Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008704.1 Hibiscus syriacus cultivar Beakdansim tig00111743_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: 516901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:453628 original size:23 final size:23
Alignment explanation
Indices: 453593--453652 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
453583 ATAAAGTAAA
* *
453593 ATAATAAATTAGGTAGCGCTTAT
1 ATAATAAAATAGGTAACGCTTAT
** *
453616 ATAATGTAATAGGTAATGCTTAT
1 ATAATAAAATAGGTAACGCTTAT
453639 ATAATAAAATAGGT
1 ATAATAAAATAGGT
453653 TAATTACTGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (23 bp):
ATAATAAAATAGGTAACGCTTAT
Found at i:453725 original size:87 final size:87
Alignment explanation
Indices: 453600--453814 Score: 340
Period size: 87 Copynumber: 2.5 Consensus size: 87
453590 AAAATAATAA
* **
453600 ATTAGGTAGCGCTTATATAATGTAATAGGTAATGCTTATATAATAAAATAGGTTAATTACTGGAA
1 ATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAA
* *
453665 ACATTATTAAGCATAATAACAT
66 ACATTATCAAGCACAATAACAT
* *
453687 ATTAGGTAGCGTTTATTTAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTGGAA
1 ATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAA
* *
453752 ATATTATCAAGTACAATAACAT
66 ACATTATCAAGCACAATAACAT
*
453774 ATTAGGTAACGTTTATATAATGTAATAGGTAGCGCTTATAT
1 ATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCTTATAT
453815 TGACCTATTC
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 116 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (87 bp):
ATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAA
ACATTATCAAGCACAATAACAT
Found at i:454151 original size:197 final size:199
Alignment explanation
Indices: 453816--454492 Score: 871
Period size: 198 Copynumber: 3.4 Consensus size: 199
453806 CGCTTATATT
* * * **
453816 GACCTATTCTATCATAAAATCATTATATTTATACC-GGTAACATTGTAAATTTACCTATTACATT
1 GACCTATTTTCTCATAAAACCGGTATATTTATACCGGGT-ACATTGTAAATTTACCTATTACATT
* * *
453880 ATAATTATCGGTTTCGATGTTTTTGGGATCGATATAATTT--TAAATGTATCGACACTTTATGCG
65 ATAATTATCCGTTTCGATATTTTTGGGATCGATAT-TTTTAATAAATGTATCGACACTTTATGCG
* * * *
453943 TGTACCTCGTTGGGCA-TCATTCTGGAAAAAAATATCAACACAAACTTAAAACGTGTCGATACAT
129 TGTACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACAT
454007 TATGTA
194 TATGTA
* * * *
454013 GACCTATTTTCTCATAAAACTGGTATATTTCTACCGGGTACATTGTAAATTTACCTATTATATTG
1 GACCTATTTTCTCATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTA
* * * *
454078 TAATTATCCGTTTGGAT-TTTTTGGGATCAATATTTTTAATAAATGTGTCGACACTTTATGTGTG
66 TAATTATCCGTTTCGATATTTTTGGGATCGATATTTTTAATAAATGTATCGACACTTTATGCGTG
* *
454142 TACCTCGTTGGAAATTCATTCTCGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTA
131 TACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTA
454207 TGTA
196 TGTA
* * * * *
454211 GACCTATTTTCTCATAAAACCGATATATTTCTACCGAGTATATTGTAAATTTACCTATTACATTG
1 GACCTATTTTCTCATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTA
** *
454276 TAATTATTTGTTTCGATATTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTG
66 TAATTATCCGTTTCGATATTTTTGGGATCGATATTTTTAATAAATGTATCGACACTTTATGCGTG
* * * *** *
454341 CACCTCGTTTGACATTCATTCTGGACAAAATGTATCGACAC-TTTTTAAATTTGTGTCGATACAT
131 TACCTCGTTGGACATTCATTCTGGA-AAAAAGTATCGACACAAACTTAAA-ATGTGTCGATACAT
454405 TATGTA
194 TATGTA
* * * * * *
