Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008552.1 Kokia drynarioides strain JFW-HI SEQ_123230, 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: 45475
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:5606 original size:462 final size:461
Alignment explanation
Indices: 4048--6328 Score: 2848
Period size: 462 Copynumber: 4.9 Consensus size: 461
4038 ATCACGAAGG
* * * * *
4048 ACAGATAATGGCTACAATCACTCACCAGAATGCAAGTATAGCAAATCCAAAAATGACGGAGGCAT
1 ACAGATAATGGTTACAATTACTCACCAGAATGCAAGTACAGCAAATCCAGAAATGACGGAGGCAC
* * * * * * *
4113 GACCAGGTCTCTATGCCATTACGGCAACAGCAGACTTATGATCTTGACATCTGATTCTTGAAGGA
66 GAGCTGGTTTCTAGGCCATTACGACAACAGCAGACTTAGGATCTTGGCATCTGATTCTTGAAGGA
* * * *
4178 GACTGCTTAACAGTAATAAAAAAGATAAATGATAATAAACCCAATCGATCGAGTATATCTGTAAT
131 GACTACCTAACAGTAATAAAAAAGATAAATGACAATAAACCCGATCGATCGAGTATATCTGTAAT
* * *
4243 TATACAAGAAATCAAACAAATTTGAGAGCATTACCTGTCCATTAT--GAGCAGAATGGCGAACCA
196 TATACAAGAAATCAAACAAATTTGAGAGCTTTACCTGTCCATT-TGCGAGGAGAACGGCGAACCA
* * * * * *
4306 AGCATGAAGTAACACATGCAATTGCAGACGATGGAAAAAAATGGTAAAATCAGATGGTGTGGATA
260 AGCATGAAGCAACGCATGCAATGGCAGACGAAGGAAAAAAATGGCAGAATCAGATGGTGTGGATA
* *
4371 GAGGAAGCCCCCAACGGTGTTGAAACAATAGCAGAACAGGATAGGGTTTCTTTGGCTTGTGTAAA
325 GAGGAAGCCCCCAACGGTGTTGAAACAATAGCAGAACAGGATAGTGTTTCTTTGGCTTGCGTAAA
* * * * *
4436 CCCAAATGTAAAAAAAAAATCGCAGGAAAAATTAAAGAAAGAGAGAGAGTGAGGAAGGGAGATTA
390 CCCAAATGT-AAAAAAGAATCACAGGAAAAATTAAAGAAAGAGAAAGAGAGAGGAAGGGGGATTA
4501 TTTTTAGA
454 TTTTTAGA
* * * * *
4509 ACAGATAATGGTTACGATTACTCACCAGAATACAAGTACAGCAGATCTAGAAATGGCGGAGGCAC
1 ACAGATAATGGTTACAATTACTCACCAGAATGCAAGTACAGCAAATCCAGAAATGACGGAGGCAC
* * * *
4574 GAGCTGGTTTCTAGGCCATTACGATAACAACGGACTTGGGATCTTGGCATCTGATTCTTGAAGGA
66 GAGCTGGTTTCTAGGCCATTACGACAACAGCAGACTTAGGATCTTGGCATCTGATTCTTGAAGGA
* *
4639 GACTGCCTAACAATAATAAAAAAGATAAATGACAATAAACCCGATCGATCGAGTATATCTGTAAT
131 GACTACCTAACAGTAATAAAAAAGATAAATGACAATAAACCCGATCGATCGAGTATATCTGTAAT
* * *
4704 TATACAATAAATCAAATAAATTTGAGAGCTTTACCTGTCCATTTGCGAGGAGAACGACGAACCAA
196 TATACAAGAAATCAAACAAATTTGAGAGCTTTACCTGTCCATTTGCGAGGAGAACGGCGAACCAA
* * * *
4769 GCATGAAGCAACGTATGCAATGGTAGACGAAGGAAAAAAATGGCAGGATCAAATGGTGTGGATAG
261 GCATGAAGCAACGCATGCAATGGCAGACGAAGGAAAAAAATGGCAGAATCAGATGGTGTGGATAG
* ** * * * * * *
4834 TGGAAGCCCTTAACGGTGTTAAAACGATAGCAAAATAGGATAGAG--T-TTTGGCTTGTGTAAAC
326 AGGAAGCCCCCAACGGTGTTGAAACAATAGCAGAACAGGATAGTGTTTCTTTGGCTTGCGTAAAC
4896 CCAAATGTAAAAAAGAATCACAGGAAAAATTAAAGAAAGAGAGAGAGAGAGAGAGAGAGGAAAAG
391 CCAAATGTAAAAAAGAATCACAGGAAAAATTAAAGAAAGAGA-A-AGAGAGAG-GA-AGG----G
4961 GGATTATTTTTAGA
448 GGATTATTTTTAGA
* * * * * ** * *
4975 ACAGATAATGGCTACAATTACTCGCTAGAATGCAAGTGCAACAAATCCA-AAAACAGCGAAGCCA
1 ACAGATAATGGTTACAATTACTCACCAGAATGCAAGTACAGCAAATCCAGAAATGA-CGGAGGCA
* * * * * * *
5039 CGAGCCGATTTCTAGGCCATTACGGCAGCAGCAGACCTAGGATCTTGGCATTTGTTTCTTGAAGG
65 CGAGCTGGTTTCTAGGCCATTACGACAACAGCAGACTTAGGATCTTGGCATCTGATTCTTGAAGG
