Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007255.1 Hibiscus syriacus cultivar Beakdansim tig00019223_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: 52689
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2309 original size:12 final size:12
Alignment explanation
Indices: 2292--2346 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
2282 TTTTTTCTTC
*
2292 AAAAAATCAAAG
1 AAAAAAACAAAG
*
2304 AAAAAAGA-AAGG
1 AAAAAA-ACAAAG
*
2316 AAAAAAAAAAAG
1 AAAAAAACAAAG
2328 AAAGAAAAC-AAG
1 AAA-AAAACAAAG
2340 AAAAAAA
1 AAAAAAA
2347 AGCGTGAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 5 0.14
12 27 0.75
13 4 0.11
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.02
Consensus pattern (12 bp):
AAAAAAACAAAG
Found at i:2326 original size:17 final size:18
Alignment explanation
Indices: 2304--2348 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
2294 AAAATCAAAG
2304 AAAAAAGAAAGGAAAA-A
1 AAAAAAGAAAGGAAAACA
2321 AAAAAAGAAA-GAAAACA
1 AAAAAAGAAAGGAAAACA
2338 AGAAAAA-AAAG
1 A-AAAAAGAAAG
2349 CGTGAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.20
17 15 0.60
18 5 0.20
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAGGAAAACA
Found at i:2333 original size:21 final size:21
Alignment explanation
Indices: 2307--2348 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2297 ATCAAAGAAA
**
2307 AAAGAAAGGAAAAAAAAAAAG
1 AAAGAAAACAAAAAAAAAAAG
*
2328 AAAGAAAACAAGAAAAAAAAG
1 AAAGAAAACAAAAAAAAAAAG
2349 CGTGAAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAGAAAACAAAAAAAAAAAG
Found at i:4287 original size:30 final size:29
Alignment explanation
Indices: 4252--4365 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 29
4242 TAAAGGATTA
*
4252 AAATAGCACAAACAGAAATTTAAAAAACT
1 AAATAGCACAAACAGAAATTTAAAAAACC
* * * *
4281 AGAATAGTAAAAATAGAAAATTT-AAAGACC
1 A-AATAGCACAAACAG-AAATTTAAAAAACC
* * *
4311 AAATATCACAAACTGAAATTTAAAAGACC
1 AAATAGCACAAACAGAAATTTAAAAAACC
* * *
4340 AAAATGGCAAAAACATGAACTTTAAA
1 -AAATAGCACAAACA-GAAATTTAAA
4366 TCCTAAAATA
Statistics
Matches: 65, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
28 6 0.09
29 17 0.26
30 27 0.42
31 15 0.23
ACGTcount: A:0.59, C:0.12, G:0.10, T:0.19
Consensus pattern (29 bp):
AAATAGCACAAACAGAAATTTAAAAAACC
Found at i:4352 original size:59 final size:60
Alignment explanation
Indices: 4230--4352 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 60
4220 TTAAATAACG
* * * *
4230 AAAATAGAAAATTAAAGGATTAAAATAGCACAAACAGAAATTTAAAAAACTAGAATAGTA
1 AAAATAGAAAATTAAAGGATCAAAATAGCACAAACAGAAATTTAAAAAACCAAAATAGCA
* * * * *
4290 AAAATAGAAAATTTAAA-GA-CCAAATATCACAAACTGAAATTTAAAAGACCAAAATGGCA
1 AAAATAGAAAA-TTAAAGGATCAAAATAGCACAAACAGAAATTTAAAAAACCAAAATAGCA
4349 AAAA
1 AAAA
4353 CATGAACTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
59 35 0.66
60 13 0.25
61 5 0.09
ACGTcount: A:0.61, C:0.10, G:0.11, T:0.19
Consensus pattern (60 bp):
AAAATAGAAAATTAAAGGATCAAAATAGCACAAACAGAAATTTAAAAAACCAAAATAGCA
Found at i:6189 original size:12 final size:13
Alignment explanation
Indices: 6174--6213 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
6164 AATTCTATTA
6174 ATAATAATAA-AT
1 ATAATAATAATAT
*
6186 ATAATAATAATAC
1 ATAATAATAATAT
6199 ATAAT-ATAATAT
1 ATAATAATAATAT
6211 ATA
1 ATA
6214 TTTTTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 19 0.76
