Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006254.1 Hibiscus syriacus cultivar Beakdansim tig00014925_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: 96214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2256 original size:12 final size:12
Alignment explanation
Indices: 2226--2260 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2216 TATCTTTCGT
2226 TTATCTTGTTT-
1 TTATCTTGTTTC
*
2237 TAATCTTGTTTC
1 TTATCTTGTTTC
2249 TTATCTTGTTTC
1 TTATCTTGTTTC
2261 CAACTCCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:5055 original size:3 final size:3
Alignment explanation
Indices: 5047--5136 Score: 173
Period size: 3 Copynumber: 30.3 Consensus size: 3
5037 CTTTTAATAC
5047 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5094 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5137 ATGTTACATA
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 84 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:18280 original size:11 final size:11
Alignment explanation
Indices: 18264--18321 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
18254 ATTTTGCCTG
18264 AAAAATGAAAA
1 AAAAATGAAAA
*
18275 AAAAATTAAAA
1 AAAAATGAAAA
18286 ATAAAATGAAAA
1 A-AAAATGAAAA
18298 ATAAAAT-AAAA
1 A-AAAATGAAAA
*
18309 AATAA-GAAAA
1 AAAAATGAAAA
18319 AAA
1 AAA
18322 GAAAAATGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
10 9 0.22
11 16 0.39
12 16 0.39
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAAATGAAAA
Found at i:18285 original size:6 final size:6
Alignment explanation
Indices: 18264--18337 Score: 50
Period size: 5 Copynumber: 12.7 Consensus size: 6
18254 ATTTTGCCTG
*
18264 AAAAAT GAAAAA- AAAATT AAAAAT -AAAAT GAAAAAT -AAAAT AAAAAAT
1 AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT -AAAAAT
* * *
18312 AAGAA- AAAAAG AAAAAT -GAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
18338 TGAGGGTTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
5 22 0.42
6 16 0.30
7 15 0.28
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:18295 original size:23 final size:24
Alignment explanation
Indices: 18265--18313 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
18255 TTTTGCCTGA
*
18265 AAAATGAAAAA-AAAATTAAAAAT
1 AAAATGAAAAATAAAATAAAAAAT
18288 AAAATGAAAAATAAAATAAAAAAT
1 AAAATGAAAAATAAAATAAAAAAT
18312 AA
1 AA
18314 GAAAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (24 bp):
AAAATGAAAAATAAAATAAAAAAT
Found at i:18298 original size:30 final size:30
Alignment explanation
Indices: 18262--18337 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
18252 GTATTTTGCC
*
18262 TGAAAAATGAAAAAAAAATTAA-AAATAAAA
1 TGAAAAATGAAAAAAAAAATAAGAAA-AAAA
18292 TGAAAAAT-AAAATAAAAAATAAGAAAAAAA
1 TGAAAAATGAAAA-AAAAAATAAGAAAAAAA
*
18322 -GAAAAATGAAATAAAA
1 TGAAAAATGAAAAAAAA
18338 TGAGGGTTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 15 0.37
30 23 0.56
31 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (30 bp):
TGAAAAATGAAAAAAAAAATAAGAAAAAAA
Found at i:18311 original size:12 final size:12
Alignment explanation
Indices: 18265--18326 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
18255 TTTTGCCTGA
*
18265 AAAATGAAAAA-
1 AAAATAAAAAAT
*
18276 AAAATTAAAAAT
1 AAAATAAAAAAT
*
18288 AAAATGAAAAAT
1 AAAATAAAAAAT
18300 AAAATAAAAAAT
1 AAAATAAAAAAT
* *
18312 AAGA-AAAAAAG
1 AAAATAAAAAAT
18323 AAAA
1 AAAA
18327 ATGAAATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
11 19 0.43
12 25 0.57
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:19720 original size:110 final size:110
