Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002096.1 Hibiscus syriacus cultivar Beakdansim tig00004279_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: 84435
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:9882 original size:26 final size:26
Alignment explanation
Indices: 9830--9880 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
9820 CATAGATTTA
9830 AGATAGTTGAACGAGTGAAAATAAAT
1 AGATAGTTGAACGAGTGAAAATAAAT
*
9856 AGATGAGTTTAAC-AGTAGAAAATAA
1 AGAT-AGTTGAACGAGT-GAAAATAA
9881 TAATATATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.24
Consensus pattern (26 bp):
AGATAGTTGAACGAGTGAAAATAAAT
Found at i:12331 original size:2 final size:2
Alignment explanation
Indices: 12324--12362 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12314 AATTTACCCC
12324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12363 CATAGGTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17839 original size:97 final size:95
Alignment explanation
Indices: 17640--17843 Score: 255
Period size: 97 Copynumber: 2.1 Consensus size: 95
17630 GAAATCACTT
* * * * * * *
17640 ATTTACTGATTTATGAACTATGGTTACTTGAAATATGTTCTCTGGTTACTGTTTTCACTATAAAA
1 ATTTACTGGTTAATGAACTATGGTTACCTAAAATATGTTATATGGTTACTGTTTTCACTAAAAAA
* *
17705 TATGATCGTTCATGATTTATGAATCATTGA
66 TATGATCATTCATGATTTATGAATCATGGA
* * * *
17735 ATCTACTGGTTAATGAATTATGGTTACCTAAAATGTGTTATATGGTTACATGTTTTCATTGAAAA
1 ATTTACTGGTTAATGAACTATGGTTACCTAAAATATGTTATATGGTTAC-TGTTTTCACT-AAAA
* *
17800 AATATGATCATTCCTGATTTATGGATCATGGA
64 AATATGATCATTCATGATTTATGAATCATGGA
17832 ATTTACTGGTTA
1 ATTTACTGGTTA
17844 CTACTTGAAT
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
95 40 0.44
96 9 0.10
97 42 0.46
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (95 bp):
ATTTACTGGTTAATGAACTATGGTTACCTAAAATATGTTATATGGTTACTGTTTTCACTAAAAAA
TATGATCATTCATGATTTATGAATCATGGA
Found at i:19906 original size:29 final size:30
Alignment explanation
Indices: 19851--19920 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
19841 TTAACGGTTC
19851 AGTGATATAATTGAAACAACAATAAAAGTTT
1 AGTGATATAATTG-AACAACAATAAAAGTTT
*
19882 AGTGCTATAATTG-ACAA-AATTAAAAGTTT
1 AGTGATATAATTGAACAACAA-TAAAAGTTT
* *
19911 ATTGGTATAA
1 AGTGATATAA
19921 ACTATACAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.06
29 21 0.60
31 12 0.34
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (30 bp):
AGTGATATAATTGAACAACAATAAAAGTTT
Found at i:20960 original size:28 final size:28
Alignment explanation
Indices: 20920--20974 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
20910 TCTTTGCTAT
* *
20920 ATTATGATGTCGAGTTAGTACTTGAAAC
1 ATTATGACGTCGAGTTAATACTTGAAAC
*
20948 ATTATGACGTCGAGTTAATGCTTGAAA
1 ATTATGACGTCGAGTTAATACTTGAAA
20975 GCAATGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.35
Consensus pattern (28 bp):
ATTATGACGTCGAGTTAATACTTGAAAC
Found at i:23454 original size:20 final size:20
Alignment explanation
Indices: 23429--23473 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
23419 ATATAAAATG
*
23429 ATATATATATAT-TTAGTTAT
1 ATATATATATATATTA-TTAA
23449 ATATATATATATATTATTAA
1 ATATATATATATATTATTAA
23469 ATATA
1 ATATA
23474 AAATGATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATATATATATATATTATTAA
Found at i:28787 original size:13 final size:13
Alignment explanation
Indices: 28740--28792 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
28730 ATCTTAATTC
28740 AAATTTTAAAAAT
1 AAATTTTAAAAAT
28753 AATATTATTAATAAAT
1 AA-ATT-TTAA-AAAT
*
28769 ATAATTTTAAATAT
1 A-AATTTTAAAAAT
*
28783 AAATTATAAA
1 AAATTTTAAA
28793 GTAAACGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 10 0.29
14 7 0.21
15 8 0.24
16 8 0.24
17 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:30754 original size:2 final size:2
Alignment explanation
