Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007537.1 Corchorus capsularis cultivar CVL-1 contig07558, 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: 44194
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:11 original size:6 final size:6
Alignment explanation
Indices: 1--177 Score: 242
Period size: 6 Copynumber: 32.2 Consensus size: 6
1 TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG
1 TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG
49 TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG -TAACG -TAACG
1 TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG
95 TTAACG -TAACG TTAACG -TAACG -TAACG -TAACG -TAACG -TAACG
1 TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG
137 -TAACG -TAACG -TAACG -TAACG -TAACG -TAACG -TAACG -TAACG
1 TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG TTAACG
177 T
1 T
178 ACGTACGTAC
Statistics
Matches: 168, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
5 80 0.48
6 88 0.52
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (6 bp):
TTAACG
Found at i:200 original size:20 final size:25
Alignment explanation
Indices: 2--198 Score: 224
Period size: 30 Copynumber: 7.5 Consensus size: 25
1 T
2 TAACGTTAACGTTAACGTTAACGTTAACG
1 TAACG-TAACG-TAACG-TAACG-TAACG
31 TTAACGTTAACGTTAACGTTAACGTTAACG
1 -TAACG-TAACG-TAACG-TAACG-TAACG
61 TTAACGTTAACGTTAACGTTAACGTAACG
1 -TAACG-TAACG-TAACG-TAACGTAACG
90 TAACGTTAACGTAACGTTAACGTAACG
1 TAACG-TAACGTAACG-TAACGTAACG
117 TAACGTAACGTAACGTAACGTAACG
1 TAACGTAACGTAACGTAACGTAACG
142 TAACGTAACGTAACGTAACGTAACG
1 TAACGTAACGTAACGTAACGTAACG
167 TAACGTAACGT-ACGT-ACGT-ACG
1 TAACGTAACGTAACGTAACGTAACG
189 T-ACGT-ACGTA
1 TAACGTAACGTA
199 CGACTACTAC
Statistics
Matches: 166, Mismatches: 0, Indels: 11
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.02
21 4 0.02
22 4 0.02
23 4 0.02
24 4 0.02
25 46 0.28
26 10 0.06
27 21 0.13
28 11 0.07
29 5 0.03
30 53 0.32
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (25 bp):
TAACGTAACGTAACGTAACGTAACG
Found at i:10067 original size:21 final size:21
Alignment explanation
Indices: 10019--10068 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
10009 CAGCAGGTCC
* * *
10019 TTCTTCATCCTCTTTTTCACT
1 TTCTTCTTCCTCATTCTCACT
10040 TTCTTCTTCCTCATTCTCACT
1 TTCTTCTTCCTCATTCTCACT
10061 TTCTTCTT
1 TTCTTCTT
10069 TTTCTTCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.08, C:0.34, G:0.00, T:0.58
Consensus pattern (21 bp):
TTCTTCTTCCTCATTCTCACT
Found at i:10213 original size:20 final size:20
Alignment explanation
Indices: 10188--10234 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
10178 TTGTTTAAAG
*
10188 TGAGTAGGTTCAAGGTACAT
1 TGAGTAGGTTCAAGGTACAC
10208 TGAGTAGGTTCAAGGTACAC
1 TGAGTAGGTTCAAGGTACAC
10228 TGAGTAG
1 TGAGTAG
10235 ATCTTCAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.32, T:0.28
Consensus pattern (20 bp):
TGAGTAGGTTCAAGGTACAC
Found at i:11183 original size:75 final size:74
Alignment explanation
Indices: 11033--11258 Score: 301
Period size: 75 Copynumber: 3.0 Consensus size: 74
11023 TGGAGTCAAC
* * * * *
11033 ATGGGCTACAAAGGCCAGAAACATCAACAGAAAAAAAGGTACTTATGGCTACGATCCTTGCTGAG
1 ATGGGCTACATAGGCCAGAAGCATCAACAG-GAAAAA--CACTTATGGTTACGATCCTTGCTGAG
11098 TATGGAATCTTG
63 TATGGAATCTTG
* * *
11110 ATGGGCTACATAGGCCAGAAGCATCAACATGGAAATACACTTATGGTTACTATCTTTGCTGAGTA
1 ATGGGCTACATAGGCCAGAAGCATCAACA-GGAAAAACACTTATGGTTACGATCCTTGCTGAGTA
11175 TGGAATCTTG
65 TGGAATCTTG
* *
11185 ATGGGCTACATAGGCCAGAAGCATCAACAAGGAAAGACACTTATAGCTT-CGATCCTTGCTGAGT
1 ATGGGCTACATAGGCCAGAAGCATCAAC-AGGAAAAACACTTAT-GGTTACGATCCTTGCTGAGT
11249 ATGGAATCTT
64 ATGGAATCTT
11259 AATGTCAAAA
Statistics
Matches: 134, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
75 98 0.73
76 4 0.03
77 31 0.23
78 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (74 bp):
ATGGGCTACATAGGCCAGAAGCATCAACAGGAAAAACACTTATGGTTACGATCCTTGCTGAGTAT
GGAATCTTG
Found at i:13528 original size:15 final size:16
Alignment explanation
Indices: 13500--13531 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
13490 TGAAAGATCC
13500 AAAATAATAAAAATTT
1 AAAATAATAAAAATTT
13516 AAAATAA-AAAAATTT
1 AAAATAATAAAAATTT
13531 A
1 A
13532 TTGCATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATAATAAAAATTT
Found at i:14890 original size:15 final size:16
Alignment explanation
Indices: 14859--14891 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
14849 CCGAACCCGA
*
14859 GAACCCGGCCGAACCT
1 GAACCCGGCCCAACCT
14875 GAACCC-GCCCAACCT
1 GAACCCGGCCCAACCT
14890 GA
1 GA
14892 TTTGACCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.27, C:0.45, G:0.21, T:0.06
