Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006778.1 Hibiscus syriacus cultivar Beakdansim tig00017141_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: 95117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3070 original size:40 final size:38
Alignment explanation
Indices: 3014--3096 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 38
3004 AGTTGACAAG
*
3014 TTGGTTGGTGGCCAACTTGTACACATGAGAAAATTCATCT
1 TTGGTAGGTGGCCAACTT-TACACATGA-AAAATTCATCT
* * * *
3054 TTGGTAGGTGGTCAACTTTGCACATGATAATTTCATCT
1 TTGGTAGGTGGCCAACTTTACACATGAAAAATTCATCT
3092 TTGGT
1 TTGGT
3097 TCCTAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 14 0.37
39 8 0.21
40 16 0.42
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (38 bp):
TTGGTAGGTGGCCAACTTTACACATGAAAAATTCATCT
Found at i:5612 original size:17 final size:17
Alignment explanation
Indices: 5592--5634 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5582 CCAAAAATTA
5592 AAAAAAAAACTAAAAAC
1 AAAAAAAAACTAAAAAC
* * * *
5609 AAAAAAAGATTGAAAAG
1 AAAAAAAAACTAAAAAC
5626 AAAAAAAAA
1 AAAAAAAAA
5635 ATGTTTATGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.81, C:0.05, G:0.07, T:0.07
Consensus pattern (17 bp):
AAAAAAAAACTAAAAAC
Found at i:9764 original size:23 final size:24
Alignment explanation
Indices: 9717--9768 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
9707 AAAGATAATT
* *
9717 ATTTTTTCAATATATTTTGTTTGA
1 ATTTTTTAAATATATTTTGTATGA
9741 ATTTTTTAAATATATTTT-TATGA
1 ATTTTTTAAATATATTTTGTATGA
9764 ATTTT
1 ATTTT
9769 AATAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (24 bp):
ATTTTTTAAATATATTTTGTATGA
Found at i:9774 original size:24 final size:24
Alignment explanation
Indices: 9725--9775 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
9715 TTATTTTTTC
* *
9725 AATATATTTTGTTTGAATTTTTTA
1 AATATATTTTGTATGAATTTTATA
9749 AATATATTTT-TATGAATTTTAATA
1 AATATATTTTGTATGAATTTT-ATA
9773 AAT
1 AAT
9776 TTTACATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (24 bp):
AATATATTTTGTATGAATTTTATA
Found at i:10901 original size:22 final size:20
Alignment explanation
Indices: 10852--10902 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
10842 TGTCTAGTTG
10852 ATATAT-TTTTTAAATATAT
1 ATATATATTTTTAAATATAT
10871 ATTATTATATTTTTAAATTACTAT
1 A-TA-TATATTTTTAAA-TA-TAT
10895 ATATATAT
1 ATATATAT
10903 AATATTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 3 0.11
22 13 0.48
23 4 0.15
24 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATATTTTTAAATATAT
Found at i:13446 original size:25 final size:25
Alignment explanation
Indices: 13418--13469 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
13408 TTATATCTCT
*
13418 TTATCTCTGTGCA-GATCATATATTA
1 TTATCTCTGTACATG-TCATATATTA
* *
13443 TTATTTCTGTACATGTCATATGTTA
1 TTATCTCTGTACATGTCATATATTA
13468 TT
1 TT
13470 GAGATATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (25 bp):
TTATCTCTGTACATGTCATATATTA
Found at i:14308 original size:20 final size:18
Alignment explanation
Indices: 14283--14320 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
14273 TTTTTTAAAA
14283 TATTAAAATAATTTATTTAT
1 TATTAAAAT-ATTT-TTTAT
14303 TATTAAAATATTTTTTAT
1 TATTAAAATATTTTTTAT
14321 AATTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTAAAATATTTTTTAT
Found at i:14647 original size:19 final size:20
Alignment explanation
Indices: 14608--14648 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
14598 ATCAGATTGT
14608 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
14628 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
14648 C
1 C
14649 TGTCTAACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.39, G:0.29, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:17432 original size:19 final size:20
Alignment explanation
Indices: 17393--17453 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
17383 ATCAAATTAT
17393 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
17413 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
17433 CCA-GGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
17452 CC
1 CC
17454 GTCTAACGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
19 16 0.42
20 22 0.58
ACGTcount: A:0.20, C:0.39, G:0.28, T:0.13
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:19911 original size:21 final size:21
Alignment explanation
Indices: 19886--19952 Score: 134
