Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000882.1 Hibiscus syriacus cultivar Beakdansim tig00001715_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: 96027
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:10307 original size:26 final size:26
Alignment explanation
Indices: 10253--10299 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
10243 TTGACCCAAT
*
10253 AAAAATAAATCACAATTACTTTTTTC
1 AAAAATAAATCACAATAACTTTTTTC
10279 AAAAATAAAT-A-AATAA-TTTTT
1 AAAAATAAATCACAATAACTTTTT
10300 GTTACAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 4 0.20
25 1 0.05
26 10 0.50
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAAATAAATCACAATAACTTTTTTC
Found at i:20251 original size:19 final size:21
Alignment explanation
Indices: 20227--20278 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
20217 CGGCCAAGAG
*
20227 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
20246 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
20267 CATGTATTTTCA
1 CATGTATTTTCA
20279 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:21021 original size:20 final size:21
Alignment explanation
Indices: 20991--21051 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
20981 TGGAGTACAA
20991 AAAGAAAGAAAAGACAAAAAAG
1 AAAG-AAGAAAAGACAAAAAAG
**
21013 -AAGAAGAAAATTCAGAAAAAG
1 AAAGAAGAAAAGACA-AAAAAG
21034 AAAAGAAGAAAAGA-AAAA
1 -AAAGAAGAAAAGACAAAA
21052 GAAATTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 9 0.28
21 12 0.38
22 1 0.03
23 10 0.31
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (21 bp):
AAAGAAGAAAAGACAAAAAAG
Found at i:21051 original size:14 final size:14
Alignment explanation
Indices: 20989--21054 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
20979 ATTGGAGTAC
20989 AAAAAGAAAGAAAAG
1 AAAAAG-AAGAAAAG
21004 ACAAAA-AAGAAGAAG
1 A-AAAAGAAGAA-AAG
***
21019 AAAATTCAGAAAA-
1 AAAAAGAAGAAAAG
21032 AGAAAAGAAGAAAAG
1 A-AAAAGAAGAAAAG
21047 AAAAAGAA
1 AAAAAGAA
21055 ATTCAAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
13 1 0.02
14 26 0.63
15 10 0.24
16 4 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (14 bp):
AAAAAGAAGAAAAG
Found at i:24361 original size:19 final size:21
Alignment explanation
Indices: 24337--24388 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
24327 CGGCCAAGAG
*
24337 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
24356 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
24377 CATGTATTTTCA
1 CATGTATTTTCA
24389 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:28156 original size:17 final size:17
Alignment explanation
Indices: 28134--28199 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 17
28124 AATAATTAAT
28134 TAATAAATTTAAATAAA
1 TAATAAATTTAAATAAA
*
28151 TAAT-AATTTATATAAA
1 TAATAAATTTAAATAAA
* * *
28167 T-ATTATTTTTAATAAA
1 TAATAAATTTAAATAAA
* *
28183 AAATAATATTTATATAA
1 TAATAA-ATTTAAATAA
28200 TTATATTAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
15 2 0.05
16 21 0.57
17 7 0.19
18 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATAAATTTAAATAAA
Found at i:28160 original size:16 final size:16
Alignment explanation
Indices: 28134--28189 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
28124 AATAATTAAT
28134 TAATAAATTTAAATAAA
1 TAAT-AATTTAAATAAA
*
28151 TAATAATTTATATAAA
1 TAATAATTTAAATAAA
* * *
28167 TATTATTTTTAATAAA
1 TAATAATTTAAATAAA
*
28183 AAATAAT
1 TAATAAT
28190 ATTTATATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATTTAAATAAA
Found at i:28214 original size:32 final size:32
Alignment explanation
Indices: 28130--28222 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 32
28120 AAAAAATAAT
* *
28130 TAATTA-ATAAATTTAAATAAATAATAATTTATA
1 TAATTATATTAATATAAA-AAATAAT-ATTTATA
* **
28163 TAAATATTATTTTTAATAAAAAATAATATTTATA
1 TAATTA-TATTAAT-ATAAAAAATAATATTTATA
*
28197 TAATTATATTAATATAAAATATAATA
1 TAATTATATTAATATAAAAAATAATA
28223 ACTATGTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
32 12 0.25
33 10 0.21
34 12 0.25
35 10 0.21
36 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TAATTATATTAATATAAAAAATAATATTTATA
Found at i:28216 original size:30 final size:34
Alignment explanation
Indices: 28143--28223 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 34
28133 TTAATAAATT
*
28143 TAAATAAATAATAATTTATATAAATATTATTTTTAA
1 TAAA-AAATAATAATTTATAT-AATATTATTATTAA
28179 TAAAAAATAAT-ATTTATAT-A-ATTA-TATTAA
1 TAAAAAATAATAATTTATATAATATTATTATTAA
28209 TATAAAATATAATAA
1 TA-AAAA-ATAATAA
28224 CTATGTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
30 7 0.17
31 8 0.20
32 6 0.15
33 1 0.02
34 8 0.20
35 7 0.17
36 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (34 bp):
TAAAAAATAATAATTTATATAATATTATTATTAA
Found at i:31655 original size:30 final size:29
Alignment explanation
Indices: 31587--31674 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 29
31577 ATATTGAAAA
* *
31587 ATAAATAAATATTAAAATAAAAATAATTT
1 ATAAATATATAATAAAATAAAAATAATTT
* *
31616 ATGACTATATAATAATAATAAAAATAATATT
1 ATAAATATATAATAA-AATAAAAATAAT-TT
31647 -TAAATATATAAATAAAATTAAAACATAA
1 ATAAATATAT-AATAAAA-TAAAA-ATAA
31675 ATAAACAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 11 0.23
