Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003694.1 Hibiscus syriacus cultivar Beakdansim tig00007895_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: 787758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:2467 original size:22 final size:20
Alignment explanation
Indices: 2437--2492 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
2427 TTGTTAGTTG
2437 TTATTTTATTTA-TTATTTACA
1 TTATTTTATTTATTTA-TTA-A
*
2458 TATTTTTTATTTATTTATTAA
1 T-TATTTTATTTATTTATTAA
2479 TTATTTTATTTATT
1 TTATTTTATTTATT
2493 CGTTTGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 12 0.39
21 3 0.10
22 13 0.42
23 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTATTTATTTATTAA
Found at i:14055 original size:105 final size:104
Alignment explanation
Indices: 13633--14356 Score: 696
Period size: 105 Copynumber: 7.0 Consensus size: 104
13623 TCGTGCCACT
* *
13633 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTTCCAAT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAA-TTTCCCAG
* ** * * *
13698 TTCAAAGCTGATTTCAACTCCAC-GACGGAGGATATCGTGCTACC
64 TTCAGAGCCAATTTCAACTTCACAG-CGAAGGATAT--TG-GACC
*
13742 CAAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAACAA-TTCCCAGCT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAG-T
* *
13806 TCAG-GACCAATTTCAACTTCACAACGGAGGATATTGGACC
65 TCAGAG-CCAATTTCAACTTCACAGCGAAGGATATTGGACC
* * * **
13846 CAAGACAGCACAAGCTCAACTTCACAGCGAAAGGG-CGGCTGACTGTCAACAAACAATTT--C-G
1 CAAGACAACACAAGTTCAACTTCACAACG-AAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAG
* * * *
13907 ----GAGCCAATCTCAACTTCACAACGAATGATATTGGACT
64 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
* *
13944 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAACAATTTCCCAGTT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAGTT
* * *
14009 CCAGGGCCAGTTTCAACTTCATAGCGAAGGATATTGGACC
66 -CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
* * * * **
14049 CAAGACAGCACAAGCTCAACTTCGCAGCGAAAGGG-CGGCTGACTGTCAACAAACAATTT--C-G
1 CAAGACAACACAAGTTCAACTTCACAACG-AAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAG
* * * *
14110 ----GAGCCAATCTCAACTTCACAACGAAGTATATTGGACT
64 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
* *
14147 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAACAATTTCCCAGTT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAGTT
* * *
14212 CCAGGGCCAGTTTCAACTTCATAGCGAAGGATATTGGACC
66 -CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
* * * * * ** * *
14252 CAAGACAGCACAAGCTCAACTTCGCAGCGAAGGGGCGGCTGACTGTCAATAAACAATTTCCCGGT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTCCCAGT
* *
14317 TCCAGAACCAATCTCAACTTCACAGC-AGAGGATATTGGAC
65 T-CAGAGCCAATTTCAACTTCACAGCGA-AGGATATTGGAC
14357 TCAGAACAAT
Statistics
Matches: 507, Mismatches: 79, Indels: 61
0.78 0.12 0.09
Matches are distributed among these distances:
97 26 0.05
98 134 0.26
99 3 0.01
100 2 0.00
103 2 0.00
104 43 0.08
105 149 0.29
106 67 0.13
107 27 0.05
108 5 0.01
109 49 0.10
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (104 bp):
CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAGTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
Found at i:14068 original size:203 final size:203
Alignment explanation
Indices: 13744--14311 Score: 1007
Period size: 203 Copynumber: 2.8 Consensus size: 203
13734 GTGCTACCCA
* *
13744 AGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAACAA-TTCCCAGCTT-
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAACAATTTCCCAG-TTC
* * * * * *
13807 CAGGACCAATTTCAACTTCACAACGGAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACA
65 CAGGGCCAGTTTCAACTTCATAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCGCA
13872 GCGAAAGGGCGGCTGACTGTCAACAAACAATTTCGGAGCCAATCTCAACTTCACAACGAA-TGAT
130 GCGAAAGGGCGGCTGACTGTCAACAAACAATTTCGGAGCCAATCTCAACTTCACAACGAAGT-AT
13936 ATTGGACTCG
194 ATTGGACTCG
13946 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAACAATTTCCCAGTTCC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAACAATTTCCCAGTTCC
14011 AGGGCCAGTTTCAACTTCATAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCGCAG
66 AGGGCCAGTTTCAACTTCATAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCGCAG
14076 CGAAAGGGCGGCTGACTGTCAACAAACAATTTCGGAGCCAATCTCAACTTCACAACGAAGTATAT
131 CGAAAGGGCGGCTGACTGTCAACAAACAATTTCGGAGCCAATCTCAACTTCACAACGAAGTATAT
14141 TGGACTCG
196 TGGACTCG
14149 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAACAATTTCCCAGTTCC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAACAATTTCCCAGTTCC
14214 AGGGCCAGTTTCAACTTCATAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCGCAG
66 AGGGCCAGTTTCAACTTCATAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCGCAG
* *
14279 CGAAGGGGCGGCTGACTGTCAATAAACAATTTC
131 CGAAAGGGCGGCTGACTGTCAACAAACAATTTC
14312 CCGGTTCCAG
Statistics
Matches: 353, Mismatches: 10, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
202 53 0.15
203 299 0.85
204 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (203 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAACAATTTCCCAGTTCC
AGGGCCAGTTTCAACTTCATAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCGCAG
CGAAAGGGCGGCTGACTGTCAACAAACAATTTCGGAGCCAATCTCAACTTCACAACGAAGTATAT
TGGACTCG
Found at i:16127 original size:4 final size:4
Alignment explanation
Indices: 16118--16243 Score: 62
Period size: 4 Copynumber: 30.5 Consensus size: 4
16108 TACATATTCT
* * *
16118 TTTA TTTA TTTCA TTTA TTCA CTTAA TTTTA TTTA TTTA TTT- TTT- TTTC
1 TTTA TTTA TTT-A TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
* * * * **
16167 TCTTG TCTA GTT- GTTA TTTA TTTA TTTA TTTA TTTACA TACA TTT- TTTA
1 T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT--A TTTA TTTA TTTA
*
16216 CTTTA TTTA TTTA ATTA TTTTA TTTA TT
1 -TTTA TTTA TTTA TTTA -TTTA TTTA TT
16244 CGTTTGTTTT
Statistics
Matches: 96, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
3 12 0.12
4 62 0.65
5 20 0.21
6 2 0.02
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:17840 original size:12 final size:12
Alignment explanation
Indices: 17823--17847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17813 TCTTCGGGGA
17823 CTTTTTCTTCTT
1 CTTTTTCTTCTT
17835 CTTTTTCTTCTT
1 CTTTTTCTTCTT
17847 C
1 C
17848 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:19344 original size:14 final size:14
Alignment explanation
Indices: 19325--19361 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
19315 CATCAATTAA
19325 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
19339 ACAAATCATCTTTT
1 ACAAATCAACATTT
19353 ACAAATCAA
1 ACAAATCAA
19362 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:21267 original size:20 final size:19
Alignment explanation
Indices: 21232--21298 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
21222 GAAACTTAAA
21232 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
21251 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
21271 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
21290 ATCGCAACG
1 ATCGCAACG
21299 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:21306 original size:14 final size:14
Alignment explanation
Indices: 21287--21344 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
21277 ATGCGAAATG
21287 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
21301 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
21317 ATGAAATCACAACGAC
1 A--AAATCGCAACGAC
21333 AAAATCGCAACG
1 AAAATCGCAACG
21345 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:21330 original size:32 final size:33
Alignment explanation
Indices: 21271--21349 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
21261 GGAAATGGCT
* *
21271 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
21304 ATCGCAACGCGAAATG-AAATCACAACGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
21336 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
21350 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGACAAA
Found at i:21378 original size:19 final size:17
Alignment explanation
Indices: 21356--21451 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 17
21346 GAAACACAAA
21356 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
21375 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
21391 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
