Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008073.1 Hibiscus syriacus cultivar Beakdansim tig00110575_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: 510636
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 3
Found at i:487131 original size:33 final size:33
Alignment explanation
Indices: 487064--487134 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
487054 AGAATGACTG
***
487064 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
487097 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
487130 TCGCA
1 TCGCA
487135 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:487152 original size:19 final size:19
Alignment explanation
Indices: 487130--487227 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
487120 GAAACCAAAA
*
487130 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
487149 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
487163 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
487182 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
487196 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
487215 TCGCGTTGCGATT
1 TCGCGTTGCGATT
487228 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:487171 original size:14 final size:14
Alignment explanation
Indices: 487152--487241 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
487142 TTTCATTTCG
487152 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
487166 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
487185 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
487199 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
487216 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
487232 CGTTGCGATT
1 CGTTGCGATT
487242 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:487177 original size:33 final size:33
Alignment explanation
Indices: 487135--487249 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
487125 CAAAATCGCA
487135 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
487168 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
487201 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
487234 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
487250 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:489177 original size:185 final size:186
Alignment explanation
Indices: 488947--489328 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
488937 TAGATTGCTT
488947 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
489012 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
489077 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
489132 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
489197 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
489262 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
489318 AGTAAATTTAT
1 AGTAAATTTAT
489329 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:489261 original size:93 final size:93
Alignment explanation
Indices: 488947--489326 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
488937 TAGATTGCTT
*
488947 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
489012 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
489040 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
489104 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
489132 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
489197 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
489225 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
489290 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
489318 AGTAAATTT
1 AGTAAATTT
489327 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:489410 original size:19 final size:19
Alignment explanation
Indices: 489370--489498 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
489360 TAGTTTACTT
* *
489370 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
489390 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
489409 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
489428 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
489442 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
489461 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
489475 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
489494 TCGCA
1 TCGCA
489499 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:489449 original size:33 final size:32
Alignment explanation
Indices: 489406--489498 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
489396 CGCGAAACCA
**
489406 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
489438 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
489471 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
489499 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:489496 original size:52 final size:52
Alignment explanation
Indices: 489370--489498 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
489360 TAGTTTACTT
**
489370 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
489422 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
489475 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
489499 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:489516 original size:19 final size:19
Alignment explanation
Indices: 489494--489628 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
489484 GAAACCAAAA
*
489494 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
489513 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
489529 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
489546 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
489562 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
489579 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
489598 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
489618 TCGTGTTGCGA
1 TCGCGTTGCGA
489629 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:489535 original size:14 final size:14
Alignment explanation
Indices: 489516--489572 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
489506 TTTCATTTCG
489516 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
489530 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
489547 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
489563 CGTTGCGATT
1 CGTTGCGATT
489573 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:489541 original size:33 final size:33
Alignment explanation
Indices: 489499--489591 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
489489 CAAAATCGCA
*
489499 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
489532 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
489565 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
489592 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:491488 original size:38 final size:38
Alignment explanation
Indices: 491445--491517 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
491435 AATTGATTGT
*
491445 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
491483 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
491518 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:491504 original size:19 final size:19
Alignment explanation
Indices: 491440--491504 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
491430 AGTTTAATTG
*
491440 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
491459 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
491477 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
491497 ATTGATTT
1 ATTGATTT
491505 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:491518 original size:14 final size:14
Alignment explanation
Indices: 491499--491534 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
491489 ATTGTTTAAT
491499 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
491513 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
491527 TGATTTGT
1 TGATTTGT
491535 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:491657 original size:19 final size:19
Alignment explanation
Indices: 491641--491742 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
491631 AAAAATGACT
491641 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
491660 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
491679 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
491693 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
491712 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
491732 ATCGCAATGCG
1 ATCGCAATGCG
491743 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:491795 original size:19 final size:19
Alignment explanation
Indices: 491771--492167 Score: 512
Period size: 19 Copynumber: 22.4 Consensus size: 19
491761 GATTATCTCG
491771 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
491790 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
491809 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
491823 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
491842 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
491861 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
491880 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
