Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014055.1 Kokia drynarioides strain JFW-HI SEQ_129086, 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: 56256
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:16736 original size:43 final size:43
Alignment explanation
Indices: 16666--16796 Score: 158
Period size: 43 Copynumber: 3.1 Consensus size: 43
16656 GAAACATTTG
* * * **
16666 ATGTATAAATGGAAAACCCATGTCTCGGGTTGAGCATGAGAAT
1 ATGTATAAATGGAAGACTCATGACTCGGAATGAGCATGAGAAT
* *
16709 TTGTATAAATGGAAGACTCGTGACTCGGAATGAGCATGAGAAT
1 ATGTATAAATGGAAGACTCATGACTCGGAATGAGCATGAGAAT
* * *
16752 ATGT-TAAA-GGAAGACTCATGTCTAGGAATGAGCATGAGATT
1 ATGTATAAATGGAAGACTCATGACTCGGAATGAGCATGAGAAT
16793 ATGT
1 ATGT
16797 TTGAAAAGGA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
41 33 0.43
42 4 0.05
43 39 0.51
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (43 bp):
ATGTATAAATGGAAGACTCATGACTCGGAATGAGCATGAGAAT
Found at i:16780 original size:41 final size:42
Alignment explanation
Indices: 16696--16852 Score: 149
Period size: 41 Copynumber: 3.7 Consensus size: 42
16686 TGTCTCGGGT
* * *
16696 TGAGCATGAGAATTTGTATAAATGGAAGACTCGTGACTCGGAA
1 TGAGCATGAGAATATGT-TAAATGGAAGACTCATGACTAGGAA
*
16739 TGAGCATGAGAATATGTTAAA-GGAAGACTCATGTCTAGGAA
1 TGAGCATGAGAATATGTTAAATGGAAGACTCATGACTAGGAA
* * * * *
16780 TGAGCATGAGATTATGTTTGAAAAGGAAGAGTTATGACTAGGTA
1 TGAGCATGAGAATATG-TT-AAATGGAAGACTCATGACTAGGAA
* * *
16824 -GAGCATAAGAATGT-TTAAAAAGGAAGACT
1 TGAGCATGAGAATATGTT-AAATGGAAGACT
16853 TACGATTTTG
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
41 45 0.46
42 6 0.06
43 30 0.31
44 16 0.16
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.25
Consensus pattern (42 bp):
TGAGCATGAGAATATGTTAAATGGAAGACTCATGACTAGGAA
Found at i:17371 original size:21 final size:21
Alignment explanation
Indices: 17346--17421 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
17336 GAATTCTACA
* *
17346 TACTTGTTTCGGTAGAACCCT
1 TACTTGTATCGATAGAACCCT
17367 TACTTGTATCGATAG-A---T
1 TACTTGTATCGATAGAACCCT
* *
17384 GTACTTGTTTCGGTAGAACCCT
1 -TACTTGTATCGATAGAACCCT
17406 TACTTGTATCGATAGA
1 TACTTGTATCGATAGA
17422 TGTACAGGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
17 1 0.02
18 13 0.30
19 1 0.02
20 1 0.02
21 27 0.61
22 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (21 bp):
TACTTGTATCGATAGAACCCT
Found at i:17390 original size:18 final size:18
Alignment explanation
Indices: 17367--17426 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
17357 GTAGAACCCT
17367 TACTTGTATCGATAGATG
1 TACTTGTATCGATAGATG
* *
17385 TACTTGTTTCGGTAGAACCCT-
1 TACTTGTATCGATAG-A---TG
17406 TACTTGTATCGATAGATG
1 TACTTGTATCGATAGATG
17424 TAC
1 TAC
17427 AGGGTAGGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 1 0.03
18 16 0.48
19 1 0.03
20 1 0.03
21 13 0.39
22 1 0.03
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (18 bp):
TACTTGTATCGATAGATG
Found at i:17400 original size:39 final size:39
Alignment explanation
Indices: 17346--17426 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
17336 GAATTCTACA
17346 TACTTGTTTCGGTAGAACCCTTACTTGTATCGATAGATG
1 TACTTGTTTCGGTAGAACCCTTACTTGTATCGATAGATG
17385 TACTTGTTTCGGTAGAACCCTTACTTGTATCGATAGATG
1 TACTTGTTTCGGTAGAACCCTTACTTGTATCGATAGATG
17424 TAC
1 TAC
17427 AGGGTAGGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (39 bp):
TACTTGTTTCGGTAGAACCCTTACTTGTATCGATAGATG
Found at i:20962 original size:26 final size:26
