Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005590.1 Hibiscus syriacus cultivar Beakdansim tig00012984_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: 151829
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1240 original size:23 final size:23
Alignment explanation
Indices: 1209--1253 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1199 ATCATCAAAA
*
1209 TCCGAGTATTGACCAATATCAAG
1 TCCGAGTATTGACCAAGATCAAG
*
1232 TCCGGGTATTGACCAAGATCAA
1 TCCGAGTATTGACCAAGATCAA
1254 ATTTCGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (23 bp):
TCCGAGTATTGACCAAGATCAAG
Found at i:2090 original size:20 final size:20
Alignment explanation
Indices: 2068--2234 Score: 178
Period size: 20 Copynumber: 8.4 Consensus size: 20
2058 AATTGGAAAA
* *
2068 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* **
2088 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
2109 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
2129 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
2149 TCGCAATGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
* *
2169 TCGCAACGTGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
2189 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
* * *
2209 T--CAACGAGATTCTAACTT
1 TCGCAACGCGATACTGACTT
2227 TCGCAACG
1 TCGCAACG
2235 AGATTCTGAA
Statistics
Matches: 129, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
18 16 0.12
19 2 0.02
20 94 0.73
21 15 0.12
22 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:2120 original size:41 final size:41
Alignment explanation
Indices: 2064--2141 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
2054 TGCGAATTGG
*
2064 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
2105 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
2142 CTGACTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:2235 original size:20 final size:20
Alignment explanation
Indices: 2109--2243 Score: 193
Period size: 20 Copynumber: 6.8 Consensus size: 20
2099 TAATACAAAA
*
2109 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
2129 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
2149 TCGCAATGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
2169 TCGCAACGTGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
2189 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
* *
2209 T--CAACGAGATTCTAACTT
1 TCGCAACGCGATTCTGACTT
*
2227 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
2244 AATTGCAATC
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
18 16 0.15
20 89 0.85
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:2521 original size:14 final size:14
Alignment explanation
Indices: 2502--2555 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
2492 GAAAATCGCA
2502 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
2516 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
2533 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
2549 TTGCGAT
1 TTGCGAT
2556 AGTCTGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:2521 original size:33 final size:33
Alignment explanation
Indices: 2484--2554 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
2474 GAAATCGCAA
2484 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
2517 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
2550 TGCGA
1 TGCGA
2555 TAGTCTGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:4559 original size:20 final size:20
Alignment explanation
Indices: 4516--4608 Score: 105
Period size: 20 Copynumber: 4.7 Consensus size: 20
4506 TAGTTTACTT
* * * *
4516 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
*
4536 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
4556 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
4576 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
*
4596 TCGCAATGCGAAA
1 TCGCAACGCGAAA
4609 TACAAATCGC
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:4617 original size:19 final size:18
Alignment explanation
Indices: 4595--4661 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 18
4585 GGAAATGGCT
*
4595 ATCGCAATGCGAAATACAA
1 ATCGCAATGCGAAACA-AA
4614 ATCGCAA--CG--ACAAA
1 ATCGCAATGCGAAACAAA
*
4628 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAA-CAAA
*
4647 ATCGCAACGCGAAAC
1 ATCGCAATGCGAAAC
4662 GCAAATCGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
14 9 0.23
15 2 0.05
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.12
Consensus pattern (18 bp):
ATCGCAATGCGAAACAAA
Found at i:4667 original size:19 final size:19
Alignment explanation
Indices: 4625--4670 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
4615 TCGCAACGAC
* *
4625 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAACG
4644 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAACG
*
4663 CAAATCGC
1 AAAATCGC
4671 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACG
Found at i:4689 original size:19 final size:19
Alignment explanation
Indices: 4667--4768 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 19
4657 GAAACGCAAA
4667 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * *
4686 TCGCATTGTGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
4702 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
4719 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
4738 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
4758 TCGTGTTGCGA
1 TCGCGTTGCGA
4769 AAGTAAACTA
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
14 6 0.09
15 3 0.05
16 2 0.03
17 2 0.03
18 3 0.05
19 31 0.48
20 17 0.27
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4749 original size:20 final size:19
Alignment explanation
Indices: 4715--4768 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
4705 TTGCGATTTT
*
4715 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
4734 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
4754 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
4769 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5331 original size:18 final size:18
Alignment explanation
Indices: 5308--5355 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
5298 CGGGTCGATC
5308 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
* *
5326 AGGTGATAGCGCTGGGTG
1 AGGTGATGGCTCTGGGTG
5344 AGGTGATGGCTC
1 AGGTGATGGCTC
5356 CCGAAGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.12, G:0.48, T:0.25
