Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014129.1 Kokia drynarioides strain JFW-HI SEQ_129162, 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: 188230
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 245 characters in sequence are not A, C, G, or T
Found at i:2070 original size:20 final size:19
Alignment explanation
Indices: 2034--2073 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2024 GAATTATAAC
*
2034 TTTTATTTATGATTTTTTT
1 TTTTATTTATGAATTTTTT
*
2053 TTTTAATTTTTGAATTTTTT
1 TTTT-ATTTATGAATTTTTT
2073 T
1 T
2074 ATAATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTATTTATGAATTTTTT
Found at i:2087 original size:19 final size:19
Alignment explanation
Indices: 2048--2087 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2038 ATTTATGATT
* * *
2048 TTTTTTTTTAATTTTTGAA
1 TTTTTTTATAATTTGTAAA
2067 TTTTTTTATAATTTGTAAA
1 TTTTTTTATAATTTGTAAA
2086 TT
1 TT
2088 ATTTACTAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTTTTATAATTTGTAAA
Found at i:11639 original size:10 final size:10
Alignment explanation
Indices: 11530--11641 Score: 51
Period size: 10 Copynumber: 11.5 Consensus size: 10
11520 TATTTTCATT
11530 TAAAA-ATTA
1 TAAAATATTA
*
11539 TAAAAAATTA
1 TAAAATATTA
*
11549 TTAAAATATCA
1 -TAAAATATTA
*
11560 TTAAA-A-TA
1 TAAAATATTA
*
11568 TCAAATATTA
1 TAAAATATTA
11578 -AAAA-ATTA
1 TAAAATATTA
* **
11586 TGTAAA-CCTA
1 T-AAAATATTA
11596 TAAAATATTA
1 TAAAATATTA
11606 TAACAAT-TTCA
1 TAA-AATATT-A
11617 TAAAAGT-TTA
1 TAAAA-TATTA
*
11627 TAAAATATAA
1 TAAAATATTA
11637 TAAAA
1 TAAAA
11642 AAACTAAAAG
Statistics
Matches: 79, Mismatches: 13, Indels: 21
0.70 0.12 0.19
Matches are distributed among these distances:
8 9 0.11
9 14 0.18
10 38 0.48
11 18 0.23
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (10 bp):
TAAAATATTA
Found at i:11732 original size:9 final size:9
Alignment explanation
Indices: 11687--11734 Score: 60
Period size: 10 Copynumber: 5.0 Consensus size: 9
11677 TAGAACATAT
11687 AAAATTATAA
1 AAAATTAT-A
11697 AAAATTCATA
1 AAAATT-ATA
11707 AAAATCTATA
1 AAAAT-TATA
*
11717 AATATTATA
1 AAAATTATA
11726 AAAATTATA
1 AAAATTATA
11735 CTAATTAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 12 0.35
10 19 0.56
11 3 0.09
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:12792 original size:24 final size:24
Alignment explanation
Indices: 12765--12810 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
12755 TTTTATCTGC
*
12765 CTTTACGGTACGTTTTTTCCTTTA
1 CTTTACGATACGTTTTTTCCTTTA
** *
12789 CTTTGTGATTCGTTTTTTCCTT
1 CTTTACGATACGTTTTTTCCTT
12811 ATGGCACGTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.09, C:0.20, G:0.13, T:0.59
Consensus pattern (24 bp):
CTTTACGATACGTTTTTTCCTTTA
Found at i:13506 original size:18 final size:18
Alignment explanation
Indices: 13468--13507 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
13458 TTTCCTATAT
*
13468 TTTTAATATTTTTTTTAA
1 TTTTAATATTTTTTGTAA
13486 TTTTAACTATTTTTTGT-A
1 TTTTAA-TATTTTTTGTAA
13504 TTTT
1 TTTT
13508 TTTAAATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTAATATTTTTTGTAA
Found at i:13911 original size:9 final size:8
Alignment explanation
Indices: 13892--13922 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
13882 AATTTTTTTA
13892 ATAAAATT
1 ATAAAATT
13900 ATAAAATAT
1 ATAAAAT-T
13909 ATAAAATT
1 ATAAAATT
13917 ATAAAA
1 ATAAAA
13923 AAAAATAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
ATAAAATT
Found at i:14602 original size:17 final size:16
Alignment explanation
Indices: 14582--14622 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
14572 TCTATGATTA
*
14582 TTTATGAATTTTATAAT
1 TTTATGAACTTTA-AAT
14599 TTTATGAACTTTAAAT
1 TTTATGAACTTTAAAT
14615 TATTATGA
1 T-TTATGA
14623 TAAAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (16 bp):
TTTATGAACTTTAAAT
Found at i:15341 original size:25 final size:25
Alignment explanation
Indices: 15313--15384 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
15303 ATTTTTAGTA
*
15313 ATTTTGTATAAATTTATTTATTTAT
1 ATTTTTTATAAATTTATTTATTTAT
**
15338 ATTTTTTACGAATTTATATT-TTTAT
1 ATTTTTTATAAATTTAT-TTATTTAT
*
15363 -TTATTTTATAAATTTATATATT
1 ATT-TTTTATAAATTTATTTATT
15385 GAAAATATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 3 0.08
25 33 0.87
26 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (25 bp):
ATTTTTTATAAATTTATTTATTTAT
Found at i:15421 original size:14 final size:14
Alignment explanation
Indices: 15402--15429 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15392 TTATAAGCTT
15402 TTATATATTTTTAA
1 TTATATATTTTTAA
15416 TTATATATTTTTAA
1 TTATATATTTTTAA
15430 AGCTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATATATTTTTAA
Found at i:16007 original size:30 final size:30
Alignment explanation
Indices: 15976--16033 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
15966 TTTATTTTAT
*
15976 TTTAAATATATT-TTTATTAGGATTTAATA
1 TTTAAAAATATTATTTATTAGGATTTAATA
* *
16005 TTTAAAAATATTATTTATTTGTATTTAAT
1 TTTAAAAATATTATTTATTAGGATTTAAT
16034 TTATGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (30 bp):
TTTAAAAATATTATTTATTAGGATTTAATA
Found at i:17170 original size:153 final size:153
Alignment explanation
Indices: 16892--17197 Score: 522
Period size: 153 Copynumber: 2.0 Consensus size: 153
16882 CGATCACGAT
*
16892 AATGGCAACATTGAAGTATGATATTTCACTGTTGGATCGCAACACCAGATTCGCGTTGTGGTAAG
1 AATGGCAACATTGAAGTATGATATTTCACTGTTGGATCGCAACACCAGATTCGCGTTGTGGCAAG
* * * *
16957 TAAAGATGCAAGTAGTTCTTGCGCAGATGGATTTGGAGGATGCCCTGTTAGGGTTAGATAAGATG
66 TAAAGATGCAAGCAGTTCTTACGCAGATAGATTTGGAGGATGCCCTGTTAGGGTTAGATAAAATG
*
17022 CCTTTGAATTTGACAGATGAAAA
131 CCTTCGAATTTGACAGATGAAAA
* * *
17045 AATGGCGACATTGAAGTATGATATTTCTCTGTTGGATCGCAACACCTGATTCGCGTTGTGGCAAG
1 AATGGCAACATTGAAGTATGATATTTCACTGTTGGATCGCAACACCAGATTCGCGTTGTGGCAAG
*
17110 TAAAGATGCAAGCAGTTCTTACGTAGATAGATTTGGAGGATGCCCTGTTAGGGTTAGATAAAATG
66 TAAAGATGCAAGCAGTTCTTACGCAGATAGATTTGGAGGATGCCCTGTTAGGGTTAGATAAAATG
17175 CCTTCGAATTTGACAGATGAAAA
131 CCTTCGAATTTGACAGATGAAAA
17198 GAGGAAACAT
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
153 143 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (153 bp):
AATGGCAACATTGAAGTATGATATTTCACTGTTGGATCGCAACACCAGATTCGCGTTGTGGCAAG
TAAAGATGCAAGCAGTTCTTACGCAGATAGATTTGGAGGATGCCCTGTTAGGGTTAGATAAAATG
CCTTCGAATTTGACAGATGAAAA
Found at i:21010 original size:15 final size:16
Alignment explanation
Indices: 20990--21019 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20980 CTTTCCTATT
20990 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
21005 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
21020 TTTTTAATTC
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:21012 original size:22 final size:22
Alignment explanation
Indices: 20985--21045 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
20975 TTCGACTTTC
20985 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
21007 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
21029 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
21046 CCTCAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:21035 original size:21 final size:22
