Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004324.1 Hibiscus syriacus cultivar Beakdansim tig00009481_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: 50976
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Found at i:1178 original size:41 final size:41
Alignment explanation
Indices: 1067--1236 Score: 215
Period size: 41 Copynumber: 4.2 Consensus size: 41
1057 GCATATTGGA
**
1067 TAAGCACTTCAGT--ACTAAGGATCGACGCAACCTTATGCG
1 TAAGCACTTCAGTGCAAAAAGGATCGACGCAACCTTATGCG
* *
1106 TAAGCACTTTAGTGC--AAAGGATCGACGCAACCTTATGTG
1 TAAGCACTTCAGTGCAAAAAGGATCGACGCAACCTTATGCG
**
1145 TAAGCACTTCAGTGCAAAAAGGATCGACGCAACCTTATATG
1 TAAGCACTTCAGTGCAAAAAGGATCGACGCAACCTTATGCG
* * *
1186 TAAGCACTTC-GACGCAAAAAGGGTCGACACAACCTTATGCG
1 TAAGCACTTCAG-TGCAAAAAGGATCGACGCAACCTTATGCG
1227 TAAGCACTTC
1 TAAGCACTTC
1237 GGTACGACTT
Statistics
Matches: 116, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
39 48 0.41
40 1 0.01
41 67 0.58
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (41 bp):
TAAGCACTTCAGTGCAAAAAGGATCGACGCAACCTTATGCG
Found at i:1203 original size:80 final size:79
Alignment explanation
Indices: 1067--1236 Score: 209
Period size: 80 Copynumber: 2.1 Consensus size: 79
1057 GCATATTGGA
** * * *
1067 TAAGCACTTCAGTACTAAGGATCGACGCAACCTTATGCGTAAGCACTTTAGTGC-AAAGGATCGA
1 TAAGCACTTCAGTAAAAAGGATCGACGCAACCTTATACGTAAGCACTTGAGCGCAAAAGGATCGA
* *
1131 CGCAACCTTATGTG
66 CACAACCTTATGCG
* *
1145 TAAGCACTTCAGTGCAAAAAGGATCGACGCAACCTTATATGTAAGCACTTCGA-CGCAAAAAGGG
1 TAAGCACTTCAGT--AAAAAGGATCGACGCAACCTTATACGTAAGCACTT-GAGCGC-AAAAGGA
1209 TCGACACAACCTTATGCG
62 TCGACACAACCTTATGCG
1227 TAAGCACTTC
1 TAAGCACTTC
1237 GGTACGACTT
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
78 13 0.17
80 33 0.42
81 1 0.01
82 31 0.40
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (79 bp):
TAAGCACTTCAGTAAAAAGGATCGACGCAACCTTATACGTAAGCACTTGAGCGCAAAAGGATCGA
CACAACCTTATGCG
Found at i:5938 original size:17 final size:17
Alignment explanation
Indices: 5912--5949 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5902 CAAAACACCG
* *
5912 CAAAATTCATAAACCCC
1 CAAAAATCATAAAACCC
5929 CAAAAATCATAAAACCC
1 CAAAAATCATAAAACCC
5946 CAAA
1 CAAA
5950 TACCTCCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.32, G:0.00, T:0.13
Consensus pattern (17 bp):
CAAAAATCATAAAACCC
Found at i:10614 original size:19 final size:20
Alignment explanation
Indices: 10571--10615 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
10561 GACTATGCTG
*
10571 GAAATTAATGTTAGAGTGTT
1 GAAATTAATGTTAGAATGTT
*
10591 GAAATTGATGTTAGAATG-T
1 GAAATTAATGTTAGAATGTT
10610 GAAATT
1 GAAATT
10616 TGGCCATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Found at i:11613 original size:70 final size:69
