Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014637.1 Kokia drynarioides strain JFW-HI SEQ_129676, 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: 74895
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 153 characters in sequence are not A, C, G, or T
Found at i:558 original size:22 final size:22
Alignment explanation
Indices: 533--574 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
523 CGAATTTGGC
533 TCGATAATTTTTT-GAATTGAGT
1 TCGA-AATTTTTTGGAATTGAGT
*
555 TCGAATTTTTTTGGAATTGA
1 TCGAAATTTTTTGGAATTGA
575 ACTCGAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (22 bp):
TCGAAATTTTTTGGAATTGAGT
Found at i:580 original size:22 final size:21
Alignment explanation
Indices: 540--580 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
530 GGCTCGATAA
**
540 TTTTTTGAATTGAGTTCGAAT
1 TTTTTTGAATTGAACTCGAAT
561 TTTTTTGGAATTGAACTCGA
1 TTTTTT-GAATTGAACTCGA
581 GTAGCTTGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (21 bp):
TTTTTTGAATTGAACTCGAAT
Found at i:1922 original size:108 final size:107
Alignment explanation
Indices: 1801--2127 Score: 582
Period size: 107 Copynumber: 3.0 Consensus size: 107
1791 TTTTTAATAA
* * *
1801 TTTTTTAATTGAATCAATTAAATCGATAAATTGATAACCTAATCAATCCAATCACCAATTGAATT
1 TTTTTTAATTGAATAAATTAAATCGATAAATTGATAACCTAACCAATTCAATCACCAATTGAATT
1866 TAAAAAACATTTGTTGACCAAAAAATGGAATCTTGATTATAT
66 TAAAAAACATTTGTTGACCAAAAAATGGAATCTTGATTATAT
*
1908 TTTTTGTAATTGAATTAATTAAATCGATAAATTGATAACCTAACCAATTCAATCACCAATTGAAT
1 TTTTT-TAATTGAATAAATTAAATCGATAAATTGATAACCTAACCAATTCAATCACCAATTGAAT
1973 TTAAAAAACATTTGTTGACCAAAAAATGGAATCTTGATTATAT
65 TTAAAAAACATTTGTTGACCAAAAAATGGAATCTTGATTATAT
* *
2016 TTTTTAAATTGAATAAATTAAATCGATAAATTGATAACCTAACCAATTCAATCACCAATTAAATT
1 TTTTTTAATTGAATAAATTAAATCGATAAATTGATAACCTAACCAATTCAATCACCAATTGAATT
*
2081 TAAAAAACATTTGTTGACCAAAAAATGAAATCTTGATTATAT
66 TAAAAAACATTTGTTGACCAAAAAATGGAATCTTGATTATAT
2123 TTTTT
1 TTTTT
2128 GTATAATGAA
Statistics
Matches: 212, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
107 108 0.51
108 104 0.49
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (107 bp):
TTTTTTAATTGAATAAATTAAATCGATAAATTGATAACCTAACCAATTCAATCACCAATTGAATT
TAAAAAACATTTGTTGACCAAAAAATGGAATCTTGATTATAT
Found at i:8371 original size:232 final size:233
Alignment explanation
Indices: 7942--8385 Score: 622
Period size: 232 Copynumber: 1.9 Consensus size: 233
7932 AAGGTACGGA
* * * *
7942 TTTGCAAGGAGACCACAACAAGCCGAAAGTCACCAGAGATGTAACAAAAATCCCATTAAAACATA
1 TTTGCAAGGAGACCACAACAAGCCAAAAGTCACCAGAGATATAAAAAAAATCCCATTAAAACAAA
* * * *
8007 AGTTAAGAAGGCTGAGAACACGACTAGATAAAAGACATAAATCAAGTTTCCTTTGTGTAAGACCT
66 AGTTAAGAAGACCGAGAACACGACTACATAAAAGACATAAATCAAGTTTCCTTCGTGTAAGACCT
* * *
8072 ATGTTACTCTGGCTCTTCATTTTTCTTTTAAGCACCCATTTCCAACACTCATGTCCGAGGAATAT
