Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014105.1 Kokia drynarioides strain JFW-HI SEQ_129136, 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: 29096
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Found at i:3804 original size:312 final size:321
Alignment explanation
Indices: 3248--3820 Score: 729
Period size: 312 Copynumber: 1.8 Consensus size: 321
3238 TTCCAACTAG
** * * * * *
3248 TTTTGCCACATTAGCACTAAAAATAGCAGGCATCAAATTTTTTTTTATGTTTGATGCCTCCTATT
1 TTTTGCCACACCAGCAATAAAAATAGCAGGCAACAAATATATTTTTATGTTTGATGCCACCTATT
* * **
3313 AATGTGGAAACAAAACTTACAAAACATGCCTTTATATAGACCCAAAGTCTTATTTTCCTTGTTTT
66 AATGTAGAAAC-AAACTTACAAAACATGCCTTTATATAGACCCAAAGTCTTATTTCCCTAATTTT
* * * * * *
3378 CATAAAAATATAGGATATGAGATATGCGTATATATAGACTCATGAATATGTTTGCAGCTTGATCT
130 CATAAAAATATAGGATATCAGATATGCGTATACATAAACTCAAGAATAAGTTTACAGCTTGATCT
* *
3443 AAGACAATGTGTGATTGCATTATCTTTTAACTAACAATGTAAGATTAAAACACTACACTATATTT
195 AAGACAATGTGAGATTGCATTATCTTTTAACTAACAATATAAGATTAAAACACTACACTATATTT
3508 TTTATCAACACTTCCAATTGGAAGAATTTTCAACAGAAAAAAAAAATACTTCCATCAAACGA
260 TTTATCAACACTTCCAATTGGAAGAATTTTCAACAGAAAAAAAAAATACTTCCATCAAACGA
* *
3570 TTTTGCCACACCAGCAATAAATATAGCA-GCAACAAATATATTTTT-T-TTTGGTGCCACCTATT
1 TTTTGCCACACCAGCAATAAAAATAGCAGGCAACAAATATATTTTTATGTTTGATGCCACCTATT
* *
3632 AATGTAGAAAC-AA-TTACAAAACATG-C-TT-TA-A-ACCCAAAGTTTTGTTTCCCTAATTTTC
66 AATGTAGAAACAAACTTACAAAACATGCCTTTATATAGACCCAAAGTCTTATTTCCCTAATTTTC
* * * * *
3690 TTAAGCAATGT-GAGATATCAGATATGTGTATACATAAACTCAAGAATAAGTTTACAGCTTGTTC
131 ATAA-AAATATAG-GATATCAGATATGCGTATACATAAACTCAAGAATAAGTTTACAGCTTGAT-
* * * * *
3754 CT-AGATAATGTGAGATTGCTTTCTCTTTTAACTAACAATATAATATTAAAATACTACACTATAT
193 CTAAGACAATGTGAGATTGCATTATCTTTTAACTAACAATATAAGATTAAAACACTACACTATAT
3818 TTT
258 TTT
3821 ATAATTTTTT
Statistics
Matches: 215, Mismatches: 33, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
311 26 0.12
312 105 0.49
313 4 0.02
314 2 0.01
315 1 0.00
316 12 0.06
317 2 0.01
319 24 0.11
320 1 0.00
321 14 0.07
322 24 0.11
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (321 bp):
TTTTGCCACACCAGCAATAAAAATAGCAGGCAACAAATATATTTTTATGTTTGATGCCACCTATT
AATGTAGAAACAAACTTACAAAACATGCCTTTATATAGACCCAAAGTCTTATTTCCCTAATTTTC
ATAAAAATATAGGATATCAGATATGCGTATACATAAACTCAAGAATAAGTTTACAGCTTGATCTA
AGACAATGTGAGATTGCATTATCTTTTAACTAACAATATAAGATTAAAACACTACACTATATTTT
TTATCAACACTTCCAATTGGAAGAATTTTCAACAGAAAAAAAAAATACTTCCATCAAACGA
Found at i:4697 original size:12 final size:11
Alignment explanation
Indices: 4673--4704 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
4663 TATTTTAAGA
4673 TTAAATTTATT
1 TTAAATTTATT
4684 TTAAATTTATTT
1 TTAAATTTA-TT
4696 TTAAATTTA
1 TTAAATTTA
4705 AAATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:4711 original size:29 final size:28
Alignment explanation
