Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003861.1 Hibiscus syriacus cultivar Beakdansim tig00008299_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: 102988
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:428 original size:2 final size:2
Alignment explanation
Indices: 421--506 Score: 142
Period size: 2 Copynumber: 44.5 Consensus size: 2
411 ATACATACAT
421 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A- AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
462 AC AC AC AC AC AC -C AC AC AC AC AC AC AA AC AC AC A- AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
502 AC AC A
1 AC AC A
507 TATATATTGG
Statistics
Matches: 79, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 3 0.04
2 76 0.96
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2647 original size:27 final size:28
Alignment explanation
Indices: 2612--2664 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
2602 AGAATGAAAA
*
2612 GATGCAAATACAGATGC-AACAAAATGTT
1 GATGCAAATACA-ATGCGAAAAAAATGTT
*
2640 GATG-AAATGCAATGCGAAAAAAATG
1 GATGCAAATACAATGCGAAAAAAATG
2665 ACACAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 4 0.18
27 14 0.64
28 4 0.18
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (28 bp):
GATGCAAATACAATGCGAAAAAAATGTT
Found at i:6025 original size:14 final size:14
Alignment explanation
Indices: 6006--6035 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5996 TACCAAAAAG
*
6006 TAAAATAATATTAA
1 TAAAATAATAATAA
6020 TAAAATAATAATAA
1 TAAAATAATAATAA
6034 TA
1 TA
6036 TTATTATTAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAATAATAATAA
Found at i:6080 original size:2 final size:2
Alignment explanation
Indices: 6075--6124 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
6065 AAATGTTACA
6075 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
6117 AT AT AT AT
1 AT AT AT AT
6125 TGATATAGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6745 original size:21 final size:18
Alignment explanation
Indices: 6721--6763 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 18
6711 AATAAGGGTT
6721 TTTTTTATAAATATAATAATA
1 TTTTTTATAAA-A-AATAA-A
6742 TTTTTTATAAAAAATAAA
1 TTTTTTATAAAAAATAAA
6760 TTTT
1 TTTT
6764 AAAATTACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 1 0.05
21 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTTTATAAAAAATAAA
Found at i:9989 original size:15 final size:15
Alignment explanation
Indices: 9956--9996 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
9946 TAATGGAAGT
* *
9956 AATCCCTGCA-AATA
1 AATCTCTGCATAAAA
9970 AATCTCTGCATAAAA
1 AATCTCTGCATAAAA
9985 AATCTCTGCATA
1 AATCTCTGCATA
9997 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (15 bp):
AATCTCTGCATAAAA
Found at i:10288 original size:15 final size:15
Alignment explanation
Indices: 10268--10314 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
10258 CCCTGGTTTT
10268 AATATGAATGATTAA
1 AATATGAATGATTAA
* *
10283 AATATGATTAATTTAA
1 AATATGAATGA-TTAA
10299 AA-ATTGAATGATTAA
1 AATA-TGAATGATTAA
10314 A
1 A
10315 TTAAAAGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (15 bp):
AATATGAATGATTAA
Found at i:17315 original size:212 final size:212
Alignment explanation
Indices: 16940--17358 Score: 757
Period size: 212 Copynumber: 2.0 Consensus size: 212
