Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001022.1 Kokia drynarioides strain JFW-HI SEQ_112235, 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: 15271
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Found at i:1234 original size:29 final size:30
Alignment explanation
Indices: 1179--1242 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
1169 TAATTTTATT
1179 ATTTTTATAATTTTTAAAGAATTAAAT-TAA
1 ATTTTTATAATTTTTAAAGAATTAAATGT-A
* *
1209 ATTTTTATCATTTTT-GAG-ATTAAAATGTA
1 ATTTTTATAATTTTTAAAGAATT-AAATGTA
1238 ATTTT
1 ATTTT
1243 ATTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.10
29 12 0.40
30 15 0.50
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAGAATTAAATGTA
Found at i:2606 original size:21 final size:19
Alignment explanation
Indices: 2572--2610 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
2562 CAATTTTAAT
2572 AATTTTTAATTATTTATAG
1 AATTTTTAATTATTTATAG
2591 AATTTATTATATTATTTATA
1 AATTT-TTA-ATTATTTATA
2611 AGTTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
AATTTTTAATTATTTATAG
Found at i:2822 original size:18 final size:19
Alignment explanation
Indices: 2782--2824 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2772 TTTTAAAAAA
*
2782 TTTAATTATTTTGAATATGT
1 TTTATTTATTTT-AATATGT
*
2802 TTTATTTATTTT-ATATTT
1 TTTATTTATTTTAATATGT
2820 TTTAT
1 TTTAT
2825 AATTTATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTATTTATTTTAATATGT
Found at i:2842 original size:28 final size:27
Alignment explanation
Indices: 2810--2913 Score: 72
Period size: 28 Copynumber: 3.7 Consensus size: 27
2800 GTTTTATTTA
2810 TTTTATATTTTTTATAATTTATTAGATT
1 TTTTATA-TTTTTATAATTTATTAGATT
* *
2838 TTTTA-AGTTTTATAATATT-TAAGTTATT
1 TTTTATATTTTTATAAT-TTATTAG--ATT
2866 TTTTATAATTTTTATAAGTTTCTATTA-A-T
1 TTTTAT-ATTTTTATAA--TT-TATTAGATT
* *
2895 TTTGATATTTTTATTATTT
1 TTTTATATTTTTATAATTT
2914 TTCTTGATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
25 1 0.02
26 14 0.23
27 3 0.05
28 22 0.36
29 6 0.10
30 10 0.16
31 1 0.02
32 2 0.03
33 2 0.03
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (27 bp):
TTTTATATTTTTATAATTTATTAGATT
Found at i:3335 original size:22 final size:25
Alignment explanation
Indices: 3308--3353 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3298 GTGGTTAAAG
3308 GATTAA-A-AAGTTCGGTT-AATTT
1 GATTAATATAAGTTCGGTTCAATTT
*
3330 GATTAATATTAGTTCGGTTCAATT
1 GATTAATATAAGTTCGGTTCAATT
3354 AACTTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 9 0.45
25 4 0.20
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (25 bp):
GATTAATATAAGTTCGGTTCAATTT
Found at i:5222 original size:24 final size:24
Alignment explanation
Indices: 5194--5254 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
5184 AGAAATAATC
5194 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
5218 TTTCAATTAAA--CTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
5240 TTTAAGTCAAACTCT
