Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004743.1 Hibiscus syriacus cultivar Beakdansim tig00010705_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: 119670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:488 original size:13 final size:13
Alignment explanation
Indices: 470--494 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
460 AACGGAATAT
470 TATATATATATAA
1 TATATATATATAA
483 TATATATATATA
1 TATATATATATA
495 CGGGGTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:2764 original size:85 final size:85
Alignment explanation
Indices: 2621--2790 Score: 322
Period size: 85 Copynumber: 2.0 Consensus size: 85
2611 TAAAGTAATC
*
2621 TAAAAGTCTCAATTCTTGGGACCATCCATTATCTATTAATACATCAGCCCATACAATTAAACGTT
1 TAAAAGTCTCAATTCTTGGGACCATCCATTATCTATTAATACATCAGCCCATACAATTAAAAGTT
2686 CATCTTCTTACCTTGTACAA
66 CATCTTCTTACCTTGTACAA
*
2706 TAAAAGTCTCAATTCTTGGGACCATCCATTATCTATTAATACATCAGCTCATACAATTAAAAGTT
1 TAAAAGTCTCAATTCTTGGGACCATCCATTATCTATTAATACATCAGCCCATACAATTAAAAGTT
2771 CATCTTCTTACCTTGTACAA
66 CATCTTCTTACCTTGTACAA
2791 ATTCCAATAC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.35
Consensus pattern (85 bp):
TAAAAGTCTCAATTCTTGGGACCATCCATTATCTATTAATACATCAGCCCATACAATTAAAAGTT
CATCTTCTTACCTTGTACAA
Found at i:9663 original size:23 final size:21
Alignment explanation
Indices: 9605--9666 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
9595 TTTATCTCCG
**
9605 AAAATCTATTTTTATT-TTTTT
1 AAAAT-TATTTTTATTAAATTT
9626 AAAATTATTTTTATTAAATTT
1 AAAATTATTTTTATTAAATTT
9647 AGAAATTATTTTTTATTAAA
1 A-AAATTA-TTTTTATTAAA
9667 AAATCATTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 6 0.17
23 11 0.31
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
AAAATTATTTTTATTAAATTT
Found at i:10848 original size:17 final size:17
Alignment explanation
Indices: 10823--10856 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
10813 CCGGTTTCGG
10823 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
10840 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
10857 ATAAAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:11289 original size:13 final size:13
Alignment explanation
Indices: 11268--11321 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
11258 AAGTTCGATA
*
11268 AATTCAAATACTT
1 AATTGAAATACTT
11281 AATTGAAATACTT
1 AATTGAAATACTT
*
11294 AATT-AACTCAAC-T
1 AATTGAAAT--ACTT
11307 AATTGAAATACTT
1 AATTGAAATACTT
11320 AA
1 AA
11322 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
12 5 0.15
13 24 0.71
14 5 0.15
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:11403 original size:32 final size:33
Alignment explanation
Indices: 11307--11405 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
11297 TAACTCAACT
* * *
11307 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
11340 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
11373 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
11405 A
1 A
11406 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:11424 original size:21 final size:21
Alignment explanation
Indices: 11400--11439 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11390 ACTTCAAGTT
11400 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
11421 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
11440 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:13743 original size:12 final size:12
Alignment explanation
Indices: 13726--13771 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
13716 TTCGGATAAA
13726 AACCGGTTTTTT
1 AACCGGTTTTTT
13738 AACCGGTTTTTTT
1 AACCGG-TTTTTT
13751 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
13765 ATCCGGT
1 AACCGGT
13772 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:13756 original size:15 final size:14
Alignment explanation
Indices: 13725--13764 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
13715 TTTCGGATAA
13725 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
13738 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
13751 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
13765 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:18401 original size:23 final size:22
Alignment explanation
Indices: 18371--18420 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 22
18361 TACAAAAAAA
18371 TTAATATATTTATTTATCTA-ATT
1 TTAATATA-TT-TTTATCTATATT
18394 TTAATATATTTTTATCTATATT
1 TTAATATATTTTTATCTATATT
