Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003416.1 Kokia drynarioides strain JFW-HI SEQ_116175, 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: 89209
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:248 original size:15 final size:15
Alignment explanation
Indices: 222--274 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
212 GGGCACTTTA
*
222 TAATTGGACCATTTG
1 TAATTGGGCCATTTG
* *
237 TATTTGGGCCATCTG
1 TAATTGGGCCATTTG
*
252 TAACTGGGCCATTTG
1 TAATTGGGCCATTTG
267 TAATTGGG
1 TAATTGGG
275 ACTTTTGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (15 bp):
TAATTGGGCCATTTG
Found at i:371 original size:17 final size:17
Alignment explanation
Indices: 311--373 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
301 TGGATTTTTC
* *
311 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
*
328 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
345 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
362 TAAACTTAAATT
1 TAAATTTAAATT
374 CAATTTCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:2192 original size:36 final size:36
Alignment explanation
Indices: 2142--2264 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 36
2132 GACATATTTG
*
2142 ATATCGTCGGTTTATCTGACTAGTGTTGGGCACAAA
1 ATATTGTCGGTTTATCTGACTAGTGTTGGGCACAAA
* ** * *
2178 ATATTGTCGGTTTATTTGACTAGTGCAGGCCAC-AC
1 ATATTGTCGGTTTATCTGACTAGTGTTGGGCACAAA
* * * * *
2213 CTATTGTCGATTTATCTGACCAGCGTTGGGCGCAAA
1 ATATTGTCGGTTTATCTGACTAGTGTTGGGCACAAA
* * *
2249 ACATTATCGTTTTATC
1 ATATTGTCGGTTTATC
2265 GGACCAGAGT
Statistics
Matches: 66, Mismatches: 20, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
35 25 0.38
36 41 0.62
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (36 bp):
ATATTGTCGGTTTATCTGACTAGTGTTGGGCACAAA
Found at i:9599 original size:8 final size:8
Alignment explanation
Indices: 9586--9611 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
9576 CACATATTTT
9586 TTTAATTA
1 TTTAATTA
9594 TTTAATTA
1 TTTAATTA
9602 TTTAATTA
1 TTTAATTA
9610 TT
1 TT
9612 ATTTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTAATTA
Found at i:21893 original size:29 final size:28
Alignment explanation
Indices: 21856--22075 Score: 185
Period size: 29 Copynumber: 7.5 Consensus size: 28
21846 AATCAAACTG
* *
21856 TTGGAAAATTTGAGGTTGAAAATGTGATTT
1 TTGGAAAGTTTGAGGTT-AAAATGT-AATT
* *
21886 TTGGAAA-TTTGAGGGTAAAAGGGTAATT
1 TTGGAAAGTTTGAGGTTAAAA-TGTAATT
21914 TTGGAAAAGTTTG-GGTTTAAAATGTAATT
1 TTGG-AAAGTTTGAGG-TTAAAATGTAATT
**
21943 TTGGAAAAGTTCAAGGTTAAAATGTAATT
1 TTGG-AAAGTTTGAGGTTAAAATGTAATT
* *
21972 TTGAAAGAGTTT-AGGGTTATAATGTAATT
1 TTGGAA-AGTTTGA-GGTTAAAATGTAATT
**
22001 TTAAAAAGTTTGAGGGTTAAAATGTAATT
1 TTGGAAAGTTTGA-GGTTAAAATGTAATT
** *
22030 TTACAAAAGTTTGAGGTTCAAAATGTGATTT