21407 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
21423 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
*
21440 TTGCATTGCGAT
1 TCGC-TTGCGAT
21452 AGCCATTTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 3 0.05
18 13 0.21
19 16 0.26
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:21397 original size:14 final size:14
Alignment explanation
Indices: 21378--21435 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
21368 TTTCATTTCG
21378 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
21392 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
21408 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
21424 CGTTGCGATTTT
1 CGTTGCGATTTT
21436 CATTTTGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:21408 original size:32 final size:33
Alignment explanation
Indices: 21361--21451 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
21351 ACAAATCGCA
21361 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
21394 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
21426 TTGCGATTTTCATTTTGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
21452 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:21470 original size:20 final size:20
Alignment explanation
Indices: 21445--21490 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
21435 TCATTTTGCA
21445 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
21465 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
21485 TTGCGA
1 TTGCGA
21491 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:21989 original size:18 final size:18
Alignment explanation
Indices: 21963--22007 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
21953 GTCGATCAGA
*
21963 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
21981 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
21999 TGATGGCTC
1 TGATGGCTC
22008 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:23351 original size:20 final size:20
Alignment explanation
Indices: 23326--23363 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23316 AATAGTTTCT
23326 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
23346 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
23364 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:23652 original size:22 final size:22
Alignment explanation
Indices: 23627--23670 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
23617 GATTTAGATA
23627 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
23649 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
23671 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:23883 original size:20 final size:20
Alignment explanation
Indices: 23858--23951 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
23848 GATTATGTAT
23858 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
23878 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
23898 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
23919 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
23939 TATCGCATTGCGA
1 TATCGCGTTGCGA
23952 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:23923 original size:41 final size:42
Alignment explanation
Indices: 23878--24013 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
23868 CGAAAGTCAG
* * * *
23878 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
23919 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
23961 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
24002 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
24014 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:23952 original size:20 final size:20
Alignment explanation
Indices: 23838--23952 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
23828 CGCTTTGAAA
*
23838 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
23859 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
23879 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
23899 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
23920 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
23940 ATCGCATTGCGAT
1 ATCGCATTGCGAT
23953 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:23985 original size:20 final size:20
Alignment explanation
Indices: 23941--24033 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
23931 ATAGTCAGTA
*
23941 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
23962 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
23982 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
24003 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
24023 TCGCATTGCGA
1 TCGCATTGCGA
24034 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:24014 original size:41 final size:41
Alignment explanation
Indices: 23941--24036 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
23931 ATAGTCAGTA
* *
23941 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
23982 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
24023 TCGCATTGCGAATT
1 TCGCATTGCGAATT
24037 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:24487 original size:5 final size:5
Alignment explanation
Indices: 24463--24511 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
24453 GTACGCTCCC
* *
24463 TTTTCA TTTTA -TTCA TTTTA TTTTA --TTA TCTTA TTTTA TTTTA TTTTA
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
24511 T
1 T
24512 CTAATTATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
3 3 0.08
4 3 0.08
5 27 0.73
6 4 0.11
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:24487 original size:14 final size:13
Alignment explanation
Indices: 24463--24502 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
24453 GTACGCTCCC
24463 TTTTCATTTTATTCA
1 TTTT-ATTTTATT-A
24478 TTTTATTTTATTA
1 TTTTATTTTATTA
*
24491 TCTTATTTTATT
1 TTTTATTTTATT
24503 TTATTTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 8 0.33
15 4 0.17
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:24498 original size:13 final size:14
Alignment explanation
Indices: 24468--24502 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
24458 CTCCCTTTTC
*
24468 ATTTTATTCATTTT
1 ATTTTATTCATCTT
24482 ATTTTATT-ATCTT
1 ATTTTATTCATCTT
24495 ATTTTATT
1 ATTTTATT
24503 TTATTTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTATTCATCTT
Found at i:24518 original size:28 final size:27
Alignment explanation
Indices: 24468--24522 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
24458 CTCCCTTTTC
* *
24468 ATTTTATTCATTTTATTTTATTATCTT
1 ATTTTATTCATTTTATCTAATTATCTT
*
24495 ATTTTATTTTATTTTATCTAATTATCTT
1 ATTTTA-TTCATTTTATCTAATTATCTT
24523 TGTCGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (27 bp):
ATTTTATTCATTTTATCTAATTATCTT
Found at i:51430 original size:2 final size:2
Alignment explanation
Indices: 51423--51450 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51413 TTTTCAACCT
51423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51451 ATGCCAATCT
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):
TA
Found at i:57313 original size:96 final size:96
Alignment explanation
Indices: 57129--57315 Score: 250
Period size: 96 Copynumber: 1.9 Consensus size: 96
57119 ACAGGATTTT
* * ** * *
57129 TCAAGCCAGGAGATGAAACTCTTCCTAATTCAGACCCAAATTGTCTTTCTTCAGCACCAAGCGAA
1 TCAAGCCAGGAGACGAAACCCTTCCTAATTCAGACCCAAACAGCCTTTCCTCAGCACCAAGCGAA
* *
57194 GGAAAATCACGTTCGAATTCAGATTTATTAA
66 GGAAAATCACGCTCGAATGCAGATTTATTAA
* * *
57225 TCAAGCCAGGAGACGAAACCCTTCCTACTTCAGACCCTACCAGCCTTTCCTCAGCACCAAGCGAA
1 TCAAGCCAGGAGACGAAACCCTTCCTAATTCAGACCCAAACAGCCTTTCCTCAGCACCAAGCGAA
*
57290 TGAAAATCACGCTCAGAA-GCAGATTT
66 GGAAAATCACGCTC-GAATGCAGATTT
57316 TTCACGGACA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 75 0.96
97 3 0.04
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (96 bp):
TCAAGCCAGGAGACGAAACCCTTCCTAATTCAGACCCAAACAGCCTTTCCTCAGCACCAAGCGAA
GGAAAATCACGCTCGAATGCAGATTTATTAA
Found at i:59626 original size:60 final size:59
Alignment explanation
Indices: 59540--59656 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 59
59530 TTCAAATTCG
** *
59540 TCCTTAAACTTTTAAATGTTCTAATTTCATCCTCAAACTATGACTC-TCATTCTAAATTAA
1 TCCTTAAACTTTTAAACATTCGAATTTCATCCT-AAACTATGAC-CGTCATTCTAAATTAA
* * *
59600 TCCTTAAACTTTTGAACATTCGAATTTCATCCTATACTATGACCGTCTTTCTAAATT
