Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001077.1 Hibiscus syriacus cultivar Beakdansim tig00002134_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: 57733
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:230 original size:17 final size:16
Alignment explanation
Indices: 208--243 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
198 TAGATTCAAG
208 TTTAATCACCTAACTAT
1 TTTAATCACCTAAC-AT
225 TTTAATCACCTAACAT
1 TTTAATCACCTAACAT
241 TTT
1 TTT
244 CTTTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTAATCACCTAACAT
Found at i:949 original size:22 final size:22
Alignment explanation
Indices: 924--965 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
914 GACGACATCC
924 GTCCCCATCTCCGAAGAAATTT
1 GTCCCCATCTCCGAAGAAATTT
* *
946 GTCCCCATCTCTGACGAAAT
1 GTCCCCATCTCCGAAGAAAT
966 CCGTCTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.33, G:0.14, T:0.26
Consensus pattern (22 bp):
GTCCCCATCTCCGAAGAAATTT
Found at i:1378 original size:14 final size:14
Alignment explanation
Indices: 1361--1392 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1351 GCGAATTTAG
1361 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
*
1375 TTTCTCGTTGCGAT
1 TTTCGCGTTGCGAT
1389 TTTC
1 TTTC
1393 ATTTTCGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:3355 original size:63 final size:64
Alignment explanation
Indices: 3249--3401 Score: 256
Period size: 63 Copynumber: 2.4 Consensus size: 64
3239 ATTGAATTTT
*
3249 ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGATATAAGAAT-TATTTTTGCTTGTTTA
1 ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATATATTTTTGCTTGTTTA
* * *
3312 ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAGAATATTTTTTTGCTTGTTTA
1 ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATATATTTTTGCTTGTTTA
3376 ATTGATTTGTAAAAGTTGATTT-TTTA
1 ATTGATTTGTAAAAGTTGATTTGTTTA
3402 TTTATTCAAT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
63 48 0.56
64 37 0.44
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (64 bp):
ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATATATTTTTGCTTGTTTA
Found at i:3560 original size:20 final size:20
Alignment explanation
Indices: 3506--3553 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3496 TGCGATAGTA
* *
3506 AAATTCGTAACGTGAAAGTC
1 AAATTCGCAACGCGAAAGTC
3526 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
3546 AAATTCGC
1 AAATTCGC
3554 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:3915 original size:18 final size:18
Alignment explanation
Indices: 3892--3927 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3882 AAGCCGGTTG
*
3892 TGATTAGGATTTTGATTT
1 TGATTACGATTTTGATTT
3910 TGATTACGATTTTGATTT
1 TGATTACGATTTTGATTT
3928 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (18 bp):
TGATTACGATTTTGATTT
Found at i:7194 original size:19 final size:20
Alignment explanation
Indices: 7170--7260 Score: 80
Period size: 19 Copynumber: 4.6 Consensus size: 20
7160 CTAAAACCTA
*
7170 TTGCGAAATT-AAATTCGTG
1 TTGCGAAATTGAAATTCGAG
*
7189 TTGCG-AATTCGAAAATCGAG
1 TTGCGAAATT-GAAATTCGAG
* *
7209 TTGCGAATTTGAAATTC-AA
1 TTGCGAAATTGAAATTCGAG
* *
7228 TTGCGAATTTGAAATTCAGTG
1 TTGCGAAATTGAAATTC-GAG
*
7249 TTGCGAATTTGA
1 TTGCGAAATTGA
7261 TTTCTTTGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.07
19 23 0.38
20 18 0.30
21 15 0.25
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (20 bp):
TTGCGAAATTGAAATTCGAG
Found at i:7213 original size:20 final size:20
Alignment explanation
Indices: 7170--7338 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
