Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004493.1 Kokia drynarioides strain JFW-HI SEQ_117926, 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: 21715
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Warning! 152 characters in sequence are not A, C, G, or T
Found at i:367 original size:38 final size:38
Alignment explanation
Indices: 320--395 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
310 TGTGCTAATG
*
320 ATGCAAATATGCAATGAAAGTGGGCAAAAAATCAGAAA
1 ATGCAAATATGCAATGAAAGTGGGAAAAAAATCAGAAA
358 ATGCAAATATGCAATGAAAGTGGGAAAAAAATCAGAAA
1 ATGCAAATATGCAATGAAAGTGGGAAAAAAATCAGAAA
396 GTATATGTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.54, C:0.09, G:0.21, T:0.16
Consensus pattern (38 bp):
ATGCAAATATGCAATGAAAGTGGGAAAAAAATCAGAAA
Found at i:6449 original size:21 final size:22
Alignment explanation
Indices: 6423--6474 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
6413 TGATTCAATG
* *
6423 AAGAAAAATAAATAAA-TAAAA
1 AAGAAAAATAAAAAAAGGAAAA
6444 AAGAAAAATAAAAAAAGGGAAAA
1 AAGAAAAATAAAAAAA-GGAAAA
6467 AAGAAAAA
1 AAGAAAAA
6475 AGGGAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 15 0.56
23 12 0.44
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (22 bp):
AAGAAAAATAAAAAAAGGAAAA
Found at i:6465 original size:16 final size:16
Alignment explanation
Indices: 6432--6482 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
6422 GAAGAAAAAT
**
6432 AAATAAATAAAAAAGAA
1 AAATAAA-AAAAGGGAA
6449 AAATAAAAAAAGGGAA
1 AAATAAAAAAAGGGAA
6465 AAA-AGAAAAAAGGGAA
1 AAATA-AAAAAAGGGAA
6481 AA
1 AA
6483 CAAAAAGGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
15 1 0.03
16 23 0.74
17 7 0.23
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
AAATAAAAAAAGGGAA
Found at i:7558 original size:49 final size:50
Alignment explanation
Indices: 7443--7652 Score: 125
Period size: 50 Copynumber: 4.3 Consensus size: 50
7433 AAAATTTGAG
* *
7443 GGGAAAGGTTGAGGCCGCAACAGTGAACCCGGTACCTTAGAAGATGAGAT
1 GGGAAAGGTTGAGGCCACAACAGTGAACCCGGTACCATAGAAGATGAGAT
* **
7493 GGGATAA-GTTNAGGCCACAATGGTGAA-CCGGATACCAT-GAAGACATGA-A-
1 GGGA-AAGGTTGAGGCCACAACAGTGAACCCGG-TACCATAGAAG--ATGAGAT
* * ** * * * *
7542 GGGAAAGGTTGAGGCCACAAC-GACGAACTCGACACCTTAGAAAACGTGAT
1 GGGAAAGGTTGAGGCCACAACAG-TGAACCCGGTACCATAGAAGATGAGAT
*** * *
7592 GGG-AAGGATTGAGGCCGTTAC-GATGAATCCGGTACCAT-GAA-ATGTGAT
1 GGGAAAGG-TTGAGGCCACAACAG-TGAACCCGGTACCATAGAAGATGAGAT
7640 GGGAAAGGTTGAG
1 GGGAAAGGTTGAG
7653 ACCGCAACGG
Statistics
Matches: 123, Mismatches: 25, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
48 19 0.15
49 43 0.35
50 55 0.45
51 6 0.05
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.17
Consensus pattern (50 bp):
GGGAAAGGTTGAGGCCACAACAGTGAACCCGGTACCATAGAAGATGAGAT
Found at i:7962 original size:39 final size:39
Alignment explanation
Indices: 7914--8146 Score: 179
Period size: 39 Copynumber: 6.0 Consensus size: 39
7904 TCATCACCCG
* * * *
7914 ATCTTTTACCCTGATCATGAGGCAGATTGCAGTCATCTA
1 ATCTCTTACCCTGATCATGAGGCAAATTGCAGCCATCCA
* * * * *
7953 ATCTCTTA-CCTCGATCAT-AGGGTAGATTGTAGCCGTCCG
1 ATCTCTTACCCT-GATCATGA-GGCAAATTGCAGCCATCCA
* *
7992 ATCTCTTACCCCGATCAT-AGGGCAAATTGCAGCCATCTA
1 ATCTCTTACCCTGATCATGA-GGCAAATTGCAGCCATCCA
* * *
8031 ATCTCTTACCCTGATCATGAGGCAAATTTCAGCCACCCG
1 ATCTCTTACCCTGATCATGAGGCAAATTGCAGCCATCCA
* * * * *
8070 ATCTTTTA-CCTCGATCATGGGGTAGATTGCAGTCATCCA
1 ATCTCTTACCCT-GATCATGAGGCAAATTGCAGCCATCCA
