Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013759.1 Kokia drynarioides strain JFW-HI SEQ_128787, 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: 100034
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:9719 original size:30 final size:28
Alignment explanation
Indices: 9619--9807 Score: 163
Period size: 29 Copynumber: 6.5 Consensus size: 28
9609 TTTTATATAG
* *
9619 AAAATGGAGA-TTTTGGAAGTTTGAGGGAA
1 AAAAT-GAGATTTTTGGAAG-TTCAGGGTA
* * *
9648 AAAACGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGAGATTTTTGGAAGTTC-AGGGTA
9677 AAAAT-AGAATTTTTGGAAGTTTCAGGGTCA
1 AAAATGAG-ATTTTTGGAAG-TTCAGGGT-A
*
9707 AAAATGAGATTTTTGGAAGTTCGAGGTTA
1 AAAATGAGATTTTTGGAAGTTC-AGGGTA
9736 AAAACTGA-ATTTTTGGAAGTTTC-GGAGTCA
1 AAAA-TGAGATTTTTGGAAG-TTCAGG-GT-A
* *
9766 AAAGTGGGATTTTTGGAAGTTCAGGGGTA
1 AAAATGAGATTTTTGGAAGTTCA-GGGTA
9795 AAAATG-GATTTTT
1 AAAATGAGATTTTT
9808 AGGGGTCAAA
Statistics
Matches: 133, Mismatches: 13, Indels: 29
0.76 0.07 0.17
Matches are distributed among these distances:
28 15 0.11
29 67 0.50
30 47 0.35
31 4 0.03
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAATGAGATTTTTGGAAGTTCAGGGTA
Found at i:9720 original size:59 final size:57
Alignment explanation
Indices: 9629--9866 Score: 235
Period size: 59 Copynumber: 4.2 Consensus size: 57
9619 AAAATGGAGA
** * * *
9629 TTTTGGAAGTTT-GAGGGAAAAAACGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAAT
1 TTTTGGAAGTTTCG-GGTCAAAAATGAGATTTTTGGAAGTTCAGGGGTAAAAAT-GAAT
*
9687 TTTTGGAAGTTTCAGGGTCAAAAATGAGATTTTTGGAAGTTC-GAGGTTAAAAACTGAAT
1 TTTTGGAAGTTTC-GGGTCAAAAATGAGATTTTTGGAAGTTCAG-GGGTAAAAA-TGAAT
* * *
9746 TTTTGGAAGTTTCGGAGTCAAAAGTGGGATTTTTGGAAGTTCAGGGGTAAAAATGGAT
1 TTTTGGAAGTTTCGG-GTCAAAAATGAGATTTTTGGAAGTTCAGGGGTAAAAATGAAT
* *
9804 TTTT---AG----GGGTCAAAAATAAGA-TTTTGGAAATTCAGGGGTAAAAATGGAAT
1 TTTTGGAAGTTTCGGGTCAAAAATGAGATTTTTGGAAGTTCAGGGGTAAAAAT-GAAT
9854 TTTTGGATAGTTT
1 TTTTGGA-AGTTT
9867 AGGAACCTCC
Statistics
Matches: 152, Mismatches: 14, Indels: 29
0.78 0.07 0.15
Matches are distributed among these distances:
49 23 0.15
50 17 0.11
51 2 0.01
54 2 0.01
55 2 0.01
58 23 0.15
59 80 0.53
60 3 0.02
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (57 bp):
TTTTGGAAGTTTCGGGTCAAAAATGAGATTTTTGGAAGTTCAGGGGTAAAAATGAAT
Found at i:9768 original size:29 final size:31
Alignment explanation
Indices: 9656--9807 Score: 121
Period size: 30 Copynumber: 5.2 Consensus size: 31
9646 AAAAAACGGG
* *
9656 ATTTTTGGAAG-TTCGGGGGT-AAAAATAGA
1 ATTTTTGGAAGTTTCAGGAGTCAAAAATAGA
9685 ATTTTTGGAAGTTTCAGG-GTCAAAAAT-GA
1 ATTTTTGGAAGTTTCAGGAGTCAAAAATAGA
*
9714 GATTTTTGGAAG-TTC--GAGGTTAAAAACT-GA
1 -ATTTTTGGAAGTTTCAGGA-GTCAAAAA-TAGA
* * *
9744 ATTTTTGGAAGTTTC-GGAGTCAAAAGTGGG
1 ATTTTTGGAAGTTTCAGGAGTCAAAAATAGA
* *
9774 ATTTTTGGAAG-TTCAGGGGT-AAAAAT-GG
1 ATTTTTGGAAGTTTCAGGAGTCAAAAATAGA
9802 ATTTTT
1 ATTTTT
9808 AGGGGTCAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 21
0.79 0.05 0.16
Matches are distributed among these distances:
27 1 0.01
28 8 0.08
29 45 0.42
30 50 0.47
31 2 0.02
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (31 bp):
ATTTTTGGAAGTTTCAGGAGTCAAAAATAGA
Found at i:9828 original size:21 final size:20
Alignment explanation
Indices: 9788--9828 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
9778 TTGGAAGTTC
*
9788 AGGGGTAAAAATGGATTTTT
1 AGGGGTAAAAATAGATTTTT
9808 AGGGGTCAAAAATAAGATTTT
1 AGGGGT-AAAAAT-AGATTTT
9829 GGAAATTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 6 0.33
22 6 0.33
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (20 bp):
AGGGGTAAAAATAGATTTTT
