Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006476.1 Kokia drynarioides strain JFW-HI SEQ_121059, 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: 23436
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:2197 original size:22 final size:22
Alignment explanation
Indices: 2149--2229 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 22
2139 ATACTTTCAA
2149 TAAAAATATAAAAAAATTTGTT
1 TAAAAATATAAAAAAATTTGTT
* * *
2171 CAAAATTA-AAAAAATATTTTTT
1 TAAAAATATAAAAAA-ATTTGTT
*
2193 TAAAAATCATTTAAAATAA--T-TT
1 TAAAAAT-A--TAAAAAAATTTGTT
2215 TAAAAATATAAAAAA
1 TAAAAATATAAAAAA
2230 TTAAAGAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
19 6 0.13
21 7 0.15
22 26 0.55
23 2 0.04
25 1 0.02
26 5 0.11
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (22 bp):
TAAAAATATAAAAAAATTTGTT
Found at i:2763 original size:20 final size:20
Alignment explanation
Indices: 2738--2781 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2728 CAGAAAATGA
2738 TTTTT-GAAAAATAAATTATT
1 TTTTTGGAAAAATAAA-TATT
*
2758 TTTTTGGAAAAATTAATATT
1 TTTTTGGAAAAATAAATATT
2778 TTTT
1 TTTT
2782 GGTGTTTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTTGGAAAAATAAATATT
Found at i:5304 original size:18 final size:18
Alignment explanation
Indices: 5283--5320 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
5273 TGAATTTTCG
5283 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
5301 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
5319 AA
1 AA
5321 AACTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.24
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:5389 original size:43 final size:43
Alignment explanation
Indices: 5328--5416 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
5318 TAAAACTATA
5328 TTATTTTTAATTTAAAATTTATATTACCCAAGCCCAATTTACT
1 TTATTTTTAATTTAAAATTTATATTACCCAAGCCCAATTTACT
* *
5371 TTATTTTTAATTTTAAATTTATATTACCCAAGCCTAATTTACT
1 TTATTTTTAATTTAAAATTTATATTACCCAAGCCCAATTTACT
5414 TTA
1 TTA
5417 CCCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.49
Consensus pattern (43 bp):
TTATTTTTAATTTAAAATTTATATTACCCAAGCCCAATTTACT
Found at i:6250 original size:4 final size:4
Alignment explanation
Indices: 6243--6278 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
6233 TTATTATTTT
*
6243 ATAA ATAA ATAA ATAA ACAA ATAA ATAA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
6279 ATTAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:7307 original size:30 final size:29
Alignment explanation
Indices: 7273--7377 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 29
7263 TCAAAATTTT
*
7273 CAAAAATTCAAATATGATCACTAAACTTTC
1 CAAAAATTCAAATTTGA-CACTAAACTTTC
* * *
7303 CAAAAATTCGAATTTGACACCAAAATTTTC
1 CAAAAATTCAAATTTGACA-CTAAACTTTC
* * * *
7333 CAAAAATTCTAATTTGACCCCTAAAGTTTT
1 CAAAAATTCAAATTTGA-CACTAAACTTTC
7363 CAAAAATTCAAATTT
1 CAAAAATTCAAATTT
7378 AACCCAATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
29 2 0.03
30 60 0.95
31 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (29 bp):
CAAAAATTCAAATTTGACACTAAACTTTC
Found at i:7338 original size:60 final size:59
Alignment explanation
Indices: 7264--7377 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 59
7254 TTTTAAACCT
* *
