Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002817.1 Hibiscus syriacus cultivar Beakdansim tig00005797_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: 77514
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3230 original size:6 final size:6
Alignment explanation
Indices: 3221--3270 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
3211 AAATGCAAAG
*
3221 ATGTGA ATGTAA ATG-AA ATGTAAA GATGTAA ATGTAAA ATG-AA ATGTAA
1 ATGTAA ATGTAA ATGTAA ATGT-AA -ATGTAA ATGT-AA ATGTAA ATGTAA
3270 A
1 A
3271 GATACAAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
5 10 0.26
6 15 0.39
7 9 0.24
8 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (6 bp):
ATGTAA
Found at i:3240 original size:25 final size:26
Alignment explanation
Indices: 3205--3273 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
3195 GCAAAGATGC
* *
3205 AAATGCAAATGCAAAGATGTGAATGT-
1 AAATG-AAATGTAAAGATGTAAATGTA
3231 AAATGAAATGTAAAGATGTAAATGTA
1 AAATGAAATGTAAAGATGTAAATGTA
3257 AAATGAAATGTAAAGAT
1 AAATGAAATGTAAAGAT
3274 ACAAATGCAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 18 0.45
26 22 0.55
ACGTcount: A:0.52, C:0.03, G:0.20, T:0.25
Consensus pattern (26 bp):
AAATGAAATGTAAAGATGTAAATGTA
Found at i:3279 original size:26 final size:25
Alignment explanation
Indices: 3226--3280 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
3216 CAAAGATGTG
**
3226 AATGTAAATGAAATGTAAAGATGTA
1 AATGTAAATGAAATGTAAAGATACA
3251 AATGTAAAATGAAATGTAAAGATACA
1 AATGT-AAATGAAATGTAAAGATACA
3277 AATG
1 AATG
3281 CAGATGCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.55, C:0.02, G:0.18, T:0.25
Consensus pattern (25 bp):
AATGTAAATGAAATGTAAAGATACA
Found at i:5344 original size:15 final size:14
Alignment explanation
Indices: 5315--5351 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
5305 TTTAAAGAAA
*
5315 AATATATATATAAT
1 AATATTTATATAAT
5329 AATATTTATAATAAT
1 AATATTTAT-ATAAT
5344 AATATTTA
1 AATATTTA
5352 AATCCTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATATTTATATAAT
Found at i:5442 original size:23 final size:23
Alignment explanation
Indices: 5412--5464 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
5402 ATACAAAAAT
5412 TATATTAACATGTGATAAACAAA
1 TATATTAACATGTGATAAACAAA
*
5435 TATATTAACATGTGATACACAAA
1 TATATTAACATGTGATAAACAAA
5458 TATATTA
1 TATATTA
5465 CCAGGCCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (23 bp):
TATATTAACATGTGATAAACAAA
Found at i:6121 original size:26 final size:26
Alignment explanation
Indices: 6080--6130 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
6070 GAACCAGACG
*
6080 AAACCATGATCAAATCTAAAACCCCA
1 AAACCATGATCAAATCCAAAACCCCA
* * *
6106 AAACCATGCTCGAATCCAAAGCCCC
1 AAACCATGATCAAATCCAAAACCCC
6131 CTCTTTTCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.43, C:0.35, G:0.08, T:0.14
Consensus pattern (26 bp):
AAACCATGATCAAATCCAAAACCCCA
Found at i:9428 original size:21 final size:21
Alignment explanation
Indices: 9377--9437 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
9367 AGCCACATTG
* * *
9377 AAGAAGTCAGCCACTTCAACT
1 AAGAAGTCAACCACATCGACT
* * *
9398 AATAAATCAACAACATCGACT
1 AAGAAGTCAACCACATCGACT
9419 AAGAAGTCAACCACATCGA
1 AAGAAGTCAACCACATCGA
9438 AGAAACTAAC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.16
Consensus pattern (21 bp):
AAGAAGTCAACCACATCGACT
Found at i:9710 original size:24 final size:24
Alignment explanation
Indices: 9660--9711 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
9650 AGTTAATTAT
*
9660 TTGTCTGAGATTGTGGAAATGATC
1 TTGTCTGAGATTGTGGAAATGAGC
*
9684 TTGTCTG-GAATTGTGGAAATTAGC
1 TTGTCTGAG-ATTGTGGAAATGAGC