16930 AATCATCATC
* *
16940 AACCTTTATTATCTTCGAACAAACACTCACTCATCGGAAACGTTAGGGTTGCACCTAAAAGTGTA
1 AACCTTCATTATCTTCGAACAAACACTCACTCATCGGAAACATTAGGGTTGCACCTAAAAGTGTA
* *
17005 TCGTTGGAAACGTTAGATACCTATTTTTAACAAAAAATTCTTTAGGCACCTAAAGTTAGCATAGG
66 TCATTGGAAACATTAGATACCTATTTTTAACAAAAAATTCTTTAGGCACCTAAAGTTAGCATAGG
** *
17070 GTTTAATTTGGGCATTTATTTTATATTAAGTCAAAATATAAACATGATGTAGATACCCGTTTTTG
131 GAATAATTTGGGCATTTATTTTATATGAAGTCAAAATATAAACATGATGTAGATACCCGTTTTTG
17135 TCCGGGTTATTATTAAT
196 TCCGGGTTATTATTAAT
17152 AACCTTCATTATCTTCGAACAAACACTCACTCATCGGAAACATTAGGGTTGCACCTAAAAGTGTA
1 AACCTTCATTATCTTCGAACAAACACTCACTCATCGGAAACATTAGGGTTGCACCTAAAAGTGTA
* *
17217 TCATTGGAAACATTAGATACCTATTTTTAACGAAAAATTCTTTAGGCACCTAAAGTTAGCATAGT
66 TCATTGGAAACATTAGATACCTATTTTTAACAAAAAATTCTTTAGGCACCTAAAGTTAGCATAGG
17282 GAATAATTTGGGCATTTATTTTATATGAAGTCAAAATATAAACATGATGTAGATACCCGTTTTTG
131 GAATAATTTGGGCATTTATTTTATATGAAGTCAAAATATAAACATGATGTAGATACCCGTTTTTG
17347 TCCGGGTTATTA
196 TCCGGGTTATTA
17359 ATATTTATTA
Statistics
Matches: 198, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
212 198 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (212 bp):
AACCTTCATTATCTTCGAACAAACACTCACTCATCGGAAACATTAGGGTTGCACCTAAAAGTGTA
TCATTGGAAACATTAGATACCTATTTTTAACAAAAAATTCTTTAGGCACCTAAAGTTAGCATAGG
GAATAATTTGGGCATTTATTTTATATGAAGTCAAAATATAAACATGATGTAGATACCCGTTTTTG
TCCGGGTTATTATTAAT
Found at i:17377 original size:19 final size:19
Alignment explanation
Indices: 17353--17394 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17343 TTTGTCCGGG
*
17353 TTATTAATATTTATTATTA
1 TTATTAATATTAATTATTA
* *
17372 TTATTATTATTAATTTTTA
1 TTATTAATATTAATTATTA
17391 TTAT
1 TTAT
17395 CATTTTTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTAATATTAATTATTA
Found at i:21303 original size:11 final size:9
Alignment explanation
Indices: 21279--21316 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
21269 AAAATATGAT
21279 AAGAGAGAA
1 AAGAGAGAA
21288 AAGAGAGAA
1 AAGAGAGAA
*
21297 AAGAGAGAT
1 AAGAGAGAA
21306 AAGAGAGAA
1 AAGAGAGAA
21315 AA
1 AA
21317 TGTCCATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (9 bp):
AAGAGAGAA
Found at i:24859 original size:20 final size:20
Alignment explanation
Indices: 24833--24877 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
24823 TATGAGAATA
*
24833 TATAAATTAGGATACATAAAC
1 TATAAATGAGGATACA-AAAC
*
24854 -ATAAATGATGATACAAAAC
1 TATAAATGAGGATACAAAAC
24873 TATAA
1 TATAA
24878 GATAAGTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.27
Consensus pattern (20 bp):
TATAAATGAGGATACAAAAC
Found at i:25551 original size:30 final size:31
Alignment explanation
Indices: 25515--25572 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
25505 AGAGTCGAGG
25515 GTTACCTATGTCCTTC-GGACATATGGACAT
1 GTTACCTATGTCCTTCGGGACATATGGACAT
* *
25545 GTTACCTATGTCTTTCGGGATATATGGA
1 GTTACCTATGTCCTTCGGGACATATGGA
25573 TAGGTCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTACCTATGTCCTTCGGGACATATGGACAT
Found at i:28943 original size:21 final size:21
Alignment explanation
Indices: 28919--28958 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28909 CTTGGTGACG
28919 TATATGACGTCCTTCGGGATA
1 TATATGACGTCCTTCGGGATA
*
28940 TATATGACTTCCTTCGGGA
1 TATATGACGTCCTTCGGGA
28959 CATAGATTTC