Alignment explanation
Indices: 20999--21045 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
20989 TTTCTATTTC
*
20999 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
21021 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
21042 TTTT
1 TTTT
21046 CCTCAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:25483 original size:14 final size:16
Alignment explanation
Indices: 25454--25483 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25444 TTTTTATGAT
25454 AATATATTTATAAAAA
1 AATATATTTATAAAAA
25470 AATATATTT-TAAAA
1 AATATATTTATAAAA
25484 TCAAATGAGA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATATTTATAAAAA
Found at i:30716 original size:25 final size:26
Alignment explanation
Indices: 30651--30717 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
30641 AAATTTAAAC
30651 TAAAAGAACATAAAAATTAAGAGAAT
1 TAAAAGAACATAAAAATTAAGAGAAT
* * * * *
30677 AAAAAAAAAAGAAAAA-TGAGA-AAGT
1 TAAAAGAACATAAAAATTAAGAGAA-T
30702 TAAAAGAACATAAAAA
1 TAAAAGAACATAAAAA
30718 GAAATTTAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
24 2 0.06
25 17 0.55
26 12 0.39
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.13
Consensus pattern (26 bp):
TAAAAGAACATAAAAATTAAGAGAAT
Found at i:37959 original size:26 final size:26
Alignment explanation
Indices: 37930--37982 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
37920 ATAAAAAATA
37930 TTACACTCGAGCTCAACCCAATCTGC
1 TTACACTCGAGCTCAACCCAATCTGC
37956 TTACACTCGAGCTCAACCCAATCTGC
1 TTACACTCGAGCTCAACCCAATCTGC
37982 T
1 T
37983 CGTATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.38, G:0.11, T:0.25
Consensus pattern (26 bp):
TTACACTCGAGCTCAACCCAATCTGC
Found at i:42624 original size:20 final size:21
Alignment explanation
Indices: 42586--42629 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
42576 CACATTATTT
*
42586 TTTATAATATATATTTTTAGTA
1 TTTATAATATATATCTTTAG-A
42608 TTTATAATATA-A-CTTTAGA
1 TTTATAATATATATCTTTAGA
42627 TTT
1 TTT
42630 TTTTGTCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 5 0.24
21 1 0.05
22 11 0.52
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTATAATATATATCTTTAGA
Found at i:42674 original size:29 final size:29
Alignment explanation
Indices: 42632--42687 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
42622 TTAGATTTTT
* *
42632 TTGTCATGATCATCTCAAATATTCATATG
1 TTGTCATAATCATCTCAAAAATTCATATG
42661 TTGTCATAATCATCTCAAAAATTCATA
1 TTGTCATAATCATCTCAAAAATTCATA
42688 CGTGCTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (29 bp):
TTGTCATAATCATCTCAAAAATTCATATG
Found at i:42992 original size:30 final size:30
Alignment explanation
Indices: 42949--43005 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
42939 AATAGTTTAT
*
42949 ATTTTTATATATTTTTTAAAAAATTAAATCA
1 ATTTTTATATA-TTTTTAAAAAACTAAATCA
42980 ATTTTT-TATATTTTTAAAAAACTAAA
1 ATTTTTATATATTTTTAAAAAACTAAA
43006 ATATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 15 0.60
30 4 0.16
31 6 0.24
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTTTTATATATTTTTAAAAAACTAAATCA
Found at i:43338 original size:27 final size:30
Alignment explanation
Indices: 43285--43347 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 30
43275 AAATCATATG
* *
43285 TATTAATTTTGATGTAAATTAATTTTTAAT
1 TATTTATTTTGATGTAAATTAAATTTTAAT
43315 TATTTATTTT-ATGT-AA-TAAATTTTAAT
1 TATTTATTTTGATGTAAATTAAATTTTAAT
*
43342 TGTTTA
1 TATTTA
43348 ATAAATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 15 0.50
28 2 0.07
29 4 0.13
30 9 0.30
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (30 bp):
TATTTATTTTGATGTAAATTAAATTTTAAT
Found at i:44885 original size:6 final size:6
Alignment explanation
Indices: 44874--44914 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
44864 CTGAAACTCT
44874 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCC
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCC
44915 TAAACTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
AACCCG
Found at i:49538 original size:3 final size:3
Alignment explanation
Indices: 49530--49592 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
49520 GTCAATTTGC
49530 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49578 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
49593 TTCTAAATGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:56096 original size:22 final size:22
Alignment explanation
Indices: 56040--56103 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
56030 ACCAAAATTA
** * *
56040 TAAAATCATGAACCGTAAATCT
1 TAAAATCACAAACCCTAAACCT
*
56062 T-AAATCCCAAAACCCTAAACCT
1 TAAAATCAC-AAACCCTAAACCT
*
56084 TAAAATCACAAACTCTAAAC
1 TAAAATCACAAACCCTAAAC
56104 TCAAATTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
21 5 0.15
22 22 0.67
23 6 0.18
ACGTcount: A:0.48, C:0.27, G:0.03, T:0.22
Consensus pattern (22 bp):
TAAAATCACAAACCCTAAACCT
Found at i:56601 original size:21 final size:21
Alignment explanation
Indices: 56559--56601 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
56549 TTAAAATATT
* *
56559 AAACCATAAATTATAGACCTC
1 AAACCATAAATCATAAACCTC
* *
56580 AAACCATAAATCCTAAATCTC
1 AAACCATAAATCATAAACCTC
56601 A
1 A
56602 CTTTACTATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (21 bp):
AAACCATAAATCATAAACCTC
Found at i:73451 original size:89 final size:90
Alignment explanation
Indices: 73358--73526 Score: 234
Period size: 90 Copynumber: 1.9 Consensus size: 90
73348 AACTTTTTTC
** * * * * *
73358 AAAAAAAAAAAAA-CAATTAAGCGTCTGCTTTTATTTTGCATTCACTTTGATATTTGAAA-TTTC
1 AAAAAAAAAAAAAGCAATTAAGCCCCTACTTTTATTTTGCACTCAATTGGATACTT-AAACTTTC
73421 AAAATGCATAAAAAAGTCCCATAATT
65 AAAATGCATAAAAAAGTCCCATAATT
73447 AAAAAAAAAAAAAGCAATTAAGCCCCTACTTTTATTTTGCACTCAATTGGATACTTAAACTTTCA
1 AAAAAAAAAAAAAGCAATTAAGCCCCTACTTTTATTTTGCACTCAATTGGATACTTAAACTTTCA
* *
73512 AAGTGCATCAAAAAG
66 AAATGCATAAAAAAG
73527 GTCCTCAAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
89 16 0.23
90 53 0.77
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.31
Consensus pattern (90 bp):
AAAAAAAAAAAAAGCAATTAAGCCCCTACTTTTATTTTGCACTCAATTGGATACTTAAACTTTCA
AAATGCATAAAAAAGTCCCATAATT
Found at i:74052 original size:93 final size:92
Alignment explanation
Indices: 73851--74070 Score: 266
Period size: 93 Copynumber: 2.4 Consensus size: 92
73841 AAGGGTCTTG
* * *
73851 TTGATGTA-TTTGACAGTTCAAGTACCCAATTGAATGCAAAAAAAATCGAGAGCTTAATTGCTTT
1 TTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAAAAAAGCGAGAGCTTAATTGCTTT
* * ***
73915 TTTTTTTTTTAAGTTTGAGGGTTTTTT
66 TTTTTTTTTTAAGTTTAAAGACCTTTT
* * *
73942 TTGATGCATTTTGAAAGTTCAAGTACTCAATTGAGTGCAAAATAAAAGC-AGATGCTTAATTGTT
1 TTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAA-AAAAGCGAGA-GCTTAATTGCT
74006 TTGTTTTTTTTTTAAGTTTAAAGACCTTTT
64 TT-TTTTTTTTTTAAGTTTAAAGACCTTTT
* * *
74036 TT-ATGCATTTTTAAAGTTTAAGTACCCAAGTGAAT
1 TTGATGCATTTTGAAAGTTCAAGTACCCAATTGAAT
74071 AAAAAACCAT
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
91 7 0.06
92 33 0.30
93 45 0.41
94 24 0.22
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.43
Consensus pattern (92 bp):
TTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAAAAAAGCGAGAGCTTAATTGCTTT
TTTTTTTTTTAAGTTTAAAGACCTTTT
Found at i:79051 original size:20 final size:21
Alignment explanation
Indices: 79028--79077 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
79018 AAAAGATTGA
*
79028 AAAACATTAAAA-ATAGATAG-
1 AAAA-ATTAAAATATAAATAGC
79048 AAAAA-TAAAATATAAATAGC
1 AAAAATTAAAATATAAATAGC
79068 AAAAATTAAA
1 AAAAATTAAA
79078 TTGAAACGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.19
19 8 0.31
20 9 0.35
21 4 0.15
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.20
Consensus pattern (21 bp):
AAAAATTAAAATATAAATAGC
Found at i:79071 original size:19 final size:18
Alignment explanation
Indices: 79035--79073 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
79025 TGAAAAACAT
*
79035 TAAAAATAGATAGAAAAA
1 TAAAAATAAATAGAAAAA
79053 TAAAATATAAATAGCAAAAA
1 TAAAA-ATAAATAG-AAAAA
79073 T
1 T
79074 TAAATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (18 bp):
TAAAAATAAATAGAAAAA
Found at i:80360 original size:20 final size:22
Alignment explanation
Indices: 80317--80377 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
80307 GCTCTCTCTC
* *
80317 TCTCTCTCTCAGCTGCTGCTTCTT
1 TCTCTCTCTC-TCT-CTTCTTCTT
*
80341 TCTTTCT-TCT-TCTTCTTCTT
1 TCTCTCTCTCTCTCTTCTTCTT
80361 TCTCTCTCTCTCTCTTC
1 TCTCTCTCTCTCTCTTC
80378 CGTAATTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 14 0.45
21 4 0.13
22 5 0.16
23 2 0.06
24 6 0.19
ACGTcount: A:0.02, C:0.38, G:0.05, T:0.56
Consensus pattern (22 bp):
TCTCTCTCTCTCTCTTCTTCTT
Found at i:80641 original size:2 final size:2
Alignment explanation
Indices: 80634--80660 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
80624 GATCACAAGG
80634 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
80661 AATCTAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:81871 original size:200 final size:202
Alignment explanation
Indices: 81523--81902 Score: 522
Period size: 200 Copynumber: 1.9 Consensus size: 202
81513 ACTCTCATTT
* *
81523 AACTGATTTGTAGCTTGAAATTGACATTTTTTTCTTTTTCTCTTAGTCGATTTTAATTTTTTCAT
1 AACTGATTTGTAGCTTGAAATTGACA-TTTTTTCCTTTTCTCTTAGTCAATTTTAATTTTTTCAT
* *
81588 TGTAACTTTAGGAGGTAAACCTTGGTAATGAATTTGGTATTATGTGTGTGTGGTTAACAGGTATT
65 TGTAACTTGAGGAGGTAAACCTTGGAAATGAATTTGGTATTATGTGTGTGTGGTTAACAGGTATT
* * *
81653 GAAATGAATGGGATTCAGCA-AAGGAAAGGTCAGAATTTTGAGAAA-TTTCCTGGAATGACTGTG
130 GAAATGAATAGAATTCAGCACAA-GAAAGGTCAGAATATTGA-AAAGTTTCCTGGAATGACTGTG
81716 CTGTCATATA
193 CTGTCATATA
* * *
81726 AACTGATTTGTAGCTTGAATTTGACA-TTTTTCCTTTTCTCTTAGTTAATTTTAATTTTCTT-TT
1 AACTGATTTGTAGCTTGAAATTGACATTTTTTCCTTTTCTCTTAGTCAATTTTAATTTT-TTCAT
** * * *
81789 TGTATGTTGA-GA-G-AAACCTTGGAAATGAATTTGGTGCTTTTGATTTGTGTGGTTAACAGGTA
65 TGTAACTTGAGGAGGTAAACCTTGGAAATGAATTTGGT-ATTATG-TGTGTGTGGTTAACAGGTA
81851 TTGAAATGAATAGAATTCAGCACAAGAAAGGTCAGAATATTGAAAAGTTTCC
128 TTGAAATGAATAGAATTCAGCACAAGAAAGGTCAGAATATTGAAAAGTTTCC
81903 AGGATGCCTG
Statistics
Matches: 157, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
198 21 0.13
199 8 0.05
200 62 0.39
201 39 0.25
202 2 0.01
203 25 0.16
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (202 bp):
AACTGATTTGTAGCTTGAAATTGACATTTTTTCCTTTTCTCTTAGTCAATTTTAATTTTTTCATT
GTAACTTGAGGAGGTAAACCTTGGAAATGAATTTGGTATTATGTGTGTGTGGTTAACAGGTATTG
AAATGAATAGAATTCAGCACAAGAAAGGTCAGAATATTGAAAAGTTTCCTGGAATGACTGTGCTG
TCATATA
Found at i:85944 original size:12 final size:12
Alignment explanation
Indices: 85927--85957 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
85917 GTGACTACCT
85927 GGTGGTGGAAAG
1 GGTGGTGGAAAG
85939 GGTGGTGGAAAG
1 GGTGGTGGAAAG
85951 GGTGGTG
1 GGTGGTG
85958 CAGAAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.61, T:0.19
Consensus pattern (12 bp):
GGTGGTGGAAAG
Found at i:90834 original size:18 final size:18
Alignment explanation
Indices: 90806--90857 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
90796 TTCAAAAAAG
*
90806 CAAAATAATTTTTAAAATT
1 CAAAAT-ATTTATAAAATT
*
90825 CAAAATATTTACAAAATT
1 CAAAATATTTATAAAATT
* *
90843 CCAAAT-TTTCTAAAA
1 CAAAATATTTATAAAA
90858 AAATATAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 7 0.25
18 15 0.54
19 6 0.21
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.37
Consensus pattern (18 bp):
CAAAATATTTATAAAATT
Found at i:93289 original size:26 final size:26
Alignment explanation
Indices: 93256--93308 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
93246 TTTGGGCGAG
93256 ATTGTTAAATAAAATAGGGCTTTAGT
1 ATTGTTAAATAAAATAGGGCTTTAGT
93282 ATTGTTAAATAAAATAGGGCTTTAGT
1 ATTGTTAAATAAAATAGGGCTTTAGT
93308 A
1 A
93309 GCTACTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (26 bp):
ATTGTTAAATAAAATAGGGCTTTAGT
Found at i:98239 original size:201 final size:194
Alignment explanation
Indices: 97796--98242 Score: 479
Period size: 195 Copynumber: 2.3 Consensus size: 194
97786 TACCAGTACT
* * * * *
97796 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAACGTATGCGATACCCCAGCCATCGGTACAGT
1 CGATGCTGCTCGCACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACAGT
* * * ** *
97861 GCCTGTCTGTACTATAAACTGTTCCCTAACAATGTTGCTCACACAAGCTGTCGAGAGTATGCAAT
66 ACCTG-CTGCACTATAAACTATTCCCTAACAATACTGCTCACACAAGCTGTCGAGAATATGCAAT
* * *
97926 AAGCATAGTCCTAGCCATCGTAGGGCTTGTAATCCATTTAGGATCCATATATCTTTCCCAAATCA
130 AAGCATAATCCTAACCATCGTAAGGCTTGTAATCCATTTAGGATCCATATATCTTTCCCAAATCA
* ** * *
97991 CGATGCTGCTAGCACGAGCTGTCGAGGACTCACAACATATGCGGTACCTTAGCCATTGATACAGT
1 CGATGCTGCTCGCACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACAGT
* * * * * *
98056 ATCTG-TGCA-TAT-AATTATTCCTTAACGATACTGCTCACACGAGCTGTCGAGAATATGCACTT
66 ACCTGCTGCACTATAAACTATTCCCTAACAATACTGCTCACACAAGCTGTCGAGAATATGCA-AT
* *
98118 ATGCATAAAT-CTCAACCATCGTAAGGCTTGTAATCCATTTAGGATCCATATTTCTTTTCTCATT
130 AAGCAT-AATCCT-AACCATCGTAAGGCTTGTAATCCATTTAGGATCCATATATC--TT-TC---
* *
98182 TCCTGACTCA
187 -CC-AAATCA
* *
98192 CGATGCTGCTCGCACGAGCTGTCGATGACTCGTAACATATACGGTACCTCA
1 CGATGCTGCTCGCACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCA
98243 CCCACCGCGT
Statistics
Matches: 206, Mismatches: 35, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
191 39 0.19
192 11 0.05
193 43 0.21
195 60 0.29
196 2 0.01
200 2 0.01
201 49 0.24
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (194 bp):
CGATGCTGCTCGCACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACAGT
ACCTGCTGCACTATAAACTATTCCCTAACAATACTGCTCACACAAGCTGTCGAGAATATGCAATA
AGCATAATCCTAACCATCGTAAGGCTTGTAATCCATTTAGGATCCATATATCTTTCCCAAATCA
Found at i:101996 original size:48 final size:48
Alignment explanation
Indices: 101951--102044 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
101941 AATGGCACAT
* *
101951 AAGTGCTGAGTAATAAAGGGCACACAAAGTGCTAATCAGAGGGCACACG
1 AAGTGCT-AATAACAAAGGGCACACAAAGTGCTAATCAGAGGGCACACG
* *
102000 AAGTGCTAATAACAGAGGGCACACAAAGTGCTGATCAGAGGGCAC
1 AAGTGCTAATAACAAAGGGCACACAAAGTGCTAATCAGAGGGCAC
102045 GAAACGTGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 34 0.83
49 7 0.17
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.14
Consensus pattern (48 bp):
AAGTGCTAATAACAAAGGGCACACAAAGTGCTAATCAGAGGGCACACG
