Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009609.1 Hibiscus syriacus cultivar Beakdansim tig00116995_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: 1078827
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:2071 original size:11 final size:12
Alignment explanation
Indices: 2038--2072 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2028 TTCTAACAAT
2038 TAAATAATAAAAA
1 TAAATAA-AAAAA
*
2051 TTAATAAAAAAA
1 TAAATAAAAAAA
2063 TAAATAAAAA
1 TAAATAAAAA
2073 TTCCATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
TAAATAAAAAAA
Found at i:2625 original size:21 final size:21
Alignment explanation
Indices: 2601--2651 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2591 CTGTGGTGAT
* *
2601 ATCTGAAATAGCTATGGTGTC
1 ATCTGAAATAGCTACGGTGCC
**
2622 ATCTGATGTAGCTACGGTGCC
1 ATCTGAAATAGCTACGGTGCC
2643 ATCTGAAAT
1 ATCTGAAAT
2652 GTCTGCAGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (21 bp):
ATCTGAAATAGCTACGGTGCC
Found at i:8827 original size:35 final size:36
Alignment explanation
Indices: 8788--8857 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 36
8778 TCAGCAATCT
**
8788 AAAAGAAATGCTACTTTCATGGTTTCAAG-TAAGCC
1 AAAAGAAAAACTACTTTCATGGTTTCAAGCTAAGCC
** *
8823 AAAAGAAAAACTACTTTGTTGGTTTTAAGCTAAGC
1 AAAAGAAAAACTACTTTCATGGTTTCAAGCTAAGC
8858 TCAACTTCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 24 0.83
36 5 0.17
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (36 bp):
AAAAGAAAAACTACTTTCATGGTTTCAAGCTAAGCC
Found at i:12326 original size:39 final size:40
Alignment explanation
Indices: 12274--12361 Score: 133
Period size: 41 Copynumber: 2.2 Consensus size: 40
12264 ACCGTTTTTT
*
12274 TTTTTTAAAAAAAACCGGA-TTTTTTCGGATAAAAATCTAG
1 TTTTTT-AAAAAAACCGGATTTTTTTCGGATAAAAAACTAG
*
12314 TTTTTTAAAAAAACCGGATTTTTTTTCGGATAAAAAACTGG
1 TTTTTTAAAAAAACCGGA-TTTTTTTCGGATAAAAAACTAG
12355 TTTTTTA
1 TTTTTTA
12362 TCCGGTTTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 12 0.27
40 6 0.14
41 26 0.59
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (40 bp):
TTTTTTAAAAAAACCGGATTTTTTTCGGATAAAAAACTAG
Found at i:12400 original size:26 final size:27
Alignment explanation
Indices: 12345--12401 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
12335 TTTTTCGGAT
* * **
12345 AAAAAACTGGTTTTTTATCCGGTTTGA
1 AAAAAACCGGTTTTTAATCCGGTTAAA
12372 AAAAAACCGGTTTTTAATCCGG-TAAA
1 AAAAAACCGGTTTTTAATCCGGTTAAA
12398 AAAA
1 AAAA
12402 CCGATCGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (27 bp):
AAAAAACCGGTTTTTAATCCGGTTAAA
Found at i:12403 original size:24 final size:23
Alignment explanation
Indices: 12319--12404 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 23
12309 TCTAGTTTTT
* *
12319 TAAAAAAACCGGATTTTTTTTCGG
1 TAAAAAAACCGG-TTTTTATCCGG
*
12343 -ATAAAAAACTGGTTTTTTATCCGG
1 TA-AAAAAACCGG-TTTTTATCCGG
12367 TTTGAAAAAAACCGGTTTTTAATCCGG
1 --T-AAAAAAACCGGTTTTT-ATCCGG
12394 TAAAAAAACCG
1 TAAAAAAACCG
12405 ATCGTTCAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
23 1 0.02
24 28 0.55
25 1 0.02
26 5 0.10
27 15 0.29
28 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (23 bp):
TAAAAAAACCGGTTTTTATCCGG
Found at i:16942 original size:39 final size:39
Alignment explanation
Indices: 16898--16974 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
16888 CAGCACAATT
* *
16898 TGGCATATTATAAAAAGAAATGGACTCATGCGCACCTGC
1 TGGCATATTATAAAAAGAAAAGGACCCATGCGCACCTGC
* * * *
16937 TGGCATATTTTCAAATGAAAAGGCCCCATGCGCACCTG
1 TGGCATATTATAAAAAGAAAAGGACCCATGCGCACCTG
16975 TGAAGAATGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (39 bp):
TGGCATATTATAAAAAGAAAAGGACCCATGCGCACCTGC
Found at i:17121 original size:33 final size:33
Alignment explanation
Indices: 17084--17146 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
17074 GAGTAGGGGT
*
17084 GACATGTGTTGGTGGAGCCTTTGGAGCATGCGC
1 GACATGTGTTGGTGGAGCCGTTGGAGCATGCGC
17117 GACATGTGTTGGTGGAGCCGTTGGAGCATG
1 GACATGTGTTGGTGGAGCCGTTGGAGCATG
17147 TGCATTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.16, C:0.16, G:0.41, T:0.27
Consensus pattern (33 bp):
GACATGTGTTGGTGGAGCCGTTGGAGCATGCGC
Found at i:20696 original size:21 final size:23
Alignment explanation
Indices: 20654--20697 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20644 TGAGCTTAAG
20654 GAAGAAGAGAGATGGCAAGGCGGA
1 GAAGAAGAGAGATGGC-AGGCGGA
*
20678 GAAGAAG-GGGATGGC-GGCGG
1 GAAGAAGAGAGATGGCAGGCGG
20698 CGGGTGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.34, C:0.09, G:0.52, T:0.05
Consensus pattern (23 bp):
GAAGAAGAGAGATGGCAGGCGGA
Found at i:20874 original size:23 final size:23
Alignment explanation
Indices: 20824--20875 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
20814 ATTTTAAGAT
20824 TTAAAAATTAATTTATAATACTAA
1 TTAAAAATTAATTTATAATAC-AA
*
20848 -TAAAAAGTTAATTTGTAATA-AA
1 TTAAAAA-TTAATTTATAATACAA
20870 TTAAAA
1 TTAAAA
20876 GACTAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 11 0.44
24 12 0.48
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
TTAAAAATTAATTTATAATACAA
Found at i:30572 original size:35 final size:35
Alignment explanation
Indices: 30533--30600 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
30523 GAACTAGCAG
* *
30533 AACACATGGAGCATAGTAAAAGAATGTCATCTCAA
1 AACACAAGGAGCATAGTAAAAGAACGTCATCTCAA
* *
30568 AACACAAGGAGCATGGTAAAAGAACGTCGTCTC
1 AACACAAGGAGCATAGTAAAAGAACGTCATCTC
30601 TCACCTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.18
Consensus pattern (35 bp):
AACACAAGGAGCATAGTAAAAGAACGTCATCTCAA
Found at i:42506 original size:146 final size:146
Alignment explanation
Indices: 42242--42535 Score: 579
Period size: 146 Copynumber: 2.0 Consensus size: 146
42232 AAAGAGAAAG
42242 AGTGAGAGATCTTCGATAATTCTTCTTATGTTTTACAATTTAAGTCACTAAAGTGAGCCCTTGAA
1 AGTGAGAGATCTTCGATAATTCTTCTTATGTTTTACAATTTAAGTCACTAAAGTGAGCCCTTGAA
42307 CCTTATTATATCCTTTTATTTTATTGGTTTTGAGCAATAAAACTATTTACCCTTTTTTTATTACA
66 CCTTATTATATCCTTTTATTTTATTGGTTTTGAGCAATAAAACTATTTACCCTTTTTTTATTACA
42372 GCTGAAATTATATAAC
131 GCTGAAATTATATAAC
42388 AGTGAGAGATCTTCGATAATTCTTCTTATGTTTTACAATTTAAGTCACTAAAGTGAGCCCTTGAA
1 AGTGAGAGATCTTCGATAATTCTTCTTATGTTTTACAATTTAAGTCACTAAAGTGAGCCCTTGAA
*
42453 CCTTATTATATCCTTTTATTTTATTGGTTTTGTGCAATAAAACTATTTACCCTTTTTTTATTACA
66 CCTTATTATATCCTTTTATTTTATTGGTTTTGAGCAATAAAACTATTTACCCTTTTTTTATTACA
42518 GCTGAAATTATATAAC
131 GCTGAAATTATATAAC
42534 AG
1 AG
42536 GCACACAGAG
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 147 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (146 bp):
AGTGAGAGATCTTCGATAATTCTTCTTATGTTTTACAATTTAAGTCACTAAAGTGAGCCCTTGAA
CCTTATTATATCCTTTTATTTTATTGGTTTTGAGCAATAAAACTATTTACCCTTTTTTTATTACA
GCTGAAATTATATAAC
Found at i:43678 original size:22 final size:21
Alignment explanation
Indices: 43660--43704 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
43650 GTTGATAGAC
43660 ATTT-AACTTGAATCTGATAG
1 ATTTCAACTTGAATCTGATAG
*
43680 ATTTCAACTTGAATCTGATAA
1 ATTTCAACTTGAATCTGATAG
43701 ATTT
1 ATTT
43705 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
ATTTCAACTTGAATCTGATAG
Found at i:44918 original size:22 final size:22
Alignment explanation
Indices: 44876--44918 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
44866 AAGAGTTAAT
* * *
44876 TTTAATATTTTTATTATAAATG
1 TTTAATATTGTTAATAAAAATG
44898 TTTAATATTGTTAATAAAAAT
1 TTTAATATTGTTAATAAAAAT
44919 AATGTATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
TTTAATATTGTTAATAAAAATG
Found at i:45720 original size:11 final size:11
Alignment explanation
Indices: 45704--45731 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
45694 TGTGATTGAA
45704 TTTTTTAATAT
1 TTTTTTAATAT
45715 TTTTTTAATAT
1 TTTTTTAATAT
45726 TTTTTT
1 TTTTTT
45732 CATCCAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTAATAT
Found at i:47830 original size:60 final size:60
Alignment explanation
Indices: 47748--47904 Score: 217
Period size: 60 Copynumber: 2.6 Consensus size: 60
47738 AAGATATTAT
* * * * *
47748 TTTTGTTAAATTCATCGATTATTAAAAATTATAAAATAATTTGTTGATTATATTATTTTA
1 TTTTGTTGAGTTCATCGATTATTAAAAATTATAAAATAATCTCTTGATTATATGATTTTA
*
47808 TTTTGTTGAGTTCATCGATTATTAAAAATTATAAAATAATCTCTTGATTATATGGTTTTA
1 TTTTGTTGAGTTCATCGATTATTAAAAATTATAAAATAATCTCTTGATTATATGATTTTA
* **
47868 TTTTGTTGAGTCTC-TCAAAAATTAAAAATTATAAAAT
1 TTTTGTTGAGT-TCATCGATTATTAAAAATTATAAAAT
47905 GATCATCCGA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 85 0.98
61 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.48
Consensus pattern (60 bp):
TTTTGTTGAGTTCATCGATTATTAAAAATTATAAAATAATCTCTTGATTATATGATTTTA
Found at i:61110 original size:36 final size:35
Alignment explanation
Indices: 61039--61163 Score: 196
Period size: 36 Copynumber: 3.5 Consensus size: 35
61029 ATGAACACTC
* * * *
61039 GAATCGAAAGTGCGATACATCCTTCCGTTCAACTT
1 GAATCGGAAGTGCGATGCTTCCTTCCGTTCGACTT
61074 GAATCGGAAGTGCTGATGCTTCCTTCCGTTCGACTT
1 GAATCGGAAGTGC-GATGCTTCCTTCCGTTCGACTT
61110 GAATCGGAAGTGTCGATGCTTCCTTCCGTTCGACTT
1 GAATCGGAAGTG-CGATGCTTCCTTCCGTTCGACTT
61146 GAATCGGAAGTGCGATGC
1 GAATCGGAAGTGCGATGC
61164 ATTCTTTCGT
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
35 18 0.21
36 65 0.77
37 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.30
Consensus pattern (35 bp):
GAATCGGAAGTGCGATGCTTCCTTCCGTTCGACTT
Found at i:64329 original size:5 final size:5