7264 CAAAATTTTCAAAAATTCAAATATGATCACTAAACTTTCCAAAAATTCGAATTTGACAC
1 CAAAATTTTCAAAAATTCAAATATGACCACTAAACTTTCCAAAAATTCAAATTTGACAC
* * * * *
7323 CAAAATTTTCCAAAAATTCTAATTTGACCCCTAAAGTTTTCAAAAATTCAAATTT
1 CAAAATTTT-CAAAAATTCAAATATGACCACTAAACTTTCCAAAAATTCAAATTT
7378 AACCCAATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 9 0.19
60 38 0.81
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.33
Consensus pattern (59 bp):
CAAAATTTTCAAAAATTCAAATATGACCACTAAACTTTCCAAAAATTCAAATTTGACAC
Found at i:7470 original size:18 final size:17
Alignment explanation
Indices: 7447--7484 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
7437 TATATTATTT
7447 TATTATATTTTATGTATG
1 TATTATATTTTAT-TATG
*
7465 TATTATTTTTTATTATG
1 TATTATATTTTATTATG
7482 TAT
1 TAT
7485 ACTTGTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (17 bp):
TATTATATTTTATTATG
Found at i:11476 original size:9 final size:9
Alignment explanation
Indices: 11462--11501 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
11452 TTTCACCCAA
11462 AAAAAAAGG
1 AAAAAAAGG
11471 AAAAAAAGG
1 AAAAAAAGG
*
11480 AAAAAGA-G
1 AAAAAAAGG
11488 AAAGAAAAGG
1 AAA-AAAAGG
11498 AAAA
1 AAAA
11502 TAGAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 4 0.15
9 19 0.70
10 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:11496 original size:27 final size:27
Alignment explanation
Indices: 11460--11522 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
11450 AATTTCACCC
11460 AAAAA-AAAAGGAAAA-A-AAGGAAAAAG
1 AAAAAGAAAAGGAAAATAGAA-G-AAAAG
*
11486 AGAAAGAAAAGGAAAATAGAAGAAAAG
1 AAAAAGAAAAGGAAAATAGAAGAAAAG
11513 AAAAAGAAAA
1 AAAAAGAAAA
11523 AGAGGAGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.12
27 24 0.75
28 2 0.06
29 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02
Consensus pattern (27 bp):
AAAAAGAAAAGGAAAATAGAAGAAAAG
Found at i:11517 original size:6 final size:6
Alignment explanation
Indices: 11473--11525 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
11463 AAAAAAGGAA
* *
11473 AAAAAGG AAAAAG AGAAAG AAAAGG AAAATAG AAGAAAAG AAAAAG AAAAAG
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAA-AG -A-AAAAG AAAAAG AAAAAG
11525 A
1 A
11526 GGAGGTGGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 26 0.67
7 7 0.18
8 3 0.08
9 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:11522 original size:11 final size:11
Alignment explanation
Indices: 11460--11522 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 11
11450 AATTTCACCC
11460 AAAAA-AAAAG
1 AAAAAGAAAAG
* *
11470 GAAAA-AAAGG
1 AAAAAGAAAAG
11480 AAAAAGAGAAAG
1 AAAAAGA-AAAG
*
11492 AAAAGGAAAA-
1 AAAAAGAAAAG
* *
11502 TAGAAGAAAAG
1 AAAAAGAAAAG
11513 AAAAAGAAAA
1 AAAAAGAAAA
11523 AGAGGAGGTG
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
10 19 0.47
11 12 0.30
12 9 0.22
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:12549 original size:49 final size:50
Alignment explanation
Indices: 12425--12555 Score: 135
Period size: 49 Copynumber: 2.7 Consensus size: 50
12415 GAAGGGATTG
* * **
12425 AAGCCG-CAACGACAAATCTGATACCCTAGAGATATGAAGAGAAAGGTTC
1 AAGCCGACAACGACGAATCTTATACCCTAGAGATATGAAGAGAAAGACTC
* * * *
12474 AAGCCGA-AACGGCGAACCTTATACCCTAGAGATGTGAAGGGAAAGACT-