18416 TTAAT
1 TTAAT
18421 TTACTCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.31
22 10 0.38
23 8 0.31
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
TTAATATATTTTTATCTATATT
Found at i:21102 original size:17 final size:15
Alignment explanation
Indices: 21072--21115 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
21062 ATATATTTAT
21072 ATAATTATAATAAAA
1 ATAATTATAATAAAA
21087 ATAATGTATGAATAAAA
1 ATAAT-TAT-AATAAAA
21104 TTATAATTATAA
1 --ATAATTATAA
21116 ACAAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.20
16 3 0.12
17 9 0.36
18 3 0.12
19 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (15 bp):
ATAATTATAATAAAA
Found at i:22751 original size:72 final size:71
Alignment explanation
Indices: 22662--22802 Score: 176
Period size: 72 Copynumber: 2.0 Consensus size: 71
22652 GATTTTGGGG
* * *
22662 CAATAATAGTGGTGTTTTCTTGACAA-ACGCCGCAATAAATCCATCTATAATGACGTTTTATCAA
1 CAATAATAGTGGCGTTTT-TTAAAAAGACGCCGCAATAAATCCATCTATAATGACG-TTTATCAA
22726 TAAAACCT
64 TAAAACCT
* * * * * *
22734 CAATAATAGTGGCGTTTTTTAAAAAGACGTCGCAATAGATTCATCTATAGTGGCGTTTATCAGTA
1 CAATAATAGTGGCGTTTTTTAAAAAGACGCCGCAATAAATCCATCTATAATGACGTTTATCAATA
22799 AAAC
66 AAAC
22803 GGCACTGTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
71 18 0.31
72 41 0.69
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (71 bp):
CAATAATAGTGGCGTTTTTTAAAAAGACGCCGCAATAAATCCATCTATAATGACGTTTATCAATA
AAACCT
Found at i:25300 original size:17 final size:18
Alignment explanation
Indices: 25259--25301 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
25249 AATTTAAATA
*
25259 AATTAAAATATTAATATG
1 AATTAAAATATCAATATG
25277 AATTAAAAT-TCAAT-TG
1 AATTAAAATATCAATATG
25293 ATATTAAAA
1 A-ATTAAAA
25302 ATATATATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 11 0.48
18 9 0.39
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (18 bp):
AATTAAAATATCAATATG
Found at i:32560 original size:31 final size:32
Alignment explanation
Indices: 32511--32584 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
32501 CATTTAATTG
* *
32511 TATGATGACGTGACATGTGTC-AAACATTTAA
1 TATGATAACGTGACATGTGCCGAAACATTTAA
* * *
32542 TATGATAATGTGATATGTGCCGCAACATTTAA
1 TATGATAACGTGACATGTGCCGAAACATTTAA
* *
32574 AATGATGACGT
1 TATGATAACGT
32585 ATTATTTATT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 17 0.50
32 17 0.50
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (32 bp):
TATGATAACGTGACATGTGCCGAAACATTTAA
Found at i:34292 original size:1 final size:1
Alignment explanation
Indices: 34286--34310 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
34276 TGTGTGTGTG
34286 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
34311 GCATTATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:36571 original size:21 final size:21
Alignment explanation
Indices: 36539--36595 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
36529 TCATTAACCT
36539 AATAA-AACTGCACTAAAAAC
1 AATAATAACTGCACTAAAAAC
*
36559 AATAATAGCTGCACTAAAAAC
1 AATAATAACTGCACTAAAAAC
36580 AATAATAACTGCACTA
1 AATAATAACTGCACTA
36596 CTTTCCATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 5 0.15
21 29 0.85
ACGTcount: A:0.54, C:0.19, G:0.07, T:0.19
Consensus pattern (21 bp):
AATAATAACTGCACTAAAAAC
Found at i:37703 original size:29 final size:32
Alignment explanation
Indices: 37662--37736 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
37652 ATAGTTATTA
37662 TATTTTATATT-AAT-ATAATTATATAAATAT
1 TATTTTATATTAAATAATAATTATATAAATAT
* *
37692 TATTTT-TATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATAATTATATAAATAT
37724 TA-TTTAT-TTAAAT
1 TATTTTATATTAAAT
37737 TTATTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 4 0.10
30 10 0.26
31 8 0.21
32 17 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATTTTATATTAAATAATAATTATATAAATAT
Found at i:37727 original size:15 final size:15
Alignment explanation
Indices: 37665--37743 Score: 72
Period size: 15 Copynumber: 5.3 Consensus size: 15
37655 GTTATTATAT
*
37665 TTTATATTAATA-TA
1 TTTATATAAATATTA
*
37679 ATTATATAAATATTA
1 TTTATATAAATATTA
* *
37694 TTTTTATTAAAATAATA
1 TTTATA-T-AAATATTA
*
37711 TTTATATAATTATTA
1 TTTATATAAATATTA
*
37726 TTTATTTAAAT-TTA
1 TTTATATAAATATTA
37740 TTTA
1 TTTA
37744 AATTTATTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 17 0.33
15 21 0.40
16 2 0.04
17 12 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATATAAATATTA
Found at i:37740 original size:10 final size:10
Alignment explanation
Indices: 37725--37751 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
37715 TATAATTATT
37725 ATTTATTTAA
1 ATTTATTTAA
37735 ATTTATTTAA
1 ATTTATTTAA
37745 ATTTATT
1 ATTTATT
37752 AATTAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTTATTTAA
Found at i:39576 original size:21 final size:21
Alignment explanation
Indices: 39552--39591 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39542 ATCTCCGCAT
*
39552 GGTTACATTCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
39573 GGTTACATGCCTAGCCCGC
1 GGTTACATGCCTAGCCCGC
39592 AGAGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.23
Consensus pattern (21 bp):
GGTTACATGCCTAGCCCGCCA
Found at i:40152 original size:34 final size:34
Alignment explanation
Indices: 40109--40215 Score: 169
Period size: 34 Copynumber: 3.1 Consensus size: 34
40099 ATAAATGTTT
40109 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
40143 TTAAAATACAAATAATATTATTCGAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* *
40177 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
40211 TTAAA
1 TTAAA
40216 TTCAAGTTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:40342 original size:14 final size:14
Alignment explanation
Indices: 40323--40352 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40313 TTTTATCATT
*
40323 AACATATATATTAA
1 AACATATACATTAA
40337 AACATATACATTAA
1 AACATATACATTAA
40351 AA
1 AA
40353 TCAACTTATC
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:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:40891 original size:127 final size:127
Alignment explanation
Indices: 40618--41468 Score: 1418
Period size: 127 Copynumber: 6.7 Consensus size: 127
40608 GTGACATGAA
* *
40618 TAGTTACCGGGGGACATAAGTGACATAATAGGGTAATGATAATATATTCTCTGACAAAATAATGG
1 TAGTTCCCGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
* * * *
40683 AAGGCGC-CCCCCGGTAACGCGCCTTCATGGTCTCATAAGGAATAATAGGTATTGACATCCT
66 AAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATCCT
* *
40744 TAGTTCACGGGGGACATAAGTGACATAATAGGATAATGATAACATATTCTCTGACAAAATAATGG
1 TAGTTCCCGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
40809 AAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATCCT
66 AAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATCCT
*
40871 TAGTTCCCAGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
1 TAGTTCCCGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
* * *
40936 AAGGCGCCCCCCCGGGAATGCGCCTTCACGGTCCCCTAATGAATAATAGGTATTGACATCCT
66 AAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATCCT
* *
40998 TAGTTCCCGGGGGATATAAGTGACATAATAGGGTAATGATAACATATTATCTGACAAAATAATGG
1 TAGTTCCCGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
* * * *
41063 AAGGCGCGCCCCCGGGAACGCGCATTCACGGTCCCTTAAGGAATAATATGTATTAACATCCT
66 AAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATCCT
41125 TAGTTCCCGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
1 TAGTTCCCGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
41190 AAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATCCT
66 AAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATCCT
*
41252 TAGTTCCTGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
1 TAGTTCCCGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
* * * ***
41317 ATGGCGC-CCCCCGGGAACGCGCCTTCACGATCCCCTAAGGAATAATAGGTATTGATATAAA
66 AAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATCCT
* *
41378 TAGTTTCTGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
1 TAGTTCCCGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
* * *
41443 AAGACGCGCCTCCGAGAACGCGCCTT
66 AAGGCGCGCCCCCGGGAACGCGCCTT
41469 AACGTGAATA
Statistics
Matches: 681, Mismatches: 42, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
126 186 0.27
127 495 0.73
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (127 bp):
TAGTTCCCGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGG
AAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATCCT
Found at i:46656 original size:14 final size:14
Alignment explanation
Indices: 46637--46663 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46627 CGCGTCGTCT
46637 CCACGCTCCGAACA
1 CCACGCTCCGAACA
46651 CCACGCTCCGAAC
1 CCACGCTCCGAAC
46664 GATGGTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.52, G:0.15, T:0.07
Consensus pattern (14 bp):
CCACGCTCCGAACA
Found at i:50916 original size:36 final size:36