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:6697 original size:20 final size:20
Alignment explanation
Indices: 6672--6709 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6662 AATAGTTTCT
6672 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
6692 GAAAATGACAATCGCAAC
1 GAAAATGAAAATCGCAAC
6710 GCAAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:7010 original size:20 final size:20
Alignment explanation
Indices: 6985--7030 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
6975 TCTGAGAGAT
6985 GGAGATAGACGGATTTCGTC
1 GGAGATAGACGGATTTCGTC
* **
7005 GGAGATGGGGGGATTTCGTC
1 GGAGATAGACGGATTTCGTC
*
7025 AGAGAT
1 GGAGAT
7031 GGGTGAGAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.11, G:0.41, T:0.24
Consensus pattern (20 bp):
GGAGATAGACGGATTTCGTC
Found at i:7031 original size:20 final size:20
Alignment explanation
Indices: 6995--7033 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6985 GGAGATAGAC
*
6995 GGATTTCGTCGGAGATGGGG
1 GGATTTCGTCAGAGATGGGG
7015 GGATTTCGTCAGAGATGGG
1 GGATTTCGTCAGAGATGGG
7034 TGAGAGAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.46, T:0.26
Consensus pattern (20 bp):
GGATTTCGTCAGAGATGGGG
Found at i:7248 original size:20 final size:20
Alignment explanation
Indices: 7218--7329 Score: 113
Period size: 20 Copynumber: 5.5 Consensus size: 20
7208 GATTATGTAT
*
7218 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
7238 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
7258 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
7278 TATCGCGTTGC-AATTTTGT-AT
1 TATCGCGTTGCGAA---AGTCAG
7299 TATCGCGTTGCGATAA-TCAG
1 TATCGCGTTGCGA-AAGTCAG
7319 TATCGCGTTGC
1 TATCGCGTTGC
7330 AATTTTCCAA
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
19 3 0.04
20 56 0.75
21 12 0.16
22 3 0.04
23 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:7319 original size:41 final size:41
Alignment explanation
Indices: 7198--7335 Score: 165
Period size: 41 Copynumber: 3.4 Consensus size: 41
7188 CGCTCTGAAA
* * * *
7198 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCAATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * * *
7239 ATTGCGTTGCGAA-ATT-AAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGC-AATTTTGTATTATCGCGTTGCGAAAGTCAGT
7279 ATCGCGTTGCAATTTTGTATTATCGCGTTGCGATAA-TCAGT
1 ATCGCGTTGCAATTTTGTATTATCGCGTTGCGA-AAGTCAGT
7320 ATCGCGTTGCAATTTT
1 ATCGCGTTGCAATTTT
7336 CCAAATTCGC
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
39 2 0.02
40 32 0.40
41 44 0.54
42 3 0.04
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCAATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:7350 original size:21 final size:21
Alignment explanation
Indices: 7321--7397 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
7311 ATAATCAGTA
* *
7321 TCGCGTTGCAATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
7342 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
7363 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
7384 TCGCATTGCGATTT
1 TCGCATTGCGATTT
7398 ACTTATTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:7351 original size:41 final size:41
Alignment explanation
Indices: 7260--7395 Score: 125
Period size: 41 Copynumber: 3.3 Consensus size: 41
7250 AAATTAAGTA
* ** *
7260 TCGCGTTGCGA-AAGTCAGTATCGCGTTGCAATTTT-GTATT
1 TCGCATTGCGATAA-TCAGTATCGCGTTGCAATTTTCCAAAT
*
7300 ATCGCGTTGCGATAATCAGTATCGCGTTGCAATTTTCCAAAT
1 -TCGCATTGCGATAATCAGTATCGCGTTGCAATTTTCCAAAT
** * * *
7342 TCGCATTGCGATTTTCCA-AATTCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATAAT-CAGTA-TCGCGTTGCAATTTTCCAAAT
7384 TCGCATTGCGAT
1 TCGCATTGCGAT
7396 TTACTTATTA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
41 45 0.55
42 37 0.45
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (41 bp):
TCGCATTGCGATAATCAGTATCGCGTTGCAATTTTCCAAAT
Found at i:13280 original size:6 final size:6
Alignment explanation
Indices: 13271--13296 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
13261 AACTCGAACT
13271 CGAGCC CGAGCC CGAGCC CGAGCC CG
1 CGAGCC CGAGCC CGAGCC CGAGCC CG
13297 GAATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.35, T:0.00
Consensus pattern (6 bp):
CGAGCC
Found at i:20582 original size:54 final size:54
Alignment explanation
Indices: 20498--20656 Score: 282
Period size: 54 Copynumber: 2.9 Consensus size: 54
20488 TCAGGGTCAG
*
20498 GGTCAGGGTCTCATCAGCAATTGTTTCATTGGCATTTTGATCATCAGTGGGCAT
1 GGTCAGGGTCTCATCAGCAATTGTTTCATTGGCATTTTGATCCTCAGTGGGCAT
* *
20552 GGTCAGGGTCTCATCAACAATTGTTCCATTGGCATTTTGATCCTCAGTGGGCAT
1 GGTCAGGGTCTCATCAGCAATTGTTTCATTGGCATTTTGATCCTCAGTGGGCAT
*
20606 GGTCAGGGTCTCATCAGCAATTGTTTCATTGGCATTTAGATCCTCAGTGGG
1 GGTCAGGGTCTCATCAGCAATTGTTTCATTGGCATTTTGATCCTCAGTGGG
20657 GTTTGAGGGT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (54 bp):
GGTCAGGGTCTCATCAGCAATTGTTTCATTGGCATTTTGATCCTCAGTGGGCAT
Found at i:23357 original size:20 final size:20
Alignment explanation
Indices: 23334--23386 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
23324 TTGAAGTAAG
23334 AGTATCGATACTATAAGGCT
1 AGTATCGATACTATAAGGCT
23354 AGTATCGATACTATAAGGCT
1 AGTATCGATACTATAAGGCT
23374 AGTATCGATACTA
1 AGTATCGATACTA
23387 AGACAAGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTATAAGGCT
Found at i:27259 original size:12 final size:12
Alignment explanation
Indices: 27244--27273 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
27234 TAAACCATGC
27244 TTTAAAAGGGAT
1 TTTAAAAGGGAT
27256 TTTAAAAGGGAT
1 TTTAAAAGGGAT
27268 TTTAAA
1 TTTAAA
27274 TTAGACAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (12 bp):
TTTAAAAGGGAT
Found at i:29174 original size:88 final size:89
Alignment explanation
Indices: 29015--29187 Score: 276
Period size: 88 Copynumber: 1.9 Consensus size: 89
29005 GTTATTTATT
* * * ***
29015 AAAAATACGAAGTGATTATAATATAATATATATTTAAAATCTTTTTTAACACACTGCTCTACACT
1 AAAAATACGAAATGATTACAAGATAATATATATTTAAAA-CAAATTTAACACACTGCTCTACACT
29080 ATTTAGTTTTAAACTAAAATCAACC
65 ATTTAGTTTTAAACTAAAATCAACC
29105 AAAAATACGAAATGATTACAAGATAATATATATTTAAAA-AAATTTAACACACTGCTCTACACTA
1 AAAAATACGAAATGATTACAAGATAATATATATTTAAAACAAATTTAACACACTGCTCTACACTA
29169 TTTAGTTTTAAACTAAAAT
66 TTTAGTTTTAAACTAAAAT
29188 TCACCTCTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 41 0.53
90 36 0.47
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (89 bp):
