Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015150.1 Kokia drynarioides strain JFW-HI SEQ_130194, 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: 411378
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 313 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:274936 original size:28 final size:29
Alignment explanation
Indices: 274900--274956 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
274890 ATATAAAATG
*
274900 AAGAGTGAAAATTGAATTATAAATTTTAA
1 AAGAGTGAAAAATGAATTATAAATTTTAA
274929 AAGA-TGAAAAATGAATTATAAATTTTAA
1 AAGAGTGAAAAATGAATTATAAATTTTAA
274957 CAGGTGTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (29 bp):
AAGAGTGAAAAATGAATTATAAATTTTAA
Found at i:276041 original size:3 final size:3
Alignment explanation
Indices: 276033--276087 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
276023 CATGACTCTG
276033 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
276081 CAT CAT C
1 CAT CAT C
276088 GTGACTGATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:277864 original size:21 final size:21
Alignment explanation
Indices: 277840--277884 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
277830 TAGCATAATT
*
277840 CAAATATAAAGTTTAGAAATC
1 CAAACATAAAGTTTAGAAATC
*
277861 CAAACATAAAGTTTATAAATC
1 CAAACATAAAGTTTAGAAATC
277882 CAA
1 CAA
277885 TCGTCGACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (21 bp):
CAAACATAAAGTTTAGAAATC
Found at i:283080 original size:27 final size:28
Alignment explanation
Indices: 283043--283095 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
283033 TATTTTTACT
*
283043 TTTCCCTCAAAACTTTTACTC-CCTCAC
1 TTTCCCCCAAAACTTTTACTCTCCTCAC
283070 TTTCCCCCAAAACTTTTACTCTCCTC
1 TTTCCCCCAAAACTTTTACTCTCCTC
283096 TCATTCCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.38
Consensus pattern (28 bp):
TTTCCCCCAAAACTTTTACTCTCCTCAC
Found at i:283849 original size:19 final size:19
Alignment explanation
Indices: 283825--283862 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
283815 GAAAGTTAAT
*
283825 AACAAATTTGATTACGGTG
1 AACAAATTTCATTACGGTG
283844 AACAAATTTCATTACGGTG
1 AACAAATTTCATTACGGTG
283863 GGTGACAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (19 bp):
AACAAATTTCATTACGGTG
Found at i:287523 original size:24 final size:24
Alignment explanation
Indices: 287495--287549 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
287485 GACTAATAAC
* *
287495 AGTTTGACTCAAACAAATAAACAG
1 AGTTTAACTCAAACAAATAAACAA
* *
287519 AGTTTAATTGAAACAAATAAACAA
1 AGTTTAACTCAAACAAATAAACAA
287543 AGTTTAA
1 AGTTTAA
287550 TTGAAAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (24 bp):
AGTTTAACTCAAACAAATAAACAA
Found at i:287550 original size:24 final size:24
Alignment explanation
Indices: 287505--287555 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
287495 AGTTTGACTC
*
287505 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
287529 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
287553 AAA
1 AAA
287556 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Found at i:298585 original size:14 final size:15
Alignment explanation
Indices: 298559--298587 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
298549 TGTTATACAA
298559 TAAATAGACAAAGAG
1 TAAATAGACAAAGAG
298574 TAAATA-ACAAAGAG
1 TAAATAGACAAAGAG
298588 AATGAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.14
Consensus pattern (15 bp):
TAAATAGACAAAGAG
Found at i:301975 original size:25 final size:25
Alignment explanation
Indices: 301939--301988 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
301929 AATTATATTT
*
301939 TTATTTAATTTAATTTAAATAAAAA