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:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TATATGACGTCCTTCGGGATA
Found at i:33663 original size:255 final size:257
Alignment explanation
Indices: 33035--33725 Score: 967
Period size: 258 Copynumber: 2.7 Consensus size: 257
33025 AGTTGTTTTG
* * * * * *
33035 AAAATGAGAAAACGAATTCCAATGTTTCTCATTTAACTTTTTTCTGAAAATGAAATTTTTGAAAA
1 AAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAA-TGTTTACAGAAAATGAAATTTTTGAAAA
* * *
33100 GTAAGAAAGCGATTTCCGAAGTTTCTTACCCAATAAATTATTTCCAAAATTAGTAAGTCCTTTGG
65 GTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTAGTAAGTCCTTCGG
* * * * *
33165 GCCATCAGTATGTCTTTCGATCATGATGATTAAATCCTTCAGGTCATATGTCAGTCTTTCGAGCA
130 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAAT-CTTCGGGTCATCTGTCAATCTTTCGAGCA
* * * * **
33230 AGATGATAAGTCATTCGGGCCATCCATAAGTCCTTCGGGCAGGATGTTTCCATATGATTTTTGA
194 AGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAGGATATTTCCACATGATTTTCAA
*
33294 AAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATG-AATTTTTGGAAAA
1 AAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAATGTTTACAGAAAATGAAATTTTT-GAAAA
* * *
33358 GTAAGAAAGTGATTTCCAATGTATCTTACCCAATTAATTATTTCCAAAATTAGTAAGTCCTTCGG
65 GTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTAGTAAGTCCTTCGG
*
33423 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTGGGTCATCTGTCAATCTTTCGAGCAA
130 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTCGGGTCATCTGTCAATCTTTCGAGCAA
* * * * *
33488 GATGTTAAGTCCTTCGGGCCGTCTATAAGACC-TCGAGCAGGATATTTTCACATGATTTTCAA
195 GATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAGGATATTTCCACATGATTTTCAA
* * * *
33550 AAAATAAGAAAGTGATTTCCAAAGTTT-TTATTTAATGTTTACAGAAAATGAAAATTTTGAAAAG
1 AAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAATGTTTACAGAAAATGAAATTTTTGAAAAG
* * *
33614 TAAGAAAGTGACTTCCAAAGTTTCTTACCCAGTAAATTATTTTCAAAATTAGTAAGTCCTTCGGG
66 TAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTAGTAAGTCCTTCGGG
* *
33679 CCATCAGTAA-TCTTTCAAGCATGATGATTAAATTCTTCGGGTTATCT
131 CCATCAGTAAGTCTTTCGAGCATGATGATTAAA-TCTTCGGGTCATCT
33726 ATCGGTCTCA
Statistics
Matches: 387, Mismatches: 42, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
254 21 0.05
255 108 0.28
256 55 0.14
257 60 0.16
258 110 0.28
259 33 0.09
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (257 bp):
AAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAATGTTTACAGAAAATGAAATTTTTGAAAAG
TAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTAGTAAGTCCTTCGGG
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTCGGGTCATCTGTCAATCTTTCGAGCAAG
ATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAGGATATTTCCACATGATTTTCAA
Found at i:33865 original size:3 final size:3
Alignment explanation
Indices: 33857--33924 Score: 68
Period size: 3 Copynumber: 22.7 Consensus size: 3
33847 TTTGTCCAGG
* * * *
33857 TTA TTA TTA ATA TTTA ATA TTA TTA TTA TT- TATA TT- GTA TTG TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
33902 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
33925 TTTTACAGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:33879 original size:16 final size:15
Alignment explanation
Indices: 33858--33892 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
33848 TTGTCCAGGT
33858 TATTATTAATATTTAA
