Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008992.1 Hibiscus syriacus cultivar Beakdansim tig00112368_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: 151563
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:7563 original size:45 final size:45
Alignment explanation
Indices: 7499--7589 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
7489 ATGCATGTAC
7499 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
1 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
* *
7544 AAGCAAATTACAAAAACAATTGAGAATGGAAATATAGAAATAAGT
1 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
7589 A
1 A
7590 CCCATTTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.59, C:0.08, G:0.14, T:0.19
Consensus pattern (45 bp):
AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
Found at i:8479 original size:161 final size:162
Alignment explanation
Indices: 8064--8774 Score: 787
Period size: 161 Copynumber: 4.4 Consensus size: 162
8054 ATACTTGAAA
* * * * * *
8064 AATCTTCAA-ATAACGGGTCTGCTCCCTTTTCTTTCA-AGGCGTATAAGACTCGAACAATCCTTG
1 AATCTTCAACA-AACGGGTCCGCTCCCTATTCCTTCAGA-GAGTATAGGACTCGAACAATCC-TC
* * * * * *
8127 GA-AAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAACAATCTTCAAAAAACGT
63 AACAAACGTGTCCGCTCCCTATTCGTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAACGG
* * * *
8190 GTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTTG
127 GTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCG
* * *
8226 AATAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTC
1 ---AATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCCTC
* * * *
8291 ATCAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTTGAATAATCTTCAACAAACGG
63 AACAAACGTGTCCGCTCCCTATTCGTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAACGG
*
8355 GTCCGCTCCCTATTCATTCAGAGAGTATA-AGACTCG
127 GTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCG
* * * * *
8391 -GTCTTCAATAAACGTGTCTGCTCCCTATTCCTTTAGAGAGTATAGGACTCGAACAATCCTCAAC
1 AATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCCTCAAC
* *
8455 AAACGTGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACCCGAACAATCTTCATA-AAACGTGTC
66 AAACGTGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTC
* *
8519 CTCTCTCTATTCCTTCAGAGAGTATAGAACTCG
130 CGCTCCCTATTCCTTCAGAGAGTATAGAACTCG
* * * * * **
8552 -ATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACATTCTTCATG
1 AATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCCTCAAC
* * * *
8616 AAACGGGTCCGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
66 AAACGTGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
*
8681 GCTCTCTATTCCTTCAGAGAGTATAGAACTCG
131 GCTCCCTATTCCTTCAGAGAGTATAGAACTCG
* *
8713 AACAATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATC
1 ---AATCTTCA-ACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATC
8775 TTCATAAAAT
Statistics
Matches: 479, Mismatches: 55, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
160 1 0.00
161 280 0.58
162 3 0.01
164 1 0.00
165 191 0.40
166 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (162 bp):
AATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCCTCAAC
AAACGTGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
GCTCCCTATTCCTTCAGAGAGTATAGAACTCG
Found at i:8779 original size:55 final size:54
Alignment explanation
Indices: 8064--8783 Score: 732
Period size: 55 Copynumber: 13.2 Consensus size: 54
8054 ATACTTGAAA
* * * * *
8064 AATCTTCAAATAACGGGTCTGCTCCCTTTTCTTTCA-AGGCGTATA-AGACTCGAAC
1 AATCTTCAAA-AACGTGTCCGCTCCCTATTCCTTCAGA-GAGTATAGA-ACTCGAAC
** * * * *
8119 AATCCTTGGAAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAAC
1 AAT-CTTCAAAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * * *
8174 AATCTTCAAAAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTTGAAT
1 AATCTTC-AAAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* *
8229 AATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA-AGACTCAAAC
1 AATCTTCAA-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * * * *
8284 AATCTTCATCAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTTGAAT
1 AATCTTCA-AAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* *
8339 AATCTTCAACAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATA-AGACTCG---
1 AATCTTCAA-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * *
8391 -GTCTTCAATAAACGTGTCTGCTCCCTATTCCTTTAGAGAGTATAGGACTCGAAC
1 AATCTTCAA-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * * *
8445 AATCCTCAACAAACGTGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACCCGAAC
1 AATCTTCAA-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
8500 AATCTTCATAAAACGTGTCCTCTCTCTATTCCTTCAGAGAGTATAGAACTCG---
1 AATCTTCA-AAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
*
8552 -ATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCAA-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * * * *
8606 ATTCTTCATGAAACGGGTCCGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCA-AAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
8661 AATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCAA-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
8716 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCA-AAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
8771 AATCTTCATAAAA
1 AATCTTCA-AAAA
8784 TAAGTTTGCT
Statistics
Matches: 580, Mismatches: 65, Indels: 40
0.85 0.09 0.06
Matches are distributed among these distances:
50 1 0.00
51 91 0.16
54 5 0.01
55 476 0.82
56 7 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (54 bp):
AATCTTCAAAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:8839 original size:37 final size:37
Alignment explanation
Indices: 8789--8869 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
8779 TAAAATAAGT
*
8789 TTGCTTCACTACTCTTCCATGAAGGTTTAAGATTGAC
1 TTGCTTCACTACTCTTCCATGAAGGCTTAAGATTGAC
*
8826 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCATGAAGGCTTAAGATTGAC
*
8863 TTACTTC
1 TTGCTTC
8870 GAATGGTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCATGAAGGCTTAAGATTGAC
Found at i:10152 original size:23 final size:22
Alignment explanation
Indices: 10131--10178 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