1 TTTCAGTTAAACTCT
5255 TATTAGTCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 18 0.60
24 12 0.40
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:8386 original size:85 final size:86
Alignment explanation
Indices: 8242--8413 Score: 292
Period size: 85 Copynumber: 2.0 Consensus size: 86
8232 TTACATGAAG
* * * *
8242 AGATTGTATATGTGAAATTGATATGAAAGCATGAATCCATGCCATTACATGTTAGTATGAA-ATA
1 AGATTGTATATGTGAAATTGACATGAAAGCATGAATACATGCCATTAAATGTTAATATGAAGATA
8306 TTGAATGTGCTTGATAAGCAT
66 TTGAATGTGCTTGATAAGCAT
*
8327 AGATTGTATATGTGAAATTGACATGAAAGCATGAATACATGCCTTTAAATGTTAATATGAAGATA
1 AGATTGTATATGTGAAATTGACATGAAAGCATGAATACATGCCATTAAATGTTAATATGAAGATA
8392 TTGAATGTGCTTGATAAGCAT
66 TTGAATGTGCTTGATAAGCAT
8413 A
1 A
8414 ACATCGATTC
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 56 0.69
86 25 0.31
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.34
Consensus pattern (86 bp):
AGATTGTATATGTGAAATTGACATGAAAGCATGAATACATGCCATTAAATGTTAATATGAAGATA
TTGAATGTGCTTGATAAGCAT
Found at i:9639 original size:8 final size:9
Alignment explanation
Indices: 9629--9971 Score: 84
Period size: 9 Copynumber: 36.7 Consensus size: 9
9619 TGTTTATTAA
9629 TTTTATAAT
1 TTTTATAAT
*
9638 TTTAATAAT
1 TTTTATAAT
*
9647 TTATTACAA-
1 TT-TTATAAT
9656 TTTTATAAT
1 TTTTATAAT
9665 TTTTATAAGTT
1 TTTTATAA--T
*
9676 TTTTATTAT
1 TTTTATAAT
*
9685 TTTTATAAA
1 TTTTATAAT
*
9694 ATTTATAA-
1 TTTTATAAT
*
9702 GTTTAT--T
1 TTTTATAAT
9709 TCTATT-TCAAT
1 T-T-TTAT-AAT
*
9720 TTTTTTAAT
1 TTTTATAAT
** *
9729 TGTCAATGAT
1 T-TTTATAAT
9739 TTTT-T--T
1 TTTTATAAT
*
9745 TTCT-T-AT
1 TTTTATAAT
*
9752 TTTTAGTGAT
1 TTTTA-TAAT
9762 TTTTATAAGT
1 TTTTATAA-T
* *
9772 TTTAAGAAT
1 TTTTATAAT
*
9781 TTTTATATGT
1 TTTTATA-AT
*
9791 TTTTATAAAA
1 TTTTAT-AAT
*
9801 TTTTAAATAT
1 TTTTATA-AT
* *
9811 TTTTTTATT
1 TTTTATAAT
*
9820 CATTTTACAAATT
1 --TTTTA-TAA-T
9833 TTTTATAAT
1 TTTTATAAT
9842 TTATTAT-AT
1 TT-TTATAAT
9851 TTTT-TAAT
1 TTTTATAAT
*
9859 ATTTTTTAAT
1 -TTTTATAAT
* *
9869 ATTTAAGTTATT
1 -TTTTA--TAAT
9881 TTTTATAATT
1 TTTTATAA-T
9891 TTTTATCAAT
1 TTTTAT-AAT
*
9901 TTTAAT-AT
1 TTTTATAAT
*
9909 TTTTATCA-
1 TTTTATAAT
*
9917 TTTAATAAAT
1 TTTTAT-AAT
9927 TTTTATAATTT
1 TTTTATAA--T
* *
9938 TTTTCTTATT
1 TTTT-ATAAT
9948 TTTTATAAT
1 TTTTATAAT
*
9957 TTTAATAAT
1 TTTTATAAT
9966 TTTTAT
1 TTTTAT
9972 GAAAAAATAT
Statistics
Matches: 245, Mismatches: 51, Indels: 76
0.66 0.14 0.20
Matches are distributed among these distances:
6 5 0.02
7 5 0.02
8 29 0.12
9 88 0.36
10 80 0.33
11 31 0.13
12 6 0.02
13 1 0.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:9645 original size:9 final size:8
Alignment explanation
Indices: 9621--9677 Score: 51
Period size: 9 Copynumber: 6.4 Consensus size: 8
9611 TTCATTATTG
9621 TTTATTAAT
1 TTTA-TAAT
9630 TTTATAAT
1 TTTATAAT
9638 TTTAATAATT
1 TTT-ATAA-T
*
9648 TATTACAAT
1 T-TTATAAT
9657 TTTATAATT
1 TTTATAA-T
9666 TTTATAAGT