1 TTATTTAATTTAACTTAAATAAAAA
*
301964 TTATTTAGTTTAACTTAAATAAAAA
1 TTATTTAATTTAACTTAAATAAAAA
301989 ATAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
TTATTTAATTTAACTTAAATAAAAA
Found at i:302727 original size:17 final size:16
Alignment explanation
Indices: 302686--302728 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
302676 AGCTGTTATA
*
302686 TTTTAA-TTTGATTTT
1 TTTTAATTTTTATTTT
*
302701 TTTTAGTTTTTATTTT
1 TTTTAATTTTTATTTT
*
302717 TTTTAAATTTTA
1 TTTTAATTTTTA
302729 GATTTTCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (16 bp):
TTTTAATTTTTATTTT
Found at i:305091 original size:42 final size:42
Alignment explanation
Indices: 305032--305115 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
305022 CTGTAGTGTG
*
305032 AGATAAAAAGTAAGTTAAATGCATCGCACTGCACCATTCATC
1 AGATAAAAAGTAAGTTAAATACATCGCACTGCACCATTCATC
*
305074 AGATAAAAAGTAAGTTAAATATATCGCACTGCACCATTCATC
1 AGATAAAAAGTAAGTTAAATACATCGCACTGCACCATTCATC
305116 CAAACCCACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (42 bp):
AGATAAAAAGTAAGTTAAATACATCGCACTGCACCATTCATC
Found at i:307383 original size:18 final size:18
Alignment explanation
Indices: 307360--307409 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
307350 AAAATGCAGG
307360 AAATGATGTTAACACTTC
1 AAATGATGTTAACACTTC
*
307378 AAATGATGTTCAA-ATTTC
1 AAATGATGTT-AACACTTC
307396 AAATGATGTTAACA
1 AAATGATGTTAACA
307410 TTGATGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 2 0.07
18 25 0.86
19 2 0.07
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (18 bp):
AAATGATGTTAACACTTC
Found at i:307937 original size:72 final size:72
Alignment explanation
Indices: 307843--308072 Score: 370
Period size: 72 Copynumber: 3.2 Consensus size: 72
307833 AATGCTAAAC
* *
307843 TAGTTTTATCAATAATTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTTTG
1 TAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATG
307908 TGTAATT
66 TGTAATT
* * *
307915 TAGGTTTATCAATAGTTATTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATG
* *
307980 TGCAATC
66 TGTAATT
* *
307987 TAATTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATG
*
308052 TGTATTT
66 TGTAATT
308059 TAGTTTTATCAATA
1 TAGTTTTATCAATA
308073 ATTAAAAATT
Statistics
Matches: 142, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 142 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (72 bp):
TAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATG
TGTAATT
Found at i:309965 original size:12 final size:12
Alignment explanation
Indices: 309950--309975 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
309940 CAAATTGATC
309950 AACAAATGAGAG
1 AACAAATGAGAG
309962 AACAAATGAGAG
1 AACAAATGAGAG
309974 AA
1 AA
309976 GTGAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.23, T:0.08
Consensus pattern (12 bp):
AACAAATGAGAG
Found at i:310391 original size:25 final size:25
Alignment explanation
Indices: 310350--310400 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
310340 ATCTTTATAC
*
310350 ATATTGAATTTTCATATCAATAAAT
1 ATATTGAATTTTAATATCAATAAAT
**
310375 ATATTG-ATTTATAATATGTATAAAT
1 ATATTGAATTT-TAATATCAATAAAT
310400 A
1 A
310401 AATTTTACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (25 bp):
ATATTGAATTTTAATATCAATAAAT
Found at i:312544 original size:15 final size:15
Alignment explanation
Indices: 312495--312544 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
312485 CTTAAAAATG
312495 TTTAAAA-AATTATA
1 TTTAAAATAATTATA
*
312509 ATTACAAATAA-TATA
1 TTTA-AAATAATTATA
312524 TATTAAAATAATTATA
1 T-TTAAAATAATTATA
312540 TTTAA
1 TTTAA
312545 TATTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 3 0.10