Alignment explanation
Indices: 19503--19952 Score: 648
Period size: 110 Copynumber: 4.1 Consensus size: 110
19493 GTTCGATCCC
* * * *
19503 GATTCAATGGATCAACTTTCCCAGATCTGATATTCCCCCAAAAAAAGCAGAACATATCCCTCTCT
1 GATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGAT-CCTCTCT
* *
19568 TTTAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCT
65 TTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCT
* * *
19614 GATTCAATGGATCAACTTTTCTAGATCTGATATTCCCTCAAAAGAAGTGGAACAGATCCTCTCTT
1 GATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCCTCTCTT
* *
19679 TCAATATTTGATATTCACTGAGTGACAGCGGAACAAGTCTACCCT
66 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCT
* * * *
19724 GATTCAATGGATCAATTTTCTCAGATCTGATATTCCCTCAGAAGAAGCGGGACAGATCCTCTCTT
1 GATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCCTCTCTT
* * * * *
19789 TGAAGATTTGATATTCCCTGAATGACATCAGAACAAGCCTACCCT
66 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCT
* *
19834 GATTAAATGGATCAACTTTCCCAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCATCTCT
1 GATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCC-TCTCT
* * **
19899 TTCAAGATTTGATATTCCATGAGTGATAATGGAACAAGTCTACCCT
65 TTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCT
19945 GATTCAAT
1 GATTCAAT
19953 CTTCCCTGAA
Statistics
Matches: 300, Mismatches: 38, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
110 200 0.67
111 100 0.33
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (110 bp):
GATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCCTCTCTT
TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCT
Found at i:20171 original size:3 final size:3
Alignment explanation
Indices: 20163--20230 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
20153 CTTTTAATAC
20163 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20211 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
20231 GTTACATATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21304 original size:2 final size:2
Alignment explanation
Indices: 21297--21321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21287 TTTGTAATAG
21297 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21322 TAAAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21829 original size:2 final size:2
Alignment explanation
Indices: 21822--21896 Score: 70
Period size: 2 Copynumber: 39.5 Consensus size: 2
21812 TTTAAGTGTT
*
21822 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA T- 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
* * *
21862 TC CA TA T- TA TG TA -A TA TA TA TA T- TA TA GTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
21897 GCATAACATG
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
1 5 0.08
2 52 0.88
3 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:21959 original size:2 final size:2
Alignment explanation
Indices: 21952--22014 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
21942 TTAAATACGA
21952 AT 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 AT
21994 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
22015 ATTTACGTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22248 original size:2 final size:2
Alignment explanation
Indices: 22241--22274 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22231 TGCATGGCTA
22241 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
22275 GTTAATATTG
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:26467 original size:62 final size:60