454411 AACCTATTCTCTCATAAAACCGGTAAATTTATACCGGTTACATTGTAAATTTATCTATTATATTA
1 GACCTATTTTCTCATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTA
**
454476 TAATTATTGGTTTCGAT
66 TAATTATCCGTTTCGAT
454493 GTAACATATG
Statistics
Matches: 419, Mismatches: 54, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
195 3 0.01
196 15 0.04
197 102 0.24
198 127 0.30
199 69 0.16
200 103 0.25
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (199 bp):
GACCTATTTTCTCATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTA
TAATTATCCGTTTCGATATTTTTGGGATCGATATTTTTAATAAATGTATCGACACTTTATGCGTG
TACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTA
TGTA
Found at i:454636 original size:31 final size:30
Alignment explanation
Indices: 454595--454688 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
454585 TTATAATAAA
*
454595 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
454625 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
* * *
454655 TTATAAAAT-T-ATAGAT-ATAATATTTTAA
1 TAATAAAATATAATA-ATAATAATTTTTTAT
454683 TAATAA
1 TAATAA
454689 TATTGACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
28 18 0.33
29 5 0.09
30 24 0.44
31 8 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:454688 original size:14 final size:14
Alignment explanation
Indices: 454606--454692 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
454596 AATAAATATA
**
454606 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
454621 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
454634 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
454648 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
454662 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
454676 ATTTTAATAATAAT
1 ATTTTAATAATAAT
454690 ATT
1 ATT
454693 GACATACATA
Statistics
Matches: 53, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
13 10 0.19
14 38 0.72
15 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:454688 original size:28 final size:28
Alignment explanation
Indices: 454620--454688 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
454610 ATAATAATTT
*
454620 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
454647 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
454675 TATTTTAATAATAA
1 TATTTTAATAATAA
454689 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:454799 original size:24 final size:24
Alignment explanation
Indices: 454728--454792 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
454718 TTCTAATATT
*
454728 TTAA-AAATATTATTATTATTTTG
1 TTAATAAATAATATTATTATTTTG
454751 TTAATAAATAATATTATTATTTTG
1 TTAATAAATAATATTATTATTTTG
454775 TTAATAAATAATATTATT
1 TTAATAAATAATATTATT
454793 TTATTGTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 4 0.10
24 36 0.90
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (24 bp):
TTAATAAATAATATTATTATTTTG
Found at i:455390 original size:31 final size:30
Alignment explanation
Indices: 455349--455442 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
455339 TTATAAAAAA
*
455349 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
455379 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
* * *
455409 TTATAAAAT-T-ATAGAT-ATAATATTTTAA
1 TAATAAAATATAATA-ATAATAATTTTTTAT
455437 TAATAA
1 TAATAA
455443 TATTTACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
28 18 0.33
29 5 0.09
30 24 0.44