Alignment explanation
Indices: 64321--64345 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
64311 AATTCAATTT
64321 GATTC GATTC GATTC GATTC GATTC
1 GATTC GATTC GATTC GATTC GATTC
64346 TCATAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
GATTC
Found at i:71837 original size:31 final size:31
Alignment explanation
Indices: 71802--71951 Score: 131
Period size: 31 Copynumber: 4.8 Consensus size: 31
71792 TGAACGTTAG
* ** *
71802 ATAAAATATTAATTTAACCCTTAAATTATAT
1 ATAAAATATCAATTTAATGCTTAAATTTTAT
* * *
71833 ATAAAATATCAAATTGATGTTTAAATTTTAT
1 ATAAAATATCAATTTAATGCTTAAATTTTAT
*
71864 ATAAAATATCAATTTAATGCTTAAATTTTAA
1 ATAAAATATCAATTTAATGCTTAAATTTTAT
* * * * * * *
71895 ATAAAAAATTAATTTGATGTTTATACTTTAG
1 ATAAAATATCAATTTAATGCTTAAATTTTAT
**
71926 ATAAAATATTTATTTAAT-CTATAAAT
1 ATAAAATATCAATTTAATGCT-TAAAT
71952 CCAGCTAAAA
Statistics
Matches: 94, Mismatches: 24, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
30 1 0.01
31 93 0.99
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (31 bp):
ATAAAATATCAATTTAATGCTTAAATTTTAT
Found at i:71899 original size:62 final size:61
Alignment explanation
Indices: 71798--71951 Score: 182
Period size: 62 Copynumber: 2.5 Consensus size: 61
71788 TATTTGAACG
* * * *
71798 TTAGATAAAATATTAATTTAACCCTTAAATTATATATAAAATATCAAATTGATGTTTAAATT
1 TTAGATAAAATATTAATTTAA-TCTTAAATTATAAATAAAAAATCAAATTGATGTTTAAACT
* * * * * *
71860 TTATATAAAATATCAATTTAATGCTTAAATTTTAAATAAAAAATTAATTTGATGTTTATACT
1 TTAGATAAAATATTAATTTAAT-CTTAAATTATAAATAAAAAATCAAATTGATGTTTAAACT
*
71922 TTAGATAAAATATTTATTTAATCTATAAAT
1 TTAGATAAAATATTAATTTAATCT-TAAAT
71952 CCAGCTAAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
61 2 0.03
62 75 0.97
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (61 bp):
TTAGATAAAATATTAATTTAATCTTAAATTATAAATAAAAAATCAAATTGATGTTTAAACT
Found at i:90006 original size:5 final size:5
Alignment explanation
Indices: 89995--90043 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
89985 ATTGATAATA
* * *
89995 TAAAT TAGAT TAAAT TAAAT TAAAT TAAA- TATAT ATAAAT TTAAT TAAA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT -TAAAT TAAAT TAAA
90044 AAAAATGTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
4 3 0.08
5 29 0.81
6 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (5 bp):
TAAAT
Found at i:97083 original size:30 final size:31
Alignment explanation
Indices: 97029--97090 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
97019 TTCTCTCCGT
97029 GATGTTCGACGCCAATCGAATCGACATGAAA
1 GATGTTCGACGCCAATCGAATCGACATGAAA
* *
97060 GATGTTC-ACGCTAATCGACTCGACATGAAA
1 GATGTTCGACGCCAATCGAATCGACATGAAA
97090 G
1 G
97091 GCGAGGCGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (31 bp):
GATGTTCGACGCCAATCGAATCGACATGAAA
Found at i:98641 original size:27 final size:27
Alignment explanation
Indices: 98603--98669 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
98593 GATAATGACT
*
98603 CTGAATCATTCAGAATATACTTCTGTG
1 CTGAATCATTCAAAATATACTTCTGTG
*
98630 CTGAATCATTCAAAATATACTTTTGTG
1 CTGAATCATTCAAAATATACTTCTGTG
98657 CTGAATCATTCAA
1 CTGAATCATTCAA
98670 TACTGTTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (27 bp):
CTGAATCATTCAAAATATACTTCTGTG
Found at i:98681 original size:23 final size:25
Alignment explanation
Indices: 98603--98687 Score: 95
Period size: 27 Copynumber: 3.3 Consensus size: 25
98593 GATAATGACT
*
98603 CTGAATCATTCAGAATATACTTCTGTG
1 CTGAATCATTC--AATATACTTTTGTG
98630 CTGAATCATTCAAAATATACTTTTGTG
1 CTGAATCATTC--AATATACTTTTGTG
98657 CTGAATCATTC-A-ATACTGTTT-TG
1 CTGAATCATTCAATATACT-TTTGTG
98680 CTGAATCA
1 CTGAATCA
98688 GTCAGTGCTG
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
23 15 0.27
24 4 0.07
27 36 0.65
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (25 bp):
CTGAATCATTCAATATACTTTTGTG
Found at i:98698 original size:15 final size:15
Alignment explanation
Indices: 98678--98707 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
98668 AATACTGTTT
98678 TGCTGAATCAGTCAG
1 TGCTGAATCAGTCAG
*
98693 TGCTGAATCATTCAG
1 TGCTGAATCAGTCAG
98708 AGGTACGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (15 bp):
TGCTGAATCAGTCAG
Found at i:104864 original size:19 final size:19
Alignment explanation
Indices: 104840--104880 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
104830 CGTTTATGTT
*
104840 TTAGTCACTAAACTTTGAA
1 TTAGTCACCAAACTTTGAA
104859 TTAGTCACCAAACTTTGAA
1 TTAGTCACCAAACTTTGAA
104878 TTA
1 TTA
104881 ATTATGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (19 bp):
TTAGTCACCAAACTTTGAA
Found at i:105974 original size:3 final size:3
Alignment explanation
Indices: 105966--105999 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
105956 GTTTGGACAT
105966 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
106000 AAAATAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:123250 original size:24 final size:24
Alignment explanation
Indices: 123218--123271 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
123208 ACAAGAATCT
123218 GATCCTGGTCCAAGATCTTATGAA
1 GATCCTGGTCCAAGATCTTATGAA
*
123242 GATCCTGGTCCAAGATCTTGTGAA
1 GATCCTGGTCCAAGATCTTATGAA
123266 GATCCT
1 GATCCT
123272 TCAGGTAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (24 bp):
GATCCTGGTCCAAGATCTTATGAA
Found at i:124566 original size:65 final size:67
Alignment explanation
Indices: 124435--124567 Score: 252
Period size: 65 Copynumber: 2.0 Consensus size: 67
124425 ACCTATGAAT
124435 TCAACAACAAAATTAGGCACTAAAGAAAATTATGCACCGGTGGATAAAGGCAGATACCAAAGGCT
1 TCAACAACAAAATTAGGCACTAAAGAAAATTATGCACCGGTGGATAAAGGCAGATACCAAAGGCT
124500 AC
66 AC
124502 TCAACAACAAAATTAGGCACTAAAGAAAA-TATGCA-CGGTGGATAAAGGCAGATACCAAAGGCT
1 TCAACAACAAAATTAGGCACTAAAGAAAATTATGCACCGGTGGATAAAGGCAGATACCAAAGGCT
124565 AC
66 AC
124567 T
1 T
124568 GGGTAAACTA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
65 31 0.47
66 6 0.09
67 29 0.44
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.17
Consensus pattern (67 bp):
TCAACAACAAAATTAGGCACTAAAGAAAATTATGCACCGGTGGATAAAGGCAGATACCAAAGGCT
AC
Found at i:126329 original size:20 final size:20
Alignment explanation
Indices: 126304--126341 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
126294 TTCGAAATGT
126304 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
126324 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
126342 CCTTCAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:126985 original size:32 final size:32
Alignment explanation
Indices: 126950--127100 Score: 205
Period size: 32 Copynumber: 4.7 Consensus size: 32
126940 AAGGTGACAC
* *
126950 TTGGGTAGGCTCTGAGGCCACAAGGTATTTCC-
1 TTGGGTAGGCTCTAAGGCCCCAAGGTA-TTCCT
126982 TTGGGTAGGCTCTAAGGCCCCAAGGTATTCCT
1 TTGGGTAGGCTCTAAGGCCCCAAGGTATTCCT
127014 TTGGGTAGGCTCTAAGGCCCCAAGGTATTCCT
1 TTGGGTAGGCTCTAAGGCCCCAAGGTATTCCT
* * * ** *
127046 TTGGGTAGGCTCTTATGCCCCAAAGTACACTT
1 TTGGGTAGGCTCTAAGGCCCCAAGGTATTCCT
*
127078 TTGGGTAGGCTCTCAGGCCCCAA
1 TTGGGTAGGCTCTAAGGCCCCAA
127101 AATAATCCCT
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 4 0.04
32 104 0.96
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (32 bp):
TTGGGTAGGCTCTAAGGCCCCAAGGTATTCCT
Found at i:128736 original size:69 final size:68
Alignment explanation
Indices: 128662--128797 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 68
128652 TAAGATTTGG
* *
128662 TTGGATCAAGTACAAAATTATAATTAAATATTAAGAGGTGTTAAATTGTATAATTTTTAAAGTTA
1 TTGGATCAAGTACAAAATTATAATTAAATATTAAGAGGTGTTAAATTGTATAA-CTTTAAAATTA
128727 TGGA
65 TGGA
* *
128731 TTGGATTAAGTACAAAATTATGATTAAATATTAAGAGGTGTTAAATTGTATAACTTTAAAATTAT
1 TTGGATCAAGTACAAAATTATAATTAAATATTAAGAGGTGTTAAATTGTATAACTTTAAAATTAT
128796 GG
66 GG
128798 GGCTTAACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 12 0.19
69 51 0.81
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (68 bp):
TTGGATCAAGTACAAAATTATAATTAAATATTAAGAGGTGTTAAATTGTATAACTTTAAAATTAT
GGA
Found at i:141378 original size:25 final size:25
Alignment explanation
Indices: 141350--141399 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
141340 CTTTAACACT
141350 TCTCCCATTTATCATTTTTAAAAAC
1 TCTCCCATTTATCATTTTTAAAAAC
141375 TCTCCCATTTATCATTTTTAAAAAC
1 TCTCCCATTTATCATTTTTAAAAAC
141400 ACACACTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (25 bp):
TCTCCCATTTATCATTTTTAAAAAC
Found at i:141685 original size:17 final size:17
Alignment explanation
Indices: 141663--141696 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
141653 TCCATAAATC
*
141663 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
*
141680 CAAAATCAAACATTCCA
1 CAAAATCAAACAATCCA
141697 AAATATTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:143691 original size:21 final size:21
Alignment explanation
Indices: 143665--143704 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
143655 CAGAACCCCA
*
143665 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
143686 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
143705 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:143739 original size:20 final size:21
Alignment explanation
Indices: 143685--143747 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
143675 GATTCCCCTG
143685 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
