Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008627.1 Hibiscus syriacus cultivar Beakdansim tig00111594_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: 1073793
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 1 of 6
Found at i:7844 original size:85 final size:82
Alignment explanation
Indices: 7731--7900 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 82
7721 TTTGAATTTT
7731 GAAGTTTCTTGAATTTGTTGGTTATTATCGAAGGTTCATCAAGAACTTTTCGATGATTATCTTCC
1 GAAGTTTCTTGAATTTGTTGGTTATTATCGAAGGTTCATCAAGAACTTTTCGATG--TATCTTCC
7796 CTCTGACCAAGCTATTGTG
64 CTCTGACCAAGCTATTGTG
7815 GAAGTTTCTTGAAATTTGTTGGTTATTATCGAAGGTTCATCAAGAACTTTTCGATGTATCTTCCC
1 GAAGTTTCTTG-AATTTGTTGGTTATTATCGAAGGTTCATCAAGAACTTTTCGATGTATCTTCCC
7880 TCTGACCAAGCTATTGTG
65 TCTGACCAAGCTATTGTG
7898 GAA
1 GAA
7901 AGACATGTTA
Statistics
Matches: 85, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
83 30 0.35
84 11 0.13
85 44 0.52
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.39
Consensus pattern (82 bp):
GAAGTTTCTTGAATTTGTTGGTTATTATCGAAGGTTCATCAAGAACTTTTCGATGTATCTTCCCT
CTGACCAAGCTATTGTG
Found at i:10774 original size:19 final size:18
Alignment explanation
Indices: 10752--10790 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
10742 CCCGTTAACC
*
10752 TTGACCCAAACCGTTGACT
1 TTGA-CCAAACAGTTGACT
*
10771 TTGACCAAATAGTTGACT
1 TTGACCAAACAGTTGACT
10789 TT
1 TT
10791 CCCGTTGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (18 bp):
TTGACCAAACAGTTGACT
Found at i:14138 original size:20 final size:21
Alignment explanation
Indices: 14099--14140 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
14089 AAGGCACACG
14099 ATACAAGACACTAGAGTGTAT
1 ATACAAGACACTAGAGTGTAT
*
14120 ATACAAGACACT-TAGTGTAT
1 ATACAAGACACTAGAGTGTAT
14140 A
1 A
14141 AGGTGGGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (21 bp):
ATACAAGACACTAGAGTGTAT
Found at i:23032 original size:22 final size:22
Alignment explanation
Indices: 22992--23033 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
22982 TTTTTTATAA
*
22992 TTTTATAATTTTTTCTATTTCT
1 TTTTATAATTTTTTATATTTCT
23014 TTTTAT-ATTTTTATATATTT
1 TTTTATAATTTTT-TATATTT
23034 TTATATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTATAATTTTTTATATTTCT
Found at i:23036 original size:10 final size:10
Alignment explanation
Indices: 22965--23039 Score: 66
Period size: 10 Copynumber: 7.6 Consensus size: 10
22955 TTTTAACAAA
22965 TTATA-ATTT
1 TTATATATTT
*
22974 TTAAATATTT
1 TTATATATTT
* *
22984 TTTTATAATT
1 TTATATATTT
22994 TTATA-ATTT
1 TTATATATTT
*
23003 TT-TCTATTTCT
1 TTATATA-TT-T
*
23014 TTTTATATTT
1 TTATATATTT
23024 TTATATATTT
1 TTATATATTT
23034 TTATAT
1 TTATAT
23040 TTTGCTAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
8 1 0.02
9 10 0.19
10 33 0.63
11 5 0.10
12 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATATATTT
Found at i:23041 original size:30 final size:28
Alignment explanation
Indices: 22965--23042 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 28
22955 TTTTAACAAA
*
22965 TTATAATTTTTAAATATTTTTTTATAATT
1 TTATAATTTTTATAT-TTTTTTTATAATT
* *
22994 TTATAATTTTTTCTATTTCTTTTTATATTT
1 TTATAA-TTTTTATATTT-TTTTTATAATT
23024 TTATATATTTTTATATTTT
1 TTATA-ATTTTTATATTTT
23043 GCTAAAATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 9 0.21
30 32 0.76
31 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.71
Consensus pattern (28 bp):
TTATAATTTTTATATTTTTTTTATAATT
Found at i:23255 original size:60 final size:60
Alignment explanation
Indices: 23140--23255 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
23130 GGCTATAGGA
* ** *
23140 TATTGCTTTATTAAGTCCTTCAACTATTAAAAGTTACAAAATAGTCTTCTAACTATATAG
1 TATTGCTTTATTAAGTCCTTCAACTATTAAAAGTTACAAAATAGCCACCCAACTATATAG
* * * * *
23200 TATTGCTTTGTTGAGTTCC-TCAACTATTAAAAGTTGCAAAATGGCCACCCGACTAT
1 TATTGCTTTATTAAG-TCCTTCAACTATTAAAAGTTACAAAATAGCCACCCAACTAT
23256 TCATTATATT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
60 43 0.93
61 3 0.07
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (60 bp):
TATTGCTTTATTAAGTCCTTCAACTATTAAAAGTTACAAAATAGCCACCCAACTATATAG
Found at i:30843 original size:18 final size:19
Alignment explanation
Indices: 30822--30857 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
30812 TTCTCTGGTT
30822 GTGCTTGTTCCTC-TGCTC
1 GTGCTTGTTCCTCGTGCTC
30840 GTGCTTGTTCCTCGTGCT
1 GTGCTTGTTCCTCGTGCT
30858 GTTCTGGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44
Consensus pattern (19 bp):
GTGCTTGTTCCTCGTGCTC
Found at i:32482 original size:22 final size:22
Alignment explanation
Indices: 32456--32517 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
32446 TGTGGGGGGG
32456 GGGGGAATCGATTCCCTTTCAAA
1 GGGGGAATCGATTCCCTTTC-AA
* *
32479 GGGGGAAACGATTCCCCTTCAA
1 GGGGGAATCGATTCCCTTTCAA
* *
32501 GAGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
32518 CTACACAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCTTTCAA
Found at i:42166 original size:20 final size:19
Alignment explanation
Indices: 42118--42165 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
42108 ATTGATTTTC
*
42118 TTTTGAAAACAAAATTAGA
1 TTTTGAAAACAAAATAAGA
42137 TTTTGGAAAACAAAATGAAG-
1 TTTT-GAAAACAAAAT-AAGA
42157 TTTTGAAAA
1 TTTTGAAAA
42166 ATGATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 15 0.58
21 2 0.08
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (19 bp):
TTTTGAAAACAAAATAAGA
Found at i:54273 original size:16 final size:17
Alignment explanation
Indices: 54252--54284 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54242 AAGATTCTAA
54252 CATATAGTTTG-AAATG
1 CATATAGTTTGTAAATG
*
54268 CATATATTTTGTAAATG
1 CATATAGTTTGTAAATG
54285 GTGTTCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (17 bp):
CATATAGTTTGTAAATG
Found at i:55462 original size:19 final size:19
Alignment explanation
Indices: 55438--55541 Score: 86
Period size: 19 Copynumber: 5.5 Consensus size: 19
55428 TGCATTGGGC
* *
55438 TATGAATTTGAAAATACGT
1 TATGAATATGAAAATAAGT
* * *
55457 TATGAATATGATAGTAAGC
1 TATGAATATGAAAATAAGT
* * *
55476 TATGAGTCTAAAAATAAGT
1 TATGAATATGAAAATAAGT
*
55495 TATGAATATGGAAATAAGT
1 TATGAATATGAAAATAAGT
* *
55514 TCTGAAT-TAGAAAATAAAT
1 TATGAATAT-GAAAATAAGT
55533 TATG-ATATG
1 TATGAATATG
55542 TGAAAGTTTT
Statistics
Matches: 64, Mismatches: 19, Indels: 5
0.73 0.22 0.06
Matches are distributed among these distances:
18 4 0.06
19 60 0.94
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (19 bp):
TATGAATATGAAAATAAGT
Found at i:55528 original size:38 final size:38
Alignment explanation
Indices: 55436--55546 Score: 111
Period size: 38 Copynumber: 2.9 Consensus size: 38
55426 TATGCATTGG
* * *
55436 GCTATGAATTTGAAAATACGTTATGAATAT-GATAGTAA
1 GCTATGAATTAGAAAATAAGTTATGAATATGGA-AATAA
*
55474 GCTATGAGTCTA-AAAATAAGTTATGAATATGGAAATAA
1 GCTATGAAT-TAGAAAATAAGTTATGAATATGGAAATAA
* * *
55512 GTTCTGAATTAGAAAATAAATTATG-ATATGTGAAA
1 GCTATGAATTAGAAAATAAGTTATGAATATG-GAAA
55547 GTTTTTGTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
37 7 0.11
38 51 0.84
39 3 0.05
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (38 bp):
GCTATGAATTAGAAAATAAGTTATGAATATGGAAATAA
Found at i:57031 original size:32 final size:32
Alignment explanation
Indices: 57003--57085 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
56993 TTAGTGTCGT
57003 ATTCAAATAATGAAAAACAATGTCAGTGTCAC
1 ATTCAAATAATGAAAAACAATGTCAGTGTCAC
* * *
57035 ATTCAGATAATGTACAACAATGTCAGTGTCAC
1 ATTCAAATAATGAAAAACAATGTCAGTGTCAC
*
57067 ATTCAAATAATAAAAAACA
1 ATTCAAATAATGAAAAACA
57086 GTTACAATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (32 bp):
ATTCAAATAATGAAAAACAATGTCAGTGTCAC
Found at i:61535 original size:32 final size:32
Alignment explanation
Indices: 61495--61616 Score: 145
Period size: 32 Copynumber: 3.8 Consensus size: 32
61485 CACAACAGAG
*
61495 TCAATATTGCATTCAGATAATGCACAGTGGAA
1 TCAATATTGCATTCAGATAATGCACAGTAGAA
* * * * *
61527 TCAGTATTGCATTCAAATAATGTATAGTAGAT
1 TCAATATTGCATTCAGATAATGCACAGTAGAA
* *
61559 TTAATATTGCATTCAGATATTGCACAGTAGAA
1 TCAATATTGCATTCAGATAATGCACAGTAGAA
** *
61591 TCAATATTATATTCATATAATGCACA
1 TCAATATTGCATTCAGATAATGCACA
61617 ACAGATCTAG
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (32 bp):
TCAATATTGCATTCAGATAATGCACAGTAGAA
Found at i:69098 original size:101 final size:101
Alignment explanation
Indices: 68923--69124 Score: 350
Period size: 101 Copynumber: 2.0 Consensus size: 101
68913 TGAAATGCTT
*
68923 GAATTTTAAAGTTAGATTAATGATTAAGGATCAAAGTGCAACTTTGGATAAATATGATGATGGAA
1 GAATTTTAAAGTTAGATTAATGATTAAGGATCAAAGTGCAAATTTGGATAAATATGATGATGGAA
*
68988 TTCCAATAGTCTAAATATTTGGAACTTAATTGTGAG
66 TTCCAATAGTCTAAATAGTTGGAACTTAATTGTGAG
* *
69024 GAATTTTAAAGTTAGGTTAATGATTAAGGATCAAAGTGCAAATTTGGATAAGTATGATGATGGAA
1 GAATTTTAAAGTTAGATTAATGATTAAGGATCAAAGTGCAAATTTGGATAAATATGATGATGGAA
* *
69089 TTCCAATAGTCTCAATAGTTGGGACTTAATTGTGAG
66 TTCCAATAGTCTAAATAGTTGGAACTTAATTGTGAG
69125 TTTTTAAAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (101 bp):
GAATTTTAAAGTTAGATTAATGATTAAGGATCAAAGTGCAAATTTGGATAAATATGATGATGGAA
TTCCAATAGTCTAAATAGTTGGAACTTAATTGTGAG
Found at i:71079 original size:24 final size:25
Alignment explanation
Indices: 71047--71103 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
71037 GAAAGTTTCA
**
71047 ATGTTTTAATTATATTA-CATTTTT
1 ATGTTTTAAACATATTATCATTTTT
* *
71071 ATGTTTTAAACATTTTATTATTTTT
1 ATGTTTTAAACATATTATCATTTTT
71096 ATGTTTTA
1 ATGTTTTA
71104 TCTCACCTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (25 bp):
ATGTTTTAAACATATTATCATTTTT
Found at i:79323 original size:22 final size:22
Alignment explanation
Indices: 79278--79323 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
79268 ACTGGTTATT
* *
79278 ATATACATGATTTTTATCATGA
1 ATATACATGATGTTTATCACGA
* *
79300 ATATATATGATGTTTATTACGA
1 ATATACATGATGTTTATCACGA
79322 AT
1 AT
79324 GTTACTTCGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (22 bp):
ATATACATGATGTTTATCACGA
Found at i:79554 original size:65 final size:61
Alignment explanation
Indices: 79473--79628 Score: 190
Period size: 60 Copynumber: 2.5 Consensus size: 61
79463 ACAAGTTTAT
* *
79473 ATTAGCACTAGTGTGTAAGGACACTAAGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAT
1 ATTAGCACTAGAGTGTAA-GAC-CT-AGTGCAGGTGGAGGGCAC-ACCTTATGTGTCATATCCAG
* * * *
79538 TTTAGCACTAGAGTGTAA-ACCTAGTGTAGGTGGTGGGCACGCCTTATGTGTCATATCCAG
1 ATTAGCACTAGAGTGTAAGACCTAGTGCAGGTGGAGGGCACACCTTATGTGTCATATCCAG
* *
79598 ATTAGCACTAGAGCGTAAG-CTTAGTGCAGGT
1 ATTAGCACTAGAGTGTAAGACCTAGTGCAGGT
79629 TTAGCACTAC
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
60 44 0.55
61 16 0.20
62 2 0.03
63 2 0.03
65 16 0.20
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (61 bp):
ATTAGCACTAGAGTGTAAGACCTAGTGCAGGTGGAGGGCACACCTTATGTGTCATATCCAG
Found at i:81379 original size:24 final size:24
Alignment explanation
Indices: 81369--81485 Score: 148
Period size: 24 Copynumber: 4.9 Consensus size: 24
81359 CATAATTCAC
*
81369 GTCAAGTATCATATCAAAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
*
81393 GTCAAGTATCAGATCAGAAT-CAA
