCCCGTAACT
508581 GGAAGAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (32 bp):
AAAACCCTTTTTATTCAATCTCCCGTAACTTG
Found at i:509357 original size:24 final size:24
Alignment explanation
Indices: 509325--509396 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
509315 CATTTGAGAC
*
509325 AAACCTATATAGTCCTTCGGGACA
1 AAACCTATATGGTCCTTCGGGACA
*
509349 AAACCTATATGGTCATTCGGGAC-
1 AAACCTATATGGTCCTTCGGGACA
*
509372 AAA-CTATGTGGTCCTTCGGGACA
1 AAACCTATATGGTCCTTCGGGACA
509395 AA
1 AA
509397 TATGTGGCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
22 17 0.40
23 5 0.12
24 21 0.49
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (24 bp):
AAACCTATATGGTCCTTCGGGACA
Found at i:509378 original size:22 final size:23
Alignment explanation
Indices: 509313--509396 Score: 98
Period size: 24 Copynumber: 3.7 Consensus size: 23
509303 GTTCTATGTA
* * *
509313 GTCATTTGAGACAAACCTATATA
1 GTCATTCGGGACAAACCTATATG
*
509336 GTCCTTCGGGACAAAACCTATATG
1 GTCATTCGGGAC-AAACCTATATG
*
509360 GTCATTCGGGACAAA-CTATGTG
1 GTCATTCGGGACAAACCTATATG
*
509382 GTCCTTCGGGACAAA
1 GTCATTCGGGACAAA
509397 TATGTGGCAC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 20 0.38
23 12 0.23
24 21 0.40
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (23 bp):
GTCATTCGGGACAAACCTATATG
Found at i:511399 original size:6 final size:6
Alignment explanation
Indices: 511388--511419 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
511378 GGTATATGTC
511388 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TT
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TT
511420 GGGAATATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (6 bp):
TTTGGG
Found at i:513399 original size:27 final size:27
Alignment explanation
Indices: 513361--513424 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
513351 ACTGGCTCTG
513361 AATCATTCAGAATGTATTTCTGTGCTT
1 AATCATTCAGAATGTATTTCTGTGCTT
513388 AATCATTCAGAATGTATTTCTGTGCTT
1 AATCATTCAGAATGTATTTCTGTGCTT
513415 AATCATTCAG
1 AATCATTCAG
513425 CACTGTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (27 bp):
AATCATTCAGAATGTATTTCTGTGCTT
Found at i:517530 original size:36 final size:36
Alignment explanation
Indices: 517490--517596 Score: 84
Period size: 36 Copynumber: 3.0 Consensus size: 36
517480 TTAGTTGGGA
*
517490 TGCTCTTCTATGTTTCTTAGCCATGTGAGATTGTTT
1 TGCTCTTCTATATTTCTTAGCCATGTGAGATTGTTT
* *
517526 TGCTC-TC-ATATTT-TTA-CTC-T-TTAGACTT-TTGGGA
1 TGCTCTTCTATATTTCTTAGC-CATGTGAGA-TTGTT---T
*
517560 TGCTCTTCTATCTTTCTTAGCCATGTGAGATTGTTT
1 TGCTCTTCTATATTTCTTAGCCATGTGAGATTGTTT
517596 T
1 T
517597 TTTTAAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 24
0.64 0.07 0.29
Matches are distributed among these distances:
31 6 0.11
32 4 0.08
33 4 0.08
34 10 0.19
35 4 0.08
36 11 0.21
37 4 0.08
38 4 0.08
39 6 0.11
ACGTcount: A:0.15, C:0.18, G:0.17, T:0.50
Consensus pattern (36 bp):
TGCTCTTCTATATTTCTTAGCCATGTGAGATTGTTT
Found at i:517967 original size:41 final size:41
Alignment explanation
Indices: 517908--517995 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
517898 GACCGGTTTG
* *
517908 ACCGGTTGAACCAATGAACCGGTAGCATGGCCGATTCGCTA
1 ACCGGTTGAACCAATGAACAGATAGCATGGCCGATTCGCTA
* *
517949 ACCGGTTGAACCAGTGAACAGATAGCATGGCCGGTTCGCTA
1 ACCGGTTGAACCAATGAACAGATAGCATGGCCGATTCGCTA
517990 ACCGGT
1 ACCGGT
517996 CCGGTTTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (41 bp):
ACCGGTTGAACCAATGAACAGATAGCATGGCCGATTCGCTA
Found at i:519266 original size:6 final size:7
Alignment explanation
Indices: 519257--519302 Score: 51
Period size: 8 Copynumber: 6.4 Consensus size: 7
519247 AAATTAAATT
519257 TATTA-A
1 TATTATA
519263 TATTATA
1 TATTATA
519270 TA-TATA
1 TATTATA
519276 TATATATA
1 TAT-TATA
519284 TATATATA
1 TAT-TATA
519292 TATATATA
1 TAT-TATA
519300 TAT
1 TAT
519303 AATAATTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 11 0.30
7 3 0.08
8 23 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TATTATA
Found at i:519273 original size:2 final size:2
Alignment explanation
Indices: 519262--519303 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
519252 AAATTTATTA
519262 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
519303 A
1 A
519304 ATAATTACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:519420 original size:29 final size:30
Alignment explanation
Indices: 519348--519423 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
519338 ACTAAACCCG
* *
519348 TCCCCGTCCCTGTTTAACATAAACGATTTT
1 TCCCCATCCCCGTTTAACATAAACGATTTT
* *
519378 TCCCCATCCTCGTTTAGCATAAACGA-TTT
1 TCCCCATCCCCGTTTAACATAAACGATTTT
*
519407 TCCCCTTCCCCGTTTAA
1 TCCCCATCCCCGTTTAA
519424 TTCGATTTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 17 0.44
30 22 0.56
ACGTcount: A:0.21, C:0.34, G:0.09, T:0.36
Consensus pattern (30 bp):
TCCCCATCCCCGTTTAACATAAACGATTTT
Found at i:527843 original size:4 final size:4
Alignment explanation
Indices: 527828--527916 Score: 169
Period size: 4 Copynumber: 22.2 Consensus size: 4
527818 TGAACGAATG
*
527828 GTAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
527876 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
527917 CAGTATGCAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 83 1.00
ACGTcount: A:0.25, C:0.01, G:0.26, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:529021 original size:55 final size:55
Alignment explanation
Indices: 528960--529072 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
528950 ATTTTATCTC
528960 AGTAATTAAAAGAATTATTATTATTCGAACACTAATTTTTATAACAGAATGATTG
1 AGTAATTAAAAGAATTATTATTATTCGAACACTAATTTTTATAACAGAATGATTG
529015 AGTAATTAAAAGAATTATTATTATTCGAACACTAATTTTTATAACAGAATGATTG
1 AGTAATTAAAAGAATTATTATTATTCGAACACTAATTTTTATAACAGAATGATTG
529070 AGT
1 AGT
529073 GTGATTAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (55 bp):
AGTAATTAAAAGAATTATTATTATTCGAACACTAATTTTTATAACAGAATGATTG
Found at i:547222 original size:14 final size:14
Alignment explanation
Indices: 547203--547229 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
547193 CTTTAAACTT
547203 TTATAATTTTTATC
1 TTATAATTTTTATC
547217 TTATAATTTTTAT
1 TTATAATTTTTAT
547230 ATAATTTTAA
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:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATAATTTTTATC
Found at i:547993 original size:60 final size:60
Alignment explanation
Indices: 547926--548040 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
547916 TTACCCCGTG
* * * *