* ** *
5104 AGACTACCTAACAGTAATAAAGAAGATAAATGACAATAAACCCGATTAATCGAGTATATTTGTAA
130 AGACTACCTAACAGTAATAAAAAAGATAAATGACAATAAACCCGATCGATCGAGTATATCTGTAA
* * *
5169 TTATACAAGAAATCAAACAAATTTGAGAGCTTTACCTGTCAATTTGTGAGGAAAACGGCGAACCA
195 TTATACAAGAAATCAAACAAATTTGAGAGCTTTACCTGTCCATTTGCGAGGAGAACGGCGAACCA
* *
5234 AGAATGAAGCAACGCATGCAATGGCAGACGAAGGAAAAAAAATGGCAGAATCAGATGGTGTAGAT
260 AGCATGAAGCAACGCATGCAATGGCAGACGAAGG-AAAAAAATGGCAGAATCAGATGGTGTGGAT
*
5299 AGAAGAAGCCCCCAACGGTGTTGAAACAATAGCAGAACAGGATAGTGTTTCTTTGGCTTGCGTAA
324 AGAGGAAGCCCCCAACGGTGTTGAAACAATAGCAGAACAGGATAGTGTTTCTTTGGCTTGCGTAA
* *
5364 ACCCAAATGTAAAAAAGAATCACAAGAAAAATTAGAGAAAGAGAAAGAGAGAGGAAGGGGGATTA
389 ACCCAAATGTAAAAAAGAATCACAGGAAAAATTAAAGAAAGAGAAAGAGAGAGGAAGGGGGATTA
*
5429 TTTTTAAA
454 TTTTTAGA
* * * **
5437 ACAGATAATGGTTGCGATTACTAACCAGAATGCAAGTACAGCAGGTCCAGAAATGACGGAGGCAC
1 ACAGATAATGGTTACAATTACTCACCAGAATGCAAGTACAGCAAATCCAGAAATGACGGAGGCAC
* * *
5502 GAGCTGGTTCCCT-GGCCATTACGACAACAGCAGACTTGGGATCTTGGCATCTGATTCTTGAATT
66 GAGCTGGTT-TCTAGGCCATTACGACAACAGCAGACTTAGGATCTTGGCATCTGATTCTTGAA-G
* * *
5566 G-GACTACCTAACAGTAATAAATAAGATAAATGACAATAAACCTGATCGATCGTGTATATCTGTA
129 GAGACTACCTAACAGTAATAAAAAAGATAAATGACAATAAACCCGATCGATCGAGTATATCTGTA
* * * * * *
5630 ATTATACAATAAATAAAACGAATTTGAGAGCTTTACCTATCCATATGCGAGAAGAACGGCGAACC
194 ATTATACAAGAAATCAAACAAATTTGAGAGCTTTACCTGTCCATTTGCGAGGAGAACGGCGAACC
* * * *
5695 AAGCATGAAGCAACGCATACAATGACAGACAAAGGAAAAAAACGGCAGAATCAGATGGTGTGGAT
259 AAGCATGAAGCAACGCATGCAATGGCAGACGAAGGAAAAAAATGGCAGAATCAGATGGTGTGGAT
* * * * *
5760 AGAGGAAGCCCCCAACGGGGTTGCAACAATAGTAGAACAAGATAGTGTTTCTTTGGCTTACAGT-
324 AGAGGAAGCCCCCAACGGTGTTGAAACAATAGCAGAACAGGATAGTGTTTCTTTGGCTTGC-GTA
* * *
5824 TACCCAAATGTAAAAAAGAATCATAGGAAAAATTAAAG--AGAGAGAGAGAGAGGAAGGGGGATT
388 AACCCAAATGTAAAAAAGAATCACAGGAAAAATTAAAGAAAGAGAAAGAGAGAGGAAGGGGGATT
5887 ATTTTTAGA
453 ATTTTTAGA
* * * * * *
5896 ACAGATAAT-GTCTGCAATTACTCACCAAAATGTAAGTACAGC-AATCTAGAAATGATGAAGGCA
1 ACAGATAATGGT-TACAATTACTCACCAGAATGCAAGTACAGCAAATCCAGAAATGACGGAGGCA
* * * ** *** * * *
5959 CGAGCTAGTTTCCAGGCCATTATGACAGTAATGGACTTCGGATCTTAGCATCTAATTCTTGAAGG
65 CGAGCTGGTTTCTAGGCCATTACGACAACAGCAGACTTAGGATCTTGGCATCTGATTCTTGAAGG
* * * * * * *
6024 AGACTACCTAACAGTAATAAAGAAGATAAAT-AAAATAAACTCGATCGGTTGAGTATATTTGTAG
130 AGACTACCTAACAGTAATAAAAAAGATAAATGACAATAAACCCGATCGATCGAGTATATCTGTAA
* **
6088 TTATACAAGAAATCAAACAAATTTAAGAGCTTTACCTGTCCATTTGCGAGGAGAACGATGAACCA
195 TTATACAAGAAATCAAACAAATTTGAGAGCTTTACCTGTCCATTTGCGAGGAGAACGGCGAACCA
* * * * * *
6153 AGCATGAAGCAATGTATGCAGTGGCAGACGAAGGAAAAAAAATGACAGAATTAGATGGTATGGAT
260 AGCATGAAGCAACGCATGCAATGGCAGACGAAGG-AAAAAAATGGCAGAATCAGATGGTGTGGAT
* * * * *
6218 AGAGGAAGCCTCCAACGGTGTTGAAACTATAGCAGAACA-GATAGTGTTTCTTCGGTTTGGGGT-
324 AGAGGAAGCCCCCAACGGTGTTGAAACAATAGCAGAACAGGATAGTGTTTCTTTGGCTT-GCGTA
* * * * *
6281 TATCCAAATGTAAAAAAGAATCATAGGAAAAATTAAAGAGAGAAAAAG