Alignment explanation
Indices: 20933--20984 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
20923 TCAAATATAA
*
20933 ATCTGA-ATATTAATTTAACAATAATT
1 ATCTGATATATTAATTT-ACAAAAATT
*
20959 ATCTGATATTTTAATTTACAAAAATT
1 ATCTGATATATTAATTTACAAAAATT
20985 GAATAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (26 bp):
ATCTGATATATTAATTTACAAAAATT
Found at i:25230 original size:33 final size:33
Alignment explanation
Indices: 25185--25251 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
25175 ACTTAAGCTC
25185 TTTTATTATTAGGAATATTTATTGGATTGAAAA
1 TTTTATTATTAGGAATATTTATTGGATTGAAAA
* * *
25218 TTTTATTGTTAGGTATATTTATTGGGTTGAAAA
1 TTTTATTATTAGGAATATTTATTGGATTGAAAA
25251 T
1 T
25252 GGTGTGCCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (33 bp):
TTTTATTATTAGGAATATTTATTGGATTGAAAA
Found at i:25748 original size:21 final size:19
Alignment explanation
Indices: 25702--25760 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 19
25692 TAGATAATTC
*
25702 ATTATTTTCTTTAAATTAAG
1 ATTATTTT-TTTAATTTAAG
25722 AGTTATTTTTTTAATTTAATG
1 A-TTATTTTTTTAATTTAA-G
* *
25743 TATTATTTGTTTATTTTA
1 -ATTATTTTTTTAATTTA
25761 TTATTTTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 10 0.30
21 22 0.67
22 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.63
Consensus pattern (19 bp):
ATTATTTTTTTAATTTAAG
Found at i:27420 original size:32 final size:32
Alignment explanation
Indices: 27379--27474 Score: 174
Period size: 32 Copynumber: 3.0 Consensus size: 32
27369 ATTCAAATTG
27379 AGTTAAGATGATAAAATAGGACTCGTCAACTC
1 AGTTAAGATGATAAAATAGGACTCGTCAACTC
*
27411 AGTTAAGATGATAAAATAGGACTTGTCAACTC
1 AGTTAAGATGATAAAATAGGACTCGTCAACTC
*
27443 CGTTAAGATGATAAAATAGGACTCGTCAACTC
1 AGTTAAGATGATAAAATAGGACTCGTCAACTC
27475 GATTAACTCG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (32 bp):
AGTTAAGATGATAAAATAGGACTCGTCAACTC
Found at i:27899 original size:15 final size:17
Alignment explanation
Indices: 27867--27899 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27857 ATGAAAAAGA
27867 TTATAATAAAAATATAT
1 TTATAATAAAAATATAT
27884 TTATAA-AAAAAT-TAT
1 TTATAATAAAAATATAT
27899 T
1 T
27900 CAACTACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTATAATAAAAATATAT
Found at i:30532 original size:28 final size:28
Alignment explanation
Indices: 30492--30549 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
30482 GATCAAACTT
* *
30492 TTGATTTTAAATTTATATTAAGTTTAAA
1 TTGATCTTAAATTTATATTAAATTTAAA
*
30520 TTGATCTTAAATTTATTTTAAATTTAAA
1 TTGATCTTAAATTTATATTAAATTTAAA
30548 TT
1 TT
30550 TAATTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (28 bp):
TTGATCTTAAATTTATATTAAATTTAAA
Found at i:30546 original size:17 final size:17
Alignment explanation
Indices: 30526--30559 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30516 TAAATTGATC
*
30526 TTAAATTTATTTTAAAT
1 TTAAATTTAATTTAAAT
30543 TTAAATTTAATTTAAAT
1 TTAAATTTAATTTAAAT
30560 CTGAAATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATTTAATTTAAAT
Found at i:30557 original size:28 final size:27
Alignment explanation
Indices: 30497--30559 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
30487 AACTTTTGAT
* *
30497 TTTAAATTTATATTAAGTTTAAATTGA
1 TTTAAATTTATATTAAATTTAAATTAA
*
30524 TCTTAAATTTATTTTAAATTTAAATTTAA
1 T-TTAAATTTATATTAAATTTAAA-TTAA
30553 TTTAAAT
1 TTTAAAT
30560 CTGAAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 26 0.84
29 4 0.13
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (27 bp):
