Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009292.1 Kokia drynarioides strain JFW-HI SEQ_123998, 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: 46823
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:8645 original size:23 final size:21
Alignment explanation
Indices: 8611--8662 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
8601 TCTTTTATCA
*
8611 ATTATTTAATGTAACTTTAATAT
1 ATTATTTTATGTAA--TTAATAT
* *
8634 ATTTTTTTATGTTATTAATAT
1 ATTATTTTATGTAATTAATAT
8655 ATTATTTT
1 ATTATTTT
8663 GGGAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 14 0.56
23 11 0.44
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTATTTTATGTAATTAATAT
Found at i:9880 original size:25 final size:25
Alignment explanation
Indices: 9851--9929 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 25
9841 CCTTCTATAG
9851 TTTGTTCATCTCTTCGATACTTAAT
1 TTTGTTCATCTCTTCGATACTTAAT
* * * *
9876 TTTG-T-AGCTTCTTC-ATGTCCTATAG
1 TTTGTTCATC-TCTTCGAT-ACTTA-AT
9901 TTTGTTCATCTCTTCGATACTTAAGT
1 TTTGTTCATCTCTTCGATACTTAA-T
9927 TTT
1 TTT
9930 CCTTTTAACA
Statistics
Matches: 39, Mismatches: 8, Indels: 13
0.65 0.13 0.22
Matches are distributed among these distances:
23 4 0.10
24 9 0.23
25 10 0.26
26 12 0.31
27 4 0.10
ACGTcount: A:0.18, C:0.19, G:0.11, T:0.52
Consensus pattern (25 bp):
TTTGTTCATCTCTTCGATACTTAAT
Found at i:9919 original size:50 final size:52
Alignment explanation
Indices: 9819--9929 Score: 190
Period size: 50 Copynumber: 2.1 Consensus size: 52
9809 CATTTTCTTC
9819 TAATTTTGTAGCTTCTTCATGTCCTTCTATAGTTTGTTCATCTCTTCGATACT
1 TAATTTTGTAGCTTCTTCATGTCC-TCTATAGTTTGTTCATCTCTTCGATACT
9872 TAATTTTGTAGCTTCTTCATGT-C-CTATAGTTTGTTCATCTCTTCGATACT
1 TAATTTTGTAGCTTCTTCATGTCCTCTATAGTTTGTTCATCTCTTCGATACT
9922 TAAGTTTT
1 TAA-TTTT
9930 CCTTTTAACA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
50 30 0.53
51 4 0.07
52 1 0.02
53 22 0.39
ACGTcount: A:0.18, C:0.19, G:0.12, T:0.51
Consensus pattern (52 bp):
TAATTTTGTAGCTTCTTCATGTCCTCTATAGTTTGTTCATCTCTTCGATACT
Found at i:12942 original size:92 final size:87
Alignment explanation
Indices: 12838--13030 Score: 235
Period size: 87 Copynumber: 2.2 Consensus size: 87
12828 TATATTAAAT
*
12838 AAATATTCAATTATAAAAAATAGAACAAATATTAAAATAATT-AATTATTTAATTAGTTATTTAT
1 AAATATTAAATTAT-AAAAATAGAACAAA-A-T-AAAT-ATTAAATTATTTAATTAGTTATTTAT
*
12902 TAAATATTAAATCGAAATATTTAATTCA
61 TAAACATT-AATCGAAATATTTAATTCA
* * * ***
12930 AAATATTAAATTATATAATTATATTTAAATAAATATTAAATTATTTAATTAGTTATTTATTAAAC
1 AAATATTAAATTATAAAAATAGAACAAAATAAATATTAAATTATTTAATTAGTTATTTATTAAAC
* *
12995 CTTAATCGAACTATTTAATTCA
66 ATTAATCGAAATATTTAATTCA
13017 AAATATTAAATTAT
1 AAATATTAAATTAT
13031 TTAATTATAT
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
87 35 0.39
88 32 0.36
89 1 0.01
90 1 0.01
91 8 0.09
92 13 0.14
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (87 bp):
AAATATTAAATTATAAAAATAGAACAAAATAAATATTAAATTATTTAATTAGTTATTTATTAAAC
ATTAATCGAAATATTTAATTCA
