Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014555.1 Kokia drynarioides strain JFW-HI SEQ_129594, 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: 156930
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1356 original size:17 final size:18
Alignment explanation
Indices: 1326--1359 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1316 ATAGATACGA
*
1326 TTCTCTTTATTTTTTTTC
1 TTCTCTTTAATTTTTTTC
1344 TTCT-TTTAATTTTTTT
1 TTCTCTTTAATTTTTTT
1360 TCCTTTACAT
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:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (18 bp):
TTCTCTTTAATTTTTTTC
Found at i:4379 original size:71 final size:71
Alignment explanation
Indices: 4263--4404 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
4253 TGATGTTTGG
*
4263 GGAATTGATTTCATGGGACCTTTTCCTAACTCATGTGAAAATCAATATATTCTATTGGCAGTAGA
1 GGAATTGATTTCATGGGACCTTTTCCTAACTCATGTGAAAATCAATATATTCTATTAGCAGTAGA
4328 TTATGT
66 TTATGT
4334 GGAATTGATTTCATGGGACCTTTTCCTAACTCATGTGAAAATCAATATATTCTATTAGCAGTAGA
1 GGAATTGATTTCATGGGACCTTTTCCTAACTCATGTGAAAATCAATATATTCTATTAGCAGTAGA
4399 TTATGT
66 TTATGT
4405 TTCCAAATGG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (71 bp):
GGAATTGATTTCATGGGACCTTTTCCTAACTCATGTGAAAATCAATATATTCTATTAGCAGTAGA
TTATGT
Found at i:11912 original size:16 final size:15
Alignment explanation
Indices: 11891--11924 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
11881 TAATGAGTTG
11891 GTTTACTTTTCAATTA
1 GTTTACTTTTCAA-TA
11907 GTTTACTTTTCAATA
1 GTTTACTTTTCAATA
11922 GTT
1 GTT
11925 AGTTGCACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (15 bp):
GTTTACTTTTCAATA
Found at i:19571 original size:16 final size:15
Alignment explanation
Indices: 19550--19583 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
19540 TGATTAAAAT
*
19550 TAATAACATAAACTAA
1 TAATAAAATAAA-TAA
19566 TAATAAAATAAATAA
1 TAATAAAATAAATAA
19581 TAA
1 TAA
19584 AGAACTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAATAAAATAAATAA
Found at i:19822 original size:15 final size:15
Alignment explanation
Indices: 19802--19833 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19792 AAGGGACCAG
19802 AACTGCAGAATGTCA
1 AACTGCAGAATGTCA
19817 AACTGCAGAATGTCA
1 AACTGCAGAATGTCA
19832 AA
1 AA
19834 ACTATCTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (15 bp):
AACTGCAGAATGTCA
Found at i:35288 original size:19 final size:20
Alignment explanation
Indices: 35260--35300 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
35250 AATAGGGAAA
35260 TTTTGGAAATTTTAG-GGTT
1 TTTTGGAAATTTTAGAGGTT
*
35279 TTTTGTAAATTTTAGAGGTT
1 TTTTGGAAATTTTAGAGGTT
35299 TT
1 TT
35301 AAGGATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (20 bp):
TTTTGGAAATTTTAGAGGTT
Found at i:37213 original size:13 final size:13
Alignment explanation
Indices: 37182--37217 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
37172 ATAATTATAG
37182 ACTTATTATTTT-
1 ACTTATTATTTTA
37194 A-TT-TTATTTTA
1 ACTTATTATTTTA
37205 ACTTATTATTTTA
