Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003724.1 Hibiscus syriacus cultivar Beakdansim tig00007965_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: 76672
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4936 original size:44 final size:44
Alignment explanation
Indices: 4850--4937 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
4840 TGAAGGAAAA
4850 TCAAATTATTAAGAAATGAACAATAAAGGGGGTCTAAAGGAATC
1 TCAAATTATTAAGAAATGAACAATAAAGGGGGTCTAAAGGAATC
**
4894 TCAAATTATTAAGAAATGAACAATAAAGGTTGTCTAAAGGAATC
1 TCAAATTATTAAGAAATGAACAATAAAGGGGGTCTAAAGGAATC
4938 AAACTAGGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (44 bp):
TCAAATTATTAAGAAATGAACAATAAAGGGGGTCTAAAGGAATC
Found at i:6374 original size:19 final size:19
Alignment explanation
Indices: 6350--6444 Score: 127
Period size: 19 Copynumber: 5.0 Consensus size: 19
6340 GAATCAGAAA
* *
6350 TTATTTCCAGATTCATAAC
1 TTATTTTCAGATTCATAGC
*
6369 TTATTTTCAGACTCATAGC
1 TTATTTTCAGATTCATAGC
*
6388 TTATTGTCAGATTCATAGC
1 TTATTTTCAGATTCATAGC
* *
6407 TTATTTTCAAATTCATATC
1 TTATTTTCAGATTCATAGC
*
6426 TTATTTTCAAATTCATAGC
1 TTATTTTCAGATTCATAGC
6445 CCAATTCATA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.45
Consensus pattern (19 bp):
TTATTTTCAGATTCATAGC
Found at i:7455 original size:690 final size:680
Alignment explanation
Indices: 6428--7803 Score: 1896
Period size: 690 Copynumber: 2.0 Consensus size: 680
6418 TTCATATCTT
* *
6428 ATTTTCAAATTCATAGCCCAATTCATATTTATGAGAATGCAATGTACGTGAGTAGAAACATAGGT
1 ATTTTCAAATTCATAGCCCAATACATATTTATGAGAATGCAACGTACGTGAGTAGAAACATAGGT
* *
6493 GCAGGGCACACCACAGTGCCAATCTTAACTGAAACATATAATGCATTCCAAGTGCAATCATAACA
66 GCAGGGCACACCACAGTGCCAATCTTAACTGAAACATATAATGCACTACAAGTGCAATCATAACA
* *
6558 TGAGTACCAACAATGCAGATCATAATGTACACAAATATACCTAAATTAACTGGAAAGTACTCAAT
131 TGAGTACCAACAATGCAGATCATAATGTA-ACAAATATACCTAAATTAACTGGAAAGCACTCAAC
** * * *
6623 TTAATGGCATGTCAAATGTACCTATGACTCTCAATACAACATACAATGGCTTTTCCATTAATTAT
195 TTAACAGCATGCCAAATGTACCTACGAATCTCAATACAACATACAATGGCTTTTCCATTAATTAT
*
6688 TATATTATTCAATTATCAAAGATATCAATATATCAACATATCCAACTATTCATATCATAACATAA
260 TATATTATTCAATTATCAAAGATATAAATATATCAACATATCCAACTATTCATATCATAACATAA
* * * * * * *
6753 TGGTAGTTCATACTCTAAACATTTCATTTCTATATAACA-TT-TATATCGTAATCACCGTCAGTT
325 TGGCACTTCATACCCTAAACATTTCATTTCCACATAACATTTATATATCATAATCACCGTCAATT
*
6816 ATCTTTCTTTAACATAT-AACATCATATTCATCATGTAATAAATATCATAACTATCATACCAATT
390 AT-ATTCTTTAACATATAAACATCATATTCATCATGTAATAAATATCAT-A--A-C-T----ATT
* *
6880 GTAATAAAGTTGACTTATTTTGAGCATTTATAATAACCTATAACATAGGAGCAACATGAAAACAT
445 GTAATAAAGTTGACTTATTTCGAGCATTTAAAATAACCTATAACATAGGAGCAACATGAAAACAT
* *
6945 AATTTATGACAAGTTTTATATGATGGCAATATGCACTACATGCAAAG-AA-ATATTCTGTATTAA
510 AATTTATGACAAGTTTTATATG-TGACAATATGCACTACATGCAAAGAAATATATTATGTATTAA
* * ** * * * * *
7008 TCTATACACTTAAAAATTATTATGTTTATACCACTAGAAATTATACTCAAAT-TGAATCTAACTA
574 TATACACACTTAAAAATTATTACATTTAT-CCAATAGAAACTAGACTCAAATAAGAATCTAACCA
* * *
7072 TATAAGGAA-CTTTTCCTGGTTCATCATATAC-ATTTATAGTGA
638 TATAAAGAACCTTTT-CTAGTTAATCATATACAATTTATAGTGA
