Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015206.1 Kokia drynarioides strain JFW-HI SEQ_130250, 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: 388724
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 703 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:277528 original size:21 final size:21
Alignment explanation
Indices: 277502--277552 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
277492 TTTCAAAAAT
*
277502 TATTTTTT-TATTT-TTATATA
1 TATTTTTTAGATTTATTAT-TA
277522 TATTTTTTAGATTTATTATTA
1 TATTTTTTAGATTTATTATTA
277543 TATTTGTTTA
1 TATTT-TTTA
277553 AAATAGTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 11 0.41
22 8 0.30
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
TATTTTTTAGATTTATTATTA
Found at i:282074 original size:29 final size:29
Alignment explanation
Indices: 282042--282098 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
282032 TGTGTCTTTT
282042 TTTTTTAAAGTA-TATATTTCTAATAATTA
1 TTTTTTAAAGTATTATATTT-TAATAATTA
***
282071 TTTTTTGGTGTATTATATTTTAATAATT
1 TTTTTTAAAGTATTATATTTTAATAATT
282099 TACTATAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTTTTAAAGTATTATATTTTAATAATTA
Found at i:284993 original size:26 final size:25
Alignment explanation
Indices: 284947--284995 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
284937 CCGTAAATAC
* * *
284947 AAAAAAATATTATTATTATAATGAT
1 AAAAAAATAGTATAATAATAATGAT
284972 AAAAAAATAGTAGTAATAATAATG
1 AAAAAAATAGTA-TAATAATAATG
284996 TAAGGAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
AAAAAAATAGTATAATAATAATGAT
Found at i:295289 original size:2 final size:2
Alignment explanation
Indices: 295282--295307 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
295272 GGGAGAACAA
295282 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
295308 CTTTGATGTG
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:295640 original size:17 final size:19
Alignment explanation
Indices: 295620--295654 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
295610 CTTGCTGAGA
295620 GTATTGTT-T-TTATTTTG
1 GTATTGTTATATTATTTTG
295637 GTATTGTTATATTATTTT
1 GTATTGTTATATTATTTT
295655 AGATTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (19 bp):
GTATTGTTATATTATTTTG
Found at i:296215 original size:21 final size:21
Alignment explanation
Indices: 296179--296237 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
296169 AATTCAATTA
*
296179 AATATT-TTTATTTTTATGAT
1 AATATTATTTATTTTTATAAT
*
296199 AATATTATTTATATTTATAAT
1 AATATTATTTATTTTTATAAT
296220 AAT-TTAATTTATTTTTAT
1 AATATT-ATTTATTTTTAT
296238 TTTTTACCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.24
21 26 0.76
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
AATATTATTTATTTTTATAAT
Found at i:299617 original size:64 final size:64
Alignment explanation
Indices: 299498--299617 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
299488 TATCGATATT
* * * *
299498 TTTAAATATTTTCGTATAATATATTTATAATCTAATTTTTAATTTATTGATAAATTGTATATCA
1 TTTAAATATTTTCGCATAATATATTTATAATCTAAGTTTTAATTTATTCACAAATTGTATATCA
* *
299562 TTTAAATATTTTTCGCAT-ATATATTTATAA-CTTAAGTTTTAGTTTCTTCACAAATT
1 TTTAAATA-TTTTCGCATAATATATTTATAATC-TAAGTTTTAATTTATTCACAAATT
299618 ATATGTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 1 0.02
64 39 0.81
65 8 0.17
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (64 bp):
TTTAAATATTTTCGCATAATATATTTATAATCTAAGTTTTAATTTATTCACAAATTGTATATCA