1 ACTTATTATTTTA
37218 TTTTCAGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.33
11 3 0.14
12 3 0.14
13 8 0.38
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (13 bp):
ACTTATTATTTTA
Found at i:37229 original size:18 final size:18
Alignment explanation
Indices: 37192--37235 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
37182 ACTTATTATT
*
37192 TTATTTTATTTTAACTTA
1 TTATTTTATTTTAACGTA
* *
37210 TTATTTTATTTTCAGGTA
1 TTATTTTATTTTAACGTA
37228 TT-TTTTAT
1 TTATTTTAT
37236 ACTTTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (18 bp):
TTATTTTATTTTAACGTA
Found at i:37415 original size:35 final size:35
Alignment explanation
Indices: 37376--37445 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
37366 GTGGATTATC
37376 GGATTGCATGTGGGTATAATTACGTAAATAACCTT
1 GGATTGCATGTGGGTATAATTACGTAAATAACCTT
37411 GGATTGCATGTGGGTATAATTACGTAAATAACCTT
1 GGATTGCATGTGGGTATAATTACGTAAATAACCTT
37446 CTGGATCCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (35 bp):
GGATTGCATGTGGGTATAATTACGTAAATAACCTT
Found at i:38498 original size:17 final size:17
Alignment explanation
Indices: 38486--38524 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
38476 CACATTTCTT
38486 CTGTCACTGCATTTTTA
1 CTGTCACTGCATTTTTA
*
38503 TTGTCACTGCATTTTTA
1 CTGTCACTGCATTTTTA
*
38520 TTGTC
1 CTGTC
38525 GTTACATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.21, G:0.13, T:0.51
Consensus pattern (17 bp):
CTGTCACTGCATTTTTA
Found at i:45764 original size:26 final size:24
Alignment explanation
Indices: 45735--45796 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
45725 TTATTTTAGG
45735 GATTTGAGTTTTTTTTAAAGGAAAGA
1 GATTTGAGTTTTTTTT--AGGAAAGA
* *
45761 GATTTGA-TATTTTTTTATGTAAGA
1 GATTTGAGT-TTTTTTTAGGAAAGA
45785 GATTTGAGTTTT
1 GATTTGAGTTTT
45797 AATCTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 16 0.50
25 2 0.06
26 14 0.44
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (24 bp):
GATTTGAGTTTTTTTTAGGAAAGA
Found at i:47459 original size:18 final size:18
Alignment explanation
Indices: 47431--47480 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
47421 TAAGAACTAT
* *
47431 CATATAAATATATACATG
1 CATATACATATATACATA
* * *
47449 TATATACATATAAATATA
1 CATATACATATATACATA
47467 CATATACATATATA
1 CATATACATATATA
47481 TTTGGACAGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (18 bp):
CATATACATATATACATA
Found at i:47465 original size:12 final size:12
Alignment explanation
Indices: 47431--47478 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
47421 TAAGAACTAT
47431 CATATAAATATA
1 CATATAAATATA
* * **
47443 TACATGTATATA
1 CATATAAATATA
47455 CATATAAATATA
1 CATATAAATATA
*
47467 CATATACATATA
1 CATATAAATATA
47479 TATTTGGACA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.35
Consensus pattern (12 bp):
CATATAAATATA
Found at i:48777 original size:27 final size:27
Alignment explanation
Indices: 48747--48808 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
48737 TTAAATTTGG