9708 TTGT
1 TTGT
9712 TGAAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.23, C:0.08, G:0.29, T:0.40
Consensus pattern (24 bp):
TTGTCTGAGATTGTGGAAATGAGC
Found at i:9768 original size:59 final size:59
Alignment explanation
Indices: 9676--9895 Score: 218
Period size: 59 Copynumber: 3.8 Consensus size: 59
9666 GAGATTGTGG
* * *
9676 AAATGATCTTGTCTGGAATTGTGGAAATTAGCTTGTTGAAATTTATAAACATATCTATA
1 AAATGATCTTGTCTGGAATTGTGAAAATTAGCTTGTTGAAAATTATGAACATATCTATA
* * * *
9735 AAATGATCTTGTCTGGAATTGTGAAAATTAGCTTGTTGAAAACTATGAACATATATGTG
1 AAATGATCTTGTCTGGAATTGTGAAAATTAGCTTGTTGAAAATTATGAACATATCTATA
* * * * ** *
9794 AAATGATATTCTCTTAGAATTGTAAAAATTAAATTGTTG-AAATATGTGAAC--ATCTATCA
1 AAATGATCTTGTC-TGGAATTGTGAAAATTAGCTTGTTGAAAAT-TATGAACATATCTAT-A
* * *
9853 ACAT-ATCTTGTCTTGAATTGTG-ACATTAGCTTG-TGAAAATTAT
1 AAATGATCTTGTCTGGAATTGTGAAAATTAGCTTGTTGAAAATTAT
9896 TTTGGAGAAA
Statistics
Matches: 130, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
55 4 0.03
56 12 0.09
57 8 0.06
58 10 0.08
59 69 0.53
60 27 0.21
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (59 bp):
AAATGATCTTGTCTGGAATTGTGAAAATTAGCTTGTTGAAAATTATGAACATATCTATA
Found at i:10211 original size:27 final size:27
Alignment explanation
Indices: 10154--10211 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
10144 TTTTGGTCTG
* **
10154 TTTTGTATGAAACAAGCAGACCTTTTG
1 TTTTGTATAAAACAAGCAGACCTTTCA
*
10181 TTTTGTATAAAACAAGCTAG-TCTTTCA
1 TTTTGTATAAAACAAGC-AGACCTTTCA
10208 TTTT
1 TTTT
10212 ACATGTAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (27 bp):
TTTTGTATAAAACAAGCAGACCTTTCA
Found at i:13342 original size:25 final size:25
Alignment explanation
Indices: 13308--13355 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
13298 ATCTAATTAA
13308 TTTGATTCAAACATTTGCATTTAGT
1 TTTGATTCAAACATTTGCATTTAGT
*
13333 TTTGTTTCAAACATTTGCATTTA
1 TTTGATTCAAACATTTGCATTTA
13356 TCCACTACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.50
Consensus pattern (25 bp):
TTTGATTCAAACATTTGCATTTAGT
Found at i:14593 original size:31 final size:31
Alignment explanation
Indices: 14557--14617 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
14547 AGATATAGTA
*
14557 TTTAATCATTTTCATTTTATTTTAATTAAGT
1 TTTAATCATTTTCATTTCATTTTAATTAAGT
* *
14588 TTTAATTATTTTCATTTCGTTTTAATTAAG
1 TTTAATCATTTTCATTTCATTTTAATTAAG
14618 ATGTGATCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.61
Consensus pattern (31 bp):
TTTAATCATTTTCATTTCATTTTAATTAAGT
Found at i:14596 original size:20 final size:20
Alignment explanation
Indices: 14573--14615 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
14563 CATTTTCATT
14573 TTATTTTAATTAAGTTTTAA
1 TTATTTTAATTAAGTTTTAA
* **
14593 TTATTTTCATTTCGTTTTAA
1 TTATTTTAATTAAGTTTTAA
14613 TTA
1 TTA
14616 AGATGTGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (20 bp):
TTATTTTAATTAAGTTTTAA
Found at i:17290 original size:31 final size:31
Alignment explanation
Indices: 17254--17330 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
17244 CAGTTACGTT
17254 GGGACCATATTGCAAACGGACTAAATGTTGG
1 GGGACCATATTGCAAACGGACTAAATGTTGG
*
17285 GGGACCATATTACAAACGGACTAAATGTTGG
1 GGGACCATATTGCAAACGGACTAAATGTTGG
**
17316 GGGACTGTATTGCAA
1 GGGACCATATTGCAA
17331 GTTTTAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGG
Found at i:17496 original size:45 final size:44
Alignment explanation
Indices: 17424--17508 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
17414 TGATAGTTTA
* *
17424 ATTCAAATATTATTTATTTATATTTTATTTTAT-AATATATCAT
1 ATTCAAATATTATTAATTTATATTTTATGTTATAAATATATCAT
*
17467 ATTCAAGTATTAATTAATCTTATATTTTATGTTATAAATATA
