Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013449.1 Kokia drynarioides strain JFW-HI SEQ_128475, 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: 72992
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Warning! 130 characters in sequence are not A, C, G, or T
Found at i:1440 original size:15 final size:15
Alignment explanation
Indices: 1420--1453 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1410 TATCTTATTT
*
1420 ATTTTTTATTAAATA
1 ATTTTTTACTAAATA
*
1435 ATTTTTTACTCAATA
1 ATTTTTTACTAAATA
1450 ATTT
1 ATTT
1454 ATAACATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTTACTAAATA
Found at i:4359 original size:19 final size:20
Alignment explanation
Indices: 4329--4370 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
4319 TAACTCCTAA
4329 TATTTTTCTAAAAATATT-TT
1 TATTTTTCT-AAAATATTATT
4349 TATTTTT-TAAAATATTATT
1 TATTTTTCTAAAATATTATT
4368 TAT
1 TAT
4371 CGATTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 6 0.29
20 7 0.33
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTCTAAAATATTATT
Found at i:11300 original size:76 final size:76
Alignment explanation
Indices: 11218--11418 Score: 244
Period size: 76 Copynumber: 2.6 Consensus size: 76
11208 AGCTAGTCAA
* * *
11218 ATAACCTGACGATATCAAAGGTGTTCCCAACACTAGTTGGATGTACCAACAATGATTTGCTTCTA
1 ATAACCTGACGATATCAAATGTGTGCCCAACACTAGTTGGATGTACCAACAATGATTTGCTCCTA
*
11283 GCGT-TATTCGG
66 GC-TCTAGTCGG
* * * ** * *
11294 ATAACCTGACAATATCAAATGTGTGCCTAGCACTAGTCAGATGTACCACCAATTATTTGCTCCTA
1 ATAACCTGACGATATCAAATGTGTGCCCAACACTAGTTGGATGTACCAACAATGATTTGCTCCTA
11359 GCTCTAGTCGG
66 GCTCTAGTCGG
* * *
11370 ATAAACC-AAGGATATCAAATGTGTGCCCATCACTAGTTGGATGTACCAA
1 AT-AACCTGACGATATCAAATGTGTGCCCAACACTAGTTGGATGTACCAA
11419 AAATTCTTCA
Statistics
Matches: 104, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
75 1 0.01
76 99 0.95
77 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (76 bp):
ATAACCTGACGATATCAAATGTGTGCCCAACACTAGTTGGATGTACCAACAATGATTTGCTCCTA
GCTCTAGTCGG
Found at i:14817 original size:13 final size:13
Alignment explanation
Indices: 14784--14820 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
14774 AAACCCAAAA
14784 CCTAAATCTCGAAC
1 CCTAAA-CTCGAAC
14798 CCTTAAACTCGAAC
1 CC-TAAACTCGAAC
14812 CCTAAACTC
1 CCTAAACTC
14821 TACCCCATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 11 0.50
15 4 0.18
ACGTcount: A:0.35, C:0.38, G:0.05, T:0.22
Consensus pattern (13 bp):
CCTAAACTCGAAC
Found at i:14870 original size:20 final size:19
Alignment explanation
Indices: 14831--14920 Score: 62
Period size: 20 Copynumber: 4.7 Consensus size: 19
14821 TACCCCATAC
*
14831 CCCAAACACTTAAACTTTAAA
1 CCCAAAC-C-TAAACATTAAA
14852 CCCAAATCCTAAACATTAAA
1 CCCAAA-CCTAAACATTAAA
* *
14872 ACC--A--TGAACATTAAA
1 CCCAAACCTAAACATTAAA
* *
14887 CCTAAACCTTAAACATTAAG
1 CCCAAACC-TAAACATTAAA
14907 CCCAAAACCTAAAC
1 CCC-AAACCTAAAC
14921 TCAAACATGA
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
15 11 0.20
17 1 0.02
18 1 0.02
20 28 0.52
21 12 0.22
22 1 0.02
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (19 bp):
CCCAAACCTAAACATTAAA
Found at i:15186 original size:50 final size:50
Alignment explanation
Indices: 15126--15225 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
15116 GAAAATATTA
*
15126 AATATAAATGAGTGTATGATAATACTTTGTTATCTTTAAGTTTTAATGAT
1 AATATAAATGAGTGTATGATAATACTTTGTTATCTTTAAATTTTAATGAT
15176 AATATAAATGAGTGTATGATAATACTTTGTTATCTTTAAATTTTAATGAT
1 AATATAAATGAGTGTATGATAATACTTTGTTATCTTTAAATTTTAATGAT
15226 GTGATACTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (50 bp):
AATATAAATGAGTGTATGATAATACTTTGTTATCTTTAAATTTTAATGAT
Found at i:22800 original size:6 final size:6
Alignment explanation
Indices: 22789--22819 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
22779 TTTGATCCAT
22789 CTGCAA CTGCAA CTGCAA CTGCAA CTGCAA C
1 CTGCAA CTGCAA CTGCAA CTGCAA CTGCAA C
22820 ATGGATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.16
Consensus pattern (6 bp):
CTGCAA
Found at i:23120 original size:49 final size:49
Alignment explanation
Indices: 23048--23143 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 49
23038 CTATTCTCAT
*
23048 AACAAGTATGATTGAAAATATGATAAGTGTTTTATTTGTTTAAATATAG
1 AACAAGTATGACTGAAAATATGATAAGTGTTTTATTTGTTTAAATATAG
* *
23097 AACAATTATGACTGAAAATATGATAAGTGTTTTATTTGTTTATATAT
1 AACAAGTATGACTGAAAATATGATAAGTGTTTTATTTGTTTAAATAT
23144 TTTTATTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.43
Consensus pattern (49 bp):