131 ATGTTACACAGGCTCTTCATTTTTCTTTTAAGCACCCAATTCCAACACTCATGTCCGAGGAATAT
8137 TTGGACATTGGCATGTACAGCGTATATCTAGACATTGG
196 TTGGACATTGGCATGTACAGCGTATATCTAGACATTGG
* * * *
8175 TTTGCAAGGGGA-C-CAACAAGGCAAAATTCACCGGAGATATAAAAAAAATCCCATTAAAACAAA
1 TTTGCAAGGAGACCACAACAAGCCAAAAGTCACCAGAGATATAAAAAAAATCCCATTAAAAC-AA
* * * * *
8238 AAGTTAAGAATACCGAGAACATGATTACATATAAGACATATATCAAGTTTCCTTCGTGTAAGACC
65 AAGTTAAGAAGACCGAGAACACGACTACATAAAAGACATAAATCAAGTTTCCTTCGTGTAAGACC
* * * * ** *
8303 TATGTTGCACAGGCTCTTCATTTTTCTTTTAAGTACTCAATTCCATCACTCATGTCCGCTGTATA
130 TATGTTACACAGGCTCTTCATTTTTCTTTTAAGCACCCAATTCCAACACTCATGTCCGAGGAATA
8368 TTTGGACATTGGCATGTA
195 TTTGGACATTGGCATGTA
8386 GTCCAGCATA
Statistics
Matches: 183, Mismatches: 27, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
231 41 0.22
232 131 0.72
233 11 0.06
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (233 bp):
TTTGCAAGGAGACCACAACAAGCCAAAAGTCACCAGAGATATAAAAAAAATCCCATTAAAACAAA
AGTTAAGAAGACCGAGAACACGACTACATAAAAGACATAAATCAAGTTTCCTTCGTGTAAGACCT
ATGTTACACAGGCTCTTCATTTTTCTTTTAAGCACCCAATTCCAACACTCATGTCCGAGGAATAT
TTGGACATTGGCATGTACAGCGTATATCTAGACATTGG
Found at i:11106 original size:51 final size:51
Alignment explanation
Indices: 11046--11149 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
11036 AATCTCGATA
*
11046 CACGTAGGTCTCATTCAAAGTTATTCTAGTTTAGGTAAATTATGTCCAAAT
1 CACGTAGGTCTCATTCAAAGTTATTCTAGTTTACGTAAATTATGTCCAAAT
11097 CACGTAGGTCTCATTCAAAGTTATTCTAGTTTACGTAAATTATGTCCAAAT
1 CACGTAGGTCTCATTCAAAGTTATTCTAGTTTACGTAAATTATGTCCAAAT
11148 CA
1 CA
11150 TGTTTTGTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (51 bp):
CACGTAGGTCTCATTCAAAGTTATTCTAGTTTACGTAAATTATGTCCAAAT
Found at i:14296 original size:37 final size:38
Alignment explanation
Indices: 14246--14322 Score: 129
Period size: 37 Copynumber: 2.0 Consensus size: 38
14236 ATTAGCCATA
14246 ACCAGAATTTGAATCTAGTGCT-CCCATAGTACAATTT
1 ACCAGAATTTGAATCTAGTGCTCCCCATAGTACAATTT
*
14283 ACCAGAATTTGAATCTAGTGCTCCCCCTTAGTACAATTT
1 ACCAGAATTTGAATCTAGTGCT-CCCCATAGTACAATTT
14322 A
1 A
14323 GGGAAATGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
37 22 0.59
39 15 0.41
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.32
Consensus pattern (38 bp):
ACCAGAATTTGAATCTAGTGCTCCCCATAGTACAATTT
Found at i:16969 original size:275 final size:278
Alignment explanation
Indices: 16485--17000 Score: 699
Period size: 275 Copynumber: 1.9 Consensus size: 278
16475 GAATATGGTC
* * *
16485 CGGTCCCTATACTTTTATTCTAGGAAATCACTTCTACTTTTCAGATTTTAAAGTTTAAGTTCAAT
1 CGGTCCCTATACTTTTATTCTAGAAAATCACTTCTACTTTTCAGATTTTAAAATTGAAGTTCAAT
*
16550 TATTAACACAGTTAAAATTATTTTTAAAATTCGAGTTCATTACAGTGCTATTCTTTTAGTTACAT
66 TATTAACACAGTTAAAATTATTTTTAAAATTCAAGTTCATTACAGTG---TTCTTTTAGTTACAT