10121 CCTCCTTTTA
10131 TTTCTC-TTTTT-TTTTTCATT
1 TTTCTCTTTTTTATTTTTCATT
10151 TTTCTCTTTTTTCATTTTTCATT
1 TTTCTCTTTTTT-ATTTTTCATT
10174 TTTCT
1 TTTCT
10179 TCCCTTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.24
21 5 0.20
23 14 0.56
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTCTCTTTTTTATTTTTCATT
Found at i:10160 original size:8 final size:9
Alignment explanation
Indices: 10140--10258 Score: 58
Period size: 9 Copynumber: 13.6 Consensus size: 9
10130 ATTTCTCTTT
*
10140 TTTTTTTCA
1 TTTTTCTCA
10149 TTTTTCTC-
1 TTTTTCTCA
10157 TTTTT-TCA
1 TTTTTCTCA
10165 -TTTT-TCA
1 TTTTTCTCA
*
10172 TTTTTCTTCC
1 TTTTTC-TCA
*
10182 CTTTTC-CA
1 TTTTTCTCA
*
10190 TTTTTTCTTCT
1 -TTTTTC-TCA
* *
10201 TTTTTTTCC
1 TTTTTCTCA
*
10210 CTTTTCGT--
1 TTTTTC-TCA
10218 TTTTTC-CA
1 TTTTTCTCA
10226 TCATTTT-TCA
1 T--TTTTCTCA
10236 TTTTTCTCA
1 TTTTTCTCA
10245 TTTTTCTCA
1 TTTTTCTCA
10254 TTTTT
1 TTTTT
10259 TCTCTTTTAT
Statistics
Matches: 85, Mismatches: 11, Indels: 28
0.69 0.09 0.23
Matches are distributed among these distances:
7 9 0.11
8 20 0.24
9 35 0.41
10 20 0.24
11 1 0.01
ACGTcount: A:0.08, C:0.21, G:0.01, T:0.71
Consensus pattern (9 bp):
TTTTTCTCA
Found at i:10160 original size:18 final size:16
Alignment explanation
Indices: 10141--10266 Score: 65
Period size: 18 Copynumber: 7.2 Consensus size: 16
10131 TTTCTCTTTT
10141 TTTTTTCATTTTTCTC
1 TTTTTTCATTTTTCTC
10157 TTTTTTCATTTTTCAT-
1 TTTTTTCATTTTTC-TC
* * *
10173 TTTTCTTCCCTTTTCCATT
1 TTTT-TT-CATTTTTC-TC
* *
10192 TTTTCTTCTTTTTTTTC
1 TTTT-TTCATTTTTCTC
** *
10209 CCTTTTCGTTTTTTCCATC
1 TTTTTTC-ATTTTT-C-TC
*
10228 ATTTTTCATTTTTCTC
1 TTTTTTCATTTTTCTC
10244 ATTTTTCTCATTTTTTCTC
1 -TTTTT-TCA-TTTTTCTC
10263 TTTT
1 TTTT
10267 ATTTCTTCTT
Statistics
Matches: 87, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
16 23 0.26
17 17 0.20
18 25 0.29
19 22 0.25
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.71
Consensus pattern (16 bp):
TTTTTTCATTTTTCTC
Found at i:19964 original size:51 final size:47
Alignment explanation
Indices: 19909--20073 Score: 140
Period size: 45 Copynumber: 3.5 Consensus size: 47
19899 TATCTACCCC
*
19909 CATGCTTTGTTATCCACAAAAAGAAATCCTAACCTCATGATATCTAATTCG
1 CATGC-TT-TTATCCA-AAAAAGAAA-CCTAACCGCATGATATCTAATTCG
* * * *
19960 CATGC--TTATTCAGAAAATAAACCTAACCGCATGATATCTAGTTCG
1 CATGCTTTTATCCAAAAAAGAAACCTAACCGCATGATATCTAATTCG
* * * * *
20005 CATGCTTGT-T-CGAAAAATAAACCTAATCGCATGATATCTAGTTCG
1 CATGCTTTTATCCAAAAAAGAAACCTAACCGCATGATATCTAATTCG
* * *
20050 CAAGCATTTATTCAAAAAATGAAA
1 CATGCTTTTATCCAAAAAA-GAAA
20074 ATAAATGACT
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
45 65 0.68
46 9 0.09
47 13 0.14
48 3 0.03
51 5 0.05
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.30
Consensus pattern (47 bp):
CATGCTTTTATCCAAAAAAGAAACCTAACCGCATGATATCTAATTCG
Found at i:19993 original size:45 final size:45
Alignment explanation
Indices: 19927--20069 Score: 180
Period size: 45 Copynumber: 3.1 Consensus size: 45
19917 GTTATCCACA
* * *
19927 AAAAGAAATCCTAACCTCATGATATCTAATTCGCATGCTTATTCAG
1 AAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCTTATTCAG
*
19973 AAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTGTTC-G
1 AAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTATTCAG
* * *
20017 AAAAATAAACCTAATCGCATGATATCTAGTTCGCAAGCATTTATTCAA
1 -AAAATAAACCTAACCGCATGATATCTAGTTCGCATGC--TTATTCAG
20065 AAAAT
1 AAAAT
20070 GAAAATAAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
44 1 0.01
45 67 0.79
46 7 0.08
47 10 0.12
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.29
Consensus pattern (45 bp):
AAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTATTCAG
Found at i:22460 original size:45 final size:45
Alignment explanation
Indices: 22396--22486 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
22386 ATGCATGTAC
22396 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
1 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
*
22441 AAGCAAATTACAAAAACAATTGAGAATGGAAACATAGAAATAAGT
1 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
22486 A
1 A
22487 CCCCTTTTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (45 bp):
AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
Found at i:26978 original size:12 final size:12
Alignment explanation
Indices: 26961--26985 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26951 CATTTGAAAT
26961 TCTAGAATCGAA
1 TCTAGAATCGAA
26973 TCTAGAATCGAA
1 TCTAGAATCGAA
26985 T
1 T
26986 TGTATCATAT
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TCTAGAATCGAA
Found at i:30599 original size:24 final size:23
Alignment explanation
Indices: 30572--30617 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
30562 AACTTTTAGC
30572 TTATACATACATATACT-TATACAA
1 TTATACAT--ATATACTATATACAA
30596 TTATACATATATACTATATACA
1 TTATACATATATACTATATACA
30618 GTGAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 6 0.29
24 8 0.38
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (23 bp):
TTATACATATATACTATATACAA
Found at i:34564 original size:21 final size:21
Alignment explanation
Indices: 34500--34568 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
34490 GTGCGGCGGT
* *
34500 GGACGGTGGTCGGAAGACGGC
1 GGACGATGGTCGGAGGACGGC
* * *
34521 GAACGGTGGTTGGAGGACGGC
1 GGACGATGGTCGGAGGACGGC
34542 GGACGATGGTCGGAGGACGGC
1 GGACGATGGTCGGAGGACGGC
34563 GGACGA
1 GGACGA
34569 CAAGCGACTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.20, C:0.17, G:0.52, T:0.10
Consensus pattern (21 bp):
GGACGATGGTCGGAGGACGGC
Found at i:40500 original size:16 final size:16
Alignment explanation
Indices: 40461--40492 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40451 TTGATCAAAT
40461 TAATAATTTAAATTTA
1 TAATAATTTAAATTTA
*
40477 TAATAATTTTAATTTA
1 TAATAATTTAAATTTA
40493 ATATAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATAATTTAAATTTA
Found at i:41282 original size:36 final size:36
Alignment explanation
Indices: 41239--41314 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
41229 ACAGAATTAA
** *
41239 ACGGGGACGGGAAAAAATTGTTTATGTTAAACGGGG
1 ACGGGGACGGGAAAAAACCGTTTATGCTAAACGGGG
*
41275 ACGGGGACGGGGAAAAACCGTTTATGCTAAACGGGG
1 ACGGGGACGGGAAAAAACCGTTTATGCTAAACGGGG
