Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006339.1 Kokia drynarioides strain JFW-HI SEQ_120914, 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: 27035
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Found at i:3327 original size:15 final size:16
Alignment explanation
Indices: 3307--3342 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3297 AATCATTTAA
3307 AAAATATAAAAAT-AT
1 AAAATATAAAAATAAT
*
3322 AAAATATTAAAATAAT
1 AAAATATAAAAATAAT
3338 AAAAT
1 AAAAT
3343 TATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATATAAAAATAAT
Found at i:10727 original size:18 final size:19
Alignment explanation
Indices: 10704--10740 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
10694 GTGTTATCAA
*
10704 AAAGAAAATAAA-AAAAAG
1 AAAGAAAAGAAAGAAAAAG
10722 AAAGAAAAGAAAGAAAAAG
1 AAAGAAAAGAAAGAAAAAG
10741 TCAAGACGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (19 bp):
AAAGAAAAGAAAGAAAAAG
Found at i:10729 original size:9 final size:9
Alignment explanation
Indices: 10704--10738 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
10694 GTGTTATCAA
*
10704 AAAGAAAAT
1 AAAGAAAAG
*
10713 AAAAAAAAG
1 AAAGAAAAG
10722 AAAGAAAAG
1 AAAGAAAAG
10731 AAAGAAAA
1 AAAGAAAA
10739 AGTCAAGACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:11623 original size:11 final size:10
Alignment explanation
Indices: 11607--11649 Score: 54
Period size: 9 Copynumber: 4.4 Consensus size: 10
11597 ATTTCACCAA
11607 AAAAAAGAGAG
1 AAAAAAGA-AG
11618 AAAAAAGAA-
1 AAAAAAGAAG
*
11627 AAAAAAAAAG
1 AAAAAAGAAG
11637 AAAAAAGAA-
1 AAAAAAGAAG
11646 AAAA
1 AAAA
11650 GAGAGGTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 12 0.41
10 9 0.31
11 8 0.28
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:11628 original size:7 final size:7
Alignment explanation
Indices: 11616--11651 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
11606 AAAAAAAGAG
11616 AGAAAAA
1 AGAAAAA
11623 AG-AAAA
1 AGAAAAA
11629 A-AAAAA
1 AGAAAAA
11635 AGAAAAA
1 AGAAAAA
11642 AGAAAAA
1 AGAAAAA
11649 AGA
1 AGA
11652 GAGGTCGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 10 0.37
7 17 0.63
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:11630 original size:19 final size:19
Alignment explanation
Indices: 11606--11654 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
11596 GATTTCACCA
11606 AAAAAAAGAGAGAAAAAAG
1 AAAAAAAGAGAGAAAAAAG
* *
11625 AAAAAAAAAAAGAAAAAAG
1 AAAAAAAGAGAGAAAAAAG
11644 -AAAAAAGAGAG
1 AAAAAAAGAGAG
11655 GTCGAGGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAGAGAAAAAAG
Found at i:11638 original size:12 final size:12
Alignment explanation
Indices: 11605--11648 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
11595 AGATTTCACC
*
11605 AAAAAAAAG-AG
1 AAAAAAAAGAAA
*
11616 AGAAAAAAGAAA
1 AAAAAAAAGAAA
11628 AAAAAAAAGAAA
1 AAAAAAAAGAAA
11640 AAAGAAAAA
1 AAA-AAAAA
11649 AGAGAGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 8 0.29
12 15 0.54
13 5 0.18
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:12321 original size:20 final size:20
Alignment explanation
Indices: 12296--12337 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
12286 GTCTTGAAAC
12296 AAATAGTTTGAATTACGACT
1 AAATAGTTTGAATTACGACT
12316 AAATAGTTTGAATTACGACT