143709 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
143729 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
143748 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:147598 original size:22 final size:21
Alignment explanation
Indices: 147556--147595 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
147546 GAGTTTGTTT
*
147556 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
147577 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
147596 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:153921 original size:21 final size:21
Alignment explanation
Indices: 153891--153938 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
153881 TAATTTTCAA
*
153891 ACATTATTGCA-CATAATTTTG
1 ACATTGTTGCATC-TAATTTTG
153912 ACATTGTTGCATCTAATTTTG
1 ACATTGTTGCATCTAATTTTG
153933 ACATTG
1 ACATTG
153939 CAATATTAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (21 bp):
ACATTGTTGCATCTAATTTTG
Found at i:155237 original size:20 final size:20
Alignment explanation
Indices: 155212--155249 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
155202 ATCATATTCT
155212 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
155232 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
155250 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:160539 original size:25 final size:23
Alignment explanation
Indices: 160506--160554 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
160496 TTTTAAAATA
*
160506 TTTAAAATATATTTATTAATATTTT
1 TTTAAAATATA-ATATT-ATATTTT
*
160531 TTTATAATATAATATTATATTTT
1 TTTAAAATATAATATTATATTTT
160554 T
1 T
160555 AATATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 4 0.18
25 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTAAAATATAATATTATATTTT
Found at i:160563 original size:22 final size:24
Alignment explanation
Indices: 160506--160566 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 24
160496 TTTTAAAATA
*
160506 TTTAA-AATATATTTATTAATATTT
1 TTTAATAATATA-ATATTAATATTT
*
160530 TTTTATAATATAATATT-ATA-TT
1 TTTAATAATATAATATTAATATTT
*
160552 TTTAATATTATAATA
1 TTTAATAATATAATA
160567 AAATAATCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 15 0.47
23 3 0.09
24 8 0.25
25 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTAATAATATAATATTAATATTT
Found at i:160735 original size:8 final size:8
Alignment explanation
Indices: 160724--160751 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
160714 TTTAATATTT
160724 ATATAATA
1 ATATAATA
160732 ATATAATA
1 ATATAATA
160740 ATATAATA
1 ATATAATA
160748 ATAT
1 ATAT
160752 TTTAATAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:160757 original size:16 final size:16
Alignment explanation
Indices: 160716--160758 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
160706 TTTATATATT
160716 TAATA-TTT-ATATAA
1 TAATATTTTAATATAA
**
160730 TAATATAATAATATAA
1 TAATATTTTAATATAA
160746 TAATATTTTAATA
1 TAATATTTTAATA
160759 ATGATATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 5 0.22
15 1 0.04
16 17 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATATTTTAATATAA
Found at i:161084 original size:14 final size:14
Alignment explanation
Indices: 161065--161097 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
161055 TAAATATTAT
*
161065 AAAATATTTTTCAG
1 AAAATATTTTTCAA
161079 AAAATATTTTTCAA
1 AAAATATTTTTCAA
161093 AAAAT
1 AAAAT
161098 CTAATGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (14 bp):
AAAATATTTTTCAA
Found at i:176122 original size:64 final size:63
Alignment explanation
Indices: 175968--176109 Score: 148
Period size: 64 Copynumber: 2.2 Consensus size: 63
175958 TCTGGGTTGT
* * *
175968 GTGCATCGATGCACTCTCA-AATAA-ACAAACATCAAATGCAATTAATGCATCGATGCATAAGGA
1 GTGCATCGATGCAC-CCCATAA-AATGCAAACATCAAATGCAATTAATGCACCGATGCATAAGGA
* * * *
176031 GTGCATCGATGCATCCCCTTAAAATGCAAACATCGAATGTC-ATTTATGCACCGATGCA-CAGGT
1 GTGCATCGATGCA-CCCCATAAAATGCAAACATCAAATG-CAATTAATGCACCGATGCATAAGG-
176094 A
63 A
176095 GTGCATCGATGCACC
1 GTGCATCGATGCACC
176110 GATAAGGAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
63 22 0.33
64 44 0.66
65 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (63 bp):
GTGCATCGATGCACCCCATAAAATGCAAACATCAAATGCAATTAATGCACCGATGCATAAGGA
Found at i:176792 original size:23 final size:23
Alignment explanation
Indices: 176748--176792 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
176738 ATTATTATAT
*
176748 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
176771 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
176793 AGTCGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:184984 original size:35 final size:35
Alignment explanation
Indices: 184938--185008 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
184928 TAACTGTGCA
184938 TATCAATTTGAGACAAAACCAATTGTTTTTAGATC
1 TATCAATTTGAGACAAAACCAATTGTTTTTAGATC
184973 TATCAATTTGAGACAAAACCAATTGTTTTTAGATC
1 TATCAATTTGAGACAAAACCAATTGTTTTTAGATC
185008 T
1 T
185009 CTGTTCTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (35 bp):
TATCAATTTGAGACAAAACCAATTGTTTTTAGATC
Found at i:197188 original size:20 final size:20
Alignment explanation
Indices: 197160--197218 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
197150 ATCAAACTAT
*
197160 TCCTAAAATTTTATAAATTC
1 TCCTCAAATTTTATAAATTC
197180 TCCTCAAATTTTATAAATTC
1 TCCTCAAATTTTATAAATTC
197200 TCCTCAAATTTTATAAATT
1 TCCTCAAATTTTATAAATT
197219 AGTACTACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (20 bp):
TCCTCAAATTTTATAAATTC
Found at i:198400 original size:13 final size:14
Alignment explanation
Indices: 198369--198398 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
198359 CTTTATCTCT
*
198369 TTTAATTTTTCTAA
1 TTTAATTTTTATAA
198383 TTTAATTTTTATAA
1 TTTAATTTTTATAA
198397 TT
1 TT
198399 AAGTCTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTTTTATAA
Found at i:198670 original size:21 final size:21
Alignment explanation
Indices: 198644--198707 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
198634 GTTTCCAAAT
* *
198644 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTAGACTA
*
198665 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTAGACTA
198686 TCGCAATGCGAACTTAGACTA
1 TCGCAATGCGAACTTAGACTA
198707 T
1 T
198708 AGTCGAAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTAGACTA
Found at i:199007 original size:42 final size:42
Alignment explanation
Indices: 198948--199089 Score: 248
Period size: 42 Copynumber: 3.4 Consensus size: 42
198938 CGTTGCGATT
198948 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* *
198990 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACACGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* *
199032 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAG
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
199074 TTGGACTATCGCAACG
1 TTGGACTATCGCAACG
199090 CGAACTTCGA
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.20
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:199106 original size:42 final size:41
Alignment explanation
Indices: 198948--199141 Score: 223
Period size: 42 Copynumber: 4.6 Consensus size: 41
198938 CGTTGCGATT
198948 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* *
198990 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACACGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* *
199032 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAG
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* *
199074 TTGGACTATCGCAACGCGAACTTCGACT-ATCGCAA--CGAAC
1 TTGGACTATCGCAA--CGAACTTGGAATAATCGCAACGCGAAC
*
199114 TTGGAATAAATCGCAACGCGAACTTGGA
1 TTGGACT--ATCGCAA--CGAACTTGGA
199142 CTGTCGCAAT
Statistics
Matches: 136, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
40 10 0.07
42 116 0.85
44 10 0.07
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (41 bp):
TTGGACTATCGCAACGAACTTGGAATAATCGCAACGCGAAC
Found at i:199106 original size:84 final size:83
Alignment explanation
Indices: 198951--199109 Score: 248
Period size: 84 Copynumber: 1.9 Consensus size: 83
198941 TGCGATTTTG
* *
198951 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAACTTCGAAT
199016 AAATCGCAACACGAACTTC
66 -AATCGCAACACGAACTTC
*
199035 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAGTTGGACTATCGCAACGCGAACTTCGA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA--CGAACTTCGA
*
199100 CT-ATCGCAAC
64 ATAATCGCAAC
199110 GAACTTGGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
84 60 0.87
86 9 0.13
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (83 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAACTTCGAAT
AATCGCAACACGAACTTC
Found at i:199148 original size:21 final size:21
Alignment explanation
Indices: 198948--199150 Score: 188
Period size: 21 Copynumber: 9.7 Consensus size: 21
198938 CGTTGCGATT
198948 TTGGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
198967 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
198990 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
199009 TTGGAATAAATCGCAACACGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
199032 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
* *
199051 TTGGAATAAATCGCAACGCGAAG
1 TTGGACT--ATCGCAACGCGAAC
199074 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
199095 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
