Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013969.1 Kokia drynarioides strain JFW-HI SEQ_129000, 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: 35729
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:846 original size:31 final size:30
Alignment explanation
Indices: 755--852 Score: 151
Period size: 31 Copynumber: 3.2 Consensus size: 30
745 AAGTGATTGT
*
755 AAGAATGGGACAAAAAGTCTTACAATGTGAA
1 AAGAATGGG-CAAAAAGTCTTACAATGTGCA
*
786 AAGAATGGGGCAAAAAGTCTTACAATGTGCT
1 AAGAAT-GGGCAAAAAGTCTTACAATGTGCA
817 AAGAATGAGGCAAAAAGTCTTACAATGTGCA
1 AAGAATG-GGCAAAAAGTCTTACAATGTGCA
848 AAGAA
1 AAGAA
853 AAGTCTTGTA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
30 1 0.02
31 58 0.94
32 3 0.05
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.19
Consensus pattern (30 bp):
AAGAATGGGCAAAAAGTCTTACAATGTGCA
Found at i:2394 original size:29 final size:30
Alignment explanation
Indices: 2270--2531 Score: 266
Period size: 30 Copynumber: 8.7 Consensus size: 30
2260 TAAAATTTGA
* * * *
2270 GGTCGAAAATGTGATTTTGGAGAAGTTTAGG
1 GGTC-AAAATGTAATTTTAGAAAAGTTTAAG
*
2301 GGTCAAAATGTAATTTTAGAAAAGTTTTAG
1 GGTCAAAATGTAATTTTAGAAAAGTTTAAG
*
2331 GGTAAAAAAT-TCAATTTTAGAAAAGTTTTAA-
1 GGT-CAAAATGT-AATTTTAGAAAAG-TTTAAG
*
2362 GGTTAAAATGTAATTTT-GAAAAGTTTAAG
1 GGTCAAAATGTAATTTTAGAAAAGTTTAAG
*
2391 GGTTAAAATGTAATTTT-GTAAAAGTTTAAG
1 GGTCAAAATGTAATTTTAG-AAAAGTTTAAG
* *
2421 GGTCAAAGTGTAATTTTGGAAAAGTTTAAG
1 GGTCAAAATGTAATTTTAGAAAAGTTTAAG
** *
2451 GGTCAAAACATAATTTTAGAAAAATTT-AG
1 GGTCAAAATGTAATTTTAGAAAAGTTTAAG
* * * *
2480 AGGTCAAAACGTAA-TTTAAAAAATTTTAGG
1 -GGTCAAAATGTAATTTTAGAAAAGTTTAAG
2510 GGTCAAAATGTAATTTTTAGAA
1 GGTCAAAATGTAA-TTTTAGAA
2532 GTTTTGGGAT
Statistics
Matches: 199, Mismatches: 21, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.03
29 49 0.25
30 108 0.54
31 33 0.17
32 4 0.02
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (30 bp):
GGTCAAAATGTAATTTTAGAAAAGTTTAAG
Found at i:2443 original size:60 final size:59
Alignment explanation
Indices: 2270--2535 Score: 254
Period size: 59 Copynumber: 4.4 Consensus size: 59
2260 TAAAATTTGA
* * * *
2270 GGTCGAAAATGTGATTTTGGAGAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTTAG
1 GGTC-AAAATGTAATTTT-GAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTTAAG
* *
2331 GGTAAAAAAT-TCAATTTTAGAAAAGTTTTAA-GGTTAAAATGTAATTTT-GAAAAGTTTAAG
1 GGT-CAAAATGT-AATTTT-GAAAAG-TTTAAGGGTCAAAATGTAATTTTAGAAAAGTTTAAG
* * *
2391 GGTTAAAATGTAATTTTGTAAAAGTTTAAGGGTCAAAGTGTAATTTTGGAAAAGTTTAAG
1 GGTCAAAATGTAATTTTG-AAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTTAAG
** * * * * *
2451 GGTCAAAACATAATTTTAGAAAAATTT-AGAGGTCAAAACGTAA-TTTAAAAAATTTTAGG
1 GGTCAAAATGTAATTTT-GAAAAGTTTAAG-GGTCAAAATGTAATTTTAGAAAAGTTTAAG
* *
2510 GGTCAAAATGTAATTTTTAGAAGTTT
1 GGTCAAAATGTAATTTTGAAAAGTTT
2536 TGGGATCTCT
Statistics
Matches: 171, Mismatches: 25, Indels: 21
0.79 0.12 0.10
Matches are distributed among these distances:
58 12 0.07
59 60 0.35
60 60 0.35
61 35 0.20
62 4 0.02
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (59 bp):
GGTCAAAATGTAATTTTGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTTAAG
Found at i:5103 original size:209 final size:210