Found at i:13024 original size:87 final size:88
Alignment explanation
Indices: 12872--13058 Score: 306
Period size: 87 Copynumber: 2.1 Consensus size: 88
12862 ACAAATATTA
*
12872 AAATAATT-AATTATTTAATTAGTTATTTATTAAATATTAAATCGAAATATTTAATTCAAAATAT
1 AAAT-ATTAAATTATTTAATTAGTTATTTATTAAACATTAAATCGAAATATTTAATTCAAAATAT
12936 TAAATTATATAATTATATTTAAAT
65 TAAATTATATAATTATATTTAAAT
* *
12960 AAATATTAAATTATTTAATTAGTTATTTATTAAACCTT-AATCGAACTATTTAATTCAAAATATT
1 AAATATTAAATTATTTAATTAGTTATTTATTAAACATTAAATCGAAATATTTAATTCAAAATATT
*
13024 AAATTATTTAATTATATTTAAAT
66 AAATTATATAATTATATTTAAAT
*
13047 AAAAATTAAATT
1 AAATATTAAATT
13059 TTTGAACAGA
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
87 61 0.66
88 32 0.34
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (88 bp):
AAATATTAAATTATTTAATTAGTTATTTATTAAACATTAAATCGAAATATTTAATTCAAAATATT
AAATTATATAATTATATTTAAAT
Found at i:13097 original size:87 final size:86
Alignment explanation
Indices: 12876--13101 Score: 203
Period size: 87 Copynumber: 2.6 Consensus size: 86
12866 ATATTAAAAT
* ** * *
12876 AATT-AATTATTTAATTAGTTATTTATTAAATATTAAATCGAAA-TATTTAATTCAAAATATTAA
1 AATTAAATTATTTAATCAGAAATTTA-TAAAAACT-AATC-AAACTATTTAATTCAAAATATTAA
12939 ATTATATAATTATATTTAAATAAA
63 ATTATATAATTATATTTAAATAAA
* * ** * * *
12963 TATTAAATTATTTAATTAGTTATTTATTAAACCTTAATCGAACTATTTAATTCAAAATATTAAAT
1 AATTAAATTATTTAATCAGAAATTTATAAAAAC-TAATCAAACTATTTAATTCAAAATATTAAAT
*
13028 TATTTAATTATATTTAAATAAA
65 TATATAATTATATTTAAATAAA
*
13050 AATTAAATT-TTTGAA-CAGAACAAATTT-TAAAAAC-AACTCAAATTATTTAATT
1 AATTAAATTATTT-AATCAG---AAATTTATAAAAACTAA-TCAAACTATTTAATT
13102 AGTTATTTAT
Statistics
Matches: 116, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
86 9 0.08
87 76 0.66
88 27 0.23
89 4 0.03
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (86 bp):
AATTAAATTATTTAATCAGAAATTTATAAAAACTAATCAAACTATTTAATTCAAAATATTAAATT
ATATAATTATATTTAAATAAA
Found at i:13126 original size:210 final size:209
Alignment explanation
Indices: 12760--13183 Score: 595
Period size: 210 Copynumber: 2.0 Consensus size: 209
12750 CCAATAATTC
* *
12760 ATTAATTAATTATTTATTTATTAAACCCTAAACTCAAATATTTAATTCAAAATATTAAATTAGTT
1 ATTATTTAATTAGTTATTTATTAAACCCTAAACTCAAATATTTAATTCAAAATATTAAATTAGTT
* * * * *
12825 AATTATATTAAATAAATATTCAATTATAAAAAATAGAACAAATATTAAAATAATTAATTATTTAA
66 AATTATATTAAATAAAAATTAAATTATAAAAAACAGAACAAATATTAAAACAATAAATTATTTAA
*
12890 TTAGTTATTTATTAAATATTAAATCGAAATATTTAATTCAAAATATTAAATTATATAATTATATT
131 TTAGTTATTTATTAAACATTAAATCGAAATATTTAATTCAAAATATTAAATTATATAATTATATT
*
12955 TAAATAAATATTAA
196 TAAATAAAAATTAA
* * *
12969 ATTATTTAATTAGTTATTTATTAAA-CCTTAA-TCGAACTATTTAATTCAAAATATTAAATTATT
1 ATTATTTAATTAGTTATTTATTAAACCCTAAACTC-AAATATTTAATTCAAAATATTAAATTAGT
*** *
13032 TAATTATATTTAAATAAAAATTAAATT-T-TTGAACAGAACAAATTTTAAAAACAACTCAAATTA
65 TAATTATA-TTAAATAAAAATTAAATTATAAAAAACAGAACAAATATT-AAAACAA-T-AAATTA
* * * *
13095 TTTAATTAGTTATTTATTAAACCTTAAATCGAACTATTTAATTCAAAATATTAAATTATTTAGTT
