Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001497.1 Hibiscus syriacus cultivar Beakdansim tig00002919_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: 1780709
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:147347 original size:20 final size:21
Alignment explanation
Indices: 147310--147350 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
147300 TTTATTTTTA
**
147310 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
147331 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
147351 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:150485 original size:2 final size:2
Alignment explanation
Indices: 150478--150528 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
150468 CTTTTAACTG
150478 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
150520 TA TA TA TA T
1 TA TA TA TA T
150529 TTATCGAATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:151044 original size:20 final size:20
Alignment explanation
Indices: 150971--151044 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
150961 ATACTTATCT
*
150971 ATATATTATTTTTTTCAATTAA
1 ATATATTATTTATTT-AA-TAA
*
150993 AT-TCTTATTTTTATTTAATAA
1 ATATATTA--TTTATTTAATAA
* **
151014 AAATAACATTTATTTAATAA
1 ATATATTATTTATTTAATAA
151034 ATATATTATTT
1 ATATATTATTT
151045 CGAGTAGGGT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
20 20 0.50
21 8 0.20
22 6 0.15
23 6 0.15
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTATTTATTTAATAA
Found at i:160507 original size:20 final size:19
Alignment explanation
Indices: 160473--160512 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
160463 AATATTGATT
160473 TCAAAAATAGATTAACAGTC
1 TCAAAAATAGATTAAC-GTC
**
160493 TCAAAAATATTTTAACGTC
1 TCAAAAATAGATTAACGTC
160512 T
1 T
160513 TTAATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (19 bp):
TCAAAAATAGATTAACGTC
Found at i:165808 original size:17 final size:18
Alignment explanation
Indices: 165775--165808 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
165765 CCACTATTAG
165775 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
165793 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
165809 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:168069 original size:80 final size:80
Alignment explanation
Indices: 167968--168188 Score: 392
Period size: 80 Copynumber: 2.8 Consensus size: 80
167958 GTTAATATTT
*
167968 TTTAATATTTTCGGTAAAACGCTACCTAAAACATTATTTTTTTCTACCGAAAATGTTAATATTAT
1 TTTAATATTTTCGGTAAAACGCTACATAAAACATTATTTTTTTCTACCGAAAATGTTAATATTAT
168033 GCGATACTTAAAATG
66 GCGATACTTAAAATG
168048 TTTAATATTTTCGGTAAAACGCTACATAAAACATTATTTTTTTCTACCGAAAATGTTAATATTAT
1 TTTAATATTTTCGGTAAAACGCTACATAAAACATTATTTTTTTCTACCGAAAATGTTAATATTAT
168113 GCGATACTTAAAATG
66 GCGATACTTAAAATG
* * *
168128 TTTAACATTTTCGGGAAAACGCTACATAAAACATTA--TTTTTCTACCGAAAATATTAATATT
1 TTTAATATTTTCGGTAAAACGCTACATAAAACATTATTTTTTTCTACCGAAAATGTTAATATT
168189 GAGTTATACC
Statistics
Matches: 137, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
78 24 0.18
80 113 0.82
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (80 bp):
TTTAATATTTTCGGTAAAACGCTACATAAAACATTATTTTTTTCTACCGAAAATGTTAATATTAT
GCGATACTTAAAATG
Found at i:168641 original size:20 final size:20
Alignment explanation
Indices: 168547--168895 Score: 418
Period size: 20 Copynumber: 17.4 Consensus size: 20
168537 GATTTTCCAT
* ** *
168547 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
168567 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
168587 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
168607 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
168627 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
168647 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
168667 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
168687 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
168707 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
168727 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
168747 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
168767 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
168787 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
168807 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
168827 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
168847 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
168867 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
168887 AATCACAAC
1 AATCGCAAC
168896 ACTGAAATTT
Statistics
Matches: 285, Mismatches: 36, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 279 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:169608 original size:24 final size:24
Alignment explanation
Indices: 169569--169615 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
169559 AAATTTGGTC
169569 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
169593 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
169616 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:169807 original size:12 final size:12
Alignment explanation
Indices: 169790--169814 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
169780 ATATAATCCT
169790 GAAGAAGAAAAA
1 GAAGAAGAAAAA
169802 GAAGAAGAAAAA
1 GAAGAAGAAAAA
169814 G
1 G
169815 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:172141 original size:19 final size:19
Alignment explanation
Indices: 172119--172444 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
172109 CGGAAAATAC
*
172119 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
172138 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
172152 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
172172 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
172186 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
172205 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
172224 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
172238 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
172257 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
172276 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
172290 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
172309 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
172328 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
172347 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
172366 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
172385 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
172399 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
172418 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
172437 AATCGCAA
1 AATCGCAA
172445 CGAGATAATC
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.04
18 4 0.01
19 174 0.65
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:172206 original size:33 final size:34
Alignment explanation
Indices: 172119--172444 Score: 321
Period size: 33 Copynumber: 9.2 Consensus size: 34
172109 CGGAAAATAC
* *
172119 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
172152 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
172186 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
172224 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
172257 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
172290 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
172328 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
172366 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
172398 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
172437 AATCGCAA
1 AATCGCAA
172445 CGAGATAATC
Statistics
Matches: 257, Mismatches: 12, Indels: 43
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 111 0.43
34 32 0.12
35 9 0.04
36 6 0.02
37 4 0.02
38 91 0.35
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:172380 original size:161 final size:157
Alignment explanation
Indices: 172147--172466 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
172137 AAATCCCAAC
*
172147 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
172212 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
172277 ATCGCAACGAGAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
172304 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAA
172368 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
*
172433 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATGCGAA
172465 AT
1 AT
172467 TATAAACGCA
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 120 0.78
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Found at i:172482 original size:52 final size:52
Alignment explanation
Indices: 172147--172466 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
172137 AAATCCCAAC
172147 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
172200 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
172252 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
172304 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
172361 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
172413 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
172465 AT
1 AT
172467 TATAAACGCA
Statistics
Matches: 255, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 184 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:172582 original size:19 final size:19
Alignment explanation
Indices: 172473--172574 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
172463 AAATTATAAA
172473 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
172492 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
172512 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
172528 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
172545 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
172564 CGCATTGCGAT
1 CGCATTGCGAT