1 GTCAAGTATCAGATCAAAATCCAA
* *
81416 GTCAAGTATCATATCAAAATCCAT
1 GTCAAGTATCAGATCAAAATCCAA
* *
81440 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAA
81464 GTCAAGTATCAGATCATAAATC
1 GTCAAGTATCAGATCA-AAATC
81486 AAATCGAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
23 23 0.28
24 52 0.64
25 6 0.07
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:81438 original size:47 final size:48
Alignment explanation
Indices: 81369--81485 Score: 175
Period size: 47 Copynumber: 2.4 Consensus size: 48
81359 CATAATTCAC
81369 GTCAAGTATCATATCAAAATCCAAGTCA-AGTATCAGATCAGAAT-CAA
1 GTCAAGTATCATATCAAAATCCAAGTCAGA-TATCAGATCAGAATCCAA
* *
81416 GTCAAGTATCATATCAAAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAAAATCCAAGTCAGATATCAGATCAGAATCCAA
*
81464 GTCAAGTATCAGATCATAAATC
1 GTCAAGTATCATATCA-AAATC
81486 AAATCGAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
47 41 0.64
48 18 0.28
49 5 0.08
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCATATCAAAATCCAAGTCAGATATCAGATCAGAATCCAA
Found at i:83879 original size:13 final size:13
Alignment explanation
Indices: 83861--83938 Score: 60
Period size: 13 Copynumber: 6.2 Consensus size: 13
83851 GACGGTCAAC
83861 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
83874 GGTCAACGGATCG
1 GGTCAACGGGTCG
83887 GGT---CGGGTCAATG
1 GGTCAACGGGTC---G
*
83900 GGT---CGGGTCA
1 GGTCAACGGGTCG
*
83910 GGTCAGCGGGTCG
1 GGTCAACGGGTCG
83923 GGTCAACGGGTCG
1 GGTCAACGGGTCG
83936 GGT
1 GGT
83939 TGGGTCAACG
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.15
13 46 0.85
ACGTcount: A:0.14, C:0.21, G:0.47, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:83890 original size:18 final size:18
Alignment explanation
Indices: 83867--83963 Score: 123
Period size: 18 Copynumber: 5.7 Consensus size: 18
83857 CAACGGTCAA
*
83867 CGGGTCGGGTCAACGGAT
1 CGGGTCGGGTCAACGGGT
*
83885 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCAACGGGT
*
83903 CGGGTCAGGTC-A---G-
1 CGGGTCGGGTCAACGGGT
83916 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
83934 CGGGTTGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
83952 CGGGTCGGGTCA
1 CGGGTCGGGTCA
83964 GGTCAGCGTT
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
13 10 0.15
14 2 0.03
17 2 0.03
18 54 0.79
ACGTcount: A:0.12, C:0.21, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:83903 original size:31 final size:30
Alignment explanation
Indices: 83861--83957 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 30
83851 GACGGTCAAC
*
83861 GGTCAACGGGTCGGGTCAACGG-ATCGGGTCG
1 GGTCAACGGGTCGGGTC-A-GGCAGCGGGTCG
*
83892 GGTCAATGGGTCGGGTCAGGTCAGCGGGTCG
1 GGTCAACGGGTCGGGTCAGG-CAGCGGGTCG
** *
83923 GGTCAACGGGTCGGGTTGGGTCAACGGGTCG
1 GGTCAACGGGTCGGGTCAGG-CAGCGGGTCG
83954 GGTC
1 GGTC
83958 GGGTCAGGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.03
30 1 0.02
31 55 0.95
ACGTcount: A:0.13, C:0.21, G:0.47, T:0.19
Consensus pattern (30 bp):
GGTCAACGGGTCGGGTCAGGCAGCGGGTCG
Found at i:86307 original size:121 final size:121
Alignment explanation
Indices: 86093--86317 Score: 450
Period size: 121 Copynumber: 1.9 Consensus size: 121
86083 ATATTAAAAA
86093 GATTTCTGACATAAGCCCCAAAGTCAGTATAATTAGAATCTAGAAAAGATTATGTGAATCATTGT
1 GATTTCTGACATAAGCCCCAAAGTCAGTATAATTAGAATCTAGAAAAGATTATGTGAATCATTGT
86158 AATGAGTCTCATAATGGTTTGGGATGTGTGTTCATACAAAGATGTGTTATTCATTT
66 AATGAGTCTCATAATGGTTTGGGATGTGTGTTCATACAAAGATGTGTTATTCATTT
86214 GATTTCTGACATAAGCCCCAAAGTCAGTATAATTAGAATCTAGAAAAGATTATGTGAATCATTGT
1 GATTTCTGACATAAGCCCCAAAGTCAGTATAATTAGAATCTAGAAAAGATTATGTGAATCATTGT
86279 AATGAGTCTCATAATGGTTTGGGATGTGTGTTCATACAA
66 AATGAGTCTCATAATGGTTTGGGATGTGTGTTCATACAA
86318 GAGGAAAAGT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 104 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (121 bp):
GATTTCTGACATAAGCCCCAAAGTCAGTATAATTAGAATCTAGAAAAGATTATGTGAATCATTGT
AATGAGTCTCATAATGGTTTGGGATGTGTGTTCATACAAAGATGTGTTATTCATTT
Found at i:89641 original size:18 final size:18
Alignment explanation
Indices: 89618--89659 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
89608 TGCTTTATAT
*
89618 GGATAGATTCTTATTTGA
1 GGATAGATTCATATTTGA
89636 GGATAGATTCATATTTGA
1 GGATAGATTCATATTTGA
*
89654 GTATAG
1 GGATAG
89660 TTTCCATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (18 bp):
GGATAGATTCATATTTGA
Found at i:90059 original size:22 final size:22
Alignment explanation
Indices: 90014--90059 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
90004 ACTGTTTATT
* *
90014 ATATACATGATTTTTATCATGA
1 ATATACATGATGTTTATCACGA
* *
90036 ATATATATGATGTTTATTACGA
1 ATATACATGATGTTTATCACGA
90058 AT
1 AT
90060 GTTACTTCGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (22 bp):
ATATACATGATGTTTATCACGA
Found at i:114710 original size:16 final size:17
Alignment explanation
Indices: 114686--114721 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
114676 TTTAGTATCA
114686 TAATATATATTT-ATAC
1 TAATATATATTTAATAC
*
114702 TAATTTATATTTAATAC
1 TAATATATATTTAATAC
114719 TAA
1 TAA
114722 CCATACTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATATATTTAATAC
Found at i:118617 original size:16 final size:16
Alignment explanation
Indices: 118587--118630 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
118577 TAATTTCTAG
*
118587 GCATATTTCACCAATTT
1 GCAT-TTTCAGCAATTT
118604 GCATTTTCAGCAATTT
1 GCATTTTCAGCAATTT
118620 GCATTTTCAGC
1 GCATTTTCAGC
118631 TTATTCACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (16 bp):
GCATTTTCAGCAATTT
Found at i:120441 original size:29 final size:28
Alignment explanation
Indices: 120390--120470 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
120380 TTATTTTGGG
*
120390 AAAATTATTACTTTAGTCCCTAAACTTTTC
1 AAAATTA-TACTTTAGTCACTAAA-TTTTC
*
120420 CAAATTATACTTTAG-CTACTAAATTTTC
1 AAAATTATACTTTAGTC-ACTAAATTTTC
* *
120448 AAAACTTATATTTTGGTCACTAA
1 AAAA-TTATACTTTAGTCACTAA
120471 CCAAAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 9 0.21
29 27 0.63
30 7 0.16
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (28 bp):
AAAATTATACTTTAGTCACTAAATTTTC
Found at i:124194 original size:22 final size:22
Alignment explanation
Indices: 124167--124209 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
124157 TAAAATATAT
* *
124167 TTTTAGTTATCATAATAAATTA
1 TTTTAGTTATAATAACAAATTA
124189 TTTTAGTTATAATAACAAATT
1 TTTTAGTTATAATAACAAATT
124210 TAAATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTTAGTTATAATAACAAATTA
Found at i:124350 original size:31 final size:32
Alignment explanation
Indices: 124308--124369 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
124298 ATGTCAAAAA
* * *
124308 TATTTAGTCAAAATAA-AATTTTTGACAAATT
1 TATTTAATCAAAATAATAATTTATAACAAATT
124339 TATTTAATCAAAATAATAATTTATAACAAAT
1 TATTTAATCAAAATAATAATTTATAACAAAT
124370 ATTAATTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (32 bp):
TATTTAATCAAAATAATAATTTATAACAAATT
Found at i:124625 original size:98 final size:98
Alignment explanation
Indices: 124330--124625 Score: 257
Period size: 101 Copynumber: 3.0 Consensus size: 98
124320 ATAAAATTTT
* * * *
124330 TGACAAATTTATTTAATCAAAATAATAATTTATAACAAATATTAATTTCTCAATATAAAAAATTG
1 TGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTTATTATAAAAATTTG
*
124395 TGAA-AAGTAATATTCTTTCACAATAACAAATTG
66 T-AACAAATAATATTCTTTCACAATAACAAATTG
* * * * * * * ** * * * *
124428 TAACAAAATAATTTAGTCACAATAACACGTTAAATTTAATCAAAGTAAAAAGTT-ATGTCA-AAA
1 TGACAAATTTATTTAATCAAAATAACA-ATT---TATAA-CAAA-TATTAATTTCTTATTATAAA
* *
124491 ATTATTTTGT--C--ATAATATT-TTGTCAAAATAAAAAATTG
60 A--A-TTTGTAACAAATAATATTCTT-TCACAATAACAAATTG
124529 TGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTTATTATAAAAATTTG
1 TGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTTATTATAAAAATTTG
124594 TAACAAATAATATTCTTTCACAATAACAAATT
66 TAACAAATAATATTCTTTCACAATAACAAATT
124626 ATTTAGTCAC
Statistics
Matches: 145, Mismatches: 35, Indels: 36
0.67 0.16 0.17
Matches are distributed among these distances:
94 5 0.03
95 7 0.05
96 8 0.06
97 8 0.06
98 42 0.29
99 4 0.03
100 4 0.03
101 43 0.30
102 8 0.06
103 5 0.03
104 7 0.05
105 4 0.03
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (98 bp):
TGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTTATTATAAAAATTTG
TAACAAATAATATTCTTTCACAATAACAAATTG
Found at i:126020 original size:20 final size:21
Alignment explanation
Indices: 125978--126027 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
125968 CCAGAAAAAA
125978 GATCGATCCCTCAACTGAAAG
1 GATCGATCCCTCAACTGAAAG
* *
125999 GATCGATCCCTTACCT-AAAG
1 GATCGATCCCTCAACTGAAAG
126019 GATCGATCC
1 GATCGATCC
126028 AAAACTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (21 bp):
GATCGATCCCTCAACTGAAAG
Found at i:146845 original size:41 final size:41
Alignment explanation
Indices: 146763--146889 Score: 177
Period size: 41 Copynumber: 3.1 Consensus size: 41
146753 AATGCATGGA
* * *
146763 TAGATGTGCTGCATTTAACAGCAAGA-T-AATGCATTGAAT
1 TAGACGTGCTGCATTTAACAGTAGGATTAAATGCATTGAAT
*
146802 TAGACTTGCTGCATTTAACAGTAGGATTAAATGCATTGAAT
1 TAGACGTGCTGCATTTAACAGTAGGATTAAATGCATTGAAT
* **
146843 TAGACGTGCTGCATTTAACAATAGGATTAAATGTTTTGAAT
1 TAGACGTGCTGCATTTAACAGTAGGATTAAATGCATTGAAT
146884 TAGACG
1 TAGACG
146890 AGGAACTAGC
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 22 0.28
40 1 0.01
41 55 0.71
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (41 bp):
TAGACGTGCTGCATTTAACAGTAGGATTAAATGCATTGAAT
Found at i:153206 original size:30 final size:30
Alignment explanation
Indices: 153170--153227 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
153160 CAAATGATTC
*
153170 CTGACTATACGACAATTCTTTGTTGAGTCA
1 CTGACTATACGACAATGCTTTGTTGAGTCA
* *
153200 CTGACTATAGGACGATGCTTTGTTGAGT
1 CTGACTATACGACAATGCTTTGTTGAGT
153228 TTTCCTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (30 bp):
CTGACTATACGACAATGCTTTGTTGAGTCA
Found at i:158214 original size:5 final size:5
Alignment explanation
Indices: 158204--158580 Score: 103
Period size: 5 Copynumber: 74.2 Consensus size: 5
158194 GGAAAATGAT
*
158204 AAATA AAAT- AAATA AGAA-A AAATA AAA-A CAAATA AAA-A TAA-A AAATA
1 AAATA AAATA AAATA A-AATA AAATA AAATA -AAATA AAATA AAATA AAATA
* * * * * * *
158251 AAA-A ATAA-A AAATA AAATG AAATT AAATT AAATT AAATT AAATT AAATT
1 AAATA A-AATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* *
158300 AAATA ATGGAATT AAATA AAATA AAATA ATAAGA AAA-A AACATA AACA-A
1 AAATA A---AATA AAATA AAATA AAATA A-AATA AAATA AA-ATA AA-ATA
* * * * * * * * * *
158349 TATATA TATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 -AAATA -AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * * * * * * * *
158401 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA TAAATA ATATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA -AAATA AAATA
* * * * * * *
158452 ATATA ATATA ATATATA TAATA TAATA TAATA TAATA TAATA TAAATA
1 AAATA AAATA A-A-ATA AAATA AAATA AAATA AAATA AAATA -AAATA
* * * * * * * * *
158500 ATATATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAAT-
