Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007351.1 Kokia drynarioides strain JFW-HI SEQ_121967, 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: 39159
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:71 original size:39 final size:38
Alignment explanation
Indices: 28--327 Score: 152
Period size: 39 Copynumber: 7.7 Consensus size: 38
18 TAGTCATCCG
*
28 ATCTTTTACCCCGAGCCTGAGGCAGATTGTAGCCATCAA
1 ATCTTTTACCCCGAGCCTGAGGCAGATT-CAGCCATCAA
** * *
67 ATCTTTTACCTTGAGCTTG-GG-ACATATCA-CCATCAGCTA
1 ATCTTTTACCCCGAGCCTGAGGCAGAT-TCAGCCATCA---A
* * **
106 ATCTCTTACCCCGAGCCT-AGGGCAGATTGCAGCTATCCG
1 ATCTTTTACCCCGAGCCTGA-GGCAGATT-CAGCCATCAA
* * *
145 ATCTTTTACCTCGAGTCTGGGGCAGA-TCA-CCATCAACCA
1 ATCTTTTACCCCGAGCCTGAGGCAGATTCAGCCATC-A--A
* *
184 ATCTCTTACCCCGAGCCT-AGGACAGATTACAGCCATCGA
1 ATCTTTTACCCCGAGCCTGAGG-CAGATT-CAGCCATCAA
* * *
223 ATCTTTTACCCTGAGCCTGGGGTAGA-TCA-CCATCAGCGA
1 ATCTTTTACCCCGAGCCTGAGGCAGATTCAGCCATCA---A
* * * * * * *
262 ATCTCTTACCCCGGGCTTGGGGTAGATTGTAGCCATCAG
1 ATCTTTTACCCCGAGCCTGAGGCAGATT-CAGCCATCAA
*
301 ATCTTTTACCCCAAGCCT-AGGGCAGAT
1 ATCTTTTACCCCGAGCCTGA-GGCAGAT
328 CACCATTAGC
Statistics
Matches: 194, Mismatches: 42, Indels: 50
0.68 0.15 0.17
Matches are distributed among these distances:
36 15 0.08
37 8 0.04
38 7 0.04
39 134 0.69
40 7 0.04
41 8 0.04
42 15 0.08
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (38 bp):
ATCTTTTACCCCGAGCCTGAGGCAGATTCAGCCATCAA
Found at i:174 original size:78 final size:78
Alignment explanation
Indices: 28--386 Score: 382
Period size: 78 Copynumber: 4.6 Consensus size: 78
18 TAGTCATCCG
* ** * * * *
28 ATCTTTTACCCCGAGCCT-GAGGCAGATTGTAGCCATCAAATCTTTTACCTTGAGCTTGGGACAT
1 ATCTCTTACCCCGAGCCTAG-GGCAGATTGTAGCCATCCGATCTTTTACCTCGAGCCTGGGGCAG
*
92 ATCACCATCAGCTA
65 ATCACCATCAGCCA
* * *
106 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCTATCCGATCTTTTACCTCGAGTCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGTAGCCATCCGATCTTTTACCTCGAGCCTGGGGCAGA
*
171 TCACCATCAACCA
66 TCACCATCAGCCA
* ** *
184 ATCTCTTACCCCGAGCCTAGGACAGATTACAGCCAT-CGAATCTTTTACC-CTGAGCCTGGGGTA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGTAGCCATCCG-ATCTTTTACCTC-GAGCCTGGGGCA
*
247 GATCACCATCAGCGA
64 GATCACCATCAGCCA
* * * * * * * *
262 ATCTCTTACCCCGGGCTTGGGGTAGATTGTAGCCATCAGATCTTTTACCCCAAGCCTAGGGCAGA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGTAGCCATCCGATCTTTTACCTCGAGCCTGGGGCAGA
*
327 TCACCATTAGCCA
66 TCACCATCAGCCA
* * * * **
340 ATGTCTTACCCCGAGCTTGGGGTAGATTGTAATCATCCGATCTTTTA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGTAGCCATCCGATCTTTTA
387 GGGTAGATCA
Statistics
Matches: 239, Mismatches: 37, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
77 3 0.01
78 233 0.97
79 3 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTAGGGCAGATTGTAGCCATCCGATCTTTTACCTCGAGCCTGGGGCAGA
TCACCATCAGCCA
Found at i:283 original size:117 final size:117
Alignment explanation
Indices: 106--627 Score: 313
Period size: 117 Copynumber: 4.6 Consensus size: 117
96 CCATCAGCTA
* * * ** * * *
106 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCTATCCGATCTTTTACCTCGAG-TCTGGGGCAG
1 ATCTTTTACCCCGAGCCTGGGGTAGATCACATC-ATCCGATCTCTTACCCCGAGCT-TGGGGCAG
* * *
170 ATCACCATCAACCAATCTCTTACCCCGAGCCTAGGACAGATTACAGCCA-T-CG
64 ATCACCATCAACCAATCTCTTACCCCAAGCCTAGGGCAGATTGCAGCCATTACG
* * * *
222 AATCTTTTACCCTGAGCCTGGGGTAGATCACCATCA-GCGAATCTCTTACCCCGGGCTTGGGGTA
1 -ATCTTTTACCCCGAGCCTGGGGTAGATCA-CATCATCCG-ATCTCTTACCCCGAGCTTGGGGCA
* * * *
286 GATTGTAGCCATC-A--GATCTTTTACCCCAAGCCTAGGGCAGA-T-CA-CCATTAGCCA
63 GA-T-CA-CCATCAACCAATCTCTTACCCCAAGCCTAGGGCAGATTGCAGCCATTA--CG
* * * * * *
340 ATGTCTTACCCCGAGCTTGGGGTAGATTGTA-ATCATCCGA--TCTT---------TTAGGGTAG
1 ATCTTTTACCCCGAGCCTGGGGTAGA-T-CACATCATCCGATCTCTTACCCCGAGCTTGGGGCAG
* * * *
393 ATCACCATCAACCAATCTCTTACCACAAG-CTTGTGGCAAATTGCAACCATT-CG
64 ATCACCATCAACCAATCTCTTACCCCAAGCCTAG-GGCAGATTGCAGCCATTACG
* * * * *
446 ATCTTTTACCCCGAGTCTGGGGTAGATTACAGTCATCCGATCTTTTACCCCGAGCTTGGAGCATA
1 ATCTTTTACCCCGAGCCTGGGGTAGATCACA-TCATCCGATCTCTTACCCCGAGCTTGGGGCAGA
* * * * *
511 TCACCATCAACCAAACTCTTACCCCGAG-CTTGAGGCAGATTGTAGCCA-TCCG
65 TCACCATCAACCAATCTCTTACCCCAAGCCTAG-GGCAGATTGCAGCCATTACG
* * * * * **
563 ATCTTTTACCCCAAGCTTGAGGCAGATCACATCAGCAAATCTCTTACCCCGAGCTTGGGGCAGAT
1 ATCTTTTACCCCGAGCCTGGGGTAGATCACATCATCCGATCTCTTACCCCGAGCTTGGGGCAGAT
628 TGCAGCCATT
Statistics
Matches: 311, Mismatches: 60, Indels: 69
0.71 0.14 0.16
Matches are distributed among these distances:
103 5 0.02
104 4 0.01
105 6 0.02
106 58 0.19
107 1 0.00
108 5 0.02
109 5 0.02
114 3 0.01
115 7 0.02
116 32 0.10
117 168 0.54
118 9 0.03
119 3 0.01
120 5 0.02
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (117 bp):
ATCTTTTACCCCGAGCCTGGGGTAGATCACATCATCCGATCTCTTACCCCGAGCTTGGGGCAGAT
CACCATCAACCAATCTCTTACCCCAAGCCTAGGGCAGATTGCAGCCATTACG
Found at i:304 original size:156 final size:156
Alignment explanation
Indices: 28--355 Score: 424
Period size: 156 Copynumber: 2.1 Consensus size: 156
18 TAGTCATCCG
* ** * * *
28 ATCTTTTACCCCGAGCCTGAGGCAGATTGTAGCCATCAAATCTTTTACCTTGAGCTTGGGACATA
1 ATCTCTTACCCCGAGCCTGAGGCAGATTACAGCCATCAAATCTTTTACCCTGAGCCTGGGACAGA