15 17 0.57
16 10 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAAAATAATTATA
Found at i:322032 original size:12 final size:12
Alignment explanation
Indices: 322015--322040 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
322005 TGAAGACCTT
322015 GGTGTCTATCTA
1 GGTGTCTATCTA
322027 GGTGTCTATCTA
1 GGTGTCTATCTA
322039 GG
1 GG
322041 CTTGCTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (12 bp):
GGTGTCTATCTA
Found at i:326733 original size:26 final size:26
Alignment explanation
Indices: 326703--326785 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
326693 TGATACGAGA
326703 TTCGAATGAGAGGTGACTAGTTGGTT
1 TTCGAATGAGAGGTGACTAGTTGGTT
* * * *
326729 TTCGAAGGTATGGGGTGA-TACG--AG-A
1 TTCGAATG-A-GAGGTGACTA-GTTGGTT
326754 TTCGAATGAGAGGTGACTAGTTGGTT
1 TTCGAATGAGAGGTGACTAGTTGGTT
326780 TTCGAA
1 TTCGAA
326786 GGTATGTGGG
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
23 7 0.17
24 3 0.07
25 8 0.19
26 14 0.33
27 3 0.07
28 7 0.17
ACGTcount: A:0.25, C:0.08, G:0.35, T:0.31
Consensus pattern (26 bp):
TTCGAATGAGAGGTGACTAGTTGGTT
Found at i:326748 original size:51 final size:51
Alignment explanation
Indices: 326689--326791 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
326679 TGCGGTGGGA
326689 GGGGTGATACGAGATTCGAATGAGAGGTGACTAGTTGGTTTTCGAAGGTAT
1 GGGGTGATACGAGATTCGAATGAGAGGTGACTAGTTGGTTTTCGAAGGTAT
326740 GGGGTGATACGAGATTCGAATGAGAGGTGACTAGTTGGTTTTCGAAGGTAT
1 GGGGTGATACGAGATTCGAATGAGAGGTGACTAGTTGGTTTTCGAAGGTAT
326791 G
1 G
326792 TGGGCAGTGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.25, C:0.08, G:0.38, T:0.29
Consensus pattern (51 bp):
GGGGTGATACGAGATTCGAATGAGAGGTGACTAGTTGGTTTTCGAAGGTAT
Found at i:328912 original size:14 final size:12
Alignment explanation
Indices: 328880--328927 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
328870 AAAATTTTTT
328880 ATATTAAAAGTAA
1 ATATTAAAAG-AA
328893 AGTATTTAAAAGATA
1 A-TA-TTAAAAGA-A
328908 ATATTAAAAGAA
1 ATATTAAAAGAA
*
328920 ATAATAAA
1 ATATTAAA
328928 TTGAAACTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 8 0.26
13 9 0.29
14 5 0.16
15 9 0.29
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.29
Consensus pattern (12 bp):
ATATTAAAAGAA
Found at i:330086 original size:15 final size:15
Alignment explanation
Indices: 330068--330099 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
330058 AGTGTTAAAA
330068 AAAATTTAAGTAGTG
1 AAAATTTAAGTAGTG
*
330083 AAAATTTAATTAGTG
1 AAAATTTAAGTAGTG
330098 AA
1 AA
330100 TTTAAGTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (15 bp):
AAAATTTAAGTAGTG
Found at i:330103 original size:13 final size:14
Alignment explanation
Indices: 330069--330106 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
330059 GTGTTAAAAA
330069 AAATTTAAGTAGTG
1 AAATTTAAGTAGTG
*
330083 AAAATTTAATTAGTG
1 -AAATTTAAGTAGTG
330098 -AATTTAAGT
1 AAATTTAAGT
330107 TCTAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 8 0.38
15 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (14 bp):
AAATTTAAGTAGTG
Found at i:330292 original size:20 final size:20
Alignment explanation
Indices: 330258--330303 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
330248 ATTCGAATTT
*
330258 TAAATATAAAGTTGAAATAAA
1 TAAA-ATAAAATTGAAATAAA
* *
330279 TAAAATAAAATTGAATTAAT
1 TAAAATAAAATTGAAATAAA
330299 TAAAA
1 TAAAA
330304 ATATTCTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (20 bp):
TAAAATAAAATTGAAATAAA
Found at i:330680 original size:21 final size:21
Alignment explanation
Indices: 330655--330698 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
330645 CACTTAAGTT