1 TCCTTAAACTTTTAAACATTCGAATTTCATCCTAAACTATGACCGTCATTCTAAATT
59657 GGTCTCCATA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 1 0.02
59 20 0.40
60 29 0.58
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (59 bp):
TCCTTAAACTTTTAAACATTCGAATTTCATCCTAAACTATGACCGTCATTCTAAATTAA
Found at i:60412 original size:2 final size:2
Alignment explanation
Indices: 60405--60432 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60395 TCCACCATTA
60405 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
60433 TGTGGTTATA
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:70525 original size:35 final size:35
Alignment explanation
Indices: 70479--70554 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
70469 AAAACAGTCC
* *
70479 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
70514 TCAATTTCATTCTAAACCCTAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
70549 TCAATT
1 TCAATT
70555 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:71098 original size:130 final size:128
Alignment explanation
Indices: 70940--71201 Score: 407
Period size: 130 Copynumber: 2.0 Consensus size: 128
70930 TTCAATCATT
* * **
70940 ATTATTTATATATAATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTA
1 ATTATTTATATATAATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA
* * *
71005 GGATTTGACATGTGTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
66 GGATCTGACATGTGTTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTA
*
71068 ATTATTTATATATGCTATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAC
1 ATTATTTATATAT--AATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAC
* * *
71133 CAGGATCTGACATGTGTTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTA
64 CAGGATCTGACATGTGTTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTA
71198 ATTA
1 ATTA
71202 GAAGAAAATT
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
128 13 0.11
130 108 0.89
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (128 bp):
ATTATTTATATATAATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA
GGATCTGACATGTGTTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTA
Found at i:71780 original size:22 final size:21
Alignment explanation
Indices: 71755--71814 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
71745 AATATACATT
* *
71755 TATATAAATATATTTTTATTCA
1 TATATAAA-ATATTTTGATTAA
*
71777 TATATTGAAATATTTTGATTAA
1 TATA-TAAAATATTTTGATTAA
*
71799 AATATAAACATATTTT
1 TATATAAA-ATATTTT
71815 AAATACTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 3 0.10
22 25 0.81
23 3 0.10
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
TATATAAAATATTTTGATTAA
Found at i:73912 original size:24 final size:24
Alignment explanation
Indices: 73884--73939 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
73874 CGTGAGCATA
73884 TTCGTTTATATATTCATCAACATG
1 TTCGTTTATATATTCATCAACATG
*
73908 TTCGTTTATATATTCGTCAACATG
1 TTCGTTTATATATTCATCAACATG
73932 TTCGTTTA
1 TTCGTTTA
73940 ATGTTTGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (24 bp):
TTCGTTTATATATTCATCAACATG
Found at i:75928 original size:27 final size:27
Alignment explanation
Indices: 75898--75956 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
75888 TATAATAATA
* *
75898 TTAATAATATATGTATATCT-AATTTTT
1 TTAATAA-ACATGTATATCTAAACTTTT
*
75925 TTAAT-AGCATGTATATCTAAACTTTT
1 TTAATAAACATGTATATCTAAACTTTT
75951 TTAATA
1 TTAATA
75957 GTAAAGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 10 0.37
26 12 0.44
27 5 0.19
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (27 bp):
TTAATAAACATGTATATCTAAACTTTT
Found at i:75942 original size:25 final size:26
Alignment explanation
Indices: 75908--75957 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
75898 TTAATAATAT
*
75908 ATGTATATCT-AATTTTTTTAATAGC
1 ATGTATATCTAAACTTTTTTAATAGC
75933 ATGTATATCTAAACTTTTTTAATAG
1 ATGTATATCTAAACTTTTTTAATAG
75958 TAAAGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (26 bp):
ATGTATATCTAAACTTTTTTAATAGC
Found at i:76362 original size:12 final size:12
Alignment explanation
Indices: 76345--76371 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
76335 ACACAATTTC
76345 TTCCTTATTAAT
1 TTCCTTATTAAT
76357 TTCCTTATTAAT
1 TTCCTTATTAAT
76369 TTC
1 TTC
76372 ACAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (12 bp):
TTCCTTATTAAT
Found at i:79026 original size:43 final size:43
Alignment explanation
Indices: 78960--79065 Score: 176
Period size: 43 Copynumber: 2.5 Consensus size: 43
78950 ATGGAGAGTT
* * *
78960 GATATGTAGATAAATATTCCTACAGTCTTCCAAAACGTGGCTG
1 GATAAGTAGATAAATATTTCTACAGTCTCCCAAAACGTGGCTG
79003 GATAAGTAGATAAATATTTCTACAGTCTCCCAAAACGTGGCTG
1 GATAAGTAGATAAATATTTCTACAGTCTCCCAAAACGTGGCTG
*
79046 GATAAGTAGATATATATTTC
1 GATAAGTAGATAAATATTTC
79066 ACCCTGCAGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (43 bp):
GATAAGTAGATAAATATTTCTACAGTCTCCCAAAACGTGGCTG
Found at i:80989 original size:81 final size:80
Alignment explanation
Indices: 80832--80989 Score: 192
Period size: 80 Copynumber: 2.0 Consensus size: 80
80822 CGCTTTGGTT
* * *
80832 TTGTTAACCGAGATGGGCTATCACGTCCACAGTGAACGGCGTAGGGTTTGTCAGGTGTTTCTTGG
1 TTGTTAACCGAGATGGGCTATCACGTCCACAGTGAACGGAGTAAGGTTTGTCAGGTATTTCTTGG
80897 TTCATACGCATCCCC
66 TTCATACGCATCCCC
* * * * ** *
80912 TTGTTAACTGAGATGGGCTGTCACGTCCATAGTTATTGAGAGTAAGGTTTGTCTA-TTATTTCTT
1 TTGTTAACCGAGATGGGCTATCACGTCCACAGTGAACG-GAGTAAGGTTTGTC-AGGTATTTCTT
*
80976 GGTTCCTACGCATC
64 GGTTCATACGCATC
80990 TCCTATCAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
80 32 0.49
81 32 0.49
82 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (80 bp):
TTGTTAACCGAGATGGGCTATCACGTCCACAGTGAACGGAGTAAGGTTTGTCAGGTATTTCTTGG
TTCATACGCATCCCC
Found at i:81242 original size:29 final size:29
Alignment explanation
Indices: 81209--81266 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
81199 TAATAGCACC
*
81209 GGTTTTTGGATAACTTTGTTCATTCCGGT
1 GGTTTTTGAATAACTTTGTTCATTCCGGT
81238 GGTTTTTGAATAACTTTGTTCATTCCGGT
1 GGTTTTTGAATAACTTTGTTCATTCCGGT
81267 CTGCACACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.48
Consensus pattern (29 bp):
GGTTTTTGAATAACTTTGTTCATTCCGGT
Found at i:81882 original size:33 final size:33
Alignment explanation
Indices: 81831--81894 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
81821 TCACCTACTA
*
81831 AAGATGAATTTTTCAATAAATTGACTACCAATC
1 AAGATGAATTTCTCAATAAATTGACTACCAATC
* *
81864 AAGATGAAATTTCT-AATAAGTTGGCTACCAA
1 AAGATG-AATTTCTCAATAAATTGACTACCAA
81895 CTAAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (33 bp):
AAGATGAATTTCTCAATAAATTGACTACCAATC
Found at i:81918 original size:9 final size:9
Alignment explanation
Indices: 81904--81968 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
81894 ACTAAAAATT
81904 TCAACTTTA
1 TCAACTTTA
81913 TCAAC-TT-
1 TCAACTTTA
*
81920 TCAACTTTG
1 TCAACTTTA
81929 TCAACTTT-
1 TCAACTTTA
81937 T-AACTTTGA
1 TCAACTTT-A
81946 -CAACTTTA
1 TCAACTTTA
*
81954 --AACTTTG
1 TCAACTTTA
81961 TCAACTTT
1 TCAACTTT
81969 CAAGCCAAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
7 17 0.35
8 6 0.12
9 25 0.52
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.45
Consensus pattern (9 bp):
TCAACTTTA
Found at i:81923 original size:16 final size:16
Alignment explanation
Indices: 81902--81971 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
81892 CAACTAAAAA
81902 TTTCAACTTTATCAAC
1 TTTCAACTTTATCAAC
*
81918 TTTCAACTTTGTCAAC
1 TTTCAACTTTATCAAC
*
81934 TTTTAACTTTGA-CAAC
1 TTTCAACTTT-ATCAAC
* *
81950 TTTAAACTTTGTCAAC
1 TTTCAACTTTATCAAC
81966 TTTCAA
1 TTTCAA
81972 GCCAAACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.44
Consensus pattern (16 bp):
TTTCAACTTTATCAAC
Found at i:81942 original size:32 final size:32
Alignment explanation
Indices: 81906--81968 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
81896 TAAAAATTTC
*
81906 AACTTT-ATCAACTTTCAACTTTGTCAACTTTT
1 AACTTTGA-CAACTTTAAACTTTGTCAACTTTT
81938 AACTTTGACAACTTTAAACTTTGTCAACTTT
1 AACTTTGACAACTTTAAACTTTGTCAACTTT
81969 CAAGCCAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (32 bp):
AACTTTGACAACTTTAAACTTTGTCAACTTTT
Found at i:83348 original size:17 final size:17
Alignment explanation
Indices: 83305--83350 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
83295 ATTTTTTTAA
83305 AATTCGG-TTAACGGTT