* * * *
8109 ATATTTTACCCCGATCATG-GGACAAATTGCAGTCATCC
1 ATCTCTTACCCTGATCATGAGG-CAAATTGCAGCCATCC
8147 GAAGCAATAA
Statistics
Matches: 156, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
38 9 0.06
39 142 0.91
40 5 0.03
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (39 bp):
ATCTCTTACCCTGATCATGAGGCAAATTGCAGCCATCCA
Found at i:8071 original size:78 final size:77
Alignment explanation
Indices: 7908--8137 Score: 243
Period size: 78 Copynumber: 2.9 Consensus size: 77
7898 GTTACATCAT
*
7908 CACCCGATCTTTTACCCTGATCATGAGGCAGATTGCAGTCATCTAATCTCTTA-CCTCGATCAT-
1 CACCCGATCTTTTACCCCGATCATG-GGCAGATTGCAGTCATCTAATCTCTTACCCT-GATCATG
* *
7971 AGGGTAGATTGTAGC
64 A-GGCAAATTGTAGC
** * * *
7986 CGTCCGATCTCTTACCCCGATCATAGGGCAAATTGCAGCCATCTAATCTCTTACCCTGATCATGA
1 CACCCGATCTTTTACCCCGATCAT-GGGCAGATTGCAGTCATCTAATCTCTTACCCTGATCATGA
8051 GGCAAATT-TCAGC
65 GGCAAATTGT-AGC
* * * * * *
8064 CACCCGATCTTTTACCTCGATCATGGGGTAGATTGCAGTCATCCAATATTTTACCCCGATCATG-
1 CACCCGATCTTTTACCCCGATCAT-GGGCAGATTGCAGTCATCTAATCTCTTACCCTGATCATGA
8128 GGACAAATTG
65 GG-CAAATTG
8138 CAGTCATCCG
Statistics
Matches: 126, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
77 3 0.02
78 118 0.94
79 5 0.04
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (77 bp):
CACCCGATCTTTTACCCCGATCATGGGCAGATTGCAGTCATCTAATCTCTTACCCTGATCATGAG
GCAAATTGTAGC
Found at i:8125 original size:117 final size:117
Alignment explanation
Indices: 7914--8145 Score: 304
Period size: 117 Copynumber: 2.0 Consensus size: 117
7904 TCATCACCCG
* * * * *
7914 ATCTTTTACCCTGATCATGAGGCAGATTGCAGTCATCTAATCTCTTACCTCGATCATAGGGTAGA
1 ATCTCTTACCCTGATCATGAGGCAAATTGCAGCCACCCAATCTCTTACCTCGATCATAGGGTAGA
* * * *
7979 TTGTAGCCGTCCGATCTCTTACCCCGATCATAGGG-CAAATTGCAGCCATCTA
66 TTGCAGCCATCCAATATCTTACCCCGATCAT-GGGACAAATTGCAGCCATCTA
* * * *
8031 ATCTCTTACCCTGATCATGAGGCAAATTTCAGCCACCCGATCTTTTACCTCGATCATGGGGTAGA
1 ATCTCTTACCCTGATCATGAGGCAAATTGCAGCCACCCAATCTCTTACCTCGATCATAGGGTAGA
* * *
8096 TTGCAGTCATCCAATATTTTACCCCGATCATGGGACAAATTGCAGTCATC
66 TTGCAGCCATCCAATATCTTACCCCGATCATGGGACAAATTGCAGCCATC
8146 CGAAGCAATA
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
116 3 0.03
117 95 0.97
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (117 bp):
ATCTCTTACCCTGATCATGAGGCAAATTGCAGCCACCCAATCTCTTACCTCGATCATAGGGTAGA
TTGCAGCCATCCAATATCTTACCCCGATCATGGGACAAATTGCAGCCATCTA
Found at i:8585 original size:48 final size:48
Alignment explanation
Indices: 8529--8701 Score: 199
Period size: 48 Copynumber: 3.6 Consensus size: 48
8519 CTTCAAACCC
* * * *
8529 CATCTTCCTAATGAGGTACAAAGAAGTGGGTTAAAGTAATAAAGCGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTTAAAGAAATAAAGCGAT
* * ***
8577 CATCTTCCTGGTGAGATACAGAGAAGTGGATTGAAA-AAATCTGGC-AGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTT-AAAGAAATAAAGCGA-T
* *
8625 CATCTTCCTGATGAGATATAGAGAAGTGGGTTAAAGAAATAAA-CTGGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTTAAAGAAATAAAGC-GAT
8673 CATCTTCCTGATGAGATACAGAGAAGTGG
1 CATCTTCCTGATGAGATACAGAGAAGTGG
8702 ACCAAATCCG
Statistics
Matches: 103, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
47 5 0.05
48 95 0.92
49 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.25
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGGTTAAAGAAATAAAGCGAT
Found at i:8693 original size:96 final size:96
Alignment explanation
Indices: 8529--8702 Score: 269
