Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009656.1 Kokia drynarioides strain JFW-HI SEQ_124374, 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: 93180
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 97 characters in sequence are not A, C, G, or T
Found at i:10429 original size:62 final size:63
Alignment explanation
Indices: 10328--10452 Score: 173
Period size: 62 Copynumber: 2.0 Consensus size: 63
10318 AAGGAAAATA
*
10328 AGGATTATTCCCTTATTAATAGAGAATGCAAATGAAAAGTT-AAAAAATAAATTATATTCTTT
1 AGGATTATTCCCTTATTAATAGAGAATGCAAAAGAAAAGTTGAAAAAATAAATTATATTCTTT
** * * *
10390 AGGATTATTCTTTTATTAATAGAGAA-GATAAAAGGAAAGTTGTAAAAATAAATTATATTCTTT
1 AGGATTATTCCCTTATTAATAGAGAATG-CAAAAGAAAAGTTGAAAAAATAAATTATATTCTTT
10453 TCAAAAAAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
61 1 0.02
62 34 0.62
63 20 0.36
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.37
Consensus pattern (63 bp):
AGGATTATTCCCTTATTAATAGAGAATGCAAAAGAAAAGTTGAAAAAATAAATTATATTCTTT
Found at i:10958 original size:274 final size:276
Alignment explanation
Indices: 10440--10993 Score: 860
Period size: 274 Copynumber: 2.0 Consensus size: 276
10430 TGTAAAAATA
* *
10440 AATTATATTCTTTTCAAAAAAACATTAATTTCCATATCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAAAACATTAATTTCCATATATTTTATATTTTGACCGAAATTAATTAA
* *
10505 TATAACTGTTTATATTAATAAATTAGGTAAAATATATACAATTAATGTTTTGTATAAATCAAATT
66 TATAACTATTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATAAATCAAATT
* * * *
10570 CATATATTAATTATATTCTTTCCGAAAGAATATTAATTTTCATGTCTTTTATATTTTTATCGAAA
131 CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGACCGAAA
* * * *
10635 TTAATTAATAAAACTATTTATATTAATAATTTCGGTAATATAAATACAATTAATATTTTGTATGA
196 TTAATTAATAAAACTATTTATATTAATAAATTAGATAAAATAAATACAATTAATATTTTGTATGA
10700 ATCAAATTCATATATT
261 ATCAAATTCATATATT
* * * *
10716 AATTATATTC-TTTC-CAAAAATATTAATTTTCATGTATTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAAAACATTAATTTCCATATATTTTATATTTTGACCGAAATTAATTAA
* *
10779 TATAACTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTATTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATAAATCAAATT
* * *
10844 CATATATTAATTTTATTTTTTTCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGACCGAAA
131 CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGACCGAAA
* * * *
10909 TTAATTAATATAATTGTTTATATTAATAAATTAGATAAAATATATACAATTAATATTTTGTATGA
196 TTAATTAATAAAACTATTTATATTAATAAATTAGATAAAATAAATACAATTAATATTTTGTATGA
*
10974 ATTAAATTCATATATT
261 ATCAAATTCATATATT
10990 AATT
1 AATT
10994 TTATCTATGT
Statistics
Matches: 252, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
274 238 0.94
275 4 0.02
276 10 0.04
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (276 bp):
AATTATATTCTTTTCAAAAAAACATTAATTTCCATATATTTTATATTTTGACCGAAATTAATTAA
TATAACTATTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATAAATCAAATT
CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGACCGAAA
TTAATTAATAAAACTATTTATATTAATAAATTAGATAAAATAAATACAATTAATATTTTGTATGA
ATCAAATTCATATATT
Found at i:10968 original size:67 final size:67
Alignment explanation
Indices: 10756--10968 Score: 159
Period size: 67 Copynumber: 3.1 Consensus size: 67
10746 CATGTATTTT
* * *
10756 ATATTTTGACCGAAATTAATTAATATAACTATTTATATTAATAAATTTGGTAAAATATATACAAT
