Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002272.1 Hibiscus syriacus cultivar Beakdansim tig00004619_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: 81524
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:143 original size:56 final size:55
Alignment explanation
Indices: 82--224 Score: 175
Period size: 52 Copynumber: 2.6 Consensus size: 55
72 CCCTATTTTC
* *
82 TAGATATATTCGATTCTGGGGCCCCTATTTTTATACTTCTTAATAGCAACAACTGA
1 TAGATATATTCGATT-TGGGGCCCCTATTTTTATACTTATTAATAGAAACAACTGA
* * * *
138 TAGATATACTCGATTT---GCCCCTATTTTTATGCTTATTAATGGAAACAACTTA
1 TAGATATATTCGATTTGGGGCCCCTATTTTTATACTTATTAATAGAAACAACTGA
* *
190 TAGATATATTCGATTTCGGGACCCCTATTTGTATA
1 TAGATATATTCGATTT-GGGGCCCCTATTTTTATA
225 TGTTAGGATT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
52 46 0.63
55 1 0.01
56 26 0.36
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (55 bp):
TAGATATATTCGATTTGGGGCCCCTATTTTTATACTTATTAATAGAAACAACTGA
Found at i:966 original size:20 final size:20
Alignment explanation
Indices: 941--995 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
931 TCGAAATGGA
941 GTGCATGGATGCACTGAATG
1 GTGCATGGATGCACTGAATG
* *
961 GTGCATTGATGCACTGCATG
1 GTGCATGGATGCACTGAATG
*
981 GTGTATGGATGCACT
1 GTGCATGGATGCACT
996 AGTGGCAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (20 bp):
GTGCATGGATGCACTGAATG
Found at i:1011 original size:23 final size:23
Alignment explanation
Indices: 980--1108 Score: 192
Period size: 23 Copynumber: 5.7 Consensus size: 23
970 TGCACTGCAT
*
980 GGTGTATGGATGCACTAGTGGCA
1 GGTGCATGGATGCACTAGTGGCA
* *
1003 GGTGCATGGATGTACTAATGGCA
1 GGTGCATGGATGCACTAGTGGCA
1026 GGTGCATGGATGCACTAGTGGCA
1 GGTGCATGGATGCACTAGTGGCA
1049 GGTGCATGGATGCACTAGTGGCA
1 GGTGCATGGATGCACTAGTGGCA
*
1072 GGTGCATGGATGCACT-GCAGG-A
1 GGTGCATGGATGCACTAG-TGGCA
1094 -GTGCATGGATGCACT
1 GGTGCATGGATGCACT
1109 TTGACACTCT
Statistics
Matches: 99, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
21 15 0.15
22 2 0.02
23 82 0.83
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.23
Consensus pattern (23 bp):
GGTGCATGGATGCACTAGTGGCA
Found at i:1068 original size:69 final size:67
Alignment explanation
Indices: 941--1108 Score: 213
Period size: 69 Copynumber: 2.5 Consensus size: 67
931 TCGAAATGGA
* * *
941 GTGCATGGATGCACTGAATG-GTGCATTGATGCAC---T-GCATGGTGTATGGATGCACTAGTGG
1 GTGCATGGATGCACTGAAGGAGTGCATGGATGCACTAGTGGCA-GGTGCATGGATGCACTAGTGG
1001 CAG
65 CAG
*
1004 GTGCATGGATGTACT-AATGGCAGGTGCATGGATGCACTAGTGGCAGGTGCATGGATGCACTAGT
1 GTGCATGGATGCACTGAA-GG-A-GTGCATGGATGCACTAGTGGCAGGTGCATGGATGCACTAGT
1068 GGCAG
63 GGCAG
*
1073 GTGCATGGATGCACTGCAGGAGTGCATGGATGCACT
1 GTGCATGGATGCACTGAAGGAGTGCATGGATGCACT
1109 TTGACACTCT
Statistics
Matches: 90, Mismatches: 6, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
62 2 0.02
63 15 0.17
66 13 0.14
67 15 0.17
68 1 0.01
69 40 0.44
70 4 0.04
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (67 bp):
GTGCATGGATGCACTGAAGGAGTGCATGGATGCACTAGTGGCAGGTGCATGGATGCACTAGTGGC
AG
Found at i:1373 original size:20 final size:21
Alignment explanation
Indices: 1324--1373 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1314 AAAATGTTTA
*
1324 ATGAAAAAGATATCAATTGTT
1 ATGAAAATGATATCAATTGTT
**
1345 AACAAAATGATATCAATTGTT
1 ATGAAAATGATATCAATTGTT
1366 -TGAAAATG
1 ATGAAAATG
1374 TTAAGCTCAC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (21 bp):
ATGAAAATGATATCAATTGTT
Found at i:5520 original size:23 final size:23
Alignment explanation
Indices: 5494--5556 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
5484 ATATAACCAC
5494 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
5517 TACCTATTACATTATATAACCGC
1 TACCTATTACATTATATAAACGA
*
5540 TACCTATTACATCATAT
1 TACCTATTACATTATAT
5557 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:5934 original size:23 final size:23
Alignment explanation
Indices: 5908--5975 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
5898 TATACTTACA
5908 ATATAACCACTACCTATTACATT
1 ATATAACCACTACCTATTACATT
*
5931 ATATAAACGA-TACCTATTACATT
1 ATAT-AACCACTACCTATTACATT
* *
5954 ATATAAGCGCTACCTATTACAT
1 ATATAACCACTACCTATTACAT
5976 ATTTTTACCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.05
23 33 0.85
24 4 0.10
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATT
Found at i:6085 original size:421 final size:430
Alignment explanation
Indices: 5318--6261 Score: 1755
Period size: 421 Copynumber: 2.2 Consensus size: 430
5308 ATATGTTTTG
*
5318 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
5383 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
5448 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
5513 ACGATACCTATTACATTATATAACCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAACCGCTACCTATTA-ATCATATTTTTACCTATTATATTGAAAG
5578 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
260 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
5643 TTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC-AAAAA
325 TTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
5707 TTATTTGATTG-TTTGATATTTTATAAAATAATATTTAGAA
390 TTATTTGATTGCTTTGATATTTTATAAAATAATATTTAGAA
5747 TTTTTAATTTAATAAT-A-ATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
5810 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
*
5874 TATAGACACTTTTAT-AAAAGGATATATAC-TTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
*
5937 ACGATACCTATTACATTATATAAGCGCTACCTATT-A-CATATTTTTACCTATTATATTGAAAGT
196 ACGATACCTATTACATTATATAACCGCTACCTATTAATCATATTTTTACCTATTATATTGAAAGT
* *
6000 GTTCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTT
261 GTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTT
6065 TTTTAA-TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
326 TTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
6129 TTATTTGATTGCTTTGATATTTTATAAAATAATATTTAGAA
390 TTATTTGATTGCTTTGATATTTTATAAAATAATATTTAGAA
6170 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
6235 AAATTAATATCTTAAAACTCACTCAAA
66 AAATTAATATCTTAAAACTCACTCAAA
6262 GATGTATATA
Statistics
Matches: 505, Mismatches: 5, Indels: 14
0.96 0.01 0.03
Matches are distributed among these distances:
420 2 0.00
421 145 0.29
422 17 0.03
423 45 0.09
424 69 0.14
425 86 0.17