1 A-A-ATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
158551 AAAT- AAATA AAA-A AAAGTA AAATA AAATA A
1 AAATA AAATA AAATA AAA-TA AAATA AAATA A
158581 TTAAAACGGG
Statistics
Matches: 331, Mismatches: 16, Indels: 50
0.83 0.04 0.13
Matches are distributed among these distances:
4 31 0.09
5 255 0.77
6 35 0.11
7 6 0.02
8 4 0.01
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (5 bp):
AAATA
Found at i:158247 original size:7 final size:7
Alignment explanation
Indices: 158208--158267 Score: 75
Period size: 7 Copynumber: 8.3 Consensus size: 7
158198 AATGATAAAT
158208 AAAATAA
1 AAAATAA
* *
158215 ATAAGAA
1 AAAATAA
158222 AAAATAA
1 AAAATAA
*
158229 AAACAAATA
1 AAA-ATA-A
158238 AAAATAA
1 AAAATAA
158245 AAAATAA
1 AAAATAA
158252 AAAATAA
1 AAAATAA
158259 AAAATAA
1 AAAATAA
158266 AA
1 AA
158268 TGAAATTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
7 37 0.82
8 4 0.09
9 4 0.09
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:158376 original size:15 final size:15
Alignment explanation
Indices: 158347--158559 Score: 359
Period size: 15 Copynumber: 14.6 Consensus size: 15
158337 AAACATAAAC
158347 AATAT-ATAT-ATAT
1 AATATAATATAATAT
158360 AATATAATATAATAT
1 AATATAATATAATAT
158375 AATATAATATAATAT
1 AATATAATATAATAT
158390 AATATAATATAATAT
1 AATATAATATAATAT
158405 AATATAATATAATAT
1 AATATAATATAATAT
158420 AATATAATATAATAT
1 AATATAATATAATAT
*
158435 AATATATAAATAATAT
1 AATATA-ATATAATAT
158451 AATATAATATAATAT
1 AATATAATATAATAT
158466 -ATATAATATAATAT
1 AATATAATATAATAT
158480 AATATAATATAATAT
1 AATATAATATAATAT
158495 AA-ATAATAT-ATAT
1 AATATAATATAATAT
158508 AATATAATATAATAT
1 AATATAATATAATAT
158523 AATATAATATAATAT
1 AATATAATATAATAT
158538 AATATAATATAATA-
1 AATATAATATAATAT
158552 AATA-AATA
1 AATATAATA
158560 AAAAAAAGTA
Statistics
Matches: 192, Mismatches: 2, Indels: 12
0.93 0.01 0.06
Matches are distributed among these distances:
13 15 0.08
14 36 0.19
15 127 0.66
16 14 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAATATAATAT
Found at i:158789 original size:12 final size:12
Alignment explanation
Indices: 158768--158801 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
158758 CTAGGGCCTT
158768 GGATCAGGTCAC
1 GGATCAGGTCAC
*
158780 GGATCGGGTCAC
1 GGATCAGGTCAC
158792 GGATCAGGTC
1 GGATCAGGTC
158802 GATGGGTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.18
Consensus pattern (12 bp):
GGATCAGGTCAC
Found at i:161534 original size:16 final size:17
Alignment explanation
Indices: 161513--161546 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
161503 TATTCTTTTC
161513 TTTTTC-TTTTTCAATT
1 TTTTTCTTTTTTCAATT
161529 TTTTTCTTTTTTCAATT
1 TTTTTCTTTTTTCAATT
161546 T
1 T
161547 AAGGCGCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTTTTCAATT
Found at i:171098 original size:30 final size:31
Alignment explanation
Indices: 171055--171119 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
171045 AAGCCTTAGA
* * *
171055 AAAATTTGGGGACCATTTTG-TAA-TTTTTG
1 AAAAGTTGGGGACCAATTCGATAATTTTTTG
171084 AAAAGTTGGAGGACCAATTCGATAATTTTTTG
1 AAAAGTTGG-GGACCAATTCGATAATTTTTTG
171116 AAAA
1 AAAA
171120 TTTGAGAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 8 0.27
30 9 0.30
31 3 0.10
32 10 0.33
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (31 bp):
AAAAGTTGGGGACCAATTCGATAATTTTTTG
Found at i:171686 original size:24 final size:24
Alignment explanation
Indices: 171659--171755 Score: 194
Period size: 24 Copynumber: 4.0 Consensus size: 24
171649 TGCATGACAT
171659 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
171683 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
171707 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
171731 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
171755 T
1 T
171756 CAGGAAGACT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:172409 original size:46 final size:46
Alignment explanation
Indices: 172314--172629 Score: 494
Period size: 46 Copynumber: 6.9 Consensus size: 46
172304 ATAAACATAC
* * * *
172314 AAATAAGCTTACGAGCTTAT-TGA-ATAATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
*
172358 AAATAAGCTTACAAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
* *
172404 AAATAAGATTAGGAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
172450 AAATAAGCTTACGAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
* * * * *
172496 AAATAAGCTTTCGATCTTATGGGATAAAAGGGCAAGCATATTGGAA
1 AAATAAGCTTACGAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
172542 AAATAAGCTTACGAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
*
172588 AAATAAGCTTACGAGCTTATGGGAT-AAATGGTAAGTATATTG
1 AAATAAGCTTACGAGCTTATGGGATAAAAGGGTAAGTATATTG
172630 ATAATTTTAT
Statistics
Matches: 249, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
44 19 0.08
45 18 0.07
46 212 0.85
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.29
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGATAAAAGGGTAAGTATATTGGTA
Found at i:172616 original size:25 final size:25
Alignment explanation
Indices: 172542--172616 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
172532 CATATTGGAA
172542 AAATAAGCTTACGAGCTTATGGGAT
1 AAATAAGCTTACGAGCTTATGGGAT
** *
172567 -AA-AAGGGTA--AG-TATATTGG-T
1 AAATAAGCTTACGAGCT-TATGGGAT
172587 AAAATAAGCTTACGAGCTTATGGGAT
1 -AAATAAGCTTACGAGCTTATGGGAT
172613 AAAT
1 AAAT
172617 GGTAAGTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
20 2 0.06
21 7 0.19
22 2 0.06
23 10 0.28
24 2 0.06
25 11 0.31
26 2 0.06
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (25 bp):
AAATAAGCTTACGAGCTTATGGGAT
Found at i:175941 original size:12 final size:12
Alignment explanation
Indices: 175910--175942 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
175900 AAAAATAGCT
175910 AAATAAAT-AAA
1 AAATAAATAAAA
175921 AAATAAAATAAAA
1 AAAT-AAATAAAA
175934 AAATAAATA
1 AAATAAATA
175943 GAGAAGGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 9 0.45
13 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
AAATAAATAAAA
Found at i:176009 original size:5 final size:5
Alignment explanation
Indices: 175976--176154 Score: 61
Period size: 5 Copynumber: 35.2 Consensus size: 5
175966 GGAAAATGAT
* * *
175976 AAAT- AAATA AAA-A TAAATA AGACA AAATA AAATA AAGTA AAAGTA AAACTA
1 AAATA AAATA AAATA -AAATA AAATA AAATA AAATA AAATA AAA-TA AAA-TA
* * *
176027 ATAA-A ATAATA AAATGGA ATAATG GAATA AAATA AAATAA AAATA AACAAA
1 A-AATA A-AATA AAAT--A A-AATA AAATA AAATA AAAT-A AAATA AA-ATA
* * * * * *
176078 AAATGG AAATA AAAAA CAAAT- ATATA ATATT AAAT- AAATA AAA-A AAA-G
1 AAAT-A AAATA AAATA -AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* *
176126 AAAGA AAA-A AAATA AAAT- AATTA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA A
176155 GAATTAAAAA
Statistics
Matches: 133, Mismatches: 24, Indels: 35
0.69 0.12 0.18
Matches are distributed among these distances:
4 26 0.20
5 73 0.55
6 27 0.20
7 4 0.03
8 3 0.02
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:181580 original size:14 final size:14
Alignment explanation
Indices: 181561--181595 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
181551 ATCTGAATCG
*
181561 AGTCAACTCATCTA
1 AGTCAACTCATCCA
181575 AGTCAACTCATCCA
1 AGTCAACTCATCCA
181589 AGTCAAC
1 AGTCAAC
181596 CTATTTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.37, C:0.31, G:0.09, T:0.23
Consensus pattern (14 bp):
AGTCAACTCATCCA
Found at i:182267 original size:26 final size:28
Alignment explanation
Indices: 182207--182258 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
182197 ACTTCGGTCA
*
182207 GGTAAAATTAAGAAAAATACCCTTATAG
1 GGTAAAATTAACAAAAATACCCTTATAG
182235 GGTAAAATT-ACAAAAATA-CCTTAT
1 GGTAAAATTAACAAAAATACCCTTAT
182259 GTTGTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 8 0.35
28 9 0.39
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (28 bp):
GGTAAAATTAACAAAAATACCCTTATAG
Found at i:183373 original size:35 final size:35
Alignment explanation
Indices: 183343--183470 Score: 150
Period size: 35 Copynumber: 3.6 Consensus size: 35
183333 AGGTTTAGCT
*
183343 CAATCAAACTGGTAATTCCTTATATAGGTTTAGAC
1 CAATCAAACTGGTAATTCCTTATATAGGTTCAGAC
* **
183378 CGATCAAACTGGTAATTCCTTACGGTAGGTTCAG-C
1 CAATCAAACTGGTAATTCCTTA-TATAGGTTCAGAC
** *
183413 TCGGTCAAATTGGTAATTCCTTATATAGGTTCAGAC
1 -CAATCAAACTGGTAATTCCTTATATAGGTTCAGAC
* *
183449 CAATCGAGCTGGTAATTCCTTA
1 CAATCAAACTGGTAATTCCTTA
183471 CGGATCTAAG
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
35 48 0.62
36 29 0.38
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (35 bp):
CAATCAAACTGGTAATTCCTTATATAGGTTCAGAC
Found at i:189748 original size:30 final size:30
Alignment explanation
Indices: 189712--189773 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
189702 AGTGAACCGG
* * *
189712 CGGTTCAAACTGGTTTTGCCGGTTTTCAGC
1 CGGTTCAAACCGGTTTTCCCGATTTTCAGC
**
189742 CGGTTCACCCCGGTTTTCCCGATTTTCAGC
1 CGGTTCAAACCGGTTTTCCCGATTTTCAGC
189772 CG
1 CG
189774 ATTCTTCCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.11, C:0.31, G:0.24, T:0.34
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTCCCGATTTTCAGC
Found at i:192041 original size:51 final size:51
Alignment explanation
Indices: 191978--192078 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
191968 ACATTACCTT
191978 TAATCGTTTTAGAAAACGAGAATTCAAATACTTGATCATAAATGCAACAAG
1 TAATCGTTTTAGAAAACGAGAATTCAAATACTTGATCATAAATGCAACAAG
*
192029 TAATCGTTTTAGAAAATGAGAATTCAAATACTTGATCATAAATGCAACAA
1 TAATCGTTTTAGAAAACGAGAATTCAAATACTTGATCATAAATGCAACAA
192079 ATAACGGAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.29
Consensus pattern (51 bp):
TAATCGTTTTAGAAAACGAGAATTCAAATACTTGATCATAAATGCAACAAG
Found at i:194590 original size:42 final size:41
Alignment explanation
Indices: 194499--194686 Score: 229
Period size: 42 Copynumber: 4.5 Consensus size: 41
194489 AAGGTGATAC
* **
194499 TGATCTAACTCCTTATGTGATGGATGAACCAA-GATGATGT
1 TGATCCAACTCCTTATGTGATGGATGAAGAAATGATGATGT
*
194539 TGATCCAACTCCTTATGTGATGGATGAGAAAAATGATGATGT
1 TGATCCAACTCCTTATGTGATGGATGA-AGAAATGATGATGT
* *
194581 TGATCCAACTCCTTATGTGATAGA-CAAGCGAAATGATGATGT
1 TGATCCAACTCCTTATGTGATGGATGAA--GAAATGATGATGT
* *
194623 TGATCCAACTCCTTATATGATAGACT-AATGAAATGATGATGT
1 TGATCCAACTCCTTATGTGATGGA-TGAA-GAAATGATGATGT
*
194665 TGATCCAACTCCTTATGCGATG
1 TGATCCAACTCCTTATGTGATG
194687 AGATCGAGCT
Statistics
Matches: 131, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
40 27 0.21
41 4 0.03
42 98 0.75
43 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (41 bp):
TGATCCAACTCCTTATGTGATGGATGAAGAAATGATGATGT
Found at i:194875 original size:117 final size:113
Alignment explanation
Indices: 194700--194921 Score: 291
Period size: 117 Copynumber: 1.9 Consensus size: 113
194690 TCGAGCTAAG
* * *
194700 GTTGAACAAGTTCTTATTATGAACTACTTCTTATTCATCGGATGAGTTCTTCTCATTATGAACTC
1 GTTGAACAAGTTCTTATTATGAACTACTTCTCACTCATCGGATGAGTTCTTCTCATTATAAACTC
*
194765 TCTACTGGAAATATTGATCATCCTCATTATGTGATGGAATCTAACCAAT
66 TC-ACTGGAAATATTGATCAACCTCATTATGTGATGGAATCTAACCAAT
* * * * * *