1 TATTATTAATATTT-A
*
33874 TATTATTATTATTTA
1 TATTATTAATATTTA
33889 TATT
1 TATT
33893 GTATTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTAATATTTA
Found at i:37168 original size:41 final size:42
Alignment explanation
Indices: 37036--37218 Score: 192
Period size: 41 Copynumber: 4.4 Consensus size: 42
37026 TTGGAGGAAG
* * * * *
37036 TTTCTGAAGGCTCATCTGTTGTGTGCAAGG-ATACCTTACCA
1 TTTCTGAAGGCTCCTCTGCTATGTCCAAGGAAGACCTTACCA
* *
37077 TTTCTGAAGGCTCCTCTACTGTG-CCAAGGTAAGACCTTACCA
1 TTTCTGAAGGCTCCTCTGCTATGTCCAAGG-AAGACCTTACCA
* * *
37119 TTTTTGAAGACTCCTCTGCTATGTACAAGG-AGACCTTACCA
1 TTTCTGAAGGCTCCTCTGCTATGTCCAAGGAAGACCTTACCA
* * *
37160 TTTCTGAAGGCTCCTTTGTTATGTGCCAGGGTAAGACCTTACCA
1 TTTCTGAAGGCTCCTCTGCTATGT-CCAAGG-AAGACCTTACCA
*
37204 TTTCTGCAGGCTCCT
1 TTTCTGAAGGCTCCT
37219 TGGCTTTGTG
Statistics
Matches: 119, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
40 5 0.04
41 51 0.43
42 33 0.28
43 5 0.04
44 25 0.21
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (42 bp):
TTTCTGAAGGCTCCTCTGCTATGTCCAAGGAAGACCTTACCA
Found at i:37207 original size:44 final size:44
Alignment explanation
Indices: 37068--37229 Score: 192
Period size: 44 Copynumber: 3.8 Consensus size: 44
37058 GTGCAAGGAT
37068 ACCTTACCATTTCTGAAGGCTCC--T-CTACTGTGCCAAGGTAAG
1 ACCTTACCATTTCTGAAGGCTCCTTTGCTA-TGTGCCAAGGTAAG
* * * *
37110 ACCTTACCATTTTTGAAGACTCCTCTGCTATGT-ACAAGG--AG
1 ACCTTACCATTTCTGAAGGCTCCTTTGCTATGTGCCAAGGTAAG
* *
37151 ACCTTACCATTTCTGAAGGCTCCTTTGTTATGTGCCAGGGTAAG
1 ACCTTACCATTTCTGAAGGCTCCTTTGCTATGTGCCAAGGTAAG
* * *
37195 ACCTTACCATTTCTGCAGGCTCCTTGGCTTTGTGC
1 ACCTTACCATTTCTGAAGGCTCCTTTGCTATGTGC
37230 TCATGATAAG
Statistics
Matches: 101, Mismatches: 13, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
41 31 0.31
42 25 0.25
43 5 0.05
44 37 0.37
45 3 0.03
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.33
Consensus pattern (44 bp):
ACCTTACCATTTCTGAAGGCTCCTTTGCTATGTGCCAAGGTAAG
Found at i:37218 original size:85 final size:83
Alignment explanation
Indices: 37036--37218 Score: 242
Period size: 83 Copynumber: 2.2 Consensus size: 83
37026 TTGGAGGAAG
* * * * *
37036 TTTCTGAAGGCTCATCTGTTGTGTGCAAGGATACCTTACCATTTCTGAAGGCTCCTCTACTGTGC
1 TTTCTGAAGGCTCCTCTGCTATGTACAAGGAGACCTTACCATTTCTGAAGGCTCCTCTACTGTGC
37101 CAAGGTAAGACCTTACCA
66 CAAGGTAAGACCTTACCA
* * *
37119 TTTTTGAAGACTCCTCTGCTATGTACAAGGAGACCTTACCATTTCTGAAGGCTCCTTTGTTA-TG
1 TTTCTGAAGGCTCCTCTGCTATGTACAAGGAGACCTTACCATTTCTGAAGGCTCC--T-CTACTG
*
37183 TGCCAGGGTAAGACCTTACCA
63 TGCCAAGGTAAGACCTTACCA
*
37204 TTTCTGCAGGCTCCT
1 TTTCTGAAGGCTCCT
37219 TGGCTTTGTG
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
83 48 0.56
85 35 0.41
86 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (83 bp):
TTTCTGAAGGCTCCTCTGCTATGTACAAGGAGACCTTACCATTTCTGAAGGCTCCTCTACTGTGC
CAAGGTAAGACCTTACCA
Found at i:37264 original size:39 final size:38
Alignment explanation
Indices: 37207--37286 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 38
37197 CTTACCATTT
* *
37207 CTGCAGGCTCCTTGGCTTTGTGCTCATGATAAGTCCTTA
1 CTGCAGGCTCCTTGGCTTTGTGCACAGGATAAG-CCTTA
*
37246 CTGCAGGCTCCTCT-GCTTTGTGCACAGGGTAAGCCTTA
1 CTGCAGGCTCCT-TGGCTTTGTGCACAGGATAAGCCTTA
37284 CTG
1 CTG
37287 GGTGTACAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 8 0.22
39 28 0.76
40 1 0.03
