Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001758.1 Hibiscus syriacus cultivar Beakdansim tig00003554_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: 55715
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:11384 original size:20 final size:18
Alignment explanation
Indices: 11359--11691 Score: 210
Period size: 19 Copynumber: 18.8 Consensus size: 18
11349 CGGGTTTCTG
11359 TTATATTATATTATGTCATA
1 TTATATTATATTAT-T-ATA
11379 TTATATGGTATA-TATTATAA
1 TTATAT--TATATTATTAT-A
*
11399 TTATAGTATA-TATTATA
1 TTATATTATATTATTATA
*
11416 -TATA-TATAATA-TATA
1 TTATATTATATTATTATA
*
11431 -TATATAATATATATTATA
1 TTATATTATAT-TATTATA
11449 TTATATATATATTATTATA
1 TTATAT-TATATTATTATA
11468 TATATATTATTATTATTATA
1 T-TATATTA-TATTATTATA
* *
11488 ATATAGTATA-TATT-TA
1 TTATATTATATTATTATA
*
11504 TTAT-TTATAGTATTTTATA
1 TTATATTATA-T-TATTATA
*
11523 TTATAGTATATTA-TATA
1 TTATATTATATTATTATA
11540 TTATATTATA-TA-TATA
1 TTATATTATATTATTATA
*
11556 TT-T-TTATATTATAATA
1 TTATATTATATTATTATA
11572 -TATA-TATA-TATATATA
1 TTATATTATATTAT-TATA
* *
11588 TATATATTATAGTAAATAATA
1 T-TATATTATA-T-TATTATA
11609 TTAT-TTATATTATTATA
1 TTATATTATATTATTATA
* *
11626 TATTTATTATA-TA-TACA
1 T-TATATTATATTATTATA
*
11643 TTATA-TATA-TATT-TC
1 TTATATTATATTATTATA
*
11658 TTATAATATATTATTTATA
1 TTATATTATATTA-TTATA
11677 TTATTATT-TATTATT
1 TTA-TATTATATTATT
11692 TTAGGTCCAA
Statistics
Matches: 253, Mismatches: 25, Indels: 72
0.72 0.07 0.21
Matches are distributed among these distances:
14 5 0.02
15 34 0.13
16 41 0.16
17 32 0.13
18 33 0.13
19 53 0.21
20 42 0.17
21 7 0.03
22 6 0.02
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (18 bp):
TTATATTATATTATTATA
Found at i:11431 original size:40 final size:38
Alignment explanation
Indices: 11387--11677 Score: 253
Period size: 38 Copynumber: 7.8 Consensus size: 38
11377 TATTATATGG
11387 TATATATTATAATTATAGTATATATTATATATATATAATA
1 TATATATTAT-ATTATA-TATATATTATATATATATAATA
* *
11427 TATATA-TATAATATATATTATATTATATATATATTAT-
1 TATATATTATATTATATA-TATATTATATATATATAATA
11464 TATATA-TATATTAT-TAT-TATTATA-ATATAGT-ATA
1 TATATATTATATTATATATATATTATATATATA-TAATA
*
11498 TATTTATTAT-TTATAGTAT-T-TTATAT-TATAGT-ATA
1 TATATATTATATTATA-TATATATTATATATATA-TAATA
*
11533 TTATATATTATATTATATATATATT-TTTATATTATAATA
1 -TATATATTATATTATATATATATTATATATA-TATAATA
11572 TATATA-TATATATATATATATATTATAGTA-A-ATAATA
1 TATATATTATAT-TATATATATATTATA-TATATATAATA
* *
11609 T-TAT-TTATATTATTATATATTTATTATATATACATTATA
1 TATATATTATATTA-TATATA--TATTATATATATATAATA
* *
11648 TATATATT-TCTTATA-ATATATTATTTATAT
1 TATATATTATATTATATATATATTATATATAT
11678 TATTATTTAT
Statistics
Matches: 215, Mismatches: 11, Indels: 54
0.77 0.04 0.19
Matches are distributed among these distances:
33 7 0.03
34 17 0.08
35 20 0.09
36 42 0.20
37 37 0.17
38 57 0.27
39 18 0.08
40 15 0.07
41 2 0.01
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (38 bp):
TATATATTATATTATATATATATTATATATATATAATA
Found at i:11553 original size:96 final size:91
Alignment explanation
Indices: 11359--11692 Score: 291
Period size: 90 Copynumber: 3.6 Consensus size: 91
11349 CGGGTTTCTG
*
11359 TTATAT-TATATTATGTCATATTATATGGTATATATTATAATTATAGTATATA-TTA-TA--TAT