Alignment explanation
Indices: 11468--11822 Score: 473
Period size: 70 Copynumber: 5.1 Consensus size: 69
11458 TGCATACCCA
* * *
11468 GTTTAGCACTAGAGTGTATACCCAAGACACTTAGTACAAGTGGT-GGCACGACCTTATGTGTCAT
1 GTTTAGCACTAGAGTGTATACCCAAGACACTTGGTGC-AGTGGTGGGCACAACCTTATGTGTCAT
11532 ATTCG
65 ATTCG
* *
11537 GTTTAGCAATAGAGTGTATACCCAAGACACTTGGTGCAGGTGGTGGGCACGACCTTATGTGTCAT
1 GTTTAGCACTAGAGTGTATACCCAAGACACTTGGTGCA-GTGGTGGGCACAACCTTATGTGTCAT
11602 ATTCG
65 ATTCG
* * * *
11607 GTTTAGCACTAGATTGTATAACCAATACACTTAGTGTGTA-TGGTGGGCACAACCTTATGTGTCA
1 GTTTAGCACTAGAGTGTATACCCAAGACACTT-G-GTGCAGTGGTGGGCACAACCTTATGTGTCA
*
11671 TATTCA
64 TATTCG
* *
11677 GTTTAGCAATAGAGTGTATACCCAAGACTCTTGGTGCAGGTGGTGGGCACAACCTTATGTGTCAT
1 GTTTAGCACTAGAGTGTATACCCAAGACACTTGGTGCA-GTGGTGGGCACAACCTTATGTGTCAT
11742 ATTCG
65 ATTCG
* * * * *
11747 GTTTAGCACTAGATTGTATACCCAATACACTTAGTGTGTA-TGGTGGGCACAAACTTATGTTTCA
1 GTTTAGCACTAGAGTGTATACCCAAGACACTT-G-GTGCAGTGGTGGGCACAACCTTATGTGTCA
11811 TATTCG
64 TATTCG
11817 GTTTAG
1 GTTTAG
11823 AACTTTGGTG
Statistics
Matches: 254, Mismatches: 24, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
68 5 0.02
69 40 0.16
70 199 0.78
71 2 0.01
72 8 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (69 bp):
GTTTAGCACTAGAGTGTATACCCAAGACACTTGGTGCAGTGGTGGGCACAACCTTATGTGTCATA
TTCG
Found at i:11719 original size:140 final size:140
Alignment explanation
Indices: 11468--11822 Score: 579
Period size: 140 Copynumber: 2.5 Consensus size: 140
11458 TGCATACCCA
* * *** *
11468 GTTTAGCACTAGAGTGTATACCCAAGACACTTAGT-ACAAGTGGT-GGCACGACCTTATGTGTCA
1 GTTTAGCACTAGATTGTATACCCAATACACTTAGTGTGTA-TGGTGGGCACAACCTTATGTGTCA
*
11531 TATTCGGTTTAGCAATAGAGTGTATACCCAAGACACTTGGTGCAGGTGGTGGGCACGACCTTATG
65 TATTCGGTTTAGCAATAGAGTGTATACCCAAGACACTTGGTGCAGGTGGTGGGCACAACCTTATG
11596 TGTCATATTCG
130 TGTCATATTCG
*
11607 GTTTAGCACTAGATTGTATAACCAATACACTTAGTGTGTATGGTGGGCACAACCTTATGTGTCAT
1 GTTTAGCACTAGATTGTATACCCAATACACTTAGTGTGTATGGTGGGCACAACCTTATGTGTCAT
* *
11672 ATTCAGTTTAGCAATAGAGTGTATACCCAAGACTCTTGGTGCAGGTGGTGGGCACAACCTTATGT
66 ATTCGGTTTAGCAATAGAGTGTATACCCAAGACACTTGGTGCAGGTGGTGGGCACAACCTTATGT
11737 GTCATATTCG
131 GTCATATTCG
* *
11747 GTTTAGCACTAGATTGTATACCCAATACACTTAGTGTGTATGGTGGGCACAAACTTATGTTTCAT
1 GTTTAGCACTAGATTGTATACCCAATACACTTAGTGTGTATGGTGGGCACAACCTTATGTGTCAT
11812 ATTCGGTTTAG
66 ATTCGGTTTAG
11823 AACTTTGGTG
Statistics
Matches: 200, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
139 36 0.18
140 164 0.82
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (140 bp):
GTTTAGCACTAGATTGTATACCCAATACACTTAGTGTGTATGGTGGGCACAACCTTATGTGTCAT
ATTCGGTTTAGCAATAGAGTGTATACCCAAGACACTTGGTGCAGGTGGTGGGCACAACCTTATGT
GTCATATTCG