Alignment explanation
Indices: 50870--51046 Score: 221
Period size: 36 Copynumber: 4.9 Consensus size: 36
50860 GAAAGATAGA
* * *
50870 ATCGACACTTTCGATTCAAGACGAACGGAATGAAGC
1 ATCGGCACTTCCGATTCAAGACGAACGGAAGGAAGC
* * *
50906 ATCGGAACTTTCGATTCAAGTA-GAACGGAATGAAGC
1 ATCGGCACTTCCGATTCAAG-ACGAACGGAAGGAAGC
*
50942 ATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGC
1 ATCGGCACTTCCGATTCAAGACGAACGGAAGGAAGC
*
50978 ATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGC
1 ATCGGCACTTCCGATTCAAGACGAACGGAAGGAAGC
** * **
51014 ATCAACACTTCCGATCCAAGTTGAACGGAAGGA
1 ATCGGCACTTCCGATTCAAGACGAACGGAAGGA
51047 TGTAGCGCAC
Statistics
Matches: 129, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
36 128 0.99
37 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.19
Consensus pattern (36 bp):
ATCGGCACTTCCGATTCAAGACGAACGGAAGGAAGC
Found at i:50977 original size:72 final size:72
Alignment explanation
Indices: 50870--51046 Score: 255
Period size: 72 Copynumber: 2.5 Consensus size: 72
50860 GAAAGATAGA
* * * *
50870 ATCGACACTTTCGATTCAAGACGAACGGAATGAAGCATCGGAACTTTCGATTCAAGTAGAACGGA
1 ATCGACACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGAACTTCCGATTCAAGTAGAACGGA
*
50935 ATGAAGC
66 AGGAAGC
* * *
50942 ATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGA
1 ATCGACACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGAACTTCCGATTCAAGTAGAACGGA
51007 AGGAAGC
66 AGGAAGC
* * *
51014 ATCAACACTTCCGATCCAAGTTGAACGGAAGGA
1 ATCGACACTTCCGATTCAAGTCGAACGGAAGGA
51047 TGTAGCGCAC
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 93 1.00
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.19
Consensus pattern (72 bp):
ATCGACACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGAACTTCCGATTCAAGTAGAACGGA
AGGAAGC
Found at i:55470 original size:36 final size:38
Alignment explanation
Indices: 55428--55505 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 38
55418 TTAATTAATA
*
55428 TTATAATTTACATTATAAAT-CTATCTTTATGA-TATT
1 TTATAATTTACATTATAAATAATATCTTTATGATTATT
* * *
55464 TTATAATTTATATTATAATTAATATTTTTATGATTATT
1 TTATAATTTACATTATAAATAATATCTTTATGATTATT
55502 TTAT
1 TTAT
55506 TCTTCTCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 18 0.50
37 10 0.28
38 8 0.22
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (38 bp):
TTATAATTTACATTATAAATAATATCTTTATGATTATT
Found at i:56105 original size:2 final size:2
Alignment explanation
Indices: 56092--56124 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
56082 GTCAAATGCT
*
56092 TA TA TA TG 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 TA T
56125 CCTTTTCTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66946 original size:20 final size:22
Alignment explanation
Indices: 66915--66954 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
66905 AGAATTAGAA
66915 TTTTAAAGATTTT-GGATTTTT
1 TTTTAAAGATTTTAGGATTTTT
66936 TTTTAAA-ATTTTAGGATTT
1 TTTTAAAGATTTTAGGATTT
66955 GAAGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (22 bp):
TTTTAAAGATTTTAGGATTTTT
Found at i:69756 original size:70 final size:70
Alignment explanation
Indices: 69643--69784 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
69633 TGTCTTGCTT
*
69643 TCGCCATAGTACCAAATTTTATGAACAAATTTCTTCAAATTGCAGTAACTTTATCAGATATGTGG
1 TCGCCATAGTACCAAATTATATGAACAAATTTCTTCAAATTGCAGTAACTTTATCAGATATGTGG
69708 CCATA
66 CCATA
69713 TCGCCATAGTACCAAATTATATGAACAAATTTCTTCAAATTGCAGTAACTTTATCAGATATGTGG
1 TCGCCATAGTACCAAATTATATGAACAAATTTCTTCAAATTGCAGTAACTTTATCAGATATGTGG
69778 CCATA
66 CCATA
69783 TC
1 TC
69785 TCTAGGAATA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (70 bp):
TCGCCATAGTACCAAATTATATGAACAAATTTCTTCAAATTGCAGTAACTTTATCAGATATGTGG
CCATA
Found at i:82967 original size:15 final size:16
Alignment explanation
Indices: 82937--82969 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
82927 TTCAAATGGA
*
82937 GACAACACATCATTGT
1 GACAACACACCATTGT
82953 GACAACAC-CCATTGT
1 GACAACACACCATTGT
82968 GA
1 GA
82970 ACAGACAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.21
Consensus pattern (16 bp):
GACAACACACCATTGT
Found at i:89728 original size:2 final size:2
Alignment explanation
Indices: 89721--89785 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
89711 ATAACGTAAT
89721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
89763 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