TTTAAATTTATATTAAATTTAAATTAA
Found at i:32393 original size:30 final size:28
Alignment explanation
Indices: 32375--32547 Score: 140
Period size: 29 Copynumber: 6.0 Consensus size: 28
32365 CATATTTTAA
32375 ACCCCAAACTTCTCAAAAATTACATTTT
1 ACCCCAAACTTCTCAAAAATTACATTTT
32403 GACCCTCAAACTT-TACAAAAATTACATTTT
1 -ACCC-CAAACTTCT-CAAAAATTACATTTT
* * *
32433 CCCCCGAACTT-TCTAAAAATTATATTTTT
1 ACCCCAAACTTCTC-AAAAATTACA-TTTT
*
32462 ACCCCAAACTTC-CAAAAAATCACATTTTT
1 ACCCCAAACTTCTC-AAAAATTACA-TTTT
* **
32491 TCCATTAAACTTC-CAAAAATTAGCATTTT
1 ACC-CCAAACTTCTCAAAAATTA-CATTTT
* *
32520 ACCCCCAGACTTC-CAAAAATCACATTTT
1 A-CCCCAAACTTCTCAAAAATTACATTTT
32548 TGCCCTCGAA
Statistics
Matches: 119, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.01
28 22 0.18
29 62 0.52
30 34 0.29
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (28 bp):
ACCCCAAACTTCTCAAAAATTACATTTT
Found at i:32466 original size:29 final size:29
Alignment explanation
Indices: 32350--32582 Score: 133
Period size: 29 Copynumber: 8.0 Consensus size: 29
32340 GAAGGTCCCT
* * * *
32350 AAACTATCTAAAAATCATATTTTAAACCCC
1 AAACTTTCTAAAAATTACATTTT-TACCCC
*
32380 AAAC-TTCTCAAAAATTACATTTTGACCCTC
1 AAACTTTCT-AAAAATTACATTTTTACCC-C
*
32410 AAACTTTAC-AAAAATTACA-TTTTCCCCC
1 AAACTTT-CTAAAAATTACATTTTTACCCC
* *
32438 GAACTTTCTAAAAATTATATTTTTACCCC
1 AAACTTTCTAAAAATTACATTTTTACCCC
* * * * **
32467 AAACTTCCAAAAAATCACATTTTTTCCATT
1 AAACTTTCTAAAAATTACATTTTTACC-CC
*
32497 AAAC-TTCCAAAAATTAGCA-TTTTACCCCC
1 AAACTTTCTAAAAATTA-CATTTTTA-CCCC
* * * *
32526 AGAC-TTCCAAAAATCACATTTTTGCCCTC
1 AAACTTTCTAAAAATTACATTTTTACCC-C
*
32555 GAAC-TTCT-AAAA-TATCATTTTTGACCCC
1 AAACTTTCTAAAAATTA-CATTTTT-ACCCC
32583 GAGTTTTCCA
Statistics
Matches: 159, Mismatches: 31, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
27 2 0.01
28 33 0.21
29 82 0.52
30 39 0.25
31 2 0.01
32 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTTCTAAAAATTACATTTTTACCCC
Found at i:32560 original size:58 final size:56
Alignment explanation
Indices: 32381--32566 Score: 178
Period size: 58 Copynumber: 3.2 Consensus size: 56
32371 TTAAACCCCA
* * * *
32381 AACTTCTCAAAAATTACATTTTGACCCTCAAACTTTACAAAAATTACA-TTTTCCCCCG
1 AACTTC-CAAAAATTACATTTT-ACCCCCAAAC-TTCCAAAAATCACATTTTTCCCTCG
* * * **
32439 AACTTTCTAAAAATTATATTTTTA-CCCCAAACTTCCAAAAAATCACATTTTTTCCATTA
1 AAC-TTCCAAAAATTACA-TTTTACCCCCAAACTTCC-AAAAATCACA-TTTTTCCCTCG
*
32498 AACTTCCAAAAATTAGCATTTTACCCCCAGACTTCCAAAAATCACATTTTTGCCCTCG
1 AACTTCCAAAAATTA-CATTTTACCCCCAAACTTCCAAAAATCACATTTTT-CCCTCG
*
32556 AACTTCTAAAA
1 AACTTCCAAAA
32567 TATCATTTTT
Statistics
Matches: 104, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
56 3 0.03
57 21 0.20
58 52 0.50
59 28 0.27
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (56 bp):
AACTTCCAAAAATTACATTTTACCCCCAAACTTCCAAAAATCACATTTTTCCCTCG
Found at i:34799 original size:89 final size:89
Alignment explanation
Indices: 34668--34942 Score: 309
Period size: 90 Copynumber: 3.1 Consensus size: 89
34658 CAAAAATTGA
* * * * * * * * **
34668 AGGTTAATATGTCGTCAGATGGTTGTGAATACATAACATATTTGCAAATGAGAG-TGCCAGAATG
1 AGGTTAATACGTTGACAGATGGTTGTGAATGCACAACGTATTTGCAAATAAGAGCTGCCAAAAAA
34732 TAGGTGGATGAACCACTAGTGTTGC
66 T-GGTGGATGAACCACTAGTGTTGC
* * * *
34757 AGGTTAATACGTTGACAAATGGTTGTGAATGCACAACGTATTTGCATATAAGAGTTGTCAAAAAA
1 AGGTTAATACGTTGACAGATGGTTGTGAATGCACAACGTATTTGCAAATAAGAGCTGCCAAAAAA
34822 TGGGTGGATGAACCACTAGTGTTGC
66 T-GGTGGATGAACCACTAGTGTTGC