126 TTTAATTAGTTATTTATTAAACATTAAATCGAAATATTTAATTCAAAATATTAAATTATATAATT
13160 ATATTTAAATAAAAATTAA
191 ATATTTAAATAAAAATTAA
13179 ATTAT
1 ATTAT
13184 AAAAATTAGA
Statistics
Matches: 190, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
207 15 0.08
208 47 0.25
209 40 0.21
210 88 0.46
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (209 bp):
ATTATTTAATTAGTTATTTATTAAACCCTAAACTCAAATATTTAATTCAAAATATTAAATTAGTT
AATTATATTAAATAAAAATTAAATTATAAAAAACAGAACAAATATTAAAACAATAAATTATTTAA
TTAGTTATTTATTAAACATTAAATCGAAATATTTAATTCAAAATATTAAATTATATAATTATATT
TAAATAAAAATTAA
Found at i:13171 original size:123 final size:121
Alignment explanation
Indices: 12960--13380 Score: 630
Period size: 122 Copynumber: 3.5 Consensus size: 121
12950 ATATTTAAAT
*
12960 AAATATTAAATTATTTAATTAGTTATTTATTAAACCTT-AATCGAACTATTTAATTCAAAATATT
1 AAATAATAAATTATTTAATTAGTTATTTATTAAACCTTAAATCGAACTATTTAATTCAAAATATT
** *
13024 AAATTATTTAATTATATTTAAATAAAAATTAAATT-TTTGAACAGAACAAATTTTAA
66 AAATTATTTAATTATATTTAAATAAAAATTAAATTATTAAAACAGAACAAATATT-A
*
13080 AAACAACTCAAATTATTTAATTAGTTATTTATTAAACCTTAAATCGAACTATTTAATTCAAAATA
1 AAATAA-T-AAATTATTTAATTAGTTATTTATTAAACCTTAAATCGAACTATTTAATTCAAAATA
* * *
13145 TTAAATTATTTAGTTATATTTAAATAAAAATTAAATTATAAAAATTAGAACAAATATTA
64 TTAAATTATTTAATTATATTTAAATAAAAATTAAATTATTAAAA-CAGAACAAATATTA
* *
13204 AAATAATTAATTATTTAATTAGTTATTTATTAAACCTTAAATCGAAATATTTAATTCAAAATATT
1 AAATAATAAATTATTTAATTAGTTATTTATTAAACCTTAAATCGAACTATTTAATTCAAAATATT
* * * *
13269 AAATTATATAATTATATTTAAATAAATATTAAATTATTAAAACATAACAAATATTG
66 AAATTATTTAATTATATTTAAATAAAAATTAAATTATTAAAACAGAACAAATATTA
* * * *
13325 AAATGATTAATTATTTAATTAGTTATTTATTAAACCCTAAATTGAACTATTTAATT
1 AAATAATAAATTATTTAATTAGTTATTTATTAAACCTTAAATCGAACTATTTAATT
13381 ATTAAAAACA
Statistics
Matches: 274, Mismatches: 22, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
120 4 0.01
121 64 0.23
122 125 0.46
123 61 0.22
124 9 0.03
125 11 0.04
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (121 bp):
AAATAATAAATTATTTAATTAGTTATTTATTAAACCTTAAATCGAACTATTTAATTCAAAATATT
AAATTATTTAATTATATTTAAATAAAAATTAAATTATTAAAACAGAACAAATATTA
Found at i:13207 original size:64 final size:63
Alignment explanation
Indices: 13139--13345 Score: 157
Period size: 64 Copynumber: 3.3 Consensus size: 63
13129 TATTTAATTC
*
13139 AAAAT-ATTAAATTATTTAGTTATATTTAAATAAAAATTAAATTATAAAAATTAGAACAAATATT
1 AAAATAATT-AATTATTTAATTATATTTAAATAAAAATTAAATTATAAAAATTA-AACAAATATT
* ** ** * * *
13203 AAAATAATTAATTATTTAATTAGTTATTT-ATTAAACCTTAAA-TCGAAATATT----TAAT-TC
1 AAAATAATTAATTATTTAATTA--TATTTAAATAAAAATTAAATTATAAAAATTAAACAAATATT
* *
13261 AAAAT-ATTAAATTATATAATTATATTTAAATAAATATTAAATTATTAAAACA-T-AACAAATAT
1 AAAATAATT-AATTATTTAATTATATTTAAATAAAAATTAAATTA-TAAAA-ATTAAACAAATAT
13323 T
63 T
* *
13324 GAAATGATTAATTATTTAATTA
1 AAAATAATTAATTATTTAATTA
13346 GTTATTTATT
Statistics
Matches: 110, Mismatches: 20, Indels: 27
0.70 0.13 0.17
Matches are distributed among these distances:
56 5 0.05