41311 ACGG
1 ACGG
41315 TGATGGGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.13, G:0.38, T:0.17
Consensus pattern (36 bp):
ACGGGGACGGGAAAAAACCGTTTATGCTAAACGGGG
Found at i:41366 original size:12 final size:12
Alignment explanation
Indices: 41332--41380 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
41322 TTTGGTAATC
*
41332 CCCGCCCCGATTA
1 CCCGGCCCGA-TA
*
41345 CCCGGGCCGATA
1 CCCGGCCCGATA
*
41357 CCTGGCCCGATA
1 CCCGGCCCGATA
*
41369 CCCGACCCGATA
1 CCCGGCCCGATA
41381 AATATTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 22 0.73
13 8 0.27
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (12 bp):
CCCGGCCCGATA
Found at i:42019 original size:23 final size:23
Alignment explanation
Indices: 41990--42058 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
41980 TTGATTTAAG
*
41990 TTCTAATTCAAACTCGAGTTCAA
1 TTCTAATTCAAATTCGAGTTCAA
* *
42013 TTTTAATTCAAATTCGAGTTCAG
1 TTCTAATTCAAATTCGAGTTCAA
*
42036 TTCTAATTCAAATTCGAGCTCAA
1 TTCTAATTCAAATTCGAGTTCAA
42059 ACCTGAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (23 bp):
TTCTAATTCAAATTCGAGTTCAA
Found at i:43610 original size:19 final size:19
Alignment explanation
Indices: 43574--43615 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
43564 TTTAAAAAGA
*
43574 AAAAATATAATATCAA-TT
1 AAAAATATAATAACAATTT
*
43592 AAAAATATATATAAGAATTT
1 AAAAATATA-ATAACAATTT
43612 AAAA
1 AAAA
43616 CTTAGAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 5 0.25
20 6 0.30
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAATATAATAACAATTT
Found at i:45030 original size:20 final size:20
Alignment explanation
Indices: 44996--45036 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
44986 GGATTCTACC
44996 TAAAAATCACAAAAATATATA
1 TAAAAATCACAAAAATA-ATA
*
45017 TAAAAAT-ACTAAAATAATA
1 TAAAAATCACAAAAATAATA
45036 T
1 T
45037 CATTTGATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 8 0.42
21 7 0.37
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAAAATCACAAAAATAATA
Found at i:45876 original size:41 final size:41
Alignment explanation
Indices: 45831--45914 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
45821 ATTCACGTTG
*
45831 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * *
45872 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
45913 CA
1 CA
45915 AATTCGTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (41 bp):
CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:46009 original size:6 final size:6
Alignment explanation
Indices: 45998--46055 Score: 116
Period size: 6 Copynumber: 9.7 Consensus size: 6
45988 GACACGTATT
45998 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
46046 ACCACG ACCA
1 ACCACG ACCA
46056 AATGGAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:46090 original size:21 final size:21
Alignment explanation
Indices: 46064--46220 Score: 117
Period size: 21 Copynumber: 7.6 Consensus size: 21
46054 CAAATGGAAA
*
46064 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAATTTGAACT
* * *
46085 ATCGCAACGCGAACTGGAA-A
1 ATCGCAACGCGAATTTGAACT
* *
46105 ATCGCAACGCGACTGT-AGACT
1 ATCGCAACGCGAATTTGA-ACT
* * *
46126 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAATTTGAACT
* *
46146 ATCGCAACGCGACTGT-AGACT
1 ATCGCAACGCGAATTTGA-ACT
* * *
46167 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAATTTGAACT
* *
46187 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATTTGAACT
46208 ATCGCAACGCGAA
1 ATCGCAACGCGAA
46221 ATGGAAACGT
Statistics
Matches: 99, Mismatches: 30, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
19 2 0.02
20 41 0.41
21 54 0.55
22 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAATTTGAACT
Found at i:46115 original size:41 final size:41
Alignment explanation
Indices: 46055--46299 Score: 337
Period size: 41 Copynumber: 6.1 Consensus size: 41
46045 GACCACGACC
*
46055 AAATGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCG
1 AAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCG
* * *
46096 AACTGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCG
1 AAATGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCG
* *
46137 AAATGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCG
1 AAATGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCG
46178 AAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCG
1 AAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCG
*
46219 AAATGG---A----AACGTGATTTTCCAACTATCGCAACGCG
1 AAATGGAAAATCGCAACGCGATTTT-CAACTATCGCAACGCG
46254 AAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCG
1 AAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCG
46295 AAATG
1 AAATG
46300 CAACGCGAAT
Statistics
Matches: 186, Mismatches: 8, Indels: 20
0.87 0.04 0.09
Matches are distributed among these distances:
34 10 0.05
35 22 0.12
38 2 0.01
40 1 0.01
41 140 0.75
42 11 0.06
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (41 bp):
AAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCG
Found at i:46244 original size:35 final size:34
Alignment explanation
Indices: 46192--46307 Score: 135
Period size: 35 Copynumber: 3.2 Consensus size: 34
46182 GGAAAATCGC
46192 AACGCGATTTTCAACTATCGCAACGCGAAATGGA
1 AACGCGATTTTCAACTATCGCAACGCGAAATGGA
*
46226 AACGTGATTTTCCAACTATCGCAACGCGAAATGGAAAA
1 AACGCGATTTT-CAACTATCGCAACGCGAAATGG---A
*
46264 TCGCAACGCGATTTTCAACTATCGCAACGCGAAAT-GC
1 ----AACGCGATTTTCAACTATCGCAACGCGAAATGGA
46301 AACGCGA
1 AACGCGA
46308 ATTTGCGATA
Statistics
Matches: 71, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
33 7 0.10
34 10 0.14
35 22 0.31
38 1 0.01
40 1 0.01
41 20 0.28
42 10 0.14
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (34 bp):
AACGCGATTTTCAACTATCGCAACGCGAAATGGA
Found at i:46289 original size:21 final size:21
Alignment explanation
Indices: 46226--46295 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 21
46216 GCGAAATGGA
*
46226 AACGTGATTTTCCAACTATCGC
1 AACGCGATTTT-CAACTATCGC
** ** *
46248 AACGCGAAATGGAA-AATCGC
1 AACGCGATTTTCAACTATCGC
46268 AACGCGATTTTCAACTATCGC
1 AACGCGATTTTCAACTATCGC
46289 AACGCGA
1 AACGCGA
46296 AATGCAACGC
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
20 15 0.42
21 14 0.39
22 7 0.19