1 AAGCCGACAACGACGAATCTTATACCCTAGAGATATGAAGAGAAAGACTC
* *
12522 AAGGCC-ACAACGACGAATCTTACACCCTAAAGAT
1 AA-GCCGACAACGACGAATCTTATACCCTAGAGAT
12556 TAGGAAAAGT
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
48 3 0.04
49 64 0.96
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.15
Consensus pattern (50 bp):
AAGCCGACAACGACGAATCTTATACCCTAGAGATATGAAGAGAAAGACTC
Found at i:12879 original size:40 final size:40
Alignment explanation
Indices: 12822--13631 Score: 470
Period size: 40 Copynumber: 20.5 Consensus size: 40
12812 GCAAGTTACA
*
12822 ACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
* **
12862 ATCATCCAATCTTTTACCCTAATAAGAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
* * ** *
12902 AACGTCCAATCTTTTACCCTAATTAGAGGGTAGATTGAAG
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
* ** * *
12942 ACCATCAAATCTTTTACCCTAATTAGAGGGCAAATTGAAT
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
* * **
12982 ACCATCCGATCTCTTACCCCGACCATGA-GGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG
* * * * * *
13022 -CAATCCAAT-TTTTACCTTAACCAGAGAGCATATTAAAA
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
* ** *
13060 ACCATCCGATCTTTTACCCCGACCATGA-GGCAGATTAAAG
1 ACCATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG
* * ** * * * *
13100 -CAATCTAATCTTTTACCCTAATTAGAAGGCAAATTAAAT
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
** * * *
13139 ACCATCTGATCTCTTA-CCTCAACTATGA-GGCAGATTAAAG
1 ACCATCCAATCTTTTACCCT-AACCA-GAGGGCAGATTGAAG
* * * *
13179 -CAATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAAT
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
** * *
13218 ACCATCTGATCTCTTACCCTAACCATG-GGGTAGATTGAAG
1 ACCATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG
* * * * *
13258 TA--ATCTAATCTTTTACCCTAACCAGAGGTCATATGGAAT
1 -ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
* * ** * *
13297 ACCATCCGATCTCTTACCCCGACTATG-GGGCAGATTAAAG
1 ACCATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG
* * * *
13337 -CAATCCAATCTTTTACACTAACTAGAGGGCAGATTGAAA
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
* * * *
13376 ACCATCCAATCTCTTA-CGTCGACCATAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCT-AACCAGAGGGCAGATTGAAG
* * * * * * *
13416 A-AATCTAATTTTTTACCCTAATCAGAGGGAAAATTAAAG
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
* * * ** * *
13455 ATCATCCGATCTCTTACCCCGACCATG-GGGCAAATAGAAG
1 ACCATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG
* * * *
13495 -CAATTCAATCTTTTACCCTAACCAAAAGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
* * * * ** * *
13534 ACCGTTCGATCTCTTACCCCGACCATGA-GGCAAATTAAAG
1 ACCATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG
* * * * *** *
13574 -CAATCTAATCTTTTACCCTAACTAAAAAACAGATTGAAA
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
*
13613 ACCATCCGATCTTTTACCC
1 ACCATCCAATCTTTTACCC
13632 CTAAAGCTAT
Statistics
Matches: 577, Mismatches: 164, Indels: 58
0.72 0.21 0.07
Matches are distributed among these distances:
37 2 0.00
38 25 0.04
39 201 0.35
40 339 0.59
41 10 0.02
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (40 bp):
ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
Found at i:13167 original size:79 final size:79