1 ATATTTTGACCGAAATTAATTAATATAATTATTTATATTAATAAATTAGATAAAATATATACAAT
10821 TA
66 TA
* * * * * * * *
10823 ATATTTTGTA-TG-AATCAAATTCATATATTAATTTTATTT-TTTTCAA-AAA-AATATTAATTT
1 ATATTTTG-ACCGAAAT-TAATT-A-ATA-TAA--TTATTTATATT-AATAAATTAGATAAAATA
* * *
10883 TCATGTC-TTTT
58 T-AT-ACAATTA
*
10894 ATATTTTGACCGAAATTAATTAATATAATTGTTTATATTAATAAATTAGATAAAATATATACAAT
1 ATATTTTGACCGAAATTAATTAATATAATTATTTATATTAATAAATTAGATAAAATATATACAAT
10959 TA
66 TA
10961 ATATTTTG
1 ATATTTTG
10969 TATGAATTAA
Statistics
Matches: 104, Mismatches: 26, Indels: 32
0.64 0.16 0.20
Matches are distributed among these distances:
66 11 0.11
67 31 0.30
68 12 0.12
69 6 0.06
70 10 0.10
71 23 0.22
72 11 0.11
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (67 bp):
ATATTTTGACCGAAATTAATTAATATAATTATTTATATTAATAAATTAGATAAAATATATACAAT
TA
Found at i:10997 original size:138 final size:138
Alignment explanation
Indices: 10440--10993 Score: 860
Period size: 138 Copynumber: 4.0 Consensus size: 138
10430 TGTAAAAATA
* * * *
10440 AATTATATTCTTTTCAAAAAAACATTAATTTCCATATCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
10505 TATAACTGTTTATATTAATAAATTAGGTAAAATATATACAATTAATGTTTTGTATAAATCAAATT
66 TATAACTATTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
10570 CATATATT
131 CATATATT
* * * * *
10578 AATTATATTCTTTCCGAAAGAATATTAATTTTCATGTCTTTTATATTTTTATCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * *
10643 TAAAACTATTTATATTAATAATTTCGGTAATATAAATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTATTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
10708 CATATATT
131 CATATATT
* *
10716 AATTATATTC-TTTC-CAAAAATATTAATTTTCATGTATTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
*
10779 TATAACTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTATTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
10844 CATATATT
131 CATATATT
* *
10852 AATTTTATTTTTTTCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * *
10917 TATAATTGTTTATATTAATAAATTAGATAAAATATATACAATTAATATTTTGTATGAATTAAATT
66 TATAACTATTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
10982 CATATATT
131 CATATATT
10990 AATT
1 AATT
10994 TTATCTATGT
Statistics
Matches: 379, Mismatches: 35, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
136 120 0.32
137 7 0.02
138 252 0.66
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (138 bp):
AATTATATTCTTTTCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAACTATTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:27325 original size:28 final size:28
Alignment explanation
Indices: 27294--27352 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
27284 AACAATCATG
27294 AATCCCAATAGAATGGG-GTTTTTTATTC
1 AATCCCAATAGAATGGGAG-TTTTTATTC
27322 AATCCCAATAGAATGGGAGTTTTTATTC
1 AATCCCAATAGAATGGGAGTTTTTATTC
27350 AAT
1 AAT
27353 AAAAACTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (28 bp):
AATCCCAATAGAATGGGAGTTTTTATTC
Found at i:33726 original size:19 final size:19
Alignment explanation
Indices: 33702--33740 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
33692 GCACTTTGCT
33702 ATAATTCTTTTTTCACAAC
1 ATAATTCTTTTTTCACAAC
33721 ATAATTCTTTTTTCACAAC
1 ATAATTCTTTTTTCACAAC
33740 A
1 A
33741 AACAATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAATTCTTTTTTCACAAC
Found at i:35865 original size:23 final size:24
Alignment explanation