* * * *
7114 ATTTTCGAATTCATAGGCCAATACATATTTATGGGAATGCAACGTATGTGAGTAG-AACATAAGG
1 ATTTTCAAATTCATAGCCCAATACATATTTATGAGAATGCAACGTACGTGAGTAGAAACAT-AGG
* **
7178 TGCCCACAGGGCACATCATGGTGCCAATCTTAACTGAAACATATAATGCACTACAAGTGCAATCA
65 TG----CAGGGCACACCACAGTGCCAATCTTAACTGAAACATATAATGCACTACAAGTGCAATCA
** * *
7243 TAACATGAGCT-CCAATGATGCAGATCATAATGT-ACGAATGTA-CTATAACTTAACTGGAAAGC
126 TAACATGAG-TACCAACAATGCAGATCATAATGTAACAAATATACCTA-AA-TTAACTGGAAAGC
* * *
7305 ACTCAACTTAACAGCATGCCAAATGTACCTACGAATCTCAATGCAATATACAATGGATTTTTCCA
188 ACTCAACTTAACAGCATGCCAAATGTACCTACGAATCTCAATACAACATACAATGG-CTTTTCCA
*
7370 TTAATTATTATATTATTCAATTATCAAA-ATATAAATATATCAACATATCCAACTCTTCATATCA
252 TTAATTATTATATTATTCAATTATCAAAGATATAAATATATCAACATATCCAACTATTCATATCA
7434 TAACATAATGGGCACTTCATACCCTAAACATTTCATTTCCACATAACATTTATATATCATAATCA
317 TAACATAAT-GGCACTTCATACCCTAAACATTTCATTTCCACATAACATTTATATATCATAATCA
*
7499 TCGTCAATTATATTCTTTAACATATAAACATCATATTCATCATGTAATAAATATCATAACTATTG
381 CCGTCAATTATATTCTTTAACATATAAACATCATATTCATCATGTAATAAATATCATAACTATTG
* * *
7564 TAATAAATTTGACTTATTTCGAGCATTTAAAATAACCTATAACATAGGAGTAATATGAAAACATA
446 TAATAAAGTTGACTTATTTCGAGCATTTAAAATAACCTATAACATAGGAGCAACATGAAAACATA
* *
7629 ATTTATGACAAGTTTTATATGTGACATTATGCACTACTTGCAAAGAAATATATTATGTATTAATA
511 ATTTATGACAAGTTTTATATGTGACAATATGCACTACATGCAAAGAAATATATTATGTATTAATA
* * *
7694 TACACACTTAAAAATTATTCCATTTATGCAATAGAAACTAGACTCGAATAAGAATCTAACCATAT
576 TACACACTTAAAAATTATTACATTTATCCAATAGAAACTAGACTCAAATAAGAATCTAACCATAT
*
7759 AAAGAACCTTTTCTAGTTAATCTTATACAATTTATAGTGA
641 AAAGAACCTTTTCTAGTTAATCATATACAATTTATAGTGA
7799 ATTTT
1 ATTTT
7804 TGAAGTTGAC
Statistics
Matches: 611, Mismatches: 61, Indels: 37
0.86 0.09 0.05
Matches are distributed among these distances:
682 21 0.03
683 104 0.17
684 68 0.11
685 26 0.04
686 54 0.09
687 4 0.01
688 10 0.02
689 104 0.17
690 151 0.25
691 17 0.03
692 52 0.09
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (680 bp):
ATTTTCAAATTCATAGCCCAATACATATTTATGAGAATGCAACGTACGTGAGTAGAAACATAGGT
GCAGGGCACACCACAGTGCCAATCTTAACTGAAACATATAATGCACTACAAGTGCAATCATAACA
TGAGTACCAACAATGCAGATCATAATGTAACAAATATACCTAAATTAACTGGAAAGCACTCAACT
TAACAGCATGCCAAATGTACCTACGAATCTCAATACAACATACAATGGCTTTTCCATTAATTATT
ATATTATTCAATTATCAAAGATATAAATATATCAACATATCCAACTATTCATATCATAACATAAT
GGCACTTCATACCCTAAACATTTCATTTCCACATAACATTTATATATCATAATCACCGTCAATTA
TATTCTTTAACATATAAACATCATATTCATCATGTAATAAATATCATAACTATTGTAATAAAGTT
GACTTATTTCGAGCATTTAAAATAACCTATAACATAGGAGCAACATGAAAACATAATTTATGACA
AGTTTTATATGTGACAATATGCACTACATGCAAAGAAATATATTATGTATTAATATACACACTTA
AAAATTATTACATTTATCCAATAGAAACTAGACTCAAATAAGAATCTAACCATATAAAGAACCTT
TTCTAGTTAATCATATACAATTTATAGTGA
Found at i:13561 original size:20 final size:21
Alignment explanation
Indices: 13531--13569 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
13521 CAGAACCCCA
*
13531 GGGGGGTATCGGTTCCCTCAT
1 GGGGGGTATCGATTCCCTCAT
13552 GGGGGG-ATCGATTCCCTC
1 GGGGGGTATCGATTCCCTC
13570 TGCACCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.10, C:0.26, G:0.38, T:0.26