199114 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
199137 TTGGACTGTCGCAA
1 TTGGACTATCGCAA
199151 TGTGAATATG
Statistics
Matches: 151, Mismatches: 17, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
19 36 0.24
21 74 0.49
23 41 0.27
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.20
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:206752 original size:2 final size:2
Alignment explanation
Indices: 206747--206777 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
206737 ACACACACAG
206747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
206778 CCAGATTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:208658 original size:5 final size:5
Alignment explanation
Indices: 208648--208677 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
208638 AAATAAATCA
208648 AAAAT AAAAT AAAAT AAAAT AAAAT GAAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAA
208678 ACGGGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:210048 original size:18 final size:18
Alignment explanation
Indices: 210002--210051 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
209992 CCTGGACCAC
*
210002 AAAACATAAT-AAATGAA
1 AAAAAATAATAAAATGAA
**
210019 ATTAAATGAATAAAATGAA
1 AAAAAAT-AATAAAATGAA
210038 AAAAAATAATAAAA
1 AAAAAATAATAAAA
210052 ATAAAAATAC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 4 0.15
18 10 0.38
19 12 0.46
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAAAATAATAAAATGAA
Found at i:210052 original size:19 final size:20
Alignment explanation
Indices: 210007--210058 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
209997 ACCACAAAAC
**
210007 ATAATAAATGAAATTAAATGA
1 ATAA-AAATGAAAAAAAATGA
210028 AT-AAAATGAAAAAAAAT-A
1 ATAAAAATGAAAAAAAATGA
210046 ATAAAAAT-AAAAA
1 ATAAAAATGAAAAA
210059 TACTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 8 0.29
19 17 0.61
20 1 0.04
21 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (20 bp):
ATAAAAATGAAAAAAAATGA
Found at i:210057 original size:18 final size:18
Alignment explanation
Indices: 210030--210072 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
210020 TTAAATGAAT
210030 AAAATGAAAAAAAATAATA
1 AAAAT-AAAAAAAATAATA
* *
210049 AAAATAAAAATACTAATA
1 AAAATAAAAAAAATAATA
*
210067 ATAATA
1 AAAATA
210073 TAGACTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAATAAAAAAAATAATA
Found at i:210190 original size:32 final size:32
Alignment explanation
Indices: 210154--210221 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
210144 ACTATATACC
210154 ATAT-AGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
210186 ATATAAGTTTTCCAAAATATTTTTAAAACTAT
1 ATATAAGTTTTCAAAAATATTTTTAAAAATAT
210218 ATAT
1 ATAT
210222 TATATAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (32 bp):
ATATAAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:210239 original size:37 final size:37
Alignment explanation
Indices: 210181--210382 Score: 111
Period size: 35 Copynumber: 5.5 Consensus size: 37
210171 GATTTTAAAA
* * *
210181 ATATTATATAAGTTTTCCAAAATATTTTTAAAACTAT
1 ATATTATATAAATTTTTCAAAATAGTTTTAAAACTAT
*
210218 ATATTATATAAATTTTTCAAAA-ATGTTTTTTTTAAACTAT
1 ATATTATATAAATTTTTCAAAATA-G---TTTTAAAACTAT
** * *
210258 GCA-T-TAT--A-TTTTCAAAAT-GATTTCAAAAATAT
1 ATATTATATAAATTTTTCAAAATAG-TTTTAAAACTAT
*
210290 ATGTTATAT--ATTTTTCAAAAT-GTTTTAAAACTTAT
1 ATATTATATAAATTTTTCAAAATAGTTTTAAAAC-TAT
* * **
210325 ATATTGTATATAAGTTTTCAAAA-ACGTTTTAAAAAAACT
1 ATATTATATA-AATTTTTCAAAATA-GTTTTAAAACTA-T
*
210364 ATATTATATATATATTTTC
1 ATATTATATAAAT-TTTTC
210383 GGAAACCGTT
Statistics
Matches: 126, Mismatches: 23, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
32 9 0.07
33 1 0.01
34 12 0.10
35 30 0.24
36 2 0.02
37 20 0.16
38 15 0.12
39 25 0.20
40 12 0.10
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (37 bp):
ATATTATATAAATTTTTCAAAATAGTTTTAAAACTAT
Found at i:210327 original size:107 final size:108
Alignment explanation
Indices: 210155--210354 Score: 266
Period size: 107 Copynumber: 1.9 Consensus size: 108
210145 CTATATACCA
* *
210155 TATAGTTTTCAAAAATGATTTTAAAAATATTATATAAGTTTTCCAAAATATTTTTAAAACTATAT
1 TATAGTTTTCAAAAATGATTTCAAAAATATTATATAAGTTTTCCAAAATAGTTTTAAAACTATAT
* *
210220 ATTATATA-AATTTTTCAAAAATGTTTTTTTTAAACTATGCAT
66 ATTATATATAAGTTTTCAAAAACGTTTTTTTTAAACTATGCAT
* *
210262 TATA-TTTTC-AAAATGATTTCAAAAATATATGTTATATA-TTTTTCAAAAT-GTTTTAAAACTT
1 TATAGTTTTCAAAAATGATTTCAAAAATAT-T-ATATA-AGTTTTCCAAAATAGTTTTAAAAC-T
*
210323 ATATATTGTATATAAGTTTTCAAAAACGTTTT
62 ATATATTATATATAAGTTTTCAAAAACGTTTT
210355 AAAAAAACTA
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
105 18 0.22
106 15 0.19
107 30 0.37
108 18 0.22
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.47
Consensus pattern (108 bp):
TATAGTTTTCAAAAATGATTTCAAAAATATTATATAAGTTTTCCAAAATAGTTTTAAAACTATAT
ATTATATATAAGTTTTCAAAAACGTTTTTTTTAAACTATGCAT
Found at i:210382 original size:39 final size:36
Alignment explanation
Indices: 210262--210382 Score: 104
Period size: 39 Copynumber: 3.2 Consensus size: 36
210252 AACTATGCAT
* * *
210262 TATATTTTCAAAATGATTT-CAAAAATATATGTTATA
1 TATATTTTCAAAACGTTTTAAAAAAATATAT-TTATA
* **
210298 TAT-TTTTCAAAATGTTTTAAAACTTATATATTGTATA
1 TATATTTTCAAAACGTTTTAAAA-AAATATATT-TATA
210335 TA-AGTTTTCAAAAACGTTTTAAAAAAACTATATTATATA
1 TATA-TTTTC-AAAACGTTTTAAAAAAA-TATATT-TATA
210374 TATATTTTC
1 TATATTTTC
210383 GGAAACCGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
35 14 0.20
36 6 0.09
37 12 0.17
38 6 0.09
39 30 0.43
40 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (36 bp):
TATATTTTCAAAACGTTTTAAAAAAATATATTTATA
Found at i:211274 original size:80 final size:80
Alignment explanation
Indices: 211070--211347 Score: 394
Period size: 80 Copynumber: 3.4 Consensus size: 80
211060 GTTTGCCTCT
* * * * * *
211070 GAGCTGAGTGTAATCGAACTAGAAGGTCTTCGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-T---TTGGCAGATAGCCCTTCTCGACTTAAGCTATG
*
211135 CTGCAAATGATGTGCCCTCG
62 CTGCAAATGATGTG-CCTTG
* * *
211155 AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
*
211220 AAATGATATGCCTTG
66 AAATGATGTGCCTTG
* *
211235 GAGCTGAGCGGAGTCGAACTCGAAGGTCTTTGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
211300 AAATGATGTGCCTTG
66 AAATGATGTGCCTTG
211315 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
211348 TCGGCACGAT
Statistics
Matches: 179, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
80 110 0.61
81 42 0.23
84 1 0.01
85 26 0.15
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (80 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
AAATGATGTGCCTTG
Found at i:211553 original size:94 final size:94
Alignment explanation
Indices: 211360--211947 Score: 1061
Period size: 94 Copynumber: 6.3 Consensus size: 94
211350 GGCACGATTC
* **
211360 CCTTCGTCGTGAAGTTGAAACCGTGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
1 CCTTCGTTGTGAAGTTGAAATTG-GGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
211425 GTTGAACTTGCGTTGTCT-GAGTCCAATAT
65 GTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
211454 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAG
1 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
211519 TTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTGAACTTGCGTTGTCTGGAGTCCAATAT
*
211548 CCTTCGTTGTGAAGTTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
1 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
211613 TTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTGAACTTGCGTTGTCTGGAGTCCAATAT
*
211642 CCTTCGTTGCGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
1 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
211707 TTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
211736 CCTTCGTTGCGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCTTCGTGAAG
1 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
211801 TTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
211830 CCTTCTTTGCGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
1 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
211895 TTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTGAACTTGCGTTGTCTGGAGTCCAATAT
*
211924 CCTTCGCTGTGAAGTTGAAATTGG
1 CCTTCGTTGTGAAGTTGAAATTGG
211948 CTCTGAAATT
Statistics
Matches: 479, Mismatches: 14, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
93 58 0.12
94 421 0.88
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (94 bp):
CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
TTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:217652 original size:18 final size:18
Alignment explanation
Indices: 217626--217660 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
217616 TCGAAAGGAC
*
217626 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
217644 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
217661 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:223056 original size:18 final size:18
Alignment explanation
Indices: 223030--223064 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
223020 TCGAAAGGAC
*
223030 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
223048 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
223065 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:227651 original size:19 final size:19
Alignment explanation