1 AAATAGTTTGAATTACGACT
12336 AA
1 AA
12338 CTCTTTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (20 bp):
AAATAGTTTGAATTACGACT
Found at i:12686 original size:49 final size:48
Alignment explanation
Indices: 12626--12950 Score: 213
Period size: 49 Copynumber: 6.6 Consensus size: 48
12616 GAGATATAAT
* *
12626 GGGAAAAGTTGAGGCCGCAACGGTGAACCTGGTACCATGAAGACATGAA
1 GGGAAAGGTTGAGGCCGCAACGGCGAACC-GGTACCATGAAGACATGAA
*
12675 GGGAAAGGTTGAGGCCGCAACGACGAATCCGGTTA-CATGAAGACATGAA
1 GGGAAAGGTTGAGGCCGCAACGGCGAA-CCGG-TACCATGAAGACATGAA
* * * *
12724 GGGAAAGCTTGAGGCCGCAACGGCGAACCCAGTACCATAAAGATATGAA
1 GGGAAAGGTTGAGGCCGCAACGGCGAA-CCGGTACCATGAAGACATGAA
** ** * *** * * * ** *
12773 ACGAAAGGTTGAGATCGTAACGATAAACCCGGTAACTTAAAGGATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAA-CCGGTACCATGAA-GACATGAA
* * * * *
12823 GGGAAAGGTTGA-GCCTGTAACAGCGAACTCGATACCGTGAAGATATGAA
1 GGGAAAGGTTGAGGCC-GCAACGGCGAAC-CGGTACCATGAAGACATGAA
* * * * * ** *
12872 GAGAAAGGTTGAGGCTGCAACGGCAAACCCGATACCTTAGAAGATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAA-CCGGTACCAT-GAAGACATGAA
** *
12922 GGGAAAATTTGAGGCCGCAACGACGAACC
1 GGGAAAGGTTGAGGCCGCAACGGCGAACC
12951 TAATACCTTA
Statistics
Matches: 216, Mismatches: 51, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
48 2 0.01
49 146 0.68
50 68 0.31
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.16
Consensus pattern (48 bp):
GGGAAAGGTTGAGGCCGCAACGGCGAACCGGTACCATGAAGACATGAA
Found at i:12934 original size:50 final size:50
Alignment explanation
Indices: 12797--12964 Score: 151
Period size: 50 Copynumber: 3.4 Consensus size: 50
12787 TCGTAACGAT
* * * * *
12797 AAACCCGGTAACTTA-AAGGATGTGATGGGAAAGGTTGAGCCTGTAACAGC
1 AAACCCGATACCTTAGAA-GATGTGATGGGAAAGGTTGAGGCTGCAACGGC
* * * * * *
12847 GAACTCGATACCGT-GAAGATATGAAGAGAAAGGTTGAGGCTGCAACGGC
1 AAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGC
** * *
12896 AAACCCGATACCTTAGAAGATGTGATGGGAAAATTTGAGGCCGCAACGAC
1 AAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGC
* **
12946 GAACCTAATACCTTAGAAG
1 AAACCCGATACCTTAGAAG
12965 CATGACGACA
Statistics
Matches: 92, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
49 37 0.40
50 55 0.60
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (50 bp):
AAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGC
Found at i:12949 original size:99 final size:97
Alignment explanation
Indices: 12624--12950 Score: 272
Period size: 99 Copynumber: 3.3 Consensus size: 97
12614 TAGAGATATA
** * * *
12624 ATGGGAAAAGTTGAGGCCGCAACGGTGAACCTGGTACCATGAAGACATGAAGGGAAAGGTTGAGG
1 ATGGGAAAAGTTGAGGCCGCAACGACGAACC-GATACCATGAAGATATGAAGAGAAAGGTTGAGG
* * * * * **
12689 CCGCAACGACGAATCCGGTTACAT-GAAGACATG
65 CTGCAACGAC-AAACCCGATACTTAGAAGATGTG
* * * *
12722 AAGGG-AAAGCTTGAGGCCGCAACGGCGAACCCAGTACCATAAAGATATGAA-ACGAAAGGTTGA
1 ATGGGAAAAG-TTGAGGCCGCAACGACGAACCGA-TACCATGAAGATATGAAGA-GAAAGGTTGA
* * * *
12785 -GATCGTAACGATAAACCCGGTAACTTA-AAGGATGTG
63 GGCT-GCAACGACAAACCCGAT-ACTTAGAA-GATGTG
* * *
12821 ATGGGAAAGGTTGA-GCCTGTAAC-AGCGAACTCGATACCGTGAAGATATGAAGAGAAAGGTTGA
1 ATGGGAAAAGTTGAGGCC-GCAACGA-CGAAC-CGATACCATGAAGATATGAAGAGAAAGGTTGA
*
12884 GGCTGCAACGGCAAACCCGATACCTTAGAAGATGTG
63 GGCTGCAACGACAAACCCGATA-CTTAGAAGATGTG
*
12920 ATGGGAAAATTTGAGGCCGCAACGACGAACC
