Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010904.1 Kokia drynarioides strain JFW-HI SEQ_125872, 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: 159986
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:9595 original size:24 final size:25
Alignment explanation
Indices: 9558--9604 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
9548 TCGCCTACTT
* *
9558 AAATAATTATATTT-TTTATTTTAA
1 AAATAATCAAATTTATTTATTTTAA
9582 AAATAATCAAATTTATTTATTTT
1 AAATAATCAAATTTATTTATTTT
9605 TAGTGTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AAATAATCAAATTTATTTATTTTAA
Found at i:14613 original size:14 final size:14
Alignment explanation
Indices: 14594--14621 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14584 ATTTAAAAAT
14594 TTTAATTAATTAAA
1 TTTAATTAATTAAA
14608 TTTAATTAATTAAA
1 TTTAATTAATTAAA
14622 GATATATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:15699 original size:106 final size:106
Alignment explanation
Indices: 15561--15773 Score: 399
Period size: 106 Copynumber: 2.0 Consensus size: 106
15551 AGTATAAATC
*
15561 TTAATAATAACAACGTGATTAACACGATTTAAATTTAAATTATATTTAAATAAAAAAATATTTTA
1 TTAATAATAACAACGTGATTAACACGATTTAAATTGAAATTATATTTAAATAAAAAAATATTTTA
* *
15626 ACCATCAAATTAACACACAGGATTTTCATTATGAGTGCTTA
66 ACCATCAAATTAACACACAAGATTCTCATTATGAGTGCTTA
15667 TTAATAATAACAACGTGATTAACACGATTTAAATTGAAATTATATTTAAATAAAAAAATATTTTA
1 TTAATAATAACAACGTGATTAACACGATTTAAATTGAAATTATATTTAAATAAAAAAATATTTTA
15732 ACCATCAAATTAACACACAAGATTCTCATTATGAGTGCTTA
66 ACCATCAAATTAACACACAAGATTCTCATTATGAGTGCTTA
15773 T
1 T
15774 CCACTAATTG
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (106 bp):
TTAATAATAACAACGTGATTAACACGATTTAAATTGAAATTATATTTAAATAAAAAAATATTTTA
ACCATCAAATTAACACACAAGATTCTCATTATGAGTGCTTA
Found at i:19370 original size:5 final size:5
Alignment explanation
Indices: 19360--19386 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19350 ATATTGCCAT
19360 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
19387 CTACTCTTTT
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:19541 original size:30 final size:29
Alignment explanation
Indices: 19481--19542 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
19471 TTTCATGTTA
* *
19481 TTTTGTAAGGGGAAAGTCAAATTTTTTTT
1 TTTTGTAAGGGGAAAGTCAAATTGTATTT
* * *
19510 TTTTTTAAGGTGAGAAGTTAAATTGTATTT
1 TTTTGTAAGGGGA-AAGTCAAATTGTATTT
19540 TTT
1 TTT
19543 AATAGTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.52
Consensus pattern (29 bp):
TTTTGTAAGGGGAAAGTCAAATTGTATTT
Found at i:31084 original size:18 final size:17
Alignment explanation
Indices: 31051--31084 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31041 AGATGACTAT
*
31051 ATAAAAAAATTTAATAA
1 ATAAAAAAATTAAATAA
31068 ATAAAAAATATTAAATA
1 ATAAAAAA-ATTAAATA
31085 TTAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAAAATTAAATAA
Found at i:31089 original size:17 final size:18
Alignment explanation
Indices: 31017--31117 Score: 50
Period size: 18 Copynumber: 5.3 Consensus size: 18
31007 ATATTACTCT
31017 AATA-TAAAT-ATTAAAA
1 AATATTAAATAATTAAAA
31033 TAATATTAAGATGACTATATAAAA
1 -AATATTAA-AT-A--AT-TAAAA
* *
31057 AA-ATTTAATAAATAAAA
1 AATATTAAATAATTAAAA
31074 AATATTAAAT-ATTAAAATA
1 AATATTAAATAATT-AAA-A
31093 AATATTTTAAA-AATTAAAA
1 AATA--TTAAATAATTAAAA
31112 TAATAT
1 -AATAT
31118 GAACGAATCT
Statistics
Matches: 66, Mismatches: 4, Indels: 27