* * * * *
93 TCACCATCAGCTAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCTATCCGATCTTTTACCTCG
66 TCACCATCAGCGAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCAGATCTTTTACCCCA
* *
158 AGTCTGGGGCAGATCACCATCAACCA
131 AGCCTAGGGCAGATCACCATCAACCA
* **
184 ATCTCTTACCCCGAGCCT-AGGACAGATTACAGCCATCGAATCTTTTACCCTGAGCCTGGGGTAG
1 ATCTCTTACCCCGAGCCTGAGG-CAGATTACAGCCATCAAATCTTTTACCCTGAGCCTGGGACAG
* * * * *
248 ATCACCATCAGCGAATCTCTTACCCCGGGCTTGGGGTAGATTGTAGCCATCAGATCTTTTACCCC
65 ATCACCATCAGCGAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCAGATCTTTTACCCC
* *
313 AAGCCTAGGGCAGATCACCATTAGCCA
130 AAGCCTAGGGCAGATCACCATCAACCA
*
340 ATGTCTTACCCCGAGC
1 ATCTCTTACCCCGAGC
356 TTGGGGTAGA
Statistics
Matches: 147, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
155 3 0.02
156 144 0.98
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (156 bp):
ATCTCTTACCCCGAGCCTGAGGCAGATTACAGCCATCAAATCTTTTACCCTGAGCCTGGGACAGA
TCACCATCAGCGAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCAGATCTTTTACCCCA
AGCCTAGGGCAGATCACCATCAACCA
Found at i:448 original size:67 final size:67
Alignment explanation
Indices: 318--453 Score: 164
Period size: 67 Copynumber: 2.0 Consensus size: 67
308 ACCCCAAGCC
* * * * * * * * *
318 TAGGGCAGATCACCATTAGCCAATGTCTTACCCCGAGCTTGGGGTAGATTGTAATCATCCGATCT
1 TAGGGCAGATCACCATCAACCAATCTCTTACCACAAGCTTGGGGCAAATTGCAACCATCCGATCT
383 TT
66 TT
* * *
385 TAGGGTAGATCACCATCAACCAATCTCTTACCACAAGCTTGTGGCAAATTGCAACCATTCGATCT
1 TAGGGCAGATCACCATCAACCAATCTCTTACCACAAGCTTGGGGCAAATTGCAACCATCCGATCT
450 TT
66 TT
452 TA
1 TA
454 CCCCGAGTCT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (67 bp):
TAGGGCAGATCACCATCAACCAATCTCTTACCACAAGCTTGGGGCAAATTGCAACCATCCGATCT
TT
Found at i:572 original size:39 final size:38
Alignment explanation
Indices: 420--765 Score: 190
Period size: 39 Copynumber: 9.0 Consensus size: 38
410 TCTTACCACA
* * *
420 AGCTTGTGGCAAATTGCAACCATTCGATCTTTTACCCCG
1 AGCTTGAGGCAGATTGC-ACCATCCGATCTTTTACCCCG
* * * *
459 AG-TCTGGGGTAGATTACAGTCATCCGATCTTTTACCCCG
1 AGCT-TGAGGCAGATTGCA-CCATCCGATCTTTTACCCCG
* * * *
498 AGCTTG-GAGCATA-T-CACCATCAACCAAACTCTTACCCCG
1 AGCTTGAG-GCAGATTGCACCAT---CCGATCTTTTACCCCG
* *
537 AGCTTGAGGCAGATTGTAGCCATCCGATCTTTTACCCCA
1 AGCTTGAGGCAGATTGCA-CCATCCGATCTTTTACCCCG
** * * ** *
576 AGCTTGAGGCAGATCACATCAGCAAATCTCTTACCCCG
1 AGCTTGAGGCAGATTGCACCATCCGATCTTTTACCCCG
* **
614 AGCTTGGGGCAGATTGCAGCCATTAGATCTTTTACCCCG
1 AGCTTGAGGCAGATTGCA-CCATCCGATCTTTTACCCCG
* * * *
653 AG-TCTGAGACAGA-T-CACCATCAGCTAATCTCTTA-CCCA
1 AGCT-TGAGGCAGATTGCACCATC--C-GATCTTTTACCCCG