Found at i:311407 original size:24 final size:25
Alignment explanation
Indices: 311371--311418 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
311361 AAAATAATCT
* *
311371 AAATTAATCAGAGTTTGATTGAAAC
1 AAATAAATCAGAGTTTAATTGAAAC
311396 AAATAAAT-AGAGTTTAATTGAAA
1 AAATAAATCAGAGTTTAATTGAAA
311419 GATTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (25 bp):
AAATAAATCAGAGTTTAATTGAAAC
Found at i:313187 original size:17 final size:18
Alignment explanation
Indices: 313152--313197 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
313142 TCAAATGTTG
*
313152 AAATTTTA-GTTCCTTT-
1 AAATTTTATTTTCCTTTA
*
313168 AAATTTTATTTTCGTTTA
1 AAATTTTATTTTCCTTTA
313186 AAATATTTATTT
1 AAAT-TTTATTT
313198 AATAAATTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 4 0.16
19 7 0.28
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (18 bp):
AAATTTTATTTTCCTTTA
Found at i:321286 original size:43 final size:43
Alignment explanation
Indices: 321224--321310 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
321214 CTGGGAACAT
*
321224 GGGCGTGTGCTAAACCGTGTGTGTATACTATTTTGTTGCACAC
1 GGGCGTGTGCTAAACCGTGTGTGTATACTATTTTGTTACACAC
*
321267 GGGCGTGTGCTAAATCGTGTGTGTATACTATTTTGTTACACAC
1 GGGCGTGTGCTAAACCGTGTGTGTATACTATTTTGTTACACAC
321310 G
1 G
321311 AACTGGGCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.36
Consensus pattern (43 bp):
GGGCGTGTGCTAAACCGTGTGTGTATACTATTTTGTTACACAC
Found at i:321412 original size:94 final size:93
Alignment explanation
Indices: 321291--321478 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 93
321281 TCGTGTGTGT
321291 ATACTATTTTGTTACACACGAACTGGGCATACGGGCGTGTGCCAGACCATGTGAATATACTGTTT
1 ATACTATTTTGTTACACACGAACTGGGCATACGGGCGTGTGCCAGACCATGTGAATATACTGTTT
321356 TGCAATTATAGGTGTAGTGGTCACACGG
66 TGCAATTATAGGTGTAGTGGTCACACGG
*
321384 ANTACTATTTTGTTACACACGAGCTGGGCATACGGGCGTGTGCCAGACCATGTGAATATACTGTT
1 A-TACTATTTTGTTACACACGAACTGGGCATACGGGCGTGTGCCAGACCATGTGAATATACTGTT
321449 TTGCAATTATAGGTGTAGTGGTCACACGG
65 TTGCAATTATAGGTGTAGTGGTCACACGG
321478 A
1 A
321479 CTAACACATG
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 1 0.01
94 92 0.99
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (93 bp):
ATACTATTTTGTTACACACGAACTGGGCATACGGGCGTGTGCCAGACCATGTGAATATACTGTTT
TGCAATTATAGGTGTAGTGGTCACACGG
Found at i:323712 original size:2 final size:2
Alignment explanation
Indices: 323705--323741 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
323695 CCAAAGTTCT
323705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
323742 TACCACAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:326770 original size:6 final size:6
Alignment explanation
Indices: 326759--326792 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
326749 AGGAAGTGGG
326759 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGG
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGG
326793 AGTAAAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:328868 original size:21 final size:20
Alignment explanation
Indices: 328826--328868 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
328816 AAAACTGTGG
328826 AAAATGTCTTACGAAAATAA
1 AAAATGTCTTACGAAAATAA
*
328846 AAAATGTCTTACGGAAATAA
1 AAAATGTCTTACGAAAATAA
328866 AAA
1 AAA
328869 GCGTAAGACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (20 bp):
AAAATGTCTTACGAAAATAA
Found at i:328936 original size:17 final size:17