Alignment explanation
Indices: 26370--26524 Score: 197
Period size: 62 Copynumber: 2.5 Consensus size: 60
26360 TAGTTTGGAA
* * * *
26370 CATTTTATAACTTTTAATAGTCGGGGGACTCAACAAAGCAACACA-TATGATAGTTGAGTGAC
1 CATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACACACTAT-A-A-TTGAGGGAC
* *
26432 CATTTTGTAACTTTTAATAGTCGAGGGATTCAACAAAACAACACACTATAATTGTGGGAC
1 CATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACACACTATAATTGAGGGAC
*
26492 TATTTTGTAACTTTTAATAGTCG-GAGGACTCAA
1 CATTTTGTAACTTTTAATAGTCGAG-GGACTCAA
26525 GAAAGTATCA
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
59 1 0.01
60 36 0.43
61 1 0.01
62 42 0.51
63 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACACACTATAATTGAGGGAC
Found at i:26541 original size:60 final size:60
Alignment explanation
Indices: 26370--26541 Score: 193
Period size: 60 Copynumber: 2.8 Consensus size: 60
26360 TAGTTTGGAA
* * * * *
26370 CATTTTATAACTTTTAATAGTCGGGGGACTCAACAAAGCAACACATATGATAGTTGAGTGAC
1 CATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACAC-TCT-ATAATTGAGGGAC
* * * *
26432 CATTTTGTAACTTTTAATAGTC-GAGGGATTCAACAAAACAACACACTATAATTGTGGGAC
1 CATTTTGTAACTTTTAATAGTCGGA-GGACTCAACAAAGCAACACTCTATAATTGAGGGAC
* * * *
26492 TATTTTGTAACTTTTAATAGTCGGAGGACTCAAGAAAGTATCACTCTATA
1 CATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACACTCTATA
26542 GTCGGGGTAC
Statistics
Matches: 92, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
60 50 0.54
61 4 0.04
62 38 0.41
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACACTCTATAATTGAGGGAC
Found at i:26565 original size:60 final size:59
Alignment explanation
Indices: 26370--26565 Score: 182
Period size: 60 Copynumber: 3.2 Consensus size: 59
26360 TAGTTTGGAA
* * * * *
26370 CATTTTATAACTTTTAATAGTCGGGGGACTCAACAAAGCAACACATATGATAGTTGAGTGAC
1 CATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACAC-TCT-ATAGTGGGGT-AC
* * * *
26432 CATTTTGTAACTTTTAATAGTC-GAGGGATTCAACAAAACAACACACTATAATTGTGGG-AC
1 CATTTTGTAACTTTTAATAGTCGGA-GGACTCAACAAAGCAACACTCTAT-AGTG-GGGTAC
* * * *
26492 TATTTTGTAACTTTTAATAGTCGGAGGACTCAAGAAAGTATCACTCTATAGTCGGGGTAC
1 CATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACACTCTATAGT-GGGGTAC
26552 CATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
26566 ACCCAAGATT
Statistics
Matches: 109, Mismatches: 18, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
59 5 0.05
60 55 0.50
61 9 0.08
62 40 0.37
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (59 bp):
CATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACACTCTATAGTGGGGTAC
Found at i:30715 original size:24 final size:24
Alignment explanation
Indices: 30688--30775 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
30678 GATATCATAA
* *
30688 ATCAAAACAGAATTCAGAACAAAT
1 ATCAGAACAGAATTCAGATCAAAT
*
30712 ATCAGAACAGAATCCAGATCAGAA-
1 ATCAGAACAGAATTCAGATCA-AAT
* * **
30736 ATCAGAATAGAATTCAGGTCATGT
1 ATCAGAACAGAATTCAGATCAAAT
30760 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
30776 AGTCAGAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
24 51 0.96
25 2 0.04
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCAAAT
Found at i:30716 original size:12 final size:13
Alignment explanation
Indices: 30688--30752 Score: 59
Period size: 12 Copynumber: 5.4 Consensus size: 13
30678 GATATCATAA
*
30688 ATCAAAACAGAAT
1 ATCAGAACAGAAT
30701 -TCAGAACA-AAT
1 ATCAGAACAGAAT
30712 ATCAGAACAGAAT
1 ATCAGAACAGAAT
* *
30725 -CCAGATCAGAA-
1 ATCAGAACAGAAT
*
30736 ATCAGAATAGAAT
