Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002573.1 Hibiscus syriacus cultivar Beakdansim tig00005216_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: 69652
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7565 original size:18 final size:15
Alignment explanation
Indices: 7530--7562 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
7520 ACGATTCCGT
7530 TAACAACAACTCCAA
1 TAACAACAACTCCAA
*
7545 TAACAACAACTCCGA
1 TAACAACAACTCCAA
7560 TAA
1 TAA
7563 TAATATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.30, G:0.03, T:0.15
Consensus pattern (15 bp):
TAACAACAACTCCAA
Found at i:10061 original size:7 final size:7
Alignment explanation
Indices: 10049--10086 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
10039 TCTCTCATTT
10049 CTTCTTC
1 CTTCTTC
10056 CTTCTTC
1 CTTCTTC
10063 CTTCTTC
1 CTTCTTC
*
10070 CTTCAT-
1 CTTCTTC
10076 CTTCTT-
1 CTTCTTC
10082 CTTCT
1 CTTCT
10087 CCCAAACGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 10 0.34
7 19 0.66
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (7 bp):
CTTCTTC
Found at i:11243 original size:23 final size:23
Alignment explanation
Indices: 11198--11245 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
11188 ATAGCACTAT
**
11198 GGTGCATTTCTACGTGGCACTTC
1 GGTGCATTTCTACACGGCACTTC
11221 GGTGCATTTCTACACGGTC-CTTC
1 GGTGCATTTCTACACGG-CACTTC
11244 GG
1 GG
11246 GAAAAATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.12, C:0.27, G:0.27, T:0.33
Consensus pattern (23 bp):
GGTGCATTTCTACACGGCACTTC
Found at i:11276 original size:24 final size:24
Alignment explanation
Indices: 11205--11277 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
11195 TATGGTGCAT
*
11205 TTCTACGTGGCACTTCGGTGC-AT
1 TTCTACGTGGCACTTCGGTGCAAA
** *
11228 TTCTACACGGTC-CTTCGG-GAAAAA
1 TTCTACGTGG-CACTTCGGTG-CAAA
11252 TTCTACGTGGCACTTCGGTGCAAA
1 TTCTACGTGGCACTTCGGTGCAAA
11276 TT
1 TT
11278 TATACGAGCT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 1 0.03
23 15 0.39
24 21 0.55
25 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.32
Consensus pattern (24 bp):
TTCTACGTGGCACTTCGGTGCAAA
Found at i:11827 original size:11 final size:11
Alignment explanation
Indices: 11813--11847 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11803 CGTTTTACGG
*
11813 AGTACTATAGC
1 AGTACTATAAC
11824 AGTACTATAAC
1 AGTACTATAAC
*
11835 AGTACTGTAAC
1 AGTACTATAAC
11846 AG
1 AG
11848 GGGAATCGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (11 bp):
AGTACTATAAC
Found at i:12357 original size:18 final size:18
Alignment explanation
Indices: 12312--12361 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
12302 ATGAACTTGA
*
12312 AAATAAGATATGAATATG
1 AAATAAGTTATGAATATG
*
12330 AAATTAAGTTATGAATCTG
1 AAA-TAAGTTATGAATATG
12349 AAATAAGTTATGA
1 AAATAAGTTATGA
12362 GTTCGGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (18 bp):
AAATAAGTTATGAATATG
Found at i:12370 original size:19 final size:18
Alignment explanation
Indices: 12312--12376 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
12302 ATGAACTTGA
* **
12312 AAATAAGATATGAATATG
1 AAATAAGTTATGAATCGG
*
12330 AAATTAAGTTATGAATCTG
1 AAA-TAAGTTATGAATCGG
*
12349 AAATAAGTTATGAGTTCGG
1 AAATAAGTTATGA-ATCGG
*
12368 AAACAAGTT
1 AAATAAGTT
12377 CTAAAATGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
18 13 0.32
19 27 0.68
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (18 bp):
AAATAAGTTATGAATCGG
Found at i:12422 original size:13 final size:13
Alignment explanation
Indices: 12398--12457 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
12388 AAATAAAGAT
*
12398 TATGAAAATGAAA
1 TATGAAAGTGAAA
*
12411 TGTGAAAGTG-AA
1 TATGAAAGTGAAA
12423 TATGAAAGTGAAA
1 TATGAAAGTGAAA
* * *
12436 GATGAAAATGAGA
1 TATGAAAGTGAAA
12449 TATGAAAGT
1 TATGAAAGT
12458 TTTGTATTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
12 11 0.29
13 27 0.71
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (13 bp):
TATGAAAGTGAAA
Found at i:12535 original size:39 final size:39
Alignment explanation
Indices: 12487--12569 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
12477 AAAAAGAATA
* *
12487 TGATATGACTGTTATGTATGATATTGTTTATCTTGGCTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
*
12526 TGATATGACTATTATGTATGATATTGTTTATCATGGTTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
12565 TGATA
1 TGATA
12570 AAATCATGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.24, C:0.06, G:0.19, T:0.51
Consensus pattern (39 bp):
TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
Found at i:14813 original size:25 final size:25
Alignment explanation
Indices: 14779--14853 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
14769 GAGTCGAGGG
14779 TTCTACGTGGTCCTTCGGGACAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
*
14804 TTCTACGTGGTCCTTTGGGACAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
* *
14829 TTCTACATGGTCCTTCAGGACAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