Alignment explanation
Indices: 4712--5112 Score: 615
Period size: 209 Copynumber: 1.9 Consensus size: 210
4702 CGCATTTTTC
* *
4712 TTCATTTGATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACCGCATCACTTGTTTTAATC
1 TTCATTTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATC
* * * *
4777 CGCTTCTCTGTATCTTATCAGGAAGATGGATTTGGTCCACTTCTCTGTGTCTCATCAAGAAGACG
66 CACTTCTCTGTATCTCATCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACG
* * **
4842 ATCACTTTATTGCTTCGACCCGCTTCTTAGTATCTCATCAAAAAACTGGGGTTTGAAGTTTCGCT
131 ACCACTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAAAAAACTGGGGTTCAAAGTTTCGCT
4907 TACATTTAGCTTTGT
196 TACATTTAGCTTTGT
* *
4922 TTCA-TTGATTTGGTATACTTCTCTTTATCTCATCAGGAAGATGACCGCATCATTTGTTTTAATC
1 TTCATTTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATC
*
4986 CATTTCTCTGTATCTCATCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACG
66 CACTTCTCTGTATCTCATCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACG
* * * ** **
5051 ACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGTTGGGGTTCAAAGTTTC
131 ACCACTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAAAAAACTGGGGTTCAAAGTTTC
5113 AACCTTCTCT
Statistics
Matches: 171, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
209 167 0.98
210 4 0.02
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.39
Consensus pattern (210 bp):
TTCATTTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATC
CACTTCTCTGTATCTCATCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACG
ACCACTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAAAAAACTGGGGTTCAAAGTTTCGCT
TACATTTAGCTTTGT
Found at i:11777 original size:23 final size:23
Alignment explanation
Indices: 11723--11779 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
11713 CGTCTATCCT
* *
11723 TGCTGACTAGACCTTCTAGAAGT
1 TGCTGACTGGACCTTCTAGAAGC
*
11746 TGTTGACTGGACCTTCTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
11769 TGCTGACTGGA
1 TGCTGACTGGA
11780 TGCCACGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
TGCTGACTGGACCTTCTAGAAGC
Found at i:16947 original size:43 final size:43
Alignment explanation
Indices: 16900--16987 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
16890 AGTTCGGCCT
*
16900 TCTCAACTTGTTTTTCTAGCAGTTCTCCTTTTATGGCGTTCTC
1 TCTCAACTTGTTTTTCTAGCAGTTCTCCTTTCATGGCGTTCTC
*
16943 TCTCAACTTGTTTTTCTAGCAGTTCTCCTTTCATGGTGTTCTC
1 TCTCAACTTGTTTTTCTAGCAGTTCTCCTTTCATGGCGTTCTC
16986 TC
1 TC
16988 GAGCTTGACC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.11, C:0.26, G:0.14, T:0.49
Consensus pattern (43 bp):
TCTCAACTTGTTTTTCTAGCAGTTCTCCTTTCATGGCGTTCTC
Found at i:19424 original size:17 final size:18
Alignment explanation
Indices: 19404--19441 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
19394 AAGTTTACAC
19404 TTATTTTAAAATT-AAAT
1 TTATTTTAAAATTAAAAT
*
19421 TTATTTTAAATTTAAAAT
1 TTATTTTAAAATTAAAAT
19439 TTA
1 TTA
19442 AAGTATGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTTTAAAATTAAAAT
Found at i:19957 original size:34 final size:34
Alignment explanation
Indices: 19914--19985 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
19904 GCAAGTTAGA
