Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008337.1 Hibiscus syriacus cultivar Beakdansim tig00111057_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: 840327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:200676 original size:14 final size:14
Alignment explanation
Indices: 200657--200692 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
200647 ACTTTATTTA
200657 TTTAATTTCAATT-C
1 TTTAATTTC-ATTGC
200671 TTTAATTTCATTGC
1 TTTAATTTCATTGC
200685 TTTAATTT
1 TTTAATTT
200693 TTTATCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 3 0.14
14 18 0.86
ACGTcount: A:0.25, C:0.11, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTAATTTCATTGC
Found at i:204982 original size:21 final size:21
Alignment explanation
Indices: 204930--204992 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
204920 AGTCGAGGGT
*
204930 TATATGAGGTACTTCGAGACA
1 TATATGAGGTCCTTCGAGACA
* *
204951 TATACGAGGTCCTTTGAGACA
1 TATATGAGGTCCTTCGAGACA
* *
204972 TATATGAGGTCATTCGGGACA
1 TATATGAGGTCCTTCGAGACA
204993 AATTTTATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (21 bp):
TATATGAGGTCCTTCGAGACA
Found at i:206432 original size:18 final size:18
Alignment explanation
Indices: 206396--206550 Score: 119
Period size: 17 Copynumber: 8.7 Consensus size: 18
206386 AGAGAGAGAG
* *
206396 AAGAAAAAAAGAATAAAAA
1 AAGAAAAGAAGAA-GAAAA
*
206415 AAGAAAAGAAGATGAAAA
1 AAGAAAAGAAGAAGAAAA
*
206433 AAGAAAAGAAGAA-AAAG
1 AAGAAAAGAAGAAGAAAA
206450 AAG-AAA-AAGAAG-AAA
1 AAGAAAAGAAGAAGAAAA
*
206465 AAGAAAAAGAAAAAAGAAAA
1 AAG-AAAAG-AAGAAGAAAA
206485 AAGAAAA-AAGAA-AAAA
1 AAGAAAAGAAGAAGAAAA
*
206501 GAA-AAAAGAAAAAGAAAA
1 -AAGAAAAGAAGAAGAAAA
* * *
206519 AA-AATAGGAGAAAAAAGA
1 AAGAAAAGAAGAAGAAA-A
206537 AAGAAAAAGAAGAA
1 AAG-AAAAGAAGAA
206551 AGAGAATAGA
Statistics
Matches: 109, Mismatches: 15, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
15 10 0.09
16 11 0.10
17 31 0.28
18 23 0.21
19 20 0.18
20 14 0.13
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (18 bp):
AAGAAAAGAAGAAGAAAA
Found at i:206444 original size:21 final size:20
Alignment explanation
Indices: 206401--206520 Score: 141
Period size: 21 Copynumber: 5.6 Consensus size: 20
206391 GAGAGAAGAA
*
206401 AAAAAGAATAAAAAAAGAAAAG
1 AAAAAGAA-AAAAGAA-AAAAG
* *
206423 AAGATGAAAAAAGAAAAGAAG
1 AAAAAGAAAAAAGAAAA-AAG
206444 AAAAAGAAGAAAAAGAAGAAAAAG
1 AAAAAG-A-AAAAAG-A-AAAAAG
206468 AAAAAGAAAAAAGAAAAAAG
1 AAAAAGAAAAAAGAAAAAAG
206488 AAAAAAGAAAAAAGAAAAAAG
1 -AAAAAGAAAAAAGAAAAAAG
206509 AAAAAGAAAAAA
1 AAAAAGAAAAAA
206521 AATAGGAGAA
Statistics
Matches: 87, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
20 20 0.23
21 34 0.39
22 13 0.15
23 7 0.08
24 10 0.11
25 3 0.03
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAAAGAAAAAAG
Found at i:206444 original size:45 final size:43
Alignment explanation
Indices: 206394--206547 Score: 181
Period size: 41 Copynumber: 3.6 Consensus size: 43
206384 AGAGAGAGAG
* *
206394 AGAAGAAAAAAAGAATAAAAAAAGAAAAGAAGATGAAAAAAGAAA
1 AGAAG-AAAAAAGAA-AAAAAAAGAAAAGAAAAAGAAAAAAGAAA
206439 AGAAG-AAAAAGAAGAAAAAGAAGAAAAAGAAAAAGAAAAAAGAAA
1 AGAAGAAAAAAGAA-AAAAA-AAG-AAAAGAAAAAGAAAAAAGAAA
* *
206484 A-AAGAAAAAAGAAAAAAGAA-AAAAGAAAAAGAAAAAA-AAT
1 AGAAGAAAAAAGAAAAAAAAAGAAAAGAAAAAGAAAAAAGAAA
* *
206524 AGGAGAAAAAAGAAAGAAAAAGAA
1 AGAAGAAAAAAGAAAAAAAAAGAA
206548 GAAAGAGAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
40 3 0.03
41 33 0.34
42 2 0.02
43 15 0.16
44 10 0.10
45 33 0.34
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (43 bp):
AGAAGAAAAAAGAAAAAAAAAGAAAAGAAAAAGAAAAAAGAAA
Found at i:206505 original size:27 final size:27
Alignment explanation
Indices: 206400--206551 Score: 139
Period size: 27 Copynumber: 5.4 Consensus size: 27
206390 AGAGAGAAGA
* * *
206400 AAAAAAGAATAAAAAAAGAAAAGAAGATG
1 AAAAAAGAA-AAAAGAA-AAAAGAAAAAG
206429 AAAAAAGAAAAGAAGAAAAAGAAGAAAAAG
1 AAAAAAGAAAA-AAG-AAAA-AAGAAAAAG
206459 AAGAAAA-AGAAAAAGAAAAAAGAAAAAAG
1 AA-AAAAGA-AAAAAGAAAAAAG-AAAAAG
206488 AAAAAAGAAAAAAGAAAAAAGAAAAAG
1 AAAAAAGAAAAAAGAAAAAAGAAAAAG
**
206515 AAAAAA-AATAGGAGAAAAAAGAAAGAA-
1 AAAAAAGAA-AAAAGAAAAAAGAAA-AAG
*
206542 AAAGAAGAAA
1 AAAAAAGAAA
206552 GAGAATAGAT
Statistics
Matches: 107, Mismatches: 6, Indels: 22
0.79 0.04 0.16
Matches are distributed among these distances:
26 2 0.02
27 31 0.29
28 26 0.24
29 26 0.24
30 15 0.14
31 7 0.07
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (27 bp):
AAAAAAGAAAAAAGAAAAAAGAAAAAG
Found at i:206531 original size:34 final size:33
Alignment explanation
Indices: 206400--206551 Score: 134
Period size: 34 Copynumber: 4.5 Consensus size: 33
206390 AGAGAGAAGA
*
206400 AAAAAAGAATAAA-AAAAGAAAAGAAGATGAAAAAAG
1 AAAAAAGAA-AAAGAAAA-AAAA-AA-AAGAAAAAAG
* *
206436 AAAAGAAGAAAAAG-AAGAAAAAGAAG-AAAAAG
1 AAAA-AAGAAAAAGAAAAAAAAAAAAGAAAAAAG
206468 -AAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAG
1 AAAAAAG-AAAAAGAAAAAA-AAAAAAGAAAAAAG
**
206502 AAAAAAGAAAAAGAAAAAAAATAGGAGAAAAAAG
1 AAAAAAGAAAAAGAAAAAAAA-AAAAGAAAAAAG
*
206536 AAAGAAA-AAGAAGAAA
1 AAA-AAAGAAAAAGAAA
206552 GAGAATAGAT
Statistics
Matches: 99, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
30 3 0.03
31 9 0.09
32 10 0.10
33 10 0.10
34 40 0.40
35 13 0.13
36 9 0.09
37 5 0.05
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (33 bp):
AAAAAAGAAAAAGAAAAAAAAAAAAGAAAAAAG
Found at i:206533 original size:21 final size:21
Alignment explanation
Indices: 206400--206551 Score: 127
Period size: 21 Copynumber: 7.1 Consensus size: 21
206390 AGAGAGAAGA
*
206400 AAAAAAGAATAAAAAAAGAAAAG
1 AAAAAAGAA-AAAAGAA-AAAAG
* *
206423 -AAGATGAAAAAAGAAAAGAAG
1 AAAAAAGAAAAAAGAAAA-AAG
206444 -AAAAAGAAGAAAAAGAAGAAAA-
1 AAAAAAG-A-AAAAAGAA-AAAAG
206466 AGAAAAAGAAAAAAGAAAAAAG
1 A-AAAAAGAAAAAAGAAAAAAG
206488 AAAAAAGAAAAAAGAAAAAAG
1 AAAAAAGAAAAAAGAAAAAAG
**
206509 -AAAAAGAAAAAA-AATAGGAG
1 AAAAAAGAAAAAAGAA-AAAAG
* *
206529 AAAAAAGAAAGAA-AAAGAAG
1 AAAAAAGAAAAAAGAAAAAAG
206549 AAA
1 AAA
206552 GAGAATAGAT
Statistics
Matches: 111, Mismatches: 9, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.02
20 24 0.22
21 50 0.45
22 16 0.14
23 11 0.10
24 8 0.07
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAAAGAAAAAAGAAAAAAG
Found at i:206534 original size:1 final size:1
Alignment explanation
Indices: 206429--206522 Score: 53
Period size: 1 Copynumber: 94.0 Consensus size: 1
206419 AAAGAAGATG
* * * * * * * * * * *
206429 AAAAAAGAAAAGAAGAAAAAGAAGAAAAAGAAGAAAAAGAAAAAGAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
206494 GAAAAAAGAAAAAAGAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
206523 TAGGAGAAAA
Statistics
Matches: 63, Mismatches: 30, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (1 bp):
A
Found at i:207442 original size:11 final size:11
Alignment explanation
Indices: 207426--207494 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 11
207416 AAGATAATAT
207426 ATTTTTTCAAA
1 ATTTTTTCAAA
*
207437 ATTTTTTATTAAA
1 A-TTTTT-TCAAA
207450 CATTTTTTCAAA
1 -ATTTTTTCAAA
*
207462 ATTTTTTATTAAA
1 A-TTTTT-TCAAA
207475 CATTTTTTCAAA
1 -ATTTTTTCAAA
207487 ATTCTTTT
1 ATT-TTTT
207495 AACTGATCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
11 5 0.11
12 22 0.47
13 18 0.38
14 2 0.04
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTTTTCAAA
Found at i:207454 original size:25 final size:25
Alignment explanation
Indices: 207426--207495 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
207416 AAGATAATAT
207426 ATTTTTTCAAAATTTTTTATTAAAC
1 ATTTTTTCAAAATTTTTTATTAAAC
207451 ATTTTTTCAAAATTTTTTATTAAAC
1 ATTTTTTCAAAATTTTTTATTAAAC
207476 ATTTTTTCAAAATTCTTTTA
1 ATTTTTTCAAAATT-TTTTA
207496 ACTGATCTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 39 0.89
26 5 0.11
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTTTTCAAAATTTTTTATTAAAC
Found at i:207455 original size:13 final size:13
Alignment explanation
Indices: 207439--207481 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
207429 TTTTCAAAAT
207439 TTTTTATTAAACA
1 TTTTTATTAAACA
*
207452 TTTTT-TCAAA-A
1 TTTTTATTAAACA
207463 TTTTTTATTAAACA
1 -TTTTTATTAAACA
207477 TTTTT
1 TTTTT
207482 TCAAAATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 1 0.04
12 9 0.36
13 14 0.56
14 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTTATTAAACA
Found at i:207456 original size:14 final size:14
Alignment explanation
Indices: 207437--207482 Score: 62
Period size: 12 Copynumber: 3.5 Consensus size: 14
207427 TTTTTTCAAA
207437 ATTTTTTATTAAAC
1 ATTTTTTATTAAAC
*
207451 A-TTTTT-TCAAA-
1 ATTTTTTATTAAAC
207462 ATTTTTTATTAAAC
1 ATTTTTTATTAAAC
207476 ATTTTTT
1 ATTTTTT
207483 CAAAATTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.33
13 9 0.33
14 8 0.30
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTTTATTAAAC
Found at i:207909 original size:19 final size:19
Alignment explanation
Indices: 207885--207922 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
207875 CATATACTCA
207885 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
207904 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
207923 AAGCCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
CCATGCAGACGAGCCATAC
Found at i:207981 original size:32 final size:32
Alignment explanation
Indices: 207937--208007 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
207927 CATATACTCA
* *
207937 CCATGCAGACGAGCCAGCCAACGGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
*