1 TTTATAA-T
9675 TTT
1 TTT
9678 TTATTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 12 0.29
9 22 0.54
10 5 0.12
11 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (8 bp):
TTTATAAT
Found at i:9687 original size:9 final size:9
Alignment explanation
Indices: 9538--9971 Score: 90
Period size: 10 Copynumber: 45.8 Consensus size: 9
9528 TTTATAATTT
9538 TTTTTATAA
1 TTTTTATAA
* *
9547 TTCATTAGAA
1 TT-TTTATAA
9557 TTTGTTAT-A
1 TTT-TTATAA
9566 TTATTTATAA
1 TT-TTTATAA
*
9576 GTTTTTAAGAA
1 -TTTTT-ATAA
9587 TTTTTATAA
1 TTTTTATAA
9596 GGCTTTTTATAAA
1 ---TTTTTAT-AA
** * *
9609 GATTCATTA
1 TTTTTATAA
9618 TTGTTTATTAA
1 TT-TTTA-TAA
9629 -TTTTATAA
1 TTTTTATAA
*
9637 TTTTAATAA
1 TTTTTATAA
*
9646 TTTATTACAA
1 TTT-TTATAA
9656 -TTTTATAA
1 TTTTTATAA
9664 TTTTTATAA
1 TTTTTATAA
*
9673 GTTTTTTATTA
1 --TTTTTATAA
9684 TTTTTATAA
1 TTTTTATAA
**
9693 AATTTATAA
1 TTTTTATAA
*
9702 -GTTTAT--
1 TTTTTATAA
9708 TTCTATT-TCAA
1 TT-T-TTAT-AA
*
9719 TTTTTTTAA
1 TTTTTATAA
** *
9728 TTGTCAATGA
1 TT-TTTATAA
9738 TTTTT-T--
1 TTTTTATAA
*
9744 TTTCT-T-A
1 TTTTTATAA
*
9751 TTTTTAGTGA
1 TTTTTA-TAA
9761 TTTTTATAA
1 TTTTTATAA
* *
9770 GTTTTAAGAA
1 -TTTTTATAA
*
9780 TTTTTATATG
1 TTTTTATA-A
9790 TTTTTATAAA
1 TTTTTAT-AA
* *
9800 ATTTTAAATA
1 TTTTTATA-A
* *
9810 TTTTTTTAT
1 TTTTTATAA
*
9819 TCATTTTACAAA
1 T--TTTTA-TAA
9831 TTTTTTATAA
1 -TTTTTATAA
9841 TTTATTAT-A
1 TTT-TTATAA
9850 TTTTT-TAA
1 TTTTTATAA
*
9858 TATTTTTTAA
1 T-TTTTATAA
* *
9868 TATTTAAGTTAT
1 T-TTTTA--TAA
9880 TTTTTATAA
1 TTTTTATAA
9889 TTTTTTATCAA
1 -TTTTTAT-AA
*
9900 TTTTAAT-A
1 TTTTTATAA
*
9908 TTTTTATCA
1 TTTTTATAA
*
9917 -TTTAATAAA
1 TTTTTAT-AA
9926 TTTTTATAA
1 TTTTTATAA
* *
9935 TTTTTTTCTTAT
1 --TTTTT-ATAA
9947 TTTTTATAA
1 TTTTTATAA
*
9956 TTTTAATAA
1 TTTTTATAA
9965 TTTTTAT
1 TTTTTAT
9972 GAAAAAATAT
Statistics
Matches: 309, Mismatches: 65, Indels: 102
0.65 0.14 0.21
Matches are distributed among these distances:
6 5 0.02
7 5 0.02
8 32 0.10
9 105 0.34
10 108 0.35
11 38 0.12
12 13 0.04
13 3 0.01
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:9715 original size:29 final size:29
Alignment explanation
Indices: 9622--9708 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 29
9612 TCATTATTGT
* *
9622 TTATTAATTTTAT-AATTTTAATAA-TTTA
1 TTATTATTTTTATAAAATTT-ATAAGTTTA
* * ** *
9650 TTA-CAATTTTATAATTTTTATAAGTTTT
1 TTATTATTTTTATAAAATTTATAAGTTTA
9678 TTATTATTTTTATAAAATTTATAAGTTTA
1 TTATTATTTTTATAAAATTTATAAGTTTA
9707 TT
1 TT
9709 TCTATTTCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
27 12 0.25
28 14 0.29
29 22 0.46
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (29 bp):
TTATTATTTTTATAAAATTTATAAGTTTA
Found at i:9864 original size:29 final size:28
Alignment explanation
Indices: 9761--9971 Score: 117
Period size: 29 Copynumber: 7.2 Consensus size: 28
9751 TTTTTAGTGA
* * *
9761 TTTTTATAAGTTTTAAGAATTTTTATAT
1 TTTTTATAATTTTTTATAATTTTTATAT