14854 CTATGTGGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (25 bp):
TTCTACGTGGTCCTTCGGGACAAAT
Found at i:18357 original size:26 final size:26
Alignment explanation
Indices: 18319--18369 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
18309 AGATAGATAC
*
18319 ATATATATTAATAAT-ATAAAATTTTT
1 ATATATATAAAT-ATGATAAAATTTTT
18345 ATATATATAAATATGATAAAATTTT
1 ATATATATAAATATGATAAAATTTT
18370 AGGGTGGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
ATATATATAAATATGATAAAATTTTT
Found at i:19326 original size:21 final size:23
Alignment explanation
Indices: 19302--19351 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
19292 TTTTGTATTA
*
19302 ATATTATTATATTA-TAC-AATT
1 ATATTATTATATAATTACTAATT
19323 ATA-TA-TATATAATTACTAATT
1 ATATTATTATATAATTACTAATT
*
19344 TTATTATT
1 ATATTATT
19352 TAAATGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 9 0.39
22 2 0.09
23 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTATTATATAATTACTAATT
Found at i:20423 original size:3 final size:3
Alignment explanation
Indices: 20417--20464 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
20407 ATATTACGTT
*
20417 TTA TTA -TA TATA TATA TATA TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20464 T
1 T
20465 ACGTATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 28 0.68
4 11 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:22337 original size:10 final size:10
Alignment explanation
Indices: 22322--22355 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
22312 TTCATTTACC
22322 ATTTATTTTT
1 ATTTATTTTT
22332 ATTTATTTTT
1 ATTTATTTTT
* *
22342 ATCTATTTCT
1 ATTTATTTTT
22352 ATTT
1 ATTT
22356 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:32786 original size:105 final size:105
Alignment explanation
Indices: 32604--33321 Score: 1328
Period size: 105 Copynumber: 6.8 Consensus size: 105
32594 AGGTTTTACC
32604 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
32669 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
32709 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
32774 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
32814 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
32879 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
32919 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
32984 ACGAAGGGACCGTTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
33024 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
33089 ACGAAGGGACCGCTGGTTGTCTACAAGCATTTCTCAAATC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
33129 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAGCTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
33194 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * *
33234 CAGAGTCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
33299 ACGAAGGGACCGCTGGTTGTCAA
66 ACGAAGGGACCGCTGGTTGTCAA
33322 TAAGCAATTT
Statistics
Matches: 593, Mismatches: 20, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 593 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:33425 original size:20 final size:20
Alignment explanation
Indices: 33400--33441 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
33390 CCAGAACTCT
33400 GAGTTCGATTTCAACTTCAC
1 GAGTTCGATTTCAACTTCAC
*
33420 GAGTTCGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
33440 GA
1 GA
33442 CGAAGGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:33688 original size:21 final size:23
Alignment explanation
Indices: 33664--33713 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
33654 TTTTGTATTA
*
33664 ATATTATTATATTA-TAC-AATT
1 ATATTATTATATAATTACTAATT
33685 ATA-TA-TATATAATTACTAATT
1 ATATTATTATATAATTACTAATT
*
33706 TTATTATT
1 ATATTATT
33714 TAAATGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 9 0.39
22 2 0.09
23 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTATTATATAATTACTAATT
Found at i:34785 original size:2 final size:2
Alignment explanation
Indices: 34780--34812 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34770 TATTACGTTT
34780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34813 TATTGTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34914 original size:18 final size:18
Alignment explanation
Indices: 34884--34950 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
34874 TTTACCCTTT
*
34884 TTATTTTTATTATTATTA
1 TTATTTATATTATTATTA
* **
34902 TTCTTTATATTATCCTTA
1 TTATTTATATTATTATTA
* *
34920 TTATTTCTATTATTACTA
1 TTATTTATATTATTATTA
*
34938 TTTTTTAT-TTATT
1 TTATTTATATTATT
34951 CATGTAATTA
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 5 0.13
18 33 0.87
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTATATTATTATTA
Found at i:34931 original size:36 final size:35
Alignment explanation
Indices: 34874--34949 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
34864 TTTATACCCT
* * * *
34874 TTTACCCTTTTTATTTTTATTATTATTATTCTTTA
