Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005320.1 Hibiscus syriacus cultivar Beakdansim tig00012040_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: 539900
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:492218 original size:4 final size:4
Alignment explanation
Indices: 492167--492221 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
492157 GTCATACATA
* * * * * *
492167 CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA CATA CATG
1 CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG
492215 CATG CAT
1 CATG CAT
492222 AATTCTTACA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (4 bp):
CATG
Found at i:492635 original size:22 final size:23
Alignment explanation
Indices: 492607--492658 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
492597 ACTATAAGTG
492607 AATTTTTTTAAGAAACTAAGCTT
1 AATTTTTTTAAGAAACTAAGCTT
492630 AATTTTTTTAAGAAACTAAGCTT
1 AATTTTTTTAAGAAACTAAGCTT
*
492653 GATTTT
1 AATTTT
492659 CAAGTATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (23 bp):
AATTTTTTTAAGAAACTAAGCTT
Found at i:493815 original size:4 final size:4
Alignment explanation
Indices: 493806--493845 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
493796 TTCATCTTGT
* * *
493806 CATA CATA CATA CATG CATA CATG CATA CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
493846 ATTCTTACAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:493817 original size:8 final size:8
Alignment explanation
Indices: 493806--493844 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
493796 TTCATCTTGT
*
493806 CATACATA
1 CATACATG
493814 CATACATG
1 CATACATG
493822 CATACATG
1 CATACATG
493830 CATACATG
1 CATACATG
493838 CATACAT
1 CATACAT
493845 AATTCTTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (8 bp):
CATACATG
Found at i:495314 original size:54 final size:54
Alignment explanation
Indices: 495173--495562 Score: 541
Period size: 54 Copynumber: 7.2 Consensus size: 54
495163 TCGAATGGAA
*
495173 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* * * *
495227 ACTGT-TGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCATATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
*
495280 ACTATGTGTGCAACCTAAGAAAGTCATAATAAGTTTATGAATTTCCGTATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* * **
495334 ACTGTGTGTGCAACCTAAGAAATTCATAATAATTTTATGAATTTCCACATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* * *
495388 ACTGTGTGTACAACCTAAGAAATTCATTATAAGTTTATGAATTTCCGTATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
**
495442 ACCGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* * ** * * *
495496 ACTATGTGTGCAAACCCATGTGATTCATAATAAG-TTGTGAATTACCATATTGGC
1 ACTATGTGTGC-AACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
**
495550 ACTACATGTGCAA
1 ACTATGTGTGCAA
495563 ACTATAGAGT
Statistics
Matches: 302, Mismatches: 32, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
53 52 0.17
54 232 0.77
55 18 0.06
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (54 bp):
ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
Found at i:496368 original size:44 final size:44
Alignment explanation
Indices: 496288--496372 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
496278 ATTGATAATG
* * * ** *
496288 TCCAGGGAGTATCGATACTATTCTGTGCAGTTGTATCGATACCT
1 TCCAGGGAGTATCAATACTACTATGTAAAGTAGTATCGATACCT
*
496332 TCCAGTGAGTATCAATACTACTATGTAAAGTAGTATCGATA
1 TCCAGGGAGTATCAATACTACTATGTAAAGTAGTATCGATA
496373 TGGAACATGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (44 bp):
TCCAGGGAGTATCAATACTACTATGTAAAGTAGTATCGATACCT
Found at i:499245 original size:20 final size:21
Alignment explanation
Indices: 499202--499252 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
499192 GTATGAACAA
*
499202 TATCGATACTCGATGATGGCAG
1 TATCGATACTC-ATGATAGCAG
*
499224 TATCGATACT-ATGATAGTAG
1 TATCGATACTCATGATAGCAG
499244 TATCGATAC
1 TATCGATAC
499253 CTAGAAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 17 0.63
22 10 0.37