57 13 0.12
58 19 0.17
59 7 0.06
60 1 0.01
62 3 0.03
63 17 0.15
64 27 0.25
65 13 0.12
66 5 0.05
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (63 bp):
AAAATAATTAATTATTTAATTATATTTAAATAAAAATTAAATTATAAAAATTAAACAAATATT
Found at i:13405 original size:26 final size:26
Alignment explanation
Indices: 13372--13426 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
13362 TAAATTGAAC
*
13372 TATTTAATTATTAAA-AACAACTCAAA
1 TATTTAATTATTAAATAA-AACCCAAA
13398 TATTTAATTATTAAATAAAACCCAAA
1 TATTTAATTATTAAATAAAACCCAAA
13424 TAT
1 TAT
13427 AACAACTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (26 bp):
TATTTAATTATTAAATAAAACCCAAA
Found at i:19379 original size:15 final size:15
Alignment explanation
Indices: 19356--19388 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19346 ATTTGAAGTT
19356 ATTGATTGGATTTGA
1 ATTGATTGGATTTGA
*
19371 ATTGGTTGGATTTGA
1 ATTGATTGGATTTGA
19386 ATT
1 ATT
19389 TACAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
ATTGATTGGATTTGA
Found at i:19529 original size:44 final size:44
Alignment explanation
Indices: 19454--19726 Score: 222
Period size: 43 Copynumber: 6.3 Consensus size: 44
19444 AATTTGTTAA
* * *
19454 CTTTAGCAGCGTTTGT-GAAAAAAACGTCGCTAAAGAACAT-TAT
1 CTTTAGCGGCGTTTGTGGGAAAAAACGTCGCTAAAGATCATGT-T
*
19497 -TTATAGCGGCGTTTGTGGGAAAAAACGTCGCTAAAGACCATGTT
1 CTT-TAGCGGCGTTTGTGGGAAAAAACGTCGCTAAAGATCATGTT
* * * * *
19541 CTTTAGCAGCGTTTATGGCAAAAGCAC-T-GCTAAAGATCATGAT
1 CTTTAGCGGCGTTTGTGGGAAAA-AACGTCGCTAAAGATCATGTT
* * *
19584 CTTTAGCGGCATTTGTGGG-TAAAGCGTCGCTAAAGATCATGTT
1 CTTTAGCGGCGTTTGTGGGAAAAAACGTCGCTAAAGATCATGTT
* * ** * *
19627 CTTTAGTGGCGTTTGTGGTAGAAGCAC--CGTTAAAGATTATGTT
1 CTTTAGCGGCGTTTGTGGGA-AAAAACGTCGCTAAAGATCATGTT
* * * * * * *
19670 CTTTAGCGTCGTTTGT-GGTAGAAGCGTTGTTAAAGACCATGTT
1 CTTTAGCGGCGTTTGTGGGAAAAAACGTCGCTAAAGATCATGTT
19713 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
19727 TTCCTCATAA
Statistics
Matches: 181, Mismatches: 38, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
41 3 0.02
42 6 0.03
43 124 0.69
44 41 0.23
45 7 0.04
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (44 bp):
CTTTAGCGGCGTTTGTGGGAAAAAACGTCGCTAAAGATCATGTT
Found at i:19652 original size:86 final size:86
Alignment explanation
Indices: 19481--19726 Score: 289
Period size: 86 Copynumber: 2.8 Consensus size: 86
19471 AAAAAAACGT
* * * *
19481 CGCTAAAGAACATTAT-TTATAGCGGCGTTTGTGGGAAAAAACGTCGCTAAAGACCATGTTCTTT
1 CGCTAAAGATCATGATCTT-TAGCGGCGTTTGTGGG-TAAAGCGTCGCTAAAGACCATGTTCTTT
*
19545 AGCAGCGTTTATGGCAAAAGCAC
64 AGCGGCGTTTATGGCAAAAGCAC
* * *
19568 TGCTAAAGATCATGATCTTTAGCGGCATTTGTGGGTAAAGCGTCGCTAAAGATCATGTTCTTTAG
1 CGCTAAAGATCATGATCTTTAGCGGCGTTTGTGGGTAAAGCGTCGCTAAAGACCATGTTCTTTAG
* * * *
19633 TGGCGTTTGTGGTAGAAGCAC
66 CGGCGTTTATGGCAAAAGCAC
* * * * * *
19654 CGTTAAAGATTATGTTCTTTAGCGTCGTTTGT-GGTAGAAGCGTTGTTAAAGACCATGTTCTTTA
1 CGCTAAAGATCATGATCTTTAGCGGCGTTTGTGGGTA-AAGCGTCGCTAAAGACCATGTTCTTTA
19718 GCGGCGTTT