Period size: 96 Copynumber: 1.8 Consensus size: 96
8519 CTTCAAACCC
* * *
8529 CATCTTCCTAATGAGGTACAAAGAAGTGGGTTAAAGTAATAAAGCGATCATCTTCCTGGTGAGAT
1 CATCTTCCTAATGAGATACAAAGAAGTGGGTTAAAGAAATAAAGCGATCATCTTCCTGATGAGAT
8594 ACAGAGAAGTGGATTGAAAAAATCTGGCAGT
66 ACAGAGAAGTGGATTGAAAAAATCTGGCAGT
* * * *
8625 CATCTTCCTGATGAGATATAGAGAAGTGGGTTAAAGAAATAAA-CTGGTCATCTTCCTGATGAGA
1 CATCTTCCTAATGAGATACAAAGAAGTGGGTTAAAGAAATAAAGC-GATCATCTTCCTGATGAGA
8689 TACAGAGAAGTGGA
65 TACAGAGAAGTGGA
8703 CCAAATCCGT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
95 1 0.01
96 69 0.99
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.25
Consensus pattern (96 bp):
CATCTTCCTAATGAGATACAAAGAAGTGGGTTAAAGAAATAAAGCGATCATCTTCCTGATGAGAT
ACAGAGAAGTGGATTGAAAAAATCTGGCAGT
Found at i:8981 original size:207 final size:207
Alignment explanation
Indices: 8625--9199 Score: 636
Period size: 207 Copynumber: 2.8 Consensus size: 207
8615 ATCTGGCAGT
* * * * * * **
8625 CATCTTCCTGATGAGATATAGAGAAGTGGGTTAAAGAAATAAACTGGTCATCTTCCTGATGAGAT
1 CATCTTCCTAATAAGATACAGAAAAGTGAGTAAAACCAATAAACTGGTCATCTTCCTGATGAGAT
* * *
8690 ACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGTGGATTTAAACAATGAGAC
66 ACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAATGAGGC
* * * ** ** *
8755 AATCATC-TTCTTGATGAGATACAAAGAAGTAGACCAAATCATTGAAGCGCAGCTCAATGTGAGT
131 -GTCATCTTTC-TGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATACGAAT
8819 AAAAATTCAAACCC
194 AAAAATTCAAACCC
* * * *
8833 CATCTTCCTGATAAGATACAGAGAAGTGAG-AAGAACCAAT-TACTGGTCATCTTCCTGACGAGA
1 CATCTTCCTAATAAGATACAGAAAAGTGAGTAA-AACCAATAAACTGGTCATCTTCCTGATGAGA
** * * * * *
8896 TGTAGAGAAGTGAATCAAATCCGTCTTCCTTATGAGATATAGAGAAGTGAATTGAAACAATGAGG
65 TACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAATGAGG
* * *
8961 CGTTCATCTTTCTAATGAGATACAGAGAAGTAGACCAACTCAATGAAGCAAAGTTCAATACGAAT
130 CG-TCATCTTTCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATACGAAT
* * *
9026 GAGACTTCAAACCC
194 AAAAATTCAAACCC
* * * * ** * *
9040 CATCTTCCTAATGAGGTACAGAAAAGTGGGTCAAAGTAATAAAGC-GATCATCTTCCTGGTGAGA
1 CATCTTCCTAATAAGATACAGAAAAGTGAGTAAAACCAATAAA-CTGGTCATCTTCCTGATGAGA
* *
9104 TACAGAGAAGTGGACCAAATCCGTCTTCCTGGTGAGATACAGAGAAGTGGATTGAAAAAATGAGG
65 TACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAATGAGG
* *
9169 CAGTCATCTTCCTGATGAGATATAGAGAAGT
130 C-GTCATCTTTCTGATGAGATACAGAGAAGT
9200 GGGTTAAAGA
Statistics
Matches: 304, Mismatches: 56, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
207 167 0.55
208 135 0.44
209 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (207 bp):
CATCTTCCTAATAAGATACAGAAAAGTGAGTAAAACCAATAAACTGGTCATCTTCCTGATGAGAT
ACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAATGAGGC
GTCATCTTTCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATACGAATAA
AAATTCAAACCC
Found at i:9198 original size:48 final size:48
Alignment explanation
Indices: 9127--9250 Score: 169
Period size: 48 Copynumber: 2.6 Consensus size: 48
9117 ACCAAATCCG
* * *
9127 TCTTCCTGGTGAGATACAGAGAAGTGGATTGAAA-AAATGAGGCAGTCA
1 TCTTCCTGATGAGATACAGAGAAGTGGATT-AAAGAAATAAAGCAGTCA
* * *
9175 TCTTCCTGATGAGATATAGAGAAGTGGGTTAAAGAAATAAAGCGGTCA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAGAAATAAAGCAGTCA
*
9223 TCTTCTTGATGAGATACAGAGAAGTGGA
1 TCTTCCTGATGAGATACAGAGAAGTGGA
9251 CCATATCAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
47 3 0.05
48 63 0.95
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.25