Found at i:16488 original size:20 final size:20
Alignment explanation
Indices: 16463--16507 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
16453 GACTATGCTG
*
16463 GAAATTAATGTTAGAGTGTT
1 GAAATTAATGTTAGAATGTT
*
16483 GAAATTGATGTTAGAATGTT
1 GAAATTAATGTTAGAATGTT
16503 -AAATT
1 GAAATT
16508 TGGTCATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.40
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Found at i:17475 original size:70 final size:70
Alignment explanation
Indices: 17357--17574 Score: 278
Period size: 70 Copynumber: 3.1 Consensus size: 70
17347 GTTGCATACC
* * ** *
17357 CGGTTTAGCACTAGAGTGCATACCCAAGACACTTAGTACAGGTAGTGGGCACGACCTTATGTGTC
1 CGGTTTAGCACTAGAGTGTATACCCAAGACACTTGGTGTAGGTGGTGGGCACGACCTTATGTGTC
17422 ATATT
66 ATATT
* * * *
17427 CAGTTTAACAATAGAGTGTATACCCAAGACAGTTGGTGTAGGTGGTGGGCACGACCTTATGTGTC
1 CGGTTTAGCACTAGAGTGTATACCCAAGACACTTGGTGTAGGTGGTGGGCACGACCTTATGTGTC
17492 ATATT
66 ATATT
* * * *
17497 CGGTTTAGCACTAGATTGTAAACCCAATACACTTAGTGTGTA--TGGTGGGCACAACCTTATGTG
1 CGGTTTAGCACTAGAGTGTATACCCAAGACACTT-G-GTGTAGGTGGTGGGCACGACCTTATGTG
*
17560 TCATTTT
64 TCATATT
17567 CGGTTTAG
1 CGGTTTAG
17575 AACTTTGGTT
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
70 122 0.95
71 1 0.01
72 5 0.04
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (70 bp):
CGGTTTAGCACTAGAGTGTATACCCAAGACACTTGGTGTAGGTGGTGGGCACGACCTTATGTGTC
ATATT
Found at i:21452 original size:19 final size:20
Alignment explanation
Indices: 21409--21453 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
21399 GACTATGCTG
* *
21409 GAAATTAATGTTGGAGTGTT
1 GAAATTAATGTTAGAATGTT
*
21429 GAAATTGATGTTAGAATG-T
1 GAAATTAATGTTAGAATGTT
21448 GAAATT
1 GAAATT
21454 TGGCCATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.38
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Found at i:22416 original size:70 final size:70
Alignment explanation
Indices: 22303--22524 Score: 252
Period size: 70 Copynumber: 3.2 Consensus size: 70
22293 GTTGCATACC
* * * *
22303 CGGTTTAGCACTAGAGTGTATACCCAAGACTCTTAGTACAGGTGGTGGGCACGACCTTATGTGTC
1 CGGTTTAGCACTAGAATGTATACCCAAGACACTTGGTGCAGGTGGTGGGCACGACCTTATGTGTC
*
22368 TTATT
66 ATATT
* * * * *
22373 CGGTTTAGCAATAGAATGTATACACAAGACACTTGGTGCAGGTGGTGGGCATGACCTTATTTCTC
1 CGGTTTAGCACTAGAATGTATACCCAAGACACTTGGTGCAGGTGGTGGGCACGACCTTATGTGTC
22438 ATATT
66 ATATT
* * * * *
22443 CGGTTTAGCACTAGATTGTATACCCAATACACTTAGTGTGTA--TAGTGGGCACAACCTTATGTG
1 CGGTTTAGCACTAGAATGTATACCCAAGACACTT-G-GTGCAGGTGGTGGGCACGACCTTATGTG
22506 TCATACTT
64 TCATA-TT
*
22514 -GATTTAGCACT
1 CGGTTTAGCACT
22525 TTGGTGCATA
Statistics
Matches: 128, Mismatches: 21, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
70 121 0.95
71 3 0.02