Indices: 35835--35886 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
35825 CTATCGTATT
* *
35835 AAAT-TAATTTTATATA-ATAAAA
1 AAATATAATTTCATACATATAAAA
35857 AAATATAATTTCATACATATAAAA
1 AAATATAATTTCATACATATAAAA
*
35881 ATATAT
1 AAATAT
35887 TAAAATGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.16
23 10 0.40
24 11 0.44
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATATAATTTCATACATATAAAA
Found at i:37370 original size:30 final size:30
Alignment explanation
Indices: 37334--37395 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
37324 TACTAATTTT
*
37334 ATCATCCAAAACGATTCTTTTCCATAAATA
1 ATCATCCAAAACGATTCATTTCCATAAATA
*
37364 ATCATCCAAAATGATTCATTTCCATAAATA
1 ATCATCCAAAACGATTCATTTCCATAAATA
37394 AT
1 AT
37396 TTTGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (30 bp):
ATCATCCAAAACGATTCATTTCCATAAATA
Found at i:38701 original size:19 final size:19
Alignment explanation
Indices: 38674--38715 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
38664 AATAAACATA
38674 TTATCTCTT-TTAAATAATT
1 TTATCTCTTATT-AATAATT
* *
38693 TTATGTCTTATTATTAATT
1 TTATCTCTTATTAATAATT
38712 TTAT
1 TTAT
38716 TTTGAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATCTCTTATTAATAATT
Found at i:40839 original size:29 final size:29
Alignment explanation
Indices: 40807--40910 Score: 81
Period size: 31 Copynumber: 3.6 Consensus size: 29
40797 TAAATATCAA
40807 AATTATATATAAATTATAATTTAATGTAT
1 AATTATATATAAATTATAATTTAATGTAT
* * * *
40836 AATTTTATACATAAATTTTGATTTTATGTA-
1 AA--TTATATATAAATTATAATTTAATGTAT
* *
40866 ATTTTATATATAAAATTTTAATTTAAT-T-T
1 A-ATTATATAT-AAATTATAATTTAATGTAT
*
40895 AATT-TTTATAAATTAT
1 AATTATATATAAATTAT
40911 TAATACAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
26 6 0.10
27 4 0.07
28 2 0.03
29 11 0.19
30 14 0.24
31 22 0.37
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (29 bp):
AATTATATATAAATTATAATTTAATGTAT
Found at i:40850 original size:31 final size:30
Alignment explanation
Indices: 40809--40904 Score: 117
Period size: 30 Copynumber: 3.2 Consensus size: 30
40799 AATATCAAAA
*
40809 TTATATATAAATTATAATTTAATGTATAATT
1 TTATATATAAATTTTAATTTAATGT-TAATT
* * *
40840 TTATACATAAATTTTGATTTTATG-TAATT
1 TTATATATAAATTTTAATTTAATGTTAATT
40869 TTATATATAAAATTTTAATTTAAT-TTAATT
1 TTATATAT-AAATTTTAATTTAATGTTAATT
40899 TT-TATA
1 TTATATA
40905 AATTATTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
29 16 0.29
30 20 0.36
31 20 0.36
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (30 bp):
TTATATATAAATTTTAATTTAATGTTAATT
Found at i:40968 original size:29 final size:30
Alignment explanation
Indices: 40936--41001 Score: 116
Period size: 29 Copynumber: 2.2 Consensus size: 30
40926 ATTTTACGTG
40936 TATAATTACATATTAAATTAAAA-TTTATA
1 TATAATTACATATTAAATTAAAATTTTATA
40965 TATAATTACATATTAAATTAAAATTTTATA
1 TATAATTACATATTAAATTAAAATTTTATA
*
40995 AATAATT
1 TATAATT
41002 TTAAGATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (30 bp):
TATAATTACATATTAAATTAAAATTTTATA
Found at i:47185 original size:4 final size:4
Alignment explanation
Indices: 47168--47256 Score: 142
Period size: 4 Copynumber: 22.2 Consensus size: 4
47158 GGCCACCATT
*
47168 ATAC ATAC ACAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
47216 ATAC ATAC TTAC ATAC ATAC AGAC ATAC AGAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