207969 CCATGCAAACGAGCCAGCCAATAGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
208001 CCATGCA
1 CCATGCA
208008 GTCTGGGCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.31, G:0.30, T:0.08
Consensus pattern (32 bp):
CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
Found at i:208098 original size:29 final size:29
Alignment explanation
Indices: 207995--208089 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
207985 GCCAATAGAG
* **
207995 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
208024 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
208053 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
208082 AGGTCGCC
1 AGGTCGCC
208090 CCGGCGTCCA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:208188 original size:49 final size:49
Alignment explanation
Indices: 208125--208230 Score: 173
Period size: 49 Copynumber: 2.2 Consensus size: 49
208115 ATGCATGCAA
*
208125 ATGCA-GCCAAATAACTTCACGTGCTCCTGCT-CCCGCTGCATGCCTGC
1 ATGCATGCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTAC
208172 ATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTAC
1 ATGCATGCCAA-ATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTAC
208222 A-GCATGCCA
1 ATGCATGCCA
208231 TGTGATCCTA
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
47 5 0.09
48 5 0.09
49 29 0.53
50 16 0.29
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (49 bp):
ATGCATGCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTAC
Found at i:208463 original size:16 final size:18
Alignment explanation
Indices: 208442--208480 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
208432 GGAGATAAGG
*
208442 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
208458 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
208476 TAAAT
1 TAAAT
208481 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:208647 original size:46 final size:48
Alignment explanation
Indices: 208584--208675 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 48
208574 TTATATAGTT
208584 AAAAAATAATTAATTAGTTTGTT-TT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTT-TTGTTAGTTAAATAGTTAAGTTATATAA
*
208629 AAAAAATTATTTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
208676 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 8 0.20
46 15 0.37
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:208720 original size:12 final size:12
Alignment explanation
Indices: 208705--208757 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
208695 TATATAAAAA
208705 ATTAGTTAGTTT
1 ATTAGTTAGTTT
208717 ATTAGTTAGTTTT
1 ATTAGTTAG-TTT
* *
208730 AGCTAGTAAGTTT
1 A-TTAGTTAGTTT
*
208743 ATTAG-TAGTAT
1 ATTAGTTAGTTT
208754 ATTA
1 ATTA
208758 TAATGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
11 8 0.24
12 12 0.35
13 8 0.24
14 6 0.18
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (12 bp):
ATTAGTTAGTTT
Found at i:208774 original size:32 final size:32
Alignment explanation
Indices: 208738--208813 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
208728 TTAGCTAGTA
208738 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAAAT
*
208770 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAT
*
208803 ATTTTATTAGT
1 AGTTTATTAGT
208814 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.28
33 19 0.49
34 5 0.13
35 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (32 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAT
Found at i:208886 original size:16 final size:16
Alignment explanation
Indices: 208854--208900 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
208844 TTTAAAAAGT
*
208854 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
208870 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
208886 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
208901 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:208895 original size:15 final size:14
Alignment explanation
Indices: 208875--208905 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
208865 GTTTATTAGT
208875 TTATTATATTATAAG
1 TTATTATATTA-AAG
208890 TTATTATATTAAAG
1 TTATTATATTAAAG
208904 TT
1 TT
208906 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:211076 original size:17 final size:17
Alignment explanation
Indices: 211054--211086 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
211044 CAATGATGTT
211054 TAGTATCAAATAATTAC
1 TAGTATCAAATAATTAC
211071 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
211087 GTATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:211090 original size:14 final size:14
Alignment explanation
Indices: 211053--211103 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
211043 ACAATGATGT
211053 TTAGTATCAAATAA
1 TTAGTATCAAATAA
211067 TTACTAGTATCAAATAA
1 -T--TAGTATCAAATAA
* *
211084 TTAGTATTAAATCA
1 TTAGTATCAAATAA
211098 TTAGTA
1 TTAGTA
211104 ATAATTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 17 0.53
15 1 0.03
16 1 0.03
17 13 0.41
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (14 bp):
TTAGTATCAAATAA
Found at i:211105 original size:21 final size:21
Alignment explanation
Indices: 211081--211124 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
211071 TAGTATCAAA
* *
211081 TAATTAGTATTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
*
211102 TAATAATTAGTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
211123 TA
1 TA
211125 TCAAATCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (21 bp):
TAATAAGTAGTAAATCATTAG
Found at i:211123 original size:11 final size:11
Alignment explanation
Indices: 211091--211124 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
211081 TAATTAGTAT
211091 TAAATCATTAG
1 TAAATCATTAG
*
211102 T-AATAATTAG
1 TAAATCATTAG
211112 TAAATCATTAG
1 TAAATCATTAG
211123 TA
1 TA
211125 TCAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (11 bp):
TAAATCATTAG
Found at i:211132 original size:14 final size:13
Alignment explanation
Indices: 211071--211135 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
211061 AAATAATTAC
*
211071 TAGTATCAAATAAT
1 TAGTAT-AAATCAT
211085 TAGTATTAAATCAT
1 TAGTA-TAAATCAT
*
211099 TAG--T-AATAAT
1 TAGTATAAATCAT
211109 TAG--TAAATCAT
1 TAGTATAAATCAT
211120 TAGTATCAAATCAT
1 TAGTAT-AAATCAT
211134 TA
1 TA
211136 AATATTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 9 0.21
11 9 0.21
13 1 0.02
14 23 0.53
15 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TAGTATAAATCAT
Found at i:211239 original size:13 final size:12
Alignment explanation
Indices: 211221--211316 Score: 81
Period size: 11 Copynumber: 7.9 Consensus size: 12
211211 TTAGTATTCT
211221 ATAATTATTAGTA
1 ATAATTATTA-TA
211234 ATAATTATTA-A
1 ATAATTATTATA
*
211245 ATCATTATTATAA
1 ATAATTATTAT-A
*
211258 ATAATTACTA-A
1 ATAATTATTATA
**
211269 ATAA-TAACATA
1 ATAATTATTATA
211280 ATAATTATTATAAA
1 ATAATTATTAT--A
*
211294 ATCATTATTATA
1 ATAATTATTATA
*
211306 ATGATTATTAT
1 ATAATTATTAT
211317 CAAATCATTA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.04
11 20 0.29
12 15 0.22
13 19 0.28
14 11 0.16
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (12 bp):
ATAATTATTATA
Found at i:211302 original size:14 final size:13
Alignment explanation
Indices: 211283--211495 Score: 82
Period size: 12 Copynumber: 15.2 Consensus size: 13
211273 TAACATAATA
211283 ATTATTATAAAATC
1 ATTATTAT-AAATC
*
211297 ATTATTAT-AATG
1 ATTATTATAAATC
211309 ATTATTATCAAATC
1 ATTATTAT-AAATC
211323 ATTACTAAATCATCAAATC
1 ATTA-T---T-AT-AAATC
*
211342 ATTAAATATTTAAATC
1 ATT--AT-TATAAATC
211358 ATTA-T-TAAATC
1 ATTATTATAAATC
* *
211369 ATTTTTAT-AATG
1 ATTATTATAAATC
211381 ATTATTACTAAATC
1 ATTATTA-TAAATC
* *
211395 ATTACTAT-AATG
1 ATTATTATAAATC
211407 ATTATTATCAAATC
1 ATTATTAT-AAATC
211421 ATTACTAAATCATCAAATC
1 ATTA-T---T-AT-AAATC
*
211440 ATTAAATATTTAAATC
1 ATT--AT-TATAAATC
211456 ATTA-T-TAAATC
1 ATTATTATAAATC
* *
211467 ATTTTTAT-AATG
1 ATTATTATAAATC
211479 ATTATTACTAAATC
1 ATTATTA-TAAATC
211493 ATT
1 ATT
211496 GTTCATTGTT
Statistics
Matches: 157, Mismatches: 16, Indels: 52
0.70 0.07 0.23
Matches are distributed among these distances:
11 18 0.11
12 43 0.27
13 5 0.03
14 39 0.25
15 2 0.01
16 16 0.10
17 2 0.01
18 6 0.04
19 22 0.14
20 2 0.01
21 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (13 bp):
ATTATTATAAATC
Found at i:211306 original size:26 final size:25
Alignment explanation
Indices: 211224--211424 Score: 111
Period size: 26 Copynumber: 8.2 Consensus size: 25
211214 GTATTCTATA
211224 ATTATTAGTAATAATTA-T-TAAATC
1 ATTATTA-TAATAATTATTATAAATC
*
211248 ATTATTATAAATAATTA--CTAAAT-
1 ATTATTAT-AATAATTATTATAAATC
* **
211271 AATAACATAATAATTATTATAAAATC
1 ATTATTATAATAATTATTAT-AAATC
*
211297 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATAATTATTAT-AAATC
* * * *
211323 ATTACTA-AATCATCAAATCATTAAAT-
1 ATTATTATAATAAT--TATTA-TAAATC
*
211349 A-T-TTA-AATCATTA-T-TAAATC
1 ATTATTATAATAATTATTATAAATC
* *
211369 ATTTTTATAATGATTATTACTAAATC
1 ATTATTATAATAATTATTA-TAAATC
* *
211395 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATAATTATTAT-AAATC
211421 ATTA
1 ATTA
211425 CTAAATCATC
Statistics
Matches: 141, Mismatches: 19, Indels: 32
0.73 0.10 0.17
Matches are distributed among these distances:
19 5 0.04
20 1 0.01
21 1 0.01
22 12 0.09
23 13 0.09
24 30 0.21
25 11 0.08
26 60 0.43
27 7 0.05
28 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTATTATAATAATTATTATAAATC
Found at i:211446 original size:98 final size:98