Alignment explanation
Indices: 12949--13632 Score: 682
Period size: 79 Copynumber: 8.7 Consensus size: 79
12939 AAGACCATCA
** * *
12949 AATCTTTTACCCTAATTAGAGGGCAAATTGAATACCATCCGATCTCTTACCCCGACCATGAGGCA
1 AATCTTTTACCCTAACCAGAAGGCAAATTAAATACCATCCGATCTCTTACCCCGACCATGAGGCA
* *
13014 GATTGAAGCAATCC
66 GATTAAAGCAATCT
* * * *
13028 AAT-TTTTACCTTAACCAG-AGAGCATATTAAAAACCATCCGATCTTTTACCCCGACCATGAGGC
1 AATCTTTTACCCTAACCAGAAG-GCAAATTAAATACCATCCGATCTCTTACCCCGACCATGAGGC
13091 AGATTAAAGCAATCT
65 AGATTAAAGCAATCT
** * * * *
13106 AATCTTTTACCCTAATTAGAAGGCAAATTAAATACCATCTGATCTCTTACCTCAACTATGAGGCA
1 AATCTTTTACCCTAACCAGAAGGCAAATTAAATACCATCCGATCTCTTACCCCGACCATGAGGCA
*
13171 GATTAAAGCAATCC
66 GATTAAAGCAATCT
* * * * ** * *
13185 AATCTTTTACCCTAACCAAAAGGCAGATTGAATACCATCTGATCTCTTACCCTAACCATGGGGTA
1 AATCTTTTACCCTAACCAGAAGGCAAATTAAATACCATCCGATCTCTTACCCCGACCATGAGGCA
* *
13250 GATTGAAGTAATCT
66 GATTAAAGCAATCT
* ** * *
13264 AATCTTTTACCCTAACCAG-AGGTCATATGGAATACCATCCGATCTCTTACCCCGACTATGGGGC
1 AATCTTTTACCCTAACCAGAAGG-CAAATTAAATACCATCCGATCTCTTACCCCGACCATGAGGC
*
13328 AGATTAAAGCAATCC
65 AGATTAAAGCAATCT
* * * * * **
13343 AATCTTTTACACTAACTAGAGGGCAGATTGAAA-ACCATCCAATCTCTTACGTCGACCAT-AGGG
1 AATCTTTTACCCTAACCAGAAGGCAAATT-AAATACCATCCGATCTCTTACCCCGACCATGA-GG
* *
13406 CAGATTGAAGAAATCT
64 CAGATTAAAGCAATCT
* * * * * * *
13422 AATTTTTTACCCTAATCAGAGGGAAAATTAAAGATCATCCGATCTCTTACCCCGACCATGGGGCA
1 AATCTTTTACCCTAACCAGAAGGCAAATTAAATACCATCCGATCTCTTACCCCGACCATGAGGCA
*
13487 -AATAGAAGCAAT-T
66 GATTA-AAGCAATCT
* * * * * *
13500 CAATCTTTTACCCTAACCAAAAGGCAGATTGAAGACCGTTCGATCTCTTACCCCGACCATGAGGC
1 -AATCTTTTACCCTAACCAGAAGGCAAATTAAATACCATCCGATCTCTTACCCCGACCATGAGGC
*
13565 AAATTAAAGCAATCT
65 AGATTAAAGCAATCT
* * ** * *
13580 AATCTTTTACCCTAACTAAAAAACAGATTGAAA-ACCATCCGATCTTTTACCCC
1 AATCTTTTACCCTAACCAGAAGGCAAATT-AAATACCATCCGATCTCTTACCCC
13633 TAAAGCTATA
Statistics
Matches: 499, Mismatches: 92, Indels: 28
0.81 0.15 0.05
Matches are distributed among these distances:
77 1 0.00
78 75 0.15
79 411 0.82
80 12 0.02
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.26
Consensus pattern (79 bp):
AATCTTTTACCCTAACCAGAAGGCAAATTAAATACCATCCGATCTCTTACCCCGACCATGAGGCA
GATTAAAGCAATCT
Found at i:13298 original size:158 final size:158
Alignment explanation
Indices: 12865--13594 Score: 790
Period size: 158 Copynumber: 4.6 Consensus size: 158
12855 ATTGAAGATC
* * * * * * **
12865 ATCCAATCTTTTACCCTAA-TAAGAGGGCAGATTGAAGAA-CGTCCAATCTTTTACCCTAATTA-
1 ATCCAATCTTTTACCCTAACCAA-AAGGCAGATTGAA-AACCATCCGATCTCTTACCCTGACCAT
* * * * *
12927 GAGGGTAGATTGAAGACCATCAAATCTTTTACCCTAATTAGAGGGCAAATTGAATACCATCCGAT
64 G-GGGCAGATTGAAG-CAATCTAATCTTTTACCCTAATCAGAGGGCAAATTAAATACCATCCGAT
*
12992 CTCTTACCCCGACCATGAGGCAGATTGAAGCA
127 CTCTTACCCCGACCATGAGGCAGATTAAAGCA
* * * * * *
13024 ATCCAAT-TTTTACCTTAACC-AGAGAGCATATTAAAAACCATCCGATCTTTTACCCCGACCATG
1 ATCCAATCTTTTACCCTAACCAAAAG-GCAGATTGAAAACCATCCGATCTCTTACCCTGACCATG
* * * * *
13087 AGGCAGATTAAAGCAATCTAATCTTTTACCCTAATTAGAAGGCAAATTAAATACCATCTGATCTC
65 GGGCAGATTGAAGCAATCTAATCTTTTACCCTAATCAGAGGGCAAATTAAATACCATCCGATCTC
* * *
13152 TTACCTCAACTATGAGGCAGATTAAAGCA
130 TTACCCCGACCATGAGGCAGATTAAAGCA
* * *
13181 ATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAATACCATCTGATCTCTTACCCTAACCATGG