Consensus pattern (16 bp):
GAACCCGGCCCAACCT
Found at i:14947 original size:16 final size:15
Alignment explanation
Indices: 14913--15046 Score: 110
Period size: 16 Copynumber: 8.5 Consensus size: 15
14903 AAAAGTAAAC
***
14913 GACCCGAACCCGCCC
1 GACCCGAACCCGAAT
14928 GACCCGAGACCCGAAT
1 GACCCGA-ACCCGAAT
14944 GACCCGCAACCC-AGAT
1 GACCCG-AACCCGA-AT
*
14960 GACCCGGGACCCGAAT
1 GACCC-GAACCCGAAT
14976 GACCCGTAACCC-AGAT
1 GACCCG-AACCCGA-AT
*
14992 GATCCGAAACCCGAAT
1 GACCCG-AACCCGAAT
*
15008 GACCCGTAACCCGAGT
1 GACCCG-AACCCGAAT
15024 GACCCGAAACCCGAAT
1 GACCCG-AACCCGAAT
*
15040 AACCCGA
1 GACCCGA
15047 GAAGTTAATC
Statistics
Matches: 98, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
15 11 0.11
16 83 0.85
17 4 0.04
ACGTcount: A:0.31, C:0.40, G:0.22, T:0.07
Consensus pattern (15 bp):
GACCCGAACCCGAAT
Found at i:14964 original size:32 final size:32
Alignment explanation
Indices: 14928--15045 Score: 166
Period size: 32 Copynumber: 3.7 Consensus size: 32
14918 GAACCCGCCC
* *
14928 GACCCGAGACCCGAATGACCCGCAACCCAGAT
1 GACCCGAAACCCGAATGACCCGTAACCCAGAT
**
14960 GACCCGGGACCCGAATGACCCGTAACCCAGAT
1 GACCCGAAACCCGAATGACCCGTAACCCAGAT
*
14992 GATCCGAAACCCGAATGACCCGTAACCC-GAGT
1 GACCCGAAACCCGAATGACCCGTAACCCAGA-T
*
15024 GACCCGAAACCCGAATAACCCG
1 GACCCGAAACCCGAATGACCCG
15046 AGAAGTTAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 2 0.03
32 76 0.97
ACGTcount: A:0.31, C:0.38, G:0.22, T:0.08
Consensus pattern (32 bp):
GACCCGAAACCCGAATGACCCGTAACCCAGAT
Found at i:14980 original size:48 final size:47
Alignment explanation
Indices: 14928--15046 Score: 125
Period size: 48 Copynumber: 2.5 Consensus size: 47
14918 GAACCCGCCC
* *
14928 GACCCGAGACCCGAATGACCCGCAACCC-AGATGACCCGGGACCCGAAT
1 GACCCGA-ACCCGAATGACCCGAAACCCGA-ATGACCCGGAACCCGAAT
* * *
14976 GACCCGTAACCC-AGATGATCCGAAACCCGAATGACCCGTAACCCGAGT
1 GACCCG-AACCCGA-ATGACCCGAAACCCGAATGACCCGGAACCCGAAT
*
15024 GACCCGAAACCCGAATAACCCGA
1 GACCCG-AACCCGAATGACCCGA
15047 GAAGTTAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
47 1 0.02
48 55 0.93
49 3 0.05
ACGTcount: A:0.32, C:0.38, G:0.22, T:0.08
Consensus pattern (47 bp):
GACCCGAACCCGAATGACCCGAAACCCGAATGACCCGGAACCCGAAT
Found at i:15028 original size:25 final size:24
Alignment explanation
Indices: 15000--15047 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
14990 ATGATCCGAA
15000 ACCCGAATGACCCG-TAACCCGAGTG
1 ACCCGAA--ACCCGATAACCCGAGTG
15025 ACCCGAAACCCGAATAACCCGAG
1 ACCCGAAACCCG-ATAACCCGAG
15048 AAGTTAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
25 16 0.76
ACGTcount: A:0.33, C:0.38, G:0.21, T:0.08
Consensus pattern (24 bp):
ACCCGAAACCCGATAACCCGAGTG
Found at i:17869 original size:13 final size:15
Alignment explanation
Indices: 17843--17882 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
17833 TTAGTATTTC
17843 TATAT-TATATTAAAT
1 TATATATATA-TAAAT
17858 TA-ATA-ATATAAAT
1 TATATATATATAAAT
17871 TATATATATATA
1 TATATATATATA
17883 TAACTGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATATATAAAT
Found at i:20220 original size:16 final size:16
Alignment explanation
Indices: 20198--20259 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
20188 TCAACCCGGA
*
20198 ACCCGAATGACCTGAG
1 ACCCGAATGACCCGAG
* *
20214 ACGCGAATGACCCGAA
1 ACCCGAATGACCCGAG
*
20230 ACCCGTATGACCCGAG
1 ACCCGAATGACCCGAG
20246 ACCCGAATGACCCG
1 ACCCGAATGACCCG
20260 GATAACTCGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.31, C:0.35, G:0.24, T:0.10
Consensus pattern (16 bp):
ACCCGAATGACCCGAG
Found at i:20233 original size:32 final size:32
Alignment explanation
Indices: 20191--20259 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
20181 CGACCGATCA
* * *
20191 ACCCGGAACCCGAATGACCTGAGACGCGAATG
1 ACCCGAAACCCGAATGACCCGAGACCCGAATG
*
20223 ACCCGAAACCCGTATGACCCGAGACCCGAATG
1 ACCCGAAACCCGAATGACCCGAGACCCGAATG
20255 ACCCG
1 ACCCG
20260 GATAACTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.36, G:0.25, T:0.09
Consensus pattern (32 bp):
ACCCGAAACCCGAATGACCCGAGACCCGAATG
Found at i:22509 original size:26 final size:26
Alignment explanation
Indices: 22480--22545 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
22470 CACGCGCGAT
* *
22480 GTCACGTGTTGAGGT-GTCCGTTGGAG
1 GTCACGTGTGGA-GTCGTACGTTGGAG
*
22506 GTCACATGTGGAGTCGTACGTTGGAG
1 GTCACGTGTGGAGTCGTACGTTGGAG
22532 GTCACGTGTGGAGT
1 GTCACGTGTGGAGT
22546 GCCAGCTGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 2 0.06
26 33 0.94
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.29
Consensus pattern (26 bp):
GTCACGTGTGGAGTCGTACGTTGGAG