7160 CTAAAACCTA
* *
7170 TTGCGAAATT-AAATTCGTG
1 TTGCGAATTTGAAATTCGAG
* *
7189 TTGCGAATTCGAAAATCGAG
1 TTGCGAATTTGAAATTCGAG
*
7209 TTGCGAATTTGAAATTC-AA
1 TTGCGAATTTGAAATTCGAG
*
7228 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAATTC-GAG
* **
7249 TTGCGAATTTG-ATTTCTTTG
1 TTGCGAATTTGAAATTC-GAG
* * *
7269 TTGCGATTTTCTAAATTCGCG
1 TTGCGAATTT-GAAATTCGAG
* *
7290 TTGCAAATTTGGAAACT-GAG
1 TTGCGAATTT-GAAATTCGAG
* * *
7310 TTGCGAAATTGGAGTTC--G
1 TTGCGAATTTGAAATTCGAG
7328 TTGCGAATTTG
1 TTGCGAATTTG
7339 TTGGTCATTT
Statistics
Matches: 115, Mismatches: 29, Indels: 13
0.73 0.18 0.08
Matches are distributed among these distances:
18 11 0.10
19 29 0.25
20 47 0.41
21 24 0.21
22 4 0.03
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGAAATTCGAG
Found at i:8466 original size:39 final size:41
Alignment explanation
Indices: 8425--8505 Score: 108
Period size: 44 Copynumber: 1.9 Consensus size: 41
8415 ATCTATCAGA
*
8425 AATTGGAATCCAATTATATATTCTGTTTGGTTGGCAGGAAATT
1 AATTGGAATCCAATTATATATTCTGTTTGGTTCGCAGG-AA-T
* *
8468 GAATTGGAATTCAATTCTATATTCTGTTTGGTTCGCAG
1 -AATTGGAATCCAATTATATATTCTGTTTGGTTCGCAG
8506 ACATGTCAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (41 bp):
AATTGGAATCCAATTATATATTCTGTTTGGTTCGCAGGAAT
Found at i:9309 original size:261 final size:263
Alignment explanation
Indices: 8803--9426 Score: 961
Period size: 261 Copynumber: 2.4 Consensus size: 263
8793 CTCCATCCGA
**
8803 GACCCGACCCGACCCGAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA-C--CC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCGACC
8865 GACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAA
66 GACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAA
* * *
8930 TATATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATTTTTT
131 AAAATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATA-TTATT
*
8995 GGTTCGGGTCAGATATTTTTCACCCTAAACCCGAACCTGACCTGACCCGAATATCACACTTAAAA
195 -GTTCGGGTCAGATATTTTTCACCCTAAACCCGAACCTGACCCGACCCGAATATCACACTTAAAA
*
9060 AAACT
259 AAACC
*
9065 GACCCGACCCGACCAAAATAAAGTTTCACCCGACTCGACCCG-ATATATGAATTAGAAATTCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA-TCGAC
*
9129 CTGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATT-GAAA
65 C-GACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAA
* *
9193 AAAAAATATATAGAGGGGTATTATTGTAATTATAT-CTAAATATATAAGGTAAAATTATATA-TA
129 AAAAAATATAGAGAGGGGTATTATTGTAATTAT-TCCTAAATATATAAGATAAAATTATATATTA
* * *
9256 TT-TTCGGGTCGGGTATTTTTCACCCTAAACCCGAA-CTCGACCCGACTCGAATATCACACTTAA
193 TTGTTCGGGTCAGATATTTTTCACCCTAAACCCGAACCT-GACCCGACCCGAATATCACACTTAA
9319 AAAAACC
257 AAAAACC
9326 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACTCGA-
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA-TCGAC
9390 --A-CCGACCCGAAATAATAAAAAAA-TATTTTTATTCAAT
65 CGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAAT
9427 TAATGAATAA
Statistics
Matches: 338, Mismatches: 16, Indels: 22
0.90 0.04 0.06
Matches are distributed among these distances:
256 14 0.04
257 22 0.07
258 1 0.00
260 2 0.01
261 117 0.35
262 59 0.17
263 4 0.01
265 61 0.18
266 58 0.17
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (263 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCGACC
GACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAA
AAAATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATTATTG
TTCGGGTCAGATATTTTTCACCCTAAACCCGAACCTGACCCGACCCGAATATCACACTTAAAAAA
ACC
Found at i:10462 original size:2 final size:2
Alignment explanation