426 21 0.04
427 103 0.20
428 1 0.00
429 16 0.03
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (430 bp):
TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
ACGATACCTATTACATTATATAACCGCTACCTATTAATCATATTTTTACCTATTATATTGAAAGT
GTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTT
TTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
TATTTGATTGCTTTGATATTTTATAAAATAATATTTAGAA
Found at i:6292 original size:25 final size:25
Alignment explanation
Indices: 6264--6328 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
6254 CACTCAAAGA
*
6264 TGTATATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
6289 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
6314 TGTACATACCTAAAT
1 TGTACATACCTAAAT
6329 TTAATGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:9357 original size:23 final size:22
Alignment explanation
Indices: 9295--9366 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
9285 ATACTTTACA
*
9295 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
9318 ATATAACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
9340 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
9363 ATAT
1 ATAT
9367 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 20 0.45
23 24 0.55
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:9751 original size:429 final size:430
Alignment explanation
Indices: 8952--9991 Score: 2003
Period size: 429 Copynumber: 2.4 Consensus size: 430
8942 TTATAATATG
*
8952 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
*
9017 TCAATTTTTTTAAGTATGTTTCATGTTTTCCGCCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
9082 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAA
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAA
*
9147 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
196 TATATATCGTAACGTAAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
9212 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAAACACTTTTATAAA
261 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAAACACTTTTATAAA
9277 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATAT-AACGATACCTATTACATTA
326 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
9341 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
9381 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
9446 TCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAA-TTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
9511 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAAT-ATATTTAGAATTTTTAATTTAATAATA
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
9575 ATATATATCGTAACGTAAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
195 ATATATATCGTAACGTAAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
*
9640 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
260 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAAACACTTTTATAA
*
9705 AAAGGATAGATACTTTACAATATAACCACTTCCTATTACATTATATAAACGATACCTATTACATT
325 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
9770 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
390 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
9811 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
9876 TCAATTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
*
9941 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTATAATTTT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTT
9992 ATTTAACAAT
Statistics
Matches: 602, Mismatches: 6, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
429 365 0.61
430 237 0.39
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (430 bp):
TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAA
TATATATCGTAACGTAAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAAACACTTTTATAAA
AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:9762 original size:23 final size:23
Alignment explanation
Indices: 9736--9796 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
9726 ATAACCACTT
9736 CCTATTACATTATATAAACGATA
1 CCTATTACATTATATAAACGATA
* *
9759 CCTATTACATTATATAAGCGCTA
1 CCTATTACATTATATAAACGATA
*
9782 CCTATTACATCATAT
1 CCTATTACATTATAT
9797 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
CCTATTACATTATATAAACGATA
Found at i:11395 original size:6 final size:6
Alignment explanation
Indices: 11384--11458 Score: 87
Period size: 6 Copynumber: 12.5 Consensus size: 6
11374 ACTTGTTTGG
* * * *
11384 ATCATC ATCATC ATCATC ATCATC GTCATC GTCATC ATCTTC ATCGTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * *
11432 ATCATC ATCGTC ATCGTC ATCTTC ATC
1 ATCATC ATCATC ATCATC ATCATC ATC
11459 GTCAGCTTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (6 bp):
ATCATC
Found at i:11404 original size:15 final size:15
Alignment explanation
Indices: 11384--11458 Score: 87
Period size: 15 Copynumber: 5.0 Consensus size: 15
11374 ACTTGTTTGG
11384 ATCATCATCATCATC
1 ATCATCATCATCATC
*
11399 ATCATCATCGTCATC
1 ATCATCATCATCATC
* *
11414 GTCATCATCTTCATC
1 ATCATCATCATCATC
* *
11429 GTCATCATCATCGTC
1 ATCATCATCATCATC
* *
11444 ATCGTCATCTTCATC
1 ATCATCATCATCATC
11459 GTCAGCTTCA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (15 bp):
ATCATCATCATCATC
Found at i:11459 original size:12 final size:12
Alignment explanation
Indices: 11385--11475 Score: 74
Period size: 12 Copynumber: 7.3 Consensus size: 12
11375 CTTGTTTGGA
* *
11385 TCATCATCATCA
1 TCATCTTCATCG
*
11397 TCATCATCATCG
1 TCATCTTCATCG
*
11409 TCATCGTCATCATCT
1 TCATC-T--TCATCG
* *
11424 TCATCGTCATCA
1 TCATCTTCATCG
*
11436 TCATCGTCATCG
1 TCATCTTCATCG
11448 TCATCTTCATCG
1 TCATCTTCATCG
* *
11460 TCAGCTTCATCT
1 TCATCTTCATCG
11472 TCAT
1 TCAT
11476 TGACCGCTTG
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
12 56 0.85
15 10 0.15
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.37
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:11459 original size:18 final size:18
Alignment explanation
Indices: 11384--11462 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
11374 ACTTGTTTGG
* *
11384 ATCATCATCATCATCATC
1 ATCATCGTCATCGTCATC
11402 ATCATCGTCATCGTCATC
1 ATCATCGTCATCGTCATC
11420 ATC-T--TCATCGTCATC
1 ATCATCGTCATCGTCATC
11435 ATCATCGTCATCGTCATC
1 ATCATCGTCATCGTCATC
*
11453 TTCATCGTCA
1 ATCATCGTCA