Consensus pattern (48 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATTAAAGAAATAAAGCAGTCA
Found at i:9264 original size:85 final size:85
Alignment explanation
Indices: 9175--9343 Score: 232
Period size: 85 Copynumber: 2.0 Consensus size: 85
9165 GAGGCAGTCA
* * * * *
9175 TCTTCCTGATGAGATATAGAGAAGTGGGTT-AAAGAAATAAAGCGGTCATCTTCTTGATGAGATA
1 TCTTCCTGATGAGATACAAAGAAGTGGATTGAAA-AAATAAAGCGATCATCTTCTTGATAAGATA
* *
9239 CAGAGAAGTGGACCATATCAG
65 CAGAGAAGTAGACCAAATCAG
* * *
9260 TCTTCCTGATGAGATACAAAGAAGTGGATTGAAATAATGAGGCGATCATCTTCTTGATAAGATAC
1 TCTTCCTGATGAGATACAAAGAAGTGGATTGAAAAAATAAAGCGATCATCTTCTTGATAAGATAC
9325 AGAGAAGTAGACCAAATCA
66 AGAGAAGTAGACCAAATCA
9344 ATGAAGTGAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 70 0.96
86 3 0.04
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAAAGAAGTGGATTGAAAAAATAAAGCGATCATCTTCTTGATAAGATAC
AGAGAAGTAGACCAAATCAG
Found at i:9283 original size:133 final size:133
Alignment explanation
Indices: 9040--9332 Score: 426
Period size: 133 Copynumber: 2.2 Consensus size: 133
9030 CTTCAAACCC
* * * * *
9040 CATCTTCCTAATGAGGTACAGAAAAGTGGGTCAAAGTAATAAAGCGATCATCTTCCTGGTGAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGAAATAAAGCGATCATCTTCCTGATGAGAT
* * *
9105 ACAGAGAAGTGGACCAAATCCGTCTTCCTGGTGAGATACAGAGAAGTGGATTGAAAAAATGAGGC
66 ACAGAGAAGTGGACCAAATCAGTCTTCCTGATGAGATACAAAGAAGTGGATTGAAAAAATGAGGC
9170 -AGT
131 GA-T
* * * *
9173 CATCTTCCTGATGAGATATAGAGAAGTGGGTTAAAGAAATAAAGCGGTCATCTTCTTGATGAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGAAATAAAGCGATCATCTTCCTGATGAGAT
* *
9238 ACAGAGAAGTGGACCATATCAGTCTTCCTGATGAGATACAAAGAAGTGGATTGAAATAATGAGGC
66 ACAGAGAAGTGGACCAAATCAGTCTTCCTGATGAGATACAAAGAAGTGGATTGAAAAAATGAGGC
9303 GAT
131 GAT
* *
9306 CATCTTCTTGATAAGATACAGAGAAGT
1 CATCTTCCTGATGAGATACAGAGAAGT
9333 AGACCAAATC
Statistics
Matches: 142, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
133 141 0.99
134 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (133 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGAAATAAAGCGATCATCTTCCTGATGAGAT
ACAGAGAAGTGGACCAAATCAGTCTTCCTGATGAGATACAAAGAAGTGGATTGAAAAAATGAGGC
GAT
Found at i:9293 original size:341 final size:339
Alignment explanation
Indices: 8877--9905 Score: 1105
Period size: 341 Copynumber: 2.9 Consensus size: 339
8867 ACCAATTACT
* * ** * * * *
8877 GGTCATCTTCCTGACGAGATGTAGAGAAGTGAATCAAATCCGTCTTCCTTATGAGATATAGAGAA
1 GGTCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAT-CGTCTTCCTGATGAGATACAGAGAA
* * * *
8942 GTGAATTGAAACAATGAGGCGTTCATCTTTCTAATGAGATACAGAGAAGTAGACCAACTCAATGA
65 GTGGATTGAAACAATGAGGCGATCATCTTTCTGATGAGATACAGAGAAGTAGACCAAATCAATGA
* * * * *
9007 AGCAAAGTTCAATACGAATGAGACTTCAAACCCCATCTTCCTAATGAGGTACAGAAAAGTGGGTC
130 AGCGAAGCTCAATACGAATGAGACTTCAAA-CCCATCTTCCTGATGAGATACAGAAAAATGGGTC
* * ** * *
9072 AAAGTAATAAAGCGATCATCTTCCTGGTGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGGT
194 AAAGCAATAAAGTGATCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGAT
* *
9137 GAGATACAGAGAAGTGGATTGAAAAAATGAGGCAGTCATCTTCCTGATGAGATATAGAGAAGTGG
259 GAGATACAAAGAAGTGGATTGAAAAAATGAGGCAGTCATCTTCCTGATGAGATATAGAGAAGTGA
*
9202 GTTAAAGAAATAAAGC
324 GTCAAAGAAATAAAGC
* *
9218 GGTCATCTTCTTGATGAGATACAGAGAAGTGGACCATATCAGTCTTCCTGATGAGATACAAAGAA
1 GGTCATCTTCTTGATGAGATACAGAGAAGTGGACCAAATC-GTCTTCCTGATGAGATACAGAGAA
* *
9283 GTGGATTGAAATAATGAGGCGATCATC-TTCTTGATAAGATACAGAGAAGTAGACCAAATCAATG