Indices: 227623--227666 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
227613 CCACAAAACA
**
227623 GAAT-AAATGAAATTAAAT
1 GAATAAAATGAAAAGAAAT
227641 GAATAAAATGAAAAGAAAT
1 GAATAAAATGAAAAGAAAT
227660 -AATAAAA
1 GAATAAAA
227667 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.20
Consensus pattern (19 bp):
GAATAAAATGAAAAGAAAT
Found at i:227667 original size:19 final size:18
Alignment explanation
Indices: 227627--227682 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
227617 AAAACAGAAT
*
227627 AAATGAAATTAAATGAAT-A
1 AAATGAAA-AAAAT-AATAA
227646 AAATGAAAAGAAATAATAA
1 AAATGAAAA-AAATAATAA
227665 AAAT-AAAAATAATAATAA
1 AAATGAAAAA-AATAATAA
227683 TAATATAGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
17 1 0.03
18 15 0.45
19 17 0.52
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATGAAAAAAATAATAA
Found at i:227674 original size:15 final size:15
Alignment explanation
Indices: 227656--227685 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
227646 AAATGAAAAG
227656 AAATAATAAAAATAA
1 AAATAATAAAAATAA
*
227671 AAATAATAATAATAA
1 AAATAATAAAAATAA
227686 TATAGACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAATAAAAATAA
Found at i:227856 original size:37 final size:37
Alignment explanation
Indices: 227798--227997 Score: 118
Period size: 35 Copynumber: 5.5 Consensus size: 37
227788 GATTTTAAAA
* * *
227798 ATATTATATAAGTTTTCCAAAATATTTTTAAAACTAT
1 ATATTATATAAATTTTTCAAAATAGTTTTAAAACTAT
*
227835 ATATTATATAAATTTTTCAAAA-ATGTTTTTTTAAACT-T
1 ATATTATATAAATTTTTCAAAATA-G--TTTTAAAACTAT
* * * *
227873 -TA-CAT-TATA-TTTTCAAAAT-GATTTCAAAAATAT
1 ATATTATATAAATTTTTCAAAATAG-TTTTAAAACTAT
*
227906 ATGTTATAT-AA-TTTTCAAAAT-GTTTTAAAACTTAT
1 ATATTATATAAATTTTTCAAAATAGTTTTAAAAC-TAT
* * *
227941 ATATTGTATATAAGTTTTCAAAA-ACGTTTTAAAA-AACT
1 ATATTATATA-AATTTTTCAAAATA-GTTTTAAAACTA-T
*
227979 ATATTATATATATATTTTC
1 ATATTATATAAAT-TTTTC
227998 GGAAACCGTT
Statistics
Matches: 126, Mismatches: 21, Indels: 31
0.71 0.12 0.17
Matches are distributed among these distances:
32 7 0.06
33 2 0.02
34 17 0.13
35 27 0.21
36 4 0.03
37 26 0.21
38 25 0.20
39 18 0.14
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (37 bp):
ATATTATATAAATTTTTCAAAATAGTTTTAAAACTAT
Found at i:227880 original size:39 final size:37
Alignment explanation
Indices: 227753--227964 Score: 112
Period size: 33 Copynumber: 5.9 Consensus size: 37
227743 TTTAAAAACG
* * **
227753 TTTTCAAAACTATATACCATAT-AGTTTTCAAAAATGA
1 TTTTTAAAACTATACATTATATAAGTTTTCAAAAAT-A
*
227790 -TTTTAAAA--AT--ATTATATAAGTTTTCCAAAATA
1 TTTTTAAAACTATACATTATATAAGTTTTCAAAAATA
* * *
227822 TTTTTAAAACTATATATTATATAAATTTTTCAAAAATGT
1 TTTTTAAAACTATACATTATAT-AAGTTTTCAAAAAT-A
* *
227861 TTTTTTAAACTTTACA-T-TAT-A-TTTTC-AAAATGA
1 TTTTTAAAACTATACATTATATAAGTTTTCAAAAAT-A
* * **
227894 -TTTCAAAAATATATGTTATATAA-TTTTC-AAAAT-
1 TTTTTAAAACTATACATTATATAAGTTTTCAAAAATA
* *
227927 GTTTTAAAACTTATATATTGTATATAAGTTTTCAAAAA
1 TTTTTAAAAC-TATACA-T-TATATAAGTTTTCAAAAA
227965 CGTTTTAAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 32
0.73 0.11 0.17
Matches are distributed among these distances:
32 15 0.11
33 27 0.20
34 17 0.12
35 19 0.14
36 8 0.06
37 17 0.12
38 18 0.13
39 17 0.12
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTTTAAAACTATACATTATATAAGTTTTCAAAAATA
Found at i:227890 original size:71 final size:70
Alignment explanation
Indices: 227691--227931 Score: 194
Period size: 71 Copynumber: 3.5 Consensus size: 70
227681 AATAATATAG
* * * * * * **
227691 ACTATATAATATATATATATCTCAAAAAAT-ATTTTTTAAACTATATATTATA-TTTAAAAACGT
1 ACTATATATTATATA-ATTTTTC-AAAAATGTTTTTTTAAACTTTATATTATATTTTCAAAATAT
227754 TTTCAAA
64 TTTCAAA
** * * * *
227761 ACTATATACCATAT-AGTTTTCAAAAATG-ATTTTAAAAATATTATA-TA-AGTTTTCCAAAATA
1 ACTATATATTATATAATTTTTCAAAAATGTTTTTTTAAACT-TTATATTATA-TTTT-CAAAATA
*
227822 TTTTTAAA
63 TTTTCAAA
*
227830 ACTATATATTATATAAATTTTTCAAAAATGTTTTTTTAAACTTTACATTATATTTTCAAAATGA-
1 ACTATATATTATAT-AATTTTTCAAAAATGTTTTTTTAAACTTTATATTATATTTTCAAAAT-AT
227894 TTTCAAA
64 TTTCAAA
* *
227901 AATATATGTTATATAA-TTTTC-AAAATGTTTT
1 ACTATATATTATATAATTTTTCAAAAATGTTTT
227932 AAAACTTATA
Statistics
Matches: 137, Mismatches: 23, Indels: 24
0.74 0.12 0.13
Matches are distributed among these distances:
66 1 0.01
67 16 0.12
68 21 0.15
69 28 0.20
70 14 0.10
71 41 0.30
72 15 0.11
73 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (70 bp):
ACTATATATTATATAATTTTTCAAAAATGTTTTTTTAAACTTTATATTATATTTTCAAAATATTT
TCAAA
Found at i:227924 original size:35 final size:35
Alignment explanation
Indices: 227881--227997 Score: 103
Period size: 38 Copynumber: 3.2 Consensus size: 35
227871 TTTACATTAT
227881 ATTTTCAAAATGATTTCAAAA-ATATA-TGTTATATA
1 ATTTTCAAAATG-TTTCAAAATATATATTG-TATATA
*
227916 ATTTTCAAAATGTTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAATGTTTCAAAA--TATATATTGTATATA
* * * *
227953 AGTTTTCAAAAACGTTTTAAAAAACTATATTATATATA
1 A-TTTTC-AAAATGTTTCAAAATA-TATATTGTATATA
227991 TATTTTC
1 -ATTTTC
227998 GGAAACCGTT
Statistics
Matches: 70, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
34 7 0.10
35 12 0.17
37 13 0.19
38 24 0.34
39 14 0.20
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (35 bp):
ATTTTCAAAATGTTTCAAAATATATATTGTATATA
Found at i:227970 original size:39 final size:37
Alignment explanation
Indices: 227902--227974 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
227892 GATTTCAAAA
*
227902 ATATATGTTATATAATTTTCAAAATGTTTTAAAACTT
1 ATATATGTTATATAATTTTCAAAACGTTTTAAAACTT
227939 ATATAT-TGTATATAAGTTTTCAAAAACGTTTTAAAA
1 ATATATGT-TATATAA-TTTTC-AAAACGTTTTAAAA
227975 AACTATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 1 0.03
37 13 0.41
38 5 0.16
39 13 0.41
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
ATATATGTTATATAATTTTCAAAACGTTTTAAAACTT
Found at i:231426 original size:22 final size:22
Alignment explanation
Indices: 231379--231450 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
231369 AAATTTAAAT
*
231379 TAGGTATCGATA-CCTAG-GGA
1 TAGGTATCGGTACCCTAGAGGA
*
231399 -GGGTATCGGTACCCTAGAGGA
1 TAGGTATCGGTACCCTAGAGGA
231420 TAGGTATCGGTACCCTAGAGGA
1 TAGGTATCGGTACCCTAGAGGA
*
231442 GAGGTATCG
1 TAGGTATCG
231451 ATACTGTGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.20
20 5 0.11
21 3 0.07
22 28 0.62
ACGTcount: A:0.26, C:0.17, G:0.35, T:0.22
Consensus pattern (22 bp):
TAGGTATCGGTACCCTAGAGGA
Found at i:241176 original size:2 final size:2
Alignment explanation
Indices: 241165--241194 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
241155 TACAAAATTG
241165 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
241195 CAAAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:246998 original size:30 final size:30
Alignment explanation
Indices: 246964--247024 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
246954 ACACTTGCCT
246964 TGATTGAATAGAGAATCAGTCCTTGGCATG
1 TGATTGAATAGAGAATCAGTCCTTGGCATG
246994 TGATTGAATAGAGAATCAGTCCTTGGCATG
1 TGATTGAATAGAGAATCAGTCCTTGGCATG
247024 T
1 T
247025 TCAGAGCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (30 bp):
TGATTGAATAGAGAATCAGTCCTTGGCATG
Found at i:248258 original size:8 final size:8
Alignment explanation
Indices: 248244--248734 Score: 235
Period size: 8 Copynumber: 61.4 Consensus size: 8
248234 ACAGCAACAA
248244 ATACATAC
1 ATACATAC
*
248252 GTACATAC
1 ATACATAC
**
248260 ATACATGT
1 ATACATAC
*
248268 ATGCATAC
1 ATACATAC
* *
248276 ATGCATGC
1 ATACATAC
*
248284 ATACATGC
1 ATACATAC
*
248292 ATACATGC
1 ATACATAC
*
248300 ATACATGC
1 ATACATAC
*
248308 ATGCATAC
1 ATACATAC
*
248316 ATGCATAC
1 ATACATAC
* *
248324 ATGCATGC
1 ATACATAC
*
248332 ATACATGC
1 ATACATAC
* *
248340 ATGCATGC
1 ATACATAC
248348 ATACATAC
1 ATACATAC
248356 ATACATAC
1 ATACATAC
248364 ATACATAC
1 ATACATAC
248372 ATACATAC
1 ATACATAC
* *
248380 ATGCATGC
1 ATACATAC
248388 ATACATAC
1 ATACATAC
248396 ATACATAC
1 ATACATAC
248404 ATACATAC
1 ATACATAC
248412 ATACATAC
1 ATACATAC
248420 ATACATAC
1 ATACATAC
248428 ATACATAC
1 ATACATAC
* *
248436 ATGCGTAC
1 ATACATAC
* *
248444 ATGCGTAC
1 ATACATAC
* *
248452 ATGCGTAC
1 ATACATAC
* *
248460 ATGCGTAC
1 ATACATAC
* *
248468 ATGCGTAC
1 ATACATAC
* *
248476 ATGCGTAC
1 ATACATAC
* *
248484 ATGCGTAC
1 ATACATAC
* *
248492 ATGCGTAC
1 ATACATAC
* *
248500 ATGCGTAC
1 ATACATAC
* *
248508 ATGCGTAC
1 ATACATAC
* *
248516 ATGCGTAC
1 ATACATAC
* *
248524 ATGCGTAC
1 ATACATAC
* *
248532 ATGCGTAC
1 ATACATAC
* *
248540 ATGCGTAC
1 ATACATAC
* *
248548 ATGCGTAC
1 ATACATAC
* *
248556 ATGCGTAC
1 ATACATAC
* *
248564 ATGCGTAC
1 ATACATAC
* *
248572 ATGCGTAC
1 ATACATAC
248580 ATACATAC
1 ATACATAC
*
248588 ATACGTAC
1 ATACATAC
* *
248596 ATGCGTAC
1 ATACATAC
** *
248604 ACGCGTAC
1 ATACATAC
*
248612 ATACGTAC
1 ATACATAC
* *
248620 ATGCGTAC
1 ATACATAC
** *
248628 ACGCGTAC
1 ATACATAC
* *
248636 ATGCGTAC
1 ATACATAC
**
248644 ACGCATAC
1 ATACATAC
*
248652 ATACGTAC
1 ATACATAC
* *
248660 ATGCGTAC
1 ATACATAC
* * *
248668 ATGCGTAT
1 ATACATAC
*
248676 ATACGTAC
1 ATACATAC
*
248684 ATGCATAC
1 ATACATAC
*
248692 ATGCATAC
1 ATACATAC
* *
248700 TTACGTAC
1 ATACATAC
*
248708 ATACGTAC
1 ATACATAC
*
248716 ATACGTAC
1 ATACATAC
248724 ATACATAC
1 ATACATAC
248732 ATA
1 ATA
248735 GAGCTGTCCT
Statistics
Matches: 435, Mismatches: 48, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 435 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (8 bp):