11463 GCTTCATCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.25
16 1 0.02
17 1 0.02
18 39 0.71
ACGTcount: A:0.24, C:0.33, G:0.08, T:0.35
Consensus pattern (18 bp):
ATCATCGTCATCGTCATC
Found at i:11469 original size:18 final size:18
Alignment explanation
Indices: 11397--11475 Score: 74
Period size: 18 Copynumber: 4.6 Consensus size: 18
11387 ATCATCATCA
* *
11397 TCATCATCATCGTCATCG
1 TCATCTTCATCGTCAGCG
* *
11415 TCA---TCATCTTCATCG
1 TCATCTTCATCGTCAGCG
* *
11430 TCATCATCATCGTCATCG
1 TCATCTTCATCGTCAGCG
*
11448 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCG
11466 TCATCTTCAT
1 TCATCTTCAT
11476 TGACCGCTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
15 14 0.26
18 39 0.74
ACGTcount: A:0.20, C:0.33, G:0.09, T:0.38
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCG
Found at i:13300 original size:199 final size:199
Alignment explanation
Indices: 12938--14308 Score: 2424
Period size: 199 Copynumber: 6.9 Consensus size: 199
12928 TTTAAATTAG
12938 TATCGACACAAACTAAA-AAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
13002 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
* * *
13067 CGACACTTTTTATATATGGATCGACACCTTATGGTTGCACACTGTTTTCCATTCATTATGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
13132 AAAA
196 AAAA
**** ** *
13136 TATCGACACTGTTTTAAA-TGGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTAT
1 TATCGACAC-AAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
* *
13200 ACTTGTACCTGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTAGGA
65 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGA
13265 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
13330 AAAAA
195 AAAAA
**** ** *
13335 TATCGACACTTTTTTAAA-TGGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAA
1 TATCGACAC-AAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
13399 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGA
65 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGA
13464 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
13529 AAAAA
195 AAAAA
*
13534 TATCGACACAAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGATATA
1 TATCGACACAAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
13599 CTTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
13664 CGCCACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
13729 AAAA
196 AAAA
13733 TATCGACACAAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
13798 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTTGGGA
* **
13863 TCGACACTTTTTATATATGGATCGACACCTTATGGTTGCAAACTGTTTTCCATTCATTCTGGACC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
13928 AAAAA
195 AAAAA
* *
13933 TATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
13998 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
14063 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
14128 AAAA
196 AAAA
14132 TATCGACACAAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
14197 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTTGGGA
*
14262 TCGACACTTTTTATATATGGTTCGACACTTTATGGTTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
14309 GGCCATATTG
Statistics
Matches: 1126, Mismatches: 43, Indels: 6
0.96 0.04 0.01
Matches are distributed among these distances:
198 13 0.01
199 859 0.76
200 254 0.23
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTAAACAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
AAAA
Found at i:14473 original size:19 final size:19
Alignment explanation
Indices: 14427--14475 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
14417 TTATATTCAC
*
14427 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
14446 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
14465 ATACAAAATTA
1 ATACAAAATTA
14476 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:16307 original size:33 final size:33
Alignment explanation
Indices: 16270--16335 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
16260 CATCTAAATA
*
16270 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
16303 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
16336 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:16394 original size:21 final size:21
Alignment explanation
Indices: 16369--16412 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16359 CCCCTTATGC
16369 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
16390 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
16411 CT
1 CT
16413 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:18472 original size:24 final size:24
Alignment explanation
Indices: 18435--18487 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
18425 CCGTTCTATC
18435 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
18459 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
18483 TATTT
1 TATTT
18488 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:18649 original size:17 final size:18
Alignment explanation
Indices: 18627--18669 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
18617 ATATATTCGG
18627 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
18644 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
18664 TATCAT
1 TATCAT
18670 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:18687 original size:20 final size:19
Alignment explanation
Indices: 18632--18678 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
18622 TTCGGTATCA
18632 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
18651 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
18672 TTTTACC
1 TTTTACC
18679 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:18912 original size:181 final size:182
Alignment explanation
Indices: 18599--19071 Score: 673
Period size: 181 Copynumber: 2.6 Consensus size: 182
18589 CGTACTTACG
* * * *
18599 AAAGTATCGACACTTTCAATATATTCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
18664 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACATTAT
* * *
18729 AGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * *
18780 AAAGTATCGACACTTTTAATATATCCGGTAACCTTTTACCGGTTTTATCGTTTTGATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * **
18845 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGATATTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACATTAT
** *
18910 AGGATTTAAAAATGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * *
18962 AAAGTACCGACACTTTAAATGTATCCGGTAGCGC-TTTACCGGTTTTATCATTTCT-ATACCGGT
1 AAAGTATCGACACTTTAAATATATCCGGTAAC-CTTTTACCGGTTTTATCATTT-TGATACCGGT
* * *
19025 TTTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACATATTTTT
64 TTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTT
19072 AATTTGGATC
Statistics
Matches: 259, Mismatches: 30, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
181 161 0.62
182 96 0.37
183 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:20217 original size:60 final size:59
Alignment explanation
Indices: 20083--20220 Score: 181
Period size: 60 Copynumber: 2.3 Consensus size: 59
20073 CATAATGAAG
* * * * *
20083 AGTTAGGTGACTC-TTTTGTAACTTTTAATAGTCGGGGACTCAACAAAGCAACACCTTAT
1 AGTTAGGAGAC-CATTTTGTAACTTTTAATAGTCGAGAACCCAACAAAGCAACACCCTAT
*
20142 AGTTAGGAGATCATTTTGTAACTTTTAATAGTCAGAGAACCCAACAAAGCAACACCCTAT
1 AGTTAGGAGACCATTTTGTAACTTTTAATAGTC-GAGAACCCAACAAAGCAACACCCTAT
20202 AGTTGAGG-GACCATTTTGT
1 AGTT-AGGAGACCATTTTGT
20221 GTACTTTACC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
58 1 0.01
59 29 0.42
60 36 0.52
61 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (59 bp):
AGTTAGGAGACCATTTTGTAACTTTTAATAGTCGAGAACCCAACAAAGCAACACCCTAT
Found at i:22057 original size:23 final size:23
Alignment explanation
Indices: 22022--22079 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
22012 ATCAAGCACA
*
22022 ATAATATATTAGGTAGCACTTAT
1 ATAATATAATAGGTAGCACTTAT
* *
22045 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCACTTAT
*
22068 ATAATAAAATAG
1 ATAATATAATAG
22080 ACATTTAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (23 bp):
ATAATATAATAGGTAGCACTTAT
Found at i:22140 original size:87 final size:87
Alignment explanation
Indices: 21994--22156 Score: 265
Period size: 87 Copynumber: 1.9 Consensus size: 87
21984 TATGTTATAT
* *
21994 CATTTAACTGGAAATATTATCAAGCACAATAATATATTAGGTAGCACTTATATAATGTAATAGGT
1 CATTTAACTGGAAATATTATCAAGCACAATAACAAATTAGGTAGCACTTATATAATGTAATAGGT
22059 AGCGCTTATATAATAAAATAGA
66 AGCGCTTATATAATAAAATAGA
* **
22081 CATTTAA-TCGGAAATATTATCAAGTACAATAACAAATTAGGTAGCGTTTATATAATGTAATAGG
1 CATTTAACT-GGAAATATTATCAAGCACAATAACAAATTAGGTAGCACTTATATAATGTAATAGG
22145 TAGCGCTTATAT
65 TAGCGCTTATAT
22157 TGACCTATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
86 1 0.01
87 69 0.99
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
CATTTAACTGGAAATATTATCAAGCACAATAACAAATTAGGTAGCACTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGA
Found at i:24390 original size:22 final size:21
Alignment explanation
Indices: 24362--24417 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
24352 AACCTGAATT
24362 TATAATAAAACTAATCATTTTA
1 TATAATAAAAC-AATCATTTTA
*
24384 TATAATAACTATACCATCATTTTA
1 TATAATAA--A-ACAATCATTTTA
*
24408 TATAAAAAAA
1 TATAATAAAA
24418 ACAAAAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
24 17 0.59
25 2 0.07
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAATAAAACAATCATTTTA
Found at i:26335 original size:20 final size:20
Alignment explanation
Indices: 26289--26335 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
26279 ACCGGTAGCG
*
26289 CTTTACCGGTTTTGTCATTT
1 CTTTACCAGTTTTGTCATTT
**
26309 CGATACCAGTTTTGTCATATT
1 CTTTACCAGTTTTGTCAT-TT
26330 -TTTACC
1 CTTTACC
26336 TATTATATTG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.13, T:0.49
Consensus pattern (20 bp):
CTTTACCAGTTTTGTCATTT
Found at i:26927 original size:183 final size:180
Alignment explanation
Indices: 26263--26912 Score: 766
Period size: 182 Copynumber: 3.6 Consensus size: 180
26253 ATTAAAGTAC
* ** * * * *
26263 CGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCAGTTTTGTCATA
1 CGACACTTTCAATATATTCAGTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * * * *
26328 TTTTTACCTATTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTTTTAGGCGCT
66 TTTTTACCTGTTATATTGCTATGGATCAATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
*
26393 ATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATTAA-TTAT
* * ** * *
26445 CTACACTTTCAATATA-TCATGTATCTTTTTACCGGTTTTATCATTTCGAGATCTGTTTTGTCAT
1 CGACACTTTCAATATATTCA-GTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCAT
* * * * *
26509 ATTCTTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACCTTATAAGCGC
65 ATTTTTACCTGTTATATTGCTATGGATCAATACATTTTTATAAAGTATCGACACTTTATAGGCGC
*
26574 TATAACTTCTTCTCTTTTAAATTCAAAAAGTTTCGATACTTATATTAATGTAT
130 TATAACTTCTTCTCTTTTAAATTC-AAAAGTGTCGATACTTATATTAAT-TAT
* * * * *
26627 CGACACTTTCAATATATCCGGTAGCTCTTTACCGATTTTATCATTTCGTGACCGGTTTTGTCATA
1 CGACACTTTCAATATATTCAGTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * * *
26692 CTTATACCTGTTATATTGTTATGGATCAATACGTTTTTATAAAGTATCGACACTTTATAGGCGCT
66 TTTTTACCTGTTATATTGCTATGGATCAATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
* * * *
26757 GTTATTTCTTCTCTTTTAAATTCTAAAAGTGTCAATACTTAT-TTAAATCTAAT
131 ATAACTTCTTCTCTTTTAAATTC-AAAAGTGTCGATACTTATATT-AAT-T-AT
* * * * * * *
26810 CGATACTTTCGATATATTTAGTAGCGGTTTACCGGTTTTATCATAAT-GAAACCGGTTTTATCAT
1 CGACACTTTCAATATATTCAGTAGCGCTTTACCGGTTTTATCAT-TTCGAGACCGGTTTTGTCAT
* *
26874 ATTTTTACATGTTATATTGCTATGGAGCAATACATTTTT
65 ATTTTTACCTGTTATATTGCTATGGATCAATACATTTTT
26913 CATTTGTATC
Statistics
Matches: 397, Mismatches: 64, Indels: 13
0.84 0.14 0.03
Matches are distributed among these distances:
181 5 0.01
182 305 0.77
183 86 0.22
184 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (180 bp):
CGACACTTTCAATATATTCAGTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
TTTTTACCTGTTATATTGCTATGGATCAATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
ATAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTATATTAATTAT
Found at i:28361 original size:34 final size:34
Alignment explanation
Indices: 28283--28364 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
28273 ATTATATTAT
* * *
28283 AATAAATAAATATAAAAAAATAATTCATAATATTA
1 AATATATAAATAT-AAAAAATAATTCAAAATATAA
* *
28318 ATTAT-TAAATATAATAAATAATT-AAAATATAA
1 AATATATAAATATAAAAAATAATTCAAAATATAA
28350 CAATATATAAATATA
1 -AATATATAAATATA