Found at i:22611 original size:23 final size:23
Alignment explanation
Indices: 22586--22755 Score: 211
Period size: 23 Copynumber: 7.4 Consensus size: 23
22576 TTGTGGTCAT
* *
22586 AAGTGGTCGAG-CGCCAGGCTTGT
1 AAGTGGTCG-GTCGCTAGGCTTGG
** * *
22609 AAGTGGTCGGGAG-TTGAGCTTGT
1 AAGTGGTCGGTCGCTAG-GCTTGG
22632 AAGTGGTCGGTCGCTAGGCTTGG
1 AAGTGGTCGGTCGCTAGGCTTGG
*
22655 AAGTGGTCGGTCACTAGGCTTGG
1 AAGTGGTCGGTCGCTAGGCTTGG
*
22678 AAGTGGTCGGTCGCTA-GCTTGT
1 AAGTGGTCGGTCGCTAGGCTTGG
22700 AAGTGGTCGGTCGCTAGGCTTGG
1 AAGTGGTCGGTCGCTAGGCTTGG
* *
22723 AAGTGGTCAGTCGCTAGACTTGG
1 AAGTGGTCGGTCGCTAGGCTTGG
22746 AAGTGGTCGG
1 AAGTGGTCGG
22756 GCGCCAAGCA
Statistics
Matches: 129, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
22 23 0.18
23 104 0.81
24 2 0.02
ACGTcount: A:0.16, C:0.16, G:0.41, T:0.26
Consensus pattern (23 bp):
AAGTGGTCGGTCGCTAGGCTTGG
Found at i:22718 original size:68 final size:69
Alignment explanation
Indices: 22601--22756 Score: 242
Period size: 68 Copynumber: 2.3 Consensus size: 69
22591 GTCGAGCGCC
* * *
22601 AGGCTTGTAAGTGGTCGGGAGTTGAGCTTGTAAGTGGTCGGTCGCTAGGCTTGGAAGTGGTCGGT
1 AGGCTTGGAAGTGGTCGGGAGCTGAGCTTGTAAGTGGTCGGTCGCTAGGCTTGGAAGTGGTCAGT
22666 CACT
66 CACT
**
22670 AGGCTTGGAAGTGGTCGGTCGCT-AGCTTGTAAGTGGTCGGTCGCTAGGCTTGGAAGTGGTCAGT
1 AGGCTTGGAAGTGGTCGGGAGCTGAGCTTGTAAGTGGTCGGTCGCTAGGCTTGGAAGTGGTCAGT
*
22734 CGCT
66 CACT
*
22738 AGACTTGGAAGTGGTCGGG
1 AGGCTTGGAAGTGGTCGGG
22757 CGCCAAGCAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
68 60 0.76
69 19 0.24
ACGTcount: A:0.16, C:0.15, G:0.41, T:0.28
Consensus pattern (69 bp):
AGGCTTGGAAGTGGTCGGGAGCTGAGCTTGTAAGTGGTCGGTCGCTAGGCTTGGAAGTGGTCAGT
CACT
Found at i:23279 original size:61 final size:57
Alignment explanation
Indices: 23177--23310 Score: 180
Period size: 61 Copynumber: 2.3 Consensus size: 57
23167 TTCTTTCTTT
* * *
23177 TCTTTTTTTTTTCTGAAATTCAAATTTTTTAATTCATTTTTTTTTTCTAGGTAGGGGGAA
1 TCTTTTTTTTTTTTTAAATTCAAATTTTTGAATTCATTTTTTTTTT-T--GTAGGGGGAA
23237 GTCTTTTTTTTTTTTTAAATTCAAATTTTTGAATTTCA-TTTTTTTTTTGTAGGGGGAA
1 -TCTTTTTTTTTTTTTAAATTCAAATTTTTGAA-TTCATTTTTTTTTTTGTAGGGGGAA
*
23295 ACTTTTTTTTTTTTTA
1 TCTTTTTTTTTTTTTA
23311 GTTAATTGGG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
57 15 0.22
58 10 0.15
60 1 0.01
61 38 0.56
62 4 0.06
ACGTcount: A:0.20, C:0.07, G:0.12, T:0.61
Consensus pattern (57 bp):
TCTTTTTTTTTTTTTAAATTCAAATTTTTGAATTCATTTTTTTTTTTGTAGGGGGAA
Found at i:23475 original size:38 final size:37
Alignment explanation
Indices: 23361--23653 Score: 415
Period size: 37 Copynumber: 7.8 Consensus size: 37
23351 GAGGTGGCCT
* * * *
23361 GTGGCGGTCGACACATTTTATCAGCTTATCGAACGAT
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
* *
23398 GTGGTGGTTGACACATTTTGTCAGCTTGTCGAGCGAC
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
*
23435 GTGGCGGTCAACACATTTTGTCAGCTATGTCGAGCGAC
1 GTGGCGGTCGACACATTTTGTCAGCT-TGTCGAGCGAC
*
23473 GTGGCGGTCGACACATTTTGTCAACTTTGTCGAGCGAC
1 GTGGCGGTCGACACATTTTGTCAGC-TTGTCGAGCGAC
* * * *
23511 GTGGCCGTCGACACATTTTGTCAACTTCTCGAACGAC
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
*
23548 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCTAC
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
* *
23585 GTGGCGGTAGACACATTTTGTCAGCTTTGTCGGGCGAC
1 GTGGCGGTCGACACATTTTGTCAGC-TTGTCGAGCGAC
*
23623 GTGGCGGTTGACACATTTTGTCAGCTTGTCG
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCG
23654 CGTGTACTTC
Statistics
Matches: 230, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
37 126 0.55
38 103 0.45
39 1 0.00
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.30
Consensus pattern (37 bp):
GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
Found at i:23636 original size:150 final size:149
Alignment explanation
Indices: 23361--23653 Score: 453
Period size: 150 Copynumber: 2.0 Consensus size: 149
23351 GAGGTGGCCT
* * * * *
23361 GTGGCGGTCGACACATTTTATCAGCTTATCGAACGATGTGGTGGTTGACACATTTTGTCAGCTTG
1 GTGGCCGTCGACACATTTTATCAACTTATCGAACGACGTGGCGGTCGACACATTTTGTCAGCTTG
23426 TCGAGCGACGTGGCGGTCAACACATTTTGTCAGCTATGTCGAGCGACGTGGCGGTCGACACATTT
66 TCGAGCGACGTGGCGGTCAACACATTTTGTCAGCTATGTCGAGCGACGTGGCGGTCGACACATTT
23491 TGTCAACTTTGTCGAGCGAC
131 TGTCAAC-TTGTCGAGCGAC
* *
23511 GTGGCCGTCGACACATTTTGTCAACTTCTCGAACGACGTGGCGGTCGACACATTTTGTCAGCTTG
1 GTGGCCGTCGACACATTTTATCAACTTATCGAACGACGTGGCGGTCGACACATTTTGTCAGCTTG
* * * *
23576 TCGAGCTACGTGGCGGT-AGACACATTTTGTCAGCTTTGTCGGGCGACGTGGCGGTTGACACATT
66 TCGAGCGACGTGGCGGTCA-ACACATTTTGTCAGCTATGTCGAGCGACGTGGCGGTCGACACATT
*
23640 TTGTCAGCTTGTCG
130 TTGTCAACTTGTCG
23654 CGTGTACTTC