Alignment explanation
Indices: 211277--211495 Score: 404
Period size: 98 Copynumber: 2.2 Consensus size: 98
211267 AAATAATAAC
* *
211277 ATAATAATTATTA-TAAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAAT
1 ATAATGATTATTACT-AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAAT
211341 CATTAAATATTTAAATCATTATTAAATCATTTTT
65 CATTAAATATTTAAATCATTATTAAATCATTTTT
211375 ATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
1 ATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
211440 ATTAAATATTTAAATCATTATTAAATCATTTTT
66 ATTAAATATTTAAATCATTATTAAATCATTTTT
211473 ATAATGATTATTACTAAATCATT
1 ATAATGATTATTACTAAATCATT
211496 GTTCATTGTT
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
98 117 0.99
99 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (98 bp):
ATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
ATTAAATATTTAAATCATTATTAAATCATTTTT
Found at i:211503 original size:7 final size:7
Alignment explanation
Indices: 211491--211517 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
211481 TATTACTAAA
211491 TCATTGT
1 TCATTGT
211498 TCATTGT
1 TCATTGT
211505 TCATTGT
1 TCATTGT
211512 TCATTG
1 TCATTG
211518 AACCAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TCATTGT
Found at i:211609 original size:14 final size:14
Alignment explanation
Indices: 211590--211637 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
211580 TTCAAGTCGT
211590 AAATCATTACTATC
1 AAATCATTACTATC
211604 AAATCATTAC--T-
1 AAATCATTACTATC
*
211615 AAATCATTAATATC
1 AAATCATTACTATC
211629 AAATCATTA
1 AAATCATTA
211638 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:211671 original size:48 final size:49
Alignment explanation
Indices: 211609--211720 Score: 181
Period size: 48 Copynumber: 2.3 Consensus size: 49
211599 CTATCAAATC
*
211609 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
* *
211658 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
211707 ATTACTAATCATTA
1 ATTACTAATCATTA
211721 CTAAATCATT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 36 0.61
49 23 0.39
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
Found at i:211729 original size:11 final size:11
Alignment explanation
Indices: 211707--211735 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
211697 TAATTTCATT
211707 ATTACT-AATC
1 ATTACTAAATC
211717 ATTACTAAATC
1 ATTACTAAATC
211728 ATTACTAA
1 ATTACTAA
211736 TGATGAGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:214789 original size:28 final size:28
Alignment explanation
Indices: 214758--214811 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
214748 ATAATCTAAT
*
214758 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
214786 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
214812 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:214818 original size:28 final size:28
Alignment explanation
Indices: 214754--214818 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
214744 TTATATAATC
*
214754 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
214782 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
214810 TAATTTATA
1 TAATATATA
214819 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:214821 original size:21 final size:21
Alignment explanation
Indices: 214788--214836 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
214778 TTAATATAAT
214788 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
214809 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
214830 ATTAACT
1 A-TAACT
214837 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:215488 original size:30 final size:30
Alignment explanation
Indices: 215448--215557 Score: 184
Period size: 30 Copynumber: 3.7 Consensus size: 30
215438 TTTGGCGAGC
215448 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
* * *
215478 TGGCCGTGCATGGAGGTCGTTGGACGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
*
215508 TGGGCATGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
215538 TGGGCGTGCATGGAGGTCGT
1 TGGGCGTGCATGGAGGTCGT
215558 GGGGTAGGTC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.11, C:0.18, G:0.47, T:0.24
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
Found at i:215605 original size:29 final size:29
Alignment explanation
Indices: 215564--215646 Score: 157
Period size: 29 Copynumber: 2.9 Consensus size: 29
215554 TCGTGGGGTA
*
215564 GGTCGCAGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
215593 GGTCGCCGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
215622 GGTCGCCGGGCGTGCATGGCGACCT
1 GGTCGCCGGGCGTGCATGGCGACCT
215647 ACCCCCGGTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.08, C:0.28, G:0.45, T:0.19
Consensus pattern (29 bp):
GGTCGCCGGGCGTGCATGGCGACCTGGTT
Found at i:218560 original size:26 final size:29
Alignment explanation
Indices: 218531--218583 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
218521 TTAAAAAATG
218531 ATATTA-TATGATTT-TCTTT-AGTTCGA
1 ATATTATTATGATTTATCTTTAAGTTCGA
*
218557 ATATTATTATGGTTTATCTTTAAGTTC
1 ATATTATTATGATTTATCTTTAAGTTC
218584 ACAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 7 0.30
28 5 0.22
29 5 0.22
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (29 bp):
ATATTATTATGATTTATCTTTAAGTTCGA
Found at i:219238 original size:345 final size:344
Alignment explanation
Indices: 218285--219403 Score: 1542
Period size: 346 Copynumber: 3.3 Consensus size: 344
218275 TTGCAGTTCA
*
218285 CAAATTTATTCAGG-TACTCATTAATGACCTTACTTTTCAGAATATATATTTCCAA--TTT-T--
1 CAAATTTATTC-GGATACTCATTAATGACCTTACTTTTCAGAATATATTTTTCCAATTTTTCTCC
* *
218344 ATGAGAAACTCTATAAATACCGTGTAAACTTATCAGGGTTAAAGGTGCACACACACGATGAATAG
65 ATGAGAAACTCTATAAATACCGTGTAAACTTATCA-GGTTAAAGGTGCACACGCACGATGTATAG
* * * * * *
218409 GCAATGCAAATGTATGGTCTGATTGGCCCTTTTGGGGGCTTGCTAATATTTTACCTATTATGAAT
129 GCGATGCGAATGTCTGGTCTGATTAGCCCTTTTGGGGGCTTGCTAATATTTTACCCACTATGAAT
** * * * *
218474 TATTCCATATTTTTCTTAAATGTGACAT-TTTTTTTGAATAATTTAAATTAAAAAATGATATTAT
194 TATTAAATATTTTCCTTAAATGTGACATATATTTTTGAATATTTTGAA-TAAAAAATGATATTAT
* * *
218538 ATGATTTTCTTTAGTTCGAATATTATTATGGTTTATCTT-TAAGTTCACAAATATATTCTATTAA
258 ATAATTTTCTTTAATTCGAATATTATTATGGTATATCTTGT-AGTTCACAAATATATTCTATTAA
*
218602 ATGGTT-TATTAATTGATTACTAT
322 A-GGTTGTATTAATTGATTACTGT
** * * * * *
218625 TGAATTTATTCGGATACTCATTAATAACCATAATTTTTAGAATATATTTTTCTAATTTTTCTCCT
1 CAAATTTATTCGGATACTCATTAATGACCTTACTTTTCAGAATATATTTTTCCAATTTTTCTCC-
* *
218690 ATGAGAAACTCTATAAATACCGTGTAAACTTATCGCGGTTAAAGGTGCACACGCACGATGTATAT
65 ATGAGAAACTCTATAAATACCGTGTAAACTTATC-AGGTTAAAGGTGCACACGCACGATGTATAG
* *
218755 GCGATGCGAATGTCTGTTTTGATTAGCCCTTTTGGGGGCTTGCTAATATTTTACCCACTATGAAT
129 GCGATGCGAATGTCTGGTCTGATTAGCCCTTTTGGGGGCTTGCTAATATTTTACCCACTATGAAT
* * **
218820 TATTAAATATTTTCCTTAAATGTCACATATCTTTTTGAATATTTTGAATTGAAAATGATATTATA
194 TATTAAATATTTTCCTTAAATGTGACATATATTTTTGAATATTTTGAATAAAAAATGATATTATA
* * *
218885 TAATTTTCTTTAATTTGAATATTATAATGGTATACCTTGTAGTTCACAAATATATTCTATTAAAG
259 TAATTTTCTTTAATTCGAATATTATTATGGTATATCTTGTAGTTCACAAATATATTCTATTAAAG
*
218950 GTTGTATTAATTGATTATTGT
324 GTTGTATTAATTGATTACTGT
*
218971 CAAATTTATTCGGATACTCATTAATGACCTTACTTTTTAGAATATATTTTTCCAATTTTTCTCCA
1 CAAATTTATTCGGATACTCATTAATGACCTTACTTTTCAGAATATATTTTTCCAATTTTTCTCC-
** *
219036 ATGAGAAGA-TCTATAAATATTGTGTAAACTTATCAGGTTAAAGGTGCACACGCAAGATGTATAG
65 ATGAGAA-ACTCTATAAATACCGTGTAAACTTATCAGGTTAAAGGTGCACACGCACGATGTATAG
* * *
219100 GCGATGTGAATGTCTGGTCCGATTAGCCCCTTTGGGGGCTTGCTAATATTTTACCCACTATGAAT
129 GCGATGCGAATGTCTGGTCTGATTAGCCCTTTTGGGGGCTTGCTAATATTTTACCCACTATGAAT
*
219165 TATTAAATATTTTCCTTAAATGAGACATATATTTTTGAATATTTTGAATAAAAAATGATATTATA
194 TATTAAATATTTTCCTTAAATGTGACATATATTTTTGAATATTTTGAATAAAAAATGATATTATA
* * * * *
219230 TTATTTTCTTTAATTCAAATATTATTATGGTATATCTTGCAGTTCACAAATATATTTTATTAAAT
259 TAATTTTCTTTAATTCGAATATTATTATGGTATATCTTGTAGTTCACAAATATATTCTATTAAAG
219295 GTTGTATTAATTGATTACTGT
324 GTTGTATTAATTGATTACTGT
* * * *
219316 CGAATTTATCCGGATACTCATTAATGACATTACTTTTCA-AACTATATTTTTCCAAATTTTCT-C
1 CAAATTTATTCGGATACTCATTAATGACCTTACTTTTCAGAA-TATATTTTTCCAATTTTTCTCC
*
219379 ATACGAGAAACTTTATAAATACCGT
65 AT--GAGAAACTCTATAAATACCGT
219404 AAGCCTACAA
Statistics
Matches: 687, Mismatches: 76, Indels: 27
0.87 0.10 0.03
Matches are distributed among these distances:
339 2 0.00
340 44 0.06
342 3 0.00
343 3 0.00
344 4 0.01
345 298 0.43
346 315 0.46
347 18 0.03
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (344 bp):
CAAATTTATTCGGATACTCATTAATGACCTTACTTTTCAGAATATATTTTTCCAATTTTTCTCCA
TGAGAAACTCTATAAATACCGTGTAAACTTATCAGGTTAAAGGTGCACACGCACGATGTATAGGC
GATGCGAATGTCTGGTCTGATTAGCCCTTTTGGGGGCTTGCTAATATTTTACCCACTATGAATTA
TTAAATATTTTCCTTAAATGTGACATATATTTTTGAATATTTTGAATAAAAAATGATATTATATA
ATTTTCTTTAATTCGAATATTATTATGGTATATCTTGTAGTTCACAAATATATTCTATTAAAGGT
TGTATTAATTGATTACTGT
Found at i:223647 original size:2 final size:2
Alignment explanation
Indices: 223640--223669 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
223630 TAAATATTAC
223640 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
223670 TATCTCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:225413 original size:18 final size:17
Alignment explanation
Indices: 225381--225433 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
225371 AAAATTAAAA
225381 TTTTATATAATTTAATT
1 TTTTATATAATTTAATT
* *
225398 TTTTATAATGATTTAATG
1 TTTTAT-ATAATTTAATT
*
225416 ATTTATA-AATTTATATT
1 TTTTATATAATTTA-ATT
225433 T
1 T