13 6 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATAATAATAT
Found at i:6193 original size:18 final size:18
Alignment explanation
Indices: 6172--6209 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
6162 ATAATTCTAT
6172 TAATAATA-ATAAATATAA
1 TAATAATACAT-AATATAA
6190 TAATAATACATAATATAA
1 TAATAATACATAATATAA
6208 TA
1 TA
6210 TATATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATAATACATAATATAA
Found at i:6623 original size:90 final size:90
Alignment explanation
Indices: 6452--6677 Score: 380
Period size: 90 Copynumber: 2.5 Consensus size: 90
6442 TTATAGATGA
* *
6452 CCCGAATGATTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAAATCTCATTTGAAAACA
1 CCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTC-TAAAATCTCATTTGAAAACA
**
6517 TCCTGCACTGAAGGTCTTATGGATGG
65 TCCTGCACTGAAGGTCTTATGGATAC
* *
6543 CCTGAAGGACTTAGAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
1 CCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
*
6608 CTTGCACTGAAGGTCTTATGGATAC
66 CCTGCACTGAAGGTCTTATGGATAC
6633 CCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCT
1 CCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCT
6678 TATTTGTCAC
Statistics
Matches: 126, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
90 86 0.68
91 40 0.32
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (90 bp):
CCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
CCTGCACTGAAGGTCTTATGGATAC
Found at i:6748 original size:43 final size:43
Alignment explanation
Indices: 6696--6914 Score: 309
Period size: 43 Copynumber: 5.1 Consensus size: 43
6686 ACCAAAGAAT
* *
6696 CCCTGCATATCACGATGGTCCCTT-AAACTTGTCATCAAGAAAC
1 CCCTACATATCACGATGGT-CCTTCAAGCTTGTCATCAAGAAAC
*
6739 CCCTACATATCACGATGGT-TTCTCAAGCTTGTCATCAA-AGAAC
1 CCCTACATATCACGATGGTCCT-TCAAGCTTGTCATCAAGA-AAC
* *
6782 CCATACATATCACGATGGTCCTTCAAGCTTGTCATCAAGGAAC
1 CCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAGAAAC
*
6825 CCCTACATATCACGATGGTCCTTCAAGCTTATCATCAAGAAAC
1 CCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAGAAAC
* * *
6868 CCCTACATATCAAGATGGTCCTTCAAGCTTTTCTTCAAGAAAC
1 CCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAGAAAC
6911 CCCT
1 CCCT
6915 GAAAAGTAGG
Statistics
Matches: 159, Mismatches: 12, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
41 1 0.01
42 2 0.01
43 155 0.97
44 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (43 bp):
CCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAGAAAC
Found at i:7015 original size:40 final size:40
Alignment explanation
Indices: 6970--7509 Score: 854
Period size: 40 Copynumber: 13.6 Consensus size: 40
6960 TATCTCAAGC
* **
6970 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
7010 AAGATAAAATCTTATTTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
7050 GAGATAAAATCTTCTGTTTCAAGGAAAAAAAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
7090 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
7130 GAGATAAAATCTTCTGTTTCAAGGAAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGG-AAAAACAATCTTGAGT
*
7171 GAGATAAAATCTTCTGTTTCAAGGAAAATCAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
7211 GATATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
7251 GAGATAAAATCTTCTGTTTCATGGAAAAACAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
7291 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