AACAAGTATGACTGAAAATATGATAAGTGTTTTATTTGTTTAAATATAG
Found at i:23622 original size:23 final size:23
Alignment explanation
Indices: 23573--23622 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
23563 CCAGCTGGCA
* * **
23573 TTTTTTTAGAGTTAGGGTTTTGC
1 TTTTTTTAAAATTAGGGTTAGGC
*
23596 TTTTTTTAAAATTAGGGTTAGGG
1 TTTTTTTAAAATTAGGGTTAGGC
23619 TTTT
1 TTTT
23623 GTGGATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.02, G:0.24, T:0.56
Consensus pattern (23 bp):
TTTTTTTAAAATTAGGGTTAGGC
Found at i:23686 original size:38 final size:38
Alignment explanation
Indices: 23643--23727 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 38
23633 AAGTTTCGAG
23643 TTTTATAAGTTATGAGTTTTTTAATATATTTTTAAG-TT
1 TTTTATAAGTTATGAGTTTTTT-ATATATTTTTAAGTTT
* * * *
23681 TTTTATATATTTTTTAGTTTTTTATATATTTTTTAGTTT
1 TTTTATA-AGTTATGAGTTTTTTATATATTTTTAAGTTT
23720 TTTTATAA
1 TTTTATAA
23728 TTTTTAAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 20 0.49
39 21 0.51
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (38 bp):
TTTTATAAGTTATGAGTTTTTTATATATTTTTAAGTTT
Found at i:23688 original size:19 final size:19
Alignment explanation
Indices: 23657--23735 Score: 115
Period size: 19 Copynumber: 4.1 Consensus size: 19
23647 ATAAGTTATG
23657 AGTTTTTTAATATATTTTTA
1 AGTTTTTT-ATATATTTTTA
*
23677 AGTTTTTTATATATTTTTT
1 AGTTTTTTATATATTTTTA
*
23696 AGTTTTTTATATATTTTTT
1 AGTTTTTTATATATTTTTA
23715 AGTTTTTT-TATAATTTTTA
1 AGTTTTTTATAT-ATTTTTA
23734 AG
1 AG
23736 ATGTAAAGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
18 3 0.05
19 45 0.80
20 8 0.14
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.68
Consensus pattern (19 bp):
AGTTTTTTATATATTTTTA
Found at i:23731 original size:9 final size:10
Alignment explanation
Indices: 23660--23733 Score: 61
Period size: 9 Copynumber: 7.6 Consensus size: 10
23650 AGTTATGAGT
23660 TTTTTAATATA
1 TTTTT-ATATA
23671 TTTTTA-AGT-
1 TTTTTATA-TA
23680 TTTTTATATA
1 TTTTTATATA
23690 TTTTT-TAGT-
1 TTTTTATA-TA
23699 TTTTTATATA
1 TTTTTATATA
*
23709 TTTTT-TAGTT
1 TTTTTATA-TA
23719 TTTTTATA-A
1 TTTTTATATA
23728 TTTTTA
1 TTTTTA
23734 AGATGTAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
9 24 0.45
10 22 0.42
11 7 0.13
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (10 bp):
TTTTTATATA
Found at i:23731 original size:38 final size:38
Alignment explanation
Indices: 23643--23732 Score: 119
Period size: 38 Copynumber: 2.3 Consensus size: 38
23633 AAGTTTCGAG
* *
23643 TTTTATAAGTTATGAGTTTTTTAATATATTTTTAAGTT
1 TTTTATAATTTTTGAGTTTTTTAATATATTTTTAAGTT
* *
23681 TTTTATATATTTTTTAGTTTTTT-ATATATTTTTTAGTTT
1 TTTTATA-ATTTTTGAGTTTTTTAATATATTTTTAAG-TT
23720 TTTTATAATTTTT
1 TTTTATAATTTTT
23733 AAGATGTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 25 0.54
39 21 0.46
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (38 bp):
TTTTATAATTTTTGAGTTTTTTAATATATTTTTAAGTT
Found at i:24845 original size:50 final size:50
Alignment explanation
Indices: 24770--24866 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
24760 ACTTCGGAGC
*
24770 GACAATGGCCTTGCAAATAGGTAAAAAATCATACTTATTATTCCAAAAGT
1 GACAATGGCCTCGCAAATAGGTAAAAAATCATACTTATTATTCCAAAAGT
24820 GACAATGGCCTCGCAAATAGGTAAAAAATCATACTTATTATTCCAAA
1 GACAATGGCCTCGCAAATAGGTAAAAAATCATACTTATTATTCCAAA
24867 TGTTGATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (50 bp):
GACAATGGCCTCGCAAATAGGTAAAAAATCATACTTATTATTCCAAAAGT
Found at i:29484 original size:52 final size:51
Alignment explanation
Indices: 29403--29694 Score: 318
Period size: 52 Copynumber: 5.6 Consensus size: 51
29393 TTCCCATTTA
* *
29403 ATACTCACGATGACATAAAGTCAGT-GGACCTTAAATCCGTAAAAGGATCCAT
1 ATACTCACGATGACACAAAGTCA-TCGGACCTTAAATCCGT-AAAGGATTCAT
* * *
29455 ATGCTCACGATGACACAAAGTCATCGGACCTTAAATCCGTAAAATGATCCAT
1 ATACTCACGATGACACAAAGTCATCGGACCTTAAATCCGT-AAAGGATTCAT
* *
29507 ATGCTCACGATGACACATAA-TCATCGGACCTTATAATCCGTAAAGGGTTCAT
1 ATACTCACGATGACACA-AAGTCATCGGACCTTA-AATCCGTAAAGGATTCAT
* * * * *
29559 ATACTCACGATGACACATAGTCATAGGACCTCATAATACGTAAAGGATTCAA
1 ATACTCACGATGACACAAAGTCATCGGACCTTA-AATCCGTAAAGGATTCAT
* ** * *
29611 ATACTCATGATGACACGTAGTCATCGGATCTCAAAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACAAAGTCATCGGACCT-TAAATCCGTAAAGGATTCAT
* ***
29663 ATACTCACAATGACATGTAGTCATCGGACCTT
1 ATACTCACGATGACACAAAGTCATCGGACCTT
29695 TTTCATTTAC
Statistics
Matches: 210, Mismatches: 25, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
51 2 0.01
52 198 0.94
53 10 0.05
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (51 bp):
