Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014924.1 Kokia drynarioides strain JFW-HI SEQ_129967, 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: 133071
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Warning! 142 characters in sequence are not A, C, G, or T
Found at i:12196 original size:30 final size:29
Alignment explanation
Indices: 12157--12542 Score: 379
Period size: 29 Copynumber: 13.2 Consensus size: 29
12147 TGGATACCCG
* *
12157 GGGGT-AAAATGGTAATTTTGGGAAATTTT
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTT
* * * ** *
12186 GGGGTTAAAATGGAATTCTT-AAACATTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
*
12214 GGGGTAAAAATGGAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
*
12243 GAGGTCAAAAATGGAATTTTTGGAAGTTTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
12273 GGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
12302 AGGGTTAAAAATGGAA-TTTTGGGAG-TTC
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTT
*
12330 GAGGGTAAAAAGGGAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
12360 GGGGGCAAAAATGAAATTTTTGGAAGTTTG
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTT
* *
12390 GGGGTAAGAATGGAATTTTTGGTAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
** *
12419 GGGGGTCAAAAATGGAATTTTTAAAAG-TTC
1 -GGGGT-AAAAATGGAATTTTTGGAAGTTTT
*
12449 GAGGGTAAAAATTGAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
12479 GAGGTTAAAAATGGTATTTTTGGAAG-TTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
12508 GAGGGTAAAAATGAAATTTTTGAAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
12538 GGGGT
1 GGGGT
12543 CTCTTAGGCA
Statistics
Matches: 297, Mismatches: 47, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
27 1 0.00
28 36 0.12
29 129 0.43
30 114 0.38
31 17 0.06
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTT
Found at i:12289 original size:59 final size:59
Alignment explanation
Indices: 12211--12543 Score: 395
Period size: 59 Copynumber: 5.7 Consensus size: 59
12201 TTCTTAAACA
12211 TTCG-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG
* * * *
12269 TTTTG-GGGTAAAAATGGAATTTTTGGAAGTTT-TAGGGTTAAAAATGGAA-TTTTGGGAG
1 -TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGA-GGTCAAAAATGGAATTTTTGGAAG
* * * * *
12327 TTCGAGGGTAAAAAGGGAATTTTTGGAAGTTTTGGGGGCAAAAATGAAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG
* * * * * * **
12386 TTTGGGGGTAAGAATGGAATTTTTGGTAGTTTTGGGGGTCAAAAATGGAATTTTTAAAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG-TTTCGAGGTCAAAAATGGAATTTTTGGAAG
* * * *
12446 TTCGAGGGTAAAAATTGAATTTTTGGAAGTTTTGAGGTTAAAAATGGTATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG
* * *
12505 TTCGAGGGTAAAAATGAAATTTTTGAAAGTTTCGGGGTC
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
12544 TCTTAGGCAA
Statistics
Matches: 230, Mismatches: 39, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
57 3 0.01
58 46 0.20
59 132 0.57
60 49 0.21
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG
Found at i:14368 original size:29 final size:27
Alignment explanation
Indices: 14352--14422 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 27
14342 TATAATAATT
14352 TTAAATTTGAAAATAAATTTAAACTTAAA
1 TTAAATTT-AAAATAAATTTAAAC-TAAA
*
14381 TTAAATTTAAAATAAATTTAAATTTTAAA
1 TTAAATTTAAAATAAATTTAAA--CTAAA
*
14410 ATAAATTTAAAAT
1 TTAAATTTAAAAT
14423 GAGTTTGAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 14 0.37
29 24 0.63
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (27 bp):
TTAAATTTAAAATAAATTTAAACTAAA
Found at i:14372 original size:18 final size:17
Alignment explanation
Indices: 14334--14420 Score: 87
Period size: 18 Copynumber: 5.4 Consensus size: 17
14324 CTTTATATAT
* *
14334 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
14351 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
*
14369 TTTAAA-CT----TAAA
1 TTTAAATTTAAAATAAA
14381 -TTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
14397 TTTAAATTTTAAAATAAA
1 TTTAAA-TTTAAAATAAA
14415 TTTAAA
1 TTTAAA
14421 ATGAGTTTGA
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
11 5 0.09
12 5 0.09
16 4 0.07
17 15 0.26
18 29 0.50
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:14387 original size:17 final size:16
Alignment explanation
Indices: 14351--14416 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
14341 TTATAATAAT
*
14351 TTTAAATTTGAAAATAAA
1 TTTAAA-TT-AAATTAAA
14369 TTTAAACTTAAATTAAA
1 TTTAAA-TTAAATTAAA
*
14386 TTTAAAATAAATTTAAA
1 TTTAAATTAAA-TTAAA
*
14403 TTTTAAAATAAATT
1 -TTTAAATTAAATT
14417 TAAAATGAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