1 AATTCGGTTTAACGGTT
* *
83321 AA-TCGATTTTAATGGTT
1 AATTCG-GTTTAACGGTT
83338 AATTCGGTTTAAC
1 AATTCGGTTTAAC
83351 CGAATTAACC
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
15 3 0.13
16 2 0.09
17 15 0.65
18 3 0.13
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (17 bp):
AATTCGGTTTAACGGTT
Found at i:83404 original size:11 final size:11
Alignment explanation
Indices: 83388--83415 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
83378 TAAGAGGCCT
83388 AATCCATTTAA
1 AATCCATTTAA
83399 AATCCATTTAA
1 AATCCATTTAA
83410 AATCCA
1 AATCCA
83416 AATCAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (11 bp):
AATCCATTTAA
Found at i:83516 original size:20 final size:17
Alignment explanation
Indices: 83475--83508 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
83465 TGAATCAAAT
*
83475 TAATTAGATATTATTTA
1 TAATTAGATATTATTAA
83492 TAATTAGATATTATTAA
1 TAATTAGATATTATTAA
83509 AACTAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TAATTAGATATTATTAA
Found at i:83866 original size:18 final size:18
Alignment explanation
Indices: 83827--83862 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
83817 TGATTATATG
83827 ATAATTATAAATTGTTTT
1 ATAATTATAAATTGTTTT
83845 ATAATTATAAATT-TTTT
1 ATAATTATAAATTGTTTT
83862 A
1 A
83863 ATAAGAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATAATTATAAATTGTTTT
Found at i:85388 original size:23 final size:23
Alignment explanation
Indices: 85355--85403 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
85345 ATGTTGAAAA
* *
85355 GTCAAAATTTTCATCTTAGAATG
1 GTCAAAATTTTCAGCTTACAATG
*
85378 GTCAAAGTTTTCAGCTTACAATG
1 GTCAAAATTTTCAGCTTACAATG
85401 GTC
1 GTC
85404 CAATTTTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (23 bp):
GTCAAAATTTTCAGCTTACAATG
Found at i:94343 original size:16 final size:16
Alignment explanation
Indices: 94322--94355 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
94312 TTACTATTCA
*
94322 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
94338 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
94354 CG
1 CG
94356 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:115520 original size:4 final size:4
Alignment explanation
Indices: 115511--115559 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
115501 AAAGGTACAA
115511 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
115559 A
1 A
115560 GTATTTGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:117695 original size:34 final size:34
Alignment explanation
Indices: 117625--117695 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
117615 TGCTATAAAA
* * *
117625 TTTTCTATTATTAATCTATTTTAATATTTTATAT
1 TTTTCTATTAATAATCTATTTTAATATTTCAAAT
*
117659 TTTTTTATTAATAATCTATTTTTAAT-TTTCAAAT
1 TTTTCTATTAATAATCTA-TTTTAATATTTCAAAT
117693 TTT
1 TTT
117696 ATAATTTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 25 0.78
35 7 0.22
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (34 bp):
TTTTCTATTAATAATCTATTTTAATATTTCAAAT
Found at i:118404 original size:112 final size:112
Alignment explanation
Indices: 118202--118419 Score: 418
Period size: 112 Copynumber: 1.9 Consensus size: 112
118192 TGTTTCGCAT
*
118202 CAGTTACTCGCTTCTAATTGGTTATTTAATGCCACGTCACCTCCCCTGCAACCTCATTCATCTAT
1 CAGTGACTCGCTTCTAATTGGTTATTTAATGCCACGTCACCTCCCCTGCAACCTCATTCATCTAT
118267 AAAACACTTGATCCAAAAGAGAATAAAATATCAAATAACTCAAACAC
66 AAAACACTTGATCCAAAAGAGAATAAAATATCAAATAACTCAAACAC
118314 CAGTGACTCGCTTCTAATTGGTTATTTAATGCCACGTCACCTCCCCTGCAACCTCATTCATCTAT
1 CAGTGACTCGCTTCTAATTGGTTATTTAATGCCACGTCACCTCCCCTGCAACCTCATTCATCTAT
*
118379 AAACCACTTGATCCAAAAGAGAATAAAATATCAAATAACTC
66 AAAACACTTGATCCAAAAGAGAATAAAATATCAAATAACTC
118420 TTCCACCCTT
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 104 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (112 bp):
CAGTGACTCGCTTCTAATTGGTTATTTAATGCCACGTCACCTCCCCTGCAACCTCATTCATCTAT
AAAACACTTGATCCAAAAGAGAATAAAATATCAAATAACTCAAACAC
Found at i:118494 original size:21 final size:21
Alignment explanation
Indices: 118469--118511 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
118459 CTACGGAGTT
118469 GTTTTGCGGTGGACGGACGAC
1 GTTTTGCGGTGGACGGACGAC
118490 GTTTTGCGGTGGACGGACGAC
1 GTTTTGCGGTGGACGGACGAC
118511 G
1 G
118512 ATGAGGGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.44, T:0.23
Consensus pattern (21 bp):
GTTTTGCGGTGGACGGACGAC
Found at i:123014 original size:37 final size:37
Alignment explanation
Indices: 122957--123045 Score: 133
Period size: 37 Copynumber: 2.4 Consensus size: 37
122947 CACCCGCAAT
* * *
122957 GAGAAGATTAATCATGGTTATCGACGATAGATACTCC
1 GAGAAGATTAGTCATAGTTATCAACGATAGATACTCC
*
122994 GAGAAGATTAGTCATAGTTATCAACGATGGATACTCC
1 GAGAAGATTAGTCATAGTTATCAACGATAGATACTCC
*
123031 GAGAATATTAGTCAT
1 GAGAAGATTAGTCAT
123046 GATAATCGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (37 bp):
GAGAAGATTAGTCATAGTTATCAACGATAGATACTCC
Found at i:123061 original size:37 final size:37
Alignment explanation
Indices: 122957--123064 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 37
122947 CACCCGCAAT
* * * * * *
122957 GAGAAGATTAATCATGGTTATCGACGATAGATACTCC
1 GAGAAGATTAGTCATAGTAATCAACAATGGATACTCC
* *
122994 GAGAAGATTAGTCATAGTTATCAACGATGGATACTCC
1 GAGAAGATTAGTCATAGTAATCAACAATGGATACTCC
* **
123031 GAGAATATTAGTCAT-GATAATCGCCAATGGATAC
1 GAGAAGATTAGTCATAG-TAATCAACAATGGATAC
123065 CCTGATTTCA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 1 0.02
37 60 0.98
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (37 bp):
GAGAAGATTAGTCATAGTAATCAACAATGGATACTCC
Found at i:125179 original size:17 final size:17
Alignment explanation
Indices: 125157--125190 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
125147 CGTTAACAAA
125157 AATTAAATCATAGCTTG
1 AATTAAATCATAGCTTG
125174 AATTAAATCATAGCTTG
1 AATTAAATCATAGCTTG
125191 TAAGCAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AATTAAATCATAGCTTG
Found at i:125201 original size:18 final size:17
Alignment explanation
Indices: 125161--125201 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
125151 AACAAAAATT
**
125161 AAATCATAGCTTGAATT
1 AAATCATAGCTTGAAGC
125178 AAATCATAGCTTGTAAGC
1 AAATCATAGCTTG-AAGC
125196 AAATCA
1 AAATCA
125202 AGATCATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (17 bp):
AAATCATAGCTTGAAGC
Found at i:126085 original size:2 final size:2
Alignment explanation
Indices: 126078--126116 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
126068 TAATAGATAA
126078 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
126117 AAACTCACAA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:126672 original size:5 final size:6
Alignment explanation
Indices: 126638--126674 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
126628 CTTGGGCTGC
*
126638 TTTAAA TTTAAA TTTAAA TTTAAA -TCAAA -TTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
126675 TTATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 8 0.29
6 20 0.71
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:131868 original size:2 final size:2
Alignment explanation
Indices: 131861--131885 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
131851 TCATGTGGTC
131861 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 A
131886 CCTTGTTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:138481 original size:2 final size:2
Alignment explanation
Indices: 138474--138503 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
138464 TTTTCCAACG
138474 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
138504 TATTATTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:139324 original size:2 final size:2
Alignment explanation
Indices: 139317--139346 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
139307 GATCATGCAC
139317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
139347 CAACCTACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:139789 original size:10 final size:10
Alignment explanation
Indices: 139774--139827 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
139764 CATTTAAATG
139774 ATAAACGAAC
1 ATAAACGAAC
*
139784 ATAAACGAATATA
1 ATAAACG-A-A-C
*
139797 ATAAACGAAT
1 ATAAACGAAC
139807 ATAAACGAAC
1 ATAAACGAAC
139817 ATAAACGAAC
1 ATAAACGAAC
139827 A
1 A
139828 ACACAAAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 27 0.71