225434 ATAAATTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 14 0.50
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
TTTTATATAATTTAATT
Found at i:225451 original size:2 final size:2
Alignment explanation
Indices: 225446--225477 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
225436 AAATTTTTTA
225446 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
225478 TAAAATTACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228409 original size:21 final size:21
Alignment explanation
Indices: 228383--228423 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
228373 AGCTCACCAA
*
228383 CTTCTATTAACATACTAACCT
1 CTTCTATTAACAGACTAACCT
228404 CTTCTATTAACAGACTAACC
1 CTTCTATTAACAGACTAACC
228424 ACCTAGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.34
Consensus pattern (21 bp):
CTTCTATTAACAGACTAACCT
Found at i:228661 original size:36 final size:35
Alignment explanation
Indices: 228580--228715 Score: 188
Period size: 35 Copynumber: 3.9 Consensus size: 35
228570 AGATGAATAA
* *
228580 TTGAATCGAAACTGCTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
*
228615 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-AC
*
228651 TTGAATCGAAAGTGCCGATGCTTCATTCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
* *
228686 TTGAATCTAAAGT---GATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
228716 TTCTTATTCA
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
32 15 0.16
35 44 0.48
36 33 0.36
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
Found at i:228698 original size:71 final size:68
Alignment explanation
Indices: 228580--228720 Score: 210
Period size: 71 Copynumber: 2.0 Consensus size: 68
228570 AGATGAATAA
* *
228580 TTGAATCGAAACTGCTGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTCCG
1 TTGAATCGAAACTGCCGATGCTTCATTCCGTTCACTTGAATCGAAAGT---GATGCTTCCTTCCG
228645 TTCTTC
63 TTCTTC
* * *
228651 TTGAATCGAAAGTGCCGATGCTTCATTCCGTTCACTTGAATCTAAAGTGATGCTTCCTTTCGTTC
1 TTGAATCGAAACTGCCGATGCTTCATTCCGTTCACTTGAATCGAAAGTGATGCTTCCTTCCGTTC
228716 TTC
66 TTC
228719 TT
1 TT
228721 ATTCACCTTC
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
68 21 0.32
71 44 0.68
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.38
Consensus pattern (68 bp):
TTGAATCGAAACTGCCGATGCTTCATTCCGTTCACTTGAATCGAAAGTGATGCTTCCTTCCGTTC
TTC
Found at i:229788 original size:61 final size:60
Alignment explanation
Indices: 229708--229878 Score: 191
Period size: 61 Copynumber: 2.8 Consensus size: 60
229698 ATTATAATCT
* * *
229708 CATTTTAAA-TGATTCTTTAATTTTTAAAATATTTTATATCAATTTTTAAATTACAACCCA
1 CATTTTAAATTGA-TCTTTAAATTTTAAAATATTTTATATCAATATTTAAAGTACAACCCA
* * * ** * ** *
229768 CATTTTTGATTTGATGTTTAAATTTTAAAATATTTTATATCAATCCTTATAGTATGACTCA
1 CA-TTTTAAATTGATCTTTAAATTTTAAAATATTTTATATCAATATTTAAAGTACAACCCA
* *
229829 CATTTTAAATTGATCTCTAAATTTTAAAATATTCTATATCAATATTTAAA
1 CATTTTAAATTGATCTTTAAATTTTAAAATATTTTATATCAATATTTAAA
229879 ATATTAGTCT
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
60 42 0.47
61 45 0.50
62 3 0.03
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (60 bp):
CATTTTAAATTGATCTTTAAATTTTAAAATATTTTATATCAATATTTAAAGTACAACCCA
Found at i:234412 original size:2 final size:2
Alignment explanation
Indices: 234405--234440 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
234395 TTCTCTAACC
234405 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
234441 CCATAATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:238349 original size:16 final size:16
Alignment explanation
Indices: 238328--238381 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
238318 AAATTGTTCT
238328 TATTAAAACGTATCAC
1 TATTAAAACGTATCAC
** *
238344 TATTAAATTGT-TC-T
1 TATTAAAACGTATCAC
238358 TATTAAAACGTATCAC
1 TATTAAAACGTATCAC
238374 TACTTAAA
1 TA-TTAAA
238382 TTGTTCTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
14 9 0.31
15 4 0.14
16 11 0.38
17 5 0.17
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (16 bp):
TATTAAAACGTATCAC
Found at i:238350 original size:61 final size:62
Alignment explanation
Indices: 238279--238394 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 62
238269 AGATGAGTAC
* * * **
238279 CACTAGTTAAATTATTTTTATTAAAACGTTTTACTGGTTAAATTGTTCTTATTAAAACGTAT
1 CACTAGTTAAATTATTCTTATTAAAACGTATCACTACTTAAATTGTTCTTATTAAAACGTAT
*
238341 CACTA-TTAAATTGTTCTTATTAAAACGTATCACTACTTAAATTGTTCTTATTAA
1 CACTAGTTAAATTATTCTTATTAAAACGTATCACTACTTAAATTGTTCTTATTAA
238395 GTAAATGTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
61 43 0.90
62 5 0.10
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (62 bp):
CACTAGTTAAATTATTCTTATTAAAACGTATCACTACTTAAATTGTTCTTATTAAAACGTAT
Found at i:238352 original size:30 final size:31
Alignment explanation
Indices: 238279--238394 Score: 162
Period size: 31 Copynumber: 3.8 Consensus size: 31
238269 AGATGAGTAC
* * * *
238279 CACTAGTTAAATTATTTTTATTAAAACGTTT
1 CACTACTTAAATTGTTCTTATTAAAACGTAT
* **
238310 TACTGGTTAAATTGTTCTTATTAAAACGTAT
1 CACTACTTAAATTGTTCTTATTAAAACGTAT
238341 CACTA-TTAAATTGTTCTTATTAAAACGTAT
1 CACTACTTAAATTGTTCTTATTAAAACGTAT
238371 CACTACTTAAATTGTTCTTATTAA
1 CACTACTTAAATTGTTCTTATTAA
238395 GTAAATGTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
30 30 0.39
31 47 0.61
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (31 bp):
CACTACTTAAATTGTTCTTATTAAAACGTAT
Found at i:238480 original size:31 final size:31
Alignment explanation
Indices: 238422--238481 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
238412 AAATTATATG
*
238422 TTTAATACATACATTATCATTTTTTTTTCTT
1 TTTAATACATAAATTATCATTTTTTTTTCTT
* *
238453 TTTAATACCTAAATT-TTATTTTATTTTTC
1 TTTAATACATAAATTATCATTTT-TTTTTC
238482 AAAATCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTAATACATAAATTATCATTTTTTTTTCTT
Found at i:239046 original size:166 final size:167
Alignment explanation
Indices: 238772--239104 Score: 659
Period size: 166 Copynumber: 2.0 Consensus size: 167
238762 ATGATTATAA
238772 AATTTGAATATGTGACACTTTAAATTAATGATTGAAAGTTTAGTCATTCAACTATAATACAAATA
1 AATTTGAATATGTGACACTTTAAATTAATGATTGAAAGTTTAGTCATTCAACTATAATACAAATA
238837 TATTTTATTATATCAAACTTAATACTTACTTGTATCATTATTAAATTAAGGCAAAAGGGTAACTT
66 TATTTTATTATATCAAACTTAATACTTACTTGTATCATTATTAAATTAAGGCAAAAGGGTAACTT
238902 TTACACTTGTA-TAGACCTAATTTATCACTTTCACCC
131 TTACACTTGTAGTAGACCTAATTTATCACTTTCACCC
238938 AATTTGAATATGTGACACTTTAAATTAATGATTGAAAGTTTAGTCATTCAACTATAATACAAATA
1 AATTTGAATATGTGACACTTTAAATTAATGATTGAAAGTTTAGTCATTCAACTATAATACAAATA
239003 TATTTTATTATATCAAACTTAATACTTACTTGTATCATTATTAAATTAAGGCAAAAGGGTAACTT
66 TATTTTATTATATCAAACTTAATACTTACTTGTATCATTATTAAATTAAGGCAAAAGGGTAACTT
239068 TTACACTTGTAGTAGACCTAATTTATCACTTTCACCC
131 TTACACTTGTAGTAGACCTAATTTATCACTTTCACCC
239105 CTATCGTATT
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
166 141 0.85
167 25 0.15
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (167 bp):
AATTTGAATATGTGACACTTTAAATTAATGATTGAAAGTTTAGTCATTCAACTATAATACAAATA
TATTTTATTATATCAAACTTAATACTTACTTGTATCATTATTAAATTAAGGCAAAAGGGTAACTT
TTACACTTGTAGTAGACCTAATTTATCACTTTCACCC
Found at i:239487 original size:23 final size:23
Alignment explanation
Indices: 239461--239527 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 23
239451 TACTTTTATG
239461 TATTTATAAAAT-TTATATTA-AA
1 TATTTATAAAATATTAT-TTATAA
239483 TTATTCT-TAAAATATTATTTATAA
1 -TATT-TATAAAATATTATTTATAA
239507 TA-TTATAAAAATATTATTTAT
1 TATTTAT-AAAATATTATTTAT
239528 TTTTTAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
21 1 0.03
22 2 0.05
23 29 0.74
24 7 0.18
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTATAAAATATTATTTATAA
Found at i:239565 original size:23 final size:22
Alignment explanation
Indices: 239516--239567 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
239506 ATATTATAAA
239516 AATATTATTTATTTTTTAAAGT
1 AATATTATTTATTTTTTAAAGT
*
239538 CATATTATTTATTTTTTTGAAA-T
1 AATATTATTTA-TTTTTT-AAAGT
239561 AATATTA
1 AATATTA
239568 CTTTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 13 0.50
24 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (22 bp):
AATATTATTTATTTTTTAAAGT
Found at i:244460 original size:20 final size:21
Alignment explanation
Indices: 244435--244473 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
244425 ATTGATATGA
*
244435 GTATCGGTACTC-CAAGAATT
1 GTATCGATACTCACAAGAATT
244455 GTATCGATACTCACAAGAA
1 GTATCGATACTCACAAGAA
244474 CAATATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (21 bp):
GTATCGATACTCACAAGAATT
Found at i:248113 original size:72 final size:75
Alignment explanation
Indices: 247931--248134 Score: 249
Period size: 72 Copynumber: 2.8 Consensus size: 75
247921 CAAAGCCAAA
* * * *
247931 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCCATAGGA-GAACCGATTCCCCCCTAAA-GC
*
247995 TTTTGGCCCCGAG
63 ATTTGGCCCCGAG
* *
248008 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGAACCGATTCCCCCCTAAA-CATT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGAACCGATTCCCCCCTAAAGCATT
*
248072 T-GCTCCGAG
66 TGGCCCCGAG
* *
248081 AATTCCA-TATGCTCGGAGGGAACCGATCCCCCCCA-AGG-GTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGAACCGATTCCCCCCT
248135 TGTACAACGT
Statistics
Matches: 114, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
70 15 0.13
71 3 0.03
72 26 0.23
73 13 0.11
74 3 0.03
75 9 0.08
76 22 0.19
77 23 0.20
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.20
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGAACCGATTCCCCCCTAAAGCATT
TGGCCCCGAG