Alignment explanation
Indices: 328911--328944 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
328901 TTTTCCCATG
*
328911 TTTGTAAAATAATTTAC
1 TTTGAAAAATAATTTAC
*
328928 TTTGAAAAATCATTTAC
1 TTTGAAAAATAATTTAC
328945 AACCAAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (17 bp):
TTTGAAAAATAATTTAC
Found at i:328989 original size:14 final size:14
Alignment explanation
Indices: 328970--328996 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
328960 GGAAAACACT
328970 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
328984 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
328997 AAGTAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:331434 original size:23 final size:23
Alignment explanation
Indices: 331319--331435 Score: 69
Period size: 23 Copynumber: 5.1 Consensus size: 23
331309 TATTCTCCTC
* *
331319 ATAAATAATAAAGTTATAAATTA
1 ATAAATAATAAAATTATAATTTA
* *
331342 ATATATAAT-AAATTATATTTTA
1 ATAAATAATAAAATTATAATTTA
* *** **
331364 TCTAAA-ACATATTTTTAATCCTTTA
1 -ATAAATA-ATAAAATT-ATAATTTA
*
331389 A-AAATAATAAAATTATAAATTA
1 ATAAATAATAAAATTATAATTTA
* *
331411 ATAAATGATAAAATTATATTTTA
1 ATAAATAATAAAATTATAATTTA
331434 AT
1 AT
331436 TTTTTTTAAA
Statistics
Matches: 67, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
22 17 0.25
23 41 0.61
24 3 0.04
25 6 0.09
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAATAATAAAATTATAATTTA
Found at i:334361 original size:2 final size:2
Alignment explanation
Indices: 334354--334383 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
334344 GCTGCCCCTT
334354 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
334384 ACAGCATTAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:335283 original size:16 final size:15
Alignment explanation
Indices: 335262--335304 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
335252 GATGAAATTT
335262 TTTTTAAAATTTTAGG
1 TTTTTAAAATTTTA-G
*
335278 TTTTTAAAATGTTAG
1 TTTTTAAAATTTTAG
335293 TATTTTAAAATT
1 T-TTTTAAAATT
335305 CATAAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (15 bp):
TTTTTAAAATTTTAG
Found at i:339594 original size:60 final size:58
Alignment explanation
Indices: 339501--339751 Score: 242
Period size: 55 Copynumber: 4.2 Consensus size: 58
339491 CTAATAAAAT
* * * * *
339501 ATTTGGTACTTGAACTTGATACTTTTTCTTAATTTTGTACCTAAACATTTTTTTGACTCA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAAC-TTTTTTTGA-TCA
* *
339561 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTT--T-T
1 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGATCA
* *
339616 ATTTGGTACCTAAACTCGACACTTTTTCCTAATTTGGTA-CTGAAACTTTTTTGGATCCA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCT-AAACTTTTTTTGAT-CA
* * * * *
339675 ATATGATACCTAAACTTGGCATTTTTTTTCCTAATTTGGCT-CCTAAGCTTTGTTTTAGATTCA
1 ATTTGGTACCTAAACTTGACA--CTTTTTCCTAATTTGG-TACCTAAACTTT-TTTT-GA-TCA
*
339738 ATTTGATACCTAAA
1 ATTTGGTACCTAAA
339752 TTTATTAAAT
Statistics
Matches: 162, Mismatches: 17, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
54 2 0.01
55 47 0.29
56 1 0.01
57 1 0.01
59 24 0.15
60 42 0.26
61 21 0.13
62 6 0.04
63 17 0.10
64 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (58 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGATCA
Found at i:339596 original size:31 final size:31
Alignment explanation
Indices: 339501--339659 Score: 110
Period size: 31 Copynumber: 5.5 Consensus size: 31