ATACATAC
Found at i:248261 original size:12 final size:12
Alignment explanation
Indices: 248244--248734 Score: 235
Period size: 12 Copynumber: 40.9 Consensus size: 12
248234 ACAGCAACAA
*
248244 ATACATACGTAC
1 ATACATACATAC
**
248256 ATACATACATGT
1 ATACATACATAC
* *
248268 ATGCATACATGC
1 ATACATACATAC
* *
248280 ATGCATACATGC
1 ATACATACATAC
*
248292 ATACATGCATAC
1 ATACATACATAC
* *
248304 ATGCATGCATAC
1 ATACATACATAC
* *
248316 ATGCATACATGC
1 ATACATACATAC
* *
248328 ATGCATACATGC
1 ATACATACATAC
* *
248340 ATGCATGCATAC
1 ATACATACATAC
248352 ATACATACATAC
1 ATACATACATAC
248364 ATACATACATAC
1 ATACATACATAC
* *
248376 ATACATGCATGC
1 ATACATACATAC
248388 ATACATACATAC
1 ATACATACATAC
248400 ATACATACATAC
1 ATACATACATAC
248412 ATACATACATAC
1 ATACATACATAC
248424 ATACATACATAC
1 ATACATACATAC
* * *
248436 ATGCGTACATGC
1 ATACATACATAC
* * *
248448 GTACATGCGTAC
1 ATACATACATAC
* * *
248460 ATGCGTACATGC
1 ATACATACATAC
* * *
248472 GTACATGCGTAC
1 ATACATACATAC
* * *
248484 ATGCGTACATGC
1 ATACATACATAC
* * *
248496 GTACATGCGTAC
1 ATACATACATAC
* * *
248508 ATGCGTACATGC
1 ATACATACATAC
* * *
248520 GTACATGCGTAC
1 ATACATACATAC
* * *
248532 ATGCGTACATGC
1 ATACATACATAC
* * *
248544 GTACATGCGTAC
1 ATACATACATAC
* * *
248556 ATGCGTACATGC
1 ATACATACATAC
* * *
248568 GTACATGCGTAC
1 ATACATACATAC
248580 ATACATACATAC
1 ATACATACATAC
* * *
248592 GTACATGCGTAC
1 ATACATACATAC
** *
248604 ACGCGTACATAC
1 ATACATACATAC
* * *
248616 GTACATGCGTAC
1 ATACATACATAC
** * *
248628 ACGCGTACATGC
1 ATACATACATAC
* **
248640 GTACACGCATAC
1 ATACATACATAC
* *
248652 ATACGTACATGC
1 ATACATACATAC
* * * *
248664 GTACATGCGTAT
1 ATACATACATAC
* *
248676 ATACGTACATGC
1 ATACATACATAC
*
248688 ATACATGCATAC
1 ATACATACATAC
* *
248700 TTACGTACATAC
1 ATACATACATAC
* *
248712 GTACATACGTAC
1 ATACATACATAC
248724 ATACATACATA
1 ATACATACATA
248735 GAGCTGTCCT
Statistics
Matches: 331, Mismatches: 148, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
12 331 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (12 bp):
ATACATACATAC
Found at i:248291 original size:20 final size:20
Alignment explanation
Indices: 248247--248453 Score: 234
Period size: 20 Copynumber: 10.3 Consensus size: 20
248237 GCAACAAATA
*
248247 CATACGTACATACATACATG
1 CATACATACATACATACATG
* * * * *
248267 TATGCATACATGCATGCATA
1 CATACATACATACATACATG
* *
248287 CATGCATACATGCATACATG
1 CATACATACATACATACATG
* *
248307 CATGCATACATGCATACATG
1 CATACATACATACATACATG
* * *
248327 CATGCATACATGCATGCATG
1 CATACATACATACATACATG
*
248347 CATACATACATACATACATA
1 CATACATACATACATACATG
*
248367 CATACATACATACATGCATG
1 CATACATACATACATACATG
*
248387 CATACATACATACATACATA
1 CATACATACATACATACATG
*
248407 CATACATACATACATACATA
1 CATACATACATACATACATG
* *
248427 CATACATACATGCGTACATG
1 CATACATACATACATACATG
*
248447 CGTACAT
1 CATACAT
248454 GCGTACATGC
Statistics
Matches: 165, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 165 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.26
Consensus pattern (20 bp):
CATACATACATACATACATG
Found at i:248469 original size:40 final size:40
Alignment explanation
Indices: 248279--248733 Score: 423
Period size: 40 Copynumber: 11.5 Consensus size: 40
248269 TGCATACATG
* * * * * *
248279 CATGCATACATGCATACATGCATACATGCATGCATACATG
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* * * * * * *
248319 CATACATGCATGCATACATGCATGCATGCATACATACATA
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* * * * * *
248359 CA----TACATACATACATACATACATGCATGCATACATA
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* * * * * * * *
248395 CATACATACATACATACATACATACATACATACATACATA
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* *
248435 CATGCGTACATGCGTACATGCGTACATGCGTACATGCGTA
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* *
248475 CATGCGTACATGCGTACATGCGTACATGCGTACATGCGTA
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* *
248515 CATGCGTACATGCGTACATGCGTACATGCGTACATGCGTA
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* * *
248555 CATGCGTACATGCGTACATGCGTACATACATACATACGTA
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* * * **
248595 CATGCGTACACGCGTACATACGTACATGCGTACACGCGTA
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* * *
248635 CATGCGTACACGCATACATACGTACATGCGTACATGCGTA
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* * * * *
248675 TATACGTACATGCATACATGCATACTTACGTACATACGTA
1 CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
* *
248715 CATACGTACATACATACAT
1 CATGCGTACATGCATACAT
248734 AGAGCTGTCC
Statistics
Matches: 368, Mismatches: 43, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
36 31 0.08
40 337 0.92
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
CATGCGTACATGCATACATGCGTACATGCGTACATACGTA
Found at i:248734 original size:16 final size:16
Alignment explanation
Indices: 248279--248733 Score: 396
Period size: 16 Copynumber: 28.7 Consensus size: 16
248269 TGCATACATG
*
248279 CATGCATACATGCATA
1 CATGCATACATGCGTA
248295 CATGCATACAT--G--
1 CATGCATACATGCGTA
*
248307 CATGCATACATGCATA
1 CATGCATACATGCGTA
* * * *
248323 CATGCATGCATACATG
1 CATGCATACATGCGTA
* * *
248339 CATGCATGCATACATA
1 CATGCATACATGCGTA
* * *
248355 CATACATACATACATA
1 CATGCATACATGCGTA
* * *
248371 CATACATACATGCATG
1 CATGCATACATGCGTA
* * *
248387 CATACATACATACATA
1 CATGCATACATGCGTA
* * *
248403 CATACATACATACATA
1 CATGCATACATGCGTA
* * *
248419 CATACATACATACATA
1 CATGCATACATGCGTA
*
248435 CATGCGTACATGCGTA
1 CATGCATACATGCGTA
*
248451 CATGCGTACATGCGTA
1 CATGCATACATGCGTA
*
248467 CATGCGTACATGCGTA
1 CATGCATACATGCGTA
*
248483 CATGCGTACATGCGTA
1 CATGCATACATGCGTA
*
248499 CATGCGTACATGCGTA
1 CATGCATACATGCGTA
*
248515 CATGCGTACATGCGTA
1 CATGCATACATGCGTA
*
248531 CATGCGTACATGCGTA
1 CATGCATACATGCGTA
*
248547 CATGCGTACATGCGTA
1 CATGCATACATGCGTA
*
248563 CATGCGTACATGCGTA
1 CATGCATACATGCGTA
* *
248579 CATACATACATACGTA
1 CATGCATACATGCGTA
* *
248595 CATGCGTACACGCGTA
1 CATGCATACATGCGTA
* *
248611 CATACGTACATGCGTA
1 CATGCATACATGCGTA
* *
248627 CACGCGTACATGCGTA
1 CATGCATACATGCGTA
* *
248643 CACGCATACATACGTA
1 CATGCATACATGCGTA
*
248659 CATGCGTACATGCGTA
1 CATGCATACATGCGTA
* * * *
248675 TATACGTACATGCATA
1 CATGCATACATGCGTA
* *
248691 CATGCATACTTACGTA
1 CATGCATACATGCGTA
* * *
248707 CATACGTACATACGTA
1 CATGCATACATGCGTA
*
248723 CATACATACAT
1 CATGCATACAT
248734 AGAGCTGTCC
Statistics
Matches: 390, Mismatches: 45, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
12 11 0.03
16 379 0.97
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (16 bp):
CATGCATACATGCGTA
Found at i:252736 original size:2 final size:2
Alignment explanation
Indices: 252729--252769 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
252719 AATGTACCAT
252729 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
252770 ACCTTCACAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:255397 original size:3 final size:3
Alignment explanation
Indices: 255382--255517 Score: 83
Period size: 3 Copynumber: 43.0 Consensus size: 3
255372 AAATTTTGCA
* * * * *
255382 TAT TAT TAG TAT TAT TAAT CAT TAT TGAT AAT AAT AAT TAT TGAT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT T-AT TAT TAT TAT TAT T-AT TAT
* * * * * *
255430 TAT AAT AAT TAT TATT TAT TAT TACT AAG TAT TAT TGT TAT TAA TAGT
1 TAT TAT TAT TAT TA-T TAT TAT TA-T TAT TAT TAT TAT TAT TAT TA-T
* * *
255478 AAT TGT TAT TAT TAAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
255518 AAACAAAATA
Statistics
Matches: 104, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
3 88 0.85
4 16 0.15
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:255434 original size:16 final size:15
Alignment explanation
Indices: 255386--255517 Score: 76
Period size: 16 Copynumber: 8.7 Consensus size: 15
255376 TTTGCATATT
* *
255386 ATTAGTATTATTAATC
1 ATTATTATTATT-ATA
* *
255402 ATTATTGATAATAATA
1 ATTATT-ATTATTATA
255418 ATTATTGATTATTATA
1 ATTATT-ATTATTATA
*
255434 ATAATTATTATT-T-
1 ATTATTATTATTATA
* * *
255447 ATTATTACTAAGTATT
1 ATTATTA-TTATTATA
* *
255463 ATTGTTATTAATAGTA
1 ATTATTATTATTA-TA
*
255479 ATTGTTATTA-T-TA
1 ATTATTATTATTATA
255492 ATTATTATTATTACT-
1 ATTATTATTATTA-TA
255507 ATTATTATTAT
1 ATTATTATTAT
255518 AAACAAAATA
Statistics
Matches: 93, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
13 17 0.18
14 5 0.05
15 23 0.25
16 44 0.47
17 4 0.04
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (15 bp):
ATTATTATTATTATA
Found at i:255437 original size:22 final size:22
Alignment explanation
Indices: 255402--255453 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
255392 ATTATTAATC
255402 ATTATTGATAATAATAATTATTG
1 ATTATT-ATAATAATAATTATTG
* *
255425 ATTATTATAATAATTATTATTT
1 ATTATTATAATAATAATTATTG
255447 ATTATTA
1 ATTATTA
255454 CTAAGTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
ATTATTATAATAATAATTATTG
Found at i:255470 original size:22 final size:21
Alignment explanation
Indices: 255403--255503 Score: 65
Period size: 22 Copynumber: 5.0 Consensus size: 21
255393 TTATTAATCA
255403 TTATTGATAATAA-TAATTATTG
1 TTATT-ATAATAAGT-ATTATTG
*
255425 ATTATTATAATAATTATTA-T-
1 -TTATTATAATAAGTATTATTG
*
255445 TTATTATTACTAAGTATTATTG
1 TTATTA-TAATAAGTATTATTG
255467 TTA-T-TAAT-AGTA--ATTG