547926 ATTATAGGATACTGTTTTGTTGAGTATCTTGACTATCAAAAGTTATAAAATAGTCCCCCA
1 ATTATAGGATACTGCTTTATTGAGTATCTAGACTATCAAAAGTTACAAAATAGTCCCCCA
* ** * *
547986 ATTATAGGGTGTTGCTTTATTGAGTCTCTAGACTATTAAAAGTTACAAAATAGTC
1 ATTATAGGATACTGCTTTATTGAGTATCTAGACTATCAAAAGTTACAAAATAGTC
548041 ACTCGATTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (60 bp):
ATTATAGGATACTGCTTTATTGAGTATCTAGACTATCAAAAGTTACAAAATAGTCCCCCA
Found at i:548887 original size:164 final size:162
Alignment explanation
Indices: 548608--548947 Score: 637
Period size: 164 Copynumber: 2.1 Consensus size: 162
548598 TTAGTCAACT
*
548608 TTAA-TATTTTGATTTAAATATAATTTGACTTTTTTTCTAATTTTGAAATTGAGCAAATAATACC
1 TTAATTATTTGGATTTAAATATAATTTGACTTTTTTTCTAATTTTGAAATTGAGCAAATAATACC
548672 TTAAAAGCATCATTTTCAACCCATCATATTAACATGGGTATTTTTATTCCAATTGGTGTTTCTAC
66 TTAAAAGCATCATTTTCAACCCATCATATTAACATGGGTATTTTTATTCCAATTGGTGTTTCTAC
548737 AAAGATTCATGATAACATAATAGTTATGTATG
131 AAAGATTCATGATAACATAATAGTTATGTATG
*
548769 TTAATTATTTGGATTTAAATATAATTTGACTTTTTTTTTCTAATTTTGAAATTGAGTAAATAATA
1 TTAATTATTTGGATTTAAATATAATTTGAC--TTTTTTTCTAATTTTGAAATTGAGCAAATAATA
548834 CCTTAAAAGCATCATTTTCAACCCATCATATTAACATGGGTATTTTTATTCCAATTGGTGTTTCT
64 CCTTAAAAGCATCATTTTCAACCCATCATATTAACATGGGTATTTTTATTCCAATTGGTGTTTCT
548899 ACAAAGATTCATGATAACATAATAGTTATGTATG
129 ACAAAGATTCATGATAACATAATAGTTATGTATG
548933 TTAATTATTTGGATT
1 TTAATTATTTGGATT
548948 AGTTAATTAC
Statistics
Matches: 174, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
161 4 0.02
162 24 0.14
164 146 0.84
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (162 bp):
TTAATTATTTGGATTTAAATATAATTTGACTTTTTTTCTAATTTTGAAATTGAGCAAATAATACC
TTAAAAGCATCATTTTCAACCCATCATATTAACATGGGTATTTTTATTCCAATTGGTGTTTCTAC
AAAGATTCATGATAACATAATAGTTATGTATG
Found at i:565567 original size:18 final size:18
Alignment explanation
Indices: 565544--565578 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
565534 GCTGAATATT
565544 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
565562 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
565579 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:567179 original size:14 final size:14
Alignment explanation
Indices: 567156--567192 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
567146 AACTGTCATT
567156 CAAA-GGAGCTTGC
1 CAAATGGAGCTTGC
567169 CAAATGGAGCTTGC
1 CAAATGGAGCTTGC
*
567183 TAAATGGAGC
1 CAAATGGAGC
567193 GAACTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.19
Consensus pattern (14 bp):
CAAATGGAGCTTGC
Found at i:570472 original size:23 final size:23
Alignment explanation
Indices: 570434--570480 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
570424 TTTAAAGTTA
570434 AGAAATGACGGAGAATATATGAT
1 AGAAATGACGGAGAATATATGAT
* *
570457 AGAAATGGCGGGGAATATATGAT
1 AGAAATGACGGAGAATATATGAT
570480 A
1 A
570481 AAAGTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.30, T:0.21
Consensus pattern (23 bp):
AGAAATGACGGAGAATATATGAT
Found at i:575346 original size:2 final size:2
Alignment explanation
Indices: 575339--575365 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
575329 CTAAACCTAC
575339 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
575366 CAAGGCAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:585885 original size:15 final size:15
Alignment explanation
Indices: 585865--585894 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
585855 CATTAGGTTC
585865 TGTTGAAAACATTTT
1 TGTTGAAAACATTTT
585880 TGTTGAAAACATTTT
1 TGTTGAAAACATTTT
585895 GATATTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
TGTTGAAAACATTTT
Found at i:591995 original size:20 final size:21
Alignment explanation
Indices: 591970--592008 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
591960 TTTTGGTGCA
591970 GAGGGAACCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
591990 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
592009 ACAGGGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.21, C:0.41, G:0.26, T:0.13
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:592014 original size:20 final size:21
Alignment explanation
Indices: 591971--592028 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
591961 TTTGGTGCAG
**
591971 AGGGAACCGA-TCCCCCCTTG
1 AGGGAACCGATTCCCCCCTAC
591991 AGGGAACCGATTCCCCCC-AC
1 AGGGAACCGATTCCCCCCTAC
* *
592011 AGGGGAATCGATACCCCC
1 A-GGGAACCGATTCCCCC
592029 TGGGGTTCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCCTAC
Found at i:594298 original size:11 final size:11
Alignment explanation
Indices: 594282--594316 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
594272 GGGGAGAAGT
594282 GTGTGTTTTAA
1 GTGTGTTTTAA
594293 GTGTGTGTGTTAA
1 GTGTGT-T-TTAA
594306 GTGTGTTTTAA
1 GTGTGTTTTAA
594317 AATAAGTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.45
12 2 0.09
13 10 0.45
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.51
Consensus pattern (11 bp):
GTGTGTTTTAA
Found at i:594300 original size:15 final size:13
Alignment explanation
Indices: 594278--594311 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
594268 AAAGGGGGAG
*
594278 AAGTGTGTGTTTT
1 AAGTGTGTGTGTT
594291 AAGTGTGTGTGTT
1 AAGTGTGTGTGTT
594304 AAGTGTGT
1 AAGTGTGT
594312 TTTAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (13 bp):
AAGTGTGTGTGTT
Found at i:594324 original size:16 final size:16
Alignment explanation
Indices: 594303--594335 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
594293 GTGTGTGTGT
594303 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
594319 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
594335 T
1 T
594336 GATAAATGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (16 bp):
TAAGTGTGTTTTAAAA
Found at i:594457 original size:15 final size:15
Alignment explanation
Indices: 594437--594467 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
594427 AAGGGGGAGA
594437 TTGTTGAAAACATTT
1 TTGTTGAAAACATTT
594452 TTGTTGAAAACATTT
1 TTGTTGAAAACATTT
594467 T
1 T
594468 GATATTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (15 bp):
TTGTTGAAAACATTT
Found at i:596477 original size:41 final size:41
Alignment explanation
Indices: 596432--596511 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
596422 TCCCAATTCA
* *
596432 ATTCAATTCAATCATAACAAAATGCAATAGTTTACCATTAG
1 ATTCAATTCAATCATAACAAAATGCAATACTTCACCATTAG
** *
596473 ATTCAATTCAATCATGGCAACATGCAATACTTCACCATT
1 ATTCAATTCAATCATAACAAAATGCAATACTTCACCATT