Indices: 4653--4721 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
4643 AACCAAACCC
*
4653 ATTTTAAATTTATTTTAAGATTAAATTT
1 ATTTTAAATTTATTTTAAGATTAAAATT
4681 ATTTTAAATTTATTTTTAA-ATTTAAAATT
1 ATTTTAAATTTA-TTTTAAGA-TTAAAATT
*
4710 ATTATAAATTTA
1 ATTTTAAATTTA
4722 ATAAAAGTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 13 0.35
29 24 0.65
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTTTAAATTTATTTTAAGATTAAAATT
Found at i:4717 original size:17 final size:18
Alignment explanation
Indices: 4683--4722 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
4673 TTAAATTTAT
* *
4683 TTTAAATTTATTTTTAAA
1 TTTAAAATTATTTATAAA
4701 TTTAAAATTA-TTATAAA
1 TTTAAAATTATTTATAAA
4718 TTTAA
1 TTTAA
4723 TAAAAGTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTAAAATTATTTATAAA
Found at i:6812 original size:30 final size:28
Alignment explanation
Indices: 6745--7066 Score: 167
Period size: 29 Copynumber: 11.1 Consensus size: 28
6735 CCCTGAATGT
** * *
6745 CCCTAAACCATCCAAAAATCATATTTGA
1 CCCTAAACTTTCCAAAAATTACATTTGA
* *
6773 CCCCCAAACTCTCCAAAAATTACATTTCGA
1 -CCCTAAACTTTCCAAAAATTACATTT-GA
** *
6803 CCCTTAAACTTTTTAAAAATTACATTTTA
1 CCC-TAAACTTTCCAAAAATTACATTTGA
* *
6832 CCCTTAAATTTTCC-AAAATTCCATTTTTGA
1 CCC-TAAACTTTCCAAAAATTACA--TTTGA
** *
6862 CCCTAAACTTTCCAAAAATTATGTTTTTA
1 CCCTAAACTTTCCAAAAATTA-CATTTGA
* *
6891 CACTCAAA-TTTCC-AAAATTCCATTTTTGA
1 CCCT-AAACTTTCCAAAAATTACA--TTTGA
* *
6920 CCCTAAACTTTCTAAAAATTACATTTTA
1 CCCTAAACTTTCCAAAAATTACATTTGA
*
6948 CCCTAAAC-TTCCAAAAATT-CTATTTTTA
1 CCCTAAACTTTCCAAAAATTAC-A-TTTGA
* * * *
6976 CCCT-GATTTCTCCTAAAATTACCATTTTA
1 CCCTAAACTT-TCCAAAAATTA-CATTTGA
*
7005 CAGCC-AAACTTT-CAAAAATTCCATTTTGA
1 C--CCTAAACTTTCCAAAAATTACA-TTTGA
* * *
7034 CCCT-GATTCTTCCAAAAATTACCATTTTA
1 CCCTAAACT-TTCCAAAAATTA-CATTTGA
7063 CCCT
1 CCCT
7067 CGAAGTTCCT
Statistics
Matches: 226, Mismatches: 42, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
26 1 0.00
27 16 0.07
28 43 0.19
29 111 0.49
30 49 0.22
31 6 0.03
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAAATTACATTTGA
Found at i:6872 original size:58 final size:57
Alignment explanation
Indices: 6788--7066 Score: 243
Period size: 58 Copynumber: 4.8 Consensus size: 57
6778 AAACTCTCCA
* * *
6788 AAAATTACA-TTTCGACCCTTAAACTTTTTAAAAATTACATTTTACCCTTAAATTTTCC
1 AAAATTCCATTTTTGACCC-TAAACTTTCTAAAAATTACATTTTACCCTTAAA-TTTCC
* ** * *
6846 AAAATTCCATTTTTGACCCTAAACTTTCCAAAAATTATGTTTTTACACTCAAATTTCC
1 AAAATTCCATTTTTGACCCTAAACTTTCTAAAAATTA-CATTTTACCCTTAAATTTCC
*
6904 AAAATTCCATTTTTGACCCTAAACTTTCTAAAAATTACATTTTACCC-TAAACTTCC
1 AAAATTCCATTTTTGACCCTAAACTTTCTAAAAATTACATTTTACCCTTAAATTTCC
* * * *
6960 AAAAATTCTATTTTT-ACCCT-GA-TTTCTCCTAAAATTACCATTTTACAGCC--AAACTTTCA
1 -AAAATTCCATTTTTGACCCTAAACTTTCT--AAAAATTA-CATTTTAC--CCTTAAA-TTTCC
* * *
7019 AAAATTCCA-TTTTGACCCT-GATTCTTCCAAAAATTACCATTTTACCCT