Found at i:11189 original size:1 final size:1
Alignment explanation
Indices: 11144--11169 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
11134 TGCTTCTGGG
11144 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
11170 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11646 original size:6 final size:6
Alignment explanation
Indices: 11635--11701 Score: 61
Period size: 6 Copynumber: 11.7 Consensus size: 6
11625 TTAAATAGAT
* * *
11635 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTAAA -ATAAA CTTAAT
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
11681 TTTAAA -ATAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTA
11702 TTGAGCCAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 35 0.71
7 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:11657 original size:17 final size:17
Alignment explanation
Indices: 11637--11701 Score: 103
Period size: 17 Copynumber: 3.8 Consensus size: 17
11627 AAATAGATTT
*
11637 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
11654 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
11671 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
11688 TAAATTTAAATTTA
1 TAAATTTAAATTTA
11702 TTGAGCCAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:13723 original size:5 final size:5
Alignment explanation
Indices: 13715--13743 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
13705 CACCTTTCCT
13715 TCTTC TCTTC TCTTC TCTTC TCTTC TCTT
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTT
13744 GTACTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCTTC
Found at i:19442 original size:30 final size:31
Alignment explanation
Indices: 19394--19459 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
19384 ATTAAAATTA
19394 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTATTATTTCAAAAAAATAAT
**
19425 TTTAATAATTTTA-TATTTTTAAAAAATAAT
1 TTTAATAATTTTATTATTTCAAAAAAATAAT
19455 TTTAA
1 TTTAA
19460 AATCATTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTAATAATTTTATTATTTCAAAAAAATAAT
Found at i:19753 original size:10 final size:10
Alignment explanation
Indices: 19734--19917 Score: 95
Period size: 10 Copynumber: 18.8 Consensus size: 10
19724 TTTTGATACA
19734 ATAA-TTTTT
1 ATAATTTTTT
19743 ATAATTTTTT
1 ATAATTTTTT
*
19753 ACGAA--TTTT
1 A-TAATTTTTT
19762 AT-ATTTCTTT
1 ATAATTT-TTT
19772 A-AATTTTTT
1 ATAATTTTTT
19781 ATAATTTTTT
1 ATAATTTTTT
*
19791 ATGA--TTTT
1 ATAATTTTTT
**
19799 ATAAAATTTT
1 ATAATTTTTT
19809 ATAATTTTTCT
1 ATAATTTTT-T
*
19820 AT-A-TTTCT
1 ATAATTTTTT
*
19828 AT-ATATTTT
1 ATAATTTTTT
19837 ATAATTTTTT
1 ATAATTTTTT
* *
19847 TTACAATTTTT
1 ATA-ATTTTTT
19858 ATAATTTGTTT
1 ATAATTT-TTT
**
19869 ACGA-TTTTT
1 ATAATTTTTT
19878 AT-ATATTTTT
1 ATAAT-TTTTT
** *
19888 ATTAAAATTTA
1 A-TAATTTTTT
19899 ATAATTTTTT
1 ATAATTTTTT
19909 ATAACTTTT
1 ATAA-TTTT
19918 ATTGATATTT
Statistics
Matches: 133, Mismatches: 23, Indels: 36
0.69 0.12 0.19
Matches are distributed among these distances:
7 1 0.01
8 12 0.09
9 26 0.20
10 66 0.50
11 27 0.20
12 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:19763 original size:19 final size:17
Alignment explanation
Indices: 19739--19919 Score: 76
Period size: 19 Copynumber: 9.4 Consensus size: 17
19729 ATACAATAAT
19739 TTTTATAATTTTTTACGAA
1 TTTTATAATTTTTTA--AA
19758 TTTTAT-ATTTCTTTAAA
1 TTTTATAATTT-TTTAAA
*
19775 TTTTTTATAATTTTTTATGA
1 --TTTTATAATTTTTTA-AA
* *
19795 TTTTATAAAATTTTATAAT
1 TTTTAT--AATTTTTTAAA
* * *
19814 TTTTCTATATTTCTATATA
1 TTTTATA-ATTT-TTTAAA
19833 TTTTATAATTTTTTTTACAA
1 TTTTATAA--TTTTTTA-AA
*
19853 TTTTTATAATTTGTTTACGAT
1 -TTTTATAATTT-TTTA--AA