1 ATGGGAAAAGTTGAGGCCGCAACGACGAACC
12951 TAATACCTTA
Statistics
Matches: 180, Mismatches: 32, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
97 11 0.06
98 65 0.36
99 90 0.50
100 14 0.08
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.16
Consensus pattern (97 bp):
ATGGGAAAAGTTGAGGCCGCAACGACGAACCGATACCATGAAGATATGAAGAGAAAGGTTGAGGC
TGCAACGACAAACCCGATACTTAGAAGATGTG
Found at i:13311 original size:43 final size:43
Alignment explanation
Indices: 13184--13446 Score: 300
Period size: 43 Copynumber: 6.0 Consensus size: 43
13174 GATTAAAGCC
* * *
13184 GCATTTCAATCTTTTATCCCTAAGTCAAGAGGGGCAGATTAAA
1 GCATTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAA
*
13227 GCTATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGTAGATTGAA
1 GC-AT--TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAA
* * *
13273 GTCATTCCAATCTTTTACCTCTAA-TCAAGAAGGGTAGATTGAA
1 G-CATTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAA
* * *
13316 G-ATTCCAATCTTATACCCCTAA-TCAAGAGGGACAGATTAAA
1 GCATTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAA
* * *
13357 GTCATTTCAATCTTTTACCCCTAA-TAAAGAGGGGTAGATTGAA
1 G-CATTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAA
* *
13400 GACATTTCCAATCTTTTACCCTTAAGTTAAGAGGGGCAGATTGAA
1 G-CA-TTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAA
13445 GC
1 GC
13447 CATCTTCCTG
Statistics
Matches: 189, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
41 35 0.19
43 58 0.31
44 39 0.21
45 18 0.10
46 38 0.20
47 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (43 bp):
GCATTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAA
Found at i:13359 original size:84 final size:85
Alignment explanation
Indices: 13168--13441 Score: 311
Period size: 84 Copynumber: 3.1 Consensus size: 85
13158 CCCCGATCAT
* * *
13168 AGGGA-AGATTAAAGCCGCATTTCAATCTTTTATCCCTAAGTCAAGAGGGGCAGATTAAAGCTAT
1 AGGGACAGATTAAAG--TCATTTCAATCTTTTA-CCCTAA-TCAAGAGGGGTAGATTGAAGC-AT
13232 CATCCAATCTTTTACCCCTAAGTCAAG
61 --TCCAATCTTTTACCCCTAAGTCAAG
** * * *
13259 AGGGGTAGATTGAAGTCATTCCAATCTTTTACCTCTAATCAAGAAGGGTAGATTGAAG-ATTCCA
1 AGGGACAGATTAAAGTCATTTCAATCTTTTACC-CTAATCAAGAGGGGTAGATTGAAGCATTCCA
*
13323 ATCTTATACCCCTAA-TCAAG
65 ATCTTTTACCCCTAAGTCAAG
*
13343 AGGGACAGATTAAAGTCATTTCAATCTTTTACCCCTAATAAAGAGGGGTAGATTGAAGACATTTC
1 AGGGACAGATTAAAGTCATTTCAATCTTTTA-CCCTAATCAAGAGGGGTAGATTGAAG-CA-TTC
* *
13408 CAATCTTTTACCCTTAAGTTAAG
63 CAATCTTTTACCCCTAAGTCAAG
*
13431 AGGGGCAGATT
1 AGGGACAGATT
13442 GAAGCCATCT
Statistics
Matches: 158, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
84 54 0.34
85 20 0.13
86 1 0.01
87 20 0.13
88 14 0.09
89 19 0.12
90 18 0.11
91 4 0.03
92 8 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (85 bp):
AGGGACAGATTAAAGTCATTTCAATCTTTTACCCTAATCAAGAGGGGTAGATTGAAGCATTCCAA
TCTTTTACCCCTAAGTCAAG
Found at i:13707 original size:122 final size:121
Alignment explanation
Indices: 13478--13801 Score: 321
Period size: 122 Copynumber: 2.7 Consensus size: 121
13468 AGAAGTGGAC
* * * * *
13478 CAAA-TCCATCTTCCTGATGAGATATATAGAAATGGATTGAAACAATGAGGCGGTAATCTTCCTG
1 CAAACTCCATCTTCCTGATGAGATACAGAGAAATGG-GTGAAACAAT-AAGTGGTAATCTTCCTG
* * * * * * *
13542 ATGGGATATAAAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTT
64 ATGAGATACAGAGAAGAAGACCAAATCAATAAAGCGAAGCTCAATACGAATGAAAATT
* * * *
13600 CAAAC-CACATGTTCCTGATGAGATACAGAGAAATGGGTCAAGCAATAAGATGGTAATCTTCCTA
1 CAAACTC-CATCTTCCTGATGAGATACAGAGAAATGGGTGAAACAATAAG-TGGTAATCTTCCTG
* * ** *
13664 ATGAGATACAGAGAAGAATACCAAATCATTAAAGCGTAA-CTCAATGTGAGTGAAAATT
64 ATGAGATACAGAGAAGAAGACCAAATCAATAAAGCG-AAGCTCAATACGAATGAAAATT
* * * * *
13722 CAAACTCCATCTTCCTGATTAGATACAGAGAAGTGGGTTGAACCAATAAGTGGTCATCTTCTTGA
1 CAAACTCCATCTTCCTGATGAGATACAGAGAAATGGG-TGAAACAATAAGTGGTAATCTTCCTGA
* *
13787 CGAGATGCAGAGAAG
65 TGAGATACAGAGAAG
13802 TGAACCAAAT
Statistics
Matches: 165, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
121 2 0.01
122 124 0.75
123 39 0.24
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (121 bp):
CAAACTCCATCTTCCTGATGAGATACAGAGAAATGGGTGAAACAATAAGTGGTAATCTTCCTGAT
GAGATACAGAGAAGAAGACCAAATCAATAAAGCGAAGCTCAATACGAATGAAAATT
Found at i:13892 original size:84 final size:84
Alignment explanation
Indices: 13729--13895 Score: 219
Period size: 84 Copynumber: 2.0 Consensus size: 84
13719 ATTCAAACTC
* * * * * * * *
13729 CATCTTCCTGATTAGATACAGAGAAGTGGGTTGAACCAATAAGTGGTCATCTTCTTGACGAGATG
1 CATCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAATAAGCGGTCATCCTCCTGACGAGATA
13794 CAGAGAAGTGAACCAAATT
66 CAGAGAAGTGAACCAAATT
* * *
13813 CATCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAGTGAGGCGGTCATCCTCCTGATGAGAT
1 CATCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAAT-AAGCGGTCATCCTCCTGACGAGAT
13878 ACAGAGAAGT-AACCAAAT
65 ACAGAGAAGTGAACCAAAT
13896 CAATGAAAAG
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 43 0.61
85 28 0.39
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (84 bp):
CATCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAATAAGCGGTCATCCTCCTGACGAGATA
CAGAGAAGTGAACCAAATT
Found at i:14070 original size:153 final size:152
Alignment explanation
Indices: 13871--14160 Score: 436
Period size: 153 Copynumber: 1.9 Consensus size: 152
13861 CATCCTCCTG
13871 ATGAGATACAGAGAAGTAACCAAATCAATGAAAAGAAGCTCAATACGAATGAGACTTCAAACCCC
1 ATGAGATACAGAGAAGTAACCAAATCAATGAAAAGAAGCTCAATACGAATGAGACTTCAAACCCC
* * * *
13936 ATCTTCTTGATGAGATAAAGAGAAATGGGTTAAAGCAATAAAGCGGTCATCTTCCTAATGAGATA
66 ATCTTCCTGATGAGATAAAGAGAAATGGATTAAAACAACAAAGCGGTCATCTTCCTAATGAGATA
14001 CAAAGAAATGAACCAAATTCGT
131 CAAAGAAATGAACCAAATTCGT
*** * *
14023 ATGAGATACAGAGAAGTAGACCAAATCAATGAGGCGAAGCTCAATACGAATGAGTCTTCAAACTC
1 ATGAGATACAGAGAAGTA-ACCAAATCAATGAAAAGAAGCTCAATACGAATGAGACTTCAAACCC
* * * * * *
14088 TATCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAACGAAGTGGTCATCTTCCTAATGAGAT
65 CATCTTCCTGATGAGATAAAGAGAAATGGATTAAAACAACAAAGCGGTCATCTTCCTAATGAGAT
14153 ACAAAGAA
130 ACAAAGAA
14161 GTAGACCCAA
Statistics
Matches: 122, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
152 18 0.15
153 104 0.85
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (152 bp):
ATGAGATACAGAGAAGTAACCAAATCAATGAAAAGAAGCTCAATACGAATGAGACTTCAAACCCC
ATCTTCCTGATGAGATAAAGAGAAATGGATTAAAACAACAAAGCGGTCATCTTCCTAATGAGATA
CAAAGAAATGAACCAAATTCGT
Found at i:14260 original size:123 final size:123
Alignment explanation
Indices: 14023--14291 Score: 398
Period size: 123 Copynumber: 2.2 Consensus size: 123
14013 CCAAATTCGT
* *