172575 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:172700 original size:14 final size:14
Alignment explanation
Indices: 172681--172717 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
172671 CATCAATTAC
172681 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
172695 ACAAATCATCTTTT
1 ACAAATCAACTTTT
172709 ACAAATCAA
1 ACAAATCAA
172718 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:172729 original size:12 final size:12
Alignment explanation
Indices: 172712--172784 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
172702 ATCTTTTACA
172712 AATCAATTAAAC
1 AATCAATTAAAC
*
172724 AATCAA--AAATTG
1 AATCAATTAAA--C
**
172736 AATCAACTTTTAC
1 AATCAA-TTAAAC
172749 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
172762 AATCAA-AAAAC
1 AATCAATTAAAC
172773 AATCAATTAAAC
1 AATCAATTAAAC
172785 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:172746 original size:38 final size:38
Alignment explanation
Indices: 172698--172770 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
172688 AACTTTTACA
*
172698 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
172736 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
172771 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:174627 original size:19 final size:19
Alignment explanation
Indices: 174587--174721 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
174577 TAGTTTACTT
* *
174587 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
174607 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
174626 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
174645 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
174659 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
174678 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
174692 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
174711 TCGCAATGCGA
1 TCGCAACGCGA
174722 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:174662 original size:14 final size:14
Alignment explanation
Indices: 174643--174699 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
174633 GCGAAATGAA
*
174643 AATCGCAACGACAG
1 AATCGCAACGAAAG
174657 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
174674 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
174690 AATCGCAACG
1 AATCGCAACG
174700 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:174666 original size:33 final size:33
Alignment explanation
Indices: 174624--174716 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
174614 GCGAAACCAA
*
174624 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
174657 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
174690 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
174717 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:174713 original size:52 final size:54
Alignment explanation
Indices: 174587--174721 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
174577 TAGTTTACTT
*
174587 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
174645 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
174692 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
174722 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:174739 original size:19 final size:19
Alignment explanation
Indices: 174717--174845 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
174707 AAAATCGCAA
174717 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
174736 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
174750 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
174769 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
174783 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
174802 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
174821 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
174841 TGCGA
1 TGCGA
174846 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:174759 original size:33 final size:33
Alignment explanation
Indices: 174717--174808 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
174707 AAAATCGCAA
174717 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
174750 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
174783 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
174809 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:175178 original size:92 final size:93
Alignment explanation
Indices: 174893--175267 Score: 709
Period size: 93 Copynumber: 4.1 Consensus size: 93
174883 ATGGATTGCA
* *
174893 TTAC-TTCAACCAATAGACAAATCAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
174957 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
174985 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
175050 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
175078 TTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
175142 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
175170 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
175235 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
175263 TTACT
1 TTACT
175268 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 96 0.35
93 182 0.65
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:175210 original size:185 final size:186
Alignment explanation
Indices: 174893--175267 Score: 709
Period size: 185 Copynumber: 2.0 Consensus size: 186
174883 ATGGATTGCA
* *
174893 TTAC-TTCAACCAATAGACAAATCAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
174957 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
175022 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
175078 TTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
175142 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
175207 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
175263 TTACT
1 TTACT
175268 AAGCAATCTA
Statistics
Matches: 186, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
185 158 0.85
186 28 0.15
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:176993 original size:14 final size:14
Alignment explanation
Indices: 176974--177063 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
176964 TTGAAATGAA
176974 AATCGCAACGAGAG
1 AATCGCAACGAGAG
176988 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
177005 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
177021 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
177040 AATCGCAACGAGAG
1 AATCGCAACGAGAG
177054 AATCGCAACG
1 AATCGCAACG
177064 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:177011 original size:33 final size:33
Alignment explanation
Indices: 176966--177080 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
176956 TCTTTTGGTT
176966 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
176999 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
177032 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
177065 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
177081 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:177012 original size:19 final size:18
Alignment explanation
Indices: 176973--177085 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
176963 GTTGAAATGA
176973 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
176988 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
177005 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
177021 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
177038 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
177054 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
177071 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
177086 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:177116 original size:14 final size:14
Alignment explanation
Indices: 177097--177151 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
177087 TTTGGTTTCG
177097 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
177111 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
177130 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
177144 CGTTGCGA
1 CGTTGCGA
177152 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:177314 original size:33 final size:33
Alignment explanation
Indices: 177272--177342 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
177262 AATACTAACT
*
177272 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
177305 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
177338 TGAAA
1 TGAAA
177343 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:177576 original size:22 final size:22
Alignment explanation
Indices: 177524--177578 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
177514 TGGTTGTGAG
**
177524 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
177546 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
177568 GGATTTCTTCG
1 GGATTTCTTCG
177579 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:177749 original size:20 final size:20
Alignment explanation
Indices: 177724--177917 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
177714 CTTTAAATAT
177724 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
177744 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
177766 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
177785 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
177805 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
177825 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
177845 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
177865 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
177885 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
177905 CGCGTTGCGATTT
1 CGCGTTGCGATTT
177918 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:177911 original size:60 final size:60
Alignment explanation
Indices: 177724--177917 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