388 AACCCAAATGTAAAAAAGAATCACAGGAAAAATTAAAGAAAGAGAAAG
6329 GAAGGAGGAG
Statistics
Matches: 1565, Mismatches: 229, Indels: 54
0.85 0.12 0.03
Matches are distributed among these distances:
457 167 0.11
458 188 0.12
459 97 0.06
460 9 0.01
461 329 0.21
462 367 0.23
463 7 0.00
465 3 0.00
466 266 0.17
467 67 0.04
468 8 0.01
469 2 0.00
470 55 0.04
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (461 bp):
ACAGATAATGGTTACAATTACTCACCAGAATGCAAGTACAGCAAATCCAGAAATGACGGAGGCAC
GAGCTGGTTTCTAGGCCATTACGACAACAGCAGACTTAGGATCTTGGCATCTGATTCTTGAAGGA
GACTACCTAACAGTAATAAAAAAGATAAATGACAATAAACCCGATCGATCGAGTATATCTGTAAT
TATACAAGAAATCAAACAAATTTGAGAGCTTTACCTGTCCATTTGCGAGGAGAACGGCGAACCAA
GCATGAAGCAACGCATGCAATGGCAGACGAAGGAAAAAAATGGCAGAATCAGATGGTGTGGATAG
AGGAAGCCCCCAACGGTGTTGAAACAATAGCAGAACAGGATAGTGTTTCTTTGGCTTGCGTAAAC
CCAAATGTAAAAAAGAATCACAGGAAAAATTAAAGAAAGAGAAAGAGAGAGGAAGGGGGATTATT
TTTAGA
Found at i:14370 original size:36 final size:36
Alignment explanation
Indices: 14302--14401 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
14292 GGTAACAGGC
* * * *
14302 ATGACCTTTAGGTC-ACAGGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTCAATAGGGAGTAAAACGAGCATA
* *
14337 ATGACCTTTGGGTCAATAGGGACTAAAACGAGCATC
1 ATGACCTTTGGGTCAATAGGGAGTAAAACGAGCATA
* *
14373 ATGACTTTTGGGGTCAATAAGGAGTAAAA
1 ATGACCTTT-GGGTCAATAGGGAGTAAAA
14402 TAAATAACGA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 13 0.24
36 24 0.44
37 17 0.31
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (36 bp):
ATGACCTTTGGGTCAATAGGGAGTAAAACGAGCATA
Found at i:15090 original size:21 final size:21
Alignment explanation
Indices: 15064--15114 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
15054 GGAGTTTTTA
* *
15064 GTATCGGTAGTATTA-TGACTT
1 GTATCGGTAGT-TGACTCACTT
15085 GTATCGGTAGTTGACTCACTT
1 GTATCGGTAGTTGACTCACTT
15106 GTATCGGTA
1 GTATCGGTA
15115 AAACTGTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (21 bp):
GTATCGGTAGTTGACTCACTT
Found at i:17502 original size:21 final size:21
Alignment explanation
Indices: 17478--17523 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
17468 TATTAGTTTT
17478 ATAATTATAATTAA-TAAGTAA
1 ATAATTAT-ATTAATTAAGTAA
*
17499 ATAATTATCTTAATTAAGTAA
1 ATAATTATATTAATTAAGTAA
17520 ATAA
1 ATAA
17524 ATCATGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (21 bp):
ATAATTATATTAATTAAGTAA
Found at i:20302 original size:30 final size:29
Alignment explanation
Indices: 20255--20351 Score: 149
Period size: 30 Copynumber: 3.3 Consensus size: 29
20245 TTTTCCAAAA
20255 AAATTTGACCCCAAACTTTCTAAAAATTC
1 AAATTTGACCCCAAACTTTCTAAAAATTC
20284 AAATTTGACCCTCAAACTTTCTAAAAATTC
1 AAATTTGACCC-CAAACTTTCTAAAAATTC
* * *
20314 CAATTTGACCCCTAAACTTTTTGAAAATTC
1 AAATTTGACCCC-AAACTTTCTAAAAATTC
20344 AAATTTGA
1 AAATTTGA
20352 TCCGGTTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
29 12 0.19
30 50 0.81
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (29 bp):