** * *
9789 GTTTTTATAAAATTTTAAATATTTTTTTAT
1 -TTTTTATAATTTTTTATA-ATTTTTATAT
*
9819 TCATTTTACAAATTTTTTATAATTTATTATA-
1 T--TTTTA-TAATTTTTTATAATTT-TTATAT
*
9850 TTTTT-TAATATTTTT-TAATATTTAAGTTAT
1 TTTTTATAAT-TTTTTATAAT-TTTTA--TAT
*
9880 TTTTTATAATTTTTTATCAATTTTAATA-
1 TTTTTATAATTTTTTAT-AATTTTTATAT
* **
9908 TTTTTATCATTTAATA-AATTTTTATAATT
1 TTTTTATAATTTTTTATAATTTTTAT-A-T
* * * *
9937 TTTTTCTTATTTTTTATAATTTTAATAA
1 TTTTTATAATTTTTTATAATTTTTATAT
9965 TTTTTAT
1 TTTTTAT
9972 GAAAAAATAT
Statistics
Matches: 142, Mismatches: 23, Indels: 35
0.71 0.12 0.17
Matches are distributed among these distances:
26 8 0.06
27 10 0.07
28 26 0.18
29 36 0.25
30 27 0.19
31 20 0.14
32 15 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTTATAATTTTTTATAATTTTTATAT
Found at i:9886 original size:48 final size:46
Alignment explanation
Indices: 9812--9937 Score: 132
Period size: 48 Copynumber: 2.7 Consensus size: 46
9802 TTTAAATATT
*
9812 TTTTTATTCATTTTACA-AATTTTTTATAATTTATTAT-ATTTTTTAATA
1 TTTTTA-TCA-TTTA-ATAATTTTTTATAATTTATTATCA-ATTTTAATA
* *
9860 TTTTTTAAT-ATTTAAGTTATTTTTTATAATTTTTTATCAATTTTAATA
1 -TTTTT-ATCATTTAA-TAATTTTTTATAATTTATTATCAATTTTAATA
*
9908 TTTTTATCATTTAATAAATTTTTATAATTT
1 TTTTTATCATTTAATAATTTTTTATAATTT
9938 TTTTCTTATT
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
46 17 0.25
47 15 0.22
48 27 0.40
49 7 0.10
50 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (46 bp):
TTTTTATCATTTAATAATTTTTTATAATTTATTATCAATTTTAATA
Found at i:9952 original size:48 final size:47
Alignment explanation
Indices: 9812--9960 Score: 128
Period size: 48 Copynumber: 3.1 Consensus size: 47
9802 TTTAAATATT
* * * *
9812 TTTTTATTCATTTTACAAATTTTTTATAA-TTTATTATATTTTTTAATA
1 TTTTTA-TCATTTAATAAA-TTTTTATAATTTTTTTCTATTTTTTAATA
* * *
9860 TTTTTTAAT-ATTTAAGTTATTTTTTATAATTTTTTATC-A-ATTTTAATA
1 -TTTTT-ATCATTTAA-TAAATTTTTATAATTTTTT-TCTATTTTTTAATA
9908 TTTTTATCATTTAATAAATTTTTATAATTTTTTTCTTATTTTTT-ATA
1 TTTTTATCATTTAATAAATTTTTATAATTTTTTTC-TATTTTTTAATA
*
9955 ATTTTA
1 TTTTTA
9961 ATAATTTTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
45 2 0.02
46 19 0.23
47 20 0.25
48 26 0.32
49 12 0.15
50 2 0.02
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (47 bp):
TTTTTATCATTTAATAAATTTTTATAATTTTTTTCTATTTTTTAATA
Found at i:10276 original size:29 final size:31
Alignment explanation
Indices: 10209--10284 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
10199 TTGATTCAAT
*
10209 TTGGTA-CTCAAACTTGACACTTTTTTTCTAAT
1 TTGGTACCT-AAACTTGA-ACTTTTTTTCTAAG
*
10241 TTAGTACCTAAACTTG-ACTTTTTTT-TAAG
1 TTGGTACCTAAACTTGAACTTTTTTTCTAAG
10270 TTGGTACCTAAACTT
1 TTGGTACCTAAACTT
10285 TTTGAGGTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 17 0.43
30 9 0.22
32 12 0.30
33 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (31 bp):
TTGGTACCTAAACTTGAACTTTTTTTCTAAG
Found at i:10558 original size:59 final size:57
Alignment explanation