1 ATCAGAACAGAAT
30749 -TCAG
1 ATCAG
30753 GTCATGTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
11 3 0.07
12 36 0.86
13 3 0.07
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (13 bp):
ATCAGAACAGAAT
Found at i:30780 original size:24 final size:24
Alignment explanation
Indices: 30688--30789 Score: 84
Period size: 24 Copynumber: 4.2 Consensus size: 24
30678 GATATCATAA
* * *
30688 ATCAAAACAGAATTC-AGAACAAAT
1 ATCAGAACAGAATTCAAG-TCAGAT
* *
30712 ATCAGAACAGAA-TCCAGATCAGAA
1 ATCAGAACAGAATTCAAG-TCAGAT
* *
30736 ATCAGAATAGAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAAGTCA-GAT
*
30760 ATCAGAACAGAATTCAAGTCAGAA
1 ATCAGAACAGAATTCAAGTCAGAT
30784 ATCAGA
1 ATCAGA
30790 TAAAATATTT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.05
24 56 0.89
25 4 0.06
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.19
Consensus pattern (24 bp):
ATCAGAACAGAATTCAAGTCAGAT
Found at i:33221 original size:13 final size:13
Alignment explanation
Indices: 33203--33231 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
33193 CCAGTCAATA
33203 GTCAACGGGTCGG
1 GTCAACGGGTCGG
33216 GTCAACGGGTCGG
1 GTCAACGGGTCGG
33229 GTC
1 GTC
33232 GGGTTGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:35318 original size:12 final size:12
Alignment explanation
Indices: 35301--35348 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
35291 CATAAATCAA
35301 AACAGAATTCAG
1 AACAGAATTCAG
*
35313 AACAGAATCCAG
1 AACAGAATTCAG
* *
35325 ATCAGAAATCAG
1 AACAGAATTCAG
35337 AACAGAATTCAG
1 AACAGAATTCAG
35349 GTCATGTATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.15
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:35359 original size:24 final size:24
Alignment explanation
Indices: 35303--35385 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
35293 TAAATCAAAA
* *
35303 CAGAATTCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAT
*
35327 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAT
* *
35351 CATG-TATCAGAACATAATTCA-AGT
1 CA-GAAATCAGAACAGAATTCAGA-T
*
35375 CGGAAATCAGA
1 CAGAAATCAGA
35386 TAAAATATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.02
24 46 0.96
25 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAT
Found at i:42736 original size:23 final size:21
Alignment explanation
Indices: 42682--42743 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
42672 TTTTTGTGTA
42682 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAATCGATTCCCCCCAT
* **
42702 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCAT
*
42723 GAAGGGGAATCGATACCCCCC
1 G-A-GGGAATCGATTCCCCCC
42744 TGGGGTTCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 10 0.30
21 8 0.24
22 1 0.03
23 14 0.42
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.16
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCAT
Found at i:47323 original size:13 final size:13
Alignment explanation
Indices: 47305--47334 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
47295 AACAGTCAAC
47305 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
47318 GGTCAACTGGTCG
1 GGTCAACGGGTCG
47331 GGTC
1 GGTC
47335 GGGTTGGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.23, G:0.43, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:48236 original size:21 final size:21
Alignment explanation
Indices: 48187--48236 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
48177 TGACCTTTAT
* *
48187 AATGCTGACATGACACTTTAC
1 AATGCTGACATCACACTCTAC
* * *
48208 AGTTCTGACATCACAGTCTAC
1 AATGCTGACATCACACTCTAC