19914 TTCACATTTCTCAGACCTTGAACCATCAGGTACT
1 TTCACATTTCTCAGACCTTGAACCATCAGGTACT
19948 TTCACATTTCTCAGACCTTGAACCATCAGGTACT
1 TTCACATTTCTCAGACCTTGAACCATCAGGTACT
19982 TTCA
1 TTCA
19986 ATGCATGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.33
Consensus pattern (34 bp):
TTCACATTTCTCAGACCTTGAACCATCAGGTACT
Found at i:20173 original size:22 final size:20
Alignment explanation
Indices: 20137--20179 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
20127 TTAATGGCAT
20137 TAATGATAAATGAATAATAA
1 TAATGATAAATGAATAATAA
20157 TAATGATATGAATGAATAATAA
1 TAATGATA--AATGAATAATAA
20179 T
1 T
20180 GAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (20 bp):
TAATGATAAATGAATAATAA
Found at i:20176 original size:19 final size:18
Alignment explanation
Indices: 20146--20181 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
20136 TTAATGATAA
20146 ATGAATAATAATAATGAT
1 ATGAATAATAATAATGAT
20164 ATGAATGAATAATAATGA
1 ATGAAT-AATAATAATGA
20182 AAAAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (18 bp):
ATGAATAATAATAATGAT
Found at i:21454 original size:59 final size:57
Alignment explanation
Indices: 21358--21821 Score: 338
Period size: 59 Copynumber: 7.9 Consensus size: 57
21348 CCCTAAACTA
* * * * *
21358 TCCAAAAATCATATTTTGATCCCT-GAATTTTCTAAAATTCCA-TTTTGACCATATTTT
1 TCCAAAAATTACATTTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTGACC-TATTTT
* * * * *
21415 TCCCCAAATATTACATTTTTGCCCTCGAACTTTCCAAAATTTCATTTTTTACTTCGATTTT
1 T--CCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGAC--CTATTTT
* *
21476 TCCAAAAAATACATTTTTACCCTCGAACATTCCAAAATTCCATTTTTGACCTCGATTTT
1 TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCT--ATTTT
* * * *
21535 TTCAAAAATTACAATTTTACCCCCGAACTTTCCAAAATTCC-TTTTTAACCCTTATTTT
1 TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGA-CC-TATTTT
*** *
21593 TTTGAAAATTACCA-TTTTA-CCTCTAAAC-TTCCTAAAATTCCATTTTTGACCTCAATTTT
1 TCCAAAAATTA-CATTTTTACCCTC-GAACTTTCC-AAAATTCCATTTTTGACCT--ATTTT
* * *
21652 TTCAAAAATTACCA-TTTTACACC-CGAACTTTCGAAAATTCCATTTTCGACCTCGATTTT
1 TCCAAAAATTA-CATTTTTAC-CCTCGAACTTTCCAAAATTCCATTTTTGACCT--ATTTT
* * * * * * *
21711 TCCAAAAATGACAATTTTACCCTCGAAC-CTCAAAAAATTCTATTTTTAACCCTGATTCT
1 TCCAAAAATTACATTTTTACCCTCGAACTTTC-CAAAATTCCATTTTTGA-CCT-ATTTT
* * *
21770 TCCAAAAATTACCA-TATTACCCTCGAA-TGTCTAAAAATTCCATTTTTGACCT
1 TCCAAAAATTA-CATTTTTACCCTCGAACTTTC-CAAAATTCCATTTTTGACCT
21822 CGAACTTTAC
Statistics
Matches: 334, Mismatches: 48, Indels: 49
0.77 0.11 0.11
Matches are distributed among these distances:
57 10 0.03
58 51 0.15
59 248 0.74
60 16 0.05
61 8 0.02
62 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (57 bp):
TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTATTTT
Found at i:21463 original size:29 final size:29
Alignment explanation
Indices: 21418--21874 Score: 146
Period size: 29 Copynumber: 15.5 Consensus size: 29
21408 ATATTTTTCC
*
21418 CCAAATATTACATTTTTGCCCTCGAACTTT
1 CCAAA-ATTACATTTTTACCCTCGAACTTT
* * **
21448 CCAAAATTTCATTTTTTA-CTTCGATTTTT
1 CCAAAATTACA-TTTTTACCCTCGAACTTT
* *
21477 CCAAAAAATACATTTTTACCCTCGAACATT
1 CC-AAAATTACATTTTTACCCTCGAACTTT
* **
21507 CCAAAATTCCATTTTTGA-CCTCGATTTTTT
1 CCAAAATTACATTTTT-ACCCTCGA-ACTTT