AAATTTGACCCCAAACTTTCTAAAAATTC
Found at i:22093 original size:15 final size:17
Alignment explanation
Indices: 22073--22105 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22063 AAATAAACCT
22073 ATTAT-AATTT-ATTTA
1 ATTATAAATTTCATTTA
22088 ATTATAAATTTCATTTA
1 ATTATAAATTTCATTTA
22105 A
1 A
22106 CAAGTATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATAAATTTCATTTA
Found at i:25969 original size:105 final size:105
Alignment explanation
Indices: 25787--25991 Score: 365
Period size: 105 Copynumber: 2.0 Consensus size: 105
25777 AGAGTGCTTT
*
25787 CAAGTTATTATACATTATTTAACGAGTGACTTCAGTGGTAAAGAAGATGTTGTTCATTCTAGGAT
1 CAAGTTATTATACATTATTTAACGAGTGACTTCAGTGGTAAAGAAGATGTTGTTCATTCTAGGAG
*
25852 ATCCGAATTCGAGCACTTGTGTGTGCAATGTGTGTTTTGA
66 ATCCGAATTCGAGCACTTGTGTGTGCAAGGTGTGTTTTGA
*
25892 CAAGTTATTATACATTATTTAACGAGTGACTTCAGTGGTAAAGAGGATGTTGTTCATTCTAGGAG
1 CAAGTTATTATACATTATTTAACGAGTGACTTCAGTGGTAAAGAAGATGTTGTTCATTCTAGGAG
* *
25957 ATCCGAGTTCGAGCACTTGTGTGTGTAAGGTGTGT
66 ATCCGAATTCGAGCACTTGTGTGTGCAAGGTGTGT
25992 GTGCCTTGTC
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (105 bp):
CAAGTTATTATACATTATTTAACGAGTGACTTCAGTGGTAAAGAAGATGTTGTTCATTCTAGGAG
ATCCGAATTCGAGCACTTGTGTGTGCAAGGTGTGTTTTGA
Found at i:35554 original size:20 final size:18
Alignment explanation
Indices: 35513--35556 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
35503 AATTTTTTAT
* *
35513 TTTTTTAAATTTAGAAAG
1 TTTTTTAAATGTAGAAAA
35531 TTTTTTAAATGTAGAATAAA
1 TTTTTTAAATGTAG-A-AAA
35551 TTTTTT
1 TTTTTT
35557 TAATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.59
19 1 0.05
20 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (18 bp):
TTTTTTAAATGTAGAAAA
Found at i:35559 original size:21 final size:18
Alignment explanation
Indices: 35511--35546 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35501 TTAATTTTTT
*
35511 ATTTTTTTAAATTTAGAA
1 ATTTTTTTAAATGTAGAA
*
35529 AGTTTTTTAAATGTAGAA
1 ATTTTTTTAAATGTAGAA
35547 TAAATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (18 bp):
ATTTTTTTAAATGTAGAA
Found at i:35620 original size:11 final size:11
Alignment explanation
Indices: 35604--35648 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
35594 ATTTATAATC
35604 ATAATTATTTT
1 ATAATTATTTT
35615 ATAATTATTTATT
1 ATAATTA-TT-TT
* *
35628 ATTATGATTTT
1 ATAATTATTTT
35639 ATAATTATTT
1 ATAATTATTT
35649 ATGTAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 17 0.61
12 4 0.14
13 7 0.25
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
ATAATTATTTT
Found at i:35766 original size:24 final size:24
Alignment explanation
Indices: 35739--35812 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
35729 GAGGTAAGTA
35739 ATTTTTATATATAATATTTATCAT
1 ATTTTTATATATAATATTTATCAT
* * * *
35763 ATTTTGATAAATACTTTTTCATCAT
1 ATTTTTATATATAATATTT-ATCAT
* * *
35788 A-ATATATATATATATATATATCAT
1 ATTTTTATATATA-ATATTTATCAT
35812 A
1 A
