Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008940.1 Hibiscus syriacus cultivar Beakdansim tig00112259_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: 476028
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:357935 original size:16 final size:16
Alignment explanation
Indices: 357903--357949 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
357893 TTTAAAAAGT
*
357903 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
357919 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
357935 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
357950 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:357944 original size:15 final size:14
Alignment explanation
Indices: 357924--357954 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
357914 GTTTATTAGT
357924 TTATTATATTATAAG
1 TTATTATATTA-AAG
357939 TTATTATATTAAAG
1 TTATTATATTAAAG
357953 TT
1 TT
357955 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:359183 original size:23 final size:23
Alignment explanation
Indices: 359155--359199 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
359145 TTTAATTATT
*
359155 ATTTAAATTAACTATATTATTTG
1 ATTTAAATAAACTATATTATTTG
* *
359178 ATTTAAATAAATTTTATTATTT
1 ATTTAAATAAACTATATTATTT
359200 TTGTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAAATAAACTATATTATTTG
Found at i:359199 original size:18 final size:20
Alignment explanation
Indices: 359149--359199 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
359139 TATTTTTTTA
359149 ATTATTATTTAAATTAACTAT
1 ATTATTATTTAAATTAAC-AT
359170 ATTATTTGATTTAAA-TAA-AT
1 ATTA-TT-ATTTAAATTAACAT
*
359190 TTTATTATTT
1 ATTATTATTT
359200 TTGTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.15
19 2 0.07
20 5 0.19
21 4 0.15
22 5 0.19
23 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTATTTAAATTAACAT
Found at i:362810 original size:28 final size:28
Alignment explanation
Indices: 362743--362803 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
362733 AATTTTTATA
*
362743 TAATATAATATAACTTAAACTAATAAAC
1 TAATATAATATAACTTAAACTAACAAAC
362771 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAACAAAC
362799 TAATA
1 TAATA
362804 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (28 bp):
TAATATAATATAACTTAAACTAACAAAC
Found at i:362813 original size:21 final size:21
Alignment explanation
Indices: 362780--362828 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
362770 CTAATATAAT
362780 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
362801 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
362822 ATTAACT
1 A-TAACT
362829 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:363328 original size:25 final size:25
Alignment explanation
Indices: 363300--363373 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
363290 ACACCGTTCG
363300 ACGTGCATGGCCATGCACAGTTCCC
1 ACGTGCATGGCCATGCACAGTTCCC
* *
363325 ACGT-C----CCATGCACAGCAT-GC
1 ACGTGCATGGCCATGCACAG-TTCCC
363345 ATC-TGCATGGCCATGCACAGTTCCC
1 A-CGTGCATGGCCATGCACAGTTCCC
363370 ACGT
1 ACGT
363374 CCCATGCACA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
20 13 0.36
21 3 0.08
24 3 0.08
25 17 0.47
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.20
Consensus pattern (25 bp):
ACGTGCATGGCCATGCACAGTTCCC
Found at i:363335 original size:20 final size:20
Alignment explanation
Indices: 363310--363384 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
363300 ACGTGCATGG
363310 CCATGCACAGTTCCCACGTC
1 CCATGCACAGTTCCCACGTC
* * *
363330 CCATGCACAGCAT-GCATCTGCATGG
1 CCATGCACAG-TTCCCA-C-G--T-C
363355 CCATGCACAGTTCCCACGTC
1 CCATGCACAGTTCCCACGTC
363375 CCATGCACAG
1 CCATGCACAG
363385 CATGCATCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
20 22 0.52
21 3 0.07
22 1 0.02
23 1 0.02
24 3 0.07
25 12 0.29
ACGTcount: A:0.23, C:0.40, G:0.19, T:0.19
Consensus pattern (20 bp):
CCATGCACAGTTCCCACGTC
Found at i:363353 original size:45 final size:45