31 8 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:455442 original size:14 final size:14
Alignment explanation
Indices: 455360--455461 Score: 57
Period size: 14 Copynumber: 7.2 Consensus size: 14
455350 AATAAATATA
**
455360 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
455375 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
455388 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
455402 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
455416 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
455430 ATTTTAATAATAAT
1 ATTTTAATAATAAT
455444 A-TTTACATAAATAAT
1 ATTTTA-AT-AATAAT
455459 ATT
1 ATT
455462 AAATAAATTA
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
13 14 0.22
14 38 0.58
15 12 0.18
16 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:455442 original size:28 final size:28
Alignment explanation
Indices: 455374--455442 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
455364 ATAATAATTT
*
455374 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
455401 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
455429 TATTTTAATAATAA
1 TATTTTAATAATAA
455443 TATTTACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:455467 original size:14 final size:15
Alignment explanation
Indices: 455425--455469 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
455415 AATTATAGAT
*
455425 ATAATATTTTAAT-A
1 ATAATATTTAAATAA
*
455439 ATAATATTTACATAA
1 ATAATATTTAAATAA
455454 ATAATA-TTAAATAA
1 ATAATATTTAAATAA
455468 AT
1 AT
455470 TATTCTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATATTTAAATAA
Found at i:455565 original size:23 final size:23
Alignment explanation
Indices: 455515--455559 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
455505 AACATATTTT
*
455515 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
455538 ATTATATAAGCGGTACCTAATA
1 ATTATATAAGCGCTACCTAATA
455560 TGTTATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:455628 original size:23 final size:23
Alignment explanation
Indices: 455593--455708 Score: 196
Period size: 23 Copynumber: 5.0 Consensus size: 23
455583 TCAGTAATTA
** *
455593 ACCTATTTTATTATATAAGCGAT
1 ACCTATTACATTATATAAGCGCT
*
455616 ATCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
455639 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
455662 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
455685 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
455708 A
1 A
455709 ACCAAAGTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 88 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:460242 original size:20 final size:20
Alignment explanation
Indices: 460217--460260 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
460207 CAACTTTCCA
*
460217 CGTCCCTTTTTTTATGAGAG
1 CGTCCCATTTTTTATGAGAG
460237 CGTCCCATTTTTTATGAGAG
1 CGTCCCATTTTTTATGAGAG
460257 CGTC
1 CGTC
460261 ATGTTCATCC
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:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (20 bp):
CGTCCCATTTTTTATGAGAG
Found at i:462897 original size:44 final size:43
Alignment explanation
Indices: 462718--462938 Score: 268
Period size: 43 Copynumber: 5.1 Consensus size: 43
462708 ATAGGTCAAG
*
462718 ATCTATAGCGGCGTTTTTGAACCAAACGCCGCAAAAGGTCGAT
1 ATCTATAGCGGCGTTTTTGAAACAAACGCCGCAAAAGGTCGAT
*