Period size: 21 Copynumber: 3.2 Consensus size: 21
19876 GTATATGATT
19886 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
19907 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
19928 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
19949 CTTA
1 CTTA
19953 TGGACATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.34
Consensus pattern (21 bp):
CTTAAGGAATGATATGTGGTC
Found at i:20826 original size:20 final size:20
Alignment explanation
Indices: 20801--20847 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
20791 CTCATCTCCA
20801 AACGGCTCCAAAACATCCCC
1 AACGGCTCCAAAACATCCCC
20821 AACGGCTCCAAAACATCCCC
1 AACGGCTCCAAAACATCCCC
20841 AACGGCT
1 AACGGCT
20848 ATATACGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.43, G:0.13, T:0.11
Consensus pattern (20 bp):
AACGGCTCCAAAACATCCCC
Found at i:21979 original size:19 final size:20
Alignment explanation
Indices: 21955--22002 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
21945 AACGATTTTC
*
21955 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
21974 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
21994 TTTTGAAAA
1 TTTTGAAAA
22003 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:23485 original size:21 final size:21
Alignment explanation
Indices: 23438--23539 Score: 154
Period size: 21 Copynumber: 5.0 Consensus size: 21
23428 ATAAGATTGT
23438 CCAGGGGGTACAGATT-CCCC
1 CCAGGGGGTACAGATTCCCCC
*
23458 CCA-GGGGTATAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
23478 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
23499 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
23520 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
23540 TCGTCTAACG
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
19 11 0.15
20 10 0.13
21 54 0.72
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:23926 original size:34 final size:32
Alignment explanation
Indices: 23887--23956 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
23877 TTTTGTAAAG
*
23887 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
23921 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
23953 GGGA
1 GGGA
23957 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:24325 original size:23 final size:23
Alignment explanation
Indices: 24276--24326 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
24266 GTGTTATATT
**
24276 ATATTTTAAAAATATTAATTATT
1 ATATTTTAAAAATATTAATTAAA
* * *
24299 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
24322 ATATT
1 ATATT
24327 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:24370 original size:17 final size:17
Alignment explanation
Indices: 24350--24387 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
24340 ATTAATATGA
24350 AATA-TATAAATAATATT
1 AATATTATAAATAAT-TT
*
24367 AATATTATTAATAATTT
1 AATATTATAAATAATTT
24384 AATA
1 AATA
24388 ATATTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATTATAAATAATTT
Found at i:24412 original size:53 final size:54
Alignment explanation
Indices: 24345--24449 Score: 160
Period size: 53 Copynumber: 2.0 Consensus size: 54
24335 ATTATATTAA
*
24345 TATGAAATATATAAATAATATTAATATTATTAATAATTTAATA-ATATTATTTC
1 TATGAAATATATAAATAATATAAATATTATTAATAATTTAATATATATTATTTC
* *
24398 TATGAAAT-TAATAAATAATATAAATTTTATTAATAATTTATTATATATTATT
1 TATGAAATAT-ATAAATAATATAAATATTATTAATAATTTAATATATATTATT
24450 AAAATAAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
52 1 0.02
53 38 0.81
54 8 0.17
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (54 bp):
TATGAAATATATAAATAATATAAATATTATTAATAATTTAATATATATTATTTC
Found at i:27160 original size:11 final size:11
Alignment explanation
Indices: 27140--27170 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
27130 GATGCCTATA
27140 TTTTTCTTTTTC
1 TTTTT-TTTTTC
27152 TTTTTTTTTTC
1 TTTTTTTTTTC
27163 TTTTTTTT
1 TTTTTTTT
27171 CAAATTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:28765 original size:14 final size:14
Alignment explanation
Indices: 28746--28791 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
28736 CATACACACA
*
28746 TATATATATATATG
1 TATATATATGTATG
*
28760 TATATATATGTGTG
1 TATATATATGTATG
* *
28774 TGTATGTATGTATG
1 TATATATATGTATG
28788 TATA
1 TATA
28792 AATGAATAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:29658 original size:77 final size:77
Alignment explanation
Indices: 29531--29685 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