Alignment explanation
Indices: 363303--363392 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
363293 CCGTTCGACG
363303 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
1 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
363348 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
1 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
363393 CCCTTCCCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (45 bp):
TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
Found at i:363394 original size:25 final size:25
Alignment explanation
Indices: 363321--363394 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
363311 CATGCACAGT
363321 TCCCACGTCCCATGCACAGCATGCA
1 TCCCACGTCCCATGCACAGCATGCA
* * *
363346 TCTGCATG-GCCATGCACAG--T---
1 TC-CCACGTCCCATGCACAGCATGCA
363366 TCCCACGTCCCATGCACAGCATGCA
1 TCCCACGTCCCATGCACAGCATGCA
363391 TCCC
1 TCCC
363395 CTTCCCCATG
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.08
20 12 0.33
22 1 0.03
23 1 0.03
25 16 0.44
26 3 0.08
ACGTcount: A:0.22, C:0.42, G:0.18, T:0.19
Consensus pattern (25 bp):
TCCCACGTCCCATGCACAGCATGCA
Found at i:363404 original size:45 final size:45
Alignment explanation
Indices: 363310--363421 Score: 158
Period size: 45 Copynumber: 2.6 Consensus size: 45
363300 ACGTGCATGG
** **
363310 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCTGCATGG
1 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCCCCATCC
*
363355 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCCCCTTCC
1 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCCCCATCC
363400 CCATG--CA-TTCCCACGTCCCATG
1 CCATGCACAGTTCCCACGTCCCATG
363422 TTGATTGCAT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
42 15 0.24
43 2 0.03
45 45 0.73
ACGTcount: A:0.21, C:0.43, G:0.16, T:0.21
Consensus pattern (45 bp):
CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCCCCATCC
Found at i:363502 original size:29 final size:29
Alignment explanation
Indices: 363459--363534 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
363449 ACACACAGGA
***
363459 CGCCCGGA-TGCCATGGCGACCTTGGAGGT
1 CGCCCGGATTG-CATGGCGACCTCCAAGGT
363488 CGCCCGGATTGCATGGCGACCTCCAAGGT
1 CGCCCGGATTGCATGGCGACCTCCAAGGT
*
363517 CGCCTGGATTGCATGGCG
1 CGCCCGGATTGCATGGCG
363535 TCCTATGACG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 40 0.95
30 2 0.05
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (29 bp):
CGCCCGGATTGCATGGCGACCTCCAAGGT
Found at i:388620 original size:67 final size:67
Alignment explanation
Indices: 388548--388681 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
388538 TTTGGACAAA
388548 TAAAAAAATAACATTTAAAACATCCATAAATTCATTAATTGAACATAATGTTAATACACACACCG
1 TAAAAAAATAACATTTAAAACATCCATAAATTCATTAATTGAACATAATGTTAATACACACACCG
388613 TC
66 TC
388615 TAAAAAAATAACATTTAAAACATCCATAAATTCATTAATTGAACATAATGTTAATACACACACCG
1 TAAAAAAATAACATTTAAAACATCCATAAATTCATTAATTGAACATAATGTTAATACACACACCG
388680 TC
66 TC
388682 GTTACCACTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.28
Consensus pattern (67 bp):
TAAAAAAATAACATTTAAAACATCCATAAATTCATTAATTGAACATAATGTTAATACACACACCG
TC
Found at i:389369 original size:19 final size:19
Alignment explanation
Indices: 389345--389383 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
389335 ATAGAGGGGT
389345 ATTAGTGTAATTATTTCTA
1 ATTAGTGTAATTATTTCTA
389364 ATTAGTGTAATTATTTCTA
1 ATTAGTGTAATTATTTCTA
389383 A
1 A
389384 ATATATAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
ATTAGTGTAATTATTTCTA
Found at i:391975 original size:21 final size:21
Alignment explanation
Indices: 391951--392003 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
391941 GTTTCCAGAT
*
391951 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
391972 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
391993 TCGCAATGCGA
1 TCGCAATGCGA
392004 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:399683 original size:46 final size:48