Indices: 10483--10647 Score: 172
Period size: 59 Copynumber: 2.8 Consensus size: 57
10473 AATATTTAAT
* *
10483 AAATTTAGATACCAAATTAGAAAAAATGTCAAATTCAAATACCAAATT-AAGTCCAAAA
1 AAATTTAGATACCAAATTA-AAAAAATGTCAAATTCAAATACAAAATTGAA-TACAAAA
* * * *
10541 AAAGTTTAGATACCAAATTAAGAAAAA-GTACTAAGTTCAAACACTAAATTGAATAGAAAA
1 AAA-TTTAGATACCAAATTAA-AAAAATGT-C-AAATTCAAATACAAAATTGAATACAAAA
* * *
10601 AAATTTAAATACCAAATTTAAAAAAATATCAAATTTAAATACAAAAT
1 AAATTTAGATACCAAA-TTAAAAAAATGTCAAATTCAAATACAAAAT
10648 CTTATATTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
58 19 0.21
59 40 0.45
60 28 0.31
61 2 0.02
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.25
Consensus pattern (57 bp):
AAATTTAGATACCAAATTAAAAAAATGTCAAATTCAAATACAAAATTGAATACAAAA
Found at i:10633 original size:17 final size:17
Alignment explanation
Indices: 10607--10639 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10597 AAAAAAATTT
10607 AAATACCAAATTTAAAA
1 AAATACCAAATTTAAAA
*
10624 AAATATCAAATTTAAA
1 AAATACCAAATTTAAA
10640 TACAAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATACCAAATTTAAAA
Found at i:10958 original size:134 final size:132
Alignment explanation
Indices: 10797--11165 Score: 360
Period size: 134 Copynumber: 2.8 Consensus size: 132
10787 AACATGCCAG
*
10797 CTTAAAAAATGTTTCTTTAAAAGAAAAAAATTTAATTGTGAAAAAGCCCATAAGAAAATGTCAAA
1 CTTAAAAAATG-TT-TTTAAAA-AAAAAAATTTAATTGTGAAAAAGCCCTTAAGAAAATGT-AAA
*
10862 AAAGAAAGT-TTTTTATTAAATTCACA-CCTAATTTTGAA-CTCCAACTTCAAAGCTTGAGTGTC
62 AAA-AAAGTCTTTGTATTAAATTCACATCC-AA--TT-AAGCTCCAACTTCAAAGCTTGAGTGTC
* *
10924 ACAGTATTCAA
122 ACAATATCCAA
* * * *
10935 CTTAAAAAATG-TTTTAAAAAAAAAAAATT-ATTGTGAAAAATGTCCTTACGAAAATGT--TAAA
1 CTTAAAAAATGTTTTTAAAAAAAAAAATTTAATTGTGAAAAA-GCCCTTAAGAAAATGTAAAAAA
* * * * * * *
10996 AAAGTCTTTGTATTAAATTCACATCCAATTAAGTTTCAATTTTAAAGTTTTAGTGTCGCAATATC
65 AAAGTCTTTGTATTAAATTCACATCCAATTAAGCTCCAACTTCAAAGCTTGAGTGTCACAATATC
*
11061 CAG
130 CAA
* * *
11064 CTTAAAAAATGTTTTTTTAAAAGAAAAAAAATTTAATTGTGAAAAAGCCGTTAAGAAATTGT-TA
1 CTTAAAAAATG--TTTTT-AAA-AAAAAAAATTTAATTGTGAAAAAGCCCTTAAGAAAATGTAAA
* *
11128 AAAAAA-TCTTTGTATTAAATTCACATCAAATTGAGCTC
62 AAAAAAGTCTTTGTATTAAATTCACATCCAATTAAGCTC
11166 TTGTCGTTAA
Statistics
Matches: 194, Mismatches: 26, Indels: 26
0.79 0.11 0.11
Matches are distributed among these distances:
128 2 0.01
129 38 0.20
130 5 0.03
131 21 0.11
132 6 0.03
133 14 0.07
134 72 0.37
135 24 0.12
136 1 0.01
138 11 0.06
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (132 bp):
CTTAAAAAATGTTTTTAAAAAAAAAAATTTAATTGTGAAAAAGCCCTTAAGAAAATGTAAAAAAA
AAGTCTTTGTATTAAATTCACATCCAATTAAGCTCCAACTTCAAAGCTTGAGTGTCACAATATCC
AA
Found at i:11323 original size:17 final size:17
Alignment explanation
Indices: 11303--11422 Score: 73
Period size: 18 Copynumber: 6.5 Consensus size: 17
11293 ATATTTTCTC
11303 ATAAAAATTATTAAAAT
1 ATAAAAATTATTAAAAT
*
11320 ATAAAAATTATTAAATT
1 ATAAAAATTATTAAAAT