596512 CAACTTGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (41 bp):
ATTCAATTCAATCATAACAAAATGCAATACTTCACCATTAG
Found at i:596542 original size:82 final size:82
Alignment explanation
Indices: 596456--596611 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 82
596446 TAACAAAATG
* * * *
596456 CAATAGTTTACCATT-AGA-TTCAATTCAATCATGGCAACATGCAATACTTCACCATTCAACTTG
1 CAATAGTTCACCATTCA-ACTT-AATTCAATCATGACAACATACAATAATTCACCATTCAACTTG
596519 ATTCGATCATGATAGCATA
64 ATTCGATCATGATAGCATA
* * *
596538 CAATAGTTCACCATTCAACTTGATTCGATCATGACAGCATACAATAATTCACCATTCAACTTGAT
1 CAATAGTTCACCATTCAACTTAATTCAATCATGACAACATACAATAATTCACCATTCAACTTGAT
596603 TCGATCATG
66 TCGATCATG
596612 GTAACATGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
82 62 0.95
83 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (82 bp):
CAATAGTTCACCATTCAACTTAATTCAATCATGACAACATACAATAATTCACCATTCAACTTGAT
TCGATCATGATAGCATA
Found at i:596630 original size:41 final size:41
Alignment explanation
Indices: 596478--596611 Score: 196
Period size: 41 Copynumber: 3.3 Consensus size: 41
596468 ATTAGATTCA
* * *
596478 ATTCAATCATGGCAACATGCAATACTTCACCATTCAACTTG
1 ATTCGATCATGACAACATACAATACTTCACCATTCAACTTG
* * *
596519 ATTCGATCATGATAGCATACAATAGTTCACCATTCAACTTG
1 ATTCGATCATGACAACATACAATACTTCACCATTCAACTTG
* *
596560 ATTCGATCATGACAGCATACAATAATTCACCATTCAACTTG
1 ATTCGATCATGACAACATACAATACTTCACCATTCAACTTG
596601 ATTCGATCATG
1 ATTCGATCATG
596612 GTAACATGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (41 bp):
ATTCGATCATGACAACATACAATACTTCACCATTCAACTTG
Found at i:598337 original size:2 final size:2
Alignment explanation
Indices: 598330--598362 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
598320 CAGCTTTTGC
598330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
598363 GCAGCCTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:604740 original size:26 final size:27
Alignment explanation
Indices: 604704--604755 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
604694 CTGTCTCTAC
*
604704 ATGTCCTTAAA-TTTTCTTCCCATTTT
1 ATGTCCCTAAATTTTTCTTCCCATTTT
*
604730 ATGTCCCTAAATTTTTCTTCCTATTT
1 ATGTCCCTAAATTTTTCTTCCCATTT
604756 CATTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.19, C:0.23, G:0.04, T:0.54
Consensus pattern (27 bp):
ATGTCCCTAAATTTTTCTTCCCATTTT
Found at i:610107 original size:21 final size:21
Alignment explanation
Indices: 610083--610125 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
610073 ACTGTTGTAT
*
610083 CCATCTTTATCCTAATTATAA
1 CCATCTTCATCCTAATTATAA
*
610104 CCATCTTCATCCTGATTATAA
1 CCATCTTCATCCTAATTATAA
610125 C
1 C
610126 AGTCCAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.40
Consensus pattern (21 bp):
CCATCTTCATCCTAATTATAA
Found at i:612765 original size:59 final size:58
Alignment explanation
Indices: 612701--612839 Score: 145
Period size: 59 Copynumber: 2.3 Consensus size: 58
612691 GAGACTAATA
* * * * * * *
612701 TAAAATAAATGTCATAATTTGGGGATAAACCTAAAATGTTAAAAATTTGATGA-CCAATT
1 TAAAATAAA-GTCACAATTTAGAGATAAAACTAAAATATTAAAAAATT-AAGATCCAATT
* * *
612760 TAAAATAAGAGTTACATTTTAGAGATAAAATTAAAATATTAAAAAATTAAGATCCAATT
1 TAAAATAA-AGTCACAATTTAGAGATAAAACTAAAATATTAAAAAATTAAGATCCAATT
612819 TAAAATAAAAGTCACAATTTA
1 TAAAAT-AAAGTCACAATTTA
612840 ATAACATATA
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
58 3 0.05
59 59 0.91
60 3 0.05
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (58 bp):
TAAAATAAAGTCACAATTTAGAGATAAAACTAAAATATTAAAAAATTAAGATCCAATT
Found at i:613061 original size:17 final size:17
Alignment explanation
Indices: 613041--613080 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
613031 TTAAAATTAA
* *
613041 TTAATTAATTTTTATTT
1 TTAATTAATTTATATCT
613058 TTAATTAATTTATATCT
1 TTAATTAATTTATATCT
613075 TTAATT
1 TTAATT
613081 GACTGTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATTAATTTATATCT
Found at i:613987 original size:14 final size:15
Alignment explanation
Indices: 613968--613999 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
613958 AAATTCGAAT
613968 ATTATA-AATAAAAA
1 ATTATACAATAAAAA
613982 ATTATACAATAAAAA
1 ATTATACAATAAAAA
613997 ATT
1 ATT
614000 TATCTACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTATACAATAAAAA
Found at i:618070 original size:16 final size:16
Alignment explanation
Indices: 618041--618075 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
618031 TTTTAGAATT
618041 TTTAAATTTCTTTATA
1 TTTAAATTTCTTTATA
* *
618057 TTTAATTTTTTTTATA
1 TTTAAATTTCTTTATA
618073 TTT
1 TTT
618076 TTTTATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAAATTTCTTTATA
Found at i:621182 original size:43 final size:42
Alignment explanation
Indices: 621121--621461 Score: 157
Period size: 43 Copynumber: 7.4 Consensus size: 42
621111 ATCAGCGGTC
*
621121 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATAT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGT-TGGAGTCCAATAT
* * * * *
621164 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTT-GATTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTTGGAGT-CCAA-TA----T
*
621214 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGT-TGGAGTCCAATAT
* * * * *
621258 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTT-GATTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTTGGAGT-CCAA-TA----T
** *
621308 CCCTTCGTCATGAAGTTGAACTTGCATTGTTTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTG-TTGGAGTCCAATAT
* * * * *
621352 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTT-GATTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTTGGAGT-CCAA-TA----T
* *
621402 CCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGT-TGGAGTCCAATAT
621446 CCTTCGTTGTGAAGTT
1 CCTTCGTTGTGAAGTT
621462 AAAATTGGCT
Statistics
Matches: 221, Mismatches: 41, Indels: 72
0.66 0.12 0.22
Matches are distributed among these distances:
43 80 0.36
44 12 0.05
45 13 0.06
46 14 0.06
48 14 0.06
49 13 0.06
50 12 0.05
51 63 0.29
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (42 bp):
CCTTCGTTGTGAAGTTGAACTTGCGTTGTTGGAGTCCAATAT
Found at i:621227 original size:51 final size:51
Alignment explanation
Indices: 621164--621421 Score: 219
Period size: 51 Copynumber: 5.4 Consensus size: 51
621154 AGTCCAATAT
*
621164 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
* * * * *
621215 CCTTCGTCGTGAAGTTGAACTTGCG---TTGTCTGGAGT-CCAA-TA----T-
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGT-T-GATTGACAACCAGCGGTC
*