1 TTATTATAATAAGTATTATTG
* *
255483 TTATTATTAATTATTATTATT
1 TTATTA-TAATAAGTATTATT
255504 ACTATTATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 21
0.72 0.04 0.24
Matches are distributed among these distances:
16 7 0.11
17 1 0.02
18 4 0.06
19 13 0.20
20 13 0.20
21 3 0.05
22 17 0.27
23 6 0.09
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (21 bp):
TTATTATAATAAGTATTATTG
Found at i:255509 original size:19 final size:19
Alignment explanation
Indices: 255382--255516 Score: 96
Period size: 19 Copynumber: 6.9 Consensus size: 19
255372 AAATTTTGCA
*
255382 TATTATTAGTATTATTAAT
1 TATTATTATTATTATTAAT
* * *
255401 CATTATTGA-TAATAATAAT
1 TATTATT-ATTATTATTAAT
*
255420 TATTGATTATTA-TAATAAT
1 TATT-ATTATTATTATTAAT
* *
255439 TATTATTTATTATTACTAAG
1 TATTA-TTATTATTATTAAT
*
255459 TATTATTGTTATTAATAGTAAT
1 TATTATTATTATT-AT--TAAT
*
255481 TGTTATTATTAATTATT-AT
1 TATTATTATT-ATTATTAAT
*
255500 TATTACTATTATTATTA
1 TATTATTATTATTATTA
255517 TAAACAAAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
18 7 0.08
19 52 0.56
20 18 0.19
22 13 0.14
23 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
TATTATTATTATTATTAAT
Found at i:256974 original size:64 final size:64
Alignment explanation
Indices: 256891--257028 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 64
256881 CATTGAATGA
*
256891 GCATCGATG-AACTCTTT-AAA-GAAGAATCATCGAATGCAAATGGTGAATCGATGCATAAGG-A
1 GCATCGATGCAACTCTTTAAAATGAA-AA-CATCGAAGGCAAATGGTGAATCGATGCAT-AGGTA
256952 GT
63 GT
* * * * * *
256954 GCATCGATGCATCTCTTTAAAATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTAGT
1 GCATCGATGCAACTCTTTAAAATGAAAACATCGAAGGCAAATGGTGAATCGATGCATAGGTAGT
257018 GCATCGATGCA
1 GCATCGATGCA
257029 CATGTTAAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
63 11 0.17
64 45 0.70
65 5 0.08
66 3 0.05
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (64 bp):
GCATCGATGCAACTCTTTAAAATGAAAACATCGAAGGCAAATGGTGAATCGATGCATAGGTAGT
Found at i:257065 original size:20 final size:22
Alignment explanation
Indices: 257017--257074 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
257007 GCATGGGTAG
257017 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
257041 TGCATCGATGCACTG-T-AGCA
1 TGCATCGATGCACTGTTAAGAA
*
257061 TGCATCGATACACT
1 TGCATCGATGCACT
257075 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 2 0.06
24 13 0.41
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:258091 original size:2 final size:2
Alignment explanation
Indices: 258084--258118 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
258074 ACATAACATG
258084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
258119 GGTATACGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:259937 original size:38 final size:39
Alignment explanation
Indices: 259876--259950 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
259866 TTGATTAACC
* * *
259876 GTTTGTGAGGATATGGTGCGCGAGTTATATAC-AGAACT
1 GTTTGTGAGGAAATGATGAGCGAGTTATATACGAGAACT
*
259914 GTTTGTGAGGAAATGATGAGCGAGTTATGTACGAGAA
1 GTTTGTGAGGAAATGATGAGCGAGTTATATACGAGAA
259951 GTATAAGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 28 0.88
39 4 0.12
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.29
Consensus pattern (39 bp):
GTTTGTGAGGAAATGATGAGCGAGTTATATACGAGAACT
Found at i:260387 original size:15 final size:15
Alignment explanation
Indices: 260367--260404 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
260357 ATCGAAAATG
260367 GGTGGCAAGCACGGC
1 GGTGGCAAGCACGGC
260382 GGTGGCAAGCACGGC
1 GGTGGCAAGCACGGC
*
260397 GATGGCAA
1 GGTGGCAA
260405 TGGCGATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.45, T:0.08
Consensus pattern (15 bp):
GGTGGCAAGCACGGC
Found at i:275658 original size:14 final size:14
Alignment explanation
Indices: 275639--275669 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
275629 GCACTCCGGG
275639 CGACCGAGGCCATC
1 CGACCGAGGCCATC
*
275653 CGACCGAGGCTATC
1 CGACCGAGGCCATC
275667 CGA
1 CGA
275670 GAGCATCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.39, G:0.29, T:0.10
Consensus pattern (14 bp):
CGACCGAGGCCATC
Found at i:275669 original size:10 final size:10
Alignment explanation
Indices: 275664--275729 Score: 73
Period size: 10 Copynumber: 6.6 Consensus size: 10
275654 GACCGAGGCT
275664 ATCCGAGAGC
1 ATCCGAGAGC
*
275674 ATCAGAG-GCC
1 ATCCGAGAG-C
275684 ATCCGAGAGC
1 ATCCGAGAGC
*
275694 ATCAGAG-GCC
1 ATCCGAGAG-C
275704 ATCCGAGAGC
1 ATCCGAGAGC
*
275714 ATCCGAGACC
1 ATCCGAGAGC
275724 ATCCGA
1 ATCCGA
275730 ACGAGCTATG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
9 2 0.04
10 43 0.91
11 2 0.04
ACGTcount: A:0.30, C:0.32, G:0.27, T:0.11
Consensus pattern (10 bp):
ATCCGAGAGC
Found at i:275687 original size:20 final size:20
Alignment explanation
Indices: 275658--275729 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
275648 CCATCCGACC
*
275658 GAGGCTATCCGAGAGCATCA
1 GAGGCCATCCGAGAGCATCA
275678 GAGGCCATCCGAGAGCATCA
1 GAGGCCATCCGAGAGCATCA
*
275698 GAGGCCATCCGAGAGCATCC
1 GAGGCCATCCGAGAGCATCA
*
275718 GAGACCATCCGA
1 GAGGCCATCCGA
275730 ACGAGCTATG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.29, C:0.31, G:0.29, T:0.11
Consensus pattern (20 bp):
GAGGCCATCCGAGAGCATCA
Found at i:275768 original size:33 final size:33
Alignment explanation
Indices: 275726--275797 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
275716 CCGAGACCAT
*
275726 CCGAACGAGCTATGCGA-GGACATCCGAGGGCAG
1 CCGAGCGAGCTATGCGAGGGA-ATCCGAGGGCAG
275759 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAG
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAG
*
275792 TCGAGC
1 CCGAGC
275798 AAGGGTAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 33 0.92
34 3 0.08
ACGTcount: A:0.25, C:0.26, G:0.39, T:0.10
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAG
Found at i:275971 original size:29 final size:29
Alignment explanation
Indices: 275929--276014 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
275919 GAGCAAGGGT
275929 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* * *
275958 AGGTCGCCCGGAGTACATGACGGCCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
275987 AGGTCGCCCGGAAG-GCATGGCGACCTAC
1 AGGTCGCCCGG-AGTGCATGGCGACCTAC
276015 GGCCAACACT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
29 48 0.96
30 2 0.04
ACGTcount: A:0.22, C:0.31, G:0.34, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:278161 original size:20 final size:20
Alignment explanation
Indices: 278136--278180 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
278126 TTATCCGGAA
*
278136 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGGAGTTT
278156 AAAAATCCGGTCTGGAGTTT
1 AAAAATCCGGTCTGGAGTTT
278176 AAAAA
1 AAAAA
278181 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGGAGTTT
Found at i:283298 original size:7 final size:7
Alignment explanation
Indices: 283286--283320 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
283276 GTTTTGAGGG
283286 TTTTGAC
1 TTTTGAC
*
283293 TTTTGAG
1 TTTTGAC
283300 TTTTGAC
1 TTTTGAC
*
283307 TTTTGAG
1 TTTTGAC
283314 TTTTGAC
1 TTTTGAC
283321 CATGATAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.14, C:0.09, G:0.20, T:0.57
Consensus pattern (7 bp):
TTTTGAC
Found at i:283304 original size:14 final size:14
Alignment explanation
Indices: 283285--283320 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
283275 TGTTTTGAGG
283285 GTTTTGACTTTTGA
1 GTTTTGACTTTTGA
283299 GTTTTGACTTTTGA
1 GTTTTGACTTTTGA
283313 GTTTTGAC
1 GTTTTGAC
283321 CATGATAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.08, G:0.22, T:0.56
Consensus pattern (14 bp):
GTTTTGACTTTTGA
Found at i:297662 original size:27 final size:27
Alignment explanation
Indices: 297632--297762 Score: 127
Period size: 27 Copynumber: 4.9 Consensus size: 27
297622 CGGCGTTGTC
* * * *
297632 GGAGTACACGGGGTTGGATTTGTTGGA
1 GGAGTACACAGGGTCGGAGTTGTCGGA
* *
297659 GGAGTACCCATGGTCGGAGTTGTCGGA
1 GGAGTACACAGGGTCGGAGTTGTCGGA
* * *
297686 GGAGTACCCATGGTCGGCGTTGTCGGA
1 GGAGTACACAGGGTCGGAGTTGTCGGA
* * *
297713 GGAGTACCCATGCTCGGAGTTGTCGGA
1 GGAGTACACAGGGTCGGAGTTGTCGGA
* * *
297740 GGAGTACCCATGGTCGGCGTTGT
1 GGAGTACACAGGGTCGGAGTTGT
297763 TGGTGTCGAG
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.17, C:0.18, G:0.40, T:0.24
Consensus pattern (27 bp):
GGAGTACACAGGGTCGGAGTTGTCGGA
Found at i:297714 original size:54 final size:54
Alignment explanation
Indices: 297651--297762 Score: 206
Period size: 54 Copynumber: 2.1 Consensus size: 54
297641 GGGGTTGGAT
* *
297651 TTGTTGGAGGAGTACCCATGGTCGGAGTTGTCGGAGGAGTACCCATGGTCGGCG
1 TTGTCGGAGGAGTACCCATGCTCGGAGTTGTCGGAGGAGTACCCATGGTCGGCG
297705 TTGTCGGAGGAGTACCCATGCTCGGAGTTGTCGGAGGAGTACCCATGGTCGGCG
1 TTGTCGGAGGAGTACCCATGCTCGGAGTTGTCGGAGGAGTACCCATGGTCGGCG
297759 TTGT
1 TTGT
297763 TGGTGTCGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.16, C:0.20, G:0.39, T:0.25
Consensus pattern (54 bp):
TTGTCGGAGGAGTACCCATGCTCGGAGTTGTCGGAGGAGTACCCATGGTCGGCG
Found at i:301416 original size:250 final size:249
Alignment explanation
Indices: 300968--301466 Score: 743
Period size: 250 Copynumber: 2.0 Consensus size: 249
300958 TTGAAACCAC
* * * * *
300968 CTCCTCTACACTCCTGCCCTCCCGGATCTTTCCCCAATCATCACAAGCAACTTATGAGAAGATAG
1 CTCCTCTACACTCCTGCCCTCACGGATCTCTACCCAATCATCACAAGCAACTGATAAGAAGATAG
