Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004223.1 Kokia drynarioides strain JFW-HI SEQ_117479, 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: 128656
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 215 characters in sequence are not A, C, G, or T
Found at i:475 original size:80 final size:80
Alignment explanation
Indices: 342--502 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
332 GTCAATTGTC
342 AATATACACAACAAAAGTCAGTCCAACTCTATATATCTACCGGAGCGAGCCGAGTCCAACTCTAG
1 AATATACACAACAAAAGTCAGTCCAACTCTATATATCTACCGGAGCGAGCCGAGTCCAACTCTAG
407 GTCCATTAAAAACCA
66 GTCCATTAAAAACCA
422 AATATACACAACAAAAGTCAGTCCAACTCTATATATCTACCGGAGCGAGCCGAGTCCAACTCTAG
1 AATATACACAACAAAAGTCAGTCCAACTCTATATATCTACCGGAGCGAGCCGAGTCCAACTCTAG
487 GTCCATTAAAAACCA
66 GTCCATTAAAAACCA
502 A
1 A
503 CTTTGACAGT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (80 bp):
AATATACACAACAAAAGTCAGTCCAACTCTATATATCTACCGGAGCGAGCCGAGTCCAACTCTAG
GTCCATTAAAAACCA
Found at i:2268 original size:18 final size:18
Alignment explanation
Indices: 2228--2268 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2218 TATTATATAA
2228 TATTTAAATATATAATTT
1 TATTTAAATATATAATTT
* *
2246 AATTTAAATATATATTTT
1 TATTTAAATATATAATTT
2264 TATTT
1 TATTT
2269 TAACTAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTAAATATATAATTT
Found at i:2278 original size:18 final size:19
Alignment explanation
Indices: 2229--2281 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
2219 ATTATATAAT
*
2229 ATTTAAATATATA-ATTTA
1 ATTTAAATATATATTTTTA
2247 ATTTAAATATATATTTTTA
1 ATTTAAATATATATTTTTA
* *
2266 TTTTAACTAATATATT
1 ATTTAAAT-ATATATT
2282 CTACTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 13 0.43
19 10 0.33
20 7 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAAATATATATTTTTA
Found at i:2396 original size:20 final size:18
Alignment explanation
Indices: 2350--2389 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2340 ATTTTAAAAA
2350 AATTAAAATATATCTGAC
1 AATTAAAATATATCTGAC
*
2368 AATTAAAATATATTTGAC
1 AATTAAAATATATCTGAC
2386 AATT
1 AATT
2390 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (18 bp):
AATTAAAATATATCTGAC
Found at i:2691 original size:19 final size:19
Alignment explanation
Indices: 2649--2694 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2639 ATGATTCCAC
*
2649 CAAAAAAATAAATTTAAAT
1 CAAAAAAATAAATATAAAT
*
2668 TAAAAAAATAAATAATAAA-
1 CAAAAAAATAAAT-ATAAAT
2687 CAAAAAAA
1 CAAAAAAA
2695 AGTACAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (19 bp):
CAAAAAAATAAATATAAAT
Found at i:3664 original size:10 final size:10
Alignment explanation
Indices: 3649--3722 Score: 50
Period size: 10 Copynumber: 7.7 Consensus size: 10
3639 AAAATTTTTA
3649 TTTTAAATTT
1 TTTTAAATTT
*
3659 TTTTAAA--A
1 TTTTAAATTT
*
3667 TTTTAACTTT
1 TTTTAAATTT
*
3677 TTTTACATATT