* * *
21537 CAAAAATTACAATTTTACCCCCGAACTTT
1 CCAAAATTACATTTTTACCCTCGAACTTT
* * **
21566 CCAAAATT-CCTTTTTAACCCT-TATTTTTT
1 CCAAAATTACATTTTT-ACCCTCGA-ACTTT
** *
21595 TGAAAATTACCA-TTTTA-CCTCTAAAC-TT
1 CCAAAATTA-CATTTTTACCCTC-GAACTTT
* *
21623 CCTAAAATTCCATTTTTGA-CCTC-AATTTTTT
1 CC-AAAATTACATTTTT-ACCCTCGAA--CTTT
*
21654 CAAAAATTACCA-TTTTACACC-CGAACTTT
1 CCAAAATTA-CATTTTTAC-CCTCGAACTTT
* * * **
21683 CGAAAATTCCATTTTCGA-CCTCGATTTTT
1 CCAAAATTACATTTT-TACCCTCGAACTTT
* * *
21712 CCAAAAATGACAATTTTACCCTCGAAC-CT
1 CC-AAAATTACATTTTTACCCTCGAACTTT
* *
21741 CAAAAAATT-CTATTTTTAACCCT-G-ATTCTT
1 C-CAAAATTAC-ATTTTT-ACCCTCGAACT-TT
* *
21771 CCAAAAATTACCA-TATTACCCTCGAA-TGT
1 CC-AAAATTA-CATTTTTACCCTCGAACTTT
* *
21800 CTAAAAATTCCATTTTTGA-CCTCGAACTTT
1 C-CAAAATTACATTTTT-ACCCTCGAACTTT
** * *
21830 ACCAAAATTACCA-TTAGACCCTCG-AGTGT
1 -CCAAAATTA-CATTTTTACCCTCGAACTTT
21859 CCAAAATTACCATTTT
1 CCAAAATTA-CATTTT
21875 GCCCCCGGTT
Statistics
Matches: 308, Mismatches: 74, Indels: 91
0.65 0.16 0.19
Matches are distributed among these distances:
28 35 0.11
29 138 0.45
30 119 0.39
31 15 0.05
32 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (29 bp):
CCAAAATTACATTTTTACCCTCGAACTTT
Found at i:21837 original size:59 final size:58
Alignment explanation
Indices: 21391--21874 Score: 337
Period size: 59 Copynumber: 8.2 Consensus size: 58
21381 TGAATTTTCT
* * * *
21391 AAAATTCCA-TTTTGACCAT--ATTTTTCCCCAAATATTA-CATTTTTGCCCTCGAACTTTCC
1 AAAATTCCATTTTTGACC-TCGATTTTT--CCAAAAATTACCA-TTTTACCCTCGAA-TGTCA
* * * * *
21450 AAAATTTCATTTTTTACTTCGATTTTTCCAAAAAATA-CATTTTTACCCTCGAACAT-TCC
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCA-TTTTACCCTCG-A-ATGTCA
* * * * *
21509 AAAATTCCATTTTTGACCTCGATTTTTTCAAAAATTACAATTTTACCCCCGAACTTTCC
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCTCGAA-TGTCA
* * *** * *
21568 AAAATTCC-TTTTTAACC-CTTATTTTTTTGAAAATTACCATTTTA-CCTCTAAACT-TCCT
1 AAAATTCCATTTTTGACCTC-GATTTTTCCAAAAATTACCATTTTACCCTC-GAA-TGT-CA
* * * *
21626 AAAATTCCATTTTTGACCTCAATTTTTTCAAAAATTACCATTTTACACC-CGAACTTTCG
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTAC-CCTCGAA-TGTCA
* * * **
21685 AAAATTCCATTTTCGACCTCGATTTTTCCAAAAATGACAATTTTACCCTCGAACCTCAA
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCTCGAATGTC-A
* * * *
21744 AAAATTCTATTTTTAACC-CTGATTCTTCCAAAAATTACCATATTACCCTCGAATGTCTA
1 AAAATTCCATTTTTGACCTC-GATTTTTCCAAAAATTACCATTTTACCCTCGAATGTC-A
* * ** * *
21803 AAAATTCCATTTTTGACCTCGAACTTTACC-AAAATTACCATTAGACCCTCGAGTGTCC
1 AAAATTCCATTTTTGACCTCG-ATTTTTCCAAAAATTACCATTTTACCCTCGAATGTCA
21861 AAAATTACCATTTT
1 AAAATT-CCATTTT
21875 GCCCCCGGTT
Statistics
Matches: 348, Mismatches: 55, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
57 6 0.02
58 55 0.16
59 260 0.75
60 18 0.05
61 9 0.03
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.39
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCTCGAATGTCA
Found at i:22230 original size:97 final size:97
Alignment explanation
Indices: 22112--22297 Score: 218
Period size: 97 Copynumber: 1.9 Consensus size: 97
22102 AAAACTTTAA
22112 AATCGAAGCAATATTCTTTTAT-TTCGAGTT-TCAAAAATTTGTGCCTGAACTTACTAGGCGC-A