1 TT-GGAAAGTTTGAGGTT-AAAATGT-AATT
*
22061 TTGGAAAGTTCGAGG
1 TTGGAAAGTTTGAGG
22076 GCCTTTTGAG
Statistics
Matches: 162, Mismatches: 17, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
28 19 0.12
29 93 0.57
30 45 0.28
31 5 0.03
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (28 bp):
TTGGAAAGTTTGAGGTTAAAATGTAATT
Found at i:21918 original size:58 final size:57
Alignment explanation
Indices: 21856--22076 Score: 209
Period size: 58 Copynumber: 3.8 Consensus size: 57
21846 AATCAAACTG
* * *
21856 TTGGAAAA-TTTGAGGTTGAAAATGTGATTTTTGGAAA-TTTGAGGGTAAAAGGGTAATT
1 TTGGAAAAGTTTGAGGTT-AAAATGT-AATTTTGGAAAGTTCGAGGGTAAAA-TGTAATT
* *
21914 TTGGAAAAGTTTG-GGTTTAAAATGTAATTTTGGAAAAGTTCAAGGTTAAAATGTAATT
1 TTGGAAAAGTTTGAGG-TTAAAATGTAATTTTGG-AAAGTTCGAGGGTAAAATGTAATT
* ** *
21972 TT-GAAAGAGTTT-AGGGTTATAATGTAATTTTAAAAAGTTTGAGGGTTAAAATGTAATT
1 TTGGAAA-AGTTTGA-GGTTAAAATGTAATTTTGGAAAGTTCGAGGG-TAAAATGTAATT
** *
22030 TTACAAAAGTTTGAGGTTCAAAATGTGATTTTTGGAAAGTTCGAGGG
1 TTGGAAAAGTTTGAGGTT-AAAATGT-AATTTTGGAAAGTTCGAGGG
22077 CCTTTTGAGC
Statistics
Matches: 134, Mismatches: 17, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
57 20 0.15
58 70 0.52
59 28 0.21
60 16 0.12
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (57 bp):
TTGGAAAAGTTTGAGGTTAAAATGTAATTTTGGAAAGTTCGAGGGTAAAATGTAATT
Found at i:21988 original size:87 final size:88
Alignment explanation
Indices: 21897--22061 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 88
21887 TGGAAATTTG
* * **
21897 AGGG-TAAAAGGGTAATTTTGGAAAAGTTTG-GGTTTAAAATGTAATTTTGGAAAAGTTCAAGGT
1 AGGGTTAAAA-GGTAATTTT-AAAAAGTTTGAGGGTTAAAATGTAATTTTACAAAAGTTCAAGGT
21960 T-AAAATGTAATTTTGAAAGAGTTT
64 TCAAAATGTAATTTTGAAAGAGTTT
* * **
21984 AGGGTTATAATGTAATTTTAAAAAGTTTGAGGGTTAAAATGTAATTTTACAAAAGTTTGAGGTTC
1 AGGGTTAAAAGGTAATTTTAAAAAGTTTGAGGGTTAAAATGTAATTTTACAAAAGTTCAAGGTTC
*
22049 AAAATGTGATTTT
66 AAAATGTAATTTT
22062 TGGAAAGTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
86 9 0.14
87 41 0.62
88 16 0.24
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (88 bp):
AGGGTTAAAAGGTAATTTTAAAAAGTTTGAGGGTTAAAATGTAATTTTACAAAAGTTCAAGGTTC
AAAATGTAATTTTGAAAGAGTTT
Found at i:23686 original size:17 final size:17
Alignment explanation
Indices: 23620--23689 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 17
23610 TAAATGGAGT
23620 TTTAAATTTAAA-TAAA
1 TTTAAATTTAAAGTAAA
23636 TTTAAATTTGAAATGTATTGGACA
1 TTTAAATTT-AAA-GTA----A-A
23660 TTTAAAATTTAAAGTAAA
1 TTT-AAATTTAAAGTAAA
23678 TTTAAATTTAAA
1 TTTAAATTTAAA
23690 ATTTGTCTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
16 9 0.20
17 12 0.27
18 4 0.09
19 3 0.07
23 4 0.09
24 7 0.16
25 6 0.13
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAGTAAA
Found at i:23706 original size:32 final size:32
Alignment explanation
Indices: 23668--23733 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
23658 CATTTAAAAT
23668 TTAAAGTAAATTTAAATTTAAAATTTGTCTTA
1 TTAAAGTAAATTTAAATTTAAAATTTGTCTTA
23700 TTAAAGTAAATTTAAATTTAAAATTTGTCTTA
1 TTAAAGTAAATTTAAATTTAAAATTTGTCTTA
23732 TT
1 TT
23734 TTGGGTTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (32 bp):
TTAAAGTAAATTTAAATTTAAAATTTGTCTTA
Found at i:24271 original size:39 final size:39
Alignment explanation
Indices: 24228--24659 Score: 238
Period size: 39 Copynumber: 11.2 Consensus size: 39
24218 TTTTTTTTTT
* * * *
24228 GTAAGATATTGGATGGTTGCAATCTGCCTCTGGCTCGGG
1 GTAAGAGATTGGATGGCTGCAATCTGCCCCAGGCTCGGG
* *
24267 GTAAGAGATTGGCTGATGG-TG--ATCTACCCCAGGCTCGGA
1 GTAAGAGATT-G--GATGGCTGCAATCTGCCCCAGGCTCGGG
* * *
24306 G-AA-AGATCGGATGGCCGTAATCTGCCCCAGGCTCGGG
1 GTAAGAGATTGGATGGCTGCAATCTGCCCCAGGCTCGGG
* *
24343 GTAAGAGATTGG-TGGCTACAATCTGCCCTAGGCTCGGG
1 GTAAGAGATTGGATGGCTGCAATCTGCCCCAGGCTCGGG
* * * *
24381 GTAAGAGATTAGCTAATGG-TG--ATCTGCCTCAAGCTCAGG
1 GTAAGAGATT-G--GATGGCTGCAATCTGCCCCAGGCTCGGG
* * * * *
24420 GTAAAAGATCGGATGGCTGCAATCTGTCCTAGGCTTGGG
1 GTAAGAGATTGGATGGCTGCAATCTGCCCCAGGCTCGGG
* *
24459 GTAAGAGATTGGCTAATGG-TG--ATCTGCCCCAAGCTCGAG
1 GTAAGAGATTGG---ATGGCTGCAATCTGCCCCAGGCTCGGG
* * * * * * *
24498 GTAAAAGATCGGATGACTGCTATCTGCCTCAAGCTCGAG
1 GTAAGAGATTGGATGGCTGCAATCTGCCCCAGGCTCGGG
* *
24537 GTAAGAGATTGGTTGAAG-TG--ATCTGCCCC-GG-GCGGG
1 GTAAGAGATTGGATG--GCTGCAATCTGCCCCAGGCTCGGG
* * * * * *
24573 GTAAAAGATCGGATGGCTTCCATCTACCCCAGGCTCGAG
1 GTAAGAGATTGGATGGCTGCAATCTGCCCCAGGCTCGGG
* *
24612 GTAAGAGATTAGCTGATGG-T--AATCTGCCCTAGGCTCGAG
1 GTAAGAGATT-G--GATGGCTGCAATCTGCCCCAGGCTCGGG
*
24651 GTAAAAGAT
1 GTAAGAGAT
24660 CAGATCTTCA
Statistics
Matches: 301, Mismatches: 61, Indels: 62
0.71 0.14 0.15
Matches are distributed among these distances:
34 6 0.02
35 2 0.01
36 23 0.08
37 34 0.11
38 47 0.16
39 162 0.54
40 4 0.01
41 6 0.02
42 17 0.06
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (39 bp):
GTAAGAGATTGGATGGCTGCAATCTGCCCCAGGCTCGGG
Found at i:24451 original size:78 final size:76
Alignment explanation
Indices: 24325--24660 Score: 322
Period size: 78 Copynumber: 4.3 Consensus size: 76
24315 GATGGCCGTA
* * * * *
24325 ATCTGCCCCAGGCTCGGGGTAAGAGATTGG-TGGCTACAATCTGCCCTAGGCTCGGGGTAAGAGA
1 ATCTG-CCCAAGCTC-GGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTCGAGGTAAGAGA
24389 TTAGCTAATGGTG
64 TTAGCTAATGGTG
* * *
24402 ATCTGCCTCAAGCTCAGGGTAAAAGATCGGATGGCTGCAATCTGTCCTAGGCTTGGGGTAAGAGA
1 ATCTGCC-CAAGCTC-GGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTCGAGGTAAGAGA
*
24467 TTGGCTAATGGTG
64 TTAGCTAATGGTG
* * *
24480 ATCTGCCCCAAGCTCGAGGTAAAAGATCGGATGACTGCTATCTG-CCTCAAGCTCGAGGTAAGAG