11 2 0.05
12 2 0.05
13 7 0.18
ACGTcount: A:0.61, C:0.15, G:0.09, T:0.15
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:139801 original size:23 final size:23
Alignment explanation
Indices: 139774--139820 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
139764 CATTTAAATG
*
139774 ATAAACGAACATAAACGAATATA
1 ATAAACGAACATAAACGAACATA
*
139797 ATAAACGAATATAAACGAACATA
1 ATAAACGAACATAAACGAACATA
139820 A
1 A
139821 ACGAACAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.13, G:0.09, T:0.17
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACATA
Found at i:139802 original size:13 final size:13
Alignment explanation
Indices: 139784--139810 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
139774 ATAAACGAAC
139784 ATAAACGAATATA
1 ATAAACGAATATA
139797 ATAAACGAATATA
1 ATAAACGAATATA
139810 A
1 A
139811 ACGAACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (13 bp):
ATAAACGAATATA
Found at i:140681 original size:13 final size:13
Alignment explanation
Indices: 140621--140681 Score: 58
Period size: 12 Copynumber: 5.0 Consensus size: 13
140611 TATAGGTTAG
*
140621 TTGAGGCACAATT
1 TTGAGACACAATT
*
140634 TT-AGACACAACT
1 TTGAGACACAATT
* *
140646 TTGAGAAACAA-C
1 TTGAGACACAATT
140658 TTGAG--ACAATT
1 TTGAGACACAATT
140669 TTGAGACACAATT
1 TTGAGACACAATT
140682 CACAAAGTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 4 0.10
11 5 0.13
12 15 0.38
13 15 0.38
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
TTGAGACACAATT
Found at i:141345 original size:34 final size:34
Alignment explanation
Indices: 141302--141403 Score: 204
Period size: 34 Copynumber: 3.0 Consensus size: 34
141292 GTATTGGCAT
141302 AAAGTACTGTTTGCATTATACACAGGTCGTTTGG
1 AAAGTACTGTTTGCATTATACACAGGTCGTTTGG
141336 AAAGTACTGTTTGCATTATACACAGGTCGTTTGG
1 AAAGTACTGTTTGCATTATACACAGGTCGTTTGG
141370 AAAGTACTGTTTGCATTATACACAGGTCGTTTGG
1 AAAGTACTGTTTGCATTATACACAGGTCGTTTGG
141404 CGAAACTCGA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (34 bp):
AAAGTACTGTTTGCATTATACACAGGTCGTTTGG
Found at i:150097 original size:40 final size:40
Alignment explanation
Indices: 150051--150137 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
150041 TATTCCCTGG
150051 TAATCTTTTATTTCAACTGATAATCTTTTATTCCCACTGA
1 TAATCTTTTATTTCAACTGATAATCTTTTATTCCCACTGA
*
150091 TAATCTTTTATTTCCACTGATAATCTTTTATTCCCACTGA
1 TAATCTTTTATTTCAACTGATAATCTTTTATTCCCACTGA
150131 TAATCTT
1 TAATCTT
150138 ACATTCCGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (40 bp):
TAATCTTTTATTTCAACTGATAATCTTTTATTCCCACTGA
Found at i:150144 original size:20 final size:20
Alignment explanation
Indices: 150051--150137 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
150041 TATTCCCTGG
* *
150051 TAATCTTTTATTTCAACTGA
1 TAATCTTTTATTCCCACTGA
150071 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCCCACTGA
*
150091 TAATCTTTTATTTCCACTGA
1 TAATCTTTTATTCCCACTGA
150111 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCCCACTGA
150131 TAATCTT
1 TAATCTT
150138 ACATTCCGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (20 bp):
TAATCTTTTATTCCCACTGA
Found at i:150707 original size:48 final size:48
Alignment explanation
Indices: 150650--150751 Score: 195
Period size: 48 Copynumber: 2.1 Consensus size: 48
150640 TTTAAATATT
*
150650 AATTTTATTTTTAATTAGATTAACGTGATCATAAGTTAATATCTGTTA
1 AATTTTATTTTTAATTAGATTAACGTGATCATAAGATAATATCTGTTA
150698 AATTTTATTTTTAATTAGATTAACGTGATCATAAGATAATATCTGTTA
1 AATTTTATTTTTAATTAGATTAACGTGATCATAAGATAATATCTGTTA
150746 AATTTT
1 AATTTT
150752 TTAAGAGTGC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (48 bp):
AATTTTATTTTTAATTAGATTAACGTGATCATAAGATAATATCTGTTA
Found at i:156137 original size:2 final size:2
Alignment explanation
Indices: 156130--156155 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
156120 ACATACATAC
156130 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
156156 CGCATGGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:162886 original size:183 final size:183
Alignment explanation
Indices: 162540--162886 Score: 527
Period size: 183 Copynumber: 1.9 Consensus size: 183
162530 AGCTCAACTT
* *
162540 AAACCATTTAAAACTCAATTAATAATTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAAT
1 AAACCATTTAAAACTCAATTAATAATTTAAGATCCAATAACTTTAAAACCTAAATCAATATTAAT
* *
162605 CAATTAAAAAAATTATATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTGTAAACT
66 CAATTAAAAAAATTATACAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACT
* *
162670 GTTTTTAATTAAAAAGTGTTAAATATATTATATATAGCATATGGGCTCAGCCC
131 GTTTTTAATTAAAAAATATTAAATATATTATATATAGCATATGGGCTCAGCCC
*
162723 AAACCATTTAAAA-TCCAATTAATAATTTAAGATCCAATAACTTTAAAATCTAAATCAATATTAA
1 AAACCATTTAAAACT-CAATTAATAATTTAAGATCCAATAACTTTAAAACCTAAATCAATATTAA
* ** * *
162787 TTAATTAAAAATTTTATCCGAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAAC
65 TCAATTAAAAAAATTATACAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAAC
* * *
162852 TTTTTTTGAATTAAAAAATATTTAAT-TTTTATATA
130 TGTTTTT-AATTAAAAAATATTAAATATATTATATA
162887 AATTAGAAAA
Statistics
Matches: 147, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
182 1 0.01
183 131 0.89
184 15 0.10
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (183 bp):
AAACCATTTAAAACTCAATTAATAATTTAAGATCCAATAACTTTAAAACCTAAATCAATATTAAT
CAATTAAAAAAATTATACAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACT
GTTTTTAATTAAAAAATATTAAATATATTATATATAGCATATGGGCTCAGCCC
Found at i:171903 original size:76 final size:78
Alignment explanation
Indices: 171786--171933 Score: 237
Period size: 76 Copynumber: 1.9 Consensus size: 78
171776 AACATATCAC
* * *
171786 AAGGAAAACCATTTGCAGTAAACTGAATGGCTTGTGATAATTAAAAACTTAAAAGC-AAAAACCC
1 AAGGAAAACCATTTGCAGTAAACAGAACGGCTTGTGATAATTAAAAAATTAAAAGCAAAAAACCC
171850 AAAAACATGTCCT
66 AAAAACATGTCCT
* *
171863 AAGGAAAA-CATTTGCAGTAAACAGAACGTCTTGTGGTAATTAAAAAATTAAAAGCAAAAAACCC
1 AAGGAAAACCATTTGCAGTAAACAGAACGGCTTGTGATAATTAAAAAATTAAAAGCAAAAAACCC
171927 AAAAACA
66 AAAAACA
171934 GACTGTAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
76 42 0.65
77 23 0.35
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (78 bp):
AAGGAAAACCATTTGCAGTAAACAGAACGGCTTGTGATAATTAAAAAATTAAAAGCAAAAAACCC
AAAAACATGTCCT
Found at i:172359 original size:67 final size:67
Alignment explanation
Indices: 172230--172362 Score: 178
Period size: 67 Copynumber: 2.0 Consensus size: 67
172220 TTAAACACAT
* *
172230 AGTAATAAAGAATGAAAAAAAATAAGCTCAAATATAGTAATAAACATCTATTGACCCGGTTTTCA
1 AGTAATAAAGAATGAAAAAAAATAAGCTCAAATATAGTAATAAACATCTATGGACCCAGTTTTCA
172295 TC
66 TC
*** * * *
172297 AGTAATAAAGAAT-AAAAAGTGTAAGCTCAAATATAGTAAATATACCTCTATGGAGCCAGTTTTC
1 AGTAATAAAGAATGAAAAAAAATAAGCTCAAATATAGT-AATAAACATCTATGGACCCAGTTTTC
172361 AT
65 AT
172363 TTTCTTATTA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 21 0.37
67 36 0.63
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.28
Consensus pattern (67 bp):
AGTAATAAAGAATGAAAAAAAATAAGCTCAAATATAGTAATAAACATCTATGGACCCAGTTTTCA
TC
Found at i:181935 original size:38 final size:37
Alignment explanation
Indices: 181817--182131 Score: 175
Period size: 38 Copynumber: 8.1 Consensus size: 37
181807 TGCAAATGGT
181817 TTTTGAAAATA-TATATAATATATAGTTTTGAAAACA
1 TTTTGAAAATACTATATAATATATAGTTTTGAAAACA
* * *
181853 TGTTTGAAAACATTTATATATTATATAGTTTTTTTGAAAACA
1 T-TTTGAAAATA-CTATATAATATATAG---TTTTGAAAACA
181895 TTTTGAAAATACGTATATAATATATAGTTTTGAAAACA
1 TTTTGAAAATAC-TATATAATATATAGTTTTGAAAACA
* * *
181933 TTTTGAAAACATTTTGAAAACGTTTAAATATTATATAGTTTTTAAAACA
1 TTTTG-AAA-A---T----AC---TATATAATATATAGTTTTGAAAACA
* * *
181982 TTTTGAAAACA-TATATAGTATATAGTTTTAAAAACA
1 TTTTGAAAATACTATATAATATATAGTTTTGAAAACA
* *
182018 TTTTTTGTAAAAT--TATATAATATATAGTTTTAAAAACTTTTT
1 --TTTTG-AAAATACTATATAATATATAGTTTTGAAAAC----A
* *
182060 TTTTG-AAA-ACT-TAT-ATA-ATATTTTTAAAAACA
1 TTTTGAAAATACTATATAATATATAGTTTTGAAAACA
* * *
182092 TTTTTG-GAA-ACTATGTAATATATAGTTTTGAAAACT
1 -TTTTGAAAATACTATATAATATATAGTTTTGAAAACA
182128 TTTT
1 TTTT
182132 TAAAGTATAT
Statistics
Matches: 225, Mismatches: 23, Indels: 63
0.72 0.07 0.20
Matches are distributed among these distances:
33 10 0.04
34 2 0.01
35 7 0.03
36 48 0.21
37 12 0.05
38 50 0.22
39 21 0.09
40 7 0.03
41 22 0.10
42 12 0.05
43 1 0.00
47 3 0.01
48 3 0.01
49 27 0.12