491894 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
491913 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
491932 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
491951 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
491970 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
491989 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
492003 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
492022 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
492041 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
492055 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
492074 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
492093 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
492107 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
492127 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
492141 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
492160 TTGCGATT
1 TTGCGATT
492168 GTATTTTCCG
Statistics
Matches: 335, Mismatches: 12, Indels: 62
0.82 0.03 0.15
Matches are distributed among these distances:
14 41 0.12
16 39 0.12
17 36 0.11
18 3 0.01
19 204 0.61
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:491811 original size:52 final size:49
Alignment explanation
Indices: 491749--492167 Score: 361
Period size: 52 Copynumber: 7.9 Consensus size: 49
491739 TGCGTTTATA
*
491749 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-T-TCGTTGCGA-TTTCATTTCGCGTTGCGATTTTC
*
491801 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-T-TTTCGTTGCGA-TTTCATTTCGCGTTGCGATTTTC
* * * **
491853 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
** *
491905 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA---T--TTTCG--TTGCGA-TTTCATTTCGCGTTGCGATTTTC
* * * *
491962 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
* * * *
492014 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
* * * *
492066 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
*
492118 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTTC--GTTGCGA-TTTCATTTCGCGTTGCGATT
492168 GTATTTTCCG
Statistics
Matches: 321, Mismatches: 26, Indels: 39
0.83 0.07 0.10
Matches are distributed among these distances:
50 18 0.06
51 9 0.03
52 212 0.66
53 29 0.09
54 6 0.02
55 7 0.02
57 29 0.09
58 4 0.01
59 7 0.02
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (49 bp):
ATTTCGCATTGCGATTTTCGTTGCGATTTCATTTCGCGTTGCGATTTTC
Found at i:491846 original size:71 final size:71
Alignment explanation
Indices: 491771--492167 Score: 527
Period size: 71 Copynumber: 5.6 Consensus size: 71
491761 GATTATCTCG
491771 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
491836 TTCGCA
66 TTCGCA
491842 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
491907 TTCGCA
66 TTCGCA
* *
491913 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
491978 TTCATTTCGCA
61 TTCATTTCGCA
*
491989 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATT
*
492047 TTC-TCTCG--
61 TTCATTTCGCA
*
492055 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
492120 TTCCGCA
66 TT-CGCA
* *
492127 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
492168 GTATTTTCCG
Statistics
Matches: 298, Mismatches: 11, Indels: 38
0.86 0.03 0.11
Matches are distributed among these distances:
66 12 0.04
67 25 0.08
68 14 0.05
69 13 0.04
70 3 0.01
71 180 0.60
72 12 0.04
73 6 0.02
74 8 0.03
76 25 0.08
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:494487 original size:12 final size:12
Alignment explanation
Indices: 494470--494494 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
494460 TCTTCGGGGA
494470 CTTTTTCTTCTT
1 CTTTTTCTTCTT
494482 CTTTTTCTTCTT
1 CTTTTTCTTCTT
494494 C
1 C
494495 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:494703 original size:24 final size:24
Alignment explanation
Indices: 494669--494715 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
494659 CTGAAACATC
494669 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
494693 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
494716 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:495417 original size:20 final size:20
Alignment explanation
Indices: 495389--495797 Score: 486
Period size: 20 Copynumber: 20.4 Consensus size: 20
495379 AAATTTCAGT
* * * *
495389 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
495409 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
495429 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
495449 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
495469 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
495489 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
495509 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
495529 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
495549 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
495569 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
495589 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
495609 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
495629 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
495649 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
495669 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
495689 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
495709 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
495729 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
495749 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
495769 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
495789 GTTGCGATT
1 GTTGCGATT
495798 ATGGAAAATC
Statistics
Matches: 343, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.02
20 331 0.97
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:496289 original size:30 final size:29
Alignment explanation
Indices: 496251--496309 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 29
496241 GAAACGCGAG
496251 TATATGACGACTGATCCCATCAACATATC
1 TATATGACGACTGATCCCATCAACATATC
496280 TATACTGACGACTGATCCCATCAACATATC
1 TATA-TGACGACTGATCCCATCAACATATC
496310 GTTTAAGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.34, C:0.29, G:0.10, T:0.27
Consensus pattern (29 bp):
TATATGACGACTGATCCCATCAACATATC
Found at i:498240 original size:67 final size:70
Alignment explanation
Indices: 498167--498318 Score: 247
Period size: 67 Copynumber: 2.2 Consensus size: 70
498157 CCTAAATTTG
* * *
498167 TTCGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAATGG-TTAAAG-AAAAAA-TTG
1 TTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTTAAAGAAAAAAAGTAG
498229 GTTAA
66 GTTAA
498234 TTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTTAAAGAAAAAAAGTAG
1 TTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTTAAAGAAAAAAAGTAG
498299 GTTAA
66 GTTAA
*
498304 TTCGGCTCGGTTAAT
1 TTCGGTTCGGTTAAT
498319 CGAACCAAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
67 45 0.58
68 6 0.08
69 6 0.08
70 21 0.27
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (70 bp):
TTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTTAAAGAAAAAAAGTAG
GTTAA
Found at i:498282 original size:37 final size:37
Alignment explanation
Indices: 498177--498282 Score: 86
Period size: 37 Copynumber: 3.1 Consensus size: 37
498167 TTCGGTTCGA
*
498177 TTAATAATTTTCAAATAAATTTTGGTTCGATTAATGG
1 TTAATAATTTTCAAATAAATTTTGGTTCGATTAACGG
* ** *
498214 TT-A-AA----GAAA-AAATTGGTTAATTCGGTT--CGG
1 TTAATAATTTTCAAATAAATT--TTGGTTCGATTAACGG
498244 TTAATAATTTTCAAATAAATTTTGGTTCGATTAACGG
1 TTAATAATTTTCAAATAAATTTTGGTTCGATTAACGG
498281 TT
1 TT
498283 TAAAGAAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 22
0.61 0.11 0.28
Matches are distributed among these distances:
30 9 0.18
31 4 0.08
32 10 0.20
35 10 0.20
36 4 0.08
37 12 0.24
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (37 bp):
TTAATAATTTTCAAATAAATTTTGGTTCGATTAACGG
Found at i:501413 original size:23 final size:24
Alignment explanation
Indices: 501373--501417 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
501363 GAACTCAAAA
501373 AAAATTAGAAGCTCGATTGAAGCT
1 AAAATTAGAAGCTCGATTGAAGCT
* *
501397 AAAATTCG-AGCTTGATTGAAG
1 AAAATTAGAAGCTCGATTGAAG
501418 TGAAAGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAATTAGAAGCTCGATTGAAGCT
Found at i:501856 original size:23 final size:21
Alignment explanation
Indices: 501830--501871 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
501820 TATAAAAAAT
501830 TATTTTTCATTAAATATTTTTGA
1 TATTTTT-ATTAAAT-TTTTTGA
*
501853 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
501872 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGA
Found at i:502120 original size:26 final size:26
Alignment explanation
Indices: 502091--502141 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
502081 TTAGTCTAAT
*
502091 GATCAATTTATAATTTTTAATAGTTG
1 GATCAATTTATAAATTTTAATAGTTG
*
502117 GATCATTTTATAAATTTTAATAGTT
1 GATCAATTTATAAATTTTAATAGTT
502142 TGTGTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (26 bp):
GATCAATTTATAAATTTTAATAGTTG
Done.