19874 TTTTATATATTTTTATTAAAA
1 TTTTATA-A-TTTT-TT-AAA
*
19895 TTTAATAATTTTTTATAA
1 TTTTATAATTTTTTA-AA
19913 CTTTTAT
1 -TTTTAT
19920 TGATATTTAT
Statistics
Matches: 126, Mismatches: 15, Indels: 42
0.69 0.08 0.23
Matches are distributed among these distances:
17 4 0.03
18 19 0.15
19 50 0.40
20 29 0.23
21 18 0.14
22 5 0.04
23 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTATAATTTTTTAAA
Found at i:19789 original size:28 final size:29
Alignment explanation
Indices: 19758--19846 Score: 105
Period size: 28 Copynumber: 3.1 Consensus size: 29
19748 TTTTTACGAA
*
19758 TTTTATATTTCTTTAAATTTTTTATAATT
1 TTTTATATTTCTTTAAATATTTTATAATT
*
19787 TTTTATGATTT-TATAAA-ATTTTATAATT
1 TTTTAT-ATTTCTTTAAATATTTTATAATT
*
19815 TTTCTATATTTC--TATATATTTTATAATT
1 TTT-TATATTTCTTTAAATATTTTATAATT
19843 TTTT
1 TTTT
19847 TTACAATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
27 4 0.08
28 31 0.58
29 14 0.26
30 4 0.08
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (29 bp):
TTTTATATTTCTTTAAATATTTTATAATT
Found at i:19903 original size:41 final size:40
Alignment explanation
Indices: 19833--19909 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
19823 TTTCTATATA
* * *
19833 TTTTATAATTTTTTTTACAATTTTTATAATTTGTTTACGAT
1 TTTTATAATTTTTATTACAAATTTAATAATTT-TTTACGAT
19874 TTTTATATATTTTTATTA-AAATTTAATAATTTTTTA
1 TTTTATA-ATTTTTATTACAAATTTAATAATTTTTTA
19910 TAACTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 4 0.12
41 19 0.59
42 9 0.28
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (40 bp):
TTTTATAATTTTTATTACAAATTTAATAATTTTTTACGAT
Found at i:22640 original size:150 final size:150
Alignment explanation
Indices: 22331--22631 Score: 469
Period size: 150 Copynumber: 2.0 Consensus size: 150
22321 ACAAAATGAC
* * *
22331 CATATTTAGTCAATCTGTTGATGACAACCATGATAACATTCTTCCCAATCGATCTAGGTAAGCCT
1 CATATTTAGCCAATCTGTCGACGACAACCATGATAACATTCTTCCCAATCGATCTAGGTAAGCCT
*
22396 TCTATGAAATCTATCGAAATGGATGACCATACTCTGTCAGGTATGGTAAAGGTTGCAGCAACCCT
66 TCTATGAAATCCATCGAAATGGATGACCATACTCTGTCAGGTATGGTAAAGGTTGCAGCAACCCT
** *
22461 GGAGTAGCCACGTTTTCACT
131 AAAGTAGCCACGTTATCACT
*
22481 CATATTTAGCCAATCTGTCGACGACCACCATGATAACATTCTT-CCAAGTCGATCTAGGTAAGCC
1 CATATTTAGCCAATCTGTCGACGACAACCATGATAACATTCTTCCCAA-TCGATCTAGGTAAGCC
* * * *
22545 TTTTATGAAGTCCATCGAAATGGATGATCATACTCTGTCAGGTATGGGTAAAGGTTGTAGCAACC
65 TTCTATGAAATCCATCGAAATGGATGACCATACTCTGTCAGGTAT-GGTAAAGGTTGCAGCAACC
22610 CTAAAGTAGCCACGTTATCACT
129 CTAAAGTAGCCACGTTATCACT
22632 TTTATTAGCT
Statistics
Matches: 137, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
149 4 0.03
150 96 0.70
151 37 0.27
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (150 bp):
CATATTTAGCCAATCTGTCGACGACAACCATGATAACATTCTTCCCAATCGATCTAGGTAAGCCT
TCTATGAAATCCATCGAAATGGATGACCATACTCTGTCAGGTATGGTAAAGGTTGCAGCAACCCT
AAAGTAGCCACGTTATCACT
Found at i:26324 original size:19 final size:19
Alignment explanation
Indices: 26300--26338 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
26290 TAATGAAATA
*
26300 AGGTTCTGTAGAATAAACC
1 AGGTTCTATAGAATAAACC
26319 AGGTTCTATAGAATAAACC
1 AGGTTCTATAGAATAAACC
26338 A
1 A
26339 ACAGTAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (19 bp):
AGGTTCTATAGAATAAACC
Found at i:29454 original size:20 final size:19
Alignment explanation
Indices: 29425--29464 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
29415 TAATTTTTTT
*
29425 TTTAAATTTTTATGAACTA
1 TTTAAATTTTAATGAACTA
29444 TTTATAATTTTAATGAACTA
1 TTTA-AATTTTAATGAACTA
29464 T
1 T
29465 ATGTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTAAATTTTAATGAACTA
Found at i:31727 original size:3 final size:3