1 ATTCAAATATT-ATTAAT-TTATATTTTATGTTATAAATATA
17509 ATTATAGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 10 0.28
44 5 0.14
45 15 0.42
46 6 0.17
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (44 bp):
ATTCAAATATTATTAATTTATATTTTATGTTATAAATATATCAT
Found at i:17664 original size:2 final size:2
Alignment explanation
Indices: 17659--17702 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
17649 TTTTACACAC
17659 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
17701 AT
1 AT
17703 TATTTATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18957 original size:20 final size:21
Alignment explanation
Indices: 18932--19015 Score: 57
Period size: 22 Copynumber: 3.8 Consensus size: 21
18922 TCTTTCTGTT
18932 TTTTTATCATC-TATTAT-TAC
1 TTTTTAT-ATCTTATTATATAC
*
18952 TTTTTAGTATCTTATTATATAT
1 TTTTTA-TATCTTATTATATAC
* *
18974 TTTTTATTATATATATATATATAG
1 TTTTTA-TATCT-TAT-TATATAC
18998 TTATTTATTAT-TTATTAT
1 TT-TTTA-TATCTTATTAT
19016 TATTGATGTA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.17
21 7 0.13
22 15 0.28
23 6 0.11
24 9 0.17
25 8 0.15
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTATATCTTATTATATAC
Found at i:18962 original size:23 final size:22
Alignment explanation
Indices: 18943--19015 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
18933 TTTTATCATC
18943 TATTAT-TACTTTTTAGTATCT
1 TATTATATACTTTTTAGTATCT
* * *
18964 TATTATATATTTTTTATTATAT
1 TATTATATACTTTTTAGTATCT
* *
18986 ATATATATATAGTTATTTATTAT-T
1 -TAT-TATATACTT-TTTAGTATCT
19010 TATTAT
1 TATTAT
19016 TATTGATGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.14
22 15 0.34
23 6 0.14
24 9 0.20
25 8 0.18
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (22 bp):
TATTATATACTTTTTAGTATCT
Found at i:19042 original size:35 final size:32
Alignment explanation
Indices: 18978--19042 Score: 69
Period size: 35 Copynumber: 1.9 Consensus size: 32
18968 ATATATTTTT
*
18978 TATTATATATATATATATAGTTATTTATTATT
1 TATTATATATATATATATAGTTATATATTATT
*
19010 TATTATTATTGATGTATATATA-TATATATATTA
1 TATTA-TA-T-ATATATATATAGT-TATATATTA
19043 GTTTTCTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
32 5 0.19
33 2 0.07
34 2 0.07
35 18 0.67
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (32 bp):
TATTATATATATATATATAGTTATATATTATT
Found at i:19055 original size:43 final size:43
Alignment explanation
Indices: 18981--19062 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
18971 TATTTTTTAT
18981 TATATATATATATATAGTTATTTATTATTTATTATTATTGATG
1 TATATATATATATATAGTTATTTATTATTTATTATTATTGATG
*
19024 TATATATATATATATA-TTAGTTT-TCTCTTTATTATTATT
1 TATATATATATATATAGTTA-TTTAT-TATTTATTATTATT
19063 ATCCTTATAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 4 0.11
43 32 0.89
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (43 bp):
TATATATATATATATAGTTATTTATTATTTATTATTATTGATG
Found at i:19098 original size:18 final size:18
Alignment explanation
Indices: 19077--19124 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
19067 TTATACATAC
*
19077 TCTTTTGTTTATCTCATT
1 TCTTTTATTTATCTCATT
*
19095 TCTTTTATTTATCTTATT
1 TCTTTTATTTATCTCATT
19113 T-TATTTATTTAT
1 TCT-TTTATTTAT
19125 TTTTCCTGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (18 bp):
TCTTTTATTTATCTCATT
Found at i:19114 original size:14 final size:13
Alignment explanation
Indices: 19092--19127 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
19082 TGTTTATCTC
*
19092 ATTTCTTTTATTT
1 ATTTATTTTATTT
19105 ATCTTATTTTATTT
1 AT-TTATTTTATTT
19119 ATTTATTTT
1 ATTTATTTT
19128 TCCTGTCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTTATTTTATTT
Found at i:19128 original size:14 final size:14
Alignment explanation
Indices: 19097--19127 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
19087 ATCTCATTTC
19097 TTTTATTTATCTTA
1 TTTTATTTATCTTA
19111 TTTTATTTAT-TTA
1 TTTTATTTATCTTA
19124 TTTT
1 TTTT
19128 TCCTGTCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTATCTTA
Found at i:20358 original size:31 final size:31
Alignment explanation
Indices: 20323--20384 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
20313 TTACAATACA
20323 ATCCCCCAACATTTAGTCCGTTTGCAATATG
1 ATCCCCCAACATTTAGTCCGTTTGCAATATG
** *
20354 ATCCCTTAACATTTAGTCTGTTTGCAATATG
1 ATCCCCCAACATTTAGTCCGTTTGCAATATG
20385 GTCTCCAACG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (31 bp):
ATCCCCCAACATTTAGTCCGTTTGCAATATG
Found at i:20445 original size:31 final size:31
Alignment explanation
Indices: 20399--20481 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 31
20389 CCAACGTAAC
* * *
20399 TGTTGGGGGATCATATTGCAAACATACTAAA
1 TGTTGGGGGACCATATTACAAACAGACTAAA
* *
20430 TGTTAGGGGACCATATTACAAACGGACTAAA
1 TGTTGGGGGACCATATTACAAACAGACTAAA
**
20461 TGTTGGGGGACTGTATTACAA
1 TGTTGGGGGACCATATTACAA
20482 GTTTTAAAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (31 bp):
TGTTGGGGGACCATATTACAAACAGACTAAA
Found at i:21602 original size:2 final size:2
Alignment explanation
Indices: 21595--21628 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21585 TGTTTTATTT
21595 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21629 ATTTTAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23419 original size:20 final size:20
Alignment explanation
Indices: 23402--23440 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
23392 ATATATTATA
23402 AAAATTTAAAAAATATTAAT
1 AAAATTTAAAAAATATTAAT
23422 AAAATTTAAAAAATATTAA
1 AAAATTTAAAAAATATTAA
23441 ATTTTCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTTAAAAAATATTAAT
Found at i:23440 original size:10 final size:10
Alignment explanation
Indices: 23394--23441 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
23384 ATGAAATAAT
23394 ATATTATAAAA
1 ATATTA-AAAA
23405 AT-TTAAAAA
1 ATATTAAAAA
23414 ATATTAATAAA
1 ATATTAA-AAA
23425 AT-TTAAAAA
1 ATATTAAAAA
23434 ATATTAAA
1 ATATTAAA
23442 TTTTCATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 11 0.32
10 16 0.47
11 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATATTAAAAA
Found at i:24163 original size:65 final size:64
Alignment explanation
Indices: 24049--24247 Score: 203
Period size: 65 Copynumber: 3.1 Consensus size: 64
24039 TCTCTTGATT
* * *
24049 CATCAAGTGCATTCGATGTTTCAA-AATAGTCA-GAGTGCATCGATGCATGGTTGGTGCATCGAT
1 CATCAAATGCATTCGATG-TTCAATAAAATTCATG-GTGCATCGATGCATGGTTGGTGCATCGAT
24112 G
64 G
*
24113 CATCAAATGCATTCGATGTTTTC-ATAAAATCCTC-T-GTGCATCGGTGCATGGTAT-GTGCATC
1 CATCAAATGCATTCGATG--TTCAATAAAAT--TCATGGTGCATCGATGCATGGT-TGGTGCATC
*
24174 GATA
61 GATG
* ** *
24178 CATGAAATGCATTCGATGTTCAATTTAATTCATGGTGCATCGATGCATGGATTGGTGCATCGGTG
1 CATCAAATGCATTCGATGTTCAATAAAATTCATGGTGCATCGATGCATGG-TTGGTGCATCGATG
24243 CATCA
1 CATCA
24248 CTTTGATAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 21
0.77 0.08 0.14
Matches are distributed among these distances:
62 2 0.02
63 4 0.04
64 39 0.35
65 64 0.57
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (64 bp):
CATCAAATGCATTCGATGTTCAATAAAATTCATGGTGCATCGATGCATGGTTGGTGCATCGATG
Found at i:26911 original size:23 final size:22
Alignment explanation
Indices: 26881--26960 Score: 81
Period size: 23 Copynumber: 3.6 Consensus size: 22
26871 GCATGACCCT
26881 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