65 GTGGATTGAAACAATGAGGCGATCATCTTTC-TGATGAGATACAGAGAAGTAGACCAAATCAATG
* *
9347 AAGTGAAGCTCAATACGAATGAGACTTCAAACTCCATCTTTCTGATGAGATACA-AAGAAATGGG
129 AAGCGAAGCTCAATACGAATGAGACTTCAAAC-CCATCTTCCTGATGAGATACAGAA-AAATGGG
* * * * **
9411 TCAAAGCAATAAAATGATCATCTTCTTATTGAGATACAAAGATTTGGACCAAATCCGCCTTCCTG
192 TCAAAGCAATAAAGTGATCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTG
* **
9476 ATGAGATACAAAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATACGAATGAGACTTCAAACCC
257 ATGAGATACAAAGAAGT-G----GAT---T---GAAAA----AAT--G-A-G-G----C--A-GT
* * *
9541 CATCTTCCTTATGAGATATAGAGAAGTGAGTCAAAGTAATAAAGT
295 CATCTTCCTGATGAGATATAGAGAAGTGAGTCAAAGAAATAAAGC
* * *
9586 GGTTATCTT-TCTGATG-GATACAGAGAAGTGGACCAAATTCGCCTTCCTGATAAGATACAGAGA
1 GGTCATCTTCT-TGATGAGATACAGAGAAGTGGACCAAA-TCGTCTTCCTGATGAGATACAGAGA
* * * * * *
9649 AGTGGATTGAATCAATGAAGCGGTCATCTTCCTGATGAGATATAGAGAAGTAGATCAAATCAATG
64 AGTGGATTGAAACAATGAGGCGATCATCTTTCTGATGAGATACAGAGAAGTAGACCAAATCAATG
* * * *
9714 AAGCGAAGCTCAATACGAATGAGACTTCAAA-CCATCTTCTTGATGAGATATAGAGAATTGGGTC
129 AAGCGAAGCTCAATACGAATGAGACTTCAAACCCATCTTCCTGATGAGATACAGAAAAATGGGTC
* *
9778 AAAGCAATAAAGTGATCATCTTCCTAATGAGATACAGAGAAGTGGATCAAATCCACCTTCCTGAT
194 AAAGCAATAAAGTGATCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGAT
** **** * *
9843 GAGATACAAAGAAGTGGATTGAATTAATGAATTTGTCATCTTTCTGATGAGATACAGAGAAGT
259 GAGATACAAAGAAGTGGATTGAAAAAATGAGGCAGTCATCTTCCTGATGAGATATAGAGAAGT
9906 AGACCAAGAA
Statistics
Matches: 571, Mismatches: 82, Indels: 73
0.79 0.11 0.10
Matches are distributed among these distances:
338 24 0.04
340 7 0.01
341 229 0.40
342 1 0.00
346 2 0.00
347 1 0.00
348 1 0.00
349 1 0.00
350 3 0.01
352 5 0.01
354 3 0.01
356 3 0.01
357 1 0.00
358 1 0.00
359 1 0.00
360 3 0.01
361 1 0.00
364 1 0.00
365 99 0.17
366 1 0.00
367 126 0.22
368 57 0.10
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (339 bp):
GGTCATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCGTCTTCCTGATGAGATACAGAGAAG
TGGATTGAAACAATGAGGCGATCATCTTTCTGATGAGATACAGAGAAGTAGACCAAATCAATGAA
GCGAAGCTCAATACGAATGAGACTTCAAACCCATCTTCCTGATGAGATACAGAAAAATGGGTCAA
AGCAATAAAGTGATCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGA
GATACAAAGAAGTGGATTGAAAAAATGAGGCAGTCATCTTCCTGATGAGATATAGAGAAGTGAGT
CAAAGAAATAAAGC
Found at i:9347 original size:48 final size:49
Alignment explanation
Indices: 9255--9347 Score: 109
Period size: 48 Copynumber: 1.9 Consensus size: 49
9245 AGTGGACCAT
* * **
9255 ATCAGTCTTCCTGATGAGATACAAAGAAGTGGATTGAAATAATGAGGCG
1 ATCAGTCTTCCTGATAAGATACAAAGAAGTAGATCCAAATAATGAGGCG
* *
9304 ATCA-TCTTCTTGATAAGATACAGAGAAGTAGA-CCAAATCAATGA
1 ATCAGTCTTCCTGATAAGATACAAAGAAGTAGATCCAAAT-AATGA
9348 AGTGAAGCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
47 4 0.11
48 29 0.78
49 4 0.11
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.25
Consensus pattern (49 bp):
ATCAGTCTTCCTGATAAGATACAAAGAAGTAGATCCAAATAATGAGGCG
Found at i:9499 original size:160 final size:159
Alignment explanation
Indices: 9309--9651 Score: 472
Period size: 160 Copynumber: 2.2 Consensus size: 159
9299 AGGCGATCAT
* **
9309 CTTCTTGATAAGATACAGAGAAGTAGACCAAATCAATGAAGTGAAGCTCAATACGAATGAGACTT
1 CTTCCTGATAAGATACAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATACGAATGAGACTT
* * * *
9374 CAAACTCCATCTTTCTGATGAGATACAAAGAAATGGGTCAAAGCAATAAAATGATCATC-TTCTT
66 CAAACCCCATCTTCCTGATGAGATACAAAGAAATGAGTCAAAGCAATAAAATGATCATCTTTCTG