65 GCGGCGTTT
19727 TTCCTCATAA
Statistics
Matches: 135, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
85 4 0.03
86 101 0.75
87 28 0.21
88 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (86 bp):
CGCTAAAGATCATGATCTTTAGCGGCGTTTGTGGGTAAAGCGTCGCTAAAGACCATGTTCTTTAG
CGGCGTTTATGGCAAAAGCAC
Found at i:24483 original size:87 final size:87
Alignment explanation
Indices: 24323--24484 Score: 191
Period size: 87 Copynumber: 1.9 Consensus size: 87
24313 ATTCGTTGAA
* * * * * *
24323 TTCATCAAGTTCGTCTCATTAGGACCACCCAAAGCCTAGGATATGAATTAATTAAGAACATTTAG
1 TTCATCAAGTTCATCCCAATAGGACCACCCAAAGCCTAGGATATGAACTAATTAAGAACATCTAA
*
24388 TGGATCATCCCATAAATATAAG
66 TAGATCATCCCATAAATATAAG
* * * * *
24410 TTCATCAAGTTCATCCCAATAGGACCACCTAAA-CACTGGGCTATGAACTCATTAAGATCATCTA
1 TTCATCAAGTTCATCCCAATAGGACCACCCAAAGC-CTAGGATATGAACTAATTAAGAACATCTA
*
24474 ATAGCTCATCC
65 ATAGATCATCC
24485 TATACATGTA
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
86 1 0.02
87 60 0.98
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (87 bp):
TTCATCAAGTTCATCCCAATAGGACCACCCAAAGCCTAGGATATGAACTAATTAAGAACATCTAA
TAGATCATCCCATAAATATAAG
Found at i:26062 original size:7 final size:7
Alignment explanation
Indices: 26050--26074 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
26040 GCACTTCAAG
26050 CATACCA
1 CATACCA
26057 CATACCA
1 CATACCA
26064 CATACCA
1 CATACCA
26071 CATA
1 CATA
26075 ATAAGTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (7 bp):
CATACCA
Found at i:27540 original size:22 final size:21
Alignment explanation
Indices: 27495--27542 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
27485 TTAAGACTTT
*
27495 CATTATTAAGCTTAATTAACC
1 CATTTTTAAGCTTAATTAACC
* *
27516 CATTTTTAATCTTGATTAAACC
1 CATTTTTAAGCTTAATT-AACC
27538 CATTT
1 CATTT
27543 ATACCTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (21 bp):
CATTTTTAAGCTTAATTAACC
Found at i:31509 original size:1 final size:1
Alignment explanation
Indices: 31505--31530 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
31495 NNNNNNNNNN
31505 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
31531 TTCAGCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32722 original size:21 final size:21
Alignment explanation
Indices: 32696--32735 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
32686 AATATTCATC
32696 TTCTTGACCTTGTAAGACCTT
1 TTCTTGACCTTGTAAGACCTT
32717 TTCTTGACCTTGTAAGACC
1 TTCTTGACCTTGTAAGACC
32736 CAGTCCAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCTTGACCTTGTAAGACCTT
Found at i:35260 original size:25 final size:26
Alignment explanation
Indices: 35222--35270 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
35212 CATAGTATAA
*
35222 ATAAAAATCAATTATTTTTATATTCG
1 ATAAAAATCAATTATTTGTATATTCG
*
35248 ATAAATAT-AATTATTTGTATATT
1 ATAAAAATCAATTATTTGTATATT
35271 TAATATCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (26 bp):
ATAAAAATCAATTATTTGTATATTCG
Found at i:35969 original size:6 final size:6