330655 AAAAA-TATATATAATCTAAAAA
1 AAAAATTATATAT-AT-TAAAAA
330677 AAAAATTATATATATTAAAAA
1 AAAAATTATATATATTAAAAA
330698 A
1 A
330699 TTGAAGTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 7 0.33
23 7 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATTATATATATTAAAAA
Found at i:332758 original size:23 final size:22
Alignment explanation
Indices: 332732--332829 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 22
332722 CTAGTGCGCT
*
332732 CTCTGTTTAGCACGTTTTGTGCC
1 CTCTGTTTAGCAC-TTGTGTGCC
* * *
332755 CTCTATTCAGCACTGTGTGTGTC
1 CTCTGTTTAGCACT-TGTGTGCC
*
332778 CTTTGTTATTAGCACTTCGTGTGCC
1 CTCTG-T-TTAGCACTT-GTGTGCC
* *
332803 CTCTGATTAGCACTTTGTGTGCT
1 CTCTGTTTAGCAC-TTGTGTGCC
332826 CTCT
1 CTCT
332830 ATTGTCCAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
22 1 0.02
23 37 0.63
24 4 0.07
25 17 0.29
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (22 bp):
CTCTGTTTAGCACTTGTGTGCC
Found at i:336739 original size:31 final size:31
Alignment explanation
Indices: 336704--336766 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
336694 TAAAATAGTT
* *
336704 ATTAAATTATTTAAAAGTTTTAATTTAAGTC
1 ATTAAACTATTCAAAAGTTTTAATTTAAGTC
* *
336735 ATTAAACTATTCGAAAGTTTTTATTTAAGTC
1 ATTAAACTATTCAAAAGTTTTAATTTAAGTC
336766 A
1 A
336767 CTAGACTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (31 bp):
ATTAAACTATTCAAAAGTTTTAATTTAAGTC
Found at i:337365 original size:102 final size:102
Alignment explanation
Indices: 337214--337418 Score: 322
Period size: 102 Copynumber: 2.0 Consensus size: 102
337204 TCATAATGAA
* * * * *
337214 TGTTAGATATATAGTTAACCCTATCTATAACAGTCACCAGCTATAACACTGTTTCACTATAACAA
1 TGTTAGAGATATAGTCAACCCTATCTATAACAATCACCAACTATAACACTATTTCACTATAACAA
337279 TCAAGTTTCTAGTAT-AATCAATTTTTTATGTTTTATT
66 TCAAGTTTCTAGT-TGAATCAATTTTTTATGTTTTATT
*
337316 TGTTAGAGATATAGTCAACCCTATCTATAACAATCCCCAACTATAACACTATTTCACTATAACAA
1 TGTTAGAGATATAGTCAACCCTATCTATAACAATCACCAACTATAACACTATTTCACTATAACAA
* *
337381 TCAAGTTTTTAGTTGAATCGATTTTTTATGTTTTATT
66 TCAAGTTTCTAGTTGAATCAATTTTTTATGTTTTATT
337418 T
1 T
337419 TAACCTTTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 1 0.01
102 93 0.99
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (102 bp):
TGTTAGAGATATAGTCAACCCTATCTATAACAATCACCAACTATAACACTATTTCACTATAACAA
TCAAGTTTCTAGTTGAATCAATTTTTTATGTTTTATT
Found at i:338018 original size:28 final size:28
Alignment explanation
Indices: 337979--338036 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
337969 TCAATAAACT
337979 ATTAAGTTCCCTAATTAAATATTCTATC
1 ATTAAGTTCCCTAATTAAATATTCTATC
338007 ATTAAGTTCCCTAATTAAATATTCTATC
1 ATTAAGTTCCCTAATTAAATATTCTATC
338035 AT
1 AT
338037 GAATTTGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.43
Consensus pattern (28 bp):
ATTAAGTTCCCTAATTAAATATTCTATC
Found at i:338356 original size:17 final size:19
Alignment explanation
Indices: 338336--338383 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
338326 AACAACCGCC
338336 TCTTTATA-ACAAA-AAAA
1 TCTTTATAGACAAATAAAA
*
338353 TCTTAATAGACAAATAAAA
1 TCTTTATAGACAAATAAAA
*
338372 TCATTATAGACA
1 TCTTTATAGACA
338384 GGGTTGAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 7 0.27
18 5 0.19
19 14 0.54
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.29
Consensus pattern (19 bp):
TCTTTATAGACAAATAAAA
Found at i:340301 original size:165 final size:165
Alignment explanation
Indices: 340029--340358 Score: 509
Period size: 165 Copynumber: 2.0 Consensus size: 165
340019 CAGGATGGGG
* *
340029 AACTCATTTTCCCAAACATGCAAAGTGCACTCAAAAGTGTATACCTCATCAATATATTGGTCAGC
1 AACTCATTTTCCCAAACATGCAAAGTGCACTCAAAAGTGTATACCTCATAAATAAATTGGTCAGC