Statistics
Matches: 130, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
149 7 0.05
150 123 0.95
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.30
Consensus pattern (149 bp):
GTGGCCGTCGACACATTTTATCAACTTATCGAACGACGTGGCGGTCGACACATTTTGTCAGCTTG
TCGAGCGACGTGGCGGTCAACACATTTTGTCAGCTATGTCGAGCGACGTGGCGGTCGACACATTT
TGTCAACTTGTCGAGCGAC
Found at i:24011 original size:49 final size:49
Alignment explanation
Indices: 23956--24050 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 49
23946 CGCCATATTG
* * *
23956 GTAGTTAGCACTTGGTTGTCTTG-TTCCTTTTTGTGTAGTATGCCACCTA
1 GTAGTTAGCACATGATTGTCTTGCTT-CTTTTTGTGTAGCATGCCACCTA
* *
24005 GTAGTTAGCACATGATTGTTTTGCTTCTTTTTGTGTCGCATGCCAC
1 GTAGTTAGCACATGATTGTCTTGCTTCTTTTTGTGTAGCATGCCAC
24051 ATTTTGATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 38 0.95
50 2 0.05
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (49 bp):
GTAGTTAGCACATGATTGTCTTGCTTCTTTTTGTGTAGCATGCCACCTA
Found at i:24441 original size:57 final size:57
Alignment explanation
Indices: 24378--24692 Score: 459
Period size: 57 Copynumber: 5.5 Consensus size: 57
24368 TAGATGCAAC
* * * * *
24378 TTGGTCGCTCGACGCGTTTCTCCTTTCTTCTTTAATCATTTCGGCATGAATGTGATT
1 TTGGTCGTTCGACGCATTTCTCCTTTCTTCTTTGACCATTTCGGCATGAACGTGATT
* * *
24435 TTGGTCGTTCGACGCATTTCTCCTTTCTTCTTTAACCATTTCGGCATGAATGTGAAT
1 TTGGTCGTTCGACGCATTTCTCCTTTCTTCTTTGACCATTTCGGCATGAACGTGATT
* * * * *
24492 TTGGTCGTTCAACACCTCTCTCCCTTCTTCTTTGACCATTTCGGCATGAACGTGATT
1 TTGGTCGTTCGACGCATTTCTCCTTTCTTCTTTGACCATTTCGGCATGAACGTGATT
* * *
24549 TTGGTTGTTCGACGCGTTTCTCCTTTCTTCTTTGAGCATTTCGGCATGAACGTGATT
1 TTGGTCGTTCGACGCATTTCTCCTTTCTTCTTTGACCATTTCGGCATGAACGTGATT
* *
24606 TTGGTCGTTCGACGCATTTCTCATTTCTTCTTTGACCATTTCGGCAAGAACGTGATT
1 TTGGTCGTTCGACGCATTTCTCCTTTCTTCTTTGACCATTTCGGCATGAACGTGATT
*
24663 TTGGTCGTTCAACGCATTTCTCCTTTCTTC
1 TTGGTCGTTCGACGCATTTCTCCTTTCTTC
24693 GTCTTGGGTG
Statistics
Matches: 232, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 232 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (57 bp):
TTGGTCGTTCGACGCATTTCTCCTTTCTTCTTTGACCATTTCGGCATGAACGTGATT
Found at i:28939 original size:40 final size:40
Alignment explanation
Indices: 28847--28926 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
28837 GAAAGCGGTT
* **
28847 AAAGATCTTAATTCATATAAATTAAGTAAAAACAACAGTTA
1 AAAGA-CTTAATTCATATAAATTAAATAAAAACAACAGAGA
*
28888 AAAGACTTAATTCATAGT-AATTAAATAAAAACATCAGAG
1 AAAGACTTAATTCATA-TAAATTAAATAAAAACAACAGAG
28927 CACAGGCTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 28 0.82
41 6 0.18
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.28
Consensus pattern (40 bp):
AAAGACTTAATTCATATAAATTAAATAAAAACAACAGAGA
Found at i:30879 original size:15 final size:12
Alignment explanation
Indices: 30825--30902 Score: 115
Period size: 12 Copynumber: 6.7 Consensus size: 12
30815 GAAATTAGGC
*
30825 AAAAGAAGACTA
1 AAAAGAAGACTG
30837 AAAAGAAGACTG
1 AAAAGAAGACTG
*
30849 GAAAGAAGACTG
1 AAAAGAAGACTG
30861 AAAAGAAGACTG
1 AAAAGAAGACTG
*
30873 AAAAAAAGACTG
1 AAAAGAAGACTG
30885 -AAAGAAGACTG
1 AAAAGAAGACTG
30896 -AAAGAAG
1 AAAAGAAG
30903 TTAGCAAAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
11 17 0.28
12 44 0.72
ACGTcount: A:0.60, C:0.08, G:0.24, T:0.08
Consensus pattern (12 bp):
AAAAGAAGACTG
Found at i:30982 original size:19 final size:19
Alignment explanation
Indices: 30923--30987 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
30913 CTTAATTTCA
30923 CAAAAATTAAGTAAATTGG
1 CAAAAATTAAGTAAATTGG
* **
30942 CAAAGACTTAA-T---TTCA
1 CAAA-AATTAAGTAAATTGG
30958 CAAAAATTAAGTAAATTGG
1 CAAAAATTAAGTAAATTGG
30977 CAAAAACTTAA
1 CAAAAA-TTAA
30988 TTGCACAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 11
0.67 0.12 0.22
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
19 13 0.38
20 9 0.26
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
CAAAAATTAAGTAAATTGG
Found at i:30982 original size:20 final size:20
Alignment explanation
Indices: 30924--30987 Score: 50
Period size: 20 Copynumber: 3.5 Consensus size: 20
30914 TTAATTTCAC
30924 AAAAATTAAGTAAATTGGCA
1 AAAAATTAAGTAAATTGGCA
* *
30944 AAGACTTAA-T---TT--CA
1 AAAAATTAAGTAAATTGGCA
30958 CAAAAATTAAGTAAATTGGCA
1 -AAAAATTAAGTAAATTGGCA
*
30979 AAAACTTAA
1 AAAAATTAA
30988 TTGCACAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 14
0.63 0.10 0.27
Matches are distributed among these distances:
14 2 0.06
15 7 0.22
16 3 0.09
19 3 0.09
20 15 0.47
21 2 0.06
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (20 bp):
AAAAATTAAGTAAATTGGCA
Found at i:31017 original size:20 final size:20
Alignment explanation