Indices: 10455--10502 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
10445 CTTCTTTTAG
10455 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
10497 AT AT AT
1 AT AT AT
10503 CAAATATCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10829 original size:14 final size:14
Alignment explanation
Indices: 10810--10846 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
10800 TGAATCATAT
10810 GTACAAACATCAGA
1 GTACAAACATCAGA
10824 GTACAAACATCAGA
1 GTACAAACATCAGA
*
10838 GTTCAAACA
1 GTACAAACA
10847 CAATCTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.22, G:0.14, T:0.16
Consensus pattern (14 bp):
GTACAAACATCAGA
Found at i:18420 original size:28 final size:28
Alignment explanation
Indices: 18363--18420 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
18353 AATAAAAAGG
*
18363 AAATTACTGTAACTAAATAGAACTTTAA
1 AAATTACTGTAACTAAATAGAACTTCAA
18391 AAATTA-TCGTAACTAAATAGAA-TATCAA
1 AAATTACT-GTAACTAAATAGAACT-TCAA
18419 AA
1 AA
18421 CAATACCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.29
Consensus pattern (28 bp):
AAATTACTGTAACTAAATAGAACTTCAA
Found at i:30087 original size:23 final size:22
Alignment explanation
Indices: 30052--30106 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
30042 GAAAAATTGG
* *
30052 AAAACCGAATTTTTTATCGGATAA
1 AAAACCG-GTTTTTTATCCGA-AA
30076 AAAACCGGTTTTTTATCCGAAA
1 AAAACCGGTTTTTTATCCGAAA
*
30098 AAACCCGGT
1 AAAACCGGT
30107 CTGGGTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 10 0.36
23 11 0.39
24 7 0.25
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (22 bp):
AAAACCGGTTTTTTATCCGAAA
Found at i:32411 original size:21 final size:21
Alignment explanation
Indices: 32387--32428 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
32377 AGTTTATTTT
*
32387 TAAATTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
32408 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
32429 AACTTGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:32532 original size:33 final size:33
Alignment explanation
Indices: 32417--32525 Score: 161
Period size: 33 Copynumber: 3.4 Consensus size: 33
32407 GTAAACTTTG
32417 TTTCAA-TTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
* *
32449 TTTAAATTTATCAAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
* *
32482 TTTGAATTTATCGAACTTGGAAGTATTT-AGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
32514 TTTCAA-TTATCG
1 TTTCAATTTATCG
32526 TAAACTTTGT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
31 6 0.09
32 14 0.20
33 50 0.71
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (33 bp):
TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
Found at i:40192 original size:26 final size:26
Alignment explanation
Indices: 40156--40205 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
40146 AGATGCGTAC
*
40156 TGACACTCACCATTGAAGCTGAAGAT
1 TGACACTCACCACTGAAGCTGAAGAT
40182 TGACACTCACCACTGAAGCTGAAG
1 TGACACTCACCACTGAAGCTGAAG
40206 CTAAAGGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (26 bp):
TGACACTCACCACTGAAGCTGAAGAT
Found at i:46660 original size:12 final size:14
Alignment explanation
Indices: 46645--46677 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
46635 AAATTGTAAA
46645 TTTAATTT-AT-TT
1 TTTAATTTGATATT
46657 TTTAATTTGATATT
1 TTTAATTTGATATT
46671 TTTAATT
1 TTTAATT
46678 CTTATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 2 0.11
14 9 0.47
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTAATTTGATATT
Found at i:52704 original size:26 final size:26
Alignment explanation
Indices: 52675--52756 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 26