1 TTATATATATATTATAT-ATATTATAT--TATATATTAT-A-TATAGTATATATTTATTATTTAT
* *
11419 ATATAATATA-TATATATAATATATATTATA
61 ATATATTATATTATATATATTATATATTATA
11449 TTATATATATATTAT-TATATATATATTATTATTATTATAATATAGTATATATTTATTATTTATA
1 TTATATATATATTATATATAT-TATATTA-TA-TATTAT-ATATAGTATATATTTATTATTTATA
*
11513 GTATTTTATATTATAGTATATTATATATTATA
62 -TATATTATATTATA-TATATTATATATTATA
* * * * *
11545 TTATATATATATT-TTTATATTATAATATATA-TATATATA-TATATATATATTATAGTAAATAA
1 TTATATATATATTATATATATTATATTATATATTATATATAGTATATATTTATTAT-TTATAT-A
11607 TATTAT-TTATAT-TATTATATATT-TA
64 TATTATATTATATATATTATATATTATA
* * * * *
11632 TTATATATACATTATATATATATTTCTTATAATATATTATTTATATTAT-TATTTATTATTT
1 TTATATATATA-T-TATATATA-TT-ATATTATATATTATATATAGTATATATTTATTATTT
11693 TAGGTCCAAA
Statistics
Matches: 207, Mismatches: 16, Indels: 40
0.79 0.06 0.15
Matches are distributed among these distances:
87 12 0.06
88 14 0.07
89 19 0.09
90 47 0.23
91 26 0.13
92 11 0.05
93 22 0.11
94 12 0.06
95 11 0.05
96 33 0.16
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (91 bp):
TTATATATATATTATATATATTATATTATATATTATATATAGTATATATTTATTATTTATATATA
TTATATTATATATATTATATATTATA
Found at i:11651 original size:76 final size:76
Alignment explanation
Indices: 11398--11687 Score: 274
Period size: 74 Copynumber: 4.0 Consensus size: 76
11388 ATATATTATA
* *
11398 ATTATAGTATATATTATATATATATAATATATATATATA-ATATATATTATATTATA-TATATAT
1 ATTATA-TATTTATTATATATATATAATATATATATATATATATATA-TATATTATAGTATATAA
*
11461 TATTATATATA-T
64 TATTATTTATATT
* * *
11473 ATTAT-TA-TTATTATA-ATATAGT-ATATATTTATTATTTATAGTATTTTATATTATAGTATAT
1 ATTATATATTTATTATATATATA-TAATATATATA-TATATATA-TA-TATATATTATAGTATAT
*
11534 TATA-TA-TTATATT
62 AATATTATTTATATT
*
11547 A-TATATATATT-TT-TATAT-TATAATATATATATATATATATATATATATTATAGTAAATAAT
1 ATTATATAT-TTATTATATATATATAATATATATATATATATATATATATATTATAGTATATAAT
11608 ATTATTTATATT
65 ATTATTTATATT
* * * * *
11620 ATTATATATTTATTATATATACATTATATATATATTTCT-TATA-ATATATTAT--T-TATATTA
1 ATTATATATTTATTATATATATATAATATATATATATATATATATATATATTATAGTATATAATA
11680 TTATTTAT
66 TTATTTAT
11688 TATTTTAGGT
Statistics
Matches: 179, Mismatches: 18, Indels: 40
0.76 0.08 0.17
Matches are distributed among these distances:
71 44 0.25
72 16 0.09
73 30 0.17
74 47 0.26
75 26 0.15
76 16 0.09
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.56
Consensus pattern (76 bp):
ATTATATATTTATTATATATATATAATATATATATATATATATATATATATTATAGTATATAATA
TTATTTATATT
Found at i:11668 original size:2 final size:2
Alignment explanation
Indices: 11387--11654 Score: 200
Period size: 2 Copynumber: 146.5 Consensus size: 2
11377 TATTATATGG
11387 TA TA TA T- TA TA -A T- TA TA GTA TA TA T- TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
11425 TA TA TA TA TA TA -A TA TA TA T- TA TA T- TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11463 T- TA TA TA TA TA T- TA T- TA T- TA T- TA TA -A TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
11500 TT TA T- TA TT TA TA GTA T- TT TA TA T- TA TA GTA TA T- 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
* *
11540 T- TA TA T- TA TA TA TA TA TT TT TA TA T- TA TA -A 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