16 4 0.09
17 20 0.47
18 19 0.44
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTAAATTAAATTAAA
Found at i:14390 original size:11 final size:11
Alignment explanation
Indices: 14365--14404 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
14355 AATTTGAAAA
*
14365 TAAATTTAAACT
1 TAAA-TTAAATT
14377 TAAATTAAATT
1 TAAATTAAATT
*
14388 TAAAATAAATT
1 TAAATTAAATT
14399 TAAATT
1 TAAATT
14405 TTAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 21 0.84
12 4 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:14407 original size:7 final size:6
Alignment explanation
Indices: 14334--14420 Score: 60
Period size: 6 Copynumber: 15.0 Consensus size: 6
14324 CTTTATATAT
* * *
14334 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* *
14381 -TTAAA TTTAAA -ATAAA TTTAAA TTTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA
14421 ATGAGTTTGA
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
4 1 0.02
5 18 0.29
6 33 0.52
7 11 0.17
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:14418 original size:11 final size:11
Alignment explanation
Indices: 14371--14422 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
14361 AAAATAAATT
* *
14371 TAAACTTAAAT
1 TAAATTTAAAA
14382 TAAATTTAAAA
1 TAAATTTAAAA
14393 TAAATTT-AAA
1 TAAATTTAAAA
14403 T---TTTAAAA
1 TAAATTTAAAA
14411 TAAATTTAAAA
1 TAAATTTAAAA
14422 T
1 T
14423 GAGTTTGAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
7 3 0.09
8 4 0.11
10 4 0.11
11 24 0.69
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:14677 original size:24 final size:24
Alignment explanation
Indices: 14642--14689 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
14632 TAAGAATATG
*
14642 AAAAGTTGAGGAAGATGAAAGGTT
1 AAAAGTTAAGGAAGATGAAAGGTT
14666 AAAAGTTAAGGAAGATGAAAGGTT
1 AAAAGTTAAGGAAGATGAAAGGTT
14690 GAACATCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (24 bp):
AAAAGTTAAGGAAGATGAAAGGTT
Found at i:14757 original size:24 final size:24
Alignment explanation
Indices: 14715--14762 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
14705 AATATTCATA
* **
14715 ATAAAAATTATATTTTAAAAATAT
1 ATAAAAATTAAATAATAAAAATAT
*
14739 ATAAAAATTAAATAATAAATATAT
1 ATAAAAATTAAATAATAAAAATAT
14763 GAACCATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAAAAATTAAATAATAAAAATAT
Found at i:17204 original size:3 final size:3
Alignment explanation
Indices: 17196--17220 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17186 TTAAGGTATG
17196 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
17221 CATTTATGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:17288 original size:117 final size:117
Alignment explanation
Indices: 17088--17311 Score: 448
Period size: 117 Copynumber: 1.9 Consensus size: 117
17078 AAAATATATG
17088 CTTCTTCTTCTTCTTCCATTTATGGTATCCATTTAATATAAAATCCACTAATAAAGCTATGAATT
1 CTTCTTCTTCTTCTTCCATTTATGGTATCCATTTAATATAAAATCCACTAATAAAGCTATGAATT
17153 TCCTTTATAAATTGGTTAACTTAGTTCTTACACTTAAGGTATGCTTCTTCTT
66 TCCTTTATAAATTGGTTAACTTAGTTCTTACACTTAAGGTATGCTTCTTCTT
17205 CTTCTTCTTCTTCTTCCATTTATGGTATCCATTTAATATAAAATCCACTAATAAAGCTATGAATT
1 CTTCTTCTTCTTCTTCCATTTATGGTATCCATTTAATATAAAATCCACTAATAAAGCTATGAATT
17270 TCCTTTATAAATTGGTTAACTTAGTTCTTACACTTAAGGTAT
66 TCCTTTATAAATTGGTTAACTTAGTTCTTACACTTAAGGTAT
17312 CCTTTTAATA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 107 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (117 bp):
CTTCTTCTTCTTCTTCCATTTATGGTATCCATTTAATATAAAATCCACTAATAAAGCTATGAATT
TCCTTTATAAATTGGTTAACTTAGTTCTTACACTTAAGGTATGCTTCTTCTT
Found at i:22628 original size:37 final size:37
Alignment explanation
Indices: 22573--22644 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
22563 AAGTGTTAAA
* * *
22573 TGTAGATAGAGAGTTTCTTATGGTTTGGAATTTAGTT
1 TGTAGACAGAGAGTTTCTTATAGTTTAGAATTTAGTT
*
22610 TGTAGACAGAGAAG-TTCTTATAGTTTAGAGTTTAG
1 TGTAGACAGAG-AGTTTCTTATAGTTTAGAATTTAG
22645 GGTTTAGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 28 0.93
38 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.42
Consensus pattern (37 bp):
TGTAGACAGAGAGTTTCTTATAGTTTAGAATTTAGTT
Found at i:24138 original size:13 final size:13
Alignment explanation
Indices: 24120--24147 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
24110 AAAAAATATC
24120 TTAATTTTTTTAT
1 TTAATTTTTTTAT
24133 TTAATTTTTTTAT
1 TTAATTTTTTTAT
24146 TT
1 TT
24148 TTTTTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTAATTTTTTTAT
Found at i:28494 original size:18 final size:17
Alignment explanation
Indices: 28452--28494 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
28442 ATTTTAAGTT
*