*
301033 TGAAAATACCAAAGTTCAACAAAAATCCACCATAACCAGTATAAAGAAAAGCTACGAAAATAAAA
66 TGAAAATACCAAAGTTCAACAAAAATCCACCACAACCAGTATAAAGAAAAGCTACGAAAATAAAA
* * * *
301098 AGTGAACCGAAATTTACTGCACTATATTCTTTTTCACCTTACTCCAAACAGAGCCGATCTGTACT
131 ACTGAACCGAAATTTACTGCACTATATTCTTTTTCACCGTACTCCAAACAGAGCCGATCGGAACT
* *
301163 AAATTTTGAGTAATGCCAACTCTTCAGTTTCCAACAAGTAAACAACCAATTGCA
196 AAATTTTGAGTAATGCCAACTCCTCAGTTTCCAACAAGCAAACAACCAATTGCA
**
301217 CTCCTCTACACTCCTGTTCTCACGGATCTCTACCCAATCATCACAAGCAA-TAGATAAGAAGATA
1 CTCCTCTACACTCCTGCCCTCACGGATCTCTACCCAATCATCACAAGCAACT-GATAAGAAGAT-
* * ** *
301281 ACG-GAAAATACCAAAGTTCACCATAAATCCACCACGGCCAGTATAAAGAAAAGCTACGAAAATC
64 A-GTGAAAATACCAAAGTTCAACAAAAATCCACCACAACCAGTATAAAGAAAAGCTACGAAAATA
*
301345 AAAACTGAACCGAAATTTATTGCACTATATAT-TTTTTCACCGTACTCCAAACAGAGCCGATCGG
128 AAAACTGAACCGAAATTTACTGCACTATAT-TCTTTTTCACCGTACTCCAAACAGAGCCGATCGG
* *
301409 AACTAAATTTTGAGTAATGCCAACTCCTCAGTTTGCAACAAGCAAGCAACCAATTGCA
192 AACTAAATTTTGAGTAATGCCAACTCCTCAGTTTCCAACAAGCAAACAACCAATTGCA
301467 TCAAGCTGCA
Statistics
Matches: 224, Mismatches: 22, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
248 1 0.00
249 54 0.24
250 167 0.75
251 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (249 bp):
CTCCTCTACACTCCTGCCCTCACGGATCTCTACCCAATCATCACAAGCAACTGATAAGAAGATAG
TGAAAATACCAAAGTTCAACAAAAATCCACCACAACCAGTATAAAGAAAAGCTACGAAAATAAAA
ACTGAACCGAAATTTACTGCACTATATTCTTTTTCACCGTACTCCAAACAGAGCCGATCGGAACT
AAATTTTGAGTAATGCCAACTCCTCAGTTTCCAACAAGCAAACAACCAATTGCA
Found at i:302124 original size:2 final size:2
Alignment explanation
Indices: 302117--302154 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
302107 TATCTTATCA
302117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
302155 CTCTTAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:310594 original size:22 final size:22
Alignment explanation
Indices: 310564--310610 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
310554 AATTACTATT
* * *
310564 ATATATATTTATGAATATAAAA
1 ATATATATTCATAAAAATAAAA
*
310586 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
310608 ATA
1 ATA
310611 CTATTAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:311556 original size:6 final size:6
Alignment explanation
Indices: 311545--311571 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
311535 TCTCTCCGGT
311545 TCTGTC TCTGTC TCTGTC TCTGTC TCT
1 TCTGTC TCTGTC TCTGTC TCTGTC TCT
311572 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (6 bp):
TCTGTC
Found at i:312040 original size:3 final size:3
Alignment explanation
Indices: 312032--312131 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
312022 TTTAATATAT
*
312032 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
312079 TAT TAA TAA TGA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
312127 TAA TA
1 TAA TA
312132 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
2 2 0.02
3 84 0.98
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:312493 original size:118 final size:118
Alignment explanation
Indices: 312286--312932 Score: 1119
Period size: 118 Copynumber: 5.5 Consensus size: 118
312276 TTCTCCAGAT
* ** * *
312286 GAGTTCTTCTCATTACGAA--CTTTCTGCTGGGGATGATGTTCCATCAAATGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTTCT-CTGGAAATGATGATCCATCAAGTGATGAATTCAAGCA
*
312349 AAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
312403 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
312468 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
312521 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
312586 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
312639 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
312704 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
312757 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAAAGATTGATCCATCAAGTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGA-TGATCCATCAAGTGATGAATTCAAGCA
*
312822 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGAT---
65 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
312873 GAGTTCTTCTCATTATGAA--CTTTCTCTGGAAAAGAATGATCCATCAAGTGATGGATTCAA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATG-ATGATCCATCAAGTGATGAATTCAA
312933 ATCTTTGCTA
Statistics
Matches: 515, Mismatches: 11, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
114 37 0.07
115 1 0.00
116 19 0.04
117 18 0.03
118 357 0.69
119 83 0.16
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (118 bp):
GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:313726 original size:48 final size:48
Alignment explanation
Indices: 313655--313746 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
313645 TGTTCTGCCC
313655 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
313703 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
313747 AGTCTCTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (48 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
Found at i:314907 original size:24 final size:23
Alignment explanation
Indices: 314879--314960 Score: 82
Period size: 24 Copynumber: 3.6 Consensus size: 23
314869 CTTGACCCCC
314879 TTTC-TTTTTCTTCTCTTTTTTCAT
1 TTTCTTTTTTCTTCTC-TTTTTC-T
* *
314903 TTTCTATTTT-TTCT-TTTCT-T
1 TTTCTTTTTTCTTCTCTTTTTCT
*
314923 TTTCTTTCTTTCTTTTCTTTTTCT
1 TTTCTTT-TTTCTTCTCTTTTTCT
314947 TTTCTTTTTTCTTC
1 TTTCTTTTTTCTTC
314961 AAGCATAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
20 7 0.15
21 3 0.06
22 7 0.15
23 10 0.21
24 16 0.34
25 4 0.09
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTCTTTTTTCTTCTCTTTTTCT
Found at i:314921 original size:5 final size:5
Alignment explanation
Indices: 314879--314954 Score: 63
Period size: 5 Copynumber: 15.6 Consensus size: 5
314869 CTTGACCCCC
* * *
314879 TTTCT TTT-T CTTCT CTT-T TTTCAT TTTCT ATT-T TTTCT TTTCT TTT-T
1 TTTCT TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT
314926 CTTTC- TTTCT TTTCTT TTTCT TTTCT TTT
1 -TTTCT TTTCT TTTC-T TTTCT TTTCT TTT
314955 TTCTTCAAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
4 14 0.24
5 35 0.59
6 10 0.17
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:314924 original size:19 final size:19
Alignment explanation
Indices: 314879--314953 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
314869 CTTGACCCCC
*
314879 TTTCTTTTTC-TTCTCTT-T
1 TTTCATTTTCTTTCT-TTCT
*
314897 TTTCATTTTCTATTTTTTCT
1 TTTCATTTTCT-TTCTTTCT
*
314917 TTTCTTTTTCTTTCTTTCT
1 TTTCATTTTCTTTCTTTCT
*
314936 TTTCTTTTTCTTTTCTTT
1 TTTCATTTTC-TTTCTTT
314954 TTTCTTCAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.18
19 19 0.39
20 21 0.43
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCATTTTCTTTCTTTCT
Found at i:326297 original size:24 final size:22
Alignment explanation
Indices: 326265--326313 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
326255 TTACTATTAT
* *
326265 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
326289 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
326311 ATA
1 ATA
326314 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:327261 original size:6 final size:6
Alignment explanation
Indices: 327250--327276 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
327240 TCTCTCCGGT
327250 TCTGTC TCTGTC TCTGTC TCTGTC TCT
1 TCTGTC TCTGTC TCTGTC TCTGTC TCT
327277 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (6 bp):
TCTGTC
Found at i:327748 original size:3 final size:3
Alignment explanation
Indices: 327740--327848 Score: 175
Period size: 3 Copynumber: 36.7 Consensus size: 3
327730 TTAATATATT
* *
327740 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA AAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
327787 TAA TAT TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
327835 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
327849 TGGATAAAAA
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.02
3 95 0.98
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:330587 original size:24 final size:24
Alignment explanation
Indices: 330560--330608 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
330550 TTAGTATCAT
330560 TTTAATAAAAATATTAATTATTAA
1 TTTAATAAAAATATTAATTATTAA
* * *
330584 TTTATTTAAAATATTATTTATTAA
1 TTTAATAAAAATATTAATTATTAA
330608 T
1 T
330609 ATTTTTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTAATAAAAATATTAATTATTAA
Found at i:330615 original size:24 final size:24
Alignment explanation
Indices: 330567--330631 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
330557 CATTTTAATA
*
330567 AAAATATTAATTATTAATTTATTT
1 AAAATATTATTTATTAATTTATTT
330591 AAAATATTATTTATTAATATT-TTT
1 AAAATATTATTTATTAAT-TTATTT
* *
330615 AACAATATAATATATTA
1 AA-AATATTATTTATTA
330632 TAATAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.61
25 14 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
AAAATATTATTTATTAATTTATTT
Found at i:330865 original size:24 final size:23
Alignment explanation
Indices: 330817--330864 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
330807 ATAGTCAAAT
330817 AATATTTTAATAAAAATATTTAA
1 AATATTTTAATAAAAATATTTAA
* *
330840 AATATATTTATTAATAAT-TTTAA
1 AATAT-TTTAATAAAAATATTTAA
330863 AA
1 AA
330865 ACATAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AATATTTTAATAAAAATATTTAA
Done.