* *
11578 TA TA TA TA TA TA TA TA T- TA TA GTA AA TA -A TA T- TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
11618 T- TA T- TA TA TA TT TA T- TA TA TA TA CA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11655 TTCTTATAAT
Statistics
Matches: 216, Mismatches: 15, Indels: 70
0.72 0.05 0.23
Matches are distributed among these distances:
1 30 0.14
2 176 0.81
3 10 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:18622 original size:86 final size:85
Alignment explanation
Indices: 18452--18626 Score: 289
Period size: 86 Copynumber: 2.0 Consensus size: 85
18442 CGCGATAATA
*
18452 TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTCGAACTTTTTCCGGAAACTCGATCCT
1 TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTCGAACTTTTTCCAGAAACTCGATCCT
*
18517 TGGCTGAGTGAATGCGCAATG
66 TGGCTGAGTAAAT-CGCAATG
*
18538 TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTCGGAATTTTTTTCCAGAAACTCGATC
1 TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTC-GAA-CTTTTTCCAGAAACTCGATC
18603 CTTGGCTGAGTAAAT-GCAATG
64 CTTGGCTGAGTAAATCGCAATG
18624 TTT
1 TTT
18627 GGTATCCATT
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
86 49 0.58
87 3 0.04
88 32 0.38
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (85 bp):
TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTCGAACTTTTTCCAGAAACTCGATCCT
TGGCTGAGTAAATCGCAATG
Found at i:20725 original size:84 final size:84
Alignment explanation
Indices: 20579--20831 Score: 463
Period size: 84 Copynumber: 3.0 Consensus size: 84
20569 CGCGATAATA
*
20579 TTTATCACCTTGTAGCCATGCCATTTGCTGATGAAGACTCGAACTTTTTCCGGAAACTCGATCCT
1 TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTCGAACTTTTTCCGGAAACTCGATCCT
20644 TGGCTGAGTGAATGCAATG
66 TGGCTGAGTGAATGCAATG
20663 TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTCGAACTTTTTCCGGAAACTCGATCCT
1 TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTCGAACTTTTTCCGGAAACTCGATCCT
20728 TGGCTGAGTGAATGCAATG
66 TGGCTGAGTGAATGCAATG
20747 TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTCGGAACTTTTTCCGGAAACTCGATCC
1 TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTC-GAACTTTTTCCGGAAACTCGATCC
*
20812 TTGACTGAGT-AAGTGCAATG
65 TTGGCTGAGTGAA-TGCAATG
20832 GTTGGTGTCC
Statistics
Matches: 165, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
84 125 0.76
85 40 0.24
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (84 bp):
TTTAGCACCTTGTAGCCATGCCATTTGCTGATGAAGACTCGAACTTTTTCCGGAAACTCGATCCT
TGGCTGAGTGAATGCAATG
Found at i:22323 original size:95 final size:95
Alignment explanation
Indices: 22160--22334 Score: 332
Period size: 95 Copynumber: 1.8 Consensus size: 95
22150 TTTAGTAAAA
*
22160 CACAGAGAACTATTTGTCTATGCTAAGCAGTACTTTCAACTACTGTGCCAAAATGCAATGCATGT
1 CACAGAGAACTATTTGTCTATGCTAAGCAGTACTTTCAACTACTGCGCCAAAATGCAATGCATGT
22225 CTAATGCCTTTCCATTGCTAAGCAGTATAG
66 CTAATGCCTTTCCATTGCTAAGCAGTATAG
*
22255 CACAGAGAACTTTTTGTCTATGCTAAGCAGTACTTTCAACTACTGCGCCAAAATGCAATGCATGT
1 CACAGAGAACTATTTGTCTATGCTAAGCAGTACTTTCAACTACTGCGCCAAAATGCAATGCATGT
22320 CTAATGCCTTTCCAT
66 CTAATGCCTTTCCAT
22335 GAGGCAGTCT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
