Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004789.1 Hibiscus syriacus cultivar Beakdansim tig00010794_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: 66284
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:5633 original size:24 final size:25
Alignment explanation
Indices: 5604--5650 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5594 TTCATCTAAC
5604 AAACTAACT-GAAATATTAACAACA
1 AAACTAACTCGAAATATTAACAACA
* *
5628 AAACTAACTCTAAATATTTACAA
1 AAACTAACTCGAAATATTAACAA
5651 TATCAACAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.26
Consensus pattern (25 bp):
AAACTAACTCGAAATATTAACAACA
Found at i:6413 original size:17 final size:17
Alignment explanation
Indices: 6391--6430 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
6381 TAGATGCAAA
6391 TAGCCTTAAGTTTCGCT
1 TAGCCTTAAGTTTCGCT
6408 TAGCCTTAAGTTTCGCT
1 TAGCCTTAAGTTTCGCT
*
6425 TTGCCT
1 TAGCCT
6431 CAATTACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.42
Consensus pattern (17 bp):
TAGCCTTAAGTTTCGCT
Found at i:12548 original size:14 final size:14
Alignment explanation
Indices: 12529--12555 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12519 TTTTCATTTA
12529 TAATATTTTTTGAT
1 TAATATTTTTTGAT
12543 TAATATTTTTTGA
1 TAATATTTTTTGA
12556 GGTAACCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TAATATTTTTTGAT
Found at i:14548 original size:41 final size:41
Alignment explanation
Indices: 14491--14572 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
14481 AGATTCAGCG
14491 TCTGCTCCTTGAACGAGGGCAAACGCAACTGGAAGAATATT
1 TCTGCTCCTTGAACGAGGGCAAACGCAACTGGAAGAATATT
14532 TCTGCTCCTTGAACGAGGGCAAACGCAACTGGAAGAATATT
1 TCTGCTCCTTGAACGAGGGCAAACGCAACTGGAAGAATATT
14573 ACGGTTTCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (41 bp):
TCTGCTCCTTGAACGAGGGCAAACGCAACTGGAAGAATATT
Found at i:16741 original size:138 final size:138
Alignment explanation
Indices: 16488--17147 Score: 978
Period size: 138 Copynumber: 4.8 Consensus size: 138
16478 TGTCAGTACC
* * *
16488 CAAAGTGGTGAAAGAGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
*
16553 TTGCCCTATTATGTCATTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
66 TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
16618 GGACTTGG
131 GGACTTGG
* * * *
16626 CAAAATGGTGAAAGCGCGCTCCCGGGGGTGCGCCTTCCATTATTTTGTGAGAGAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * * *
16691 TTACCTTATTATGTCATTCATGTCCCCCGGGGAACTATAGATGGCAGTACCTATTATTTCTGAGG
66 TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
16756 GGACTTGG
131 GGACTTGG
** * *
16764 CAAAGTGGTGAAAGCGCGTTGTCGGGGGCGCGCATTCCATTATTTTGTCAGAGAATATATTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * * ** * *
16829 TTGTCCTATTATGTCACTCATGTCCCCCAGAGAACTATTCATGTCAGTACCTATTATTTATGAGG
66 TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
16894 GGACTTGG
131 GGACTTGG
* * *
16902 CAAAGTGGTAAAAGCGCGTTCTCGGGGGCGCGCATTCCATTATTTTGTCAGAGAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * **
16967 TTGCCCTATTATGTCACTCATGTCCCCCGGAGAAATATTCATGCCAGTACCTATTATTTCTGAGG
66 TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
17032 GGACTTGG
131 GGACTTGG
* * * * * *
17040 CAAAGTGGTGAAAGCGCTTTCCCGGGGGCGCACCTTCAATTATTTTTTTAGAGAATATATTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
* *
17105 TTTCCCTATTATGTCAATCATGTCCCCCGGGGAACTATAGATG
66 TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATG
17148 GATGGTGAAA
Statistics
Matches: 471, Mismatches: 51, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