Indices: 30994--31053 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
30984 TTAATTGCAC
30994 AAGAATTAAGTAAATTAGCA
1 AAGAATTAAGTAAATTAGCA
*
31014 AAG-ACT---T-AATT-GCA
1 AAGAATTAAGTAAATTAGCA
31028 CAAGAATTAAGTAAAATTAGCA
1 -AAGAATTAAGT-AAATTAGCA
31050 AAGA
1 AAGA
31054 CTTGATTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 15
0.64 0.04 0.32
Matches are distributed among these distances:
14 3 0.10
15 7 0.23
16 3 0.10
19 3 0.10
20 3 0.10
21 8 0.27
22 3 0.10
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.23
Consensus pattern (20 bp):
AAGAATTAAGTAAATTAGCA
Found at i:31052 original size:36 final size:35
Alignment explanation
Indices: 30903--31089 Score: 266
Period size: 35 Copynumber: 5.3 Consensus size: 35
30893 CTGAAAGAAG
* *
30903 TTAGCAAAGACTTAATTTCACAAAAATTAAGTAAA
1 TTAGCAAAGACTTAATTGCACAAGAATTAAGTAAA
* * *
30938 TTGGCAAAGACTTAATTTCACAAAAATTAAGTAAA
1 TTAGCAAAGACTTAATTGCACAAGAATTAAGTAAA
* *
30973 TTGGCAAAAACTTAATTGCACAAGAATTAAGTAAA
1 TTAGCAAAGACTTAATTGCACAAGAATTAAGTAAA
31008 TTAGCAAAGACTTAATTGCACAAGAATTAAGTAAAA
1 TTAGCAAAGACTTAATTGCACAAGAATTAAGT-AAA
* *
31044 TTAGCAAAGACTTGATTCCACAAGAATTAAGTAAA
1 TTAGCAAAGACTTAATTGCACAAGAATTAAGTAAA
*
31079 GTCAGCAAAGA
1 -TTAGCAAAGA
31090 TATTATCCAT
Statistics
Matches: 141, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
35 99 0.70
36 42 0.30
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (35 bp):
TTAGCAAAGACTTAATTGCACAAGAATTAAGTAAA
Found at i:31185 original size:22 final size:22
Alignment explanation
Indices: 31160--31279 Score: 150
Period size: 22 Copynumber: 5.4 Consensus size: 22
31150 AAAAGAAATT
31160 AGACTGAAATTAGACTGAAAGA
1 AGACTGAAATTAGACTGAAAGA
* **
31182 AGACTGAAATTAGATTGAAATT
1 AGACTGAAATTAGACTGAAAGA
* **
31204 ATACTGAAAGAAGACTGAAAAGA
1 AGACTGAAATTAGACTG-AAAGA
31227 AGACTGAAATTAGACTGAAAGA
1 AGACTGAAATTAGACTGAAAGA
* * *
31249 GGACTGAAATAAGACTGAGAGA
1 AGACTGAAATTAGACTGAAAGA
31271 AGACTGAAA
1 AGACTGAAA
31280 GAAGACTGGC
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
22 64 0.79
23 17 0.21
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.18
Consensus pattern (22 bp):
AGACTGAAATTAGACTGAAAGA
Found at i:31191 original size:33 final size:33
Alignment explanation
Indices: 31154--31287 Score: 178
Period size: 33 Copynumber: 4.0 Consensus size: 33
31144 TTAGGCAAAA
*
31154 GAAATTAGACTGAAATTAGACTGAAAGAAGACT
1 GAAATAAGACTGAAATTAGACTGAAAGAAGACT
* * *
31187 GAAATTAGATTGAAATTATACTGAAAGAAGACT
1 GAAATAAGACTGAAATTAGACTGAAAGAAGACT
* *
31220 GAAAAGAAGACTGAAATTAGACTGAAAGAGGACT
1 G-AAATAAGACTGAAATTAGACTGAAAGAAGACT
* **
31254 GAAATAAGACTGAGAGAAGACTGAAAGAAGACT
1 GAAATAAGACTGAAATTAGACTGAAAGAAGACT
31287 G
1 G
31288 GCTTAGTTTC
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
33 60 0.68
34 28 0.32
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.19
Consensus pattern (33 bp):
GAAATAAGACTGAAATTAGACTGAAAGAAGACT
Found at i:31273 original size:11 final size:11
Alignment explanation
Indices: 31160--31287 Score: 130
Period size: 11 Copynumber: 11.5 Consensus size: 11
31150 AAAAGAAATT
**
31160 AGACTGAAATT
1 AGACTGAAAGA
31171 AGACTGAAAGA
1 AGACTGAAAGA
**
31182 AGACTGAAATT
1 AGACTGAAAGA
* **
31193 AGATTGAAATT
1 AGACTGAAAGA
*
31204 ATACTGAAAGA
1 AGACTGAAAGA
31215 AGACTGAAAAGA
1 AGACTG-AAAGA
**
31227 AGACTGAAATT
1 AGACTGAAAGA
31238 AGACTGAAAGA
1 AGACTGAAAGA
* *
31249 GGACTGAAATA
1 AGACTGAAAGA
*
31260 AGACTGAGAGA
1 AGACTGAAAGA
31271 AGACTGAAAGA
1 AGACTGAAAGA
31282 AGACTG
1 AGACTG
31288 GCTTAGTTTC
Statistics
Matches: 96, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
11 85 0.89
12 11 0.11
ACGTcount: A:0.49, C:0.09, G:0.24, T:0.18
Consensus pattern (11 bp):
AGACTGAAAGA
Found at i:31334 original size:36 final size:36
Alignment explanation
Indices: 31281--32051 Score: 861
Period size: 36 Copynumber: 21.7 Consensus size: 36
31271 AGACTGAAAG
* *
31281 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* ** *
31317 TAGACTATCTTAATTTCAAGGAAATTAAGTGAAA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGT-AAAGAA
* * *
31353 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
31389 TAGACTGGCTTAATTTCAAGGTAATTAAGTAAA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * * *
31424 GAGAACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAA
1 AAG-ACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
31461 AAGACTGGCTTAGTTTCAAGGTAATTAAGTAAA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
31496 AAGAACTGACTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAG-ACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
*