* * * * *
16615 GACTACTAAATGAGTATTTTTTTTTTATTTCAATATGTCACACCAAAAATTTAATGGTGTTACCA
128 GACTACTAAATGAGTATTATTTTTTTATTTCAAAATATCACACCAAAAATTTAATGGTATTAACA
* * * *
16680 ATTGGATTTGAATTTTGAAATCTGAAAAAATAGAGAGATTAAATTCCTAAAATAAAAGTACAGGT
193 ATTGGATCTGAATTTTAAAATCTGAAAAAATAAAGAGACTAAATTCCTAAAATAAAAGTACAGGT
16745 GCTCTTCCCAATTTGGGAATA
258 GCTCTTCCCAATTTGGGAATA
16766 CGGTCCCTATACTTTTATTCTAAGAATTCAATCAC-TCTACTTTTCAGA-TTTAAAATTGAAG-T
1 CGGTCCCTATACTTTTATTCT-AGAA---AATCACTTCTACTTTTCAGATTTTAAAATTGAAGTT
* * * *
16828 CTATTTATTAACACTGTTAAAATTATTTTTTAAATTCAAGTTCATTAC-G-G-TCTTTTAGTTCC
62 C-AATTATTAACACAGTTAAAATTATTTTTAAAATTCAAGTTCATTACAGTGTTCTTTTAGTTAC
* * *
16890 CTGGCTACT-AA-GTG-ATTATTTTTTTATTTCAAAATATCACACCAAAAAATTTAATGGTATTA
126 ATGACTACTAAATGAGTATTATTTTTTTATTTCAAAATATCACACC-AAAAATTTAATGGTATTA
*
16952 ACAATTGGATCTGAATTTTAAAATCTGAAAAAGTAAAGAGACTAAATTC
190 ACAATTGGATCTGAATTTTAAAATCTGAAAAAATAAAGAGACTAAATTC
17001 AAAATTTTGG
Statistics
Matches: 208, Mismatches: 21, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
274 26 0.12
275 62 0.30
276 2 0.01
277 18 0.09
281 22 0.11
282 6 0.03
283 53 0.25
284 13 0.06
285 6 0.03
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (278 bp):
CGGTCCCTATACTTTTATTCTAGAAAATCACTTCTACTTTTCAGATTTTAAAATTGAAGTTCAAT
TATTAACACAGTTAAAATTATTTTTAAAATTCAAGTTCATTACAGTGTTCTTTTAGTTACATGAC
TACTAAATGAGTATTATTTTTTTATTTCAAAATATCACACCAAAAATTTAATGGTATTAACAATT
GGATCTGAATTTTAAAATCTGAAAAAATAAAGAGACTAAATTCCTAAAATAAAAGTACAGGTGCT
CTTCCCAATTTGGGAATA
Found at i:22160 original size:17 final size:20
Alignment explanation
Indices: 22138--22180 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
22128 TTAAACCATG
22138 TTATAAA-AATA-AAT-AAA
1 TTATAAATAATATAATAAAA
22155 TTATAAATTAATATAATAAAA
1 TTATAAA-TAATATAATAAAA
22176 TTATA
1 TTATA
22181 TTTAAATTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.32
19 4 0.18
20 3 0.14
21 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TTATAAATAATATAATAAAA
Found at i:22256 original size:22 final size:23
Alignment explanation
Indices: 22213--22256 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
22203 AAATTAATAC
* * *
22213 ATAATAAATTTATATTTTAATTT
1 ATAATAAAATTATAATTAAATTT
22236 ATAA-AAAATTATAATTAAATT
1 ATAATAAAATTATAATTAAATT
22257 CCGACCCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAATAAAATTATAATTAAATTT
Found at i:24299 original size:20 final size:20
Alignment explanation
Indices: 24254--24292 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
24244 ATCATTTTAT
24254 CTTTTTAATAATTAATTTTG
1 CTTTTTAATAATTAATTTTG
24274 CGTTTTT-ATAATTAATTTT
1 C-TTTTTAATAATTAATTTT
24293 AGTTTTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (20 bp):
CTTTTTAATAATTAATTTTG
Found at i:27860 original size:53 final size:51