1 AAAATTCCATTTTTGACCCTAAACT-TTCTAAAAATTA-CATTTTACCCT
7067 CGAAGTTCCT
Statistics
Matches: 186, Mismatches: 22, Indels: 27
0.79 0.09 0.11
Matches are distributed among these distances:
54 5 0.03
55 1 0.01
56 21 0.11
57 32 0.17
58 99 0.53
59 25 0.13
60 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (57 bp):
AAAATTCCATTTTTGACCCTAAACTTTCTAAAAATTACATTTTACCCTTAAATTTCC
Found at i:7082 original size:58 final size:58
Alignment explanation
Indices: 6817--7125 Score: 251
Period size: 58 Copynumber: 5.3 Consensus size: 58
6807 TAAACTTTTT
* * **
6817 AAAAATTA-CATTTTACCCTTAAATTTTCCAAAATTCCATTTTTGACCCT-AAACTTTCC
1 AAAAATTACCATTTTACCCTCAAA-CTTCCAAAATTCCATTTTTGACCCTGATTC-TTCC
*** * * ** *
6875 AAAAATTATGTTTTTACACTCAAATTTCCAAAATTCCATTTTTGACCCT-AAACTTTCT
1 AAAAATTACCATTTTACCCTCAAACTTCCAAAATTCCATTTTTGACCCTGATTC-TTCC
*
6933 AAAAATTA-CATTTTACCCT-AAACTTCCAAAAATTCTATTTTT-ACCCTGATT-TCTCC
1 AAAAATTACCATTTTACCCTCAAACTTCC-AAAATTCCATTTTTGACCCTGATTCT-TCC
* * *
6989 TAAAATTACCATTTTACAGC-CAAACTTTCAAAAATTCCA-TTTTGACCCTGATTCTTCC
1 AAAAATTACCATTTTAC-CCTCAAAC-TTCCAAAATTCCATTTTTGACCCTGATTCTTCC
* * * * * * *
7047 AAAAATTACCATTTTACCCTCGAAGTTCCTGAAATTCTATTTTTAACCCCGATTTTTTTCC
1 AAAAATTACCATTTTACCCTCAAACTTCC-AAAATTCCATTTTTGACCCTGA--TTCTTCC
7108 -AAAATTACCATTTTACCC
1 AAAAATTACCATTTTACCC
7126 CCGGATGTCT
Statistics
Matches: 209, Mismatches: 27, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
55 1 0.00
56 21 0.10
57 38 0.18
58 100 0.48
59 25 0.12
60 18 0.09
61 6 0.03
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCTCAAACTTCCAAAATTCCATTTTTGACCCTGATTCTTCC
Found at i:7142 original size:60 final size:60
Alignment explanation
Indices: 7043--7187 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 60
7033 ACCCTGATTC
* * * * ***
7043 TTCCAAAAATTACCATTTTACCCTC-GAAGTTCCTGAAATTCTATTTTTAACCCCGATTTTT
1 TTCC-AAAATTACCATTTTACCCCCGGAAGTTCCTAAAATTCCATTTTAAACCCC-AAACTT
*
7104 TTCCAAAATTACCATTTTACCCCCGGATG-T-CTCAAAATTCCATTTTAAACCCCAAACTT
1 TTCCAAAATTACCATTTTACCCCCGGAAGTTCCT-AAAATTCCATTTTAAACCCCAAACTT
*
7163 TTCAAAAATTACCATTTTACCCCCG
1 TTCCAAAATTACCATTTTACCCCCG
7188 AACGTTTAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 29 0.40
60 37 0.51
61 7 0.10
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (60 bp):
TTCCAAAATTACCATTTTACCCCCGGAAGTTCCTAAAATTCCATTTTAAACCCCAAACTT
Found at i:7184 original size:29 final size:29
Alignment explanation
Indices: 6774--7185 Score: 121
Period size: 29 Copynumber: 14.1 Consensus size: 29
6764 CATATTTGAC
* * *
6774 CCCCAAACTCTCCAAAAATTA-CATTTCGA
1 CCCCAAACTTTTCAAAAATTACCATTT-TA
* *
6803 CCCTTAAACTTTTTAAAAATTA-CATTTTA
1 CCC-CAAACTTTTCAAAAATTACCATTTTA
* *
6832 CCCTTAAA-TTTTCCAAAATT-CCATTTTTGA
1 CCC-CAAACTTTTCAAAAATTACCA-TTTT-A
* * ***
6862 CCCTAAACTTTCCAAAAATTATGTTTTTA
1 CCCCAAACTTTTCAAAAATTACCATTTTA
* *
6891 CACTCAAA--TTTCCAAAATT-CCATTTTTGA