621258 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
* * * * ** ***
621309 CCTTCGTCATGAAGTTGAACTT--G-CATTGTT--TGGA-GTCCA-ATAT-
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
*
621352 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
621403 CCTTCGTCGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
621422 CTTGCATTGT
Statistics
Matches: 154, Mismatches: 33, Indels: 40
0.68 0.15 0.18
Matches are distributed among these distances:
43 41 0.27
44 5 0.03
45 8 0.05
46 14 0.09
48 14 0.09
49 8 0.05
50 5 0.03
51 59 0.38
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (51 bp):
CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
Found at i:621256 original size:94 final size:94
Alignment explanation
Indices: 621095--621678 Score: 830
Period size: 94 Copynumber: 6.0 Consensus size: 94
621085 TGGAACTGGA
* * * **
621095 AAATTGTTTATTGACAATCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
621160 ATATCCTTCGTTGTGAAGTTGAAATTGGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGG
*
621189 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
621254 ATATCCTTCGTTGTGAAGTTGAAATTGGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGG
* *
621283 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTTTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
621348 ATATCCTTCGTTGTGAAGTTGAAATTGGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGG
621377 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
*
621442 ATATCCTTCGTTGTGAAGTTAAAATTGGCTCTG
66 ATATCCTTCGTTGTGAAGTTGAAATTGG----G
621475 AAATTGAGAAATGTTTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
1 AAA-T------TG-TTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
*
621539 GGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTG
58 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----G
*
621580 AAATTGAGAAATGTTTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 AAA-T------TG-TTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
*
621644 GGAGTCCAATATCCTTCGTTGAGAAGTTGAAATTG
58 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
621679 ACTATGGGTA
Statistics
Matches: 463, Mismatches: 15, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
94 271 0.59
98 4 0.01
99 1 0.00
105 184 0.40
106 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (94 bp):
AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGG
Found at i:621572 original size:105 final size:105
Alignment explanation
Indices: 621367--621678 Score: 554
Period size: 105 Copynumber: 3.0 Consensus size: 105
621357 GTTGTGAAGT
*
621367 TGAAATTGGGAAAT-TGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTG
1 TGAAATTGAGAAATGT-TTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTG
*
621431 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTC
64 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
621473 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
*
621538 TGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
621578 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
*
621643 TGGAGTCCAATATCCTTCGTTGAGAAGTTGAAATTG
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
621679 ACTATGGGTA
Statistics
Matches: 199, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
105 182 0.91
106 16 0.08
107 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:622535 original size:13 final size:13
Alignment explanation
Indices: 622514--622552 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
622504 TTCTTTTCTT
622514 CTTCTTTTTTTTTC
1 CTTC-TTTTTTTTC
622528 CTTCTTTTTTTTC
1 CTTCTTTTTTTTC
622541 CTT-TTTTTTTTC
1 CTTCTTTTTTTTC
622553 AACTTAGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 9 0.36
13 12 0.48
14 4 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTCTTTTTTTTC
Found at i:631995 original size:20 final size:20
Alignment explanation
Indices: 631957--632000 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
631947 ATAGTTAGTA
*
631957 AAATAAAAATAAATGGAAAT
1 AAATAAAAATAAATAGAAAT
631977 AAATAAAAATAACA-AGAAAT
1 AAATAAAAATAA-ATAGAAAT
631997 AAAT
1 AAAT
632001 GGCAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAATAGAAAT
Found at i:637340 original size:59 final size:60
Alignment explanation
Indices: 637242--637358 Score: 173
Period size: 59 Copynumber: 2.0 Consensus size: 60
637232 AATGGTCCCC
* * * * *
637242 GATTATATGATATTATTTTATTAAGTACTTTGATTATTAAAAGTTACAACATGGTCATTT
1 GATTATATAATATTATTTTATTAAGTACTTCGACTATTAAAAGTTACAAAATGATCATTT
*
637302 GATTATATAATATTATTTT-TTAAGTTCTTCGACTATTAAAAGTTACAAAATGATCAT
1 GATTATATAATATTATTTTATTAAGTACTTCGACTATTAAAAGTTACAAAATGATCAT
637359 CCAACTATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
59 33 0.65
60 18 0.35
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (60 bp):
GATTATATAATATTATTTTATTAAGTACTTCGACTATTAAAAGTTACAAAATGATCATTT
Found at i:639010 original size:17 final size:17
Alignment explanation
Indices: 638983--639021 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
638973 TTTTTACAAT
638983 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
638999 TAATTATAAATAATATC
1 TAATTATAAATAATATC
639016 TAATTA
1 TAATTA
639022 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:644464 original size:24 final size:24
Alignment explanation
Indices: 644432--644498 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
644422 TAGAGCAGTG
644432 GAGTGCTGAAACACTGAAGCTCTA
1 GAGTGCTGAAACACTGAAGCTCTA
644456 GAGTGCTGAAACACTGAAGCTCTA
1 GAGTGCTGAAACACTGAAGCTCTA
* *
644480 GAGTGTTGAAGCACTGAAG
1 GAGTGCTGAAACACTGAAG
644499 TGCTGGAGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (24 bp):
GAGTGCTGAAACACTGAAGCTCTA
Found at i:651724 original size:2 final size:2
Alignment explanation
Indices: 651717--651756 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
651707 TGATACAATA
651717 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
651757 GTTAAAAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:653087 original size:15 final size:16
Alignment explanation
Indices: 653069--653101 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
653059 GTGGCAGATC
653069 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
653084 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
653100 AA
1 AA
653102 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:663017 original size:2 final size:2
Alignment explanation
Indices: 663010--663037 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