0.68 0.04 0.28
Matches are distributed among these distances:
17 13 0.20
18 14 0.21
19 8 0.12
20 8 0.12
21 10 0.15
22 4 0.06
23 4 0.06
24 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (18 bp):
AATATTAAATAATTAAAA
Found at i:36577 original size:24 final size:24
Alignment explanation
Indices: 36550--36599 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
36540 CATGAAATAA
36550 TAAAATAATCAAAATAT-CATTATG
1 TAAAA-AATCAAAATATACATTATG
**
36574 TAAAAAATGTAAATATACATTATG
1 TAAAAAATCAAAATATACATTATG
36598 TA
1 TA
36600 GGAACTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (24 bp):
TAAAAAATCAAAATATACATTATG
Found at i:39290 original size:59 final size:59
Alignment explanation
Indices: 39206--39324 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 59
39196 TATCAAAGAA
* * * *
39206 TCTAATTTGAAATTATTGTTGAATTTTGAGCTTGAACTGCCAAAGGAGGAAATAAATAT
1 TCTAATTTGAAACTATTATTCAATTTTGAACTTGAACTGCCAAAGGAGGAAATAAATAT
* ** * *
39265 TCTAATTTGAAACTATTATTCAATTTTGAACTTTAACTGCCATTGGATGATATAAATAT
1 TCTAATTTGAAACTATTATTCAATTTTGAACTTGAACTGCCAAAGGAGGAAATAAATAT
39324 T
1 T
39325 GTCTGCAAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39
Consensus pattern (59 bp):
TCTAATTTGAAACTATTATTCAATTTTGAACTTGAACTGCCAAAGGAGGAAATAAATAT
Found at i:50402 original size:168 final size:168
Alignment explanation
Indices: 50124--50459 Score: 620
Period size: 168 Copynumber: 2.0 Consensus size: 168
50114 GAGACTCTCA
*
50124 TTCACTTTCAACCTAAACCTTTTTAGTTCTTTTTCTTTTGATTCATTCTGGGAAAGTCAATGACT
1 TTCACTTTCAACCTAAACCTTTCTAGTTCTTTTTCTTTTGATTCATTCTGGGAAAGTCAATGACT
*
50189 TGCATGTCCTGGTTTCCAAATTCTCAACACTTTAGTTCAGCAAATTATTCTTAAAATTGTTTTTT
66 TGCATGTCCTGGTTTCCAAATTCTCAACAATTTAGTTCAGCAAATTATTCTTAAAATTGTTTTTT
*
50254 GCCCCTTAGTAAAAAACTTAAGATTAATTTTTTCAGTT
131 GCCCCTTAGTAAAAAACTTAAGATTAATTGTTTCAGTT
50292 TTCACTTTCAACCTAAACCTTTCTAGTTCTTTTTCTTTTGATTCATTCTGGGAAAGTCAATGACT
1 TTCACTTTCAACCTAAACCTTTCTAGTTCTTTTTCTTTTGATTCATTCTGGGAAAGTCAATGACT
50357 TGCATGTCCTGGTTTCCAGAA-TCTCAACAATTTAGTTCAGCAAATTATTCTTAAAATTGTTTTT
66 TGCATGTCCTGGTTTCCA-AATTCTCAACAATTTAGTTCAGCAAATTATTCTTAAAATTGTTTTT
*
50421 TGCCCCTTAGTAAAAAACTTAAGATTGATTGTTTCAGTT
130 TGCCCCTTAGTAAAAAACTTAAGATTAATTGTTTCAGTT
50460 GTTGCTTAGA
Statistics
Matches: 163, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
168 161 0.99
169 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (168 bp):
TTCACTTTCAACCTAAACCTTTCTAGTTCTTTTTCTTTTGATTCATTCTGGGAAAGTCAATGACT
TGCATGTCCTGGTTTCCAAATTCTCAACAATTTAGTTCAGCAAATTATTCTTAAAATTGTTTTTT
GCCCCTTAGTAAAAAACTTAAGATTAATTGTTTCAGTT
Found at i:62393 original size:30 final size:30
Alignment explanation
Indices: 62359--62448 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
62349 GGTCCCTGAA
*
62359 TTTGGTTCAATTTTTAATTTGATACTTGAG
1 TTTGGTTCAATTTTTAATTTGATATTTGAG
* *
62389 TTTGGCTTCAA-TGTTAATTTTAGTATTTGAG
1 TTTGG-TTCAATTTTTAATTTGA-TATTTGAG
** *
62420 -TTACTTCAATATTTAATTTGATATTTGAG
1 TTTGGTTCAATTTTTAATTTGATATTTGAG
62449 CTTTTTTTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
29 13 0.27
30 24 0.49
31 12 0.24
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.52
Consensus pattern (30 bp):
TTTGGTTCAATTTTTAATTTGATATTTGAG
Found at i:65517 original size:20 final size:20
Alignment explanation
Indices: 65492--65531 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
65482 AAAAGGAAAA
65492 AAGGAAGAGAAAACTGAGTT
1 AAGGAAGAGAAAACTGAGTT