26903 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
26925 GTGTATCGATGCACGTTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
26947 ATGCATCAATGCAC
1 GTGCATCGATGCAC
26961 TGTTAGGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.33
22 15 0.33
23 16 0.35
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:32889 original size:65 final size:63
Alignment explanation
Indices: 32790--32981 Score: 185
Period size: 65 Copynumber: 3.0 Consensus size: 63
32780 GCACTAAGAG
* **
32790 TGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAA
1 TGCATTCGATGTTTCATAAA-ATCCTCAGTGCATCGATGCATGG-TGGTGCATCGATGCATCAAA
* * * *
32854 TGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTATGTGCAACGATGCATGAAA
1 TGCATTCGATG-TTTCATAAAATCCTCAGTGCATCGATGCATGGT-GGTGCATCGATGCATCAAA
** *
32919 TGCATTCGATG-TTCAATTTAAT--TCATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATC
1 TGCATTCGATGTTTC-ATAAAATCCTCA--GTGCATCGATGCATGG--TGGTGCATCGATGCATC
32981 A
61 A
32982 CTTTGATAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 32 0.30
65 64 0.60
66 4 0.04
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (63 bp):
TGCATTCGATGTTTCATAAAATCCTCAGTGCATCGATGCATGGTGGTGCATCGATGCATCAAA
Found at i:33423 original size:34 final size:34
Alignment explanation
Indices: 33375--33447 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
33365 TATCACACTT
* *
33375 AAAAAAACCTGACCCGA-ACCTAATTTTTTTTATA
1 AAAAAAACCTGACCCGATACCGAATTGTTTTTA-A
*
33409 AAAAAAATCC-GACCCGATCCCGAATTGTTTTTAA
1 AAAAAAA-CCTGACCCGATACCGAATTGTTTTTAA
33443 AAAAA
1 AAAAA
33448 TTTGACCCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 20 0.59
35 14 0.41
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (34 bp):
AAAAAAACCTGACCCGATACCGAATTGTTTTTAA
Found at i:34037 original size:28 final size:29
Alignment explanation
Indices: 34004--34063 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
33994 ATTATGTTAA
* *
34004 TTATTTATTAAAA-TAATAA-TATTATATT
1 TTATTT-TAAAAAGTAATAATTAATATATT
*
34032 TTATTTTAAAAAGTATTAATTAATATATT
1 TTATTTTAAAAAGTAATAATTAATATATT
34061 TTA
1 TTA
34064 AATATATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 11 0.41
29 11 0.41
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TTATTTTAAAAAGTAATAATTAATATATT
Found at i:34076 original size:23 final size:23
Alignment explanation
Indices: 34033--34104 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
34023 TATTATATTT
* *
34033 TATTTTAAAAAGTATTAATTAATA
1 TATTTTAAATA-TATTTATTAATA
*
34057 TATTTTAAATATATTTATTAAAA
1 TATTTTAAATATATTTATTAATA
*
34080 TATTATTAGAT-TATTATATTAATA
1 TATT-TTAAATATATT-TATTAATA
34104 T
1 T
34105 TAAATGCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 18 0.44
24 23 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
TATTTTAAATATATTTATTAATA
Found at i:35559 original size:15 final size:15
Alignment explanation
Indices: 35539--35568 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35529 TTCACCTTCA
35539 CTTTCCTCTCCCTCG
1 CTTTCCTCTCCCTCG
*
35554 CTTTCCTCTTCCTCG
1 CTTTCCTCTCCCTCG
35569 TCACTCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.50, G:0.07, T:0.43
Consensus pattern (15 bp):
CTTTCCTCTCCCTCG
Found at i:35565 original size:21 final size:21
Alignment explanation
Indices: 35516--35567 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
35506 CCCTTCCCTC
*
35516 TCCTC-TCCTCTCCTTCACCT
1 TCCTCTTCCTCTCCCTCACCT
* *
35536 TCACT-TTCCTCTCCCTCGCTT
1 TC-CTCTTCCTCTCCCTCACCT
35557 TCCTCTTCCTC
1 TCCTCTTCCTC
35568 GTCACTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.04, C:0.52, G:0.02, T:0.42
Consensus pattern (21 bp):