* * * * *
691 AGCCTG-GGCAGAATGCAACCGTCCGATCTCTTACCCCA
1 AGCTTGAGGCAGATTGC-ACCATCCGATCTTTTACCCCG
*
729 AGCTT-AGGTAGATTGCAACCATCCGATCTTTTACCCC
1 AGCTTGAGGCAGATTGC-ACCATCCGATCTTTTACCCC
766 AATCATGGGG
Statistics
Matches: 234, Mismatches: 51, Indels: 45
0.71 0.15 0.14
Matches are distributed among these distances:
36 7 0.03
37 17 0.07
38 79 0.34
39 118 0.50
40 8 0.03
41 1 0.00
42 4 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (38 bp):
AGCTTGAGGCAGATTGCACCATCCGATCTTTTACCCCG
Found at i:629 original size:77 final size:78
Alignment explanation
Indices: 446--741 Score: 311
Period size: 77 Copynumber: 3.8 Consensus size: 78
436 CAACCATTCG
* * * * *
446 ATCTTTTACCCCGAG-TCTGGGGTAGATTACAGTCATCCGATCTTTTACCCCGAGCTTG-GAGCA
1 ATCTCTTACCCCGAGCT-TGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAG-GCA
* *
509 TATCACCATCAACCAA
64 GATCACCATC-AGCAA
* *
525 A-CTCTTACCCCGAGCTTGAGGCAGATTGTAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
589 TCA-CATCAGCAA
66 TCACCATCAGCAA
** * *
601 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTAGATCTTTTACCCCGAG-TCTGAGACAG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCT-TGAGGCAG
*
665 ATCACCATCAGCTA
65 ATCACCATCAGCAA
* * * * * * *
679 ATCTCTTA-CCCAAGCCT-GGGCAGAATGCAACCGTCCGATCTCTTACCCCAAGCTT-AGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
741 T
66 T
742 TGCAACCATC
Statistics
Matches: 184, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
75 6 0.03
76 35 0.19
77 70 0.38
78 70 0.38
79 3 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
TCACCATCAGCAA
Found at i:746 original size:38 final size:38
Alignment explanation
Indices: 679--767 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 38
669 CCATCAGCTA
* *
679 ATCTCTTA-CCCAAGCCTGGGCAGAATGCAACCGTCCG
1 ATCTCTTACCCCAAGCCTAGGCAGAATGCAACCATCCG
* * *
716 ATCTCTTACCCCAAGCTTAGGTAGATTGCAACCATCCG
1 ATCTCTTACCCCAAGCCTAGGCAGAATGCAACCATCCG
*
754 ATCTTTTACCCCAA
1 ATCTCTTACCCCAA
768 TCATGGGGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
37 8 0.18
38 37 0.82
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.25
Consensus pattern (38 bp):
ATCTCTTACCCCAAGCCTAGGCAGAATGCAACCATCCG
Found at i:988 original size:28 final size:29
Alignment explanation
Indices: 951--1019 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
941 ATCATTTAAC
951 CCCTAAACTTTTATAAAATTACA-ACTAA
1 CCCTAAACTTTTATAAAATTACATACTAA
* **
979 CCCTAAACTTTTCTAAAATTACATTTTAA
1 CCCTAAACTTTTATAAAATTACATACTAA
1008 CCCTAAACTTTT
1 CCCTAAACTTTT
1020 CCAAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 22 0.59