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATACTATATAATATATAGTTTTGAAAACA
Found at i:181938 original size:11 final size:11
Alignment explanation
Indices: 181922--181953 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
181912 TAATATATAG
181922 TTTTGAAAACA
1 TTTTGAAAACA
181933 TTTTGAAAACA
1 TTTTGAAAACA
181944 TTTTGAAAAC
1 TTTTGAAAAC
181954 GTTTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:181941 original size:49 final size:48
Alignment explanation
Indices: 181884--181993 Score: 159
Period size: 49 Copynumber: 2.2 Consensus size: 48
181874 TATATAGTTT
*
181884 TTTTGAAAACATTTTGAAAATACG-TATATAATATATAGTTTTGAAAACA
1 TTTTGAAAACATTTTG-AAA-ACGTTAAATAATATATAGTTTTGAAAACA
* *
181933 TTTTGAAAACATTTTGAAAACGTTTAAATATTATATAGTTTTTAAAACA
1 TTTTGAAAACATTTTGAAAACG-TTAAATAATATATAGTTTTGAAAACA
181982 TTTTGAAAACAT
1 TTTTGAAAACAT
181994 ATATAGTATA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
47 3 0.05
48 3 0.05
49 50 0.89
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (48 bp):
TTTTGAAAACATTTTGAAAACGTTAAATAATATATAGTTTTGAAAACA
Found at i:182042 original size:74 final size:68
Alignment explanation
Indices: 181933--182185 Score: 185
Period size: 74 Copynumber: 3.6 Consensus size: 68
181923 TTTGAAAACA
* * * * *
181933 TTTTGAAAACA-TTTTGAAAACGTTTAAATATTATATAGTTTTTAAAACATTTTGAAAACATATA
1 TTTTAAAAACATTTTTGAAAAC---TATATAATATATAGTTTTAAAAACTTTTTGAAAAC-T-TA
181997 TAGTATATAG
61 TA-TA-ATAG
*
182007 TTTTAAAAACATTTTTTGTAAAATTATATAATATATAGTTTTAAAAACTTTTTTTTTGAAAACTT
1 TTTTAAAAACA-TTTTTG-AAAACTATATAATATATAGTTTTAAAAAC----TTTTTGAAAACTT
*
182072 ATATAATAT
60 ATATAATAG
* * * * * *
182081 TTTTAAAAACATTTTTGGAAACTATGTAATATATAGTTTTGAAAACTTTTT-TAAA-GTATATAG
1 TTTTAAAAACATTTTTGAAAACTATATAATATATAGTTTTAAAAACTTTTTGAAAACTTATATAA
182144 T--
66 TAG
* *
182145 TTTCTAAAAAATATTTTTGAAATA-TATATATTATATAGTTT
1 TTT-T-AAAAACATTTTTGAAA-ACTATATAATATATAGTTT
182186 ATTTCATATT
Statistics
Matches: 151, Mismatches: 18, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
64 3 0.02
65 1 0.01
66 36 0.24
67 4 0.03
68 5 0.03
72 25 0.17
73 6 0.04
74 45 0.30
75 2 0.01
76 9 0.06
77 5 0.03
78 10 0.07
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (68 bp):
TTTTAAAAACATTTTTGAAAACTATATAATATATAGTTTTAAAAACTTTTTGAAAACTTATATAA
TAG
Found at i:182132 original size:36 final size:36
Alignment explanation
Indices: 181964--182132 Score: 175
Period size: 36 Copynumber: 4.6 Consensus size: 36
181954 GTTTAAATAT
* * *
181964 TATATAGTTTTTAAAAC-ATTTTGAAAACATATATAG
1 TATATAGTTTTAAAAACTTTTTTGAAAAC-TATATAA
*
182000 TATATAGTTTTAAAAACATTTTTTGTAAAATTATATAA
1 TATATAGTTTTAAAAAC-TTTTTTG-AAAACTATATAA
182038 TATATAGTTTTAAAAACTTTTTTTTTGAAAACT-TAT-A
1 TATATAGTTTTAAAAAC---TTTTTTGAAAACTATATAA
* * * *
182075 TA-ATATTTTTAAAAACATTTTTGGAAACTATGTAA
1 TATATAGTTTTAAAAACTTTTTTGAAAACTATATAA
*
182110 TATATAGTTTTGAAAACTTTTTT
1 TATATAGTTTTAAAAACTTTTTT
182133 AAAGTATATA
Statistics
Matches: 112, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
33 11 0.10
34 2 0.02
35 3 0.03
36 46 0.41
37 3 0.03
38 31 0.28
39 9 0.08
40 7 0.06
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (36 bp):
TATATAGTTTTAAAAACTTTTTTGAAAACTATATAA
Found at i:182171 original size:30 final size:26
Alignment explanation
Indices: 182108--182172 Score: 67
Period size: 30 Copynumber: 2.3 Consensus size: 26
182098 GAAACTATGT
* *
182108 AATATATAGTTTTGAAAACTTTTTTA
1 AATATATAGTTTTAAAAAATTTTTTA
182134 AAGTATATAGTTTTCTAAAAAATATTTTTGA
1 AA-TATATAG-TTT-TAAAAAAT-TTTTT-A
182165 AATATATA
1 AATATATA
182173 TATTATATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 7 0.22
28 3 0.09
29 6 0.19
30 11 0.34
31 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (26 bp):
AATATATAGTTTTAAAAAATTTTTTA
Found at i:182199 original size:10 final size:10
Alignment explanation
Indices: 182183--182253 Score: 65
Period size: 10 Copynumber: 7.3 Consensus size: 10
182173 TATTATATAG
182183 TTTATTTCAT
1 TTTATTTCAT
* *
182193 ATTATTTTAT
1 TTTATTTCAT
*
182203 TTTATTTTAT
1 TTTATTTCAT
*
182213 TTTATTTCTT
1 TTTATTTCAT
*
182223 TTTA-TTAAT
1 TTTATTTCAT
*
182232 TTAATTTCAT
1 TTTATTTCAT
*
182242 TTCATTT-AT
1 TTTATTTCAT
182251 TTT
1 TTT
182254 TGTTTTTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
9 10 0.20
10 39 0.80
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATTTCAT
Found at i:182204 original size:5 final size:5
Alignment explanation
Indices: 182183--182228 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
182173 TATTATATAG
* *
182183 TTTAT TTCAT ATTAT TTTAT TTTAT TTTAT TTTAT TTCT-T TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT TTTAT T
182229 AATTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 1 0.03
5 33 0.94
6 1 0.03
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:182233 original size:19 final size:19
Alignment explanation
Indices: 182211--182253 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
182201 ATTTTATTTT
* *
182211 ATTTTATTTCTTTTTATTA
1 ATTTTATTTCATTTCATTA
* *
182230 ATTTAATTTCATTTCATTT
1 ATTTTATTTCATTTCATTA
182249 ATTTT
1 ATTTT
182254 TGTTTTTTTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTATTTCATTTCATTA
Found at i:183641 original size:12 final size:11
Alignment explanation
Indices: 183617--183711 Score: 68
Period size: 11 Copynumber: 8.5 Consensus size: 11
183607 ACTTTACTAC
183617 ATTTTTTTATT
1 ATTTTTTTATT
*
183628 ATTTTTATTCTT
1 ATTTTT-TTATT
183640 ATTTATTTGT-TT
1 ATTT-TTT-TATT
* *
183652 GTTTTTTTAACT
1 ATTTTTTT-ATT
* *
183664 AATCTTTTATT
1 ATTTTTTTATT
*
183675 ATTATTTTATT
1 ATTTTTTTATT
*
183686 ATTATTTT-TT
1 ATTTTTTTATT
*
183696 ATTATTTTATT
1 ATTTTTTTATT
183707 ATTTT
1 ATTTT
183712 CTTTTTCCTT
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
10 11 0.16
11 34 0.50
12 20 0.29
13 3 0.04
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (11 bp):
ATTTTTTTATT
Found at i:183676 original size:3 final size:3
Alignment explanation
Indices: 183670--183709 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
183660 AACTAATCTT
183670 TTA TTA TTA TT- TTA TTA TTA TT- TT- TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
183710 TTCTTTTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 8 0.24
3 26 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (3 bp):
TTA
Found at i:183677 original size:50 final size:49
Alignment explanation
Indices: 183589--183692 Score: 124
Period size: 49 Copynumber: 2.1 Consensus size: 49
183579 TTTTAATTTA
*
183589 ATTTAATTTGTTTATTTTACTTTACTACATTTTTTTATTATTTTTATTCTT
1 ATTTAATTTGTTTATTTTA-TTTACTACATTTTTTTATTA-TTTTATTATT
*
183640 ATTT-ATTTGTTTGTTTT-TTTAACTA-ATCTTTTATTATTATTTTATTATT
1 ATTTAATTTGTTTATTTTATTT-ACTACAT-TTTT-TTATTATTTTATTATT
183689 ATTT
1 ATTT
183693 TTTATTATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
48 5 0.10
49 21 0.44
50 18 0.38
51 4 0.08
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (49 bp):
ATTTAATTTGTTTATTTTATTTACTACATTTTTTTATTATTTTATTATT
Found at i:183686 original size:8 final size:8
Alignment explanation
Indices: 183673--183711 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
183663 TAATCTTTTA
183673 TTATTATT
1 TTATTATT
183681 TTATTA--
1 TTATTATT
183687 TTATT-TT
1 TTATTATT
183694 TTATTATT
1 TTATTATT
183702 TTATTATT
1 TTATTATT
183710 TT
1 TT
183712 CTTTTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 5 0.18
7 5 0.18
8 18 0.64
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTATT
Found at i:183699 original size:21 final size:22
Alignment explanation
Indices: 183668--183709 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
183658 TTAACTAATC
183668 TTTTATTATTATTTTATTATTA
1 TTTTATTATTATTTTATTATTA
183690 TTTT-TTATTATTTTATTATT
1 TTTTATTATTATTTTATTATT
183710 TTCTTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTATTATTATTTTATTATTA
Found at i:197686 original size:85 final size:84
Alignment explanation
Indices: 197501--197700 Score: 217
Period size: 85 Copynumber: 2.4 Consensus size: 84
197491 AAAAATGATT
* * * *
197501 AAATTAGGGGCCTAAACTATAAAAGTAAAAAGTATAATTGAAAAAATTAGAGACCTTAATTATAG
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTATAATTGAAAAAATTAGAGACCTAAATTATAG
*
197566 AGGTAAAAAGTGATAAAAA
66 AGGTAAAAAATGATAAAAA
* * * * *
197585 AAAATAGGGGCATCAATTTTAAAGGTAAAAAGTGAT-GTTGAAAAAAATTAGGGACCTAAATTAT