31533 AAGATTGGCTTAATTTCAAGGAAATTAGGTAAA-AGA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGA-A
* * *
31569 TAGACTGGCTTTATTTCAAGGAAATTAAGTAAA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
31604 AAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAG-ACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * * *
31641 AAGACTAGCTTAGTTTCAAGAAAACTAGGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
31676 TAGACTGACTTAATTTCAAGGAAATTAGGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
31711 TAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-AC
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
31746 AATACTGGCTTAGTTTCAAGGAAACTAGGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
31781 TAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-AC
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
31816 AAGACTGTCTTAGTTTCAAGGAAACTAGGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
31851 TAGACTGGCTTAATTTCAAGGAAATTAAGT-AA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
31885 AAGAACTGGCTTAATTTCAAGGAAACTAGGTAAAGGA
1 AAG-ACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
31922 AAGACTGACTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
31958 AAGACTGACTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
31994 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
32029 GACACAGGCTTAATTTC-AGGAAA
1 AAGACTGGCTTAATTTCAAGGAAA
32052 GGAAATTAAG
Statistics
Matches: 624, Mismatches: 94, Indels: 36
0.83 0.12 0.05
Matches are distributed among these distances:
34 11 0.02
35 227 0.36
36 365 0.58
37 21 0.03
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
Found at i:32091 original size:32 final size:31
Alignment explanation
Indices: 32055--32162 Score: 119
Period size: 32 Copynumber: 3.3 Consensus size: 31
32045 CAGGAAAGGA
*
32055 AATTAAGTAAAATAAAGAACTTAATTCAGTGT
1 AATTAAGTACAATAAAGAACTTAATTCAG-GT
*
32087 AATTAAGTGAGGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT-A---CAATAAAGA-ACTTAATTCA-GGT
32123 AATTAAGTACAATAAAGAACTTAATTCAAGGT
1 AATTAAGTACAATAAAGAACTTAATTC-AGGT
32155 AATTAAGT
1 AATTAAGT
32163 GAAGTCAATA
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
32 34 0.52
33 3 0.05
35 2 0.03
36 25 0.38
37 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (31 bp):
AATTAAGTACAATAAAGAACTTAATTCAGGT
Found at i:32105 original size:36 final size:34
Alignment explanation
Indices: 32065--32183 Score: 138
Period size: 36 Copynumber: 3.4 Consensus size: 34
32055 AATTAAGTAA
32065 AATAAAGAACTTAATTCAGTGTAATTAAGTGAGGTC
1 AATAAAGAACTTAATTCAG-GTAATTAAGTGA-GTC
*
32101 AATAAA-AGGCTTAATTCAGGGTAATTAAGT-A--C
1 AATAAAGA-ACTTAATTCA-GGTAATTAAGTGAGTC
32133 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTC
1 AATAAAGAACTTAATTC-AGGTAATTAAGTG-AGTC
*
32169 AATAAAGAGCTTAAT
1 AATAAAGAACTTAAT
32184 CTAGAAAAGA
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
32 26 0.36
33 2 0.03
34 1 0.01
35 2 0.03
36 40 0.56
37 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (34 bp):
AATAAAGAACTTAATTCAGGTAATTAAGTGAGTC
Found at i:32137 original size:68 final size:68
Alignment explanation
Indices: 32055--32183 Score: 208
Period size: 68 Copynumber: 1.9 Consensus size: 68
32045 CAGGAAAGGA
*
32055 AATTAAGTAAAATAAAGAACTTAATTC-AGTGTAATTAAGTGAGGTCAATAAA-AGGCTTAATTC
1 AATTAAGTAAAATAAAGAACTTAATTCAAG-GTAATTAAGTGAAGTCAATAAAGA-GCTTAATTC
32118 AGGGT
64 AGGGT
*
32123 AATTAAGTACAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAAT
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAAT
32184 CTAGAAAAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
68 54 0.95
69 3 0.05
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.29
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAATTCAG
GGT
Found at i:33029 original size:89 final size:90
Alignment explanation
Indices: 32873--33051 Score: 306
Period size: 89 Copynumber: 2.0 Consensus size: 90
32863 ATCTCCTGCC
* *
32873 AGTTGGGGGCCATGCTAGGTCAAGGTCGATTCTTGTCGATCGCCCAGCCTGCTGGCGTTGAGCCC
1 AGTTGGGGGCCATGCTAGGTCAAGGTCAAATCTTGTCGATCGCCCAGCCTGCTGGCGTTGAGCCC
*
32938 CTTGGGGGCGTTCGTCATTCCCATA
66 CTTGGGGGCGTTCATCATTCCCATA
* *
32963 AGTT-GGGGCCATGCTAGGTCAGGGTCAAATCTTGTCGATCGCCCCGCCTGCTGGCGTTGAGCCC
1 AGTTGGGGGCCATGCTAGGTCAAGGTCAAATCTTGTCGATCGCCCAGCCTGCTGGCGTTGAGCCC
33027 CTTGGGGGCGTTCATCATTCCCATA
66 CTTGGGGGCGTTCATCATTCCCATA
33052 CTTTGTCCAA
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 80 0.95
90 4 0.05
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.26
Consensus pattern (90 bp):
AGTTGGGGGCCATGCTAGGTCAAGGTCAAATCTTGTCGATCGCCCAGCCTGCTGGCGTTGAGCCC
