Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004562.1 Hibiscus syriacus cultivar Beakdansim tig00010139_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: 81706
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2407 original size:26 final size:26
Alignment explanation
Indices: 2378--2455 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
2368 TAATGCACCG
2378 TTATGCATTTTCATTTGTTGCACCTT
1 TTATGCATTTTCATTTGTTGCACCTT
** *
2404 TTATGC-----CGA-TAAT-GCACCGT
1 TTATGCATTTTC-ATTTGTTGCACCTT
2424 TTATGCATTTTCATTTGTTGCACCTT
1 TTATGCATTTTCATTTGTTGCACCTT
2450 TTATGC
1 TTATGC
2456 TGATAATTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
20 12 0.32
21 3 0.08
22 1 0.03
24 1 0.03
25 3 0.08
26 18 0.47
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.47
Consensus pattern (26 bp):
TTATGCATTTTCATTTGTTGCACCTT
Found at i:2437 original size:46 final size:44
Alignment explanation
Indices: 2223--2499 Score: 330
Period size: 43 Copynumber: 6.3 Consensus size: 44
2213 ACCATGAGTG
* *
2223 GCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATTAGT
1 GCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTGT
* * * * *
2267 GTACCATTTAT-CCGATATTGCACTGTTATGCATTTTCATTAGT
1 GCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTGT
*
2310 G-ACCCTTTTAT-CCGATAATGCACCGTTATGCATTTTTTATTTGT
1 GCA-CCTTTTATGCCGATAATGCACCGTTATGCA-TTTTCATTTGT
* *
2354 GCACATTTTAT--TGATAATGCACCGTTATGCATTTTCATTTGTT
1 GCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTG-T
2397 GCACCTTTTATGCCGATAATGCACCGTTTATGCATTTTCATTTGTT
1 GCACCTTTTATGCCGATAATGCACCG-TTATGCATTTTCATTTG-T
* * * * *
2443 GCACCTTTTATGCTGATAATTCACCGTTATACATTTTCGTTTAT
1 GCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTGT
2487 GGCACCTTTTATG
1 -GCACCTTTTATG
2500 TCTATTCATA
Statistics
Matches: 205, Mismatches: 20, Indels: 15
0.85 0.08 0.06
Matches are distributed among these distances:
42 10 0.05
43 86 0.42
44 27 0.13
45 39 0.19
46 43 0.21
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (44 bp):
GCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTGT
Found at i:8623 original size:22 final size:22
Alignment explanation
Indices: 8594--8645 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
8584 ACATGTATGT
8594 GAAGTTGGTTTGCAAGG-CAT-A
1 GAAGTTGGTTTGC-AGGCCATGA
8615 GTAAGTTGGTTTGCAGGCCATGA
1 G-AAGTTGGTTTGCAGGCCATGA
8638 GAAGTTGG
1 GAAGTTGG
8646 AATTCTTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.14
22 22 0.79
23 2 0.07
ACGTcount: A:0.25, C:0.10, G:0.37, T:0.29
Consensus pattern (22 bp):
GAAGTTGGTTTGCAGGCCATGA
Found at i:8730 original size:41 final size:41
Alignment explanation
Indices: 8685--8786 Score: 145
Period size: 40 Copynumber: 2.5 Consensus size: 41
8675 AGGCATGTAA
* *
8685 AAAGCATGGAGAT-TTCACCAGGCTATGTTGAAGACTCATGG
1 AAAGCATGAAG-TCTTCACCAGGCCATGTTGAAGACTCATGG
* *
8726 AAAGCATGAAGTCATCACCA-GCCATGTTGAAGACTCGTGG
1 AAAGCATGAAGTCTTCACCAGGCCATGTTGAAGACTCATGG
8766 AAAGCATGAAGTCTTCACCAG
1 AAAGCATGAAGTCTTCACCAG
8787 CTCACTATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 38 0.70
41 16 0.30
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (41 bp):
AAAGCATGAAGTCTTCACCAGGCCATGTTGAAGACTCATGG
Found at i:8810 original size:41 final size:40
Alignment explanation