Alignment explanation
Indices: 399616--399711 Score: 169
Period size: 46 Copynumber: 2.0 Consensus size: 48
399606 ATCAAGAATG
399616 AATCTCGACAACCAAATATCCATG-AAAA-ATGGAAGAAACCCTTGAA
1 AATCTCGACAACCAAATATCCATGAAAAACATGGAAGAAACCCTTGAA
399662 AATCTCGACAACCAAATATCCATGAAAAATCATGGAAGAAACCCTTGAA
1 AATCTCGACAACCAAATATCCATGAAAAA-CATGGAAGAAACCCTTGAA
399711 A
1 A
399712 CCACCCATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
46 24 0.51
47 4 0.09
49 19 0.40
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.18
Consensus pattern (48 bp):
AATCTCGACAACCAAATATCCATGAAAAACATGGAAGAAACCCTTGAA
Found at i:429367 original size:31 final size:31
Alignment explanation
Indices: 429329--429395 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
429319 TGTAATGTTC
* *
429329 ATTTTGTAATAATTTAATAAATTAAATGATT
1 ATTTTGTAACAATTTAATAAATTAAATGACT
* *
429360 ATTTTGTAACAATTTGATAAATTTAATGACT
1 ATTTTGTAACAATTTAATAAATTAAATGACT
429391 ATTTT
1 ATTTT
429396 CATAAGCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.49
Consensus pattern (31 bp):
ATTTTGTAACAATTTAATAAATTAAATGACT
Found at i:430326 original size:21 final size:21
Alignment explanation
Indices: 430302--430345 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
430292 AAATTAAAAG
430302 AAATCACTGAGTCAATTTGGA
1 AAATCACTGAGTCAATTTGGA
430323 AAATCACTGAGTCAATTTGGA
1 AAATCACTGAGTCAATTTGGA
430344 AA
1 AA
430346 GGAAGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (21 bp):
AAATCACTGAGTCAATTTGGA
Found at i:431465 original size:23 final size:23
Alignment explanation
Indices: 431436--431493 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
431426 TCAATGCCCT
*
431436 TTTTACACTTATTTGTCTGATTC
1 TTTTACACGTATTTGTCTGATTC
* *
431459 TTTTACACGTATTTGTTTGATTT
1 TTTTACACGTATTTGTCTGATTC
431482 TTTTACACGTAT
1 TTTTACACGTAT
431494 ATCAATCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (23 bp):
TTTTACACGTATTTGTCTGATTC
Found at i:432656 original size:2 final size:2
Alignment explanation
Indices: 432649--432680 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
432639 ATTGAAAGGA
432649 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
432681 GAAATCTGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:434293 original size:165 final size:169
Alignment explanation
Indices: 434009--434325 Score: 462
Period size: 165 Copynumber: 1.9 Consensus size: 169
433999 CGATTAAGTT
* *
434009 TGTGCATATTTTGTCAATTGTTACAACATGTGTAGAAGGAATATTTTTTTCACAATAAAAAATAT
1 TGTGCATATTTTGTCAATTGTTACAACATGTGTAGAAAGAATATATTTTTCACAATAAAAAATAT
* *
434074 AATTTTTCTGAAGAATTGAATTAAAGATCAACAGATGAACGATTGTTGCGTTATATATATTGAAA
66 -ATTTTTCTGAAGAATTAAATTAAAGATCAACAGATGAACGATTGTTCCGTTATATATATTGAAA
* * *
434139 AATATTTTTTAATAACGTGATAAGATCAATTATTACAACA
130 AATAATTTTTAACAACATGATAAGATCAATTATTACAACA
* * * *
434179 TGTGTATATTTTGTCAATTGTTACAACGTGTGTAGAAAGAATA-ATTTTT-GCGATAAAAAATAT
1 TGTGCATATTTTGTCAATTGTTACAACATGTGTAGAAAGAATATATTTTTCACAATAAAAAATAT
* * * *
434242 -TTTTT-TTAAGAATTAAATTAAAGATTAATAGATTAACGATTGTTCCGTTATATATATTGAAAA
66 ATTTTTCTGAAGAATTAAATTAAAGATCAACAGATGAACGATTGTTCCGTTATATATATTGAAAA
434305 ATAATTTTTAACAACATGATA
131 ATAATTTTTAACAACATGATA
434326 TGATGGACTC
Statistics
Matches: 132, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
165 70 0.53
166 5 0.04
168 12 0.09
169 5 0.04
170 40 0.30
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (169 bp):
TGTGCATATTTTGTCAATTGTTACAACATGTGTAGAAAGAATATATTTTTCACAATAAAAAATAT
ATTTTTCTGAAGAATTAAATTAAAGATCAACAGATGAACGATTGTTCCGTTATATATATTGAAAA
ATAATTTTTAACAACATGATAAGATCAATTATTACAACA
Found at i:437916 original size:29 final size:29
Alignment explanation
Indices: 437884--437942 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
437874 TTTTTAAAAT
** * *
437884 TTTTAAATTTGTCACTATATTCGATGAGA
1 TTTTAAATCCGTCACTACATTCGATAAGA
*
437913 TTTTAACTCCGTCACTACATTCGATAAGA
1 TTTTAAATCCGTCACTACATTCGATAAGA
437942 T
1 T