CTTGGGGGCGTTCATCATTCCCATA
Found at i:33984 original size:48 final size:49
Alignment explanation
Indices: 33911--34022 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 49
33901 ACTTGCTTTT
* *
33911 CATCCGGAAAGGGCAATTTAAGAAAAAGCGAGT-AAAACTAATGCCTTC
1 CATCCGGGAAGGGCAATTTAAGAAAAAGCAAGTAAAAACTAATGCCTTC
** * * *
33959 CATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAGTGCCTTC
1 CATCCGGGAAGGGCAATTTAAGAAAAAGCAAGTAAAAACTAATGCCTTC
* *
34008 CGTCGGGGAAGGGCA
1 CATCCGGGAAGGGCA
34023 CTTTGGGGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
48 28 0.53
49 25 0.47
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.19
Consensus pattern (49 bp):
CATCCGGGAAGGGCAATTTAAGAAAAAGCAAGTAAAAACTAATGCCTTC
Found at i:34101 original size:84 final size:86
Alignment explanation
Indices: 33955--34211 Score: 279
Period size: 84 Copynumber: 2.9 Consensus size: 86
33945 AAACTAATGC
* * * *
33955 CTTCCATCCGGGAAGGGCGTTTTAGGAAAA-AGCAAGTAAAAATTAGTGCCTTCCGTCGGGGAAG
1 CTTCCATCCGGGAAGGGCATTTTTGGAAAATAGCAAGT-AAAATAAGTGCCTTCCGTCTGGGAAG
34019 GGCACTTTGGGGAAAAAC-GT-
65 GGCACTTTGGGGAAAAACAGTA
34039 CTTCCATCCGGGAAGGGCATTTTTGGAAAATAGCAAGTAAAATAAGTGCCTTCCGTCTGGGAAGG
1 CTTCCATCCGGGAAGGGCATTTTTGGAAAATAGCAAGTAAAATAAGTGCCTTCCGTCTGGGAAGG
*
34104 GCA-TTTTGGGAAAAACAGGTAAAGATTA
66 GCACTTTGGGGAAAAAC------AG--TA
* * *
34132 GTGCCTTCCGTCCGGGAAGGGCGTTTTTTGGAAAATAGCAAGTAAAATAAGTGGCTTCCGTCTGG
1 ----CTTCCATCCGGGAAGGGC-ATTTTTGGAAAATAGCAAGTAAAATAAGTGCCTTCCGTCTGG
*
34197 GAAGGGCGCTTTGGG
61 GAAGGGCACTTTGGG
34212 AAATAGCAAG
Statistics
Matches: 146, Mismatches: 10, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
83 12 0.08
84 56 0.38
85 7 0.05
90 1 0.01
92 1 0.01
97 17 0.12
98 47 0.32
99 5 0.03
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (86 bp):
CTTCCATCCGGGAAGGGCATTTTTGGAAAATAGCAAGTAAAATAAGTGCCTTCCGTCTGGGAAGG
GCACTTTGGGGAAAAACAGTA
Found at i:34116 original size:49 final size:49
Alignment explanation
Indices: 34039--34511 Score: 408
Period size: 49 Copynumber: 9.6 Consensus size: 49
34029 GGAAAAACGT
* * * *
34039 CTTCCATCCGGGAAGGGCATTTTTGGAAAATAGCAAGTAAAATAAGTGC
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAAATAGCAAGTAAAATAAGTGC
* * *
34088 CTTCCGTCTGGGAAGGGCATTTTGGGAAAA-A-CAGGTAAAGATTAGTGC
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAAATAGCAAGTAAA-ATAAGTGC
* * *
34136 CTTCCGTCCGGGAAGGGCGTTTTTTGGAAAATAGCAAGTAAAATAAGTGG
1 CTTCCGTCTGGGAAGGGCG-TTTTGGGAAAATAGCAAGTAAAATAAGTGC
* *
34186 CTTCCGTCTGGGAAGGGCGCTTTGGG-AAATAGCAAGTAAAATAAGTGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAAATAGCAAGTAAAATAAGTGC
* * * *
34234 CTTCCGTCTGGGAAGGGTGTTTTGGG-AGATAGCACGTAAAA-AATGAATGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAAATAGCAAGTAAAATAA-G--TGC
* * * * * *
34284 CTTCCGTCTGGGAAGGGCGCTTTAGG-AAATAGCTAGCAAAAATAAATGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAAATAGCAAG-TAAAATAAGTGC
* * * *
34333 TTTCCGTCTGGGAAGGGCATTTTTGGG-AAATAGCAAATAAAAGAAGTGC
1 CTTCCGTCTGGGAAGGGC-GTTTTGGGAAAATAGCAAGTAAAATAAGTGC
** * * *
34382 CTTCCGTCCAGGAAGGGCGTTTAGGGAAAA-AGCAAAATAAAAATTGAGTGC
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAAATAGC-AAGT-AAAA-TAAGTGC
* * * ** *
34433 CTTCCGTCCGGGAAGAGCGTTTTGGGAAAA-AGTTAA-TAAAAATAAACGT
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAAATAG-CAAGT-AAAATAAGTGC
* * *
34482 CTTCCATCCGGGAAGGGCGTTTTGGAAAAA
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAAA
34512 GTAGGTAAAG
Statistics
Matches: 355, Mismatches: 54, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
47 9 0.03
48 94 0.26
49 122 0.34
50 81 0.23
51 47 0.13
52 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (49 bp):
CTTCCGTCTGGGAAGGGCGTTTTGGGAAAATAGCAAGTAAAATAAGTGC
Found at i:34166 original size:132 final size:132
Alignment explanation
Indices: 33911--34153 Score: 346
Period size: 132 Copynumber: 1.8 Consensus size: 132
33901 ACTTGCTTTT
* *
33911 CATCCGGAAAGGGCAATTTAAGAAAAAGCGAGTAAAACTAATGCCTTCCATCCGGGAAGGGCGTT
1 CATCCGGAAAGGGCAATTTAAGAAAAAGCAAGTAAAACTAATGCCTTCCATCCGGGAAGGGCATT
*
33976 TTAGGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCGGGGAAGGGCACTTTGGGGAAAAACGTCT
66 TTAGGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGGAAGGGCACTTTGGGGAAAAACGTCT
34041 TC
131 TC
* * ** * *
34043 CATCCGGGAAGGGCATTTTTGGAAAATAGCAAGTAAAA-TAAGTGCCTTCCGTCTGGGAAGGGCA
1 CATCCGGAAAGGGCAATTTAAGAAAA-AGCAAGTAAAACTAA-TGCCTTCCATCCGGGAAGGGCA
* * *
34107 TTTTGGGAAAAA-CAGGTAAAGATTAGTGCCTTCCGTCCGGGAAGGGC
64 TTTTAGGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGGAAGGGC
34154 GTTTTTTGGA
