Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014076.1 Kokia drynarioides strain JFW-HI SEQ_129107, 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: 30195
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:397 original size:15 final size:15
Alignment explanation
Indices: 379--449 Score: 88
Period size: 15 Copynumber: 4.7 Consensus size: 15
369 AGTTTGGGCT
*
379 TTTGTAATTGGGTCA
1 TTTGTAATTGGGCCA
*
394 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
* * *
409 TCTGTAACTGGGCCT
1 TTTGTAATTGGGCCA
*
424 TTTGTTATTGGGCCA
1 TTTGTAATTGGGCCA
439 TTTGTAATTGG
1 TTTGTAATTGG
450 ACTTTGTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.15, C:0.13, G:0.27, T:0.45
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:504 original size:17 final size:16
Alignment explanation
Indices: 482--554 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 16
472 TTGGACTTTC
482 TAAATTT-AATCTTATAA
1 TAAATTTAAAT-TTA-AA
499 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
516 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
*
533 TAAACTTAAATTTAAA
1 TAAATTTAAATTTAAA
549 TAAATT
1 TAAATT
555 CAATTTCCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
16 8 0.16
17 39 0.76
18 4 0.08
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:533 original size:7 final size:6
Alignment explanation
Indices: 499--549 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
489 AATCTTATAA
* *
499 TAAATT TAAATT TCAAA-- TAAATT TAAATT TAAA-A TAAACT TAAATT
1 TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT
545 TAAAT
1 TAAAT
550 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 3 0.08
5 5 0.13
6 27 0.71
7 3 0.08
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:566 original size:16 final size:17
Alignment explanation
Indices: 497--567 Score: 92
Period size: 17 Copynumber: 4.3 Consensus size: 17
487 TTAATCTTAT
497 AATAAATTTAAATTTCA
1 AATAAATTTAAATTTCA
*
514 AATAAATTTAAATTTAA
1 AATAAATTTAAATTTCA
*
531 AATAAACTTAAATTT-A
1 AATAAATTTAAATTTCA
* *
547 AATAAA-TTCAATTTCC
1 AATAAATTTAAATTTCA
563 AATAA
1 AATAA
568 GCCCAGACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
15 7 0.14
16 12 0.24
17 30 0.61
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAATTTAAATTTCA
Found at i:1346 original size:140 final size:139
Alignment explanation
Indices: 1010--1602 Score: 788
Period size: 139 Copynumber: 4.3 Consensus size: 139
1000 CGTGGGTTTG
* * * *
1010 GTTT-GGTCTTCTTCTTAGTATCTCATCAGGAAGATGA-CCACGTCATCTGTCTCAA-----TTC
1 GTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCC-CATCA-CTGTTTCAATCCGCTTC
* * ** * * *
1068 GCT-TATCTCATTAGGAAGATAAATTTGGTTCACTTCTCAATACCTCATCTAGAAGATCTGCTCG
64 TCTGTATCTCATCAGGAAGACGAATTTAGTTCACTTCTCAGTACCTCATCTAGAAGATTTGCTCG
1132 TTTCGAGCCTC
129 TTTCGAGCCTC
* * * *
1143 ATTTGGGTCTTCTTCTTAGTGTCTCATCCGGAAGATGATCCCATCACTGTTTCAATCCACTTCTC
1 GTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCCGCTTCTC
* * * * *
1208 TGTATCTTATCAGGAATATGAATTTAGTTCACTTCTCAGTACCTAATCTGGAAGATTTGCTCGTT
66 TGTATCTCATCAGGAAGACGAATTTAGTTCACTTCTCAGTACCTCATCTAGAAGATTTGCTCGTT
1273 TCGAGCCTC
131 TCGAGCCTC
*