7331 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
7371 GAGATAAAATCTTCTGTTTCATGGAAAAAACAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGG-AAAAACAATCTTGAGT
7412 GAGATAAAATCTTCTGTTTCAAGGAAAAACAA--TTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
7450 GAGATAAAATC-TATGTTT-AAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
7488 GAGATAAAATCTTCTGTTTCAA
1 GAGATAAAATCTTCTGTTTCAA
7510 TAAAACATGT
Statistics
Matches: 462, Mismatches: 32, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
36 12 0.03
37 6 0.01
38 33 0.07
39 6 0.01
40 328 0.71
41 77 0.17
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:7324 original size:23 final size:23
Alignment explanation
Indices: 7298--7366 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
7288 AGCGAGATAA
7298 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
** * *
7321 AATC-T-TGAGT-GA-G-ATAA-
1 AATCTTCTGTTTCAAGGAAAAAC
7338 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
7361 AATCTT
1 AATCTT
7367 GAATGAGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 4 0.12
20 2 0.06
21 4 0.12
22 4 0.12
23 10 0.31
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:7399 original size:241 final size:239
Alignment explanation
Indices: 6970--7509 Score: 913
Period size: 241 Copynumber: 2.3 Consensus size: 239
6960 TATCTCAAGC
* ** * *
6970 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAACAAGATAAAATCTTATTTTTCAAGGA
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
*
7035 AAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAAAAATCTTGAATGAGATAAAAT
66 AAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAAGGAAAAAAAATCTTGAATGAGATAAAAT
7100 CTTCTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGAAAAAACAATC
131 CTTCTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGAAAAAACAATC
* *
7165 TTGAATGAGATAAAATCTTCTGTTTCAAGGAAAATCAATCTTGAGT
196 TTGAACGAGATAAAATCTTCTGTTTCAAGGAAAAACAA--TTGAGT
* *
7211 GATATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCATGGA
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
* *
7276 AAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAAT
66 AAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAAGGAAAAAAAATCTTGAATGAGATAAAAT
*
7341 CTTCTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCATGGAAAAAACAATC
131 CTTCTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGAAAAAACAATC
*
7406 TTGAGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATTGAGT
196 TTGAACGAGATAAAATCTTCTGTTTCAAGGAAAAACAATTGAGT
*
7450 GAGATAAAATC-TATGTTT-AAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAA
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAA
7510 TAAAACATGT
Statistics
Matches: 282, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
237 40 0.14
238 7 0.02
239 16 0.06
241 219 0.78
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (239 bp):
GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
AAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAAGGAAAAAAAATCTTGAATGAGATAAAAT
CTTCTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGAAAAAACAATC
TTGAACGAGATAAAATCTTCTGTTTCAAGGAAAAACAATTGAGT
Found at i:7827 original size:34 final size:34
Alignment explanation
Indices: 7783--7903 Score: 179
Period size: 34 Copynumber: 3.6 Consensus size: 34
7773 TCTCAGAGAA
*
7783 AAATTATCTCAAGCGAGACGGAATTTGTTTTGAG