1 C-CCCAAACTTTTCAAAAATTACCA-TTTT-A
*
6920 CCCTAAAC-TTTCTAAAAATTA-CATTTTA
1 CCCCAAACTTTTC-AAAAATTACCATTTTA
* * *
6948 CCCTAAAC-TTCCAAAAATT-CTATTTTTA
1 CCCCAAACTTTTCAAAAATTACCA-TTTTA
** *
6976 -CCCTGA-TTTCTCCTAAAATTACCATTTTA
1 CCCCAAACTTT-T-CAAAAATTACCATTTTA
*
7005 CAGCCAAAC-TTTCAAAAATT-CCATTTTGA
1 C-CCCAAACTTTTCAAAAATTACCATTTT-A
**
7034 -CCCTGA-TTCTTCCAAAAATTACCATTTTA
1 CCCCAAACTT-TT-CAAAAATTACCATTTTA
* * * ** *
7063 CCCTCGAA-GTTCCTGAAATT-CTATTTTTAA
1 CCC-CAAACTTTTCAAAAATTACCA-TTTT-A
*** *
7093 CCCCGATTTTTTTCCAAAATTACCATTTTA
1 CCCC-AAACTTTTCAAAAATTACCATTTTA
** *
7123 CCCCCGGA-TGTCTC-AAAATT-CCATTTTAAA
1 -CCCCAAACT-TTTCAAAAATTACCATTTT--A
7153 CCCCAAACTTTTCAAAAATTACCATTTTA
1 CCCCAAACTTTTCAAAAATTACCATTTTA
7182 CCCC
1 CCCC
7186 CGAACGTTTA
Statistics
Matches: 284, Mismatches: 59, Indels: 80
0.67 0.14 0.19
Matches are distributed among these distances:
27 17 0.06
28 64 0.23
29 92 0.32
30 78 0.27
31 31 0.11
32 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (29 bp):
CCCCAAACTTTTCAAAAATTACCATTTTA
Found at i:7198 original size:29 final size:29
Alignment explanation
Indices: 7108--7201 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
7098 ATTTTTTTCC
* * * *
7108 AAAATTACCATTTTACCCCCGGATGTCTC
1 AAAATTACCATTTTACCCCCGAACGTTTA
* * *
7137 AAAATT-CCATTTTAAACCCCAAACTTTTCA
1 AAAATTACCATTTT-ACCCCCGAACGTTT-A
7167 AAAATTACCATTTTACCCCCGAACGTTTA
1 AAAATTACCATTTTACCCCCGAACGTTTA
7196 AAAATT
1 AAAATT
7202 TTGTTTTTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
28 7 0.13
29 21 0.40
30 17 0.33
31 7 0.13
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAACGTTTA
Found at i:7200 original size:59 final size:59
Alignment explanation
Indices: 6846--7239 Score: 188
Period size: 58 Copynumber: 6.7 Consensus size: 59
6836 TAAATTTTCC
* * * *** * * * *
6846 AAAATTCCATTTTTGACCCTAAACTTTCCAAAAATTATGTTTTTACACTC-AA-ATTTCC
1 AAAATTCCATTTTTAACCCCAAACTTTTCAAAAATTACCATTTTACCCCCGAACGTTT-A
* * ** *
6904 AAAATTCCATTTTTGACCCTAAAC-TTTCTAAAAATTA-CATTTTA-CCCTAAAC-TTCCA
1 AAAATTCCATTTTTAACCCCAAACTTTTC-AAAAATTACCATTTTACCCCCGAACGTT-TA
* ** * ** *
6961 AAAATTCTATTTTT-A-CCCTGA-TTTCTCCTAAAATTACCATTTTACAGCCAAAC-TTTCA
1 AAAATTCCATTTTTAACCCCAAACTTT-T-CAAAAATTACCATTTTACCCCCGAACGTTT-A
* ** *
7019 AAAATTCCA-TTTTGA-CCCTGA-TTCTTCCAAAAATTACCATTTTACCCTCGAA-GTTCCT-
1 AAAATTCCATTTTTAACCCCAAACTT-TT-CAAAAATTACCATTTTACCCCCGAACGTT--TA
* * *** * * * * *
7077 GAAATTCTATTTTTAACCCCGATTTTTTTCCAAAATTACCATTTTACCCCCGGATGTCTC
1 AAAATTCCATTTTTAACCCC-AAACTTTTCAAAAATTACCATTTTACCCCCGAACGTTTA
*
7137 AAAATTCCATTTTAAACCCCAAACTTTTCAAAAATTACCATTTTACCCCCGAACGTTTA
1 AAAATTCCATTTTTAACCCCAAACTTTTCAAAAATTACCATTTTACCCCCGAACGTTTA
*** * * * *
7196 AAAATTTTGTTTTTAACCTCTAACTTTCCTAAAATTACCATTTT
1 AAAATTCCATTTTTAACCCCAAACTTTTCAAAAATTACCATTTT
7240 GCCCTCGAGT
Statistics