1 AATCGAAGCAATATTCTTTTATCTTCGA-TTCT-AAAAATTTGTGCCTGAACTTACTAGGCGCGA
22174 ATTTTCCCCCAAATCGAAATAATCGAATACCCTTT
64 ATTTT-CCCCAAATCGAAATAATCGAATACCCTTT
* * * * * * *
22209 AATCGAGGCAATGTT-TCTTTATCTTTGATTCTGAAAATTTGTGCCTTAACTTACTAGGTGCGAC
1 AATCGAAGCAATATTCT-TTTATCTTCGATTCTAAAAATTTGTGCCTGAACTTACTAGGCGCGAA
** *
22273 TTTTCTTCAAATCGAGATAATCGAA
65 TTTTCCCCAAATCGAAATAATCGAA
22298 CATCCTTTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
96 1 0.01
97 64 0.85
98 10 0.13
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (97 bp):
AATCGAAGCAATATTCTTTTATCTTCGATTCTAAAAATTTGTGCCTGAACTTACTAGGCGCGAAT
TTTCCCCAAATCGAAATAATCGAATACCCTTT
Found at i:27072 original size:67 final size:65
Alignment explanation
Indices: 26963--27095 Score: 248
Period size: 67 Copynumber: 2.0 Consensus size: 65
26953 TTACCAGCAA
26963 TTGTATGACCAACATGCAATGGCCCCATACTACACGGAGCCAGTACAACCACCTTTTCCAAAATG
1 TTGTATGACCAACATGCAATGGCCCCATACTACACGGAGCCAGTACAACCACC-TTTCCAAAATG
27028 G
65 G
27029 TNTGTATGACCAACATGCAATGGCCCCATACTACACGGAGCCAGTACAACCACCTTTCCAAAATG
1 T-TGTATGACCAACATGCAATGGCCCCATACTACACGGAGCCAGTACAACCACCTTTCCAAAATG
27094 G
65 G
27095 T
1 T
27096 ATGACTCCAA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 14 0.21
67 52 0.79
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (65 bp):
TTGTATGACCAACATGCAATGGCCCCATACTACACGGAGCCAGTACAACCACCTTTCCAAAATGG
Found at i:29012 original size:31 final size:32
Alignment explanation
Indices: 28962--29025 Score: 121
Period size: 31 Copynumber: 2.0 Consensus size: 32
28952 GAATGAGGCT
28962 TAAAGAGGAAGAGAACACTGGAAGAGTTATGA
1 TAAAGAGGAAGAGAACACTGGAAGAGTTATGA
28994 TAAAGAGGAAG-GAACACTGGAAGAGTTATGA
1 TAAAGAGGAAGAGAACACTGGAAGAGTTATGA
29025 T
1 T
29026 GGAGTTGGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.66
32 11 0.34
ACGTcount: A:0.45, C:0.06, G:0.31, T:0.17
Consensus pattern (32 bp):
TAAAGAGGAAGAGAACACTGGAAGAGTTATGA
Found at i:29385 original size:19 final size:18
Alignment explanation
Indices: 29357--29395 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
29347 CTTGAATTTG
*
29357 TATACATACACTCATACT
1 TATACATACAATCATACT
*
29375 TATACCATACAATCATTCT
1 TATA-CATACAATCATACT
29394 TA
1 TA
29396 AATTTACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (18 bp):
TATACATACAATCATACT
Found at i:33471 original size:49 final size:49
Alignment explanation
Indices: 33319--33696 Score: 213
Period size: 49 Copynumber: 7.7 Consensus size: 49
33309 CTATAGGTCT
* * * *
33319 CAGTACCACGAAA-CATGAAGGGAAAGATCTAAGCCGCAAC-GACGGATC
1 CAGTACCACAAAAGCATAAAGGGAAAGATTTAAGCCGCAACTG-CAGATC
* * * * * *
33367 TAGTACCGCAAAGATACA-AAAGGGAAAGGTTTAAGTCGCAAC-G-ACGAAC
1 CAGTACCACAAA-A-GCATAAAGGGAAAGATTTAAGCCGCAACTGCA-GATC
* *
33416 CTAGTACCTCAAAAGCATAAAGGGAAAGATTTAAGCCACAACTGCAGATC
1 C-AGTACCACAAAAGCATAAAGGGAAAGATTTAAGCCGCAACTGCAGATC
* * * * *
33466 CAGTACCGC-AAAGACACAGAAGGGAAAGATTTAAGCCACAACGGCAAATC
1 CAGTACCACAAAAG-CATA-AAGGGAAAGATTTAAGCCGCAACTGCAGATC
* * * * *
33516 CAGTACCA-TAGAGACATAAAGGGAAAGATCTAAGCCGTAACTGCGGATC
1 CAGTACCACAAAAG-CATAAAGGGAAAGATTTAAGCCGCAACTGCAGATC
* * * * * *
33565 CAGTACCAC-AAAGACACAAAGTGAAGGGTTTAAGTCGCAA-TG-ACGAAC
1 CAGTACCACAAAAG-CATAAAGGGAAAGATTTAAGCCGCAACTGCA-GATC