Found at i:102021 original size:25 final size:23
Alignment explanation
Indices: 101967--102105 Score: 140
Period size: 23 Copynumber: 6.0 Consensus size: 23
101957 TGAGTAATAA
101967 AGGGCACACAAAGTGCTAATCAG
1 AGGGCACACAAAGTGCTAATCAG
*
101990 AGGGCACACGAAGTGCTAATAACAG
1 AGGGCACACAAAGTGCTAAT--CAG
*
102015 AGGGCACACAAAGTGCTGATCAG
1 AGGGCACACAAAGTGCTAATCAG
* *
102038 AGGGCACGA-AACGTGCTAAACAG
1 AGGGCAC-ACAAAGTGCTAATCAG
* * *
102061 AGAGCACACACAGTGCTGATCAG
1 AGGGCACACAAAGTGCTAATCAG
* *
102084 A-AGCACACACAA-TGCTGATCAG
1 AGGGCACACA-AAGTGCTAATCAG
102106 TAAGCGCGCT
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
22 19 0.19
23 58 0.59
24 1 0.01
25 21 0.21
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (23 bp):
AGGGCACACAAAGTGCTAATCAG
Found at i:102054 original size:48 final size:45
Alignment explanation
Indices: 101967--102092 Score: 157
Period size: 48 Copynumber: 2.7 Consensus size: 45
101957 TGAGTAATAA
*
101967 AGGGCACACAAAGTGCTAATCAGAGGGCACACGAAGTGCTAATAACAG
1 AGGGCACACAAAGTGCTGATCAGAGGGCACAC-AAGTGCT-A-AACAG
102015 AGGGCACACAAAGTGCTGATCAGAGGGCACGA-AACGTGCTAAACAG
1 AGGGCACACAAAGTGCTGATCAGAGGGCAC-ACAA-GTGCTAAACAG
* * *
102061 AGAGCACACACAGTGCTGATCAGA-AGCACACA
1 AGGGCACACAAAGTGCTGATCAGAGGGCACACA
102093 CAATGCTGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
44 1 0.01
45 5 0.07
46 27 0.38
47 3 0.04
48 34 0.48
49 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.11
Consensus pattern (45 bp):
AGGGCACACAAAGTGCTGATCAGAGGGCACACAAGTGCTAAACAG
Found at i:102730 original size:10 final size:10
Alignment explanation
Indices: 102715--102744 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
102705 TCAGTCTCTA
102715 ATATTTTTCT
1 ATATTTTTCT
102725 ATATTTTTCT
1 ATATTTTTCT
102735 ATGATTTTTC
1 AT-ATTTTTC
102745 AAAGTCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (10 bp):
ATATTTTTCT
Found at i:105290 original size:18 final size:19
Alignment explanation
Indices: 105249--105296 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
105239 TGATGATGTC
* *
105249 ATAAAAATATAAAGGATAA
1 ATAAAATTATAAAGGAAAA
105268 A-AAAATTATAAA-GAAAA
1 ATAAAATTATAAAGGAAAA
105285 ATAAAATATATA
1 ATAAAAT-TATA
105297 TTAATAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (19 bp):
ATAAAATTATAAAGGAAAA
Found at i:106159 original size:40 final size:39
Alignment explanation
Indices: 106073--106164 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 39
106063 TTAAAATTTA
* * * *
106073 TATTTAATAAAATAAAATATTTATTATATTTATTTGTGTT
1 TATTTAATATAATAAAACATTTATTATAGTTA-TTGTGTG
*
106113 TTTTTAATATAATAAAACATTTATTATAGTTA-TGATAGTG
1 TATTTAATATAATAAAACATTTATTATAGTTATTG-T-GTG
106153 TATTTAATATAA
1 TATTTAATATAA
106165 AAACTTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
38 2 0.05
39 1 0.02
40 41 0.93
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (39 bp):
TATTTAATATAATAAAACATTTATTATAGTTATTGTGTG
Found at i:107124 original size:22 final size:23
Alignment explanation
Indices: 107080--107124 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
107070 TTAATCTTTT
* * *
107080 AAAAATTGCACTTTTACTATCGA
1 AAAAATTACAATTTAACTATCGA
107103 AAAAATTACAATTTAACT-TCGA
1 AAAAATTACAATTTAACTATCGA
107125 TCCCCTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (23 bp):
AAAAATTACAATTTAACTATCGA
Found at i:114351 original size:28 final size:28
Alignment explanation
Indices: 114313--114367 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
114303 AAATGAGCAT
*
114313 CATGACCTTTGGGTCAACAGGGAGTAAG
1 CATGACCTTTGGGTCAACAAGGAGTAAG
*
114341 CATGACCTTTGGGTCAATAAGGAGTAA
1 CATGACCTTTGGGTCAACAAGGAGTAA
114368 ATCGAATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACAAGGAGTAAG
Found at i:119612 original size:5 final size:5
Alignment explanation
Indices: 119602--119629 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
119592 TTCAATTCCT
119602 CCCCA CCCCA CCCCA CCCCA CCCCA CCC
1 CCCCA CCCCA CCCCA CCCCA CCCCA CCC
119630 ATCCCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCCA
Found at i:119917 original size:3 final size:3
Alignment explanation
Indices: 119909--119951 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
119899 GTATCTAACA
* *
119909 ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT CTT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
119952 ACTAGGGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:129389 original size:9 final size:9
Alignment explanation
Indices: 129371--129405 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
129361 TAGTTTGGTG
*
129371 TTCGATTTA
1 TTCGAATTA
129380 TTCGAATTA
1 TTCGAATTA
*
129389 TTCGAGTTA
1 TTCGAATTA
129398 TTCGAATT
1 TTCGAATT
129406 CAAAAACTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (9 bp):
TTCGAATTA
Found at i:129398 original size:18 final size:18
Alignment explanation
Indices: 129371--129405 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
129361 TAGTTTGGTG
*
129371 TTCGATTTATTCGAATTA
1 TTCGAGTTATTCGAATTA
129389 TTCGAGTTATTCGAATT
1 TTCGAGTTATTCGAATT
129406 CAAAAACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TTCGAGTTATTCGAATTA
Found at i:129929 original size:6 final size:6
Alignment explanation
Indices: 129918--129951 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
129908 AGTGAGCAAC
129918 AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGC
1 AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGC
129952 GTAGATACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.35, T:0.15
Consensus pattern (6 bp):
AGGCAT
Found at i:134854 original size:27 final size:26
Alignment explanation
Indices: 134793--134844 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
134783 AACTGCAAAG
134793 AAATCTTAATTCAACTCAATTTTTTT
1 AAATCTTAATTCAACTCAATTTTTTT
134819 AAATCTTAATTCAACTCAATTTTTTT
1 AAATCTTAATTCAACTCAATTTTTTT
134845 TCTATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (26 bp):
AAATCTTAATTCAACTCAATTTTTTT
Found at i:135691 original size:20 final size:20
Alignment explanation
Indices: 135666--135716 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
135656 GGCTTGGGAT
*
135666 TTCTATCGGTAAAACTTCAC
1 TTCTATCGATAAAACTTCAC
* *
135686 TTCTATCGATATAACTTCAG
1 TTCTATCGATAAAACTTCAC
*
135706 TTCTACCGATA
1 TTCTATCGATA
135717 CCTTGAAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (20 bp):
TTCTATCGATAAAACTTCAC
Found at i:137340 original size:69 final size:68
Alignment explanation
Indices: 137260--137395 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 68
137250 TAATTAAACT
* * ** * *
137260 TAATCACTTTAATATTAAATTAACATAATATTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATAATAAATTAACAAAATA-CAATCAAAATAAATATTAAATTAAATTTAATATT
137325 AAAA
65 AAAA
* * * *
137329 TAATCATTTTAATAATAAATTAATAAAATACAATTAAAATAAGTATTAAATTAAATTTAATATTA
1 TAATCACTTTAATAATAAATTAACAAAATACAATCAAAATAAATATTAAATTAAATTTAATATTA
137394 AA
66 AA
137396 CTATTAAAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
68 31 0.54
69 26 0.46
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (68 bp):
TAATCACTTTAATAATAAATTAACAAAATACAATCAAAATAAATATTAAATTAAATTTAATATTA