1 TTTTAAAT-TT
* *
3688 GTTTAGA-TT
1 TTTTAAATTT
3697 TTTT-AATGTT
1 TTTTAAAT-TT
3707 TTTT-AATTT
1 TTTTAAATTT
3716 TTTTAAA
1 TTTTAAA
3723 AAATATATAA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
8 7 0.14
9 11 0.22
10 24 0.49
11 7 0.14
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:3719 original size:19 final size:19
Alignment explanation
Indices: 3649--3721 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
3639 AAAATTTTTA
*
3649 TTTTAAATTTTTTTAA-A-
1 TTTTTAATTTTTTTAATAT
*
3666 ATTTTAACTTTTTTTACATAT
1 TTTTTAA-TTTTTTTA-ATAT
* *
3687 TGTTTAGA-TTTTTTAATGT
1 TTTTTA-ATTTTTTTAATAT
3706 TTTTTAATTTTTTTAA
1 TTTTTAATTTTTTTAA
3722 AAAATATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
17 5 0.11
18 9 0.20
19 17 0.39
20 8 0.18
21 4 0.09
22 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (19 bp):
TTTTTAATTTTTTTAATAT
Found at i:5614 original size:15 final size:15
Alignment explanation
Indices: 5594--5640 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
5584 TTGTCTCGTA
5594 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* *
5609 TTATATTTAAAATA-
1 TTATATTTTAATTAT
*
5623 TTAT-TTTTAGTTAT
1 TTATATTTTAATTAT
5637 TTAT
1 TTAT
5641 GTTATTGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 6 0.23
14 8 0.31
15 12 0.46
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:5794 original size:18 final size:18
Alignment explanation
Indices: 5771--5813 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5761 TTTTCAGTTG
5771 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
5789 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
5807 TAATTAA
1 TAATTAA
5814 AAATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:9832 original size:22 final size:22
Alignment explanation
Indices: 9779--9832 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
9769 AAAAAATTTC
*
9779 AATAAATA-AAAAATAAAAAAT
1 AATAAATATTAAAATAAAAAAT
9800 AATTAAATATTAAAATAAAACAAT
1 AA-TAAATATTAAAATAAAA-AAT
9824 -ATAAATATT
1 AATAAATATT
9833 TTTAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.07
22 14 0.48
23 10 0.34
24 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAAATATTAAAATAAAAAAT
Found at i:9930 original size:13 final size:13
Alignment explanation
Indices: 9912--9937 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9902 CGAATTTAAA
9912 CAAAATTTTAAGT
1 CAAAATTTTAAGT
9925 CAAAATTTTAAGT
1 CAAAATTTTAAGT
9938 TGGATCGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
CAAAATTTTAAGT
Found at i:10173 original size:5 final size:5
Alignment explanation
Indices: 10163--10189 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
10153 AAATTGTGTC
10163 TCAGT TCAGT TCAGT TCAGT TCAGT TC
1 TCAGT TCAGT TCAGT TCAGT TCAGT TC
10190 GTGCACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (5 bp):
TCAGT
Found at i:17005 original size:15 final size:15