29 15 0.41
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTTATAAAATTACATACTAA
Found at i:1176 original size:28 final size:29
Alignment explanation
Indices: 945--1202 Score: 245
Period size: 29 Copynumber: 8.9 Consensus size: 29
935 ATCATCATCA
**
945 TTTAACCCCTAAACTTTTATAAAATTACA-
1 TTTAA-CCCTAAACTTTTCCAAAATTACAT
** *
974 ACTAACCCTAAACTTTTCTAAAATTACAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
* *
1003 TTTAACCCTAAACTTTTCCAAAAATATAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
* *
1032 TTTAACCCCTAAACTTCTCCAAAATCACAT
1 TTTAA-CCCTAAACTTTTCCAAAATTACAT
* *
1062 TTTAAACCCTAAAATCTTCCAAAATTACAT
1 TTT-AACCCTAAACTTTTCCAAAATTACAT
* * * *
1092 TTT-TCTCTAAAC-TTTCTTAAAATCACAT
1 TTTAACCCTAAACTTTTC-CAAAATTACAT
* * *
1120 TTTGACCCTAAACTTCTCCAAAATCACAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
*
1149 TTTAACCC-AAATTTTTCCAAAATTACAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
* * * *
1177 TTTACCCCCAAATTTTTCTAAAATTA
1 TTTAACCCTAAACTTTTCCAAAATTA
1203 TGTTTTCACA
Statistics
Matches: 190, Mismatches: 32, Indels: 14
0.81 0.14 0.06
Matches are distributed among these distances:
27 3 0.02
28 64 0.34
29 72 0.38
30 49 0.26
31 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.37
Consensus pattern (29 bp):
TTTAACCCTAAACTTTTCCAAAATTACAT
Found at i:2604 original size:26 final size:25
Alignment explanation
Indices: 2542--2602 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 25
2532 TCTTTTTAAA
*
2542 AATTT-AATTTATTTGTTTAACAAT
1 AATTTAAATTTATTTGTTTAAGAAT
2566 AATTTAAACTTTATTTGTTTAAGAAT
1 AATTTAAA-TTTATTTGTTTAAGAAT
2592 AATTTAAATTT
1 AATTTAAATTT
2603 TAGTTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 5 0.15
25 5 0.15
26 24 0.71
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (25 bp):
AATTTAAATTTATTTGTTTAAGAAT
Found at i:4039 original size:30 final size:30
Alignment explanation
Indices: 3952--4259 Score: 256
Period size: 30 Copynumber: 10.4 Consensus size: 30
3942 TCTTTAAATT
* *
3952 TTACATTTTGACCACT-AACTTTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
*
3981 TTACATTTTAACCCC-AAATTTTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
4010 TTGCATTTTTACCCCTTAAACTTTTCAAAAA
1 TTACATTTTAACCCC-TAAACTTTTCCAAAA
* *
4041 TTGCATTTTAACCTCTAAACTTTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
*
4071 TTACATTTTAACCCCTAAACTTCTT-TAAAA
1 TTACATTTTAACCCCTAAACTT-TTCCAAAA
* * * * *
4101 TCACATTTTAAACCTTAAAATCTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
4131 CTACATTTTATCCCCCAAACATTCTT--AAAA
1 TTACATTTTAACCCCTAAAC-TT-TTCCAAAA