462761 ATATATAGCGGCGTTTTTTG-AACAAACGCCGCAAAAGGTCGAT
1 ATCTATAGCGGCG-TTTTTGAAACAAACGCCGCAAAAGGTCGAT
* * * * *
462804 ATATATAGCGACATTTTTGGAACAAACACCGCAAAA-GTCGAT
1 ATCTATAGCGGCGTTTTTGAAACAAACGCCGCAAAAGGTCGAT
* * ** *
462846 ATCTATAGCGGCGTTTTTGCAAAAAAACGCCACAAAATATCGAA
1 ATCTATAGCGGCGTTTTTG-AAACAAACGCCGCAAAAGGTCGAT
* *
462890 ATCTATAGCGGCGTTTTT-AGAACAAACGCCGCAAAAGGTCAAG
1 ATCTATAGCGGCGTTTTTGA-AACAAACGCCGCAAAAGGTCGAT
462933 ATCTAT
1 ATCTAT
462939 CATATCTATA
Statistics
Matches: 153, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
42 29 0.19
43 96 0.63
44 28 0.18
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (43 bp):
ATCTATAGCGGCGTTTTTGAAACAAACGCCGCAAAAGGTCGAT
Found at i:468125 original size:82 final size:82
Alignment explanation
Indices: 468027--468207 Score: 213
Period size: 82 Copynumber: 2.2 Consensus size: 82
468017 TAATCTTTAA
* * * ** *
468027 GGCGTTTATTGAAAAAACCCCACTATA-AGTGAACACTATTGTGGCATTTTTATAAAAACGCCGC
1 GGCGTTTGTCGAAAAATCCCCACTATAGA-TGAAC-CTATTACGGCATTTGTATAAAAACGCCGC
468091 TAAAGTA-TTAATATGTTGT
64 TAAAGTACTT-ATATGTTGT
* * * *
468110 GGCGTTTGTCGAAAAATCGCCACTATAGATGGACCTATTACGGCGTTTGTATAAAAACGCCTCTA
1 GGCGTTTGTCGAAAAATCCCCACTATAGATGAACCTATTACGGCATTTGTATAAAAACGCCGCTA
*
468175 AAGTACTTATCTGTTGT
66 AAGTACTTATATGTTGT
*
468192 GGTGTTTGTCGAAAAA
1 GGCGTTTGTCGAAAAA
468208 ACGCCGCTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
82 54 0.64
83 29 0.35
84 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (82 bp):
GGCGTTTGTCGAAAAATCCCCACTATAGATGAACCTATTACGGCATTTGTATAAAAACGCCGCTA
AAGTACTTATATGTTGT
Found at i:468218 original size:42 final size:41
Alignment explanation
Indices: 468080--468250 Score: 141
Period size: 42 Copynumber: 4.1 Consensus size: 41
468070 GCATTTTTAT
* *
468080 AAAAACGCCGCTAAAGTATTAATATGTTGTGGCGTTTGTCGA
1 AAAAACGCCGCTAAAGTATT-ATCTGTTATGGCGTTTGTCGA
* * * * * * *
468122 AAAATCGCCACTATAG-ATGGACCTATTACGGCGTTTGT--A
1 AAAAACGCCGCTAAAGTAT-TATCTGTTATGGCGTTTGTCGA
* * *
468161 TAAAAACGCCTCTAAAGTACTTATCTGTTGTGGTGTTTGTCGA
1 -AAAAACGCCGCTAAAGTA-TTATCTGTTATGGCGTTTGTCGA
* * *
468204 AAAAACGCCGCTAAAGTACTACTCTTTTATGGCGTTTTTCGA
1 AAAAACGCCGCTAAAGTATTA-TCTGTTATGGCGTTTGTCGA
468246 AAAAA
1 AAAAA
468251 TGCCACTACA
Statistics
Matches: 98, Mismatches: 24, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
39 1 0.01
40 13 0.13
41 31 0.32
42 52 0.53
43 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGTATTATCTGTTATGGCGTTTGTCGA
Found at i:468324 original size:124 final size:124
Alignment explanation
Indices: 468080--468345 Score: 277
Period size: 124 Copynumber: 2.1 Consensus size: 124
468070 GCATTTTTAT
* * * *
468080 AAAAACGCCGCTAAAGTATTAATATGTTGTGGCGTTTGTCGAAAAATCGCCACTATAGATGGACC
1 AAAAACGCCGCTAAAGTACTAATATGTTATGGCGTTTGTCGAAAAATCGCCACTACAGATGAACC
* ** * * * * **
468145 TATTACGGCGTTTGTATAAAAACGCCTCTAAAGTACTTATCTGTTGTGGTGTTTGTCGA
66 TATTACGGCGTTTATATAAAAACGCCGATAAAGAACTTACCTATTGCGGCATTTGTCGA
* * * * *
468204 AAAAACGCCGCTAAAGTACTACTCTTTTATGGCGTTTTTCGAAAAAAT-GCCACTACATATGAAC
1 AAAAACGCCGCTAAAGTACTAATATGTTATGGCGTTTGTCG-AAAAATCGCCACTACAGATGAAC
* **
468268 CTATTGCGGCGTTTATATAAAAACGCCGATAACA-AAC-TACCCTATTGCGGCATTTGTTTA
65 CTATTACGGCGTTTATATAAAAACGCCGATAA-AGAACTTA-CCTATTGCGGCATTTGTCGA
* *
468328 AGAAACGCTGCTAAAGTA
1 AAAAACGCCGCTAAAGTA
468346 TCATTTTGTG
Statistics