1 TTTATCCTTATTATTTCTATTATTACTATTCTTTA
*
34909 TATTATCCTTATTATTTCTATTATTACTATTTTTTA
1 T-TTATCCTTATTATTTCTATTATTACTATTCTTTA
34945 TTTAT
1 TTTAT
34950 TCATGTAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 5 0.14
36 30 0.86
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (35 bp):
TTTATCCTTATTATTTCTATTATTACTATTCTTTA
Found at i:38169 original size:2 final size:2
Alignment explanation
Indices: 38162--38211 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
38152 GAAATTCAGG
38162 TA TA TA TA 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 TA TA TA TA
38204 TA TA TA TA
1 TA TA TA TA
38212 CACAAGTCCA
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):
TA
Found at i:50219 original size:64 final size:63
Alignment explanation
Indices: 50150--50306 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 63
50140 TAATGAAGGT
* **
50150 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATAGTTTTATT-TTAA-AA
50213 G
63 G
* * * *
50214 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATATTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATAGTTTTATTTTAAAAG
*
50277 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
50307 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 3 0.04
64 66 0.85
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATAGTTTTATTTTAAAAG
Found at i:52387 original size:13 final size:13
Alignment explanation
Indices: 52369--52415 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
52359 ATGAATGTTG
52369 GAATCTGTTATGA
1 GAATCTGTTATGA
52382 GAATCTGTTATG-
1 GAATCTGTTATGA
* *
52394 GAGTCAGTTATGA
1 GAATCTGTTATGA
52407 G--TCTGTTAT
1 GAATCTGTTAT
52416 TGAGGTAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 7 0.23
12 10 0.33
13 13 0.43
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (13 bp):
GAATCTGTTATGA
Found at i:52419 original size:12 final size:11
Alignment explanation
Indices: 52372--52415 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
52362 AATGTTGGAA
52372 TCTGTTATGAG
1 TCTGTTATGAG
52383 AATCTGTTATGGAG
1 --TCTGTTAT-GAG
*
52397 TCAGTTATGAG
1 TCTGTTATGAG
52408 TCTGTTAT
1 TCTGTTAT
52416 TGAGGTAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 10 0.36
12 7 0.25
13 8 0.29
14 3 0.11
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (11 bp):
TCTGTTATGAG
Found at i:52535 original size:26 final size:26
Alignment explanation
Indices: 52499--52550 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
52489 AAAATTACAG
52499 AGCATTATTCATTGAGTTTTAAACTT
1 AGCATTATTCATTGAGTTTTAAACTT
52525 AGCATTATTCATTGAGTTTTAAACTT
1 AGCATTATTCATTGAGTTTTAAACTT
52551 CTCAACAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (26 bp):
AGCATTATTCATTGAGTTTTAAACTT
Found at i:58307 original size:22 final size:22
Alignment explanation
Indices: 58279--58388 Score: 148
Period size: 22 Copynumber: 4.9 Consensus size: 22
58269 CATTCGAAAA
58279 TGTTCATGGTACTGTTCACTAC
1 TGTTCATGGTACTGTTCACTAC
*
58301 TGTTCATGGTATTGTTCACTAC
1 TGTTCATGGTACTGTTCACTAC
* *
58323 TGTTCATGGTATTGTTCATTAC
1 TGTTCATGGTACTGTTCACTAC
* *
58345 TGTTTATGGTACTGTTCATTAC
1 TGTTCATGGTACTGTTCACTAC
*
58367 TGTTCATACGGTACTATTCACT
1 TGTTCAT--GGTACTGTTCACT
58389 GTTCATACCG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
22 68 0.86
24 11 0.14
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.45
Consensus pattern (22 bp):
TGTTCATGGTACTGTTCACTAC
Found at i:58367 original size:10 final size:10
Alignment explanation
Indices: 58288--58373 Score: 73
Period size: 10 Copynumber: 8.0 Consensus size: 10
58278 ATGTTCATGG
*
58288 TACTGTTCAC
1 TACTGTTCAT
58298 TACTGTTCAT
1 TACTGTTCAT
* *
58308 GGTATTGTTCAC
1 --TACTGTTCAT
58320 TACTGTTCAT
1 TACTGTTCAT
*
58330 GGTATTGTTCAT
1 --TACTGTTCAT
*
58342 TACTGTTTAT
1 TACTGTTCAT
58352 GGTACTGTTCAT
1 --TACTGTTCAT
58364 TACTGTTCAT
1 TACTGTTCAT
58374 ACGGTACTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
10 35 0.57
12 26 0.43
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (10 bp):
TACTGTTCAT
Found at i:59365 original size:32 final size:32
Alignment explanation
Indices: 59342--59414 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
59332 AAGGGTCTGG
*
59342 TTAACGGGTCAACGATTGGGTCAACGGCCAGA
1 TTAACGGGTCAACGATTAGGTCAACGGCCAGA
*
59374 TTAACGGGTCAACGATTAGGTCAATGGCCAGA
1 TTAACGGGTCAACGATTAGGTCAACGGCCAGA
59406 TTAACGGGT
1 TTAACGGGT
59415 TGATGGTCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (32 bp):
TTAACGGGTCAACGATTAGGTCAACGGCCAGA
Found at i:62154 original size:21 final size:21
Alignment explanation
Indices: 62129--62186 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
62119 GCGACGGCCA
62129 CAATAGCACCCACGACAGTCG
1 CAATAGCACCCACGACAGTCG
* **
62150 TAATAGTGCCCACGACAGTCG
1 CAATAGCACCCACGACAGTCG
*
62171 CAATAGCACCCGCGAC
1 CAATAGCACCCACGAC
62187 GACTGCAGTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.36, G:0.21, T:0.12
Consensus pattern (21 bp):
CAATAGCACCCACGACAGTCG
Done.