339491 CTAATAAAAT
* * *
339501 ATTTGGTACTTGAACTTGATACTTTTTCTTA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTA
* * *
339532 ATTTTGTACCT-AA----ACATTTTTTTGACTCA
1 ATTTGGTACCTGAACTTGACA-CTTTTT-CCT-A
339561 ATTTGGTACCTGAACTTGACACTTTTTCCTA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTA
* *
339592 ATTTGGTACCTAAACTT-----TTTTT--TT
1 ATTTGGTACCTGAACTTGACACTTTTTCCTA
* *
339616 ATTTGGTACCTAAACTCGACACTTTTTCCTA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTA
339647 ATTTGGTA-CTGAA
1 ATTTGGTACCTGAA
339660 ACTTTTTTGG
Statistics
Matches: 99, Mismatches: 14, Indels: 31
0.69 0.10 0.22
Matches are distributed among these distances:
24 17 0.17
26 7 0.07
27 5 0.05
28 1 0.01
29 16 0.16
30 8 0.08
31 35 0.35
32 2 0.02
33 5 0.05
34 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.47
Consensus pattern (31 bp):
ATTTGGTACCTGAACTTGACACTTTTTCCTA
Found at i:339702 original size:115 final size:116
Alignment explanation
Indices: 339500--339730 Score: 265
Period size: 115 Copynumber: 2.0 Consensus size: 116
339490 GCTAATAAAA
* * * * * * * *
339500 TATTTGGTACTTGAACTTGATACTTTTTCTTAATTTTGTACCTAAACATTTTTTTGACTCAATTT
1 TATTTGGTACCTAAACTCGACACTTTTTCCTAATTTGGTACCTAAACATTTTTTGGACTCAATAT
* * *
339565 GGTACCTGAACTTGACA-CTTTTTCCTAATTTGG-TACCTAAACTTTTTTTT
66 GATACCTAAACTTGACATCTTTTTCCTAATTTGGCT-CCTAAACTTTGTTTT
339615 TATTTGGTACCTAAACTCGACACTTTTTCCTAATTTGGTA-CTGAAAC-TTTTTTGGA-TCCAAT
1 TATTTGGTACCTAAACTCGACACTTTTTCCTAATTTGGTACCT-AAACATTTTTTGGACT-CAAT
* * *
339677 ATGATACCTAAACTTGGCATTTTTTTTCCTAATTTGGCTCCTAAGCTTTGTTTT
64 ATGATACCTAAACTTGACA-TCTTTTTCCTAATTTGGCTCCTAAACTTTGTTTT
339731 AGATTCAATT
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
113 1 0.01
114 29 0.30
115 38 0.39
116 28 0.29
117 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (116 bp):
TATTTGGTACCTAAACTCGACACTTTTTCCTAATTTGGTACCTAAACATTTTTTGGACTCAATAT
GATACCTAAACTTGACATCTTTTTCCTAATTTGGCTCCTAAACTTTGTTTT
Found at i:340460 original size:26 final size:28
Alignment explanation
Indices: 340428--340479 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
340418 ATTGTTTCAG
*
340428 ATGTAATTGATAAT-A-TTTATAAAAAT
1 ATGTAATTAATAATGATTTTATAAAAAT
*
340454 ATGTAATTAATTATGATTTTATAAAA
1 ATGTAATTAATAATGATTTTATAAAA
340480 CCTAGTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 1 0.05
28 9 0.41
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (28 bp):
ATGTAATTAATAATGATTTTATAAAAAT
Found at i:353244 original size:18 final size:18
Alignment explanation
Indices: 353219--353255 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
353209 AAAGTTAAAA
*
353219 ATAAAATTTTAC-ATTAT
1 ATAAAAATTTACAATTAT
353236 ATAAAAATTTACAATTAT
1 ATAAAAATTTACAATTAT
353254 AT
1 AT
353256 GAGATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAAAAATTTACAATTAT
Found at i:354742 original size:25 final size:23
Alignment explanation
Indices: 354714--354776 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
354704 TCGTCCATAT
354714 TATTTTATTTTTTTAAAACTATTT-A
1 TATTTTATTTTTTT--AA-TATTTAA
* *
354739 TATTATATTATTTTAATATTTAA
1 TATTTTATTTTTTTAATATTTAA
354762 TATTTTTATTTTTTT
1 TA-TTTTATTTTTTT
354777 TATTTATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 5 0.16
23 5 0.16
24 10 0.31
25 12 0.38
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
TATTTTATTTTTTTAATATTTAA
Found at i:357278 original size:277 final size:277
Alignment explanation