138 471 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (138 bp):
CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
GGACTTGG
Found at i:17353 original size:63 final size:63
Alignment explanation
Indices: 17272--17399 Score: 193
Period size: 63 Copynumber: 2.0 Consensus size: 63
17262 GTTATGTGAA
* * *
17272 GTTTGAATAAATTAGATAAAATGTTATAAATAAGTTGAATAAATGTGAAGTGATCATTTGGTT
1 GTTTGAATAAATTAGATAAAATGTTATAAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
* * **
17335 GTTTGAATATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
1 GTTTGAATAAATTAGATAAAATGTTATAAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
17398 GT
1 GT
17400 GACATTTAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.39, C:0.01, G:0.22, T:0.38
Consensus pattern (63 bp):
GTTTGAATAAATTAGATAAAATGTTATAAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
Found at i:17484 original size:14 final size:14
Alignment explanation
Indices: 17465--17495 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
17455 TGATAAGTTG
17465 GTTTTAATGTATAT
1 GTTTTAATGTATAT
17479 GTTTTAATGTATAT
1 GTTTTAATGTATAT
17493 GTT
1 GTT
17496 AAGGATAAAA
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:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:17645 original size:34 final size:34
Alignment explanation
Indices: 17603--17675 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
17593 TTAAGTTGAA
17603 TTTAATTTTAAATTTCGAATACCATAATTTATAT
1 TTTAATTTTAAATTTCGAATACCATAATTTATAT
* * *
17637 TTTAATTTTAAATTTTGAATACTATAATTTGTAT
1 TTTAATTTTAAATTTCGAATACCATAATTTATAT
*
17671 ATTAA
1 TTTAA
17676 AAACATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.52
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATACCATAATTTATAT
Found at i:18216 original size:21 final size:20
Alignment explanation
Indices: 18189--18258 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
18179 GTCATAAAAC
*
18189 CCTGCGGGCTAGGTATGTAA
1 CCTGCGGGCTAGGAATGTAA
18209 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
18230 CCCTGAGGGCTAGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
18251 CCCTGCGG
1 -CCTGCGG
18259 AGATGGCATA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.21, C:0.23, G:0.36, T:0.20
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:20116 original size:30 final size:30
Alignment explanation
Indices: 20035--20116 Score: 73
Period size: 30 Copynumber: 2.8 Consensus size: 30
20025 TAATTAGCAC
*
20035 AAAAAATAATTAATTA-ATAA--ATTTAAAT
1 AAAAAATAA-TATTTATATAATTATTTAAAT
* * * *
20063 AAATAATAAT-TATATAAATATTATTTGAAT
1 AAAAAATAATATTTATATA-ATTATTTAAAT
20093 AAAAAATAATATTTATATAATTAT
1 AAAAAATAATATTTATATAATTAT
20117 ATTACTATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
26 2 0.05
27 3 0.07
28 9 0.22
30 21 0.51
31 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (30 bp):
AAAAAATAATATTTATATAATTATTTAAAT
Found at i:20439 original size:60 final size:60
Alignment explanation
Indices: 20342--20484 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 60
20332 TTAATAGAAG
* * * * *
20342 GCGCGTCCTCGGGGATGCGCCTTACCCACGTGACATCCGACTCAGCA-GAACCC-TGTGAAA
1 GCGCGTCCCCGGGGATGTGCCTTACACACGTGACATCC-ACTCAGCATAAACCCAGGT-AAA
* * *
20402 GCGCGTCCCCGGGGATATGCCTTACACACGTGGCATCCAGTCAGCATAAACCCAGGTAAA
1 GCGCGTCCCCGGGGATGTGCCTTACACACGTGACATCCACTCAGCATAAACCCAGGTAAA
*
20462 GCGCATCCCCGGGGATGTGCCTT
1 GCGCGTCCCCGGGGATGTGCCTT
20485 TGTGCCACCT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
59 7 0.10
60 62 0.87