* * * *
340094 ATTGATTGAGGCGTGAGCACAAGTAGTAACGATGTGCGCATAGGGTGTAATAAAGTGACTGGAAC
66 ATTGATCGAGGCGTGAGCACAAGTAGCAACGACGTGCGCATAGGGGGTAATAAAGTGACTGGAAC
* *
340159 CTCTCGCAATCGCACCGTCTATTTCAGAGATCAAC
131 CTCTCACAATCGCACCGTCTATTTCAAAGATCAAC
*
340194 AACTCATTTTCCCAAACATGTAAAGTGCACTCAATAA-TGTATACCTCATAAATAAATTGGTCAG
1 AACTCATTTTCCCAAACATGCAAAGTGCACTCAA-AAGTGTATACCTCATAAATAAATTGGTCAG
* *
340258 TATTGATCGAGGCGTGAGCACAAGTAGCAACGACGTGCGCATAGGGGGTAATGAAGTGACTGGAA
65 CATTGATCGAGGCGTGAGCACAAGTAGCAACGACGTGCGCATAGGGGGTAATAAAGTGACTGGAA
* * **
340323 CCTCTCATAATTGCATTGTCTATTTCAAAGATCAAC
130 CCTCTCACAATCGCACCGTCTATTTCAAAGATCAAC
340359 TTCGTAAGAC
Statistics
Matches: 149, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
165 147 0.99
166 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (165 bp):
AACTCATTTTCCCAAACATGCAAAGTGCACTCAAAAGTGTATACCTCATAAATAAATTGGTCAGC
ATTGATCGAGGCGTGAGCACAAGTAGCAACGACGTGCGCATAGGGGGTAATAAAGTGACTGGAAC
CTCTCACAATCGCACCGTCTATTTCAAAGATCAAC
Found at i:345110 original size:80 final size:80
Alignment explanation
Indices: 344888--345094 Score: 299
Period size: 80 Copynumber: 2.6 Consensus size: 80
344878 ACGATTATGG
*
344888 CACCCAGTGTCTAGCGGATAAACCGCAAATGTGAGCCCAACTCTAGTTGGTTTAACCAACAAATA
1 CACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAACTCTAGTTGGTTTAACCAACAAATA
* * *
344953 TCTGTCAATTCCTGG
66 TCCGTCAACTCCTGA
* * *
344968 CACCCATTGCTTAGCGGATAAACCGCAAATGTGAGTCCAACTCTAGTTGGTTTAACCAACAAATA
1 CACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAACTCTAGTTGGTTTAACCAACAAATA
*
345033 TCCGTTAACTCCTGA
66 TCCGTCAACTCCTGA
* * *
345048 CATCTAGTGCCTAGCGGATAAACCACGAAA-GTGAGCCCAACTCTAGT
1 CACCCAGTGCCTAGCGGATAAACCGC-AAATGTGAGCCCAACTCTAGT
345095 CAGTTAAACT
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
80 109 0.97
81 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (80 bp):
CACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAACTCTAGTTGGTTTAACCAACAAATA
TCCGTCAACTCCTGA
Found at i:346810 original size:49 final size:49
Alignment explanation
Indices: 346756--346853 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
346746 CAATGATTTG
*
346756 TTTTTTTAAATATTTATATAAGATATTAAAATGTAAAAATAATCTAATA
1 TTTTTTAAAATATTTATATAAGATATTAAAATGTAAAAATAATCTAATA
*
346805 TTTTTTAAAATATTTATATAAGATATTAAAATGTAAAAATAGTCTAATA
1 TTTTTTAAAATATTTATATAAGATATTAAAATGTAAAAATAATCTAATA
346854 ATTTGTTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (49 bp):
TTTTTTAAAATATTTATATAAGATATTAAAATGTAAAAATAATCTAATA
Found at i:362233 original size:24 final size:23
Alignment explanation
Indices: 362159--362238 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
362149 AATGTTCACA
*
362159 AACATGTTCATTTAAC-TTAATCG
1 AACATGTTCA-TGAACATTAATCG
* *
362182 AACATGGTCATGAACATTAAACG
1 AACATGTTCATGAACATTAATCG
* *
362205 AACATGTTCATGACCATATAATTG
1 AACATGTTCATGAACAT-TAATCG
362229 AACATGTTCA
1 AACATGTTCA
362239 CAAATAATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 4 0.08
23 30 0.62
24 14 0.29
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (23 bp):
AACATGTTCATGAACATTAATCG
Found at i:362407 original size:18 final size:18
Alignment explanation
Indices: 362384--362420 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
362374 ACCGAACATA
362384 CTTATGTTCGTGTTCGTT
1 CTTATGTTCGTGTTCGTT
362402 CTTATGTTCGTGTTCGTT
1 CTTATGTTCGTGTTCGTT
362420 C
1 C
362421 GTTTATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.19, G:0.22, T:0.54
Consensus pattern (18 bp):
CTTATGTTCGTGTTCGTT
Found at i:363552 original size:31 final size:31
Alignment explanation