28452 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
28469 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
28487 TATAATTT
1 TATAATTT
28495 AGAATACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:28664 original size:89 final size:90
Alignment explanation
Indices: 28549--28715 Score: 219
Period size: 90 Copynumber: 1.9 Consensus size: 90
28539 TTAATATAAC
* * * * * *** *
28549 ATTTGGTACTTGAACTTGACACTTTTTTT-AATTTGGTACCTAAATTTTTTTTTGTCCAATTTGG
1 ATTTGGTACCTAAACTTGACAATTTTTTTAAAGTTCGTACCTAAATTTTTTGGGGTCCAAATTGG
28613 TACTCAAACTTGACACGTTTTGCTA
66 TACTCAAACTTGACACGTTTTGCTA
*
28638 ATTTGGTACCTAAACTTGACAATTTTTTTAAAGTTCGTACTTAAATTTTTTGGGGTCCAAATTGG
1 ATTTGGTACCTAAACTTGACAATTTTTTTAAAGTTCGTACCTAAATTTTTTGGGGTCCAAATTGG
**
28703 TACTTGAACTTGA
66 TACTCAAACTTGA
28716 ATATTTTTCC
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
89 26 0.40
90 39 0.60
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (90 bp):
ATTTGGTACCTAAACTTGACAATTTTTTTAAAGTTCGTACCTAAATTTTTTGGGGTCCAAATTGG
TACTCAAACTTGACACGTTTTGCTA
Found at i:29013 original size:63 final size:62
Alignment explanation
Indices: 28890--29080 Score: 252
Period size: 63 Copynumber: 3.2 Consensus size: 62
28880 TTAATACATT
** * * * *
28890 AGGTACCAAATTGAATCTAAAAAAAA-CTTAGGTGCCAAATTAGG-AAAAAATGTCATGTTC
1 AGGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGTCAAGTTC
*
28950 AGGTACCAAATTGGGTCCAAAAAAAAGTTTAGGCACCAAATTAGGGAAAAAAATGTCAAGTTC
1 AGGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTA-GGAAAAAAATGTCAAGTTC
29013 AGGTACCAAATTGGGT-C-AAAAAAAGTTTAGGTACC--ATTA-GAAAAAAATGTCAAGTTC
1 AGGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGTCAAGTTC
*
29070 AAGTACCAAAT
1 AGGTACCAAAT
29081 ATTATATTAT
Statistics
Matches: 119, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
57 28 0.24
59 4 0.03
60 23 0.19
61 30 0.25
62 3 0.03
63 31 0.26
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (62 bp):
AGGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGTCAAGTTC
Found at i:30839 original size:122 final size:123
Alignment explanation
Indices: 30692--31057 Score: 537
Period size: 123 Copynumber: 3.0 Consensus size: 123
30682 GATTTCGTTA
* * *
30692 AATATT-AAAACATGGAAGGTAATATCCTTTTGGAAAGGATATAATGCTTTAAT-AACTTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
* *
30755 ATATTTCTCTAAAGGAATAATTTCATTTTAATATGAGATATTAAATAAAAGGAAATTG
66 ATATTTCTATAAAGGAATAATTTCGTTTTAATATGAGATATTAAATAAAAGGAAATTG
*
30813 AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
* *
30878 ATAATTT-TTTAAAGGAAT-ATTTCCGTTTTAATATGAGATATTAAATAAAA-AAAAGTTG
66 AT-ATTTCTATAAAGGAATAATTT-CGTTTTAATATGAGATATTAAATAAAAGGAAA-TTG
*
30936 AATATTAAAAATATGGAAGTTAATAGT-CTTTTGGAAAGGATATAATGGTTTTAATAAACCTTCC
1 AATATTAAAAACATGGAAGTTAATA-TCCTTTTGGAAAGGATATAAT-GTTTTAATAAACCTTCC
* * *
31000 ATATATTTCTATAAAAGAATAATTTTGTTTTAATATGATATATTAAATAAAAGGAAAT
64 ATATATTTCTATAAAGGAATAATTTCGTTTTAATATGAGATATTAAATAAAAGGAAAT
31058 ATAGCAAAAT
Statistics
Matches: 221, Mismatches: 14, Indels: 17
0.88 0.06 0.07
Matches are distributed among these distances:
121 6 0.03
122 51 0.23
123 96 0.43
124 61 0.28
125 7 0.03
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.37
Consensus pattern (123 bp):
AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
ATATTTCTATAAAGGAATAATTTCGTTTTAATATGAGATATTAAATAAAAGGAAATTG
Found at i:33408 original size:15 final size:15
Alignment explanation
Indices: 33388--33419 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
33378 GAAACCCCTA
33388 AAAGTATGAATTCAT
1 AAAGTATGAATTCAT
33403 AAAGTATGAATTCAT
1 AAAGTATGAATTCAT
33418 AA
1 AA
33420 TTAATCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (15 bp):
AAAGTATGAATTCAT
Found at i:37933 original size:21 final size:21
Alignment explanation
Indices: 37909--37970 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
37899 CAAGAATCAA
37909 GTTATGGGTTTAGGGTTTAAG
1 GTTATGGGTTTAGGGTTTAAG
* * * *
37930 GTTATGAGTTAAGAGTTTGAG
1 GTTATGGGTTTAGGGTTTAAG
37951 GTT-TAGGGTTT-GGGTTTAAG
1 GTTAT-GGGTTTAGGGTTTAAG
37971 TGTTTAAGGT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 8 0.25
21 24 0.75
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (21 bp):
GTTATGGGTTTAGGGTTTAAG
Found at i:37940 original size:28 final size:28
Alignment explanation
Indices: 37908--37995 Score: 68
Period size: 28 Copynumber: 3.4 Consensus size: 28
37898 TCAAGAATCA
37908 AGTTATGGGTTTAGGGTTTAAGGTTATG
1 AGTTATGGGTTTAGGGTTTAAGGTTATG
* *
37936 AGTTAAGAGTTT-GAGGTTT-A-G----G
1 AGTTATGGGTTTAG-GGTTTAAGGTTATG
*
37958 -GTT-TGGGTTTAAGTGTTTAAGGTTATG
1 AGTTATGGGTTT-AGGGTTTAAGGTTATG
37985 AGTTATGGGTT
1 AGTTATGGGTT