ATACTCACGATGACACAAAGTCATCGGACCTTAAATCCGTAAAGGATTCAT
Found at i:29687 original size:156 final size:156
Alignment explanation
Indices: 29403--29694 Score: 365
Period size: 156 Copynumber: 1.9 Consensus size: 156
29393 TTCCCATTTA
* * * * *
29403 ATACTCACGATGACATAAAGTCAGTGGACCTTAAATCCGTAAAAGGATCCATATGCTCACGATGA
1 ATACTCACGATGACACAAAGTCAGTGGACCTCAAATACGTAAAAGGATCCAAATACTCACGATGA
* * * *
29468 CACAAAGTCATCGGACCTTAAATCCGTAAAATGATCCATATGCTCACGATGACACATAATCATCG
66 CACAAAGTCATCGGACCTAAAATCCGTAAAAGGATCCATATACTCACAATGACACATAATCATCG
29533 GACCTTATAATCCGTAAAGGGTTCAT
131 GACCTTATAATCCGTAAAGGGTTCAT
* * *
29559 ATACTCACGATGACACATAGTCA-TAGGACCTCATAATACGT-AAAGGATTCAAATACTCATGAT
1 ATACTCACGATGACACAAAGTCAGT-GGACCTCA-AATACGTAAAAGGATCCAAATACTCACGAT
** * * ** *
29622 GACACGTAGTCATCGGATCTCAAAATCCGT-AAAGGATTCATATACTCACAATGACATGTAGTCA
64 GACACAAAGTCATCGGACCT-AAAATCCGTAAAAGGATCCATATACTCACAATGACACATAATCA
29686 TCGGACCTT
128 TCGGACCTT
29695 TTTCATTTAC
Statistics
Matches: 114, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
155 1 0.01
156 99 0.87
157 14 0.12
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (156 bp):
ATACTCACGATGACACAAAGTCAGTGGACCTCAAATACGTAAAAGGATCCAAATACTCACGATGA
CACAAAGTCATCGGACCTAAAATCCGTAAAAGGATCCATATACTCACAATGACACATAATCATCG
GACCTTATAATCCGTAAAGGGTTCAT
Found at i:34035 original size:20 final size:19
Alignment explanation
Indices: 33997--34036 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
33987 TCTCCCCCTG
*
33997 AAGGGAATTTTTATTAAAA
1 AAGGGAATTTTTATGAAAA
*
34016 AAGGGAATGTTTTCTGAAAA
1 AAGGGAAT-TTTTATGAAAA
34036 A
1 A
34037 GTAACATCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33
Consensus pattern (19 bp):
AAGGGAATTTTTATGAAAA
Found at i:42297 original size:15 final size:15
Alignment explanation
Indices: 42274--42303 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42264 AAAGACATAC
*
42274 CTTATTAACTGTCAA
1 CTTAATAACTGTCAA
42289 CTTAATAACTGTCAA
1 CTTAATAACTGTCAA
42304 TACTCTGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (15 bp):
CTTAATAACTGTCAA
Found at i:42836 original size:21 final size:20
Alignment explanation
Indices: 42812--42898 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
42802 TTGGTTTTTG
42812 AAAATTATTAAAAAAATTATA
1 AAAATTA-TAAAAAAATTATA
* * *
42833 AAAACTATAAGAAAGTTATA
1 AAAATTATAAAAAAATTATA
* * * *
42853 GATAATTATATAAAATTTATT
1 -AAAATTATAAAAAAATTATA
* * *
42874 AAAATGATAATAAAATTTTA
1 AAAATTATAAAAAAATTATA
42894 AAAAT
1 AAAAT
42899 GTTAAAATAT
Statistics
Matches: 49, Mismatches: 16, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
20 29 0.59
21 20 0.41
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAATTATAAAAAAATTATA
Found at i:42985 original size:22 final size:23
Alignment explanation
Indices: 42949--42991 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
42939 TAAAACTTTA
42949 TAATATTAATATTTTA-AATAAT
1 TAATATTAATATTTTATAATAAT
42971 TAATATATAAT-TTTTATAATA
1 TAATAT-TAATATTTTATAATA
42992 TTTTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATATTAATATTTTATAATAAT
Found at i:43017 original size:32 final size:31
Alignment explanation
Indices: 42955--43018 Score: 83
Period size: 34 Copynumber: 2.0 Consensus size: 31
42945 TTTATAATAT
*
42955 TAATATTTTAAATAATTAATATATAATTTTTA
1 TAATATTTTAAAAAATTAATATAT-ATTTTTA
*
42987 TAATATTTTAATAAAAATTAATATATTTTTTT
1 TAATATTTT-A-AAAAATTAATATATATTTTT
43019 CATCACTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 9 0.32
33 6 0.21
34 13 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TAATATTTTAAAAAATTAATATATATTTTTA
Found at i:43526 original size:30 final size:31
Alignment explanation
Indices: 43463--43537 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
43453 TAAATGATTA
* *
43463 AAAAATCAATTAAGTTCTCATAAAAGAAATT
1 AAAAATTAATTAAGTTCTCATAAAACAAATT
*
43494 AAAAATTAATTAA-TTCCTCAT-AAACTAATT
1 AAAAATTAATTAAGTT-CTCATAAAACAAATT
43524 AAAAATTCAATTAA
1 AAAAATT-AATTAA
43538 ACCCTCCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 16 0.41
31 23 0.59
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAAATTAATTAAGTTCTCATAAAACAAATT
Found at i:48016 original size:18 final size:18
Alignment explanation
Indices: 47995--48039 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
47985 AAACTTTCAA
47995 TTTCAATGAAACAAAAAT
1 TTTCAATGAAACAAAAAT
48013 TTTCAATGAAACAAAAAT
1 TTTCAATGAAACAAAAAT
48031 TTTCAATGA
1 TTTCAATGA
48040 TTTATCAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (18 bp):
TTTCAATGAAACAAAAAT