194814 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGATTTCTTCTTATTATAAA
1 GTTGAACAAGTTC-T-T-ATTATGAACTACTTCTCACTCATCGGATGAGTTCTTCTCATTATAAA
* * *
194879 CTCTCATTGGAAATGTTGATCAACCTCATTCTGTGATGGAATC
63 CTCTCACTGGAAATATTGATCAACCTCATTATGTGATGGAATC
194922 GAACAAAATG
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
114 13 0.14
115 1 0.01
116 35 0.38
117 43 0.47
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (113 bp):
GTTGAACAAGTTCTTATTATGAACTACTTCTCACTCATCGGATGAGTTCTTCTCATTATAAACTC
TCACTGGAAATATTGATCAACCTCATTATGTGATGGAATCTAACCAAT
Found at i:195177 original size:203 final size:202
Alignment explanation
Indices: 194791--195682 Score: 1036
Period size: 203 Copynumber: 4.4 Consensus size: 202
194781 ATCATCCTCA
* * * * * *
194791 TTATGTGATGGAATCTAACCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTT
1 TTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAA-TTCTTCTCCCTCATC
* * * * * *
194856 GGATGATTTCTTCTTATTAT-AAA-CTCTCATTGGAAATGTTGATCAACCTCATTCTGTGATGGA
65 GGATGAGTTCTTCTCATTATGAAATCTC-CACTGGAAATATTGATCCACCTCATTCTGTGATGAA
* * * * * *
194919 ATCGAACAAAATGATGATGATGATCCAACTCTATATGCAATGGATGACCCAAGTATTGGTACTAT
129 ATCGAACAAAGTGATGATGCTGATCCAACTCCATATGCAATGGATGAGCCAAGTATTAGTGCTAT
194984 TCCAACTCC
194 TCCAACTCC
* * * * * *
194993 TTATATGATGGAATCAAGTTGAGGTTGAACAAGTTCTTCTCATTATGAATGTCTTCTCACTCGTC
1 TTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAAT-TCTTCTCCCTCATC
* * ** * *
195058 GGATGAGTTCTTCTCATTATGAAATATCTACTGGAAATGCTGATCCACCTCTTTATGTGATGAAA
65 GGATGAGTTCTTCTCATTATGAAATCTCCACTGGAAATATTGATCCACCTCATTCTGTGATGAAA
* * ** * *
195123 TCGAACAAAGTGATGATGCTAATACAACTCCATATGTGATGGATGAGCCAAGTATTTGTGCTGTT
130 TCGAACAAAGTGATGATGCTGATCCAACTCCATATGCAATGGATGAGCCAAGTATTAGTGCTATT
195188 CCAACTCC
195 CCAACTCC
* * *
195196 TTATGTGATGGAATCGAGCTAAGGTTAAACTAGTTCTTCTTATTATGAATTTCTTCTCCCTCATC
1 TTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAA-TTCTTCTCCCTCATC
* * * *
195261 GGATGAGTT-TT-TC-TCAT----TCTCCGCTGGAAATATTGATTCACCTCATTCTGTGATGGAA
65 GGATGAGTTCTTCTCATTATGAAATCTCCACTGGAAATATTGATCCACCTCATTCTGTGATGAAA
* * * * *
195319 TCAAACAAAGTGATGATGCTGGTCCAACTCTATATGAAATGGATGAGCCAAGTTTTAGTGCTATT
130 TCGAACAAAGTGATGATGCTGATCCAACTCCATATGCAATGGATGAGCCAAGTATTAGTGCTATT
195384 CCAACT-C
195 CCAACTCC
* * *
195391 TTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGACCTTATTTTCCCTCATC
1 TTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGA-ATTCTTCTCCCTCATC
* * * *
195456 GGATGAGTTCTTCTCATTATGAACTCTCCCATTGGAAATATTGATCCACCTCTTTTTGTGAT-AG
65 GGATGAGTTCTTCTCATTATGAAATCT-CCACTGGAAATATTGATCCACCTCATTCTGTGATGA-
* * * * * *
195520 AATTGAACAAATTGATGATGTTGATCCAACTCCATATGCGATGGATGAGCCAAGTATTAGTGTTG
128 AATCGAACAAAGTGATGATGCTGATCCAACTCCATATGCAATGGATGAGCCAAGTATTAGTGCTA
*
195585 TTCCAACTCT
193 TTCCAACTCC
*
195595 TTATGTGATGTAATCGAGCTATA-GTTGAACAAGTTCTTCTCATTATGAACTTAC-TCTCCCTCA
1 TTATGTGATGGAATCGAGCTA-AGGTTGAACAAGTTCTTCTCATTATGAA-TT-CTTCTCCCTCA
195658 TCGGATGAGTTCTTCTCATTATGAA
63 TCGGATGAGTTCTTCTCATTATGAA
195683 CCCTACCATT
Statistics
Matches: 584, Mismatches: 88, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
195 68 0.12
196 95 0.16
197 2 0.00
198 3 0.01
200 3 0.01
201 3 0.01
202 77 0.13
203 249 0.43
204 83 0.14
205 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (202 bp):
TTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAATTCTTCTCCCTCATCG
GATGAGTTCTTCTCATTATGAAATCTCCACTGGAAATATTGATCCACCTCATTCTGTGATGAAAT
CGAACAAAGTGATGATGCTGATCCAACTCCATATGCAATGGATGAGCCAAGTATTAGTGCTATTC
CAACTCC
Found at i:195348 original size:399 final size:400
Alignment explanation
Indices: 194791--195678 Score: 1153
Period size: 399 Copynumber: 2.2 Consensus size: 400
194781 ATCATCCTCA
* * * * * *
194791 TTATGTGATGGAATCTAACCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTT
1 TTATGTGATGGAATCGAGCTAA-GTTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCCTCATC
* * *
194856 GGATGA-TTTCTTCTTATTATAAACTCTCATTGGAAATGTTGATCAACCTCATTCTGTGATGGAA
65 GGATGAGTTT-TTCTCA-T-T--ACTCTCACTGGAAATATTGATCAACCTCATTCTGTGATGGAA
* * *
194920 TCGAACAAAATGATGATGATGATCCAACTCTATATGCAATGGATGACCCAAGTATTGGTACTATT
125 TCAAACAAAATGATGATGATGATCCAACTCTATATGAAATGGATGACCCAAGTATTAGTACTATT
* * *
194985 CCAACTCCTTATATGATGGAATCAAGTTGAGGTTGAACAAGTTCTTCTCATTATGA-ATGTCTTC
190 CCAACT-CTTATATGATGGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGACAT-TATTC
* * *
195049 TCACTCGTCGGATGAGTTCTTCTCATTATGAAATAT-CTACTGGAAATGCTGATCCACCTCTTTA
253 TCACTCATCGGATGAGTTCTTCTCATTATGAAATATCCCACTGGAAATACTGATCCACCTCTTTA
*
195113 TGTGAT-GAAATCGAACAAAGTGATGATGCTAATACAACTCCATATGTGATGGATGAGCCAAGTA
318 TGTGATAG-AATCGAACAAAGTGATGATGCTAATACAACTCCATATGCGATGGATGAGCCAAGTA
*
195177 TTTGTGCTGTTCCAACTCC
382 TTAGTGCTGTTCCAACTCC
* * *
195196 TTATGTGATGGAATCGAGCTAAGGTTAAACTAGTTCTTCTTATTATGAATTTCTTCTCCCTCATC
1 TTATGTGATGGAATCGAGCTAA-GTTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCCTCATC
*
195261 GGATGAGTTTTTCTCATT-CTC-CGCTGGAAATATTGATTC-ACCTCATTCTGTGATGGAATCAA
65 GGATGAGTTTTTCTCATTACTCTCACTGGAAATATTGA-TCAACCTCATTCTGTGATGGAATCAA
* * * * * *
195323 ACAAAGTGATGATGCTGGTCCAACTCTATATGAAATGGATGAGCCAAGTTTTAGTGCTATTCCAA
129 ACAAAATGATGATGATGATCCAACTCTATATGAAATGGATGACCCAAGTATTAGTACTATTCCAA
* * * * *
195388 CTCTTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGACCTTATTTTCCCTC
194 CTCTTATATGATGGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGACATTATTCTCACTC
* * * * *
195453 ATCGGATGAGTTCTTCTCATTATGAACTCTCCCATTGGAAATATTGATCCACCTCTTTTTGTGAT
259 ATCGGATGAGTTCTTCTCATTATGAAATATCCCACTGGAAATACTGATCCACCTCTTTATGTGAT
* * * * * *
195518 AGAATTGAACAAATTGATGATGTTGATCCAACTCCATATGCGATGGATGAGCCAAGTATTAGTGT
324 AGAATCGAACAAAGTGATGATGCTAATACAACTCCATATGCGATGGATGAGCCAAGTATTAGTGC
*
195583 TGTTCCAACTCT
389 TGTTCCAACTCC
* *
195595 TTATGTGATGTAATCGAGCTATAGTTGAACAAGTTCTTCTCATTATGAACTTAC-TCTCCCTCAT
1 TTATGTGATGGAATCGAGCTA-AGTTGAACAAGTTCTTCTCATTATGAA-TTTCTTCTCCCTCAT
*
195659 CGGATGAGTTCTTCTCATTA
64 CGGATGAGTTTTTCTCATTA
195679 TGAACCCTAC
Statistics
Matches: 421, Mismatches: 54, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
398 80 0.19
399 260 0.62
400 10 0.02
403 1 0.00
404 1 0.00
405 66 0.16
406 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (400 bp):
TTATGTGATGGAATCGAGCTAAGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCCTCATCG
GATGAGTTTTTCTCATTACTCTCACTGGAAATATTGATCAACCTCATTCTGTGATGGAATCAAAC
AAAATGATGATGATGATCCAACTCTATATGAAATGGATGACCCAAGTATTAGTACTATTCCAACT
CTTATATGATGGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGACATTATTCTCACTCAT
CGGATGAGTTCTTCTCATTATGAAATATCCCACTGGAAATACTGATCCACCTCTTTATGTGATAG
AATCGAACAAAGTGATGATGCTAATACAACTCCATATGCGATGGATGAGCCAAGTATTAGTGCTG
TTCCAACTCC
Found at i:197298 original size:55 final size:54
Alignment explanation
Indices: 197120--197594 Score: 352
Period size: 54 Copynumber: 8.7 Consensus size: 54
197110 CAAATGACTT
* * * * ** * **
197120 ATCATCAAGAAACCTTTGAAAACCAGACTTGGCTTCTTCAAAAATTCATTTACATTT
1 ATCATCAAGAAACC-TTGAAAATCAGGCTTAGTTTCTTTGAAAACTCATTTA-A-AA
* * * * * * *
197177 ATCATCAAGAAATCCTTAAAAAATTAGG-TTAGCTTCTTTAAAAATTCATTTGAAG
1 ATCATCAAGAAA-CCTT-GAAAATCAGGCTTAGTTTCTTTGAAAACTCATTTAAAA
* ** * *
197232 A-CATCAAGAAACCCTTGAAAATTAGGCTTAAATTCTTTGAAAACTCGTTTATAA
1 ATCATCAAGAAA-CCTTGAAAATCAGGCTTAGTTTCTTTGAAAACTCATTTAAAA
* * * * *
197286 ATCATCACGAAA-CTTCAGAAAATCAGACTTAGTTTCTTTGAAAATTCTTTTGAAA
1 ATCATCAAGAAACCTT--GAAAATCAGGCTTAGTTTCTTTGAAAACTCATTTAAAA
* * * * *
197341 AT-ATTATGAAACCCCTGAAAATCAGGCTTAGCTTCTTTGAAAACTTATTTAAAA
1 ATCATCAAGAAA-CCTTGAAAATCAGGCTTAGTTTCTTTGAAAACTCATTTAAAA
* * * * *
197395 ATCATCAAGAAACTTTTAAAATCAGACTTAGTTTATTTGAAAACTCGTTTAAAA
1 ATCATCAAGAAACCTTGAAAATCAGGCTTAGTTTCTTTGAAAACTCATTTAAAA
* * * *
197449 ATCATCAAGAAACTTCTGAAAATAAGACTTTGTTTCTTTGAAAACTCATTTAAAA
1 ATCATCAAGAAACCT-TGAAAATCAGGCTTAGTTTCTTTGAAAACTCATTTAAAA
* * * * *
197504 ATCATCAAGAAA-CTTCCAAAAATC-GGACTTAGATTCTTTTAAAATTCATTTGAAA
1 ATCATCAAGAAACCTT--GAAAATCAGG-CTTAGTTTCTTTGAAAACTCATTTAAAA
* *
197559 AT-ATCAAGAAACCCTTGAAAATTATGCTTAGTTTCT
1 ATCATCAAGAAA-CCTTGAAAATCAGGCTTAGTTTCT
197595 AAAAAAATCA
Statistics
Matches: 337, Mismatches: 65, Indels: 35
0.77 0.15 0.08
Matches are distributed among these distances:
53 13 0.04
54 149 0.44
55 126 0.37
56 6 0.02
57 35 0.10
58 8 0.02
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (54 bp):
ATCATCAAGAAACCTTGAAAATCAGGCTTAGTTTCTTTGAAAACTCATTTAAAA
Found at i:197338 original size:109 final size:108
Alignment explanation
Indices: 197177--197594 Score: 453
Period size: 109 Copynumber: 3.8 Consensus size: 108
197167 ATTTACATTT
* * * * * *
197177 ATCATCAAGAAATCCTTAAAAAATTAG-GTTAGCTTCTTTAAAAATTCATTTGAAGACATCAAGA
1 ATCATCAAGAAA--CTTCAAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAAACATCAAGA
* * *
197241 AACCCTTGAAAATTAGGCTTAAATTCTTTGAAAACTCGTTTATAA
64 AACCCTTGAAAATTAGGCTTAGATTCTTTGAAAACTCATTTAAAA
* * * * *
197286 ATCATCACGAAACTTCAGAAAATCAGACTTAGTTTCTTTGAAAATTCTTTTGAAAATATTATGAA
1 ATCATCAAGAAACTTCA-AAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAAACATCAAGAA
* * * *
197351 ACCCCTGAAAATCAGGCTTAGCTTCTTTGAAAACTTATTTAAAA
65 ACCCTTGAAAATTAGGCTTAGATTCTTTGAAAACTCATTTAAAA
** * * * *
197395 ATCATCAAGAAACTTTTAAAATCAGACTTAGTTTATTTGAAAACTCGTTTAAAAATCATCAAGAA
1 ATCATCAAGAAACTTCAAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAAA-CATCAAGAA
* * * * *
197460 A-CTTCTGAAAATAAGACTTTGTTTCTTTGAAAACTCATTTAAAA
65 ACCCT-TGAAAATTAGGCTTAGATTCTTTGAAAACTCATTTAAAA
* * * *
197504 ATCATCAAGAAACTTCCAAAAATCGGACTTAGATTCTTTTAAAATTCATTTGAAAATATCAAGAA
1 ATCATCAAGAAACTT-CAAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAAACATCAAGAA
* *
197569 ACCCTTGAAAATTATGCTTAGTTTCT
65 ACCCTTGAAAATTAGGCTTAGATTCT
197595 AAAAAAATCA
Statistics
Matches: 253, Mismatches: 50, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
107 4 0.02
108 42 0.17
109 174 0.69
110 33 0.13
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.34
Consensus pattern (108 bp):
ATCATCAAGAAACTTCAAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAAACATCAAGAAA
CCCTTGAAAATTAGGCTTAGATTCTTTGAAAACTCATTTAAAA
Found at i:199568 original size:13 final size:12
Alignment explanation
Indices: 199552--199604 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
199542 TCTTGATGTA
199552 TTTTTCTTTCTTAT
1 TTTTTCTTTC-T-T
*
199566 TTTTTCTTTATT
1 TTTTTCTTTCTT
*
199578 TTTGTCTTTCTT
1 TTTTTCTTTCTT
199590 TTTTGTCTTTCTT
1 TTTT-TCTTTCTT
199603 TT
1 TT
199605 CTTTGAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.41
13 11 0.32
14 9 0.26
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:199593 original size:25 final size:25
Alignment explanation
Indices: 199552--199604 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
199542 TCTTGATGTA
*
199552 TTTTTCTTTCTTATTTTTTCTTTAT
1 TTTTTCTTTCTTATTTTGTCTTTAT
*
199577 TTTTGTCTTTCTT-TTTTGTCTTTCT
1 TTTT-TCTTTCTTATTTTGTCTTTAT
199602 TTT
1 TTT
199605 CTTTGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.79
Consensus pattern (25 bp):
TTTTTCTTTCTTATTTTGTCTTTAT
Found at i:211874 original size:20 final size:20