177714 CTTTAAATAT
**
177724 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
177785 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
177845 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
177905 CGCGTTGCGATTT
1 CGCGTTGCGATTT
177918 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:177934 original size:21 final size:20
Alignment explanation
Indices: 177910--177986 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
177900 ATATTCGCGT
177910 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
177931 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
177951 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
177973 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
177987 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:177997 original size:20 final size:20
Alignment explanation
Indices: 177972--178023 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
177962 AAGAATCGCG
*
177972 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
177992 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
178012 TTGCGATTCTGG
1 TTGCGATTCTGG
178024 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:179027 original size:19 final size:19
Alignment explanation
Indices: 178977--179027 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
178967 ATAGAATTAT
178977 ATTTTCTATTTT-TTTCTTC
1 ATTTTC-ATTTTCTTTCTTC
*
178996 ATTTTC-TTCTTCTTTTTTC
1 ATTTTCATT-TTCTTTCTTC
*
179015 CTTTTCATTTTCT
1 ATTTTCATTTTCT
179028 CTTTATCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 21 0.78
20 2 0.07
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTCATTTTCTTTCTTC
Found at i:179215 original size:84 final size:85
Alignment explanation
Indices: 179103--179258 Score: 278
Period size: 84 Copynumber: 1.8 Consensus size: 85
179093 CCCAAAATTT
179103 CATAGGTTTTACAAAATTCTACGGTATAATATAAGAAAAACTCTAATGTTTGATTAAATAATCAC
1 CATAGGTTTTACAAAATTCTACGGTATAATATAAGAAAAACTCTAATGTTTGATTAAATAATCAC
179168 TTTGATATATATATATATTG
66 TTTGATATATATATATATTG
** *
179188 CATAGGTTTTA-TTAATTCTACGGTATAATATAAGAAAAACTCTAATGTTTGATTAAATAGTCAC
1 CATAGGTTTTACAAAATTCTACGGTATAATATAAGAAAAACTCTAATGTTTGATTAAATAATCAC
179252 TTTGATA
66 TTTGATA
179259 CATTTTTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
84 57 0.84
85 11 0.16
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.39
Consensus pattern (85 bp):
CATAGGTTTTACAAAATTCTACGGTATAATATAAGAAAAACTCTAATGTTTGATTAAATAATCAC
TTTGATATATATATATATTG
Found at i:179324 original size:99 final size:99
Alignment explanation
Indices: 179178--179364 Score: 311
Period size: 99 Copynumber: 1.9 Consensus size: 99
179168 TTTGATATAT
* * *
179178 ATATATATTGCATAGGTTTTATTAATTCTACGGTATAATATAAGAAAAACTCTAATGTTTGATTA
1 ATATATATCGCATAGATTTTATTAATTCTACGATATAATATAAGAAAAACTCTAATGTTTGATTA
* *
179243 AATAGTCACTTTGATACATTTTTTTTCTTTTGAA
66 AATAATCAATTTGATACATTTTTTTTCTTTTGAA
* *
179277 ATATATATCGCATAGATTTTATTAATTTTGCGATATAATATAAGAAAAACTCTAATGTTTGATTA
1 ATATATATCGCATAGATTTTATTAATTCTACGATATAATATAAGAAAAACTCTAATGTTTGATTA
179342 AATAATCAATTTGATACATTTTT
66 AATAATCAATTTGATACATTTTT
179365 CCTTTTGAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 81 1.00
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (99 bp):
ATATATATCGCATAGATTTTATTAATTCTACGATATAATATAAGAAAAACTCTAATGTTTGATTA
AATAATCAATTTGATACATTTTTTTTCTTTTGAA
Found at i:181129 original size:17 final size:16
Alignment explanation
Indices: 181109--181142 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
181099 TTAAATACCT
*
181109 AAAATTAACAAATTAAA
1 AAAATTAA-AAAGTAAA
181126 AAAATTAAAAAGTAAA
1 AAAATTAAAAAGTAAA
181142 A
1 A
181143 TGGATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAATTAAAAAGTAAA
Found at i:183485 original size:113 final size:114
Alignment explanation
Indices: 183296--183516 Score: 399
Period size: 113 Copynumber: 1.9 Consensus size: 114
183286 TAAAAATACA
**
183296 TAGGCAGTAAGATCTATATTAAAGAAATACAACCATGCAATCAAAACCATTCGCAATTTTAATTT
1 TAGGCAGTAAGATCTATATTAAAGAAATACAACCATGCAATCAAAACCATTCGCAATCATAATTT
183361 CCTAAATAAAAGAAATGTAGAAAGACAAAACCTAGCTAAAAAAATGAGC
66 CCTAAATAAAAGAAATGTAGAAAGACAAAACCTAGCTAAAAAAATGAGC
*
183410 TAGGCAGTAAGATCTAT-TTAAAGAAATACAACCCTGCAATCAAAACCATTCGCAATCATAATTT
1 TAGGCAGTAAGATCTATATTAAAGAAATACAACCATGCAATCAAAACCATTCGCAATCATAATTT
*
183474 CCTAAATAAAAGAAATGTAGAAAGACAAAACCTAGCTACAAAA
66 CCTAAATAAAAGAAATGTAGAAAGACAAAACCTAGCTAAAAAA
183517 TTGCAACTCA
Statistics
Matches: 103, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
113 86 0.83
114 17 0.17
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (114 bp):
TAGGCAGTAAGATCTATATTAAAGAAATACAACCATGCAATCAAAACCATTCGCAATCATAATTT
CCTAAATAAAAGAAATGTAGAAAGACAAAACCTAGCTAAAAAAATGAGC
Found at i:185908 original size:37 final size:35
Alignment explanation
Indices: 185849--185962 Score: 167
Period size: 35 Copynumber: 3.2 Consensus size: 35
185839 ATCCCATTAT
* *
185849 CATTTTTCAACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAGAAACATTTACCAAACTTTG-AAAAC
*
185885 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTC-AAGAAACATTTACCAAACTTTGAAAAC
185921 CA-TTTTCAAGAAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAG-AAACATTTACCAAACTTTGAAAAC
185956 CATTTTT
1 CATTTTT
185963 TCAAAGTTAG
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
34 3 0.04
35 31 0.44
36 17 0.24
37 20 0.28
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.32
Consensus pattern (35 bp):
CATTTTTCAAGAAACATTTACCAAACTTTGAAAAC
Found at i:185924 original size:21 final size:21
Alignment explanation
Indices: 185900--185960 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
185890 TTCAAAGAAA
185900 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
185921 CATTT-TC-AA----GAAAA-
1 CATTTACCAAACTTTGAAAAC
185935 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
185956 CATTT
1 CATTT
185961 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 6 0.19
16 2 0.06
19 2 0.06
20 6 0.19
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:185977 original size:35 final size:35
Alignment explanation
Indices: 185851--185995 Score: 136
Period size: 35 Copynumber: 4.1 Consensus size: 35
185841 CCCATTATCA
* * *
185851 TTTTTCAACAAACATCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGACATTTACCAAACTTTGAAAACCAT
185886 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG--ACATTTACCAAACTTTGAAAACCAT
*
185923 -TTTTCAAGAAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTC-A-AAGACATTTACCAAACTTTGAAAACCAT
** * *
185959 TTTTTCAAAGTTAGTTACCAAAC-TTGAAAATCAT
1 TTTTTCAAAGACATTTACCAAACTTTGAAAACCAT
185993 TTT
1 TTT
185996 AACAATCTCC
Statistics
Matches: 93, Mismatches: 9, Indels: 16
0.79 0.08 0.14
Matches are distributed among these distances:
34 13 0.14
35 42 0.45
36 10 0.11
37 28 0.30
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.34
Consensus pattern (35 bp):
TTTTTCAAAGACATTTACCAAACTTTGAAAACCAT
Found at i:190509 original size:37 final size:36
Alignment explanation
Indices: 190450--190569 Score: 147
Period size: 37 Copynumber: 3.3 Consensus size: 36
190440 ATCCTATTAT
* *
190450 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
190486 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
* *
190522 CA-TTTTCAAGGAAACATTTACCAAAC-TTAAAAAGC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAA-C
190557 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
190570 TTTATTACTA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
34 6 0.08
35 26 0.36
36 13 0.18
37 28 0.38
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:190536 original size:35 final size:34
Alignment explanation
Indices: 190453--190562 Score: 132
Period size: 35 Copynumber: 3.1 Consensus size: 34
190443 CTATTATCAT
* * *
190453 TTTTCAACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAGAAACATTTACCAAACTTTG-AAAACCA
190488 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 -TTTTC-AAGAAACATTTACCAAACTTTGAAAACCA
*
190524 TTTTCAAGGAAACATTTACCAAAC-TTAAAAAGCCA
1 TTTTCAA-GAAACATTTACCAAACTTTGAAAA-CCA
190559 TTTT
1 TTTT
190563 TTCAAAGTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
34 8 0.12
35 28 0.42
36 11 0.16
37 20 0.30
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (34 bp):
TTTTCAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:195076 original size:33 final size:33
Alignment explanation
Indices: 195024--195333 Score: 406
Period size: 33 Copynumber: 9.4 Consensus size: 33
195014 CTCCGGAGCT
* * *
195024 GGCGGCGGCTG-AAGTGGGTTTGGAGGCAGAACG
1 GGCGGCGGCAGAAAG-GGGTTCGGAGGAAGAACG
*
195057 GGCGGCGGCAGAAAGGGGTTCGGAGGCAGAACG
1 GGCGGCGGCAGAAAGGGGTTCGGAGGAAGAACG
195090 GGCGGCGGCAGAAAGGGGTTCGGAGGAAGAACG
1 GGCGGCGGCAGAAAGGGGTTCGGAGGAAGAACG
* *
195123 GGTGGCGGCAGAACGGGGTTCGGAGGAAGAACG
1 GGCGGCGGCAGAAAGGGGTTCGGAGGAAGAACG
* *
195156 GGTGGCGGCAGAATGGGGTTCGGAGGAAGAACG
1 GGCGGCGGCAGAAAGGGGTTCGGAGGAAGAACG
* * *
195189 GGTGGCGGCAGAATGGGGTTCGGAGGAAGAACA
1 GGCGGCGGCAGAAAGGGGTTCGGAGGAAGAACG
* * * * *
195222 GGAGGCGGTAGAATGGGGTTCGGTGGAAGAACA
1 GGCGGCGGCAGAAAGGGGTTCGGAGGAAGAACG
* * *
195255 GGCGGCGGTAGAAAAGGGTTCGGTGGAAGAACG
1 GGCGGCGGCAGAAAGGGGTTCGGAGGAAGAACG
* * *
195288 GGCGGCGGTAGAAAAGGGTTTGGAGGAAGAACG
1 GGCGGCGGCAGAAAGGGGTTCGGAGGAAGAACG
195321 GGCGGCGGCAGAA
1 GGCGGCGGCAGAA
195334 GCTGGTCCGG
Statistics
Matches: 259, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
33 256 0.99
34 3 0.01
ACGTcount: A:0.25, C:0.14, G:0.50, T:0.11
Consensus pattern (33 bp):
GGCGGCGGCAGAAAGGGGTTCGGAGGAAGAACG
Found at i:198431 original size:16 final size:18
Alignment explanation
Indices: 198406--198450 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
198396 TTTAATCATC
*
198406 AAATTAAATT-TT-TTAT
1 AAATTTAATTATTATTAT
198422 AAATTTAATTATTATTAT
1 AAATTTAATTATTATTAT
198440 -AATTTAATTAT