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
AACGCGATTTTCAACTATCGC
Found at i:46303 original size:21 final size:21
Alignment explanation
Indices: 46238--46303 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
46228 CGTGATTTTC
46238 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
46259 GAA-AATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
46279 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
46300 CAAC
1 CAAC
46304 GCGAATTTGC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:48457 original size:42 final size:42
Alignment explanation
Indices: 48267--48471 Score: 211
Period size: 42 Copynumber: 4.8 Consensus size: 42
48257 TCGATGTTAG
*
48267 AGCTTGGGATTTCAGCAC-CTG-ACGAGGAACTTTCAATGTTTA
1 AGCTTGGGATTTCAGCACACGGCA-G-GGAACTTTCAATGTTTA
* * *
48309 AGCTTGGGATTTCTTCAGCAGACGGCAAGGAACGTTCAATGTTTA
1 AGCTTGGGA--T-TTCAGCACACGGCAGGGAACTTTCAATGTTTA
* *
48354 AGCTTGAGATTTCAGCACCCGGC-GAGGAACTTTCAATGTTTA
1 AGCTTGGGATTTCAGCACACGGCAG-GGAACTTTCAATGTTTA
* * * *
48396 CA-CTTGGAAATTCATCACACGGCAGGGGACTTTCAATGTTTA
1 -AGCTTGGGATTTCAGCACACGGCAGGGAACTTTCAATGTTTA
* *
48438 AGCTTGGGATTTCAGCACACAGCAAGGAACTTTC
1 AGCTTGGGATTTCAGCACACGGCAGGGAACTTTC
48472 GTCTTCACCG
Statistics
Matches: 133, Mismatches: 21, Indels: 18
0.77 0.12 0.10
Matches are distributed among these distances:
41 1 0.01
42 94 0.71
43 3 0.02
44 1 0.01
45 31 0.23
46 2 0.02
47 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (42 bp):
AGCTTGGGATTTCAGCACACGGCAGGGAACTTTCAATGTTTA
Found at i:48466 original size:84 final size:85
Alignment explanation
Indices: 48267--48471 Score: 254
Period size: 84 Copynumber: 2.4 Consensus size: 85
48257 TCGATGTTAG
* * * *
48267 AGCTTGGGATTTCAGCACCTGACGAGGAACTTTCAATGTTTAAGCTTGGGATTTCTTCAGCAGAC
1 AGCTTGGGATTTCAGCACCAG-CGAGGAACTTTCAATGTTTAAGCTTGGAAATTCATCAGCA-AC
48332 GGCAAGGAACGTTCAATGTTTA
64 GGCAAGGAACGTTCAATGTTTA
* *
48354 AGCTTGAGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTACA-CTTGGAAATTCATCA-C-AC
1 AGCTTGGGATTTCAGCA-CCAGCGAGGAACTTTCAATGTTTA-AGCTTGGAAATTCATCAGCAAC
* * *
48416 GGCAGGGGACTTTCAATGTTTA
64 GGCAAGGAACGTTCAATGTTTA
*
48438 AGCTTGGGATTTCAGCACACAGCAAGGAACTTTC
1 AGCTTGGGATTTCAGCAC-CAGCGAGGAACTTTC
48472 GTCTTCACCG
Statistics
Matches: 104, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
83 1 0.01
84 50 0.48
86 1 0.01
87 48 0.46
88 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (85 bp):
AGCTTGGGATTTCAGCACCAGCGAGGAACTTTCAATGTTTAAGCTTGGAAATTCATCAGCAACGG
CAAGGAACGTTCAATGTTTA
Found at i:52161 original size:263 final size:260
Alignment explanation
Indices: 51672--52170 Score: 707
Period size: 263 Copynumber: 1.9 Consensus size: 260
51662 ATTGCATTTT
* * * *
51672 AACATATAAAAAAAACCATCCTATAAATCAAGAACTCATATTTTGATCCCATGGTCATTAACATT
1 AACATAT-AAAAAAACCATCCTATAAATCAAGAACTCATATATAGATCCCATGATCATGAACATT
* * * *
51737 AACCATAAATGCATACACATTGATTTTTAACTTATAAACAATCAACAAAACTGGGAATTTAACCT
65 AACCATAAAAGCATACACATTGATTTGTAACTTACAAACAATCAACAAAACTGGAAATTTAACCT
* * * * *
51802 AGCAACCAAACTTTCCAACCAGATTCTGAAAACCAGAAAACGGCATCAATGCCTCATCTTTAGAT
130 AGCAACCAAACTTTCCAACAAAAATCTGAAAACCAGAAAACGACATCAATGCCTCATCTCTAGAT
* * * *
51867 CCTATTAGGATTATCAAAACAAAATTATCTCATTAAACCATACCCATAAATTGCATTAAAAGTTA
195 CCTATTAGCATAATCAAAACAAAAATATCTCATGAAACCATACCCATAAATTGCATTAAAAGTTA
51932 A
260 A
*
51933 AACATAT-AAAAAACCATCCCTATAAATCAATAACTCATATATAGATCCCATGATCATGAACATT
1 AACATATAAAAAAACCAT-CCTATAAATCAAGAACTCATATATAGATCCCATGATCATGAACATT
*
51997 AACCATAAACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACAAAAACTGGAAATTTAA
65 AACCATAAA--AGCATACACATTGATTTGTAACTTACAAACAATCAAC-AAAACTGGAAATTTAA
* *
52062 CCTAG-AAGCCGAACTTTCCAACAAAAATCTGAAGACCAGAAAACGACATCAATGCCTCATCTCT
127 CCTAGCAA-CCAAACTTTCCAACAAAAATCTGAAAACCAGAAAACGACATCAATGCCTCATCTCT
**
52126 AGATCCTATTAGCATCAAT-GTAACAAAAATATCTCATGAAACCAT
191 AGATCCTATTAGCAT-AATCAAAACAAAAATATCTCATGAAACCAT
52171 CCCTGTAAAT
Statistics
Matches: 209, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
259 10 0.05
260 50 0.24
261 7 0.03
262 35 0.17
263 105 0.50
264 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (260 bp):
AACATATAAAAAAACCATCCTATAAATCAAGAACTCATATATAGATCCCATGATCATGAACATTA
ACCATAAAAGCATACACATTGATTTGTAACTTACAAACAATCAACAAAACTGGAAATTTAACCTA
GCAACCAAACTTTCCAACAAAAATCTGAAAACCAGAAAACGACATCAATGCCTCATCTCTAGATC
CTATTAGCATAATCAAAACAAAAATATCTCATGAAACCATACCCATAAATTGCATTAAAAGTTAA
Found at i:52565 original size:227 final size:225
Alignment explanation
Indices: 51943--52902 Score: 1321
Period size: 221 Copynumber: 4.3 Consensus size: 225
51933 AACATATAAA
* *
51943 AAACCATCCCTATAAATCAATAACTCATATATAGATCCCATGATCATG----AACATTAACCATA
1 AAACCATCCCTATAAATCAAGAACTCATATTTAGATCCCATGATCATGAAATAACATTAACCATA
*
52004 AACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACAAAAACTGGAAATTTAACCTAGAA
66 AACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACAAAAACTGGGAATTTAACCTAGAA
* *
52069 GCCGAACTTTCCAACAAAAATCTGAAGACCAGAAAACGACATCAATGCCTCATCTCTAGATCCTA
131 GCCGAACTTTCCAACAAAAATCTGAAGACCAGAAAACAACATCAATGCCTCATCTTTAGATCCTA
*
52134 TTAGCATCAATG-TAACAAAAATATCTCATG
196 TTAGCATCAA-GATAACAAAAATCTCTCATG
* *
52164 AAACCATCCCTGTAAATCAAGAACTCATATTTAGATCCCATGATCATG----AACATTAACTATA
1 AAACCATCCCTATAAATCAAGAACTCATATTTAGATCCCATGATCATGAAATAACATTAACCATA
52225 AACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACAAAAACTGGGAATTTAACCTAGAA
66 AACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACAAAAACTGGGAATTTAACCTAGAA
* * * *
52290 GCCGGACTATCCAACAAAAAACTGAAGACCAGAAAATGAA-ATCAATGCCTCATCTTTAGATCCT
131 GCCGAACTTTCCAACAAAAATCTGAAGACCAGAAAA-CAACATCAATGCCTCATCTTTAGATCCT
52354 ATTAGCATCAAGATAACAAAAATCTCTCATG
195 ATTAGCATCAAGATAACAAAAATCTCTCATG
* **
52385 AAGCCATCCCTGCAAATCAAGAACTCATATTTAGATCCCATGATCATGAAAATTAACATTAACCA
1 AAACCATCCCTATAAATCAAGAACTCATATTTAGATCCCATGATCATG-AAA-TAACATTAACCA
* *
52450 TAAACCAGCCTACACATTGATTTGTAACTTGCAAACAATCAACAAAAACTGGGAATTCAACCTAG
64 TAAACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACAAAAACTGGGAATTTAACCTAG
* * * * *
52515 AAGCCAAACTTTCCAACCAGAATCTGAGGACCAGAAAACAACATCAATGCCTCATTTTTAGATCC
129 AAGCCGAACTTTCCAACAAAAATCTGAAGACCAGAAAACAACATCAATGCCTCATCTTTAGATCC
*
52580 TATTAGCATCAAGACAACAAAAATCTCTCATG