663000 TCAAACCCGA
663010 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
663038 TAGAAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:666671 original size:28 final size:27
Alignment explanation
Indices: 666635--666703 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 27
666625 AAAAAAAAAA
* * * *
666635 TAAAAAATTAATCAATTTTATTATTCT
1 TAAATAATTAATCAAATTTAATATCCT
* *
666662 TAACATAATTTATGAAATTTAATATCCT
1 TAA-ATAATTAATCAAATTTAATATCCT
*
666690 TAAGTAATTAATCA
1 TAAATAATTAATCA
666704 TAAAATAATA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (27 bp):
TAAATAATTAATCAAATTTAATATCCT
Found at i:671153 original size:13 final size:13
Alignment explanation
Indices: 671135--671159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
671125 TTACCGAACA
671135 TTAAATGAACATG
1 TTAAATGAACATG
671148 TTAAATGAACAT
1 TTAAATGAACAT
671160 ATTCACGAAA
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:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (13 bp):
TTAAATGAACATG
Found at i:674422 original size:18 final size:18
Alignment explanation
Indices: 674380--674423 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
674370 TGGTGGCGGG
*
674380 GGGGAGGTGGATGATGTA
1 GGGGAGGTGGATGAAGTA
674398 GGCGGAGGT-GATGAAGTA
1 GG-GGAGGTGGATGAAGTA
674416 GAGGGAGG
1 G-GGGAGG
674424 AGGACGGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.25, C:0.02, G:0.57, T:0.16
Consensus pattern (18 bp):
GGGGAGGTGGATGAAGTA
Found at i:674546 original size:48 final size:47
Alignment explanation
Indices: 674494--674622 Score: 152
Period size: 48 Copynumber: 2.7 Consensus size: 47
674484 TGGAATAGCA
*
674494 GGTGGTGGGGAAGGAGTAGTAGTTGGCGGCGGAGCCGCAGCGGCTGGT
1 GGTGGTGTGGAAGGAGT-GTAGTTGGCGGCGGAGCCGCAGCGGCTGGT
** * * *
674542 GGTGGTGTGG-AGGAAGTGGTAGTTGGCGGCGGAGTTGCTGCTGTTGGT
1 GGTGGTGTGGAAGG-AGT-GTAGTTGGCGGCGGAGCCGCAGCGGCTGGT
*
674590 GGGGGTGTGGAAGGAGTGCTAGTTGGCGGCGGA
1 GGTGGTGTGGAAGGAGTG-TAGTTGGCGGCGGA
674623 ACTGAAGCTA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
47 4 0.06
48 63 0.90
49 3 0.04
ACGTcount: A:0.13, C:0.11, G:0.54, T:0.22
Consensus pattern (47 bp):
GGTGGTGTGGAAGGAGTGTAGTTGGCGGCGGAGCCGCAGCGGCTGGT
Found at i:675063 original size:25 final size:21
Alignment explanation
Indices: 675012--675063 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
675002 ATTTATATAT
675012 TCAATTAATTCAGTTATAGTG
1 TCAATTAATTCAGTTATAGTG
675033 TCAATTAATTCAGTTATAGTG
1 TCAATTAATTCAGTTATAGTG
* *
675054 TAAAATAATT
1 TCAATTAATT
675064 TAATAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (21 bp):
TCAATTAATTCAGTTATAGTG
Found at i:675854 original size:23 final size:24
Alignment explanation
Indices: 675808--675867 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
675798 AGAACATGCT
675808 ACAAGAGTAGAGAAAAAATATGTC
1 ACAAGAGTAGAGAAAAAATATGTC
* *
675832 ACAAGAGTATAG-AAAAATGTGTC
1 ACAAGAGTAGAGAAAAAATATGTC
675855 ACAATGA-TAGAGA
1 ACAA-GAGTAGAGA
675868 TTCTTATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 18 0.58
24 13 0.42
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.18
Consensus pattern (24 bp):
ACAAGAGTAGAGAAAAAATATGTC
Found at i:676377 original size:6 final size:6
Alignment explanation
Indices: 676366--676419 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
676356 TACACGTATT
676366 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
676412 ACC-CG ACC
1 ACCACG ACC
676420 CGAGACGAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.31
6 33 0.69
ACGTcount: A:0.30, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:676428 original size:5 final size:5
Alignment explanation
Indices: 676420--676447 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
676410 CGACCCGACC
676420 CGAGA CGAGA CGAGA CGAGA CGAGA CGA
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGA
676448 ACGGCGGCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.39, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:677093 original size:40 final size:41
Alignment explanation
Indices: 677048--677125 Score: 122
Period size: 42 Copynumber: 1.9 Consensus size: 41
677038 TGCGATTTTG
677048 GACTATCGCAA-CGAACTTGGACTATCGCAATGCGATAGTC
1 GACTATCGCAACCGAACTTGGACTATCGCAATGCGATAGTC
* *
677088 GACTATCGCAACGCGAACTTGGACTATCGTATTGCGAT
1 GACTATCGCAAC-CGAACTTGGACTATCGCAATGCGAT
677126 TTACATATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 11 0.32
42 23 0.68
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (41 bp):
GACTATCGCAACCGAACTTGGACTATCGCAATGCGATAGTC
Found at i:677124 original size:21 final size:21
Alignment explanation
Indices: 677045--677116 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
677035 CGTTGCGATT
677045 TTGGACTATCGCAA--CGAAC
1 TTGGACTATCGCAATGCGAAC
677064 TTGGACTATCGCAATGCGATA-
1 TTGGACTATCGCAATGCGA-AC
* * *
677085 GTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAATGCGAAC
677106 TTGGACTATCG
1 TTGGACTATCG
677117 TATTGCGATT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 14 0.32
20 1 0.02
21 28 0.64
22 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:677163 original size:21 final size:21
Alignment explanation
Indices: 677137--677248 Score: 113
Period size: 21 Copynumber: 5.4 Consensus size: 21
677127 TACATATTCA
*
677137 CATTGCGATAGTCCAAGTTTG
1 CATTGCGATAGTCCAAGTTCG
* *
677158 CATTGCGATAGT-CGACTATCG
1 CATTGCGATAGTCCAAGT-TCG
* *
677179 CATTGCGAT-TTACATA-TTCG
1 CATTGCGATAGTCCA-AGTTCG
677199 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
* *
677220 CAATGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
677241 CGTTGCGA
1 CATTGCGA
677249 ATCTGGAAAC
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
20 17 0.23
21 57 0.76
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (21 bp):
CATTGCGATAGTCCAAGTTCG
Found at i:677248 original size:62 final size:62
Alignment explanation
Indices: 677109--677234 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 62
677099 CGCGAACTTG
* * *
677109 GACTATCGTATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTTGCATTGCGATAGTC
1 GACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCGCAATGCGATAGTC
*
677171 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCAATGCGATAGTC
1 GACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCGCAATGCGATAGTC
677233 GA
1 GA
677235 AGTTCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (62 bp):
GACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCGCAATGCGATAGTC
Found at i:677872 original size:18 final size:19
Alignment explanation
Indices: 677845--677885 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
677835 AATCTTTATT
677845 TTTTTAAATAAAAATAATA
1 TTTTTAAATAAAAATAATA
* *
677864 TTTTT-AATAAATATATTA
1 TTTTTAAATAAAAATAATA
677882 TTTT
1 TTTT
677886 GGATTGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTAAATAAAAATAATA
Found at i:681791 original size:21 final size:20
Alignment explanation
Indices: 681748--681794 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
681738 TCTCTTCATT
**
681748 TTCTTTTTTTTCTTTCTTTC
1 TTCTTTTTTTTCTTTCTACC
681768 TTCTGTTTTTTTCTTTCTACC
1 TTCT-TTTTTTTCTTTCTACC
681789 TTCTTT
1 TTCTTT
681795 GACTTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (20 bp):
TTCTTTTTTTTCTTTCTACC
Found at i:683721 original size:29 final size:29
Alignment explanation
Indices: 683679--683771 Score: 159
Period size: 29 Copynumber: 3.2 Consensus size: 29
683669 ATCAAACTAA
* *
683679 AATTTATTTGAAAATTATTAACCGAATCG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
683708 AATTAATTTGAAAATTATTAACCAAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
683737 AATTAATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
683766 AATTAA
1 AATTAA
683772 CCGATTGTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:683885 original size:29 final size:29
Alignment explanation
Indices: 683835--683911 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
683825 ATCGGTTTGC
* * *
683835 TTAATCGAATCAAAATTTATTTGAAAATTA
1 TTAATCGAA-CCAAATTAATTTAAAAATTA
683865 TTAATCGAACCAAATTAATTTAAAAATTA
1 TTAATCGAACCAAATTAATTTAAAAATTA
*
683894 TTAACCGAACCAAATTAA
1 TTAATCGAACCAAATTAA
683912 CCGTTTTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 34 0.79
30 9 0.21
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (29 bp):
TTAATCGAACCAAATTAATTTAAAAATTA
Found at i:684005 original size:30 final size:29
Alignment explanation
Indices: 683971--684035 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
683961 TTTTGGTTCG
* *
683971 ATTAATCGAACCAAAATTTACTTGAAAATT
1 ATTAACCGAACC-AAATTAACTTGAAAATT
* *
684001 ATTAACCGAACCGAATTAATTTGAAAATT
1 ATTAACCGAACCAAATTAACTTGAAAATT
684030 ATTAAC
1 ATTAAC
684036 TAAATCGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (29 bp):
ATTAACCGAACCAAATTAACTTGAAAATT
Found at i:684044 original size:29 final size:29
Alignment explanation
Indices: 683992--684048 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
683982 CAAAATTTAC
*
683992 TTGAAAATTATTAACCGAACCGAATTAAT
1 TTGAAAATTATTAACCAAACCGAATTAAT
* *
684021 TTGAAAATTATTAACTAAATCGAATTAA
1 TTGAAAATTATTAACCAAACCGAATTAA
684049 CCAAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (29 bp):
TTGAAAATTATTAACCAAACCGAATTAAT
Found at i:684047 original size:137 final size:138
Alignment explanation
Indices: 683715--684050 Score: 453
Period size: 137 Copynumber: 2.4 Consensus size: 138
683705 TCGAATTAAT
*
683715 TTGAAAATTATTAACCAAACCGAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATTGT
1 TTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGA-TGT
* * * *
683780 TTTTGAAAATTATTAACCGAATTAATCGAAGCAAAAATTCGGTTAATCGGTTTGCTTAATCGAAT
65 TTTT-AAAACTATTAACCGAATTAATCGAAGCAAAAATTCGGTTAATCGGTTCGATTAATCGAAC
*
683845 CAAAATTTAT
129 CAAAATTTAC
* * * *
683855 TTGAAAATTATTAATCGAACCAAATTAATTTAAAAATTATTAACCGAACCAAATTAACCG-T-TT
1 TTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATGTT
** * * *
683918 TTT-CCACTATTAATCGAATTAATCGAAGTAAAAATTCGGTTAATTTTGGTTCGATTAATCGAAC
66 TTTAAAACTATTAACCGAATTAATCGAAGCAAAAATTCGGTTAA--TCGGTTCGATTAATCGAAC
683982 CAAAATTTAC
129 CAAAATTTAC
** *
683992 TTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACTAAATCGAATTAACC
1 TTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACCGAACCGAATTAACC
684051 AAAATTTTTT
Statistics
Matches: 172, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
135 35 0.20
137 81 0.47
138 1 0.01
140 55 0.32
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (138 bp):
TTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATGTT
TTTAAAACTATTAACCGAATTAATCGAAGCAAAAATTCGGTTAATCGGTTCGATTAATCGAACCA
AAATTTAC
Found at i:692317 original size:31 final size:31
Alignment explanation
Indices: 692279--692346 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
692269 ATTTAAGCTA
* *
692279 AGGGACTAAAATGGAACGGATCAATAATATT
1 AGGGACTAAAATCGAACAGATCAATAATATT
* * *
692310 AGGGACTAAAATCGAATAGATTAATAATGTT
1 AGGGACTAAAATCGAACAGATCAATAATATT
692341 AGGGAC
1 AGGGAC
692347 CATTTATACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.24
Consensus pattern (31 bp):
AGGGACTAAAATCGAACAGATCAATAATATT
Found at i:692458 original size:18 final size:18
Alignment explanation
Indices: 692435--692469 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
692425 ACCGCATAGT
692435 TTACCCATATTAAAAAGC
1 TTACCCATATTAAAAAGC
692453 TTACCCATATTAAAAAG
1 TTACCCATATTAAAAAG
692470 TTTGACGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (18 bp):
TTACCCATATTAAAAAGC
Found at i:697904 original size:20 final size:19
Alignment explanation
Indices: 697879--697918 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
697869 TAAACATTTT
697879 TTTCTGCCCAGTTTCAAAAC
1 TTTCTG-CCAGTTTCAAAAC
**
697899 TTTCTGGGAGTTTCAAAAC
1 TTTCTGCCAGTTTCAAAAC
697918 T
1 T
697919 ATGACCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTCTGCCAGTTTCAAAAC
Found at i:698583 original size:21 final size:20
Alignment explanation
Indices: 698559--698598 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
698549 TGGCTACAAC
*
698559 AAACTAAGCTTAGAATACTTG
1 AAACTAAGCTT-GAAAACTTG
698580 AAACTAAGCTTGAAAACTT
1 AAACTAAGCTTGAAAACTT
698599 ACAAAATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (20 bp):
AAACTAAGCTTGAAAACTTG
Found at i:700190 original size:57 final size:57
Alignment explanation
Indices: 700095--700255 Score: 250
Period size: 57 Copynumber: 2.8 Consensus size: 57
700085 CACAGTTTCT
* *
700095 AAAATCGCGTTGCGATGGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
1 AAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATTAGCGTTGCGAATTTG
* ** * *
700152 AAAATCGTGTTGCGATAACACTGTTTACCTACAGCGGTAATTAGCGTTGTGAATTTG
1 AAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATTAGCGTTGCGAATTTG
*
700209 AAAATCGCGTTGCGATAGTACTATTTACCTACATCGGTAATTAGCGT
1 AAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATTAGCGT
700256 ATTTCGATAA
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 92 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (57 bp):
AAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATTAGCGTTGCGAATTTG
Found at i:700317 original size:20 final size:20
Alignment explanation
Indices: 700294--700337 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
700284 GTAATTAGCT
700294 TTGCGAATTTGTAAATCGCG
1 TTGCGAATTTGTAAATCGCG
*
700314 TTGCGAATTTTTAAATCGCG
1 TTGCGAATTTGTAAATCGCG
700334 TTGC
1 TTGC
700338 TCCTGTGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGTAAATCGCG
Found at i:702004 original size:20 final size:20
Alignment explanation
Indices: 701979--702024 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
701969 GTAATTAGCG
*
701979 TTGCGAATTTGAAAATCTCA
1 TTGCGAATTTGAAAATCGCA
701999 TTGCGAATTTGAAAATCGCA
1 TTGCGAATTTGAAAATCGCA
702019 TTGCGA
1 TTGCGA
702025 TAGTACTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCGCA
Found at i:702080 original size:20 final size:20
Alignment explanation
Indices: 702055--702135 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
702045 GGTAATCAGT
702055 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
** * * *
702075 GTTGCGATTTTGGAAAATGGC
1 GTTGCGA-TTTACATATTCGC
* **
702096 GCTGCGATTTACATATTATC
1 GTTGCGATTTACATATTCGC
*
702116 ATTGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
702136 ATTGTGAATT
Statistics
Matches: 44, Mismatches: 16, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:702080 original size:77 final size:78
Alignment explanation
Indices: 701933--702092 Score: 200
Period size: 77 Copynumber: 2.1 Consensus size: 78
701923 CACAGTTTCC
** * * *
701933 AAAATCGTGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCTC
1 AAAATCGCATTGCGATAGTACTGTTTACCTACATCGGTAATCAGCGTTGCGAATTTGAAAATCGC
701998 ATTGCGAATTT-G
66 ATTGCGAATTTGG
* *
702010 AAAATCGCATTGCGATAGTACTGTTTACCTACATCGGTAATCAGTGTTGCG-ATTT-ACATATTC
1 AAAATCGCATTGCGATAGTACTGTTTACCTACATCGGTAATCAGCGTTGCGAATTTGA-A-AATC
* *
702073 GCGTTGCGATTTTGG
64 GCATTGCGAATTTGG
702088 AAAAT
1 AAAAT
702093 GGCGCTGCGA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
75 1 0.01
76 5 0.07
77 59 0.83
78 6 0.08
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (78 bp):
AAAATCGCATTGCGATAGTACTGTTTACCTACATCGGTAATCAGCGTTGCGAATTTGAAAATCGC
ATTGCGAATTTGG
Found at i:702961 original size:23 final size:23
Alignment explanation
Indices: 702896--702964 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
702886 CACCACAGCT
* * *
702896 CGTATAATTGCACAGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
*
702919 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
* *
702942 CGTAGAATTGCATCGTAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
702965 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:704663 original size:20 final size:20
Alignment explanation
Indices: 704587--704662 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
704577 ACAGGTTCCA
** *
704587 AAATCGCAACGCGAATAGGT
1 AAATCGCAACGATAATATGT
*
704607 AAATCGCAAC-ATGAATATAT
1 AAATCGCAACGAT-AATATGT
*
704627 AAATCGCAACGATAATTTGT
1 AAATCGCAACGATAATATGT
*
704647 AAATCGCAACGCTAAT
1 AAATCGCAACGATAAT
704663 TACCGATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 45 0.96
21 2 0.04
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGATAATATGT
Found at i:704859 original size:20 final size:20
Alignment explanation
Indices: 704836--704873 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
704826 TTGCAATGCG
*
704836 AATATGTAAATCGCAACGAT
1 AATATGTAAATCACAACGAT
704856 AATATGTAAATCACAACG
1 AATATGTAAATCACAACG
704874 CGATTTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (20 bp):
AATATGTAAATCACAACGAT
Found at i:704958 original size:57 final size:57
Alignment explanation
Indices: 704869--705052 Score: 253
Period size: 57 Copynumber: 3.2 Consensus size: 57
704859 ATGTAAATCA
* * *
704869 CAACGCGATTTTCCAAAATCGCAACACTAATTACCGATGTAGGTAAACAGAACTATCG
1 CAACGCGATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACAGAACTATCG
* ***
704927 CAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTTATCG
1 CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGAACTATCG
*
704984 CAACGCGATTTTCAAATTCGCAATGCTAATTACCGATATAGGTAAACA-ATACTATCG
1 CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGA-ACTATCG
* *
705041 TAACGTGATTTT
1 CAACGCGATTTT
705053 GGAAAATGTG
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
57 100 0.90
58 11 0.10
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (57 bp):
CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGAACTATCG
Found at i:705084 original size:21 final size:20
Alignment explanation
Indices: 705059--705120 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
705049 TTTTGGAAAA
705059 TGTGTTGCGAATTTACAAAT
1 TGTGTTGCGAATTTACAAAT
* ** *
705079 TCGTGTTGCGATTTTGGAAAC
1 T-GTGTTGCGAATTTACAAAT
705100 TGTGTTGCGAATTTACAAAT
1 TGTGTTGCGAATTTACAAAT
705120 T
1 T
705121 TGCGGTGCGA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (20 bp):
TGTGTTGCGAATTTACAAAT
Found at i:705104 original size:20 final size:20
Alignment explanation
Indices: 705047--705109 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
705037 ATCGTAACGT
705047 GATTTTGGAAAATGTGTTGC
1 GATTTTGGAAAATGTGTTGC
* ** *
705067 GAATTTACAAATTCGTGTTGC
1 GATTTTGGAAAAT-GTGTTGC
*
705088 GATTTTGGAAACTGTGTTGC
1 GATTTTGGAAAATGTGTTGC
705108 GA
1 GA
705110 ATTTACAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (20 bp):
GATTTTGGAAAATGTGTTGC
Found at i:705130 original size:41 final size:41
Alignment explanation
Indices: 705047--705133 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
705037 ATCGTAACGT
* *
705047 GATTTTGGAAAATGTGTTGCGAATTTACAAATTCGTGTTGC
1 GATTTTGGAAAATGTGTTGCGAATTTACAAATTCGCGGTGC
* *
705088 GATTTTGGAAACTGTGTTGCGAATTTACAAATTTGCGGTGC
1 GATTTTGGAAAATGTGTTGCGAATTTACAAATTCGCGGTGC
705129 GATTT
1 GATTT
705134 ACCTATTCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.39
Consensus pattern (41 bp):
GATTTTGGAAAATGTGTTGCGAATTTACAAATTCGCGGTGC
Found at i:724336 original size:16 final size:17
Alignment explanation
Indices: 724315--724347 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
724305 CTTCAGTTCA
724315 TATTTTAATTTA-ATTT
1 TATTTTAATTTATATTT
*
724331 TATTTTATTTTATATTT
1 TATTTTAATTTATATTT
724348 CGTTTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTTTAATTTATATTT
Found at i:724370 original size:12 final size:12
Alignment explanation
Indices: 724355--724418 Score: 60