Indices: 356774--357318 Score: 849
Period size: 277 Copynumber: 2.0 Consensus size: 277
356764 TTCCTTAGTG
* * * * ** *
356774 CTCAGATTTATCGAGTCAGCATTCCTCTCATACAAAACATCATTGGTTAGATAAATTGCTGACAA
1 CTCAGATCTACCGAGTCAACATTCCTCCCATACAAAACATCACCGATTAGATAAATTGCTGACAA
* *
356839 TACCTTTGTCCCAACCTTTATGTCTCGATTTATCGACACAACAGATCGTGATTGTAGATCACCAA
66 TACCTTGGTCCCAACCTTTATGTCTCGATTTATCGACACAACAGATCGTGATTGCAGATCACCAA
*
356904 ATATATGAATGCAATCGTTAAAGGAAAAAGACACGCCATAATTTTGCCAAGGAAGTTCAAGCTAA
131 ATATATGAATGCAATCGTTAAAGGAAAAAGACACGCCATAATTTTGCCAAGGAAGTTCAAGCCAA
*
356969 GAACAAAATCATAGTCATTTAAACAGATTACCTCAAAATCTTCCTTGCCCTTCCACTCGTCGATT
196 GAACAAAATCATAGTCATCTAAACAGATTACCTCAAAATCTTCCTTGCCCTTCCACTCGTCGATT
357034 TGTAGCTTCACCTCGTA
261 TGTAGCTTCACCTCGTA
* * * * *
357051 CTCAGATCTACCGAGTCAATATTCCTCCCATACAAAACATCCCCGATTAGCTAGATTGTTGACAA
1 CTCAGATCTACCGAGTCAACATTCCTCCCATACAAAACATCACCGATTAGATAAATTGCTGACAA
**
357116 TACCTTGGTCCCAACCTTTATGTCTCGATTTATCGACACATTAGATCGTGATTGCAGATCACCAA
66 TACCTTGGTCCCAACCTTTATGTCTCGATTTATCGACACAACAGATCGTGATTGCAGATCACCAA
* * ** *
357181 ATATATGAATGCAATTGTTAAAGGAAAAAGACATGCTTTAATTTTGTCAAGGAAGTTCAAGCCAA
131 ATATATGAATGCAATCGTTAAAGGAAAAAGACACGCCATAATTTTGCCAAGGAAGTTCAAGCCAA
* *
357246 GAATAAAATCATAGTCATCTAAAC-GAATTACCTTAAAATCTTCCTTGCCCTTCCACTCGTCGAT
196 GAACAAAATCATAGTCATCTAAACAG-ATTACCTCAAAATCTTCCTTGCCCTTCCACTCGTCGAT
357310 TTGTAGCTT
260 TTGTAGCTT
357319 TAGTCCTCGT
Statistics
Matches: 242, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
276 1 0.00
277 241 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (277 bp):
CTCAGATCTACCGAGTCAACATTCCTCCCATACAAAACATCACCGATTAGATAAATTGCTGACAA
TACCTTGGTCCCAACCTTTATGTCTCGATTTATCGACACAACAGATCGTGATTGCAGATCACCAA
ATATATGAATGCAATCGTTAAAGGAAAAAGACACGCCATAATTTTGCCAAGGAAGTTCAAGCCAA
GAACAAAATCATAGTCATCTAAACAGATTACCTCAAAATCTTCCTTGCCCTTCCACTCGTCGATT
TGTAGCTTCACCTCGTA
Found at i:358755 original size:28 final size:27
Alignment explanation
Indices: 358693--358767 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
358683 TGGATACCCG
*
358693 AGGGTAAAATGGTAATTTTAAATTCTC
1 AGGGTAAAATGGTAATTTTAAATTCTA
*
358720 AGGAGTAAAATGGTAATTTTGGATATTC-A
1 AGG-GTAAAATGGTAATTTT--AAATTCTA
*
358749 AGGGTAAAACGGTAATTTT
1 AGGGTAAAATGGTAATTTT
358768 TAGAAAAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.07
28 31 0.74
29 3 0.07
30 5 0.12
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (27 bp):
AGGGTAAAATGGTAATTTTAAATTCTA
Found at i:358816 original size:29 final size:27
Alignment explanation
Indices: 358784--359055 Score: 124
Period size: 29 Copynumber: 9.3 Consensus size: 27
358774 AATCGAGATA
358784 AAAAATAGAATTTTTGGACATTCTGGGGT
1 AAAAATAGAATTTTTGGA-ATT-TGGGGT
* * * *
358813 -AAAATGGTAATTTTTAAGAGTTTTGAGGT
1 AAAAATAG-AATTTTT-GGA-ATTTGGGGT
* * *
358842 TAAAATGGAGTTTTTGGACATTTGGGGGT
1 AAAAATAGAATTTTTGGA-ATTT-GGGGT
**
358871 -AAAAT-GATATTTTTTTAAAGTTTTGGGGT
1 AAAAATAGA-A-TTTTTGGAA--TTTGGGGT
*
358900 CAAAAATAGAATTTTTGGAGGTTTGGGGGT
1 -AAAAATAGAATTTTTGGA-ATTT-GGGGT
*
358930 AAAAAT-GTAATTTTTGGAAGTTTCGAGGT
1 AAAAATAG-AATTTTTGGAA-TTT-GGGGT
*
358959 CAAAAA-ATGAAATTTTTGGAAGTTCGGGGAT
1 -AAAAATA-G-AATTTTTGGAA-TTTGGGG-T
*
358990 AAAAAT-GTAATTTTTGAAAGTTTCGGGGT
1 AAAAATAG-AATTTTTGGAA-TTT-GGGGT
*
359019 CAAAAATGGAATTTTTGGAATTTTGAGGGT
1 -AAAAATAGAATTTTTGGAA-TTTG-GGGT
359049 AAAAATA
1 AAAAATA
359056 TATTTTCAAA
Statistics
Matches: 191, Mismatches: 28, Indels: 48