Matches: 263, Mismatches: 52, Indels: 41
0.74 0.15 0.12
Matches are distributed among these distances:
55 5 0.02
56 10 0.04
57 37 0.14
58 88 0.33
59 74 0.28
60 43 0.16
61 4 0.02
62 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCAAACTTTTCAAAAATTACCATTTTACCCCCGAACGTTTA
Found at i:18649 original size:18 final size:18
Alignment explanation
Indices: 18626--18660 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18616 CATCTAACAC
*
18626 TGTTCCTTGTAATTATTT
1 TGTTCCTTGTAAATATTT
18644 TGTTCCTTGTAAATATT
1 TGTTCCTTGTAAATATT
18661 CAGCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.57
Consensus pattern (18 bp):
TGTTCCTTGTAAATATTT
Found at i:19240 original size:49 final size:48
Alignment explanation
Indices: 19090--19455 Score: 221
Period size: 49 Copynumber: 7.4 Consensus size: 48
19080 GTATCGCGAA
* * *
19090 ACATGAAGGGAAAGATTTAAGCCGAAACGGCGAATCCAGTACCACGAAG
1 ACATGAAGGGAAAGATTTAAG-CGCAACGGCGAATCCAATACCATGAAG
* * * * ** * * *
19139 ATATGGAGGGAAAAGGTTTAAGTCGTAATAGC-AAACCTAGTACC-TCAGAG
1 ACATGAAGGG-AAAGATTTAAG-CGCAACGGCGAATCC-AATACCATGA-AG
*
19189 ACATGAAGGGAAAGATTTAAGCAGCAACGGTGAATCCAATACCATGAAG
1 ACATGAAGGGAAAGATTTAAGC-GCAACGGCGAATCCAATACCATGAAG
* * *
19238 ACATGAAGGGAAAG-GTTCAGTCGCAATGGCGAA-CCTTAA-ACTTCA-GAAG
1 ACATGAAGGGAAAGATTTAAG-CGCAACGGCGAATCC--AATAC--CATGAAG
* *
19287 ACATGAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCAAGAAA
1 ACATG-AAGGGAAAGATTTAAG-CGCAACGGCGAATCCAATACCATGAAG
* * * * *
19337 ACAAGAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTTATACC-TCAAAG
1 ACATGAAGGGAAAGATTTAAG-CGCAACGGCGAATCC-AATACCAT-GAAG
* * * * *
19386 ACATTAAAGGGAAATATTTAAGCCGCAACGGCG-ATCTAGTACCACGAAG
1 ACA-TGAAGGGAAAGATTTAAG-CGCAACGGCGAATCCAATACCATGAAG
* *
19435 ACA-CAAGGGGAAAGGTTTAAG
1 ACATGAA-GGGAAAGATTTAAG
19456 TCTCAATGGC
Statistics
Matches: 244, Mismatches: 51, Indels: 45
0.72 0.15 0.13
Matches are distributed among these distances:
47 4 0.02
48 30 0.12
49 109 0.45
50 82 0.34
51 17 0.07
52 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (48 bp):
ACATGAAGGGAAAGATTTAAGCGCAACGGCGAATCCAATACCATGAAG
Found at i:19297 original size:99 final size:100
Alignment explanation
Indices: 19090--19512 Score: 535
Period size: 99 Copynumber: 4.3 Consensus size: 100
19080 GTATCGCGAA
* * * *
19090 ACATG-AAGGGAAAGATTTAAGCCGAAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAAG
1 ACATGAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGACATGAAGGG-AAAG
* * *
19154 GTTTAAGTCGTAATAGCAAACC-TAGTACCTCAG-AG
65 GTTTAAGTCGCAATGGCGAACCTTA-TACCTCAGAAG
* * *
19189 ACATG-AAGGGAAAGATTTAAGCAGCAACGGTGAATCCAATACCATGAAGACATGAAGGGAAAGG
1 ACATGAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGACATGAAGGGAAAGG
* * *
19253 -TTCAGTCGCAATGGCGAACCTTAAACTTCAGAAG
66 TTTAAGTCGCAATGGCGAACCTTATACCTCAGAAG
* * *