47257 GGAATATTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 77 1.00
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.22
Consensus pattern (4 bp):
ATAC
Found at i:49425 original size:6 final size:6
Alignment explanation
Indices: 49414--49439 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
49404 TGGGGCATAG
49414 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
49440 GAAAGAAAAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:52923 original size:17 final size:16
Alignment explanation
Indices: 52899--52947 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
52889 AGATATCACG
52899 AATTTTAAAAAAAATT
1 AATTTTAAAAAAAATT
* * *
52915 ATTTTTTAAATATAATT
1 A-ATTTTAAAAAAAATT
52932 AATTTTAAATAAAAAT
1 AATTTTAAA-AAAAAT
52948 AATCATTAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTTAAAAAAAATT
Found at i:52937 original size:16 final size:16
Alignment explanation
Indices: 52899--52950 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
52889 AGATATCACG
*
52899 AATTTTAAAAAAAATT
1 AATTTTAAATAAAATT
* *
52915 ATTTTTTAAATATAATT
1 A-ATTTTAAATAAAATT
*
52932 AATTTTAAATAAAAAT
1 AATTTTAAATAAAATT
52948 AAT
1 AAT
52951 CATTAACTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTTAAATAAAATT
Found at i:56693 original size:45 final size:45
Alignment explanation
Indices: 56642--56831 Score: 188
Period size: 45 Copynumber: 4.2 Consensus size: 45
56632 GATCAGGTTG
* * *
56642 TTTTGGAAGGAAACAAGATTGATCTTACATCTGAAACTGATACTA
1 TTTTGGAAGAAAAGAAGATTGATCTTACATCTGAAAATGATACTA
* * * ** * *
56687 TTTTGGAAGAAAAGAGGATTGATCTTGCATC-CATTGACGATACTT
1 TTTTGGAAGAAAAGAAGATTGATCTTACATCTGA-AAATGATACTA
* *
56732 TTTTGGAAGAAAAG-AGAATTGATCTTACATC-AAATAATGATACTC
1 TTTTGGAAGAAAAGAAG-ATTGATCTTACATCTGAA-AATGATACTA
* * * *
56777 TTTTGGAAGAAAAGAGGATTGATCCTGCATCAGAAAATGATACTA
1 TTTTGGAAGAAAAGAAGATTGATCTTACATCTGAAAATGATACTA
56822 TTTTGGAAGA
1 TTTTGGAAGA
56832 GTATAGCTCT
Statistics
Matches: 118, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
44 2 0.02
45 113 0.96
46 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (45 bp):
TTTTGGAAGAAAAGAAGATTGATCTTACATCTGAAAATGATACTA
Found at i:56795 original size:90 final size:90
Alignment explanation
Indices: 56642--56807 Score: 248
Period size: 90 Copynumber: 1.8 Consensus size: 90
56632 GATCAGGTTG
* *
56642 TTTTGGAAGGAAACAAGATTGATCTTACATCTGAAACTGATACTATTTTGGAAGAAAAGAGGATT
1 TTTTGGAAGGAAACAAGATTGATCTTACATCTAAAAATGATACTATTTTGGAAGAAAAGAGGATT
*
56707 GATCTTGCATCCATTGACGATACTT
66 GATCCTGCATCCATTGACGATACTT
*
56732 TTTTGGAA-GAAA-AGAGAATTGATCTTACATC-AAATAATGATACTCTTTTGGAAGAAAAGAGG
1 TTTTGGAAGGAAACA-AG-ATTGATCTTACATCTAAA-AATGATACTATTTTGGAAGAAAAGAGG
56794 ATTGATCCTGCATC
63 ATTGATCCTGCATC
56808 AGAAAATGAT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
88 1 0.01
89 8 0.12
90 60 0.87
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (90 bp):
TTTTGGAAGGAAACAAGATTGATCTTACATCTAAAAATGATACTATTTTGGAAGAAAAGAGGATT
GATCCTGCATCCATTGACGATACTT
Found at i:56819 original size:90 final size:89
Alignment explanation
Indices: 56642--56831 Score: 233
Period size: 90 Copynumber: 2.1 Consensus size: 89
56632 GATCAGGTTG
* *
56642 TTTTGGAAGGAAACAAGATTGATCTTACATCTGAAACTGATACTATTTTGGAAGAAAAGAGGATT
1 TTTTGGAA-GAAACAAGATTGATCTTACATCTAAAAATGATACTATTTTGGAAGAAAAGAGGATT
* *** *