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (38 bp):
CTGCAGGCTCCTTGGCTTTGTGCACAGGATAAGCCTTA
Found at i:57345 original size:7 final size:7
Alignment explanation
Indices: 57322--57367 Score: 64
Period size: 7 Copynumber: 7.1 Consensus size: 7
57312 CCATCAAAGG
57322 AAAAT-A
1 AAAATAA
57328 AAAAT--
1 AAAATAA
57333 AAAATAA
1 AAAATAA
57340 AAAAT-A
1 AAAATAA
57346 AAAATAA
1 AAAATAA
57353 AAAATAA
1 AAAATAA
57360 AAAATAA
1 AAAATAA
57367 A
1 A
57368 TAGATTAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.14
6 11 0.30
7 21 0.57
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:57349 original size:13 final size:13
Alignment explanation
Indices: 57322--57367 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
57312 CCATCAAAGG
57322 AAAAT-AAAAAT-
1 AAAATAAAAAATA
57333 AAAATAAAAAATA
1 AAAATAAAAAATA
57346 AAAATAAAAAATAA
1 AAAATAAAAAAT-A
57360 AAAATAAA
1 AAAATAAA
57368 TAGATTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.16
12 6 0.19
13 12 0.38
14 9 0.28
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:57368 original size:18 final size:19
Alignment explanation
Indices: 57322--57369 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
57312 CCATCAAAGG
57322 AAAATAAA-AATAAAATAA
1 AAAATAAATAATAAAATAA
57340 AAAATAAA-AATAAAAAATAA
1 AAAATAAATAAT--AAAATAA
57360 AAAATAAATA
1 AAAATAAATA
57370 GATTAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.41
20 15 0.56
21 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAATAAATAATAAAATAA
Found at i:64381 original size:17 final size:17
Alignment explanation
Indices: 64358--64396 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
64348 TTAAGTGACC
64358 AAAGTATAAACTTTGGA
1 AAAGTATAAACTTTGGA
*
64375 TAAGTATAAACTTTGGA
1 AAAGTATAAACTTTGGA
64392 AAAGT
1 AAAGT
64397 TTAGAGAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (17 bp):
AAAGTATAAACTTTGGA
Found at i:67785 original size:47 final size:46
Alignment explanation
Indices: 67695--67791 Score: 115
Period size: 47 Copynumber: 2.1 Consensus size: 46
67685 ATATCGTGTG
* * * *
67695 TGTTTATTTATTGTTCACGAACATATTCGGTTAATGTTCATGAATA
1 TGTTTATTTATTGTTCACGAACATATTCAGTTAACGTTAATGAACA
* *
67741 TGTTTATTTATATGTTCATGAACGA-ATTCATTTAACGTTAATGAACA
1 TGTTTATTTAT-TGTTCACGAAC-ATATTCAGTTAACGTTAATGAACA
67788 TGTT
1 TGTT
67792 CGTTCAGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
46 11 0.26
47 31 0.72
48 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.45
Consensus pattern (46 bp):
TGTTTATTTATTGTTCACGAACATATTCAGTTAACGTTAATGAACA
Found at i:71181 original size:20 final size:20
Alignment explanation
Indices: 71156--71194 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
71146 TACATGCATA
*
71156 CAGTTACAAGCTACTAACAT
1 CAGTTACAAACTACTAACAT
71176 CAGTTACAAACTACTAACA
1 CAGTTACAAACTACTAACA
71195 ATCCTAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.23
Consensus pattern (20 bp):
CAGTTACAAACTACTAACAT
Found at i:75358 original size:23 final size:23
Alignment explanation
Indices: 75327--75395 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
75317 CACCACAGCT
* *
75327 CGTATAATTGCATCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
75350 CGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
75373 TGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