1 AAATTATCTCAAGCGAGACGGAATTTATTTTGAG
* *
7817 AAATTGTCTCAAGCGAGACGAAATTTATTTTGAG
1 AAATTATCTCAAGCGAGACGGAATTTATTTTGAG
* * *
7851 AAATTGTCTCAAGTGAGACAGAATTTATTTTGAG
1 AAATTATCTCAAGCGAGACGGAATTTATTTTGAG
*
7885 AAATTATCTCAAGTGAGAC
1 AAATTATCTCAAGCGAGAC
7904 AAAAAAAATA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 80 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (34 bp):
AAATTATCTCAAGCGAGACGGAATTTATTTTGAG
Found at i:8085 original size:32 final size:32
Alignment explanation
Indices: 8011--8128 Score: 164
Period size: 32 Copynumber: 3.7 Consensus size: 32
8001 ACTTCAGGAC
* * * *
8011 GTTGAATCTCTAAAAATGCCCCAACATTTTTAA
1 GTTGAATCTCCAAAGATGCCCCAACA-TTTGAT
*
8044 GTTGAATCTCCAAAGACGCCCCAACATTTGAT
1 GTTGAATCTCCAAAGATGCCCCAACATTTGAT
*
8076 GTTGAATCTCCAAATATGCCCCAACATTTGAT
1 GTTGAATCTCCAAAGATGCCCCAACATTTGAT
*
8108 GTTGAATTTCCAAAGATGCCC
1 GTTGAATCTCCAAAGATGCCC
8129 TCTATTGCTT
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
32 53 0.70
33 23 0.30
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (32 bp):
GTTGAATCTCCAAAGATGCCCCAACATTTGAT
Found at i:8513 original size:32 final size:32
Alignment explanation
Indices: 8472--8551 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
8462 GGTTATTGTG
8472 TTTGGTCAATGGTTTGAATGTCTCAGGTTATT
1 TTTGGTCAATGGTTTGAATGTCTCAGGTTATT
*
8504 TTTGGTCAATGGTTTGAATGTCTCAGGTTGTT
1 TTTGGTCAATGGTTTGAATGTCTCAGGTTATT
8536 TTTGGTCAATGGTTTG
1 TTTGGTCAATGGTTTG
8552 GCCTTCTTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.16, C:0.09, G:0.28, T:0.47
Consensus pattern (32 bp):
TTTGGTCAATGGTTTGAATGTCTCAGGTTATT
Found at i:9273 original size:31 final size:31
Alignment explanation
Indices: 9211--9274 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
9201 TTTTTTTTCC
* * *
9211 TTTTTGCTCTTTGTTTTTTTTTCTTTGATTT
1 TTTTTACTCTTTGTTTTTTTCTCTTTAATTT
9242 TTTTTACTCTTTGTTTTTTTACTC-TTAATTT
1 TTTTTACTCTTTGTTTTTTT-CTCTTTAATTT
9273 TT
1 TT
9275 CTTTGTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.08, C:0.11, G:0.06, T:0.75
Consensus pattern (31 bp):
TTTTTACTCTTTGTTTTTTTCTCTTTAATTT
Found at i:9295 original size:11 final size:12
Alignment explanation
Indices: 9270--9316 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
9260 TTACTCTTAA
9270 TTTTTCTTTGTT
1 TTTTTCTTTGTT
9282 TTTTTCTTTGTTT
1 TTTTTCTTTG-TT
9295 TTTTTCTCTT-TAT
1 TTTTTCT-TTGT-T
9308 TTTTTCTTT
1 TTTTTCTTT
9317 ATTATCATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 13 0.41
13 17 0.53
14 2 0.06
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTGTT
Found at i:9304 original size:15 final size:15
Alignment explanation
Indices: 9211--9312 Score: 78
Period size: 15 Copynumber: 7.3 Consensus size: 15
9201 TTTTTTTTCC
*
9211 TTTTTGCTCTTTGTT
1 TTTTTTCTCTTTGTT
9226 TTTTTT-TCTTTGATT
1 TTTTTTCTCTTTG-TT
9241 TTTTTTACTCTTTGTT
1 TTTTTT-CTCTTTGTT
*
9257 TTTTTACTC----TT
1 TTTTTTCTCTTTGTT
**
9268 AATTTT-TCTTTG--
1 TTTTTTCTCTTTGTT
9280 TTTTTT-TCTTTGTT
1 TTTTTTCTCTTTGTT
*
9294 TTTTTTCTCTTTATT
1 TTTTTTCTCTTTGTT
9309 TTTT
1 TTTT
9313 CTTTATTATC
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
10 2 0.03
11 5 0.07
12 10 0.14
14 12 0.17
15 27 0.39
16 7 0.10
17 6 0.09
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.77
Consensus pattern (15 bp):
TTTTTTCTCTTTGTT
Found at i:9317 original size:11 final size:12
Alignment explanation