Indices: 30747--30778 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30737 TTACAAAAGG
30747 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
30779 GCCATATTTT
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:32505 original size:3 final size:3
Alignment explanation
Indices: 32499--32530 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
32489 TGTAAATTAT
32499 TAA TAA TAA TTAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA T
32531 GAAATATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:32515 original size:13 final size:13
Alignment explanation
Indices: 32493--32530 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
32483 CCTGCATGTA
*
32493 AATTATTAATAAT
1 AATTAATAATAAT
32506 AATTAATAATAAT
1 AATTAATAATAAT
32519 AA-TAATAATAAT
1 AATTAATAATAAT
32531 GAAATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:34736 original size:21 final size:21
Alignment explanation
Indices: 34692--34736 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
34682 AAACTATACA
*
34692 TTTAGTACCTAAATTATCAGT
1 TTTAGTACCTAAATTATCAAT
34713 TTTAGTACCTAAACTT-TCAAT
1 TTTAGTACCTAAA-TTATCAAT
34734 TTT
1 TTT
34737 TTCAAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTAGTACCTAAATTATCAAT
Found at i:38965 original size:16 final size:16
Alignment explanation
Indices: 38944--38977 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
38934 TTACTATTCA
*
38944 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
38960 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
38976 CG
1 CG
38978 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:64399 original size:18 final size:18
Alignment explanation
Indices: 64373--64419 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
64363 TTGATTTTAT
64373 TAAAATAATATCTAAAAC
1 TAAAATAATATCTAAAAC
* * *
64391 TATAATAATATCTATAAT
1 TAAAATAATATCTAAAAC
64409 TAAAATAATAT
1 TAAAATAATAT
64420 TTTTATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATAATATCTAAAAC
Found at i:67672 original size:81 final size:81
Alignment explanation
Indices: 67532--67773 Score: 340
Period size: 81 Copynumber: 3.0 Consensus size: 81
67522 CTAGGATTGA
** * * *
67532 TACTGATTTATCTCCTCTGCGAAAACGGAGGGTTCGGAATGAAACACCATCACCTGAACCTTTAG
1 TACTGATTTATCTCCTCCACGAAAACGGAGGGTTCGGAATGATACACAATCACCAGAACCTTTAG
*
67597 TAAACAGTGCAGATGG
66 TAAACAGAGCAGATGG
* * *
67613 TACTGATTTATCTCCTCCACGGAAACAGAGGGTTCGGAATGATACACAATCATCAGAACCTTTAG
1 TACTGATTTATCTCCTCCACGAAAACGGAGGGTTCGGAATGATACACAATCACCAGAACCTTTAG
*
67678 TGAACAGAGCAGATGG
66 TAAACAGAGCAGATGG
* * * * * *
67694 TACTGATTTATCTCCTCCACGTAAATGGAGGGCTCGGAATGATACACATTCACCAAAACCTTTAA
1 TACTGATTTATCTCCTCCACGAAAACGGAGGGTTCGGAATGATACACAATCACCAGAACCTTTAG
67759 TAAACAGAGCAGATG
66 TAAACAGAGCAGATG
67774 CTGATTTATC
Statistics
Matches: 142, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 142 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (81 bp):
TACTGATTTATCTCCTCCACGAAAACGGAGGGTTCGGAATGATACACAATCACCAGAACCTTTAG
TAAACAGAGCAGATGG
Found at i:67825 original size:78 final size:78
Alignment explanation
Indices: 67533--67818 Score: 288
Period size: 81 Copynumber: 3.6 Consensus size: 78
67523 TAGGATTGAT
** * * * * **
67533 ACTGATTTATCTCCTCTGCGAAAACGGAGGGTTCGGAATGAAACACCATCACCTGAACCTTTAGT
1 ACTGATTTATCTCCTCCACGGAAATGGAGGG-T-GGAATGATACACAATCACCAAAACCTTTAGT
*
67598 AAACAGTGCAGATGG
64 AAACAGAGCAGATGG
** * *
67613 TACTGATTTATCTCCTCCACGGAAACAGAGGGTTCGGAATGATACACAATCATCAGAACCTTTAG
1 -ACTGATTTATCTCCTCCACGGAAATGGAGGG-T-GGAATGATACACAATCACCAAAACCTTTAG
*
67678 TGAACAGAGCAGATGG
63 TAAACAGAGCAGATGG
* * *
67694 TACTGATTTATCTCCTCCACGTAAATGGAGGGCTCGGAATGATACACATTCACCAAAACCTTTAA
1 -ACTGATTTATCTCCTCCACGGAAATGGAGGG-T-GGAATGATACACAATCACCAAAACCTTTAG
67759 TAAACAGAGCAGAT-G
63 TAAACAGAGCAGATGG
* * *
67774 -CTGATTTATCACCACCTCGGAAATGGAGGGTGAGAAATGATACAC