48229 AATGCTGA
1 AATGCTGA
48237 TGTAGCAATC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (21 bp):
AATGCTGACATCACACTCTAC
Found at i:48382 original size:15 final size:15
Alignment explanation
Indices: 48364--48433 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
48354 AAATTATTTT
48364 AAATTTAAAATATAA
1 AAATTTAAAATATAA
48379 AAATATT-AAATATAA
1 AAAT-TTAAAATATAA
* *
48394 AAATACTAAAA-CTAA
1 AAAT-TTAAAATATAA
*
48409 AAA-TTAAATTACTAA
1 AAATTTAAAATA-TAA
*
48424 AAAATTAAAA
1 AAATTTAAAA
48434 AAAATATTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
13 4 0.09
15 30 0.68
16 10 0.23
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTTAAAATATAA
Found at i:48442 original size:28 final size:27
Alignment explanation
Indices: 48377--48442 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
48367 TTTAAAATAT
48377 AAAAATATTAAATATAAAAATACTAAA
1 AAAAATATTAAATATAAAAATACTAAA
*
48404 ACTAAAA-ATTAAATTACTAAAAA-ATTAAA
1 A--AAAATATTAAA-TA-TAAAAATACTAAA
48433 AAAAATATTA
1 AAAAATATTA
48443 TTAGTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
27 5 0.15
28 10 0.30
29 12 0.36
30 6 0.18
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAATATTAAATATAAAAATACTAAA
Found at i:50150 original size:28 final size:28
Alignment explanation
Indices: 50117--50202 Score: 90
Period size: 25 Copynumber: 3.1 Consensus size: 28
50107 TCAATTTAGT
50117 TATATTTTTAATAAATTAAAATAAATTA
1 TATATTTTTAATAAATTAAAATAAATTA
*
50145 TATA-TTTT--TAAATTAAAA-AAATAA
1 TATATTTTTAATAAATTAAAATAAATTA
* *
50169 AATATTTTTAAATTAAATTAATAATAAAATA
1 TATATTTTT-AA-TAAATTAA-AATAAATTA
50200 TAT
1 TAT
50203 TTAATAAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
24 8 0.17
25 14 0.30
27 4 0.09
28 4 0.09
29 8 0.17
30 2 0.04
31 6 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TATATTTTTAATAAATTAAAATAAATTA
Found at i:50162 original size:25 final size:24
Alignment explanation
Indices: 50128--50236 Score: 105
Period size: 24 Copynumber: 4.3 Consensus size: 24
50118 ATATTTTTAA
* *
50128 TAAATTAAAATAAATTATATATTTT
1 TAAATTAAAA-AAATAAAATATTTT
50153 TAAATTAAAAAAATAAAATATTTT
1 TAAATTAAAAAAATAAAATATTTT
50177 TAAATTAAATTAATAATAAAATATATTT
1 TAAATTAAA--AA-AATAAAATAT-TTT
* *
50205 AATAAGTT-AATAAA-AAAATATTTT
1 --TAAATTAAAAAAATAAAATATTTT
50229 TAAATTAA
1 TAAATTAA
50237 TATATAAAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
22 5 0.07
23 1 0.01
24 24 0.33
25 17 0.24
26 4 0.06
27 11 0.15
28 3 0.04
29 2 0.03
30 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
TAAATTAAAAAAATAAAATATTTT
Found at i:50192 original size:52 final size:53
Alignment explanation
Indices: 50118--50236 Score: 133
Period size: 52 Copynumber: 2.3 Consensus size: 53
50108 CAATTTAGTT
*
50118 ATATTTTT-AA-TAAATT-AA-AATAAATTATATATTT-TTAAATTAAAAAAATAAA
1 ATATTTTTAAATTAAATTAAATAATAAA--ATATATTTAATAAATT-AAAAAA-AAA
* *
50170 ATATTTTTAAATTAAATT-AATAATAAAATATATTTAATAAGTTAATAAAAAA
1 ATATTTTTAAATTAAATTAAATAATAAAATATATTTAATAAATTAAAAAAAAA
50222 ATATTTTTAAATTAA
1 ATATTTTTAAATTAA
50237 TATATAAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
52 26 0.43
53 15 0.25
54 13 0.22
55 6 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (53 bp):
ATATTTTTAAATTAAATTAAATAATAAAATATATTTAATAAATTAAAAAAAAA
Found at i:50206 original size:22 final size:22
Alignment explanation
Indices: 50181--50252 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 22
50171 TATTTTTAAA
50181 TTAAATTAATAATAAAATATAT
1 TTAAATTAATAATAAAATATAT
* *
50203 TTAATAAGTTAATAAAAAAATATTT