**
11337 ATTAAAAATATAAAAAAAT
1 A-TAAAAAT-TATTAAAAT
*
11356 ATATTAAAATTGA-TACGAACTT
1 ATA--AAAATT-ATTA--AA-AT
*
11378 ATAAAAATTATAAAAAT
1 ATAAAAATTATTAAAAT
11395 AATAAAAACTTA-TAAATATT
1 -ATAAAAA-TTATTAAA-A-T
11415 ATAAAAAT
1 ATAAAAAT
11423 CAAATTAATT
Statistics
Matches: 81, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
17 18 0.22
18 22 0.27
19 21 0.26
20 14 0.17
21 2 0.02
22 4 0.05
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAAAAATTATTAAAAT
Found at i:11390 original size:9 final size:9
Alignment explanation
Indices: 11303--11531 Score: 117
Period size: 10 Copynumber: 23.8 Consensus size: 9
11293 ATATTTTCTC
11303 ATAAAAATT
1 ATAAAAATT
*
11312 ATTAAAA-T
1 ATAAAAATT
11320 ATAAAAATT
1 ATAAAAATT
*
11329 AT-TAAATT
1 ATAAAAATT
11337 ATTAAAAATAT
1 A-TAAAAAT-T
*
11348 AAAAAAATAT
1 ATAAAAAT-T
*
11358 ATTAAAATT
1 ATAAAAATT
* *
11367 GATACGAACTT
1 -ATA-AAAATT
11378 ATAAAAATT
1 ATAAAAATT
*
11387 ATAAAAATA
1 ATAAAAATT
11396 ATAAAAACTT
1 ATAAAAA-TT
*
11406 ATAAATATT
1 ATAAAAATT
*
11415 ATAAAAATC
1 ATAAAAATT
*
11424 A-AATTAATT
1 ATAA-AAATT
*
11433 CTAATAAATT
1 ATAA-AAATT
11443 ATAAACAATT
1 ATAAA-AATT
*
11453 TTATAAAATT
1 ATA-AAAATT
11463 AATAAAACA-T
1 -ATAAAA-ATT
*
11473 ATTTAAAATT
1 A-TAAAAATT
*
11483 CTATAAAATGT
1 ATA-AAAAT-T
11494 ATAAAAAATCCT
1 AT-AAAAAT--T
11506 -TAAAAACTT
1 ATAAAAA-TT
11515 ATAAAAATT
1 ATAAAAATT
11524 CATAAAAA
1 -ATAAAAA
11532 AAAATTATTA
Statistics
Matches: 169, Mismatches: 29, Indels: 43
0.70 0.12 0.18
Matches are distributed among these distances:
8 15 0.09
9 50 0.30
10 82 0.49
11 20 0.12
12 2 0.01
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:11402 original size:19 final size:19
Alignment explanation
Indices: 11380--11421 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11370 ACGAACTTAT
11380 AAAAATTATAAAAATAATA
1 AAAAATTATAAAAATAATA
* * *
11399 AAAACTTATAAATATTATA
1 AAAAATTATAAAAATAATA
11418 AAAA
1 AAAA
11422 TCAAATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTATAAAAATAATA
Found at i:11500 original size:20 final size:21
Alignment explanation
Indices: 11477--11530 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
11467 AAACATATTT
11477 AAAATTCTATAAAA-TGTATAA
1 AAAATTCTATAAAACT-TATAA
*
11498 AAAATCCT-TAAAAACTTAT-A
1 AAAATTCTAT-AAAACTTATAA
11518 AAAATTC-ATAAAA
1 AAAATTCTATAAAA
11531 AAAAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
19 4 0.14
20 9 0.32
21 14 0.50
22 1 0.04
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATTCTATAAAACTTATAA
Found at i:11543 original size:24 final size:23
Alignment explanation
Indices: 11507--11554 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
11497 AAAAATCCTT
* *
11507 AAAAACTTATAAAAATTCATAAA
1 AAAAAATTATAAAAAATCATAAA
11530 AAAAAATTATTAAAAAATCATAAA
1 AAAAAATTA-TAAAAAATCATAAA
11554 A
1 A
11555 CTTGAACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAAAATTATAAAAAATCATAAA
Done.