Indices: 8699--8811 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 40
8689 CATGGAGATT
* * * *
8699 TCACCAGGCTATGTTGAAGACTCATGGAAAGCATGAAGTCA
1 TCACCA-GCCATGATGAAGACTCGTAGAAAGCATGAAGTCA
* * *
8740 TCACCAGCCATGTTGAAGACTCGTGGAAAGCATGAAGTCT
1 TCACCAGCCATGATGAAGACTCGTAGAAAGCATGAAGTCA
8780 TCACCAGCTCACT-ATGAAGACGT-GTAGAAAGC
1 TCACCAGC-CA-TGATGAAGAC-TCGTAGAAAGC
8812 GTTGAGTCTT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
40 39 0.61
41 23 0.36
42 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (40 bp):
TCACCAGCCATGATGAAGACTCGTAGAAAGCATGAAGTCA
Found at i:10223 original size:26 final size:26
Alignment explanation
Indices: 10184--10252 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 26
10174 TGTTAAAATA
*
10184 ATATATTCAATTATATTATAATATATAT
1 ATATATTC-ATTATATTA-AAAATATAT
*
10212 ATATATTC-TTATTTTAAAAATATAT
1 ATATATTCATTATATTAAAAATATAT
* *
10237 ATAAATTAATTATATT
1 ATATATTCATTATATT
10253 TATTAATGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 14 0.40
26 13 0.37
28 8 0.23
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATATTCATTATATTAAAAATATAT
Found at i:11080 original size:367 final size:363
Alignment explanation
Indices: 9902--11354 Score: 2345
Period size: 367 Copynumber: 4.0 Consensus size: 363
9892 GTATCTTTGG
9902 TTATTAATGGTTTTGACCCCGACAAATGGAACGATC-GTGGTGGTGTTCTTGACCGAGAAAGGTA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGA-CGGTGGTGGTGTTCTTGACCGAGAAAGGTA
*
9966 ACATTTTGAATTATTTTTCTCTCA-ATTCTAAATCATTACGGTTTGGTTTTCCTTAAGTTATTTT
65 ACATTTTGAATTATTTTTCTCT-AGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTT
**
10030 TTGAATTTTTCACTTTAAA-ACATAATTACTCAAAATAATATTATTTATATATTTAATACCAATA
129 TCAAATTTTTCACTTTAAATA-ATAATTACTCAAAATAATATTATTTATATATTTAATACCAATA
*
10094 TATTATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAGTA
193 TATTATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATA
*
10159 TATAATATTTTCCAATGTTAAAATAATATATTCAATTATATTATAATATAT-ATA-TATATTCTT
258 TATAATATTTTCCAATGTTATAATAATATATTCAATTATATTATAATATATGATATTATATTCTT
*
10222 ATTTT-A-AA-A-AT-AT--A-TA-T--AAATTAATTATAT
323 ATTTTAACAATATATAATAAATTATTAAAAAATAATTATAT
* * *
10252 TTATTAATGGTTTTGACCTCGACAAATGGAACGACAGTAGTGGTGTTCTTGACCGAGAAAGGTAA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
*
10317 CATTTTGAATTATTTTTCTCTCGATTCTAAATCATTACGGTTTGA-TTTCCTTAAGTTATTTTTC
66 CATTTTGAATTATTTTTCTCTAGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTTC
** *
10381 AAATTTTTCACTTTAAAGCATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATAA
131 AAATTTTTCACTTTAAATAATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATAT
* *
10446 TATATTATTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAT
196 TATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAT
*
10511 AATA-TTTCCAATGTTATAATAATATATTTAATTATATTATAATATATGATATTATATTCTTATT
261 AATATTTTCCAATGTTATAATAATATATTCAATTATATTATAATATATGATATTATATTCTTATT
10575 TTAACAATATATAATAAATTATTAAAAAATTAATTATAT
326 TTAACAATATATAATAAATTATTAAAAAA-TAATTATAT
10614 TTATTAACT-GTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGT-
1 TTATTAA-TGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTA
* *
10677 ACAATTTTGAATTATTTTTCTCTCGATTCTAAATCATTATGGTTTGATTTTCCTTAAGTTATTTT
65 AC-ATTTTGAATTATTTTTCTCTAGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTT
**
10742 TTGAATTTTTCACTTTAAATAATAATTACTCAAAATAATATTATTTATATATTTAATACCAATAT
129 TCAAATTTTTCACTTTAAATAATAATTACTCAAAATAATATTATTTATATATTTAATACCAATAT
10807 ATTATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATAT
194 ATTATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATAT
*
10872 ATAATATTTTCCAATGTTATAATAATATATTCAATTATATTGTAATAATATATGATATTGTATTC
259 ATAATATTTTCCAATGTTATAATAATATATTCAATTATA-T-T-ATAATATATGATATTATATTC
* *
10937 TTATTTTAACAATATATAATAAACTCTTAAAAAAATAATTATAT
321 TTATTTTAACAATATATAATAAATTATT-AAAAAATAATTATAT
10981 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
* * * *
11046 CATTTTGAATTATTTTTCTCTAGAATCAAAATCATTATGGTGTGATTTTCCTTAAGTTATTTTTC
66 CATTTTGAATTATTTTTCTCTAGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTTC
* *
11111 AAAATTTTCATTTTAAAGT-ATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATA
131 AAATTTTTCACTTTAAA-TAATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATA
* *
11175 GTATTTTAGTATTATTTTAATAAATTAATTACTAAGATATAATTTTTAATCATTTTAATAATATA
195 TTATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATA
*
11240 TAATATTTTCCAATGTTATAATAATATATTAAATTATATTATAATAATATATGATATTATATTCT
260 TAATATTTTCCAATGTTATAATAATATATTCAATTATA-T-T-ATAATATATGATATTATATTCT
11305 TATTTTAACAATATATAATAAATTATTAAAAAATAATTATAT
322 TATTTTAACAATATATAATAAATTATTAAAAAATAATTATAT
11347 TTATTAAT
1 TTATTAAT
11355 TTCATAAAAT
Statistics
Matches: 1031, Mismatches: 44, Indels: 40
0.92 0.04 0.04
Matches are distributed among these distances:
348 41 0.04
349 149 0.14
350 117 0.11
351 1 0.00
352 2 0.00
353 1 0.00
354 2 0.00
355 2 0.00
357 1 0.00
358 2 0.00
359 1 0.00
361 5 0.00
362 110 0.11
363 147 0.14
364 31 0.03
365 1 0.00
366 25 0.02
367 384 0.37
368 9 0.01
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (363 bp):
TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
CATTTTGAATTATTTTTCTCTAGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTTC
AAATTTTTCACTTTAAATAATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATAT
TATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAT
AATATTTTCCAATGTTATAATAATATATTCAATTATATTATAATATATGATATTATATTCTTATT
TTAACAATATATAATAAATTATTAAAAAATAATTATAT
Found at i:11281 original size:23 final size:23
Alignment explanation
Indices: 11255--11302 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
11245 TTTTCCAATG
*
11255 TTATAATAATATATTAAATTATA
1 TTATAATAATATATGAAATTATA
*
11278 TTATAATAATATATGATATTATA
1 TTATAATAATATATGAAATTATA
11301 TT
1 TT
11303 CTTATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTATAATAATATATGAAATTATA
Found at i:39508 original size:18 final size:19
Alignment explanation
Indices: 39480--39536 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
39470 TCTTCTTATT
39480 TTTACTTTAATTATTTTTA
1 TTTACTTTAATTATTTTTA
* *
39499 TTTA-TTTAATCACTTTTA
1 TTTACTTTAATTATTTTTA
* *
39517 -TTATTTTAATATCTTTTTA
1 TTTACTTTAAT-TATTTTTA
39536 T
1 T
39537 CAAAATTCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 3 0.10
18 18 0.60
19 9 0.30
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTACTTTAATTATTTTTA
Found at i:42999 original size:24 final size:24
Alignment explanation
Indices: 42972--43020 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 24
42962 CTAACGAGTT