48747 GTTAATTATTTTCTCAAAAAAAATTGA
1 GTTAATTATTTTCTCAAAAAAAATTGA
*
48774 GTTAATTATTTTCTCAAAAAAAATTGG
1 GTTAATTATTTTCTCAAAAAAAATTGA
48801 GTTAATTA
1 GTTAATTA
48809 CAATATCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (27 bp):
GTTAATTATTTTCTCAAAAAAAATTGA
Found at i:51270 original size:16 final size:18
Alignment explanation
Indices: 51244--51277 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
51234 TTAAAATTGG
51244 ATTGAGAAAATT-ATTTA
1 ATTGAGAAAATTAATTTA
51261 ATTG-GAAAATTAATTTA
1 ATTGAGAAAATTAATTTA
51278 TCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
ATTGAGAAAATTAATTTA
Found at i:54926 original size:23 final size:22
Alignment explanation
Indices: 54893--54942 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
54883 CTTTATTTGA
54893 TAAAATA-TTTTGATATAACAAGT
1 TAAAATATTTTTGA-AT-ACAAGT
* *
54916 TAAAATGTTTTTGAATAGAAGT
1 TAAAATATTTTTGAATACAAGT
54938 TAAAA
1 TAAAA
54943 CTGACAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.42
23 8 0.33
24 6 0.25
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (22 bp):
TAAAATATTTTTGAATACAAGT
Found at i:61191 original size:20 final size:19
Alignment explanation
Indices: 61166--61215 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
61156 TACAATTTGG
* *
61166 TATCGATACTTATTTAAAAT
1 TATCGATACTT-TATAAAAA
61186 TATCGATACGTTTATAAAAA
1 TATCGATAC-TTTATAAAAA
61206 TATCGATACT
1 TATCGATACT
61216 CGAGGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (19 bp):
TATCGATACTTTATAAAAA
Found at i:66252 original size:39 final size:40
Alignment explanation
Indices: 66208--66300 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 40
66198 TTGTAACCTA
* *
66208 TCTTCAATTTGCCCTCTGAAT-GGGTAAAAGATCGGATGG
1 TCTTCAATCTGCCCTCTGAATAGGGTAAAAGATCGAATGG
* ** *
66247 TCTTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGAATGG
1 TCTTCAATCTGCCCTCTGAATAGGGTAAAAGATCGAATGG
66287 TCTTCAATCTGCCC
1 TCTTCAATCTGCCC
66301 AATGGTTGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 17 0.36
40 30 0.64
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (40 bp):
TCTTCAATCTGCCCTCTGAATAGGGTAAAAGATCGAATGG
Found at i:66348 original size:42 final size:40
Alignment explanation
Indices: 66229--66531 Score: 340
Period size: 42 Copynumber: 7.5 Consensus size: 40
66219 CCCTCTGAAT
* * ** *
66229 GGGTAAAAGATCGGATGGTCTTCAATCTGCCCTTTGGTTA
1 GGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATGGTTG
* * *
66269 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCAATGGTTG
1 GGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATGGTTG
*
66309 GGGTAAGAGATTGGATGGTATCTTCAATCTGCCCCATGGTCG
1 GGGTAAGAGATTGGATGG--TCTTCAATCTGCCCCATGGTTG
* *
66351 AGGTAAGAGATTGGATGG-CTTCAATCTGCCCCATGGTTA
1 GGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATGGTTG
* * * *
66390 GGGTAAGAGATTGGAGGGTGTCTTCAATCTACCTCATGGTCG
1 GGGTAAGAGATTGGA-TG-GTCTTCAATCTGCCCCATGGTTG
* *
66432 GGGTAAGAGATTGGATGG-CTTCAATCTACCCCAAGGTTG
1 GGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATGGTTG
* **
66471 GGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTCA
1 GGGTAAGAGATTGGAT-G-GTCTTCAATCTGCCCCATGGTTG
**
66513 ATGTAAGAGATTGGATGGT
1 GGGTAAGAGATTGGATGGT
66532 AGCTTTGCCT
Statistics
Matches: 225, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
39 66 0.29
40 56 0.25
41 4 0.02
42 99 0.44
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (40 bp):
GGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATGGTTG
Found at i:66395 original size:81 final size:81
Alignment explanation
Indices: 66229--66530 Score: 394
Period size: 81 Copynumber: 3.7 Consensus size: 81
66219 CCCTCTGAAT
* ** * * *
66229 GGGTAAAAGATCGGAT-G-GTCTTCAATCTGCCCTTTGGT-TAGGGTAAAAGATTGAATGGTCTT
1 GGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTCGA-GGTAAGAGATTGGATGG-CTT
*
66291 CAATCTGCCCAATGGTTG
64 CAATCTGCCCCATGGTTG
* *
66309 GGGTAAGAGATTGGATGGTATCTTCAATCTGCCCCATGGTCGAGGTAAGAGATTGGATGGCTTCA
1 GGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTCGAGGTAAGAGATTGGATGGCTTCA
*
66374 ATCTGCCCCATGGTTA
66 ATCTGCCCCATGGTTG
* * * * *
66390 GGGTAAGAGATTGGAGGGTGTCTTCAATCTACCTCATGGTCGGGGTAAGAGATTGGATGGCTTCA
1 GGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTCGAGGTAAGAGATTGGATGGCTTCA
* *
66455 ATCTACCCCAAGGTTG
66 ATCTGCCCCATGGTTG
* *
66471 GGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTCAATGTAAGAGATTGGATGG
1 GGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTCGAGGTAAGAGATTGGATGG
66531 TAGCTTTGCC
Statistics
Matches: 194, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
80 14 0.07
81 146 0.75
82 33 0.17
83 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (81 bp):
GGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTCGAGGTAAGAGATTGGATGGCTTCA
ATCTGCCCCATGGTTG
Found at i:68613 original size:29 final size:28
Alignment explanation
Indices: 68577--68651 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 28
68567 CCTCGTTTTA
* * *
68577 TTTTAAAATTATATTTCAGCCTCTAAAC
1 TTTTAAAATTAAATTTAACCCTCTAAAC
68605 TTTTCAAAAATTTAAATTTAACCCTCTAAAC
1 TTTT--AAAA-TTAAATTTAACCCTCTAAAC
* *
68636 TTCTAAAATTACATTT
1 TTTTAAAATTAAATTT
68652 TAGACCCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 11 0.28
29 4 0.10
30 4 0.10
31 20 0.51
ACGTcount: A:0.39, C:0.17, G:0.01, T:0.43
Consensus pattern (28 bp):
TTTTAAAATTAAATTTAACCCTCTAAAC
Found at i:68653 original size:29 final size:30
Alignment explanation
Indices: 68599--68816 Score: 198
Period size: 30 Copynumber: 7.3 Consensus size: 30
68589 ATTTCAGCCT
* *
68599 CTAAACTTT-TCAAAAATTTAAATTTAACCC
1 CTAAACTTTCT-AAAAATTTCATTTTAACCC
*
68629 TCTAAAC-TTCT-AAAATTACATTTTAGA-CC
1 -CTAAACTTTCTAAAAATTTCATTTTA-ACCC
* *
68658 C-AAACTTTCTAAAAATTTCATTTTGATCC
1 CTAAACTTTCTAAAAATTTCATTTTAACCC
* * * *
68687 TTGAACTTTCTAAAAATTTTATTTTGACCC
1 CTAAACTTTCTAAAAATTTCATTTTAACCC
*
68717 CTAAACTTTCTAAAAATTACATTTTAACCC
1 CTAAACTTTCTAAAAATTTCATTTTAACCC
* **
68747 CTAAACTATT-TGAAAATTTTGTTTTAA-CC
1 CTAAACT-TTCTAAAAATTTCATTTTAACCC
* * *
68776 CTCAAACTTTTTGAAAATTTCATTTTACCCC