19287 ACATGAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCAAGAAAACAAGAAGGGAAAGG
1 ACATGAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGACATGAAGGGAAAGG
19352 TTTAAGTCGCAATGGCGAACCTTATACCTCA-AAG
66 TTTAAGTCGCAATGGCGAACCTTATACCTCAGAAG
* * * * *
19386 ACATTAAAGGGAAATATTTAAGCCGCAACGGCG-ATCTAGTACCACGAAGACA-CAAGGGGAAAG
1 ACATGAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGACATGAA-GGGAAAG
* *
19449 GTTTAAGTCTCAATGGCGAGCCTTATACCTCAGAAG
65 GTTTAAGTCGCAATGGCGAACCTTATACCTCAGAAG
19485 -CATGAAA-GGAAA-ATTTAAGCCGCAACGG
1 ACATGAAAGGGAAAGATTTAAGCCGCAACGG
19513 TAAATTTAGT
Statistics
Matches: 287, Mismatches: 31, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
96 16 0.06
97 29 0.10
98 72 0.25
99 143 0.50
100 27 0.09
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (100 bp):
ACATGAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGACATGAAGGGAAAGG
TTTAAGTCGCAATGGCGAACCTTATACCTCAGAAG
Found at i:19925 original size:17 final size:16
Alignment explanation
Indices: 19903--19944 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
19893 CAAACCCATT
19903 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAA-A
*
19920 TTAAATTTGTTTTAAA
1 TTAAATTTATTTTAAA
19936 TTAAATTTA
1 TTAAATTTA
19945 AATTTAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TTAAATTTATTTTAAA
Found at i:19950 original size:17 final size:16
Alignment explanation
Indices: 19903--19950 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
19893 CAAACCCATT
*
19903 TTAAATTTATTTTAAGA
1 TTAAATTTAATTTAA-A
**
19920 TTAAATTTGTTTTAAA
1 TTAAATTTAATTTAAA
19936 TTAAATTTAAATTTA
1 TTAAATTT-AATTTA
19951 GTTTAAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 9 0.33
17 18 0.67
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (16 bp):
TTAAATTTAATTTAAA
Found at i:19956 original size:17 final size:16
Alignment explanation
Indices: 19936--19996 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 16
19926 TTGTTTTAAA
19936 TTAAATTTAAATTTAGT
1 TTAAATTTAAATTTA-T
*
19953 TTAAGTTTAAATTTATT
1 TTAAATTTAAATTTA-T
* *
19970 TTAATTTTAAAATTAT
1 TTAAATTTAAATTTAT
19986 TATAAATTTAA
1 T-TAAATTTAA
19997 TAAAAGTCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
16 2 0.05
17 36 0.95
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:20899 original size:3 final size:3
Alignment explanation
Indices: 20891--20956 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
20881 ATAGTTTTAT
* ** **
20891 TAA TAA TAAA TACA TTAA TAA TAG TAA TAA TAA TTT TAA TAA TAA TTT
1 TAA TAA T-AA TA-A -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
20939 TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
20957 ATGAATAAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
3 41 0.85
4 5 0.10
5 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:20921 original size:12 final size:12
Alignment explanation