Found at i:249149 original size:172 final size:172
Alignment explanation
Indices: 248863--249206 Score: 688
Period size: 172 Copynumber: 2.0 Consensus size: 172
248853 TCTTGAGTCG
248863 ATTCGGGAAGAGTTATATCGATTATTAAAGTTATCAATGGCCTCCGCTTCAAACTTCGACTCCGG
1 ATTCGGGAAGAGTTATATCGATTATTAAAGTTATCAATGGCCTCCGCTTCAAACTTCGACTCCGG
248928 TCTTGATTCGATGCCCGTCAACAAGCCTCCTTTCTTCAATGGAGCTAATTACGCCTATTGGAAGA
66 TCTTGATTCGATGCCCGTCAACAAGCCTCCTTTCTTCAATGGAGCTAATTACGCCTATTGGAAGA
248993 ATAGAATGATGTACTTCATTCAAGCAAGTGATATGGGAGCAT
131 ATAGAATGATGTACTTCATTCAAGCAAGTGATATGGGAGCAT
249035 ATTCGGGAAGAGTTATATCGATTATTAAAGTTATCAATGGCCTCCGCTTCAAACTTCGACTCCGG
1 ATTCGGGAAGAGTTATATCGATTATTAAAGTTATCAATGGCCTCCGCTTCAAACTTCGACTCCGG
249100 TCTTGATTCGATGCCCGTCAACAAGCCTCCTTTCTTCAATGGAGCTAATTACGCCTATTGGAAGA
66 TCTTGATTCGATGCCCGTCAACAAGCCTCCTTTCTTCAATGGAGCTAATTACGCCTATTGGAAGA
249165 ATAGAATGATGTACTTCATTCAAGCAAGTGATATGGGAGCAT
131 ATAGAATGATGTACTTCATTCAAGCAAGTGATATGGGAGCAT
249207 GGAATGCCGT
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (172 bp):
ATTCGGGAAGAGTTATATCGATTATTAAAGTTATCAATGGCCTCCGCTTCAAACTTCGACTCCGG
TCTTGATTCGATGCCCGTCAACAAGCCTCCTTTCTTCAATGGAGCTAATTACGCCTATTGGAAGA
ATAGAATGATGTACTTCATTCAAGCAAGTGATATGGGAGCAT
Found at i:253932 original size:21 final size:21
Alignment explanation
Indices: 253906--253968 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
253896 TTTTGGTGCA
*
253906 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
253927 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
253948 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
253969 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:253976 original size:21 final size:21
Alignment explanation
Indices: 253950--253989 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
253940 CCCCCTTTGA
*
253950 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
253971 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
253990 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:255950 original size:17 final size:17
Alignment explanation
Indices: 255917--255961 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
255907 TTTCAACATT
*
255917 TTGGATATTTTTGGATTG
1 TTGGAT-TTTGTGGATTG
*
255935 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
255952 TTGGATTTTG
1 TTGGATTTTG
255962 GGTTTATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:256726 original size:76 final size:77
Alignment explanation
Indices: 256567--256776 Score: 282
Period size: 76 Copynumber: 2.8 Consensus size: 77
256557 CAAAGCCAAA
* * * **
256567 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCTATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCC-ATAGGAGGAACCGATTCCCCCCTAAACAG
256631 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
* *
256644 ATTTCCAGAATGCTCGGAGGGAACCAATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
256709 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * * *
256720 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
256777 TGTACAACGG
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 19 0.16
76 55 0.47
77 44 0.37
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:258019 original size:27 final size:27
Alignment explanation
Indices: 257987--258058 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
257977 CCAGAGGAGG
* *
257987 AGGAAGAGTACGAGAAGAGCTAGGAAT
1 AGGAAGAGCACGAGAAGAGCTAGGAAC
258014 AGGAAGAGCACGAGAAGAGCTAGGAAC
1 AGGAAGAGCACGAGAAGAGCTAGGAAC
* * *
258041 AGGAGGAGCTCGTGAAGA
1 AGGAAGAGCACGAGAAGA
258059 ACTGGCTCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.42, C:0.11, G:0.39, T:0.08
Consensus pattern (27 bp):
AGGAAGAGCACGAGAAGAGCTAGGAAC
Found at i:259662 original size:21 final size:21
Alignment explanation
Indices: 259636--259711 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
259626 CAAGGAATGC
259636 ATCGATGCATCTTCATGATGT
1 ATCGATGCATCTTCATGATGT
* *
259657 ATCGATGCA-CATTCAAAGGGATGC
1 ATCGATGCATC-TTC--A-TGATGT
*
259681 ATCGATGCACCTTCAT-AGTGT
1 ATCGATGCATCTTCATGA-TGT
259702 ATCGATGCAT
1 ATCGATGCAT
259712 TATACACAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
20 2 0.05
21 23 0.52
22 1 0.02
23 1 0.02
24 16 0.36
25 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (21 bp):
ATCGATGCATCTTCATGATGT
Found at i:259684 original size:24 final size:23
Alignment explanation
Indices: 259610--259695 Score: 88
Period size: 24 Copynumber: 3.8 Consensus size: 23
259600 CATGGCATTG
* *
259610 TGCATCGATGTACATTCAAGGAA
1 TGCATCGATGCACATTCAAGGGA
*
259633 TGCATCGATGCATC-TTC-A-TGA
1 TGCATCGATGCA-CATTCAAGGGA
*
259654 TGTATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
*
259678 TGCATCGATGCACCTTCA
1 TGCATCGATGCACATTCA
259696 TAGTGTATCG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 15 0.29
22 1 0.02
23 16 0.31
24 18 0.35
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:259695 original size:45 final size:44
Alignment explanation
Indices: 259613--259710 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 44
259603 GGCATTGTGC
* *
259613 ATCGATGTACATTCAAGGAATGCATCGATGCATCTTCAT-GATGT
1 ATCGATGCACATTCAAGGAATGCATCGATGCACCTTCATAG-TGT
*
259657 ATCGATGCACATTCAAAGGGATGCATCGATGCACCTTCATAGTGT
1 ATCGATGCACATTC-AAGGAATGCATCGATGCACCTTCATAGTGT
259702 ATCGATGCA
1 ATCGATGCA
259711 TTATACACAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
44 13 0.27
45 35 0.71
46 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAATGCATCGATGCACCTTCATAGTGT
Found at i:265562 original size:64 final size:65
Alignment explanation
Indices: 265491--265627 Score: 174
Period size: 64 Copynumber: 2.1 Consensus size: 65
265481 TACATTGAGG
* *
265491 GTGCATCGATGCATAAAA-CACATTCAATGTTTTAA-AATAGCCTGG-GTGCATCGATGCATAGC
1 GTGCATCGATGCATAAAATCA-ATTCAATGTTTTAATAATA-CATGGAGTGCATCGATGCAT-GA
265553 T-T
63 TAT
* * *
265555 GTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATATATGGAGTGCATCGATGCATGATAT
1 GTGCATCGATGCATAAAATCAATTCAATGTTTTAATAATACATGGAGTGCATCGATGCATGATAT
265620 GTGCATCG
1 GTGCATCG
265628 GTACACAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
64 35 0.55
65 29 0.45
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATCAATTCAATGTTTTAATAATACATGGAGTGCATCGATGCATGATAT
Found at i:265626 original size:65 final size:63
Alignment explanation
Indices: 265491--265650 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 63
265481 TACATTGAGG
* * * *
265491 GTGCATCGATGCATAAAACACATTCAATGTTTTAAAATAGCCTGGGTGCATCGATGCATAGCTT
1 GTGCATCGGTGCATAAAACA-ATTCGATGTTTTAAAATAGCATGGGTGCATCGATGCATAGATT
*
265555 GTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATA-TATGGAGTGCATCGATGCAT-GAT
1 GTGCATCGGTGCATAAAA-CAATTCGATGTTTTAA-AATAGCATGG-GTGCATCGATGCATAGAT
265618 AT
63 -T
* * *
265620 GTGCATCGGTACACAAAAGCCATTCGATGTT
1 GTGCATCGGTGCATAAAA-CAATTCGATGTT
265651 CAATTAAAAC
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 35 0.42
65 48 0.58
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (63 bp):
GTGCATCGGTGCATAAAACAATTCGATGTTTTAAAATAGCATGGGTGCATCGATGCATAGATT
Found at i:273875 original size:15 final size:16
Alignment explanation
Indices: 273848--273880 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
273838 TAAATTAGTT
273848 AAAAATTTAAAAATAA
1 AAAAATTTAAAAATAA
273864 AAAAATTT-AAAATAA
1 AAAAATTTAAAAATAA
273879 AA
1 AA
273881 TATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATTTAAAAATAA
Found at i:274476 original size:24 final size:24
Alignment explanation
Indices: 274433--274508 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
274423 ATTTATAAAT
274433 ATATACAT-TTTAAAAT-ATAATTA
1 ATATA-ATATTTAAAATAATAATTA
*
274456 ATATAATATTTAAAATAATAATAA
1 ATATAATATTTAAAATAATAATTA
*
274480 ATTTAATATTTTAAAATAA-AATTCA
1 ATATAATA-TTTAAAATAATAATT-A
274505 ATAT
1 ATAT
274509 GTATAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
22 2 0.04
23 13 0.29
24 16 0.36
25 14 0.31
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATAATATTTAAAATAATAATTA
Found at i:277048 original size:6 final size:6
Alignment explanation
Indices: 277037--277066 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
277027 ACAGACCTTC
*
277037 TATTTT TATTTT TATTTC TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT
277067 ATAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:281024 original size:11 final size:11
Alignment explanation
Indices: 281008--281034 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
280998 GACTAAAATA
281008 AAATAATAATT
1 AAATAATAATT
281019 AAATAATAATT
1 AAATAATAATT
281030 AAATA
1 AAATA
281035 TTATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATT
Found at i:281336 original size:22 final size:21
Alignment explanation
Indices: 281311--281356 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
281301 ATTAATAGGA
*
281311 TTAAAATA-TGAAATATTTTAAT
1 TTAAAATACT-AAATATGTT-AT
281333 TTAAAATACTAAATATGTTAT
1 TTAAAATACTAAATATGTTAT
281354 TTA
1 TTA
281357 CCCCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 16 0.73
23 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAAAATACTAAATATGTTAT
Found at i:282535 original size:3 final size:3
Alignment explanation
Indices: 282529--282593 Score: 100
Period size: 3 Copynumber: 22.7 Consensus size: 3
282519 AATAATTATT
282529 TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
282575 TAA T-A TTA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
282594 GGGATAATAG