56707 GATCTTGCATCCATTGACGATACTT
65 GATCCTGCATCCAAAAACGATACTA
*
56732 TTTTGGAAGAAA-AGAGAATTGATCTTACATC-AAATAATGATACTCTTTTGGAAGAAAAGAGGA
1 TTTTGGAAGAAACA-AG-ATTGATCTTACATCTAAA-AATGATACTATTTTGGAAGAAAAGAGGA
*
56795 TTGATCCTGCAT-CAGAAAATGATACTA
63 TTGATCCTGCATCCA-AAAACGATACTA
56822 TTTTGGAAGA
1 TTTTGGAAGA
56832 GTATAGCTCT
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
88 1 0.01
89 10 0.11
90 76 0.87
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (89 bp):
TTTTGGAAGAAACAAGATTGATCTTACATCTAAAAATGATACTATTTTGGAAGAAAAGAGGATTG
ATCCTGCATCCAAAAACGATACTA
Found at i:72004 original size:29 final size:28
Alignment explanation
Indices: 71960--72132 Score: 163
Period size: 30 Copynumber: 5.9 Consensus size: 28
71950 CCCCGAAGGT
71960 CCCTAAACCTTCCAAAAATTACCATTTTAC
1 CCCTAAA-CTTCCAAAAA-TACCATTTTAC
* *
71990 CCCTAAACTTCCAAAAATCCCATTTTTGGC
1 CCCTAAACTTCCAAAAATACCA-TTTT-AC
* *
72020 CCCGAACCTTCCAAAAATTACCATTTTA-
1 CCCTAAACTTCCAAAAA-TACCATTTTAC
*
72048 CCCTCAAACTTCTAAAAAT-CTCATTTTGAC
1 CCCT-AAACTTCCAAAAATAC-CATTTT-AC
* *
72078 CCCGAACCTTCCAAAAAATACCATTTTA-
1 CCCTAAACTTCC-AAAAATACCATTTTAC
*
72106 CCCTCAAACTTCCAAAAATCCCATTTT
1 CCCT-AAACTTCCAAAAATACCATTTT
72133 TGACCTCGAA
Statistics
Matches: 118, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.01
28 30 0.25
29 40 0.34
30 42 0.36
31 5 0.04
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATACCATTTTAC
Found at i:72057 original size:59 final size:59
Alignment explanation
Indices: 71965--72153 Score: 292
Period size: 59 Copynumber: 3.2 Consensus size: 59
71955 AAGGTCCCTA
*
71965 AACCTTCCAAAAATTACCATTTTACCC-CTAAACTTCCAAAAATCCCATTTTTGGCCCCG
1 AACCTTCCAAAAATTACCATTTTACCCTC-AAACTTCCAAAAATCCCATTTTTGACCCCG
* *
72024 AACCTTCCAAAAATTACCATTTTACCCTCAAACTTCTAAAAATCTCA-TTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
* *
72082 AACCTTCCAAAAAATACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCG
1 AACCTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
* *
72141 AAACATCCAAAAA
1 AACCTTCCAAAAA
72154 AAAAATACTA
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
58 54 0.45
59 64 0.54
60 1 0.01
ACGTcount: A:0.37, C:0.32, G:0.04, T:0.28
Consensus pattern (59 bp):
AACCTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:72133 original size:29 final size:29
Alignment explanation
Indices: 71968--72153 Score: 170
Period size: 29 Copynumber: 6.3 Consensus size: 29
71958 GTCCCTAAAC
*
71968 CTTCCAAAAATTACCATTTTACCC-CTAAA
1 CTTCCAAAAA-TACCATTTTACCCTCGAAA
* * *
71997 CTTCCAAAAATCCCATTTTTGGCCC-CGAAC
1 CTTCCAAAAATACCA-TTTT-ACCCTCGAAA
72027 CTTCCAAAAATTACCATTTTACCCTC-AAA
1 CTTCCAAAAA-TACCATTTTACCCTCGAAA
* *
72056 CTTCTAAAAAT-CTCATTTTGACCC-CGAAC
1 CTTCCAAAAATAC-CATTTT-ACCCTCGAAA
72085 CTTCCAAAAAATACCATTTTACCCTC-AAA
1 CTTCC-AAAAATACCATTTTACCCTCGAAA
*
72114 CTTCCAAAAATCCCATTTTTGA-CCTCGAAA
1 CTTCCAAAAATACCA-TTTT-ACCCTCGAAA
*
72144 CATCCAAAAA
1 CTTCCAAAAA
72154 AAAAATACTA
Statistics
Matches: 131, Mismatches: 13, Indels: 25
0.78 0.08 0.15
Matches are distributed among these distances:
27 1 0.01
28 21 0.16
29 57 0.44
30 47 0.36
31 5 0.04
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.28
Consensus pattern (29 bp):
CTTCCAAAAATACCATTTTACCCTCGAAA
Found at i:72152 original size:30 final size:29
Alignment explanation
Indices: 71968--72153 Score: 157