194 TATTAGCATCAAGATAACAAAAATCTCTCATG
*
52612 AAGCCATCCCTATAAATCAAGAACTCATATTTAGATCCCATGATCATGATCATGAACATGAACAT
1 AAACCATCCCTATAAATCAAGAACTCATATTTAGAT-CC-----CATGATCATGAA-AT-AACAT
* * * * ** *
52677 TAACCATAAACCATCCTACACATTGATTTTTAACTTATATACGGTCAACAAAAATTGGGAATTTA
58 TAACCATAAACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACAAAAACTGGGAATTTA
** * * *
52742 ACCTAGCTGCC-AACTTTCCAACCAGAATCTGAAAACCAGAAAACAACATCAATGCCTCATCTTT
123 ACCTAGAAGCCGAACTTTCCAACAAAAATCTGAAGACCAGAAAACAACATCAATGCCTCATCTTT
* * **
52806 AGATCCTACTAGCATCAAGATGACAAATCTCTCTCATG
188 AGATCCTATTAGCATCAAGATAACAAAAATCTCTCATG
* * * *
52844 AAACCATCCCTATAAATCAAGAACTCGTATTGAGATCACATAATCATGAACATTAACAT
1 AAACCATCCCTATAAATCAAGAACTCATATTTAGATCCCATGATCATGAA-A-TAACAT
52903 GAACAAACAA
Statistics
Matches: 668, Mismatches: 53, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
220 1 0.00
221 251 0.38
222 1 0.00
226 20 0.03
227 192 0.29
228 2 0.00
231 1 0.00
232 119 0.18
233 81 0.12
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (225 bp):
AAACCATCCCTATAAATCAAGAACTCATATTTAGATCCCATGATCATGAAATAACATTAACCATA
AACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACAAAAACTGGGAATTTAACCTAGAA
GCCGAACTTTCCAACAAAAATCTGAAGACCAGAAAACAACATCAATGCCTCATCTTTAGATCCTA
TTAGCATCAAGATAACAAAAATCTCTCATG
Found at i:52841 original size:232 final size:232
Alignment explanation
Indices: 51981--52907 Score: 1271
Period size: 227 Copynumber: 4.1 Consensus size: 232
51971 ATATAGATCC
*
51981 CATGATCATGAACATTAACCATAAACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACA
1 CATGAACATGAACATTAACCATAAACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACA
* * * * *
52046 AAAACTGGAAATTTAACCTAGAAGCCGAACTTTCCAACAAAAATCTGAAGACCAGAAAACGACAT
66 AAAACTGGGAATTTAACCTAGAAGCCAAACTTTCCAACCAGAATCTGAAGACCAGAAAACAACAT
* * *
52111 CAATGCCTCATCTCTAGATCCTATTAGCATCAATG-TAACAAAAATATCTCATGAAACCATCCCT
131 CAATGCCTCATCTTTAGATCCTATTAGCATCAA-GATAACAAAAATCTCTCATGAAGCCATCCCT
*
52175 GTAAATCAAGAACTCATATTTAGAT-CC-----CATG-
195 ATAAATCAAGAACTCATATTTAGATCCCATGATCATGA
*
52206 -AT---CATGAACATTAACTATAAACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACA
1 CATGAACATGAACATTAACCATAAACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACA
** * * * * *
52267 AAAACTGGGAATTTAACCTAGAAGCCGGACTATCCAACAAAAAACTGAAGACCAGAAAATGAA-A
66 AAAACTGGGAATTTAACCTAGAAGCCAAACTTTCCAACCAGAATCTGAAGACCAGAAAA-CAACA
52331 TCAATGCCTCATCTTTAGATCCTATTAGCATCAAGATAACAAAAATCTCTCATGAAGCCATCCCT
130 TCAATGCCTCATCTTTAGATCCTATTAGCATCAAGATAACAAAAATCTCTCATGAAGCCATCCCT
**
52396 GCAAATCAAGAACTCATATTTAGATCCCATGATCATG-
195 ATAAATCAAGAACTCATATTTAGATCCCATGATCATGA
* *
52433 -A--AA-ATTAACATTAACCATAAACCAGCCTACACATTGATTTGTAACTTGCAAACAATCAACA
1 CATGAACATGAACATTAACCATAAACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACA
* *
52494 AAAACTGGGAATTCAACCTAGAAGCCAAACTTTCCAACCAGAATCTGAGGACCAGAAAACAACAT
66 AAAACTGGGAATTTAACCTAGAAGCCAAACTTTCCAACCAGAATCTGAAGACCAGAAAACAACAT
* *
52559 CAATGCCTCATTTTTAGATCCTATTAGCATCAAGACAACAAAAATCTCTCATGAAGCCATCCCTA
131 CAATGCCTCATCTTTAGATCCTATTAGCATCAAGATAACAAAAATCTCTCATGAAGCCATCCCTA
52624 TAAATCAAGAACTCATATTTAGATCCCATGATCATGA
196 TAAATCAAGAACTCATATTTAGATCCCATGATCATGA
* * * * **
52661 TCATGAACATGAACATTAACCATAAACCATCCTACACATTGATTTTTAACTTATATACGGTCAAC
1 -CATGAACATGAACATTAACCATAAACCAGCCTACACATTGATTTGTAACTTACAAACAATCAAC
* ** *
52726 AAAAATTGGGAATTTAACCTAGCTGCC-AACTTTCCAACCAGAATCTGAAAACCAGAAAACAACA
65 AAAAACTGGGAATTTAACCTAGAAGCCAAACTTTCCAACCAGAATCTGAAGACCAGAAAACAACA
* * ** *
52790 TCAATGCCTCATCTTTAGATCCTACTAGCATCAAGATGACAAATCTCTCTCATGAAACCATCCCT
130 TCAATGCCTCATCTTTAGATCCTATTAGCATCAAGATAACAAAAATCTCTCATGAAGCCATCCCT
* * * *
52855 ATAAATCAAGAACTCGTATTGAGATCACATAATCATGAA
195 ATAAATCAAGAACTCATATTTAGATCCCATGATCATG-A
*
52894 CATTAACATGAACA
1 CATGAACATGAACA
52908 AACAATCCAT
Statistics
Matches: 631, Mismatches: 53, Indels: 29
0.88 0.07 0.04
Matches are distributed among these distances:
220 1 0.00
221 198 0.31
222 3 0.00
224 2 0.00
226 2 0.00
227 210 0.33
230 1 0.00
232 141 0.22
233 73 0.12
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (232 bp):
CATGAACATGAACATTAACCATAAACCAGCCTACACATTGATTTGTAACTTACAAACAATCAACA
AAAACTGGGAATTTAACCTAGAAGCCAAACTTTCCAACCAGAATCTGAAGACCAGAAAACAACAT
CAATGCCTCATCTTTAGATCCTATTAGCATCAAGATAACAAAAATCTCTCATGAAGCCATCCCTA
TAAATCAAGAACTCATATTTAGATCCCATGATCATGA
Found at i:53639 original size:21 final size:19
Alignment explanation
Indices: 53614--53659 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
53604 TATATTTCAA
53614 AATATATACTGAGAAAAAT
1 AATATATACTGAGAAAAAT
53633 AATATATACTGAGAAAAAT
1 AATATATACTGAGAAAAAT
53652 AATATATA
1 AATATATA
53660 ATATAGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.28
Consensus pattern (19 bp):
AATATATACTGAGAAAAAT
Found at i:54215 original size:20 final size:19
Alignment explanation
Indices: 54192--54238 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
54182 TAATTATCTC
54192 TATTTAAATATTATTTTAAT
1 TATTTAAAT-TTATTTTAAT
*
54212 TATTT--ATTTATTTTACT
1 TATTTAAATTTATTTTAAT
54229 TATTATAAAT
1 TATT-TAAAT
54239 GGAAACTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 13 0.57
18 3 0.13
20 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTAAATTTATTTTAAT
Found at i:59982 original size:41 final size:41
Alignment explanation
Indices: 59925--60006 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
59915 TGCTATGGCA
59925 AACTTTCATCTAGCATTAGCAGATGAAGTATTGTCAAGCAT
1 AACTTTCATCTAGCATTAGCAGATGAAGTATTGTCAAGCAT
59966 AACTTTCATCTAGCATTAGCAGATGAAGTATTGTCAAGCAT
1 AACTTTCATCTAGCATTAGCAGATGAAGTATTGTCAAGCAT
60007 CGAGGAGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (41 bp):
AACTTTCATCTAGCATTAGCAGATGAAGTATTGTCAAGCAT
Found at i:66610 original size:59 final size:58
Alignment explanation
Indices: 66537--66700 Score: 188
Period size: 59 Copynumber: 2.7 Consensus size: 58
66527 CTTCATTTTC
*
66537 AATTGGTCCTTAAACTTTTGAATATTCTAATTTCATCCTCAAATTATGACTCTCATT-CT-
1 AATT-GTCCTTAAACTTTTGAATATTCTAATTTCATCC-CAAATTATGACCCTC-TTCCTA
* *
66596 AGTTAGTCCTTAAACTTTTGAACATTCTAATTTCATCCCTAAATTATGACCCTCTTCCTA
1 AATT-GTCCTTAAACTTTTGAATATTCTAATTTCATCCC-AAATTATGACCCTCTTCCTA
** * *
66656 AATTGATCCCCAAACTTTTGAATATTATAACTTCATCCCCAAATT