72 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (70 bp):
CGGTTTAGCACTAGAATGTATACCCAAGACACTTGGTGCAGGTGGTGGGCACGACCTTATGTGTC
ATATT
Found at i:27275 original size:19 final size:20
Alignment explanation
Indices: 27231--27276 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27221 GACTATACTG
* *
27231 GAAATTAATGTTAGAGTGTA
1 GAAATTTATGTTAGAATGTA
27251 GAAATTTATGTTAGAATGT-
1 GAAATTTATGTTAGAATGTA
27270 GAAATTT
1 GAAATTT
27277 GGCCATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (20 bp):
GAAATTTATGTTAGAATGTA
Found at i:28241 original size:70 final size:70
Alignment explanation
Indices: 28128--28349 Score: 268
Period size: 70 Copynumber: 3.2 Consensus size: 70
28118 GTTGCATACC
* * * ** *
28128 CGGTTTAGCACTAGAGTGTATACCCAAGACACTTAGTACAAGTGGTGGAAACGACTTTATGTGTC
1 CGGTTTAGCACTAGAATGTATACCCAAGATACTTAGTGCAAGTGGTGGGCACGACATTATGTGTC
28193 ATATT
66 ATATT
* * *
28198 CGGTTTAGCAATAGAATGTATACCCAAGATACTTGGTGCAAGTGGTGGGCACGACATTATTTGTC
1 CGGTTTAGCACTAGAATGTATACCCAAGATACTTAGTGCAAGTGGTGGGCACGACATTATGTGTC
28263 ATATT
66 ATATT
* * * * * *
28268 CAGTTTAGCACTAGATTGTATACCCAATACT-CTTAGTGCGTA-TGGTGGGCACAACCTTATGTG
1 CGGTTTAGCACTAGAATGTATACCCAAGA-TACTTAGTGC-AAGTGGTGGGCACGACATTATGTG
28331 TCATATT
64 TCATATT
*
28338 CGATTTAGCACT
1 CGGTTTAGCACT
28350 TTGGTGCATA
Statistics
Matches: 130, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
70 128 0.98
71 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (70 bp):
CGGTTTAGCACTAGAATGTATACCCAAGATACTTAGTGCAAGTGGTGGGCACGACATTATGTGTC
ATATT
Found at i:35975 original size:18 final size:18
Alignment explanation
Indices: 35943--35983 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35933 ATAAAGAGCT
*
35943 AGTTT-AATTAATGAACC
1 AGTTTAAATGAATGAACC
*
35960 AGTTTAAATGAATGAACT
1 AGTTTAAATGAATGAACC
35978 AGTTTA
1 AGTTTA
35984 GTTAGAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (18 bp):
AGTTTAAATGAATGAACC
Found at i:36162 original size:20 final size:20
Alignment explanation
Indices: 36124--36162 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
36114 CAACTTAATG
* *
36124 TCATGCAAATTTATTAACAC
1 TCATGCAAATTCATGAACAC
36144 TCATGCAAATTCATGAACA
1 TCATGCAAATTCATGAACA
36163 AGTAAAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (20 bp):
TCATGCAAATTCATGAACAC
Found at i:37407 original size:25 final size:25
Alignment explanation
Indices: 37380--37426 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
37370 CATAATTACA
*
37380 AAAAT-ATTTTTTCATGAAAAAACT
1 AAAATCATTTTTTAATGAAAAAACT
*
37404 AAAATCATTTTTTAATTAAAAAA
1 AAAATCATTTTTTAATGAAAAAA
37427 TAATTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAATCATTTTTTAATGAAAAAACT
Found at i:38296 original size:418 final size:410