Consensus pattern (21 bp):
GGGGGGTATCGATTCCCTCAT
Found at i:17400 original size:22 final size:21
Alignment explanation
Indices: 17358--17397 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17348 GAGTTTGTTT
*
17358 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
17379 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
17398 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:31909 original size:31 final size:32
Alignment explanation
Indices: 31864--31924 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
31854 ATCGGATTAA
** *
31864 TTGATTTTTGGATCAGATCAA-ATCGGATCGG
1 TTGATTTTCAGATCAGATCAATATCCGATCGG
*
31895 TTGATTTTCAGATCATATCAATATCCGATC
1 TTGATTTTCAGATCAGATCAATATCCGATC
31925 AATTAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (32 bp):
TTGATTTTCAGATCAGATCAATATCCGATCGG
Found at i:33982 original size:15 final size:16
Alignment explanation
Indices: 33953--34009 Score: 80
Period size: 17 Copynumber: 3.5 Consensus size: 16
33943 CCGTGTCCCG
33953 ACCCGGATGTTTCGGGT
1 ACCCGGAT-TTTCGGGT
33970 ACCCGG-TTTTCGGGT
1 ACCCGGATTTTCGGGT
*
33985 ACCTGGATTTTACGGGT
1 ACCCGGATTTT-CGGGT
34002 ACCCGGAT
1 ACCCGGAT
34010 ACCCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
15 13 0.36
16 5 0.14
17 18 0.50
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.30
Consensus pattern (16 bp):
ACCCGGATTTTCGGGT
Found at i:34314 original size:24 final size:24
Alignment explanation
Indices: 34258--34307 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
34248 TTGTTTACTT
* * *
34258 TAATTTAATATATAATATTATTAA
1 TAATTAAATATATAATAATATAAA
34282 TAATTAAATATATAATAATAGTAAA
1 TAATTAAATATATAATAATA-TAAA
34307 T
1 T
34308 CATAAATCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATTAAATATATAATAATATAAA
Found at i:35869 original size:17 final size:17
Alignment explanation
Indices: 35843--35878 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
35833 GTCATTCACC
35843 GTTAACATTTAACAAAA
1 GTTAACATTTAACAAAA
*
35860 GTTAATATTTAACAAAA
1 GTTAACATTTAACAAAA
35877 GT
1 GT
35879 GATGACGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (17 bp):
GTTAACATTTAACAAAA
Found at i:36261 original size:31 final size:31
Alignment explanation
Indices: 36214--36296 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 31
36204 TTAAATACAT
*
36214 TTTATTCTT-GTTTTAACTTAAAAAAATATAC
1 TTTATTCTTAG-TTTAACTTAAAAAAATATAA
36245 TTTAGTT-TTA-TCTTAACTT-AAAAAATATAA
1 TTTA-TTCTTAGT-TTAACTTAAAAAAATATAA
36275 TTTATTCTTAGTTTAACTTAAA
1 TTTATTCTTAGTTTAACTTAAA
36297 TATTTATATT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
29 2 0.04
30 25 0.56
31 16 0.36
32 2 0.04
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (31 bp):
TTTATTCTTAGTTTAACTTAAAAAAATATAA
Found at i:36369 original size:29 final size:29
Alignment explanation
Indices: 36332--36448 Score: 111
Period size: 29 Copynumber: 4.1 Consensus size: 29
36322 TAATATTATA
*
36332 AAAACAAGAATAAAATATATTTTAAAATT
1 AAAATAAGAATAAAATATATTTTAAAATT
* *
36361 AAAATAAGAAGAAAATATACATTTTAAAATG