37996 CATGGTTCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 21
0.63 0.07 0.30
Matches are distributed among these distances:
20 5 0.11
21 7 0.16
22 3 0.07
23 1 0.02
26 1 0.02
27 3 0.07
28 18 0.41
29 6 0.14
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (28 bp):
AGTTATGGGTTTAGGGTTTAAGGTTATG
Found at i:37975 original size:14 final size:13
Alignment explanation
Indices: 37915--37975 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 13
37905 TCAAGTTATG
37915 GGTTTAGGGTTTAA
1 GGTTT-GGGTTTAA
*
37929 GGTTATGAG-TTAA
1 GGTT-TGGGTTTAA
*
37942 GAGTTTGAGGTTTAG
1 G-GTTTG-GGTTTAA
37957 GGTTTGGGTTTAA
1 GGTTTGGGTTTAA
37970 GTGTTT
1 G-GTTT
37976 AAGGTTATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
13 14 0.37
14 19 0.50
15 5 0.13
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (13 bp):
GGTTTGGGTTTAA
Found at i:39379 original size:57 final size:58
Alignment explanation
Indices: 39316--39424 Score: 166
Period size: 58 Copynumber: 1.9 Consensus size: 58
39306 GTGGGTATTA
* * *
39316 AAAATATTATTAAATTATATATTA-TTTTATTAAATTGCATTTAATAATAATTATGTT
1 AAAATATAATTAAATTATATATTATTTTTATTAAATTACATTTAAAAATAATTATGTT
* *
39373 AAAATATAATTAAATTATTTATTATTTTTATTAAATTATATTTAAAAATAAT
1 AAAATATAATTAAATTATATATTATTTTTATTAAATTACATTTAAAAATAAT
39425 ATTATTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 22 0.48
58 24 0.52
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (58 bp):
AAAATATAATTAAATTATATATTATTTTTATTAAATTACATTTAAAAATAATTATGTT
Found at i:39433 original size:58 final size:57
Alignment explanation
Indices: 39311--39440 Score: 163
Period size: 58 Copynumber: 2.2 Consensus size: 57
39301 TTGGCGTGGG
* * *
39311 TATTAAAAATATTATTAAATTATATATTATTTTATTAAATTGCATTTAATAATAATTA
1 TATT-AAAATATAATTAAATTATATATTATTTTATTAAATTACATTTAAAAATAATTA
* * *
39369 TGTTAAAATATAATTAAATTATTTATTATTTTTATTAAATTATATTTAAAAATAA-TA
1 TATTAAAATATAATTAAATTATATATTA-TTTTATTAAATTACATTTAAAAATAATTA
*
39426 TTATTAAAATTTAAT
1 -TATTAAAATATAAT
39441 AACAATAATC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 24 0.39
58 38 0.61
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (57 bp):
TATTAAAATATAATTAAATTATATATTATTTTATTAAATTACATTTAAAAATAATTA
Found at i:40991 original size:47 final size:48
Alignment explanation
Indices: 40906--41000 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 48
40896 AACGGAGGAA
* * ** *
40906 TTAGTCAACAGTTTATTTGCTCGACCAGTGGTTTATCCACAACGTATT
1 TTAGTCAACAGTTCATCTGCTCGACCAGTGGTCCATCCAAAACGTATT
* *
40954 TTAGTCAACAG-TCATCTGCTCGACTAGTTGTCCATCCAAAACGTATT
1 TTAGTCAACAGTTCATCTGCTCGACCAGTGGTCCATCCAAAACGTATT
41001 AAATAGCTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 29 0.73
48 11 0.28
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (48 bp):
TTAGTCAACAGTTCATCTGCTCGACCAGTGGTCCATCCAAAACGTATT
Found at i:41137 original size:44 final size:47
Alignment explanation
Indices: 41024--41137 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 47
41014 CTGCACCCAT
* * * * *
41024 GGATGGTTCATCCACCATATTTTTAGTCGGTAGTTTATCTACACGGCC
1 GGATGGTTCATCCACCACA-TATTAGTCAGTAGTTTATCTACACAGAC
* * *
41072 AG-TGGTTCATCCACAACATATTAGT-AGT-TTTTATCTACACAGAC
1 GGATGGTTCATCCACCACATATTAGTCAGTAGTTTATCTACACAGAC
41116 GGATGGTTCATCCACCA-ATATT
1 GGATGGTTCATCCACCACATATT
41138 CTTATTGTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
44 19 0.35
45 15 0.27
46 6 0.11
47 14 0.25
48 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (47 bp):
GGATGGTTCATCCACCACATATTAGTCAGTAGTTTATCTACACAGAC
Found at i:44738 original size:29 final size:27
Alignment explanation
Indices: 44656--44738 Score: 67
Period size: 29 Copynumber: 2.8 Consensus size: 27
44646 GAATTGGATC
*
44656 AAATTAAAATTTTATGTATAAAATTACACA
1 AAATT-AAAGTTTATGTAT--AATTACACA
* * *
44686 AAATCAAAGTTCATATATACAATTACACA
1 AAATTAAAGTT--TATGTATAATTACACA
44715 TTAAATTAAAGTTTATGTATAATT
1 --AAATTAAAGTTTATGTATAATT
44739 TCGAGATTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
29 23 0.55
30 4 0.10
31 15 0.36
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.37
Consensus pattern (27 bp):
AAATTAAAGTTTATGTATAATTACACA
Found at i:46388 original size:29 final size:29
Alignment explanation
Indices: 46356--46413 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
46346 GTCAAATTAC
* *
46356 CGTGTGGC-AGCTCGTGTGGGTCACATGGG
1 CGTGTGGCAAGC-CATGTGGGCCACATGGG
*
46385 CGTGTGTCAAGCCATGTGGGCCACATGGG
1 CGTGTGGCAAGCCATGTGGGCCACATGGG
46414 TTGGGTCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.14, C:0.22, G:0.41, T:0.22
Consensus pattern (29 bp):
CGTGTGGCAAGCCATGTGGGCCACATGGG
Found at i:51695 original size:21 final size:21