65512 AAGGAAGAGAAAACTGAGTT
1 AAGGAAGAGAAAACTGAGTT
65532 GTCTGCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.30, T:0.15
Consensus pattern (20 bp):
AAGGAAGAGAAAACTGAGTT
Found at i:68240 original size:18 final size:18
Alignment explanation
Indices: 68212--68253 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
68202 CTAATAATAT
68212 AATATTCATTT-TAAAAA
1 AATATTCATTTATAAAAA
68229 AATATCTCATTTATAAAAA
1 AATAT-TCATTTATAAAAA
*
68248 ATTATT
1 AATATT
68254 TATGCCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 10 0.45
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATTCATTTATAAAAA
Found at i:68241 original size:17 final size:18
Alignment explanation
Indices: 68212--68249 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
68202 CTAATAATAT
68212 AATATTCATTTTA-AAAA
1 AATATTCATTTTATAAAA
68229 AATATCTCA-TTTATAAAA
1 AATAT-TCATTTTATAAAA
68247 AAT
1 AAT
68250 TATTTATGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
AATATTCATTTTATAAAA
Found at i:71774 original size:2 final size:2
Alignment explanation
Indices: 71767--71793 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
71757 AATTTGTCTT
71767 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
71794 CCCAACGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71887 original size:2 final size:2
Alignment explanation
Indices: 71880--71905 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71870 TGGATGTAAT
71880 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
71906 AACTTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:74266 original size:17 final size:19
Alignment explanation
Indices: 74230--74269 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
74220 ACTATTATTC
*
74230 TAAATTGATTTTTAATTTT
1 TAAATTGATTTATAATTTT
74249 TAAATT-ATTTAT-ATTTT
1 TAAATTGATTTATAATTTT
74266 TAAA
1 TAAA
74270 ATTTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 5 0.25
19 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (19 bp):
TAAATTGATTTATAATTTT
Found at i:74271 original size:18 final size:17
Alignment explanation
Indices: 74240--74277 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
74230 TAAATTGATT
74240 TTTAATTTTTAAA-TTA
1 TTTAATTTTTAAATTTA
74256 TTTATATTTTTAAAATTTA
1 TTTA-ATTTTT-AAATTTA
74275 TTT
1 TTT
74278 TAAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 3 0.16
19 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAATTTTTAAATTTA
Found at i:75310 original size:71 final size:71
Alignment explanation
Indices: 75194--75328 Score: 261
Period size: 71 Copynumber: 1.9 Consensus size: 71
75184 AATTATCGTT
*
75194 CCTTTAAATGAAGAGGATAATGCATTTCAGCATACTCGAATTTATGTGCTTTTGTACTGATAATT
1 CCTTTAAATGAAGAGGATAATACATTTCAGCATACTCGAATTTATGTGCTTTTGTACTGATAATT
75259 TTTCAA
66 TTTCAA
75265 CCTTTAAATGAAGAGGATAATACATTTCAGCATACTCGAATTTATGTGCTTTTGTACTGATAAT
1 CCTTTAAATGAAGAGGATAATACATTTCAGCATACTCGAATTTATGTGCTTTTGTACTGATAAT
75329 AATATTCATG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (71 bp):
CCTTTAAATGAAGAGGATAATACATTTCAGCATACTCGAATTTATGTGCTTTTGTACTGATAATT
TTTCAA
Found at i:83308 original size:17 final size:18
Alignment explanation
Indices: 83277--83310 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
83267 TTTTCTAACT
83277 TTTTCTAATTATTTATAA
1 TTTTCTAATTATTTATAA
*
83295 TTTT-TAATTTTTTATA
1 TTTTCTAATTATTTATA
83311 TATACATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCTAATTATTTATAA
Found at i:83825 original size:96 final size:95
Alignment explanation
Indices: 83661--83895 Score: 389
Period size: 96 Copynumber: 2.5 Consensus size: 95
83651 GCTAAAATTG
* *
83661 AATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATAGTTAAGTGATTATTTTGTAAT
1 AATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATAGTTAAGTGATCATTTTATAAT
*
83726 TTTTCATAGTTGGACGACCAAAAAAATTACT
66 TTTTCATAGTTGAACGACC-AAAAAATTACT
83757 AATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATAGTTAAGTGATCATTTTATAAT
1 AATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATAGTTAAGTGATCATTTTATAAT
*
83822 TTTTCATAGTTGAACGATCAAAAAATTACT
66 TTTTCATAGTTGAACGACCAAAAAATTACT
* ** *
83852 AACAGTTAAGTGAATAAATAAGGATCATTTTATAATTTTTTATA
1 AATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATA
83896 ATTGGACGAT
Statistics
Matches: 131, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
95 51 0.39
96 80 0.61
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (95 bp):
AATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATAGTTAAGTGATCATTTTATAAT
TTTTCATAGTTGAACGACCAAAAAATTACT
Found at i:83840 original size:29 final size:29
Alignment explanation
Indices: 83779--83841 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
83769 AATAAATAGG
* *
83779 GATCATTTTATAATTTTTTATAGTTAAGT
1 GATCATTTTATAATTTTTCATAGTTAAGC
83808 GATCATTTTATAATTTTTCATAGTTGAA-C
1 GATCATTTTATAATTTTTCATAGTT-AAGC
83837 GATCA
1 GATCA
83842 AAAAATTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 29 0.94
30 2 0.06
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (29 bp):
GATCATTTTATAATTTTTCATAGTTAAGC
Found at i:83888 original size:66 final size:68
Alignment explanation
Indices: 83803--83931 Score: 199
Period size: 66 Copynumber: 1.9 Consensus size: 68
83793 TTTTTATAGT
* *
83803 TAAGTGATCATTTTATAATTTTTCATAGTTGAACGAT-CAAAAAATTACTAACAGTTAAGTGAAT
1 TAAGTGATCATTTTATAATTTTTCATAATTGAACGATAAAAAAAATTACTAACAGTTAAGTGAAT
83867 AAA
66 AAA
* * *
83870 TAAG-GATCATTTTATAATTTTTTATAATTGGACGATAAAAAAAATTACTAATAGTTAAGTGA
1 TAAGTGATCATTTTATAATTTTTCATAATTGAACGATAAAAAAAATTACTAACAGTTAAGTGA
83932 TTAGTAGTGG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 29 0.52
67 27 0.48
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.37
Consensus pattern (68 bp):
TAAGTGATCATTTTATAATTTTTCATAATTGAACGATAAAAAAAATTACTAACAGTTAAGTGAAT
AAA
Found at i:89909 original size:15 final size:15
Alignment explanation
Indices: 89889--89923 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
89879 AACCACACGT
89889 TATATTCAATATGAA
1 TATATTCAATATGAA
**
89904 TATATTTTATATGAA
1 TATATTCAATATGAA
89919 TATAT
1 TATAT
89924 CTGGCCTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (15 bp):
TATATTCAATATGAA
Found at i:90791 original size:7 final size:7
Alignment explanation
Indices: 90781--90805 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
90771 GTTTATTCAC
90781 CTCTTGT
1 CTCTTGT
90788 CTCTTGT
1 CTCTTGT
90795 CTCTTGT
1 CTCTTGT
90802 CTCT
1 CTCT
90806 GTCAGTTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.12, T:0.56
Consensus pattern (7 bp):
CTCTTGT
Found at i:95457 original size:50 final size:51
Alignment explanation
Indices: 95287--95523 Score: 282
Period size: 51 Copynumber: 4.6 Consensus size: 51
95277 TTTCGTTTAA
** * *
95287 TACTCACGATGACA-TATAGTCATCGAACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGAACCT-TTAATCCATAAAGG-ATTCATT