42972 TCCACGCCACCCGCTCCTCTCTAC
1 TCCACGCCACCCGCTCCTCTCTAC
42996 T-----CCACCCGCTCCTCTCTAC
1 TCCACGCCACCCGCTCCTCTCTAC
43015 TCCACG
1 TCCACG
43021 ACGGTGTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 10
0.67 0.00 0.33
Matches are distributed among these distances:
19 19 0.95
24 1 0.05
ACGTcount: A:0.12, C:0.57, G:0.08, T:0.22
Consensus pattern (24 bp):
TCCACGCCACCCGCTCCTCTCTAC
Found at i:43002 original size:19 final size:19
Alignment explanation
Indices: 42978--43019 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
42968 AGTTTCCACG
42978 CCACCCGCTCCTCTCTACT
1 CCACCCGCTCCTCTCTACT
42997 CCACCCGCTCCTCTCTACT
1 CCACCCGCTCCTCTCTACT
43016 CCAC
1 CCAC
43020 GACGGTGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.12, C:0.60, G:0.05, T:0.24
Consensus pattern (19 bp):
CCACCCGCTCCTCTCTACT
Found at i:53316 original size:5 final size:6
Alignment explanation
Indices: 53303--53329 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53293 TTTAATTTAA
53303 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
53330 GCAGGAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:56375 original size:18 final size:19
Alignment explanation
Indices: 56347--56403 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
56337 TCTTCTTATT
56347 TTTACTTTAATTATTTTTA
1 TTTACTTTAATTATTTTTA
* *
56366 TTTA-TTTAATCACTTTTA
1 TTTACTTTAATTATTTTTA
* *
56384 -TTATTTTAATATCTTTTTA
1 TTTACTTTAAT-TATTTTTA
56403 T
1 T
56404 CAAAATTCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 3 0.10
18 18 0.60
19 9 0.30
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTACTTTAATTATTTTTA
Found at i:57887 original size:12 final size:12
Alignment explanation
Indices: 57870--57915 Score: 92
Period size: 12 Copynumber: 3.8 Consensus size: 12
57860 CAATCAGATG
57870 AGCCATATTTTT
1 AGCCATATTTTT
57882 AGCCATATTTTT
1 AGCCATATTTTT
57894 AGCCATATTTTT
1 AGCCATATTTTT
57906 AGCCATATTT
1 AGCCATATTT
57916 CAATTGCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (12 bp):
AGCCATATTTTT
Found at i:61777 original size:15 final size:17
Alignment explanation
Indices: 61748--61780 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
61738 TATTTTTATC
61748 TTTACTTTTTGTTTCAT
1 TTTACTTTTTGTTTCAT
61765 TTTA-TTTTT-TTTCAT
1 TTTACTTTTTGTTTCAT
61780 T
1 T
61781 CAAGCATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTACTTTTTGTTTCAT
Found at i:61812 original size:5 final size:6
Alignment explanation
Indices: 61799--61825 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
61789 TTTAATTTAA
61799 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
61826 GCAGGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:66039 original size:31 final size:31
Alignment explanation
Indices: 65938--66040 Score: 78
Period size: 31 Copynumber: 3.4 Consensus size: 31
65928 TGTACGTAGG
*
65938 TAAATTAA-TTT-ATATTATTATT-T-TTGTT
1 TAAATTAAGTTTAAT-TTTTTATTGTATTGTT
*
65966 TAAATTTAG-TTAGATTATTTT-TTGTATTGATT
1 TAAATTAAGTTTA-ATT-TTTTATTGTATTG-TT
*
65998 T--GTTATAGTTTAATTTTTTATTGTATTGTT
1 TAAATTA-AGTTTAATTTTTTATTGTATTGTT
66028 TAAATTAAGTTTA
1 TAAATTAAGTTTA
66041 GTTTGTTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 21
0.69 0.06 0.25
Matches are distributed among these distances:
28 9 0.16
29 3 0.05
30 15 0.26
31 22 0.38
32 9 0.16