Alignment explanation
Indices: 16985--17014 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16975 TAAATTTTAT
16985 ATAAAAAATATAAAA
1 ATAAAAAATATAAAA
*
17000 ATAAAAACTATAAAA
1 ATAAAAAATATAAAA
17015 TTATATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAAAAAATATAAAA
Found at i:29555 original size:2 final size:2
Alignment explanation
Indices: 29548--29575 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29538 CTAAAAAGTA
29548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29576 GTTCTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30611 original size:18 final size:18
Alignment explanation
Indices: 30571--30613 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30561 ATTCAATGTG
30571 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
30589 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
30607 TAATTAA
1 TAATTAA
30614 AAACATATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:32549 original size:29 final size:30
Alignment explanation
Indices: 32514--32571 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
32504 ATGGTTTAAC
*
32514 GTGTAATTGTATACA-TGAATTTTGATTTT
1 GTGTAATTGTATACATTAAATTTTGATTTT
*
32543 GTGTAATTTTATACATTAAATTTTGATTT
1 GTGTAATTGTATACATTAAATTTTGATTT
32572 GATCCAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.53
Consensus pattern (30 bp):
GTGTAATTGTATACATTAAATTTTGATTTT
Found at i:46296 original size:31 final size:32
Alignment explanation
Indices: 46247--46306 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
46237 ATAAAACTGA
46247 ATTTTAATCCCTCCAAAAATGATAAAAATTTG
1 ATTTTAATCCCTCCAAAAATGATAAAAATTTG
* * *
46279 ATTTTAAT-CTTCTAAAAATTATAAAAAT
1 ATTTTAATCCCTCCAAAAATGATAAAAAT
46307 ATAGGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (32 bp):
ATTTTAATCCCTCCAAAAATGATAAAAATTTG
Found at i:70184 original size:16 final size:16
Alignment explanation
Indices: 70163--70196 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
70153 AAAGCTGCGC
70163 TATCAAATATATTCAG
1 TATCAAATATATTCAG
70179 TATCAAATATATTCAG
1 TATCAAATATATTCAG
70195 TA
1 TA
70197 GGCGGCCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
TATCAAATATATTCAG
Found at i:78348 original size:3 final size:3
Alignment explanation
Indices: 78340--78368 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
78330 CTTCAAACCA
78340 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
78369 AGGCCCGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:81651 original size:141 final size:140
Alignment explanation
Indices: 81395--81668 Score: 408
Period size: 141 Copynumber: 1.9 Consensus size: 140
81385 TTTCATGTAT
** * *
81395 TTGGAATATTTGTGGAGTGTCATATGACATAGATATATCCCGGTATGCATCAGACAGTGACTTCG
1 TTGGAATATTCATGGAGTGTCATATGACATACATATATCCCAGTATGCATCAGACAGTGACTTCG
* *
81460 GGAAAAATGAAGACTCAGAGAATCAAAATACTAAACCCGAAAAAGACCCAACCTTAGATAGGAAT