1282 GTTTTGGGTCTTCTTCTCAGCGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCCGCTTCT
1 G-TTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCCGCTTCT
*
1347 CTGTATCTCATCAAGAAGACGAATTTAGTTCACTTCTCAGTACCTCATCTAGAAGATTTGCTCGT
65 CTGTATCTCATCAGGAAGACGAATTTAGTTCACTTCTCAGTACCTCATCTAGAAGATTTGCTCGT
1412 TTCGAGCCTC
130 TTCGAGCCTC
* * * *
1422 GTTTGAGTTTTCTTCTCAGTGTCTTATCAGGAAGATGATCCCATCACTGTTTCAATCTGCTTCTC
1 GTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCCGCTTCTC
* * * * * * * *
1487 TGTATCTTATTAGAAAGACGAATTTGGTTTATTTCTCAGTACCTCATCTGGAAGTTTTGCTCGTT
66 TGTATCTCATCAGGAAGACGAATTTAGTTCACTTCTCAGTACCTCATCTAGAAGATTTGCTCGTT
1552 TCGAGCCTC
131 TCGAGCCTC
*
1561 GTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATAATCCC
1 GTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCC
1603 GCTGTTTTGT
Statistics
Matches: 407, Mismatches: 44, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
133 11 0.03
134 35 0.09
135 2 0.00
138 5 0.01
139 225 0.55
140 129 0.32
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.37
Consensus pattern (139 bp):
GTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCCGCTTCTC
TGTATCTCATCAGGAAGACGAATTTAGTTCACTTCTCAGTACCTCATCTAGAAGATTTGCTCGTT
TCGAGCCTC
Found at i:12819 original size:29 final size:28
Alignment explanation
Indices: 12786--13033 Score: 173
Period size: 29 Copynumber: 8.4 Consensus size: 28
12776 TAGGATCTTG
*
12786 GGAAGTTCGAGGGT-AATATGGTAATTTTT
1 GGAAGTTCG-GGGTAAAAATGG-AATTTTT
* * * *
12815 AGAAGATCCGAGGTCAAAAATGGGA-TTTT
1 GGAAG-TTCGGGGT-AAAAATGGAATTTTT
*
12844 GGGAGTTCGGAGGT-AAAATGGTAATTTTT
1 GGAAGTTCGG-GGTAAAAATGG-AATTTTT
* *
12873 GGAAGGTTCGAGGCTAAAAATGGGATTTTT
1 GGAA-GTTCG-GGGTAAAAATGGAATTTTT
*
12903 GGGAGTTCGGGGGT-AAAATGGTAATTTTT
1 GGAAGTTC-GGGGTAAAAATGG-AATTTTT
* *
12932 GGAAGATTTGGGGTAAAAAATGGGATTTTT
1 GGAAG-TTCGGGGT-AAAAATGGAATTTTT
* *
12962 GGAAGGTTCGGGGTCAAAATAGGGATTTTT
1 GGAA-GTTCGGGGTAAAAAT-GGAATTTTT
*
12992 GGAAGTTTGGGGGT-AAAATGGTAATTTTT
1 GGAAG-TTCGGGGTAAAAATGG-AATTTTT
*
13021 AGAAGGTTCGGGG
1 GGAA-GTTCGGGG
13034 GCCTATGGGG
Statistics
Matches: 175, Mismatches: 25, Indels: 38
0.74 0.11 0.16
Matches are distributed among these distances:
27 7 0.04
28 13 0.07
29 72 0.41
30 61 0.35
31 22 0.13
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.32
Consensus pattern (28 bp):
GGAAGTTCGGGGTAAAAATGGAATTTTT
Found at i:12852 original size:58 final size:57
Alignment explanation
Indices: 12771--12996 Score: 249
Period size: 59 Copynumber: 3.8 Consensus size: 57
12761 GTTCAGAATA
* * * * *
12771 AAAAATAGGATCTTGGGAAGTTCGAGGGTAATATGGTAATTTTTAGAAGATCCGAGGTC
1 AAAAATGGGATTTTGGG-AGTTCG-GGGTAAAATGGTAATTTTTGGAAGATTCGAGGTC
*
12830 AAAAATGGGATTTTGGGAGTTCGGAGGTAAAATGGTAATTTTTGGAAGGTTCGAGG-C
1 AAAAATGGGATTTTGGGAGTTCGG-GGTAAAATGGTAATTTTTGGAAGATTCGAGGTC
* * *
12887 TAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTGGAAGATTTGGGGTA
1 -AAAAATGGGA-TTTTGGGAGTTC-GGGGTAAAATGGTAATTTTTGGAAGATTCGAGGTC
* *
12947 AAAAATGGGATTTTTGGAAGGTTCGGGGTCAAAATAGG-GATTTTTGGAAG
1 AAAAATGGGA-TTTTGGGA-GTTCGGGGT-AAAAT-GGTAATTTTTGGAAG
12997 TTTGGGGGTA
Statistics
Matches: 147, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
57 2 0.01
58 43 0.29
59 78 0.53