35813 ATTTGTCTTA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
24 28 0.76
25 9 0.24
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (24 bp):
ATTTTTATATATAATATTTATCAT
Found at i:36416 original size:15 final size:15
Alignment explanation
Indices: 36396--36425 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
36386 ACGTTTACAT
36396 AAGCTCCACAATTAC
1 AAGCTCCACAATTAC
36411 AAGCTCCACAATTAC
1 AAGCTCCACAATTAC
36426 TTGGTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (15 bp):
AAGCTCCACAATTAC
Found at i:42461 original size:93 final size:93
Alignment explanation
Indices: 42343--42518 Score: 316
Period size: 93 Copynumber: 1.9 Consensus size: 93
42333 TTTGCCTATC
*
42343 TTTTCACTACTATTGGTGTTAATGGATTATTTACTAAAATAATTCAAATTTGGTCATCACACTCT
1 TTTTCACTACTATTGGTGTTAATGGACTATTTACTAAAATAATTCAAATTTGGTCATCACACTCT
42408 TTTCCTATGCCATTGAATATGAGTGCAA
66 TTTCCTATGCCATTGAATATGAGTGCAA
* * *
42436 TTTTCACTCCTATTGGTGTTAATGGACTATTTACTAAAATGATTCAAATTTGGTCATGACACTCT
1 TTTTCACTACTATTGGTGTTAATGGACTATTTACTAAAATAATTCAAATTTGGTCATCACACTCT
42501 TTTCCTATGCCATTGAAT
66 TTTCCTATGCCATTGAAT
42519 TGTTCTAAGT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (93 bp):
TTTTCACTACTATTGGTGTTAATGGACTATTTACTAAAATAATTCAAATTTGGTCATCACACTCT
TTTCCTATGCCATTGAATATGAGTGCAA
Found at i:45041 original size:13 final size:13
Alignment explanation
Indices: 45025--45059 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
45015 GGGTTTTTTT
45025 CAAAAAAATACGA
1 CAAAAAAATACGA
45038 C--AAAAATACGA
1 CAAAAAAATACGA
45049 CAAAAAAATAC
1 CAAAAAAATAC
45060 CTGACACCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.09
Consensus pattern (13 bp):
CAAAAAAATACGA
Found at i:45309 original size:11 final size:11
Alignment explanation
Indices: 45293--45349 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
45283 GGGGACCAAC
* *
45293 GAAAAATGAAG
1 GAAAAAAGAAA
45304 GAAAAAAGAAA
1 GAAAAAAGAAA
45315 GAAAAAAGAGAAA
1 G-AAAAA-AGAAA
*
45328 GAAAGAAAGGAA
1 GAAA-AAAGAAA
*
45340 GAAAGAAGAA
1 GAAAAAAGAA
45350 GGAAGAAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 14 0.37
12 16 0.42
13 8 0.21
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:45317 original size:4 final size:4
Alignment explanation
Indices: 45304--45346 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
45294 AAAAATGAAG
* *
45304 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GGAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
45347 GAAGGAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.82
5 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:45319 original size:21 final size:21
Alignment explanation
Indices: 45304--45345 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
45294 AAAAATGAAG
45304 GAAA-AAAGAAAGAAAAAAGA
1 GAAAGAAAGAAAGAAAAAAGA
*
45324 GAAAGAAAGAAAGGAAGAAAGA
1 GAAAGAAAGAAA-GAAAAAAGA
45346 AGAAGGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAAAAAGA
Done.