30 21 0.44
31 12 0.25
32 4 0.08
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (29 bp):
ATAAATATATAATAAAATAAAAATAATTT
Found at i:32580 original size:18 final size:17
Alignment explanation
Indices: 32547--32580 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
32537 GGTTTACTTG
*
32547 CTTTTTTTTTCTTGTTT
1 CTTTTTTTTCCTTGTTT
32564 CTTTTTTTTCCTCTGTT
1 CTTTTTTTTCCT-TGTT
32581 GGTTGCCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (17 bp):
CTTTTTTTTCCTTGTTT
Found at i:33048 original size:3 final size:3
Alignment explanation
Indices: 33042--33074 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
33032 ATAATAATAA
33042 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
33075 AATAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:33462 original size:124 final size:124
Alignment explanation
Indices: 33233--34217 Score: 632
Period size: 112 Copynumber: 8.4 Consensus size: 124
33223 GTTGAATAAA
* * * * * *
33233 TTCTTCTAT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG---GGATGATGTTGA
1 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAAGTTGATGCTAA
* * * * ** * *
33294 CCTATTTCCTTCTGTGATAGAGTCATTTAAAAGGTTGAATAAGCTCTTTTCATTATGAAC
65 TCTATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
*
33354 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTAATGCTAAT
1 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAAT
*
33419 CTATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC
66 CTATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
33478 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAAT
1 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAAT
*
33543 CTATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC
66 CTATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
** * * * *
33602 TTCTTC-TTCTT-TAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGAT-C--
1 TTCTTCTTTCTTCTTCA-GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGCTA
*** ** **
33661 --C-A--T-C--AAATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
64 ATCTATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* * * *
33714 TTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGAT-C----
1 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAAT
** * * **
33774 C-A--T-C--AAGTGATGGATTTGA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-
66 CTATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* * *
33826 -T-TTC-TTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGAT-C
1 TTCTTCTTTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGC
*** ** **
33886 ----C-A--T-C--AAATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
62 TAATCTATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* * * *
33939 TTCTTCTTCCTTATTTAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTT-AT-C---
1 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG-TTGATGCTAA
** * * **
33999 -C-A--T-C--AAGTGATGGATTTGA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-
65 TCTATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* * *
34051 -T-TTC-TTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGAT-C
1 TTCTTCTTTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGC
*** ** **
34111 ----C-A--T-C--AAATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
62 TAATCTATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
*
34164 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
1 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
34218 CTGGTCCATC
Statistics
Matches: 749, Mismatches: 81, Indels: 76
0.83 0.09 0.08
Matches are distributed among these distances:
109 21 0.03
110 6 0.01
111 19 0.03
112 193 0.26
113 184 0.25
114 17 0.02
115 7 0.01
116 22 0.03
117 1 0.00
118 1 0.00
121 13 0.02
122 36 0.05
123 40 0.05
124 189 0.25
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (124 bp):
TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAAT
CTATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
Found at i:33692 original size:112 final size:112
Alignment explanation
Indices: 33569--34204 Score: 855
Period size: 112 Copynumber: 5.7 Consensus size: 112
33559 TAGAATTATG
** *
33569 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTTAGATGACGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTAGATGACGAGTTCTTCTCAT
33634 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
** *
33681 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTA-GATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTT-TAGATGACGAGTTCTTCTC
* ** * * * * * ** *
33745 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
64 ATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
* *
33794 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTAGATGACGAGTTCTTCTCAT
33859 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
* ** *
33906 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTATTTAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTAGAT-GACGAGTTCTTCTCA
* ** * * * * ** *
33971 TTATGAACTTTTTCTGGAAAAGCTT-ATCCATCAAGTGATGGATTTGAG
65 TTATGAACTCTACCTGGCAATG-TTGATCCATCAAATGATGAATTCAAA
* *
34019 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTAGATGACGAGTTCTTCTCAT
34084 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
** *
34131 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTT-TAGATGACGAGTTCTTCTC
34195 ATTATGAACT
64 ATTATGAACT
34205 TTCTCTGGAA
Statistics
Matches: 446, Mismatches: 70, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
111 3 0.01
112 225 0.50
113 213 0.48
114 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTAGATGACGAGTTCTTCTCAT
TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
Found at i:33798 original size:113 final size:113
Alignment explanation
Indices: 33569--34227 Score: 846
Period size: 113 Copynumber: 5.9 Consensus size: 113
33559 TAGAATTATG
** *
33569 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTT-TAGATGACGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTAGATGACGAGTTCTTCTCA
* * *
33633 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
** *
33681 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTA-GATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTAGATGACGAGTTCTTCTC
* ** * * ** *
33745 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
65 ATTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
*
33794 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTC-AGATGACGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTAGATGACGAGTTCTTCTCA
* * *
33858 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
* ** *
33906 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT-TATTTAGATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTAGAT-GACGAGTTCTTCTC
* ** * * * ** *
33970 ATTATGAACTTTTTCTGGAAAAGCTTATCCATCAAGTGATGGATTTGAG
65 ATTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
*
34019 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTC-AGATGACGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTAGATGACGAGTTCTTCTCA
* * *
34083 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
** *
34131 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTAGATGACGAGTTCTTCTC
* *
34195 ATTATGAACT-TTCTCTGGAAAAGCTGGTCCATC
65 ATTATGAACTCTAC-CTGGAAAAGCTGATCCATC
34228 TGGTGATGGA
Statistics
Matches: 463, Mismatches: 75, Indels: 17
0.83 0.14 0.03
Matches are distributed among these distances:
111 1 0.00
112 229 0.49
113 230 0.50
114 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTAGATGACGAGTTCTTCTCA
TTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
Found at i:33836 original size:225 final size:225
Alignment explanation
Indices: 33568--34240 Score: 1238
Period size: 225 Copynumber: 3.0 Consensus size: 225
33558 ATAGAATTAT
** * * *
33568 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTTAGATGACGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCA
33633 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
66 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
33698 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
33763 AAAAGCTGATCCATCAAGTGATGGATTTGA
196 AAAAGCTGATCCATCAAGTGATGGATTTGA
33793 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCA
33858 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
66 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
*
33923 TCTTCTCATTATGAACTTCTTCTTCCTTATTTAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
*
33988 AAAAGCTTATCCATCAAGTGATGGATTTGA
196 AAAAGCTGATCCATCAAGTGATGGATTTGA
34018 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCA
34083 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
66 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
* *
34148 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
* **
34213 AAAAGCTGGTCCATCTGGTGATGGATTT
196 AAAAGCTGATCCATCAAGTGATGGATTT
34241 TAATCTTTGC
Statistics
Matches: 434, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
225 434 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (225 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCA
TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
AAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:35092 original size:114 final size:113
Alignment explanation
Indices: 34929--35265 Score: 523
Period size: 114 Copynumber: 3.0 Consensus size: 113
34919 GATCATGCAG
* ** * * * * * *
34929 TTCATCTTTCAATTCCAATGATTGGTTTT-GTGATTCTTACCGAACCAGATCAGATGACTCAAAG
1 TTCATCTTTCAAATCCAATGATTAATTTTAG-GGTTCATATCAAATCAGATCAGATAACTCAAAG
34993 AACACTTCCAGAAGATGCTATTGGATCTTCTTATTTCTACTATGAGCAAA
65 AACACTTCCAGAAGATGCTATTGG-TCTTCTTATTTCTACTATGAGCAAA
*
35043 TTCATCTTTCAAATCTAATGATTAATTTTAGGGTTCATATCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTAATTTTAGGGTTCATATCAAATCAGATCAGATAACTCAAAGA
35108 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATT-GGTCTTCTTATTTCTACTATGAGCAAA
* *
35157 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATATCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTAATTTTAGGGTTCATATCAAATCAGATCAGATAACTCAAAGA
35222 ACACTTCCAGAAGATGCTATTGTGTCTTCTTATTTCTACTATGA
66 ACACTTCCAGAAGATGCTATTG-GTCTTCTTATTTCTACTATGA
35266 TAACGTGACA
Statistics
Matches: 207, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
113 1 0.00
114 203 0.98
115 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (113 bp):