Alignment explanation
Indices: 211851--211890 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
211841 TCCTGATGAG
211851 GATTTGATGGAAATATCAGT
1 GATTTGATGGAAATATCAGT
*
211871 GATTTGATGGCAATATCAGT
1 GATTTGATGGAAATATCAGT
211891 AAGAAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (20 bp):
GATTTGATGGAAATATCAGT
Found at i:214578 original size:86 final size:87
Alignment explanation
Indices: 214444--214625 Score: 249
Period size: 86 Copynumber: 2.1 Consensus size: 87
214434 GTGGAACAAT
* * * * *
214444 TTCTTTCCAAGTCAATCCGATCTCCATGGAAGAGTAGTGGAAGCAAATCATCCTTGAGTCTGATC
1 TTCTTTCCAAGTCAATCCGATCACCATGAAAGAGTAGTGGAAGCAAATCAACCTTAAATCTGATC
* *
214509 TTCATG-GAATAGTGAAACAGA
66 TTCACGAGAATAGTAAAACAGA
* *
214530 TTCTTTCCAAGTTAATCCGATCACCATGAAAGAGTAGTGGAAGGAAATCAACCTTAAATCTGATC
1 TTCTTTCCAAGTCAATCCGATCACCATGAAAGAGTAGTGGAAGCAAATCAACCTTAAATCTGATC
*
214595 TTCACGAAAGAGTAGTAAAACAGA
66 TTCACG--AGAATAGTAAAACAGA
214619 TTCTTTC
1 TTCTTTC
214626 AATACAAATC
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
86 63 0.76
89 20 0.24
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (87 bp):
TTCTTTCCAAGTCAATCCGATCACCATGAAAGAGTAGTGGAAGCAAATCAACCTTAAATCTGATC
TTCACGAGAATAGTAAAACAGA
Found at i:214671 original size:35 final size:35
Alignment explanation
Indices: 214632--214698 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
214622 TTTCAATACA
* **
214632 AATCAAGCCTTCTTAAAAGAGTAGTAAAGCAATGC
1 AATCAAGCATTCACAAAAGAGTAGTAAAGCAATGC
*
214667 AATCAAGCATTCACAAAAGAGTAGTGAAGCAA
1 AATCAAGCATTCACAAAAGAGTAGTAAAGCAA
214699 GAATATATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.19
Consensus pattern (35 bp):
AATCAAGCATTCACAAAAGAGTAGTAAAGCAATGC
Found at i:219195 original size:21 final size:21
Alignment explanation
Indices: 219146--219187 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
219136 GCGATCCCTG
219146 CGTATACTTTAGAAACTGCGA
1 CGTATACTTTAGAAACTGCGA
*
219167 CGTATACTTTAGAAATTGCGA
1 CGTATACTTTAGAAACTGCGA
219188 TTCTTACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (21 bp):
CGTATACTTTAGAAACTGCGA
Found at i:221743 original size:15 final size:14
Alignment explanation
Indices: 221721--221764 Score: 70
Period size: 15 Copynumber: 3.0 Consensus size: 14
221711 GTATTGGTAC
221721 TGTACTCACAATAT
1 TGTACTCACAATAT
221735 TGATACTCACAATATT
1 TG-TACTCACAATA-T
221751 TGTACTCACAATAT
1 TGTACTCACAATAT
221765 ATATACTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.11
15 22 0.79
16 3 0.11
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (14 bp):
TGTACTCACAATAT
Found at i:221771 original size:15 final size:14
Alignment explanation
Indices: 221723--221772 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
221713 ATTGGTACTG
221723 TACTCACAATATTGA
1 TACTCACAATATT-A
*
221738 TACTCACAATATTTG
1 TACTCACAATA-TTA
221753 TACTCACAATATATA
1 TACTCACAATAT-TA
221768 TACTC
1 TACTC
221773 TCCCTGGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.90
16 2 0.06
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (14 bp):
TACTCACAATATTA
Found at i:224689 original size:11 final size:10
Alignment explanation
Indices: 224617--224691 Score: 59
Period size: 11 Copynumber: 7.6 Consensus size: 10
224607 ATTTAACTAA
224617 TTAAATGAAT
1 TTAAATGAAT
*
224627 TTAAAATGCAT
1 TT-AAATGAAT
*
224638 TTAACT-AA-
1 TTAAATGAAT
224646 TTAAATGAAT
1 TTAAATGAAT
*
224656 TTAAAATGCAT
1 TT-AAATGAAT
*
224667 TT-AATTAA-
1 TTAAATGAAT
224675 TTAAATGAATT
1 TTAAATGAA-T
224686 TTAAAT
1 TTAAAT
224692 TCATTTAATG
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
8 7 0.14
9 12 0.24
10 7 0.14
11 24 0.48
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (10 bp):
TTAAATGAAT
Found at i:224700 original size:29 final size:29
Alignment explanation
Indices: 224606--224699 Score: 161
Period size: 29 Copynumber: 3.2 Consensus size: 29
224596 ATACACTTAA
224606 CATTTAACTAATTAAATGAATTTAAAATG
1 CATTTAACTAATTAAATGAATTTAAAATG
224635 CATTTAACTAATTAAATGAATTTAAAATG
1 CATTTAACTAATTAAATGAATTTAAAATG
* * *
224664 CATTTAATTAATTAAATGAATTTTAAATT
1 CATTTAACTAATTAAATGAATTTAAAATG
224693 CATTTAA
1 CATTTAA
224700 TGAGAAATTC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.41
Consensus pattern (29 bp):
CATTTAACTAATTAAATGAATTTAAAATG
Found at i:246031 original size:54 final size:54
Alignment explanation
Indices: 245889--246034 Score: 186
Period size: 54 Copynumber: 2.7 Consensus size: 54
245879 GGAAATACAC
* * * * *
245889 AAACTTATTATGAA-TTCTATAGATTGCACACATACTGCCGATACGGTCATCCAT
1 AAACTCATTATGAATTTC-ATGGGTTGCACACATAGTGCCGAGACGGTCATCCAT
* * * *
245943 AAACTTATTATGAATTTCATGGGTTGCACACATAGTGTCGAGATGGTCATTCAT
1 AAACTCATTATGAATTTCATGGGTTGCACACATAGTGCCGAGACGGTCATCCAT
*
245997 AAACTCATTATGAATTTCGTGGGTTGCACACATAGTGC
1 AAACTCATTATGAATTTCATGGGTTGCACACATAGTGC
246035 TGAAAGTACA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 78 0.96
55 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (54 bp):
AAACTCATTATGAATTTCATGGGTTGCACACATAGTGCCGAGACGGTCATCCAT
Found at i:249720 original size:46 final size:46
Alignment explanation
Indices: 249645--249771 Score: 202
Period size: 46 Copynumber: 2.8 Consensus size: 46
249635 ATATAAAATT
* *
249645 CTTACCATTT-ATCCCATTAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
249690 CTTACCATTTAATACCATAAGCTCATAAGCTTAGTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
249736 CTTATCATTTAATACCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTT
249772 GCATTACCAT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 10 0.14
46 64 0.86
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (46 bp):
CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:253709 original size:17 final size:16
Alignment explanation
Indices: 253665--253715 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
253655 TTTTCTCTTT
253665 TTCTTTTCTTTTCTTT-
1 TTCTTTTCTTTT-TTTC
* *
253681 TTCTATTATTTTTTTC
1 TTCTTTTCTTTTTTTC
253697 TTCGTTTTCTTTTTTTC
1 TTC-TTTTCTTTTTTTC
253714 TT
1 TT
253716 ATATTATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 3 0.10
16 13 0.45
17 13 0.45
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (16 bp):
TTCTTTTCTTTTTTTC
Found at i:256108 original size:46 final size:46
Alignment explanation
Indices: 256034--256160 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
256024 TATAAAATTT
256034 CTTACCATTT-AT-CCTATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACC-ATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
256079 CTTACCATTTAATATCATAAGCTCATAAGCTTAGTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
256125 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTT
256161 GCATGCTTAC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
45 10 0.14
46 63 0.85
47 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (46 bp):
CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:257894 original size:46 final size:46
Alignment explanation
Indices: 257819--257945 Score: 211
Period size: 46 Copynumber: 2.8 Consensus size: 46
257809 ATATAAAATT
* *
257819 CTTACCATTT-ATCCCATTAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
257864 CTTACCATTTAATACCATAAGCTCATAAGCTTAGTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
257910 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTT
257946 GAATGCTTAC
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
45 10 0.13
46 65 0.87
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (46 bp):
CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:258099 original size:40 final size:40
Alignment explanation
Indices: 258020--258099 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
258010 ATAGGAGTCA
* * * *
258020 AATATTGCACCGAAGTGTTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCTTTACCCACCT
* *
258060 AATAATGCACCGTAGTGCTGAGGTCGGGCTTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCTTTACCCACCT
258100 TGTACACCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGCTTTACCCACCT
Found at i:261814 original size:24 final size:24
Alignment explanation
Indices: 261780--261829 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
261770 CTCTCATCAT
*
261780 TTTTCTCTTTCTCTT-TTTCTTTTC
1 TTTTCTCTTTCTATTATTT-TTTTC
*
261804 TTTTCTTTTTCTATTATTTTTTTC
1 TTTTCTCTTTCTATTATTTTTTTC
261828 TT
1 TT
261830 ATATTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTCTCTTTCTATTATTTTTTTC
Found at i:264197 original size:46 final size:46
Alignment explanation
Indices: 264123--264249 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
264113 TATAAAATTT
264123 CTTACCATTT-AT-CCTATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACC-ATAAGCTCGTAAGCTTATTTTACCAATATA
* *
264168 CTTACCATTTAATACCATAAGCTCATAAGCTTAGTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
264214 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTT
264250 GCATGCTTAC
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
45 10 0.13
46 64 0.84
47 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (46 bp):
CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:264976 original size:2 final size:2
Alignment explanation
Indices: 264969--265010 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
264959 TATAAATTCT
*
264969 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
265011 AATAAATACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:269513 original size:18 final size:18
Alignment explanation
Indices: 269490--269533 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
269480 CATAAAATAT
269490 TCAAACTATATGTTAGTA
1 TCAAACTATATGTTAGTA
269508 TCAAACTATATGTTAGTA
1 TCAAACTATATGTTAGTA
269526 TCAAACTA
1 TCAAACTA
269534 ACATAATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (18 bp):
TCAAACTATATGTTAGTA
Found at i:271786 original size:160 final size:158
Alignment explanation
Indices: 271503--271825 Score: 495
Period size: 160 Copynumber: 2.0 Consensus size: 158
271493 CCTTAATGTT
* * * *
271503 TCAATTTGGGTAAAAAAATATCTCGTTGGATCAAAATCGTTAGTCAATTAACGGTCAATTCTTAT
1 TCAATTTGGGTAAAAAAATACCTCGTTAGATAAAAATCGTTAGTCAAATAACGGTCAATTCTTAT
* * * *
271568 ATTTGACTAAGCAAGAACACGTGGAGGGAGATGCTAATGTGGCACGTCCGCGTGTGATGCCACGT
66 AGTTGACTAAGCAAGAACACGTGGAGGGAGATGCTAATATGACACGTCCACGTGTGATGCCACGT
271633 CAACAATTTTTTTTCAAATTAATTATAAA
131 CAACAA-TTTTTTTCAAATTAATTATAAA
* *
271662 TCAATTTGGGTCAAAAAATACCCTCGTTAGATAAAAATCGTTAGTCAAATAACGGTCAATTCTTG
1 TCAATTTGGGTAAAAAAATA-CCTCGTTAGATAAAAATCGTTAGTCAAATAACGGTCAATTCTTA
* * * *
271727 TAGTTGACTAAGCAAGAACATGTGGATGGAGATGCTAATATGACATGTCCACTTGTGATGCCACG
65 TAGTTGACTAAGCAAGAACACGTGGAGGGAGATGCTAATATGACACGTCCACGTGTGATGCCACG
271792 TCAACAATTTTTTTCAAATTAATTATAAA
130 TCAACAATTTTTTTCAAATTAATTATAAA
271821 T-AATT
1 TCAATT
271826 ATTTTTATTA
Statistics
Matches: 149, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
158 4 0.03
159 42 0.28
160 103 0.69
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (158 bp):
TCAATTTGGGTAAAAAAATACCTCGTTAGATAAAAATCGTTAGTCAAATAACGGTCAATTCTTAT
AGTTGACTAAGCAAGAACACGTGGAGGGAGATGCTAATATGACACGTCCACGTGTGATGCCACGT