Found at i:48690 original size:15 final size:15
Alignment explanation
Indices: 48670--48711 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
48660 ATTCAATTAT
48670 TAAATAAACTTTTTA
1 TAAATAAACTTTTTA
*
48685 TAAATATA-TTTTTA
1 TAAATAAACTTTTTA
*
48699 -ATATAAACTTTTT
1 TAAATAAACTTTTT
48712 TCTACCGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 5 0.22
14 11 0.48
15 7 0.30
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAATAAACTTTTTA
Found at i:49524 original size:3 final size:3
Alignment explanation
Indices: 49516--49548 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
49506 CAATATTCTT
49516 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49549 AAGATGTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53693 original size:98 final size:98
Alignment explanation
Indices: 53435--53728 Score: 378
Period size: 98 Copynumber: 3.0 Consensus size: 98
53425 TAAACCTTGA
* * * * *
53435 AAAAGGGTATTTGATTATCCCTGTTTGAAGAAAAGTCACGCCTAGTAAGTTAAGGCACAAATTTC
1 AAAAGGGTATTCGATTATCCC-GTTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTT
* *
53500 CAAAACCCGAGATAAAGAAATATTGCCTCGATTT
65 CAAAACCCGAAATAAAGGAATATTGCCTCGATTT
* * * * *
53534 --AAGGGCATCCGATTGTCCCGGTTTGAAGAAAAATCGTACCTAGTAAGTTAAGGCACGAATTTT
1 AAAAGGGTATTCGATTATCCC-GTTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTT
**
53597 CAAAATTCGAAATAAAGGAATATTG-CTCGATTT
65 CAAAACCCGAAATAAAGGAATATTGCCTCGATTT
* **
53630 AAAAGGGTATTCGATTATCCCGATTTGAAGAAAAATCGCACCTAGTAAATTAAAACACAAATTTT
1 AAAAGGGTATTCGATTATCCCG-TTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTT
*
53695 CAAAACCCGAAATAAAGGAATATTGTCTCGATTT
65 CAAAACCCGAAATAAAGGAATATTGCCTCGATTT
53729 TAAATATTTT
Statistics
Matches: 166, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
96 8 0.05
97 74 0.45
98 76 0.46
99 8 0.05
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (98 bp):
AAAAGGGTATTCGATTATCCCGTTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTC
AAAACCCGAAATAAAGGAATATTGCCTCGATTT
Found at i:53892 original size:14 final size:16
Alignment explanation
Indices: 53860--53898 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
53850 CAAATATACG
53860 AAAATAAATATGAG-A
1 AAAATAAATATGAGAA
*
53875 AAAATAAA-ATGCGAA
1 AAAATAAATATGAGAA
53890 AAAATAAAT
1 AAAATAAAT
53899 GAGAAATNNN
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (16 bp):
AAAATAAATATGAGAA
Found at i:54065 original size:30 final size:28
Alignment explanation
Indices: 53986--54353 Score: 273
Period size: 29 Copynumber: 12.6 Consensus size: 28
53976 AAAGGGGTCG
* *
53986 AAAATG-AAGTTTTGGAGAGTTT-GGGGCT
1 AAAATGTAATTTTTAGA-AGTTTAGGGG-T
54014 AAAATGTAATTTTTAGAAAGTTTTAGGGGT
1 AAAATGTAATTTTTAG-AAG-TTTAGGGGT
*
54044 AAAATTGTAATTTTTAGAAGTTT-GAGGGC
1 AAAA-TGTAATTTTTAGAAGTTTAG-GGGT
* *
54073 AAAATGTAGTTTTTGGAAGTTTAGGGGT
1 AAAATGTAATTTTTAGAAGTTTAGGGGT
* *
54101 AAAAATGTATTTTTTAAGAAGTTT-GAGG-
1 -AAAATGTAATTTTT-AGAAGTTTAGGGGT
* **
54129 ACAAATTTGTATTTTTTGAGAAGTTCGGGGGTT
1 A-AAA--TGTAATTTTT-AGAAGTTTAGGGG-T
* * *
54162 AAAATGTGATTTTTGGAAGTTTGAGGGCT
1 AAAATGTAATTTTTAGAAGTTT-AGGGGT
* *
54191 AACAT-TATACTTTTTGGAAGTTT-GAGGGT
1 AAAATGTA-A-TTTTTAGAAGTTTAG-GGGT
* *
54220 AAAATGTAATTTTTGAGAAGTTCAAGGGT
1 AAAATGTAATTTTT-AGAAGTTTAGGGGT
* * *
54249 CAAAATGTATTTTTTGGAAGTTTAGGGGGC
1 -AAAATGTAATTTTTAGAAGTTTA-GGGGT
*
54279 AAAATGTAATTTTTAGAAGTTTAAGGGT
1 AAAATGTAATTTTTAGAAGTTTAGGGGT
*
54307 AAAATGTAATTTTTAAGAAGTTTAGGGGCC
1 AAAATGTAATTTTT-AGAAGTTTAGGGG-T
* *
54337 AAAATATGATTTTTAGA
1 AAAATGTAATTTTTAGA
54354 TAATTCAAGG
Statistics
Matches: 276, Mismatches: 38, Indels: 51
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.00
28 53 0.19
29 109 0.39
30 90 0.33
31 19 0.07
32 3 0.01
33 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (28 bp):
AAAATGTAATTTTTAGAAGTTTAGGGGT
Found at i:54123 original size:58 final size:57
Alignment explanation
Indices: 53986--54353 Score: 332
Period size: 58 Copynumber: 6.3 Consensus size: 57
53976 AAAGGGGTCG
* * *
53986 AAAATG-AAGTTTTGGAGAGTTTG-GGGCTAAAATGTAATTTTTAGAAAGTTTTAGGGGTA
1 AAAATGTAATTTTTAGA-AGTTTGAGGGC-AAAATGTAATTTTT-GGAAG-TTTAGGGGTA
* *
54045 AAATTGTAATTTTTAGAAGTTTGAGGGCAAAATGTAGTTTTTGGAAGTTTAGGGGTA
1 AAAATGTAATTTTTAGAAGTTTGAGGGCAAAATGTAATTTTTGGAAGTTTAGGGGTA
* * * * ** *
54102 AAAATGTATTTTTTAAGAAGTTTGAGGACAAATTTGTATTTTTTGAGAAGTTCGGGGGTT
1 AAAATGTAATTTTT-AGAAGTTTGAGGGCAAA-ATGTAATTTTTG-GAAGTTTAGGGGTA
* * *
54162 AAAATGTGATTTTTGGAAGTTTGAGGGCTAACAT-TATACTTTTTGGAAGTTT-GAGGGT-