95 78 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (95 bp):
CACAGAGAACTATTTGTCTATGCTAAGCAGTACTTTCAACTACTGCGCCAAAATGCAATGCATGT
CTAATGCCTTTCCATTGCTAAGCAGTATAG
Found at i:25308 original size:15 final size:15
Alignment explanation
Indices: 25285--25321 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
25275 TTATTATGAC
25285 AAATCTAATTTTGTCA
1 AAAT-TAATTTTGTCA
25301 AAATTAATTTTGTCA
1 AAATTAATTTTGTCA
*
25316 CAATTA
1 AAATTA
25322 GTAGTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (15 bp):
AAATTAATTTTGTCA
Found at i:25874 original size:182 final size:178
Alignment explanation
Indices: 25624--26038 Score: 395
Period size: 180 Copynumber: 2.3 Consensus size: 178
25614 ACAAATTTTG
* ** * *
25624 TTTGTAATTATATATTTTAATTATAGTGACAAAACGTATAGTCACAAATGATTATCTCCAATTTT
1 TTTGTAGTTATATATTTTAATTATAGTGACAAAATATATTGTCATAAA-GATT-TCTCCAATTTT
* * ** * *
25689 TTTTGTACAAAAACAAAATCATATAGTAACATGTTTTGTAACTATAAGCT-ATAATTATTGTTAC
64 TTTTGCAC-AAAA-AAAACCATATAGTAACAAATTTTGTAACTATAAG-TGATAATAATTATTAC
* * * *
25753 AAAAAA-GTTGTCACAACAAATAATGAGATTCAAGTTTTTAGTAAAAAACAATT
126 AAAAAACATTGTCAAAAAAAATAATGAGATTCAAGTTTTT-GTAAAAAACAATA
* * *
25806 TTTGTCGTTATATGTTTTAATTATAGTGACAAAATATATTGTCATAAAGATTTC-CCTTCATATT
1 TTTGTAGTTATATATTTTAATTATAGTGACAAAATATATTGTCATAAAGATTTCTCC--AAT-TT
* * * * * *
25870 TTTTTGCGCCAAAAAAGCCATATAGTGATAAATTTTGTAACTATAAGTGTTAATAATTATTACAA
63 TTTTTGCACAAAAAAAACCATATAGTAACAAATTTTGTAACTATAAGTGATAATAATTATTACAA
** * * * **
25935 AAAACATTGTCAAAAAAAATAATGTTATTCACGTTTTTGTGACAAATTATA
128 AAAACATTGTCAAAAAAAATAATGAGATTCAAGTTTTTGTAAAAAACAATA
* * * ** *
25986 TTTGTAGTTATAAATTTTAACTATAGTGATAGCATATATTGTCATAAATATTT
1 TTTGTAGTTATATATTTTAATTATAGTGACAAAATATATTGTCATAAAGATTT
26039 TTTTCTCAAC
Statistics
Matches: 189, Mismatches: 39, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
179 3 0.02
180 100 0.53
181 36 0.19
182 50 0.26
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (178 bp):
TTTGTAGTTATATATTTTAATTATAGTGACAAAATATATTGTCATAAAGATTTCTCCAATTTTTT
TTGCACAAAAAAAACCATATAGTAACAAATTTTGTAACTATAAGTGATAATAATTATTACAAAAA
ACATTGTCAAAAAAAATAATGAGATTCAAGTTTTTGTAAAAAACAATA
Found at i:26563 original size:416 final size:417
Alignment explanation
Indices: 25827--26622 Score: 1221
Period size: 416 Copynumber: 1.9 Consensus size: 417
25817 ATGTTTTAAT
* *
25827 TATAGTGACAAAATATATTGTCATAAAGATTTCCCTTCATATTTTTTTGCGCCAAAAAAGCCATA
1 TATAGTAACAAAATATATTGTCATAAAGATTTCCCTACATATTTTTTTGCGCCAAAAAAGCCATA
*
25892 TAGTGATAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAACATTGTCAAAAAAAATAA
66 TAGTGATAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAAATTGTCAAAAAAAATAA
* * * *
25957 TGTTATTCACGTTTTTGTGACAAATTATATTTGTAGTTATAAATTTTAACTATAGTGATAGCATA
131 TGATATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAATTTTAACTATAGTGATAACATA
* *
26022 TATTGTCATAAATATTTTTTTCTCAACTTTTTTTGTTTCAAAAGTTATATTGAAATTTTTATAAT
196 TATTGTCATAAATA-TTTTTTCTCAACTTTTTTTGTTTCAAAAGTTATATTGAAAGTTTCATAAT
* *
26087 TATAATTTATAGTTATTGTTATAGAAAAAATTATCACATCAAATAATAAAATTCAAGTTTTTTGT
260 TATAATTTATAATTATTATTATAGAAAAAATTATCACATCAAATAATAAAATTCAAGTTTTTTGT