CAACAATTTTTTTCAAATTAATTATAAA
Found at i:272505 original size:14 final size:14
Alignment explanation
Indices: 272486--272517 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
272476 ATATTTTTGA
272486 AATAAAGTTATGAT
1 AATAAAGTTATGAT
*
272500 AATAAATTTATGAT
1 AATAAAGTTATGAT
272514 AATA
1 AATA
272518 TACTATAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (14 bp):
AATAAAGTTATGAT
Found at i:272896 original size:6 final size:6
Alignment explanation
Indices: 272885--272926 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
272875 TGTTTTAGTC
* *
272885 AATTTA AATTTA TATTTTA AATTTA AA-TTA ATTTTA AATTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA
272927 TAAATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 4 0.13
6 21 0.70
7 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
AATTTA
Found at i:272908 original size:7 final size:7
Alignment explanation
Indices: 272887--272938 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
272877 TTTTAGTCAA
272887 TTTAAA-
1 TTTAAAT
*
272893 TTTATAT
1 TTTAAAT
272900 TTTAAA-
1 TTTAAAT
272906 TTTAAA-
1 TTTAAAT
272912 -TT-AAT
1 TTTAAAT
272917 TTTAAAT
1 TTTAAAT
272924 TTATAAAT
1 TT-TAAAT
272932 TTTAAAT
1 TTTAAAT
272939 AAGAAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 13 0.33
7 15 0.38
8 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTAAAT
Found at i:272930 original size:19 final size:20
Alignment explanation
Indices: 272885--272932 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
272875 TGTTTTAGTC
*
272885 AATTTA-AATTTATATTTTA
1 AATTTATAAATTATATTTTA
272904 AA-TT-TAAATTA-ATTTTA
1 AATTTATAAATTATATTTTA
272921 AATTTATAAATT
1 AATTTATAAATT
272933 TTAAATAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 8 0.32
18 9 0.36
19 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTTATAAATTATATTTTA
Found at i:278609 original size:24 final size:24
Alignment explanation
Indices: 278544--278609 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 24
278534 AACAATTGTT
* *
278544 TATATA-TATATATTATGTATAAAC
1 TATATAGTTTATATT-TATATAAAC
278568 TATATAGTTTGATA---ATATAAAC
1 TATATAGTTT-ATATTTATATAAAC
278590 TATATAGTTTATATTTATAT
1 TATATAGTTTATATTTATAT
278610 TATTATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
21 3 0.09
22 17 0.49
24 10 0.29
25 2 0.06
26 3 0.09
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (24 bp):
TATATAGTTTATATTTATATAAAC
Found at i:278627 original size:11 final size:11
Alignment explanation
Indices: 278598--278639 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
278588 ACTATATAGT
*
278598 TTATATTTATA
1 TTATATATATA
278609 TTAT-TATATA
1 TTATATATATA
*
278619 TTATATATAAA
1 TTATATATATA
278630 TTATATATAT
1 TTATATATAT
278640 TATGTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTATATATATA
Found at i:279418 original size:73 final size:74
Alignment explanation
Indices: 279341--279503 Score: 251
Period size: 74 Copynumber: 2.2 Consensus size: 74
279331 TTAAATGACT
*
279341 AAGGGTATCGGTACCTCTA-G-GGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTTGGAGCCA
1 AAGGGTATCGGTACCT-TATGAAGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTTGGAGCC-
*
279404 AAAAT-AATAC
64 AAAATCAACAC
*
279414 AAGGGTATCGGTACCTTATGAAGGGTATCGGTACCCATTTGGCATTCTGTTTTTCTTGGAGCCAA
1 AAGGGTATCGGTACCTTATGAAGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTTGGAGCCAA
*
279479 AATCAACAT
66 AATCAACAC
279488 AAGGGTATCGGTACCT
1 AAGGGTATCGGTACCT
279504 ATAACTTAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
72 2 0.02
73 22 0.27
74 59 0.71
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (74 bp):
AAGGGTATCGGTACCTTATGAAGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTTGGAGCCAA
AATCAACAC
Found at i:279844 original size:12 final size:13
Alignment explanation
Indices: 279822--279858 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
279812 TAAGATTTTC
279822 TTTGAAAATTAGT
1 TTTGAAAATTAGT
279835 TTTG-AAATTAGT
1 TTTGAAAATTAGT
279847 TTTGGAAAATTA
1 TTT-GAAAATTA
279859 CTCTCCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.50
13 5 0.23
14 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (13 bp):
TTTGAAAATTAGT
Found at i:280103 original size:22 final size:22
Alignment explanation
Indices: 280078--280122 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
280068 TGATGCAAAA
280078 ATTAATAT-AAACCAATATAAAC
1 ATTAATATCAAACCAAT-TAAAC
* *
280100 ATTAATTTCAAACCACTTAAAC
1 ATTAATATCAAACCAATTAAAC
280122 A
1 A
280123 ACCAAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (22 bp):
ATTAATATCAAACCAATTAAAC
Found at i:281985 original size:21 final size:21
Alignment explanation
Indices: 281952--282012 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
281942 ATACATGTTG
* *
281952 AAGGA-GTACCGATACCTAGC
1 AAGGAGGTATCGATACCTAGA
*
281972 AAGGAGGTATCGATACCTATA
1 AAGGAGGTATCGATACCTAGA
*
281993 AAGGGGGTATCGATACCTAG
1 AAGGAGGTATCGATACCTAG
282013 TGCACAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 5 0.14
21 30 0.86
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (21 bp):
AAGGAGGTATCGATACCTAGA
Found at i:283294 original size:17 final size:17
Alignment explanation
Indices: 283273--283312 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
283263 TTCCCTTTTG
283273 AAAAACCTTTTTTCTATC
1 AAAAA-CTTTTTTCTATC
*
283291 AAAAAGTTTTTTCTATC
1 AAAAACTTTTTTCTATC
283308 AAAAA
1 AAAAA
283313 GTTTGACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (17 bp):
AAAAACTTTTTTCTATC
Found at i:283313 original size:17 final size:17
Alignment explanation
Indices: 283280--283316 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
283270 TTGAAAAACC
283280 TTTTTTCTATCAAAAAG
1 TTTTTTCTATCAAAAAG
283297 TTTTTTCTATCAAAAAG
1 TTTTTTCTATCAAAAAG
283314 TTT
1 TTT
283317 GACAATCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTTTTCTATCAAAAAG
Found at i:287740 original size:73 final size:74
Alignment explanation
Indices: 287661--287815 Score: 217
Period size: 74 Copynumber: 2.1 Consensus size: 74
287651 TTAAATGACT
* * *
287661 AAGGGTATCGGTA-CCTCTAG-GGGGTATCGGTCCCCATTGGGCATTCTGTTTTTCTTGGAGCCA
1 AAGGGTATCGGTATCCT-AAGAGGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGCC-
287724 AAAAT-AACAC
64 AAAATCAACAC
* *
287734 AAGGGTATTGGTATCCTAAGAGGGGTATCGGTACCCATTTGGCATTCTGTTTTTCTCGGAGCCAA
1 AAGGGTATCGGTATCCTAAGAGGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGCCAA
*
287799 AATCAACAT
66 AATCAACAC
287808 AAGGGTAT
1 AAGGGTAT
287816 TGGCACCTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
73 19 0.26
74 54 0.74
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (74 bp):
AAGGGTATCGGTATCCTAAGAGGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGCCAA
AATCAACAC
Found at i:287781 original size:74 final size:74
Alignment explanation
Indices: 287681--287818 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 74
287671 GTACCTCTAG
* *
287681 GGGGTATCGGTCCCCATTGGGCATTCTGTTTTTCTTGGAGCCAAAAAT-AACACAAGGGTATTGG
1 GGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGCC-AAAATCAACACAAGGGTATTGG
287745 TATCCTAAGA
65 TATCCTAAGA
* *
287755 GGGGTATCGGTACCCATTTGGCATTCTGTTTTTCTCGGAGCCAAAATCAACATAAGGGTATTGG
1 GGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGCCAAAATCAACACAAGGGTATTGG
287819 CACCTATGAC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
73 5 0.08
74 54 0.92
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (74 bp):
GGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGCCAAAATCAACACAAGGGTATTGGT
ATCCTAAGA
Found at i:288138 original size:11 final size:11
Alignment explanation
Indices: 288122--288211 Score: 53
Period size: 11 Copynumber: 8.5 Consensus size: 11
288112 ACTATTGAAC
288122 TATATATAAAT
1 TATATATAAAT
**
288133 TATATAGTTTAT
1 TATATA-TAAAT
288145 TA-ATATAAA-
1 TATATATAAAT
**
288154 -ATATATATTT
1 TATATATAAAT
*
288164 TATATAAAAAT
1 TATATATAAAT
*
288175 TATATATGAAT
1 TATATATAAAT
* *
288186 TGTATTTAAA-
1 TATATATAAAT
* *
288196 TATATACAGAT
1 TATATATAAAT
288207 TATAT
1 TATAT
288212 TTATATATTA
Statistics
Matches: 56, Mismatches: 18, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
8 1 0.02
9 5 0.09
10 8 0.14
11 37 0.66
12 5 0.09
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (11 bp):
TATATATAAAT
Found at i:288150 original size:22 final size:20
Alignment explanation
Indices: 288122--288180 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 20
288112 ACTATTGAAC
288122 TATATATAAATTATATAGTT
1 TATATATAAATTATATAGTT
* *
288142 TATTAATATAAAATATATATTT
1 TA-T-ATATAAATTATATAGTT
*
288164 TATATAAAAATTATATA
1 TATATATAAATTATATA
288181 TGAATTGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 14 0.42
21 2 0.06
22 17 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TATATATAAATTATATAGTT
Found at i:288181 original size:22 final size:22
Alignment explanation
Indices: 288122--288181 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 22
288112 ACTATTGAAC
288122 TATATATAAATTATATAGTTTAT
1 TATATATAAATTATATA-TTTAT
*
288145 TA-ATATAAAATATATA-TT-T
1 TATATATAAATTATATATTTAT
*
288164 TATATAAAAATTATATAT
1 TATATATAAATTATATAT
288182 GAATTGTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.09
20 14 0.44
22 13 0.41
23 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATATATAAATTATATATTTAT
Found at i:288310 original size:2 final size:2
Alignment explanation
Indices: 288305--289823 Score: 382
Period size: 2 Copynumber: 759.0 Consensus size: 2
288295 AACTATAAAT
288305 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
288347 TA TA GTA TA -A T- TA TA AA GA CTA AA GTA TA TA -A GTA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA -TA TA TA TA
* * * *
288388 TA TA TA TA AA GTA TA TA AA TA TA AA GTA TA -A GTA TT TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * * *
288430 TA AA GTA TA -A T- TA TA -A GA CTA AA GTA TA TA -A GCA TA TA -A
1 TA TA -TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA -TA TA TA TA
* *
288469 TA TA AA GTA TA TA -A GTA TA TA -A TA TA -A AA TA TA TA -A GTA
1 TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
288508 T- TA -A TA TA -A AA TA TA TA AA GTA TA -A T- TA TA AA GA CTA AA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* *
288547 GTA TA TA -A TA TA AA GTA TA TA -A GTA TA TA TA TA TA TA AA GTA
1 -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA -TA
* * *
288589 TA -A GTA TG TA TA TA TG TA TA TA TA TA TA TA TA -A GT- TT TA GTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
288631 TA AA GTA TA TA TA CA TA TA TA -A TA -A TA TA AA GTA TA -A GTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * *
288671 TA T- TA TA TA TA TA TA TA AA GTA TA -A T- TA TA AA GA CTA AA GTA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA -TA
* * *
288713 TA CA -A GCA TA TA -A TA TA AA GTA TA TA -A GTA TA TA -A TA TA
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA
* * * *
288752 AA GTA TCA AA GTA T- TA AA TA TA -A GTA TA TA -A GTA T- TA AA TA