1 ATCTG-CCCAAGCTCG-GGTAAAAGATCGGATGGCTGCAATCTGCCCT-AGGCTCGAGGTAAGAG
* *
24544 ATTGGTTGAA--GTG
63 ATTAGCT-AATGGTG
** * * * * *
24557 ATCTGCCCCGGGC-GGGGTAAAAGATCGGATGGCTTCCATCTACCCCAGGCTCGAGGTAAGAGAT
1 ATCTG-CCCAAGCTCGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTCGAGGTAAGAGAT
* *
24621 TAGCTGATGGTA
65 TAGCTAATGGTG
*
24633 ATCTGCCCTAGGCTCGAGGTAAAAGATC
1 ATCTGCCC-AAGCTCG-GGTAAAAGATC
24661 AGATCTTCAA
Statistics
Matches: 218, Mismatches: 29, Indels: 23
0.81 0.11 0.09
Matches are distributed among these distances:
74 1 0.00
75 46 0.21
76 15 0.07
77 42 0.19
78 110 0.50
79 4 0.02
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (76 bp):
ATCTGCCCAAGCTCGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTCGAGGTAAGAGATT
AGCTAATGGTG
Found at i:32747 original size:24 final size:24
Alignment explanation
Indices: 32702--32747 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
32692 CGTCATTTGT
* *
32702 TCCTGCAACTGCTCTTGCATTTTA
1 TCCTGCAACTCCTCTTGAATTTTA
* *
32726 TCCTGCATCTCCTTTTGAATTT
1 TCCTGCAACTCCTCTTGAATTT
32748 GCTCTAGCCT
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:0.15, C:0.28, G:0.11, T:0.46
Consensus pattern (24 bp):
TCCTGCAACTCCTCTTGAATTTTA
Found at i:36922 original size:29 final size:30
Alignment explanation
Indices: 36860--36915 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 30
36850 CTTTAGGGTC
* *
36860 AAAATTGAATTTTTTGGAAAATTTGGGATT
1 AAAATTGAATCTTTTGGAAAATTTGAGATT
36890 AAAATTGAA-CTTTTGGAAAATTTGAG
1 AAAATTGAATCTTTTGGAAAATTTGAG
36916 TTGAAAACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (30 bp):
AAAATTGAATCTTTTGGAAAATTTGAGATT
Found at i:36932 original size:29 final size:29
Alignment explanation
Indices: 36860--36940 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
36850 CTTTAGGGTC
* *
36860 AAAATTGAATTTTTTGGAAAATTTGGGATT
1 AAAAGTGAA-TTTTTGGAAAATTTGAGATT
* *
36890 AAAATTGAACTTTTGGAAAATTTGAG-TT
1 AAAAGTGAATTTTTGGAAAATTTGAGATT
36918 GAAAACGTG-ATTTTT-GAAAATTT
1 -AAAA-GTGAATTTTTGGAAAATTT
36941 AGGGTAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.22
29 24 0.53
30 11 0.24
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.41
Consensus pattern (29 bp):
AAAAGTGAATTTTTGGAAAATTTGAGATT
Found at i:37006 original size:30 final size:29
Alignment explanation
Indices: 36871--37175 Score: 297
Period size: 29 Copynumber: 10.5 Consensus size: 29
36861 AAATTGAATT
36871 TTTTGGAAAA-TTT-GGGATTAAAAT-TGAA
1 TTTTGGAAAAGTTTAGGG-TTAAAATGT-AA
* * *
36899 CTTTTGGAAAA-TTT-GAGTTGAAAACGTGA
1 -TTTTGGAAAAGTTTAGGGTT-AAAATGTAA
* * *
36928 TTTTTGAAAA-TTTAGGGTAAAAAGGTAA
1 TTTTGGAAAAGTTTAGGGTTAAAATGTAA
* * *
36956 TTTTGGAAAAGTTCAAGGCTAAAATGTAA
1 TTTTGGAAAAGTTTAGGGTTAAAATGTAA
*
36985 TTTTGGAAAAGTTTATGGGCTAAAATGTAA