26152 AATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCATAACCATTTC
325 AATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCATAACCATTTC
26217 TCTCTATTTTTTAGTGTAAAAAATGTTA
390 TCTCTATTTTTTAGTGTAAAAAATGTTA
* ** * *
26245 TATAGTAACACAATATATTGTCATAAAGATTTTTCTACATA-TTTTTTGTGCCAAAAAA-TCATA
1 TATAGTAACAAAATATATTGTCATAAAGATTTCCCTACATATTTTTTTGCGCCAAAAAAGCCATA
* *
26308 TAGT-A-ACAATTTTCGTAACTATAAGTGTTTATAATTATTACAAAAAAAATTGTCACAAAAAAT
66 TAGTGATA-AATTTT-GTAACTATAAGTGTTAATAATTATTACAAAAAAAATTGTCAAAAAAAAT
* *
26371 AATGATATTCACATTTTT-TGGCAAATTATACTTGTAGTTATAAATTTTAATTATAGTGATAACA
129 AATGATATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAATTTTAACTATAGTGATAACA
* * *
26435 TATATTGTGATAAATA-TTTTTCTCCAC-TTTTTTGTTTCAAAAGTTTATATTGATAAGTTTCGT
194 TATATTGTCATAAATATTTTTTCTCAACTTTTTTTGTTTCAAAAG-TTATATTGA-AAGTTTCAT
* *
26498 AATTATAATTTATAATTATTATTATTATAGAAAAAATTATCACATTAGATAATAAAATT-AAGTT
257 AATTATAATTTAT-A--ATTATTATTATAGAAAAAATTATCACATCAAATAATAAAATTCAAGTT
* *
26562 TTTTGTAATCAATTATTTTTGTAGTTATATATTTTAATCATTATGAAAAATTATACTATCA
319 TTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCA
26623 ACAAAAATAA
Statistics
Matches: 344, Mismatches: 27, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
412 16 0.05
413 19 0.06
414 20 0.06
415 65 0.19
416 134 0.39
417 54 0.16
418 36 0.10
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (417 bp):
TATAGTAACAAAATATATTGTCATAAAGATTTCCCTACATATTTTTTTGCGCCAAAAAAGCCATA
TAGTGATAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAAATTGTCAAAAAAAATAA
TGATATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAATTTTAACTATAGTGATAACATA
TATTGTCATAAATATTTTTTCTCAACTTTTTTTGTTTCAAAAGTTATATTGAAAGTTTCATAATT
ATAATTTATAATTATTATTATAGAAAAAATTATCACATCAAATAATAAAATTCAAGTTTTTTGTA
ATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCATAACCATTTCT
CTCTATTTTTTAGTGTAAAAAATGTTA
Found at i:29641 original size:21 final size:21
Alignment explanation
Indices: 29617--29656 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29607 TTTATTTTAT
29617 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
29638 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
29657 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:29704 original size:33 final size:33
Alignment explanation
Indices: 29651--29749 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
29641 TTTGTTTCAA
29651 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
29683 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
29716 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
29749 T
1 T
29750 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:29778 original size:13 final size:13
Alignment explanation
Indices: 29735--29789 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
29725 TTGGAAGTAT
29735 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
29748 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
29762 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
29775 TTAAGTATTTGAA
1 TTAAGTATTTCAA
29788 TT
1 TT
29790 TATCAAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:30011 original size:21 final size:21
Alignment explanation