75396 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:75582 original size:103 final size:103
Alignment explanation
Indices: 75414--75628 Score: 385
Period size: 103 Copynumber: 2.1 Consensus size: 103
75404 TGTCCATAAG
* *
75414 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
*
75479 TTCACACATGTTCCAATGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
75517 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
*
75582 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
75620 GACCACATA
1 GACCACATA
75629 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:80552 original size:23 final size:23
Alignment explanation
Indices: 80526--80594 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
80516 CACCACAGCT
*
80526 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
80549 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
80572 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
80595 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:80782 original size:103 final size:103
Alignment explanation
Indices: 80610--80827 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
80600 TAATGTCCAT
* * *
80610 AAGGACCACATATCATTCCTTAAGAATCATATACAAATACTAGGGATCAAGTATGTGTCTCACCG
1 AAGGACCACATATCATTCCTTAAGAATCATATACAAATACCAAGGATCAAGTATGTGTCTCACCA
80675 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
80713 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACAAATACCAAGGATCAAGTATGTGTCTCACCA
*
80778 GACTTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
80816 AAGGACCACATA
1 AAGGACCACATA
80828 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACAAATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:81803 original size:18 final size:19
Alignment explanation
Indices: 81780--81816 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
81770 TTAGTCATGC
81780 ATACATACAATCA-ATGTA
1 ATACATACAATCACATGTA
*
81798 ATACATATAATCACATGTA
1 ATACATACAATCACATGTA
81817 GTTATAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (19 bp):
ATACATACAATCACATGTA
Found at i:87192 original size:20 final size:20
Alignment explanation
Indices: 87167--87214 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
87157 AATAATTTTA
*
87167 TGATTTATATTTTTTTTATT
1 TGATTTAGATTTTTTTTATT
* *
87187 TGATTTGGGTTTTTTTTATT
1 TGATTTAGATTTTTTTTATT
87207 TGAGTTTA
1 TGA-TTTA
87215 AAATTAATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.69
Consensus pattern (20 bp):
TGATTTAGATTTTTTTTATT
Found at i:87324 original size:14 final size:14
Alignment explanation
Indices: 87305--87338 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
87295 TGGACTAAAT
87305 ATAAACAAATGAAC
1 ATAAACAAATGAAC
87319 ATAAACAAATGAAC
1 ATAAACAAATGAAC
87333 ATAAAC
1 ATAAAC
87339 GATCGATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.65, C:0.15, G:0.06, T:0.15
Consensus pattern (14 bp):
ATAAACAAATGAAC
Found at i:96875 original size:24 final size:24
Alignment explanation
Indices: 96836--96893 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
96826 AGAACATGAT
*
96836 GATGGTAGAAGAGAAGATGA-GGAA
1 GATGGTAGATGAGAAGATGATGG-A
* *
96860 GATGGTAGATGTGAAGTTGATGGA
1 GATGGTAGATGAGAAGATGATGGA
96884 GATGG-AGATG
1 GATGGTAGATG
96894 GAGATGGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.17
24 23 0.77