1 AAAATGTAATTTTTAGAAGTTTGAGGGC-AAAATGTA-A-TTTTTGGAAGTTTAG-GGGTA
** * **
54220 AAAATGTAATTTTTGAGAAGTTCAAGGGTCAAAATGTATTTTTTGGAAGTTTAGGGGGC
1 AAAATGTAATTTTT-AGAAGTTTGAGGG-CAAAATGTAATTTTTGGAAGTTTAGGGGTA
* * * **
54279 AAAATGTAATTTTTAGAAGTTTAAGGGTAAAATGTAATTTTTAAGAAGTTTAGGGGCC
1 AAAATGTAATTTTTAGAAGTTTGAGGGCAAAATGTAATTTTT-GGAAGTTTAGGGGTA
* *
54337 AAAATATGATTTTTAGA
1 AAAATGTAATTTTTAGA
54354 TAATTCAAGG
Statistics
Matches: 259, Mismatches: 35, Indels: 31
0.80 0.11 0.10
Matches are distributed among these distances:
57 35 0.14
58 92 0.36
59 86 0.33
60 46 0.18
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (57 bp):
AAAATGTAATTTTTAGAAGTTTGAGGGCAAAATGTAATTTTTGGAAGTTTAGGGGTA
Found at i:55782 original size:17 final size:16
Alignment explanation
Indices: 55762--55809 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
55752 GACATTATTT
55762 ATTTTAGATTTAAATAA
1 ATTTTA-ATTTAAATAA
* *
55779 ATTTAAATTTAAATTA
1 ATTTTAATTTAAATAA
55795 ATTTTAAGTTTAAAT
1 ATTTTAA-TTTAAAT
55810 TTAATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
ATTTTAATTTAAATAA
Found at i:55810 original size:17 final size:17
Alignment explanation
Indices: 55764--55874 Score: 84
Period size: 17 Copynumber: 6.4 Consensus size: 17
55754 CATTATTTAT
*
55764 TTTAGATTTAAA-TAAA
1 TTTAAATTTAAATTAAA
*
55780 TTTAAATTTAAATTAAT
1 TTTAAATTTAAATTAAA
*
55797 TTTAAGTTTAAATTTAATAA
1 TTTAAATTTAAA-TT-A-AA
*
55817 TTTTAAACTTAAAATT-AA
1 -TTTAAA-TTTAAATTAAA
55835 TTTAAATTTAAGA-TAAA
1 TTTAAATTTAA-ATTAAA
** *
55852 TTTAAACCTAAAATAAA
1 TTTAAATTTAAATTAAA
55869 TTTAAA
1 TTTAAA
55875 AAATGAGCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
16 17 0.22
17 42 0.55
18 4 0.05
19 1 0.01
20 1 0.01
21 7 0.09
22 5 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:55822 original size:38 final size:39
Alignment explanation
Indices: 55764--55845 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 39
55754 CATTATTTAT
* * *
55764 TTTAGATTTAAATAAATTTAAA-TTTAAATTAATTTTAAG
1 TTTAAATTTAAATAAATTTAAACTTAAAATTAA-TTTAAA
*
55803 TTTAAATTT-AATAATTTTAAACTTAAAATTAATTTAAA
1 TTTAAATTTAAATAAATTTAAACTTAAAATTAATTTAAA
55841 TTTAA
1 TTTAA
55846 GATAAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 21 0.55
39 17 0.45
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (39 bp):
TTTAAATTTAAATAAATTTAAACTTAAAATTAATTTAAA
Found at i:55864 original size:34 final size:32
Alignment explanation
Indices: 55798--55874 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 32
55788 TAAATTAATT
* *
55798 TTAAGTTTAAATTTAATAATTTTAAACTTAAAA
1 TTAA-TTTAAATTTAATAAATTTAAACCTAAAA
55831 TTAATTTAAATTTAAGATAAATTTAAACCTAAAA
1 TTAATTTAAATTT-A-ATAAATTTAAACCTAAAA
*
55865 TAAATTTAAA
1 TTAATTTAAA
55875 AAATGAGCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 9 0.23
33 5 0.13
34 25 0.64
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.42
Consensus pattern (32 bp):
TTAATTTAAATTTAATAAATTTAAACCTAAAA
Found at i:55874 original size:6 final size:6
Alignment explanation
Indices: 55764--55857 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
55754 CATTATTTAT
* * *
55764 TTTAGA TTTAAA --TAAA TTTAAA TTTAAA -TTAAT TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
55809 TTTAATAA TTTTAAA CTTAAA ATT-AA TTTAAA TTTAAGA --TAAA TTTAAA
1 TTT-A-AA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
55858 CCTAAAATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
4 5 0.07
5 11 0.15
6 45 0.63
7 4 0.06
8 3 0.04
9 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:56343 original size:39 final size:38
Alignment explanation
Indices: 56299--56427 Score: 136
Period size: 39 Copynumber: 3.3 Consensus size: 38
56289 CCCATTATCG
*
56299 GGGTAAGAGATTTGCCAATGGTGATCTGCCCCAAGCTC-
1 GGGTAAGAGATTTG-CAATGGTGATCTGCCTCAAGCTCA
* * * * *
56337 GAGGTAATAGATTTG-AATGATTGCAATCTACCTCATGATCA
1 G-GGTAAGAGATTTGCAATG-GTG--ATCTGCCTCAAGCTCA
56378 GGGTAAGAGATTTGCTAATGGTGATCTGCCTCAAGCTCA
1 GGGTAAGAGATTTGC-AATGGTGATCTGCCTCAAGCTCA
56417 GGGTAAGAGAT
1 GGGTAAGAGAT
56428 CAAATGATTG
Statistics
Matches: 73, Mismatches: 11, Indels: 13
0.75 0.11 0.13
Matches are distributed among these distances:
37 4 0.05
38 3 0.04
39 36 0.49
40 23 0.32
41 3 0.04
42 4 0.05
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (38 bp):
GGGTAAGAGATTTGCAATGGTGATCTGCCTCAAGCTCA
Found at i:56389 original size:40 final size:39
Alignment explanation
Indices: 56339--56469 Score: 108
Period size: 39 Copynumber: 3.3 Consensus size: 39
56329 CCAAGCTCGA
*
56339 GGTAATAGATTTGAATGATTGCAATCTACCTCATGATCAG