1 TT-A-AA-TTAATAATAAAATATAT
50228 TTAAATTAATATATAAAATTATAT
1 TTAAATTAATA-ATAAAA-TATAT
50252 T
1 T
50253 ATATATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 8 0.20
23 8 0.20
24 8 0.20
25 17 0.41
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (22 bp):
TTAAATTAATAATAAAATATAT
Found at i:50245 original size:25 final size:26
Alignment explanation
Indices: 50146--50236 Score: 109
Period size: 25 Copynumber: 3.6 Consensus size: 26
50136 AATAAATTAT
50146 ATATTTTTAAATTAAA-AA-AATAAA
1 ATATTTTTAAATTAAATAATAATAAA
50170 ATATTTTTAAATTAAATTAATAATAAA
1 ATATTTTTAAATTAAA-TAATAATAAA
* * *
50197 ATATATTT-AA-TAAGTTAATAAAAAA
1 ATATTTTTAAATTAA-ATAATAATAAA
50222 ATATTTTTAAATTAA
1 ATATTTTTAAATTAA
50237 TATATAAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 16 0.28
25 19 0.33
26 6 0.11
27 16 0.28
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (26 bp):
ATATTTTTAAATTAAATAATAATAAA
Found at i:50628 original size:2 final size:2
Alignment explanation
Indices: 50623--50679 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
50613 AAAAAAAAAA
50623 AT 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 AT
50665 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
50680 ATAAATAAGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51075 original size:31 final size:32
Alignment explanation
Indices: 51023--51087 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
51013 GGGTGACCAC
51023 ATCTTAATTAAATAAAAAACGAAAATGATCAT
1 ATCTTAATTAAATAAAAAACGAAAATGATCAT
* *
51055 ATCTTAATTAAAT-AAAAACGAAAGTGATTAT
1 ATCTTAATTAAATAAAAAACGAAAATGATCAT
51086 AT
1 AT
51088 TTTATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (32 bp):
ATCTTAATTAAATAAAAAACGAAAATGATCAT
Found at i:51150 original size:2 final size:2
Alignment explanation
Indices: 51143--51231 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
51133 CATAATTACC
51143 AT 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 AT
51185 AT 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 AT
51227 AT AT A
1 AT AT A
51232 GTTAACTGGA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51477 original size:23 final size:23
Alignment explanation
Indices: 51451--51526 Score: 152
Period size: 23 Copynumber: 3.3 Consensus size: 23
51441 TCTGATCTCA
51451 AAGGAAGAAGGCCTTGTTTGATG
1 AAGGAAGAAGGCCTTGTTTGATG
51474 AAGGAAGAAGGCCTTGTTTGATG
1 AAGGAAGAAGGCCTTGTTTGATG
51497 AAGGAAGAAGGCCTTGTTTGATG
1 AAGGAAGAAGGCCTTGTTTGATG
51520 AAGGAAG
1 AAGGAAG
51527 CGATGGAGAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.33, C:0.08, G:0.36, T:0.24
Consensus pattern (23 bp):
AAGGAAGAAGGCCTTGTTTGATG
Found at i:53049 original size:1 final size:1
Alignment explanation
Indices: 53043--53067 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
53033 ATTGCCGATA
53043 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
53068 GCATTTGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:55841 original size:322 final size:322
Alignment explanation
Indices: 55256--55899 Score: 1216
Period size: 322 Copynumber: 2.0 Consensus size: 322
55246 ACTCTGCAAG
* *
55256 CAATGTCAGAGGAACTCCCAATACTAATGTCGATAACTGCATAGGATCGATTTTTTAACCTGAAA
1 CAATGTCAAAGGAACTCCCAATACTAATGTCGATAACTGCATAGGATCGATTCTTTAACCTGAAA
55321 TGGTGAGTAACAGTGTAAACTTTGGGAAAGCTCAGTAATAAAGAACTACAAGATGACACTGAAGG
66 TGGTGAGTAACAGTGTAAACTTTGGGAAAGCTCAGTAATAAAGAACTACAAGATGACACTGAAGG
55386 ACATGTAGACAAATGACAAAAGCATAAAACTTTTTTATTGATCCAGGCATATACAGGTTCTAGTG
131 ACATGTAGACAAATGACAAAAGCATAAAACTTTTTTATTGATCCAGGCATATACAGGTTCTAGTG