Alignment explanation
Indices: 27779--27877 Score: 126
Period size: 53 Copynumber: 1.9 Consensus size: 51
27769 TAAATTTGTT
* *
27779 ATTTAATAATGATCTAAAAACAAACAAAAATCAGATTTAATTGGATTTCACAA
1 ATTTAATAATGATCTAAAAACAAAC-AAAA-CACATTTAAGTGGATTTCACAA
* * * *
27832 ATTTAATTATTATCTAAAAATAACCAAAACACATTTAAGTGGATTT
1 ATTTAATAATGATCTAAAAACAAACAAAACACATTTAAGTGGATTT
27878 AATTTCGATG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
51 15 0.38
52 4 0.10
53 21 0.52
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (51 bp):
ATTTAATAATGATCTAAAAACAAACAAAACACATTTAAGTGGATTTCACAA
Found at i:30631 original size:2 final size:2
Alignment explanation
Indices: 30624--30649 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30614 TTATACACTC
30624 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
30650 TTAAAATGGG
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:37610 original size:16 final size:17
Alignment explanation
Indices: 37591--37622 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
37581 AATTTAATAT
37591 TATTTT-TATTTTTTTA
1 TATTTTCTATTTTTTTA
37607 TATTTTCTATTTTTTT
1 TATTTTCTATTTTTTT
37623 TTTACTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (17 bp):
TATTTTCTATTTTTTTA
Found at i:38046 original size:30 final size:30
Alignment explanation
Indices: 38012--38068 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
38002 GTTAGACTTG
38012 AATTTTAAAACCTGAAAAGTATAAGGATTA
1 AATTTTAAAACCTGAAAAGTATAAGGATTA
***
38042 AATTTTAAATTTTGAAAAGTATAAGGA
1 AATTTTAAAACCTGAAAAGTATAAGGA
38069 CTTATGAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (30 bp):
AATTTTAAAACCTGAAAAGTATAAGGATTA
Found at i:45139 original size:24 final size:25
Alignment explanation
Indices: 45111--45158 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
45101 GATATATTAT
45111 ATAATTTTCATA-TTTTTAATAATA
1 ATAATTTTCATATTTTTTAATAATA
*
45135 ATAATTTTTATATTTTTTAATAAT
1 ATAATTTTCATATTTTTTAATAAT
45159 TTTTATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
ATAATTTTCATATTTTTTAATAATA
Found at i:52153 original size:16 final size:15
Alignment explanation
Indices: 52134--52177 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
52124 CTTAAATTTG
52134 GATCATTTTAAGTTTT
1 GATCATTTTAAG-TTT
*
52150 GATCATTTCAAGTTT
1 GATCATTTTAAGTTT
52165 GAGTCGATTTTAA
1 GA-TC-ATTTTAA
52178 TTAGATTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 13 0.54
17 6 0.25
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (15 bp):
GATCATTTTAAGTTT
Found at i:52328 original size:32 final size:34
Alignment explanation
Indices: 52266--52330 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 34
52256 AGAGATTACC
52266 AGGTTTTGATCACATTTCAAGTTTAGGTCATTTT
1 AGGTTTTGATCACATTTCAAGTTTAGGTCATTTT
*