1 GGTAAGAGATTTGAATGATTG-AATCTACCTCATGATCAG
* * * *
56379 GGTAAGAGATTTGCTAATG-GTG-ATCTGCCTCAAGCTCAG
1 GGTAAGAGATTTG--AATGATTGAATCTACCTCATGATCAG
** * *
56418 GGTAAGAGA-TCAAATGATTGTAATTTACC-CTATGATCGG
1 GGTAAGAGATTTGAATGATTG-AATCTACCTC-ATGATCAG
56457 GGTAAGAGATTTG
1 GGTAAGAGATTTG
56470 TTGGTGATGA
Statistics
Matches: 69, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
36 4 0.06
37 2 0.03
38 2 0.03
39 42 0.61
40 13 0.19
41 2 0.03
42 4 0.06
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (39 bp):
GGTAAGAGATTTGAATGATTGAATCTACCTCATGATCAG
Found at i:56481 original size:78 final size:78
Alignment explanation
Indices: 56270--56956 Score: 585
Period size: 78 Copynumber: 8.8 Consensus size: 78
56260 CTTTATTGCT
* * * ** * *** *
56270 TCGAATGATTGTCATCTGCCCCATTATCGGGGTAAGAGATTTGCCAATGGTGATCTGCCCCAAGC
1 TCGAATGACTGTAATCTGCCCTAAGATCGGGGTAAGAGATTGGCTGGTGATGATCTGCCCCAAGC
* *
56335 TCGAGGTAATAGA
66 TCGGGGTAAGAGA
* * * * * * * ** * *
56348 TTTGAATGATTGCAATCT-ACCTCATGATCAGGGTAAGAGATTTGCTAATGGTGATCTGCCTCAA
1 -TCGAATGACTGTAATCTGCCCT-AAGATCGGGGTAAGAGATTGGCTGGTGATGATCTGCCCCAA
*
56412 GCTCAGGGTAAGAGA
64 GCTCGGGGTAAGAGA
* * * * * * * ** * * *
56427 TCAAATGATTGTAATTTACCCTATGATCGGGGTAAGAGATTTGTTGGTGATGATCTATCCTAGGT
1 TCGAATGACTGTAATCTGCCCTAAGATCGGGGTAAGAGATTGGCTGGTGATGATCTGCCCCAAGC
56492 TCGGGGTAAGAGA
66 TCGGGGTAAGAGA
* * * * * * *
56505 TCGAATGGCTGCAATTTGCCCCAAGCTCGGGGTAAGAGATTGGCTGGGGGTGATCTGCCCCAAGC
1 TCGAATGACTGTAATCTGCCCTAAGATCGGGGTAAGAGATTGGCTGGTGATGATCTGCCCCAAGC
56570 TCGGGGTAAGAGA
66 TCGGGGTAAGAGA
* * * * * * * * *
56583 TCCAACGACTGTAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGAG-GGTGATCTGTCTCAGG
1 TCGAATGACTGTAATCTGCCCTAAGATCGGGGTAAGAGATTGGCTG-GTGATGATCTGCCCCAAG
56647 CTCGGGGTAAGAGA
65 CTCGGGGTAAGAGA
* * * ** * *
56661 TCGAATGGCTGTAATCTGCCCTATGATCGAGGTAAGAGATTTACTGGTGATGAACTGTCCCAAGC
1 TCGAATGACTGTAATCTGCCCTAAGATCGGGGTAAGAGATTGGCTGGTGATGATCTGCCCCAAGC
*
56726 TTGGGGTAAGAGA
66 TCGGGGTAAGAGA
* * * *
56739 TCGAATGGCTGCAATCTACCC-AAGCTCGGGGTAAGAGATTGGCTGGTGATGATCTGCCCCAAGC
1 TCGAATGACTGTAATCTGCCCTAAGATCGGGGTAAGAGATTGGCTGGTGATGATCTGCCCCAAGC
*
56803 TCAGGGTAAGAGA
66 TCGGGGTAAGAGA
* * * * *
56816 TCGAATGGA-TATAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGGTGATGATCTGCCCTAGG
1 TCGAAT-GACTGTAATCTGCCCTAAGATCGGGGTAAGAGATTGGCTGGTGATGATCTGCCCCAAG
56880 CTCGGGGTAAGAGA
65 CTCGGGGTAAGAGA
** * * * **
56894 TCGAATGACTACAATCTTCCATAA-ACTCGGGGTAAAAGATTGGCTCACTG-TGATCTGCCCCAA
1 TCGAATGACTGTAATCTGCCCTAAGA-TCGGGGTAAGAGATTGGCT-GGTGATGATCTGCCCCAA
56957 ACTTGAGGTA
Statistics
Matches: 500, Mismatches: 99, Indels: 19
0.81 0.16 0.03
Matches are distributed among these distances:
77 65 0.13
78 366 0.73
79 69 0.14
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (78 bp):
TCGAATGACTGTAATCTGCCCTAAGATCGGGGTAAGAGATTGGCTGGTGATGATCTGCCCCAAGC
TCGGGGTAAGAGA
Found at i:56535 original size:39 final size:38
Alignment explanation
Indices: 56492--56900 Score: 290
Period size: 39 Copynumber: 10.5 Consensus size: 38
56482 TATCCTAGGT
*
56492 TCGGGGTAAGAGATCGAATGGCTGCAATTTGCCCCAAGC
1 TCGGGGTAAGAGATCGAATGGCTG-AATCTGCCCCAAGC
* ** *
56531 TCGGGGTAAGAGATTGGCTGGGGGTG-ATCTGCCCCAAGC
1 TCGGGGTAAGAGATCGAAT--GGCTGAATCTGCCCCAAGC
* * *
56570 TCGGGGTAAGAGATCCAACGACTGTAATCTGCCCCAAGC
1 TCGGGGTAAGAGATCGAATGGCTG-AATCTGCCCCAAGC
* ** * * * *
56609 TCGGGGTAAGAGATTGGTTGAGGGTG-ATCTGTCTCAGGC
1 TCGGGGTAAGAGATCGAAT--GGCTGAATCTGCCCCAAGC
* * *
56648 TCGGGGTAAGAGATCGAATGGCTGTAATCTGCCCTATGA
1 TCGGGGTAAGAGATCGAATGGCTG-AATCTGCCCCAAGC
* ** * * *
56687 TCGAGGTAAGAGATTTACTGG-TGATGAACTGTCCCAAGC
1 TCGGGGTAAGAGATCGAATGGCTGA--ATCTGCCCCAAGC
* *
56726 TTGGGGTAAGAGATCGAATGGCTGCAATCT-ACCCAAGC
1 TCGGGGTAAGAGATCGAATGGCTG-AATCTGCCCCAAGC
* **
56764 TCGGGGTAAGAGATTGGCTGG-TGATGATCTGCCCCAAGC
1 TCGGGGTAAGAGATCGAATGGCTGA--ATCTGCCCCAAGC
* * * * *
56803 TCAGGGTAAGAGATCGAATGGATATAATCTGCCCTAGGC
1 TCGGGGTAAGAGATCGAATGGCT-GAATCTGCCCCAAGC
* ** * *
56842 TCGGGGTAAGAGATTGGCTGG-TGATGATCTGCCCTAGGC
1 TCGGGGTAAGAGATCGAATGGCTGA--ATCTGCCCCAAGC
56881 TCGGGGTAAGAGATCGAATG
1 TCGGGGTAAGAGATCGAATG
56901 ACTACAATCT
Statistics
Matches: 284, Mismatches: 67, Indels: 38
0.73 0.17 0.10
Matches are distributed among these distances:
36 1 0.00
37 11 0.04
38 31 0.11
39 229 0.81
40 3 0.01
41 9 0.03
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.23
Consensus pattern (38 bp):
TCGGGGTAAGAGATCGAATGGCTGAATCTGCCCCAAGC
Found at i:56959 original size:39 final size:39
Alignment explanation