** * * * * *
95340 TACTCACGATGACACTGGGTCATCGGACCTTTAATCCATCATGAATTCATG
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATT
* *
95391 TACTCACAATGACACTTAGTCATCGAACCTTTAATCCGT-AAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATT
*
95441 TACTCACGATGACACTTAGTCATC-AGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGA-ACCTTTAATCCATAAAGGATTCATT
*
95492 TACTCACGATGACACTTAGTCATCGGACCTTT
1 TACTCACGATGACACTTAGTCATCGAACCTTT
95524 TCATTTATAG
Statistics
Matches: 160, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 44 0.28
51 81 0.51
52 8 0.05
53 25 0.16
54 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATT
Found at i:95470 original size:101 final size:103
Alignment explanation
Indices: 95287--95523 Score: 309
Period size: 101 Copynumber: 2.3 Consensus size: 103
95277 TTTCGTTTAA
**
95287 TACTCACGATGACA-TATAGTCATCGAACCTCTTGTTCCATATAGGAATTCATATACTCACGATG
1 TACTCACGATGACACT-TAGTCATCGAACCT-TTAATCCATATAGGAATTCATATACTCACGATG
* * * *
95351 ACACTGGGTCATCGGACCTTTAATCCATCATGAATTCATG
64 ACACTGAGTCATCAGACCTTTAATCCATAAAGAATTCATG
* * *
95391 TACTCACAATGACACTTAGTCATCGAACCTTTAATCCGTA-AGG-ATTCATTTACTCACGATGAC
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCATATAGGAATTCATATACTCACGATGAC
* * * *
95454 ACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
66 ACTGAGTCATCAGACCTTTAATCCATAAAGAATTCATG
*
95492 TACTCACGATGACACTTAGTCATCGGACCTTT
1 TACTCACGATGACACTTAGTCATCGAACCTTT
95524 TCATTTATAG
Statistics
Matches: 117, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
101 79 0.68
102 3 0.03
103 7 0.06
104 27 0.23
105 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (103 bp):
TACTCACGATGACACTTAGTCATCGAACCTTTAATCCATATAGGAATTCATATACTCACGATGAC
ACTGAGTCATCAGACCTTTAATCCATAAAGAATTCATG
Found at i:101356 original size:17 final size:18
Alignment explanation
Indices: 101331--101364 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
101321 TTTTAACTTT
101331 ATTTATAT-ATTTTTTAG
1 ATTTATATAATTTTTTAG
*
101348 ATTTTTATAATTTTTTA
1 ATTTATATAATTTTTTA
101365 AAAGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTATATAATTTTTTAG
Found at i:101489 original size:9 final size:9
Alignment explanation
Indices: 101475--101504 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
101465 ACATTAATAT
*
101475 ATTATTCAA
1 ATTATTTAA
101484 ATTATTTAA
1 ATTATTTAA
101493 ATTATTTAA
1 ATTATTTAA
101502 ATT
1 ATT
101505 TTAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (9 bp):
ATTATTTAA
Found at i:105173 original size:35 final size:35
Alignment explanation
Indices: 105132--105208 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
105122 GTAATTCTGT
105132 AAATAAAATATTTTATTTAGAATTAAACCGTGTTC
1 AAATAAAATATTTTATTTAGAATTAAACCGTGTTC
*
105167 AAATAAAATATTTTATTTAGAGTTAAACCGTGTTC
1 AAATAAAATATTTTATTTAGAATTAAACCGTGTTC
105202 AAATAAA
1 AAATAAA
105209 TTTCATGTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (35 bp):
AAATAAAATATTTTATTTAGAATTAAACCGTGTTC
Found at i:123291 original size:5 final size:5
Alignment explanation
Indices: 123281--123305 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
123271 ATTTTTAAAT
123281 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
123306 ATATTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:123384 original size:17 final size:17
Alignment explanation
Indices: 123283--123384 Score: 52