Period size: 12 Copynumber: 5.3 Consensus size: 12
724345 TTTCGTTTAT
*
724355 TATTATTACATA
1 TATTATTATATA
* * *
724367 TATTTTTTTATT
1 TATTATTATATA
724379 TATTATTATATTA
1 TATTATTATA-TA
724392 TATT-TTATATA
1 TATTATTATATA
724403 TA-TATATATATA
1 TATTAT-TATATA
724415 TATT
1 TATT
724419 TTTGATGGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
10 1 0.02
11 5 0.12
12 29 0.71
13 6 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATTATATA
Found at i:724397 original size:24 final size:24
Alignment explanation
Indices: 724329--724421 Score: 79
Period size: 24 Copynumber: 3.9 Consensus size: 24
724319 TTAATTTAAT
*
724329 TTTATT-TTATTTTATATTTCGTTTA
1 TTTATTATTATATTATATTT--TTTA
*
724354 -TTATTATTACA-TATATTTTTTTA
1 TTTATTATTATATTATA-TTTTTTA
*
724377 TTTATTATTATATTATATTTTATA
1 TTTATTATTATATTATATTTTTTA
*
724401 TATA-TA-TATATATATATTTTT
1 TTTATTATTATAT-TATATTTTT
724422 GATGGTGGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
22 5 0.09
23 14 0.25
24 28 0.49
25 10 0.18
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (24 bp):
TTTATTATTATATTATATTTTTTA
Found at i:724540 original size:47 final size:47
Alignment explanation
Indices: 724444--724610 Score: 225
Period size: 47 Copynumber: 3.6 Consensus size: 47
724434 GATTTGATAA
* * *
724444 GTAGTGGTTGATTATTTTAATATGTAG-GGTTT-ATTATTTTAACAT
1 GTAGTAGTTGATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
* * *
724489 GTAGT-GTTGATTATTTTTAATAGATAGTGGTTTGATTATTTTTATAG
1 GTAGTAGTTGATTA-TTTTAATAGGTAGTGGTTTGATTATTTTAATAT
*
724536 GTAGTAGTTTATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
1 GTAGTAGTTGATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
*
724583 GTTGT-GTTGATTATTTTAATAGGTAGTG
1 GTAGTAGTTGATTATTTTAATAGGTAGTG
724611 ATCTTAATAT
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
44 8 0.07
45 16 0.15
46 27 0.25
47 49 0.46
48 7 0.07
ACGTcount: A:0.26, C:0.01, G:0.22, T:0.52
Consensus pattern (47 bp):
GTAGTAGTTGATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
Found at i:724609 original size:69 final size:69
Alignment explanation
Indices: 724445--724609 Score: 212
Period size: 69 Copynumber: 2.4 Consensus size: 69
724435 ATTTGATAAG
* * *
724445 TAGTGGTTGATTATTTTAATATGTAG-GGTTTATTATTTTAACATGTAGTGTTGATTATTTTTAA
1 TAGTGGTTGATTATTTTAATAGGTAGTAGTTTATTATTTTAACAGGTAGTGTTGATTATTTTTAA
724509 TAGA
66 TAGA
* *
724513 TAGTGGTTTGATTATTTTTATAGGTAGTAGTTTATTATTTTAATAGGTAGTGGTTTGATTA-TTT
1 TAGTGG-TTGATTATTTTAATAGGTAGTAGTTTATTATTTTAACAGGTAGT-G-TTGATTATTTT
724577 TAATATG-
63 TAATA-GA
*
724584 TTGT-GTTGATTATTTTAATAGGTAGT
1 TAGTGGTTGATTATTTTAATAGGTAGT
724610 GATCTTAATA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
68 6 0.07
69 38 0.45
70 21 0.25
71 12 0.14
72 8 0.09
ACGTcount: A:0.26, C:0.01, G:0.21, T:0.53
Consensus pattern (69 bp):
TAGTGGTTGATTATTTTAATAGGTAGTAGTTTATTATTTTAACAGGTAGTGTTGATTATTTTTAA
TAGA
Found at i:724628 original size:38 final size:38
Alignment explanation
Indices: 724576--724648 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
724566 TTTGATTATT
*
724576 TTAATATGTTGTGTTGATTATTTTAATAGGTAGTGATC
1 TTAATATGTAGTGTTGATTATTTTAATAGGTAGTGATC
*
724614 TTAATATGTAGTGTTGATTATTTTATTAGGTAGTG
1 TTAATATGTAGTGTTGATTATTTTAATAGGTAGTG
724649 GGGTAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.26, C:0.01, G:0.22, T:0.51
Consensus pattern (38 bp):
TTAATATGTAGTGTTGATTATTTTAATAGGTAGTGATC
Found at i:724646 original size:22 final size:22
Alignment explanation
Indices: 724444--724648 Score: 188
Period size: 22 Copynumber: 9.3 Consensus size: 22
724434 GATTTGATAA
*
724444 GTAGTGGTTGATTATTTTAATAT
1 GTAGT-GTTGATTATTTTAATAG
* * * *
724467 GTAGGGTTTATTATTTTAACAT
1 GTAGTGTTGATTATTTTAATAG
724489 GTAGTGTTGATTATTTTTAATAG
1 GTAGTGTTGATTA-TTTTAATAG
* *
724512 ATAGTGGTTTGATTATTTTTATAG
1 GTAGT-G-TTGATTATTTTAATAG
*
724536 GTAGTAGTTTATTATTTTAATAG
1 GTAGT-GTTGATTATTTTAATAG
*
724559 GTAGTGGTTTGATTATTTTAATAT
1 GTAGT-G-TTGATTATTTTAATAG
*
724583 GTTGTGTTGATTATTTTAATAG
1 GTAGTGTTGATTATTTTAATAG
* *
724605 GTA--G-TG---ATCTTAATAT
1 GTAGTGTTGATTATTTTAATAG
*
724621 GTAGTGTTGATTATTTTATTAG
1 GTAGTGTTGATTATTTTAATAG
724643 GTAGTG
1 GTAGTG
724649 GGGTAATTAT
Statistics
Matches: 148, Mismatches: 24, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
16 11 0.07
18 1 0.01
19 4 0.03
20 1 0.01
22 56 0.38
23 36 0.24
24 32 0.22
25 7 0.05
ACGTcount: A:0.26, C:0.01, G:0.21, T:0.52
Consensus pattern (22 bp):
GTAGTGTTGATTATTTTAATAG
Found at i:724786 original size:17 final size:17
Alignment explanation
Indices: 724764--724796 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
724754 CTTTCTTTCC
724764 TACTTTTATT-ATATTAA
1 TACTTTT-TTCATATTAA
724781 TACTTTTTTCATATTA
1 TACTTTTTTCATATTA
724797 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (17 bp):
TACTTTTTTCATATTAA
Found at i:726225 original size:32 final size:31
Alignment explanation
Indices: 726184--726260 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
726174 TTAACTCGGG
726184 GTGACCACATCTTAATTAAATAAAAAACGAAA
1 GTGACCACATCTTAATTAAAT-AAAAACGAAA
* *
726216 GTGACCACATCGTAATTAAATAAAAATGAAA
1 GTGACCACATCTTAATTAAATAAAAACGAAA
* *
726247 GTGATCATATCTTA
1 GTGACCACATCTTA
726261 TATTGTTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 20 0.50
32 20 0.50
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (31 bp):
GTGACCACATCTTAATTAAATAAAAACGAAA
Found at i:726247 original size:31 final size:32
Alignment explanation
Indices: 726184--726250 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
726174 TTAACTCGGG
*
726184 GTGACCACATCTTAATTAAATAAAAAACGAAA
1 GTGACCACATCGTAATTAAATAAAAAACGAAA
*
726216 GTGACCACATCGTAATTAAAT-AAAAATGAAA
1 GTGACCACATCGTAATTAAATAAAAAACGAAA
726247 GTGA
1 GTGA
726251 TCATATCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (32 bp):
GTGACCACATCGTAATTAAATAAAAAACGAAA
Found at i:728724 original size:23 final size:23
Alignment explanation
Indices: 728672--728754 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
728662 ATAAAGAACA
*
728672 TGTCACAAGAGCAAGAGAAAAAACG
1 TGTCACAAGAACAA-AG-AAAAACG
* *
728697 GGTCACAATAACAAAGAAAAACG
1 TGTCACAAGAACAAAGAAAAACG
* *
728720 TGTCACAATAACAAA-AAAAAAG
1 TGTCACAAGAACAAAGAAAAACG
728742 TGTCACAAGAACA
1 TGTCACAAGAACA
728755 TATATTCTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 18 0.35
23 21 0.40
24 2 0.04
25 11 0.21
ACGTcount: A:0.55, C:0.17, G:0.17, T:0.11
Consensus pattern (23 bp):
TGTCACAAGAACAAAGAAAAACG
Done.