AAAAATACGAAATGATTACAAGATAATATATATTTAAAACAAATTTAACACACTGCTCTACACTA
TTTAGTTTTAAACTAAAATCAACC
Found at i:29770 original size:26 final size:26
Alignment explanation
Indices: 29741--29793 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
29731 AACACTAACC
* *
29741 TTAGAACTTGAGACCTTACATTATAA
1 TTAGAACTTGAGACATTAAATTATAA
29767 TTAGAACTTGAGACATTAAATTATAA
1 TTAGAACTTGAGACATTAAATTATAA
29793 T
1 T
29794 CACTAAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (26 bp):
TTAGAACTTGAGACATTAAATTATAA
Found at i:29815 original size:28 final size:28
Alignment explanation
Indices: 29779--29836 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
29769 AGAACTTGAG
*
29779 ACATTAAATTAT-AATCACTAAATCCTAA
1 ACATCAAATTATAAAT-ACTAAATCCTAA
* *
29807 ACATCAAATTTTAAATACTAAATCTTAA
1 ACATCAAATTATAAATACTAAATCCTAA
29835 AC
1 AC
29837 CCAAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (28 bp):
ACATCAAATTATAAATACTAAATCCTAA
Found at i:29848 original size:28 final size:29
Alignment explanation
Indices: 29825--29879 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
29815 TTTTAAATAC
29825 TAAATCTT-AAACCCAAAAAATTAAACAA
1 TAAATCTTAAAACCCAAAAAATTAAACAA
* *
29853 TAAATTTTAAAATCCAAAAAATTAAAC
1 TAAATCTTAAAACCCAAAAAATTAAAC
29880 TAAGTGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (29 bp):
TAAATCTTAAAACCCAAAAAATTAAACAA
Found at i:34125 original size:18 final size:18
Alignment explanation
Indices: 34102--34200 Score: 139
Period size: 18 Copynumber: 5.6 Consensus size: 18
34092 TGTTTATGAG
34102 GGAATTAGAATCTGTTAA
1 GGAATTAGAATCTGTTAA
*
34120 GGAATTAGAATCTATTAA
1 GGAATTAGAATCTGTTAA
*
34138 GGAATTGGAATCTGTTAA
1 GGAATTAGAATCTGTTAA
*
34156 GGAATTAGAATCTATTAA
1 GGAATTAGAATCTGTTAA
*
34174 GGAATTGGAATCTG-T-A
1 GGAATTAGAATCTGTTAA
*
34190 GGAATTGGAAT
1 GGAATTAGAAT
34201 TGGAATCTGA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
16 12 0.16
17 1 0.01
18 61 0.82
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.32
Consensus pattern (18 bp):
GGAATTAGAATCTGTTAA
Found at i:34149 original size:36 final size:36
Alignment explanation
Indices: 34102--34200 Score: 166
Period size: 36 Copynumber: 2.8 Consensus size: 36
34092 TGTTTATGAG
*
34102 GGAATTAGAATCTGTTAAGGAATTAGAATCTATTAA
1 GGAATTGGAATCTGTTAAGGAATTAGAATCTATTAA
34138 GGAATTGGAATCTGTTAAGGAATTAGAATCTATTAA
1 GGAATTGGAATCTGTTAAGGAATTAGAATCTATTAA
*
34174 GGAATTGGAATCTG-T-AGGAATTGGAAT
1 GGAATTGGAATCTGTTAAGGAATTAGAAT
34201 TGGAATCTGA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 11 0.18
35 1 0.02
36 49 0.80
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.32
Consensus pattern (36 bp):
GGAATTGGAATCTGTTAAGGAATTAGAATCTATTAA
Found at i:34841 original size:38 final size:38
Alignment explanation
Indices: 34770--34877 Score: 110
Period size: 38 Copynumber: 2.8 Consensus size: 38
34760 TGAACCTGAT
* * * *
34770 TATTTCACTT-AAAAAACCCAACCCGAACACGACCCGGA
1 TATTACACTTAAAAAAACCCGACCC-AACCCGACCCGAA
* *
34808 TATTACACTTAAAAAAACCCGACCCTACCCGACCTGAA
1 TATTACACTTAAAAAAACCCGACCCAACCCGACCCGAA
* * * *
34846 TATCAAACTTAAAAAAACTCGACCCGACCCGA
1 TATTACACTTAAAAAAACCCGACCCAACCCGA
34878 TCCTGATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 46 0.78
39 13 0.22
ACGTcount: A:0.41, C:0.33, G:0.09, T:0.17
Consensus pattern (38 bp):
TATTACACTTAAAAAAACCCGACCCAACCCGACCCGAA
Found at i:34985 original size:28 final size:30
Alignment explanation
Indices: 34954--35016 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 30
34944 TCACACTTAA
34954 AAAAACCCGACCCGAACCCG-A-TTTTTTT
1 AAAAACCCGACCCGAACCCGAATTTTTTTT
* * *
34982 AAAAATCCGACCCGATCCTGAATTTTTTTT
1 AAAAACCCGACCCGAACCCGAATTTTTTTT
35012 AAAAA
1 AAAAA
35017 AACTGACCCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 17 0.57
29 1 0.03
30 12 0.40
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.29
Consensus pattern (30 bp):
AAAAACCCGACCCGAACCCGAATTTTTTTT
Found at i:34994 original size:91 final size:94
Alignment explanation
Indices: 34829--35027 Score: 235
Period size: 91 Copynumber: 2.1 Consensus size: 94
34819 AAAAAACCCG
* * * * *
34829 ACCCTACCCGACCTGAATATCAAACTTAAAAAAACTCGACCCGACCCGATCCTGATTTTTTTTTA
1 ACCCGACCCGACCCGAATATCAAACTTAAAAAAA--C-ACCCGACCCGAACCCGATTTTTTTTAA
34894 AAATCGACCCGATCC-CAAAATTTTTTAAAAA
63 AAATCGACCCGATCCTCAAAATTTTTTAAAAA
*
34925 ACCCGACCCGACCCGAATATCACACTT-AAAAAA-ACCCGACCCGAACCCGA-TTTTTTTAAAAA
1 ACCCGACCCGACCCGAATATCAAACTTAAAAAAACACCCGACCCGAACCCGATTTTTTTTAAAAA
* **
34987 TCCGACCCGATCCTGAATTTTTTTTAAAAA
66 T-CGACCCGATCCTCAAAATTTTTTAAAAA
* *
35017 AACTGACCCGA
1 ACCCGACCCGA
35028 ATACCAAAAG
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
90 12 0.13
91 26 0.29
92 22 0.24
95 6 0.07
96 24 0.27
ACGTcount: A:0.36, C:0.30, G:0.10, T:0.25
Consensus pattern (94 bp):
ACCCGACCCGACCCGAATATCAAACTTAAAAAAACACCCGACCCGAACCCGATTTTTTTTAAAAA
TCGACCCGATCCTCAAAATTTTTTAAAAA
Found at i:36504 original size:49 final size:49
Alignment explanation
Indices: 36432--36531 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
36422 CCCTGTTTGG
36432 TTAGCATGGGAATCTCATTCCCGGTAATGTAAGATTATCAATAGTGGAT
1 TTAGCATGGGAATCTCATTCCCGGTAATGTAAGATTATCAATAGTGGAT
36481 TTAGCATGGGAATCTCATTCCCGGTAATGTAAGATTATCAATAGTGGAT
1 TTAGCATGGGAATCTCATTCCCGGTAATGTAAGATTATCAATAGTGGAT
36530 TT
1 TT
36532 TTTGGGGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (49 bp):
TTAGCATGGGAATCTCATTCCCGGTAATGTAAGATTATCAATAGTGGAT
Found at i:38007 original size:2 final size:2
Alignment explanation
Indices: 38000--38038 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
37990 ATTTCTACCA
38000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38039 CAAATATTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41268 original size:31 final size:31
Alignment explanation
Indices: 41233--41564 Score: 546
Period size: 31 Copynumber: 10.8 Consensus size: 31
41223 TTGCCATTTC
*
41233 CAATACTAGTGGATTGAGCATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
41264 CAATACTAG-TGAATTGAGCATTATTAACATT
1 CAATACTAGTTG-ATTGAGCATTATTAACATT
*
41295 CAATACTAG-TGTATTGAGCATTATCAACATT
1 CAATACTAGTTG-ATTGAGCATTATTAACATT
41326 CAATACTAGTTGATTGAGCATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
41357 CAATACTAGTTGATTGAGCATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
41388 CAATACTAGTTGATTGAGCATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