1 TA -TA T-A TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* * *
288793 TA AA GTA TA TA -A GTA TA TA TA TA AA CTA TA AA GTA TA TA TA TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * * * *
288836 TA AA CTA TA -A AA TA TA TA TA TA TA TA AA GT- TT TA GTA TA AA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * *
288877 T- TA TG TA TA CA TA TA TA -A TA -A TA TA AA GTA TA -A CTA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * * * *
288916 TA TA TA TA GA GA GA GTA TA -A T- TA TA AA GA CTA AA GTA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA -TA TA TA
* *
288957 -A GTA TA TA -A TA TA TA TA CTT TA TA GTT TA TA TA TA TA CT- TA
1 TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA
* * * *
288998 TA TA CTT TA TA T- TA T- TA TA TA TG TA TA TA TA CTT TA TT TA -A
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * **
289039 T- TA AA TA TG TG TA TA TA TA AA TA TA CT- TA TA CC T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * ** * *
289079 T- TT TA TA TA TG TA TA TA TA CC T- TA TA CTA -A AA CTT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * * *
289120 TA TA TA TA TA CA CTT TA TA GTT TA TA TA TA TA CT- TA TA TGC TT
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA T-A TA
* *
289163 TA TA TT TA -A TA CT- TA TA TA CT- TA TA TT TA -A TA CT- TA TA
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* *
289201 TA CTT TA TA T- TA TA TA CT- TA -A TA CTT TA TA T- TA T- TA TA
1 TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * * *
289239 TA CA TA TA TA TA CTT TA TA TT TA TA TA CT- TA TA TA CTT TGG TC
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA T-A TA
* * * * *
289282 TT TA TA TT TA TA TT TA TA TA TA -A CA TA CT- TA TA CTT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * *
289323 TA T- TA TA TA TG TA TA TA CA CTT TA TA CTA -A AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* *
289365 TA TA TA TA TA TA TA TA TA TA TA CT- TA TA CTT TA TA TT TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * *
289407 CT- TA TA TA CT- TA TA TT TA -A TA CT- TA TA TGC TT TA TA T- TA
1 -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA T-A TA TA TA TA TA
289446 TA CT- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
289488 TA TA TA TA TA TA TA TA TA TA TT TA CTT TA TC TT TA TT TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
289531 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
289572 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA CTA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
289614 TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A AA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
289654 TA TA AA GTA TA TA -A TA TA TA TA AA GT- TT TA GTA TA AA T- TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* *
289694 TA TA TA CTT TA TA GTT TA TA TA TA GTA TA TA TA T- TA TA TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * * * *
289736 CTT TA TA GTT TA CA TT TA TA TA TA TA TT TA TA CT- TA TA TT TT
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
289778 TT TA TA TA TG TA TA TT TA AA TA -A GTA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
289820 TA TA
1 TA TA
289824 ACGTGTTAAT
Statistics
Matches: 1111, Mismatches: 217, Indels: 378
0.65 0.13 0.22
Matches are distributed among these distances:
1 94 0.08
2 920 0.83
3 97 0.09
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:288724 original size:43 final size:42
Alignment explanation
Indices: 288329--288815 Score: 300
Period size: 43 Copynumber: 11.4 Consensus size: 42
288319 TATATATATA
*
288329 TATATATA-TATATATATATATAGTATAATTATAAAGACTAAAG
1 TATATA-AGTATATATATATAAAGTATAATTATAAAGA-TAAAG
* *
288372 TATATAAGTATATATATATATA-TA-AAGTATATAAATATAAAG
1 TATATAAGTATATATATATAAAGTATAA-T-TATAAAGATAAAG
*
288414 --TATAAGTATTTATATATAAAGTATAATTAT-AAGACTAAAG
1 TATATAAGTATATATATATAAAGTATAATTATAAAGA-TAAAG
* * * *
288454 TATATAAGCATATA-ATATAAAGTATATAAGTATATAATATAAAA
1 TATATAAGTATATATATATAAAG--TATAATTATA-AAGATAAAG
288498 TATATAAGTATTAATATAAAATATATAAAGTATAATTATAAAGACTAAAG
1 TATATAAG---T-ATAT---ATATATAAAGTATAATTATAAAGA-TAAAG
* * *
288548 TATATAA-TATAAAGTATAT-AAGTAT-A-TATATATATAAAG
1 TATATAAGTATATA-TATATAAAGTATAATTATAAAGATAAAG
* ** * **
288587 --TATAAGTATGTATATATGTA-TATATATATATATAAGTTTTAG
1 TATATAAGTATATATATATAAAGTATA-AT-TATA-AAGATAAAG
* *
288629 TATA-AAGTATATATACATATA-TAATAA-TATAAAG-TATAAG
1 TATATAAGTATATATATATAAAGT-ATAATTATAAAGATA-AAG
*
288669 TATATTA-TATATATATATAAAGTATAATTATAAAGACTAAAG
1 TATATAAGTATATATATATAAAGTATAATTATAAAGA-TAAAG
* * * *
288711 TATACAAGCATATA-ATATAAAGTATATAAGTATATAATATAAAG
1 TATATAAGTATATATATATAAAG--TATAATTATA-AAGATAAAG
* * *
288755 TATCA-AAGTAT-TAAATAT-AAGTATATAAGTATTAAATATAAAG
1 TAT-ATAAGTATATATATATAAAG--TATAATTA-TAAAGATAAAG
288798 TATATAAGTATATATATA
1 TATATAAGTATATATATA
288816 AACTATAAAG
Statistics
Matches: 358, Mismatches: 39, Indels: 93
0.73 0.08 0.19
Matches are distributed among these distances:
37 13 0.04
38 5 0.01
39 10 0.03
40 57 0.16
41 31 0.09
42 49 0.14
43 96 0.27
44 50 0.14
45 10 0.03
46 1 0.00
48 4 0.01
49 3 0.01
50 20 0.06
51 1 0.00
52 8 0.02
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (42 bp):
TATATAAGTATATATATATAAAGTATAATTATAAAGATAAAG
Found at i:289059 original size:242 final size:242
Alignment explanation
Indices: 288471--288969 Score: 659
Period size: 242 Copynumber: 2.1 Consensus size: 242
288461 GCATATAATA
* * * * * *
288471 TAAAGTATATAAGTATATAATATAAAATATATAAGTAT-TAATATAAAATATATAAAGTA-TAAT
1 TAAAGTATACAAGCATATAATATAAACTATATAAGTATATAATATAAAGTAT-CAAAGTATTAAA
*
288534 TATAAAG-ACTA-AAGTA-TATAATATAAAGTATATAAGTATATATAT--ATATAAAGTATA-AG
65 TAT-AAGTA-TATAAGTATTA-AATATAAAGTAAATAAGTATATATATAAATATAAAGTATATA-
* **
288593 TATGT--A-TAT-ATGTATATATATATATATAAGTTTTAGTATAAAGTATATATACATATATAAT
126 TATATAAACTATAAAATATATATATATATATAAGTTTTAGTATAAAGTATATATACATATATAAT
* * *
288654 AATATAAAGTATAAGTATATTATATATATATATAAAGTATAATTATAAAGAC
191 AATATAAAGTATAACTATATTATATATATAGAGAAAGTATAATTATAAAGAC
*
288706 TAAAGTATACAAGCATATAATATAAAGTATATAAGTATATAATATAAAGTATCAAAGTATTAAAT
1 TAAAGTATACAAGCATATAATATAAACTATATAAGTATATAATATAAAGTATCAAAGTATTAAAT
*
288771 ATAAGTATATAAGTATTAAATATAAAGTATATAAGTATATATATAAACTATAAAGTATATATATA
66 ATAAGTATATAAGTATTAAATATAAAGTAAATAAGTATATATATAAA-TATAAAGTATATATATA
* *
288836 TAAACTATAAAATATATATATATATA-AAGTTTTAGTATAAATTATGTATACATATATAATAATA
130 TAAACTATAAAATATATATATATATATAAGTTTTAGTATAAAGTATATATACATATATAATAATA
*
288900 TAAAGTATAACTATA-T-TATATATAGAGAGAGTATAATTATAAAGAC
195 TAAAGTATAACTATATTATATATATAGAGAAAGTATAATTATAAAGAC
* *
288946 TAAAGTATATAAGTATATAATATA
1 TAAAGTATACAAGCATATAATATA
288970 TATACTTTAT
Statistics
Matches: 234, Mismatches: 17, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
235 46 0.20
236 50 0.21
237 2 0.01
238 1 0.00
239 15 0.06
240 50 0.21
241 2 0.01
242 53 0.23
243 15 0.06
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (242 bp):
TAAAGTATACAAGCATATAATATAAACTATATAAGTATATAATATAAAGTATCAAAGTATTAAAT
ATAAGTATATAAGTATTAAATATAAAGTAAATAAGTATATATATAAATATAAAGTATATATATAT
AAACTATAAAATATATATATATATATAAGTTTTAGTATAAAGTATATATACATATATAATAATAT
AAAGTATAACTATATTATATATATAGAGAAAGTATAATTATAAAGAC
Found at i:289097 original size:242 final size:244
Alignment explanation
Indices: 288471--288969 Score: 654
Period size: 236 Copynumber: 2.1 Consensus size: 244
288461 GCATATAATA
* * * * * *
288471 TAAAGTATATAAGTATATAATATAAAATATATAAGTAT-TAATATAAAATATATAAAGTA-TAAT
1 TAAAGTATACAAGCATATAATATAAACTATATAAGTATATAATATAAAGTAT-CAAAGTATTAAA
*
288534 TATAAAG-ACTA-AAGTA-TATAATATAAAGTATATAAGTATATATAT--A-TATAAAGTATA-A
65 TAT-AAGTA-TATAAGTATTA-AATATAAAGTAAATAAGTATATATATAAACTATAAAGTATATA
* *
288592 -GTAT---GTATATATGTATATATATATATATAAGTTTTAGTATAAAGTATATATACATATATAA
127 TATATAAACTATATATGTATATATATATATATAAGTTTTAGTATAAAGTATATATACATATATAA
* * *
288653 TAATATAAAGTATAAGTATATTATATATATATATAAAGTATAATTATAAAGAC
192 TAATATAAAGTATAACTATATTATATATATAGAGAAAGTATAATTATAAAGAC
*
288706 TAAAGTATACAAGCATATAATATAAAGTATATAAGTATATAATATAAAGTATCAAAGTATTAAAT
1 TAAAGTATACAAGCATATAATATAAACTATATAAGTATATAATATAAAGTATCAAAGTATTAAAT
*
288771 ATAAGTATATAAGTATTAAATATAAAGTATATAAGTATATATATAAACTATAAAGTATATATATA
66 ATAAGTATATAAGTATTAAATATAAAGTAAATAAGTATATATATAAACTATAAAGTATATATATA
** * *
288836 TAAACTATA-AAATATATATATATATA-AAGTTTTAGTATAAATTATGTATACATATATAATAAT
131 TAAACTATATATGTATATATATATATATAAGTTTTAGTATAAAGTATATATACATATATAATAAT
*
288899 ATAAAGTATAACTATA-T-TATATATAGAGAGAGTATAATTATAAAGAC
196 ATAAAGTATAACTATATTATATATATAGAGAAAGTATAATTATAAAGAC
* *
288946 TAAAGTATATAAGTATATAATATA
1 TAAAGTATACAAGCATATAATATA
288970 TATACTTTAT
Statistics
Matches: 233, Mismatches: 18, Indels: 21
0.86 0.07 0.08
Matches are distributed among these distances:
235 46 0.20
236 50 0.21
237 2 0.01
238 1 0.00
239 11 0.05
240 50 0.21
241 4 0.02
242 50 0.21
243 15 0.06
244 4 0.02
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (244 bp):
TAAAGTATACAAGCATATAATATAAACTATATAAGTATATAATATAAAGTATCAAAGTATTAAAT
ATAAGTATATAAGTATTAAATATAAAGTAAATAAGTATATATATAAACTATAAAGTATATATATA
TAAACTATATATGTATATATATATATATAAGTTTTAGTATAAAGTATATATACATATATAATAAT
ATAAAGTATAACTATATTATATATATAGAGAAAGTATAATTATAAAGAC
Found at i:289130 original size:60 final size:61
Alignment explanation
Indices: 288982--289148 Score: 162
Period size: 69 Copynumber: 2.6 Consensus size: 61
288972 TACTTTATAG
* *
288982 TTTATATATATACTTATATA-CTTTATATTATTATATATGTATATATACTTTATTTAATTAAATA
1 TTTATATATATA--TATATACCTTTATATT-TTATATATGTATATATACCTTA-TTAACTAAATA
289046 TGTGTATATATAAATATACTTATACCTTATATATTTTATATATGTATATATACCTTA-T-ACTAA
1 T-T-TATATAT--ATATA--TATACCTT-TATATTTTATATATGTATATATACCTTATTAACTAA
289109 A-A
59 ATA
*
289111 CTTTATATATATATATATACACTTTATAGTTTATATAT
1 -TTTATATATATATATATAC-CTTTATATTTTATATAT
289149 ATACTTATAT
Statistics
Matches: 90, Mismatches: 3, Indels: 24
0.77 0.03 0.21
Matches are distributed among these distances:
60 18 0.20
61 3 0.03
62 5 0.06
64 8 0.09
65 3 0.03
66 15 0.17
67 1 0.01
68 7 0.08
69 24 0.27
70 6 0.07
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (61 bp):
TTTATATATATATATATACCTTTATATTTTATATATGTATATATACCTTATTAACTAAATA
Found at i:289260 original size:91 final size:91
Alignment explanation
Indices: 289110--289491 Score: 264
Period size: 91 Copynumber: 4.2 Consensus size: 91
289100 TTATACTAAA
* * *
289110 ACTTTATA-TATATA-TATATACACTTTATAGTTTATATATATAC-T-TATATGCTTTATATTTA
1 ACTTTATATTATATACT-TA-ATACTTTATA-CTTAT-TATATACATATATATACTTTATATTTA
289171 ATACTTATATACTTATATTTAATACTTATAT
62 ATACTTATATACTTATATTTAATA-TTATAT
289202 ACTTTATATTATATACTTAATACTTTATA-TTATTATATACATATATATACTTTATATTTATATA
1 ACTTTATATTATATACTTAATACTTTATACTTATTATATACATATATATACTTTATATTTA-ATA
* *
289266 CTTATATACTT-TGGTCTTTATATT-TAT
65 CTTATATACTTAT-AT-TTAATATTATAT
* ** * **
289293 A-TTTATATATAACATACTT-ATACTTTATA-TTATTATATATGTATATACACTTTATACTAAAA
1 ACTTTATAT-T-ATATACTTAATACTTTATACTTATTATATACATATATATACTTTATA-TTTAA
*
289355 TA-TATATATA-TATATATATATATATATATAT
63 TACT-TATATACT-TATATTTA-ATAT-TATAT
* * *