66 AGAAAAATGAAGACTCA-AGAATCAAAATACTAAACCCGAAAAAGACCCAACCTTAGAGAGGAAT
81525 AAACCACATAC
130 AAACCACATAC
*
81536 TTGGAATATTCATGGAGTGTCATATGACATACATATATCCCAGTATGCGTCAGACATGGTGACTT
1 TTGGAATATTCATGGAGTGTCATATGACATACATATATCCCAGTATGCATCAGACA--GTGACTT
* * *
81601 CGAGAAAAATGAAGAGTC-AGAA-CAACAATACTAAACCCGTAAAAGGCCCAACCTTAGAGAGGA
64 CGAGAAAAATGAAGACTCAAGAATCAA-AATACTAAACCCGAAAAAGACCCAACCTTAGAGAGGA
81664 ATAAA
128 ATAAA
81669 AAATGCACTT
Statistics
Matches: 120, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
140 3 0.03
141 94 0.78
143 23 0.19
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (140 bp):
TTGGAATATTCATGGAGTGTCATATGACATACATATATCCCAGTATGCATCAGACAGTGACTTCG
AGAAAAATGAAGACTCAAGAATCAAAATACTAAACCCGAAAAAGACCCAACCTTAGAGAGGAATA
AACCACATAC
Found at i:84647 original size:101 final size:98
Alignment explanation
Indices: 84536--84726 Score: 242
Period size: 101 Copynumber: 1.9 Consensus size: 98
84526 GTTCTATAAA
* * *
84536 AAAATTATGAAAATACCGTTT-CGTAAATAAAATAATTCATATTATTT-GAGGGTATTTTAATTT
1 AAAATTATGAAAAT-CCATTTCCGTAAATAAAATAAGTCATATTATTTAG-GGGCATTTTAA---
84599 TTTTTTATTTTAACAAAAATTAAGAAAAATTTGATTAG
61 TTTTTTATTTTAACAAAAATTAAGAAAAATTTGATTAG
** * * *
84637 AAAATTATGAAAATGTATTTCCGTAATTAAGATGAGTCATATTATTTAGGGGCATTTTAATTTTT
1 AAAATTATGAAAATCCATTTCCGTAAATAAAATAAGTCATATTATTTAGGGGCATTTTAATTTTT
*
84702 TATTTTAACAAAAATTAAGGAAAAT
66 TATTTTAACAAAAATTAAGAAAAAT
84727 ATGCATATGT
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
98 29 0.37
100 3 0.04
101 46 0.58
102 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (98 bp):
AAAATTATGAAAATCCATTTCCGTAAATAAAATAAGTCATATTATTTAGGGGCATTTTAATTTTT
TATTTTAACAAAAATTAAGAAAAATTTGATTAG
Found at i:86015 original size:45 final size:45
Alignment explanation
Indices: 85964--86246 Score: 415
Period size: 45 Copynumber: 6.3 Consensus size: 45
85954 GGCCGGTTCG
* *
85964 TCCATTTCTCTTCGACATGGTACCGAACAGGACTAGATGGCTTAT
1 TCCATTTCTCTTCGACACGATACCGAACAGGACTAGATGGCTTAT
* * * * *
86009 TCCATTTCTCTTCGGCACCATAACGAGCAGGACTAGATGGTTTAT
1 TCCATTTCTCTTCGACACGATACCGAACAGGACTAGATGGCTTAT
* * *
86054 TCCATTTCTCTTCAACAGGGTACCGAACAGGACTAGATGGCTTAT
1 TCCATTTCTCTTCGACACGATACCGAACAGGACTAGATGGCTTAT
* *
86099 TCCATTTCTCTTC-AGCACCATAACGAACAGGACTAGATGGCTTAT
1 TCCATTTCTCTTCGA-CACGATACCGAACAGGACTAGATGGCTTAT
*
86144 TCCATTTCTCTTCGACACGATACCGAACAGGACTCGATGGCTTAT
1 TCCATTTCTCTTCGACACGATACCGAACAGGACTAGATGGCTTAT
* *
86189 TCCATTTCTCTTCGACACGATACCGAACGGGACTAGAAGGCTTAT
1 TCCATTTCTCTTCGACACGATACCGAACAGGACTAGATGGCTTAT
86234 TCCATTTCTCTTC
1 TCCATTTCTCTTC
86247 AGTATGATAC
Statistics
Matches: 211, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
44 1 0.00
45 209 0.99
46 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (45 bp):
TCCATTTCTCTTCGACACGATACCGAACAGGACTAGATGGCTTAT
Found at i:86284 original size:135 final size:135