14023 ATGAGATACAGAGAAGTAGACCAAATCAATGAGGCGAAGCTCAATACGAATGAGTCTTCAAACTC
1 ATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGTCTTCAAACCC
* * * * *
14088 TATCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAACGAAGTGGTCATCTTCCTA
66 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAACAAAGAGGTCATCTTCCTA
* *
14146 ATGAGATACAAAGAAGTAGACCCAATCAATGAAGCGAAGCTCAATACGAATGAAG-CTTCAAACC
1 ATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATG-AGTCTTCAAACC
* * *
14210 CCATCTTCTTGATGAGATACAGAGAAGTAGG-TCAAAGCAATAAAGAGGTCATCTTCCTA
65 CCATCTTCCTGATGAGATACAGAGAAGT-GGATCAAAACAACAAAGAGGTCATCTTCCTA
14269 ATGAGATACAGAGAAGTAGACCA
1 ATGAGATACAGAGAAGTAGACCA
14292 TCCATCTTCT
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
123 126 0.97
124 4 0.03
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (123 bp):
ATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGTCTTCAAACCC
CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAACAAAGAGGTCATCTTCCTA
Found at i:14327 original size:206 final size:208
Alignment explanation
Indices: 14089--14499 Score: 605
Period size: 206 Copynumber: 2.0 Consensus size: 208
14079 TTCAAACTCT
14089 ATCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAACGAAGTGGTCATCTTCCTAATGAGATA
1 ATCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAACGAAGTGGTCATCTTCCTAATGAGATA
*
14154 CAAAGAAGTAGACCCAA-TC-AATGAAGCGAAGCTCAATACGAATGAAGCTTCAAACCCC-ATCT
66 CAAAGAAGTAGA-CCAATTCAAATGAAGCAAAGCTCAATACGAATGAAGCTTCAAACCCCTATCT
* * *
14216 TCTTGATGAGATACAGAGAAGTAGG-TCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAG
130 TCCTGATGAGATACAGAAAAGT-GGACCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAG
*
14280 AGAAGTAGACCATCC
194 AGAAGTAAACCATCC
* * * *
14295 ATCTTCTTGATGAGATACAGAGAAGTGGATTAAATTAATGAAGTGGTCATCTTTCTAATGAGATA
1 ATCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAACGAAGTGGTCATCTTCCTAATGAGATA
* * * * *
14360 CAGAGACGTAGACCAATTCAAATGAAGCAAAGTTTAATACGAGTGAAGCTTCAAACCCCTATCTT
66 CAAAGAAGTAGACCAATTCAAATGAAGCAAAGCTCAATACGAATGAAGCTTCAAACCCCTATCTT
* * * * *
14425 CCTGATGAGATACAGAAAAGTGGACCGAAGCAATAAAGTGGTTATCTTCCTGATGAGATATAGAG
131 CCTGATGAGATACAGAAAAGTGGACCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAGAG
14490 AAGTAAACCA
196 AAGTAAACCA
14500 AGAGATGAAG
Statistics
Matches: 182, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
205 4 0.02
206 73 0.40
207 37 0.20
208 68 0.37
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (208 bp):
ATCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAACGAAGTGGTCATCTTCCTAATGAGATA
CAAAGAAGTAGACCAATTCAAATGAAGCAAAGCTCAATACGAATGAAGCTTCAAACCCCTATCTT
CCTGATGAGATACAGAAAAGTGGACCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAGAG
AAGTAAACCATCC
Found at i:14353 original size:83 final size:83
Alignment explanation
Indices: 14210--14374 Score: 251
Period size: 83 Copynumber: 2.0 Consensus size: 83
14200 GCTTCAAACC
14210 CCATCTTCTTGATGAGATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGAGA
1 CCATCTTCTTGATGAGATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGAGA
14275 TACAGAGAAGTAGACCAT
66 TACAGAGAAGTAGACCAT
* ** * * *
14293 CCATCTTCTTGATGAGATACAGAGAAGT-GGATTAAATTAATGAAGTGGTCATCTTTCTAATGAG
1 CCATCTTCTTGATGAGATACAGAGAAGTAGG-TCAAAGCAATAAAGAGGTCATCTTCCTAATGAG
*