* * *
4161 TCACATTTTGA-CCC-AAACTTCTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
4189 TTACATTTTGA-CCC-ACACTTTGCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
4217 TTACATTTTTACCCCTAAATTTTTTCTAAAA
1 TTACATTTTAACCCCTAAA-CTTTTCCAAAA
**
4248 TTATGTTTTAAC
1 TTACATTTTAAC
4260 AACGTATTAT
Statistics
Matches: 223, Mismatches: 44, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.00
27 2 0.01
28 42 0.19
29 46 0.21
30 85 0.38
31 45 0.20
32 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
TTACATTTTAACCCCTAAACTTTTCCAAAA
Found at i:5827 original size:31 final size:34
Alignment explanation
Indices: 5755--5829 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
5745 ATATATACCA
*
5755 ATATATATACGTTTATTTATTTTTTTATACTGCAT
1 ATATATATACGTTTATTTATTTTTCTATACTG-AT
* *
5790 ACATATATTCGTTTA-TTATTTTTCTATAC-G-T
1 ATATATATACGTTTATTTATTTTTCTATACTGAT
5821 ATATATATA
1 ATATATATA
5830 GACATATGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 8 0.23
33 1 0.03
34 13 0.37
35 13 0.37
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (34 bp):
ATATATATACGTTTATTTATTTTTCTATACTGAT
Found at i:26338 original size:19 final size:17
Alignment explanation
Indices: 26304--26350 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
26294 GATTAGGCAG
26304 TAAAAGAAAAAGAAGAA
1 TAAAAGAAAAAGAAGAA
26321 TAAAAGAAAAGGAGAAGAA
1 TAAAAGAAAA--AGAAGAA
* *
26340 GAAGAGAAAAA
1 TAAAAGAAAAA
26351 TTCTAGAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
19 15 0.58
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.04
Consensus pattern (17 bp):
TAAAAGAAAAAGAAGAA
Found at i:27710 original size:24 final size:24
Alignment explanation
Indices: 27681--27737 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
27671 ATCCCACTAC
*
27681 ATATCCTACTACATGGATTGTGGT
1 ATATCCTACTACATGGATTATGGT
*
27705 ATATCCAACTACATGGATTATGGT
1 ATATCCTACTACATGGATTATGGT
27729 ATATCCTAC
1 ATATCCTAC
27738 ATCAATCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (24 bp):
ATATCCTACTACATGGATTATGGT
Found at i:30396 original size:30 final size:29
Alignment explanation
Indices: 30335--30437 Score: 75
Period size: 30 Copynumber: 3.4 Consensus size: 29
30325 AAAATCCAAC
* * *
30335 TTAACCATCAAATTTTAATAAAAGTTGAAA
1 TTAACCCTTAAATTTT-ATAAAAGTTCAAA
30365 TTAACCCTTAAATTTTATTAAAA-TTACAAA
1 TTAACCCTTAAATTTTA-TAAAAGTT-CAAA
* * * *
30395 TTAGTCCC-TAAATTTTACAAAATTTCCAAT
1 TTA-ACCCTTAAATTTTATAAAAGTT-CAAA
*
30425 TTAATCCTTAAAT
1 TTAACCCTTAAAT
30438 AAATTTTGGG
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
29 9 0.15
30 47 0.80