1 AAATTTAATTAT
198451 CATCGATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 9 0.35
17 13 0.50
18 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTTAATTATTATTAT
Found at i:215496 original size:23 final size:23
Alignment explanation
Indices: 215461--215520 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
215451 ATCAAGCACA
* *
215461 ATAACATATTAGGTACCGCTTAT
1 ATAATATAATAGGTACCGCTTAT
**
215484 ATAATATAATAGGTAGTGCTTAT
1 ATAATATAATAGGTACCGCTTAT
*
215507 ATAATAAAATAGGT
1 ATAATATAATAGGT
215521 TAATTACTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (23 bp):
ATAATATAATAGGTACCGCTTAT
Found at i:215663 original size:23 final size:23
Alignment explanation
Indices: 215637--215686 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
215627 ATCAAGCACA
*
215637 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
215660 ATAACGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
215683 ATAA
1 ATAA
215687 TAAAATATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:215693 original size:23 final size:23
Alignment explanation
Indices: 215637--215693 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
215627 ATCAAGCACA
* *
215637 ATAACATATTAGGTAGCGCTTAT
1 ATAACAAAATAGGTAGCGCTTAT
** *
215660 ATAACGTAATAGGTAGTGCTTAT
1 ATAACAAAATAGGTAGCGCTTAT
*
215683 ATAATAAAATA
1 ATAACAAAATA
215694 TGTTAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (23 bp):
ATAACAAAATAGGTAGCGCTTAT
Found at i:215699 original size:87 final size:87
Alignment explanation
Indices: 215441--215702 Score: 391
Period size: 89 Copynumber: 3.0 Consensus size: 87
215431 ATCATTTAAT
* * *
215441 TGGAAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATATAATAGGTAGTGCTTA
1 TGGAAAAATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATGTAATAGGTAGTGCTTA
215506 TATAATAAAATAGGTTAATTAC
66 TATAATAAAATAGGTTAATTAC
** * **
215528 TGGAATCATTATCAAGCACAATAATATATATTAGGTAAAACTTATATAATGTAATAGGTA-TCGC
1 TGGAAAAATTATCAAGCACAAT-A-ACATATTAGGTAACGCTTATATAATGTAATAGGTAGT-GC
215592 TTATATAATAAAATAGGTTAATTAC
63 TTATATAATAAAATAGGTTAATTAC
* *
215617 TGGAAAAATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGTGCTTA
1 TGGAAAAATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATGTAATAGGTAGTGCTTA
*
215682 TATAATAAAATATGTTAATTA
66 TATAATAAAATAGGTTAATTA
215703 TTTAATTTGT
Statistics
Matches: 156, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
87 75 0.48
88 4 0.03
89 77 0.49
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
TGGAAAAATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATGTAATAGGTAGTGCTTA
TATAATAAAATAGGTTAATTAC
Found at i:216777 original size:60 final size:60
Alignment explanation
Indices: 216702--216872 Score: 200
Period size: 60 Copynumber: 2.9 Consensus size: 60
216692 TTATAACCTA
* * * * *
216702 CATTTTAAATTAGTCTTTTAATTTTTAAATATTTTAATTTCATCCCTAAAGTATGACTTT
1 CATTCTAAATTAGTCTTTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGACTCT
* * * *
216762 CATTCTAAATTAGTCTTTAAACTTTTGAACAATCTAATTTCATCCCTAAACTATGACTCT
1 CATTCTAAATTAGTCTTTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGACTCT
* *** *
216822 CTTTCTAAATT-GATCTCCGAACTTTTAAATATTTCAATTTCATCCCTAAAC
1 CATTCTAAATTAG-TCTTTAAACTTTTAAATATTTTAATTTCATCCCTAAAC
216873 CCATCCAAAC
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
59 1 0.01
60 91 0.99
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (60 bp):
CATTCTAAATTAGTCTTTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGACTCT
Found at i:222821 original size:37 final size:38
Alignment explanation
Indices: 222735--222828 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
222725 TTTTCACCCT
**
222735 AAACCCGAACCCGACCCGGTCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTTAAAA
* *
222774 AAATCCGACCCGACTCGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
*
222811 AAACCCGACCCAACCCGA
1 AAACCCGACCCGACCCGA
222829 ACAAAATAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 18 0.38
38 24 0.50
39 6 0.12
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (38 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:225623 original size:183 final size:183
Alignment explanation
Indices: 225267--225643 Score: 604
Period size: 183 Copynumber: 2.1 Consensus size: 183
225257 TAAATATATT
225267 ATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAATTTAAGATC
1 ATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAATTTAAGATC
* *
225332 CAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATCTTTTATTTTATA
66 CAATAACTTTTAAACTTAAATAAATATTAATTAATTAAAAAATTATATAAATCTTTTACTTTATA
*
225397 ATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAAAAATATTAA
131 ATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAAAAATATTAA
225450 ATATATTATATATAACATATGGGCT-AAGCCCAAA-CTATTTAAAACCCAATTAATAATTTAAGA
1 ATATATTATATATAACATATGGGCTCAA-CCCAAATC-ATTTAAAACCCAATTAATAATTTAAGA
*
225513 TCCAATAACTTTTAAACTTAAATAAATATTAATTAATTAAAAAATTTATTTAAAAT-TTTTACTT
64 TCCAATAACTTTTAAACTTAAATAAATATTAATTAATTAAAAAA-TTATAT-AAATCTTTTACTT
* *
225577 TATAATTATATATTATTTAAATTAATTAT-AA-TTTTTTTTGAATTAAAAAATATTTA
127 TATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-AATTAAAAAATATTAA
*
225633 AT-TTTTATATA
1 ATATATTATATA
225644 AATTAGAAAA
Statistics
Matches: 182, Mismatches: 7, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
182 18 0.10
183 120 0.66
184 40 0.22
185 4 0.02
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
ATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAATTTAAGATC
CAATAACTTTTAAACTTAAATAAATATTAATTAATTAAAAAATTATATAAATCTTTTACTTTATA
ATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAAAAATATTAA
Found at i:225658 original size:26 final size:25
Alignment explanation
Indices: 225600--225659 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
225590 TATTTAAATT
* * *
225600 AATTATAATTTTTTTTGAATTAAAA
1 AATTTTAATTTTTTATAAATTAAAA
*
225625 AATATTTAATTTTTATATAAATTAGAA
1 AAT-TTTAATTTTT-TATAAATTAAAA
225652 AATTTTAA
1 AATTTTAA
225660 AAAAAAAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 3 0.10
26 14 0.48
27 12 0.41
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
AATTTTAATTTTTTATAAATTAAAA
Found at i:226723 original size:16 final size:15
Alignment explanation
Indices: 226702--226732 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
226692 TAAATAAATT
226702 TAAAAAATTATCAAAA
1 TAAAAAATTA-CAAAA
226718 TAAAAAATTACAAAA
1 TAAAAAATTACAAAA
226733 GAATACTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAAAATTACAAAA
Found at i:236296 original size:17 final size:16
Alignment explanation
Indices: 236261--236321 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 16
236251 GACAAATTTA
*
236261 TAAAATTTAAAAAAAT
1 TAAAATATAAAAAAAT
*
236277 TAAAATATAAAATTAAT
1 TAAAATATAAAA-AAAT
*
236294 TAAAAATTTAAAAAATAT
1 T-AAAATATAAAAAA-AT
236312 CTAAAATATA
1 -TAAAATATA
236322 TATTAATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 11 0.31
17 5 0.14
18 19 0.53
19 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATATAAAAAAAT
Found at i:236327 original size:35 final size:34
Alignment explanation
Indices: 236262--236337 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 34
236252 ACAAATTTAT
236262 AAAATTTAAAAAAATTAAAATATAAAATTAATTA
1 AAAATTTAAAAAAATTAAAATATAAAATTAATTA
* *
236296 AAAATTTAAAAAATATCTAAAATAT-ATATTAATTT
1 AAAATTTAAAAAA-AT-TAAAATATAAAATTAATTA
236331 AAAATTT
1 AAAATTT
236338 TCAAATGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 13 0.34
35 17 0.45
36 8 0.21
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (34 bp):
AAAATTTAAAAAAATTAAAATATAAAATTAATTA
Found at i:236333 original size:36 final size:35
Alignment explanation
Indices: 236255--236334 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 35
236245 AGATATGACA
236255 AATTTATAAAATTTAAAAAAATTAAAATATAAAATT
1 AATTTA-AAAATTTAAAAAAATTAAAATATAAAATT
*
236291 AA-TTAAAAATTTAAAAAATATCTAAAATAT-ATATT
1 AATTTAAAAATTTAAAAAA-AT-TAAAATATAAAATT
236326 AATTTAAAA
1 AATTTAAAA
236335 TTTTCAAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
34 13 0.32
35 11 0.28
36 16 0.40
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (35 bp):
AATTTAAAAATTTAAAAAAATTAAAATATAAAATT
Found at i:236620 original size:2 final size:2
Alignment explanation
Indices: 236613--236646 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
236603 TAATCACATA
236613 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
236647 TATTTCACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:236867 original size:30 final size:30
Alignment explanation
Indices: 236831--236907 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
236821 CATGCGGAAG
236831 ACTAAATTGAATAAAATGTAAAGTTAAAGT
1 ACTAAATTGAATAAAATGTAAAGTTAAAGT
236861 ACTAAATTGAATAAAATGTAAAGTTAAAGT
1 ACTAAATTGAATAAAATGTAAAGTTAAAGT
*
236891 ACTAAATTGAAAAAAAT
1 ACTAAATTGAATAAAAT
236908 AGAAATTTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.29
Consensus pattern (30 bp):
ACTAAATTGAATAAAATGTAAAGTTAAAGT
Found at i:245687 original size:2 final size:2
Alignment explanation
Indices: 245680--245710 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
245670 ACATACATAC
245680 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 A
245711 CTACCCCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:247677 original size:30 final size:30
Alignment explanation
Indices: 247643--247701 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
247633 CTTAATCTAT
* *
247643 ATTATTTATGATATGGTATGATAATTATTA
1 ATTATTTATCAGATGGTATGATAATTATTA
*
247673 ATTATTTATCAGATGGTATGATATTTATT
1 ATTATTTATCAGATGGTATGATAATTATT
247702 CTTTGGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.51
Consensus pattern (30 bp):
ATTATTTATCAGATGGTATGATAATTATTA
Found at i:254481 original size:79 final size:80