1 CT-AAACTTTCTAAAAATTTCATTTTAACCC
68807 CTAAACTTTC
1 CTAAACTTTC
68817 CTTATTTTTC
Statistics
Matches: 155, Mismatches: 22, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
27 4 0.03
28 6 0.04
29 33 0.21
30 99 0.64
31 13 0.08
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (30 bp):
CTAAACTTTCTAAAAATTTCATTTTAACCC
Found at i:83145 original size:17 final size:18
Alignment explanation
Indices: 83110--83148 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
83100 TATCACTTAG
*
83110 TTGTCATTGCATCTTTAT
1 TTGTCACTGCATCTTTAT
83128 TTGTCACTGCAT-TTTAT
1 TTGTCACTGCATCTTTAT
83145 TTGT
1 TTGT
83149 TAGTACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.56
Consensus pattern (18 bp):
TTGTCACTGCATCTTTAT
Found at i:89312 original size:2 final size:2
Alignment explanation
Indices: 89261--89300 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
89251 ACTTCTTTTG
*
89261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89301 TTGTTTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:89665 original size:15 final size:15
Alignment explanation
Indices: 89644--89679 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
89634 ATTATTTTTT
*
89644 TAAAAAAAGGAAAA-
1 TAAAAAAAGAAAAAC
89658 TAAAAAAAGAAAAAC
1 TAAAAAAAGAAAAAC
89673 TAAAAAA
1 TAAAAAA
89680 GGACTGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.81, C:0.03, G:0.08, T:0.08
Consensus pattern (15 bp):
TAAAAAAAGAAAAAC
Found at i:110522 original size:49 final size:49
Alignment explanation
Indices: 110466--111047 Score: 286
Period size: 49 Copynumber: 12.0 Consensus size: 49
110456 CACAAAGGCG
* * *
110466 AACCTTGTACCTTAGAGACGTGATGGGAAAGATTGAAGCCACAATGATG
1 AACCTTGTACCTTAGAGAAGTGATGGGAAAGATTGAAGCCGCAATGATA
* * * * * *
110515 AATCTTGTACCAT-GAAGATA-TGGA-GGGAAAGGTTAAAGCCGCAACGGTA
1 AACCTTGTACCTTAG-AGA-AGT-GATGGGAAAGATTGAAGCCGCAATGATA
* * * ** * *
110564 AACCATGTACCTTAAAGAAGTGATGGGAAGGATTGAAGCTACAACGACA
1 AACCTTGTACCTTAGAGAAGTGATGGGAAAGATTGAAGCCGCAATGATA
* * * * *
110613 AATCTTGTACCAT-GAAGATA-TGGA-GGGAAAGGTTAAAGCCGCAATGGTA
1 AACCTTGTACCTTAG-AGA-AGT-GATGGGAAAGATTGAAGCCGCAATGATA
* * * ** * *
110662 AACCATGTACCTTAAAGAAGTGATGGGAAGGATTGAAGCTACAA-CAGCA
1 AACCTTGTACCTTAGAGAAGTGATGGGAAAGATTGAAGCCGCAATGA-TA
* * * * * *
110711 AATCTTGTACCAT-GAAGATA-TGGA-GGGAAAGGTTAAAGCCTCAATGACA
1 AACCTTGTACCTTAG-AGA-AGT-GATGGGAAAGATTGAAGCCGCAATGATA
* * * * * * *
110760 AACCTTGTACCTCAAAGAAGTGATTGGAAGGATTGAAGTCGCAACGATG
1 AACCTTGTACCTTAGAGAAGTGATGGGAAAGATTGAAGCCGCAATGATA
* * * *
110809 AATCTTGTACCAT-GAAGATA-TGGA-GGGAAAGGTTAAAGCCGCAATGATA
1 AACCTTGTACCTTAG-AGA-AGT-GATGGGAAAGATTGAAGCCGCAATGATA
* * **
110858 AACCTTGTACCTCAGAGAAGTGAT--G--AGATTGAAGCCGCAACGGCA
1 AACCTTGTACCTTAGAGAAGTGATGGGAAAGATTGAAGCCGCAATGATA
* * * * *
110903 AACCTTGTACGTCAAAGAAGTGATGGGAAATATTGAAGCCGCAATGGTGA
1 AACCTTGTACCTTAGAGAAGTGATGGGAAAGATTGAAGCCGCAATGAT-A
* * * * * * * **
110953 ATCC-TGTACCATAGAGATA-TGA-AGGAAAAAGTTGAAGCTGTAACGGCA
1 AACCTTGTACCTTAGAGA-AGTGATGGGAAAGA-TTGAAGCCGCAATGATA