0.72 0.10 0.18
Matches are distributed among these distances:
27 2 0.01
28 18 0.09
29 81 0.42
30 65 0.34
31 23 0.12
32 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (27 bp):
AAAAATAGAATTTTTGGAATTTGGGGT
Found at i:358826 original size:28 final size:28
Alignment explanation
Indices: 358694--358826 Score: 76
Period size: 28 Copynumber: 4.6 Consensus size: 28
358684 GGATACCCGA
358694 GGGTAAAATGGTAATTTT--AAATTCTCAG
1 GGGTAAAATGGTAATTTTGGAAATTCT--G
* * **
358722 GAGTAAAATGGTAATTTTGGATATTCAA
1 GGGTAAAATGGTAATTTTGGAAATTCTG
* * *
358750 GGGTAAAACGGTAATTTTTAGAAAAATC-G
1 GGGTAAAATGGTAA-TTTT-GGAAATTCTG
* * * *
358779 AGATAAAAAATAG-AATTTTTGGACATTCTG
1 GGGT--AAAATGGTAA-TTTTGGAAATTCTG
358809 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
358827 TAAGAGTTTT
Statistics
Matches: 77, Mismatches: 20, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
28 39 0.51
29 13 0.17
30 20 0.26
31 5 0.06
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTGGAAATTCTG
Found at i:358915 original size:30 final size:30
Alignment explanation
Indices: 358888--359101 Score: 169
Period size: 29 Copynumber: 7.2 Consensus size: 30
358878 TATTTTTTTA
*
358888 AAGTTTTGGGGTCAAAAATAGAATTTTTGG
1 AAGTTTCGGGGTCAAAAATAGAATTTTTGG
* *
358918 AGGTTTGGGGGT-AAAAAT-GTAATTTTTGG
1 AAGTTTCGGGGTCAAAAATAG-AATTTTTGG
*
358947 AAGTTTCGAGGTCAAAAA-ATGAAATTTTTGG
1 AAGTTTCGGGGTCAAAAATA-G-AATTTTTGG
*
358978 AAG-TTCGGGGAT-AAAAAT-GTAATTTTTGA
1 AAGTTTCGGGG-TCAAAAATAG-AATTTTTGG
*
359007 AAGTTTCGGGGTCAAAAATGGAATTTTTGG
1 AAGTTTCGGGGTCAAAAATAGAATTTTTGG
* * **
359037 AA-TTTTGAGGGT-AAAAATA-TA-TTTTCA
1 AAGTTTCG-GGGTCAAAAATAGAATTTTTGG
* * *
359064 AATTTTTTGGGGTCAAAAATGGAATTTTTGG
1 AA-GTTTCGGGGTCAAAAATAGAATTTTTGG
359095 ACAGTTT
1 A-AGTTT
359102 AGGGACCTTC
Statistics
Matches: 148, Mismatches: 20, Indels: 31
0.74 0.10 0.16
Matches are distributed among these distances:
27 6 0.04
28 6 0.04
29 58 0.39
30 54 0.36
31 23 0.16
32 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (30 bp):
AAGTTTCGGGGTCAAAAATAGAATTTTTGG
Found at i:358917 original size:59 final size:58
Alignment explanation
Indices: 358784--359097 Score: 284
Period size: 58 Copynumber: 5.3 Consensus size: 58
358774 AATCGAGATA
*
358784 AAAAATAGAATTTTTGGACATTCT-GGGGTAAAATGGTAATTTTT-AAGAGTTTTGAGGT-
1 AAAAATAGAATTTTTGGACATT-TGGGGGTAAAAT-GTAATTTTTGAA-AGTTTTGGGGTC
* * * * *
358842 TAAAATGGAGTTTTTGGACATTTGGGGGTAAAATGATATTTTTTTAAAGTTTTGGGGTC
1 AAAAATAGAATTTTTGGACATTTGGGGGTAAAATG-TAATTTTTGAAAGTTTTGGGGTC
** * * *
358901 AAAAATAGAATTTTTGGAGGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTC
1 AAAAATAGAATTTTTGGACATTTGGGGGT-AAAATGTAATTTTTGAAAGTTTTGGGGTC
* * *
358960 AAAAA-ATGAAATTTTTGGA-AGTTCGGGGATAAAAATGTAATTTTTGAAAGTTTCGGGGTC
1 AAAAATA-G-AATTTTTGGACA-TTTGGGGGT-AAAATGTAATTTTTGAAAGTTTTGGGGTC
* * * * *
359020 AAAAATGGAATTTTTGGA-ATTTTGAGGGTAAAA-AT-ATATTTTCAAATTTTTTGGGGTC
1 AAAAATAGAATTTTTGGACA-TTTGGGGGTAAAATGTAAT-TTTTGAAA-GTTTTGGGGTC
*
359078 AAAAATGGAATTTTTGGACA
1 AAAAATAGAATTTTTGGACA
359098 GTTTAGGGAC
Statistics
Matches: 215, Mismatches: 29, Indels: 23
0.81 0.11 0.09
Matches are distributed among these distances:
56 2 0.01
57 10 0.05
58 78 0.36
59 68 0.32
60 57 0.27
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.38
Consensus pattern (58 bp):
AAAAATAGAATTTTTGGACATTTGGGGGTAAAATGTAATTTTTGAAAGTTTTGGGGTC
Found at i:358973 original size:60 final size:59