Alignment explanation
Indices: 254376--254537 Score: 231
Period size: 79 Copynumber: 2.0 Consensus size: 80
254366 AATATATATT
* *
254376 TTTAACATTTCTGGTAAAACGATACCTAAAACATTATTTTTTTCTACCAGAAATGTTAAATATTG
1 TTTAACATTTCTGGTAAAACGATACCTAAAACATTATTTTTTTCTACAAAAAATGTT-AATATTG
254441 -GACGCTA-CTAAAATG
65 AG-CGCTACCTAAAATG
* * *
254456 TTTAATATTTC-GGTAAAACGCTACCTAAAACATTATTTTTTTTTACAAAAAATGTTAATATTGA
1 TTTAACATTTCTGGTAAAACGATACCTAAAACATTATTTTTTTCTACAAAAAATGTTAATATTGA
*
254520 GTGCTACCTAAAATG
66 GCGCTACCTAAAATG
254535 TTT
1 TTT
254538 TTTTTTCTAC
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
78 11 0.15
79 53 0.72
80 10 0.14
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (80 bp):
TTTAACATTTCTGGTAAAACGATACCTAAAACATTATTTTTTTCTACAAAAAATGTTAATATTGA
GCGCTACCTAAAATG
Found at i:259068 original size:88 final size:88
Alignment explanation
Indices: 258919--259087 Score: 329
Period size: 88 Copynumber: 1.9 Consensus size: 88
258909 TTTAATTAGA
258919 AAAATATTGTTCGTGTATTATTGCACATGGGAGCTGGCTAACCCCGTGTGTGTTTCAGTATTTTA
1 AAAATATTGTTCGTGTATTATTGCACATGGGAGCTGGCTAACCCCGTGTGTGTTTCAGTATTTTA
258984 ATGGTGATAAATTATAGTCTTTC
66 ATGGTGATAAATTATAGTCTTTC
*
259007 AAAATATTGTTTGTGTATTATTGCACATGGGAGCTGGCTAACCCCGTGTGTGTTTCAGTATTTTA
1 AAAATATTGTTCGTGTATTATTGCACATGGGAGCTGGCTAACCCCGTGTGTGTTTCAGTATTTTA
259072 ATGGTGATAAATTATA
66 ATGGTGATAAATTATA
259088 ATTACGAAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (88 bp):
AAAATATTGTTCGTGTATTATTGCACATGGGAGCTGGCTAACCCCGTGTGTGTTTCAGTATTTTA
ATGGTGATAAATTATAGTCTTTC
Found at i:268235 original size:15 final size:15
Alignment explanation
Indices: 268215--268246 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
268205 TTGATCCCCA
268215 TGGAGAATTTGACTT
1 TGGAGAATTTGACTT
268230 TGGAGAATTTGACTT
1 TGGAGAATTTGACTT
268245 TG
1 TG
268247 AGTATTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.41
Consensus pattern (15 bp):
TGGAGAATTTGACTT
Found at i:271147 original size:25 final size:25
Alignment explanation
Indices: 271119--271168 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
271109 GATCAGAATT
271119 GAGCTACCTCCTCTCGATGAAATCG
1 GAGCTACCTCCTCTCGATGAAATCG
271144 GAGCTACCTCCTCTCGATGAAATCG
1 GAGCTACCTCCTCTCGATGAAATCG
271169 AAATAGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (25 bp):
GAGCTACCTCCTCTCGATGAAATCG
Found at i:281322 original size:32 final size:33
Alignment explanation
Indices: 281281--281344 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
281271 CTGCGCAACC
281281 TAAAATGTTAAT-TTTTAAACATTTTC-GTAACT
1 TAAAATGTTAATATTTT-AACATTTTCGGTAACT
*
281313 TAAAATGTTAATATTTTTACATTTTCGGTAAC
1 TAAAATGTTAATATTTTAACATTTTCGGTAAC
281345 AATCGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (33 bp):
TAAAATGTTAATATTTTAACATTTTCGGTAACT
Found at i:287540 original size:7 final size:7
Alignment explanation
Indices: 287528--287556 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
287518 AGGCAATAGC
287528 TCCGATT
1 TCCGATT
287535 TCCGATT
1 TCCGATT
287542 TCCGATT
1 TCCGATT
287549 TCCGATT
1 TCCGATT
287556 T
1 T
287557 GTCAACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCCGATT
Found at i:300130 original size:22 final size:21
Alignment explanation
Indices: 300088--300127 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
300078 GAGTTTATTT
*
300088 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
300109 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
300128 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:306694 original size:16 final size:17
Alignment explanation
Indices: 306666--306701 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
306656 TGTATCGCCG
306666 ACAAAATTTTACTATTC
1 ACAAAATTTTACTATTC
306683 ACAAAA-TTTACTATTC
1 ACAAAATTTTACTATTC
306699 ACA
1 ACA
306702 TGAATAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.36
Consensus pattern (17 bp):
ACAAAATTTTACTATTC
Found at i:309864 original size:26 final size:26
Alignment explanation
Indices: 309828--309877 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
309818 AGTGGTCGGC
309828 GACGAGGGTGGCCGAAGATGGCCGGT
1 GACGAGGGTGGCCGAAGATGGCCGGT
309854 GACGAGGGTGGCCGAAGATGGCCG
1 GACGAGGGTGGCCGAAGATGGCCG
309878 ACGACGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.50, T:0.10
Consensus pattern (26 bp):
GACGAGGGTGGCCGAAGATGGCCGGT
Found at i:309883 original size:26 final size:26
Alignment explanation
Indices: 309827--309883 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
309817 AAGTGGTCGG
*
309827 CGACGAGGGTGGCCGAAGATGGCCGG
1 CGACGAGGGTGGCCGAAGATGGCCGA
*
309853 TGACGAGGGTGGCCGAAGATGGCCGA
1 CGACGAGGGTGGCCGAAGATGGCCGA
309879 CGACG
1 CGACG
309884 GTTGGTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.47, T:0.09
Consensus pattern (26 bp):
CGACGAGGGTGGCCGAAGATGGCCGA
Found at i:312198 original size:54 final size:54
Alignment explanation
Indices: 312139--312248 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
312129 AATATTCTAA
312139 ATAAAATTCGACTTCTTTTTCCCTACATATAAATTGTCTAAAAAAATTATGATT
1 ATAAAATTCGACTTCTTTTTCCCTACATATAAATTGTCTAAAAAAATTATGATT
* *
312193 ATAAAATTCGACTTCTTTTTCCCTACGTATATATTGTCTAAAAAAATTATGATT
1 ATAAAATTCGACTTCTTTTTCCCTACATATAAATTGTCTAAAAAAATTATGATT
312247 AT
1 AT
312249 GAGCTTAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (54 bp):
ATAAAATTCGACTTCTTTTTCCCTACATATAAATTGTCTAAAAAAATTATGATT
Found at i:320224 original size:16 final size:16
Alignment explanation
Indices: 320200--320233 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
320190 TATCGCCGAC
*
320200 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
320216 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
320232 CG
1 CG
320234 TGAATAGTAA
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:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:332257 original size:371 final size:370
Alignment explanation
Indices: 331530--332275 Score: 1317
Period size: 371 Copynumber: 2.0 Consensus size: 370
331520 TTAAAATTAA
331530 ATTGTTTGTTTAATTTTTTCAACGAATTTCTTTGAAAATGTTAATTGATAAAATTTTAGAATATA
1 ATTGTTTGTTTAATTTTTTCAACGAATTTCTTTGAAAATGTTAATTGATAAAATTTTAGAATATA
331595 AATTTCTTTTTATTTTATTTTATTTATTTCCTTTAATTATATTACTTTTTAAATTTACATTTTTT
66 AATTTCTTTTTATTTTA--TTATTTATTTCCTTTAATTATATTACTTTTTAAATTTACATTTTTT
331660 AAATAATCTATCTATATCAAATATTTAAGTCACTAACAGGGTTGGTTCAAGTGGTAAACAATTTG
129 AAATAATCTATCTATATCAAATATTTAAGTCACTAACAGGGTTGGTTCAAGTGGTAAACAATTTG
331725 ATATCACTTAAGTAAAGTATTGAGTTCGAGTCTTTGGATACCAGTTATTAATAGACTGTAAATGA
194 ATATCACTT-A-TAAAGTATTGAGTTCGAGTCTTTGGATACCAGTTATTAATAGACTGTAAATGA
331790 GACGAGACGATCGCGAGCTACTCGAGATCGACTTGGTCAAGGCTCGATAAATACTCGGATCGAAT
257 GACGAGACGATCGCGAGCTACTC-AGATCGACTTGGTCAAGGCTCGATAAATACTCGGATCGAAT
*
331855 GGACTTGACTCGAGCTCGACTCGAATTCTTAACGAGCCGAAACAAGCTAC
321 GGACTTGACTCGAGCTCGACTCGAATTCTTAACGAACCGAAACAAGCTAC
331905 ATTGTTTGTTTAA-TTTTTCAACGAATTTCTTTTGAAAATGTTAAATTGATAAAAATTTTAGAAT
1 ATTGTTTGTTTAATTTTTTCAACGAATTTC-TTTGAAAATGTT-AATTGAT-AAAATTTTAGAAT
331969 ATAAATTTCTTTTTATTTTA-T-TTTATTTCCTTTAATTATATTACTTTTTAAAATTTACATTTT
63 ATAAATTTCTTTTTATTTTATTATTTATTTCCTTTAATTATATTACTTTTT-AAATTTACATTTT
332032 TTAAATAATCTATCTATATCAAATATTTAAGTTCACTAACAGGGGTTGGTTCAAGTGGTAAACAA
127 TTAAATAATCTATCTATATCAAATATTTAAG-TCACTAACA-GGGTTGGTTCAAGTGGTAAACAA
332097 TTTGATATCAC-T-TAAAGTATTGAGTTCGAGTCTTTGGATACCAGTTATTAATAGGA-TGTAAA
190 TTTGATATCACTTATAAAGTATTGAGTTCGAGTCTTTGGATACCAGTTATTAATA-GACTGTAAA
332159 TGAGACGAGACAGATCGCGAGCTACTC-GATCGACTTGGTCAAGGCTCGATAAATACTCGGATCG
254 TGAGACGAGAC-GATCGCGAGCTACTCAGATCGACTTGGTCAAGGCTCGATAAATACTCGGATCG
332223 AATGGACTTGACTCGAGCTCGACTCGAATTCTTAACGAACCGAAACAAGCTAC
318 AATGGACTTGACTCGAGCTCGACTCGAATTCTTAACGAACCGAAACAAGCTAC
332276 TTGATACTCG
Statistics
Matches: 362, Mismatches: 1, Indels: 20
0.95 0.00 0.05
Matches are distributed among these distances:
371 89 0.25
372 58 0.16
373 45 0.12
374 61 0.17
375 35 0.10
376 41 0.11
377 33 0.09
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (370 bp):
ATTGTTTGTTTAATTTTTTCAACGAATTTCTTTGAAAATGTTAATTGATAAAATTTTAGAATATA
AATTTCTTTTTATTTTATTATTTATTTCCTTTAATTATATTACTTTTTAAATTTACATTTTTTAA
ATAATCTATCTATATCAAATATTTAAGTCACTAACAGGGTTGGTTCAAGTGGTAAACAATTTGAT
ATCACTTATAAAGTATTGAGTTCGAGTCTTTGGATACCAGTTATTAATAGACTGTAAATGAGACG
AGACGATCGCGAGCTACTCAGATCGACTTGGTCAAGGCTCGATAAATACTCGGATCGAATGGACT
TGACTCGAGCTCGACTCGAATTCTTAACGAACCGAAACAAGCTAC
Found at i:332392 original size:371 final size:369
Alignment explanation
Indices: 331624--332364 Score: 1002
Period size: 371 Copynumber: 2.0 Consensus size: 369
331614 TTATTTATTT
331624 CCTTTAATTATATTACTTTTT-AAATTTACATTTTTTAAATAATCTATCTATATCAAATATTTAA
1 CCTTTAATTATATTACTTTTTAAAATTTACATTTTTTAAATAATCTATCTATATCAAATATTTAA
331688 GTCACTAACAGGGTTGGTTCAAGTGGTAAACAATTTGATATCACTTAAGTAAAGTATTGAGTTCG
66 GTCACTAACAGGGTTGGTTCAAGTGGTAAACAATTTGATATCACTT-A-TAAAGTATTGAGTTCG
331753 AGTCTTTGGATACCAGTTATTAATAGACTGTAAATGAGACGAGACGATCGCGAGCTACTCGAGAT
129 AGTCTTTGGATACCAGTTATTAATAGACTGTAAATGAGACGAGACGATCGCGAGCTACTC-AGAT
331818 CGACTTGGTCAAGGCTCGATAAATACTCGGATCGAATGGACTTGACTCGAGCTCGACTCGAATTC
193 CGACTTGGTCAAGGCTCGATAAATACTCGGATCGAATGGACTTGACTCGAGCTCGACTCGAATTC
* * ** **** ** * *
331883 TTAACGAGCCGAAACAAGCTACATTGTTTGTTTAATTTTTCAACGAATTTCTTTTGAAAATGTTA
258 TTAACGAACCGAAACAAGCTACATTGTTCGTCGAAAAGCTCAACGAATAGC-TTCGAAAATGATA
* *** * * * * *
331948 AATTGATAAAAATTTTAGAATATAAATTTCTTTTTATTTTATTTTATTT
322 AATTGATAAAAATTTTAGAAAATAAATAAATTATTATATAATATTA-TA
331997 CCTTTAATTATATTACTTTTTAAAATTTACATTTTTTAAATAATCTATCTATATCAAATATTTAA
1 CCTTTAATTATATTACTTTTTAAAATTTACATTTTTTAAATAATCTATCTATATCAAATATTTAA
332062 GTTCACTAACAGGGGTTGGTTCAAGTGGTAAACAATTTGATATCAC-T-TAAAGTATTGAGTTCG
66 G-TCACTAACA-GGGTTGGTTCAAGTGGTAAACAATTTGATATCACTTATAAAGTATTGAGTTCG
332125 AGTCTTTGGATACCAGTTATTAATAGGA-TGTAAATGAGACGAGACAGATCGCGAGCTACTC-GA