*
41419 CAATACTAGTTTATTGAGCATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
*
41450 CAATA--AGTTTATTGAGCATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
*
41479 CAATAATAGTTGATTGAGCATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
* *
41510 CAATACTAGTTAATTGAGCATTATTAATATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
*
41541 CAATACTAGTTGAATGAGCATTAT
1 CAATACTAGTTGATTGAGCATTAT
41565 CCAATACTAG
Statistics
Matches: 286, Mismatches: 11, Indels: 8
0.94 0.04 0.03
Matches are distributed among these distances:
29 29 0.10
30 1 0.00
31 254 0.89
32 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (31 bp):
CAATACTAGTTGATTGAGCATTATTAACATT
Found at i:41896 original size:34 final size:32
Alignment explanation
Indices: 41834--41903 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
41824 ACCTTACAAC
* *
41834 TCCCTAGTTTTTCCGGGTTAAACTAGAACCTT
1 TCCCTAGTTTTTACGGGCTAAACTAGAACCTT
*
41866 TCCCTAGCTTTTATACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTT-TACGGGCTAAACTAGAACCTT
41900 TCCC
1 TCCC
41904 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTTACGGGCTAAACTAGAACCTT
Found at i:42212 original size:21 final size:21
Alignment explanation
Indices: 42186--42227 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
42176 CCAGAATGGG
*
42186 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
42207 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
42228 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:42293 original size:21 final size:21
Alignment explanation
Indices: 42263--42306 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
42253 CTGTTGAACA
*
42263 GGGGGGGAATCGGTACCCCCT
1 GGGGGAGAATCGGTACCCCCT
42284 GGGGGAGAATCGGTACCCCCT
1 GGGGGAGAATCGGTACCCCCT
42305 GG
1 GG
42307 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.43, T:0.14
Consensus pattern (21 bp):
GGGGGAGAATCGGTACCCCCT
Found at i:42365 original size:21 final size:21
Alignment explanation
Indices: 42339--42418 Score: 82
Period size: 21 Copynumber: 4.1 Consensus size: 21
42329 AAAACCTGCA
42339 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
42360 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
* *
42377 --GGGGTATCTGTACCCCCTA
1 GGGGGGAATCTGTACCCCCTG
*
42396 GGGGGGAATCTATACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
42417 GG
1 GG
42419 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 31 0.63
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:42382 original size:15 final size:15
Alignment explanation
Indices: 42362--42391 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42352 ACCCCCTGGG
42362 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
42377 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
42392 CCTAGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:42386 original size:36 final size:36
Alignment explanation
Indices: 42341--42412 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
42331 AACCTGCAGG
* * *
42341 GGGGAATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCTGTACCCCCTAGGGGGGAATCTATACCC
*
42377 GGGGTATCTGTACCCCCTAGGGGGGAATCTATACCC
1 GGGGAATCTGTACCCCCTAGGGGGGAATCTATACCC
42413 CCTGGGCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (36 bp):
GGGGAATCTGTACCCCCTAGGGGGGAATCTATACCC
Found at i:42540 original size:29 final size:31
Alignment explanation
Indices: 42508--42567 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
42498 AAACTTTGAA
42508 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
42537 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
42568 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:42757 original size:22 final size:22
Alignment explanation
Indices: 42726--42772 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
42716 AAGCTCCCTC
42726 TTTTTCATTAAGAAATTGAATT
1 TTTTTCATTAAGAAATTGAATT
*
42748 TTTTTTATTAAGAAATTGAATT
1 TTTTTCATTAAGAAATTGAATT
42770 TTT
1 TTT
42773 CAAACCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (22 bp):
TTTTTCATTAAGAAATTGAATT
Found at i:43889 original size:19 final size:20
Alignment explanation
Indices: 43846--43893 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
43836 TCTAAATCCT
*
43846 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
43866 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
43885 TTTTCAAAA
1 TTTTCAAAA
43894 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:45177 original size:29 final size:31
Alignment explanation
Indices: 45145--45204 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
45135 AAACTTTGAA
45145 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
45174 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
45205 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:50574 original size:31 final size:31
Alignment explanation
Indices: 50536--50900 Score: 522
Period size: 31 Copynumber: 11.8 Consensus size: 31
50526 TTGCCATTTC
*
50536 CAATACTAGTGGATTGAGCATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
50567 CAATACTAG-TGAATTGAGCATTATTAACATT
1 CAATACTAGTTG-ATTGAGCATTATTAACATT
*
50598 CAATACTAG-TGAATTGAGCATTATGAACATT
1 CAATACTAGTTG-ATTGAGCATTATTAACATT
* *
50629 CAATACTAG-TGTATTGAGCATTATCAATATT
1 CAATACTAGTTG-ATTGAGCATTATTAACATT
* *
50660 TAATACTAGTTGATTGAGTATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
* *
50691 CAATACTAGTTGATTAAGCATTATTAATATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
* *
50722 CAATACTAGTTTATT-AGGCATTTTTAACATT
1 CAATACTAGTTGATTGA-GCATTATTAACATT
* *
50753 CAATACTAGTTGATTGGGCATTATTAATATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
* *
50784 CAATACTAGTTTATTGAGCATTATTAATATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
*
50815 CAATACTAGTTTATTGAGCATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
50846 CAATACTAGTTGATTGAGCATTATTAACATT
1 CAATACTAGTTGATTGAGCATTATTAACATT
*
50877 CAATACTAGTTGAATGAGCATTAT
1 CAATACTAGTTGATTGAGCATTAT
50901 CCAATACTAG
Statistics
Matches: 305, Mismatches: 25, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
30 2 0.01
31 301 0.99
32 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (31 bp):
CAATACTAGTTGATTGAGCATTATTAACATT
Found at i:51313 original size:29 final size:29
Alignment explanation
Indices: 51281--51341 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
51271 AAAGCAGTTA