1 AATTG-TCCTTAAACTTTTGAATATTCTAATTTCAT-CCCAAATT
66701 CATCCAAATA
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
58 3 0.03
59 51 0.57
60 33 0.37
61 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (58 bp):
AATTGTCCTTAAACTTTTGAATATTCTAATTTCATCCCAAATTATGACCCTCTTCCTA
Found at i:66692 original size:60 final size:59
Alignment explanation
Indices: 66512--66700 Score: 177
Period size: 60 Copynumber: 3.2 Consensus size: 59
66502 GTGTCATATG
* * * * * **
66512 TCCCTAAACTATGATCTTCATTTTCAATTGGTCCTTAAACTTTTGAATATTCTAATTTCA
1 TCCCTAAATTATGACCCTCATTCT-AATTAGTCCCCAAACTTTTGAATATTCTAATTTCA
* * ** *
66572 T-CCTCAAATTATGACTCTCATTCTAGTTAGTCCTTAAACTTTTGAACATTCTAATTTCA
1 TCCCT-AAATTATGACCCTCATTCTAATTAGTCCCCAAACTTTTGAATATTCTAATTTCA
* *
66631 TCCCTAAATTATGACCCTC-TTCCTAAATT-GATCCCCAAACTTTTGAATATTATAACTTCA
1 TCCCTAAATTATGACCCTCATT-CT-AATTAG-TCCCCAAACTTTTGAATATTCTAATTTCA
*
66691 TCCCCAAATT
1 TCCCTAAATT
66701 CATCCAAATA
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
58 2 0.02
59 52 0.48
60 54 0.50
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.41
Consensus pattern (59 bp):
TCCCTAAATTATGACCCTCATTCTAATTAGTCCCCAAACTTTTGAATATTCTAATTTCA
Found at i:68992 original size:23 final size:23
Alignment explanation
Indices: 68966--69018 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
68956 TCTCGAAAGA
* * *
68966 CCACATAGGTTTGCATCGAAGTG
1 CCACATAGATTTACACCGAAGTG
68989 CCACATAGATTTACACCGAAGTG
1 CCACATAGATTTACACCGAAGTG
69012 CCACATA
1 CCACATA
69019 TTTGTCACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (23 bp):
CCACATAGATTTACACCGAAGTG
Found at i:69029 original size:21 final size:21
Alignment explanation
Indices: 68940--69050 Score: 77
Period size: 21 Copynumber: 5.1 Consensus size: 21
68930 AGACAATACT
* *
68940 AAGTGCCACATAATTGTCTCG
1 AAGTGCCACATATTTGTCACG
*
68961 AAAG-ACCACATAGGTTTG-CATCG
1 -AAGTGCCACATA--TTTGTCA-CG
*
68984 AAGTGCCACATAGATTT-ACACCG
1 AAGTGCCACAT--ATTTGTCA-CG
69007 AAGTGCCACATATTTGTCACG
1 AAGTGCCACATATTTGTCACG
*
69028 AA-TGACCACATATTTGTCCCG
1 AAGTG-CCACATATTTGTCACG
69049 AA
1 AA
69051 AGACCACATA
Statistics
Matches: 73, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
20 2 0.03
21 32 0.44
22 9 0.12
23 29 0.40
25 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (21 bp):
AAGTGCCACATATTTGTCACG
Found at i:69055 original size:21 final size:21
Alignment explanation
Indices: 69012--69060 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
69002 CACCGAAGTG
*
69012 CCACATATTTGTCACGAATGA
1 CCACATATTTGTCACGAAAGA
*
69033 CCACATATTTGTCCCGAAAGA
1 CCACATATTTGTCACGAAAGA
69054 CCACATA
1 CCACATA
69061 AACCCTCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (21 bp):
CCACATATTTGTCACGAAAGA
Found at i:69721 original size:21 final size:21
Alignment explanation
Indices: 69697--69739 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
69687 CCCAGAATAG
*
69697 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
69718 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
69739 A
1 A
69740 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:69815 original size:20 final size:19
Alignment explanation
Indices: 69775--69811 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
69765 CTGTTGAACA
69775 GGGGGGAATCGGTACCCCT
1 GGGGGGAATCGGTACCCCT
69794 GGGGGGAATCGGTACCCC
1 GGGGGGAATCGGTACCCC
69812 CTGGACATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.27, G:0.43, T:0.14
Consensus pattern (19 bp):
GGGGGGAATCGGTACCCCT
Found at i:69874 original size:21 final size:21
Alignment explanation
Indices: 69849--69947 Score: 122
Period size: 21 Copynumber: 5.0 Consensus size: 21
69839 AAAACCTGCA
69849 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
69870 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
69886 -GGGG-ATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
*
69905 GGGGGGATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
69926 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
69947 G
1 G
69948 CAATCTTGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
14 7 0.10
15 4 0.06
16 3 0.04
19 3 0.04
20 4 0.06
21 48 0.70
ACGTcount: A:0.12, C:0.28, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:69895 original size:14 final size:15
Alignment explanation
Indices: 69871--69899 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
69861 ACCCCCTGGG
69871 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
69886 GGGG-ATCTGTACCC
1 GGGGTATCTGTACCC
69900 CCTGGGGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.28, G:0.34, T:0.24
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:69901 original size:35 final size:36
Alignment explanation
Indices: 69850--69920 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
69840 AAACCTGCAG
*
69850 GGGGTATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGGATCTGTACCC
69886 GGGG-ATCTGTACCCCCTGGGGGGGGATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGGATCTGTACCC
69921 CCTGGGGGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 30 0.88
36 4 0.12
ACGTcount: A:0.11, C:0.28, G:0.38, T:0.23
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGGATCTGTACCC
Found at i:70069 original size:29 final size:31
Alignment explanation
Indices: 70037--70096 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
70027 AAACTTTGAA
70037 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
70066 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
70097 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:72315 original size:34 final size:32
Alignment explanation
Indices: 72262--72331 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
72252 ACCTTACAAC
* *
72262 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
72294 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
72328 TCCC
1 TCCC
72332 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:72570 original size:20 final size:22
Alignment explanation
Indices: 72545--72584 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
72535 AGTCGTATAT
72545 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
72565 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