Indices: 363517--363579 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
363507 ATAAAGGAGT
363517 AAACTTGATACTAACCTTAGGTAGAGGAGGA
1 AAACTTGATACTAACCTTAGGTAGAGGAGGA
363548 AAACTTGATACTAACCTTAGGTAGAGGAGGA
1 AAACTTGATACTAACCTTAGGTAGAGGAGGA
363579 A
1 A
363580 TATCCGTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (31 bp):
AAACTTGATACTAACCTTAGGTAGAGGAGGA
Found at i:370743 original size:28 final size:28
Alignment explanation
Indices: 370711--370769 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
370701 AATAATTTTC
370711 AAAATT-TA-AAATATTTATAAAACTTCCA
1 AAAATTATATAAATATTTA-AAAA-TTCCA
* *
370739 AAAATTATATATATATTTAAAAATTCTA
1 AAAATTATATAAATATTTAAAAATTCCA
370767 AAA
1 AAA
370770 GATGTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.48
29 6 0.22
30 8 0.30
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAATTATATAAATATTTAAAAATTCCA
Found at i:371780 original size:30 final size:31
Alignment explanation
Indices: 371730--371788 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
371720 CTATTTTATT
371730 ATATATTATATTTATTATTTTTAAAGAATTTA
1 ATATATTATATTTATTATTTTTAAA-AATTTA
*
371762 ATATA-TAT-TTTTTTATTTTTAAAAATT
1 ATATATTATATTTATTATTTTTAAAAATT
371789 AAAGTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 4 0.15
30 14 0.54
31 3 0.12
32 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (31 bp):
ATATATTATATTTATTATTTTTAAAAATTTA
Found at i:371810 original size:31 final size:30
Alignment explanation
Indices: 371745--371811 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
371735 TTATATTTAT
* * **
371745 TATTTTTAAAGAATTTAATATATATTTTTT
1 TATTTTTAAAGAATTAAATATATATTATCG
371775 TATTTTTAAA-AATTAAAGTATAATATTATCG
1 TATTTTTAAAGAATTAAA-TAT-ATATTATCG
371806 TATTTT
1 TATTTT
371812 AATTTATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 6 0.19
30 13 0.42
31 12 0.39
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (30 bp):
TATTTTTAAAGAATTAAATATATATTATCG
Found at i:372207 original size:2 final size:2
Alignment explanation
Indices: 372200--372225 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
372190 GCATACATAC
372200 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
372226 TTACATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:376683 original size:101 final size:101
Alignment explanation
Indices: 376508--376712 Score: 410
Period size: 101 Copynumber: 2.0 Consensus size: 101
376498 ATACATTTTT
376508 ATGATAATTGTACTAACTTGGTTATCTTGTCTTATTTCACATTGCATCCTCATATTAGGAAATGT
1 ATGATAATTGTACTAACTTGGTTATCTTGTCTTATTTCACATTGCATCCTCATATTAGGAAATGT
376573 ATTGATTTAAGTTCAATTATTAGTAGAGAACTGGTC
66 ATTGATTTAAGTTCAATTATTAGTAGAGAACTGGTC
376609 ATGATAATTGTACTAACTTGGTTATCTTGTCTTATTTCACATTGCATCCTCATATTAGGAAATGT
1 ATGATAATTGTACTAACTTGGTTATCTTGTCTTATTTCACATTGCATCCTCATATTAGGAAATGT
376674 ATTGATTTAAGTTCAATTATTAGTAGAGAACTGGTC
66 ATTGATTTAAGTTCAATTATTAGTAGAGAACTGGTC
376710 ATG
1 ATG
376713 GAAAAAGGGT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 104 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (101 bp):
ATGATAATTGTACTAACTTGGTTATCTTGTCTTATTTCACATTGCATCCTCATATTAGGAAATGT
ATTGATTTAAGTTCAATTATTAGTAGAGAACTGGTC
Found at i:386345 original size:25 final size:25
Alignment explanation
Indices: 386304--386354 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
386294 ATCTTTATAC
*
386304 ATATTGAATTTTCATATCAATAAAT
1 ATATTGAATTTTAATATCAATAAAT
**
386329 ATATTG-ATTTATAATATGTATAAAT
1 ATATTGAATTT-TAATATCAATAAAT
386354 A
1 A
386355 AATTTTACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (25 bp):
ATATTGAATTTTAATATCAATAAAT
Found at i:393936 original size:20 final size:21
Alignment explanation