AAA
Found at i:138876 original size:7 final size:8
Alignment explanation
Indices: 138846--138880 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
138836 AAGTTAACTG
138846 ATTTTTATA
1 ATTTTT-TA
138855 TATTTTTTA
1 -ATTTTTTA
138864 ATTTTTTA
1 ATTTTTTA
138872 ATTTTTTA
1 ATTTTTTA
138880 A
1 A
138881 ATAATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 2 0.08
10 6 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
ATTTTTTA
Found at i:140443 original size:109 final size:109
Alignment explanation
Indices: 140243--140499 Score: 329
Period size: 109 Copynumber: 2.4 Consensus size: 109
140233 ATAAATATTA
* * * * *
140243 GCAAATACCGTTGGTTTATCCAATTAGAGTTGGGTTCACTATTTAATTCATCAGTTTATTTGACT
1 GCAAATACCGTTGGTTTATCCAACTAGAGCTGGGCTCACTAGTTAATTCATCAGTTTATCTGACT
*
140308 AGTGCTTAACACATATTCATCTGTTTATCCGACTAGCGCTGGGT
66 AGTGCTTAACACATATTCATCTGTTTATCCGACTAGCGCTGGGC
* * *
140352 TCAAATACCGTTGGTTTATCCAACTAGAGCTGGGCTCACTAGTTCATTCGTCAGTTTATCTGACT
1 GCAAATACCGTTGGTTTATCCAACTAGAGCTGGGCTCACTAGTTAATTCATCAGTTTATCTGACT
* ** *
140417 AGTG-TTGGACACATATTTGT-TGGTTTATCCGACTAGCGTTGGGC
66 AGTGCTT-AACACATATTCATCT-GTTTATCCGACTAGCGCTGGGC
* * * *
140461 GCAAACATCATTGATTTATCCAACTAGAGCTGGGCTCAC
1 GCAAATACCGTTGGTTTATCCAACTAGAGCTGGGCTCAC
140500 ATGTAATATT
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
108 3 0.02
109 125 0.98
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (109 bp):
GCAAATACCGTTGGTTTATCCAACTAGAGCTGGGCTCACTAGTTAATTCATCAGTTTATCTGACT
AGTGCTTAACACATATTCATCTGTTTATCCGACTAGCGCTGGGC
Found at i:140549 original size:109 final size:109
Alignment explanation
Indices: 140330--140560 Score: 249
Period size: 109 Copynumber: 2.1 Consensus size: 109
140320 ATATTCATCT
** * * *
140330 GTTTATCCGACTAGCGCTGGGTTCAAATACCGTTGGTTTATCCAACTAGAGCTGGGCTCACTAGT
1 GTTTATCCGACTAGCGCTGGGCGCAAACACCATTGATTTATCCAACTAGAGCTGGGCTCACTAGT
* * * * * *
140395 TCATTCGTCAGTTTATCTGACTAGTGTTGGACACATATTTGTTG
66 TCATTCGTCAGTTTATCCGAATAGCGCTGGACACAAATCTGTTG
* *
140439 GTTTATCCGACTAGCGTTGGGCGCAAACATCATTGATTTATCCAACTAGAGCTGGGCTCAC-ATG
1 GTTTATCCGACTAGCGCTGGGCGCAAACACCATTGATTTATCCAACTAGAGCTGGGCTCACTA-G
*
140503 TAAT-ATT-GTC-GATTTATCCGAATAGCGCTGGGCACAAACTCT-TTG
65 T--TCATTCGTCAG-TTTATCCGAATAGCGCTGGACACAAA-TCTGTTG
140548 GTTTATCC-ACTAG
1 GTTTATCCGACTAG
140561 GCATCGGGTG
Statistics
Matches: 103, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
108 7 0.07
109 90 0.87
110 5 0.05
111 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33
Consensus pattern (109 bp):
GTTTATCCGACTAGCGCTGGGCGCAAACACCATTGATTTATCCAACTAGAGCTGGGCTCACTAGT
TCATTCGTCAGTTTATCCGAATAGCGCTGGACACAAATCTGTTG
Found at i:146205 original size:41 final size:41
Alignment explanation
Indices: 146140--146229 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 41
146130 AGTCATAAAA
*
146140 CTTCCTCTTTAAAAGATCTCATGCT-T-CAC-AGGTTTATAAGT
1 CTTCCTTTTTAAAAGATCTCATGCTCTAC-CGAGG--TATAAGT
*
146181 CTTCCTTTTTAAACA-ATCTTATGCTCTACCGAGGTATAAGT
1 CTTCCTTTTTAAA-AGATCTCATGCTCTACCGAGGTATAAGT
146222 CTTCCTTT
1 CTTCCTTT
146230 AAACATAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
41 36 0.84
42 3 0.07
43 4 0.09
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.41
Consensus pattern (41 bp):
CTTCCTTTTTAAAAGATCTCATGCTCTACCGAGGTATAAGT
Found at i:146270 original size:42 final size:42
Alignment explanation
Indices: 146219--146406 Score: 272
Period size: 42 Copynumber: 4.4 Consensus size: 42
146209 CCGAGGTATA
*
146219 AGTCTTCCTTTAAACATAATCTCATTCTCA-TCCTGAGACATG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATTCC-GAGACATG
*
146261 AGTCTTCCTTTAAACATAATCTCATCCTCA-TCACGAGACATG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATTC-CGAGACATG
*
146303 AGTCTTCCTTCTTAAACATATTCTCATGCTCATTCCGAGACATG
1 AGTCTTCC-T-TTAAACATAATCTCATGCTCATTCCGAGACATG
*
146347 AGTCTTCCTTTAAACATATTCTCATGCTCATTCCGAGACATG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATTCCGAGACATG
*
146389 AGTCTTCCATTTATACAT
1 AGTCTTCC-TTTAAACAT
146407 CAAGTGTTTC
Statistics
Matches: 137, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
42 88 0.64
43 11 0.08
44 36 0.26
45 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.36
Consensus pattern (42 bp):
AGTCTTCCTTTAAACATAATCTCATGCTCATTCCGAGACATG
Found at i:146335 original size:86 final size:84
Alignment explanation
Indices: 146219--146406 Score: 272
Period size: 86 Copynumber: 2.2 Consensus size: 84
146209 CCGAGGTATA
*
146219 AGTCTTCCTTTAAACATAATCTCATTCTCA-TCCTGAGACATGAGTCTTCCTTTAAACATAATCT
1 AGTCTTCCTTTAAACATAATCTCATGCTCATTCC-GAGACATGAGTCTTCCTTTAAACATAATCT
146283 CATCCTCA-TCACGAGACATG
65 CATCCTCATTC-CGAGACATG
* *
146303 AGTCTTCCTTCTTAAACATATTCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATATTC
1 AGTCTTCC-T-TTAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATAATC
*
146368 TCATGCTCATTCCGAGACATG
64 TCATCCTCATTCCGAGACATG
*
146389 AGTCTTCCATTTATACAT
1 AGTCTTCC-TTTAAACAT
146407 CAAGTGTTTC
Statistics
Matches: 94, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
84 8 0.09
85 8 0.09
86 73 0.78
87 5 0.05
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.36
Consensus pattern (84 bp):
AGTCTTCCTTTAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATAATCTC
ATCCTCATTCCGAGACATG
Found at i:146364 original size:128 final size:126
Alignment explanation
Indices: 146178--146406 Score: 327
Period size: 128 Copynumber: 1.8 Consensus size: 126
146168 CAGGTTTATA
* * **
146178 AGTCTTCCTTTTTAAACAATCTTATGCTCTACCGAGGTATAAGTCTTCCTTTAAACATAATCTCA
1 AGTCTTCCTTCTTAAACAATCTCATGCTCTACCGAGACATAAGTCTTCCTTTAAACATAATCTCA
*
146243 TTCTCA-TCCTGAGACATGAGTCTTCC-TTTAAACATAATCTCATCCTCATCACGAGACATG
66 TGCTCATTCC-GAGACATGAGTCTTCCATTTAAACATAATCTCATCCTCATCACGAGACATG
* * *
146303 AGTCTTCCTTCTTAAACATATTCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATATTC
1 AGTCTTCCTTCTTAAACA-A-TCTCATGCTC-TACCGAGACATAAGTCTTCCTTTAAACATAATC
*
146368 TCATGCTCATTCCGAGACATGAGTCTTCCATTTATACAT
63 TCATGCTCATTCCGAGACATGAGTCTTCCATTTAAACAT
146407 CAAGTGTTTC
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
125 17 0.19
126 1 0.01
127 9 0.10
128 52 0.58
129 11 0.12
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (126 bp):
AGTCTTCCTTCTTAAACAATCTCATGCTCTACCGAGACATAAGTCTTCCTTTAAACATAATCTCA
TGCTCATTCCGAGACATGAGTCTTCCATTTAAACATAATCTCATCCTCATCACGAGACATG
Found at i:150348 original size:20 final size:20
Alignment explanation
Indices: 150323--150360 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
150313 ATGAAGAAGA
150323 AAGGTTAATGTTAGTTGTTT
1 AAGGTTAATGTTAGTTGTTT
150343 AAGGTTAATGTTAGTTGT
1 AAGGTTAATGTTAGTTGT
150361 CATTATGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (20 bp):
AAGGTTAATGTTAGTTGTTT
Found at i:153725 original size:87 final size:87
Alignment explanation
Indices: 153567--153733 Score: 239
Period size: 87 Copynumber: 1.9 Consensus size: 87
153557 TTCGATGATC
** * * *
153567 TCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGTGTAAATTTTCAAAATCGAAGATAAGGAA
1 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAATCGAAGATAAAGAA
153632 ACATTGCCTCGATTTGATTATT
66 ACATTGCCTCGATTTGATTATT