Alignment explanation
Indices: 85987--86286 Score: 339
Period size: 135 Copynumber: 2.2 Consensus size: 135
85977 GACATGGTAC
** * ** * * *
85987 CGAACAGGACTAGATGGCTTATTCCATTTCTCTTCGGCACCATAACGAGCAGGACTAGATGGTTT
1 CGAACAGGACTAGAACGCTCACGCCATTTCTCTTCGACACCATAACGAACAGGACTAGATGGCTT
* * *
86052 ATTCCATTTCTCTTCAACAGGGTACCGAACAGGACTAGATGGCTTATTCCATTTCTCTTCAGCAC
66 ATTCCATTTCTCTTCAACACGATACCGAACAGGACTAGAAGGCTTATTCCATTTCTCTTCAGCAC
86117 CATAA
131 CATAA
** * ** * * *
86122 CGAACAGGACTAGATGGCTTATTCCATTTCTCTTCGACACGATACCGAACAGGACTCGATGGCTT
1 CGAACAGGACTAGAACGCTCACGCCATTTCTCTTCGACACCATAACGAACAGGACTAGATGGCTT
* * * *
86187 ATTCCATTTCTCTTCGACACGATACCGAACGGGACTAGAAGGCTTATTCCATTTCTCTTCAGTAT
66 ATTCCATTTCTCTTCAACACGATACCGAACAGGACTAGAAGGCTTATTCCATTTCTCTTCAGCAC
* *
86252 GATAC
131 CATAA
* * * *
86257 CGTACAGGACTTGAACTCTCCCGCCATTTC
1 CGAACAGGACTAGAACGCTCACGCCATTTC
86287 CCGGGACTTA
Statistics
Matches: 141, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
135 141 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (135 bp):
CGAACAGGACTAGAACGCTCACGCCATTTCTCTTCGACACCATAACGAACAGGACTAGATGGCTT
ATTCCATTTCTCTTCAACACGATACCGAACAGGACTAGAAGGCTTATTCCATTTCTCTTCAGCAC
CATAA
Found at i:98496 original size:2 final size:2
Alignment explanation
Indices: 98489--98528 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
98479 TCAGTGATAA
98489 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
98529 CTTAATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:99904 original size:30 final size:29
Alignment explanation
Indices: 99864--99933 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
99854 GTTAATAATT
* *
99864 TATAAGAATTGAATTAAATCAAAATTTCATA
1 TATAA-AATTGAATAAAATC-AAAGTTCATA
* *
99895 TATAAAATTGCATAAAATCAAAGTTCATG
1 TATAAAATTGAATAAAATCAAAGTTCATA
*
99924 TATATAATTG
1 TATAAAATTG
99934 TACAGTAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 17 0.50
30 12 0.35
31 5 0.15
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.36
Consensus pattern (29 bp):
TATAAAATTGAATAAAATCAAAGTTCATA
Found at i:108478 original size:20 final size:20
Alignment explanation
Indices: 108449--108500 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 20
108439 AATCGAAATT
108449 AAATTATAATTTTAAAAAAGA
1 AAATTATAATTTTAAAAAA-A
108470 AAA-TATAA--TTAAAAAAA
1 AAATTATAATTTTAAAAAAA
*
108487 AAATTAAAATTTTA
1 AAATTATAATTTTA
108501 TTATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 4 0.15
18 12 0.44
20 8 0.30
21 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAATTATAATTTTAAAAAAA
Found at i:110391 original size:127 final size:127
Alignment explanation
Indices: 110168--110403 Score: 332
Period size: 127 Copynumber: 1.9 Consensus size: 127
110158 TGTCTTTTTC
** * * *
110168 AATATGATTTATCATTTTTTATATAAACTTGAGAATTCAATTCTATCAATCTGAGCATTAACTTT