* * *
111001 AACCTTGTACCTTAGAGATGTAATGGGAAAGATTGAAGCTGCAATGA
1 AACCTTGTACCTTAGAGAAGTGATGGGAAAGATTGAAGCCGCAATGA
111048 CAAATCTTAT
Statistics
Matches: 386, Mismatches: 111, Indels: 72
0.68 0.20 0.13
Matches are distributed among these distances:
45 37 0.10
47 2 0.01
48 23 0.06
49 300 0.78
50 24 0.06
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.21
Consensus pattern (49 bp):
AACCTTGTACCTTAGAGAAGTGATGGGAAAGATTGAAGCCGCAATGATA
Found at i:110617 original size:98 final size:98
Alignment explanation
Indices: 110439--110882 Score: 622
Period size: 98 Copynumber: 4.5 Consensus size: 98
110429 TACAGGTTTA
* * * ** * * *
110439 GAGGGAAAGGTTGAAGCCACAAAGGCGAACCTTGTACCTTAGAGACGTGATGGGAAAGATTGAAG
1 GAGGGAAAGGTTAAAGCCGCAATGGTAAACCTTGTACCTTAAAGAAGTGATGGGAAGGATTGAAG
* * **
110504 CCACAATGATGAATCTTGTACCATGAAGATATG
66 CTACAACGACAAATCTTGTACCATGAAGATATG
* *
110537 GAGGGAAAGGTTAAAGCCGCAACGGTAAACCATGTACCTTAAAGAAGTGATGGGAAGGATTGAAG
1 GAGGGAAAGGTTAAAGCCGCAATGGTAAACCTTGTACCTTAAAGAAGTGATGGGAAGGATTGAAG
110602 CTACAACGACAAATCTTGTACCATGAAGATATG
66 CTACAACGACAAATCTTGTACCATGAAGATATG
*
110635 GAGGGAAAGGTTAAAGCCGCAATGGTAAACCATGTACCTTAAAGAAGTGATGGGAAGGATTGAAG
1 GAGGGAAAGGTTAAAGCCGCAATGGTAAACCTTGTACCTTAAAGAAGTGATGGGAAGGATTGAAG
110700 CTACAAC-AGCAAATCTTGTACCATGAAGATATG
66 CTACAACGA-CAAATCTTGTACCATGAAGATATG
* ** * *
110733 GAGGGAAAGGTTAAAGCCTCAATGACAAACCTTGTACCTCAAAGAAGTGATTGGAAGGATTGAAG
1 GAGGGAAAGGTTAAAGCCGCAATGGTAAACCTTGTACCTTAAAGAAGTGATGGGAAGGATTGAAG
* **
110798 -TCGCAACGATGAATCTTGTACCATGAAGATATG
66 CT-ACAACGACAAATCTTGTACCATGAAGATATG
* * *
110831 GAGGGAAAGGTTAAAGCCGCAATGATAAACCTTGTACCTCAGAGAAGTGATG
1 GAGGGAAAGGTTAAAGCCGCAATGGTAAACCTTGTACCTTAAAGAAGTGATG
110883 AGATTGAAGC
Statistics
Matches: 316, Mismatches: 27, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
97 2 0.01
98 313 0.99
99 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.20
Consensus pattern (98 bp):
GAGGGAAAGGTTAAAGCCGCAATGGTAAACCTTGTACCTTAAAGAAGTGATGGGAAGGATTGAAG
CTACAACGACAAATCTTGTACCATGAAGATATG
Found at i:110939 original size:143 final size:143
Alignment explanation
Indices: 110758--111018 Score: 344
Period size: 143 Copynumber: 1.8 Consensus size: 143
110748 GCCTCAATGA
* * * *
110758 CAAACCTTGTACCTCAAAGAAGTGATTGGAAGGATTGAAGTCGCAACGATGAATCTTGTACCAT-
1 CAAACCTTGTACCTCAAAGAAGTGATGGGAAAGATTGAAGCCGCAACGATGAATCCTGTACCATA
* * * * *
110822 GAAGATATGGAGGGAAAGGTTAAAGCCGCAATGATAAACCTTGTACCTCAGAGAAGTGATGAGAT
66 G-AGATATGAAGGAAAAAGTTAAAGCCGCAACGACAAACCTTGTACCTCAGAGAAGTGATGAGAT
110887 TGAAGCCGCAACGG
130 TGAAGCCGCAACGG
* * * *
110901 CAAACCTTGTACGTCAAAGAAGTGATGGGAAATATTGAAGCCGCAATGGTGAATCCTGTACCATA
1 CAAACCTTGTACCTCAAAGAAGTGATGGGAAAGATTGAAGCCGCAACGATGAATCCTGTACCATA
* * * * *
110966 GAGATATGAAGGAAAAAGTTGAAGCTGTAACGGCAAACCTTGTACCTTAGAGA
66 GAGATATGAAGGAAAAAGTTAAAGCCGCAACGACAAACCTTGTACCTCAGAGA
111019 TGTAATGGGA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
143 98 0.99
144 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.21