Indices: 20888--20956 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
20878 TAAATAGTTT
20888 TATTAATAATAA
1 TATTAATAATAA
20900 -A-TACATTAATAA
1 TATTA-A-TAATAA
*
20912 TAGTAATAATAA
1 TATTAATAATAA
*
20924 TTTTAATAATAA
1 TATTAATAATAA
* *
20936 TTTTAATATTAA
1 TATTAATAATAA
*
20948 TAATAATAA
1 TATTAATAA
20957 ATGAATAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 2 0.04
11 2 0.04
12 39 0.83
13 2 0.04
14 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (12 bp):
TATTAATAATAA
Found at i:22161 original size:58 final size:58
Alignment explanation
Indices: 22055--22596 Score: 365
Period size: 59 Copynumber: 9.2 Consensus size: 58
22045 CAAAAGTCAT
* *
22055 ATTTTGACCCCTAAACTCTCCAAAAATTACA-TTTCAATCC-CTAAACTTTCCAAAAATTAC
1 ATTTT-ACCCCTAAACT-TCCAAAAATTCCATTTTTAA-CCTC-AAACTTTCCAAAAATTAC
* * * *
22115 ATTTTACCCTTAAAATTTCC-AAAATTCCATTTTTAACCGCAAACTTTCTAAAAATTAC
1 ATTTTACCCCT-AAACTTCCAAAAATTCCATTTTTAACCTCAAACTTTCCAAAAATTAC
* * * * *
22173 ATTTGTACCCCTAAATTTTCTAAAATTCCATTTTTAA-CTCTAAACTTTCTAAAAA-TAT
1 ATTT-TACCCCTAAACTTCCAAAAATTCCATTTTTAACCTC-AAACTTTCCAAAAATTAC
*
22231 ATTTTACCCTTAAACTTCCAAAAATTCCA-TTTTAACCTC--ACTTTTCCAAAAATTAC
1 ATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCAAAC-TTTCCAAAAATTAC
* ** *
22287 TATTTTACCCCTAAACTTCCAAAAATTTCATTTTTAACCTCGATTCTTTCAAAAAATTACC
1 -ATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTC-AAACTTTCCAAAAATTA-C
* * * * * *
22348 ATTTTACCCCCAAACTTCTAAAATTTCCATTTTTGA--TCATGATTCTTCCAAAAAATTACC
1 ATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCA-AACT-TTCC-AAAAATTA-C
* * * * * * ** * *
22408 ATTTAAACCCC-GAACTTCCTAAAATTCTATTTTTGACCCCAATTTTTTTTCTAAAATTACC
1 ATTT-TACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCAA--ACTTTCCAAAAATTA-C
** * * *
22469 ATTTTA-CCCTCGGA-TGTCTAAAAATTCTATTTTAAACCTCAAACTTTCCAAAAATTATC
1 ATTTTACCCCT-AAACT-TCCAAAAATTCCATTTTTAACCTCAAACTTTCCAAAAATTA-C
* ** * * * *
22528 ATTTTACCCCCAAA-TGTTTAAAATTTCCATTTTTGACCCCAAACTTTCCCAAAATTACC
1 ATTTTACCCCTAAACT-TCCAAAAATTCCATTTTTAACCTCAAACTTTCCAAAAATTA-C
*
22587 ATTTTGCCCC
1 ATTTTACCCC
22597 CAAGTGTCCA
Statistics
Matches: 392, Mismatches: 63, Indels: 55
0.77 0.12 0.11
Matches are distributed among these distances:
54 2 0.01
55 9 0.02
56 8 0.02
57 52 0.13
58 59 0.15
59 121 0.31
60 91 0.23
61 43 0.11
62 5 0.01
63 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.38
Consensus pattern (58 bp):
ATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCAAACTTTCCAAAAATTAC
Found at i:22321 original size:29 final size:29
Alignment explanation
Indices: 22055--22381 Score: 193
Period size: 29 Copynumber: 11.2 Consensus size: 29
22045 CAAAAGTCAT
*
22055 ATTTTGACCCCTAAACTCTCCAAAAATTAC
1 ATTTTTACCCCTAAACT-TCCAAAAATTAC
** *
22085 ATTTCAATCCCTAAACTTTCCAAAAATTAC
1 ATTTTTACCCCTAAAC-TTCCAAAAATTAC
* * *
22115 A-TTTTACCCTTAAAATTTCC-AAAATTCC