TCCTCTTCCTCTCCCTCACCT
Found at i:36021 original size:19 final size:18
Alignment explanation
Indices: 35999--36034 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
35989 ACAATTTATT
*
35999 GTTAGTTTGTTAGCTTGCG
1 GTTAGTTGGTTAG-TTGCG
36018 GTTAGTTGGTTAGTTGC
1 GTTAGTTGGTTAGTTGC
36035 CACAAATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.11, C:0.08, G:0.33, T:0.47
Consensus pattern (18 bp):
GTTAGTTGGTTAGTTGCG
Found at i:39063 original size:20 final size:21
Alignment explanation
Indices: 39034--39081 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
39024 ATTTATGGAT
* *
39034 AAAT-TATAAAATATATTTA-
1 AAATATATAAAATAAAATTAG
39053 AAATATAT-AAATAAAATTAG
1 AAATATATAAAATAAAATTAG
39073 AAATATATA
1 AAATATATA
39082 CAACCATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATATATAAAATAAAATTAG
Found at i:39303 original size:14 final size:14
Alignment explanation
Indices: 39274--39319 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
39264 GTCAAATTAA
*
39274 TATATCTTTTAAAAT
1 TATAT-TTTAAAAAT
39289 TATATTTTAAAAAT
1 TATATTTTAAAAAT
39303 TATATTTTAAAAAT
1 TATATTTTAAAAAT
39317 TAT
1 TAT
39320 TATATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 25 0.83
15 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATTTTAAAAAT
Found at i:39327 original size:14 final size:14
Alignment explanation
Indices: 39284--39329 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
39274 TATATCTTTT
*
39284 AAAATTATATTTTA
1 AAAATTATATTATA
*
39298 AAAATTATATTTTA
1 AAAATTATATTATA
39312 AAAATTAT-TATATA
1 AAAATTATAT-TATA
39326 AAAA
1 AAAA
39330 AGAAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 1 0.03
14 29 0.97
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATTATATTATA
Found at i:39327 original size:28 final size:29
Alignment explanation
Indices: 39274--39329 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
39264 GTCAAATTAA
* *
39274 TATATCTTTTAAAATTATATTTTAAAAAT
1 TATATCTTTAAAAATTATATTATAAAAAT
39303 TATAT-TTTAAAAATTAT-TATATAAAAA
1 TATATCTTTAAAAATTATAT-TATAAAAA
39330 AGAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.04
28 18 0.75
29 5 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
TATATCTTTAAAAATTATATTATAAAAAT
Found at i:40797 original size:29 final size:29
Alignment explanation
Indices: 40762--40843 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
40752 AAACTAAATT
*
40762 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
40791 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
40820 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
40844 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:45566 original size:29 final size:29
Alignment explanation
Indices: 45531--45612 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
45521 AAACTAAATT
*
45531 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
45560 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
45589 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
45613 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:49851 original size:21 final size:21
Alignment explanation
Indices: 49827--49866 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49817 AATAATATTT
*
49827 ATAAAT-TTTATTCTTTTTAAG
1 ATAAATCTTTACT-TTTTTAAG
49848 ATAAATCTTTACTTTTTTA
1 ATAAATCTTTACTTTTTTA
49867 CTACATGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (21 bp):
ATAAATCTTTACTTTTTTAAG
Found at i:50668 original size:40 final size:40
Alignment explanation
Indices: 50611--50687 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
50601 GTTATATTTT
50611 TTTATTAAAATAATATTTAT-ATAATTATTATTTATTTAAA