29521 TTTGCCCTAA
29531 ATCGTTAACTTCGTTAAAAAACACGAGACTAAATTATATATTTAGTCACTCAATTATTCTTATGG
1 ATCGTTAACTTCGTTAAAAAACACGAGACTAAATTATATATTTAGTCACTCAATTATTCTTATGG
29596 TTCTGTTTTGAT
66 TTCTGTTTTGAT
29608 ATCGTTAACTTCGTTAAAAAACACGAGACTAAATTATATATTTAGTCACTCAATTATTCTTATGG
1 ATCGTTAACTTCGTTAAAAAACACGAGACTAAATTATATATTTAGTCACTCAATTATTCTTATGG
29673 TTCTGTTTTGAT
66 TTCTGTTTTGAT
29685 A
1 A
29686 ATCTAATTAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (77 bp):
ATCGTTAACTTCGTTAAAAAACACGAGACTAAATTATATATTTAGTCACTCAATTATTCTTATGG
TTCTGTTTTGAT
Found at i:32588 original size:41 final size:38
Alignment explanation
Indices: 32540--32657 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 38
32530 TTTATTTTTC
32540 AAACGCCACTATAGTACAAACTATTACGGCATTTTTAAAT
1 AAACGCCACTA-AGTACAAACTATTACGGCATTTTT-AAT
* * * **
32580 AACACGCCACTAACGTTCTAAACTATTATGGCGTTTTTTTT
1 AA-ACGCCACTAA-GTAC-AAACTATTACGGCATTTTTAAT
* *
32621 AAATGCCACGAAAGTATCAAACTATTACGGCATTTTT
1 AAACGCCAC-TAAGTA-CAAACTATTACGGCATTTTT
32658 CCAACAATGA
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
40 28 0.44
41 18 0.29
42 17 0.27
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (38 bp):
AAACGCCACTAAGTACAAACTATTACGGCATTTTTAAT
Found at i:32854 original size:12 final size:12
Alignment explanation
Indices: 32824--32856 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
32814 TTTTGCATGT
*
32824 AAAACGCCGCTA
1 AAAACGTCGCTA
32836 AAAACGTCGCTA
1 AAAACGTCGCTA
32848 AAAACGTCG
1 AAAACGTCG
32857 ATACTAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.27, G:0.18, T:0.12
Consensus pattern (12 bp):
AAAACGTCGCTA
Found at i:51029 original size:32 final size:32
Alignment explanation
Indices: 50978--51043 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 32
50968 TCCCTTCAAA
50978 TATACTTTTTTTATAAAAAAAGTTATTTTAAAT
1 TATACTTTTTTTATAAAAAAAGTTA-TTTAAAT
51011 TATACTTTTTTTATAAAAAAAGTTATTTAAAT
1 TATACTTTTTTTATAAAAAAAGTTATTTAAAT
51043 T
1 T
51044 GATCTCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.24
33 25 0.76
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (32 bp):
TATACTTTTTTTATAAAAAAAGTTATTTAAAT
Found at i:52340 original size:43 final size:43
Alignment explanation
Indices: 52291--52599 Score: 247
Period size: 43 Copynumber: 7.2 Consensus size: 43
52281 TGTGATATAA
* * *
52291 AAACGCCACAAAAAGTCAAGATCTATAGTGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAAC
** * **
52334 AAACGCCGCAATCGGTCGAGATCTATAGCGGCGTTTTTTTATAC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGA-AC
* * * *
52378 AAACGCCACAAAATGTCAAGTTCTCTAGCGGCGTTTTTGGCAA-
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGG-AAC
* * * *
52421 AAGCACCGCAAAAGGGT--AGATATATAGCGGCGTTGTTGGATAC
1 AAACGCCGCAAAA-GGTCAAGATCTATAGCGGCGTTTTTGGA-AC
*
52464 AAACGCCGCAAAAGGTCAAGATCTATAGCGG-GTTTTTGGAAAAA
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGG--AAC
* ** * *
52508 AAACGTCGCAAAAGGT-TTGATATATAACGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGA-AC
* * * *
52551 AAACACTGCAAATA--TC-AGATCTATAACGGCGTTTTTGGATAT
1 AAACGCCGCAAA-AGGTCAAGATCTATAGCGGCGTTTTTGGA-AC
52593 AAACGCC
1 AAACGCC
52600 ACTAATTACC
Statistics
Matches: 208, Mismatches: 45, Indels: 27
0.74 0.16 0.10
Matches are distributed among these distances:
41 1 0.00
42 51 0.25
43 81 0.39
44 73 0.35
45 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAAC
Found at i:52547 original size:87 final size:86
Alignment explanation
Indices: 52273--52589 Score: 286
Period size: 87 Copynumber: 3.7 Consensus size: 86
52263 GCTAATGTTG
* * * * *
52273 GCGGCGTTTGTGATATAAAAACGCCACAAAAAGTCAAGATCTATAGTGGCGTTTTTGG--AACAA
1 GCGGCGTTTTTG-GATACAAACGCCAC-AAAAGTCAAGATCTATAGCGGCGTTTTTGGAAAAAAA
** * *
52336 ACGCCGCAATCGGTCGAGATCTATA
64 ACG-CGCAAAAGGT-TAGATATATA
** * * * **
52361 GCGGCGTTTTTTTATACAAACGCCACAAAATGTCAAGTTCTCTAGCGGCGTTTTTGGCAAAAGCA
1 GCGGCGTTTTTGGATACAAACGCCACAAAA-GTCAAGATCTATAGCGGCGTTTTTGGAAAAAAAA
*
52426 C-CGCAAAAGGGTAGATATATA
65 CGCGCAAAAGGTTAGATATATA
* *
52447 GCGGCGTTGTTGGATACAAACGCCGCAAAAGGTCAAGATCTATAGCGG-GTTTTTGGAAAAAAAA
1 GCGGCGTTTTTGGATACAAACGCCACAAAA-GTCAAGATCTATAGCGGCGTTTTTGGAAAAAAAA
*
52511 CGTCGCAAAAGGTTTGATATATA
65 CG-CGCAAAAGGTTAGATATATA
* * * ** *
52534 ACGGCGTTTTTGGACACAAACACTGCAAATA-TC-AGATCTATAACGGCGTTTTTGGA
1 GCGGCGTTTTTGGATACAAACGCCACAAA-AGTCAAGATCTATAGCGGCGTTTTTGGA
52590 TATAAACGCC