**
9438 ATTGAGATACAAAGATTTGGACCAAATCCGC
131 A-TG-GATACAAAGAAGTGGACCAAATCCGC
* *
9469 CTTCCTGATGAGATACAAAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATACGAATGAGACTT
1 CTTCCTGATAAGATACAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATACGAATGAGACTT
* * * * * * * *
9534 CAAACCCCATCTTCCTTATGAGATATAGAGAAGTGAGTCAAAGTAATAAAGTGGTTATCTTTCTG
66 CAAACCCCATCTTCCTGATGAGATACAAAGAAATGAGTCAAAGCAATAAAATGATCATCTTTCTG
* *
9599 ATGGATACAGAGAAGTGGACCAAATTCGC
131 ATGGATACAAAGAAGTGGACCAAATCCGC
9628 CTTCCTGATAAGATACAGAGAAGT
1 CTTCCTGATAAGATACAGAGAAGT
9652 GGATTGAATC
Statistics
Matches: 159, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
159 44 0.28
160 110 0.69
161 5 0.03
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.24
Consensus pattern (159 bp):
CTTCCTGATAAGATACAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATACGAATGAGACTT
CAAACCCCATCTTCCTGATGAGATACAAAGAAATGAGTCAAAGCAATAAAATGATCATCTTTCTG
ATGGATACAAAGAAGTGGACCAAATCCGC
Found at i:9894 original size:206 final size:206
Alignment explanation
Indices: 9469--9912 Score: 649
Period size: 206 Copynumber: 2.2 Consensus size: 206
9459 CCAAATCCGC
*
9469 CTTCCTGATGAGATACAAAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATACGAATGAGACTT
1 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATACGAATGAGACTT
* * * * *
9534 CAAACCCCATCTTCCTTATGAGATATAGAGAAGTGAGTCAAAGTAATAAAGTGGTTATCTTTCTG
66 CAAA-CCCATCTTCCTTATGAGATATAGAGAAGTGAGTCAAAGCAATAAAGTGATCATCTTCCTA
* * *
9599 ATGGATACAGAGAAGTGGACCAAATTCGCCTTCCTGATAAGATACAGAGAAGTGGATTGAATCAA
130 ATGGATACAGAGAAGTGGACCAAATCCACCTTCCTGATAAGATACAAAGAAGTGGATTGAATCAA
9664 TGAAGCGGTCAT
195 TGAAGCGGTCAT
* * **
9676 CTTCCTGATGAGATATAGAGAAGTAGATCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTT
1 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATACGAATGAGACTT
* *
9741 CAAA-CCATCTT-CTTGATGAGATATAGAGAATTGGGTCAAAGCAATAAAGTGATCATCTTCCTA
66 CAAACCCATCTTCCTT-ATGAGATATAGAGAAGTGAGTCAAAGCAATAAAGTGATCATCTTCCTA
* * *
9804 ATGAGATACAGAGAAGTGGATCAAATCCACCTTCCTGATGAGATACAAAGAAGTGGATTGAATTA
130 ATG-GATACAGAGAAGTGGACCAAATCCACCTTCCTGATAAGATACAAAGAAGTGGATTGAATCA
***
9869 ATGAATTTGTCAT
194 ATGAAGCGGTCAT
*
9882 CTTTCTGATGAGATACAGAGAAGTAGACCAA
1 CTTCCTGATGAGATACAGAGAAGTAGACCAA
9913 GAAAGGAAGC
Statistics
Matches: 211, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
204 3 0.01
205 51 0.24
206 93 0.44
207 64 0.30
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (206 bp):
CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATACGAATGAGACTT
CAAACCCATCTTCCTTATGAGATATAGAGAAGTGAGTCAAAGCAATAAAGTGATCATCTTCCTAA
TGGATACAGAGAAGTGGACCAAATCCACCTTCCTGATAAGATACAAAGAAGTGGATTGAATCAAT
GAAGCGGTCAT
Found at i:11988 original size:31 final size:30
Alignment explanation
Indices: 11953--12070 Score: 139
Period size: 31 Copynumber: 3.9 Consensus size: 30
11943 TTAAAATTAT
* *
11953 ATTTTGACCCCTAAATTTTTCCCAAAATCAC
1 ATTTTAACCCCTAAA-CTTTCCCAAAATCAC
* *
11984 ATTTTAACCCCTAAACTTTCTCTAAATCAC
1 ATTTTAACCCCTAAACTTTCCCAAAATCAC
* * *
12014 ATTTTGACCCCTTAAACTTTCCAAAAATTAC
1 ATTTTAACCCC-TAAACTTTCCCAAAATCAC
*
12045 ATTTTAACCCC-AAACTTTCCTAAAAT
1 ATTTTAACCCCTAAACTTTCCCAAAAT
12071 TATGTTTTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
29 14 0.19
30 22 0.29
31 39 0.52
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.36
Consensus pattern (30 bp):
ATTTTAACCCCTAAACTTTCCCAAAATCAC