Alignment explanation
Indices: 31719--31763 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
31709 AATTTCAAAC
31719 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31764 GAAGATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:32728 original size:21 final size:21
Alignment explanation
Indices: 32702--32759 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
32692 TCAGAAATAA
32702 TTTTATAA-TTTATAAAATTGT
1 TTTTATAATTTTATAAAATT-T
*
32723 TTTTATAATTTTTATACAATTT
1 TTTTATAA-TTTTATAAAATTT
**
32745 TTTTATGGTTTTATA
1 TTTTATAATTTTATA
32760 TAATGCAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 15 0.47
22 7 0.22
23 10 0.31
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTATAATTTTATAAAATTT
Found at i:32761 original size:23 final size:23
Alignment explanation
Indices: 32702--32750 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
32692 TCAGAAATAA
32702 TTTTATAA--TTTATAAAATTGT
1 TTTTATAATTTTTATAAAATTGT
*
32723 TTTTATAATTTTTATACAATT-T
1 TTTTATAATTTTTATAAAATTGT
32745 TTTTAT
1 TTTTAT
32751 GGTTTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 8 0.32
22 7 0.28
23 10 0.40
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTATAATTTTTATAAAATTGT
Found at i:32837 original size:3 final size:3
Alignment explanation
Indices: 32829--32855 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
32819 AATTTCAAAC
32829 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
32856 GAAGATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:37341 original size:20 final size:19
Alignment explanation
Indices: 37298--37342 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
37288 CTTTTAAAGA
*
37298 CCAAAAGTTTTTTTATGGG
1 CCAAAAGTTTTTTTACGGG
37317 CCAAAAGTTTTTTTACGGG
1 CCAAAAGTTTTTTTACGGG
37336 CTCAAAA
1 C-CAAAA
37343 AAAAATTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (19 bp):
CCAAAAGTTTTTTTACGGG
Found at i:37948 original size:11 final size:11
Alignment explanation
Indices: 37934--37981 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
37924 ATATTCAAAT
37934 AATAATAACAA
1 AATAATAACAA
37945 AATAATAACAA
1 AATAATAACAA
* **
37956 CATAATAGTAA
1 AATAATAACAA
* *
37967 AATTATAGCAA
1 AATAATAACAA
37978 AATA
1 AATA
37982 TGGAGAAAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (11 bp):
AATAATAACAA
Found at i:40631 original size:22 final size:21
Alignment explanation
Indices: 40606--40649 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
40596 AAATTATATA
40606 TTTATATATTAATAT-TTAATTT
1 TTTATA-ATTAATATATT-ATTT
*
40628 TTTATAATTTATATATTATTT
1 TTTATAATTAATATATTATTT
40649 T
1 T
40650 GACAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTATAATTAATATATTATTT
Found at i:40739 original size:23 final size:21
Alignment explanation
Indices: 40704--40751 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
40694 ACATCTATAT
* *
40704 AAAAAATTCAAAATATTTTTA
1 AAAAAATTCAAAAAACTTTTA
40725 AAAAAATTCATAAAAAACTTTTA
1 AAAAAATTC--AAAAAACTTTTA
40748 AAAA
1 AAAA
40752 TTATCCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAATTCAAAAAACTTTTA
Found at i:43314 original size:28 final size:28
Alignment explanation
Indices: 43274--43327 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
43264 TTAATATTCT
43274 TTCATGTCAATCCCTCTAGAAAATTTCC
1 TTCATGTCAATCCCTCTAGAAAATTTCC
43302 TTCATGTCAATCCCTCTAGAAAATTT
1 TTCATGTCAATCCCTCTAGAAAATTT
43328 TGACGCTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (28 bp):
TTCATGTCAATCCCTCTAGAAAATTTCC
Found at i:44177 original size:17 final size:17
Alignment explanation