Statistics
Matches: 190, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
85 26 0.14
86 64 0.34
87 85 0.45
88 11 0.06
89 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (86 bp):
GCGGCGTTTTTGGATACAAACGCCACAAAAGTCAAGATCTATAGCGGCGTTTTTGGAAAAAAAAC
GCGCAAAAGGTTAGATATATA
Found at i:61530 original size:2 final size:2
Alignment explanation
Indices: 61523--61562 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
61513 AGAATTAGTA
61523 AT AT AT AT 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 AT AT AT AT
61563 CAATTTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62519 original size:15 final size:15
Alignment explanation
Indices: 62495--62531 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
62485 ATATTTAGTT
62495 GGGT-GGGCGGATGC
1 GGGTCGGGCGGATGC
62509 GGGTCGGGCGGATGC
1 GGGTCGGGCGGATGC
*
62524 GGGGCGGG
1 GGGTCGGG
62532 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.05, C:0.16, G:0.68, T:0.11
Consensus pattern (15 bp):
GGGTCGGGCGGATGC
Found at i:65084 original size:12 final size:12
Alignment explanation
Indices: 65069--65096 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
65059 TATAGTAAAA
65069 TTTATTATTATT
1 TTTATTATTATT
65081 TTTATTATTATT
1 TTTATTATTATT
65093 TTTA
1 TTTA
65097 AATTTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTATTATT
Found at i:65289 original size:14 final size:15
Alignment explanation
Indices: 65259--65295 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
65249 TTAAATTAGT
65259 TAAAA-ATTTAAAGA
1 TAAAATATTTAAAGA
*
65273 TAAATTATTTAAA-A
1 TAAAATATTTAAAGA
65287 TAAAATATT
1 TAAAATATT
65296 AATTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAAGA
Found at i:66346 original size:20 final size:20
Alignment explanation
Indices: 66314--66387 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
66304 TTTTCCCAAT
*
66314 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
* ** *
66334 TCGTAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
66355 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
66375 TCGCAACGCGAAT
1 TCGCAACGCGAAT
66388 TGGGAAAATC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:66357 original size:21 final size:21
Alignment explanation
Indices: 66331--66406 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
66321 GCGAATAAGT
*
66331 AAATCGTAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
66352 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
66372 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
66393 AAATCGCAATGCGA
1 AAATCGCAACGCGA
66407 TAATAAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:66359 original size:41 final size:41
Alignment explanation
Indices: 66314--66424 Score: 179
Period size: 41 Copynumber: 2.7 Consensus size: 41
66304 TTTTCCCAAT
*
66314 TCGCAATGCGAATAAGTAAATCGTAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
66355 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
66396 TCGCAATGCGATAATAA-AAAATCGCAACG
1 TCGCAATGCG--AATAAGTAAATCGCAACG
66425 AGATACTTAC
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 50 0.76
42 11 0.17
43 5 0.08
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:66442 original size:20 final size:20
Alignment explanation
Indices: 66417--66469 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
66407 TAATAAAAAA
* *
66417 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
66437 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
66457 TCGCAACGCGATA
1 TCGCAACGCGATA
66470 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:66685 original size:22 final size:22
Alignment explanation
Indices: 66657--66700 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
66647 CACTCTCTCA
66657 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
66679 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
66701 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:66989 original size:20 final size:20
Alignment explanation
Indices: 66964--67001 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
66954 CGATTCTCTC
66964 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
66984 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
67002 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:68341 original size:18 final size:18
Alignment explanation
Indices: 68320--68364 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