1 AAAATAAGAATAAAATAT--ATTTTAAAATT
*
36392 AAAAT-A-AA-AAAATAT-TTTT--AGTT
1 AAAATAAGAATAAAATATATTTTAAAATT
* *
36415 AAAATAAGAATAAAATATATATTTTAAGTT
1 AAAATAAGAATAAAATATAT-TTTAAAATT
36445 AAAA
1 AAAA
36449 ATAAATTATA
Statistics
Matches: 74, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
23 7 0.09
24 1 0.01
25 6 0.08
26 7 0.09
27 1 0.01
28 10 0.14
29 18 0.24
30 9 0.12
31 15 0.20
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAATAAGAATAAAATATATTTTAAAATT
Found at i:36468 original size:54 final size:54
Alignment explanation
Indices: 36340--36468 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 54
36330 TAAAAACAAG
* *
36340 AATAAAATATATTTTAA-AATTAAAATAAGAAGAAAATATACATTTTAAAATGAA
1 AATAAAATATA-TTTAATAGTTAAAATAAGAAGAAAATATACATTTTAAAATAAA
* * * * **
36394 AATAAAAAAATATTT-TTAGTTAAAATAAGAATAAAATATATATTTTAAGTTAAA
1 AAT-AAAATATATTTAATAGTTAAAATAAGAAGAAAATATACATTTTAAAATAAA
*
36448 AATAAATTATATTTAATAGTT
1 AATAAAATATATTTAATAGTT
36469 TAACTTATTA
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
53 9 0.15
54 45 0.74
55 7 0.11
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.36
Consensus pattern (54 bp):
AATAAAATATATTTAATAGTTAAAATAAGAAGAAAATATACATTTTAAAATAAA
Found at i:42811 original size:2 final size:2
Alignment explanation
Indices: 42800--42832 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
42790 AACAAGATCC
42800 AT AT -T 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
42833 TCCAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:56087 original size:24 final size:25
Alignment explanation
Indices: 56047--56093 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
56037 AATCCTTGTA
*
56047 ACACGTTTTTCTTTGCTCTTGTGTC
1 ACACGTTTTTCTCTGCTCTTGTGTC
56072 ACAC-TTTTTCTCTGCTCTTGTG
1 ACACGTTTTTCTCTGCTCTTGTG
56094 GCACGTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.09, C:0.26, G:0.15, T:0.51
Consensus pattern (25 bp):
ACACGTTTTTCTCTGCTCTTGTGTC
Found at i:56878 original size:2 final size:2
Alignment explanation
Indices: 56873--56938 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
56863 CATTTTACTT
56873 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56915 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
56939 ACCTCAAATT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62249 original size:11 final size:11
Alignment explanation
Indices: 62233--62259 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
62223 ATTTCATATG
62233 CATAAGTACGA
1 CATAAGTACGA
62244 CATAAGTACGA
1 CATAAGTACGA
62255 CATAA
1 CATAA
62260 CTCTATATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.19
Consensus pattern (11 bp):
CATAAGTACGA
Found at i:63801 original size:14 final size:14
Alignment explanation
Indices: 63782--63810 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
63772 GACAAGGGTG
63782 TGATTAGTGTATAT
1 TGATTAGTGTATAT
63796 TGATTAGTGTATAT
1 TGATTAGTGTATAT
63810 T
1 T
63811 CCACGAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (14 bp):
TGATTAGTGTATAT
Found at i:68597 original size:20 final size:20