28365 GTAATTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
32 7 0.18
33 14 0.36
34 15 0.38
35 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (34 bp):
AATATATAAATATAAAAAATAATTCAAAATATAA
Found at i:28464 original size:19 final size:19
Alignment explanation
Indices: 28442--28498 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 19
28432 AATTATATTA
28442 TAATAAATAAATATAATAT
1 TAATAAATAAATATAATAT
*
28461 TAATTAAT-AATATTAATAT
1 TAATAAATAAATA-TAATAT
28480 TAAATATAATAATATATAA
1 T-AATA-AATAA-ATATAA
28499 ATATAGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 4 0.13
19 14 0.45
20 3 0.10
21 3 0.10
22 4 0.13
23 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATAAATAAATATAATAT
Found at i:28499 original size:16 final size:16
Alignment explanation
Indices: 28436--28659 Score: 70
Period size: 16 Copynumber: 14.6 Consensus size: 16
28426 ATGAAAAATT
* *
28436 ATATTATAATAAATAA
1 ATATAATAATATATAA
* *
28452 ATATAATATTA-ATTA
1 ATATAATAATATATAA
*
28467 ATAATATTAATAT-TAA
1 AT-ATAATAATATATAA
28483 ATATAATAATATATAA
1 ATATAATAATATATAA
*
28499 ATATAGTAAT-TA-AA
1 ATATAATAATATATAA
* * *
28513 ATA-GATATTTTATAA
1 ATATAATAATATATAA
28528 A-A-AATAAT-TAT-A
1 ATATAATAATATATAA
* * *
28540 ATA-CAT--TTTGTAA
1 ATATAATAATATATAA
* *
28553 ATTTTGA-AATA-ATGAA
1 A-TATAATAATATAT-AA
* * *
28569 AAATTATATTATAATAA
1 ATATAATAATAT-ATAA
*
28586 ATA-AATAATA-ATTA
1 ATATAATAATATATAA
*
28600 ATAATATTAATAT-TAA
1 AT-ATAATAATATATAA
28616 ATATAATACATA-ATTAAA
1 ATATAATA-ATATA-T-AA
28634 ATATAATAATATATAA
1 ATATAATAATATATAA
*
28650 ATATAGTAAT
1 ATATAATAAT
28660 TAAAATAGAT
Statistics
Matches: 153, Mismatches: 31, Indels: 48
0.66 0.13 0.21
Matches are distributed among these distances:
11 1 0.01
12 4 0.03
13 11 0.07
14 18 0.12
15 29 0.19
16 68 0.44
17 9 0.06
18 13 0.08
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.40
Consensus pattern (16 bp):
ATATAATAATATATAA
Found at i:28580 original size:138 final size:143
Alignment explanation
Indices: 28343--28795 Score: 582
Period size: 151 Copynumber: 3.1 Consensus size: 143
28333 AAATAATTAA
* * *
28343 AATATAACAATATATAAATATAGTAATTAAAATAGAAATTTTATAAAAAAACAATTATAATATAT
1 AATATAATAATATAT-AA-ATAGTAATTAAAATAGATATTTTAT-AAAAAATAATTATAATATAT
* *
28408 TTTTTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAATATAATATTAATTAATAATA
63 TTTGTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAATATAATAATAA-TAATAATA
28473 TTAATATTAAATATAAT
127 TTAATATTAAATATAAT
*
28490 AATAT-AT-A-A-AT--ATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATACATTTT
1 AATATAATAATATATAAATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATATATTTT
*
28549 GTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAATAATAATTAATAATATTAATATT
66 GTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAAT-ATAA-TAATAATAATAATATT
*
28614 AA-ATATAATACATAATT
129 AATAT-TAA-ATATAA-T
*
28631 AAAATATAATAATATATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTAAAATATA
1 --AATATAATAATATAT-AA-ATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATATA
* * *
28696 TTTTGTAAATTTTGAAATAATGAAAATTTATATTATAATGAATATA-ATAATAATAACTAATAAT
62 TTTTGTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAATATAATAATAA-TAATAAT
28760 ATTAATTATTAAATATAAT
126 ATTAA-TATTAAATATAAT
*
28779 AA-ATAATTAAAATATAA
1 AATATAA-TAATATATAA
28796 TAATATGTAA
Statistics
Matches: 271, Mismatches: 16, Indels: 40
0.83 0.05 0.12
Matches are distributed among these distances:
138 65 0.24
139 42 0.15
140 10 0.04
141 1 0.00
143 7 0.03
144 3 0.01
145 8 0.03
146 11 0.04
147 7 0.03
148 7 0.03
149 20 0.07
150 3 0.01
151 87 0.32
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (143 bp):
AATATAATAATATATAAATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATATATTTT
GTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAATATAATAATAATAATAATATTAA
TATTAAATATAAT
Found at i:28621 original size:18 final size:18
Alignment explanation
Indices: 28600--28659 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
28590 ATAATAATTA
*
28600 ATAATATTAATATTAAAT
1 ATAATAATAATATTAAAT
*
28618 ATAATACATAAT-TAAAAT
1 ATAATA-ATAATATTAAAT
28636 ATAATAAT-ATA-TAAAT
1 ATAATAATAATATTAAAT
*
28652 ATAGTAAT
1 ATAATAAT
28660 TAAAATAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 13 0.36
17 2 0.06
18 17 0.47
19 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATAATAATAATATTAAAT
Found at i:28636 original size:25 final size:29
Alignment explanation
Indices: 28630--28696 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 29
28620 AATACATAAT
*
28630 TAAAATATAATAATATATAAATATAGTAAT
1 TAAAATAT-ATAATATATAAATACAGTAAT
* * * *
28660 TAAAATAGATATTTTATAAA-A-AATAAT
1 TAAAATATATAATATATAAATACAGTAAT
28687 TAAAATATAT
1 TAAAATATAT
28697 TTTGTAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 14 0.44
28 1 0.03
29 10 0.31
30 7 0.22
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
TAAAATATATAATATATAAATACAGTAAT
Found at i:28641 original size:30 final size:30
Alignment explanation
Indices: 28574--28797 Score: 122
Period size: 30 Copynumber: 7.3 Consensus size: 30
28564 ATGAAAAATT
* *
28574 ATATTATAATAAATA-AAT-AATAATTAATA
1 ATATAATATTAAATATAATAAATAATTAA-A
*
28603 ATATTAATATTAAATATAATACATAATTAAA
1 ATA-TAATATTAAATATAATAAATAATTAAA
* * *
28634 ATATAATAATATATA-AATATAGTAATTAAA
1 ATATAATATTAAATATAATA-AATAATTAAA
* * *
28664 ATA-GATATT--TTATAAAAAATAATTAAA
1 ATATAATATTAAATATAATAAATAATTAAA
* * * *
28691 ATATATTTTGTAAAT-T-TTGAAATAATGAAA
1 ATATAATAT-TAAATATAAT-AAATAATTAAA
* * *
28721 ATTTATATTATAATGAATATAATAATAATAACTAATA
1 A--TATA--ATATTAAATATAAT-A-AATAATTAA-A
28758 ATATTAATTATTAAATATAATAAATAATTAAA
1 ATA-TAA-TATTAAATATAATAAATAATTAAA
28790 ATATAATA
1 ATATAATA
28798 ATATGTAAAT
Statistics
Matches: 145, Mismatches: 30, Indels: 39
0.68 0.14 0.18
Matches are distributed among these distances:
27 14 0.10
28 5 0.03
29 12 0.08
30 45 0.31
31 11 0.08
32 16 0.11
33 12 0.08
34 4 0.03
35 15 0.10
36 9 0.06
37 2 0.01
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (30 bp):
ATATAATATTAAATATAATAAATAATTAAA
Found at i:28646 original size:151 final size:156
Alignment explanation
Indices: 28436--28838 Score: 623
Period size: 151 Copynumber: 2.7 Consensus size: 156