Indices: 44155--44197 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
44145 GCAGAATTTG
44155 AATTTATTTTAAAATTA
1 AATTTATTTTAAAATTA
*
44172 AATTTATTTTAAATTTA
1 AATTTATTTTAAAATTA
44189 AATTTATTT
1 AATTTATTT
44198 AAATAATGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTTATTTTAAAATTA
Found at i:44843 original size:3 final size:3
Alignment explanation
Indices: 44835--44864 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
44825 TAAATGAAAG
44835 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44865 ATTTAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:44926 original size:3 final size:3
Alignment explanation
Indices: 44906--44967 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
44896 AATGGCAACT
* * *
44906 ATA ATTA ATA TTA TTA ATA AT- ATA ATA ATA ATA ATA ATA GATA TTA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
44952 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
44968 ATCGAAAGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:44955 original size:22 final size:20
Alignment explanation
Indices: 44905--44967 Score: 81
Period size: 22 Copynumber: 3.0 Consensus size: 20
44895 TAATGGCAAC
* *
44905 TATAATTAATATTATTAATAA
1 TATAA-TAATAATAATAATAA
44926 TATAATAATAATAATAATAGA
1 TATAATAATAATAATAATA-A
44947 TATTAATAATAATAATAATAA
1 TA-TAATAATAATAATAATAA
44968 ATCGAAAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.32
21 9 0.24
22 17 0.45
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TATAATAATAATAATAATAA
Found at i:46088 original size:30 final size:29
Alignment explanation
Indices: 46029--46248 Score: 164
Period size: 30 Copynumber: 7.5 Consensus size: 29
46019 TAATCTATCA
*
46029 AAAAATTCCATTTTTACCCTCG-AACTTCC
1 AAAAATTCCATTTTTA-CCTCGAAATTTCC
46058 AAAAATTCCATTTTTGACCTCGAAATTTCC
1 AAAAATTCCATTTTT-ACCTCGAAATTTCC
* * *
46088 AAAAATCCCATTTTTGACCTCTAAACTTCC
1 AAAAATTCCATTTTT-ACCTCGAAATTTCC
** * *
46118 AAAAATTCCA-TTTGCCCCCG-AATGTCC
1 AAAAATTCCATTTTTACCTCGAAATTTCC
* *
46145 AAAAACTCCATTTTCTACCTCGAAA-CTCTC
1 AAAAATTCCATTTT-TACCTCGAAATTTC-C
* * * * *
46175 AAAAATACC-CTTTTACCCTTG-AATATCT
1 AAAAATTCCATTTTTA-CCTCGAAATTTCC
* *
46203 AAAAATTCCATTTTTAACCCCAAAATTTCC
1 AAAAATTCCATTTTT-ACCTCGAAATTTCC
*
46233 CAAAATTACCATTTTT
1 AAAAATT-CCATTTTT
46249 CCCCCGGGTA
Statistics
Matches: 149, Mismatches: 30, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
27 14 0.09
28 18 0.12
29 44 0.30
30 65 0.44
31 8 0.05
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCTCGAAATTTCC
Found at i:47437 original size:17 final size:17
Alignment explanation
Indices: 47399--47441 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
47389 TTAAATTTAT
47399 AAATTTT-AAAATGCTA
1 AAATTTTAAAAATGCTA
*
47415 ATATTTTAAAAAT-CTCA
1 AAATTTTAAAAATGCT-A
47432 AAATTTTAAA
1 AAATTTTAAA
47442 TTTTTCAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATTTTAAAAATGCTA
Found at i:47793 original size:18 final size:18
Alignment explanation
Indices: 47772--47807 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
47762 TGAATTTTCG
*
47772 AATTCGAATAACTCAAAT
1 AATTCGAATAAATCAAAT
47790 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
47808 TTCAAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.28
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:48112 original size:152 final size:150
Alignment explanation
Indices: 47863--48141 Score: 329
Period size: 152 Copynumber: 1.8 Consensus size: 150
47853 TTTATTTTTG
* *
47863 CCTCAAAACTTTTATTCCTTCCCAATTTCCTCCAAAACTTTTACTTCCCTTTCATCCCACTCCCA
1 CCTCAAAACTTTTATTCCTTCCCAATTTCCTCCAAAACTTTTACTTCCCTCTCATCCAACTCCCA