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (21 bp):
TATCGATACTCATGATAGCAG
Found at i:503131 original size:55 final size:55
Alignment explanation
Indices: 503063--503206 Score: 207
Period size: 55 Copynumber: 2.6 Consensus size: 55
503053 ATTTGTATGA
* * *
503063 GTGTATCGATACACTGAGGAGTGTATCGATTCCTTCAAAACACCAAATACCATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACACCAAATACCATTT
** * * * *
503118 GTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACGTCGAGTGCTATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACACCAAATACCATTT
503173 GTGTATCGGTACACTGAGGAGTGTATCGATACCC
1 GTGTATCGGTACACTGAGGAGTGTATCGATACCC
503207 CCAAGTATGA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 80 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (55 bp):
GTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACACCAAATACCATTT
Found at i:503806 original size:22 final size:23
Alignment explanation
Indices: 503757--503808 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
503747 CCGTGACAAA
*
503757 TATGTGGCATTTCGATACAACCC
1 TATGTGGCACTTCGATACAACCC
* *
503780 TATGTGGCACTTCGGTGCAA-CC
1 TATGTGGCACTTCGATACAACCC
503802 TATGTGG
1 TATGTGG
503809 TCCTTCAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (23 bp):
TATGTGGCACTTCGATACAACCC
Found at i:510012 original size:55 final size:55
Alignment explanation
Indices: 509946--510067 Score: 181
Period size: 55 Copynumber: 2.2 Consensus size: 55
509936 GCGTGTATCA
*
509946 GTACACTGAGGAGTGTATGGATACCCTCAAAACATCAAATGCCATTTGTGCATCG
1 GTACACTGAGGAGTGTATCGATACCCTCAAAACATCAAATGCCATTTGTGCATCG
** * ** *
510001 GTACACTGAGGAGTGTATCGATACCCTCAAAACATTGAGTGTTATTTGTGTATCG
1 GTACACTGAGGAGTGTATCGATACCCTCAAAACATCAAATGCCATTTGTGCATCG
510056 GTACACTGAGGA
1 GTACACTGAGGA
510068 CTCTTTATGA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (55 bp):
GTACACTGAGGAGTGTATCGATACCCTCAAAACATCAAATGCCATTTGTGCATCG
Found at i:519808 original size:104 final size:104
Alignment explanation
Indices: 519603--519809 Score: 292
Period size: 104 Copynumber: 2.0 Consensus size: 104
519593 TCACGAGATG
519603 ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTAGGATGGTAGG
1 ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTAGGATGGTAGG
** **
519668 TGTGATGGGCTGACTCCCCTCGAAGCAGTGTTAAAAAAA
66 TGTGATAAGCTGACTCCCCTCGAAGCAGTGAAAAAAAAA
* *
519707 ACTCTACCTGATTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTA-G
1 ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTAGGATGGTAGG
* * * * * *
519771 TGTGTTAAGTTGACTCTCCTTGAAGTA-TGCAAAAAAAA
66 TGTGATAAGCTGACTCCCCTCGAAGCAGTGAAAAAAAAA
519809 A
1 A
519810 GTTGAAGTTA
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 10 0.11
103 21 0.23
104 61 0.66
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (104 bp):
ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTAGGATGGTAGG
TGTGATAAGCTGACTCCCCTCGAAGCAGTGAAAAAAAAA
Found at i:522417 original size:21 final size:21
Alignment explanation
Indices: 522372--522420 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
522362 GTCGAGGGTC
* *
522372 TATGTGGTCCTTCGAGACAAT
1 TATGTGGTCCTCCGAGACAAA
* *
522393 TATGTGGTCCTCCGGGATAAA
1 TATGTGGTCCTCCGAGACAAA
522414 TATGTGG
1 TATGTGG
522421 CACTTCGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTCCGAGACAAA
Found at i:522463 original size:22 final size:23
Alignment explanation
Indices: 522414--522464 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
522404 CCGGGATAAA
* **
522414 TATGTGGCACTTCGGTGCAATCC
1 TATGTGACACTTAAGTGCAATCC
522437 TATGTGACACTTAAGTGCAA-CC
1 TATGTGACACTTAAGTGCAATCC
522459 TATGTG
1 TATGTG
522465 GTTTTTGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (23 bp):
TATGTGACACTTAAGTGCAATCC
Found at i:526393 original size:82 final size:82
Alignment explanation
Indices: 526293--526487 Score: 275
Period size: 82 Copynumber: 2.4 Consensus size: 82
526283 TGTTTTAAAA
* * * *
526293 TAAAAGCCTAGCTATGCATTTGGCACAAATGTGTCAATAATGTCAGTTAGATGAAAGGTTAAATG
1 TAAAAGCCTAGCTATGCATTTGGCACAAAGGTGCCAATAATGCCAATTAGATGAAAGGTTAAATG