Alignment explanation
Indices: 358784--359101 Score: 271
Period size: 59 Copynumber: 5.4 Consensus size: 59
358774 AATCGAGATA
* *
358784 AAAAAT-AGAATTTTTGGACA-TTCT-GGGGT-AAAATGGTAATTTTT-AAGAGTTTTGAGGT-
1 AAAAATGA-AATTTTTGGA-AGTT-TGGGGGTAAAAAT-GTAATTTTTGAA-AGTTTCGGGGTC
* * * * * *
358842 TAAAATGGAGTTTTTGGACA-TTTGGGGGT-AAAATGATATTTTTTTAAAGTTTTGGGGTC
1 AAAAATGAAATTTTTGGA-AGTTTGGGGGTAAAAATG-TAATTTTTGAAAGTTTCGGGGTC
* * *
358901 AAAAAT-AGAATTTTTGGAGGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTC
1 AAAAATGA-AATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTC
* *
358960 AAAAAATGAAATTTTTGGAAGTTCGGGGATAAAAATGTAATTTTTGAAAGTTTCGGGGTC
1 -AAAAATGAAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTC
* * * * * * *
359020 AAAAATGGAATTTTTGGAATTTTGAGGGTAAAAATAT-A-TTTTCAAATTTTTTGGGGTC
1 AAAAATGAAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAAA-GTTTCGGGGTC
*
359078 AAAAATGGAATTTTTGGACAGTTT
1 AAAAATGAAATTTTTGGA-AGTTT
359102 AGGGACCTTC
Statistics
Matches: 219, Mismatches: 29, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
57 9 0.04
58 73 0.33
59 78 0.36
60 58 0.26
61 1 0.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (59 bp):
AAAAATGAAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTC
Found at i:360126 original size:19 final size:19
Alignment explanation
Indices: 360102--360138 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
360092 ATTAATATTG
* *
360102 TTAATATCATTATTATTAA
1 TTAATACCATTAGTATTAA
360121 TTAATACCATTAGTATTA
1 TTAATACCATTAGTATTA
360139 TACTTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (19 bp):
TTAATACCATTAGTATTAA
Found at i:360155 original size:9 final size:9
Alignment explanation
Indices: 360091--360169 Score: 52
Period size: 9 Copynumber: 8.7 Consensus size: 9
360081 TAATATTTAA
360091 TATTAATAT
1 TATTAATAT
*
360100 TGTTAATAT
1 TATTAATAT
* *
360109 CATTATTAT
1 TATTAATAT
*
360118 TAATTAATAC
1 T-ATTAATAT
* *
360128 CATTAGTAT
1 TATTAATAT
*
360137 TA-TACTTAT
1 TATTA-ATAT
360146 TATTAATAT
1 TATTAATAT
*
360155 TATTATTAT
1 TATTAATAT
*
360164 CATTAA
1 TATTAA
360170 GGCTATTTAT
Statistics
Matches: 51, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
8 2 0.04
9 41 0.80
10 8 0.16
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (9 bp):
TATTAATAT
Found at i:360160 original size:15 final size:15
Alignment explanation
Indices: 360087--360163 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
360077 TTTTTAATAT
* *
360087 TTAATATTAATATTG
1 TTAATATTATTATTA
*
360102 TTAATATCATTATTA
1 TTAATATTATTATTA
* **
360117 TTAATTAATACCATTA
1 TTAA-TATTATTATTA
* *
360133 GTATTA-TACTTATTA
1 TTAATATTA-TTATTA
360148 TTAATATTATTATTA
1 TTAATATTATTATTA
360163 T
1 T
360164 CATTAAGGCT
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
14 2 0.04
15 33 0.72
16 11 0.24
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (15 bp):
TTAATATTATTATTA
Found at i:360895 original size:5 final size:6
Alignment explanation
Indices: 360858--360920 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
360848 TTTAGACATT
* * * *
360858 AATTTA AATTTA AATTTA AACTTA AA-ATA AATTTA ATTTTA AA-ATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
360904 AATTT- AATTTA TATTTA
1 AATTTA AATTTA AATTTA
360921 GCCCGGATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
5 13 0.28
6 33 0.72
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:360911 original size:17 final size:17