52665 GGTCCTTAAT
52675 TTTTTAATTTTATAAAATGGTCTCAC
1 TTTTTAATTTTATAAAATGGTCTCAC
** * *
52701 -TTTTACCTTTATAGTTAA-GGGCTC-C
1 TTTTTAATTTTATA--AAATGGTCTCAC
52726 TATTTTTAATTTTAT-AAATGGTCTCAC
1 --TTTTTAATTTTATAAAATGGTCTCAC
52753 TTTT
1 TTTT
52757 ACCTTTATAG
Statistics
Matches: 41, Mismatches: 8, Indels: 15
0.64 0.12 0.23
Matches are distributed among these distances:
25 18 0.44
26 10 0.24
27 3 0.07
28 10 0.24
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (26 bp):
TTTTTAATTTTATAAAATGGTCTCAC
Found at i:52756 original size:52 final size:53
Alignment explanation
Indices: 52675--52780 Score: 205
Period size: 52 Copynumber: 2.0 Consensus size: 53
52665 GGTCCTTAAT
52675 TTTTTAATTTTATAAAATGGTCTCACTTTTACCTTTATAGTTAAGGGCTCCTA
1 TTTTTAATTTTATAAAATGGTCTCACTTTTACCTTTATAGTTAAGGGCTCCTA
52728 TTTTTAATTTTAT-AAATGGTCTCACTTTTACCTTTATAGTTAAGGGCTCCTA
1 TTTTTAATTTTATAAAATGGTCTCACTTTTACCTTTATAGTTAAGGGCTCCTA
52780 T
1 T
52781 AAAATTCTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 40 0.75
53 13 0.25
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (53 bp):
TTTTTAATTTTATAAAATGGTCTCACTTTTACCTTTATAGTTAAGGGCTCCTA
Found at i:55863 original size:21 final size:21
Alignment explanation
Indices: 55839--55880 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
55829 AGTTTATTTT
55839 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
55860 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
55881 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:55917 original size:33 final size:33
Alignment explanation
Indices: 55875--55977 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
55865 TTTGTTTCAA
55875 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
55908 TTATCGAACTTGAAAGTTTTTAAATATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
55941 TTATCGAACTTGGAAGTATTT-AGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
55972 TTATCG
1 TTATCG
55978 TAAACTTTGT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 6 0.09
32 8 0.12
33 50 0.78
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:57184 original size:24 final size:26
Alignment explanation
Indices: 57134--57195 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
57124 TTTTGAGAGC
*
57134 AGTTTTCG-AAAATATATATATATTAT
1 AGTTTT-GAAAAACATATATATATTAT
57160 AGTTTTGAAAAACATATAT-TA-TAT
1 AGTTTTGAAAAACATATATATATTAT
57184 AGTTTTGAAAAA
1 AGTTTTGAAAAA
57196 TAGTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
24 15 0.44
25 3 0.09
26 16 0.47
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (26 bp):
AGTTTTGAAAAACATATATATATTAT
Found at i:57224 original size:40 final size:43
Alignment explanation
Indices: 57162--57351 Score: 125
Period size: 35 Copynumber: 4.9 Consensus size: 43
57152 TATATTATAG
57162 TTTTGAAAAACATATAT--TATATAG-TTTTGAAAAATAGTTTT
1 TTTTGAAAAACATATATAATATATAGTTTTTG-AAAATAGTTTT
*
57203 TTTTG-AAAATATATATAATATATAGTTTTTGAAAATAG----
1 TTTTGAAAAACATATATAATATATAGTTTTTGAAAATAGTTTT
* *
57241 TTTT---AAA-ATATTTAATATATAGTTTTTGAAAA-CG--TT
1 TTTTGAAAAACATATATAATATATAGTTTTTGAAAATAGTTTT
**
57277 TTTAAAAAAACATATAT--TATATAG-TTTTGAAAATA-TTTT
1 TTTTGAAAAACATATATAATATATAGTTTTTGAAAATAGTTTT
** * * *
57316 TAAT-ATATATATATAT-ATAATATAGTTTTTGAAAAT
1 TTTTGAAAAACATATATAAT-ATATAGTTTTTGAAAAT
57352 TTTGAAAACA
Statistics
Matches: 122, Mismatches: 12, Indels: 30
0.74 0.07 0.18
Matches are distributed among these distances:
34 1 0.01
35 24 0.20
36 6 0.05
37 9 0.07
38 20 0.16
39 7 0.06
40 21 0.17
41 15 0.12
42 14 0.11
43 5 0.04