51281 GTTAATTCAGATTATTTTTAGATAGAATT
1 GTTAATTCAGATTATTTTTAGATAGAATT
* *
51310 GTTATTTTAGATTATTTTTAGATAGAATT
1 GTTAATTCAGATTATTTTTAGATAGAATT
51339 GTT
1 GTT
51342 CTTGTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (29 bp):
GTTAATTCAGATTATTTTTAGATAGAATT
Found at i:52080 original size:4 final size:4
Alignment explanation
Indices: 52073--52126 Score: 74
Period size: 4 Copynumber: 13.8 Consensus size: 4
52063 TAAAATGTAA
* *
52073 ACAT ACAT ACAT ACAT ACAT ACAT ATAT ATAT ACAT ACAT ACAT A-AT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
52120 ATAT ACA
1 ACAT ACA
52127 CGCATACACA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
3 3 0.07
4 43 0.93
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.30
Consensus pattern (4 bp):
ACAT
Found at i:52132 original size:19 final size:20
Alignment explanation
Indices: 52073--52134 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
52063 TAAAATGTAA
* * *
52073 ACATACATACATACATACAT
1 ACATATATATATACACACAT
*
52093 ACATATATATATACATACAT
1 ACATATATATATACACACAT
*
52113 ACATA-ATATATACACGCAT
1 ACATATATATATACACACAT
52132 ACA
1 ACA
52135 CACACATACA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
19 15 0.39
20 23 0.61
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (20 bp):
ACATATATATATACACACAT
Found at i:54334 original size:23 final size:24
Alignment explanation
Indices: 54299--54356 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
54289 ATTTTCAAAT
54299 TATTAATTAAAAAACATA-TA-ACTTA
1 TATT-ATTAAAAAA-ATATTATA-TTA
54324 TATTATTAAAAAAATATTATATTA
1 TATTATTAAAAAAATATTATATTA
54348 -ATTATTAAA
1 TATTATTAAA
54357 CATACATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 12 0.39
24 14 0.45
25 5 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (24 bp):
TATTATTAAAAAAATATTATATTA
Found at i:55022 original size:14 final size:14
Alignment explanation
Indices: 55003--55032 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54993 TTTAGATTTT
*
55003 TTAAAATTACATTA
1 TTAAAAATACATTA
55017 TTAAAAATACATTA
1 TTAAAAATACATTA
55031 TT
1 TT
55033 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:55074 original size:19 final size:20
Alignment explanation
Indices: 55037--55074 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
55027 ATTATTGATA
*
55037 ATTATAAAATTTTAAAATAT
1 ATTATAAAATTCTAAAATAT
*
55057 ATTA-AAAATTCTATAATA
1 ATTATAAAATTCTAAAATA
55075 CAACTAAGAC
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:55131 original size:14 final size:14
Alignment explanation
Indices: 55112--55154 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
55102 TATGTGATAG
*
55112 GATTTAGGGTTTAT
1 GATTTAGGGTTTAA
*
55126 GATTTATGGTTTAA
1 GATTTAGGGTTTAA
*
55140 GGTTTAGGGTTTAA
1 GATTTAGGGTTTAA
55154 G
1 G
55155 TTATGCACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
GATTTAGGGTTTAA
Found at i:55768 original size:225 final size:225
Alignment explanation
Indices: 55377--55827 Score: 839
Period size: 225 Copynumber: 2.0 Consensus size: 225
55367 CACAGATTGA
55377 GCTAACATCGACCCATGTTCGCAAATAGAGAAGTTATTAAAGGTGCAATAGAACATACGTTAAAT
1 GCTAACATCGACCCATGTTCGCAAATAGAGAAGTTATTAAAGGTGCAATAGAACATACGTTAAAT
*
55442 GGAATGTAAGCATGTATGCCATTGACAGGACCAACGGTGAAGCCTGTATACCCGACCATTGCTCT
66 GGAATGTAAGCATGTATGCCATTGACAGGACCAACGGTGAAGCCTGTATACCCGACCATTGCTCC
* *
55507 ATGAACTGCGACGTGAGCAAGTAGGGCGCAGTAGACATTATCCGAAAGTGTTGGAGTTTGGGTGG
131 ATGAACTGCGACGTGAGCAAATAGGGCGCAGTAGACATTATCCGAAAGTGTTGGAGTTTAGGTGG
*
55572 AAGGAATGGAGAAGAAGCTGATATATAGTG
196 AAGGAACGGAGAAGAAGCTGATATATAGTG
55602 GCTAACATCGACCCATGTTCGCAAATAGAGAAGTTATTAAAGGTGCAATAGAACATACGTTAAAT
1 GCTAACATCGACCCATGTTCGCAAATAGAGAAGTTATTAAAGGTGCAATAGAACATACGTTAAAT
* * *
55667 GGGATGTAAGTATGTATGCCATTGACAGGACCAACGGTGAAGCCTGTATACCCGAGCATTGCTCC
66 GGAATGTAAGCATGTATGCCATTGACAGGACCAACGGTGAAGCCTGTATACCCGACCATTGCTCC
55732 ATGAACTGCGACGTGAGCAAATAGGGCGCAGTAGACATTATCCGAAAGTGTTGGAGTTTAGGTGG
131 ATGAACTGCGACGTGAGCAAATAGGGCGCAGTAGACATTATCCGAAAGTGTTGGAGTTTAGGTGG
55797 AAGGAACGGAGAAGAAGCTGATATATAGTG
196 AAGGAACGGAGAAGAAGCTGATATATAGTG
55827 G
1 G
55828 GGTTTGTCTT
Statistics
Matches: 219, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
225 219 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (225 bp):
GCTAACATCGACCCATGTTCGCAAATAGAGAAGTTATTAAAGGTGCAATAGAACATACGTTAAAT
GGAATGTAAGCATGTATGCCATTGACAGGACCAACGGTGAAGCCTGTATACCCGACCATTGCTCC
ATGAACTGCGACGTGAGCAAATAGGGCGCAGTAGACATTATCCGAAAGTGTTGGAGTTTAGGTGG
AAGGAACGGAGAAGAAGCTGATATATAGTG
Found at i:57318 original size:21 final size:21
Alignment explanation
Indices: 57278--57318 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
57268 AGATAAAATA
* *
57278 TTATATAAAACATTATTATTT
1 TTATATAAAACATAAATATTT
*
57299 TTATATAAAATATAAATATT
1 TTATATAAAACATAAATATT
57319 GTTTTTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATATAAAACATAAATATTT
Found at i:57493 original size:24 final size:23
Alignment explanation
Indices: 57451--57503 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
57441 TTGAAATAAT
* **
57451 AATATTTTTAATAATTATTATTA
1 AATATTTTTAATAAATATTAAAA
*
57474 AATATTTTATCATAAATATTAAAA
1 AATATTTT-TAATAAATATTAAAA
57498 AATATT
1 AATATT
57504 AATGATTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTTTTAATAAATATTAAAA
Found at i:64904 original size:20 final size:19
Alignment explanation
Indices: 64878--64955 Score: 74
Period size: 19 Copynumber: 4.2 Consensus size: 19
64868 TTCAAGATTG
64878 CCCAGGGGGTACAGATTCC
1 CCCAGGGGGTACAGATTCC
*
64897 CCCTAGGGGGTACAGA-TAC
1 CCC-AGGGGGTACAGATTCC
*
64916 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGAT--TCC
*
64934 CCCAGGGGGTACCGATTCC
1 CCCAGGGGGTACAGATTCC
64953 CCC
1 CCC
64956 CTGTCTAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
15 9 0.19
18 4 0.09
19 13 0.28
20 12 0.26
21 9 0.19
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.14
Consensus pattern (19 bp):
CCCAGGGGGTACAGATTCC
Found at i:64924 original size:15 final size:15
Alignment explanation
Indices: 64904--64933 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
64894 TCCCCCTAGG
64904 GGGTACAGATACCCC
1 GGGTACAGATACCCC
64919 GGGTACAGATACCCC
1 GGGTACAGATACCCC
64934 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:64934 original size:35 final size:36
Alignment explanation
Indices: 64884--64954 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