72585 TATACTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:72636 original size:21 final size:21
Alignment explanation
Indices: 72612--72654 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
72602 CCCAGAATAG
*
72612 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
72633 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
72654 A
1 A
72655 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:72716 original size:21 final size:21
Alignment explanation
Indices: 72690--72732 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
72680 CTGTTGAACA
72690 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
72711 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
72732 G
1 G
72733 ACATTCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:72810 original size:15 final size:15
Alignment explanation
Indices: 72790--72819 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
72780 CCCCCTGGGG
72790 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
72805 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
72820 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:72829 original size:21 final size:21
Alignment explanation
Indices: 72767--72846 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
72757 AAACCTGCAT
72767 GGGGGTATCTGTACCCCCTGGG
1 GGGGGTATCTGTACCCCCT-GG
72789 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
72805 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* * *
72825 GGGGGAATCTATACTCCCTGG
1 GGGGGTATCTGTACCCCCTGG
72846 G
1 G
72847 CAATTTTGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
20 3 0.06
21 18 0.37
22 13 0.27
ACGTcount: A:0.12, C:0.26, G:0.38, T:0.24
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:72968 original size:29 final size:31
Alignment explanation
Indices: 72936--72995 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
72926 AAACTTTGAA
72936 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
72965 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
72996 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:73091 original size:16 final size:16
Alignment explanation
Indices: 73070--73103 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
73060 TGTTTAATCA
73070 TTATTCACA-ATGTTTC
1 TTATTCACATA-GTTTC
73086 TTATTCACATAGTTTC
1 TTATTCACATAGTTTC
73102 TT
1 TT
73104 TCTCATAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (16 bp):
TTATTCACATAGTTTC
Found at i:73643 original size:54 final size:54
Alignment explanation
Indices: 73541--73685 Score: 161
Period size: 54 Copynumber: 2.7 Consensus size: 54
73531 GATACTCCCC
* ** * *
73541 TTCAAGGGTATTGATACCTCCTCATGGTACCGATATTGATATATCATTCGATG-T
1 TTCAAGGGTATTGATACCTCCTCAAGGTACCGATA-CCAAATAGCATTCGATGAT
*
73595 TTCAAGGGTATTGATACCTCCTCAAGGTACCGATACCAAACTGGCATTCGATGAT
1 TTCAAGGGTATTGATACCTCCTCAAGGTACCGATACCAAA-TAGCATTCGATGAT
* *
73650 TT-AAGGGTATCGATACCATCCTTC-AGGTATCGATAC
1 TTCAAGGGTATTGATACC-TCC-TCAAGGTACCGATAC
73686 TACCCTTACA
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
53 2 0.03
54 58 0.73
55 17 0.22
56 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (54 bp):
TTCAAGGGTATTGATACCTCCTCAAGGTACCGATACCAAATAGCATTCGATGAT
Found at i:73692 original size:20 final size:21
Alignment explanation
Indices: 73655--73735 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
73645 ATGATTTAAG
*
73655 GGTATCGATACCATCCTT-CA
1 GGTATCGATACCACCCTTACA
*
73675 GGTATCGATACTACCCTTACA
1 GGTATCGATACCACCCTTACA
* * *
73696 -ATATCAATACCACTCTTAACA
1 GGTATCGATACCACCCTT-ACA
*
73717 GGTATCGATACAACCCTTA
1 GGTATCGATACCACCCTTA
73736 AAAAATACTC
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
20 29 0.60
21 6 0.12
22 13 0.27
ACGTcount: A:0.32, C:0.28, G:0.11, T:0.28
Consensus pattern (21 bp):
GGTATCGATACCACCCTTACA
Found at i:80061 original size:28 final size:28
Alignment explanation
Indices: 80029--80084 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
80019 CTCCAATATT
*
80029 TATTTAAATAGATTTTTATTTTT-TTAAA
1 TATTTAAATAG-TTTTAATTTTTATTAAA
* *
80057 TATTTTAATTGTTTTAATTTTTATTAAA
1 TATTTAAATAGTTTTAATTTTTATTAAA
80085 ATAATCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (28 bp):
TATTTAAATAGTTTTAATTTTTATTAAA
Found at i:80095 original size:29 final size:27
Alignment explanation
Indices: 80041--80095 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
80031 TTTAAATAGA
* * *
80041 TTTTTATTTTTTTAAATATTTTAATTG
1 TTTTAATTTTTTTAAATAATCTAATTG
80068 TTTTAATTTTTATTAAAATAATCTAATT
1 TTTTAATTTTT-TT-AAATAATCTAATT
80096 TACTAACGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 2 0.09
29 11 0.48
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTAATTTTTTTAAATAATCTAATTG
Found at i:82697 original size:15 final size:15
Alignment explanation
Indices: 82677--82712 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
82667 AAAGAAGAGT
82677 GGCTGTTTTATATCC
1 GGCTGTTTTATATCC
82692 GGCTGTTTTATATCC
1 GGCTGTTTTATATCC
82707 GGCTGT
1 GGCTGT
82713 ATTAAGAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.44
Consensus pattern (15 bp):
GGCTGTTTTATATCC
Found at i:97098 original size:22 final size:22
Alignment explanation
Indices: 97070--97132 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
97060 ACTGAATATT
*
97070 TGTCCCGAATGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
97092 TGTCCCGAAGGACCAC----TA
1 TGTCCCGAAGGACCACTGTATA
*
97110 TGTCCTGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
97132 T
1 T
97133 CCCTCGACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
18 17 0.49
22 18 0.51
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGTATA
Found at i:97113 original size:18 final size:18
Alignment explanation
Indices: 97090--97126 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
97080 GACCACTGTA
97090 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
*
97108 TATGTCCTGAAGGACCAC
1 TATGTCCCGAAGGACCAC
97126 T
1 T
97127 GTATATCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:100370 original size:14 final size:14
Alignment explanation
Indices: 100324--100369 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
100314 CGTTCGTGAA
100324 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
100338 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