Alignment explanation
Indices: 51671--51744 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
51661 TATTACACAT
*
51671 TTCTACCGATATAAGTGACAG
1 TTCTACCGATATAAGTGACAC
* * *
51692 TTCTACCAATACAAGTGACTC
1 TTCTACCGATATAAGTGACAC
* * ***
51713 TTCTATCGAAATAAGTCTTAC
1 TTCTACCGATATAAGTGACAC
51734 TTCTACCGATA
1 TTCTACCGATA
51745 CTAAAAACTC
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (21 bp):
TTCTACCGATATAAGTGACAC
Found at i:52488 original size:19 final size:18
Alignment explanation
Indices: 52455--52532 Score: 102
Period size: 19 Copynumber: 4.2 Consensus size: 18
52445 TACGAACCAA
52455 TATTGCTCAACGAGCTAG
1 TATTGCTCAACGAGCTAG
*
52473 TATTGCTCTTACGAGCTAG
1 TATTGCTC-AACGAGCTAG
*
52492 TATTTGCTCAACGAGATAG
1 TA-TTGCTCAACGAGCTAG
*
52511 TATTTGCTCGACGAGCTAG
1 TA-TTGCTCAACGAGCTAG
52530 TAT
1 TAT
52533 GTTATTCCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
18 9 0.17
19 38 0.72
20 6 0.11
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (18 bp):
TATTGCTCAACGAGCTAG
Found at i:52503 original size:38 final size:38
Alignment explanation
Indices: 52457--52532 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
52447 CGAACCAATA
* *
52457 TTGCTCAACGAGCTAGTA-TTGCTCTTACGAGCTAGTAT
1 TTGCTCAACGAGATAGTATTTGCTC-GACGAGCTAGTAT
52495 TTGCTCAACGAGATAGTATTTGCTCGACGAGCTAGTAT
1 TTGCTCAACGAGATAGTATTTGCTCGACGAGCTAGTAT
52533 GTTATTCCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 29 0.83
39 6 0.17
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (38 bp):
TTGCTCAACGAGATAGTATTTGCTCGACGAGCTAGTAT
Found at i:54191 original size:20 final size:20
Alignment explanation
Indices: 54166--54209 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
54156 AAACTTGTTG
54166 AATTTTTATATTTA-AAGTCA
1 AATTTTTATATTTAGAA-TCA
54186 AATTTTTATATTTAGAATCA
1 AATTTTTATATTTAGAATCA
54206 AATT
1 AATT
54210 AATGGAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
AATTTTTATATTTAGAATCA
Found at i:54589 original size:29 final size:30
Alignment explanation
Indices: 54538--54594 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
54528 AAAAAAAAAA
*
54538 AAAATCAAGTTTAAAACTAAA-TTAGTTTC
1 AAAATCAAATTTAAAACTAAATTTAGTTTC
* * *
54567 AAAATCAAATTTAAGAGTTAATTTAGTT
1 AAAATCAAATTTAAAACTAAATTTAGTT
54595 CAGTAAGACC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (30 bp):
AAAATCAAATTTAAAACTAAATTTAGTTTC
Found at i:56904 original size:15 final size:16
Alignment explanation
Indices: 56884--56913 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56874 CTTCCCTATT
56884 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
56899 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
56914 TTTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:56907 original size:22 final size:22
Alignment explanation
Indices: 56879--56939 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
56869 TTTGACTTCC
56879 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
56901 CTATTTTCTTTTATTTTTAA-T
1 CTATTTTCTTTTACTTTTAATT
*
56922 -TATGTTTCTTTTATTTTT
1 CTAT-TTTCTTTTACTTTT
56940 CCTTAGATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 3 0.08
21 18 0.50
22 15 0.42
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:58969 original size:7 final size:6
Alignment explanation
Indices: 58946--58975 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
58936 TCTCCTTTCT
58946 CCCTTC CCCTTC CCCTTCC CCCTTC CCCTT
1 CCCTTC CCCTTC CCCTT-C CCCTTC CCCTT
58976 TGAGAGACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCCTTC
Found at i:58969 original size:13 final size:12
Alignment explanation
Indices: 58946--58975 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
58936 TCTCCTTTCT
58946 CCCTTCCCCTTC
1 CCCTTCCCCTTC
58958 CCCTTCCCCCTTC
1 CCCTT-CCCCTTC
58971 CCCTT
1 CCCTT
58976 TGAGAGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (12 bp):
CCCTTCCCCTTC
Found at i:62073 original size:14 final size:14
Alignment explanation
Indices: 62054--62087 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
62044 AAAATAATTT
*
62054 ATTTTCTAGAAATC
1 ATTTTCCAGAAATC
*
62068 ATTTTCCGGAAATC
1 ATTTTCCAGAAATC
62082 ATTTTC
1 ATTTTC
62088 AACCAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (14 bp):
ATTTTCCAGAAATC
Found at i:63459 original size:21 final size:20
Alignment explanation
Indices: 63430--63484 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
63420 TACTAAGTTA
63430 ATTTTTTTATAATTACGGTT
1 ATTTTTTTATAATTACGGTT
* *
63450 ATTTTCTTTA-AAGTAAGGGTT
1 ATTTT-TTTATAA-TTACGGTT
*
63471 ATTTTTTTTTAATT
1 ATTTTTTTATAATT
63485 TAATGTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.60