89786 TTGATAAATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:94656 original size:8 final size:7
Alignment explanation
Indices: 94632--94673 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
94622 TTTTCATACA
94632 TGCA-TT
1 TGCATTT
94638 TGCATTT
1 TGCATTT
94645 TGCATCTT
1 TGCAT-TT
94653 TGCATTT
1 TGCATTT
* *
94660 TTCATTG
1 TGCATTT
94667 TGCATTT
1 TGCATTT
94674 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:94656 original size:15 final size:14
Alignment explanation
Indices: 94632--94673 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
94622 TTTTCATACA
94632 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
94645 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
94660 TTCATTGTGCATTT
1 TGCATTTTGCATTT
94674 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:94764 original size:27 final size:26
Alignment explanation
Indices: 94733--94792 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
94723 CATTCACATA
*
94733 TTTACATTTGAATTTGCATTTGCATTT
1 TTTACATTTGAATTTACATTTGCA-TT
* * *
94760 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGAATTTACATTTGCATT
94786 TTTACAT
1 TTTACAT
94793 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTACATTTGAATTTACATTTGCATT
Found at i:96783 original size:15 final size:15
Alignment explanation
Indices: 96757--96833 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
96747 TCCAGCAAAG
96757 AAAGGAAAAAAGAAAA
1 AAAGG-AAAAAGAAAA
*
96773 AGAGGAAAAAGAAAA
1 AAAGGAAAAAGAAAA
96788 AAAGG--AAAGAAATA
1 AAAGGAAAAAGAAA-A
** *
96802 GAAAACAAAAA-CAAA
1 -AAAGGAAAAAGAAAA
96817 AAA-GAAAAAGAAAA
1 AAAGGAAAAAGAAAA
96831 AAA
1 AAA
96834 TTAAATCAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
13 12 0.24
14 10 0.20
15 18 0.37
16 6 0.12
17 3 0.06
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (15 bp):
AAAGGAAAAAGAAAA
Found at i:96789 original size:24 final size:26
Alignment explanation
Indices: 96762--96832 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
96752 CAAAGAAAGG
* *
96762 AAAAAAGAAAAAGAGGAAA-AAGAA-
1 AAAAAAGAAAAAGAGAAAACAAAAAC
* *
96786 AAAAAGGAAAGAAATAGAAAACAAAAAC
1 AAAAAAG-AA-AAAGAGAAAACAAAAAC
*
96814 AAAAAAGAAAAAGAAAAAA
1 AAAAAAGAAAAAGAGAAAA
96833 ATTAAATCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
24 6 0.17
25 2 0.06
26 16 0.44
27 6 0.17
28 6 0.17
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.01
Consensus pattern (26 bp):
AAAAAAGAAAAAGAGAAAACAAAAAC
Found at i:99267 original size:114 final size:114
Alignment explanation
Indices: 99059--99284 Score: 362
Period size: 114 Copynumber: 2.0 Consensus size: 114
99049 AAGTGCCATG
*
99059 TGCTCATAGTAGAAATAAGAAGACTCAACAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAACAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * *
99124 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
* *
99173 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAACAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
99238 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
99285 CTGCATGATC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAACAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:101880 original size:22 final size:22
Alignment explanation
Indices: 101849--101901 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
101839 ATCTACACTC
**
101849 TTCAAAGATGGTAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
101871 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
101893 TTCAAAGAT
1 TTCAAAGAT
101902 AAAGCTTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:102498 original size:113 final size:113
Alignment explanation
Indices: 102301--102846 Score: 685
Period size: 112 Copynumber: 4.9 Consensus size: 113
102291 TTAGCAAAGT
* *
102301 TCAAATCCATCATTCAATGGATCAACA-TTCCAG-GACGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGA-GAGTTCATAATGAGAAGAACTCATCTG
* *
102364 AATAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
102413 TCAAATCCATCATTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
* *
102478 AGAAGGAAGAAGAATTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * ** *
102526 TTAAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATTTGA
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
* *
102591 AGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* ** * * * * **
102638 TTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
*
102703 AG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-C