Indices: 393900--393938 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
393890 GGATTTTTTA
*
393900 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
393921 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
393939 AATTCCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:402872 original size:50 final size:50
Alignment explanation
Indices: 402797--402894 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 50
402787 GGCATGGTGT
* *
402797 CACATTAGTGCTAGAACTTAGGCAAAAAATGATCAATGACGACCTAAGAA
1 CACATCAGTGCTAGAACTTAGGCAAAAAACGATCAATGACGACCTAAGAA
* *
402847 CACATCAGTGTTAGAACTTAGGCAAAAGACGATCAATGACGACCTAAG
1 CACATCAGTGCTAGAACTTAGGCAAAAAACGATCAATGACGACCTAAG
402895 GACTAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (50 bp):
CACATCAGTGCTAGAACTTAGGCAAAAAACGATCAATGACGACCTAAGAA
Found at i:403234 original size:50 final size:50
Alignment explanation
Indices: 403078--403218 Score: 194
Period size: 50 Copynumber: 2.8 Consensus size: 50
403068 GACAAAATAA
* * ****
403078 TGAATCTTATACCCCTAAAGCTGTAGAGAAATAGATTGAAGCCGCAATGG
1 TGAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGG
*
403128 TGAATCTCATACACTTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGG
1 TGAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGG
*
403178 CGAATCTCATACACCTAAAGCTGTAG-GCGGGCAGATTGAAG
1 TGAATCTCATACACCTAAAGCTGTAGAG-GGGCAGATTGAAG
403219 TCGTAAGGGT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 80 0.99
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (50 bp):
TGAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGG
Found at i:403249 original size:50 final size:50
Alignment explanation
Indices: 403078--403269 Score: 188
Period size: 50 Copynumber: 3.8 Consensus size: 50
403068 GACAAAATAA
* * * ****
403078 TGAATCTTATACCCCTAAAGCTGTAGAGAAATAGATTGAAGCCGCAATGG
1 TGAATCTCATACACTTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGG
403128 TGAATCTCATACACTTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGG
1 TGAATCTCATACACTTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGG
* * * * *
403178 CGAATCTCATACACCTAAAGCTGTAG-GCGGGCAGATTGAAGTCGTAAGGG
1 TGAATCTCATACACTTAAAGCTGTAGAG-GGGCAGATTGAAGCCGCAATGG
* * * * * * * *
403228 TAAATCTTATACTCTTGAAGCTGAAAAAGGGCAAATTGAAGC
1 TGAATCTCATACACTTAAAGCTGTAGAGGGGCAGATTGAAGC
403270 TTAAAGAGCA
Statistics
Matches: 117, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
49 1 0.01
50 116 0.99
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (50 bp):
TGAATCTCATACACTTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGG
Found at i:403502 original size:101 final size:101
Alignment explanation
Indices: 403373--403611 Score: 275
Period size: 101 Copynumber: 2.4 Consensus size: 101
403363 GGAGTGAAGC
* *
403373 CAAATCCTATATCCCTGAAGTTACAGTGGATCAGATTAAAGCT-ACGAAGGCAAATCCTTATCTC
1 CAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATT-AAGCTCACGAAAGCAAATCCTTATCTC
* * *
403437 TCTAAAGTTGCAGTAGAGCAGGATGAAGTTACAAAAT
65 CCTAAAGTTGCAGTAGAGCAAGATGAAGCTACAAAAT
* * * * * *
403474 CAAATCTTATACCCCTGAAGTTGCAGTGGGTCAGATTAAGGTCATGAAAGCAAATCTTTATCTCC
1 CAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTAAGCTCACGAAAGCAAATCCTTATCTCC
* * * * *
403539 CTGAAGTTGCAGTGGAGCAATATGAAGCTACGACAT
66 CTAAAGTTGCAGTAGAGCAAGATGAAGCTACAAAAT
* * *
403575 CAAGTCCTATATCCCTGCAA-TTGTAGTGGATTAGATT
1 CAAATCCTATATCCCTG-AAGTTGCAGTGGATCAGATT
403612 GAAGTTACAT
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
100 4 0.04
101 108 0.95
102 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (101 bp):
CAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTAAGCTCACGAAAGCAAATCCTTATCTCC