61 2 0.03
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.17
Consensus pattern (60 bp):
GCGCGTCCCCGGGGATGTGCCTTACACACGTGACATCCACTCAGCATAAACCCAGGTAAA
Found at i:21077 original size:22 final size:20
Alignment explanation
Indices: 21031--21088 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 20
21021 AAATTTAAGA
*
21031 AAACAA-AAAAAAAGTAAAT
1 AAACAATAAAAAAAATAAAT
*
21050 ACACAATAAAAATAAATAAATT
1 AAACAATAAAAA-AAATAAA-T
21072 AAACAAATAAAACAAAA
1 AAAC-AATAAAA-AAAA
21089 ATGAATTGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.16
20 5 0.16
21 6 0.19
22 4 0.13
23 10 0.32
24 1 0.03
ACGTcount: A:0.76, C:0.09, G:0.02, T:0.14
Consensus pattern (20 bp):
AAACAATAAAAAAAATAAAT
Found at i:24266 original size:24 final size:24
Alignment explanation
Indices: 24239--24306 Score: 127
Period size: 24 Copynumber: 2.8 Consensus size: 24
24229 CATTGACTAC
24239 TCAGATAAGTTAGTTTTCATAAAA
1 TCAGATAAGTTAGTTTTCATAAAA
24263 TCAGATAAGTTAGTTTTCATAAAA
1 TCAGATAAGTTAGTTTTCATAAAA
*
24287 TCAGATAAGTTAGTCTTCAT
1 TCAGATAAGTTAGTTTTCAT
24307 CACTTTATAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (24 bp):
TCAGATAAGTTAGTTTTCATAAAA
Found at i:28192 original size:21 final size:21
Alignment explanation
Indices: 28163--28202 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28153 CATATAAAAT
*
28163 TGTCCCGAATGACCTCATATA
1 TGTCCCGAATGACCACATATA
*
28184 TGTCTCGAATGACCACATA
1 TGTCCCGAATGACCACATA
28203 GAACCCTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTCCCGAATGACCACATATA
Found at i:30756 original size:26 final size:27
Alignment explanation
Indices: 30713--30765 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
30703 TTAACCTCAA
* * *
30713 AATTCATTTACAATCTC-TATATTAAC
1 AATTCACTTAAAAACTCTTATATTAAC
30739 AATTCACTTAAAAACTCTTTATATTAA
1 AATTCACTTAAAAACTC-TTATATTAA
30766 ATCTTTCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 14 0.64
28 8 0.36
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTCACTTAAAAACTCTTATATTAAC
Found at i:35214 original size:19 final size:19
Alignment explanation
Indices: 35192--35230 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
35182 TTCCTTATGT
* *
35192 GGTATCGATACCCTTCTTC
1 GGTACCGATACCCTCCTTC
35211 GGTACCGATACCCTCCTTC
1 GGTACCGATACCCTCCTTC
35230 G
1 G
35231 ATACTGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.15, C:0.36, G:0.18, T:0.31
Consensus pattern (19 bp):
GGTACCGATACCCTCCTTC
Found at i:35239 original size:19 final size:19
Alignment explanation
Indices: 35197--35239 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
35187 TATGTGGTAT
* *
35197 CGATACCCTTCTTCGGTAC
1 CGATACCCTCCTTCGATAC
35216 CGATACCCTCCTTCGATAC
1 CGATACCCTCCTTCGATAC
*
35235 TGATA
1 CGATA
35240 TCATTTCAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.21, C:0.35, G:0.14, T:0.30
Consensus pattern (19 bp):
CGATACCCTCCTTCGATAC
Found at i:39956 original size:5 final size:6
Alignment explanation
Indices: 39931--39961 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39921 TTTATAAATC
*
39931 AAAGAA AAAGAA AAATAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A
39962 GTACATCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:41189 original size:58 final size:58
Alignment explanation
Indices: 41069--41180 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
41059 GAGGAGGAAT
* * * * *
41069 GGGGAGGGGGGAGTTGAGAGTGAAATCATATTTTTTTTTGTTTCAAACAATGAAATGG
1 GGGGAGGGGAGAGTTGAGAGTAAAATCATATATATATTTGTTTCAAACAATGAAATGG
*