** * *
47928 ATCTACCCCAAACCCATTTCCCCCAATTTTTTTTTTTAATATTT-TCTATCCAAAATTTTACTCT
66 ATCTACCCCAAACCCATCCCCCCCAA--TTTTTTTTGAATATTTCCCT-TCCAAAATTTTACTCT
47992 TCCTATATACTTTCCCCCAAAAC
128 TCCTATATACTTTCCCCCAAAAC
* *
48015 CCTCAAAACTTTTATTTCC-TCCCACTTT-CTCCCTAAAATTTTTAC-TCTCCTCTCATCCTAAC
1 CCTCAAAACTTTTA-TTCCTTCCCAATTTCCT-CC-AAAACTTTTACTTC-CCTCTCATCC-AAC
* *
48077 -CCC-ATTTACCCCAAACTCATCCCCCCCTCAA-TTTTTTTGAATATTTCCCTTCCAAAATTTTA
61 TCCCAATCTACCCCAAACCCAT-CCCCCC-CAATTTTTTTTGAATATTTCCCTTCCAAAATTTTA
48139 CTC
124 CTC
48142 CCCTATTTAC
Statistics
Matches: 109, Mismatches: 10, Indels: 17
0.80 0.07 0.12
Matches are distributed among these distances:
151 31 0.28
152 43 0.39
153 30 0.28
154 5 0.05
ACGTcount: A:0.25, C:0.36, G:0.00, T:0.39
Consensus pattern (150 bp):
CCTCAAAACTTTTATTCCTTCCCAATTTCCTCCAAAACTTTTACTTCCCTCTCATCCAACTCCCA
ATCTACCCCAAACCCATCCCCCCCAATTTTTTTTGAATATTTCCCTTCCAAAATTTTACTCTTCC
TATATACTTTCCCCCAAAAC
Found at i:48944 original size:12 final size:12
Alignment explanation
Indices: 48927--48955 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
48917 GATTTAAATC
48927 GAAATTATACTT
1 GAAATTATACTT
48939 GAAATTATACTT
1 GAAATTATACTT
48951 GAAAT
1 GAAAT
48956 GATAAACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (12 bp):
GAAATTATACTT
Found at i:53703 original size:5 final size:5
Alignment explanation
Indices: 53688--53729 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
53678 ATAATATTAT
*
53688 TTTAA -TTAA TTTAA TTTAA TTTAA TATTAAA TTTAA TCTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA T-TT-AA TTTAA TTTAA T
53730 ATTTATTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
4 4 0.12
5 22 0.67
6 4 0.12
7 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (5 bp):
TTTAA
Found at i:53722 original size:17 final size:17
Alignment explanation
Indices: 53679--53767 Score: 73
Period size: 17 Copynumber: 5.6 Consensus size: 17
53669 ATTCTAAAAA
*
53679 TAATATT-ATTTTAA-T
1 TAATATTAAATTTAATT
53694 TAAT-TT-AATTTAATT
1 TAATATTAAATTTAATT
*
53709 TAATATTAAATTTAATC
1 TAATATTAAATTTAATT
* * *
53726 TAATATTTATTTTGA-T
1 TAATATTAAATTTAATT
* *
53742 AAATATTATA-TTAATT
1 TAATATTAAATTTAATT
53758 TAATATTAAA
1 TAATATTAAA
53768 ATAATTAAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
14 8 0.14
15 12 0.21
16 17 0.30
17 20 0.35
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TAATATTAAATTTAATT
Found at i:57914 original size:16 final size:16
Alignment explanation
Indices: 57893--57923 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
57883 ACAAATATAG
57893 GTATAAATATTTAATT
1 GTATAAATATTTAATT
57909 GTATAAATATTTAAT
1 GTATAAATATTTAAT
57924 ATAGGTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
GTATAAATATTTAATT
Found at i:58333 original size:461 final size:461
Alignment explanation
Indices: 57471--58339 Score: 1657
Period size: 461 Copynumber: 1.9 Consensus size: 461
57461 TGGATGGTTC
57471 ACTTTCAACTATTTTGGAAGTTATGTCAAGGTAGGCACTTTTATTGTTCATATTTATTTGCATGA
1 ACTTTCAACTATTTTGGAAGTTATGTCAAGGTAGGCACTTTTATTGTTCATATTTATTTGCATGA
* *
57536 ACAATGATATTTCTATTTCCATGTTTAATGTTTTGGTCGGAATGATACTTGCCTGGAAATGTTGA
66 ACAATGATATTTCTATTTCCATGTTTAATGTTTTGATCGGAATGATACTTGCCTAGAAATGTTGA
*
57601 ATTCCAGTTTGGGCACAATAGGAAAGTATATTAATTTTAAATTCTAGTTTCTGTCCAAGAAATTT
131 ATTCCAGTTTCGGCACAATAGGAAAGTATATTAATTTTAAATTCTAGTTTCTGTCCAAGAAATTT
*
57666 GACTTGGATATCTTGTGGTGATAGTGACATGATATTTAGTTGAAGCCAAATTTCCTCTTTGGTTT
196 GACTTGGATATCTTGTGGTGATACTGACATGATATTTAGTTGAAGCCAAATTTCCTCTTTGGTTT
*
57731 TTCTCTCCGTCTTTCCTTATTGCCATGAGCATGCTAGGTGTCAATATTGTTTTAATAATTATGAA
261 TTCTCTCCGTCTTTCCTTATTGCCATGAGCATGCTAGGTGTCAATATTGTTTTAATAATTATAAA