289386 AC-TTATACTT-TATATTTAATACTTATATACTTA-TATTTA-ATACTTATATGCTTTATA-TT-
1 ACTTTATA-TTATATACTTAATACTT-TATACTTATTATATACATA--TATATACTTTATATTTA
*
289445 ATACTTATATA-TATATATATATATATATATAT
62 ATACTTATATACT-TATATTTA-ATAT-TATAT
*
289477 A-TATATATATATATA
1 ACTTTATAT-TATATA
289492 TATATATATA
Statistics
Matches: 241, Mismatches: 22, Indels: 54
0.76 0.07 0.17
Matches are distributed among these distances:
89 7 0.03
90 16 0.07
91 112 0.46
92 58 0.24
93 32 0.13
94 16 0.07
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (91 bp):
ACTTTATATTATATACTTAATACTTTATACTTATTATATACATATATATACTTTATATTTAATAC
TTATATACTTATATTTAATATTATAT
Found at i:289329 original size:30 final size:29
Alignment explanation
Indices: 289283--289401 Score: 73
Period size: 27 Copynumber: 4.5 Consensus size: 29
289273 ACTTTGGTCT
289283 TTATA-TTTATA-T-TTATATATAACATAC
1 TTATACTTTATATTATTATATAT-ACATAC
**
289310 TTATACTTTATATTATTATATATGTATA-
1 TTATACTTTATATTATTATATATACATAC
* * * *
289338 -TACACTTTATACTA--AAATATATATA-
1 TTATACTTTATATTATTATATATACATAC
* *
289363 -TATA-TATATA-TA-TATATATATATAC
1 TTATACTTTATATTATTATATATACATAC
289388 TTATACTTTATATT
1 TTATACTTTATATT
289402 TAATACTTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
23 2 0.03
24 15 0.20
25 12 0.16
26 4 0.05
27 22 0.30
28 7 0.09
29 4 0.05
30 8 0.11
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (29 bp):
TTATACTTTATATTATTATATATACATAC
Found at i:289411 original size:13 final size:13
Alignment explanation
Indices: 289384--289434 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
289374 ATATATATAT
289384 ATACTTATACTTT-
1 ATACTTATA-TTTA
* *
289397 ATATTTAATACTTA
1 ATACTT-ATATTTA
289411 TATACTTATATTTA
1 -ATACTTATATTTA
289425 ATACTTATAT
1 ATACTTATAT
289435 GCTTTATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 17 0.55
14 9 0.29
15 5 0.16
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (13 bp):
ATACTTATATTTA
Found at i:290179 original size:33 final size:34
Alignment explanation
Indices: 290142--290212 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
290132 CCTTTACAAC
*
290142 TCCCTAG-TTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
* * *
290175 TCCCTAGCTTTTACACGGGCTTAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
290209 TCCC
1 TCCC
290213 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:290463 original size:21 final size:21
Alignment explanation
Indices: 290429--290468 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
290419 AGTCGTATCT
290429 AGCCATTAGGGATG-TTTTAG
1 AGCCATTAGGGATGATTTTAG
*
290449 AGCCATTTGGGGATGATTTT
1 AGCCA-TTAGGGATGATTTT
290469 TCTTCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.38
Consensus pattern (21 bp):
AGCCATTAGGGATGATTTTAG
Found at i:290845 original size:2 final size:2
Alignment explanation
Indices: 290838--290878 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
290828 TAATTCAACA
290838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
290879 GATGCATGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:291759 original size:24 final size:24
Alignment explanation
Indices: 291714--291759 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
291704 TTTAGTCCTT
*
291714 TTTTATATTAATATCAGCTTCACA
1 TTTTATATTAATATCAACTTCACA
*
291738 TTTTATAATTAAT-TCAATTTCA
1 TTTTAT-ATTAATATCAACTTCA
291760 TCCCTCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTATATTAATATCAACTTCACA
Found at i:291873 original size:8 final size:8
Alignment explanation
Indices: 291857--292000 Score: 57
Period size: 8 Copynumber: 19.2 Consensus size: 8
291847 AACTATAAAG
291857 TATAAGTA
1 TATAAGTA
*
291865 TATATGTA
1 TATAAGTA
* *
291873 TCTGTA-TA
1 TAT-AAGTA
291881 TATAAAGTA
1 TAT-AAGTA
*
291890 TA-AAGTG
1 TATAAGTA
291897 TA-AAGTA
1 TATAAGTA
291904 TATAA-TA
1 TATAAGTA
291911 TA-AAGTA
1 TATAAGTA
*
291918 -ATAAAGTG
1 TAT-AAGTA
* *
291926 T-T-TGGA
1 TATAAGTA
291932 TATAAGTA
1 TATAAGTA
291940 CTA-AAGTA
1 -TATAAGTA
291948 TATAA--A
1 TATAAGTA
291954 TATAAGTA
1 TATAAGTA
*
291962 T-TAAATA
1 TATAAGTA
291969 TA-AAGTA
1 TATAAGTA
291976 TATAAGTA
1 TATAAGTA
*
291984 CTA-AAATA
1 -TATAAGTA
291992 TATAA-TA
1 TATAAGTA
291999 TA
1 TA
292001 AAATATTAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 35
0.66 0.12 0.23
Matches are distributed among these distances:
6 11 0.11
7 39 0.39
8 43 0.43
9 8 0.08
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (8 bp):
TATAAGTA
Found at i:291956 original size:22 final size:21
Alignment explanation
Indices: 291897--292035 Score: 111
Period size: 22 Copynumber: 6.4 Consensus size: 21
291887 GTATAAAGTG
*
291897 TAAAGTATATAATATAAAGTAA
1 TAAAGTATATAATAT-AAGTAT
* * * *
291919 TAAAGTGTTTGGATATAAGTAC
1 TAAAGTATAT-AATATAAGTAT
291941 TAAAGTATATAAATATAAGTAT
1 TAAAGTATAT-AATATAAGTAT
* *
291963 TAAA-TATAAAGTATATAAGTAC
1 TAAAGTATATA--ATATAAGTAT
* *
291985 TAAAATATATAATATAAAATAT
1 TAAAGTATATAATAT-AAGTAT
* *
292007 TAAACTATATAACATAAGTAT
1 TAAAGTATATAATATAAGTAT
292028 TAAA-TATA
1 TAAAGTATA
292036 AAGTATATTA
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
20 5 0.05
21 17 0.18
22 64 0.67
23 9 0.09
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.35
Consensus pattern (21 bp):
TAAAGTATATAATATAAGTAT
Found at i:291968 original size:13 final size:15
Alignment explanation
Indices: 291880--292043 Score: 92
Period size: 14 Copynumber: 10.9 Consensus size: 15
291870 GTATCTGTAT
291880 ATATAAAGTATA-AA
1 ATATAAAGTATATAA
* *
291894 GTGTAAAGTATAT-A
1 ATATAAAGTATATAA
291908 ATATAAAGTA-ATAA
1 ATATAAAGTATATAA
* ** *
291922 AGTGT-TTGGATATAA
1 A-TATAAAGTATATAA
*
291937 GTACTAAAGTATATAA
1 ATA-TAAAGTATATAA
291953 ATAT-AAGTAT-TAA
1 ATATAAAGTATATAA
291966 ATATAAAGTATATAA
1 ATATAAAGTATATAA
* *
291981 GTACTAAAATATAT-A
1 ATA-TAAAGTATATAA
*
291996 ATATAAAATAT-TAA
1 ATATAAAGTATATAA
*
292010 ACTATATAACATAAGTATTAA
1 A-TATA-AA-GT-A-TA-TAA
292031 ATATAAAGTATAT
1 ATATAAAGTATAT
292044 TAATGATCAT
Statistics
Matches: 115, Mismatches: 18, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
13 10 0.09
14 46 0.40
15 21 0.18
16 22 0.19
17 3 0.03
18 2 0.02
19 3 0.03
20 4 0.03
21 4 0.03
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (15 bp):
ATATAAAGTATATAA
Found at i:292008 original size:44 final size:45
Alignment explanation
Indices: 291881--292015 Score: 145
Period size: 44 Copynumber: 3.1 Consensus size: 45
291871 TATCTGTATA
* * *
291881 TATAAAGTATA-AAGT-GTAAAGTATATAATATAAAGTAATAAAG
1 TATAAAGTATATAAGTACTAAAGTATATAATATAAAGTATTAAAC
* ** *
291924 TGT-TTGGATATAAGTACTAAAGTATATAA-ATATAAGTATTAAA-
1 TATAAAGTATATAAGTACTAAAGTATATAATATA-AAGTATTAAAC
* *
291967 TATAAAGTATATAAGTACTAAAATATATAATATAAAATATTAAAC
1 TATAAAGTATATAAGTACTAAAGTATATAATATAAAGTATTAAAC
292012 TATA
1 TATA
292016 TAACATAAGT
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
42 4 0.05
43 11 0.15
44 52 0.70
45 7 0.09
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.34
Consensus pattern (45 bp):
TATAAAGTATATAAGTACTAAAGTATATAATATAAAGTATTAAAC
Found at i:292065 original size:21 final size:21
Alignment explanation
Indices: 292039--292100 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
292029 AAATATAAAG
292039 TATATTAATGATCATAATTAA
1 TATATTAATGATCATAATTAA
*
292060 TATATTAA-G-T-AT-ATTTA
1 TATATTAATGATCATAATTAA
*
292077 T-TATTAAATTATCATAATTAA
1 TATATT-AATGATCATAATTAA
292098 TAT
1 TAT
292101 TTTATTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
16 4 0.12
17 7 0.22
18 2 0.06
19 2 0.06
20 3 0.09
21 13 0.41
22 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (21 bp):
TATATTAATGATCATAATTAA
Found at i:297791 original size:2 final size:2
Alignment explanation
Indices: 297784--297814 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
297774 TCGCATGAAT
297784 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
297815 CTTCAAGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:306507 original size:27 final size:27
Alignment explanation
Indices: 306476--306542 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
306466 TCAATCTGAG
*
306476 TTACCACATAGTAAGACAGGCAATGTC
1 TTACCACATAGTAAGACAGACAATGTC
306503 TTACCACATAGTAAGACAGACAATGTC
1 TTACCACATAGTAAGACAGACAATGTC
306530 TTACCACATAGTA
1 TTACCACATAGTA
306543 GTACGGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (27 bp):
TTACCACATAGTAAGACAGACAATGTC
Found at i:313117 original size:20 final size:19
Alignment explanation
Indices: 313081--313124 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
313071 AAAATAATCA
* *
313081 AATTTTACATTCCAACATC
1 AATTTTACACTCAAACATC
*
313100 AATTTTAACACTCAAACATT
1 AATTTT-ACACTCAAACATC
313120 AATTT
1 AATTT
313125 CCAGCATAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTTTACACTCAAACATC
Found at i:318989 original size:32 final size:32
Alignment explanation
Indices: 318943--319065 Score: 102
Period size: 32 Copynumber: 3.8 Consensus size: 32
318933 AGTATTAGTG
* * * * *
318943 TTGCATTTAGATAATGCACATTATAGTCAGTA
1 TTGCATTCAAATAATGCACAATAGAGTCAATA
** * * *
318975 TTGCATTCAAATAATATATAACAGAGTAAATA
1 TTGCATTCAAATAATGCACAATAGAGTCAATA
* * * *
319007 TTGCATTCCAATAATGCTCAGTAGAATCAATA
1 TTGCATTCAAATAATGCACAATAGAGTCAATA
* *
319039 TTGCATTCAGATAATGCACAACAGAGT
1 TTGCATTCAAATAATGCACAATAGAGT
319066 TAGTGTTATA
Statistics
Matches: 66, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.32
Consensus pattern (32 bp):
TTGCATTCAAATAATGCACAATAGAGTCAATA
Found at i:321007 original size:23 final size:23
Alignment explanation
Indices: 320979--321070 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
320969 CACTGAAGTG
320979 CCACATAGAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* * * **
321002 CTACATAGTATTGTCCCGAAAAA
1 CCACATAGAAATGTCCCGAAGGA
321025 CCACATAGAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* * *
321048 CCACGTAGAATTATCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
321071 TCGCGTAGAA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAGGA
Found at i:321080 original size:46 final size:46
Alignment explanation
Indices: 320979--321067 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
320969 CACTGAAGTG
* * *
320979 CCACATAGAAATGTCCCGAAGGACTACATAGTATTGTCCCGAAAAA
1 CCACATAGAAATGTCCCGAAGGACCACATAGAATTATCCCGAAAAA
*
321025 CCACATAGAAATGTCCCGAAGGACCACGTAGAATTATCCCGAA
1 CCACATAGAAATGTCCCGAAGGACCACATAGAATTATCCCGAA
321068 GGATCGCGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (46 bp):
CCACATAGAAATGTCCCGAAGGACCACATAGAATTATCCCGAAAAA
Found at i:321709 original size:24 final size:19
Alignment explanation
Indices: 321657--321742 Score: 145
Period size: 19 Copynumber: 4.5 Consensus size: 19
321647 TCTCATTGTG
*
321657 GTATAGATACTATACTTCA
1 GTATCGATACTATACTTCA
321676 GTATCGATACTATACTTCA
1 GTATCGATACTATACTTCA
*
321695 GTATCGATATTATACTTCA
1 GTATCGATACTATACTTCA
321714 GTATCGATACTATACTTCA
1 GTATCGATACTATACTTCA
*
321733 GTATCAATAC
1 GTATCGATAC
321743 CGTACCTACA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 63 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (19 bp):
GTATCGATACTATACTTCA
Done.