Matches: 116, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
123 2 0.02
124 107 0.92
125 7 0.06
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (124 bp):
AAAAACGCCGCTAAAGTACTAATATGTTATGGCGTTTGTCGAAAAATCGCCACTACAGATGAACC
TATTACGGCGTTTATATAAAAACGCCGATAAAGAACTTACCTATTGCGGCATTTGTCGA
Found at i:476799 original size:393 final size:392
Alignment explanation
Indices: 476075--477266 Score: 2276
Period size: 392 Copynumber: 3.0 Consensus size: 392
476065 ACTCAACTTT
* *
476075 TAAATTGCTCCTATTTTAATCACTCTAATTTATTTTATTAATAAATTTTGTGACATTACTTTTTA
1 TAAATTGCTCCTATTTTAATCACTCTAATTTATTTTATTAATAACTTTTGTGACATGACTTTTTA
476140 TTATTATATTATTAATATATAATTAAAAATAAAAAATAAATTTGAAAGTTAGAGTGATTAAATTA
66 TTATTATATTATTAATATATAATTAAAAATAAAAAATAAATTTGAAAGTTAGAGTGATTAAATTA
*
476205 TGAGTAATTTAAGTAATTAAATTAAAAAAATAAACTTTAGTGGCCAAAATAGGAGTGGAAAAATA
131 TGAGTAATTTAAGTAATTAAATTAAAAAAATAAACTTTAGTGACCAAAATAGGAGTGGAAAAATA
* *
476270 GTTGAGTGATGAATAATGTAATTTACCGATAAAAAGGTATCACATGCAAATCACCTGATAAGTTT
196 GTTGAGTGATGAATAATGCAATTTACCCATAAAAAGGTATCACATGCAAATCACCTGATAAGTTT
476335 TTAACGATGGGGGTACTAAAACGAAACAAAAGCTAAACATTAAGTATAGTCTTAAGAAAATTGAA
261 TTAACGATGGGGGTACTAAAACGAAACAAAAGCTAAACATTAAGTATAGTCTTAAGAAAATTGAA
476400 AAATTAGGCTCTAAAATGAACAAAAACTGAAAGTTATGTACTAAACGTGCAATTTACCCTATGTA
326 AAATTAGGCTCTAAAATGAACAAAAACTGAAAGTTATGTACTAAACGTGCAATTTACCCTATGTA
476465 TA
391 TA
*
476467 TAAATTGCTCCTATTTTAATCACTCTAATTTATTTTATTAATAACTTTTGTGACATGACTTATTA
1 TAAATTGCTCCTATTTTAATCACTCTAATTTATTTTATTAATAACTTTTGTGACATGACTTTTTA
476532 TTATTATATTATTAATATATAATTAAAAATAAAAAATAAATTTGAAAGTTAGAGTGATTAAATTA
66 TTATTATATTATTAATATATAATTAAAAATAAAAAATAAATTTGAAAGTTAGAGTGATTAAATTA
476597 TGAGTAATTTAAGTAATTAAATTAAAAAAAATAAACTTTAGTGACCAAAATAGGAGTGGAAAAAT
131 TGAGTAATTTAAGTAATTAAATT-AAAAAAATAAACTTTAGTGACCAAAATAGGAGTGGAAAAAT
476662 AGTTGAGTGATGAATAATGCAATTTACCCATAAAAAGGTATCACATGCAAATCACCTGATAAGTT
195 AGTTGAGTGATGAATAATGCAATTTACCCATAAAAAGGTATCACATGCAAATCACCTGATAAGTT
476727 TTTAACGATGGGGGTACTAAAACGAAACAAAAGCTAAACATTAAGTATAGTCTTAAGAAAATTGA
260 TTTAACGATGGGGGTACTAAAACGAAACAAAAGCTAAACATTAAGTATAGTCTTAAGAAAATTGA
476792 AAAATTAGGCTCTAAAATGAACAAAAACTGAAAGTTATGTACTAAACGTGCAATTTACCCTATGT
325 AAAATTAGGCTCTAAAATGAACAAAAACTGAAAGTTATGTACTAAACGTGCAATTTACCCTATGT
476857 ATA
390 ATA
476860 TAAATTGCTCCTATTTTAATCACTCTAATTTATTTTATTAATAACTTTTGTGACATGACTTTTTA
1 TAAATTGCTCCTATTTTAATCACTCTAATTTATTTTATTAATAACTTTTGTGACATGACTTTTTA
*
476925 TTATTATTTTATTAATATATAATTAAAAATAAAAAATAAATTTGAAAGTTAGAGTGATTAAATTA
66 TTATTATATTATTAATATATAATTAAAAATAAAAAATAAATTTGAAAGTTAGAGTGATTAAATTA
*
476990 TGAGTAATTTAAGTAATTAAATTAAAAAAATAAACTTTATTGACCAAAATAGGAGTGGAAAAATA
131 TGAGTAATTTAAGTAATTAAATTAAAAAAATAAACTTTAGTGACCAAAATAGGAGTGGAAAAATA
*
477055 GTTGAGTGATGAATAATGCAATTTACCCATACAAAGGTATCACATGCAAATCACCTGATAAGTTT
196 GTTGAGTGATGAATAATGCAATTTACCCATAAAAAGGTATCACATGCAAATCACCTGATAAGTTT
477120 TTAACGATGGGGGTACTAAAACGAAACAAAAGCTAAACATTAAGTATAGTCTTAAGAAAATTGAA
261 TTAACGATGGGGGTACTAAAACGAAACAAAAGCTAAACATTAAGTATAGTCTTAAGAAAATTGAA
* *
477185 AAATTAGGCACTAAAATGAACAAAAACTTAAAGTTATGTACTAAACGTGCAATTTACCCTATGTA
326 AAATTAGGCTCTAAAATGAACAAAAACTGAAAGTTATGTACTAAACGTGCAATTTACCCTATGTA
477250 TA
391 TA
477252 TAAATTGCTCCTATT
1 TAAATTGCTCCTATT
477267 AGGTGATATA
Statistics
Matches: 787, Mismatches: 12, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