* *
57796 ATAGCATTTTGTTCCATTGTTGTCTGTCGAGTCTGTAGTTTTGTTTTTAATATAGGTATACTTGC
326 ATAGCATTTTGTTCCATTGTTGTCTGTCGAGTCTGTAGTTGTGTTTTTAATATAGGTATAATTGC
57861 ATGTATTTGTATAAATATTTATACAAATATAGGTATAAATATTTAATTGTATAAATATTTAATAT
391 ATGTATTTGTATAAATATTTATACAAATATAGGTATAAATATTTAATTGTATAAATATTTAATAT
57926 AGGTAT
456 AGGTAT
57932 ACTTTCAACTATTTTGGAAGTTATGTCAAGGTAGGCACTTTTATTGTTCATATTTATTTGCATGA
1 ACTTTCAACTATTTTGGAAGTTATGTCAAGGTAGGCACTTTTATTGTTCATATTTATTTGCATGA
57997 ACAATGATATTTCTATTTCCATGTTTAATGTTTTGATCGGAATGATACTTGCCTAGAAATGTTGA
66 ACAATGATATTTCTATTTCCATGTTTAATGTTTTGATCGGAATGATACTTGCCTAGAAATGTTGA
58062 ATTCCAGTTTCGGCACAATAGGAAAGTATATTAATTTTAAATTCTAGTTTCTGTCCAAGAAATTT
131 ATTCCAGTTTCGGCACAATAGGAAAGTATATTAATTTTAAATTCTAGTTTCTGTCCAAGAAATTT
*
58127 GACTTGGATATCTTGTGGTGATACTGACATGATATTTAGTTGAAGCCAAGTTTCCTCTTTGGTTT
196 GACTTGGATATCTTGTGGTGATACTGACATGATATTTAGTTGAAGCCAAATTTCCTCTTTGGTTT
58192 TTCTCTCCGTCTTTCCTTATTGCCATGAGCATGCTAGGTGTCAATATTGTTTTAATAATTATAAA
261 TTCTCTCCGTCTTTCCTTATTGCCATGAGCATGCTAGGTGTCAATATTGTTTTAATAATTATAAA
*
58257 ATAGCATTTTGTTCCATTGTTGTCTGTTGAGTCTGTAGTTGTGTTTTTAATATAGGTATAATTGC
326 ATAGCATTTTGTTCCATTGTTGTCTGTCGAGTCTGTAGTTGTGTTTTTAATATAGGTATAATTGC
58322 ATGTATTTGTATAAATAT
391 ATGTATTTGTATAAATAT
58340 GTGCTCCAGT
Statistics
Matches: 399, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
461 399 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.43
Consensus pattern (461 bp):
ACTTTCAACTATTTTGGAAGTTATGTCAAGGTAGGCACTTTTATTGTTCATATTTATTTGCATGA
ACAATGATATTTCTATTTCCATGTTTAATGTTTTGATCGGAATGATACTTGCCTAGAAATGTTGA
ATTCCAGTTTCGGCACAATAGGAAAGTATATTAATTTTAAATTCTAGTTTCTGTCCAAGAAATTT
GACTTGGATATCTTGTGGTGATACTGACATGATATTTAGTTGAAGCCAAATTTCCTCTTTGGTTT
TTCTCTCCGTCTTTCCTTATTGCCATGAGCATGCTAGGTGTCAATATTGTTTTAATAATTATAAA
ATAGCATTTTGTTCCATTGTTGTCTGTCGAGTCTGTAGTTGTGTTTTTAATATAGGTATAATTGC
ATGTATTTGTATAAATATTTATACAAATATAGGTATAAATATTTAATTGTATAAATATTTAATAT
AGGTAT
Found at i:65009 original size:52 final size:52
Alignment explanation
Indices: 64948--65057 Score: 220
Period size: 52 Copynumber: 2.1 Consensus size: 52
64938 AGTGGTTGAG
64948 AATATGGAGTAAACTGAGAATAGAAAGGGTTGTAAAGTTGCTGCAATTCATA
1 AATATGGAGTAAACTGAGAATAGAAAGGGTTGTAAAGTTGCTGCAATTCATA
65000 AATATGGAGTAAACTGAGAATAGAAAGGGTTGTAAAGTTGCTGCAATTCATA
1 AATATGGAGTAAACTGAGAATAGAAAGGGTTGTAAAGTTGCTGCAATTCATA
65052 AATATG
1 AATATG
65058 CTTTAGGGAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.27
Consensus pattern (52 bp):
AATATGGAGTAAACTGAGAATAGAAAGGGTTGTAAAGTTGCTGCAATTCATA
Found at i:67646 original size:20 final size:20
Alignment explanation
Indices: 67607--67668 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
67597 GATCGTTAAC
*
67607 CCGTTGGCTGTTGACCGTTGA
1 CCGTTGACT-TTGACCGTTGA
** *
67628 GTGTTGACTTTGACTGTTGA
1 CCGTTGACTTTGACCGTTGA
*
67648 CCGTTGACTTTGACCATTGA
1 CCGTTGACTTTGACCGTTGA
67668 C
1 C
67669 TTTTTCGAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 27 0.82
21 6 0.18
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (20 bp):
CCGTTGACTTTGACCGTTGA
Found at i:67667 original size:27 final size:27
Alignment explanation
Indices: 67614--67669 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
67604 AACCCGTTGG
* *
67614 CTGTTGACCGTTGAGTGTTGACTTTGA
1 CTGTTGACCGTTGACTGTTGACATTGA
67641 CTGTTGACCGTTGACT-TTGACCATTGA
1 CTGTTGACCGTTGACTGTTGA-CATTGA
67668 CT
1 CT
67670 TTTTCGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (27 bp):
CTGTTGACCGTTGACTGTTGACATTGA
Found at i:70548 original size:39 final size:39
Alignment explanation
Indices: 70471--70549 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