14357 ATACAGAGACGTAGACCA
65 ATACAGAGAAGTAGACCA
14375 ATTCAAATGA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
82 2 0.03
83 72 0.97
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (83 bp):
CCATCTTCTTGATGAGATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGAGA
TACAGAGAAGTAGACCAT
Found at i:14754 original size:57 final size:57
Alignment explanation
Indices: 14666--14781 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
14656 CACAACATTG
*
14666 AATCCTACTTTCCTAAAGTCGTAGAGAAGCAGATGCAGTGAAAACGAATGACTAATA
1 AATCCTACTTTCCTAAAGTCGTAGAGAAGCAGATGCAGTGAAAACGAACGACTAATA
* *
14723 AATCCTACTTTCCTAAAGTTGTAGAGAAGCAGATGCAGTGAAATCGAACGACTAATA
1 AATCCTACTTTCCTAAAGTCGTAGAGAAGCAGATGCAGTGAAAACGAACGACTAATA
14780 AA
1 AA
14782 GCGAATGGTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (57 bp):
AATCCTACTTTCCTAAAGTCGTAGAGAAGCAGATGCAGTGAAAACGAACGACTAATA
Found at i:17335 original size:18 final size:17
Alignment explanation
Indices: 17298--17350 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
17288 TTCAAAAATG
*
17298 AAATTTTATAAAAGTTA
1 AAATTTTATAAAACTTA
*
17315 AAATTTTATAAATTCTTA
1 AAATTTTATAAA-ACTTA
*
17333 AAA--TTATAAAAATTA
1 AAATTTTATAAAACTTA
17348 AAA
1 AAA
17351 AAAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 6 0.19
16 7 0.23
17 12 0.39
18 6 0.19
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATTTTATAAAACTTA
Found at i:17858 original size:19 final size:20
Alignment explanation
Indices: 17827--17864 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
17817 ATTTCCATAC
*
17827 AAATTATTAAAATTTATAAA
1 AAATTATTAAAATATATAAA
17847 AAATTA-TAAAATATATAA
1 AAATTATTAAAATATATAA
17865 CAATAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTATTAAAATATATAAA
Found at i:26463 original size:67 final size:67
Alignment explanation
Indices: 26384--26516 Score: 257
Period size: 67 Copynumber: 2.0 Consensus size: 67
26374 TATTTTCTTC
26384 CATGTAAATTTTTTACCCACAATCAATATCAAAATAGATATTCAAAATACAAAATCAAGAGTTTT
1 CATGTAAATTTTTTACCCACAATCAATATCAAAATAGATATTCAAAATACAAAATCAAGAGTTTT
26449 TG
66 TG
*
26451 CATGTAAATTTTTTACCCATAATCAATATCAAAATAGATATTCAAAATACAAAATCAAGAGTTTT
1 CATGTAAATTTTTTACCCACAATCAATATCAAAATAGATATTCAAAATACAAAATCAAGAGTTTT
26516 T
66 T
26517 TGTTTGCTCA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (67 bp):
CATGTAAATTTTTTACCCACAATCAATATCAAAATAGATATTCAAAATACAAAATCAAGAGTTTT
TG
Found at i:26935 original size:89 final size:88
Alignment explanation
Indices: 26809--26982 Score: 190
Period size: 89 Copynumber: 2.0 Consensus size: 88
26799 TATAGAATTA
* ** * * * *
26809 ATATGTATATATATTTATATTGATTTTATACTCTATTTAT-TTTATGTTTTTTTTTCTC-TATTT
1 ATATATATATATATACATATTGATTCTATACTATATTT-TCTTT-T-TTTTTTTCTCACTTATTT
*
26872 CGAAAATAAGTATTAAGTAAATATAT
63 CGAAAATAAATATTAAGTAAATATAT
* * *
26898 ATATATATATATATACATATTTATTCTATATTATATTTTCTTTTTTTTTTTCTCACTTATTTTGA
1 ATATATATATATATACATATTGATTCTATACTATATTTTCTTTTTTTTTTTCTCACTTATTTCGA
* *
26963 AAATAAATGTTAGGTAAATA
66 AAATAAATATTAAGTAAATA
26983 AAATATAAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
87 10 0.14
88 26 0.37
89 34 0.49
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (88 bp):
ATATATATATATATACATATTGATTCTATACTATATTTTCTTTTTTTTTTTCTCACTTATTTCGA
AAATAAATATTAAGTAAATATAT
Done.