526358 CCTTTGGAATAAAAGAC
66 CCTTTGGAATAAAAGAC
* * * *
526375 TAAAAGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAATTAGATGAAAGGTTAAATT
1 TAAAAGCCTAGCTATGCATTTGGCACAAAGGTGCCAATAATGCCAATTAGATGAAAGGTTAAATG
*
526440 CCTTTGGGATAAAAGAC
66 CCTTTGGAATAAAAGAC
* *
526457 TAAATGACC-AGCTATGCATTTGGCAAAAAGG
1 TAAAAG-CCTAGCTATGCATTTGGCACAAAGG
526488 ATGACATAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 97 0.98
83 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (82 bp):
TAAAAGCCTAGCTATGCATTTGGCACAAAGGTGCCAATAATGCCAATTAGATGAAAGGTTAAATG
CCTTTGGAATAAAAGAC
Found at i:527656 original size:16 final size:16
Alignment explanation
Indices: 527635--527680 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
527625 AGAAAATGAG
*
527635 TAAGCGGTAAATA-CAT
1 TAAGCGCTAAA-AGCAT
527651 TAAGCGCTAAAAGCAT
1 TAAGCGCTAAAAGCAT
527667 TAAGCGCTAAAAGC
1 TAAGCGCTAAAAGC
527681 TTATAGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 1 0.04
16 27 0.96
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (16 bp):
TAAGCGCTAAAAGCAT
Found at i:531799 original size:54 final size:54
Alignment explanation
Indices: 531350--531797 Score: 657
Period size: 54 Copynumber: 8.3 Consensus size: 54
531340 TTACCGAATG
* *
531350 GGCACTATGTGTGAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * *
531404 GGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATTAATTTTCGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
531458 GGCACTGTGTGTGCAACCTAAGAAATTCATAGTAAGTTTATGAATTTTCGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* *
531512 GGCACTGTGTGTGCAACCTAAGAAATTCATAATACGTTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
531566 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
531620 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * *
531674 AGTACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * * * **
531728 GGCACTCTGTTTGCAAACCCACA-TAATTCATAATAAG-TTGTGAATTACCGTATT
1 GGCACTGTGTGTGC-AACCTA-AGAAATTCATAATAAGTTTATGAATTTTCGTATT
**
531782 GGCACTACGTGTGCAA
1 GGCACTGTGTGTGCAA
531798 ACTATAGAGT
Statistics
Matches: 357, Mismatches: 35, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
53 2 0.01
54 336 0.94
55 18 0.05
56 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (54 bp):
GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
Found at i:531964 original size:82 final size:82
Alignment explanation
Indices: 531873--532061 Score: 281
Period size: 82 Copynumber: 2.3 Consensus size: 82
531863 TGTTTTAAAA
* *
531873 TAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAATATTAAACT
1 TAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAAATGAAAGATTAAA-T
*
531938 -CCTTTGGGATAAAAGAC
65 GCCTTTCGGATAAAAGAC
* * * *
531955 TAAAAGCCTAGTTGTGTATTTGGCAGAAAGGTGCCAATAATTCCAGTTAAATGAAAGGTTAAATG
1 TAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAAATGAAAGATTAAATG
532020 CCTTTCGGATAAAAGAC
66 CCTTTCGGATAAAAGAC
**
532037 TAAATTCCTAGCTGTGCATTTGGCA
1 TAAAAGCCTAGCTGTGCATTTGGCA
532062 AAACGGATGT
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 1 0.01
82 94 0.99
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (82 bp):
TAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAAATGAAAGATTAAATG
CCTTTCGGATAAAAGAC
Found at i:533568 original size:131 final size:131
Alignment explanation
Indices: 533215--533638 Score: 521
Period size: 131 Copynumber: 3.2 Consensus size: 131
533205 GAAGACAAGA
* * * * *
533215 GAACAAGTCTGCCTCGATTCAATCTTTCCT-GAGAATAGTGGAATGAATCAACATTTACATATCT
1 GAACAAGTCTACCTCAATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACATTTCCATATCT
* * * * * *
533279 GATCTACCCTAAAGAGCATCGGAGTAGATCCTCGTT-TTCCAGATTTGATCTTCCTTGAGGATTA
66 GATCTACCCTAAAGAGCAGCGGAGCATATCC-CCTTCTT-CAGATTTGATCTTCCCTGAGGATAA
533343 GTG
129 GTG
* * * * *
533346 GAACAAGTTTGCCTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCT
1 GAACAAGTCTACCTCAATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACATTTCCATATCT
* **