70461 AATGAACTGG
* * * *
70471 TGACCTAATCGGTTTGACCACCAATCCAGTTTTGAAAAC
1 TGACCTAATCGGTTTAACCACCAATCCAATTCTAAAAAC
*
70510 TGACCTAATTGGTTTAACCACCAATCCAATTCTAAAAAC
1 TGACCTAATCGGTTTAACCACCAATCCAATTCTAAAAAC
70549 T
1 T
70550 TTGGCTAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.29
Consensus pattern (39 bp):
TGACCTAATCGGTTTAACCACCAATCCAATTCTAAAAAC
Found at i:73497 original size:22 final size:23
Alignment explanation
Indices: 73471--73523 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
73461 TAATATCATT
*
73471 ATATTAAATGTTT-TAATA-ATAA
1 ATATTAAATATTTATAATATA-AA
* *
73493 ATATTTACTATTTATAATATAAA
1 ATATTAAATATTTATAATATAAA
73516 ATATTAAA
1 ATATTAAA
73524 CAATGATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 10 0.42
23 13 0.54
24 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATTAAATATTTATAATATAAA
Found at i:74814 original size:11 final size:11
Alignment explanation
Indices: 74798--74822 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
74788 TTTAAAAATA
74798 TTTTTTTATAT
1 TTTTTTTATAT
74809 TTTTTTTATAT
1 TTTTTTTATAT
74820 TTT
1 TTT
74823 ATATAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTATAT
Found at i:75431 original size:16 final size:17
Alignment explanation
Indices: 75397--75433 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
75387 CTTGATTCTT
* *
75397 AAAATTTTAAAATTAAA
1 AAAATTTCAAAAATAAA
75414 AAAATTTCAAAAATAAA
1 AAAATTTCAAAAATAAA
75431 AAA
1 AAA
75434 CAATAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATTTCAAAAATAAA
Found at i:76091 original size:20 final size:20
Alignment explanation
Indices: 76062--76099 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
76052 TGTGGTGTTT
76062 TAAAAATATTATTTTATTTA
1 TAAAAATATTATTTTATTTA
*
76082 TAAAATTATTATTTTATT
1 TAAAAATATTATTTTATT
76100 AAATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAAAATATTATTTTATTTA
Found at i:76108 original size:20 final size:20
Alignment explanation
Indices: 76062--76106 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
76052 TGTGGTGTTT
* *
76062 TAAAAATATTATTTTATTTA
1 TAAAATTATTATTTTATTAA
76082 TAAAATTATTATTTTATTAAA
1 TAAAATTATTATTTTATT-AA
76103 TAAA
1 TAAA
76107 TTTCATGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAATTATTATTTTATTAA
Found at i:86394 original size:22 final size:22
Alignment explanation
Indices: 86368--86419 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
86358 CATTTTGTCA
*
86368 CCCATAAAGGGCTTTCATACGT
1 CCCATAAAGGGCTCTCATACGT
* *
86390 CCCATACATGGCTCTCATACGT
1 CCCATAAAGGGCTCTCATACGT
86412 CCCATAAA
1 CCCATAAA
86420 AGAGATCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.25
Consensus pattern (22 bp):
CCCATAAAGGGCTCTCATACGT
Found at i:92954 original size:42 final size:42
Alignment explanation
Indices: 92895--92975 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
92885 TTTAAAGACG
92895 ACAATATTACTACTGCAGGAGCACATAAGATATTTCAATCAT
1 ACAATATTACTACTGCAGGAGCACATAAGATATTTCAATCAT
*
92937 ACAATATTACTGCTGCAGGAGCACATAAGATATTTCAAT
1 ACAATATTACTACTGCAGGAGCACATAAGATATTTCAAT
92976 AATAGCAAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (42 bp):
ACAATATTACTACTGCAGGAGCACATAAGATATTTCAATCAT
Found at i:99648 original size:21 final size:21
Alignment explanation
Indices: 99630--99671 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
99620 CAATATTTTT
99630 GTCAAAAGAACAACAATTTAA
1 GTCAAAAGAACAACAATTTAA
* *
99651 GTCAACAGAGCAACAATTTAA
1 GTCAAAAGAACAACAATTTAA
99672 CTTTTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (21 bp):
GTCAAAAGAACAACAATTTAA
Done.