437943 CACACTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (29 bp):
TTTTAAATCCGTCACTACATTCGATAAGA
Found at i:439035 original size:15 final size:15
Alignment explanation
Indices: 439015--439044 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
439005 GCATTTGCTG
439015 AGGATACATGGAACC
1 AGGATACATGGAACC
*
439030 AGGATACATTGAACC
1 AGGATACATGGAACC
439045 CATCTGGCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (15 bp):
AGGATACATGGAACC
Found at i:449332 original size:32 final size:32
Alignment explanation
Indices: 449291--449378 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 32
449281 TGAATTTATT
449291 AAATAATTATTTAAATTTATTAAATTATAATA
1 AAATAATTATTTAAATTTATTAAATTATAATA
* *
449323 AAATAATTA-TTAAATTTATCATAA-TATTATA
1 AAATAATTATTTAAATTTATTA-AATTATAATA
* *
449354 AAATAATCATCT-AATTTATTTAAAT
1 AAATAATTATTTAAATTTA-TTAAAT
449379 ATATTATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
31 33 0.70
32 14 0.30
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.45
Consensus pattern (32 bp):
AAATAATTATTTAAATTTATTAAATTATAATA
Found at i:450147 original size:60 final size:59
Alignment explanation
Indices: 450018--450191 Score: 183
Period size: 60 Copynumber: 2.9 Consensus size: 59
450008 TGTACAACTC
* * *
450018 TCATTTTAAATTGGT-CTCTAAACTTTTAAATATTCCAA-TTCATCCCTAGACTATGAATA
1 TCATTTTAAATTGGTCCTC-AAACTTTTGAATATTCCAATTTCATCCC-AAACTATGAACA
* * * *
450077 TCATTCTAAATTAGTCCTCAAACTTTTGAATATTTCAATTTCATTCCCAAACTATGACCA
1 TCATTTTAAATTGGTCCTCAAACTTTTGAATATTCCAATTTCA-TCCCAAACTATGAACA
* * * *
450137 TCATTTTAAATCGGTCCCCAAGCTTTTTGAACATTCCAAATTT-ATCCCAAACTAT
1 TCATTTTAAATTGGTCCTCAAAC-TTTTGAATATTCC-AATTTCATCCCAAACTAT
450192 AGTATACACT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
59 30 0.31
60 45 0.47
61 16 0.17
62 5 0.05
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (59 bp):
TCATTTTAAATTGGTCCTCAAACTTTTGAATATTCCAATTTCATCCCAAACTATGAACA
Found at i:459362 original size:21 final size:22
Alignment explanation
Indices: 459332--459372 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
459322 CAAGCATCGG
*
459332 TAATTGTCAA-ATAAATAAACC
1 TAATTCTCAATATAAATAAACC
*
459353 TAATTCTCAATTTAAATAAA
1 TAATTCTCAATATAAATAAA
459373 TAAAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATTCTCAATATAAATAAACC
Found at i:459515 original size:15 final size:15
Alignment explanation
Indices: 459492--459531 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
459482 TATTGAATTT
* *
459492 AATTGAATAAACTAA
1 AATTAAATAAAATAA
459507 AATTAAATAAAATAA
1 AATTAAATAAAATAA
*
459522 AAATAAATAA
1 AATTAAATAA
459532 TTGAAAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (15 bp):
AATTAAATAAAATAA
Found at i:459937 original size:34 final size:34
Alignment explanation
Indices: 459897--459963 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
459887 GAATTAAACG
459897 GGGACGG-GAAAAACCGTTTATGCTAAACGGGGAT
1 GGGACGGAG-AAAACCGTTTATGCTAAACGGGGAT
* *
459931 GGGACGGAGAAAACTGTTTATGTTAAACGGGGA
1 GGGACGGAGAAAACCGTTTATGCTAAACGGGGA
459964 CGGGGATGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.36, T:0.19
Consensus pattern (34 bp):
GGGACGGAGAAAACCGTTTATGCTAAACGGGGAT
Found at i:460143 original size:17 final size:16
Alignment explanation
Indices: 460059--460141 Score: 59
Period size: 15 Copynumber: 5.4 Consensus size: 16
460049 ATTATTTTAC
*
460059 ATATATATAATATTA-
1 ATATATTTAATATTAT
* *
460074 ATAAATTTAA-ATTAA
1 ATATATTTAATATTAT
**
460089 AT-TAAATATATATATAT
1 ATATATTTA-ATAT-TAT
460106 ATATATTTAATATT-T
1 ATATATTTAATATTAT
*
460121 ATATATTTAAT-TTAA
1 ATATATTTAATATTAT
460136 ATATAT
1 ATATAT
460142 ATATCCGGCC
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 9 0.17
15 29 0.55
16 3 0.06
17 8 0.15
18 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATTTAATATTAT
Found at i:468965 original size:30 final size:30
Alignment explanation
Indices: 468908--468965 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