Indices: 56916--57007 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
56906 AATCTTCCAT
56916 AAACTCGGGGTAAAAGATTGGCTCACT-GTGATCTGCCCC
1 AAACTCGGGGTAAAAGATTGGCTCA-TGGTGATCTGCCCC
* * * * *
56955 AAACTTGAGGTAAAAGATTGGTTGATGGTGATTTGCCCC
1 AAACTCGGGGTAAAAGATTGGCTCATGGTGATCTGCCCC
**
56994 AGGCTCGGGGTAAA
1 AAACTCGGGGTAAA
57008 GGATCGAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
38 1 0.02
39 42 0.98
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (39 bp):
AAACTCGGGGTAAAAGATTGGCTCATGGTGATCTGCCCC
Found at i:66609 original size:99 final size:99
Alignment explanation
Indices: 66373--66665 Score: 398
Period size: 99 Copynumber: 3.0 Consensus size: 99
66363 AAACCTTGAA
* *
66373 AAAGGGTATTTGATTATCC-CAGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTT
1 AAAGGGTATTCGATTA-CCTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTT
* * * *
66437 C-AAACCTGAGATAAAGAAATATTACCTCGA--TT
65 CAAAACCCGAAATAAAGGAATATTGCCTCGATTTT
** * **
66469 AAA-GGTATTCGATTGTCTTGGTTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCACAAATTTTC
1 AAAGGGTATTCGATTACCTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
*
66533 AAAACCCAAAATAAAGGAATATTGCCTCGATTTT
66 AAAACCCGAAATAAAGGAATATTGCCTCGATTTT
* * * *
66567 AAAGGGTATTCGATTACCTCGGTTTGAAGAAAAATCGTGCCTAGTAAGTTAAAGTACGAATTTTC
1 AAAGGGTATTCGATTACCTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
66632 AAAACCCGAAATAAAGGAATATTGCCTCGATTTT
66 AAAACCCGAAATAAAGGAATATTGCCTCGATTTT
66666 TAATATTTTG
Statistics
Matches: 170, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
94 1 0.01
95 52 0.31
96 27 0.16
98 5 0.03
99 85 0.50
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (99 bp):
AAAGGGTATTCGATTACCTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
AAAACCCGAAATAAAGGAATATTGCCTCGATTTT
Found at i:66802 original size:14 final size:15
Alignment explanation
Indices: 66792--66823 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
66782 CAAATATACG
66792 AAAATAAATATGAGA
1 AAAATAAATATGAGA
66807 AAAAT-AA-ATGAGA
1 AAAATAAATATGAGA
66820 AAAA
1 AAAA
66824 AACAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 10 0.59
14 2 0.12
15 5 0.29
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (15 bp):
AAAATAAATATGAGA
Found at i:66984 original size:29 final size:29
Alignment explanation
Indices: 66932--67360 Score: 331
Period size: 29 Copynumber: 14.8 Consensus size: 29
66922 GTTTGGGGCT
*
66932 AAAATGTAA-TTTTGGAAAGTTTTAAGGGTA
1 AAAATGTAATTTTTAG-AAG-TTTAAGGGTA
*
66962 AAAATTTAATTTTTAGAAGTTTAAGGGTA
1 AAAATGTAATTTTTAGAAGTTTAAGGGTA
* * **
66991 AAAATATAAATTTTGAGAAGTTCGAGGGT-
1 AAAATGT-AATTTTTAGAAGTTTAAGGGTA
* * * *
67020 AAAATGTGATTTTAAGAAGTTCAGGGGTA
1 AAAATGTAATTTTTAGAAGTTTAAGGGTA
**
67049 AAAATGTAATTTTT-GAAAGTTCGAGGG-A
1 AAAATGTAATTTTTAG-AAGTTTAAGGGTA
* ** *
67077 AAAATGTAACTTTTGAGAAGTTCGAGGG-C
1 AAAATGTAA-TTTTTAGAAGTTTAAGGGTA
* *
67106 AAAATGTAATTTTTTAAAAGTTTAGGGGT-
1 AAAATGTAA-TTTTTAGAAGTTTAAGGGTA
* * *
67135 AAAATGTAATTTTTAAAAGTTT-GGGGGA
1 AAAATGTAATTTTTAGAAGTTTAAGGGTA
* * *
67163 AAAATATAATTTTTGAGAAGTTTAGGGGTT
1 AAAATGTAATTTTT-AGAAGTTTAAGGGTA
* * *
67193 AAAATGTGATTTTTAGAAGTTT-CGAGGAA
1 AAAATGTAATTTTTAGAAGTTTAAG-GGTA
* * *
67222 AAAATATAATTTTTGGAAGTTTAAGGATA
1 AAAATGTAATTTTTAGAAGTTTAAGGGTA
67251 AAAATGTAATTTTTAAGAAGTTTAAGGGT-
1 AAAATGTAATTTTT-AGAAGTTTAAGGGTA
* **
67280 -AAATGTAATTTTGAGAAGTTCGAGGGT-
1 AAAATGTAATTTTTAGAAGTTTAAGGGTA
* * *
67307 AAAATGTACTTTTTGAGAAGTTTAGGGGTC
1 AAAATGTAATTTTT-AGAAGTTTAAGGGTA
* * *
67337 AAAATATGATTTTTTGATAGTTTA
1 AAAATGTAATTTTTAGA-AGTTTA
67361 GGGACCTTTT
Statistics
Matches: 328, Mismatches: 54, Indels: 34
0.79 0.13 0.08
Matches are distributed among these distances:
27 16 0.05
28 78 0.24
29 153 0.47
30 76 0.23
31 5 0.02
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTAGAAGTTTAAGGGTA
Found at i:67103 original size:86 final size:85
Alignment explanation
Indices: 66957--67350 Score: 368
Period size: 86 Copynumber: 4.6 Consensus size: 85
66947 AAAGTTTTAA
* *
66957 GGGTAAAAATTTAATTTTT-AGAAGTTTAAGGGTAAAAATATAAATTTTGAGAAGTTCGAGGGTA
1 GGGTAAAAATGTAATTTTTGA-AAGTTTAAGGG-AAAAATATAATTTTTGAGAAGTTCGAGGGTA
*
67021 AAATGTGATTTTAAGAAGTTCAG
64 AAATGTAATTTTAAGAAGTTC-G
** * * *
67044 GGGTAAAAATGTAATTTTTGAAAGTTCGAGGGAAAAATGTAACTTTTGAGAAGTTCGAGGGCAAA
1 GGGTAAAAATGTAATTTTTGAAAGTTTAAGGGAAAAATATAATTTTTGAGAAGTTCGAGGGTAAA
*
67109 ATGTAATTTTTTAA-AAGTTTAG
66 ATGTAA--TTTTAAGAAG-TTCG
* ** *
67131 GGGT-AAAATGTAATTTTTAAAAGTTTGGGGGAAAAATATAATTTTTGAGAAGTT-TAGGGGTTA