Found at i:12081 original size:61 final size:62
Alignment explanation
Indices: 11936--12078 Score: 179
Period size: 61 Copynumber: 2.4 Consensus size: 62
11926 TTGACCCTCG
* * *
11936 AACTTT-TTTAAAATTATATTTTGACCCCTAAATTTTTCCCAAAATCACATTTTAACCCCTA
1 AACTTTCTCTAAAATTATATTTTGACCCCTAAATCTTTCCAAAAATCACATTTTAACCCCTA
* * *
11997 AACTTTCTCT-AAATCACATTTTGACCCCTTAAA-CTTTCCAAAAATTACATTTTAACCCC-A
1 AACTTTCTCTAAAATTATATTTTGACCCC-TAAATCTTTCCAAAAATCACATTTTAACCCCTA
*
12057 AACTTTC-CTAAAATTATGTTTT
1 AACTTTCTCTAAAATTATATTTT
12079 TGATCTCGAA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
59 2 0.03
60 17 0.24
61 45 0.64
62 6 0.09
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (62 bp):
AACTTTCTCTAAAATTATATTTTGACCCCTAAATCTTTCCAAAAATCACATTTTAACCCCTA
Found at i:14982 original size:20 final size:20
Alignment explanation
Indices: 14959--15024 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
14949 AAATACCTAT
14959 AAAAACCAATAAAAACACCC
1 AAAAACCAATAAAAACACCC
* * **
14979 AAAAACC-TTAAATAC-CTAT
1 AAAAACCAATAAAAACAC-CC
*
14998 AAAAACCAATAGAAACACCC
1 AAAAACCAATAAAAACACCC
15018 AAAAACC
1 AAAAACC
15025 TTCATCTTCT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
18 1 0.03
19 13 0.38
20 19 0.56
21 1 0.03
ACGTcount: A:0.61, C:0.27, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAAACCAATAAAAACACCC
Found at i:15000 original size:39 final size:39
Alignment explanation
Indices: 14936--15026 Score: 155
Period size: 39 Copynumber: 2.3 Consensus size: 39
14926 AATTCTAATA
* *
14936 ACCCTAAAATCTTAAATACCTATAAAAACCAATAAAAAC
1 ACCCAAAAACCTTAAATACCTATAAAAACCAATAAAAAC
*
14975 ACCCAAAAACCTTAAATACCTATAAAAACCAATAGAAAC
1 ACCCAAAAACCTTAAATACCTATAAAAACCAATAAAAAC
15014 ACCCAAAAACCTT
1 ACCCAAAAACCTT
15027 CATCTTCTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.55, C:0.26, G:0.01, T:0.18
Consensus pattern (39 bp):
ACCCAAAAACCTTAAATACCTATAAAAACCAATAAAAAC
Found at i:16444 original size:23 final size:23
Alignment explanation
Indices: 16397--16545 Score: 165
Period size: 23 Copynumber: 6.4 Consensus size: 23
16387 ATCATGTTTA
16397 AATGTGATTATATG-TGCTAAATATT
1 AATGTGATT-TATGCT--TAAATATT
*
16422 AATGTGATTTGTGCTTAAATATT
1 AATGTGATTTATGCTTAAATATT
* * *
16445 AATGTGATTTGTGCCTAAATGTT
1 AATGTGATTTATGCTTAAATATT
*
16468 AATATGATTTATGCTTAAATATT
1 AATGTGATTTATGCTTAAATATT
* *
16491 AATGTGATTTATGATTAAATGTT
1 AATGTGATTTATGCTTAAATATT
* * *
16514 AATATAATTTATGCTAAAATATT
1 AATGTGATTTATGCTTAAATATT
*
16537 CATGTGATT
1 AATGTGATT
16546 AAATGTGATT
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
23 92 0.88
24 3 0.03
25 10 0.10
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.46
Consensus pattern (23 bp):
AATGTGATTTATGCTTAAATATT
Found at i:16470 original size:46 final size:45
Alignment explanation
Indices: 16409--16545 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 45
16399 TGTGATTATA
* * *
16409 TGTGCTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
1 TGTGCTAAATGTTAATATGATTTATGCTTAAATATTAATGTGATT
16454 TGTGCCTAAATGTTAATATGATTTATGCTTAAATATTAATGTGATT
1 TGTG-CTAAATGTTAATATGATTTATGCTTAAATATTAATGTGATT
* * * * *
16500 TATGATTAAATGTTAATATAATTTATGCTAAAATATTCATGTGATT
1 TGTG-CTAAATGTTAATATGATTTATGCTTAAATATTAATGTGATT
16546 AAATGTGATT
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 4 0.05
46 78 0.95
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (45 bp):