Period size: 17 Copynumber: 6.2 Consensus size: 17
123273 TTTTAAATTT
*
123283 TTATTTT-AT-TTTATT
1 TTATTTTAATATTTATA
123298 TTATTTTAATATTTA-A
1 TTATTTTAATATTTATA
* *
123314 TAATTTTATATATTTTTA
1 TTATTTTA-ATATTTATA
* * *
123332 TT-TATTGAAAATTTTTA
1 TTAT-TTTAATATTTATA
** * * *
123349 -TATAGTCATCTTAATA
1 TTATTTTAATATTTATA
123365 TTATTTTAATATTTATA
1 TTATTTTAATATTTATA
123382 TTA
1 TTA
123385 GAGTAATATT
Statistics
Matches: 61, Mismatches: 19, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
15 7 0.11
16 15 0.25
17 34 0.56
18 5 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
TTATTTTAATATTTATA
Found at i:125184 original size:78 final size:75
Alignment explanation
Indices: 125061--125232 Score: 182
Period size: 78 Copynumber: 2.2 Consensus size: 75
125051 GAGGGTGCAA
* * * * *
125061 CAACGCCGGAGGTTGCTTTGAAGCAGAAGAAGGTCTCGTTCTCTGATGTTAAAAGCGTTATCACG
1 CAACACCGGAGATTGCTTTGAACCAGAAGAAGGTCTCGTTCTCTGA---TAAAAGCATAATCACG
*
125126 GAAGATATTGAGT
63 GAAGATACTGAGT
* * * * **
125139 CAACACCGGAGATTGGTTTGAACCGGAAGAAGGTTTCGTTTTCTGATAAAAGCATAATCATTGAA
1 CAACACCGGAGATTGCTTTGAACCAGAAGAAGGTCTCGTTCTCTGATAAAAGCATAATCACGGAA
125204 GATACTGAGT
66 GATACTGAGT
* *
125214 CAACCCCAGAGATTAGCTT
1 CAACACCGGAGATT-GCTT
125233 ATGCCAGAAG
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
75 36 0.46
76 3 0.04
78 39 0.50
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (75 bp):
CAACACCGGAGATTGCTTTGAACCAGAAGAAGGTCTCGTTCTCTGATAAAAGCATAATCACGGAA
GATACTGAGT
Found at i:126318 original size:123 final size:123
Alignment explanation
Indices: 126099--126345 Score: 458
Period size: 123 Copynumber: 2.0 Consensus size: 123
126089 AGGCACCTAA
* * *
126099 AGTTTGATCCCAGTGTAATGGAGCCTGTAAGTGTGAGAGATGCTGGAACTGAACTATTTGATAAC
1 AGTTTGATCCCAATGTAATGGAGCCTGTAAGTGAGAGAGATGCTGAAACTGAACTATTTGATAAC
126164 AAGCCTTACCGAGAGATTGAAGCAGATGATGCAGTAGAAGAAGATGATGATGAACAAG
66 AAGCCTTACCGAGAGATTGAAGCAGATGATGCAGTAGAAGAAGATGATGATGAACAAG
126222 AGTTTGATCCCAATGTAATGGAGCCTGTAAGTGAGAGAGATGCTGAAACTGAACTATTTGATAAC
1 AGTTTGATCCCAATGTAATGGAGCCTGTAAGTGAGAGAGATGCTGAAACTGAACTATTTGATAAC
*
126287 AAGCCTTACCGAGAGATTGAAGCAGATGATGCAGTAGAAGGAGATGATGATGAACAAG
66 AAGCCTTACCGAGAGATTGAAGCAGATGATGCAGTAGAAGAAGATGATGATGAACAAG
126345 A
1 A
126346 AAATCAAGAG
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 120 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (123 bp):
AGTTTGATCCCAATGTAATGGAGCCTGTAAGTGAGAGAGATGCTGAAACTGAACTATTTGATAAC
AAGCCTTACCGAGAGATTGAAGCAGATGATGCAGTAGAAGAAGATGATGATGAACAAG
Found at i:127707 original size:126 final size:126
Alignment explanation
Indices: 127449--127810 Score: 638
Period size: 126 Copynumber: 2.9 Consensus size: 126
127439 AGATTAGGAC
* *
127449 TTAATTGTACTGTTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTTGCTTTCAATTCTT
1 TTAATTGTACTATTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCTT
* *
127514 T-TT-TTCACAGTTGCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATGCATATTAACTGGAT
66 TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATGCATATTAACTGGAT
*
127573 TTAATTGTACTATTATTCATTGTTCTTTCCATAACTTCGAATAGCACTCTTAGCTTTCAATTCTT
1 TTAATTGTACTATTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCTT
127638 TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATGCATATTAACTGGAT
66 TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATGCATATTAACTGGAT
* *
127699 TTAATTGTACTATTATTCGTTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCCT
1 TTAATTGTACTATTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCTT
*
127764 TCTTCTTCACAATTCCTTAGTGTCTGGTAGCTTGGTTGAGAAGTATG
66 TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATG
127811 AGATCAAATG
Statistics
Matches: 227, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
124 63 0.28
125 2 0.01
126 162 0.71
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (126 bp):
TTAATTGTACTATTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCTT
TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATGCATATTAACTGGAT
Found at i:143643 original size:23 final size:23
Alignment explanation
Indices: 143612--143669 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
143602 TCTTCATTAA
* *
143612 TTTAGAATTTAATTTTTTTAATT
1 TTTAAAATTTAATCTTTTTAATT
*
143635 TTTAAAATTTAATCTTTTTATTT
1 TTTAAAATTTAATCTTTTTAATT
* *
143658 TTTTAATTTTAA
1 TTTAAAATTTAA
143670 AATTTAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTAAAATTTAATCTTTTTAATT
Found at i:143644 original size:30 final size:28
Alignment explanation
Indices: 143610--143684 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 28
143600 ATTCTTCATT
143610 AATTTAGAATTTAATTTTTTTAATTTTTAA
1 AATTTA-AATTTAATTTTTTTAA-TTTTAA
* *
143640 AATTTAATCTTTTTATTTTTTTAATTTTAA
1 AATTTAA--ATTTAATTTTTTTAATTTTAA
*
143670 AATTTAAATTCAATT
1 AATTTAAATTTAATT
143685 GTTAATATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 5 0.13
29 1 0.03
30 19 0.50
31 13 0.34
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (28 bp):
AATTTAAATTTAATTTTTTTAATTTTAA
Found at i:143698 original size:22 final size:22
Alignment explanation
Indices: 143673--143718 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
143663 ATTTTAAAAT
143673 TTAAATTCAATTG-TTAATATTA
1 TTAAATT-AATTGATTAATATTA
* *
143695 TTAAATTTATTGATTAGTATTA
1 TTAAATTAATTGATTAATATTA
143717 TT
1 TT
143719 TTTAAAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (22 bp):
TTAAATTAATTGATTAATATTA
Found at i:150790 original size:21 final size:21
Alignment explanation
Indices: 150764--150803 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
150754 CCAAGCTCCT
* *
150764 ATCTTCTTCCTCTTCATCGTC
1 ATCTTCTTCATCGTCATCGTC
150785 ATCTTCTTCATCGTCATCG
1 ATCTTCTTCATCGTCATCG
150804 AACTCCGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.07, T:0.45
Consensus pattern (21 bp):
ATCTTCTTCATCGTCATCGTC
Found at i:150794 original size:15 final size:15
Alignment explanation
Indices: 150774--150802 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
150764 ATCTTCTTCC
150774 TCTTCATCGTCATCT
1 TCTTCATCGTCATCT
150789 TCTTCATCGTCATC
1 TCTTCATCGTCATC
150803 GAACTCCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.07, T:0.45
Consensus pattern (15 bp):
TCTTCATCGTCATCT
Found at i:158315 original size:40 final size:41
Alignment explanation
Indices: 158240--158321 Score: 148
Period size: 40 Copynumber: 2.0 Consensus size: 41
158230 TGATGATTAA
158240 AATTTTGGGTAAGACGGTAGATTTGTATCCGTGGATAGTTTT
1 AATTTTGGGTAAGACGGTA-ATTTGTATCCGTGGATAGTTTT
158282 AATTTTGGGTAAGACGGT-ATTTGTATCCGTGGATAGTTTT
1 AATTTTGGGTAAGACGGTAATTTGTATCCGTGGATAGTTTT
158322 CTCACAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 22 0.55
42 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.41
Consensus pattern (41 bp):
AATTTTGGGTAAGACGGTAATTTGTATCCGTGGATAGTTTT
Done.