25 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (24 bp):
GATGGTAGATGAGAAGATGATGGA
Found at i:96952 original size:24 final size:25
Alignment explanation
Indices: 96889--96955 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 25
96879 ATGGAGATGG
96889 AGATGGAGATGGTAGAAGTGAATGT
1 AGATGGAGATGGTAGAAGTGAATGT
** * *
96914 -GATAAATATGGTAGATGTGAA-GT
1 AGATGGAGATGGTAGAAGTGAATGT
*
96937 AGATGGAGATGATAGAAGT
1 AGATGGAGATGGTAGAAGT
96956 TGAGATAATG
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
23 2 0.06
24 30 0.94
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.25
Consensus pattern (25 bp):
AGATGGAGATGGTAGAAGTGAATGT
Found at i:98229 original size:40 final size:39
Alignment explanation
Indices: 98173--98305 Score: 140
Period size: 41 Copynumber: 3.3 Consensus size: 39
98163 TAAATATTTG
* *
98173 TACTTTAATGGCGTTTTAATATAAACACCGCTAAAGACTA
1 TACTTTAGTGGTGTTTT-ATATAAACACCGCTAAAGACTA
* * * * *
98213 TACTTTAGTGTTGTTTTTCTACAAACGCCGCTAAAGACTTG
1 TACTTTAGTGGTG-TTTTATATAAACACCGCTAAAGAC-TA
* *
98254 TACTTTAGTGGTGTTTCTACATAAACACCGCAAAAGACTAA
1 TACTTTAGTGGTGTTT-TATATAAACACCGCTAAAGACT-A
98295 TACTTTAGTGG
1 TACTTTAGTGG
98306 CATTTTTTGA
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
40 31 0.41
41 44 0.59
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (39 bp):
TACTTTAGTGGTGTTTTATATAAACACCGCTAAAGACTA
Found at i:98278 original size:81 final size:82
Alignment explanation
Indices: 98152--98304 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 82
98142 CGTTTTTTGA
* * * * *
98152 ACAAATGCCGCTAAATATTTGTACTTTAATGGCGTTTTAATATAAACACCGCTAAAGACT-ATAC
1 ACAAACGCCGCTAAAGACTTGTACTTTAATGGCGTTTTAACATAAACACCGCAAAAGACTAATAC
98216 TTTAGTGTTGTTTTTCT
66 TTTAGTGTTGTTTTTCT
* *
98233 ACAAACGCCGCTAAAGACTTGTACTTTAGTGGTGTTTCT-ACATAAACACCGCAAAAGACTAATA
1 ACAAACGCCGCTAAAGACTTGTACTTTAATGGCGTTT-TAACATAAACACCGCAAAAGACTAATA
98297 CTTTAGTG
65 CTTTAGTG
98305 GCATTTTTTG
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 51 0.81
82 12 0.19
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (82 bp):
ACAAACGCCGCTAAAGACTTGTACTTTAATGGCGTTTTAACATAAACACCGCAAAAGACTAATAC
TTTAGTGTTGTTTTTCT
Found at i:100573 original size:31 final size:31
Alignment explanation
Indices: 100525--100588 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
100515 GTTTGCAAGG
*
100525 TTATCACATATCGACTTATTTTCAACAGAAA
1 TTATCACATATCAACTTATTTTCAACAGAAA
*
100556 TTATCACGTATCAACTTATTTTCAACAGAAA
1 TTATCACATATCAACTTATTTTCAACAGAAA
100587 TT
1 TT
100589 CTCTCATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (31 bp):
TTATCACATATCAACTTATTTTCAACAGAAA
Found at i:101225 original size:35 final size:35
Alignment explanation
Indices: 101149--101262 Score: 149
Period size: 35 Copynumber: 3.3 Consensus size: 35
101139 ATCCTATTAT
* *
101149 CATTTTC-AACAAATATCTACCAAACTTTGAAAAC
1 CATTTTCAAAGAAATATTTACCAAACTTTGAAAAC
**
101183 TGTTTTTCAAAGAAATATTTACCAAACTTTGAAAAC
1 -CATTTTCAAAGAAATATTTACCAAACTTTGAAAAC
* *
101219 CATTTTCAAAGAAACATTTACCAAACTTTGAATAC
1 CATTTTCAAAGAAATATTTACCAAACTTTGAAAAC
*
101254 AATTTTCAA
1 CATTTTCAA
101263 CACTAGTCTG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 44 0.64
36 25 0.36
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.33
Consensus pattern (35 bp):
CATTTTCAAAGAAATATTTACCAAACTTTGAAAAC
Done.