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
2 6 0.10
3 52 0.90
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:282540 original size:17 final size:18
Alignment explanation
Indices: 282529--282593 Score: 100
Period size: 17 Copynumber: 3.8 Consensus size: 18
282519 AATAATTATT
282529 TAATAATAATAATAA-AA
1 TAATAATAATAATAATAA
282546 TAATAATAATAATAATAA
1 TAATAATAATAATAATAA
282564 TAAT-ATAATAATAAT-A
1 TAATAATAATAATAATAA
*
282580 TTATAATAATAATA
1 TAATAATAATAATA
282594 GGGATAATAG
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
16 4 0.09
17 35 0.78
18 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATAATAA
Found at i:282593 original size:14 final size:14
Alignment explanation
Indices: 282506--282593 Score: 96
Period size: 14 Copynumber: 6.6 Consensus size: 14
282496 ACTCGGCCTG
*
282506 TAATAATATT-T-G
1 TAATAATATTATAA
282518 TAATAATTATT-TAA
1 TAATAA-TATTATAA
* *
282532 TAATAATAATAAAA
1 TAATAATATTATAA
282546 TAATAATA--ATAA
1 TAATAATATTATAA
*
282558 TAATAATAATATAA
1 TAATAATATTATAA
282572 TAATAATATTATAA
1 TAATAATATTATAA
282586 TAATAATA
1 TAATAATA
282594 GGGATAATAG
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
12 17 0.26
13 8 0.12
14 41 0.62
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (14 bp):
TAATAATATTATAA
Found at i:283345 original size:177 final size:176
Alignment explanation
Indices: 282905--283674 Score: 1218
Period size: 177 Copynumber: 4.4 Consensus size: 176
282895 TCAAGTGAGA
* *
282905 TAAAATTTATATTTGAAAACATCCTACACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
1 TAAAATTT-CATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
** *
282970 CAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAATAAACCCCTTTGTTGGGCTTAGCTTCCT
65 CAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCT
* *
283035 TTAACAGCTCTTTTGAGATAATTAGTAAACCCTGAAGGCTTGATTTC
130 TTAACAGCTCTTTTGAGATAATTAGTAAACCCCGAAGGCTTGGTTTC
* * * *
283082 TAAAATTTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGACCCGTAGGACTTACAAATT
1 TAAAATTTCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* * *
283147 AAGAAACCCCCGAATGCTTAGTTTCTTATTTGTCAAGGAACCTCTTTGTTAGGCTTAGCTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
283212 TAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
131 TAACAGCTCTTTTGAGATAATTAGTAAA-CCCCGAAGGCTTGGTTTC
* * **
283259 TAAAATTTCATTTGAAAACATTCTGCACTAAAGGTCTTAAGGATGGCATGTAGGACTTACAAATC
1 TAAAATTTCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* * *
283324 AAGAAACCCTCGAAGGCTTAGTTTCTTAGTTATCAAGGAACCCCTTTATTAGGCTTAGCTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
* *
283389 TAACAACTCTTTTGAGATAATTAG-AAAACCCGAAGGCTTGGTTTC
131 TAACAGCTCTTTTGAGATAATTAGTAAACCCCGAAGGCTTGGTTTC
* * *
283434 TAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
1 TAAAATTTCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* * *
283499 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCATTTGTTGGGATTAGCTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
*
283564 TAACAGCTATTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
131 TAACAGCTCTTTTGAGATAATTAGTAAA-CCCCGAAGGCTTGGTTTC
* *
283611 TAAAATCTCATCTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
1 TAAAATTTCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
283675 TTCGGAAATA
Statistics
Matches: 543, Mismatches: 47, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
175 156 0.29
176 146 0.27
177 241 0.44
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (176 bp):
TAAAATTTCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
TAACAGCTCTTTTGAGATAATTAGTAAACCCCGAAGGCTTGGTTTC
Found at i:283564 original size:352 final size:353
Alignment explanation
Indices: 282905--283674 Score: 1267
Period size: 352 Copynumber: 2.2 Consensus size: 353
282895 TCAAGTGAGA
* *
282905 TAAAATTTATATTTGAAAACATCCTACACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
1 TAAAATTT-CATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
* * * *
282970 CAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAATAAACCCCTTTGTTGGGCTTAGCTTCCT
65 CAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTATCAAGAAACCCCTTTATTAGGCTTAGCTTCCT
* * *
283035 TTAACAGCTCTTTTGAGATAATTAGTAAACCCTGAAGGCTTGATTTCTAAAATTTCATTTGAAAA
130 TTAACAACTCTTTTGAGATAATTAGAAAACCCTGAAGGCTTGATTTCTAAAATCTCATTTGAAAA
* *
283100 CATCCTACACTGAAGGTCTTATGGATGACCCGTAGGACTTACAAATTAAGAAACCCCCGAATGCT
195 CATCCTACACTGAAGGTCTTATGGATGACCCGTAGGACTTACAAATCAAGAAACCCCCGAAGGCT
* * *
283165 TAGTTTCTTATTTGTCAAGGAACCTCTTTGTTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGAT
260 TAGTTTCTTAGTTGTCAAGGAACCTCTTTGTTAGGATTAGCTTCCTTTAACAGCTATTTTGAGAT
283230 AATTAGTAAACCCCCGAAGGCTTGGTTTC
325 AATTAGTAAACCCCCGAAGGCTTGGTTTC
* * **
283259 TAAAATTTCATTTGAAAACATTCTGCACTAAAGGTCTTAAGGATGGCATGTAGGACTTACAAATC
1 TAAAATTTCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* *
283324 AAGAAACCCTCGAAGGCTTAGTTTCTTAGTTATCAAGGAACCCCTTTATTAGGCTTAGCTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTATCAAGAAACCCCTTTATTAGGCTTAGCTTCCTT
*
283389 TAACAACTCTTTTGAGATAATTAGAAAACCC-GAAGGCTTGGTTTCTAAAATCTCATTTGAAAAC
131 TAACAACTCTTTTGAGATAATTAGAAAACCCTGAAGGCTTGATTTCTAAAATCTCATTTGAAAAC
*
283453 ATCC-AGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATCAAGAAACCCCCGAAGGCT
196 ATCCTA-CACTGAAGGTCTTATGGATGACCCGTAGGACTTACAAATCAAGAAACCCCCGAAGGCT
*
283517 TAGTTTCTTAGTTGTCAAGGAACC-CATTTGTTGGGATTAGCTTCCTTTAACAGCTATTTTGAGA
260 TAGTTTCTTAGTTGTCAAGGAACCTC-TTTGTTAGGATTAGCTTCCTTTAACAGCTATTTTGAGA
283581 TAATTAGTAAACCCCCGAAGGCTTGGTTTC
324 TAATTAGTAAACCCCCGAAGGCTTGGTTTC
* *
283611 TAAAATCTCATCTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
1 TAAAATTTCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
283675 TTCGGAAATA
Statistics
Matches: 385, Mismatches: 29, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
351 2 0.01
352 236 0.61
353 139 0.36
354 8 0.02
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (353 bp):
TAAAATTTCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTATCAAGAAACCCCTTTATTAGGCTTAGCTTCCTT
TAACAACTCTTTTGAGATAATTAGAAAACCCTGAAGGCTTGATTTCTAAAATCTCATTTGAAAAC
ATCCTACACTGAAGGTCTTATGGATGACCCGTAGGACTTACAAATCAAGAAACCCCCGAAGGCTT
AGTTTCTTAGTTGTCAAGGAACCTCTTTGTTAGGATTAGCTTCCTTTAACAGCTATTTTGAGATA
ATTAGTAAACCCCCGAAGGCTTGGTTTC
Found at i:284819 original size:54 final size:55
Alignment explanation
Indices: 284730--284839 Score: 168
Period size: 54 Copynumber: 2.0 Consensus size: 55
284720 CATTGGTTCA
* * * *
284730 TAAAACATTTGACAATACATTCATCTTTTCCTGTGGCTTCTGCCCATATTT-TTG
1 TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTTCTTG
*
284784 TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTTTGCCCAGATTTCTTG
1 TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTTCTTG
284839 T
1 T
284840 CAGTGAAGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 46 0.92
55 4 0.08
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.41
Consensus pattern (55 bp):
TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTTCTTG
Found at i:285383 original size:51 final size:51
Alignment explanation
Indices: 285306--285499 Score: 300
Period size: 51 Copynumber: 3.8 Consensus size: 51
285296 GTATCTCAAC
* * * *
285306 CTTTTCATACTGGTGTGAGCCGTCAAGATACCCCAGATGGATTACTTCTAT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTAT
*
285357 CTTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATTACTTCTAT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTAT
* * *
285408 TTTTTCATGCTTATGTGAGCCTTTAAGATACCCCACATGGATTACTTCTAT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTAT
*
285459 CTTTTGATGCTGATGTGAGCCTTCAAGATA-CCCACATGGAT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGAT
285500 AATATGGACC
Statistics
Matches: 130, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 11 0.08
51 119 0.92
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (51 bp):
CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTAT
Found at i:287015 original size:14 final size:13
Alignment explanation
Indices: 286996--287071 Score: 70
Period size: 12 Copynumber: 6.0 Consensus size: 13
286986 CTTGATTCAA
286996 TTTCTTTTTCTTCT
1 TTTCTTTTTC-TCT
287010 TTTC-TTTTCTCT
1 TTTCTTTTTCTCT
287022 TTTCTCTTTTCTCT
1 TTTCT-TTTTCTCT
* *
287036 TTT-TTTTCCCCT
1 TTTCTTTTTCTCT
*
287048 TCT-TTTTTCTCT
1 TTTCTTTTTCTCT
*
287060 TTT-TTTTCCTCT
1 TTTCTTTTTCTCT
287072 GATGGATGAG
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
12 32 0.60
13 6 0.11
14 15 0.28
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTTTTTCTCT
Found at i:287018 original size:19 final size:19
Alignment explanation
Indices: 286996--287043 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
286986 CTTGATTCAA
286996 TTTCTTTTTCTTCTTTTCT-
1 TTTCTTTTTC-TCTTTTCTC
287015 TTTCTCTTTTCTCTTTTCTC
1 TTTCT-TTTTCTCTTTTCTC
287035 TTT-TTTTTC
1 TTTCTTTTTC
287044 CCCTTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.19
19 14 0.52
20 8 0.30
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTCTTTTTCTCTTTTCTC
Found at i:287041 original size:24 final size:23
Alignment explanation
Indices: 286996--287068 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 23
286986 CTTGATTCAA
*
286996 TTTCTTTTTCTTCTTTTCTTTTCTCT
1 TTTCTTTTTC-TCTTTT-TTTTC-CC
287022 TTTCTCTTTTCTCTTTTTTTTCCC
1 TTTCT-TTTTCTCTTTTTTTTCCC
*
287046 CTTCTTTTTTCTCTTTTTTTTCC
1 TTTC-TTTTTCTCTTTTTTTTCC
287069 TCTGATGGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 21 0.49