TTCATCTTTCAAATCCAATGATTAATTTTAGGGTTCATATCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:35586 original size:19 final size:17
Alignment explanation
Indices: 35558--35606 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
35548 AAAATAAAAG
*
35558 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
35577 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
35593 AATAAATTGAATTT
1 AATAAATTGAATTT
35607 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:35977 original size:13 final size:13
Alignment explanation
Indices: 35959--36013 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
35949 CTTGACCCCC
35959 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
35972 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
* *
35985 CTTTATTCTT-TT
1 TTTTTTTCTTCTT
* *
35997 TTATTTT-TTATT
1 TTTTTTTCTTCTT
36009 TTTTT
1 TTTTT
36014 CAAGCATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
11 2 0.06
12 12 0.34
13 21 0.60
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:35983 original size:16 final size:15
Alignment explanation
Indices: 35959--36014 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 15
35949 CTTGACCCCC
35959 TTTTTTTCTTCTTTT
1 TTTTTTTCTTCTTTT
35974 TTTTTCTTCTTCTTTAT
1 TTTTT-TTCTTCTTT-T
*
35991 TCTTTTTTATT-TTTT
1 T-TTTTTTCTTCTTTT
36006 ATTTTTTTC
1 -TTTTTTTC
36015 AAGCATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
15 12 0.34
16 13 0.37
17 6 0.17
18 4 0.11
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTCTTCTTTT
Found at i:43371 original size:15 final size:15
Alignment explanation
Indices: 43348--43379 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43338 TGAAATTAAT
43348 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
43363 AATGTATGTATGCAA
1 AATGAATGTATGCAA
43378 AA
1 AA
43380 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:47443 original size:30 final size:29
Alignment explanation
Indices: 47375--47453 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 29
47365 ATATTGAAAA
* *
47375 ATAAATAAATATTAAAATAAAAATAATTT
1 ATAAATATATAATAAAATAAAAATAATTT
* *
47404 ATGACTATATAATAATAATAAAAATAATATT
1 ATAAATATATAATAA-AATAAAAATAAT-TT
47435 -TAAATATAT-AT-AAATAAAA
1 ATAAATATATAATAAAATAAAA
47454 TTAAAACATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 7 0.17
28 1 0.02
29 13 0.31
30 19 0.45
31 2 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (29 bp):
ATAAATATATAATAAAATAAAAATAATTT
Found at i:47451 original size:21 final size:21
Alignment explanation
Indices: 47417--47480 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
47407 ACTATATAAT
* *
47417 AATA-ATAAAAATAATATTTA
1 AATATATATAAATAATATTAA
*
47437 AATATATATAAATAAAATTAA
1 AATATATATAAATAATATTAA
* * * *
47458 AACATAAATAAACAATAATAA
1 AATATATATAAATAATATTAA
47479 AA
1 AA
47481 ATACAATTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 4 0.11
21 31 0.89
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AATATATATAAATAATATTAA
Found at i:48563 original size:9 final size:10
Alignment explanation
Indices: 48473--48563 Score: 63
Period size: 9 Copynumber: 9.9 Consensus size: 10
48463 TTTGGGCCTG
*
48473 TAATAATATT
1 TAATAATATA
* *
48483 TATTATTAT-
1 TAATAATATA
48492 TAATAATA-A
1 TAATAATATA
48501 TAATAATA-A
1 TAATAATATA
* *
48510 TTATTAT-TA
1 TAATAATATA
* *
48519 TTATTAT-TA
1 TAATAATATA
48528 TAATAAT-TA
1 TAATAATATA
48537 TAATAATA-A
1 TAATAATATA
48546 TAATAATATA
1 TAATAATATA
48556 -AATAATAT
1 TAATAATAT
48564 TTAAATGAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
9 61 0.88
10 8 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TAATAATATA
Found at i:49303 original size:2 final size:2
Alignment explanation
Indices: 49286--49321 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
49276 ACACACACAC
* *
49286 AT AT AC AT AT AC 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
49322 CAATAAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:57819 original size:6 final size:6
Alignment explanation
Indices: 57808--57849 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
57798 AGACCCATAT
** *
57808 GTCATG GTCATG GTCACA GTCATG GTCATG GTCACG GTCATG
1 GTCATG GTCATG GTCATG GTCATG GTCATG GTCATG GTCATG
57850 ACACAAGGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (6 bp):
GTCATG
Found at i:57831 original size:18 final size:18
Alignment explanation
Indices: 57808--57849 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
57798 AGACCCATAT
57808 GTCATGGTCATGGTCACA
1 GTCATGGTCATGGTCACA
*
57826 GTCATGGTCATGGTCACG
1 GTCATGGTCATGGTCACA
57844 GTCATG
1 GTCATG
57850 ACACAAGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (18 bp):
GTCATGGTCATGGTCACA
Found at i:95802 original size:32 final size:31
Alignment explanation
Indices: 95727--95803 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
95717 CTAATATGAC
* * * *
95727 TCTTAGGTAGGCTCTGTGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
*
95758 TCTCAGGTAGGCCCTGCGACCCTAAGAT-ATGT
1 TCTTAGGTAGGCCCTGCGACCCTAAGATCA--T
95790 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
95804 ATGGCCCCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 1 0.03
31 23 0.61
32 14 0.37
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
Done.