* ** * * * * *
34847 AAGTTAATACACTGCCAGATGGTTATGAATGCACAACGTATTTGCAGATAAAAGCTACCAAAAAA
1 AGGTTAATACGTTGACAGATGGTTGTGAATGCACAACGTATTTGCAAATAAGAGCTGCCAAAAAA
*
34912 TGGATGGATGAACCACGAGTGTTGC
66 TGG-TGGATGAACCACTAGTGTTGC
34937 AGGTTA
1 AGGTTA
34943 TTAAACTGCC
Statistics
Matches: 157, Mismatches: 27, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
89 47 0.30
90 110 0.70
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.27
Consensus pattern (89 bp):
AGGTTAATACGTTGACAGATGGTTGTGAATGCACAACGTATTTGCAAATAAGAGCTGCCAAAAAA
TGGTGGATGAACCACTAGTGTTGC
Found at i:37802 original size:6 final size:6
Alignment explanation
Indices: 37791--37816 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
37781 TACACTGGCT
37791 TGGACC TGGACC TGGACC TGGACC TG
1 TGGACC TGGACC TGGACC TGGACC TG
37817 TACCAGTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.19
Consensus pattern (6 bp):
TGGACC
Found at i:38398 original size:2 final size:2
Alignment explanation
Indices: 38391--38416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38381 TTTCCCACCC
38391 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
38417 TCATTTTCAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:40096 original size:14 final size:14
Alignment explanation
Indices: 40077--40103 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40067 CAATAGCCCA
40077 AACCTAAACCCAAT
1 AACCTAAACCCAAT
40091 AACCTAAACCCAA
1 AACCTAAACCCAA
40104 AGTGAACCAC
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:0.52, C:0.37, G:0.00, T:0.11
Consensus pattern (14 bp):
AACCTAAACCCAAT
Found at i:40099 original size:20 final size:20
Alignment explanation
Indices: 40061--40100 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
40051 CTTTTAAAAT
*
40061 TAAAACCAATAGCCCAAACC
1 TAAAACCAATAACCCAAACC
* *
40081 TAAACCCAATAACCTAAACC
1 TAAAACCAATAACCCAAACC
40101 CAAAGTGAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.35, G:0.03, T:0.12
Consensus pattern (20 bp):
TAAAACCAATAACCCAAACC
Found at i:41273 original size:3 final size:3
Alignment explanation
Indices: 41223--41262 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
41213 ACAAATTTAC
41223 ATT ATT -TT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41263 TTGGATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:46766 original size:20 final size:20
Alignment explanation
Indices: 46741--46786 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
46731 TATTTTAAAT
46741 TAAACCCAATAGCCCAAACC
1 TAAACCCAATAGCCCAAACC
*
46761 TAAACCCAATAGTCCAAACC
1 TAAACCCAATAGCCCAAACC
*
46781 CAAACC
1 TAAACC
46787 AAGTTAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.39, G:0.04, T:0.11
Consensus pattern (20 bp):
TAAACCCAATAGCCCAAACC
Found at i:46812 original size:11 final size:11
Alignment explanation
Indices: 46794--46823 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
46784 ACCAAGTTAA
46794 ACCGTTGACCG
1 ACCGTTGACCG
*
46805 ATCGTTGACCG
1 ACCGTTGACCG
46816 ACCGTTGA
1 ACCGTTGA
46824 TCATTGACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (11 bp):
ACCGTTGACCG
Found at i:46849 original size:19 final size:20
Alignment explanation
Indices: 46820--46857 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
46810 TGACCGACCG
*
46820 TTGATCATTGACTGTTGACT
1 TTGATCATTGACCGTTGACT
46840 TTGA-CATTGACCGTTGAC
1 TTGATCATTGACCGTTGAC
46858 CGTTCATCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGATCATTGACCGTTGACT
Found at i:46854 original size:33 final size:34
Alignment explanation
Indices: 46815--46891 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
46805 ATCGTTGACC
* *
46815 GACCGTTGATCATTGA-CTGTTGACTTTGA-CATT
1 GACCGTTGACCATTCATC-GTTGACTTTGACCATT
* *
46848 GACCGTTGACCGTTCATCGTTGACTTTGACCGTT
1 GACCGTTGACCATTCATCGTTGACTTTGACCATT
46882 GACCGTTGAC
1 GACCGTTGAC
46892 TTTTTCCAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 24 0.63
34 14 0.37
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.35
Consensus pattern (34 bp):
GACCGTTGACCATTCATCGTTGACTTTGACCATT
Found at i:46878 original size:20 final size:20
Alignment explanation
Indices: 46853--46894 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
46843 ACATTGACCG
*
46853 TTGACCGTTCATCGTTGACT
1 TTGACCGTTCACCGTTGACT
*
46873 TTGACCGTTGACCGTTGACT
1 TTGACCGTTCACCGTTGACT
46893 TT
1 TT
46895 TTCCAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGACCGTTCACCGTTGACT
Found at i:47987 original size:3 final size:3
Alignment explanation
Indices: 47940--47976 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
47930 ACAAATTTAC
47940 ATT ATT -TT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
47977 TTGGATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:51974 original size:4 final size:4
Alignment explanation
Indices: 51965--52030 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
51955 AAATAAACGG
* * *
51965 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* *
52015 G-AA GAAG GAAA TAAA G
1 GAAA GAAA GAAA GAAA G
52031 TTAATGTGTG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 40 0.78
5 8 0.16
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:51991 original size:21 final size:21
Alignment explanation
Indices: 51966--52017 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
51956 AATAAACGGG
51966 AAAGAAAGAAAGAAA-AGAAAG
1 AAAGAAAGAAAGAAAGAG-AAG
* * *
51987 AAAGAAAGGAAGAAGGAGAGG
1 AAAGAAAGAAAGAAAGAGAAG
52008 AAAGAAAGAA
1 AAAGAAAGAA
52018 GAAGGAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAGAAAGAGAAG
Found at i:51994 original size:25 final size:25
Alignment explanation
Indices: 51965--52025 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
51955 AAATAAACGG
51965 GAAAGAAAGAAAGAAAAGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
* * * *
51990 GAAAGGAAGAAGGAGAGGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
*
52015 G-AAGAAGGAAA
1 GAAAGAAAGAAA
52026 TAAAGTTAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (25 bp):
GAAAGAAAGAAAGAAAAGAAAGAAA
Found at i:52018 original size:17 final size:15
Alignment explanation
Indices: 51969--52030 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 15
51959 AAACGGGAAA
51969 GAAAGAAAGAA-AA-
1 GAAAGAAAGAAGAAG
51982 GAAAGAAAG-A-AAG
1 GAAAGAAAGAAGAAG
*
51995 G-AAG-AAGGAG-AG
1 GAAAGAAAGAAGAAG
52007 GAAAGAAAGAAGAAG
1 GAAAGAAAGAAGAAG
*
52022 GAAATAAAG
1 GAAAGAAAG
52031 TTAATGTGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
11 3 0.07
12 10 0.24
13 13 0.32
14 5 0.12
15 10 0.24
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (15 bp):
GAAAGAAAGAAGAAG
Found at i:52100 original size:14 final size:14
Alignment explanation
Indices: 52083--52109 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52073 TTAAAATCGT
52083 ATTTTATTTATTTA
1 ATTTTATTTATTTA
52097 ATTTTATTTATTT
1 ATTTTATTTATTT
52110 TTTAACAGAT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTATTTATTTA
Done.