64874 ATTGCCCAGG
* *
64884 GGGTACAGAT-TCCCCCTAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
* *
64919 GGGTACAGATACCCCCCCAGGGGGTACCGATTCCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
64955 CCTGTCTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 10 0.32
36 21 0.68
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.15
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:64956 original size:20 final size:20
Alignment explanation
Indices: 64878--64956 Score: 78
Period size: 20 Copynumber: 4.2 Consensus size: 20
64868 TTCAAGATTG
64878 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
* *
64898 CCTAGGGGGTACAGA-T-AC
1 CCCAGGGGGTACAGATTCCC
*
64916 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGAT-TCCC
*
64934 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
64954 CCC
1 CCC
64957 TGTCTAAAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
15 9 0.20
18 7 0.15
19 1 0.02
20 20 0.43
21 9 0.20
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.14
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:65065 original size:21 final size:21
Alignment explanation
Indices: 65039--65080 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
65029 ATTTGAATAT
*
65039 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
65060 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
65081 CCCATTCTGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:65143 original size:21 final size:21
Alignment explanation
Indices: 65109--65148 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
65099 TTTGAGTAGA
*
65109 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
65131 AAAAT-ATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
65149 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:65403 original size:34 final size:32
Alignment explanation
Indices: 65364--65433 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
65354 TTTTGTAAAG
* *
65364 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
65398 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
65430 GGGA
1 GGGA
65434 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:66429 original size:15 final size:15
Alignment explanation
Indices: 66407--66450 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
66397 GATGATGGTG
66407 AAGGAAGAAGAAGAA
1 AAGGAAGAAGAAGAA
*
66422 AGGGAAG-AGAAGAA
1 AAGGAAGAAGAAGAA
**
66436 AAACAAGAAGAAGAA
1 AAGGAAGAAGAAGAA
66451 GAATGAGGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (15 bp):
AAGGAAGAAGAAGAA
Found at i:68260 original size:34 final size:30
Alignment explanation
Indices: 68222--68290 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
68212 TTGATATAAC
68222 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTA
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTA
* *
68256 AATTT-ACAATATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTA
68285 AATTTA
1 AATTTA
68291 TTCAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 9 0.28
30 12 0.38
31 5 0.16
33 1 0.03
34 5 0.16
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTA
Found at i:68405 original size:21 final size:20
Alignment explanation
Indices: 68379--68457 Score: 78
Period size: 21 Copynumber: 4.1 Consensus size: 20
68369 TTCAAGATTG
68379 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGA-TCCCC
*
68400 CCCAGGGGGTACAGAT--AC
1 CCCAGGGGGTACAGATCCCC
*
68418 CCC---GGGTACAGATACCC
1 CCCAGGGGGTACAGATCCCC
*
68435 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGA-TCCCC
68456 CC
1 CC
68458 TGACTAAAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 10 0.21
17 4 0.08
18 4 0.08
20 9 0.19
21 21 0.44
ACGTcount: A:0.20, C:0.39, G:0.28, T:0.13
Consensus pattern (20 bp):
CCCAGGGGGTACAGATCCCC
Found at i:68426 original size:15 final size:15
Alignment explanation
Indices: 68406--68435 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
68396 CCCCCCCAGG
68406 GGGTACAGATACCCC
1 GGGTACAGATACCCC
68421 GGGTACAGATACCCC
1 GGGTACAGATACCCC
68436 CCAGGGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:68443 original size:35 final size:36
Alignment explanation
Indices: 68385--68455 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
68375 ATTGCCCAGG
*
68385 GGGTACAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATTACCCCCCAGGGGGTACAGATACCCC
* *
68421 GGGTACAGA-TACCCCCCAGGGGGTACCGATTCCCC
1 GGGTACAGATTACCCCCCAGGGGGTACAGATACCCC
68456 CCTGACTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 23 0.72
36 9 0.28
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.14
Consensus pattern (36 bp):
GGGTACAGATTACCCCCCAGGGGGTACAGATACCCC
Found at i:68523 original size:20 final size:21
Alignment explanation
Indices: 68483--68526 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
68473 AATAGAATGT
68483 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
68504 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
68525 CC
1 CC
68527 TGTTCAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.45, G:0.27, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:68588 original size:21 final size:21
Alignment explanation
Indices: 68562--68603 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
68552 ATTTGAATAT
*
68562 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
68583 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
68604 CCCATTATGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:68666 original size:21 final size:21
Alignment explanation
Indices: 68632--68671 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
68622 TTTGAGTAGA
*
68632 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
68654 AAAAT-ATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
68672 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:68925 original size:34 final size:32
Alignment explanation
Indices: 68886--68955 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
68876 TTTTGTAAAG
* *
68886 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
68920 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
68952 GGGA
1 GGGA
68956 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:70423 original size:7 final size:7
Alignment explanation
Indices: 70411--70435 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
70401 TTTTCGAAAC
70411 TTATATA
1 TTATATA
70418 TTATATA
1 TTATATA
70425 TTATATA