31 3 0.05
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.39
Consensus pattern (29 bp):
TTAACCCTTAAATTTTATAAAAGTTCAAA
Found at i:33568 original size:349 final size:351
Alignment explanation
Indices: 32892--33585 Score: 955
Period size: 349 Copynumber: 2.0 Consensus size: 351
32882 CACAGTCTAA
32892 TAATATGAATAGAATATCAACATGCGATACGCATCACGGAATAAAATGATACAAATATCACAACA
1 TAATATGAATAGAATATCAACATGCGATACGCATCACGGAATAAAATGATACAAATATCACAACA
* * *
32957 CATAATAATATCACACAAGGTGTGGAACACCGTCACACAACAAAATGTAGCACAGGAAGAAACAC
66 CAGAAGAATATCACACAAGGTATGGAACACCGTCACACAACAAAATGTAGCACAGGAAGAAACAC
* * *
33022 ACCTTTAGCGGGTAAAAGCTTTAAAGTCATGAAGGACGCCTCTCACACTTAGATCTAACTTCGAC
131 ACCTCTAGCGGGCAAAAGCTCTAAAGTCATGAAGGACGCCTCTCACACTTAGATCTAACTTCGAC
** * * * * *
33087 TCTAGTTGAATTAGGACTTATGAGAATAAACTCTGCATTAAAATCTATCACTAGGCCACTTACTA
196 TCTAACTGAATTAAGACCTATGACAATAAACTCTACATTAAAATCTATCACTAGGCCACCTACTA
* * * * *
33152 ACACAATACTAAATTGAATACGCTCATGTGCAGCACTCGTAACTCGTGCAGGGGTAGTCAACATA
261 ACACAATACTAAATCGAATACACTCATGTGCAGCACTCGTAACTCGTGCAAGAGCAGTCAACATA
33217 GGT-GA-AGGAGGTAACTTGTCAGCC
326 GGTAGAGAGGAGGTAACTTGTCAGCC
* * * * *
33241 TAATATGTATGGAATATTAACATGTGATACGCATCACGGAATAAAATGATATAAATATCACAACA
1 TAATATGAATAGAATATCAACATGCGATACGCATCACGGAATAAAATGATACAAATATCACAACA
* * *
33306 CAGAAGAATATCACACAAGGTATGGAACATCGTCACACAATAAAATGTAGCACATGAAGAAACAC
66 CAGAAGAATATCACACAAGGTATGGAACACCGTCACACAACAAAATGTAGCACAGGAAGAAACAC
* * * * * * * *
33371 ACCTCTAGTGGGCAGAAGCTCTAACGTCGTGGAGGACGCCTCTCATAGTTAGATCTAAC-TCTGG
131 ACCTCTAGCGGGCAAAAGCTCTAAAGTCATGAAGGACGCCTCTCACACTTAGATCTAACTTC-GA
* * *
33435 GTCTAACTGAATTAAGACCTATGACAATAAACTTTACATTAAAATCTAAT-ACTATGCCACCTAC
195 CTCTAACTGAATTAAGACCTATGACAATAAACTCTACATTAAAATCT-ATCACTAGGCCACCTAC
* * * **
33499 TAACATAATACTAAATCGAATACACTCATGTGCAGTACTTGTAACTCGTGCAAGAGCAGTCCGCA
259 TAACACAATACTAAATCGAATACACTCATGTGCAGCACTCGTAACTCGTGCAAGAGCAGTCAACA
33564 TAGGTAGAGGAGGAGGTAACTT
324 TAGGTAGA-GAGGAGGTAACTT
33586 ATTGGCTTTA
Statistics
Matches: 298, Mismatches: 42, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
348 2 0.01
349 280 0.94
350 4 0.01
352 12 0.04
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (351 bp):
TAATATGAATAGAATATCAACATGCGATACGCATCACGGAATAAAATGATACAAATATCACAACA
CAGAAGAATATCACACAAGGTATGGAACACCGTCACACAACAAAATGTAGCACAGGAAGAAACAC
ACCTCTAGCGGGCAAAAGCTCTAAAGTCATGAAGGACGCCTCTCACACTTAGATCTAACTTCGAC
TCTAACTGAATTAAGACCTATGACAATAAACTCTACATTAAAATCTATCACTAGGCCACCTACTA
ACACAATACTAAATCGAATACACTCATGTGCAGCACTCGTAACTCGTGCAAGAGCAGTCAACATA
GGTAGAGAGGAGGTAACTTGTCAGCC
Done.