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (43 bp):
TTTTGAAAAACATATATAATATATAGTTTTTGAAAATAGTTTT
Found at i:57226 original size:42 final size:41
Alignment explanation
Indices: 57162--57351 Score: 136
Period size: 38 Copynumber: 4.9 Consensus size: 41
57152 TATATTATAG
*
57162 TTTTGAAAAACATATATTATATAG-TTTTGAAAAATAGTTTT
1 TTTTGAAAAACATATAATATATAGTTTTTG-AAAATAGTTTT
*
57203 TTTTGAAAATATATATAATATATAGTTTTTGAAAATAG----
1 TTTTGAAAA-ACATATAATATATAGTTTTTGAAAATAGTTTT
* * *
57241 TTTT--AAAATATTTAATATATAGTTTTTGAAAA-CG--TT
1 TTTTGAAAAACATATAATATATAGTTTTTGAAAATAGTTTT
** *
57277 TTTAAAAAAACATATATTATATAG-TTTTGAAAATA-TTTT
1 TTTTGAAAAACATATAATATATAGTTTTTGAAAATAGTTTT
** * * *
57316 TAAT-ATATATATATATATAATATAGTTTTTGAAAAT
1 TTTTGAAAAACATATA-AT-ATATAGTTTTTGAAAAT
57352 TTTGAAAACA
Statistics
Matches: 121, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
34 1 0.01
35 24 0.20
36 6 0.05
37 9 0.07
38 27 0.22
39 4 0.03
40 6 0.05
41 19 0.16
42 20 0.17
43 5 0.04
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (41 bp):
TTTTGAAAAACATATAATATATAGTTTTTGAAAATAGTTTT
Found at i:57259 original size:35 final size:35
Alignment explanation
Indices: 57203--57382 Score: 127
Period size: 35 Copynumber: 4.9 Consensus size: 35
57193 AAATAGTTTT
57203 TTTTGAAAATATATATAATATATAGTTTTTGAAAATAG
1 TTTT-AAAATAT-T-TAATATATAGTTTTTGAAAATAG
*
57241 TTTTAAAATATTTAATATATAGTTTTTGAAAA-CG
1 TTTTAAAATATTTAATATATAGTTTTTGAAAATAG
* * * *
57275 TTTTTAAAAAAACATATATTATATAG-TTTTGAAAATAT
1 -TTTT---AAAATATTTAATATATAGTTTTTGAAAATAG
57313 TTTTAATATATATATATATATAATATAGTTTTTGAAAAT--
1 TTTTAA-A-ATAT-T-TA-AT-ATATAGTTTTTGAAAATAG
* * * *
57352 TTTGAAAACATATATTATATAG-TTTTGAAAA
1 TTTTAAAATATTTAATATATAGTTTTTGAAAA
57383 CATATATATA
Statistics
Matches: 117, Mismatches: 13, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
32 9 0.08
33 6 0.05
34 4 0.03
35 27 0.23
36 4 0.03
37 23 0.20
38 22 0.19
39 6 0.05
40 6 0.05
41 10 0.09
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (35 bp):
TTTTAAAATATTTAATATATAGTTTTTGAAAATAG
Found at i:57292 original size:73 final size:73
Alignment explanation
Indices: 57215--57382 Score: 213
Period size: 73 Copynumber: 2.3 Consensus size: 73
57205 TTGAAAATAT
*
57215 ATATAATATATAGTTTTTGAAAATAGTTTTAA-A-ATAT-T-TA-AT-ATATAGTTTTTGAAAAC
1 ATATATTATATAG-TTTTGAAAATAGTTTTAATATATATATATATATAATATAGTTTTTGAAAA-
57274 GTTTTTAAAAAAAC
64 --TTTT--AAAAAC
*
57288 ATATATTATATAGTTTTGAAAATATTTTTAATATATATATATATATAATATAGTTTTTGAAAATT
1 ATATATTATATAGTTTTGAAAATAGTTTTAATATATATATATATATAATATAGTTTTTGAAAATT
*
57353 TTGAAAAC
66 TTAAAAAC
57361 ATATATTATATAGTTTTGAAAA
1 ATATATTATATAGTTTTGAAAA
57383 CATATATATA
Statistics
Matches: 86, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
72 17 0.20
73 40 0.47
74 4 0.05
75 5 0.06
76 2 0.02
77 2 0.02
78 16 0.19
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (73 bp):
ATATATTATATAGTTTTGAAAATAGTTTTAATATATATATATATATAATATAGTTTTTGAAAATT
TTAAAAAC
Found at i:57297 original size:115 final size:110
Alignment explanation
Indices: 57167--57383 Score: 294
Period size: 113 Copynumber: 1.9 Consensus size: 110
57157 TATAGTTTTG
**
57167 AAAAACATATATTATATAGTTTTGAAAAATAGTTTTTTTTGAAA-ATATATATA-ATATATAGTT
1 AAAAACATATATTATATAGTTTTG-AAAATA-TTTTTAAT-AAATATATATATATA-ATATAGTT
* * *
57230 TTTGAAAATAGTTTTAAAATATTTAATATATAGTTTTTGAAAACGTTTTTAA
62 TTTGAAAAT--TTTGAAAACATATAATATATAG-TTTTGAAAACGTTTTTAA
*
57282 AAAAACATATATTATATAGTTTTGAAAATATTTTTAATATATATATATATATAATATAGTTTTTG
1 AAAAACATATATTATATAGTTTTGAAAATATTTTTAATAAATATATATATATAATATAGTTTTTG
*