* * * * * * *
33613 CTTGTACCTCAGAAGCATGAAGGGAAAGATCTAAGCCACGA-TGGCAGATC
1 C-AGTACCACAAAAGCATAAAGGGAAAGATTTAAGCCGCAACT-GCAGATC
* *
33663 CAGTACCACAAAGATACA-AAAGGGAAAGGTTTAA
1 CAGTACCACAAA-A-GCATAAAGGGAAAGATTTAA
33697 ATCGCAACGA
Statistics
Matches: 252, Mismatches: 59, Indels: 36
0.73 0.17 0.10
Matches are distributed among these distances:
48 21 0.08
49 124 0.49
50 101 0.40
51 6 0.02
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (49 bp):
CAGTACCACAAAAGCATAAAGGGAAAGATTTAAGCCGCAACTGCAGATC
Found at i:33508 original size:99 final size:97
Alignment explanation
Indices: 33332--33895 Score: 487
Period size: 99 Copynumber: 5.8 Consensus size: 97
33322 TACCACGAAA
* *
33332 CATGAAGGGAAAGATCTAAGCCGCAAC-GACGGATCTAGTACCGCAAAGATACAAAAGGGAAAGG
1 CATGAAGGGAAAGATCTAAGCCGCAACTG-C-GATCCAGTACCGCAAAGACAC-AAAGGGAAAGG
*
33396 TTTAAGTCGCAACGACGAACCTAGTACCTCAAAAG
63 TTTAAGTCGCAACGACGAACCTAGTACCTCAAGAG
* * * *
33431 CATAAAGGGAAAGATTTAAGCCACAACTGCAGATCCAGTACCGCAAAGACACAGAAGGGAAAGAT
1 CATGAAGGGAAAGATCTAAGCCGCAACTGC-GATCCAGTACCGCAAAGACACA-AAGGGAAAGGT
* * * *
33496 TTAAGCCACAACGGCAAATCC-AGTA-C-CATAGAG
64 TTAAGTCGCAACGACGAA-CCTAGTACCTCA-AGAG
* * * * *
33529 ACATAAAGGGAAAGATCTAAGCCGTAACTGCGGATCCAGTACCACAAAGACACAAAGTGAAGGGT
1 -CATGAAGGGAAAGATCTAAGCCGCAACTGC-GATCCAGTACCGCAAAGACACAAAGGGAAAGGT
* *
33594 TTAAGTCGCAATGACGAACCTTGTACCTC-AGAAG
64 TTAAGTCGCAACGACGAACCTAGTACCTCAAG-AG
* * * *
33628 CATGAAGGGAAAGATCTAAGCCACGA-TGGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGG
1 CATGAAGGGAAAGATCTAAGCCGCAACT-GC-GATCCAGTACCGCAAAGACAC-AAAGGGAAAGG
* *
33692 TTTAAATCGCAACGACGAACCTAG------GAGA-
63 TTTAAGTCGCAACGACGAACCTAGTACCTCAAGAG
* * *
33720 CATGAAGGGAAAGGTTTAAGCCGCAACGGCGAATCCAGTACCGCAATGAAGACACAAAGGGAAAG
1 CATGAAGGGAAAGATCTAAGCCGCAACTGCG-ATCCAGTACCGC-A--AAGACACAAAGGGAAAG
* * * * * *
33785 GTTTAAGTCACAATGGCAAACTTAGTACCTC-GGAG
62 GTTTAAGTCGCAACGACGAACCTAGTACCTCAAGAG
* *
33820 ACATGAAGGGAAAGATTTAAGCCGCAA-TGGCGAATCCAGTACCGCGAAA-ACAC-CAGAGGAAA
1 -CATGAAGGGAAAGATCTAAGCCGCAACT-GCG-ATCCAGTACCGC-AAAGACACAAAG-GGAAA
*
33882 GGTTTACGTCGCAA
61 GGTTTAAGTCGCAA
33896 AGGCGAGCCT
Statistics
Matches: 381, Mismatches: 57, Indels: 55
0.77 0.12 0.11
Matches are distributed among these distances:
91 1 0.00
92 35 0.09
93 2 0.01
94 31 0.08
95 6 0.02
97 7 0.02
98 96 0.25
99 157 0.41
100 4 0.01
101 42 0.11
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (97 bp):
CATGAAGGGAAAGATCTAAGCCGCAACTGCGATCCAGTACCGCAAAGACACAAAGGGAAAGGTTT
AAGTCGCAACGACGAACCTAGTACCTCAAGAG
Found at i:33662 original size:197 final size:189
Alignment explanation
Indices: 33331--33872 Score: 601
Period size: 197 Copynumber: 2.8 Consensus size: 189
33321 GTACCACGAA
* *
33331 ACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCTAGTACCGCAAAGATACAAAAGGGAAAGG
1 ACATGAAGGGAAAGATCTAAGCCGCAACG-CGGATCCAGTACCGCAAAGACAC-AAAGGGAAAGG
* * * *
33396 TTTAAGTCGCAACGACGAACCTAGTACCTCAAAAGCATAAAGGGAAAGATTTAAGCCACAACT-G
64 TTTAAGTCGCAATGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCACAA-TGG
* * *
33460 CAGATCCAGTACCGCAAAGACACAGAAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCAT
128 CAGATCCAGTACCGCAAAGACACAAAAGGGAAAGATTTAAACCACAAC-G---A--C-GAACC-T