1 AATATGATTTATCAAATTTGATATAAACTTGAGAATTCAATTCCATCAATCCGA-CATTAACTTT
* * *
110233 TTGTATGATAATAAAGTGTTAACAAACCAATTCAACTCCAACTTAAATGATATGATATTTTAA
65 TGGTATGATAATAAAATGTTAACAAACCAATTCAACTCAAACTTAAATGATATGATATTTTAA
*
110296 AATATGATTTATCAAATTTGATATAAACTTGAGAA-TCTAATTCCATCAATCCGA-ATATGACTT
1 AATATGATTTATCAAATTTGATATAAACTTGAGAATTC-AATTCCATCAATCCGACAT-TAACTT
* *
110359 TTGGTATGATAATAAAATGTTAAGAAACCAATTCAATTCAAACTT
64 TTGGTATGATAATAAAATGTTAACAAACCAATTCAACTCAAACTT
110404 GAATTCGTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
126 2 0.02
127 47 0.49
128 46 0.48
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (127 bp):
AATATGATTTATCAAATTTGATATAAACTTGAGAATTCAATTCCATCAATCCGACATTAACTTTT
GGTATGATAATAAAATGTTAACAAACCAATTCAACTCAAACTTAAATGATATGATATTTTAA
Found at i:112849 original size:59 final size:60
Alignment explanation
Indices: 112643--112976 Score: 258
Period size: 59 Copynumber: 5.7 Consensus size: 60
112633 AAATAAATCA
* ** *
112643 TTTTTAGTGTTGGTCATTGC-ATGGCCGACATTTCTTTTTTGAGAAAAAAAACTTCAAATT
1 TTTTTGGTGTTGGTCATTGCAATGGCCGACACCTCTTTTTTGAGAAAAAAAA-TTCAAAAT
* * * * * *
112703 TTTTTGGTGTTGGTCA-TGCAATAGTCGACACTTTCTTTTTT-CGAAAAAAAATT-TACAT
1 TTTTTGGTGTTGGTCATTGCAATGGCCGACAC-CTCTTTTTTGAGAAAAAAAATTCAAAAT
* * * * *
112761 TTTTGGGTGTTGG-CATTGC-ATGTCCGACACCCCCTTTTTGAGAAAAAAATTTCAAAAT
1 TTTTTGGTGTTGGTCATTGCAATGGCCGACACCTCTTTTTTGAGAAAAAAAATTCAAAAT
* * * **
112819 TTTTTGGTGTTGGTCA-TGCAATGGCCGACACTATTTTTTCTTGAAAAAAAAAATT--GTAT
1 TTTTTGGTGTTGGTCATTGCAATGGCCGACAC-CTCTTTT-TTGAGAAAAAAAATTCAAAAT
* ** * ** * *
112878 TTTTGGGTGTTGACCATTG-TATGGTTGACACCTCCTTTTTGAGAAAAAAAATTCAAATT
1 TTTTTGGTGTTGGTCATTGCAATGGCCGACACCTCTTTTTTGAGAAAAAAAATTCAAAAT
* * * * *
112937 TTTTTTGTGTAGGTCA-TGAAATGGCCGAGACCTTTTTTTT
1 TTTTTGGTGTTGGTCATTGCAATGGCCGACACCTCTTTTTT
112977 TCGGATAAAA
Statistics
Matches: 208, Mismatches: 53, Indels: 27
0.72 0.18 0.09
Matches are distributed among these distances:
56 6 0.03
57 34 0.16
58 41 0.20
59 68 0.33
60 37 0.18
61 22 0.11
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (60 bp):
TTTTTGGTGTTGGTCATTGCAATGGCCGACACCTCTTTTTTGAGAAAAAAAATTCAAAAT
Found at i:112867 original size:117 final size:116
Alignment explanation
Indices: 112641--112999 Score: 404
Period size: 118 Copynumber: 3.1 Consensus size: 116
112631 CCAAATAAAT
* * ** *
112641 CATTTTT-AGTGTTGGTCATTGCATGGCCGACATTTCTTTTTTGAGAAAAAAAACTTCAAATTTT
1 CATTTTTGGGTGTTGG-CATTGCATGTCCGACACCTCCTTTTTGAGAAAAAAAA-TTCAAATTTT
* * *
112705 TTTGGTGTTGGTCATGCAATAGTCGACACTTTCTTTTTTCGAAAAAAAATTTA
64 TTTGGTGTTGGTCATGCAATGGCCGACACTTTCTTTTTTCGAAAAAAAAATTA
* * *
112758 CATTTTTGGGTGTTGGCATTGCATGTCCGACACCCCCTTTTTGAGAAAAAAATTTCAAAATTTTT
1 CATTTTTGGGTGTTGGCATTGCATGTCCGACACCTCCTTTTTGAGAAAAAAAATTCAAATTTTTT
*
112823 TGGTGTTGGTCATGCAATGGCCGACACTATT-TTTTCTT-GAAAAAAAAAATTG
66 TGGTGTTGGTCATGCAATGGCCGACACT-TTCTTTT-TTCG-AAAAAAAAATTA