Alignment explanation
Indices: 68574--68641 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
68564 GTTTCCAATT
68574 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
** * * * **
68594 TCGCATTGTGATTTTCCAAA
1 TCGCAACGCGAATATGTAAA
*
68614 TTCACAACGCGAATATGTAAA
1 -TCGCAACGCGAATATGTAAA
68635 TCGCAAC
1 TCGCAAC
68642 ACATAAGTCA
Statistics
Matches: 31, Mismatches: 16, Indels: 2
0.63 0.33 0.04
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:68658 original size:20 final size:21
Alignment explanation
Indices: 68610--68794 Score: 122
Period size: 20 Copynumber: 9.2 Consensus size: 21
68600 TGTGATTTTC
* *
68610 CAAATTCACAACGCGAATATGT
1 CAAATTCGCAACGCG-ATAAGT
*
68632 -AAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGATAAGT
68650 CAAATTCGCAACGCGAT-AGT
1 CAAATTCGCAACGCGATAAGT
* * * *
68670 CAAATTCGTAACAC-AAAAAT
1 CAAATTCGCAACGCGATAAGT
* * * **
68690 AAAATTCGCAACTCAAATTTGT
1 CAAATTCGCAACGC-GATAAGT
* *
68712 -AAA-TCGCAACAC-AGAAGT
1 CAAATTCGCAACGCGATAAGT
68730 CAAATTCGCAACGCGAT-AGT
1 CAAATTCGCAACGCGATAAGT
* *
68750 CACATTCGTAACGCGAT-AGT
1 CAAATTCGCAACGCGATAAGT
*
68770 CAAATTTGCAACGCGA-AAGT
1 CAAATTCGCAACGCGATAAGT
68790 CAAAT
1 CAAAT
68795 GTTTTTACGC
Statistics
Matches: 127, Mismatches: 26, Indels: 22
0.73 0.15 0.13
Matches are distributed among these distances:
18 8 0.06
19 7 0.06
20 101 0.80
21 9 0.07
22 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (21 bp):
CAAATTCGCAACGCGATAAGT
Found at i:68665 original size:40 final size:40
Alignment explanation
Indices: 68610--68745 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 40
68600 TGTGATTTTC
* *
68610 CAAATTCACAACGCGAATATGTAAATCGCAACACATAAGT
1 CAAATTCGCAACGCGAATATGTAAATCGCAACACAAAAGT
* *
68650 CAAATTCGCAACGCG-ATA-GTCAAATTCGTAACACAAAAAT
1 CAAATTCGCAACGCGAATATGT-AAA-TCGCAACACAAAAGT
* * * * *
68690 AAAATTCGCAACTCAAATTTGTAAATCGCAACACAGAAGT
1 CAAATTCGCAACGCGAATATGTAAATCGCAACACAAAAGT
68730 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
68746 TAGTCACATT
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
38 2 0.03
39 6 0.08
40 63 0.81
41 5 0.06
42 2 0.03
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.20
Consensus pattern (40 bp):
CAAATTCGCAACGCGAATATGTAAATCGCAACACAAAAGT
Found at i:68781 original size:80 final size:80
Alignment explanation
Indices: 68611--68761 Score: 248
Period size: 80 Copynumber: 1.9 Consensus size: 80
68601 GTGATTTTCC
* * * * *
68611 AAATTCACAACGCGAATATGTAAATCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATT
1 AAATTCGCAACTCAAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATT
68676 CGTAACACAAAAATA
66 CGTAACACAAAAATA
*
68691 AAATTCGCAACTCAAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCACATT
1 AAATTCGCAACTCAAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATT
68756 CGTAAC
66 CGTAAC
68762 GCGATAGTCA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.21
Consensus pattern (80 bp):
AAATTCGCAACTCAAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATT
CGTAACACAAAAATA