25 6 0.14
26 11 0.26
27 5 0.12
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTCTTTTTCTCTTTTTTTTCCC
Found at i:287062 original size:7 final size:7
Alignment explanation
Indices: 286998--287038 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
286988 TGATTCAATT
286998 TCTTTT-
1 TCTTTTC
*
287004 TCTTCTTT
1 TCTT-TTC
287012 TCTTTTC
1 TCTTTTC
287019 TCTTTTC
1 TCTTTTC
287026 TCTTTTC
1 TCTTTTC
287033 TCTTTT
1 TCTTTT
287039 TTTTCCCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 4 0.12
7 24 0.75
8 4 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TCTTTTC
Found at i:295644 original size:3 final size:3
Alignment explanation
Indices: 295638--295681 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
295628 AATTATTATT
* *
295638 TAA TAA TAA TAA TAA -AA TAA TAT TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
295682 GAAGGATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:306847 original size:20 final size:20
Alignment explanation
Indices: 306824--306861 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
306814 TTCCCCTGTG
*
306824 GGGGGAATCGGTTCCCTCAA
1 GGGGGAATCGATTCCCTCAA
*
306844 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
306862 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.26, G:0.37, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAA
Found at i:306847 original size:21 final size:20
Alignment explanation
Indices: 306801--306861 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
306791 CCAGAACCCT
*
306801 AGGGGGGTATCGATTCCC-CTG
1 AGGGGGG-ATCGATTCCCTC-A
* *
306822 TGGGGGGAATCGGTTCCCTCA
1 AGGGGGG-ATCGATTCCCTCA
306843 AGGGGGGATCGATTCCCTC
1 AGGGGGGATCGATTCCCTC
306862 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 11 0.33
21 21 0.64
22 1 0.03
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.23
Consensus pattern (20 bp):
AGGGGGGATCGATTCCCTCA
Found at i:308120 original size:21 final size:20
Alignment explanation
Indices: 308096--308134 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
308086 TCTATAAAAA
308096 ATATTAAATATAAATTTTAAT
1 ATATTAAATA-AAATTTTAAT
308117 ATATTAAATAAAATTTTA
1 ATATTAAATAAAATTTTA
308135 GTTTGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTAAATAAAATTTTAAT
Found at i:311493 original size:19 final size:19
Alignment explanation
Indices: 311469--311506 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
311459 ACAGCTCGGC
311469 TCAGACCAGTCCAACCGGT
1 TCAGACCAGTCCAACCGGT
* *
311488 TCAGACCGGTCCAATCGGT
1 TCAGACCAGTCCAACCGGT
311507 CAACCGATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.34, G:0.24, T:0.18
Consensus pattern (19 bp):
TCAGACCAGTCCAACCGGT
Found at i:313252 original size:20 final size:20
Alignment explanation
Indices: 313227--313270 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
313217 TCGGTGGAAG
313227 ATCCAATCCTGTGCCTTTAA
1 ATCCAATCCTGTGCCTTTAA
*
313247 ATCCAATCCTGTGCTTTTAA
1 ATCCAATCCTGTGCCTTTAA
313267 ATCC
1 ATCC
313271 TTTCTTGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.30, G:0.09, T:0.36
Consensus pattern (20 bp):
ATCCAATCCTGTGCCTTTAA
Found at i:316966 original size:58 final size:58
Alignment explanation
Indices: 316885--316995 Score: 204
Period size: 58 Copynumber: 1.9 Consensus size: 58
316875 AAAAATTATA
*
316885 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATATAAAT
1 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTACATATATATAAAT
*
316943 TATAAACTATATTTATATTATAAACTATATAATTATTATAAGCTACATATATA
1 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTACATATATA
316996 AATTATGTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (58 bp):
TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTACATATATATAAAT
Found at i:316979 original size:18 final size:19
Alignment explanation
Indices: 316881--316983 Score: 126
Period size: 18 Copynumber: 5.5 Consensus size: 19
316871 TTAAAAAAAT
*
316881 TATA-TATAAACTATAT-T
1 TATATTATAAACTATATAA
316898 TATATTATAAACTATATAA
1 TATATTATAAACTATATAA
316917 T-TATTATAAACTATATATA
1 TATATTATAAACTATATA-A
*
316936 TATAAATTATAAACTATAT-T
1 TAT--ATTATAAACTATATAA
316956 TATATTATAAACTATATAA
1 TATATTATAAACTATATAA
316975 T-TATTATAA
1 TATATTATAA
316984 GCTACATATA
Statistics
Matches: 76, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.05
18 50 0.66
19 4 0.05
20 4 0.05
22 14 0.18
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATTATAAACTATATAA
Found at i:316994 original size:40 final size:39
Alignment explanation
Indices: 316880--316973 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 39
316870 ATTAAAAAAA
316880 TTATA-TATAAACTATAT-T-TAT-ATTATAAACTATA-
1 TTATATTATAAACTATATATATATAATTATAAACTATAT
*
316914 TAATTATTATAAACTATATATATATAAATTATAAACTATAT
1 TTA-TATTATAAACTATATATATAT-AATTATAAACTATAT
316955 TTATATTATAAACTATATA
1 TTATATTATAAACTATATA
316974 ATTATTATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
34 2 0.04
35 2 0.04
36 12 0.24
37 1 0.02
38 3 0.06
40 29 0.57
41 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (39 bp):
TTATATTATAAACTATATATATATAATTATAAACTATAT
Found at i:317000 original size:20 final size:19
Alignment explanation
Indices: 316885--317001 Score: 75
Period size: 18 Copynumber: 6.2 Consensus size: 19
316875 AAAAATTATA
* *
316885 TATAAACT-ATATTTATAT
1 TATAAACTAATATATAAAT
*
316903 TATAAACT-ATATA-ATTAT
1 TATAAACTAATATATA-AAT
316921 TATAAACTATATATATATAAAT
1 TATAAAC--TA-ATATATAAAT
* *
316943 TATAAACT-ATATTTATAT
1 TATAAACTAATATATAAAT
*
316961 TATAAACT-ATATA-ATTAT
1 TATAAACTAATATATA-AAT
*
316979 TATAAGCTACATATATAAAT
1 TATAAACTA-ATATATAAAT
316999 TAT
1 TAT
317002 GTTTATGTGA
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
17 2 0.02
18 52 0.63
20 12 0.15
21 1 0.01
22 14 0.17
23 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (19 bp):
TATAAACTAATATATAAAT
Found at i:317036 original size:15 final size:15
Alignment explanation
Indices: 316989--317055 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 15
316979 TATAAGCTAC
*
316989 ATATATAAATTATGT
1 ATATATAAACTATGT
* * *
317004 TTATGTGAACTA--T
1 ATATATAAACTATGT
317017 ATATATAAACTATG-
1 ATATATAAACTATGT
*
317031 -TATATAAACTATAT
1 ATATATAAACTATGT
*
317045 ATGTATAAACT
1 ATATATAAACT
317056 TTGAAAAGTA
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
13 22 0.56
15 17 0.44
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (15 bp):
ATATATAAACTATGT
Found at i:317097 original size:18 final size:18
Alignment explanation
Indices: 317048--317087 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
317038 ACTATATATG
* *
317048 TATAAACTTTGAAAAGTA
1 TATAAACTATAAAAAGTA
317066 TATAAACTATAAAAAGTA
1 TATAAACTATAAAAAGTA
317084 TATA
1 TATA
317088 GTTTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (18 bp):
TATAAACTATAAAAAGTA
Found at i:317120 original size:10 final size:10
Alignment explanation
Indices: 317105--317204 Score: 50
Period size: 11 Copynumber: 10.1 Consensus size: 10
317095 AAATATTATT
317105 TATATA-ATA
1 TATATATATA
317114 TAGTATATATA
1 TA-TATATATA
*
317125 TATATATAAA
1 TATATATATA
*
317135 CTATATATGTA
1 -TATATATATA
*
317146 TAAACTATATA
1 TATA-TATATA
*
317157 -AAATATATA
1 TATATATATA
* *
317166 GTTTATATGT-
1 -TATATATATA
*
317176 TATA-ATTTA
1 TATATATATA
317185 TAT-TA-ATA
1 TATATATATA
317193 TAGTATATATA
1 TA-TATATATA
317204 T
1 T
317205 GTATGTATTA
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
8 7 0.10
9 16 0.23
10 19 0.28
11 27 0.39
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (10 bp):
TATATATATA
Found at i:317122 original size:2 final size:2
Alignment explanation
Indices: 317105--317204 Score: 50
Period size: 2 Copynumber: 50.5 Consensus size: 2
317095 AAATATTATT
* *
317105 TA TA TA -A TA TA GTA TA TA TA TA TA TA TA AA CTA TA TA TG TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * *
317148 AA CTA TA TA -A AA TA TA TA GTT TA TA TG T- TA TA -A TT 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
317188 TA -A TA TA GTA TA TA TA T
1 TA TA TA TA -TA TA TA TA T
317205 GTATGTATTA
Statistics
Matches: 75, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
1 6 0.08
2 62 0.83
3 7 0.09
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:317122 original size:14 final size:14
Alignment explanation
Indices: 317083--317130 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
317073 TATAAAAAGT
*
317083 ATATAGTTTATAAA
1 ATATAGTTTATATA
317097 ATATTA-TTTATATA
1 ATA-TAGTTTATATA
*
317111 ATATAGTATATATA
1 ATATAGTTTATATA
317125 TATATA
1 -ATATA
317131 TAAACTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 20 0.69
15 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (14 bp):
ATATAGTTTATATA
Found at i:317139 original size:13 final size:14
Alignment explanation
Indices: 317111--317156 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 14
317101 TATTTATATA
*
317111 ATATAGTATATA-T
1 ATATAGTATAAACT
317124 ATATA-TATAAACT
1 ATATAGTATAAACT
317137 ATATATGTATAAACT
1 ATATA-GTATAAACT
317152 ATATA
1 ATATA
317157 AAATATATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 5 0.17
13 11 0.38
15 13 0.45
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (14 bp):
ATATAGTATAAACT
Found at i:317139 original size:15 final size:15
Alignment explanation
Indices: 317121--317156 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
317111 ATATAGTATA
317121 TATATATATATAAAC
1 TATATATATATAAAC
*
317136 TATATATGTATAAAC
1 TATATATATATAAAC