Period size: 30 Copynumber: 6.3 Consensus size: 29
71958 GTCCCTAAAC
* * *
71968 CTTCCAAAAATTACCATTTT-ACCCCTAAA
1 CTTCCAAAAA-TCCCATTTTGACCTCGAAA
* * *
71997 CTTCCAAAAATCCCATTTTTGGCCCCGAAC
1 CTTCCAAAAATCCCA-TTTTGACCTCGAAA
*
72027 CTTCCAAAAATTACCATTTT-ACCCTC-AAA
1 CTTCCAAAAA-TCCCATTTTGA-CCTCGAAA
* * * *
72056 CTTCTAAAAATCTCATTTTGACCCCGAAC
1 CTTCCAAAAATCCCATTTTGACCTCGAAA
*
72085 CTTCCAAAAAATACCATTTT-ACCCTC-AAA
1 CTTCC-AAAAATCCCATTTTGA-CCTCGAAA
72114 CTTCCAAAAATCCCATTTTTGACCTCGAAA
1 CTTCCAAAAATCCCA-TTTTGACCTCGAAA
*
72144 CATCCAAAAA
1 CTTCCAAAAA
72154 AAAAATACTA
Statistics
Matches: 126, Mismatches: 20, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
28 23 0.18
29 48 0.38
30 51 0.40
31 4 0.03
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.28
Consensus pattern (29 bp):
CTTCCAAAAATCCCATTTTGACCTCGAAA
Found at i:74077 original size:12 final size:12
Alignment explanation
Indices: 74060--74091 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
74050 AATAAAATAC
74060 GCTCTCTCTCTT
1 GCTCTCTCTCTT
74072 GCTCTCTCTCTT
1 GCTCTCTCTCTT
74084 GCTCTCTC
1 GCTCTCTC
74092 ATTCTCTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.44, G:0.09, T:0.47
Consensus pattern (12 bp):
GCTCTCTCTCTT
Found at i:77468 original size:49 final size:49
Alignment explanation
Indices: 77394--77497 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
77384 ACCCATTATA
*
77394 TGTATACACAGGACACTTTAACCTAGGACAAAGTTTATTGAATTGTAGT
1 TGTATACACAGGACACTTTAACCTAGGACAAAGTTTATTCAATTGTAGT
* *
77443 TTTATACACAGGACACTTTAACCTAGTACAAAGTTTATTCAATTGTAGT
1 TGTATACACAGGACACTTTAACCTAGGACAAAGTTTATTCAATTGTAGT
77492 TGTATA
1 TGTATA
77498 TATCTTTAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (49 bp):
TGTATACACAGGACACTTTAACCTAGGACAAAGTTTATTCAATTGTAGT
Found at i:87243 original size:19 final size:19
Alignment explanation
Indices: 87219--87283 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
87209 TATACATTGA
*
87219 AATTTTTATAAATATTTTG
1 AATTTTTAAAAATATTTTG
87238 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAA-TATTTTG
87257 AATTTTTTAAAAATATTTTG
1 AA-TTTTTAAAAATATTTTG
87277 AATTTTT
1 AATTTTT
87284 TTTGTAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
18 8 0.19
19 16 0.38
20 9 0.21
21 9 0.21
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
AATTTTTAAAAATATTTTG
Found at i:87284 original size:20 final size:20
Alignment explanation
Indices: 87215--87284 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
87205 TATATATACA
* *
87215 TTGAAATTTTTATAAATATT
1 TTGAATTTTTTAAAAATATT
87235 TTGAA--TTTTAAAAATTATT
1 TTGAATTTTTTAAAAA-TATT
87254 TTGAATTTTTTAAAAATATT
1 TTGAATTTTTTAAAAATATT
87274 TTGAATTTTTT
1 TTGAATTTTTT
87285 TTGTAATTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
18 8 0.17
19 9 0.20
20 20 0.43
21 9 0.20
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGAATTTTTTAAAAATATT
Found at i:88475 original size:31 final size:31
Alignment explanation
Indices: 88437--88502 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
88427 ATAATTATGC
* * *
88437 ACATAAAACTTTGATTTTTATTTAAATGTAT
1 ACATAAAACTTCGATTTTAATTCAAATGTAT
*
88468 ACATAAAACTTCGATTTTAATTCAATTGTAT
1 ACATAAAACTTCGATTTTAATTCAAATGTAT
88499 ACAT
1 ACAT
88503 TTAATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (31 bp):
ACATAAAACTTCGATTTTAATTCAAATGTAT
Done.