392 400 0.51
393 387 0.49
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (392 bp):
TAAATTGCTCCTATTTTAATCACTCTAATTTATTTTATTAATAACTTTTGTGACATGACTTTTTA
TTATTATATTATTAATATATAATTAAAAATAAAAAATAAATTTGAAAGTTAGAGTGATTAAATTA
TGAGTAATTTAAGTAATTAAATTAAAAAAATAAACTTTAGTGACCAAAATAGGAGTGGAAAAATA
GTTGAGTGATGAATAATGCAATTTACCCATAAAAAGGTATCACATGCAAATCACCTGATAAGTTT
TTAACGATGGGGGTACTAAAACGAAACAAAAGCTAAACATTAAGTATAGTCTTAAGAAAATTGAA
AAATTAGGCTCTAAAATGAACAAAAACTGAAAGTTATGTACTAAACGTGCAATTTACCCTATGTA
TA
Found at i:480083 original size:14 final size:13
Alignment explanation
Indices: 480044--480094 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 13
480034 CATAATATAA
480044 TTTTAATAATATT
1 TTTTAATAATATT
**
480057 TTATTTTTAATATT
1 TT-TTAATAATATT
*
480071 TTTTAAT-ATATA
1 TTTTAATAATATT
*
480083 TTATAATAATAT
1 TTTTAATAATAT
480095 ATGATATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
12 10 0.33
13 9 0.30
14 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTAATAATATT
Found at i:480429 original size:30 final size:29
Alignment explanation
Indices: 480344--480444 Score: 114
Period size: 30 Copynumber: 3.4 Consensus size: 29
480334 CCCGTAAAAT
*
480344 GTAATT-ATTTTACATAAAACATTTTTAG
1 GTAATTCATTTTACATAAAACATTTTCAG
* * *
480372 GTAATTCACTTTACGTAAAACAATTTTCAT
1 GTAATTCATTTTACATAAAAC-ATTTTCAG
*
480402 GTAATTCATTTTACATAAAACGGTTTTCAG
1 GTAATTCATTTTACATAAAAC-ATTTTCAG
* *
480432 GCAATCCATTTTA
1 GTAATTCATTTTA
480445 ACTAAATTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 6 0.10
29 12 0.20
30 42 0.70
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.42
Consensus pattern (29 bp):
GTAATTCATTTTACATAAAACATTTTCAG
Found at i:483132 original size:30 final size:30
Alignment explanation
Indices: 483070--483132 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
483060 ATGAAATTAT
* *
483070 AAAAATTAGGGGTCCTAATTATAATTATAA
1 AAAAATTAGGGGTCCTAATTATAAATACAA
* *
483100 AAAAATTGGAGGGT-CTAATTGTAAATACAA
1 AAAAATTAG-GGGTCCTAATTATAAATACAA
483130 AAA
1 AAA
483133 TTTGAGGACC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (30 bp):
AAAAATTAGGGGTCCTAATTATAAATACAA
Found at i:490225 original size:15 final size:15
Alignment explanation
Indices: 490200--490271 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
490190 TGGTTTTCCA
490200 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
490215 GAATTTGAATTACTG
1 GAAAATGAATTACTG
490230 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
490245 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
490259 GAAAATGAATTAC
1 GAAAATGAATTAC
490272 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.25
15 36 0.75
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:490269 original size:29 final size:30
Alignment explanation
Indices: 490200--490271 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
490190 TGGTTTTCCA
490200 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
490230 GAAAATGAATTACTGGAATTTGAATT-CTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
490259 GAAAATGAATTAC
1 GAAAATGAATTAC
490272 ATTTCTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (30 bp):
GAAAATGAATTACTGGAATTTGAATTACTG
Found at i:490277 original size:20 final size:20
Alignment explanation
Indices: 490254--490323 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