1 GGGTAAAAATGTAATTTTTGAAAGTTTAAGGGAAAAATATAATTTTTGAGAAGTTCGA-GGG-TA
* *
67194 AAATGTGATTTTTAGAAGTTTCG
64 AAATGTAATTTTAAGAAG-TTCG
* * * * * * * **
67217 AGGAAAAAATATAATTTTTGGAAGTTTAAGGATAAAAATGTAATTTTTAAGAAGTTTAAGGGT-A
1 GGGTAAAAATGTAATTTTTGAAAGTTTAAGG-GAAAAATATAATTTTTGAGAAGTTCGAGGGTAA
*
67281 AATGTAATTTTGAGAAGTTCG
65 AATGTAATTTTAAGAAGTTCG
* * * *
67302 AGGGT-AAAATGTACTTTTTGAGAAGTTTAGGGGTCAAAATATGATTTTT
1 -GGGTAAAAATGTAATTTTTGA-AAGTTTAAGGG-AAAAATATAATTTTT
67351 TGATAGTTTA
Statistics
Matches: 253, Mismatches: 41, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
85 23 0.09
86 131 0.52
87 65 0.26
88 33 0.13
89 1 0.00
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (85 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTAAGGGAAAAATATAATTTTTGAGAAGTTCGAGGGTAAA
ATGTAATTTTAAGAAGTTCG
Found at i:67199 original size:144 final size:144
Alignment explanation
Indices: 66961--67359 Score: 466
Period size: 144 Copynumber: 2.8 Consensus size: 144
66951 TTTTAAGGGT
* * *
66961 AAAAATTTAATTTTTAGAAGTTTAAGGGTAAAAATATAAATTTTGAGAAGTTCGAGGGTAAAATG
1 AAAAATGTAATTTTTAAAAGTTTAAGGGT-AAAATGT-AATTTTGAGAAGTTCGAGGGTAAAATG
* * * * * *
67026 TGA-TTTTAAGAAGTTCAGGGGTAAAAATGTAATTTTT-GAAAG-TTCGAGGGAAAAATGTAACT
64 TAATTTTTGAGAAGTTTAGGGGTAAAAATGTGATTTTTAG-AAGTTTCGAGGAAAAAATATAACT
*
67088 TTTGAGAAGTTCGAGG-G
128 TTTG-GAAGTTCAAGGAG
* * * * * * * *
67105 CAAAATGTAATTTTTTAAAAGTTTAGGGGTAAAATGTAATTTTTAAAAGTTTGGGGGAAAAATAT
1 AAAAATGTAA-TTTTTAAAAGTTTAAGGGTAAAATGTAATTTTGAGAAGTTCGAGGGTAAAATGT
* *
67170 AATTTTTGAGAAGTTTAGGGGTTAAAATGTGATTTTTAGAAGTTTCGAGGAAAAAATATAATTTT
65 AATTTTTGAGAAGTTTAGGGGTAAAAATGTGATTTTTAGAAGTTTCGAGGAAAAAATATAACTTT
* *
67235 TGGAAGTTTAAGGAT
130 TGGAAGTTCAAGGAG
67250 AAAAATGTAATTTTTAAGAAGTTTAAGGGT-AAATGTAATTTTGAGAAGTTCGAGGGTAAAATGT
1 AAAAATGTAATTTTTAA-AAGTTTAAGGGTAAAATGTAATTTTGAGAAGTTCGAGGGTAAAATGT
* * * *
67314 ACTTTTTGAGAAGTTTAGGGGTCAAAATATGATTTTTTGATAGTTT
65 AATTTTTGAGAAGTTTAGGGGTAAAAATGTGATTTTTAGA-AGTTT
67360 AGGGACCTTT
Statistics
Matches: 214, Mismatches: 34, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
143 23 0.11
144 127 0.59
145 64 0.30
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (144 bp):
AAAAATGTAATTTTTAAAAGTTTAAGGGTAAAATGTAATTTTGAGAAGTTCGAGGGTAAAATGTA
ATTTTTGAGAAGTTTAGGGGTAAAAATGTGATTTTTAGAAGTTTCGAGGAAAAAATATAACTTTT
GGAAGTTCAAGGAG
Found at i:68889 original size:6 final size:6
Alignment explanation
Indices: 68878--68953 Score: 65
Period size: 6 Copynumber: 13.7 Consensus size: 6
68868 TAGATTTGAA
* * *
68878 TAAATT TAAA-T TAAA-- TAATTT TAAATT TAAA-A TAAATT TAAACT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
68922 TAAAAT T-AATT TAAATT TAAA-C TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
68954 CCTAAAACAA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
4 3 0.05
5 17 0.30
6 36 0.64
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:68892 original size:11 final size:11
Alignment explanation
Indices: 68878--68953 Score: 75
Period size: 11 Copynumber: 6.9 Consensus size: 11
68868 TAGATTTGAA
68878 TAAATTTAAAT
1 TAAATTTAAAT
*
68889 TAAA--TAATTT
1 TAAATTTAA-AT
*
68899 TAAATTTAAAA
1 TAAATTTAAAT
68910 TAAATTTAAACT
1 TAAATTTAAA-T
* *
68922 TAAAATTAATT
1 TAAATTTAAAT
*
68933 TAAATTTAAAC
1 TAAATTTAAAT
68944 TAAATTTAAA
1 TAAATTTAAA
68954 CCTAAAACAA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
9 3 0.06
10 5 0.10
11 33 0.63
12 11 0.21
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:68912 original size:17 final size:17
Alignment explanation
Indices: 68876--68970 Score: 113
Period size: 17 Copynumber: 5.7 Consensus size: 17
68866 TTTAGATTTG
68876 AATAAATTTAAA-TT-A
1 AATAAATTTAAATTTAA
*
68891 AATAATTTTAAATTTAA
1 AATAAATTTAAATTTAA
*
68908 AATAAATTTAAACTTAA
1 AATAAATTTAAATTTAA
*
68925 AATTAATTTAAATTTAA
1 AATAAATTTAAATTTAA
* **
68942 ACTAAATTTAAACCTAA
1 AATAAATTTAAATTTAA
*
68959 AACAAATTTAAA
1 AATAAATTTAAA
68971 AAATGAGCTA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
15 11 0.16
16 2 0.03
17 54 0.81
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:69467 original size:36 final size:36
Alignment explanation
Indices: 69406--69476 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
69396 GATAGTAGAC
* *
69406 ATATATGAAGTGATGATGAATTGAAA-TGAGAATATG
1 ATATATGAAGTGATGATAAAATGAAATTGA-AATATG
* *
69442 ATATATGAATTGATTATAAAATGAAATTGAAATAT
1 ATATATGAAGTGATGATAAAATGAAATTGAAATAT
69477 CGATGCCCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (36 bp):
ATATATGAAGTGATGATAAAATGAAATTGAAATATG
Done.