41127 GGGGAGGGGAGAGTTGAGAGTAAAAAT-ATATATATATTT-TTTCAGACAATGAAA
1 GGGGAGGGGAGAGTTGAGAGT-AAAATCATATATATATTTGTTTCAAACAATGAAA
41181 GGTCGGGGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 14 0.30
58 29 0.62
59 4 0.09
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.30
Consensus pattern (58 bp):
GGGGAGGGGAGAGTTGAGAGTAAAATCATATATATATTTGTTTCAAACAATGAAATGG
Found at i:45159 original size:29 final size:29
Alignment explanation
Indices: 45114--45171 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
45104 CTGTTGGCCG
*
45114 TAGGTCGCCATGCCTTCCGGGAGACCTAC
1 TAGGTCGCCATGCCTTCCCGGAGACCTAC
* *
45143 TAGGTCGCCATGTCTTCCCGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGAGACCTAC
45172 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGAGACCTAC
Found at i:45224 original size:10 final size:10
Alignment explanation
Indices: 45211--45281 Score: 65
Period size: 10 Copynumber: 6.7 Consensus size: 10
45201 ACACGCTGGG
45211 CATCCGAGGC
1 CATCCGAGGC
45221 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
*
45235 CATCCGAAAG-
1 CATCCG-AGGC
45245 CATCCGAGGC
1 CATCCGAGGC
45255 CATCCGAGAG-
1 CATCCGAG-GC
45265 CATCCGAGGC
1 CATCCGAGGC
45275 CATCCGA
1 CATCCGA
45282 CCGAGGCCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
9 3 0.06
10 33 0.65
11 5 0.10
13 2 0.04
14 8 0.16
ACGTcount: A:0.25, C:0.38, G:0.27, T:0.10
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:45253 original size:20 final size:20
Alignment explanation
Indices: 45228--45281 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
45218 GGCCATCCGA
45228 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
45248 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
45268 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
45282 CCGAGGCCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.37, G:0.28, T:0.09
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:45295 original size:10 final size:10
Alignment explanation
Indices: 45228--45281 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
45218 GGCCATCCGA
45228 CCGAGGCCAT
1 CCGAGGCCAT
*
45238 CCGAAAG-CAT
1 CCG-AGGCCAT
45248 CCGAGGCCAT
1 CCGAGGCCAT
45258 CCGAGAG-CAT
1 CCGAG-GCCAT
45268 CCGAGGCCAT
1 CCGAGGCCAT
45278 CCGA
1 CCGA
45282 CCGAGGCCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 3 0.08
10 32 0.84
11 3 0.08
ACGTcount: A:0.26, C:0.37, G:0.28, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:45452 original size:23 final size:23
Alignment explanation
Indices: 45394--45453 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
45384 CTCGGTTGCC
* **
45394 CTCGGATTCCCTCTTATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
*
45417 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
45440 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
45454 GTCGGATGGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.10, C:0.35, G:0.25, T:0.30
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:45458 original size:14 final size:14
Alignment explanation
Indices: 45436--45468 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
45426 CCTCGCATAG
*
45436 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
45450 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
45464 CTCGG
1 CTCGG
45469 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:45504 original size:14 final size:14
Alignment explanation
Indices: 45485--45540 Score: 85
Period size: 14 Copynumber: 4.0 Consensus size: 14
45475 TCGGATGCTT
45485 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