533411 GATCTACCCTAAAGAGCAGCGGAGCATATCCCCTTGCTTCATATTTGATCTTCCCTGAGGAGCAG
66 GATCTACCCTAAAGAGCAGCGGAGCATATCCCCTT-CTTCAGATTTGATCTTCCCTGAGGATAAG
533476 TG
130 TG
* ** *
533478 GAA-AAGTCTACCTCAATTCAATCTTCCCTAAATAATAGTGGAATGAATCAATGTTTCCATATAT
1 GAACAAGTCTACCTCAATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACATTTCCATATCT
* * * *
533542 GATCTACTCTGAAGAGTAGCGAAGCATATCCCCTTTCTTCAGATTTGATCTTCCCTGAGGATAAG
66 GATCTACCCTAAAGAGCAGCGGAGCATATCCCC-TTCTTCAGATTTGATCTTCCCTGAGGATAAG
533607 TG
130 TG
* * *
533609 GAATAAATCTACCTCAATTCAATTTTCCCT
1 GAACAAGTCTACCTCAATTCAATCTTCCCT
533639 GAAAAGTGAA
Statistics
Matches: 256, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
131 143 0.56
132 111 0.43
133 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (131 bp):
GAACAAGTCTACCTCAATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACATTTCCATATCT
GATCTACCCTAAAGAGCAGCGGAGCATATCCCCTTCTTCAGATTTGATCTTCCCTGAGGATAAGT
G
Found at i:533708 original size:48 final size:47
Alignment explanation
Indices: 533655--533749 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 47
533645 TGAATCAAAG
* * * *
533655 TTTCCAAATCTT-ATTTACCTTGAAGTGCAGCGGAGCAGATCTCCTTTT
1 TTTCCAAAT-TTGATCTACCCTAAAGAGCAGCGGAGCAGATCT-CTTTT
*
533703 TTTCCAAATTTGATCTACCCTAAAGAGTAGCGGAGCAGATCTCTTTT
1 TTTCCAAATTTGATCTACCCTAAAGAGCAGCGGAGCAGATCTCTTTT
533750 CAGATTTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
47 7 0.17
48 34 0.83
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (47 bp):
TTTCCAAATTTGATCTACCCTAAAGAGCAGCGGAGCAGATCTCTTTT
Found at i:534503 original size:18 final size:19
Alignment explanation
Indices: 534480--534518 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
534470 AAAGAACAAC
*
534480 AACAAAGAATA-AAAAAGA
1 AACAAAGAAAAGAAAAAGA
534498 AACAAAGAAAAGAAAAAGA
1 AACAAAGAAAAGAAAAAGA
534517 AA
1 AA
534519 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (19 bp):
AACAAAGAAAAGAAAAAGA
Found at i:534515 original size:19 final size:18
Alignment explanation
Indices: 534480--534537 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
534470 AAAGAACAAC
*
534480 AACAAAGAATAAAAAAGA
1 AACAAAGAAAAAAAAAGA
534498 AACAAAGAAAAGAAAAAGA
1 AACAAAGAAAA-AAAAAGA
*
534517 AA-AAATTTAAAAAAAAAGA
1 AACAAA--GAAAAAAAAAGA
534536 AA
1 AA
534538 AGGGAGAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 13 0.37
19 18 0.51
20 4 0.11
ACGTcount: A:0.79, C:0.03, G:0.10, T:0.07
Consensus pattern (18 bp):
AACAAAGAAAAAAAAAGA
Found at i:535333 original size:45 final size:45
Alignment explanation
Indices: 535264--535522 Score: 448
Period size: 45 Copynumber: 5.8 Consensus size: 45
535254 TATAAAATTT
* * *
535264 CTTATCATTTATCCTATAAGCTCGTAAGCTTATTTTAACAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
535309 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
535354 CTTATCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
535399 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
535444 CTTACCATTTATCCCATAAGCTCTTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
535489 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
535523 GCATGCTTAC
Statistics
Matches: 205, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
44 25 0.12
45 180 0.88
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:535681 original size:40 final size:40
Alignment explanation
Indices: 535626--535789 Score: 256
Period size: 40 Copynumber: 4.1 Consensus size: 40
535616 ACCGTAGTGC
*
535626 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
535666 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTGT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
535706 TACATATAAGGTCGTACCCACCATATACACCGAAGTGTAA
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
535746 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAC
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
535786 TACA
1 TACA
535790 AACTTGCAGC
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 112 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Done.