1 TTTTGGAAAAGTTTA-GGGTTAAAATGTAA
37015 TTTTGGAAAAGTTT-GGTGTTAAAATGTAA
1 TTTTGGAAAAGTTTAGG-GTTAAAATGTAA
* *
37044 TTTTGGAAAAGTTTAGGGGTCAAATGTAA
1 TTTTGGAAAAGTTTAGGGTTAAAATGTAA
* *
37073 TTTTGGAAGAGTTTAGGTGTCAAAATGTAA
1 TTTTGGAAAAGTTTAGG-GTTAAAATGTAA
37103 TTTT-GAAAGAGTTTAAGGGTTAAAATGTAA
1 TTTTGGAAA-AGTTT-AGGGTTAAAATGTAA
* *
37133 TTTTGG-GAAGTTTAGGGGTTAAAATGTGAT
1 TTTTGGAAAAGTTTA-GGGTTAAAATGT-AA
37163 TTTTGG-AAAGTTT
1 TTTTGGAAAAGTTT
37176 GAGGACCTCC
Statistics
Matches: 235, Mismatches: 28, Indels: 25
0.82 0.10 0.09
Matches are distributed among these distances:
28 33 0.14
29 121 0.51
30 77 0.33
31 4 0.02
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTTGGAAAAGTTTAGGGTTAAAATGTAA
Found at i:37021 original size:59 final size:56
Alignment explanation
Indices: 36927--37175 Score: 245
Period size: 59 Copynumber: 4.3 Consensus size: 56
36917 TGAAAACGTG
* * *
36927 ATTTTTGAAAA-TTTAGGGTAAAAAGGTAATTTTGGAAAAGTTCAAGGCTAAAATGTA
1 ATTTTGGAAAAGTTTAGGGT-AAAATGTAATTTTGGAAAAGTT-TAGGCTAAAATGTA
* *
36984 ATTTTGGAAAAGTTTATGGGCTAAAATGTAATTTTGGAAAAGTTTGGTGTTAAAATGTA
1 ATTTTGGAAAAGTTTA-GGG-TAAAATGTAATTTTGGAAAAGTTTAG-GCTAAAATGTA
* * *
37043 ATTTTGGAAAAGTTTAGGGGTCAAATGTAATTTTGGAAGAGTTTAGGTGTCAAAATGTA
1 ATTTTGGAAAAGTTTA-GGGTAAAATGTAATTTTGGAAAAGTTTAGG-CT-AAAATGTA
* *
37102 ATTTT-GAAAGAGTTTAAGGGTTAAAATGTAATTTTGG-GAAGTTTAGGGGTTAAAATGTGA
1 ATTTTGGAAA-AGTTT-AGGG-TAAAATGTAATTTTGGAAAAGTTTA--GGCTAAAATGT-A
*
37162 TTTTTGG-AAAGTTT
1 ATTTTGGAAAAGTTT
37176 GAGGACCTCC
Statistics
Matches: 164, Mismatches: 15, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
57 11 0.07
58 33 0.20
59 92 0.56
60 25 0.15
61 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (56 bp):
ATTTTGGAAAAGTTTAGGGTAAAATGTAATTTTGGAAAAGTTTAGGCTAAAATGTA
Found at i:38779 original size:64 final size:64
Alignment explanation
Indices: 38678--38807 Score: 233
Period size: 64 Copynumber: 2.0 Consensus size: 64
38668 TTAGGCATTA
* *
38678 GGGTTCTGAAAAACTTTGTAAAATTAGACCTATTGGGTTGTAATTTTTTGGGCCGTGTTAATTG
1 GGGTTCTGAAAAACTTTGTAAAATTAGACCTATTGGGTTGTAATTTGTTGGGCCATGTTAATTG
*
38742 GGGTTCTGAAAAACTTTGTAAAATTAGGCCTATTGGGTTGTAATTTGTTGGGCCATGTTAATTG
1 GGGTTCTGAAAAACTTTGTAAAATTAGACCTATTGGGTTGTAATTTGTTGGGCCATGTTAATTG
38806 GG
1 GG
38808 TTTAGGTTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.25, C:0.09, G:0.27, T:0.39
Consensus pattern (64 bp):
GGGTTCTGAAAAACTTTGTAAAATTAGACCTATTGGGTTGTAATTTGTTGGGCCATGTTAATTG
Found at i:38835 original size:18 final size:18
Alignment explanation
Indices: 38812--38853 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
38802 ATTGGGTTTA
38812 GGTTTAGGTGGGTAATTG
1 GGTTTAGGTGGGTAATTG
38830 GGTTTAGGTGGGTAATTG
1 GGTTTAGGTGGGTAATTG
38848 GGTTTA
1 GGTTTA