Consensus pattern (20 bp):
ATTTTTTTATAATTACGGTT
Found at i:63829 original size:16 final size:17
Alignment explanation
Indices: 63790--63831 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
63780 TAAAAAAAAA
63790 TTGAACTTTTTGCTCGT
1 TTGAACTTTTTGCTCGT
* *
63807 TTG-ACTTTTT-TTCTT
1 TTGAACTTTTTGCTCGT
63822 TTGAACTTTT
1 TTGAACTTTT
63832 CCTCTTCTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 13 0.59
17 3 0.14
ACGTcount: A:0.12, C:0.14, G:0.12, T:0.62
Consensus pattern (17 bp):
TTGAACTTTTTGCTCGT
Found at i:76397 original size:162 final size:162
Alignment explanation
Indices: 76130--76449 Score: 559
Period size: 162 Copynumber: 2.0 Consensus size: 162
76120 AGGCATTTAG
* * **
76130 AATCCTGAAAATCAACAAGACCAATCTAGCATCACTCATCTGTCAACTCAACATGACAACTATGT
1 AATCCTGAAAATCAACAAGACCAATCCAGCATCACTAATCTGTCAACTCAACATGACAACTACAT
*
76195 TCATAATAAAGGATGAGTTATACATTCCACTACATAATGTATAAAGGCAAAGCTAAACAAGCTGA
66 TCATAATAAAGGATAAGTTATACATTCCACTACATAATGTATAAAGGCAAAGCTAAACAAGCTGA
* *
76260 GCTTTGAAGCGATAAATCAAAAGTTAGCCACT
131 GATTTGAAGCAATAAATCAAAAGTTAGCCACT
76292 AATCCTGAAAATCAACAAGACCAATCCAGCATCACTAATCTGTCAACTCAACATGACAACTACAT
1 AATCCTGAAAATCAACAAGACCAATCCAGCATCACTAATCTGTCAACTCAACATGACAACTACAT
* *
76357 TCGTGATAAAGGATAAGTTATACATTCCACTACATAATGTATAAAGGCAAAGCTAAACAAGCTGA
66 TCATAATAAAGGATAAGTTATACATTCCACTACATAATGTATAAAGGCAAAGCTAAACAAGCTGA
76422 GATTTGAAGCAATAAATCAAAAGTTAGC
131 GATTTGAAGCAATAAATCAAAAGTTAGC
76450 AACCCAAAAA
Statistics
Matches: 149, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 149 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.23
Consensus pattern (162 bp):
AATCCTGAAAATCAACAAGACCAATCCAGCATCACTAATCTGTCAACTCAACATGACAACTACAT
TCATAATAAAGGATAAGTTATACATTCCACTACATAATGTATAAAGGCAAAGCTAAACAAGCTGA
GATTTGAAGCAATAAATCAAAAGTTAGCCACT
Found at i:80274 original size:6 final size:6
Alignment explanation
Indices: 80263--80293 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
80253 ATCATTTTTT
80263 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
80294 TTTCAAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:80687 original size:67 final size:65
Alignment explanation
Indices: 80640--80776 Score: 231
Period size: 67 Copynumber: 2.1 Consensus size: 65
80630 TTAAGTATAT
80640 TATATATATATATATATGAAAGATAAGGGCAAAGGTATAAAATAATTTAAGGGATCAAAATTAAA
1 TATATATATATATATATGAAAGATAAGGGCAAAGGTATAAAATAATTTAA--GATCAAAATTAAA
80705 TA
64 TA
80707 TATATATATATATATATGAAAGATAAGGGCAAAGGTATAAAATAATTTAAGGGATCAAAATTAAA
1 TATATATATATATATATGAAAGATAAGGGCAAAGGTATAAAATAATTTAA--GATCAAAATTAAA
80772 T-
64 TA
80773 TATA
1 TATA
80777 ATTTTTTAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 4 0.06
67 66 0.94
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.31
Consensus pattern (65 bp):
TATATATATATATATATGAAAGATAAGGGCAAAGGTATAAAATAATTTAAGATCAAAATTAAATA
Found at i:81311 original size:27 final size:26
Alignment explanation
Indices: 81255--81318 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
81245 CCAAAAATTG
*
81255 ATAAATTG-TAATATATTTTTTATTA
1 ATAAAATGTTAATATATTTTTTATTA
*
81280 TTAAAATGTTAATATAATTTTTT-TCTA
1 ATAAAATGTTAATAT-ATTTTTTAT-TA
*
81307 ATAAAATATTAA
1 ATAAAATGTTAA
81319 AAAGATTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 6 0.19
26 7 0.22
27 19 0.59
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
ATAAAATGTTAATATATTTTTTATTA
Found at i:81768 original size:11 final size:11
Alignment explanation
Indices: 81741--81774 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
81731 TCCATTTCCT
81741 TCTTTTCTTTCTC
1 TCTTTT-TTT-TC
81754 TCTTTTTTTTC
1 TCTTTTTTTTC
81765 TCTTTTTTTT
1 TCTTTTTTTT
81775 TTTCACCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 3 0.14
13 6 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TCTTTTTTTTC
Found at i:81776 original size:13 final size:13
Alignment explanation
Indices: 81741--81775 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
81731 TCCATTTCCT
*
81741 TCTTTTCTTTCTC
1 TCTTTTTTTTCTC
81754 TCTTTTTTTTCTC
1 TCTTTTTTTTCTC
81767 T-TTTTTTTT
1 TCTTTTTTTT
81776 TTCACCTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TCTTTTTTTTCTC
Found at i:85940 original size:3 final size:3
Alignment explanation
Indices: 85934--85983 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
85924 TTCTTGAGGA
85934 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
85982 GT
1 GT
85984 GTGTGTGTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
GTT
Found at i:86513 original size:25 final size:25
Alignment explanation
Indices: 86484--86562 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