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * ** * *
102749 CCTGAATTCATCACTT-GATGAAT-TATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCT
1 TC-AAATTCATCA-TTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCT
*
102812 GAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTT
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTT
102847 ATCTGAAGAG
Statistics
Matches: 383, Mismatches: 46, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
111 65 0.17
112 179 0.47
113 137 0.36
114 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:102699 original size:225 final size:222
Alignment explanation
Indices: 102303--102846 Score: 719
Period size: 225 Copynumber: 2.4 Consensus size: 222
102293 AGCAAAGTTC
* ** * *
102303 AAATCCATCATTCAATGGATCAACATTCCAGGACGAGTTCATAATGAGAAGAACTCATCTGAATA
1 AAATTCATCATTTGATGGATCATCATTCCAGGA-GAGTTCATAATGAGAAGAACTCATCTGAAGA
* * **
102368 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGG
65 A-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACCCGATGG
* * *
102433 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTTCAT
129 ATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCAT
* * *
102498 AATGAGAAGAACTTGTTCAACTTTTTGCTT
193 AATGAGAAGAACTTGTTCAACCTTTTCCCT
* *
102528 AAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAG
1 AAATTCATCATTTGATGGATCATCATT-CCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
102593 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGG
64 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACCCGATGG
* ** *
102658 ATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATA
129 ATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATA
*
102723 ATGAGAAGAATTTGTTCAACCTTTTCCCT
194 ATGAGAAGAACTTGTTCAACCTTTTCCCT
* * * * ** * *
102752 GAATTCATCACTTGATGAATTATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AAATTCATCATTTGATGGATCATCATTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
102817 GGAAGAAGAAGTTCATAATGAGAAGAACTT
65 AGAAGAAGAAGTTCATAATGAGAAGAACTT
102847 ATCTGAAGAG
Statistics
Matches: 279, Mismatches: 38, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
223 62 0.22
224 63 0.23
225 119 0.43
226 34 0.12
227 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (222 bp):
AAATTCATCATTTGATGGATCATCATTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACCCGATGGAT
CAACAGTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAAT
GAGAAGAACTTGTTCAACCTTTTCCCT
Found at i:102823 original size:19 final size:19
Alignment explanation
Indices: 102799--102862 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
102789 TTCATAATGA
102799 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
**
102818 GAAGAA-GAAGTTCAT-AATGA-
1 GAAGAACTTA--TC-TGAA-GAG
102838 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
102857 GAAGAA
1 GAAGAA
102863 GAAGTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 4 0.12
19 16 0.47
20 10 0.29
21 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.19
Consensus pattern (19 bp):
GAAGAACTTATCTGAAGAG
Found at i:102825 original size:22 final size:22
Alignment explanation
Indices: 102798--102865 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
102788 GTTCATAATG
102798 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
* *
102820 AGAAGAA-GT-TC--ATA-ATG-
1 AGAAGAACTTATCTGA-AGAGGA
102837 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
102859 AGAAGAA
1 AGAAGAA
102866 GTTCATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
17 7 0.20
18 4 0.11
19 3 0.09
20 3 0.09
21 4 0.11
22 14 0.40
ACGTcount: A:0.49, C:0.07, G:0.26, T:0.18
Consensus pattern (22 bp):
AGAAGAACTTATCTGAAGAGGA
Found at i:102840 original size:39 final size:39
Alignment explanation
Indices: 102786--102885 Score: 200
Period size: 39 Copynumber: 2.6 Consensus size: 39
102776 TTTCCAGAGA
102786 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
102825 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
102864 AAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
102886 GTTTAACCTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.46, C:0.08, G:0.24, T:0.22
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
Found at i:102854 original size:150 final size:151
Alignment explanation
Indices: 102676--102994 Score: 534
Period size: 150 Copynumber: 2.1 Consensus size: 151
102666 TGCCAGTTAG
*