1 ACTGATTTATCTCCTCCACGGAAATGGAGGGTG-G-AATGATACAC
67819 CTTCACCGAA
Statistics
Matches: 180, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
76 1 0.01
77 2 0.01
78 36 0.20
80 1 0.01
81 140 0.78
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (78 bp):
ACTGATTTATCTCCTCCACGGAAATGGAGGGTGGAATGATACACAATCACCAAAACCTTTAGTAA
ACAGAGCAGATGG
Found at i:71465 original size:2 final size:2
Alignment explanation
Indices: 71454--71555 Score: 93
Period size: 2 Copynumber: 57.0 Consensus size: 2
71444 GAACCCAAAA
*
71454 AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
71490 AT -T AT AT AA AT A- AT -T A- AT AT -T A- AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71526 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
71556 CGAGGCGGGT
Statistics
Matches: 84, Mismatches: 4, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
1 12 0.14
2 72 0.86
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:71494 original size:34 final size:36
Alignment explanation
Indices: 71454--71538 Score: 138
Period size: 34 Copynumber: 2.4 Consensus size: 36
71444 GAACCCAAAA
71454 ATATTATATATATAATTAATA-TAAAATATATA-AT
1 ATATTATATATATAATTAATATTAAAATATATATAT
*
71488 ATATTATATAAATAATTAATATTAAAATATATATAT
1 ATATTATATATATAATTAATATTAAAATATATATAT
71524 ATATATATATATATA
1 ATAT-TATATATATA
71539 TATATATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
34 20 0.43
35 11 0.24
36 6 0.13
37 9 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
ATATTATATATATAATTAATATTAAAATATATATAT
Found at i:73869 original size:82 final size:82
Alignment explanation
Indices: 73714--73872 Score: 180
Period size: 82 Copynumber: 1.9 Consensus size: 82
73704 AGAGGTTATT
*** * * *
73714 GATACTGTAAGGCCAGTATCGATACCAAGGGTATGGTTTGAGCTTTAAAGCAAGAGTAAGTGTAG
1 GATACTGTAAGGCCAGTATCGATACCAAGGGTATGAAATGAGCTTTAAAGCAAGAGAAAATATAG
73779 AGGCAAGTGAGGGTGTC
66 AGGCAAGTGAGGGTGTC
* *
73796 GATATTGTAAGGCCAGTATCGATACCAA-GGTCGA-GAAATGGGCTTT-AAGTCAAGAGAAAATA
1 GATACTGTAAGGCCAGTATCGATACCAAGGGT--ATGAAATGAGCTTTAAAG-CAAGAGAAAATA
* *
73858 TATAGGTAAGTGAGG
63 TAGAGGCAAGTGAGG
73873 TTTTGCACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
81 6 0.09
82 57 0.89
83 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.31, T:0.24
Consensus pattern (82 bp):
GATACTGTAAGGCCAGTATCGATACCAAGGGTATGAAATGAGCTTTAAAGCAAGAGAAAATATAG
AGGCAAGTGAGGGTGTC
Found at i:77528 original size:80 final size:80
Alignment explanation
Indices: 77350--77573 Score: 315
Period size: 80 Copynumber: 2.8 Consensus size: 80
77340 GCTTGCCCTC
* ** *
77350 AGCACACAGCAAAAAGGGAAGCCAACCTAAGGATATACCTTAGATCTACCCAAGGACATCCTTAG
1 AGCACACAGC-AAAAGGGAA-CCAACCTAAGGATATACCTTGGGCCTACCCAA-GATATCCTTAG
*
77415 ATCCGTAGGGTTACCTTA
63 ATCCATAGGGTTACCTTA
* *
77433 AGCACACAGC-TAAGGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGGTC
1 AGCACACAGCAAAAGGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGATC
77497 CATAGGGTTACCTTA
66 CATAGGGTTACCTTA
* *
77512 TGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATACCTT
1 AGCACACAGCAAAAGGGAACCAACCTAAGGATATACCTTGGG-CCTACCCAAGATAT-CCTT
77574 GGGACCTACC
Statistics
Matches: 128, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
79 34 0.27
80 59 0.46
81 21 0.16
82 4 0.03
83 10 0.08
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (80 bp):
AGCACACAGCAAAAGGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGATC
CATAGGGTTACCTTA
Found at i:77568 original size:23 final size:23
Alignment explanation
Indices: 77541--77595 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
77531 CCAACCTAAG
77541 GATATACCTTGGGACCTACCCAA
1 GATATACCTTGGGACCTACCCAA
77564 GATATACCTTGGGACCTACCCAA
1 GATATACCTTGGGACCTACCCAA
77587 GATAT-CCTT
1 GATATACCTT
77596 AGGTCCGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (23 bp):
GATATACCTTGGGACCTACCCAA