86474 AAACCAAACC
*
86484 AAGCATTTGTGGCGAGTTATGTGTA
1 AAGCATTTGTGGCGAGTTATCTGTA
* *
86509 AAGCATTTGAGGTGAGTTATCTGTA
1 AAGCATTTGTGGCGAGTTATCTGTA
* * *
86534 AATC-TCTTGTGGCGAATTATCTGAA
1 AAGCAT-TTGTGGCGAGTTATCTGTA
86559 AAGC
1 AAGC
86563 CTATGTGATG
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 1 0.02
25 43 0.98
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (25 bp):
AAGCATTTGTGGCGAGTTATCTGTA
Found at i:86611 original size:26 final size:24
Alignment explanation
Indices: 86582--86641 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
86572 GTATTATTTG
* *
86582 GGAAGCCTTAGTGGCGAGGTTATCTA
1 GGAAGCCTTA-TGGC-AAGTCATCTA
86608 GGAAGCCTTTATGGCAAGTCATCTA
1 GGAAGCC-TTATGGCAAGTCATCTA
*
86633 GAAAGCCTT
1 GGAAGCCTT
86642 TCCAGATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.07
25 14 0.47
26 11 0.37
27 3 0.10
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (24 bp):
GGAAGCCTTATGGCAAGTCATCTA
Found at i:90069 original size:24 final size:24
Alignment explanation
Indices: 90011--90069 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
90001 CAGAAGCATT
*
90011 CCACAAGACAG-AGAAAAAGTTTG
1 CCACAAGACAGAAGAAAAAGTGTG
*
90034 CCACAAGGCAGAAG-AAAAGTGTG
1 CCACAAGACAGAAGAAAAAGTGTG
*
90057 TCACAAAGACAGA
1 CCAC-AAGACAGA
90070 TAAAAACTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.10
Consensus pattern (24 bp):
CCACAAGACAGAAGAAAAAGTGTG
Found at i:90821 original size:5 final size:5
Alignment explanation
Indices: 90811--90843 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
90801 AGCACCTCCT
90811 TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCC
1 TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCC
90844 ATTCTTCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.61, G:0.00, T:0.21
Consensus pattern (5 bp):
TCCCA
Found at i:92840 original size:25 final size:26
Alignment explanation
Indices: 92790--92840 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
92780 ACGAATTTTC
92790 TTAAAATTTTACCAAGGGTAAAATTG
1 TTAAAATTTTACCAAGGGTAAAATTG
**
92816 TTAAAATTTTACTGA-GGTAAAATTG
1 TTAAAATTTTACCAAGGGTAAAATTG
92841 AGATGAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (26 bp):
TTAAAATTTTACCAAGGGTAAAATTG
Found at i:93642 original size:113 final size:113
Alignment explanation
Indices: 93420--93649 Score: 340
Period size: 113 Copynumber: 2.0 Consensus size: 113
93410 ATATGAAAAC
* *
93420 ACAAGTACGTATTCTGTTAAGGTTTATTACTATAAATATCACAATCTGGGTCTGTTTTCAAAATT
1 ACAAGTACGTATTCAGTTAAGGTTTATTACTATAAATATCACAATCTGAGTCTGTTTTCAAAATT
*
93485 TTAATTTTTTGCTGTGTAAGAAAATCGTTTTCAAACCAGATTTTTCCA
66 TTAATTTTTTGCTGTGCAAGAAAATCGTTTTCAAACCAGATTTTTCCA
*
93533 ACAAGTACGTATTCAGTTAAGGTTTATTGCTATAAATATCACAAAT-TGAGTC-GATTTTCAAAA
1 ACAAGTACGTATTCAGTTAAGGTTTATTACTATAAATATCAC-AATCTGAGTCTG-TTTTCAAAA
* * * *
93596 TTTTAATTTTTT-TTGTGCAAGAAAATTGTTTTCAAATCAGGTTTTTTCCA
64 TTTTAATTTTTTGCTGTGCAAGAAAATCGTTTTCAAACCA-GATTTTTCCA
93646 ACAA
1 ACAA
93650 TTGCATCTTG
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
112 24 0.23
113 79 0.75
114 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (113 bp):
ACAAGTACGTATTCAGTTAAGGTTTATTACTATAAATATCACAATCTGAGTCTGTTTTCAAAATT
TTAATTTTTTGCTGTGCAAGAAAATCGTTTTCAAACCAGATTTTTCCA
Found at i:101523 original size:114 final size:113
Alignment explanation
Indices: 101368--101594 Score: 296
Period size: 114 Copynumber: 2.0 Consensus size: 113
101358 GTACCATTAA
* * ** * *** *
101368 ATAATGTAATTTATTTTAATACGAAATAATATTTTTGTAATTTCTCTAATTGTTTTGGTGTTCGG
1 ATAATATAATCTATTTTAATACGAAATAATATTTTCATAATTTCTCTAACTAAGTTGGTGTCCGG
101433 TTGACTCATGACATC-AACTCAATC-AGAGACTTAAATAATAATATAGAT
66 TTGACTCATGACA-CAAACTCAATCAAGA-ACTTAAATAATAATATAGAT
* *
101481 ATAATATAATCTATTTTAATCACGAAATGATATTTTCATAATTTCTCTAACTAAGTTGGTGTCCT
1 ATAATATAATCTATTTTAAT-ACGAAATAATATTTTCATAATTTCTCTAACTAAGTTGGTGTCCG
* *
101546 GTTGATTCATGACACAAACTCATTCAAGAACTTAAATAATAATATAGAT
65 GTTGACTCATGACACAAACTCAATCAAGAACTTAAATAATAATATAGAT
101595 GATGAACAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
113 19 0.19
114 76 0.78
115 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (113 bp):
ATAATATAATCTATTTTAATACGAAATAATATTTTCATAATTTCTCTAACTAAGTTGGTGTCCGG
TTGACTCATGACACAAACTCAATCAAGAACTTAAATAATAATATAGAT
Found at i:101801 original size:18 final size:19
Alignment explanation
Indices: 101780--101816 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
101770 AAAAAAATCT
*
101780 AATTT-AACACTAAAAATA
1 AATTTAAACACAAAAAATA
101798 AATTTAAACACAAAAAATA
1 AATTTAAACACAAAAAATA
101817 CCCATATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (19 bp):