*
153654 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCGAAACTCGAA-ATAAA-A
1 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-AAAATCGAAGATAAAGA
*
153717 GAATATTGCCTCGATTT
65 -AACATTGCCTCGATTT
153734 TAAAGTATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
86 1 0.01
87 62 0.87
88 8 0.11
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (87 bp):
TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAATCGAAGATAAAGAA
ACATTGCCTCGATTTGATTATT
Found at i:154253 original size:30 final size:29
Alignment explanation
Indices: 154126--154274 Score: 187
Period size: 29 Copynumber: 5.1 Consensus size: 29
154116 GGAGGTTTAA
* *
154126 GGGT-AAAAATGTAATTTTTGGAATTTTCG
1 GGGTCAAAAATGGAATTTTTGGAAGTTT-G
* * *
154155 AGGTCAAAATTGGAA-TTTTGGAAGTTCG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTG
*
154183 AGGGT-AAAAATGGAATTTTTGGAAGTTCG
1 -GGGTCAAAAATGGAATTTTTGGAAGTTTG
154212 GGGTCAAAAATGGAATTTTTGGAAGTTTG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTG
154241 GGGTCAAAAAATGGAATTTTTGGAAGTTTAG
1 GGGTC-AAAAATGGAATTTTTGGAAGTTT-G
154272 GGG
1 GGG
154275 GTAANNNNNN
Statistics
Matches: 106, Mismatches: 8, Indels: 10
0.85 0.06 0.08
Matches are distributed among these distances:
28 14 0.13
29 57 0.54
30 31 0.29
31 4 0.04
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (29 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTTG
Found at i:154427 original size:29 final size:29
Alignment explanation
Indices: 154380--154665 Score: 300
Period size: 29 Copynumber: 9.8 Consensus size: 29
154370 NGAGGTTTAA
*
154380 GGGT-AAAAATGTAATTTTTGGAATTTTCG
1 GGGTCAAAAATGGAATTTTTGGAA-TTTCG
* * *
154409 AGGTCAAAATTGGAA-TTTTGGAAGTTCG
1 GGGTCAAAAATGGAATTTTTGGAATTTCG
*
154437 AGGGT-AAAAATGGAATTTTTGGAAGTTCG
1 -GGGTCAAAAATGGAATTTTTGGAATTTCG
154466 GGGTCAAAAATGGAATTTTTGGAAGTTT-G
1 GGGTCAAAAATGGAATTTTTGGAA-TTTCG
*
154495 GGGTCAAAAAATGGAATTTTTGGAAGTTTAGG
1 GGGTC-AAAAATGGAATTTTTGGAA-TTT-CG
*
154527 GGGT-AAAAATGGAATTTTTGGAAGTTTTG
1 GGGTCAAAAATGGAATTTTTGGAA-TTTCG
* *
154556 GGGTCAAAAATGGAATTTTTAGAAGTTCTG
1 GGGTCAAAAATGGAATTTTTGGAATTTC-G
154586 GGGT-AAAAATGGAATTTTTGGAAGTTTCG
1 GGGTCAAAAATGGAATTTTTGGAA-TTTCG
* * *
154615 AGGTCAAAAATAGAA-TTTTGGAAGTTCG
1 GGGTCAAAAATGGAATTTTTGGAATTTCG
* *
154643 ATGGT-AAAAATGTAATTTTTGGA
1 -GGGTCAAAAATGGAATTTTTGGA
154666 CAGTTTAGGG
Statistics
Matches: 224, Mismatches: 19, Indels: 28
0.83 0.07 0.10
Matches are distributed among these distances:
28 29 0.13
29 99 0.44
30 91 0.41
32 5 0.02
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
GGGTCAAAAATGGAATTTTTGGAATTTCG
Found at i:154521 original size:59 final size:57
Alignment explanation
Indices: 154380--154671 Score: 349
Period size: 58 Copynumber: 5.0 Consensus size: 57
154370 NGAGGTTTAA
* * * * *
154380 GGGT-AAAAATGTAATTTTTGGAATTTTCGAGGTCAAAATTGGAA-TTTTGGAAGTTCG
1 GGGTCAAAAATGGAATTTTTGGAA-GTTCGGGGT-AAAAATGGAATTTTTGGAAGTTTG
154437 AGGGT-AAAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTG
1 -GGGTCAAAAATGGAATTTTTGGAAGTTCGGGGT-AAAAATGGAATTTTTGGAAGTTTG
*
154495 GGGTCAAAAAATGGAATTTTTGGAAGTTTAGGGGGTAAAAATGGAATTTTTGGAAGTTTTG
1 GGGTC-AAAAATGGAATTTTTGGAAG-TT-CGGGGTAAAAATGGAATTTTTGGAAG-TTTG
*
154556 GGGTCAAAAATGGAATTTTTAGAAGTTCTGGGGTAAAAATGGAATTTTTGGAAGTTTCG
1 GGGTCAAAAATGGAATTTTTGGAAGTTC-GGGGTAAAAATGGAATTTTTGGAAGTTT-G
* * * *
154615 AGGTCAAAAATAGAA-TTTTGGAAGTTCGATGGTAAAAATGTAATTTTTGGACAGTTT
1 GGGTCAAAAATGGAATTTTTGGAAGTTCG-GGGTAAAAATGGAATTTTTGGA-AGTTT
154672 AGGGACATCC
Statistics
Matches: 211, Mismatches: 13, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
57 22 0.10
58 68 0.32
59 66 0.31
60 41 0.19
61 14 0.07
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (57 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTTGGAAGTTTG
Found at i:155767 original size:3 final size:3
Alignment explanation
Indices: 155761--155856 Score: 59
Period size: 3 Copynumber: 32.0 Consensus size: 3
155751 TTATTAATGT
* ** * * * *
155761 TTA TTA TTA TTA TTG TCG TCA TTA ATA TTA TTAA TGA -TA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* * * ** *
155806 ATA TTA GTA ATA TTA TTA TTA TTA TTA TTA TTA TTA CCA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
155854 TTA
1 TTA
155857 AAGCCTTATT
Statistics
Matches: 71, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
2 1 0.01
3 68 0.96
4 2 0.03
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:155793 original size:9 final size:9
Alignment explanation
Indices: 155781--155856 Score: 71
Period size: 9 Copynumber: 8.1 Consensus size: 9
155771 TATTGTCGTC
155781 ATTAATATT
1 ATTAATATT
155790 ATTAATGATATT
1 ATT-A--ATATT
*
155802 AGTAATATT
1 ATTAATATT
*
155811 AGTAATATT
1 ATTAATATT
*
155820 ATTATTATT
1 ATTAATATT
*
155829 ATTATTATT
1 ATTAATATT
**
155838 ATTACCATT
1 ATTAATATT
155847 ATTAATATT
1 ATTAATATT
155856 A
1 A
155857 AAGCCTTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
9 48 0.84
10 1 0.02
11 1 0.02
12 7 0.12
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (9 bp):
ATTAATATT
Found at i:156538 original size:6 final size:6
Alignment explanation
Indices: 156522--156589 Score: 74
Period size: 6 Copynumber: 12.0 Consensus size: 6
156512 TTAAGTCAAA
**
156522 TTAAA- TTAAAT TTAAAT TTAAA- CCAAAT TTAAAT TTAAGA- -TAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT
156567 TTAAAT TTAAAT TT-AAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT
156590 CAATTTAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
4 1 0.02
5 16 0.30
6 35 0.66
7 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:156538 original size:11 final size:11
Alignment explanation
Indices: 156519--156598 Score: 65
Period size: 11 Copynumber: 7.3 Consensus size: 11
156509 GTCTTAAGTC
156519 AAATTAAA-TT
1 AAATTAAATTT
156529 AAATTTAAATTT
1 AAA-TTAAATTT
**
156541 AAACCAAATTT
1 AAATTAAATTT
* **
156552 AAATTTAAGAT
1 AAATTAAATTT
156563 AAATTTAAATTT
1 AAA-TTAAATTT
*
156575 AAATTTAATTT
1 AAATTAAATTT
*
156586 AAA-TCAATTT
1 AAATTAAATTT
156596 AAA
1 AAA
156599 CCCAACTTAA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
10 12 0.22
11 30 0.55
12 13 0.24
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:156542 original size:17 final size:17
Alignment explanation
Indices: 156522--156589 Score: 93
Period size: 17 Copynumber: 4.0 Consensus size: 17
156512 TTAAGTCAAA
156522 TTAAATTAAATTTAAAT
1 TTAAATTAAATTTAAAT
**
156539 TTAAACCAAATTTAAAT
1 TTAAATTAAATTTAAAT
156556 TTAAGA-TAAATTTAAAT
1 TTAA-ATTAAATTTAAAT
*
156573 TTAAATTTAATTTAAAT
1 TTAAATTAAATTTAAAT
156590 CAATTTAAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
16 1 0.02
17 43 0.96
18 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TTAAATTAAATTTAAAT
Found at i:157595 original size:205 final size:206
Alignment explanation
Indices: 156941--157815 Score: 1227
Period size: 205 Copynumber: 4.3 Consensus size: 206
156931 TCTGGTTTCA
* * * *** ** ** *
156941 TTGACTTGGCCTTCTTCTCAGTATCTCATCAGGAAGACGACCATATCACTTGTTTTGATCCTCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
* * * ** * * * *
157006 CTCTGTGTTTCATCAGGAAGATGGTTTTGGTTCACTTCCCTGTATTTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
157071 TTTATTACTTCGACTTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
157136 CGAGCGTGGGT
196 CGAGCGTGGGT
* *
157147 TTGATTTGGTCTTC-TCTTCTGTGTCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCT
1 TTGATTTGGTCTTCTTC-TCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCT
* * * * * *
157211 TCTTTATATCTCAACAGGAAGACGAATTTGGTTCACTTCTTAGTATCTCATTAGGAAGCTAACCA
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * *
157276 TTTTATTACTTCAATCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAGGATTTGCTCACA
130 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
*
157341 TCGAGCGGGGGT
195 TCGAGCGTGGGT
* * *
157353 TTGATTTGGTCTTCTTCACAATATCTCATCAGGAAGATGATCGCGTCGTTTGTTTCAA-CTCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATC-CGCT
*
157417 TCTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC-
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
** *
157481 TTTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
130 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
157546 TCGAGCGTGGGT
195 TCGAGCGTGGGT
*
157558 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
* * * * *
157623 TTCTGTATCTTATCAGGAAGACGAATTTGGTCCACTTCTCATTATTTCATCAGGAAGCTAA-CTT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * *
157687 TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCACAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
157752 CGAGCGTGGGT
196 CGAGCGTGGGT
*
157763 TTGATTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGACCGCGTCGTTTGT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGT
157816 AGATAATCAC
Statistics
Matches: 598, Mismatches: 66, Indels: 11
0.89 0.10 0.02
Matches are distributed among these distances:
204 1 0.00
205 314 0.53
206 281 0.47
207 2 0.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
CGAGCGTGGGT
Found at i:169506 original size:57 final size:58
Alignment explanation
Indices: 169380--169541 Score: 159
Period size: 58 Copynumber: 2.8 Consensus size: 58
169370 ACTCGGGGAC
* * * *
169380 AAAATGGTAATTTTG-GA-TTCTCAAGGTCAAAAATAGAATTTTTAGACATTCGGGGGT
1 AAAATGGTAATTTTGAGAGTT-TCGAGGCCAAAAATAGAATTTTTAGACATCCCGGGGT
* * * *
169437 AAAAGGGTAATTTTGAGAGTTTCGAGGCCGAAAATAGAGTTTTTGGACATCCCGGGG-
1 AAAATGGTAATTTTGAGAGTTTCGAGGCCAAAAATAGAATTTTTAGACATCCCGGGGT
* * * * * *
169494 AAATTGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAATTTTAGA
1 AAAATGGTAA-TTTTGAGAGTTTCGAGGCCAAAAATAGAATTTTTAGA
169542 GGTTTGAGGG
Statistics
Matches: 84, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
57 22 0.26
58 60 0.71
59 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (58 bp):
AAAATGGTAATTTTGAGAGTTTCGAGGCCAAAAATAGAATTTTTAGACATCCCGGGGT
Found at i:169571 original size:38 final size:38
Alignment explanation
Indices: 169529--169616 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
169519 GGGTCAAAAA
* * *
169529 TGGAAATTTTAGAGGTTTGAGGGTAAATA-TGTAATTTT
1 TGGAAATTTTAGAAGTTCGAGGGTAAAAATTG-AATTTT
* *
169567 TGGAATTTTTGGAAGTTCGAGGGTAAAAATTGAATTTT
1 TGGAAATTTTAGAAGTTCGAGGGTAAAAATTGAATTTT
*
169605 TGGAAGTTTTAG
1 TGGAAATTTTAG
169617 GGTCAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 40 0.95
39 2 0.05
ACGTcount: A:0.31, C:0.01, G:0.27, T:0.41
Consensus pattern (38 bp):
TGGAAATTTTAGAAGTTCGAGGGTAAAAATTGAATTTT
Found at i:169632 original size:30 final size:29
Alignment explanation
Indices: 169567--169671 Score: 158
Period size: 29 Copynumber: 3.6 Consensus size: 29
169557 ATGTAATTTT
**
169567 TGGAATTTTTGGAAGTTCGAGGGTAAAAA
1 TGGAATTTTTGGAAGTTTTAGGGTAAAAA
*
169596 TTGAATTTTTGGAAGTTTTAGGGTCAAAAA
1 TGGAATTTTTGGAAGTTTTAGGGT-AAAAA
169626 TGGAATTTTTGGAAG-TTTAGGGGTAAAAA
1 TGGAATTTTTGGAAGTTTTA-GGGTAAAAA
169655 TGGAATTTTTGGAAGTT
1 TGGAATTTTTGGAAGTT
169672 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
29 45 0.65
30 24 0.35
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (29 bp):
TGGAATTTTTGGAAGTTTTAGGGTAAAAA
Found at i:169633 original size:68 final size:68
Alignment explanation
Indices: 169497--169639 Score: 173
Period size: 68 Copynumber: 2.1 Consensus size: 68
169487 CCCGGGGAAA
* * *
169497 TTGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAATTTTAGAGGTTTGAGGGTAAATATGTA
1 TTGG-AATTTTTGAAAGTTTCGGGGTCAAAAATGGAAATTTTAGAAGTTTGAGGGTAAAAATGGA
169562 ATTT
65 ATTT
* * * * *
169566 TTGGAATTTTTGGAAG-TTCGAGGGT-AAAAATTGAATTTTTGGAAGTTTTAGGGTCAAAAATGG
1 TTGGAATTTTTGAAAGTTTCG-GGGTCAAAAATGGAAATTTTAGAAGTTTGAGGGT-AAAAATGG
169629 AATTT
64 AATTT
169634 TTGGAA
1 TTGGAA
169640 GTTTAGGGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
67 28 0.44
68 32 0.50
69 4 0.06
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (68 bp):
TTGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAATTTTAGAAGTTTGAGGGTAAAAATGGAA
TTT
Found at i:178663 original size:57 final size:58
Alignment explanation
Indices: 178537--178698 Score: 159
Period size: 58 Copynumber: 2.8 Consensus size: 58
178527 ACTCGGGGAC
* * * *
178537 AAAATGGTAATTTTG-GA-TTCTCAAGGTCAAAAATAGAATTTTTAGACATTCGGGGGT
1 AAAATGGTAATTTTGAGAGTT-TCGAGGCCAAAAATAGAATTTTTAGACATCCCGGGGT
* * * *
178594 AAAAGGGTAATTTTGAGAGTTTCGAGGCCGAAAATAGAGTTTTTGGACATCCCGGGG-
1 AAAATGGTAATTTTGAGAGTTTCGAGGCCAAAAATAGAATTTTTAGACATCCCGGGGT
* * * * * *
178651 AAATTGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAATTTTAGA
1 AAAATGGTAA-TTTTGAGAGTTTCGAGGCCAAAAATAGAATTTTTAGA
178699 GGTTTGAGGG
Statistics
Matches: 84, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
57 22 0.26
58 60 0.71
59 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (58 bp):
AAAATGGTAATTTTGAGAGTTTCGAGGCCAAAAATAGAATTTTTAGACATCCCGGGGT
Found at i:178728 original size:38 final size:38
Alignment explanation
Indices: 178686--178773 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
178676 GGGTCAAAAA
* * *
178686 TGGAAATTTTAGAGGTTTGAGGGTAAATA-TGTAATTTT
1 TGGAAATTTTAGAAGTTCGAGGGTAAAAATTG-AATTTT
* *
178724 TGGAATTTTTGGAAGTTCGAGGGTAAAAATTGAATTTT
1 TGGAAATTTTAGAAGTTCGAGGGTAAAAATTGAATTTT
*
178762 TGGAAGTTTTAG
1 TGGAAATTTTAG
178774 GGTCAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 40 0.95
39 2 0.05
ACGTcount: A:0.31, C:0.01, G:0.27, T:0.41
Consensus pattern (38 bp):
TGGAAATTTTAGAAGTTCGAGGGTAAAAATTGAATTTT
Found at i:178796 original size:59 final size:59
Alignment explanation
Indices: 178724--178937 Score: 312
Period size: 58 Copynumber: 3.7 Consensus size: 59
178714 ATGTAATTTT
*
178724 TGGAATTTTTGGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTTAGGGTCAAAAA
1 TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAA
*
178783 TGGAATTTTTGGAAGTT-TAGGGGTAAAAATGGAATTTTTGGAAG-TTTAGGGGT-AAAAA
1 TGGAATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTGGAAGTTTTA-GGGTCAAAAA
* *
178841 TGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAGTTTT-GAGGTCAAAAA
1 TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAG-GGTCAAAAA
* *
178900 TGGAA-TTTTGGAAGTTCAAGGGTAAAAATGTAATTTTT
1 TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTT
178938 AGACAATTTA
Statistics
Matches: 141, Mismatches: 8, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