33525 A-GAG
185 AGGAG
* * * * *
33529 ACATAAAGGGAAAGATCTAAGCCGTAACTGCGGATCCAGTACCACAAAGACACAAAGTGAAGGGT
1 ACATGAAGGGAAAGATCTAAGCCGCAAC-GCGGATCCAGTACCGCAAAGACACAAAGGGAAAGGT
* *
33594 TTAAGTCGCAATGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATCTAAGCCACGATGGCA
65 TTAAGTCGCAATGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCACAATGGCA
* * * * *
33659 GATCCAGTACCACAAAGATACAAAAGGGAAAGGTTTAAATCGCAACGACGAACCTAGGAG
130 GATCCAGTACCGCAAAGACACAAAAGGGAAAGATTTAAACCACAACGACGAACCTAGGAG
* * *
33719 ACATGAAGGGAAAGGTTTAAGCCGCAACGGCGAATCCAGTACCGCAATGAAGACACAAAGGGAAA
1 ACATGAAGGGAAAGATCTAAGCCGCAAC-GCGGATCCAGTACCGC-A--AAGACACAAAGGGAAA
* * * * *
33784 GGTTTAAGTCACAATGGC-AAACTTAGTACCTC-GGAGACATGAAGGGAAAGATTTAAGCCGCAA
62 GGTTTAAGTCGCAATGACGAACCTT-GTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCACAA
33847 TGGC-GAATCCAGTACCGCGAAA-ACAC
125 TGGCAG-ATCCAGTACCGC-AAAGACAC
33873 CAGAGGAAAG
Statistics
Matches: 295, Mismatches: 39, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
189 2 0.01
190 45 0.15
191 2 0.01
192 9 0.03
193 79 0.27
194 3 0.01
196 2 0.01
197 106 0.36
198 46 0.16
199 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (189 bp):
ACATGAAGGGAAAGATCTAAGCCGCAACGCGGATCCAGTACCGCAAAGACACAAAGGGAAAGGTT
TAAGTCGCAATGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCACAATGGCAG
ATCCAGTACCGCAAAGACACAAAAGGGAAAGATTTAAACCACAACGACGAACCTAGGAG
Found at i:33848 original size:49 final size:49
Alignment explanation
Indices: 33710--33862 Score: 155
Period size: 49 Copynumber: 3.1 Consensus size: 49
33700 GCAACGACGA
* * *
33710 ACCTAGGAGACATGAAGGGAAAGGTTTAAGCCGCAACGGCGAATCCAGT
1 ACCTCGGAGACATGAAGGGAAAGGTTTAAGCCGCAATGGCAAATCCAGT
* * ** * * *
33759 ACCGCAATGAAGACACAAAGGGAAAGGTTTAAGTCACAATGGCAAA-CTTAGT
1 ACCTC---GGAGACATGAAGGGAAAGGTTTAAGCCGCAATGGCAAATC-CAGT
* *
33811 ACCTCGGAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGT
1 ACCTCGGAGACATGAAGGGAAAGGTTTAAGCCGCAATGGCAAATCCAGT
33860 ACC
1 ACC
33863 GCGAAAACAC
Statistics
Matches: 80, Mismatches: 19, Indels: 10
0.73 0.17 0.09
Matches are distributed among these distances:
49 40 0.50
50 1 0.01
51 1 0.01
52 38 0.47
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16
Consensus pattern (49 bp):
ACCTCGGAGACATGAAGGGAAAGGTTTAAGCCGCAATGGCAAATCCAGT
Found at i:33881 original size:49 final size:49
Alignment explanation
Indices: 33724--33901 Score: 153
Period size: 49 Copynumber: 3.6 Consensus size: 49
33714 AGGAGACATG
* * *
33724 AAGGGAAAGGTTTAAGCCGCAACGGCGAATCCAGTACCGCAATGAAGACACA
1 AAGGGAAAGGTTTAAGCCGCAATGGCGAATCCAGTACCGC---GAAAACACC
* * * * * * * **
33776 AAGGGAAAGGTTTAAGTCACAATGGC-AAACTTAGTACCTCGGAGACATG
1 AAGGGAAAGGTTTAAGCCGCAATGGCGAATC-CAGTACCGCGAAAACACC
*
33825 AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCGCGAAAACACC
1 AAGGGAAAGGTTTAAGCCGCAATGGCGAATCCAGTACCGCGAAAACACC
* * *
33874 -AGAGGAAAGGTTTACGTCGCAAAGGCGA
1 AAG-GGAAAGGTTTAAGCCGCAATGGCGA
33902 GCCTTATACC
Statistics
Matches: 100, Mismatches: 23, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
48 2 0.02
49 62 0.62
50 3 0.03
51 3 0.03
52 30 0.30
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.15