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (31 bp):
TAAATTAAGTTTAATTTTTTATTGTATTGTT
Found at i:66061 original size:14 final size:14
Alignment explanation
Indices: 66042--66071 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
66032 TTAAGTTTAG
*
66042 TTTGTTTTATTTTT
1 TTTGTTTAATTTTT
66056 TTTGTTTAATTTTT
1 TTTGTTTAATTTTT
66070 TT
1 TT
66072 ACTTTATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTGTTTAATTTTT
Found at i:66108 original size:11 final size:10
Alignment explanation
Indices: 66086--66126 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
66076 TATTGTTTAA
*
66086 ATTAATTTAT
1 ATTAAATTAT
66096 ATTAAACTTAT
1 ATTAAA-TTAT
66107 ATTAAATTAT
1 ATTAAATTAT
*
66117 ATTAAGTTAT
1 ATTAAATTAT
66127 TGTTTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (10 bp):
ATTAAATTAT
Found at i:68395 original size:31 final size:31
Alignment explanation
Indices: 68357--68432 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
68347 ATTATAGTTG
*
68357 AAATAATATTTACAAAC-ACTCGTTCAAATAA
1 AAATAATATTTACAAACAAC-CATTCAAATAA
*
68388 AAATAATATTTACAAACAACCATTCAAATAT
1 AAATAATATTTACAAACAACCATTCAAATAA
**
68419 AAATAGGATTTACA
1 AAATAATATTTACA
68433 TTATAGAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.29
Consensus pattern (31 bp):
AAATAATATTTACAAACAACCATTCAAATAA
Found at i:68529 original size:27 final size:27
Alignment explanation
Indices: 68499--68565 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
68489 GAGTTTACTA
* * **
68499 ACATTAATTCAAATGTAGATATTTATC
1 ACATTCATTCAAATATAGATATCCATC
*
68526 ACATTCATTAAAATATAGATATCCATC
1 ACATTCATTCAAATATAGATATCCATC
68553 ACATTCATTCAAA
1 ACATTCATTCAAA
68566 AAAAATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.36
Consensus pattern (27 bp):
ACATTCATTCAAATATAGATATCCATC
Found at i:72584 original size:45 final size:45
Alignment explanation
Indices: 72525--72810 Score: 351
Period size: 45 Copynumber: 6.4 Consensus size: 45
72515 GAATACCATG
72525 AGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATT
* * * * *
72570 AGTGGTACCATTTAT-TTCGATATTGCACTGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCT-GATAATGCACCGTTATGCATTTTCATT
* * * *
72615 AGTGACACCTTTTATCCCGATAATGCACCGTTATGCATTTTTATT
1 AGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATT
* * *
72660 TGTGGCACATTTTATGTTGATAATGCACCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATT
* * * *
72705 TGTTGCACCTTTTATGCCGATAATGCACCGTTATCCATTTTCATT
1 AGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATT
* * * * *
72750 TGTTGCACCTTTTATGCTGATAATTCACCGTTATACATTTTCGTTT
1 AGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTC-ATT
72796 A-TGGCACCTTTTATG
1 AGTGGCACCTTTTATG
72811 TCTATTCATA
Statistics
Matches: 207, Mismatches: 31, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
44 1 0.00
45 204 0.99
46 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (45 bp):
AGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATT
Found at i:75923 original size:20 final size:20
Alignment explanation
Indices: 75889--75963 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 20
75879 AGGCTCAATA
* * *
75889 GTATCGGTACCTCTACTATG
1 GTATCGATACTTCTACGATG
75909 GTATCGATACTTCTATACGATG
1 GTATCGATACTTC--TACGATG
*
75931 GTACCGATACTTCTATACGATG