* *
45499 TCGGATGACCTCTG
1 TCGGATGGCCTCGG
45513 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
*
45527 TCGGATGGCATCGG
1 TCGGATGGCCTCGG
45541 ATGCCCAGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.11, C:0.27, G:0.39, T:0.23
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:45791 original size:22 final size:22
Alignment explanation
Indices: 45755--45801 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
45745 AAATTTAGCG
*
45755 AAACCGAAAGCAACCCAAACCA
1 AAACCGAAAGCAACCCAAACAA
** *
45777 AAACCGAAATTAACCCGAACAA
1 AAACCGAAAGCAACCCAAACAA
45799 AAA
1 AAA
45802 ATAACCCCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.30, G:0.09, T:0.04
Consensus pattern (22 bp):
AAACCGAAAGCAACCCAAACAA
Found at i:45866 original size:32 final size:32
Alignment explanation
Indices: 45771--45879 Score: 134
Period size: 32 Copynumber: 3.4 Consensus size: 32
45761 AAAGCAACCC
* * *
45771 AAACCAAAACCGAAATTAACCCGAACAAAAA-
1 AAACCCAAACTGAAACTAACCCGAACAAAAAG
* *
45802 ATAACCCCAA-TCGAAACT-ACCCGAACAGAAAG
1 A-AACCCAAACT-GAAACTAACCCGAACAAAAAG
45834 AAACCCAAACTGAAACTAACCCGAACAAAAAG
1 AAACCCAAACTGAAACTAACCCGAACAAAAAG
45866 AAACCCAAACTGAA
1 AAACCCAAACTGAA
45880 TTTTAACCCG
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
31 26 0.39
32 40 0.61
ACGTcount: A:0.55, C:0.28, G:0.09, T:0.07
Consensus pattern (32 bp):
AAACCCAAACTGAAACTAACCCGAACAAAAAG
Found at i:45870 original size:16 final size:16
Alignment explanation
Indices: 45820--45871 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
45810 AATCGAAACT
45820 ACCCGAACAGAAAGAA
1 ACCCGAACAGAAAGAA
* * **
45836 ACCCAAACTGAAACTA
1 ACCCGAACAGAAAGAA
*
45852 ACCCGAACAAAAAGAA
1 ACCCGAACAGAAAGAA
45868 ACCC
1 ACCC
45872 AAACTGAATT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.54, C:0.31, G:0.12, T:0.04
Consensus pattern (16 bp):
ACCCGAACAGAAAGAA
Found at i:45903 original size:33 final size:33
Alignment explanation
Indices: 45820--45923 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 33
45810 AATCGAAACT
**
45820 ACCCGAACAGAAAGAAACCCAAACTGAA-ACTA
1 ACCCGAACAGAAAGAAACCCAAACTGAATTTTA
*
45852 ACCCGAACAAAAAGAAACCCAAACTGAATTTTA
1 ACCCGAACAGAAAGAAACCCAAACTGAATTTTA
* * *
45885 ACCCGAATC-GAAATAAACCCGAACCGAATTTTA
1 ACCCGAA-CAGAAAGAAACCCAAACTGAATTTTA
45918 ACCCGA
1 ACCCGA
45924 TCCGAAAGCA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
32 27 0.43
33 35 0.56
34 1 0.02
ACGTcount: A:0.48, C:0.28, G:0.12, T:0.12
Consensus pattern (33 bp):
ACCCGAACAGAAAGAAACCCAAACTGAATTTTA
Found at i:45922 original size:17 final size:17
Alignment explanation
Indices: 45867--45929 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
45857 AACAAAAAGA
* *
45867 AACCCAAACTGAATTTT
1 AACCCGAACCGAATTTT
* * *
45884 AACCCGAATCGAA-ATA
1 AACCCGAACCGAATTTT
45900 AACCCGAACCGAATTTT
1 AACCCGAACCGAATTTT
*
45917 AACCCGATCCGAA
1 AACCCGAACCGAA
45930 AGCAGCTTGA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 13 0.36
17 23 0.64
ACGTcount: A:0.41, C:0.29, G:0.11, T:0.19
Consensus pattern (17 bp):
AACCCGAACCGAATTTT
Found at i:46588 original size:14 final size:14
Alignment explanation
Indices: 46565--46594 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
46555 TTGCATTGAG
46565 TTTCTCAATAAAAC
1 TTTCTCAATAAAAC
*
46579 TTTCTTAATAAAAC
1 TTTCTCAATAAAAC
46593 TT
1 TT
46595 AAAAGATCAA
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:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTCTCAATAAAAC
Found at i:47266 original size:21 final size:21