1 ATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAAAACCATCCGATCTCTTACCCTGACCATGG
* * * * * **
13246 GGTAGATTGAAGTAATCTAATCTTTTACCCTAACCAGAGGTCATATGGAATACCATCCGATCTCT
66 GGCAGATTGAAGCAATCTAATCTTTTACCCTAATCAGAGGGCAAATTAAATACCATCCGATCTCT
* *
13311 TACCCCGACTATGGGGCAGATTAAAGCA
131 TACCCCGACCATGAGGCAGATTAAAGCA
* * * * * * *
13339 ATCCAATCTTTTACACTAACTAGAGGGCAGATTGAAAACCATCCAATCTCTTA-CGTCGACCATA
1 ATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAAAACCATCCGATCTCTTACCCT-GACCATG
* * * * *
13403 GGGCAGATTGAAGAAATCTAATTTTTTACCCTAATCAGAGGGAAAATTAAAGATCATCCGATCTC
65 GGGCAGATTGAAGCAATCTAATCTTTTACCCTAATCAGAGGGCAAATTAAATACCATCCGATCTC
* *
13468 TTACCCCGACCATGGGGCA-AATAGAAGCA
130 TTACCCCGACCATGAGGCAGATTA-AAGCA
* * * * * *
13497 ATTCAATCTTTTACCCTAACCAAAAGGCAGATTGAAGACCGTTCGATCTCTTACCCCGACCATGA
1 ATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAAAACCATCCGATCTCTTACCCTGACCATGG
* *
13562 GGCAAATTAAAGCAATCTAATCTTTTACCCTAA
66 GGCAGATTGAAGCAATCTAATCTTTTACCCTAA
13595 CTAAAAAACA
Statistics
Matches: 474, Mismatches: 88, Indels: 19
0.82 0.15 0.03
Matches are distributed among these distances:
157 87 0.18
158 375 0.79
159 12 0.03
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (158 bp):
ATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAAAACCATCCGATCTCTTACCCTGACCATGG
GGCAGATTGAAGCAATCTAATCTTTTACCCTAATCAGAGGGCAAATTAAATACCATCCGATCTCT
TACCCCGACCATGAGGCAGATTAAAGCA
Found at i:13316 original size:237 final size:236
Alignment explanation
Indices: 12869--13630 Score: 827
Period size: 237 Copynumber: 3.2 Consensus size: 236
12859 AAGATCATCC
* * * * ** *
12869 AATCTTTTACCCTAA-TAAGAGGGCAGATTGAAGAA-CGTCCAATCTTTTACC-CTAATTAGAGG
1 AATCTTTTACCCTAACT-AGAAGGCAAATTGAA-AACCATCCAATCTCTTACCTC-AACCATAGG
* * * * *
12931 GTAGATTGAAGACCATCAAATCTTTTACCCTAATTAGAGGGCAAATTGAATACCATCCGATCTCT
63 GCAGATTAAAGA-AATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAATACCATCCGATCTCT
* * * *
12996 TACCCCGACCATGAGGCAGATTGAAGCAATCCAAT-TTTTACCTTAACCAGAGAGCATATTAAAA
127 TACCCCGACCATGGGGCAGATTGAAGCAATCTAATCTTTTACCCTAACCAGAG-GCATATTGAAA
*
13060 ACCATCCGATCTTTTACCCCGACCATGAGGCAGATTAAAGCAATCT
191 ACCATCCGATCTCTTACCCCGACCATGAGGCAGATTAAAGCAATCT
* ** *
13106 AATCTTTTACCCTAATTAGAAGGCAAATT-AAATACCATCTGATCTCTTACCTCAACTAT-GAGG
1 AATCTTTTACCCTAACTAGAAGGCAAATTGAAA-ACCATCCAATCTCTTACCTCAACCATAG-GG
* * * * * *
13169 CAGATTAAAGCAATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAATACCATCTGATCTCTTA
64 CAGATTAAAGAAATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAATACCATCCGATCTCTTA
** * * * *
13234 CCCTAACCATGGGGTAGATTGAAGTAATCTAATCTTTTACCCTAACCAGAGGTCATATGGAATAC
129 CCCCGACCATGGGGCAGATTGAAGCAATCTAATCTTTTACCCTAACCAGAGG-CATATTGAAAAC
* * *
13299 CATCCGATCTCTTACCCCGACTATGGGGCAGATTAAAGCAATCC
193 CATCCGATCTCTTACCCCGACCATGAGGCAGATTAAAGCAATCT
* * * * *
13343 AATCTTTTACACTAACTAGAGGGCAGATTGAAAACCATCCAATCTCTTACGTCGACCATAGGGCA
1 AATCTTTTACCCTAACTAGAAGGCAAATTGAAAACCATCCAATCTCTTACCTCAACCATAGGGCA
* * * * * * *
13408 GATTGAAGAAATCTAATTTTTTACCCTAATCAGAGGGAAAATTAAAGATCATCCGATCTCTTACC
66 GATTAAAGAAATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAATACCATCCGATCTCTTACC
* * * * *