Indices: 29985--30041 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
29975 TGGAGCGTGG
*
29985 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
30006 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
30027 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
30042 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:30258 original size:16 final size:16
Alignment explanation
Indices: 30215--30262 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
30205 TTAAAATCGG
* *
30215 TTTTTTTATAACCGGT
1 TTTTTTTAAAACCGAT
**
30231 TTTTCTAAAAAACCGAT
1 TTTT-TTTAAAACCGAT
30248 TTTTTTTAAAACCGA
1 TTTTTTTAAAACCGA
30263 AACCGGTTAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (16 bp):
TTTTTTTAAAACCGAT
Found at i:32839 original size:17 final size:17
Alignment explanation
Indices: 32817--32854 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
32807 CGGTACCGAG
32817 TAGAGGTATTGATACCA
1 TAGAGGTATTGATACCA
32834 TAGAGGTATTGATACCA
1 TAGAGGTATTGATACCA
32851 TAGA
1 TAGA
32855 AGAGTAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (17 bp):
TAGAGGTATTGATACCA
Found at i:34017 original size:22 final size:22
Alignment explanation
Indices: 33989--34051 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
33979 AGTAGAGGGT
* *
33989 TACATAGGTCCTTTGGGACATA
1 TACATAGGTCATTCGGGACATA
34011 TACATAGGTCATTCGGGAC--A
1 TACATAGGTCATTCGGGACATA
*
34031 TACATGAGGTCTTTCGGGACA
1 TACAT-AGGTCATTCGGGACA
34052 AATTTCACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 6 0.17
21 13 0.36
22 17 0.47
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (22 bp):
TACATAGGTCATTCGGGACATA
Found at i:34046 original size:21 final size:20
Alignment explanation
Indices: 33989--34051 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
33979 AGTAGAGGGT
33989 TACATAGGTCCTTT-GGGACATA
1 TACATAGGT-CTTTCGGGAC--A
*
34011 TACATAGGTCATTCGGGACA
1 TACATAGGTCTTTCGGGACA
34031 TACATGAGGTCTTTCGGGACA
1 TACAT-AGGTCTTTCGGGACA
34052 AATTTCACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
20 6 0.16
21 17 0.46
22 14 0.38
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (20 bp):
TACATAGGTCTTTCGGGACA
Found at i:36895 original size:95 final size:95
Alignment explanation
Indices: 36732--36904 Score: 328
Period size: 95 Copynumber: 1.8 Consensus size: 95
36722 TTAGTAAAAC
*
36732 ACAGAGAACTATTTGTCTATGCTAAGCAGTACTTTCAACTACTGTGCCAAAATGCAATGCATGTC
1 ACAGAGAACTATTTGTCTATGCTAAGCAGTACTTTCAACTACTGCGCCAAAATGCAATGCATGTC
36797 TAATGCCTTTCCAGTGCTAAGCAGTATAGG
66 TAATGCCTTTCCAGTGCTAAGCAGTATAGG
*
36827 ACAGAGAACTTTTTGTCTATGCTAAGCAGTACTTTCAACTACTGCGCCAAAATGCAATGCATGTC
1 ACAGAGAACTATTTGTCTATGCTAAGCAGTACTTTCAACTACTGCGCCAAAATGCAATGCATGTC
36892 TAATGCCTTTCCA
66 TAATGCCTTTCCA
36905 TGAGGCAGTC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 76 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (95 bp):
ACAGAGAACTATTTGTCTATGCTAAGCAGTACTTTCAACTACTGCGCCAAAATGCAATGCATGTC
TAATGCCTTTCCAGTGCTAAGCAGTATAGG
Found at i:43966 original size:14 final size:14
Alignment explanation
Indices: 43947--43977 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
43937 AGAAGTATCA
43947 ATACTTAAAGAATG
1 ATACTTAAAGAATG