38854 TTTGGTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (18 bp):
GGTTTAGGTGGGTAATTG
Found at i:44290 original size:30 final size:30
Alignment explanation
Indices: 44254--44314 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
44244 AATAATCTAC
44254 TGGATTTTAGGAATTCAAATTTAAAAAGAA
1 TGGATTTTAGGAATTCAAATTTAAAAAGAA
44284 TGGATTTTAGGAATTCAAATTTAAAAAGAA
1 TGGATTTTAGGAATTCAAATTTAAAAAGAA
44314 T
1 T
44315 TTGTTATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.34
Consensus pattern (30 bp):
TGGATTTTAGGAATTCAAATTTAAAAAGAA
Found at i:44474 original size:18 final size:19
Alignment explanation
Indices: 44448--44485 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
44438 CCTCAAACAT
*
44448 ATATACAAA-ACATACTTC
1 ATATACAAAGACATAATTC
*
44466 ATATGCAAAGACATAATTC
1 ATATACAAAGACATAATTC
44485 A
1 A
44486 ATATCATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.26
Consensus pattern (19 bp):
ATATACAAAGACATAATTC
Found at i:49629 original size:14 final size:15
Alignment explanation
Indices: 49614--49643 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
49604 TCACAGCGTA
49614 GTTTTCAGAATCTAG
1 GTTTTCAGAATCTAG
49629 TGTTTTCAGAATCTA
1 -GTTTTCAGAATCTA
49644 AAGTCTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (15 bp):
GTTTTCAGAATCTAG
Found at i:49693 original size:29 final size:29
Alignment explanation
Indices: 49631--49694 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
49621 GAATCTAGTG
*
49631 TTTTCAGAATCTAAAGTCTTACATAACAA
1 TTTTCAGAATCTAAAGTCTTACAGAACAA
* * *
49660 CTTTCAGAGTCTAAAGT-TTCACAGAATAA
1 TTTTCAGAATCTAAAGTCTT-ACAGAACAA
49689 TTTTCA
1 TTTTCA
49695 AAAAATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (29 bp):
TTTTCAGAATCTAAAGTCTTACAGAACAA
Found at i:51293 original size:22 final size:23
Alignment explanation
Indices: 51248--51295 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
51238 TGAGTAATAG
* *
51248 GAATCACATAAATCAGTATCACA
1 GAATCACACAAATCAGCATCACA
51271 GAATCACACAAATCA-CATCACA
1 GAATCACACAAATCAGCATCACA
51293 GAA
1 GAA
51296 CTCAGATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.50, C:0.25, G:0.08, T:0.17
Consensus pattern (23 bp):
GAATCACACAAATCAGCATCACA
Found at i:53402 original size:192 final size:193
Alignment explanation
Indices: 53031--53473 Score: 547
Period size: 192 Copynumber: 2.3 Consensus size: 193
53021 TACCAGTACT
* * * * * *
53031 CGATGCTGCTCACACGAACTGTCGAGGACTCGCAACGTATGCGGTACCCCATCCATCGGTACGGT
1 CGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGGT
* * * *
53096 GTCTGTCTGTACTATAAATTGTTCCCTAACGATGCTACTCACACGAGCTATCGAGAGTATGCATA
66 ATCTG-CTGCACTATAAATCGTTCCCTAACGATGCTACTCACACGAGCTATCGAGAATATGCATA
* *
53161 AAGCATAGTCCTAGCCATCGTACGGCCTGCAATCCATTTCGGATCCATATCTCTTTCCCGAGTCA