60 22 0.15
61 2 0.01
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (57 bp):
AAAAATGGGATTTTGGGAGTTCGGGGTAAAATGGTAATTTTTGGAAGATTCGAGGTC
Found at i:12990 original size:89 final size:90
Alignment explanation
Indices: 12858--13025 Score: 259
Period size: 89 Copynumber: 1.9 Consensus size: 90
12848 GTTCGGAGGT
*
12858 AAAATGGTAATTTTTGGAAGGTTCGAGGCTAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATG
1 AAAATGGTAATTTTTGGAAGGTTCGAGGCTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
*
12923 GTAATTTTTGGAAGATTTGGGGTAA
66 GTAATTTTTAGAAGATTTGGGGTAA
* * * *
12948 AAAATGG-GATTTTTGGAAGGTTCG-GGGTCAAAATAGGGATTTTTGGAAGTTTGGGGGTAAAAT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGCTAAAAAT-GGGATTTTTGGAAGTTCGGGGGTAAAAT
13011 GGTAATTTTTAGAAG
65 GGTAATTTTTAGAAG
13026 GTTCGGGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
88 8 0.11
89 56 0.79
90 7 0.10
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (90 bp):
AAAATGGTAATTTTTGGAAGGTTCGAGGCTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
GTAATTTTTAGAAGATTTGGGGTAA
Found at i:13001 original size:59 final size:56
Alignment explanation
Indices: 12771--13033 Score: 235
Period size: 59 Copynumber: 4.5 Consensus size: 56
12761 GTTCAGAATA
* * * * * ** *
12771 AAAAATAGGATCTTGGGAAGTTCGAGGGTAATATGGTAATTTTTAGAAGATCCGAGGT
1 AAAAATGGGATTTTTGGAAGTTCG-GGGTAAAATGGTAATTTTTGGAAG-TTTGGGGT
* * *
12829 CAAAAATGGGA-TTTTGGGAGTTCGGAGGTAAAATGGTAATTTTTGGAAGGTTCGAGGCT
1 -AAAAATGGGATTTTTGGAAGTTCGG-GGTAAAATGGTAATTTTTGGAA-GTTTG-GGGT
*
12888 AAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTGGAAGATTTGGGGT
1 AAAAATGGGATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTGGAAG-TTTGGGGT
*
12946 AAAAAATGGGATTTTTGGAAGGTTCGGGGTCAAAATAGG-GATTTTTGGAAGTTTGGGGGT
1 -AAAAATGGGATTTTTGGAA-GTTCGGGGT-AAAAT-GGTAATTTTTGGAAGTTT-GGGGT
* *
13006 -AAAATGGTAATTTTTAGAAGGTTCGGGG
1 AAAAATGG-GATTTTTGGAA-GTTCGGGG
13034 GCCTATGGGG
Statistics
Matches: 177, Mismatches: 15, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
57 1 0.01
58 54 0.31
59 93 0.53
60 27 0.15
61 2 0.01
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.32
Consensus pattern (56 bp):
AAAAATGGGATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTTGGAAGTTTGGGGT
Found at i:13034 original size:30 final size:30
Alignment explanation
Indices: 12830--13034 Score: 176
Period size: 30 Copynumber: 7.0 Consensus size: 30
12820 ATCCGAGGTC
* * *
12830 AAAAATGGGA-TTTTGGGA-GTTCGGAGGT
1 AAAAATGGAATTTTTGGAAGGTTCGGGGGT
* *
12858 -AAAATGGTAATTTTTGGAAGGTTCGAGGCT
1 AAAAATGG-AATTTTTGGAAGGTTCGGGGGT
* *
12888 AAAAATGGGATTTTTGGGA-GTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGGTTCGGGGGT
* *
12917 -AAAATGGTAATTTTTGGAAGATT-TGGGGT
1 AAAAATGG-AATTTTTGGAAGGTTCGGGGGT
*
12946 AAAAAATGGGATTTTTGGAAGGTTC-GGGGT
1 -AAAAATGGAATTTTTGGAAGGTTCGGGGGT
* * *
12976 CAAAATAGGGATTTTTGGAA-GTTTGGGGGT
1 AAAAAT-GGAATTTTTGGAAGGTTCGGGGGT
*
13006 -AAAATGGTAATTTTTAGAAGGTTCGGGGG
1 AAAAATGG-AATTTTTGGAAGGTTCGGGGG
13035 CCTATGGGGT
Statistics
Matches: 144, Mismatches: 20, Indels: 24
0.77 0.11 0.13
Matches are distributed among these distances:
27 7 0.05
28 10 0.07
29 51 0.35
30 62 0.43