Found at i:69326 original size:20 final size:19
Alignment explanation
Indices: 69291--69344 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
69281 AAATCGCAAC
69291 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
69310 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
69330 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
69345 AGAAACTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.27
20 18 0.60
21 4 0.13
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:71037 original size:21 final size:21
Alignment explanation
Indices: 71013--71062 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
71003 GTTAGGGGAA
*
71013 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTACT
*
71034 TTACGTCATGAGGTCGGTACT
1 TTACGTGATGAGGTCGGTACT
71055 TTACGTGA
1 TTACGTGA
71063 AGATAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTACT
Found at i:71294 original size:4 final size:4
Alignment explanation
Indices: 71285--71334 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
71275 TTTTTCGGCA
* * * *
71285 TTAT TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
71333 TT
1 TT
71335 TCAGCGGTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:73039 original size:61 final size:65
Alignment explanation
Indices: 72965--73087 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 65
72955 AAGTTGATTA
72965 TTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGTAAAAGTTGATTTGTTTAAT
1 TTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGTAAAAGTTGATTTGTTTAAT
* * * *
73026 TTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTGTAAAAGTTGATTTGTT
73088 GTTTCTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
61 14 0.26
62 1 0.02
63 1 0.02
64 6 0.11
66 31 0.58
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (65 bp):
TTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGTAAAAGTTGATTTGTTTAAT
Found at i:73196 original size:20 final size:20
Alignment explanation
Indices: 73171--73214 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
73161 AATAAGCGTT
73171 GCGAAAGTCAAATTCACAAC
1 GCGAAAGTCAAATTCACAAC
*
73191 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCACAAC
73211 GCGA
1 GCGA
73215 TTTTCGGTTT
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:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (20 bp):
GCGAAAGTCAAATTCACAAC
Found at i:73554 original size:18 final size:18
Alignment explanation
Indices: 73531--73566 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
73521 AAGCCGGTTG
*
73531 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
73549 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
73567 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:75996 original size:12 final size:12
Alignment explanation
Indices: 75975--76008 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
75965 GGTTGTGGGT
*
75975 TTTGAGATTGTG
1 TTTGATATTGTG
75987 TTTGATATTGTG
1 TTTGATATTGTG
*
75999 TTTGGTATTG
1 TTTGATATTG
76009 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Done.