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGT-ATAATTG-AAAAAATTAGAGACCTAAATTAT
**
197649 -GA-GTAAAAAATAGGATTGAAA
64 AGAGGTAAAAAAT--GATAAAAA
* *
197670 AAATTAGGGACCTCAATTATAAAGGGAAAAA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAA
197701 AGCGAGAATT
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
83 8 0.08
84 32 0.34
85 55 0.58
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (84 bp):
AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTATAATTGAAAAAATTAGAGACCTAAATTATAG
AGGTAAAAAATGATAAAAA
Found at i:197701 original size:43 final size:43
Alignment explanation
Indices: 197501--197700 Score: 176
Period size: 41 Copynumber: 4.7 Consensus size: 43
197491 AAAAATGATT
* * * *
197501 AAATTAGGGGCCTAAACTATAAAAGTAAAAAGTATAATTGAAA
1 AAATTAGGGACCTAAATTATAAAGGTAAAAAGTATGATTGAAA
* * * **
197544 AAATTAGAGACCTTAATTATAGAGGTAAAAAG--TGATAAAAA
1 AAATTAGGGACCTAAATTATAAAGGTAAAAAGTATGATTGAAA
* * * * *
197585 AAAATAGGGGCATCAATTTTAAAGGTAAAAAGTGATG-TTGAAAA
1 AAATTAGGGACCTAAATTATAAAGGTAAAAAGT-ATGATTG-AAA
* * *
197629 AAATTAGGGACCTAAATTAT-GA-GTAAAAAATAGGATTGAAA
1 AAATTAGGGACCTAAATTATAAAGGTAAAAAGTATGATTGAAA
* *
197670 AAATTAGGGACCTCAATTATAAAGGGAAAAA
1 AAATTAGGGACCTAAATTATAAAGGTAAAAA
197701 AGCGAGAATT
Statistics
Matches: 121, Mismatches: 29, Indels: 14
0.74 0.18 0.09
Matches are distributed among these distances:
41 55 0.45
42 12 0.10
43 34 0.28
44 20 0.17
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (43 bp):
AAATTAGGGACCTAAATTATAAAGGTAAAAAGTATGATTGAAA
Found at i:204690 original size:30 final size:31
Alignment explanation
Indices: 204635--204693 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
204625 AGAATGACCG
204635 GAAACATTATTAGACGCCAAAAAAATAACTA
1 GAAACATTATTAGACGCCAAAAAAATAACTA
* *
204666 GAAACATTATTAGGC-CCTAAAAAATAAC
1 GAAACATTATTAGACGCCAAAAAAATAAC
204694 CGAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (31 bp):
GAAACATTATTAGACGCCAAAAAAATAACTA
Found at i:206912 original size:19 final size:19
Alignment explanation
Indices: 206891--206926 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
206881 ACAATATTTA
206891 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
206909 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
206927 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:208164 original size:3 final size:3
Alignment explanation
Indices: 208156--208229 Score: 103
Period size: 3 Copynumber: 24.7 Consensus size: 3
208146 TTATTTGTTA
* * *
208156 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT GAT AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
208204 ATT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
208230 AATGGATAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:209053 original size:114 final size:114
Alignment explanation
Indices: 208521--209200 Score: 1105
Period size: 114 Copynumber: 6.0 Consensus size: 114
208511 CAGATGATAT
*
208521 CAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 CAAA-AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* ** * *
208586 TCATTCATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAA
64 TCATT-ATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTTAAA
208638 C-AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
208702 ATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGA-TTCAG
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTTAAA
** * * *
208750 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
208815 ATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAG
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTTAAA
*
208864 C-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
208928 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTTAAA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTTAAA
208977 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
209042 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTTAAA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTTAAA
209091 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
209156 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATT
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATT
209201 CAAATCTTTG
Statistics
Matches: 533, Mismatches: 27, Indels: 9
0.94 0.05 0.02
Matches are distributed among these distances:
112 3 0.01
113 243 0.46
114 281 0.53
115 3 0.01
116 2 0.00
117 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (114 bp):
CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTTAAA
Found at i:209816 original size:51 final size:51
Alignment explanation
Indices: 209639--210090 Score: 823
Period size: 51 Copynumber: 8.8 Consensus size: 51
209629 TCTGTCCAAT
209639 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCT-AAC
*
209691 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
209743 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
*
209794 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATATTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
*
209845 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
209896 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
*
209947 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
*
209999 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
210051 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
210091 TGAGCACATA
Statistics
Matches: 391, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
51 199 0.51
52 190 0.49
53 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (51 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
Found at i:211044 original size:6 final size:6
Alignment explanation
Indices: 211033--211107 Score: 50
Period size: 6 Copynumber: 12.7 Consensus size: 6
211023 CTTGACCCCC
* *
211033 TTTCTT TTTC-T TCTCTTT TTTCAT TTTCTAT TTT-TT CTTTCTT TTTC-T
1 TTTCTT TTTCTT TTTC-TT TTTCTT TTTCT-T TTTCTT -TTTCTT TTTCTT
* * *
211081 CTTCTT TTT-TT TTTTTT TTTTTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC
211108 AAGCATAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
5 14 0.25
6 31 0.56
7 10 0.18
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:211085 original size:11 final size:10
Alignment explanation
Indices: 211032--211107 Score: 65
Period size: 9 Copynumber: 8.1 Consensus size: 10
211022 CCTTGACCCC
211032 CTTTCTTTTT
1 CTTTCTTTTT
*
211042 C-TTCTCTTT
1 CTTTCTTTTT
*
211051 -TTTCATTTT
1 CTTTCTTTTT
*
211060 CTAT-TTTTT
1 CTTTCTTTTT
211069 CTTTCTTTTT
1 CTTTCTTTTT
211079 CTCTTCTTTTT
1 CT-TTCTTTTT
211090 -TTT-TTTTT
1 CTTTCTTTTT
*
211098 -TTTTTTTTT
1 CTTTCTTTTT
211107 C
1 C
211108 AAGCATAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
8 8 0.15
9 27 0.50
10 11 0.20
11 8 0.15
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:211092 original size:24 final size:25
Alignment explanation
Indices: 211032--211102 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
211022 CCTTGACCCC
*
211032 CTTTCTTTTTCTTCTCTTTTTTCATTTT
1 CTTT-TTTTTCTT-TC-TTTTTCATCTT
*
211060 CTATTTTTTCTTTCTTTTTC-TCTT
1 CTTTTTTTTCTTTCTTTTTCATCTT
* *
211084 CTTTTTTTTTTTTTTTTTT
1 CTTTTTTTTCTTTCTTTTT
211103 TTTTCAAGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
24 19 0.50
25 6 0.16
26 2 0.05
27 8 0.21
28 3 0.08
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (25 bp):
CTTTTTTTTCTTTCTTTTTCATCTT
Found at i:221645 original size:18 final size:18
Alignment explanation
Indices: 221622--221656 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
221612 ATACTTGCAA
221622 ATAAAACAT-ATAAATATT
1 ATAAAA-ATAATAAATATT
221640 ATAAAAATAATAAATAT
1 ATAAAAATAATAAATAT
221657 AAAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATAATAAATATT
Found at i:221663 original size:18 final size:18
Alignment explanation
Indices: 221631--221665 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
221621 AATAAAACAT
* *
221631 ATAAATATTATAAAAATA
1 ATAAATATAAAAAAAATA
221649 ATAAATATAAAAAAAAT
1 ATAAATATAAAAAAAAT
221666 TTGAAAAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATATAAAAAAAATA
Found at i:222438 original size:19 final size:19
Alignment explanation
Indices: 222417--222452 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
222407 ACAATATTTA
222417 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
222435 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