52300 AGGTTTTGAT-A-ATTTCATGTTT-GAGTCATTT
1 AGGTTTTGATCACATTTCAAGTTTAG-GTCATTT
52331 GCAATTTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 1 0.03
32 17 0.59
33 1 0.03
34 10 0.34
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.49
Consensus pattern (34 bp):
AGGTTTTGATCACATTTCAAGTTTAGGTCATTTT
Found at i:52861 original size:108 final size:108
Alignment explanation
Indices: 52667--52882 Score: 369
Period size: 108 Copynumber: 2.0 Consensus size: 108
52657 TCGACTCGAA
*
52667 GTTCGATCAGTTTTGGTGACCCGTTATCTGATCCGAAAAACTCTTTTAAATACATTTCAAAAGAT
1 GTTCGATCAGTTTTGGTGACCCGGTATCTGATCCGAAAAACTCTTTTAAATACATTTCAAAAGAT
*
52732 CCTTTTTAGAGGGTCTACTCTCCAGATAATTCACCTCTTATCT
66 CCTTTTTAGAGGGTCTACTCTCCAAATAATTCACCTCTTATCT
* * *
52775 GTTCGATCCGTTTTGGTGACCCGGTATTTGATCCGAAAAACTCTTTTAAATACATTTCGAAAGAT
1 GTTCGATCAGTTTTGGTGACCCGGTATCTGATCCGAAAAACTCTTTTAAATACATTTCAAAAGAT
* *
52840 CTTTTTTAGAGGGTCTGCTCTCCAAATAATTCACCTCTTATCT
66 CCTTTTTAGAGGGTCTACTCTCCAAATAATTCACCTCTTATCT
52883 TTTCCTTTTC
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 101 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (108 bp):
GTTCGATCAGTTTTGGTGACCCGGTATCTGATCCGAAAAACTCTTTTAAATACATTTCAAAAGAT
CCTTTTTAGAGGGTCTACTCTCCAAATAATTCACCTCTTATCT
Found at i:56014 original size:16 final size:16
Alignment explanation
Indices: 55993--56023 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55983 AAATCAAATT
55993 ATTTTAATTTTTTAAA
1 ATTTTAATTTTTTAAA
*
56009 ATTTTATTTTTTTAA
1 ATTTTAATTTTTTAA
56024 TCAGATTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTAATTTTTTAAA
Found at i:60863 original size:186 final size:185
Alignment explanation
Indices: 60515--60881 Score: 644
Period size: 185 Copynumber: 2.0 Consensus size: 185
60505 TCATATATAT
* *
60515 ATATATATATTTTTTTTTTTAAATAATAAAATTAAACATTTAATTTAAATAAATAGGAAGCTCAA
1 ATATATATATATATTTTTTTAAATAATAAAATTAAACATTTAATTTAAATAAATAGGAAGCTCAA
60580 AGTCAAACAAATATCAATAGCCCAAAGTAGAAAAAGAAAAAAAAAGAAAAAAATTTCAAAAGTAA
66 AGTCAAACAAATATCAATAGCCCAAAGTAGAAAAAGAAAAAAAAAGAAAAAAATTTCAAAAGTAA
*
60645 GTTTCATAATAAAAGAAAATAAAGTAACAAAACCAATAAAGTAAATAGAAAGTTC
131 GTTTCATAATAAAAGAAAATAAAGTAACAAAACCAATAAAATAAATAGAAAGTTC
60700 ATATATATATATATTTTTTTAAATAATAAAATTAAACATTTAATTTAAATAAATAGGAAGCTCAA
1 ATATATATATATATTTTTTTAAATAATAAAATTAAACATTTAATTTAAATAAATAGGAAGCTCAA
* *****
60765 AGTCAAACAAATATCAATAGCCCAAAGTAGAAAAAGAAAAAGAAAGAATTTTTTTTTCAAAAGTA
66 AGTCAAACAAATATCAATAGCCCAAAGTAGAAAAAGAAAAAAAAAGAA-AAAAATTTCAAAAGTA
60830 AGTTTCATAATAAAAGAAAATAAAGTAACAAAACCAATAAAATAAATAGAAA
130 AGTTTCATAATAAAAGAAAATAAAGTAACAAAACCAATAAAATAAATAGAAA
60882 AATGTCAAGT
Statistics
Matches: 172, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
185 110 0.64
186 62 0.36
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.27