1 TTATATA
70432 TTAT
1 TTAT
70436 TCCAAGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATATA
Found at i:70497 original size:38 final size:37
Alignment explanation
Indices: 70455--70554 Score: 123
Period size: 38 Copynumber: 2.7 Consensus size: 37
70445 ATTTAAAAAC
* *
70455 TATATATACGTTTTCAAAATATGTTTTCAAAACTATA
1 TATATATACGTTTTCAAAATATGTTTTCAAAACAAGA
* * * *
70492 TTATATATATGTTTTTAAAAAATGTTTTTAAAACAAGA
1 -TATATATACGTTTTCAAAATATGTTTTCAAAACAAGA
70530 TAT-TATACGTTTTCAAAAT-TGTTTT
1 TATATATACGTTTTCAAAATATGTTTT
70555 ATATATGTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
35 6 0.11
36 13 0.25
37 3 0.06
38 31 0.58
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (37 bp):
TATATATACGTTTTCAAAATATGTTTTCAAAACAAGA
Found at i:70524 original size:12 final size:13
Alignment explanation
Indices: 70500--70524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
70490 TATTATATAT
70500 ATGTTTTTAAAAA
1 ATGTTTTTAAAAA
70513 ATGTTTTTAAAA
1 ATGTTTTTAAAA
70525 CAAGATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
ATGTTTTTAAAAA
Found at i:70615 original size:60 final size:61
Alignment explanation
Indices: 70478--70615 Score: 176
Period size: 60 Copynumber: 2.3 Consensus size: 61
70468 TCAAAATATG
* * *
70478 TTTTCAAAACTATATTATATATATGTTTTTAAAAAATGTTTTTAAAACAAGATATTATACG
1 TTTTCAAAAATATATTTTATATATGTTTTTAAAAAATGTTTTTAAAACAAGATATTATACA
* * * *
70539 TTTTC-AAAAT-TGTTTTATATATGTTTTTTCAAAAATGTTTTTAAAACCATATA-TATACA
1 TTTTCAAAAATATATTTTATATATG-TTTTTAAAAAATGTTTTTAAAACAAGATATTATACA
70598 TTTTCAAAAATAT-TTTTA
1 TTTTCAAAAATATATTTTA
70616 AAACCATATA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
59 21 0.31
60 40 0.60
61 6 0.09
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (61 bp):
TTTTCAAAAATATATTTTATATATGTTTTTAAAAAATGTTTTTAAAACAAGATATTATACA
Found at i:70642 original size:35 final size:35
Alignment explanation
Indices: 70564--70681 Score: 123
Period size: 34 Copynumber: 3.3 Consensus size: 35
70554 TATATATGTT
* *
70564 TTTTCAAAAATGTTTTTAAAACCATATA-TATACA
1 TTTTAAAAAATATTTTTAAAACCATATATTATACA
*
70598 TTTTCAAAAATATTTTTAAAACCATATATTATAC-
1 TTTTAAAAAATATTTTTAAAACCATATATTATACA
* * *
70632 TTCTTAAAAAATAAGTTTTCAAAAACTATATATTATATA
1 TT-TTAAAAAAT-A-TTTT-TAAAACCATATATTATACA
*
70671 TTTTTAAAAAT
1 TTTTAAAAAAT
70682 TATATTTGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
34 29 0.40
35 13 0.18
36 1 0.01
37 4 0.06
38 23 0.32
39 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (35 bp):
TTTTAAAAAATATTTTTAAAACCATATATTATACA
Found at i:85504 original size:22 final size:22
Alignment explanation
Indices: 85478--85557 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 22
85468 ATAGGGCAGA
*
85478 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
85500 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
85523 GGGAACCGTTTCCCCC-T--AG
1 GGGAACCGATACCCCCTTGAAG
*
85542 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
85558 CTGGGGTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 15 0.29
21 1 0.02
22 14 0.27
23 21 0.41
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.19
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:85520 original size:23 final size:23
Alignment explanation
Indices: 85478--85539 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
85468 ATAGGGCAGA
* *
85478 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
85500 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
85523 GGGAACCGTTTCCCCCT
1 GGGAACCGATTCCCCCT
85540 AGGGGAATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:102480 original size:159 final size:158
Alignment explanation
Indices: 102190--102504 Score: 589
Period size: 159 Copynumber: 2.0 Consensus size: 158
102180 TTTTTGTGCA
102190 TAACTTATTCTCTAGAAACATTTTAAAAGGGAAGTGTTCTGCATTTATATTTCTATTATTAGGCT
1 TAACTTATTCTCTAGAAACATTTTAAAAGGGAAGTGTTCTGCATTTATATTTCTATTATTAGGCT
102255 AGAATTATGGCATGATCTTGGGCACCACACAGTCCAACGTGATAGTTTCTAGAAGGTCCAATCAG
66 AGAATTATGGCATGATCTTGGGCACCACACAGTCCAACGTGATAGTTTCTAGAAGGTCCAATCAG
102320 CAGC-AC-ACAGTTTCTGTAAGGTCAAG
131 CAGCAACAACAGTTTCTGTAAGGTCAAG
102346 TAACTTATTCTCTAGAAACAATTTTAAAAGGGAAGTGTTCTGCATTTTATATTTCTATTATTATG
1 TAACTTATTCTCTAGAAAC-ATTTTAAAAGGGAAGTGTTCTGCA-TTTATATTTCTATTATTA-G
102411 GCTAGAATTATGGCATGATCTTGGGCACCACACAGTCCAACGTGATAGTTTCTAGAAGGTCCAAT
63 GCTAGAATTATGGCATGATCTTGGGCACCACACAGTCCAACGTGATAGTTTCTAGAAGGTCCAAT
102476 CAGCAGCAACAACAGTTTCTGTAAGGTCA
128 CAGCAGCAACAACAGTTTCTGTAAGGTCA
102505 TGTCAGTACT
Statistics
Matches: 154, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
156 19 0.12
157 24 0.16
158 18 0.12
159 73 0.47
160 2 0.01
161 18 0.12
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (158 bp):
TAACTTATTCTCTAGAAACATTTTAAAAGGGAAGTGTTCTGCATTTATATTTCTATTATTAGGCT
AGAATTATGGCATGATCTTGGGCACCACACAGTCCAACGTGATAGTTTCTAGAAGGTCCAATCAG
CAGCAACAACAGTTTCTGTAAGGTCAAG
Found at i:106489 original size:18 final size:18
Alignment explanation
Indices: 106466--106510 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
106456 TATTACTAAC
106466 TTGATGTTCGGTTTCATT
1 TTGATGTTCGGTTTCATT
106484 TTGATGTTCGGTTTCATT
1 TTGATGTTCGGTTTCATT
*
106502 TAGATGTTC
1 TTGATGTTC
106511 TTACAAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.11, G:0.22, T:0.53
Consensus pattern (18 bp):
TTGATGTTCGGTTTCATT
Found at i:111862 original size:24 final size:20
Alignment explanation
Indices: 111809--111866 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
111799 TTCCCATTGA
*
111809 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
111829 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
111852 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
111867 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:115867 original size:20 final size:22
Alignment explanation
Indices: 115842--115901 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 22
115832 TTCCCATTGA
115842 AGTGCATCGATGCACTC-TT-C
1 AGTGCATCGATGCACTCTTTAC
*
115862 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCACTCTTT-AC
115885 ATGTGCATCGATGCACT
1 A-GTGCATCGATGCACT
115902 ACCAGGCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.47
21 2 0.06
23 2 0.06
24 14 0.41
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
AGTGCATCGATGCACTCTTTAC
Found at i:119895 original size:3 final size:3
Alignment explanation