57 1 0.01
58 83 0.59
59 57 0.40
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (59 bp):
TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAA
Found at i:178950 original size:29 final size:28
Alignment explanation
Indices: 178724--178937 Score: 268
Period size: 29 Copynumber: 7.4 Consensus size: 28
178714 ATGTAATTTT
*
178724 TGGAATTTTTGGAAGTTCGAGGGTAAAAA
1 TGGAATTTTTGGAAGTT-TAGGGTAAAAA
*
178753 TTGAATTTTTGGAAGTTTTAGGGTCAAAAA
1 TGGAATTTTTGGAAG-TTTAGGGT-AAAAA
178783 TGGAATTTTTGGAAGTTTAGGGGTAAAAA
1 TGGAATTTTTGGAAGTTTA-GGGTAAAAA
178812 TGGAATTTTTGGAAGTTTAGGGGTAAAAA
1 TGGAATTTTTGGAAGTTTA-GGGTAAAAA
**
178841 TGGAATTTTTGGAAGTTCGGGGGTAAAAA
1 TGGAATTTTTGGAAGTT-TAGGGTAAAAA
* *
178870 TGGAATTTTTGAAAGTTTTGAGGTCAAAAA
1 TGGAATTTTTGGAAGTTTAG-GGT-AAAAA
*
178900 TGGAA-TTTTGGAAGTTCAAGGGTAAAAA
1 TGGAATTTTTGGAAGTT-TAGGGTAAAAA
*
178928 TGTAATTTTT
1 TGGAATTTTT
178938 AGACAATTTA
Statistics
Matches: 165, Mismatches: 12, Indels: 16
0.85 0.06 0.08
Matches are distributed among these distances:
28 10 0.06
29 119 0.72
30 36 0.22
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (28 bp):
TGGAATTTTTGGAAGTTTAGGGTAAAAA
Found at i:180075 original size:3 final size:3
Alignment explanation
Indices: 180069--180094 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
180059 ATGATATTAG
180069 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
180095 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:180099 original size:3 final size:3
Alignment explanation
Indices: 180093--180148 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
180083 ATAATAATAA
180093 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
180141 TAT TAT TA
1 TAT TAT TA
180149 AAGCCTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:180867 original size:6 final size:6
Alignment explanation
Indices: 180850--180923 Score: 64
Period size: 6 Copynumber: 12.3 Consensus size: 6
180840 GTCTTAAGTC
**
180850 AATTTA AA-TTA AATTTA AATTTAAA AACATA AATTTA AATTTA AGA--TA
1 AATTTA AATTTA AATTTA AATTT--A AATTTA AATTTA AATTTA A-ATTTA
**
180898 AATTTA AATTTA AAAATA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AA
180924 CCCAACTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
4 1 0.02
5 8 0.15
6 40 0.74
7 1 0.02
8 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (6 bp):
AATTTA
Found at i:180870 original size:17 final size:18
Alignment explanation
Indices: 180850--180923 Score: 98
Period size: 17 Copynumber: 4.1 Consensus size: 18
180840 GTCTTAAGTC
*
180850 AATTT-AAATTAAATTTA
1 AATTTAAAAATAAATTTA
180867 AATTTAAAAACATAAATTTA
1 AATTT-AAAA-ATAAATTTA
*
180887 AATTT-AAGATAAATTTA
1 AATTTAAAAATAAATTTA
180904 AATTTAAAAATAAATTTA
1 AATTTAAAAATAAATTTA
180922 AA
1 AA
180924 CCCAACTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
17 19 0.38
18 15 0.30
19 3 0.06
20 13 0.26
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (18 bp):
AATTTAAAAATAAATTTA
Found at i:180900 original size:37 final size:35
Alignment explanation
Indices: 180850--180923 Score: 114
Period size: 37 Copynumber: 2.1 Consensus size: 35
180840 GTCTTAAGTC
180850 AATTTAAATTAAATTTAAATTTAAAAACATAAATTTA
1 AATTTAAATTAAATTTAAATTT-AAAA-ATAAATTTA
180887 AATTTAAGA-TAAATTTAAATTTAAAAATAAATTTA
1 AATTTAA-ATTAAATTTAAATTTAAAAATAAATTTA
180922 AA
1 AA
180924 CCCAACTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 11 0.31
36 4 0.11
37 20 0.56
38 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (35 bp):
AATTTAAATTAAATTTAAATTTAAAAATAAATTTA
Found at i:180958 original size:24 final size:24
Alignment explanation
Indices: 180927--180977 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
180917 ATTTAAACCC
*
180927 AACTTAAAATAAAAGGTTTAATCT
1 AACTTAAAATAAAAGGCTTAATCT
180951 AACTTAAAATAAAAGGCTTAATCT
1 AACTTAAAATAAAAGGCTTAATCT
180975 AAC
1 AAC
180978 ACTCGGGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.29
Consensus pattern (24 bp):
AACTTAAAATAAAAGGCTTAATCT
Found at i:183042 original size:53 final size:54
Alignment explanation
Indices: 182959--183066 Score: 209
Period size: 53 Copynumber: 2.0 Consensus size: 54
182949 GATGCAACCT
182959 TTTGCTGCTTCTCTTTCCTGCAAGTACTCTTTATGTCTTCAACATTAGATTTTG
1 TTTGCTGCTTCTCTTTCCTGCAAGTACTCTTTATGTCTTCAACATTAGATTTTG
183013 TTTGCTGCTTCTCTTTCCTGC-AGTACTCTTTATGTCTTCAACATTAGATTTTG
1 TTTGCTGCTTCTCTTTCCTGCAAGTACTCTTTATGTCTTCAACATTAGATTTTG
183066 T
1 T
183067 CCTAATCTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 33 0.61
54 21 0.39
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (54 bp):
TTTGCTGCTTCTCTTTCCTGCAAGTACTCTTTATGTCTTCAACATTAGATTTTG
Found at i:183416 original size:23 final size:23
Alignment explanation
Indices: 183379--183481 Score: 179
Period size: 23 Copynumber: 4.4 Consensus size: 23
183369 TTTCACTCTA
183379 ATTTTTTTATAAAAAAAAATTATG
1 ATTTTTTTAT-AAAAAAAATTATG
*
183403 ATTTTTTTATAAAAAAATTTATG
1 ATTTTTTTATAAAAAAAATTATG
*
183426 ATTTTTTTATAAAAAAATTTATG
1 ATTTTTTTATAAAAAAAATTATG
183449 ATTTTTTTATAAAAAAAATTATG
1 ATTTTTTTATAAAAAAAATTATG
183472 ATTTTTTTAT
1 ATTTTTTTAT
183482 TTTATCAATA
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
23 67 0.87
24 10 0.13
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
ATTTTTTTATAAAAAAAATTATG
Found at i:184485 original size:8 final size:8
Alignment explanation
Indices: 184472--184531 Score: 61
Period size: 8 Copynumber: 7.5 Consensus size: 8
184462 TTAAAAAATC
184472 TTTTTATT
1 TTTTTATT
184480 TTTTTATT
1 TTTTTATT
* *
184488 TTTTGA-A
1 TTTTTATT
*
184495 TTTTAATGAT
1 TTTTTAT--T
184505 TTTTTA-T
1 TTTTTATT
184512 TTTTTATT
1 TTTTTATT
184520 TTTTTATT
1 TTTTTATT
184528 TTTT
1 TTTT
184532 AAAAAAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
7 12 0.28
8 26 0.60
10 5 0.12
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (8 bp):
TTTTTATT
Found at i:184521 original size:6 final size:7
Alignment explanation
Indices: 184472--184532 Score: 59
Period size: 7 Copynumber: 7.9 Consensus size: 7
184462 TTAAAAAATC
184472 TTTTTATT
1 TTTTTA-T
184480 TTTTTAT
1 TTTTTAT
184487 TTTTTGAAT
1 TTTTT--AT
*
184496 TTTAATGAT
1 TTT--TTAT
184505 TTTTTAT
1 TTTTTAT
184512 TTTTTATT
1 TTTTTA-T
184520 TTTTTAT
1 TTTTTAT
184527 TTTTTA
1 TTTTTA
184533 AAAAAAATAG
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
7 22 0.48
8 13 0.28
9 10 0.22
11 1 0.02
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (7 bp):
TTTTTAT
Found at i:184770 original size:15 final size:16
Alignment explanation
Indices: 184740--184773 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
184730 AATTTTAAAT
*
184740 TTTTTTAATATTTTTA
1 TTTTTTAATATATTTA
184756 TTTTTTAATA-ATTTA
1 TTTTTTAATATATTTA
184771 TTT
1 TTT
184774 GCTTTGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTAATATATTTA
Found at i:185739 original size:14 final size:14
Alignment explanation
Indices: 185720--185747 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
185710 AAGATAACTT
185720 ATGTTATCAATGTG
1 ATGTTATCAATGTG
185734 ATGTTATCAATGTG
1 ATGTTATCAATGTG
185748 GTGTATGCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
ATGTTATCAATGTG
Done.