Alignment explanation
Indices: 35958--35994 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
35948 AGGGAGCCAG
35958 CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT C
1 CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT C
35995 TTCATCATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.49
Consensus pattern (6 bp):
CATCTT
Found at i:36002 original size:18 final size:18
Alignment explanation
Indices: 35958--36002 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
35948 AGGGAGCCAG
*
35958 CATCTTCATCTTCATCTT
1 CATCATCATCTTCATCTT
*
35976 CATCTTCATCTTCATCTT
1 CATCATCATCTTCATCTT
*
35994 CTTCATCAT
1 CATCATCAT
36003 TCCTCTCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (18 bp):
CATCATCATCTTCATCTT
Found at i:45307 original size:23 final size:22
Alignment explanation
Indices: 45256--45316 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
45246 AGTGATTGAA
*
45256 ATTAAATTATAATTTTTACGAT
1 ATTAAATTATAATTTTTACAAT
**
45278 AAAAAATATATAATTTTTA-AAT
1 ATTAAAT-TATAATTTTTACAAT
*
45300 GATTAAATTAAAATTTT
1 -ATTAAATTATAATTTT
45317 ATCATTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (22 bp):
ATTAAATTATAATTTTTACAAT
Found at i:46192 original size:17 final size:17
Alignment explanation
Indices: 46159--46192 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46149 TTGACACGTG
* *
46159 TTTTTTTTATTTTTTTA
1 TTTTTTTTATATATTTA
46176 TTTTTTTTATATATTTA
1 TTTTTTTTATATATTTA
46193 AAAATAAAAA
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:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTTATATATTTA
Found at i:46345 original size:27 final size:27
Alignment explanation
Indices: 46301--46360 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
46291 CCTGACACCC
46301 AATGGAGGAACACAAAGTGGCGGCACT
1 AATGGAGGAACACAAAGTGGCGGCACT
*
46328 AATGGAGGAATATC-AAGTGGCGGCACT
1 AATGGAGGAACA-CAAAGTGGCGGCACT
46355 AA-GGAG
1 AATGGAG
46361 TGTTTTGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 4 0.13
27 26 0.84
28 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.35, T:0.13
Consensus pattern (27 bp):
AATGGAGGAACACAAAGTGGCGGCACT
Found at i:46540 original size:11 final size:11
Alignment explanation
Indices: 46524--46573 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
46514 GGGGACCAAC
* *
46524 GAAAAATGAAG
1 GAAAAAAGAAA
46535 GAAAAAAGAAA
1 GAAAAAAGAAA
46546 GAAAAAAGAGAAA
1 G-AAAAA-AGAAA
46559 GAAATAAAGAAA
1 GAAA-AAAGAAA
46571 GAA
1 GAA
46574 GAAGGAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 10 0.29
12 16 0.47
13 8 0.24
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:46551 original size:12 final size:12
Alignment explanation
Indices: 46536--46573 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
46526 AAAATGAAGG
46536 AAAAAAGAAAGA
1 AAAAAAGAAAGA
46548 AAAAAGAGAAAGA
1 AAAAA-AGAAAGA
*
46561 AATAAAGAAAGA
1 AAAAAAGAAAGA
46573 A
1 A
46574 GAAGGAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAAGA
Done.