55451 ATGAGTTGAGGTTCCACAAATATTTTTAAGGTAATGATACATGCATGATCATGACCAACTTTCTC
196 ATGAGTTGAGGTTCCACAAATATTTTTAAGGTAATGATACATGCATGATCATGACCAACTTTCTC
55516 CATAACTTGATTATTCCATGGACGTTCTTCATTGCTACTTCTAAGGGAGTTCTTCCTTACTC
261 CATAACTTGATTATTCCATGGACGTTCTTCATTGCTACTTCTAAGGGAGTTCTTCCTTACTC
* *
55578 CAATGTCAAAGGAACTCCCAATACTGATGTCGATAACTGCATATGATCGATTCTTTAACCTGAAA
1 CAATGTCAAAGGAACTCCCAATACTAATGTCGATAACTGCATAGGATCGATTCTTTAACCTGAAA
55643 TGGTGAGTAACAGTGTAAACTTTGGGAAAGCTCAGTAATAAAGAACTACAAGATGACACTGAAGG
66 TGGTGAGTAACAGTGTAAACTTTGGGAAAGCTCAGTAATAAAGAACTACAAGATGACACTGAAGG
* * *
55708 ACATGTAGATAAATGACAAAAGGATAAAACTTTTTTATTGATCCATGCATATACAGGTTCTAGTG
131 ACATGTAGACAAATGACAAAAGCATAAAACTTTTTTATTGATCCAGGCATATACAGGTTCTAGTG
55773 ATGAGTTGAGGTTCCACAAATATTTTTAAGGTAATGATACATGCATGATCATGACCAACTTTCTC
196 ATGAGTTGAGGTTCCACAAATATTTTTAAGGTAATGATACATGCATGATCATGACCAACTTTCTC
*
55838 CATAACTTGATTATTCCATGGTCGTTCTTCATTGCTACTTCTAAGGGAGTTCTTCCTTACTC
261 CATAACTTGATTATTCCATGGACGTTCTTCATTGCTACTTCTAAGGGAGTTCTTCCTTACTC
55900 TATCTTATAT
Statistics
Matches: 314, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
322 314 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (322 bp):
CAATGTCAAAGGAACTCCCAATACTAATGTCGATAACTGCATAGGATCGATTCTTTAACCTGAAA
TGGTGAGTAACAGTGTAAACTTTGGGAAAGCTCAGTAATAAAGAACTACAAGATGACACTGAAGG
ACATGTAGACAAATGACAAAAGCATAAAACTTTTTTATTGATCCAGGCATATACAGGTTCTAGTG
ATGAGTTGAGGTTCCACAAATATTTTTAAGGTAATGATACATGCATGATCATGACCAACTTTCTC
CATAACTTGATTATTCCATGGACGTTCTTCATTGCTACTTCTAAGGGAGTTCTTCCTTACTC
Found at i:57060 original size:19 final size:20
Alignment explanation
Indices: 57036--57086 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
57026 CGGCCAAGAG
*
57036 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
57055 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
*
57075 CATGCATTTTCA
1 CATGTATTTTCA
57087 AAGGGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:71740 original size:15 final size:15
Alignment explanation
Indices: 71720--71757 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
71710 TCGTTCTTTG
71720 ATATTGTCCCAATCA
1 ATATTGTCCCAATCA
71735 ATATTGTCCCAATCA
1 ATATTGTCCCAATCA
71750 ATATTGTC
1 ATATTGTC
71758 GTCCGTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (15 bp):
ATATTGTCCCAATCA
Found at i:72990 original size:25 final size:26
Alignment explanation
Indices: 72956--73020 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 26
72946 ATCGGAAAAT
*
72956 AAAGT-ATTTGGTC-CAGACTTAGAC
1 AAAGTGATTTGGCCTCAGACTTAGAC
72980 AAAGTGATTT-GCCTCAGACTTAGAC
1 AAAGTGATTTGGCCTCAGACTTAGAC
73005 AAAGTGATTT-GCCTCA
1 AAAGTGATTTGGCCTCA
73021 AAAGGTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
24 7 0.18
25 31 0.82
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (26 bp):
AAAGTGATTTGGCCTCAGACTTAGAC
Found at i:89776 original size:12 final size:12
Alignment explanation
Indices: 89756--89789 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
89746 TGCTCGATCG
*
89756 AAATGAAAAATA
1 AAATAAAAAATA
89768 AAATAAAAAAATA
1 AAAT-AAAAAATA
89781 AAATAAAAA
1 AAATAAAAA
89790 TGTAAAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:89795 original size:13 final size:13
Alignment explanation
Indices: 89761--89789 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
89751 GATCGAAATG
89761 AAAAATAAAATAA
1 AAAAATAAAATAA
89774 AAAAATAAAATAA
1 AAAAATAAAATAA
89787 AAA
1 AAA
89790 TGTAAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAATAA
Done.