Indices: 9256--9351 Score: 52
Period size: 12 Copynumber: 7.6 Consensus size: 12
9246 TACTCTTTGT
9256 TTTTTTACTCTTAA
1 TTTTTT-CT-TTAA
**
9270 -TTTTTCTTTGT
1 TTTTTTCTTTAA
**
9281 TTTTTTCTTTGTT
1 TTTTTTCTTT-AA
*
9294 TTTTTTCTCTTTA
1 TTTTTTCT-TTAA
9307 TTTTTTCTTT-A
1 TTTTTTCTTTAA
*
9318 TTATCATTGCTTTAA
1 TT-T--TTTCTTTAA
*
9333 TTTTTTTTTTAA
1 TTTTTTCTTTAA
9345 TTTTTTC
1 TTTTTTC
9352 CTCTTTTTTC
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
11 5 0.07
12 27 0.40
13 23 0.34
14 9 0.13
15 3 0.04
ACGTcount: A:0.11, C:0.10, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTTTCTTTAA
Found at i:10371 original size:41 final size:41
Alignment explanation
Indices: 10322--10402 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
10312 GATATCAAAA
* *
10322 TCGTAACCCTCGGGATATATG-GACTCTTTTCTCATATCATT
1 TCGTAACCCTCGGGATAT-GGAGACTCTTTTCTCAGATCATT
10363 TCGTAACCCTCGGGATATGGAGACTCTTTTCTCAGATCAT
1 TCGTAACCCTCGGGATATGGAGACTCTTTTCTCAGATCAT
10403 CTGGAAGGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (41 bp):
TCGTAACCCTCGGGATATGGAGACTCTTTTCTCAGATCATT
Found at i:14368 original size:30 final size:30
Alignment explanation
Indices: 14299--14374 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
14289 CAAAATAGAT
* *
14299 AAAACA-AAAACTTTAAGTATTAAAATAACG
1 AAAACAGAAAA-TTAAAGGATTAAAATAACG
* *
14329 AAAATAGAAAATTAAAGGATTAAAATAGC-
1 AAAACAGAAAATTAAAGGATTAAAATAACG
*
14358 ACAAACAGAAATTTAAA
1 A-AAACAGAAAATTAAA
14375 AAGCTAGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.87
31 4 0.11
ACGTcount: A:0.62, C:0.08, G:0.09, T:0.21
Consensus pattern (30 bp):
AAAACAGAAAATTAAAGGATTAAAATAACG
Found at i:14386 original size:30 final size:28
Alignment explanation
Indices: 14351--14434 Score: 69
Period size: 30 Copynumber: 2.9 Consensus size: 28
14341 TAAAGGATTA
*
14351 AAATAGCACAAACAGAAATTTAAAAAGCT
1 AAATAGCACAAACAGAAATTTAAAAA-CC
* * * * *
14380 AGAATAGTAAAAATAGAAAATTTGAAGACC
1 A-AATAGCACAAACAG-AAATTTAAAAACC
* *
14410 AAATATCACAAACTGAAATTTAAAA
1 AAATAGCACAAACAGAAATTTAAAA
14435 GTCCAAAATG
Statistics
Matches: 40, Mismatches: 13, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
28 8 0.20
29 10 0.25
30 13 0.32
31 9 0.22
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (28 bp):
AAATAGCACAAACAGAAATTTAAAAACC
Found at i:17657 original size:23 final size:24
Alignment explanation
Indices: 17606--17659 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
17596 AAGATTTCAT
* * *
17606 ACAT-AAATTTAACATAAAAGTTA
1 ACATAAAATTTAAAATAAAACTGA
17629 AC-TAAAATTTAAAAT-AAACTGA
1 ACATAAAATTTAAAATAAAACTGA
17651 ACATAAAAT
1 ACATAAAAT
17660 CCAAGTAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.28
Consensus pattern (24 bp):
ACATAAAATTTAAAATAAAACTGA
Found at i:23760 original size:18 final size:19
Alignment explanation
Indices: 23737--23780 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
23727 TCAGTAATCC
* *
23737 TATTCC-CTGGTAATCTTT
1 TATTCCACTGATAATCTTA
23755 TATTCCCACTGATAATCTTA
1 TATT-CCACTGATAATCTTA
23775 TATTCC
1 TATTCC
23781 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (19 bp):
TATTCCACTGATAATCTTA
Found at i:26129 original size:17 final size:17
Alignment explanation
Indices: 26103--26209 Score: 62
Period size: 17 Copynumber: 6.2 Consensus size: 17
26093 CCTATATTGT
26103 TATT-TTTATTATTTTA
1 TATTATTTATTATTTTA