Indices: 119857--119914 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
119847 GTTCTGCTCA
* * * * *
119857 AAT AAT AAA AAT ATT AAT ACT AAT ACT AAG AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
119905 AAT AAT AAT A
1 AAT AAT AAT A
119915 TCGGAACGAA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:129049 original size:21 final size:21
Alignment explanation
Indices: 129023--129085 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
129013 ATTATCAAAT
*
129023 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
129044 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
129065 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
129086 CAATACGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.51, C:0.25, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:129100 original size:42 final size:41
Alignment explanation
Indices: 129023--129102 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 41
129013 ATTATCAAAT
*
129023 AAACTTGACATCCATAACAACAAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAACAAAC-TGAAATCCATAACAAC
*
129065 AAACTTGAAATCCATAACAACCAATAC-GAATTCCATAA
1 AAACTTGAAATCCATAACAA-CAA-ACTGAAATCCATAA
129103 TAATAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 29 0.85
43 3 0.09
44 2 0.06
ACGTcount: A:0.50, C:0.25, G:0.05, T:0.20
Consensus pattern (41 bp):
AAACTTGAAATCCATAACAACAAACTGAAATCCATAACAAC
Found at i:134208 original size:16 final size:16
Alignment explanation
Indices: 134187--134221 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
134177 CCGTATCTCG
134187 TTGACTCATCCGATAC
1 TTGACTCATCCGATAC
134203 TTGACTCATCCGATAC
1 TTGACTCATCCGATAC
134219 TTG
1 TTG
134222 CTTTAGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (16 bp):
TTGACTCATCCGATAC
Found at i:135007 original size:9 final size:10
Alignment explanation
Indices: 134986--135010 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
134976 CATCTTTGAG
134986 TTTTAAGCTT
1 TTTTAAGCTT
134996 TTTTAAGCTT
1 TTTTAAGCTT
135006 TTTTA
1 TTTTA
135011 TCATCTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (10 bp):
TTTTAAGCTT
Found at i:139924 original size:26 final size:26
Alignment explanation
Indices: 139895--139948 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
139885 AGTAAGAATT
139895 TTCGGGCTCAAAATGTAATTTCTGGG
1 TTCGGGCTCAAAATGTAATTTCTGGG
139921 TTCGGGCTCAAAATGTAATTTCTGGG
1 TTCGGGCTCAAAATGTAATTTCTGGG
139947 TT
1 TT
139949 GTGTGCATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (26 bp):
TTCGGGCTCAAAATGTAATTTCTGGG
Found at i:141383 original size:2 final size:2
Alignment explanation
Indices: 141376--141403 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
141366 AATGTATGTG
141376 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
141404 GTGTGTGTGT
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:141678 original size:16 final size:16
Alignment explanation
Indices: 141657--141689 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
141647 TGCATGATCA
141657 CAATAATTCCCTTAAG
1 CAATAATTCCCTTAAG
141673 CAATAATTCCCTTAAG
1 CAATAATTCCCTTAAG
141689 C
1 C
141690 TATCTTAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.30
Consensus pattern (16 bp):
CAATAATTCCCTTAAG
Found at i:144334 original size:53 final size:53
Alignment explanation
Indices: 144276--144379 Score: 181
Period size: 53 Copynumber: 2.0 Consensus size: 53
144266 ATTTAGAATG
* *
144276 CTTAGACATTTGAGCAGAAGCTAAACAAAGACTGTTTAAGGTACAAAGAAATA
1 CTTAGACATTTGAGCAGAAGCTAAACAAAAACTGTATAAGGTACAAAGAAATA
*
144329 CTTAGACATTTGAGCAGAAGCTAAACAAAAATTGTATAAGGTACAAAGAAA
1 CTTAGACATTTGAGCAGAAGCTAAACAAAAACTGTATAAGGTACAAAGAAA
144380 GAGGAGGACG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.22
Consensus pattern (53 bp):
CTTAGACATTTGAGCAGAAGCTAAACAAAAACTGTATAAGGTACAAAGAAATA
Found at i:146799 original size:83 final size:83
Alignment explanation
Indices: 146671--146915 Score: 194
Period size: 82 Copynumber: 3.0 Consensus size: 83
146661 AATAAACACA
* * * * * ** *
146671 GCTAAAGTATTATTCCGTTGCGGCGCTTGTTG-AGAAAACATCACTATAAATAAACTCTATTACA
1 GCTAAAGTACTACTCTGTTGCGACGTTTGTTGAAG-AAACGCCACTATAGATAAACTCTATTACA
*
146735 GTGTTTGTATAAAAACTCC
65 GTGTTTGTATAAAAACGCC
*** * *
146754 GC-AAACGTACTACTCTGTTGCGGTTTTTGTTGAA-AACACGCCACTATAGATTAA-TCCTATTG
1 GCTAAA-GTACTACTCTGTTGCGACGTTTGTTGAAGAA-ACGCCACTATAGATAAACT-CTATTA
* * *
146816 CGGTGTTTTTGTAAAAA-GCC
63 CAGTGTTTGTATAAAAACGCC
* * * * * * *
146836 GCTAAATTACTACTTTGTTGCGACGTTTGTTGAAGAAATGTCATTATAGATGAACCCTATTACAG
1 GCTAAAGTACTACTCTGTTGCGACGTTTGTTGAAGAAACGCCACTATAGATAAACTCTATTACAG
*
146901 CGTTTGTATAAAAAC
66 TGTTTGTATAAAAAC
146916 ACAGTTACAG
Statistics
Matches: 124, Mismatches: 30, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
82 64 0.52
83 59 0.48
84 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (83 bp):
GCTAAAGTACTACTCTGTTGCGACGTTTGTTGAAGAAACGCCACTATAGATAAACTCTATTACAG
TGTTTGTATAAAAACGCC
Found at i:146913 original size:82 final size:83
Alignment explanation
Indices: 146712--146915 Score: 198
Period size: 82 Copynumber: 2.5 Consensus size: 83
146702 GAGAAAACAT
* * * * *
146712 CACTATAAATAAACTCTATTACAGTGTTTGTATAAAAACTCCGCAAACGTACTACTCTGTTGCGG
1 CACTATAGATGAACCCTATTACAGTGTTTGTATAAAAACGCCGCAAACGTACTACTCTGTTGCGA
**
146777 TTTTTGTTGAAAACACGC
66 CGTTTGTTGAAAACACGC
* * * * * * * *
146795 CACTATAGATTAATCCTATTGCGGTGTTTTTGTAAAAA-GCCGCTAAA-TTACTACTTTGTTGCG
1 CACTATAGATGAACCCTATTACAGTGTTTGTATAAAAACGCCGC-AAACGTACTACTCTGTTGCG
* *
146858 ACGTTTGTTGAAGAA-ATGT
65 ACGTTTGTTGAA-AACACGC
* *
146877 CATTATAGATGAACCCTATTACAGCGTTTGTATAAAAAC
1 CACTATAGATGAACCCTATTACAGTGTTTGTATAAAAAC
146916 ACAGTTACAG
Statistics
Matches: 94, Mismatches: 24, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
82 59 0.63
83 35 0.37
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (83 bp):
CACTATAGATGAACCCTATTACAGTGTTTGTATAAAAACGCCGCAAACGTACTACTCTGTTGCGA
CGTTTGTTGAAAACACGC
Found at i:150315 original size:16 final size:16
Alignment explanation
Indices: 150291--150331 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
150281 ATGGACGAAA
*
150291 CTCCACCCGACCTCCG
1 CTCCCCCCGACCTCCG
*
150307 CTCCCCCCGACCTCTG
1 CTCCCCCCGACCTCCG
150323 CTCCCCCCG
1 CTCCCCCCG
150332 GTGACCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.07, C:0.66, G:0.12, T:0.15
Consensus pattern (16 bp):
CTCCCCCCGACCTCCG
Done.