CTAAAGTTGCAGTAGAGCAAGATGAAGCTACAAAAT
Found at i:403550 original size:51 final size:49
Alignment explanation
Indices: 403373--403553 Score: 145
Period size: 51 Copynumber: 3.6 Consensus size: 49
403363 GGAGTGAAGC
* * * * * *
403373 CAAATCCTATATCCCTGAAGTTACAGTGGATCAGATTAAAG-CTACGAAGG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGGTCAGATTAAGGTC-A-GAAAG
* * * * * *
403423 CAAATCCTTATCTCTCTAAAGTTGCAGTAGAG-CAGGATGAAGTTACA-AAAT
1 CAAAT-CTTATCTCCCTGAAGTTGCAGT-GGGTCA-GATTAAGGT-CAGAAAG
403474 CAAATCTTATAC-CCCTGAAGTTGCAGTGGGTCAGATTAAGGTCATGAAAG
1 CAAATCTTAT-CTCCCTGAAGTTGCAGTGGGTCAGATTAAGGTCA-GAAAG
403524 CAAATCTTTATCTCCCTGAAGTTGCAGTGG
1 CAAATC-TTATCTCCCTGAAGTTGCAGTGG
403554 AGCAATATGA
Statistics
Matches: 102, Mismatches: 18, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
48 2 0.02
49 9 0.09
50 35 0.34
51 48 0.47
52 6 0.06
53 1 0.01
54 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (49 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGGTCAGATTAAGGTCAGAAAG
Found at i:406112 original size:24 final size:24
Alignment explanation
Indices: 406085--406131 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
406075 TTTTCTTTCT
*
406085 ATTTTATTTATT-TTTTACTTTAAA
1 ATTTTATTT-TTATTTTAATTTAAA
406109 ATTTTATTTTTATTTTAATTTAA
1 ATTTTATTTTTATTTTAATTTAA
406132 CCTTGTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTATTTTTATTTTAATTTAAA
Found at i:407203 original size:26 final size:26
Alignment explanation
Indices: 407174--407228 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
407164 AAAACAAAAA
*
407174 TTTGAGACTTTTTTAAAAAAAAATGT
1 TTTGAGACTTTTTAAAAAAAAAATGT
407200 TTTGAGACTTTTTAAAAAAAAAATGT
1 TTTGAGACTTTTTAAAAAAAAAATGT
407226 TTT
1 TTT
407229 TGACAATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (26 bp):
TTTGAGACTTTTTAAAAAAAAAATGT
Found at i:409613 original size:2 final size:2
Alignment explanation
Indices: 409606--409711 Score: 104
Period size: 2 Copynumber: 51.5 Consensus size: 2
409596 ATCATCACAA
* * * *
409606 AT AT AT AT GT AT AC AT AT AT AT AT AT AT GT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
409648 AT AT AT GT AT CAT AT AT AT AT GT AT CAT AT AT AT AT GT AT AT GT
1 AT AT AT AT AT -AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
*
409692 AT CAT AT AT AT AT GT AT AT A
1 AT -AT AT AT AT AT AT AT AT A
409712 AATGATTTTA
Statistics
Matches: 83, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
2 77 0.93
3 6 0.07
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (2 bp):
AT
Found at i:409698 original size:15 final size:15
Alignment explanation
Indices: 409606--409687 Score: 104
Period size: 15 Copynumber: 5.8 Consensus size: 15
409596 ATCATCACAA
409606 ATATATATGTATACAT
1 ATATATATGTAT-CAT
409622 ATATATA--TAT-AT
1 ATATATATGTATCAT
*
409634 GTATATA--TA-CAT
1 ATATATATGTATCAT
409646 ATATATATGTATCAT
1 ATATATATGTATCAT
409661 ATATATATGTATCAT
1 ATATATATGTATCAT
409676 ATATATATGTAT
1 ATATATATGTAT
409688 ATGTATCATA
Statistics
Matches: 60, Mismatches: 2, Indels: 9
0.85 0.03 0.13
Matches are distributed among these distances:
12 18 0.30
14 5 0.08
15 30 0.50
16 7 0.12
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (15 bp):
ATATATATGTATCAT
Found at i:410874 original size:16 final size:16
Alignment explanation
Indices: 410840--410874 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
410830 GATTAAAAAG
*
410840 AAATCAAGAATACATC
1 AAATCAAGAATACAGC
*
410856 AAATCAAGAATATAGC
1 AAATCAAGAATACAGC
410872 AAA
1 AAA
410875 ATCAGAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.17
Consensus pattern (16 bp):
AAATCAAGAATACAGC
Done.