490244 GGAATTTGAA
490254 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
490274 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
490294 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
490314 TTCTGGAAAA
1 TTCTGGAAAA
490324 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:490546 original size:30 final size:28
Alignment explanation
Indices: 490489--490591 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 28
490479 CTTTACTAAA
*
490489 ATATTATTGAAATATATAAATAATATTAT
1 ATATTATT-AAATATATAAAAAATATTAT
490518 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATATAAAAAA--TATTAT
490548 ATATTATTAAA-ATA-AAATATAATATCT-T
1 ATATTATTAAATATATAAA-A-AATAT-TAT
490576 ATATTATTATAATATA
1 ATATTATTA-AATATA
490592 ATTGATTATT
Statistics
Matches: 64, Mismatches: 1, Indels: 17
0.78 0.01 0.21
Matches are distributed among these distances:
28 30 0.47
29 13 0.20
30 20 0.31
31 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAAATATTAT
Found at i:490589 original size:23 final size:22
Alignment explanation
Indices: 490563--490662 Score: 62
Period size: 23 Copynumber: 4.2 Consensus size: 22
490553 ATTAAAATAA
490563 AATATAATATCTTATATTATTAT
1 AATATAATAT-TTATATTATTAT
*
490586 AATATAATTGATTATTTTATATATATTAA
1 AATAT-A---A-TA-TTTATAT-TATTAT
490615 AATATAATA-TTATATTATTAT
1 AATATAATATTTATATTATTAT
**
490636 AAATATTAATAAATATATT-TTA-
1 -AATA-TAATATTTATATTATTAT
490658 AATAT
1 AATAT
490663 TTTAATAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 23
0.71 0.03 0.26
Matches are distributed among these distances:
20 1 0.02
21 9 0.14
22 10 0.16
23 13 0.20
24 9 0.14
25 1 0.02
27 1 0.02
28 9 0.14
29 11 0.17
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (22 bp):
AATATAATATTTATATTATTAT
Found at i:490589 original size:28 final size:27
Alignment explanation
Indices: 490542--490637 Score: 94
Period size: 28 Copynumber: 3.6 Consensus size: 27
490532 ATAAAAAATT
*
490542 TATTATATATTATTAAAATAAAATATAA
1 TATT-TATATTATTATAATAAAATATAA
* *
490570 TATCTTATATTATTATAATATAAT-TGAT
1 TAT-TTATATTATTATAATAAAATAT-AA
*
490598 TATTT-TA-TA-TATATTAAAATATAA
1 TATTTATATTATTATAATAAAATATAA
490622 TA-TTATATTATTATAA
1 TATTTATATTATTATAA
490638 ATATTAATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
23 2 0.04
24 14 0.25
25 5 0.09
26 6 0.11
27 3 0.05
28 24 0.44
29 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
TATTTATATTATTATAATAAAATATAA
Found at i:490627 original size:22 final size:23
Alignment explanation
Indices: 490602--490677 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 23
490592 ATTGATTATT
490602 TTATATATATTAAAATA-TAATA
1 TTATATATATTAAAATATTAATA
490624 TTATAT-TATTATAAATATTAATA
1 TTATATATATTA-AAATATTAATA
* * *
490647 -AATATATTTTAAATATTTTAATAA
1 TTATATATATTAAA-ATATTAAT-A
490671 TTA-ATAT
1 TTATATAT
490678 TTTGATGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
21 5 0.11
22 17 0.39
23 16 0.36
24 5 0.11
25 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATATATATTAAAATATTAATA
Found at i:490650 original size:32 final size:31
Alignment explanation
Indices: 490576--490652 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
490566 ATAATATCTT
* *
490576 ATATTATTATAATATAATTGATTATTTTATAT
1 ATATTAATA-AATATAATTGATTATTTTATAA
*
490608 ATATT-A-AAATATAATATTA-TATTATTATAA
1 ATATTAATAAATATAAT-TGATTATT-TTATAA