130 AAGCATAATCCTAGCCATCGTACGGCCTACAATCCATTTC-GATCCATATCTCTTTCCCGAGTCA
* * * * *
53226 CGATGCTGCTCATACGAGCTATCGAGGACTCGTAACATATGTGGTACCTCAGCCATTGATATGGT
1 CGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGGT
* * *
53291 ATCTG-TGCA-TAT-AATCGTT-CCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTT
66 ATCTGCTGCACTATAAATCGTTCCCTAACGATGCTACTCACACGAGCTATCGAGAATATGCA-TA
* * *
53352 ATGCATAAAT-CTCAGCCATCGTAGGGCCTATAATCCATTTAC-ACTCCATATCTCTTTCCCGAG
130 AAGCAT-AATCCT-AGCCATCGTACGGCCTACAATCCATTT-CGA-TCCATATCTCTTTCCCGAG
53415 TCA
191 TCA
* * *
53418 TGATGCTGCTCACACGAGTTATCGAGGACTCGCAACACATGCGGTACCTCAGCCAT
1 CGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCGGTACCTCAGCCAT
53474 AATGTCGGTT
Statistics
Matches: 214, Mismatches: 29, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
190 36 0.17
191 15 0.07
192 101 0.47
193 4 0.02
195 58 0.27
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (193 bp):
CGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGGT
ATCTGCTGCACTATAAATCGTTCCCTAACGATGCTACTCACACGAGCTATCGAGAATATGCATAA
AGCATAATCCTAGCCATCGTACGGCCTACAATCCATTTCGATCCATATCTCTTTCCCGAGTCA
Found at i:53975 original size:16 final size:16
Alignment explanation
Indices: 53951--53982 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53941 TCCTTACAAA
*
53951 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
53967 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
53983 AAAAATTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:54291 original size:33 final size:35
Alignment explanation
Indices: 54249--54321 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 35
54239 AGGGTTCGAC
54249 TTTAGAGGAAGAAG-AA-AAGAAGAATGATAAAAT
1 TTTAGAGGAAGAAGAAAGAAGAAGAATGATAAAAT
54282 TTTAGAGGAAGAAGAAAAGAAGAAGAATGATAAAAT
1 TTTAGAGGAAGAAG-AAAGAAGAAGAATGATAAAAT
54318 TTTA
1 TTTA
54322 ACTTTTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
33 14 0.38
35 2 0.05
36 21 0.57
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (35 bp):
TTTAGAGGAAGAAGAAAGAAGAAGAATGATAAAAT
Found at i:59225 original size:2 final size:2
Alignment explanation
Indices: 59218--59247 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59208 TACATCCGCA
59218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59248 TAGCTCAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64453 original size:33 final size:33
Alignment explanation
Indices: 64413--64481 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
64403 TCGATAAAGC
64413 ATAATAATGCTCTCAATCTCGGTATTTTTTTTA
1 ATAATAATGCTCTCAATCTCGGTATTTTTTTTA
64446 ATAATAATGCTCTCAATCTCGGTATTTTTTTTA
1 ATAATAATGCTCTCAATCTCGGTATTTTTTTTA
64479 ATA
1 ATA
64482 TTGTAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (33 bp):
ATAATAATGCTCTCAATCTCGGTATTTTTTTTA