100352 CGTTTGGTTATGTT
1 CGTTCGGTTATGTT
100366 CGTT
1 CGTT
100370 TATGTTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.07, C:0.13, G:0.28, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:105989 original size:166 final size:167
Alignment explanation
Indices: 105659--105992 Score: 661
Period size: 166 Copynumber: 2.0 Consensus size: 167
105649 TTTAAAAACT
105659 TTCATGTCATAAATTCTATTAATCAATTAACGTTCATGATTTGATTGATCAATTTTCTTAATGTT
1 TTCATGTCATAAATTCTATTAATCAATTAACGTTCATGATTTGATTGATCAATTTTCTTAATGTT
105724 AGTGACTTAATTGAAAACAAAATTAGTTTAGTGACCAAAATAAACATACTAATAGTTAGATGACC
66 AGTGACTTAATTGAAAACAAAATTAGTTTAGTGACCAAAATAAACATACTAATAGTTAGATGACC
105789 AACATGTTTGTTTACCCTTTTATTTTATTTTATAAAA
131 AACATGTTTGTTTACCCTTTTATTTTATTTTATAAAA
105826 TTCATGTCATAAATTCTATTAATCAATTAACGTTCATGATTTGATTGATCAATTTTCTTAATGTT
1 TTCATGTCATAAATTCTATTAATCAATTAACGTTCATGATTTGATTGATCAATTTTCTTAATGTT
105891 AGTGACTTAATTGAAAA-AAAATTAGTTTAGTGACCAAAATAAACATACTAATAGTTAGATGACC
66 AGTGACTTAATTGAAAACAAAATTAGTTTAGTGACCAAAATAAACATACTAATAGTTAGATGACC
105955 AACATGTTTGTTTACCCTTTTATTTTATTTTATAAAA
131 AACATGTTTGTTTACCCTTTTATTTTATTTTATAAAA
105992 T
1 T
105993 GTGTTATCCT
Statistics
Matches: 167, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
166 85 0.51
167 82 0.49
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (167 bp):
TTCATGTCATAAATTCTATTAATCAATTAACGTTCATGATTTGATTGATCAATTTTCTTAATGTT
AGTGACTTAATTGAAAACAAAATTAGTTTAGTGACCAAAATAAACATACTAATAGTTAGATGACC
AACATGTTTGTTTACCCTTTTATTTTATTTTATAAAA
Found at i:112682 original size:13 final size:12
Alignment explanation
Indices: 112657--112681 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
112647 AAAAATAATA
112657 TGATAATTTTTT
1 TGATAATTTTTT
112669 TGATAATTTTTT
1 TGATAATTTTTT
112681 T
1 T
112682 TTGAAAAATA
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TGATAATTTTTT
Found at i:115904 original size:83 final size:83
Alignment explanation
Indices: 115784--116102 Score: 413
Period size: 83 Copynumber: 3.8 Consensus size: 83
115774 AATTTTTTCA
* * *
115784 ATCCCATCCAAAATGAAAGACACGTTCTAGGGGAAGCATTTTCCATTAGTATTCAGAGAATATCT
1 ATCCCATCCAAAATGAAAGACACGTTCCAGGGGAAGCATTTTCCATTATTATTCAGAGAATCTCT
* *
115849 GCCATGTCATAGTGTTCC
66 ACCATGTTATAGTGTTCC
** **** * *
115867 ATCTTATCCAAAATGAAAGGTGTGTTCTAGGGAAAGCATTTTCCATTATTATTCAGAGAATCTCT
1 ATCCCATCCAAAATGAAAGACACGTTCCAGGGGAAGCATTTTCCATTATTATTCAGAGAATCTCT
115932 ACCATGTTATAGTGTTCC
66 ACCATGTTATAGTGTTCC
* ** * **
115950 ATCCCATCCAAAATGAAAGGCACGTTCCAGATGAAGCGTTTTCCATTATTAGACAGAGAATCTCT
1 ATCCCATCCAAAATGAAAGACACGTTCCAGGGGAAGCATTTTCCATTATTATTCAGAGAATCTCT
* * *
116015 ATCATGTTTTAGTGTTTC
66 ACCATGTTATAGTGTTCC
* * *
116033 ATCCCATCCGAAATGAAAGACGCGTTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCT
1 ATCCCATCCAAAATGAAAGACACGTTCCAGGGGAAGCATTTTCCATTATTATTCAGAGAATCTCT
116098 ACCAT
66 ACCAT
116103 TTCACATAAT
Statistics
Matches: 202, Mismatches: 34, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 202 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (83 bp):
ATCCCATCCAAAATGAAAGACACGTTCCAGGGGAAGCATTTTCCATTATTATTCAGAGAATCTCT
ACCATGTTATAGTGTTCC
Found at i:126161 original size:17 final size:16
Alignment explanation
Indices: 126138--126183 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
126128 TATATGATTT
126138 AAAAAATAATTAAATA
1 AAAAAATAATTAAATA
*
126154 ACAAAAATAA--AATTA
1 A-AAAAATAATTAAATA
*
126169 AAATAATAATTAAAT
1 AAAAAATAATTAAAT
126184 GGTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
14 7 0.29
15 5 0.21
16 4 0.17
17 8 0.33
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAATAATTAAATA
Found at i:127201 original size:16 final size:17
Alignment explanation
Indices: 127165--127202 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
127155 TTGATTTGCA
*
127165 AATTTCTTTAGCGATAT
1 AATTTCTTTAGCGATAG
*
127182 AATTT-TTTAGCGGTAG
1 AATTTCTTTAGCGATAG
127198 AATTT
1 AATTT
127203 GGGGTTAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (17 bp):
AATTTCTTTAGCGATAG
Found at i:127967 original size:16 final size:16
Alignment explanation
Indices: 127942--127983 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
127932 ATATCATTTT
127942 AATA-ATTATTTAAAA
1 AATATATTATTTAAAA
*
127957 AATATATTATTTTAAA
1 AATATATTATTTAAAA
127973 AAT-TATT-TTTA
1 AATATATTATTTA
127984 TTGTGATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 8 0.33
16 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATATTATTTAAAA
Found at i:127968 original size:28 final size:27
Alignment explanation
Indices: 127928--127980 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
127918 TACACCTTAT
*
127928 AAAAATATCATTTTAATAATTATTTAA
1 AAAAATATCATTTTAAAAATTATTTAA
*
127955 AAAATATATTATTTTAAAAATTATTT
1 AAAA-ATATCATTTTAAAAATTATTT
127981 TTATTGTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
AAAAATATCATTTTAAAAATTATTTAA
Found at i:145116 original size:28 final size:30
Alignment explanation
Indices: 145042--145116 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 30
145032 TTTTTTTGTA
*
145042 AAAATAAGTACCTAAAGTTATCTTTTTGGTC
1 AAAAT-AGTACCTAAAGTTATCTTTATGGTC
* *
145073 AAAATAACTACTTAAAG-TA-CTTTAT-GTC
1 AAAAT-AGTACCTAAAGTTATCTTTATGGTC
145101 AAAATAGTTACCTAAA
1 AAAATAG-TACCTAAA
145117 CTATTCAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 15 0.39
29 5 0.13
30 2 0.05
31 15 0.39
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (30 bp):
AAAATAGTACCTAAAGTTATCTTTATGGTC
Found at i:149420 original size:2 final size:2
Alignment explanation
Indices: 149413--149448 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
149403 TTTTACTAAT
149413 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
149449 CGAAAATGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:151412 original size:20 final size:21
Alignment explanation
Indices: 151369--151432 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
151359 TGATTAACAA
*
151369 TTCACGGTACTGAAGTGGCGG
1 TTCACGGTACTGAAGTGGCAG
*
151390 TTCATGGTACTGAA-TGGCAG
1 TTCACGGTACTGAAGTGGCAG
* * *
151410 TTCACGATACTGACGTGGTAG
1 TTCACGGTACTGAAGTGGCAG
151431 TT
1 TT
151433 TAGGGTGGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (21 bp):
TTCACGGTACTGAAGTGGCAG
Done.