26119 TATTATTTATT-TTGTTA
1 TATTATTTATTATT-TTA
**
26136 TATATACGTATT-TTTTA
1 TAT-TATTTATTATTTTA
*
26153 TATATATTTTTTATTTGTA
1 TAT-TATTTATTATTT-TA
* * *
26172 TACCTA-TTATTAATATA
1 TA-TTATTTATTATTTTA
*
26189 TATTTTTTAATTATTTT-
1 TATTATTT-ATTATTTTA
26206 TATT
1 TATT
26210 TGAATATTTC
Statistics
Matches: 70, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
16 7 0.10
17 34 0.49
18 23 0.33
19 6 0.09
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TATTATTTATTATTTTA
Found at i:26299 original size:31 final size:33
Alignment explanation
Indices: 26248--26327 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 33
26238 CTTATAATTG
* * *
26248 TATATATATATTTTTCTATTTTTGGTTTTTTTA-C
1 TATATATATATATAT-TATTTTTAG-TTTTTTACC
26282 TAT-TATAT-TATATTATTTTTAGTTTTTTACC
1 TATATATATATATATTATTTTTAGTTTTTTACC
26313 TATATATATATATAT
1 TATATATATATATAT
26328 ACATTATCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 7 0.17
31 12 0.30
32 8 0.20
33 10 0.25
34 3 0.08
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.64
Consensus pattern (33 bp):
TATATATATATATATTATTTTTAGTTTTTTACC
Found at i:26485 original size:10 final size:9
Alignment explanation
Indices: 26466--26517 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
26456 TTTATTTTTA
26466 TTTTTTATT
1 TTTTTTATT
26475 TTTTCTTATT
1 TTTT-TTATT
*
26485 TATTTTACTT
1 TTTTTTA-TT
26495 TGTTATTTATT
1 T-TT-TTTATT
*
26506 TTCTTTATT
1 TTTTTTATT
26515 TTT
1 TTT
26518 CTATTTTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 15 0.43
10 12 0.34
11 4 0.11
12 4 0.11
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTTTATT
Found at i:26486 original size:14 final size:13
Alignment explanation
Indices: 26456--26562 Score: 51
Period size: 13 Copynumber: 8.0 Consensus size: 13
26446 TTCTCTTGTC
26456 TTTATTTTTATTT
1 TTTATTTTTATTT
26469 TTTATTTTT-TCTT
1 TTTATTTTTAT-TT
26482 ATTTA-TTTTACTTT
1 -TTTATTTTTA-TTT
* *
26496 GTTATTTATT-TTC
1 TTTATTT-TTATTT
* *
26509 TTTATTTTTCTAT
1 TTTATTTTTATTT
* * *
26522 TTTGTTTCTGTTT
1 TTTATTTTTATTT
*
26535 CTTTATTTTCATTT
1 -TTTATTTTTATTT
26549 TGCTTA-TTTTATTT
1 T--TTATTTTTATTT
26563 ACTTTTTTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 19
0.68 0.14 0.18
Matches are distributed among these distances:
12 3 0.04
13 37 0.53
14 24 0.34
15 6 0.09
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTATTTTTATTT
Found at i:26486 original size:27 final size:27
Alignment explanation
Indices: 26456--26517 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
26446 TTCTCTTGTC
* *
26456 TTTATTTTTA-TTTTTTATTTTTTCTTA
1 TTTATTTTTACTTTGTTATTTATT-TTA
*
26483 TTTA-TTTTACTTTGTTATTTATTTTC
1 TTTATTTTTACTTTGTTATTTATTTTA
26509 TTTATTTTT
1 TTTATTTTT
26518 CTATTTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 11 0.37
27 19 0.63
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.79
Consensus pattern (27 bp):
TTTATTTTTACTTTGTTATTTATTTTA
Found at i:26500 original size:17 final size:16
Alignment explanation
Indices: 26480--26511 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
26470 TTATTTTTTC
26480 TTATTTATTTTACTTTG
1 TTATTTATTTT-CTTTG
26497 TTATTTATTTTCTTT
1 TTATTTATTTTCTTT
26512 ATTTTTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (16 bp):
TTATTTATTTTCTTTG
Found at i:26516 original size:53 final size:55
Alignment explanation
Indices: 26454--26589 Score: 136