Alignment explanation
Indices: 47242--47301 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
47232 AAAAAAAAGT
* *
47242 AAAAATGAAAAATATTAAATG
1 AAAAATGAAAAATATAAAATA
*
47263 AAAAATGAAAAATAAAAAATA
1 AAAAATGAAAAATATAAAATA
*
47284 AAAAAGTTAAAAATATAA
1 AAAAA-TGAAAAATATAA
47302 GAAACTTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAAATGAAAAATATAAAATA
Found at i:47275 original size:14 final size:13
Alignment explanation
Indices: 47235--47287 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
47225 AAATTATAAA
47235 AAAAAGTAAAAATG
1 AAAAA-TAAAAATG
*
47249 AAAAATATTAAATG
1 AAAAATA-AAAATG
*
47263 AAAAATGAAAAATA
1 AAAAAT-AAAAATG
47277 AAAAATAAAAA
1 AAAAATAAAAA
47288 AGTTAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 7 0.21
14 26 0.76
15 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (13 bp):
AAAAATAAAAATG
Found at i:47288 original size:7 final size:7
Alignment explanation
Indices: 47242--47298 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
47232 AAAAAAAAGT
*
47242 AAAAATG
1 AAAAATA
47249 AAAAATA
1 AAAAATA
** *
47256 TTAAATG
1 AAAAATA
*
47263 AAAAATG
1 AAAAATA
47270 AAAAATA
1 AAAAATA
47277 AAAAATA
1 AAAAATA
*
47284 AAAAAGTT
1 AAAAA-TA
47292 AAAAATA
1 AAAAATA
47299 TAAGAAACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
7 34 0.85
8 6 0.15
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (7 bp):
AAAAATA
Found at i:47288 original size:14 final size:14
Alignment explanation
Indices: 47242--47298 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
47232 AAAAAAAAGT
47242 AAAAATGAAAAATA
1 AAAAATGAAAAATA
** *
47256 TTAAATGAAAAATG
1 AAAAATGAAAAATA
*
47270 AAAAATAAAAAATA
1 AAAAATGAAAAATA
*
47284 AAAAAGTTAAAAATA
1 AAAAA-TGAAAAATA
47299 TAAGAAACTT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
14 26 0.76
15 8 0.24
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (14 bp):
AAAAATGAAAAATA
Found at i:52024 original size:20 final size:20
Alignment explanation
Indices: 52010--52060 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
52000 GCAAAAGTTT
52010 ATTTTGAAAAACAAAATGAA
1 ATTTTGAAAAACAAAATGAA
52030 ATTTTGAAAAACAAAATGAA
1 ATTTTGAAAAACAAAATGAA
52050 ATTTTGAAAAA
1 ATTTTGAAAAA
52061 ATGATTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.27
Consensus pattern (20 bp):
ATTTTGAAAAACAAAATGAA
Found at i:56501 original size:21 final size:20
Alignment explanation
Indices: 56443--56514 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
56433 AGTAGGTTTG
* *
56443 GGATCAATCCCTTCACCAAAA
1 GGATTAATCCCTTC-CCTAAA
56464 GGATTAATCCCTTCCCTAAA
1 GGATTAATCCCTTCCCTAAA
* *
56484 GGATTGATCTCTTTCCCTAAA
1 GGATTAATC-CCTTCCCTAAA
* *
56505 TGATCAATCC
1 GGATTAATCC
56515 ATTTCTTGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (20 bp):
GGATTAATCCCTTCCCTAAA
Found at i:58884 original size:18 final size:17
Alignment explanation
Indices: 58852--58885 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
58842 ATTTCATGCA
*
58852 ATTTTATTTTTTATATG
1 ATTTTATTGTTTATATG
58869 ATTTTATATGTTTATAT
1 ATTTTAT-TGTTTATAT
58886 ATATGATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
ATTTTATTGTTTATATG
Found at i:65307 original size:20 final size:20
Alignment explanation
Indices: 65270--65311 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
65260 GAATTCCACC
*
65270 ATGCAACTATATGCTCCTAA
1 ATGCAACTACATGCTCCTAA
* *
65290 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
65310 AT
1 AT
65312 TGGCTCTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Done.