102676 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
**
102741 ACCTTTTCC-CTGAATTCATCACTTGATGAATT-ATTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 ACCTTTTCCTC-GAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGA
102804 ACTTATCTGAAGAGGAAGAAGA
130 ACTTATCTGAAGAGGAAGAAGA
* * *
102826 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
* *
102891 ACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
102956 CTTATCTGAAGAGGAAGAAGA
131 CTTATCTGAAGAGGAAGAAGA
*
102977 AATTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
102995 TTTGTTTAAC
Statistics
Matches: 158, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
150 89 0.56
151 69 0.44
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (151 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
CTTATCTGAAGAGGAAGAAGA
Found at i:102864 original size:262 final size:264
Alignment explanation
Indices: 102564--103106 Score: 849
Period size: 262 Copynumber: 2.1 Consensus size: 264
102554 TACCAGTTAG
*
102564 AGTTCATAATGAGAAGAACTCATTTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * ** *
102629 ACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
102694 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
131 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
* *
102759 TCACTTGATGAATT-A-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAA
196 TCACTTGATGAATTAACTTTTT-CAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAA
102821 GAAGA
260 GAAGA
* * *
102826 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* ** * * *
102891 ACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
* * *
102956 CTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCA
131 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
*
103021 TCACTTGATGGATTAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
196 TCACTTGATGAATTAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
103086 AAGA
261 AAGA
103090 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
103107 TCTTGTTCAA
Statistics
Matches: 255, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
262 188 0.74
263 35 0.14
264 32 0.13
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (264 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
TCACTTGATGAATTAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
AAGA
Found at i:102971 original size:112 final size:112
Alignment explanation
Indices: 102825--103121 Score: 497
Period size: 112 Copynumber: 2.6 Consensus size: 112
102815 GAGGAAGAAG
102825 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
102890 AACCTTTTG-CTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
66 AACCTTTTGCCT-GAATTCATCACTTGATGGATTAACATTTCCAGAGA
* *
102937 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
* *
103002 AACCTTTTGCCTGAATTCATCACTTGATGGATTAACTTTTTCAGAGA
66 AACCTTTTGCCTGAATTCATCACTTGATGGATTAACATTTCCAGAGA
* * *
103049 AAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGATCTTGTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
103114 CAACCTTT
65 TAACCTTT
103122 GTTTGATGCT
Statistics
Matches: 173, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
112 133 0.77
113 40 0.23
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.30
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
AACCTTTTGCCTGAATTCATCACTTGATGGATTAACATTTCCAGAGA
Found at i:110159 original size:6 final size:6
Alignment explanation
Indices: 110075--110158 Score: 134
Period size: 6 Copynumber: 14.2 Consensus size: 6
110065 AAAATACTGC
110075 TGCCAG TGCCAG TGCCAG TGCCAG TGCCAG TGCCAG TGCCAG TGCCAG
1 TGCCAG TGCCAG TGCCAG TGCCAG TGCCAG TGCCAG TGCCAG TGCCAG
* * *
110123 TGCCA- TGCCAG TGCCAG TGCCAA TACCAG TACCAG T
1 TGCCAG TGCCAG TGCCAG TGCCAG TGCCAG TGCCAG T
110159 AGTGTCTGAA
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
5 5 0.07
6 69 0.93
ACGTcount: A:0.20, C:0.33, G:0.29, T:0.18
Consensus pattern (6 bp):
TGCCAG
Found at i:118766 original size:26 final size:27
Alignment explanation
Indices: 118726--118777 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
118716 AATATTTCTT
118726 TTAAAAGTAAACTAATATAATTAAATAA
1 TTAAAAGTAAACTAATA-AATTAAATAA
*
118754 TTAAAA-T-AACTAATAAATTTAATA
1 TTAAAAGTAAACTAATAAATTAAATA
118778 TTCATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 8 0.35
27 1 0.04
28 6 0.26
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (27 bp):
TTAAAAGTAAACTAATAAATTAAATAA
Done.