Consensus pattern (143 bp):
CAAACCTTGTACCTCAAAGAAGTGATGGGAAAGATTGAAGCCGCAACGATGAATCCTGTACCATA
GAGATATGAAGGAAAAAGTTAAAGCCGCAACGACAAACCTTGTACCTCAGAGAAGTGATGAGATT
GAAGCCGCAACGG
Found at i:116668 original size:30 final size:30
Alignment explanation
Indices: 116608--116830 Score: 177
Period size: 30 Copynumber: 7.4 Consensus size: 30
116598 TTATATTTCG
* * *
116608 ACCCCTAAACTTTCCAAAAAAT-CAAATTTA
1 ACCCCTAAACTTTCTAAAAATTGC-ATTTTA
116638 ACCCCTTAAACTTTCT-AAAATTGCATTTTA
1 ACCCC-TAAACTTTCTAAAAATTGCATTTTA
* * * *
116668 AACCCTAAACTTTCTAAAATTTTCATTTTG
1 ACCCCTAAACTTTCTAAAAATTGCATTTTA
* * * *
116698 ATCTCTAAACTTTCTAAAAA-TGTTAGTTTA
1 ACCCCTAAACTTTCTAAAAATTG-CATTTTA
* *
116728 ACCCCCAAACTTTCTAAAAATTGAATTTT-
1 ACCCCTAAACTTTCTAAAAATTGCATTTTA
* * **
116757 AGCCTTCAAACTTTCTAAAAATTTTATTTTA
1 ACCCCT-AAACTTTCTAAAAATTGCATTTTA
* *
116788 ATCCCC-AAACTTTCTAAAAATTTCATTTTG
1 A-CCCCTAAACTTTCTAAAAATTGCATTTTA
* *
116818 CCCCCCAAACTTT
1 ACCCCTAAACTTT
116831 TCGATATTTT
Statistics
Matches: 155, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
29 18 0.12
30 122 0.79
31 13 0.08
32 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
ACCCCTAAACTTTCTAAAAATTGCATTTTA
Found at i:116748 original size:90 final size:89
Alignment explanation
Indices: 116634--116830 Score: 238
Period size: 90 Copynumber: 2.2 Consensus size: 89
116624 AAAAATCAAA
* *
116634 TTTAACCCCTTAAACTTTCTAAAATTGCATTTTAAACCCT-AAACTTTCT-AAAATTTTCATTTT
1 TTTAACCCC-CAAACTTTCTAAAATTGAATTTT-AACCCTCAAACTTTCTAAAAATTTT-ATTTT
* * *
116697 GATCTCTAAACTTTCTAAAAATGTT-AG
63 AATCCCCAAACTTTCTAAAAAT-TTCAG
* *
116724 TTTAACCCCCAAACTTTCTAAAAATTGAATTTTAGCCTTCAAACTTTCTAAAAATTTTATTTTAA
1 TTTAACCCCCAAACTTTCT-AAAATTGAATTTTAACCCTCAAACTTTCTAAAAATTTTATTTTAA
*
116789 TCCCCAAACTTTCTAAAAATTTCAT
65 TCCCCAAACTTTCTAAAAATTTCAG
**
116814 TTTGCCCCCCAAACTTT
1 TTTAACCCCCAAACTTT
116831 TCGATATTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
89 15 0.16
90 70 0.75
91 8 0.09
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.41
Consensus pattern (89 bp):
TTTAACCCCCAAACTTTCTAAAATTGAATTTTAACCCTCAAACTTTCTAAAAATTTTATTTTAAT
CCCCAAACTTTCTAAAAATTTCAG
Found at i:116847 original size:60 final size:59
Alignment explanation
Indices: 116645--116830 Score: 212
Period size: 60 Copynumber: 3.1 Consensus size: 59
116635 TTAACCCCTT
** * * * *
116645 AAACTTTCT-AAAATTGCATTTTAAACCCTAAACTTTCTAAAATTTTCATTTTGATCTCT
1 AAACTTTCTAAAAATTTTATTTTAAACCCCAAACTTTCTAAAAATTTCATTTTG-CCTCC
* * * ** *
116704 AAACTTTCTAAAAATGTTAGTTTAACCCCCAAACTTTCTAAAAATTGAATTTTAGCCTTC
1 AAACTTTCTAAAAATTTTATTTTAAACCCCAAACTTTCTAAAAATTTCATTTT-GCCTCC
* *
116764 AAACTTTCTAAAAATTTTATTTTAATCCCCAAACTTTCTAAAAATTTCATTTTGCCCCCC
1 AAACTTTCTAAAAATTTTATTTTAAACCCCAAACTTTCTAAAAATTTCATTTTG-CCTCC
116824 AAACTTT
1 AAACTTT
116831 TCGATATTTT
Statistics
Matches: 105, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
59 10 0.10
60 94 0.90
61 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (59 bp):