468898 TACAAGGTCA
* *
468908 TATTTGAATACTAATTAAAGTTTAAGGGCT
1 TATTTGAATACTAATAAAAGTTAAAGGGCT
468938 TATTTGAATAC-AATAAAAGTATAAAGGG
1 TATTTGAATACTAATAAAAGT-TAAAGGG
468966 TTGTTTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.34
Consensus pattern (30 bp):
TATTTGAATACTAATAAAAGTTAAAGGGCT
Found at i:470059 original size:28 final size:28
Alignment explanation
Indices: 470019--470078 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
470009 TGCTTTCAAG
470019 CACTGACTCCACGACATAATACTTAAAA
1 CACTGACTCCACGACATAATACTTAAAA
* *
470047 CACTGACTCCACGACATTATGCTTAAAA
1 CACTGACTCCACGACATAATACTTAAAA
470075 CACT
1 CACT
470079 AGCTCAACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.23
Consensus pattern (28 bp):
CACTGACTCCACGACATAATACTTAAAA
Found at i:470088 original size:28 final size:28
Alignment explanation
Indices: 470019--470094 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
470009 TGCTTTCAAG
*
470019 CACTGACTCCACGACATAATACTTAAAA
1 CACTGACTCAACGACATAATACTTAAAA
* * *
470047 CACTGACTCCACGACATTATGCTTAAAA
1 CACTGACTCAACGACATAATACTTAAAA
*
470075 CACT-AGCTCAACGACGTAAT
1 CACTGA-CTCAACGACATAAT
470095 GTAAATAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 1 0.02
28 41 0.98
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (28 bp):
CACTGACTCAACGACATAATACTTAAAA
Found at i:471049 original size:29 final size:29
Alignment explanation
Indices: 470988--471057 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
470978 AGACAAAAAT
* ** *
470988 AAAGTTTTGAGGGTCAAAAGAAGTGTAATA
1 AAAG-TTTAAGGGTCAAAAGAAGCATAACA
471018 AAAGTTTAAGGGTCAAAAGAAGCATAACA
1 AAAGTTTAAGGGTCAAAAGAAGCATAACA
*
471047 AAAATTTAAGG
1 AAAGTTTAAGG
471058 ACTAATATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.23
Consensus pattern (29 bp):
AAAGTTTAAGGGTCAAAAGAAGCATAACA
Found at i:472113 original size:96 final size:96
Alignment explanation
Indices: 471957--472186 Score: 291
Period size: 96 Copynumber: 2.4 Consensus size: 96
471947 TGATTTTTCT
* * * * *
471957 AACTCAGTTTGTTTCATTTGCAATATTATGATTTGAACTATAGATGTTGTCTAAGAGATATAACA
1 AACTCAATTTGCTTCATTTGCAATATTATAATTTGAACCATAGATATTGTCTAAGAGATATAACA
* * *
472022 CCTCATAGACTAACTTAGAGGTGATT-ATCCC
66 CCTCATAGACCAACTTAGAGATAATTCA-CCC
* * * * *
472053 AACTCAATTTGCTTCATTTGCAATGTTATAATTTGAACCGTAGATATTGTTTAAGGGATATAGCA
1 AACTCAATTTGCTTCATTTGCAATATTATAATTTGAACCATAGATATTGTCTAAGAGATATAACA
*
472118 CCTTATAGACCAACTTAGAGATAATTCACCC
66 CCTCATAGACCAACTTAGAGATAATTCACCC
* * *
472149 AACTCAATTTGCTTCATTCGCAAAATTATAATATGAAC
1 AACTCAATTTGCTTCATTTGCAATATTATAATTTGAAC
472187 TCTCGATGAT
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
96 114 0.99
97 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (96 bp):
AACTCAATTTGCTTCATTTGCAATATTATAATTTGAACCATAGATATTGTCTAAGAGATATAACA
CCTCATAGACCAACTTAGAGATAATTCACCC
Found at i:472490 original size:3 final size:3
Alignment explanation
Indices: 472484--472525 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
472474 ATTCTACTAC
472484 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
472526 CAAGTTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:472958 original size:31 final size:31
Alignment explanation
Indices: 472902--472960 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
472892 GTCTTAAAAT
*
472902 TTATCAAATTATTACAAAATGATCTTTATGC
1 TTATCAAATTATTACAAAATCATCTTTATGC
472933 TTATCGAAA-TATTACAAACA-CATCTTTA
1 TTATC-AAATTATTACAAA-ATCATCTTTA
472961 AATTATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (31 bp):
TTATCAAATTATTACAAAATCATCTTTATGC
Found at i:474463 original size:12 final size:12
Alignment explanation
Indices: 474446--474472 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
474436 GAATCAGTTT
474446 TTGGATAATTAA
1 TTGGATAATTAA
474458 TTGGATAATTAA
1 TTGGATAATTAA
474470 TTG
1 TTG
474473 TTTATTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (12 bp):
TTGGATAATTAA
Done.