57347 AAAATTTTGAAAACATATATTATATAGTTTTGAAAAC
66 AAAATTTTGAAAACATATAATATATAGTTTTGAAAAC
57384 ATATATATAT
Statistics
Matches: 93, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
110 10 0.11
111 18 0.19
112 2 0.02
113 32 0.34
114 7 0.08
115 24 0.26
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (110 bp):
AAAAACATATATTATATAGTTTTGAAAATATTTTTAATAAATATATATATATAATATAGTTTTTG
AAAATTTTGAAAACATATAATATATAGTTTTGAAAACGTTTTTAA
Found at i:57371 original size:40 final size:40
Alignment explanation
Indices: 57288--57372 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
57278 TTAAAAAAAC
* ** *
57288 ATATATTATATAGTTTTGAAAATATTTTTAATATATATAT
1 ATATATAATATAGTTTTGAAAATATTTAAAACATATATAT
57328 ATATATAATATAGTTTTTGAAAAT-TTTGAAAACATATAT-T
1 ATATATAATATAG-TTTTGAAAATATTT-AAAACATATATAT
57368 ATATA
1 ATATA
57373 GTTTTGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 21 0.54
41 18 0.46
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (40 bp):
ATATATAATATAGTTTTGAAAATATTTAAAACATATATAT
Found at i:57378 original size:23 final size:24
Alignment explanation
Indices: 57351--57396 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
57341 TTTTTGAAAA
57351 TTTTGAAAACATATAT-TATATAG
1 TTTTGAAAACATATATATATATAG
57374 TTTTGAAAACATATATATATATA
1 TTTTGAAAACATATATATATATA
57397 TATAGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (24 bp):
TTTTGAAAACATATATATATATAG
Found at i:57400 original size:28 final size:27
Alignment explanation
Indices: 57361--57415 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
57351 TTTTGAAAAC
*
57361 ATATATTATATAGTTTTGAAAACATAT
1 ATATATTATATAGTTTTGAAAAAATAT
*
57388 ATATATATATATAGTTTTTAAAAAATAT
1 ATATAT-TATATAGTTTTGAAAAAATAT
57416 TATTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (27 bp):
ATATATTATATAGTTTTGAAAAAATAT
Found at i:57428 original size:29 final size:28
Alignment explanation
Indices: 57368--57428 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
57358 AACATATATT
* * *
57368 ATATAGTTTTGAAAACATATATATATAT
1 ATATAGTTTTGAAAAAATATATATAAAA
* *
57396 ATATAGTTTTTAAAAAATATTATTTAAAA
1 ATATAGTTTTGAAAAAATA-TATATAAAA
57425 ATAT
1 ATAT
57429 CTATATAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (28 bp):
ATATAGTTTTGAAAAAATATATATAAAA
Found at i:57466 original size:101 final size:98
Alignment explanation
Indices: 57288--57482 Score: 220
Period size: 101 Copynumber: 1.9 Consensus size: 98
57278 TTAAAAAAAC
*
57288 ATATATTATATAGTTTTGAAAATATTTTTAATATATATATATATATAATATAGTTTTTGAAAATT
1 ATATATTATATAGTTTTAAAAATATTTTTAATATATATATATATATAATATA-TTTTTGAAAATT
**
57353 TTGAAAACATATATTATATAGTTTTGAAAACATAT
65 TTGAAAACATATAAAATATAG-TTTGAAAACATAT
*
57388 ATATATATATATAGTTTTTAAAAAATATTATTTAA-A-A-ATATCTATATAAT-T-TTTTTGAAA
1 ATATAT-TATATAG-TTTT-AAAAATATT-TTTAATATATATATATATATAATATATTTTTG-AA
* *
57448 ACATTTTTAAATATATATAAAATATAGTTTGAAAA
61 A-ATTTTGAAA-ACATATAAAATATAGTTTGAAAA
57483 TGTTTTGAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
98 6 0.07
99 3 0.04
100 23 0.28
101 31 0.38
102 5 0.06
103 9 0.11
104 5 0.06
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (98 bp):
ATATATTATATAGTTTTAAAAATATTTTTAATATATATATATATATAATATATTTTTGAAAATTT
TGAAAACATATAAAATATAGTTTGAAAACATAT
Found at i:57567 original size:20 final size:20
Alignment explanation
Indices: 57530--57567 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
57520 TATATATTTG
*
57530 TTTTTATTTTATTTTTTTCA
1 TTTTTATTTTATTATTTTCA
57550 TTTTTA-TTTATTAATTTT
1 TTTTTATTTTATT-ATTTT
57568 TCCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTATTTTATTATTTTCA
Done.