490638 ATATTAATAAATATA
1 ATATTAATAAATATA
490653 TTTTAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 12 0.32
30 13 0.34
31 1 0.03
32 12 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATATTAATAAATATAATTGATTATTTTATAA
Found at i:490654 original size:21 final size:22
Alignment explanation
Indices: 490606--490663 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
490596 ATTATTTTAT
*
490606 ATATATTA-AAATA-TAATATT
1 ATATATTATAAATATTAATATA
490626 ATATTATTATAAATATTAATA-A
1 ATA-TATTATAAATATTAATATA
*
490648 ATATATTTTAAATATT
1 ATATATTATAAATATT
490664 TTAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 3 0.09
21 17 0.52
22 8 0.24
23 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATATTATAAATATTAATATA
Found at i:490676 original size:53 final size:50
Alignment explanation
Indices: 490560--490678 Score: 141
Period size: 53 Copynumber: 2.3 Consensus size: 50
490550 ATTATTAAAA
** *
490560 TAAAATATAATATCTTATATTATTATAATATAATTGATTATTTTATATATAT
1 TAAAATATAATA--TTATATTATTATAATATAATAAATTATTTTAAATATAT
*
490612 TAAAATATAATATTATATTATTATAAATATTAATAAATATATTTTAAATATTT
1 TAAAATATAATATTATATTATTAT-AATA-TAATAAAT-TATTTTAAATATAT
490665 TAATAAT-TAATATT
1 TAA-AATATAATATT
490679 TTGATGAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
50 12 0.20
51 4 0.07
52 18 0.31
53 22 0.37
54 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (50 bp):
TAAAATATAATATTATATTATTATAATATAATAAATTATTTTAAATATAT
Found at i:490911 original size:42 final size:42
Alignment explanation
Indices: 490852--491013 Score: 288
Period size: 42 Copynumber: 3.9 Consensus size: 42
490842 ATGAATTACA
* *
490852 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
490894 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
490936 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
490978 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
491014 TTCGGGGAAA
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 117 1.00
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:491791 original size:2 final size:2
Alignment explanation
Indices: 491784--491811 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
491774 CAAATAGGGA
491784 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
491812 TGTATAGAAA
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:501303 original size:15 final size:15
Alignment explanation
Indices: 501283--501312 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
501273 AGGAAATATT
501283 AGAAACCAATATGGC
1 AGAAACCAATATGGC
501298 AGAAACCAATATGGC
1 AGAAACCAATATGGC
501313 TGGGAGGGGA
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:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (15 bp):
AGAAACCAATATGGC
Found at i:511640 original size:43 final size:44
Alignment explanation
Indices: 511592--511685 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 44
511582 CACTTCATTT
*
511592 TGTGATGGAA-TGAGCAAAATGTTGATGCTAATCCAACTCCTTA
1 TGTGATGGAATTGAGCAAAATGGTGATGCTAATCCAACTCCTTA
* ** *
511635 TGTGATGGAATTGAGCAAAATGGTGATGTTGGTCTAACTCCTTA
1 TGTGATGGAATTGAGCAAAATGGTGATGCTAATCCAACTCCTTA
511679 TGTGATG
1 TGTGATG
511686 TGATCGAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 10 0.22
44 35 0.78
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (44 bp):
TGTGATGGAATTGAGCAAAATGGTGATGCTAATCCAACTCCTTA
Done.