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
132 57 0.59
133 40 0.41
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (132 bp):
CATCCGGAAAGGGCAATTTAAGAAAAAGCAAGTAAAACTAATGCCTTCCATCCGGGAAGGGCATT
TTAGGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGGAAGGGCACTTTGGGGAAAAACGTCT
TC
Found at i:38044 original size:42 final size:42
Alignment explanation
Indices: 37973--38120 Score: 228
Period size: 42 Copynumber: 3.5 Consensus size: 42
37963 CTCGGAGGCG
*
37973 TTCATCACATT-TGGTTATTCT-AGGAAGCTGTCGTTCGACACT
1 TTCATCAC-TTCTGGTTGTTCTGAGG-AGCTGTCGTTCGACACT
*
38015 TTCATCACTTCTGGTTGTTCTGAGGAGCTGTCGTTTGACACT
1 TTCATCACTTCTGGTTGTTCTGAGGAGCTGTCGTTCGACACT
38057 TTCATCACTTCTGGTTGTTCTGAGGAGCTGTCGTTCGACACT
1 TTCATCACTTCTGGTTGTTCTGAGGAGCTGTCGTTCGACACT
* *
38099 TTCAACACTTTTGGTTGTTCTG
1 TTCATCACTTCTGGTTGTTCTG
38121 GCTATTAGAG
Statistics
Matches: 99, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
41 2 0.02
42 94 0.95
43 3 0.03
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (42 bp):
TTCATCACTTCTGGTTGTTCTGAGGAGCTGTCGTTCGACACT
Found at i:40591 original size:18 final size:18
Alignment explanation
Indices: 40545--40663 Score: 114
Period size: 18 Copynumber: 6.6 Consensus size: 18
40535 GCACCAGGCG
* * *
40545 CCACACCCAGTAGCCGCA
1 CCACACCAAGTGGTCGCA
* *
40563 CCATC-CCAAGTGGTTGCG
1 CCA-CACCAAGTGGTCGCA
40581 CCACACCAAGTGGTCGCA
1 CCACACCAAGTGGTCGCA
*
40599 CCACACCAAGTGGCCGCA
1 CCACACCAAGTGGTCGCA
*
40617 CCACACTAAGTGGTCGCA
1 CCACACCAAGTGGTCGCA
* * * *
40635 CCGCACCTAGTGGCCACA
1 CCACACCAAGTGGTCGCA
*
40653 CCGCACCAAGT
1 CCACACCAAGT
40664 TGCCACACTT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
17 1 0.01
18 81 0.98
19 1 0.01
ACGTcount: A:0.25, C:0.41, G:0.22, T:0.12
Consensus pattern (18 bp):
CCACACCAAGTGGTCGCA
Found at i:40628 original size:54 final size:54
Alignment explanation
Indices: 40545--40663 Score: 132
Period size: 54 Copynumber: 2.2 Consensus size: 54
40535 GCACCAGGCG
* * * * *
40545 CCACACCCAGTAGCCGCACCATCCCAAGTGGTTGCGCCACACCAAGTGGTCGCA
1 CCACACCAAGTAGCCGCACCATCCCAAGTGGTCGCACCACACCAAGTGGCCACA
* * * *
40599 CCACACCAAGTGGCCGCACCA-CACTAAGTGGTCGCACCGCACCTAGTGGCCACA
1 CCACACCAAGTAGCCGCACCATC-CCAAGTGGTCGCACCACACCAAGTGGCCACA
*
40653 CCGCACCAAGT
1 CCACACCAAGT
40664 TGCCACACTT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 1 0.02
54 53 0.98
ACGTcount: A:0.25, C:0.41, G:0.22, T:0.12
Consensus pattern (54 bp):
CCACACCAAGTAGCCGCACCATCCCAAGTGGTCGCACCACACCAAGTGGCCACA
Found at i:40808 original size:15 final size:15
Alignment explanation
Indices: 40788--40826 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
40778 AAGTGGTGCC
*
40788 AGTGCAGAAAGATCT
1 AGTGCAGAAACATCT
40803 AGTGCAGAAACATCT
1 AGTGCAGAAACATCT
*
40818 GGTGC-GAAA
1 AGTGCAGAAA
40827 AGATGCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.18
Consensus pattern (15 bp):
AGTGCAGAAACATCT
Found at i:41935 original size:30 final size:30
Alignment explanation
Indices: 41899--41978 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
41889 GAAGATGATG
* * *
41899 GCACCCAAAATGGTGGCACCGAAGTCTACT
1 GCACCCAAAATGGTGGCACCAAAATCAACT
41929 GCACCCAAAATGGTGGCACCAAAATCAACT
1 GCACCCAAAATGGTGGCACCAAAATCAACT
* *
41959 GCACCCAAGATGATGGCACC
1 GCACCCAAAATGGTGGCACC
41979 TCAGGTGACG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.34, C:0.31, G:0.21, T:0.14
Consensus pattern (30 bp):
GCACCCAAAATGGTGGCACCAAAATCAACT
Found at i:41977 original size:15 final size:15
Alignment explanation
Indices: 41959--42053 Score: 86
Period size: 15 Copynumber: 6.3 Consensus size: 15
41949 AAAATCAACT
*
41959 GCACCCAAGATGATG
1 GCACCCAAGGTGATG
*
41974 GCACCTC-AGGTGACG
1 GCACC-CAAGGTGATG
*
41989 GCACTCAAGGTGATG
1 GCACCCAAGGTGATG
*
42004 GCACCTC-AGGTGACG
1 GCACC-CAAGGTGATG
*
42019 GCACTCAAGGTGATG
1 GCACCCAAGGTGATG
* * *
42034 GCACCGAAGATGATA
1 GCACCCAAGGTGATG
42049 GCACC
1 GCACC
42054 GAAAGTGTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
14 2 0.03
15 60 0.94
16 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.31, T:0.15
Consensus pattern (15 bp):
GCACCCAAGGTGATG
Found at i:42003 original size:30 final size:30
Alignment explanation
Indices: 41959--42038 Score: 142
Period size: 30 Copynumber: 2.7 Consensus size: 30
41949 AAAATCAACT
* *
41959 GCACCCAAGATGATGGCACCTCAGGTGACG
1 GCACTCAAGGTGATGGCACCTCAGGTGACG
41989 GCACTCAAGGTGATGGCACCTCAGGTGACG
1 GCACTCAAGGTGATGGCACCTCAGGTGACG
42019 GCACTCAAGGTGATGGCACC
1 GCACTCAAGGTGATGGCACC
42039 GAAGATGATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.15
Consensus pattern (30 bp):
GCACTCAAGGTGATGGCACCTCAGGTGACG
Done.