Period size: 53 Copynumber: 2.5 Consensus size: 55
26444 TTTTCTCTTG
26454 TCTTTATTTTTATTTTTTATTTTTTCTTATTTATTTT-ACTTTG-TTA-TTTATTT
1 TCTTTATTTTTATTTTTTATTTTTT-TTATTTATTTTCACTTTGCTTATTTTATTT
* * * * * *
26507 TCTTTATTTTTCTATTTTGTTTCTGTTTCTTTATTTTCATTTTGCTTATTTTATTT
1 TCTTTATTTTTATTTTTTATTT-TTTTTATTTATTTTCACTTTGCTTATTTTATTT
* *
26563 ACTTT-TTTTTCATTTTATTATCTTTTT
1 TCTTTATTTTT-ATTTT-TTATTTTTTT
26590 AGTTTTATTC
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
53 29 0.45
54 7 0.11
55 8 0.12
56 17 0.26
57 4 0.06
ACGTcount: A:0.13, C:0.09, G:0.03, T:0.75
Consensus pattern (55 bp):
TCTTTATTTTTATTTTTTATTTTTTTTATTTATTTTCACTTTGCTTATTTTATTT
Found at i:36363 original size:32 final size:33
Alignment explanation
Indices: 36298--36382 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 33
36288 TTATTATTTT
* * *
36298 TATTATTTTATATTATTTATTTTGTTGTATATACG
1 TATT-TTTTATA-TATATATTTTATTGTATATACC
*
36333 TATTTTTTATATATATATTTTATT-TGTATACC
1 TATTTTTTATATATATATTTTATTGTATATACC
* * *
36365 TACTATTAATATATATAT
1 TATTTTTTATATATATAT
36383 ATTAATTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 21 0.49
33 11 0.26
34 7 0.16
35 4 0.09
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (33 bp):
TATTTTTTATATATATATTTTATTGTATATACC
Found at i:36490 original size:40 final size:43
Alignment explanation
Indices: 36437--36525 Score: 114
Period size: 41 Copynumber: 2.1 Consensus size: 43
36427 CTTATAATTG
*
36437 TATATATATATTTTT-CTATTTTTGGTTTTTTTTA-CTATTATA
1 TATATATATATTTTTACTATTTTTAGTTTTTTTTACCT-TTATA
* *
36479 T-TATAT-TATTTTTAGTTTTTTTAGTTTTTTTTACCTTTATA
1 TATATATATATTTTTACTATTTTTAGTTTTTTTTACCTTTATA
36520 TATATA
1 TATATA
36526 ACATTATCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 7 0.17
41 27 0.66
42 7 0.17
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (43 bp):
TATATATATATTTTTACTATTTTTAGTTTTTTTTACCTTTATA
Found at i:36663 original size:35 final size:35
Alignment explanation
Indices: 36624--36697 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
36614 TTTGCATATA
36624 TTTTATTTATTAAATTTTT-TT-TCTATTGTCTTTAT
1 TTTTATTT-TT-AATTTTTCTTATCTATTGTCTTTAT
* * *
36659 TTTTATTTTTTATTTTTCTTATTTATTTTCTTTAT
1 TTTTATTTTTAATTTTTCTTATCTATTGTCTTTAT
36694 TTTT
1 TTTT
36698 CTATTTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 6 0.18
34 4 0.12
35 24 0.71
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77
Consensus pattern (35 bp):
TTTTATTTTTAATTTTTCTTATCTATTGTCTTTAT
Found at i:36680 original size:22 final size:21
Alignment explanation
Indices: 36655--36710 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
36645 TCTATTGTCT
*
36655 TTATTTTTATTTTTTATTTTTC
1 TTATTTTT-TTCTTTATTTTTC
36677 TTATTTATTTTCTTTATTTTTC
1 TTATTT-TTTTCTTTATTTTTC
36699 -TATTTTCTTTCT
1 TTATTTT-TTTCT
36711 GTTTCTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 10 0.32
22 18 0.58
23 2 0.06
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (21 bp):
TTATTTTTTTCTTTATTTTTC
Found at i:36695 original size:13 final size:13
Alignment explanation
Indices: 36654--36687 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
36644 TTCTATTGTC
*
36654 TTTATTTTTATTT
1 TTTATTTTTATTA
*
36667 TTTATTTTTCTTA
1 TTTATTTTTATTA
36680 TTTATTTT
1 TTTATTTT
36688 CTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTATTTTTATTA
Found at i:36745 original size:9 final size:9