1 TTTATTAAAATAATATTTATGATAATTA-TATTTATTTAAA
* * *
50651 TTTATT-AATTAATTATTTGTGCTAATTATATTTATTT
1 TTTATTAAAATAA-TATTTATGATAATTATATTTATTT
50688 GCCTATAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.16
40 21 0.66
41 6 0.19
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (40 bp):
TTTATTAAAATAATATTTATGATAATTATATTTATTTAAA
Found at i:53023 original size:14 final size:14
Alignment explanation
Indices: 53004--53037 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
52994 TTAAGAGAGA
*
53004 ATCAAAGAGAAAGC
1 ATCAAAGAGAAAAC
53018 ATCAAAGAGAAAAC
1 ATCAAAGAGAAAAC
53032 ATCAAA
1 ATCAAA
53038 CCTCAAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.09
Consensus pattern (14 bp):
ATCAAAGAGAAAAC
Found at i:58476 original size:95 final size:94
Alignment explanation
Indices: 58280--58533 Score: 316
Period size: 95 Copynumber: 2.7 Consensus size: 94
58270 GGCTAGCTAG
* * ** *
58280 ATCCATAAAGCTGAGGCGTTTAACCAATTGCTCTAGAGTTACAACTCAA--TTGTA-TATATATA
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTT-TATTGTATAT-
*
58342 ATTATCACATTTATCAGGCTAGCTGAATATT
64 ATAATCACATTTATCAGGCTAGCTGAATATT
* *
58373 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGAAAACTCAAGCTTTATTGTATAGTA
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATA-TA
* * *
58438 TAATCACCTTTATCAGGCTAGCTGACTCTT
65 TAATCACATTTATCAGGCTAGCTGAATATT
* * ** *
58468 ATCCATAAAGCTAGGGCGTTTAACCAATTGGTTTAGAGGGACATTTTAAGCTTTATTGTATATAT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATAT
58533 A
66 A
58534 TAATATTATA
Statistics
Matches: 139, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
93 43 0.31
94 6 0.04
95 89 0.64
96 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (94 bp):
ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATAT
AATCACATTTATCAGGCTAGCTGAATATT
Found at i:62262 original size:20 final size:19
Alignment explanation
Indices: 62215--62269 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
62205 AAAGTGTTAG
62215 ATAAAATAAATAATAAGATA
1 ATAAAATAAATAA-AAGATA
*
62235 AAATAAATAAATAAAAGATA
1 ATA-AAATAAATAAAAGATA
*
62255 GGTAAAATAAATAAA
1 -ATAAAATAAATAAA
62270 TTATAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (19 bp):
ATAAAATAAATAAAAGATA
Found at i:62491 original size:34 final size:34
Alignment explanation
Indices: 62425--62493 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 34
62415 AAGAATATAT
*
62425 ATATATGTATAATAAAACAAATAAATAAAAAATA
1 ATATATATATAATAAAACAAATAAATAAAAAATA
*
62459 ATATATATATACATAAAA-AATTAAA-AATAAAATA
1 ATATATATATA-ATAAAACAAATAAATAA-AAAATA
62493 A
1 A
62494 AAGTAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 2 0.06
34 23 0.74
35 6 0.19
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (34 bp):
ATATATATATAATAAAACAAATAAATAAAAAATA
Found at i:63717 original size:21 final size:20
Alignment explanation
Indices: 63669--63717 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
63659 TAGTGGGCTT
*
63669 GTTGGGCCACTGTGTATTAT
1 GTTGGGCCACTGTGTATTAA
*
63689 GCTGGGCCAC-GTGTAATGTAA
1 GTTGGGCCACTGTGT-AT-TAA
63710 GTTGGGCC
1 GTTGGGCC
63718 TGATACAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.16, C:0.18, G:0.35, T:0.31
Consensus pattern (20 bp):
GTTGGGCCACTGTGTATTAA
Found at i:63791 original size:17 final size:17
Alignment explanation
Indices: 63771--63812 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
63761 AATAATAATA
*
63771 ATATTTATACAATATAT
1 ATATATATACAATATAT
*
63788 ATATATATATAATATAT
1 ATATATATACAATATAT
*
63805 AAATATAT
1 ATATATAT
63813 GTTTATTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATATACAATATAT
Done.