Consensus pattern (185 bp):
ATATATATATATATTTTTTTAAATAATAAAATTAAACATTTAATTTAAATAAATAGGAAGCTCAA
AGTCAAACAAATATCAATAGCCCAAAGTAGAAAAAGAAAAAAAAAGAAAAAAATTTCAAAAGTAA
GTTTCATAATAAAAGAAAATAAAGTAACAAAACCAATAAAATAAATAGAAAGTTC
Found at i:61632 original size:2 final size:2
Alignment explanation
Indices: 61625--61664 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
61615 TACCCAAATC
61625 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
61665 GAAAATGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66384 original size:18 final size:18
Alignment explanation
Indices: 66361--66397 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
66351 TTTATTTTGG
*
66361 TATTCAATTTATTCGAAT
1 TATTCAAATTATTCGAAT
66379 TATTCAAATTATTCGAAT
1 TATTCAAATTATTCGAAT
66397 T
1 T
66398 CAAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (18 bp):
TATTCAAATTATTCGAAT
Found at i:67571 original size:25 final size:26
Alignment explanation
Indices: 67527--67581 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
67517 GGTTAAGTTT
* *
67527 TTTTTTCTTTTCATTTTTAGATTAAA
1 TTTTCTCTTTTCATTGTTAGATTAAA
*
67553 TTTTCTCTTTTC-TTGTTAGATTAGA
1 TTTTCTCTTTTCATTGTTAGATTAAA
67578 TTTT
1 TTTT
67582 ATTTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.18, C:0.09, G:0.07, T:0.65
Consensus pattern (26 bp):
TTTTCTCTTTTCATTGTTAGATTAAA
Found at i:67588 original size:25 final size:26
Alignment explanation
Indices: 67527--67588 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
67517 GGTTAAGTTT
* *
67527 TTTTTTCTTTTCATTTTTAGATTAAA
1 TTTTATCTTTTCATTGTTAGATTAAA
* *
67553 TTTTCTCTTTTC-TTGTTAGATTAGA
1 TTTTATCTTTTCATTGTTAGATTAAA
*
67578 TTTTATTTTTT
1 TTTTATCTTTT
67589 TCTTTCTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 20 0.65
26 11 0.35
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.68
Consensus pattern (26 bp):
TTTTATCTTTTCATTGTTAGATTAAA
Found at i:72557 original size:29 final size:30
Alignment explanation
Indices: 72524--72582 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
72514 AAAATTATAC
**
72524 TCCTAAATTTTCTT-AAAATTTTAATTAGA
1 TCCTAAATTTTCTTGAAAAAATTAATTAGA
*
72553 TCCTAAATTTTTTTGAAAAAATTAATTAGA
1 TCCTAAATTTTCTTGAAAAAATTAATTAGA
72583 CCCCTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (30 bp):
TCCTAAATTTTCTTGAAAAAATTAATTAGA
Found at i:74401 original size:30 final size:31
Alignment explanation
Indices: 74367--74428 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
74357 TTCAAGAAAA
* *
74367 TTTTAAAATTTTAATTAAATCC-TCAAAATT
1 TTTTAAAATTATAATTAAACCCTTCAAAATT
*
74397 TTTTAAAATTATAATTAGACCCTTCAAAATT
1 TTTTAAAATTATAATTAAACCCTTCAAAATT
74428 T
1 T
74429 AATGCCAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (31 bp):
TTTTAAAATTATAATTAAACCCTTCAAAATT
Done.