28426 ATGAAAAATT
* * *
28436 ATATTATAATAAATAAAT-ATAATATTAATTAAT-AATAT--T-AAT-ATTAA-ATATAATAATA
1 ATATAATAAT-AATAACTAATAATATTAATTATTAAATATAATAAATAATTAAAATATAATAATA
*
28494 TATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATACATTTTGTAAATTTTG
65 TATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTAAAATACATTTTGTAAATTTTG
28559 AAATAATGAAAAATTATATTATAAT-A
130 AAATAATGAAAAATTATATTATAATGA
* *
28585 A-AT-A-AATAATAATTAATAATATTAA-TATTAAATATAATACATAATTAAAATATAATAATAT
1 ATATAATAATAATAACTAATAATATTAATTATTAAATATAATAAATAATTAAAATATAATAATAT
*
28646 ATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTAAAATATATTTTGTAAATTTTGA
66 ATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTAAAATACATTTTGTAAATTTTGA
*
28711 AATAATGAAAATTTATATTATAATGA
131 AATAATGAAAAATTATATTATAATGA
28737 ATATAATAATAATAACTAATAATATTAATTATTAAATATAATAAATAATTAAAATATAATAATAT
1 ATATAATAATAATAACTAATAATATTAATTATTAAATATAATAAATAATTAAAATATAATAATAT
* *
28802 GTAAATATAGTTATTAAAATAGATATTTTATAAAAAA
66 ATAAATATAGTAATTAAAATAGATATTTTATAAAAAA
28839 AGTATAATAT
Statistics
Matches: 232, Mismatches: 10, Indels: 17
0.90 0.04 0.07
Matches are distributed among these distances:
145 9 0.04
146 18 0.08
147 1 0.00
148 3 0.01
149 3 0.01
150 5 0.02
151 98 0.42
152 2 0.01
153 2 0.01
154 1 0.00
155 20 0.09
156 70 0.30
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (156 bp):
ATATAATAATAATAACTAATAATATTAATTATTAAATATAATAAATAATTAAAATATAATAATAT
ATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTAAAATACATTTTGTAAATTTTGA
AATAATGAAAAATTATATTATAATGA
Found at i:28741 original size:9 final size:8
Alignment explanation
Indices: 28729--28801 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 8
28719 AAATTTATAT
28729 TATAATGAA
1 TATAAT-AA
28738 TATAATAA
1 TATAATAA
28746 TAATAACTAA
1 T-ATAA-TAA
*
28756 TAATATTAA
1 T-ATAATAA
*
28765 T-TATTAA
1 TATAATAA
28772 -AT-ATAA
1 TATAATAA
28778 TA-AATAA
1 TATAATAA
28785 T-TAA-AA
1 TATAATAA
28791 TATAATAA
1 TATAATAA
28799 TAT
1 TAT
28802 GTAAATATAG
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
6 6 0.11
7 18 0.33
8 8 0.15
9 14 0.26
10 8 0.15
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (8 bp):
TATAATAA
Found at i:31349 original size:66 final size:65
Alignment explanation
Indices: 31222--31354 Score: 144
Period size: 66 Copynumber: 2.0 Consensus size: 65
31212 AACTAAAATA
* * *
31222 TTTGTATTAAACTATTTTATTTTGAGTTAATGAAAATCTTTTCTGTTATGCAAAATATTTTA-TT
1 TTTGTACTAAACTATTTTATTTTGAGTTAATGAAAA--TTTGCAGTTATGCAAAATATTTTAGTT
31286 AT
64 AT
* * * *
31288 TTTGTACTAAACTATTTTATTTTGAGTTAATTGAGCAA-TTGCAGTTTATGGAACATTTTTTAGT
1 TTTGTACTAAACTATTTTATTTTGAGTTAA-TGA-AAATTTGCAG-TTATGCAAAATATTTTAGT
31352 TAT
63 TAT
31355 GTGAACTATT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
65 4 0.07
66 43 0.77
67 7 0.12
68 2 0.04
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (65 bp):
TTTGTACTAAACTATTTTATTTTGAGTTAATGAAAATTTGCAGTTATGCAAAATATTTTAGTTAT
Found at i:34073 original size:15 final size:15
Alignment explanation
Indices: 34053--34083 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34043 ATACACCCTG
34053 CAGTGTATCCATGCA
1 CAGTGTATCCATGCA
*
34068 CAGTGTATCGATGCA
1 CAGTGTATCCATGCA
34083 C
1 C
34084 CCTGCAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (15 bp):
CAGTGTATCCATGCA
Found at i:34098 original size:35 final size:35
Alignment explanation
Indices: 34034--34104 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
34024 AGGGTGTGAA
** * *
34034 AGTGTATCCATACACCCTGCAGTGTATCCATGCAC
1 AGTGTATCCATACACCCTGCAAAGCATCCATACAC
* *
34069 AGTGTATCGATGCACCCTGCAAAGCATCCATACAC
1 AGTGTATCCATACACCCTGCAAAGCATCCATACAC
34104 A
1 A
34105 TGTGACTGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.23
Consensus pattern (35 bp):
AGTGTATCCATACACCCTGCAAAGCATCCATACAC
Found at i:34594 original size:34 final size:33
Alignment explanation
Indices: 34555--34625 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
34545 TTTTGTAAAG
*
34555 GGGAAAGGTTCTAGCTAAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAAGCCCGTG-AAAAACTA
* * *
34589 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
34622 GGGA
1 GGGA
34626 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
Found at i:37338 original size:22 final size:21
Alignment explanation
Indices: 37308--37349 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
37298 TGGTATATTT
*
37308 TTAATAATTGATATCCTTTTTG
1 TTAACAATTGATAT-CTTTTTG
*
37330 TTAACAATTGGTATCTTTTT
1 TTAACAATTGATATCTTTTT
37350 CATTAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (21 bp):
TTAACAATTGATATCTTTTTG
Found at i:37355 original size:22 final size:22
Alignment explanation
Indices: 37308--37355 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
37298 TGGTATATTT
* *
37308 TTAATAATTGATATCCTTTTTG
1 TTAACAATTGATATCCTTTTTA
*
37330 TTAACAATTGGTAT-CTTTTTCA
1 TTAACAATTGATATCCTTTTT-A
37352 TTAA
1 TTAA
37356 ACATTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (22 bp):
TTAACAATTGATATCCTTTTTA
Found at i:37624 original size:20 final size:20
Alignment explanation
Indices: 37573--37661 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
37563 ATGGTATCAA
*
37573 AGTGTATCCATACACCCTGC
1 AGTGTATCCATGCACCCTGC
*
37593 AGTGTATCCATGCACTCTGC
1 AGTGTATCCATGCACCCTGC
37613 AGTGTATCCATGCA---T--
1 AGTGTATCCATGCACCCTGC
* *
37628 AGTGTATCAATGTACCCTGC
1 AGTGTATCCATGCACCCTGC
*
37648 AGTGCATCCATGCA
1 AGTGTATCCATGCA
37662 ACTGTGACTA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
15 12 0.21
17 1 0.02
18 1 0.02
20 43 0.75
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (20 bp):
AGTGTATCCATGCACCCTGC
Found at i:37648 original size:35 final size:35
Alignment explanation
Indices: 37593--37661 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
37583 TACACCCTGC
* * *
37593 AGTGTATCCATGCACTCTGCAGTGTATCCATGCAT
1 AGTGTATCAATGCACCCTGCAGTGCATCCATGCAT
*
37628 AGTGTATCAATGTACCCTGCAGTGCATCCATGCA
1 AGTGTATCAATGCACCCTGCAGTGCATCCATGCA
37662 ACTGTGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (35 bp):
AGTGTATCAATGCACCCTGCAGTGCATCCATGCAT
Found at i:38171 original size:34 final size:33
Alignment explanation
Indices: 38114--38181 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