1 GTATCGATACTTC--TACGATG
*
75953 GTACCGATACT
1 GTATCGATACT
75964 CTCTTTCAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.22
22 38 0.78
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACTTCTACGATG
Found at i:75938 original size:22 final size:22
Alignment explanation
Indices: 75906--75963 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
75896 TACCTCTACT
*
75906 ATGGTATCGATACTTCTATACG
1 ATGGTACCGATACTTCTATACG
75928 ATGGTACCGATACTTCTATACG
1 ATGGTACCGATACTTCTATACG
75950 ATGGTACCGATACT
1 ATGGTACCGATACT
75964 CTCTTTCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (22 bp):
ATGGTACCGATACTTCTATACG
Found at i:76032 original size:21 final size:20
Alignment explanation
Indices: 76006--76074 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 20
75996 AGAATCCGTG
76006 GTATCGATACTAATTGCACCA
1 GTATCGATACTAATT-CACCA
** **
76027 GTATCGATACCCA-T-AGGA
1 GTATCGATACTAATTCACCA
*
76045 GTATCGATACTAATTACACTA
1 GTATCGATACTAATT-CACCA
76066 GTATCGATA
1 GTATCGATA
76075 TTGTTCATCG
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
18 13 0.35
19 1 0.03
20 1 0.03
21 22 0.59
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (20 bp):
GTATCGATACTAATTCACCA
Found at i:79199 original size:22 final size:22
Alignment explanation
Indices: 79170--79221 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
79160 ACATGTATGT
79170 GAAGTTGGTTTGCAAGG-CAT-A
1 GAAGTTGGTTTGC-AGGCCATGA
79191 GTAAGTTGGTTTGCAGGCCATGA
1 G-AAGTTGGTTTGCAGGCCATGA
79214 GAAGTTGG
1 GAAGTTGG
79222 AATTCTTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.14
22 22 0.79
23 2 0.07
ACGTcount: A:0.25, C:0.10, G:0.37, T:0.29
Consensus pattern (22 bp):
GAAGTTGGTTTGCAGGCCATGA
Found at i:79306 original size:41 final size:41
Alignment explanation
Indices: 79261--79362 Score: 145
Period size: 40 Copynumber: 2.5 Consensus size: 41
79251 AGGCATGTAA
* *
79261 AAAGCATGGAGAT-TTCACCAGGCTATGTTGAAGACTCATGG
1 AAAGCATGAAG-TCTTCACCAGGCCATGTTGAAGACTCATGG
* *
79302 AAAGCATGAAGTCATCACCA-GCCATGTTGAAGACTCGTGG
1 AAAGCATGAAGTCTTCACCAGGCCATGTTGAAGACTCATGG
79342 AAAGCATGAAGTCTTCACCAG
1 AAAGCATGAAGTCTTCACCAG
79363 CTCACTATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 38 0.70
41 16 0.30
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (41 bp):
AAAGCATGAAGTCTTCACCAGGCCATGTTGAAGACTCATGG
Found at i:79386 original size:41 final size:40
Alignment explanation
Indices: 79275--79387 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 40
79265 CATGGAGATT
* * * *
79275 TCACCAGGCTATGTTGAAGACTCATGGAAAGCATGAAGTCA
1 TCACCA-GCCATGATGAAGACTCGTAGAAAGCATGAAGTCA
* * *
79316 TCACCAGCCATGTTGAAGACTCGTGGAAAGCATGAAGTCT
1 TCACCAGCCATGATGAAGACTCGTAGAAAGCATGAAGTCA
79356 TCACCAGCTCACT-ATGAAGACGT-GTAGAAAGC
1 TCACCAGC-CA-TGATGAAGAC-TCGTAGAAAGC
79388 GTTGAGTCTT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
40 39 0.61
41 23 0.36
42 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (40 bp):
TCACCAGCCATGATGAAGACTCGTAGAAAGCATGAAGTCA
Found at i:81555 original size:349 final size:352
Alignment explanation
Indices: 80542--81706 Score: 1654
Period size: 349 Copynumber: 3.3 Consensus size: 352
80532 GGTATCTTGG
80542 TTATTAATGGTTTTGACCCCGA-AAATGGAACGATC-GTGGTGGTGTTTCTTGACCGAGAAAGGT
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGA-CGGTGGTGGTG-TTCTTGACCGAGAAAGGT