Alignment explanation
Indices: 36622--36759 Score: 53
Period size: 9 Copynumber: 16.0 Consensus size: 9
36612 TATTTGCATA
36622 TATTTTATT
1 TATTTTATT
**
36631 TATTAAATT
1 TATTTTATT
*
36640 T-TTTT-TC
1 TATTTTATT
* *
36647 TATTGTCTT
1 TATTTTATT
36656 TATTTT-TAT
1 TATTTTAT-T
36665 T-TTTTATT
1 TATTTTATT
36673 T-TTCTTATT
1 TATT-TTATT
*
36682 TATTTTCTT
1 TATTTTATT
*
36691 TATTTT-TC
1 TATTTTATT
*
36699 TATTTTCTT
1 TATTTTATT
* *
36708 TCTGTTTCTT
1 TAT-TTTATT
36718 TA--TT-TT
1 TATTTTATT
* * *
36724 CATTTTGTC
1 TATTTTATT
36733 TATTTTATT
1 TATTTTATT
36742 TATTTT-TT
1 TATTTTATT
36750 TCATTTTATT
1 T-ATTTTATT
36760 ATCTTTTTAG
Statistics
Matches: 98, Mismatches: 18, Indels: 25
0.70 0.13 0.18
Matches are distributed among these distances:
6 3 0.03
7 4 0.04
8 26 0.27
9 54 0.55
10 11 0.11
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (9 bp):
TATTTTATT
Found at i:36766 original size:17 final size:18
Alignment explanation
Indices: 36716--36767 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
36706 TTTCTGTTTC
36716 TTTATTT-TCATTTTGTCTAT
1 TTTATTTATC-TTTT-TC-AT
*
36736 TTTATTTATTTTTTTCAT
1 TTTATTTATCTTTTTCAT
36754 TTTA-TTATCTTTTT
1 TTTATTTATCTTTTT
36768 AGCTTTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 9 0.31
18 6 0.21
19 2 0.07
20 11 0.38
21 1 0.03
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTATTTATCTTTTTCAT
Found at i:52009 original size:171 final size:171
Alignment explanation
Indices: 51606--52130 Score: 654
Period size: 171 Copynumber: 3.0 Consensus size: 171
51596 GATACAAATG
* * * *
51606 AAAAATGTATCGCTCCATAGAAATATTACAGGTAAAAATATGACAAAACCGGTCTCGAATGATAA
1 AAAAATGTATCGATCCATA-ACATA--ACAGGTAAAAATATGACAAAACCGGTCTCAAATGA-CA
* * *
51671 AACCGGTAAAACAATA-GAATATGTTGAAAGTGTCGATAA-TTAATATAAGTATCGACACTTTTG
62 AACCGGTAAAGCACTACGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTG
*
51734 AATTTAAAAG-AAA-TTATAGCGCCT-ATAAGTGTCGATACTTTA
127 AATTTAAAAGAAAAGTTATAGCGCCTAAAAAGTGTCGATACTTTA
* *
51776 AAAAATATATCGATCCATAACATATAACAGGTAAAAATATGACAAAACCGGTCCCAAAATGACAA
1 AAAAATGTATCGATCCATAAC--ATAACAGGTAAAAATATGACAAAACCGGTCTC-AAATGACAA
* *
51841 ACCGGTAAAGCTCTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCAACACTTTTT
63 ACCGGTAAAGCACTA-CGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACAC-TTTT
*
51906 GAATTTAAAAGAATAAGTT-TAGCGTCTAAAAAGTGTCGATACTTTA
126 GAATTTAAAAGAA-AAGTTATAGCGCCTAAAAAGTGTCGATACTTTA
* *
51952 TGAAAATGTATCGATCCATAACATAACAGCT-AAAATATGAC-AAA-CGGTCTCAAATGACAAAA
1 -AAAAATGTATCGATCCATAACATAACAGGTAAAAATATGACAAAACCGGTCTCAAATGAC-AAA
* * * * *
52014 CCGATAAAGAACTACGGATATGTTGAAAGTGTCGATATTTTAATATAAGTAACGACACTTTAGAA
64 CCGGTAAAGCACTACGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTGAA
* *
52079 TTTAAAAGAGAAGAAGTTATAGTGCCTATAAAGTGTCGATACTTTA
129 TTT-AAA-AGAA-AAGTTATAGCGCCTAAAAAGTGTCGATACTTTA
52125 AAAAAT
1 AAAAAT
52131 AGTAAACAAA
Statistics
Matches: 310, Mismatches: 29, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
169 43 0.14
170 31 0.10
171 76 0.25
172 52 0.17
173 42 0.14
174 11 0.04
175 17 0.05
176 19 0.06
177 19 0.06
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (171 bp):
AAAAATGTATCGATCCATAACATAACAGGTAAAAATATGACAAAACCGGTCTCAAATGACAAACC
GGTAAAGCACTACGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTGAATT
TAAAAGAAAAGTTATAGCGCCTAAAAAGTGTCGATACTTTA
Done.