TGTGCTAAATGTTAATATGATTTATGCTTAAATATTAATGTGATT
Found at i:16553 original size:10 final size:11
Alignment explanation
Indices: 16538--16630 Score: 57
Period size: 10 Copynumber: 8.1 Consensus size: 11
16528 TAAAATATTC
16538 ATGTGATTAA-
1 ATGTGATTAAT
16548 ATGTGATTAAT
1 ATGTGATTAAT
*
16559 ATGTGATGTGATAA
1 ATGTGAT-T-A-AT
* * *
16573 ATACTGAAATATT
1 AT-GTG-ATTAAT
16586 CATGTGATTAA-
1 -ATGTGATTAAT
*
16597 ATGTGACTAA-
1 ATGTGATTAAT
16607 ATGTGATTAAT
1 ATGTGATTAAT
16618 ATGTGATGTAAT
1 ATGTGAT-TAAT
16630 A
1 A
16631 AATGTTGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
10 28 0.44
11 14 0.22
12 9 0.14
13 3 0.05
14 6 0.09
15 3 0.05
16 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (11 bp):
ATGTGATTAAT
Found at i:16608 original size:59 final size:58
Alignment explanation
Indices: 16538--16715 Score: 230
Period size: 58 Copynumber: 3.1 Consensus size: 58
16528 TAAAATATTC
* *
16538 ATGTGATTAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTGATTAA
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTGAGT-A
* ** *
16597 ATGTGACTAAATGTGATTAATATGTGATGTAATAAATGTTGAAATATTCATGTAAGTA
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTGAGTA
* * * * * * *
16655 ATGTAACTAAATGTGATTAATATGTGCTGTGTTAAATACTTAAGTACTCATGTGAATA
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTGAGTA
16713 ATG
1 ATG
16716 CGATTAATGT
Statistics
Matches: 102, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
58 51 0.50
59 51 0.50
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (58 bp):
ATGTGACTAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTGAGTA
Found at i:16691 original size:58 final size:59
Alignment explanation
Indices: 16545--16694 Score: 221
Period size: 59 Copynumber: 2.6 Consensus size: 59
16535 TTCATGTGAT
* * *
16545 TAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTGATTAAATGTGAC
1 TAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTAAGTAAATGTAAC
* **
16604 TAAATGTGATTAATATGTGATGTAATAAATGTTGAAATATTCATGTAAGT-AATGTAAC
1 TAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTAAGTAAATGTAAC
* *
16662 TAAATGTGATTAATATGTGCTGTGTTAAATACT
1 TAAATGTGATTAATATGTGATGTGATAAATACT
16695 TAAGTACTCA
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
58 35 0.44
59 45 0.56
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (59 bp):
TAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTAAGTAAATGTAAC
Found at i:19138 original size:23 final size:23
Alignment explanation
Indices: 19092--19304 Score: 275
Period size: 23 Copynumber: 9.2 Consensus size: 23
19082 ATTGTGTTTA
*
19092 AATGTGATTATATGTGTTAAATATT
1 AATGTGATT-TATG-CTTAAATATT
*
19117 AATGTGATTTCTGCTTAAATATT
1 AATGTGATTTATGCTTAAATATT
* * *
19140 -ATGTGATTTGTTCTTAACTATT
1 AATGTGATTTATGCTTAAATATT
*
19162 AATGTGATTTGTGCTTAAATATT
1 AATGTGATTTATGCTTAAATATT
*
19185 AATGTGATTTATGCTTAAATGTT
1 AATGTGATTTATGCTTAAATATT
* *
19208 AATGTGATTTATTCTTAAATGTT
1 AATGTGATTTATGCTTAAATATT
*
19231 AATATGATTTATGCTTAAATATT
1 AATGTGATTTATGCTTAAATATT
*
19254 AATGTGATTTATGCTTAAATGTT
1 AATGTGATTTATGCTTAAATATT
* *
19277 AATATGATTTATGCTGAAATATT
1 AATGTGATTTATGCTTAAATATT
*
19300 CATGT
1 AATGT
19305 AACTAATGTG
Statistics
Matches: 167, Mismatches: 20, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
22 19 0.11
23 136 0.81
24 3 0.02
25 9 0.05
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.48
Consensus pattern (23 bp):
AATGTGATTTATGCTTAAATATT
Done.