129 AGTCTTTGGATACCAGTTATTAATA-GACTGTAAATGAGACGAGAC-GATCGCGAGCTACTCAGA
332188 TCGACTTGGTCAAGGCTCGATAAATACTCGGATCGAATGGACTTGACTCGAGCTCGACTCGAATT
192 TCGACTTGGTCAAGGCTCGATAAATACTCGGATCGAATGGACTTGACTCGAGCTCGACTCGAATT
** *
332253 CTTAACGAACCGAAACAAGCTAC-TTGATACTCGACTCGAAAAGCTC-GTGAGTAGC-TCGAAAA
257 CTTAACGAACCGAAACAAGCTACATTG-T--TCG--TCGAAAAGCTCAACGAATAGCTTCGAAAA
* * *
332315 T-AT-AATAT-ATCAAGATTTTATTTAAAATAAATAAATTATTA-ATAATATTA
317 TGATAAAT-TGATAAAAATTTTA--GAAAATAAATAAATTATTATATAATATTA
332365 ACACTTATGT
Statistics
Matches: 329, Mismatches: 26, Indels: 28
0.86 0.07 0.07
Matches are distributed among these distances:
370 16 0.05
371 98 0.30
372 78 0.24
373 40 0.12
374 48 0.15
375 15 0.05
376 34 0.10
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (369 bp):
CCTTTAATTATATTACTTTTTAAAATTTACATTTTTTAAATAATCTATCTATATCAAATATTTAA
GTCACTAACAGGGTTGGTTCAAGTGGTAAACAATTTGATATCACTTATAAAGTATTGAGTTCGAG
TCTTTGGATACCAGTTATTAATAGACTGTAAATGAGACGAGACGATCGCGAGCTACTCAGATCGA
CTTGGTCAAGGCTCGATAAATACTCGGATCGAATGGACTTGACTCGAGCTCGACTCGAATTCTTA
ACGAACCGAAACAAGCTACATTGTTCGTCGAAAAGCTCAACGAATAGCTTCGAAAATGATAAATT
GATAAAAATTTTAGAAAATAAATAAATTATTATATAATATTATA
Found at i:346859 original size:30 final size:25
Alignment explanation
Indices: 346802--346849 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
346792 AAACACGTAC
*
346802 TTATCTTGAAATTTAAATTTTCTAA
1 TTATCTTAAAATTTAAATTTTCTAA
346827 TTATCTTAAAATTTAAATTTTCT
1 TTATCTTAAAATTTAAATTTTCT
346850 TCGATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.54
Consensus pattern (25 bp):
TTATCTTAAAATTTAAATTTTCTAA
Found at i:348926 original size:28 final size:28
Alignment explanation
Indices: 348870--348927 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
348860 TCATGCTATT
* * *
348870 TTCTCATATTATGATCGTGTTGTTGTTG
1 TTCTCATATTATGATCGGGTTCTTCTTG
* *
348898 TTCTCGTATTATGATTGGGTTCTTCTTG
1 TTCTCATATTATGATCGGGTTCTTCTTG
348926 TT
1 TT
348928 GTTTTTCTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (28 bp):
TTCTCATATTATGATCGGGTTCTTCTTG
Found at i:351480 original size:14 final size:14
Alignment explanation
Indices: 351432--351490 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
351422 CATCAACATT
351432 TAAAGTAAATAATT-
1 TAAA-TAAATAATTA
*
351446 TAAATTAAAT-ATCA
1 TAAA-TAAATAATTA
351460 T-AA-AAATAATTA
1 TAAATAAATAATTA
*
351472 TAAATAAATAATAA
1 TAAATAAATAATTA
351486 TAAAT
1 TAAAT
351491 TTTGAACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 4 0.11
12 4 0.11
13 6 0.16
14 23 0.62
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
TAAATAAATAATTA
Found at i:354098 original size:135 final size:135
Alignment explanation
Indices: 353856--354124 Score: 360
Period size: 135 Copynumber: 2.0 Consensus size: 135
353846 GATCAGCATG
* * *
353856 TGTTTGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACTATCAACCTCTGTT
1 TGTTTGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCAACCTCTGCT
* * * * * *
353921 TGTTTTTTAGACTCAAAGCGTTTGTATAGAACTTCATCATATCCCCAGCAGCAACCAGAGCCTCT
66 CGTTTTTCAGACGCAAAGCCTTTGTATAGAACTTCATCATATCCCCACCAGCAACCAGAGCCTCA
353986 CTTCA
131 CTTCA
* * * * * * *
353991 TGTTTGATACTGAAGATGTTCAAGAAGGCAAGAGATGGTCTTCTCAGCCACAACCATCTTCTGCT
1 TGTTTGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCAACCTCTGCT
**
354056 CGTTTTTCAGGA-GCAAAGCCTTTGTATAGAACTTCATCATATCCTGACCAGCAACCAGAGCCTC
66 CGTTTTTCA-GACGCAAAGCCTTTGTATAGAACTTCATCATATCCCCACCAGCAACCAGAGCCTC
354120 ACTTC
130 ACTTC
354125 TCAAGAGAAC
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
135 113 0.98
136 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (135 bp):
TGTTTGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCAACCTCTGCT
CGTTTTTCAGACGCAAAGCCTTTGTATAGAACTTCATCATATCCCCACCAGCAACCAGAGCCTCA
CTTCA
Found at i:361694 original size:14 final size:14
Alignment explanation
Indices: 361675--361702 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
361665 CAATCATTCA
361675 TGACCCAGAAAAGG
1 TGACCCAGAAAAGG
361689 TGACCCAGAAAAGG
1 TGACCCAGAAAAGG
361703 CTTAACAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.29, T:0.07
Consensus pattern (14 bp):
TGACCCAGAAAAGG
Found at i:367583 original size:18 final size:19
Alignment explanation
Indices: 367548--367584 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
367538 CACGGAATGT
367548 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
367568 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
367585 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:370266 original size:17 final size:17
Alignment explanation
Indices: 370244--370277 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
370234 TTCATAAATC
*
370244 TAAAATCCAACAATCCA
1 TAAAATCAAACAATCCA
370261 TAAAATCAAACAATCCA
1 TAAAATCAAACAATCCA
370278 AAATATTGAA
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:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (17 bp):
TAAAATCAAACAATCCA
Found at i:372259 original size:21 final size:21
Alignment explanation
Indices: 372233--372272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
372223 CAGAACCCCA
*
372233 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
372254 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
372273 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:372307 original size:20 final size:21
Alignment explanation
Indices: 372253--372315 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
372243 GATTCCCCTG
372253 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
372277 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
372297 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
372316 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:394242 original size:25 final size:26
Alignment explanation
Indices: 394199--394254 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
394189 AACGAAAATG
*
394199 AACAA-AATAAAAATAAAAAAAAGGA
1 AACAAGAATAAAAATAAAAAAAAGAA
* *
394224 AACAAGAATGAAAAT-AAAAATAGAA
1 AACAAGAATAAAAATAAAAAAAAGAA
394249 AACAAG
1 AACAAG
394255 GTTAATAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.75, C:0.05, G:0.11, T:0.09
Consensus pattern (26 bp):
AACAAGAATAAAAATAAAAAAAAGAA
Found at i:394334 original size:17 final size:16
Alignment explanation
Indices: 394312--394343 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
394302 TATGTACAAC
394312 CAATGAATAAATAAATA
1 CAATGAATAAA-AAATA
394329 CAATGAATAAAAAAT
1 CAATGAATAAAAAAT
394344 GACCATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (16 bp):
CAATGAATAAAAAATA
Found at i:394457 original size:2 final size:2
Alignment explanation
Indices: 394450--394481 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
394440 CTATAAAGTA
394450 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
394482 TAAAGTATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:394553 original size:2 final size:2
Alignment explanation
Indices: 394546--394570 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
394536 AAAATAAATA
394546 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
394571 AATTAGAAAA
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:394556 original size:21 final size:20
Alignment explanation
Indices: 394513--394556 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
394503 AATAATCCAA
*
394513 ATAAAAAAAATAATATACGT
1 ATAAAAAAAATAATATACAT
*
394533 ATAAAAATAAATAATATATAT
1 ATAAAAA-AAATAATATACAT
394554 ATA
1 ATA
394557 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
ATAAAAAAAATAATATACAT
Found at i:394638 original size:21 final size:19
Alignment explanation
Indices: 394602--394642 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
394592 ATAGTTATAT
394602 TAATATATAAAAATAATAA
1 TAATATATAAAAATAATAA
* *
394621 TAATATATACATAT-ATAA
1 TAATATATAAAAATAATAA
394639 TAAT
1 TAAT
394643 TACTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATATATAAAAATAATAA
Found at i:394749 original size:2 final size:2
Alignment explanation
Indices: 394742--394788 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
394732 GCTACTTTAT
394742 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
394783 TA TA TA
1 TA TA TA
394789 CTTTTAATAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:394916 original size:17 final size:16
Alignment explanation
Indices: 394889--394920 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
394879 TTTGATGGTC
394889 ATTTTTTATTCATTGT
1 ATTTTTTATTCATTGT
394905 ATTTTATTATTCATTG
1 ATTTT-TTATTCATTG
394921 GTTGTACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (16 bp):
ATTTTTTATTCATTGT
Found at i:398019 original size:98 final size:98
Alignment explanation
Indices: 397783--398451 Score: 1154
Period size: 98 Copynumber: 6.9 Consensus size: 98
397773 AATTGGGAAG
* * * *
397783 TTGTTTGTTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGGACTTGCGTTGTCTGAAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
397848 TCCTTCGTTGTGAAGTTGAAATTGG----GAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
397877 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* *
397942 TCCTTCGTTGTGACGTTGAAATTGGCTCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
* *
397975 TTGTTTATTGACAACCAGCGGTTCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
398040 TCCTTCGTTGTGCAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
*
398073 TTGTTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
398138 TCCTTCG-T-TG-AGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
* *
398168 TTATTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
1 TT-GTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
*
398233 ATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAA
65 ATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