AAACTTTCTAAAAATTTTATTTTAAACCCCAAACTTTCTAAAAATTTCATTTTGCCTCC
Found at i:122562 original size:52 final size:52
Alignment explanation
Indices: 122484--122670 Score: 313
Period size: 52 Copynumber: 3.6 Consensus size: 52
122474 TTCCCATTTA
122484 ATACTCACGATGACACA-ACGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATA-GTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
122536 ATACTCACGATGACACATAGTTATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
122588 ATACTTACAATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
122640 ATACTCATGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
122671 TTTTTCATTT
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
52 124 0.99
53 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:128736 original size:15 final size:15
Alignment explanation
Indices: 128716--128745 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
128706 AGTACATATG
*
128716 CTCTTTTTTCTTTTT
1 CTCTTTTTCCTTTTT
128731 CTCTTTTTCCTTTTT
1 CTCTTTTTCCTTTTT
128746 TTTTAGCATC
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:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
CTCTTTTTCCTTTTT
Found at i:130048 original size:18 final size:18
Alignment explanation
Indices: 130027--130063 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
130017 TGTCTTCAAT
*
130027 TTCCACAGGATCTTCTTC
1 TTCCACAGGATCCTCTTC
*
130045 TTCCTCAGGATCCTCTTC
1 TTCCACAGGATCCTCTTC
130063 T
1 T
130064 AGATCTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.35, G:0.11, T:0.41
Consensus pattern (18 bp):
TTCCACAGGATCCTCTTC
Found at i:130079 original size:18 final size:18
Alignment explanation
Indices: 130058--130099 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
130048 CTCAGGATCC
130058 TCTTCTAGATCTTCTTAT
1 TCTTCTAGATCTTCTTAT
* * *
130076 TCTTCAAGGTCTTCTTCT
1 TCTTCTAGATCTTCTTAT
130094 TCTTCT
1 TCTTCT
130100 TCTTAAGCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.26, G:0.07, T:0.55
Consensus pattern (18 bp):
TCTTCTAGATCTTCTTAT
Found at i:130884 original size:26 final size:24
Alignment explanation
Indices: 130855--130914 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
130845 TTAATTAGTA
*
130855 TAAAATATTAATAATTTAAATTAAAT
1 TAAAA-ATTAATAAATTAAA-TAAAT
*
130881 TAAAGAGTTAATAAATTAAATAAAT
1 TAAA-AATTAATAAATTAAATAAAT
130906 TAAAAATTA
1 TAAAAATTA
130915 GAAGATGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 4 0.13
25 9 0.30
26 16 0.53
27 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
TAAAAATTAATAAATTAAATAAAT
Found at i:140800 original size:22 final size:23
Alignment explanation
Indices: 140758--140801 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
140748 GCATGTAAAA
140758 ATGCAATACTAATGAATACATTT
1 ATGCAATACTAATGAATACATTT
140781 ATGCAATA-TAA-GAAATACATT
1 ATGCAATACTAATG-AATACATT
140802 GATTCTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.05
22 11 0.55
23 8 0.40
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (23 bp):
ATGCAATACTAATGAATACATTT
Done.