*
80605 AACA-TTTGAATTATTTTTCTCA-ATTCTAAATCATTACGGTTTG-GTTTCCTTAAGTTATTTTT
64 AACATTTTGAATTATTTTTCTCAGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTT
*
80667 TGAATTTTTCACTTTAAAACATATTACTCAAATAATATTATTTATATATTTAATACCAATATATT
129 TGAATTTTTCACTTTAAAATA-ATTACTCAAATAATATTATTTATATATTTAATACCAATATATT
*
80732 ATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAGTATAAT
193 ATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAAT
* * **
80797 ATTTTCCAATGT-TAA-AATA-ATTCAATTATATTATAATAATATATGATATT-ATATTCTTATT
258 ATTTTCCAATTTATAATAATATATTCAATTATATTATAATAATATATGATATTCTTATT-TTAAC
** * *
80858 TTTA-AAAATATA-TAATAAATTAATTATAT
322 AATATATAATATATTAAAAAATTAATTATAT
* * *
80887 TTATTAATGGTTTTGACCTCGACAAAT-GAACGACAGTAGTGGTGTTCTTGACCGAGAAAGGTAA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
* *
80951 C-TTTTGAATTATTTTTCTCTCGATTCTAAATC-TTACGGTTTGA-TTTCCTTAAGTTATTTTTC
66 CATTTTGAATTATTTTTCTC-AGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTTT
* *
81013 AAATTTTTCACTTTAAAGCATAATTACTCAAATAATATTATTTATATATTTAATACC-ATATAAT
130 GAATTTTTCACTTTAAA--ATAATTACTCAAATAATATTATTTATATATTTAATACCAATATATT
*
81077 ATATTAGTATTATTTT-ATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATATA
193 ATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATA-A
* *
81141 TATTTT-CAATGTTATAAT-ATAT-TTTAATTATATTATAATATATATATTATATTCTTATTTTA
257 TATTTTCCAAT-TTATAATAATATATTCAATTATATTATAATA-ATATATGATATTCTTATTTTA
81203 ACAATATATAATATTATTAAAAAATTAATTATAT
320 ACAATATATAATA-TATTAAAAAATTAATTATAT
81237 TTATTAACT-GTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGT-
1 TTATTAA-TGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTA
* *
81300 ACATTTTGAATTATTTTTCTCACGATTCTAAATCATTATGGTTTGATTTTCTTTAAGTTATTTTT
65 ACATTTTGAATTATTTTTCTCA-GATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTT
*
81365 TGAA-TTTTCACTTTAATATAATTACTCAAAT-ATATTA-TT-TATATTTAATACCAATAT-TTA
129 TGAATTTTTCACTTTAAAATAATTACTCAAATAATATTATTTATATATTTAATACCAATATATTA
81425 TTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTTAATCATTTTAATATATATAA
194 TTTTAGTATTATTTTAATAAATTAATTATTAAGATATAA-TTTTTAATCATTTTAATA-ATATAA
* *
81490 TATTTTCCAATTTATAATAATATATTCAA-T-TATTGTAATAATATATGATGTTTCTTATTTTAA
257 TATTTTCCAATTTATAATAATATATTCAATTATATTATAATAATATATGAT-ATTCTTATTTTAA
*
81553 CAATATATAATAAACTCTTAAAAAA-TAATTATA-
321 CAATATATAAT--A-TATTAAAAAATTAATTATAT
81586 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
* * * *
81651 CATTTTGAATTATTTTTCTCTAGAATCAAAATCATTATGGTGTGATTTTCCTTAAG
66 CATTTTGAATTATTTTTCTC-AGATTCTAAATCATTACGGTTTGATTTTCCTTAAG
Statistics
Matches: 743, Mismatches: 40, Indels: 69
0.87 0.05 0.08
Matches are distributed among these distances:
344 88 0.12
345 108 0.15
346 72 0.10
347 47 0.06
348 47 0.06
349 133 0.18
350 129 0.17
351 78 0.10
352 22 0.03
353 19 0.03
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (352 bp):
TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
CATTTTGAATTATTTTTCTCAGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTTTG
AATTTTTCACTTTAAAATAATTACTCAAATAATATTATTTATATATTTAATACCAATATATTATT
TTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAATATT
TTCCAATTTATAATAATATATTCAATTATATTATAATAATATATGATATTCTTATTTTAACAATA
TATAATATATTAAAAAATTAATTATAT
Done.