43961 ATACTTAAAGAATG
1 ATACTTAAAGAATG
43975 ATA
1 ATA
43978 TCGGTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (14 bp):
ATACTTAAAGAATG
Found at i:45289 original size:21 final size:20
Alignment explanation
Indices: 45230--45292 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 20
45220 AGTCGAGGGT
*
45230 TACATAGGTCCTTTGGGACATA
1 TACATAGGTCCTTCGGGAC--A
*
45252 TACATAGGTCATTCGGGACA
1 TACATAGGTCCTTCGGGACA
*
45272 TACATGATGTCCTTCGGGACA
1 TACAT-AGGTCCTTCGGGACA
45293 AATTTCACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 6 0.17
21 13 0.36
22 17 0.47
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (20 bp):
TACATAGGTCCTTCGGGACA
Found at i:46546 original size:20 final size:19
Alignment explanation
Indices: 46508--46546 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
46498 GTATGGATAA
*
46508 GAGTGCAGTTTGATAAGTT
1 GAGTGAAGTTTGATAAGTT
*
46527 GAGTGAAGTGTTGTTAAGTT
1 GAGTGAAGT-TTGATAAGTT
46547 AATTCTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.03, G:0.33, T:0.38
Consensus pattern (19 bp):
GAGTGAAGTTTGATAAGTT
Found at i:47024 original size:27 final size:27
Alignment explanation
Indices: 46992--47050 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
46982 GTTTCAGAAG
46992 AGTTTAAGAATAGATACATTGGTGATC
1 AGTTTAAGAATAGATACATTGGTGATC
*
47019 AGTTTAAGAATGGATACATTGGTGATC
1 AGTTTAAGAATAGATACATTGGTGATC
47046 AGTTT
1 AGTTT
47051 GTGAAACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.36
Consensus pattern (27 bp):
AGTTTAAGAATAGATACATTGGTGATC
Found at i:49671 original size:2 final size:2
Alignment explanation
Indices: 49664--49697 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
49654 ATTTAGGTGA
49664 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
49698 GATAACAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50363 original size:21 final size:20
Alignment explanation
Indices: 50333--50373 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
50323 AGTTGGGGGT
50333 TACATAGGTCATTCGGGACA
1 TACATAGGTCATTCGGGACA
*
50353 TACATGAGGTCCTTCGGGACA
1 TACAT-AGGTCATTCGGGACA
50374 AATTTCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (20 bp):
TACATAGGTCATTCGGGACA
Found at i:52815 original size:82 final size:82
Alignment explanation
Indices: 52675--52884 Score: 280
Period size: 82 Copynumber: 2.5 Consensus size: 82
52665 GAACTGCGTC
* * *
52675 CGTATAGCTTACCTTAAGCACACAGCAAAAAGGAAGCCAACCTAAGGATAGGCTTTGGGGCTTGT
1 CGTATAGCTTACCCTAAGCACACA--ACAAAGGAAGCCAACCTAAGGATAGGCTTTGGGGCCTGT
*
52740 ATCCTTAAGTCCGTAAG-T
64 AACCTTAAGTCCGTAAGTT
*
52758 CTGTATAGCTTACCCTAAGCACACAACAAAGGAAGCCAACTTAAGGATAGGCTTTGGGGCCTGTA
1 C-GTATAGCTTACCCTAAGCACACAACAAAGGAAGCCAACCTAAGGATAGGCTTTGGGGCCTGTA
52823 ACCTTAAGTCCGTAAGTT
65 ACCTTAAGTCCGTAAGTT
* * * *
52841 CGTAT-GACTTACCCTAAGCATACAGCAAAAGGGAGCCGACCTAA
1 CGTATAG-CTTACCCTAAGCACACAAC-AAAGGAAGCCAACCTAA
52885 TGGAGCATCT
Statistics
Matches: 113, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
81 1 0.01
82 73 0.65
83 17 0.15
84 22 0.19
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (82 bp):
CGTATAGCTTACCCTAAGCACACAACAAAGGAAGCCAACCTAAGGATAGGCTTTGGGGCCTGTAA
CCTTAAGTCCGTAAGTT
Done.