13473 CCGACCATGGGGCAAATAGAAGCAAT-TCAATCTTTTACCCTAACCAAAAGGCAGATTGAAGACC
131 CCGACCATGGGGCAGATTGAAGCAATCT-AATCTTTTACCCTAACC-AGAGGCATATTGAAAACC
* * *
13537 GTTCGATCTCTTACCCCGACCATGAGGCAAATTAAAGCAATCT
194 ATCCGATCTCTTACCCCGACCATGAGGCAGATTAAAGCAATCT
* ** * * *
13580 AATCTTTTACCCTAACTAAAAAACAGATTGAAAACCATCCGATCTTTTACC
1 AATCTTTTACCCTAACTAGAAGGCAAATTGAAAACCATCCAATCTCTTACC
13631 CCTAAAGCTA
Statistics
Matches: 435, Mismatches: 79, Indels: 22
0.81 0.15 0.04
Matches are distributed among these distances:
235 1 0.00
236 79 0.18
237 345 0.79
238 10 0.02
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (236 bp):
AATCTTTTACCCTAACTAGAAGGCAAATTGAAAACCATCCAATCTCTTACCTCAACCATAGGGCA
GATTAAAGAAATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAATACCATCCGATCTCTTACC
CCGACCATGGGGCAGATTGAAGCAATCTAATCTTTTACCCTAACCAGAGGCATATTGAAAACCAT
CCGATCTCTTACCCCGACCATGAGGCAGATTAAAGCAATCT
Found at i:15294 original size:29 final size:30
Alignment explanation
Indices: 15258--15406 Score: 189
Period size: 29 Copynumber: 5.0 Consensus size: 30
15248 TATTTTTGAT
*
15258 CCTAAAATTTCCAAAAATTCAAATTTGACC
1 CCTAAATTTTCCAAAAATTCAAATTTGACC
15288 CCTAAATTTTCCAAAAATTC-AATTTGACC
1 CCTAAATTTTCCAAAAATTCAAATTTGACC
*
15317 CCTAAACTTTT-CAAAAATTCAAATTT-AAC
1 CCTAAA-TTTTCCAAAAATTCAAATTTGACC
* *
15346 CCTAAATTTTTCCAAAAATTCTAATTTGACT
1 CCTAAA-TTTTCCAAAAATTCAAATTTGACC
* * *
15377 CCGAAGTTTT-CTAAAATTCAAATTTGACC
1 CCTAAATTTTCCAAAAATTCAAATTTGACC
15406 C
1 C
15407 GATTTTAATG
Statistics
Matches: 104, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
29 53 0.51
30 46 0.44
31 5 0.05
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (30 bp):
CCTAAATTTTCCAAAAATTCAAATTTGACC
Found at i:15337 original size:59 final size:61
Alignment explanation
Indices: 15258--15406 Score: 207
Period size: 59 Copynumber: 2.5 Consensus size: 61
15248 TATTTTTGAT
*
15258 CCTAAAATTTCCAAAAATTCAAATTTGACCCCTAAA-TTTTCCAAAAATTC-AATTTGACC
1 CCTAAAATTTTCAAAAATTCAAATTTGACCCCTAAATTTTTCCAAAAATTCTAATTTGACC
* * *
15317 CCTAAACTTTTCAAAAATTCAAATTT-AACCCTAAATTTTTCCAAAAATTCTAATTTGACT
1 CCTAAAATTTTCAAAAATTCAAATTTGACCCCTAAATTTTTCCAAAAATTCTAATTTGACC
* * *
15377 CC-GAAGTTTTCTAAAATTCAAATTTGACCC
1 CCTAAAATTTTCAAAAATTCAAATTTGACCC
15407 GATTTTAATG
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
58 8 0.10
59 58 0.73
60 13 0.16
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (61 bp):
CCTAAAATTTTCAAAAATTCAAATTTGACCCCTAAATTTTTCCAAAAATTCTAATTTGACC
Found at i:23265 original size:15 final size:16
Alignment explanation
Indices: 23237--23270 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
23227 AGTATTTATC
23237 AAAAGAAAAATATAAA
1 AAAAGAAAAATATAAA
*
23253 AAAAG-AAATTATAAA
1 AAAAGAAAAATATAAA
23268 AAA
1 AAA
23271 GACAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAAGAAAAATATAAA
Found at i:23277 original size:16 final size:15
Alignment explanation
Indices: 23237--23278 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
23227 AGTATTTATC
*
23237 AAAAGAAAAATATAA
1 AAAAGAAAATTATAA
23252 AAAA-AGAAATTATAA
1 AAAAGA-AAATTATAA
23267 AAAAGACAAATT
1 AAAAGA-AAATT
23279 TCAAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.04
15 16 0.70
16 6 0.26
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAAGAAAATTATAA
Done.