222453 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:223689 original size:3 final size:3
Alignment explanation
Indices: 223681--223754 Score: 103
Period size: 3 Copynumber: 24.7 Consensus size: 3
223671 TTATTTGTTA
* * *
223681 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT GAT AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
223729 ATT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
223755 AATGGATAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:231322 original size:15 final size:15
Alignment explanation
Indices: 231302--231334 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
231292 GAGGGACTAA
231302 AACTGGATAGAAGTT
1 AACTGGATAGAAGTT
231317 AACTGGATAGAAGTT
1 AACTGGATAGAAGTT
231332 AAC
1 AAC
231335 GGTTGAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.24
Consensus pattern (15 bp):
AACTGGATAGAAGTT
Found at i:232487 original size:35 final size:35
Alignment explanation
Indices: 232441--232509 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
232431 AAAATTTCAA
*
232441 TGAGCTTAATGAGCAATGAGACAAGCAACGAGCAT
1 TGAGCTTAATGAGCAACGAGACAAGCAACGAGCAT
*
232476 TGAGCTTAATGAGCAACGAGGCAAGCAACGAGCA
1 TGAGCTTAATGAGCAACGAGACAAGCAACGAGCA
232510 ACGATACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (35 bp):
TGAGCTTAATGAGCAACGAGACAAGCAACGAGCAT
Found at i:232510 original size:19 final size:19
Alignment explanation
Indices: 232486--232547 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
232476 TGAGCTTAAT
*
232486 GAGCAACGAGGC-AAGCAAC
1 GAGCAACGAGACGAA-CAAC
*
232505 GAGCAACGATACGAACAAC
1 GAGCAACGAGACGAACAAC
*
232524 GAGCAACGATACGAACAAC
1 GAGCAACGAGACGAACAAC
232543 GAGCA
1 GAGCA
232548 TCGAATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 38 0.95
20 2 0.05
ACGTcount: A:0.45, C:0.26, G:0.26, T:0.03
Consensus pattern (19 bp):
GAGCAACGAGACGAACAAC
Found at i:243112 original size:2 final size:2
Alignment explanation
Indices: 243105--243157 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
243095 TAGGTCATTA
243105 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
243147 AT AT AT AT AT A
1 AT AT AT AT AT A
243158 AAAGAATGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:256164 original size:18 final size:18
Alignment explanation
Indices: 256141--256175 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
256131 ACATGATGAC
256141 TGAGA-TATGATAGTCATT
1 TGAGATTATGATA-TCATT
256159 TGAGATTATGATATCAT
1 TGAGATTATGATATCAT
256176 ATTTTATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (18 bp):
TGAGATTATGATATCATT
Found at i:256662 original size:32 final size:32
Alignment explanation
Indices: 256545--256662 Score: 92
Period size: 32 Copynumber: 3.7 Consensus size: 32
256535 ATAACGTATG
* * * *
256545 ACATATTATGTAATCATTTTAAGTGATGTAAC
1 ACATATTATATAATCATCTTAAGTGATGTGAT
* * * *
256577 ACATGTTATATAATTATCTTAAATGACGTGAT
1 ACATATTATATAATCATCTTAAGTGATGTGAT
* * * * * * *
256609 ATATGTCATATCACCACCTTAAGTGATATGAT
1 ACATATTATATAATCATCTTAAGTGATGTGAT
*
256641 ACATATTATATTATCATCTTAA
1 ACATATTATATAATCATCTTAA
256663 ATAAATGATA
Statistics
Matches: 63, Mismatches: 23, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (32 bp):
ACATATTATATAATCATCTTAAGTGATGTGAT
Found at i:258974 original size:6 final size:6
Alignment explanation
Indices: 258963--258988 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
258953 TAATACATCG
258963 TCGGGC TCGGGC TCGGGC TCGGGC TC
1 TCGGGC TCGGGC TCGGGC TCGGGC TC
258989 AAATCCATAG
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:0.00, C:0.35, G:0.46, T:0.19
Consensus pattern (6 bp):
TCGGGC
Found at i:263349 original size:15 final size:16
Alignment explanation
Indices: 263310--263376 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 16
263300 GATATTTTTT
263310 TATTTTT-TATTAAAG
1 TATTTTTCTATTAAAG
*
263325 ---TTTTCTATTAAGG
1 TATTTTTCTATTAAAG
263338 TATTTTTCATTATTAAAG
1 TATTTTTC--TATTAAAG
263356 --TTTTT-TATTAAAG
1 TATTTTTCTATTAAAG
263369 TATTTTTC
1 TATTTTTC
263377 ATTTATTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 17
0.68 0.03 0.28
Matches are distributed among these distances:
12 4 0.10
13 15 0.37
15 5 0.12
16 10 0.24
18 7 0.17
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.60
Consensus pattern (16 bp):
TATTTTTCTATTAAAG
Found at i:263353 original size:18 final size:17
Alignment explanation
Indices: 263330--263379 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
263320 TAAAGTTTTC
263330 TATTAAGGTATTTTTCAT
1 TATTAA-GTATTTTTCAT
263348 TATTAAAGT-TTTTT-AT
1 TATT-AAGTATTTTTCAT
263364 TA--AAGTATTTTTCAT
1 TATTAAGTATTTTTCAT
263379 T
1 T
263380 TATTTCTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.14
14 5 0.17
15 3 0.10
16 4 0.14
17 5 0.17
18 6 0.21
19 2 0.07
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (17 bp):
TATTAAGTATTTTTCAT
Found at i:263354 original size:31 final size:31
Alignment explanation
Indices: 263316--263379 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
263306 TTTTTATTTT
*
263316 TTATTAAAGTTTTCTATTAAGGTATTTTTCA
1 TTATTAAAGTTTTCTATTAAAGTATTTTTCA
*
263347 TTATTAAAGTTTTTTATTAAAGTATTTTTCA
1 TTATTAAAGTTTTCTATTAAAGTATTTTTCA
263378 TT
1 TT
263380 TATTTCTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.58
Consensus pattern (31 bp):
TTATTAAAGTTTTCTATTAAAGTATTTTTCA
Found at i:267444 original size:14 final size:14
Alignment explanation
Indices: 267425--267453 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
267415 AAACCGTACT
267425 ACTCGACTACCCTG
1 ACTCGACTACCCTG
267439 ACTCGACTACCCTG
1 ACTCGACTACCCTG
267453 A
1 A
267454 TCAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.41, G:0.14, T:0.21
Consensus pattern (14 bp):
ACTCGACTACCCTG
Found at i:279066 original size:15 final size:15
Alignment explanation
Indices: 279043--279082 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
279033 AAATTTAAAA
279043 TTTTA-ATTAATTAT
1 TTTTATATTAATTAT
279057 TTTTATATTAATTAT
1 TTTTATATTAATTAT
* *
279072 ATTTATCTTAA
1 TTTTATATTAA
279083 AATTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTATATTAATTAT
Found at i:279086 original size:17 final size:18
Alignment explanation
Indices: 279066--279099 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
279056 TTTTTATATT
279066 AATTATATTTAT-CTTAA
1 AATTATATTTATACTTAA
*
279083 AATTTTATTTATACTTA
1 AATTATATTTATACTTA
279100 TTACGAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTATATTTATACTTAA
Found at i:279394 original size:3 final size:3
Alignment explanation
Indices: 279386--279413 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
279376 ATTTGAGCTT
279386 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
279414 AAGTTTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:279592 original size:19 final size:20
Alignment explanation
Indices: 279556--279594 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
279546 TAAAATATAT
*
279556 TTTTTAAAATTAATTAAATA
1 TTTTTAAAATTAAATAAATA
*
279576 TTTTTCAAA-TAAATAAATA
1 TTTTTAAAATTAAATAAATA
279595 ATCTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTTAAAATTAAATAAATA
Found at i:279601 original size:24 final size:25
Alignment explanation
Indices: 279574--279621 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
279564 ATTAATTAAA
279574 TATTTT-TCAAATAAATA-AATAATC
1 TATTTTAT-AAATAAATAGAATAATC
*
279598 TATTTTATATATAAATAGAATAAT
1 TATTTTATAAATAAATAGAATAAT
279622 TTGAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
TATTTTATAAATAAATAGAATAATC
Found at i:280782 original size:3 final size:3
Alignment explanation
Indices: 280774--280856 Score: 139
Period size: 3 Copynumber: 27.7 Consensus size: 3
280764 TTTTTATCCA
* *
280774 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
280822 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
280857 AATATATTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:280896 original size:20 final size:19
Alignment explanation
Indices: 280855--280899 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
280845 CTATTATTAT
* *
280855 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
280874 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
280894 TAAATA
1 TAAATA
280900 ATAAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Done.