* * * *
112875 TATTTTTGGGTGTTGACCATTGTATGGT-TGACACCTCCTTTTTGAGAAAAAAAATTCAAATTTT
1 CATTTTTGGGTGTTG-GCATTGCAT-GTCCGACACCTCCTTTTTGAGAAAAAAAATTCAAATTTT
* * * * * *
112939 TTTTGTGTAGGTCATGAAATGGCCGAGACCTTT-TTTTTTCGGATAAAAAATTA
64 TTTGGTGTTGGTCATGCAATGGCCGACA-CTTTCTTTTTTCGAAAAAAAAATTA
112992 CAATTTTT
1 C-ATTTTT
113000 TTTTATATTG
Statistics
Matches: 206, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
116 42 0.20
117 77 0.37
118 83 0.40
119 4 0.02
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (116 bp):
CATTTTTGGGTGTTGGCATTGCATGTCCGACACCTCCTTTTTGAGAAAAAAAATTCAAATTTTTT
TGGTGTTGGTCATGCAATGGCCGACACTTTCTTTTTTCGAAAAAAAAATTA
Found at i:112988 original size:61 final size:61
Alignment explanation
Indices: 112922--113066 Score: 156
Period size: 61 Copynumber: 2.4 Consensus size: 61
112912 CTTTTTGAGA
* *
112922 AAAAAAATTCAAATTTTTTTTGTGTAGGTCATGAAATGGCCGAGA-CCTTTTTT-TTTCGG-
1 AAAAAAATTCAAATTTTTTTTGTGTAGGTCATGAAATAGCCGACACCCTTTTTTATTT-GGT
* * * * * *
112981 ATAAAAAATTACAATTTTTTTTTATATTGGTCATGTAATAGTCGACACCCTTTTTTATTTGGT
1 A-AAAAAATT-CAAATTTTTTTTGTGTAGGTCATGAAATAGCCGACACCCTTTTTTATTTGGT
113044 AAAAAAATT-AAA-TTTTTTTGTGT
1 AAAAAAATTCAAATTTTTTTTGTGT
113067 TGACCATATA
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
59 10 0.14
60 10 0.14
61 28 0.40
62 18 0.26
63 4 0.06
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (61 bp):
AAAAAAATTCAAATTTTTTTTGTGTAGGTCATGAAATAGCCGACACCCTTTTTTATTTGGT
Found at i:118577 original size:22 final size:22
Alignment explanation
Indices: 118547--118605 Score: 55
Period size: 27 Copynumber: 2.5 Consensus size: 22
118537 TTTAACAACA
* *
118547 ATAAGTTAATTAATATAATATT
1 ATAATTTAATTAATATAATACT
118569 ATAATTTAATAAAATTAATATAATACT
1 ATAA-TT--T--AATTAATATAATACT
118596 ATAATTTAAT
1 ATAATTTAAT
118606 AAAATGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
22 7 0.23
23 1 0.03
24 1 0.03
25 1 0.03
26 2 0.07
27 18 0.60
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAATTTAATTAATATAATACT
Found at i:118592 original size:27 final size:27
Alignment explanation
Indices: 118554--118610 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
118544 ACAATAAGTT
*
118554 AATTAATATAATATTATAATTTAATAA
1 AATTAATATAATACTATAATTTAATAA
118581 AATTAATATAATACTATAATTTAATAA
1 AATTAATATAATACTATAATTTAATAA
118608 AAT
1 AAT
118611 GTTATTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTAATATAATACTATAATTTAATAA
Found at i:120547 original size:21 final size:21
Alignment explanation
Indices: 120521--120563 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
120511 CAGGTAATAC
120521 TTAGTTTTAGTTGCATTAAGT
1 TTAGTTTTAGTTGCATTAAGT
120542 TTAGTTTTAGTTGCATTAAGT
1 TTAGTTTTAGTTGCATTAAGT
120563 T
1 T
120564 CTTTCAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.19, T:0.53
Consensus pattern (21 bp):
TTAGTTTTAGTTGCATTAAGT
Done.