1 ATTTTTACCCCT-AAACTTCCAAAAATTAC
* *
22143 ATTTTTAACCGC-AAACTTTCTAAAAATTAC
1 ATTTTT-ACCCCTAAAC-TTCCAAAAATTAC
* * * * *
22173 ATTTGTACCCCTAAATTTTCTAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTAC
* * * *
22202 ATTTTTAACTCTAAACTTTCTAAAAA-TAT
1 ATTTTTACCCCTAAAC-TTCCAAAAATTAC
* *
22231 A-TTTTACCCTTAAACTTCCAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTAC
* * ***
22259 ATTTTAACCTC-ACTTTTCCAAAAATTAC
1 ATTTTTACCCCTAAACTTCCAAAAATTAC
*
22287 -TATTTTACCCCTAAACTTCCAAAAATTTC
1 AT-TTTTACCCCTAAACTTCCAAAAATTAC
* * ** *
22316 ATTTTTAACCTCGATTCTTTCAAAAAATTACC
1 ATTTTT-ACCCCTAAAC-TTCCAAAAATTA-C
* * * *
22348 A-TTTTACCCCCAAACTTCTAAAATTTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTAC
22376 ATTTTT
1 ATTTTT
22382 GATCATGATT
Statistics
Matches: 218, Mismatches: 62, Indels: 35
0.69 0.20 0.11
Matches are distributed among these distances:
27 9 0.04
28 46 0.21
29 80 0.37
30 66 0.30
31 15 0.07
32 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.01, T:0.39
Consensus pattern (29 bp):
ATTTTTACCCCTAAACTTCCAAAAATTAC
Found at i:22614 original size:28 final size:28
Alignment explanation
Indices: 22519--22648 Score: 143
Period size: 28 Copynumber: 4.5 Consensus size: 28
22509 AAACTTTCCA
* * * **
22519 AAAATTATCATTTTACCCCCAAATGTTT
1 AAAATTACCATTTTGCCCCCAAGTGTCC
* * * *
22547 AAAATTTCCATTTTTGACCCCAAACTTTCCC
1 AAAATTACCA-TTTTG-CCCCCAAGTGT-CC
22578 AAAATTACCATTTTGCCCCCAAGTGTCC
1 AAAATTACCATTTTGCCCCCAAGTGTCC
*
22606 AAAATTACCATTTTGCCCCCGAGTGTCC
1 AAAATTACCATTTTGCCCCCAAGTGTCC
22634 AAAATTACCATTTTG
1 AAAATTACCATTTTG
22649 TCCATGGGTA
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
28 52 0.60
29 12 0.14
30 13 0.15
31 9 0.10
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.34
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCCAAGTGTCC
Found at i:22665 original size:28 final size:28
Alignment explanation
Indices: 22578--22665 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
22568 AAACTTTCCC
* * * *
22578 AAAATTACCATTTTGCCCCCAAGTGTCC
1 AAAATTACCATTTTGCCCACGAGTATCA
* * *
22606 AAAATTACCATTTTGCCCCCGAGTGTCC
1 AAAATTACCATTTTGCCCACGAGTATCA
* * *
22634 AAAATTACCATTTTGTCCATGGGTATCA
1 AAAATTACCATTTTGCCCACGAGTATCA
22662 AAAA
1 AAAA
22666 ATCTCATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCACGAGTATCA
Found at i:25249 original size:29 final size:31
Alignment explanation
Indices: 25191--25249 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
25181 ATTAAAACAC
*
25191 AAATATCCAAAATCCATGAAAATTAAAAATT
1 AAATATCCAAAATCCATAAAAATTAAAAATT
* *
25222 AAATAT-CAAAA-CCTTAAAAATTCAAAAT
1 AAATATCCAAAATCCATAAAAATTAAAAAT
25250 AATCAAGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.56
30 5 0.20
31 6 0.24
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (31 bp):
AAATATCCAAAATCCATAAAAATTAAAAATT
Done.