68310 TCCACTTCGG
*
68320 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
68338 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
68356 GAGCCATCA
1 GAGCCATCA
68365 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:68900 original size:19 final size:20
Alignment explanation
Indices: 68846--68912 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
68836 TAGTTTACTT
* *
68846 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
68866 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
68886 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
68905 TCGCAACG
1 TCGCAACG
68913 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:68920 original size:14 final size:14
Alignment explanation
Indices: 68901--68958 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
68891 ATGCGAAATG
*
68901 AAAATCGCAACGAC
1 AAAATCGCAACGAA
*
68915 AAAATCGCAATGCCAA
1 AAAATCGCAA--CGAA
68931 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
68947 AAAATCGCAACG
1 AAAATCGCAACG
68959 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:68943 original size:32 final size:33
Alignment explanation
Indices: 68885--68975 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
68875 GGAAATGGCT
*
68885 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
68918 ATCGCAATGCCAAATG-AAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
68950 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
68976 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.55
33 24 0.45
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:69011 original size:14 final size:14
Alignment explanation
Indices: 68992--69082 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
68982 TTGTGTTTCG
68992 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
69006 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
69022 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
69038 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
69055 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
69071 CGTTGCGATTTT
1 CGTTGCGATTTT
69083 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 31 0.48
15 3 0.05
16 6 0.09
17 2 0.03
18 14 0.22
19 8 0.12
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:69021 original size:19 final size:18
Alignment explanation
Indices: 68987--69139 Score: 114
Period size: 19 Copynumber: 8.9 Consensus size: 18
68977 GCGATTTGTG
68987 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
69003 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
69019 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
69035 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
69052 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
69068 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
* **
69085 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
*
69104 TTTCTGCGTTGCGATAGTCA
1 TTTC-GCGTTGCGAT-TTCA
69124 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
69140 TAAGTTTCAT
Statistics
Matches: 109, Mismatches: 12, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
14 27 0.25
15 6 0.06
16 8 0.07
17 4 0.04
18 16 0.15
19 31 0.28
20 17 0.16
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:69056 original size:33 final size:33
Alignment explanation
Indices: 68987--69140 Score: 211
Period size: 33 Copynumber: 4.5 Consensus size: 33
68977 GCGATTTGTG
68987 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
69019 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
69052 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
* * **
69085 TTTCGCATTGCGATAGCCATTTCTGCGTTGCGATAGTCA
1 TTTCGCGTTGCGAT-----TTTGT-CGTTGCGATTTTCA
69124 TTTCGCGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
69141 AAGTTTCATG
Statistics
Matches: 110, Mismatches: 5, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
32 27 0.25
33 51 0.46
34 3 0.03
38 4 0.04
39 25 0.23
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:69117 original size:20 final size:19
Alignment explanation
Indices: 69083--69137 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
69073 TTGCGATTTT
*
69083 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
69102 CATTTCTGCGTTGCGATAGT
1 CATTTC-GCGTTGCGATAGC
69122 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
69138 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:71027 original size:13 final size:13