38104 TTTTGCAAAG
* * *
38114 GGGAAAGGTTCTATCTAAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTAAGCCCGTG-AAAAACTA
* *
38148 GGGAAAGGTTATAGCTTATCCCGTGAAAAACTA
1 GGGAAAGGTTATAGCTAAGCCCGTGAAAAACTA
38181 G
1 G
38182 TAGTTGTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 8 0.28
34 21 0.72
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTATAGCTAAGCCCGTGAAAAACTA
Found at i:40510 original size:23 final size:23
Alignment explanation
Indices: 40480--40528 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
40470 ACACATTGTA
*
40480 TTTATGACACATTTTCTTATGTT
1 TTTATGACACATTTTCTTATCTT
*
40503 TTTATGACACATTTTTTTATCTT
1 TTTATGACACATTTTCTTATCTT
40526 TTT
1 TTT
40529 GATATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.12, G:0.06, T:0.61
Consensus pattern (23 bp):
TTTATGACACATTTTCTTATCTT
Found at i:43874 original size:17 final size:17
Alignment explanation
Indices: 43844--43888 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
43834 TTTTTTATAA
*
43844 TTTTAGAAAAATAAGAT
1 TTTTATAAAAATAAGAT
* *
43861 TTTTATAAATATAATAT
1 TTTTATAAAAATAAGAT
*
43878 TTTTTTAAAAA
1 TTTTATAAAAA
43889 CTTATTTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (17 bp):
TTTTATAAAAATAAGAT
Found at i:44038 original size:18 final size:18
Alignment explanation
Indices: 43998--44039 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
43988 CGTTAGACAC
*
43998 TTAAATCATTAAAAAAAC
1 TTAAATCATTAAAAAAAA
*
44016 CTAAATCATTAAAAAAAA
1 TTAAATCATTAAAAAAAA
44034 TTAAAT
1 TTAAAT
44040 ACCTATCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAATCATTAAAAAAAA
Found at i:44821 original size:2 final size:2
Alignment explanation
Indices: 44814--44841 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44804 AATGTTATTA
44814 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
44842 TAATAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45356 original size:2 final size:2
Alignment explanation
Indices: 45349--45399 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
45339 TACCTTTTAA
45349 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
45391 AT AT AT AT A
1 AT AT AT AT A
45400 CACGCACACG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48999 original size:19 final size:20
Alignment explanation
Indices: 48962--48999 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
48952 ATTATTGATA
*
48962 ATTATAAAATTTTAAAATAT
1 ATTATAAAATTCTAAAATAT
*
48982 ATTA-AAAATTCTATAATA
1 ATTATAAAATTCTAAAATA
49000 CAACTAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTATAAAATTCTAAAATAT
Found at i:52527 original size:14 final size:14
Alignment explanation
Indices: 52508--52534 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52498 GTAATTCTTA
52508 AAATTATTTTTTAG
1 AAATTATTTTTTAG
52522 AAATTATTTTTTA
1 AAATTATTTTTTA
52535 TTTTATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
AAATTATTTTTTAG
Found at i:56049 original size:75 final size:74
Alignment explanation
Indices: 55943--56140 Score: 224
Period size: 75 Copynumber: 2.7 Consensus size: 74
55933 ATATTTTTCT
* *
55943 ACTTAATATTATGGTTTGAGTCTT-AAGATTTGATACTTTAATATTATGATTTGATTATGGATTT
1 ACTTAATATTGTGGTTTGAGTCTTGAA-ATTTGA-ACTTTAATATTATGATTTGATTATGAATTT
* *
56007 TATTATTCTAG
64 TACTATTCTAA
* * * ** * *
56018 AGTTAATATTGTGGTTTGAATCTTGAAATTTGACATTTTAATATCGTGGTTTGTTTATGAATTTT
1 ACTTAATATTGTGGTTTGAGTCTTGAAATTTGA-ACTTTAATATTATGATTTGATTATGAATTTT
*
56083 ACTGTTCTAA
65 ACTATTCTAA
*
56093 ACTTAATATTGTGGTTTGAGTCTTGATATTTG-ACTTT-AT-TTATGATTT
1 ACTTAATATTGTGGTTTGAGTCTTGAAATTTGAACTTTAATATTATGATTT
56141 TTTATATATA
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
71 6 0.06
72 2 0.02
73 4 0.04
75 88 0.86
76 2 0.02
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (74 bp):
ACTTAATATTGTGGTTTGAGTCTTGAAATTTGAACTTTAATATTATGATTTGATTATGAATTTTA
CTATTCTAA
Found at i:56257 original size:12 final size:12
Alignment explanation
Indices: 56242--56266 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56232 CCTGTCCCAA
56242 TCCCCGTATCCG
1 TCCCCGTATCCG
56254 TCCCCGTATCCG
1 TCCCCGTATCCG
56266 T
1 T
56267 ATCAGTGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.48, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCCCGTATCCG
Found at i:61195 original size:77 final size:76
Alignment explanation
Indices: 60968--61253 Score: 466
Period size: 77 Copynumber: 3.8 Consensus size: 76
60958 AGAAAACGCG
* *
60968 GAGGTGGGACAATTGGCCACCCTTTACAAGTTGCTTTGTGGTCAATTAGGACCCATAACGCGGAG
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTGGTCAATTAGGACCCATAACGCGGAG
61033 GTGGCAATT-A
66 GTGGCAATTAA
*
61043 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTAGTCAATTAGGACCCATAACGCGGAG
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTGGTCAATTAGGACCCATAACGCGGAG
61108 GTGGCAATTAA
66 GTGGCAATTAA
* *
61119 GAGGTGGGACAATCGGCCACCCTTTTCGAGTCGCTTTGCTGGTCAATTAGGACCCATAACGCGGA
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTG-TGGTCAATTAGGACCCATAACGCGGA
61184 GGTGGCAATTAA
65 GGTGGCAATTAA
* * * *
61196 GAGGTGGGACAATCGGTCACCCTCTACAAGTTGCTTTCCTGGTCAATTAGGACCCATA
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTT-GTGGTCAATTAGGACCCATA
61254 TATATTATAT
Statistics
Matches: 196, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
75 71 0.36
76 37 0.19
77 88 0.45
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (76 bp):
GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTGGTCAATTAGGACCCATAACGCGGAG
GTGGCAATTAA
Found at i:61813 original size:31 final size:31
Alignment explanation
Indices: 61753--61827 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
61743 TTAATTAACA
* * ** *
61753 TAAGTTTTGGTCACTTATGTTATTGTTTTAT
1 TAAGTTTTGGTTACTTACGTTATCATTTTAG
61784 TGAA-TTTTGGTTACTTACGTTATCATTTTAG
1 T-AAGTTTTGGTTACTTACGTTATCATTTTAG
61815 TAAGTTTTGGTTA
1 TAAGTTTTGGTTA
61828 GTTTGATAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 2 0.05
31 33 0.89
32 2 0.05
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (31 bp):
TAAGTTTTGGTTACTTACGTTATCATTTTAG
Found at i:67640 original size:21 final size:21
Alignment explanation
Indices: 67614--67655 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
67604 CCGTTAGACA