31 14 0.10
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGGTTCGGGGGT
Found at i:14817 original size:15 final size:15
Alignment explanation
Indices: 14797--14867 Score: 106
Period size: 15 Copynumber: 4.7 Consensus size: 15
14787 AGTTTGGGCT
*
14797 TTTGTAATTGGGTCA
1 TTTGTAATTGGGCCA
*
14812 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
*
14827 TCTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
*
14842 TTTGTTATTGGGCCA
1 TTTGTAATTGGGCCA
14857 TTTGTAATTGG
1 TTTGTAATTGG
14868 ACTTTGTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.45
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:14922 original size:17 final size:15
Alignment explanation
Indices: 14900--14961 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 15
14890 TTGGACTTTC
14900 TAAATTTAATCTTATAA
1 TAAATTTAAT-TTA-AA
14917 TAAATTTAAATTTAAAA
1 TAAATTT-AATTT-AAA
*
14934 TAAACTTAAATTTAAA
1 TAAA-TTTAATTTAAA
*
14950 TAAATTCAATTT
1 TAAATTTAATTT
14962 CCAATAAGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 7 0.17
16 7 0.17
17 20 0.50
18 6 0.15
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTTAATTTAAA
Found at i:15185 original size:30 final size:32
Alignment explanation
Indices: 15139--15220 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 32
15129 ATTTATTATA
*
15139 AATTATTGTTAATATTTTAATAT-ATGAAATATT
1 AATTATT-TAAATATTTTAATATAAT-AAATATT
*
15172 AA-T-TTTAAATATTTCTAA-ATAATTAATATT
1 AATTATTTAAATATTT-TAATATAATAAATATT
15202 AATTATTTAAA-ATTTTAAT
1 AATTATTTAAATATTTTAAT
15221 TAAATTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
30 21 0.50
31 12 0.29
32 7 0.17
33 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (32 bp):
AATTATTTAAATATTTTAATATAATAAATATT
Found at i:15203 original size:24 final size:23
Alignment explanation
Indices: 15165--15209 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
15155 TTAATATATG
*
15165 AAATATTAATTTTAAATATTTCT
1 AAATATTAATATTAAATATTTCT
*
15188 AAATAATTAATATTAATTATTT
1 AAAT-ATTAATATTAAATATTT
15210 AAAATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATTAATATTAAATATTTCT
Found at i:19125 original size:35 final size:35
Alignment explanation
Indices: 19086--19202 Score: 103
Period size: 35 Copynumber: 3.6 Consensus size: 35
19076 CTGAGGTGCC
*
19086 ATCAATAAACTTTGCCGAGGTTGAGAGGAAAAACT
1 ATCAATCAACTTTGCCGAGGTTGAGAGGAAAAACT
* *
19121 ATCAATTAACGTTTG-C-----T--GAGG---ATCT
1 ATCAATCAAC-TTTGCCGAGGTTGAGAGGAAAAACT
*
19146 ATCAATCAACTTTGCTGAGGTTGAGAGGAAAAACT
1 ATCAATCAACTTTGCCGAGGTTGAGAGGAAAAACT
*
19181 ATCAATCAACTTTGCTGAGGTT
1 ATCAATCAACTTTGCCGAGGTT
19203 ATCAACTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
24 4 0.06
25 12 0.18
28 4 0.06
30 2 0.03
32 4 0.06
35 35 0.54
36 4 0.06
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (35 bp):
ATCAATCAACTTTGCCGAGGTTGAGAGGAAAAACT
Found at i:19150 original size:60 final size:58
Alignment explanation
Indices: 19037--19229 Score: 254
Period size: 60 Copynumber: 3.3 Consensus size: 58
19027 ACAGTCAACT
* *
19037 TTTGCTGAGGTTGAGAGGAAAAACTATCAA-TCACTTTTGCTGAGGTGCCATCAATAAAC
1 TTTGCTGAGGTTGAGAGGAAAAACTATCAATTAAC-TTTGCTGAGGT-CTATCAATAAAC
* *