Alignment explanation
Indices: 70992--71043 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
70982 TTGATTGTTT
70992 AATTGATTTGTAA
1 AATTGATTTGTAA
*
71005 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
* **
71019 TATTGATTTGTTT
1 AATTGATTTGTAA
*
71032 AATTGATGTGTA
1 AATTGATTTGTA
71044 CATAATTTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:71235 original size:20 final size:20
Alignment explanation
Indices: 71178--71235 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
71168 TCGCATTGCG
* *
71178 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
71198 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
71218 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
71236 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:72109 original size:20 final size:20
Alignment explanation
Indices: 72084--72177 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
72074 GATTATGTAT
72084 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
72104 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
72124 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
72145 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
72165 TATCGCATTGCGA
1 TATCGCGTTGCGA
72178 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:72178 original size:20 final size:20
Alignment explanation
Indices: 72064--72178 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
72054 CGCTTTGAAA
*
72064 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
72085 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
72105 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
72125 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
72146 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
72166 ATCGCATTGCGAT
1 ATCGCATTGCGAT
72179 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:72196 original size:21 final size:21
Alignment explanation
Indices: 72167--72259 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
72157 ATAGTCAGTA
72167 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
72188 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
72208 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
72229 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
72249 TCGCATTGCGA
1 TCGCATTGCGA
72260 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:72197 original size:41 final size:41
Alignment explanation
Indices: 72106--72240 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
72096 AAAGTCAGTA
* * * ** *
72106 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
72146 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
72188 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
72229 TCGCGTTGCGAT
1 TCGCGTTGCGAT
72241 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:72241 original size:41 final size:41
Alignment explanation
Indices: 72167--72259 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
72157 ATAGTCAGTA
72167 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
72208 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
72249 TCGCATTGCGA
1 TCGCATTGCGA
72260 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:76528 original size:30 final size:30
Alignment explanation
Indices: 76494--76552 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
76484 AGGGTGAATT
* *
76494 ATATG-TTTAGTATTTAAATTATTAGTTTTA
1 ATATGTTTTAGTACTTAAATT-TTAATTTTA
76524 ATATGTTTTAGTACTTAAATTTTAATTTT
1 ATATGTTTTAGTACTTAAATTTTAATTTT
76553 TTTAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (30 bp):
ATATGTTTTAGTACTTAAATTTTAATTTTA
Found at i:86993 original size:15 final size:15
Alignment explanation
Indices: 86973--87002 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
86963 GAGTCGAAGT
86973 TTGAAGTAGAGGCAA
1 TTGAAGTAGAGGCAA
86988 TTGAAGTAGAGGCAA
1 TTGAAGTAGAGGCAA
87003 ATGAGTTAGG
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:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (15 bp):
TTGAAGTAGAGGCAA
Found at i:93056 original size:21 final size:21
Alignment explanation
Indices: 93030--93071 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
93020 ATTCGAATCC
93030 CAGCATCTGTAACTCTTTTCT
1 CAGCATCTGTAACTCTTTTCT
93051 CAGCATCTGTAACTCTTTTCT
1 CAGCATCTGTAACTCTTTTCT
93072 TTACAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.43
Consensus pattern (21 bp):
CAGCATCTGTAACTCTTTTCT
Done.