398267 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
398332 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
398365 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
398430 TCCTTCGTTGTGAAGTTAAAAT
66 TCCTTCGTTGTGAAGTTGAAAT
398452 CGACTCTGGG
Statistics
Matches: 547, Mismatches: 20, Indels: 12
0.94 0.03 0.02
Matches are distributed among these distances:
94 85 0.16
95 22 0.04
96 69 0.13
97 2 0.00
98 347 0.63
99 22 0.04
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (98 bp):
TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
Found at i:398267 original size:292 final size:288
Alignment explanation
Indices: 397530--398439 Score: 1347
Period size: 292 Copynumber: 3.1 Consensus size: 288
397520 AGCCTTGAAT
* * *
397530 TGGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
1 TGGAGTCCAATATCCTTCG-T-TGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC
* * * * *
397595 CTTCGTCGTGAAGTTGAACTTTCATTGTCTTGAGTCCAATATCATTCGCTGTGGAGTTGAAATTG
64 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* * *
397660 GCTCTGAAATTGGGAAATTATTTATTGACAACCAGCGG-TCTCTTCATCATTAAGTTGAACTTAC
129 GCTCTGAAATT--G------TTTATTGACAACCAGCGGTTC-CTTCGTCATGAAGTTGAACTTGC
*
397724 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
185 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTG--A-----AA-TTGTTT
* * *
397789 GTTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGGACTTGCGTTGTC
242 ATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
397836 TGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC
1 TGGAGTCCAATATCCTTCG-T-TGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC
* *
397901 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGACGTTGAAATTG
64 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
397966 GCTCTGAAATTGTTTATTGACAACCAGCGGTTCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGG
129 GCTCTGAAATTGTTTATTGACAACCAGCGGTTCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGG
* *
398031 AGTCCAATATCCTTCGTTGTGCAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCAGTC
194 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTC
398096 CCTTCGTCGTGAAGTTGAACTTGCGTTGTC
259 CCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
398126 TGGAGTCCAATATCCTTCGTTG-AGTTGAAATTGGCCCTGAAATTATTTTATTGACAACCAGCGG
1 TGGAGTCCAATATCCTTCGTTGAAGTTGAAATTGG----GAAATT-GTTTATTGACAACCAGCGG
*
398190 TCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
61 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
* * *
398255 TTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
126 TTGGCTCTGAAATTGTTTATTGACAACCAGCGGTTCCTTCGTCATGAAGTTGAACTTGCGTTGTC
398320 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCG
191 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCG
398385 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
256 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
398418 TGGAGTCCAATATCCTTCGTTG
1 TGGAGTCCAATATCCTTCGTTG
398440 TGAAGTTAAA
Statistics
Matches: 568, Mismatches: 30, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
287 12 0.02
288 2 0.00
289 1 0.00
290 67 0.12
291 8 0.01
292 260 0.46
296 1 0.00
298 84 0.15
299 2 0.00
304 1 0.00
306 130 0.23
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (288 bp):
TGGAGTCCAATATCCTTCGTTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCT
TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC
TCTGAAATTGTTTATTGACAACCAGCGGTTCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAG
TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTC
Found at i:398340 original size:390 final size:393
Alignment explanation
Indices: 397530--398451 Score: 1371
Period size: 390 Copynumber: 2.3 Consensus size: 393
397520 AGCCTTGAAT
* * *
397530 TGGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGG---GAAGTTGTTTGTTGACAACCAGCGG
1 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCTGAAATTGTTTATTGACAACCAGCGG
* * * * * *
397592 TCCCTTCGTCGTGAAGTTGAACTTTCATTGTCTTGAGTCCAATATCATTCGCTGTGGAGTTGAAA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * * *
397657 TTGGCTCTGAAATTGGGAAATTATTTATTGACAACCAGCGGTCTCTTCATCATTAAGTTGAACTT
131 TTGGCCCTGAAATT-GG-----ATTTATTGACAACCAGCAGTCCCTTCATCATGAAGTTGAACTT
*
397722 ACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGT
190 ACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATT--G-AG-TGT
* * * *
397787 TTGTTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGGACTTGCGTTGTCTGAAGTCCAATATCCT
251 TTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCT
*
397852 TCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
316 TCGCTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
397917 AACTTGCGTTGTC
381 AACTTGCGTTGTC
*
397930 TGGAGTCCAATATCCTTCGTTGTGACGTTGAAATTGGCTCTGAAATTGTTTATTGACAACCAGCG
1 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC-CTGAAATTGTTTATTGACAACCAGCG
* * *
397995 GTTCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGCAGTTGAA
65 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
* * *
398060 ATTGGCCCTGAAATT-G-TTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
130 ATTGGCCCTGAAATTGGATTTATTGACAACCAGCAGTCCCTTCATCATGAAGTTGAACTTACGTT
398123 GTCTGGAGTCCAATATCCTTCG-T-TG-AGTTGAAATTGGCCCTGAAATT-A-T-TTTATTGACA
195 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGTGTTTATTGACA
*
398182 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGA
260 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGCTGTGA
398247 AGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
325 AGTTGAAATTGG----GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
398312 GCGTTGTC
386 GCGTTGTC
398320 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCG
1 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG-CCTGAAATTGTTTATTGACAACCAGCG
*
398385 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAA
65 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
398450 AT
130 AT
398452 CGACTCTGGG
Statistics
Matches: 482, Mismatches: 31, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
386 81 0.17
387 1 0.00
389 1 0.00
390 182 0.38
391 1 0.00
393 21 0.04
394 2 0.00
395 1 0.00
396 63 0.13
400 35 0.07
402 1 0.00
404 93 0.19
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (393 bp):
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCTGAAATTGTTTATTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
TTGGCCCTGAAATTGGATTTATTGACAACCAGCAGTCCCTTCATCATGAAGTTGAACTTACGTTG
TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGTGTTTATTGACAA
CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
GTC
Found at i:398351 original size:43 final size:43
Alignment explanation
Indices: 398290--398446 Score: 116
Period size: 43 Copynumber: 3.4 Consensus size: 43
398280 ACCAGCGGTC
398290 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** ***
398333 CCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTT-G--C-G---TTG--TCTGGA-GTCCA-ATAT
398387 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
398431 CCTTCGTTGTGAAGTT
1 CCTTCGTCGTGAAGTT
398447 AAAATCGACT
Statistics
Matches: 83, Mismatches: 19, Indels: 24
0.66 0.15 0.19
Matches are distributed among these distances:
43 35 0.42
44 2 0.02
45 3 0.04
46 5 0.06
47 1 0.01
48 3 0.04
50 3 0.04
51 1 0.01
52 5 0.06
53 3 0.04
54 2 0.02
55 20 0.24
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:407791 original size:17 final size:16
Alignment explanation
Indices: 407765--407796 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
407755 TTTGATGGCC
407765 ATTTTTTATTCATTGT
1 ATTTTTTATTCATTGT
407781 ATTTATTTATTCATTG
1 ATTT-TTTATTCATTG
407797 GTTGTACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (16 bp):
ATTTTTTATTCATTGT
Found at i:407882 original size:25 final size:25
Alignment explanation
Indices: 407854--407903 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
407844 GCTTATTAAC
*
407854 CTTGTTTTCTATTTTTATCTTCATT
1 CTTGTTTCCTATTTTTATCTTCATT
* * *
407879 CTTGTTTCCTTTTTTTTTGTTCATT
1 CTTGTTTCCTATTTTTATCTTCATT
407904 TTCGTTCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.08, C:0.16, G:0.06, T:0.70
Consensus pattern (25 bp):
CTTGTTTCCTATTTTTATCTTCATT
Found at i:415567 original size:16 final size:16
Alignment explanation
Indices: 415554--415588 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
415544 AGGGAATTAG
415554 AATCTGTAGGAATTGA
1 AATCTGTAGGAATTGA
415570 AATCTGTAGGAATTGA
1 AATCTGTAGGAATTGA
415586 AAT
1 AAT
415589 TCAATTCCAT
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:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (16 bp):
AATCTGTAGGAATTGA
Found at i:415987 original size:21 final size:21
Alignment explanation
Indices: 415958--416010 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
415948 ATTCTGACTA
415958 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
415979 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
416000 TCGCAATGCGA
1 TCGCATTGCGA
416011 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:416025 original size:20 final size:20
Alignment explanation
Indices: 416000--416093 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
415990 TTTTCCTAAT
416000 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
416020 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
416040 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
416061 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
416081 TCGCAATGCGAAT
1 TCGCAATGCGAAT
416094 CTGACTATCG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 47 0.72
21 18 0.28
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:416031 original size:41 final size:40
Alignment explanation
Indices: 416000--416093 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 40
415990 TTTTCCTAAT
*