Found at i:64789 original size:56 final size:57
Alignment explanation
Indices: 64684--64815 Score: 169
Period size: 57 Copynumber: 2.3 Consensus size: 57
64674 TTAATATAAT
* * *
64684 ATTTGGTATTAGAATTTAATATTTTTTTTAATTTGATATTTAAA-TTTTTTAGATTCA
1 ATTTGGTATTA-AATTTAATATTTTTTCTAATTTGATATCTAAACTTTTTTAAATTCA
* *
64741 ATTTGGTATTTAAATTTGAT-TTTTTTCTAATTTGATATCTAAGCTTTTTTAAATTCA
1 ATTTGGTA-TTAAATTTAATATTTTTTCTAATTTGATATCTAAACTTTTTTAAATTCA
*
64798 ATTTGGTACTTATATTTA
1 ATTTGGTA-TTAAATTTA
64816 TTAAATATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
56 20 0.31
57 42 0.65
58 3 0.05
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (57 bp):
ATTTGGTATTAAATTTAATATTTTTTCTAATTTGATATCTAAACTTTTTTAAATTCA
Found at i:65058 original size:57 final size:58
Alignment explanation
Indices: 64948--65067 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 58
64938 AGTTAATATT
* * * *
64948 AAAAAAAGATTAGGTACCAAATTAGGAAAAGTAGTTAAGTTTAGGTACCAAATTGGATA
1 AAAAAAAGATTAAGTACCAAATTAGAAAAAGTAGTCAAGTTTAGGTACCAAATTAGA-A
* * **
65007 AAAAAAAGTTTAAGTACCAACTTA-AAAAAGT-GTCAAGTTTAGGTATTAAATTAGAA
1 AAAAAAAGATTAAGTACCAAATTAGAAAAAGTAGTCAAGTTTAGGTACCAAATTAGAA
65063 AAAAA
1 AAAAA
65068 TGTCAATTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
56 6 0.11
57 20 0.38
58 6 0.11
59 21 0.40
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.26
Consensus pattern (58 bp):
AAAAAAAGATTAAGTACCAAATTAGAAAAAGTAGTCAAGTTTAGGTACCAAATTAGAA
Found at i:79148 original size:17 final size:18
Alignment explanation
Indices: 79113--79149 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
79103 TCTTTCGAGG
79113 GAGAATTTGGTTCCAATA
1 GAGAATTTGGTTCCAATA
*
79131 GAGACTTTGGTT-CAATA
1 GAGAATTTGGTTCCAATA
79148 GA
1 GA
79150 AGTCTAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (18 bp):
GAGAATTTGGTTCCAATA
Found at i:81855 original size:31 final size:31
Alignment explanation
Indices: 81818--81890 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
81808 AAAAGAAAGC
81818 TTATTATTGTCATTTGATCATGATGAGTCTA
1 TTATTATTGTCATTTGATCATGATGAGTCTA
81849 TTATTATTGTCATTTGATCATGATGAGTCTA
1 TTATTATTGTCATTTGATCATGATGAGTCTA
*
81880 TT-TAATTGTCA
1 TTATTATTGTCA
81891 CGTTTGGGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 8 0.20
31 33 0.80
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (31 bp):
TTATTATTGTCATTTGATCATGATGAGTCTA
Found at i:83676 original size:20 final size:21
Alignment explanation
Indices: 83638--83676 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
83628 TTTAGGTTTC
*
83638 TTGATTATATTTTTATTTTAG
1 TTGATTATATTTTCATTTTAG
*
83659 TTGATT-TATTTTCCTTTT
1 TTGATTATATTTTCATTTT
83677 GTAATAGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (21 bp):
TTGATTATATTTTCATTTTAG
Done.