Alignment explanation
Indices: 37474--38312 Score: 1023
Period size: 418 Copynumber: 2.0 Consensus size: 410
37464 TATAAAACTT
* * * * * *
37474 TTACTATATAACATTTTTGGCACCAAAAAATAGGGATAAATTTTTTTATAGAGTAATTTTTCATA
1 TTACTATATAACATTTTTGACACCAAAAAATAGGGAGAAATGTTCTAATAGAGTAATGTTTCATA
* *
37539 ATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAACTTGAATTTTATTATATGATGT
66 ATAATTAAAATATATAAATACAAAAATAATTGATTACAAAAAACTTGAATTTTATTATATGATGT
**
37604 GATAATTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTATCAATATAGTTTTTTGAA
131 GATAATTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTATCAATATAGACTTTTGAA
* *
37669 ACAAAAAAAAAAGTGGAGAAAAATATTTATCAGAATATATGTTATCACTATAATTAAAATTTATA
196 AC---AAAAAAAGTGGAGAAAAATAGTTATCAGAATATATGCTATCACTATAATTAAAATTTATA
*
37734 ACTACAAGTCCTCACAAAAATGTGAATACCATTATTTTTTGTGACAATATTTTTTGTAATAATTA
258 ACTACAAGTCCTCACAAAAACGTGAATACCATTATTTTTTGTGACAATATTTTTTGTAATAATTA
* ** * *
37799 TAAATACGTATAATTACAAAAATTGTTACTATATGATTTTTCTGGTGCAAAATAATATGGAGGAA
323 TAAACACGTATAATTACAAAAATTGCAACTATATGATTTTTCTGGCGCAAAATAATATAGAGGAA
37864 AATCTTTATGATAATATATTTTG
388 AATCTTTATGATAATATATTTTG
**
37887 TTACTATATAACATTTTTGACATTAAAAAATAGGGAGAAATGGTTCTAATAGTA-TAATGTTTCA
1 TTACTATATAACATTTTTGACACCAAAAAATAGGGAGAAAT-GTTCTAATAG-AGTAATGTTTCA
* * * * *
37951 TTATAATTAAAATATATAAATACAAAGATAATTTATTACAAAAAAAACTTGAATTTTATTTTTTG
64 TAATAATTAAAATATATAAATACAAAAATAATTGATTAC--AAAAAACTTGAATTTTATTATATG
* * ** *
38016 ATGTGATAATTTTTTCTATAATAATAATTATAAATTATAATTTTTAAAA-TTGTCAATATA-ACT
127 ATGTGATAA-TTTTTCTATAACAATAACTATAAATTATAA-TTACAAAACTTATCAATATAGACT
* *
38079 TTTGAAAC-AAAAAAGTGGAG-AAAATAGTTATGACAATTAATATATGCTATCACTATAGTTAAA
190 TTTGAAACAAAAAAAGTGGAGAAAAATAGTTAT--C-A-GAATATATGCTATCACTATAATTAAA
* ** *
38142 ATTTATAACTACAAATATAATTTGTCACAAAAACGTGAATATCATTA-TTTTTGTGAC-A-ATTT
251 ATTTATAACTAC------AAGTCCTCACAAAAACGTGAATACCATTATTTTTTGTGACAATATTT
* * * *
38204 TTTGTAATAATTATTAACACTTATAATTACAAAATTTGCAACTATATGACTTTTT-TTGCGCTAA
310 TTTGTAATAATTATAAACACGTATAATTACAAAAATTGCAACTATATGA-TTTTTCTGGCGC-AA
* * *
38268 AA-CATATAGAGGGAAATCTTTGTGATAATATATTTTG
373 AATAATATAGAGGAAAATCTTTATGATAATATATTTTG
*
38305 TCACTATA
1 TTACTATA
38313 ATTAAAACAT
Statistics
Matches: 364, Mismatches: 44, Indels: 31
0.83 0.10 0.07
Matches are distributed among these distances:
411 10 0.03
412 12 0.03
413 38 0.10
414 51 0.14
415 36 0.10
416 40 0.11
417 38 0.10
418 95 0.26
419 10 0.03
420 10 0.03
421 24 0.07
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (410 bp):
TTACTATATAACATTTTTGACACCAAAAAATAGGGAGAAATGTTCTAATAGAGTAATGTTTCATA
ATAATTAAAATATATAAATACAAAAATAATTGATTACAAAAAACTTGAATTTTATTATATGATGT
GATAATTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTATCAATATAGACTTTTGAA
ACAAAAAAAGTGGAGAAAAATAGTTATCAGAATATATGCTATCACTATAATTAAAATTTATAACT
ACAAGTCCTCACAAAAACGTGAATACCATTATTTTTTGTGACAATATTTTTTGTAATAATTATAA
ACACGTATAATTACAAAAATTGCAACTATATGATTTTTCTGGCGCAAAATAATATAGAGGAAAAT
CTTTATGATAATATATTTTG
Found at i:40332 original size:26 final size:26
Alignment explanation
Indices: 40293--40343 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
40283 CCCTTGCTTG
40293 AACCTGAATGGCCTTCAATGGGTGAT
1 AACCTGAATGGCCTTCAATGGGTGAT
* *
40319 AACCTTGAAT-GCCTTGAATTGGTGA
1 AACC-TGAATGGCCTTCAATGGGTGA
40344 ATTAAGATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (26 bp):
AACCTGAATGGCCTTCAATGGGTGAT
Found at i:40757 original size:17 final size:17
Alignment explanation
Indices: 40735--40785 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
40725 TATAAAAACT
40735 AGTTTAATTAATGAACC
1 AGTTTAATTAATGAACC
* *
40752 AGTTTAAATAAATGAACT
1 AGTTT-AATTAATGAACC
*
40770 AGTTTAATTAGTGAAC
1 AGTTTAATTAATGAAC
40786 TAGCTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (17 bp):
AGTTTAATTAATGAACC
Found at i:40793 original size:18 final size:17
Alignment explanation
Indices: 40731--40802 Score: 83
Period size: 17 Copynumber: 4.1 Consensus size: 17
40721 AACATATAAA
40731 AACTAGTTTAATTAATG
1 AACTAGTTTAATTAATG
* *
40748 AACCAGTTTAAATAAATG
1 AACTAGTTT-AATTAATG
*
40766 AACTAGTTTAATTAGTG
1 AACTAGTTTAATTAATG
40783 AACTAGCTTT-ATTGAATG
1 AACTAG-TTTAATT-AATG
40801 AA
1 AA
40803 ATATGATACT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
17 23 0.50
18 23 0.50
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (17 bp):
AACTAGTTTAATTAATG
Found at i:41303 original size:70 final size:70
Alignment explanation
Indices: 41185--41316 Score: 221
Period size: 70 Copynumber: 1.9 Consensus size: 70
41175 AGGATTGCAT
*
41185 CACTTAGTGCAGGTGGTGGGCATGACCTTATGTGTCATATTCTGTTTAGCACTAGAGTGTATACC
1 CACTTAGTGCAGGTGGTGGGCACGACCTTATGTGTCATATTCTGTTTAGCACTAGAGTGTATACC
41250 CACGA
66 CACGA
* *
41255 CACTTAGTGCAGGTGGTGGGCACGACCTTATGTGTCGTATTC-GATTTAGTACTAGAGTGTAT
1 CACTTAGTGCAGGTGGTGGGCACGACCTTATGTGTCATATTCTG-TTTAGCACTAGAGTGTAT
41317 GGTGGGTACG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 1 0.02
70 57 0.98
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (70 bp):
CACTTAGTGCAGGTGGTGGGCACGACCTTATGTGTCATATTCTGTTTAGCACTAGAGTGTATACC
CACGA
Found at i:42146 original size:9 final size:9
Alignment explanation
Indices: 42132--42159 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
42122 TCCATTAATC
42132 ACATAACCT
1 ACATAACCT
42141 ACATAACCT
1 ACATAACCT
42150 ACATAACCT
1 ACATAACCT
42159 A
1 A
42160 ACAACAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.21
Consensus pattern (9 bp):
ACATAACCT
Done.