67614 GGGGGAATCGGTACCCCCTAG
1 GGGGGAATCGGTACCCCCTAG
*
67635 GGGGGAATCTGTACCCCCTAG
1 GGGGGAATCGGTACCCCCTAG
67656 ACATTCTGTT
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:0.19, C:0.29, G:0.36, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTAG
Found at i:67728 original size:23 final size:22
Alignment explanation
Indices: 67684--67726 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
67674 GCCAAAAACC
67684 TGCGGGGGGAATCTGTACCCCT
1 TGCGGGGGGAATCTGTACCCCT
67706 TGCGGGGGGAATCTGTACCCC
1 TGCGGGGGGAATCTGTACCCC
67727 CTGGACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (22 bp):
TGCGGGGGGAATCTGTACCCCT
Found at i:69167 original size:19 final size:20
Alignment explanation
Indices: 69124--69171 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
69114 TCTAAATCCT
*
69124 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
69144 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
69163 TTTTCAAAA
1 TTTTCAAAA
69172 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:70092 original size:34 final size:33
Alignment explanation
Indices: 70030--70101 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
70020 CCTTACAAAC
* *
70030 TCCCTAGTTTTTCAGGGCTAAACTAGAAC-CTT
1 TCCCTAGTTTTACAGGGATAAACTAGAACACTT
* *
70062 TCCCTAGCTTTTACACGGGATAAGCTAGAACATTT
1 TCCCTAG-TTTTACA-GGGATAAACTAGAACACTT
70097 TCCCT
1 TCCCT
70102 TTACAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 7 0.21
33 6 0.18
34 13 0.39
35 7 0.21
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.33
Consensus pattern (33 bp):
TCCCTAGTTTTACAGGGATAAACTAGAACACTT
Found at i:70517 original size:20 final size:20
Alignment explanation
Indices: 70447--70525 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
70437 CTGTTAGACA
70447 GGGGGAATCGGTACCCCT-G
1 GGGGGAATCGGTACCCCTGG
** *
70466 GGGGGAATCTATTCCCCCTGG
1 GGGGGAATC-GGTACCCCTGG
* *
70487 GGGGAAAAATCGGTACCCGTGG
1 GGGG--GAATCGGTACCCCTGG
*
70509 GGGGGAATCTGTACCCC
1 GGGGGAATCGGTACCCC
70526 CTGGACATTC
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
19 9 0.20
20 16 0.36
21 5 0.11
22 11 0.24
23 4 0.09
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCTGG
Found at i:73031 original size:30 final size:32
Alignment explanation
Indices: 72972--73061 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 32
72962 CATAAAAATA
*
72972 TTTTTAAGTTAAACATAAGAGTAAAATATAAT
1 TTTTTAAGTTAAACATAAGAATAAAATATAAT
* *
73004 TTTTTATGTT-AA-ATAAGAATAACATAT-AT
1 TTTTTAAGTTAAACATAAGAATAAAATATAAT
** * *
73033 TTAATAAATTAAA-ATAAAAATAAAATATA
1 TTTTTAAGTTAAACATAAGAATAAAATATA
73062 TATTATCAAG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 8 0.17
30 28 0.60
31 2 0.04
32 9 0.19
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (32 bp):
TTTTTAAGTTAAACATAAGAATAAAATATAAT
Found at i:74911 original size:199 final size:199
Alignment explanation
Indices: 74536--75444 Score: 872
Period size: 199 Copynumber: 4.6 Consensus size: 199
74526 CATGTGTATC
* * ** * * *
74536 GATACTTGATGTTTACACCTATTATCATTATACTGGTAGA-TTTTACCGTTTTCATTGTAAATTA
1 GATACTTG-TATTTACGCCTATTATCATTATACCAGTAGACTTTTATCGTTTACATTGTAAATTT
* ** * *
74600 ACCTATTATTTTAAAGTAATAGGTTTCAAAATT-ATAA-TCATTGATACTTTATAGAGGTGTATC
65 ACCTATTATTTTAAAGTAATAGGTTTCGAAATTCA-AAGT-ATCAATACTTTATACATGTGTATC
*
74663 GATACATTTTGCGTGCAAGTTGTTTGAGAAACATACTAGAATAAAAGTATCGATACCTATATAGA
128 GATACATTTTGCGTGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCGATACCTATATAGA
*
74728 CAATATT
193 CAATACT
*** *
74735 GATACTTGGTATTTATTTCTATTATCAATATACCAGTAGACTTTTATCGTTTACATTGTAAATTT
1 GATACTT-GTATTTACGCCTATTATCATTATACCAGTAGACTTTTATCGTTTACATTGTAAATTT
* * * **
74800 ACCTATTAATTTAAAGCAATTGGTTTCGAAATTCAAAGTATCTCTACTTTATACATGTGTATCGA
65 ACCTATTATTTTAAAGTAATAGGTTTCGAAATTCAAAGTATCAATACTTTATACATGTGTATCGA
* * *
74865 TACATTTTGAGTGCAAATT-ATTGAGAAACATACTAGACTAAAAGTATCGATACAC-ATAT-GTA
130 TACATTTTGCGTGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCGATAC-CTATATAG-A
* *
74927 -ATGTACC
193 CA-ATACT
* * * * ** * *
74934 GATACTTGGTATATACGCCTATTATCATTATATCGGTAAACTTTTGGCCTTTACAATT-TTAATT
1 GATACTT-GTATTTACGCCTATTATCATTATACCAGTAGACTTTTATCGTTTAC-ATTGTAAATT
* * *
74998 TACCTATTATTTTATAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTTGTACATGTGTATCG
64 TACCTATTATTTTAAAGTAATAGGTTTCGAAATTCAAAGTATCAATACTTTATACATGTGTATCG
* * * * * * *
75063 ATAC-TTTTGCGTGTACATTGTTTGAGAATCATACTGGAATAAAAGTATCGATATCTATATAAAA
129 ATACATTTTGCGTGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCGATACCTATATAGAC
*
75127 AATATT
194 AATACT
* * *
75133 GATACTT-TACGTTTACGCCTATTATCATTAAACCAATAGATTTTTATCGTTTACATTGTAAATT
1 GATACTTGTA--TTTACGCCTATTATCATTATACCAGTAGACTTTTATCGTTTACATTGTAAATT
* * * * *
75197 TACCTTTTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTACCAATACTATATATATATGTGTAT
64 TACCTATTATTTTAAAGTAATAGGTTTCGAAATTCAAAGTATCAATACT-T-TATACATGTGTAT
* * * ** * *
75262 CAATACTTTTTGCGTACAAATTGTTTGAGATGCATACTGGAATTAAAGTATCGATA-CTGATATA
127 CGATACATTTTGCGTGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCGATACCT-ATATA
75326 -ACAAAGTACT
191 GAC-AA-TACT
* * * * *
75336 GATACGATGTGTTTATG-CTATTATCATTATATCAGTAGACTTTTA-CAATTTACATTGTAAATT
1 GATAC-TTGTATTTACGCCTATTATCATTATACCAGTAGACTTTTATC-GTTTACATTGTAAATT
* *
75399 TA--T-CTA----AAAGTAATAGGTTTCGAAATT-ACAAGTATCGATACTTTAT
64 TACCTATTATTTTAAAGTAATAGGTTTCGAAATTCA-AAGTATCAATACTTTAT
75445 TGCGGACAAA
Statistics
Matches: 589, Mismatches: 96, Indels: 56
0.79 0.13 0.08
Matches are distributed among these distances:
193 3 0.01
194 1 0.00
195 32 0.05
197 2 0.00
198 18 0.03
199 307 0.52
200 98 0.17
201 22 0.04
202 91 0.15
203 13 0.02
204 1 0.00
205 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (199 bp):
GATACTTGTATTTACGCCTATTATCATTATACCAGTAGACTTTTATCGTTTACATTGTAAATTTA
CCTATTATTTTAAAGTAATAGGTTTCGAAATTCAAAGTATCAATACTTTATACATGTGTATCGAT
ACATTTTGCGTGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCGATACCTATATAGACAA
TACT
Found at i:81150 original size:3 final size:3
Alignment explanation
Indices: 81142--81166 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
81132 TGGTACGTGG
81142 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
81167 TTGGCTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Done.