Found at i:77652 original size:103 final size:103
Alignment explanation
Indices: 77461--77675 Score: 380
Period size: 103 Copynumber: 2.1 Consensus size: 103
77451 CCAACCTAAG
*
77461 GATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCATAGGGTTACCTTATGCACACAACAAAA
1 GATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCATAGGGTTAACTTATGCACACAACAAAA
77526 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
66 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
* *
77564 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGC-AA
1 GATATACCTTGGG-CCTACCCAAGATATCCTTAGGTCCATAGGGTTAACTTATGCACACAACAAA
77628 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
65 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
77667 GATAT-CCTT
1 GATATACCTT
77676 AGGTCCGTAG
Statistics
Matches: 108, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
102 4 0.04
103 59 0.55
104 45 0.42
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (103 bp):
GATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCATAGGGTTAACTTATGCACACAACAAAA
GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
Found at i:77697 original size:80 final size:80
Alignment explanation
Indices: 77564--77764 Score: 366
Period size: 80 Copynumber: 2.5 Consensus size: 80
77554 ACCTACCCAA
77564 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAAA
1 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAAA
77629 GGGAACCAACCTAAG
66 GGGAACCAACCTAAG
*
77644 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAGCAAA
1 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAAA
77709 GGGAACCAACCTAAG
66 GGGAACCAACCTAAG
* * *
77724 GATATGCCTTGGGGCCTACCTAAGATATCCTTAGGTCCGTA
1 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTA
77765 AGGACTTACA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 117 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (80 bp):
GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAAA
GGGAACCAACCTAAG
Found at i:77712 original size:183 final size:183
Alignment explanation
Indices: 77381--77757 Score: 607
Period size: 183 Copynumber: 2.1 Consensus size: 183
77371 CCAACCTAAG
* * *
77381 GATATACCTTAGATCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAGCTAA
1 GATATACCTTAGACCTACCCAAGGACATCCTTAGATCCGTAGGGTTAACTTAAGCACACAGCAAA
77446 GGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCATAGGGTTACCTT
66 GGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCATAGGGTTACCTT
77511 ATGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
131 ATGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
* * * *
77564 GATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAA
1 GATATACCTT-AGACCTACCCAAGGACATCCTTAGATCCGTAGGGTTAACTTAAGCACACAGCAA
*
77628 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACC
65 AGGGAACCAACCTAAGGATATACCTTGGG-CCTACCCAAGATATCCTTAGGTCCATAGGGTTACC
* * * *
77693 TTATGCACACAGC-AAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACCTAA
129 TTATGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
77747 GATAT-CCTTAG
1 GATATACCTTAG
77758 GTCCGTAAGG
Statistics
Matches: 179, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
181 1 0.01
182 4 0.02
183 118 0.66
184 56 0.31
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (183 bp):
GATATACCTTAGACCTACCCAAGGACATCCTTAGATCCGTAGGGTTAACTTAAGCACACAGCAAA
GGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCATAGGGTTACCTT
ATGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
Found at i:79625 original size:17 final size:18
Alignment explanation
Indices: 79592--79625 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
79582 TCCATTCTGT
79592 CTTATTATTTAATTCCAA
1 CTTATTATTTAATTCCAA
79610 CTTATTATTT-ATTCCA
1 CTTATTATTTAATTCCA
79626 GACCTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (18 bp):
CTTATTATTTAATTCCAA
Done.