Consensus pattern (49 bp):
AAGGGAAAGGTTTAAGCCGCAATGGCGAATCCAGTACCGCGAAAACACC
Found at i:33922 original size:291 final size:291
Alignment explanation
Indices: 33332--33946 Score: 730
Period size: 291 Copynumber: 2.1 Consensus size: 291
33322 TACCACGAAA
* * * * * *
33332 CATGAAGGGAAAGATCTAAGCCGCAACGACGGATCTAGTACCGCAAAGATACAAAAGGGAAAGGT
1 CATGAAGGGAAAGATCTAAGCCACAATGGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGGT
* *
33397 TTAAGTCGCAACGACGAACCTAGTACCTCAAAAGCATAAAGGGAAAGATTTAAGCCACAACTGCA
66 TTAAATCGCAACGACGAACCTAG-----CAAAAGCATAAAGGGAAAGATTTAAGCCACAACGGCA
33462 GATCCAGTACCGCAAAGACACAGAAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCATAG
126 GATCCAGTACCGCAAAGACACAGAAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCATAG
* * *
33527 AGACATAAAGGGAAAGATCTAAGCCGTAACTGCGGATCCAGTACCACAAAGACACAAAGTGAAGG
191 AGACATAAAGGGAAAGATCTAAGCCGCAACTGCGAATCCAGTACCACAAAGACACAAAGTGAAAG
* *
33592 GTTTAAGTCGCAATGACGAACCTTGTACCTCAGAAG
256 GTTTAAGTCGCAAAGACGAACCTTATACCTCAGAAG
*
33628 CATGAAGGGAAAGATCTAAGCCACGATGGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGGT
1 CATGAAGGGAAAGATCTAAGCCACAATGGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGGT
* * * * *
33693 TTAAATCGCAACGACGAACCTAG-GAGA-CATGAAGGGAAAGGTTTAAGCCGCAACGGC-GAATC
66 TTAAATCGCAACGACGAACCTAGCAAAAGCATAAAGGGAAAGATTTAAGCCACAACGGCAG-ATC
* * * * *
33755 CAGTACCGCAATGAAGACACA-AAGGGAAAGGTTTAAGTCACAATGGCAAA-CTTAGTACC-TCG
130 CAGTACCGC-A--AAGACACAGAAGGGAAAGATTTAAGCCACAACGGCAAATC-CAGTACCAT-A
* * * *
33817 GAGACATGAAGGGAAAGATTTAAGCCGCAA-TGGCGAATCCAGTACCGCGAAA-ACACCAGAG-G
190 GAGACATAAAGGGAAAGATCTAAGCCGCAACT-GCGAATCCAGTACCAC-AAAGACA-CAAAGTG
* * *
33879 AAAGGTTTACGTCGCAAAGGCGAGCCTTATACCTCAGAAG
252 AAAGGTTTAAGTCGCAAAGACGAACCTTATACCTCAGAAG
*
33919 CATGTAA-GGAAA-ATTTAAGCCACAATGG
1 CATG-AAGGGAAAGATCTAAGCCACAATGG
33947 AAAATTTTAT
Statistics
Matches: 276, Mismatches: 33, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
288 1 0.00
289 38 0.14
290 20 0.07
291 120 0.43
292 17 0.06
296 80 0.29
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (291 bp):
CATGAAGGGAAAGATCTAAGCCACAATGGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGGT
TTAAATCGCAACGACGAACCTAGCAAAAGCATAAAGGGAAAGATTTAAGCCACAACGGCAGATCC
AGTACCGCAAAGACACAGAAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCATAGAGACA
TAAAGGGAAAGATCTAAGCCGCAACTGCGAATCCAGTACCACAAAGACACAAAGTGAAAGGTTTA
AGTCGCAAAGACGAACCTTATACCTCAGAAG
Found at i:34976 original size:22 final size:20
Alignment explanation
Indices: 34940--34982 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
34930 TTAATGGCAT
34940 TAATGATAAATGAATAATAA
1 TAATGATAAATGAATAATAA
34960 TAATGATATGAATGAATAATAA
1 TAATGATA--AATGAATAATAA
34982 T
1 T
34983 GAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (20 bp):
TAATGATAAATGAATAATAA
Found at i:34979 original size:19 final size:18
Alignment explanation
Indices: 34949--34984 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
34939 TTAATGATAA
34949 ATGAATAATAATAATGAT
1 ATGAATAATAATAATGAT
34967 ATGAATGAATAATAATGA
1 ATGAAT-AATAATAATGA
34985 AAAAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (18 bp):
ATGAATAATAATAATGAT
Done.