416000 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGAAAATCGCAACGCGATTACGTAAA
* * *
416040 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGAAAATCGCAACGCGATTACGTAAA
416081 TCGCAATGCGAAT
1 TCGCAATGCGAAT
416094 CTGACTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 13 0.27
41 36 0.73
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCGCAACGCGATTACGTAAA
Found at i:416639 original size:20 final size:19
Alignment explanation
Indices: 416568--416647 Score: 99
Period size: 20 Copynumber: 4.1 Consensus size: 19
416558 TTAGTGATTC
416568 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
* **
416587 TCGCGTTGCGATAGTCATT
1 TCTCGTTGCGATTTTCATT
416606 TACGT-GTTGCGATTTTCATT
1 T-C-TCGTTGCGATTTTCATT
416626 CTCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATTTTCATT
416646 TC
1 TC
416648 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
19 20 0.39
20 30 0.59
21 1 0.02
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TCTCGTTGCGATTTTCATT
Found at i:418547 original size:94 final size:94
Alignment explanation
Indices: 418340--418810 Score: 756
Period size: 94 Copynumber: 5.1 Consensus size: 94
418330 TAGATTGCTT
* * * * *
418340 AGTAAATTTATTCGGTTGTTGCCAATACTGCTAAA-T-TGT-TT-ATTAACAGTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
418401 ATTTGTCTTTTGTGTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGT-TTTGTCTTTTGGTTGAA
*
418431 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
418496 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
418525 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
418590 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
418619 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
418684 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
418713 AGTAAATTTGTTCGTTTGATGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTAAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
418778 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
418806 AGTAA
1 AGTAA
418811 TGCAATCCAT
Statistics
Matches: 359, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
91 33 0.09
92 1 0.00
93 24 0.07
94 276 0.77
95 25 0.07
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:418927 original size:20 final size:20
Alignment explanation
Indices: 418902--418963 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
418892 TTTTGGTTGA
418902 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
418922 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
418941 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
418961 AAT
1 AAT
418964 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:418970 original size:33 final size:33
Alignment explanation
Indices: 418926--419023 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
418916 CGAGAGAATG
*
418926 AAAATCGCAACGCGAAACGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
* * *
418959 AGAATCGCAACGCGAAATGAAGATCGCAACGAC
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
*
418992 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAA-CGAAAATCGCAACG
419024 CGAAACTATA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 45 0.80
34 11 0.20
ACGTcount: A:0.47, C:0.26, G:0.20, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACGAAAATCGCAACGAC
Found at i:419015 original size:20 final size:20
Alignment explanation
Indices: 418992--419029 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
418982 TCGCAACGAC
418992 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
419012 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
419030 TATAATCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.29, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:419134 original size:20 final size:19
Alignment explanation
Indices: 419035--419150 Score: 125
Period size: 19 Copynumber: 6.3 Consensus size: 19
419025 GAAACTATAA
419035 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
419054 TCGTATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
419068 TCTCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
419087 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
419106 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
419125 CTCTCGTTGCTATTTTCATT
1 -TCGCGTTGCGATTTTCATT
419145 TCGCGT
1 TCGCGT
419151 GAAAATGATT
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
14 7 0.09
16 3 0.04
17 3 0.04
19 48 0.62
20 17 0.22
ACGTcount: A:0.09, C:0.22, G:0.20, T:0.49
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:419147 original size:39 final size:38
Alignment explanation
Indices: 419035--419150 Score: 125
Period size: 33 Copynumber: 3.2 Consensus size: 38
419025 GAAACTATAA
**
419035 TCGCGTTGCGATTTTCATTTCGTATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
419068 TCTCGTTGTGATTTTCATTTCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
419106 TCGCGTTGCGATTTTCATTCTCTCGTTGCTATTTTCATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
419145 TCGCGT
1 TCGCGT
419151 GAAAATGATT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
33 26 0.38
35 3 0.04
38 17 0.25
39 22 0.32
ACGTcount: A:0.09, C:0.22, G:0.20, T:0.49
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:419207 original size:25 final size:25
Alignment explanation
Indices: 419179--419226 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
419169 GTAGGTTTTA
419179 GATGTATAGAAAGTGTTGTTTGAAG
1 GATGTATAGAAAGTGTTGTTTGAAG
*
419204 GATGTGTAGAAAGTGTTGTTTGA
1 GATGTATAGAAAGTGTTGTTTGA
419227 GCAAATGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (25 bp):
GATGTATAGAAAGTGTTGTTTGAAG
Found at i:419598 original size:33 final size:33
Alignment explanation
Indices: 419551--419677 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
419541 ACTAAATTCG
* * *
419551 CGTTACGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
419584 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
419617 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
419650 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
419678 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:419610 original size:19 final size:19
Alignment explanation
Indices: 419586--419697 Score: 100
Period size: 19 Copynumber: 6.4 Consensus size: 19
419576 GATTCCCTCG
419586 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
419605 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
419619 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
419638 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
419652 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
419671 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
419691 TTGCGAT
1 TTGCGAT
419698 AGACATTAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
14 16 0.21
16 10 0.13
17 10 0.13
19 29 0.39
20 10 0.13
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:419622 original size:14 final size:14
Alignment explanation
Indices: 419603--419659 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
419593 TTTCATTTCG
419603 CATTGCGATTCTCT
1 CATTGCGATTCTCT
*
419617 CATTGCGATTTTCATTTCG
1 CATTGCGA--TTC---TCT
419636 CATTGCGATTCTCT
1 CATTGCGATTCTCT
*
419650 CGTTGCGATT
1 CATTGCGATT
419660 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (14 bp):
CATTGCGATTCTCT
Found at i:419696 original size:20 final size:20
Alignment explanation
Indices: 419650--419743 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
419640 GCGATTCTCT
**
419650 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
419669 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
419689 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
419708 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
419730 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
419744 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:422024 original size:15 final size:14
Alignment explanation
Indices: 421988--422026 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
421978 CTCCCGTGGC
421988 ATTTTTCTTCGGGG
1 ATTTTTCTTCGGGG
* *
422002 ACTTTTCTTTGGGG
1 ATTTTTCTTCGGGG
422016 ATTTCTTCTTC
1 ATTT-TTCTTC
422027 TTCTTTTTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.08, C:0.18, G:0.21, T:0.54
Consensus pattern (14 bp):
ATTTTTCTTCGGGG
Found at i:422251 original size:24 final size:24
Alignment explanation
Indices: 422217--422270 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
422207 CTGAAAAATC
422217 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
422241 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
422265 ATCAAA
1 ATCAAA
422271 TTTCGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:422284 original size:24 final size:24
Alignment explanation
Indices: 422217--422284 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
422207 CTGAAAAATC
* * *
422217 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
422241 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
422265 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
422285 TAGTACTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:423141 original size:20 final size:20
Alignment explanation
Indices: 423110--423240 Score: 88
Period size: 21 Copynumber: 6.5 Consensus size: 20
423100 GAAATTCAGT
*
423110 ATTGCGATTACGTAAATCGC
1 ATTGCGAATACGTAAATCGC
*
423130 AATGCGAATACGT-AATCGC
1 ATTGCGAATACGTAAATCGC
* * * *
423149 ATTGCGATTTTCCTAATTCGC
1 ATTGCGA-ATACGTAAATCGC
*
423170 ATTGCGATTTACGT-AATCGC
1 ATTGCGA-ATACGTAAATCGC
* *
423190 ATTGCGAATTAGGAAAATCGC
1 ATTGCGAA-TACGTAAATCGC
** *
423211 AACGCGAATTTA-GGAAATCGC
1 ATTGCGAA--TACGTAAATCGC
423232 ATTGCGAAT
1 ATTGCGAAT
423241 CTGGAAACTG
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
19 13 0.15
20 29 0.33
21 43 0.49
22 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (20 bp):
ATTGCGAATACGTAAATCGC
Done.