AATTTAAACACAAAAAATA
Found at i:110046 original size:3 final size:3
Alignment explanation
Indices: 110040--110070 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
110030 TGTTGTTTAG
110040 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
110071 AGAATTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:111766 original size:31 final size:31
Alignment explanation
Indices: 111731--111827 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 31
111721 ATACCAAATA
111731 TTAAACTTTGAATCTATCAACCAATATGCCC
1 TTAAACTTTGAATCTATCAACCAATATGCCC
** * * *
111762 TTAAA-TGGGCACCTCATCTCATACCAA-AT---A
1 TTAAACTTTG-A-ATC-TATCA-ACCAATATGCCC
111792 TTAAACTTTGAATCTATCAACCAATATGCCC
1 TTAAACTTTGAATCTATCAACCAATATGCCC
111823 TTAAA
1 TTAAA
111828 TGGGCACCTC
Statistics
Matches: 47, Mismatches: 10, Indels: 18
0.63 0.13 0.24
Matches are distributed among these distances:
27 5 0.11
28 6 0.13
29 2 0.04
30 8 0.17
31 13 0.28
32 2 0.04
33 6 0.13
34 5 0.11
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.31
Consensus pattern (31 bp):
TTAAACTTTGAATCTATCAACCAATATGCCC
Found at i:111795 original size:61 final size:61
Alignment explanation
Indices: 111720--111850 Score: 262
Period size: 61 Copynumber: 2.1 Consensus size: 61
111710 ACCATCAAAA
111720 CATACCAAATATTAAACTTTGAATCTATCAACCAATATGCCCTTAAATGGGCACCTCATCT
1 CATACCAAATATTAAACTTTGAATCTATCAACCAATATGCCCTTAAATGGGCACCTCATCT
111781 CATACCAAATATTAAACTTTGAATCTATCAACCAATATGCCCTTAAATGGGCACCTCATCT
1 CATACCAAATATTAAACTTTGAATCTATCAACCAATATGCCCTTAAATGGGCACCTCATCT
111842 CATACCAAA
1 CATACCAAA
111851 CATAACATTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.28
Consensus pattern (61 bp):
CATACCAAATATTAAACTTTGAATCTATCAACCAATATGCCCTTAAATGGGCACCTCATCT
Found at i:112620 original size:45 final size:45
Alignment explanation
Indices: 112532--112634 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
112522 TTTCAACTAA
* * *
112532 GGTCTTATAACATATCATATATGAAGTCGTGGTATCTCTCAACCAC
1 GGTCTTA-AACATATCAGAAATGAAGTCGTGGAATCTCTCAACCAC
* *
112578 GGTCTTAAACATATCAGAAATGATGTCTTGGAATCT-TGCAACCAC
1 GGTCTTAAACATATCAGAAATGAAGTCGTGGAATCTCT-CAACCAC
* *
112623 GATCTTATACAT
1 GGTCTTAAACAT
112635 TTCAATTCCA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.02
45 41 0.84
46 7 0.14
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (45 bp):
GGTCTTAAACATATCAGAAATGAAGTCGTGGAATCTCTCAACCAC
Found at i:117604 original size:2 final size:2
Alignment explanation
Indices: 117599--117626 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
117589 ACACAATCTA
117599 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
117627 TCTAAGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:118869 original size:23 final size:25
Alignment explanation
Indices: 118843--118888 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
118833 CCAATTAGGG
118843 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
118866 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
118889 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:122893 original size:17 final size:17
Alignment explanation
Indices: 122871--122911 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
122861 AAAAAATATA
122871 TTTATTTTCATTTTCA-T
1 TTTATTTT-ATTTTCATT
*
122888 TTTATTTTATTTTTATT
1 TTTATTTTATTTTCATT
122905 TTTATTT
1 TTTATTT
122912 CAATTATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTATTTTCATT
Found at i:123890 original size:19 final size:19
Alignment explanation
Indices: 123868--123904 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
123858 AAAAAATTGA
123868 AAAAAAATTTGA-AAAAAGG
1 AAAAAAA-TTGAGAAAAAGG
123887 AAAAAAATTGAGAAAAAG
1 AAAAAAATTGAGAAAAAG
123905 AAGAGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (19 bp):
AAAAAAATTGAGAAAAAGG
Found at i:124972 original size:25 final size:23
Alignment explanation
Indices: 124931--124976 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
124921 CCAATTAGGG
124931 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
124954 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
124977 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:132010 original size:13 final size:13
Alignment explanation
Indices: 131975--132014 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
131965 TAAAGAAGTG
131975 ATATAGTAAAA-AA
1 ATATA-TAAAAGAA
131988 ATA-A-AAAAGAA
1 ATATATAAAAGAA
131999 ATATATAAAAGAA
1 ATATATAAAAGAA
132012 ATA
1 ATA
132015 AAATACATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.17
11 5 0.21
12 2 0.08
13 13 0.54
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (13 bp):
ATATATAAAAGAA
Done.