19096 TTTGCCGAGGTTGAGAGGAAAAACTATCAATTAACGTTTGCTGAGGATCTATCAATCAAC
1 TTTGCTGAGGTTGAGAGGAAAAACTATCAATTAAC-TTTGCTGAGG-TCTATCAATAAAC
*
19156 TTTGCTGAGGTTGAGAGGAAAAACTATCAATCAACTTTGCTGAGGT-TATC----AAC
1 TTTGCTGAGGTTGAGAGGAAAAACTATCAATTAACTTTGCTGAGGTCTATCAATAAAC
19209 TTTTGCTGAGGTTGAGAGGAA
1 -TTTGCTGAGGTTGAGAGGAA
19230 CTTTTGTCGA
Statistics
Matches: 124, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
53 3 0.02
54 20 0.16
57 4 0.03
58 1 0.01
59 39 0.31
60 56 0.45
61 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.30
Consensus pattern (58 bp):
TTTGCTGAGGTTGAGAGGAAAAACTATCAATTAACTTTGCTGAGGTCTATCAATAAAC
Found at i:19163 original size:24 final size:25
Alignment explanation
Indices: 19119--19165 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
19109 AGAGGAAAAA
*
19119 CTATCAATTAACGTTTGCTGAGGAT
1 CTATCAATCAACGTTTGCTGAGGAT
19144 CTATCAATCAAC-TTTGCTGAGG
1 CTATCAATCAACGTTTGCTGAGG
19166 TTGAGAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (25 bp):
CTATCAATCAACGTTTGCTGAGGAT
Found at i:19208 original size:18 final size:19
Alignment explanation
Indices: 19185--19221 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19175 AAAACTATCA
19185 ATCAAC-TTTGCTGAGGTT
1 ATCAACTTTTGCTGAGGTT
19203 ATCAACTTTTGCTGAGGTT
1 ATCAACTTTTGCTGAGGTT
19222 GAGAGGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (19 bp):
ATCAACTTTTGCTGAGGTT
Found at i:19614 original size:28 final size:27
Alignment explanation
Indices: 19549--19615 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
19539 TTTAATAACT
19549 TATATATTTATAATTTTTAAAAAATTA
1 TATATATTTATAATTTTTAAAAAATTA
* *
19576 AATTAAATTTATATATTTTTAAAAAATTA
1 TA-TATATTTATA-ATTTTTAAAAAATTA
*
19605 TATATTTTTAT
1 TATATATTTAT
19616 CTTTATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 1 0.03
28 16 0.48
29 16 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TATATATTTATAATTTTTAAAAAATTA
Found at i:22458 original size:22 final size:25
Alignment explanation
Indices: 22410--22460 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 25
22400 GGTTTTAGTC
* *
22410 TTTGAACTCAGTAATCGTTTTGGTA
1 TTTGAACTCAGTAATCGGTTTGATA
22435 TTTGAACTC-GT-AT-GGTTTGATA
1 TTTGAACTCAGTAATCGGTTTGATA
22457 TTTG
1 TTTG
22461 GTATTTGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.46
23 2 0.08
24 2 0.08
25 9 0.38
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.47
Consensus pattern (25 bp):
TTTGAACTCAGTAATCGGTTTGATA
Found at i:26898 original size:26 final size:26
Alignment explanation
Indices: 26868--26976 Score: 66
Period size: 26 Copynumber: 4.3 Consensus size: 26
26858 ATTCAAATAC
*
26868 CAAATACCAAAACCATTCACTGAGTT
1 CAAATACCAAAACAATTCACTGAGTT
* * *
26894 CAAATACTAAAGACAAAT-A-T-AG-A
1 CAAATACCAAA-ACAATTCACTGAGTT
* * *
26917 AAAATAACC-ATACTAATTCACCGAGTT
1 CAAAT-ACCAAAAC-AATTCACTGAGTT
* *
26944 CAAATACCCAAACCATTCACTGAGTT
1 CAAATACCAAAACAATTCACTGAGTT
*
26970 TAAATAC
1 CAAATAC
26977 ACTGAGCATA
Statistics
Matches: 60, Mismatches: 15, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
22 2 0.03
23 8 0.13
24 5 0.08
25 1 0.02
26 33 0.55
27 11 0.18
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (26 bp):
CAAATACCAAAACAATTCACTGAGTT
Done.