317151 TATATA
1 TATATA
317157 AAATATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:317163 original size:39 final size:39
Alignment explanation
Indices: 317066--317172 Score: 105
Period size: 39 Copynumber: 2.7 Consensus size: 39
317056 TTGAAAAGTA
* *
317066 TATAAACTATA-AAAAGTATATAGTTTATAAAATATTATT
1 TATAAACTATATAAAA-TATATAGTATATAAAATATTATG
* *
317105 TATATAA-TATAGT-ATATATATA-TATATAAACTATATATG
1 TATA-AACTATA-TAAAATATATAGTATATAAAATAT-TATG
*
317144 TATAAACTATATAAAATATATAGTTTATA
1 TATAAACTATATAAAATATATAGTATATA
317173 TGTTATAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
38 13 0.24
39 33 0.60
40 9 0.16
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (39 bp):
TATAAACTATATAAAATATATAGTATATAAAATATTATG
Found at i:317187 original size:62 final size:60
Alignment explanation
Indices: 317064--317208 Score: 132
Period size: 62 Copynumber: 2.3 Consensus size: 60
317054 CTTTGAAAAG
* * * * *
317064 TATATAAACTATAAAAAGTATATAGTTTATAAAATATTATTTATATAATATAGTATATATAT
1 TATATAAACTAT-ATATGTATAAACTATATAAAATATTATTTATATAATATAG-ATATATAT
** *
317126 ATATATAAACTATATATGTATAAACTATATAAAATATATAGTTTATATGTTATA-ATTTATAT
1 -TATATAAACTATATATGTATAAACTATATAAAATAT-TA-TTTATATAATATAGATATATAT
*
317188 TAATATAGTA-TATATATGTAT
1 T-ATATA-AACTATATATGTAT
317209 GTATTAGTCT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
61 1 0.01
62 42 0.61
63 15 0.22
64 11 0.16
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.45
Consensus pattern (60 bp):
TATATAAACTATATATGTATAAACTATATAAAATATTATTTATATAATATAGATATATAT
Found at i:317325 original size:2 final size:2
Alignment explanation
Indices: 317320--317377 Score: 73
Period size: 2 Copynumber: 29.0 Consensus size: 2
317310 TTATATAGTT
**
317320 TA TA TA TA TA TA TA GG 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
*
317362 GTT TA TA TA TA T- TA TA
1 -TA TA TA TA TA TA TA TA
317378 CATGGTTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 46 0.96
3 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:317377 original size:20 final size:21
Alignment explanation
Indices: 317311--317388 Score: 88
Period size: 24 Copynumber: 3.6 Consensus size: 21
317301 TAATTTACTT
317311 TATATAGTTTATATATATATA
1 TATATAGTTTATATATATATA
317332 TAGGTATA-TATATATATATATATA
1 TA--TATAGT-T-TATATATATATA
317356 TATATAGTTTATATATAT-TA
1 TATATAGTTTATATATATATA
* *
317376 TACATGGTTTATA
1 TATATAGTTTATA
317389 CATACATTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
20 13 0.26
21 11 0.22
22 6 0.12
23 6 0.12
24 14 0.28
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (21 bp):
TATATAGTTTATATATATATA
Found at i:317416 original size:7 final size:7
Alignment explanation
Indices: 317395--317475 Score: 72
Period size: 7 Copynumber: 11.4 Consensus size: 7
317385 TATACATACA
*
317395 TTAGAGT
1 TTAGGGT
*
317402 TTATGGT
1 TTAGGGT
317409 TTAGGGT
1 TTAGGGT
317416 TTAGGGT
1 TTAGGGT
317423 TTAGGGT
1 TTAGGGT
**
317430 TTAAAGT
1 TTAGGGT
**
317437 TTAATGT
1 TTAGGGT
317444 TTAGGGT
1 TTAGGGT
* *
317451 TTATGAT
1 TTAGGGT
317458 TTAGAGGT
1 TTAG-GGT
*
317466 TTAAGGT
1 TTAGGGT
317473 TTA
1 TTA
317476 TATAAACTAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
7 55 0.92
8 5 0.08
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:317727 original size:20 final size:20
Alignment explanation
Indices: 317689--317743 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
317679 CAACTTCCCA
*
317689 AAATTTT-CTATTT-CCTCT
1 AAATTTTCCAATTTCCCTCT
317707 AAATTTTCCAATTTCCCTCT
1 AAATTTTCCAATTTCCCTCT
*
317727 AAA-TTCCCAATTTCCCT
1 AAATTTTCCAATTTCCCT
317744 ATATTCTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 7 0.21
19 18 0.55
20 8 0.24
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTTTCCAATTTCCCTCT
Found at i:318437 original size:19 final size:20
Alignment explanation
Indices: 318415--318459 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
318405 TTGAGAATAT
*
318415 AGGGAAATTG-GGAATTTAG
1 AGGGAAATTGAGAAATTTAG
318434 AGGGAAATTGAGAAATTTAG
1 AGGGAAATTGAGAAATTTAG
318454 AGGGAA
1 AGGGAA
318460 TAGAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.22
Consensus pattern (20 bp):
AGGGAAATTGAGAAATTTAG
Found at i:318958 original size:23 final size:24
Alignment explanation
Indices: 318932--318981 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
318922 TTATTTTTTG
318932 TTTATATAAATTAAACTACA-TAA
1 TTTATATAAATTAAACTACATTAA
*
318955 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTACATTAA
318979 TTT
1 TTT
318982 TCCTTTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTATATAAATTAAACTACATTAA
Found at i:319017 original size:28 final size:24
Alignment explanation
Indices: 318985--319060 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 24
318975 TTAATTTTCC
*
318985 TTTACATTATTAATAATGTTTTATCTAA
1 TTTACATT-TAAATAA--TTTTAT-TAA
319013 TTTACATTTAAATAATTTTATTAA
1 TTTACATTTAAATAATTTTATTAA
*
319037 TTT-TA-TTAAATAATTTTATATAA
1 TTTACATTTAAATAATTTTAT-TAA
319060 T
1 T
319061 AGGTCTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.31
23 5 0.11
24 6 0.13
25 6 0.13
27 6 0.13
28 8 0.18
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (24 bp):
TTTACATTTAAATAATTTTATTAA
Found at i:319262 original size:16 final size:16
Alignment explanation
Indices: 319237--319287 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
319227 CGGATCATTT
*
319237 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
*
319253 ACATGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
319269 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
319285 ACA
1 ACA
319288 AGTCGGGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:319963 original size:2 final size:2
Alignment explanation
Indices: 319956--319991 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
319946 GCCGGAAGCC
319956 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
319992 GTAATGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:320271 original size:31 final size:31
Alignment explanation
Indices: 320229--320287 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
320219 AACTTAAAAG
* * *
320229 AGTTTTGCAATACTTAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
320260 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
320288 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:320338 original size:22 final size:22
Alignment explanation
Indices: 320312--320354 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
320302 TAATAAATTA
320312 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
320334 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
320355 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:320360 original size:18 final size:18
Alignment explanation
Indices: 320339--320395 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
320329 CATATTTTAA
320339 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
* *
320357 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
*
320371 AATTAATCAATTCATACT
1 AATAAATCAATTCATACT
320389 AATAAAT
1 AATAAAT
320396 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 6 0.21
15 5 0.17
17 5 0.17
18 13 0.45
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:320363 original size:22 final size:22
Alignment explanation
Indices: 320314--320362 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
320304 ATAAATTATT
**
320314 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
320336 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
320359 TAAA
1 TAAA
320363 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:320367 original size:54 final size:54
Alignment explanation
Indices: 320302--320931 Score: 504
Period size: 54 Copynumber: 11.4 Consensus size: 54
320292 ACAACTATAA
320302 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
* * ** * ** * * *
320356 TAATAAATTATTTAAAATTAATCAATTCATACTAATAAATTATTTAAAAT-A-AA
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATTCATAC
** *
320409 TCAATCTA-TATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATA
1 T-AATAAATTA-TTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATTCATA
320473 C
54 C
* *
320474 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
*
320528 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
320582 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
** * ** * * * *
320636 TAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT-AAAT
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATTCATAC
** * * * * * *
320690 TAATCCATAATTTAAAATAAATCAATCCATA----CAAATAAAT-TATTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
*
320739 TAAATCAATCCA-TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATC
1 T-AAT-AA---ATTA-TTTAAAATAAATCAA-TC---C--AT--A-T-TTTAAAATAAATCAATT
320803 CATAC
50 CATAC
*
320808 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAA-TCTATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC-ATAC
* *
320856 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
*
320910 TAATAAATTATTTTAAATAAAT
1 TAATAAATTATTTAAAATAAAT
320932 TATTTTAAAA
Statistics
Matches: 465, Mismatches: 63, Indels: 96
0.75 0.10 0.15
Matches are distributed among these distances:
47 1 0.00
48 24 0.05
49 12 0.03
50 5 0.01
52 3 0.01
53 5 0.01
54 311 0.67
55 26 0.06
56 1 0.00
57 2 0.00
58 14 0.03
60 5 0.01
62 3 0.01
63 11 0.02
64 22 0.05
65 4 0.01
67 3 0.01
68 9 0.02
69 4 0.01
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
Done.