Alignment explanation
Indices: 360868--360913 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
360858 AATTTAAATT
**
360868 TAAATTTAAACTTAAAA
1 TAAATTTAATTTTAAAA
360885 TAAATTTAATTTTAAAA
1 TAAATTTAATTTTAAAA
360902 TAAATTTAATTT
1 TAAATTTAATTT
360914 ATATTTAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTAATTTTAAAA
Found at i:361710 original size:2 final size:2
Alignment explanation
Indices: 361703--361728 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
361693 TGAATTGTTT
361703 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
361729 ACCCCTAAAT
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):
TA
Found at i:369400 original size:15 final size:15
Alignment explanation
Indices: 369382--369416 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
369372 TCAATTATCG
*
369382 TTTTTTTTTTGTAAA
1 TTTTTTTTTTATAAA
*
369397 TTTTATTTTTATAAA
1 TTTTTTTTTTATAAA
369412 TTTTT
1 TTTTT
369417 CATAGTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTTTTTTATAAA
Found at i:369454 original size:19 final size:19
Alignment explanation
Indices: 369403--369455 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
369393 TAAATTTTAT
*
369403 TTTTATAAATTTTTCATAG
1 TTTTATATATTTTTCATAG
* *
369422 TTTATATGTTTTTTTC-TAG
1 TTT-TATATATTTTTCATAG
369441 ATTTTATATATTTTT
1 -TTTTATATATTTTT
369456 TTTCTGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.66
Consensus pattern (19 bp):
TTTTATATATTTTTCATAG
Found at i:369458 original size:22 final size:21
Alignment explanation
Indices: 369422--369499 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 21
369412 TTTTTCATAG
369422 TTTATATGTTTTTTTCTAGATT
1 TTTATAT-TTTTTTTCTAGATT
369444 TTATATATTTTTTTTCT-GAATTT
1 TT-TATATTTTTTTTCTAG-A-TT
* * *
369467 TTTATATATTTATT-TACATT
1 TTTATATTTTTTTTCTAGATT
369487 TTTATATTTTTTT
1 TTTATATTTTTTT
369500 AATATGTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 13 0.28
21 3 0.06
22 22 0.47
23 9 0.19
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTATATTTTTTTTCTAGATT
Found at i:379498 original size:20 final size:20
Alignment explanation
Indices: 379473--379514 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
379463 AAAGCTTAGA
*
379473 TACAAATTGATTGAATCAAT
1 TACAAATTAATTGAATCAAT
379493 TACAAATTAATTGAATCAAT
1 TACAAATTAATTGAATCAAT
379513 TA
1 TA
379515 AGTTTACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (20 bp):
TACAAATTAATTGAATCAAT
Found at i:383517 original size:68 final size:67
Alignment explanation
Indices: 383330--383523 Score: 205
Period size: 69 Copynumber: 2.8 Consensus size: 67
383320 ATTTTTTTTT
* *
383330 ATAGAAATGACATGAAATCACAGTTTCATAC-AATCATTTCTCATAGTAAATGATATTTATTAAA
1 ATAG-AATGACATGAAATCACAGTTTCATACTAATC-TTT-TCATAGTAAATAATATCTATTAAA
383394 AAGGA
63 AAGGA
* * * * * *
383399 ATAGGGATGTCATAAAATCATAGTTTCATA-TAATCCCTTCTCATAATAAATAATATCTATTAAA
1 ATA-GAATGACATGAAATCACAGTTTCATACTAAT--CTTTTCATAGTAAATAATATCTATT-AA
383463 AAAGG-
62 AAAGGA
* *
383468 ATAGAATGACATGAAATCACAATTTCATACTGTATCTTTTCATAGTAAATAATATC
1 ATAGAATGACATGAAATCACAGTTTCATACT-AATCTTTTCATAGTAAATAATATC
383524 ATCTCATTAA
Statistics
Matches: 102, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
68 40 0.39
69 49 0.48
70 12 0.12
71 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (67 bp):
ATAGAATGACATGAAATCACAGTTTCATACTAATCTTTTCATAGTAAATAATATCTATTAAAAAG
GA
Done.