Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014734.1 Kokia drynarioides strain JFW-HI SEQ_129773, 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: 222657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:188171 original size:151 final size:153
Alignment explanation
Indices: 187840--188183 Score: 341
Period size: 151 Copynumber: 2.3 Consensus size: 153
187830 ACGAAGACAC
* * * * * * *
187840 AAGGGAAAGTTCTAAGCCGTAACGGTGGATCCAGTACCACGAAGATAC------AAGGGAACGAT
1 AAGGGAAAGATCTAAGCCGCAACAGTGAATCCAGTACCACAAAGACACAAGGGAAAGGGAAAGAT
** * * * * *
187899 CTAAGCCGCAATGGCGGATCCATTACCTTCGAAGACACGAAAGGGAAAGGTTTAAGTCGCTATGG
66 CTAAGCCGCAACAGCGGATCCAGTACCTACGAAGACAC-AAAGGGAAAGATCTAAGTCGCTATGA
* * * *
187964 TGAACCTATTACGTCCGAGACATC
130 CGAACCTATTACCTCAGAGACATA
* * *
187988 AAGGGAAAGATCTAAGCCGCAATAGTGGATCCAGTACCACGAAGACACAAGGGAAAGGGAAAGAT
1 AAGGGAAAGATCTAAGCCGCAACAGTGAATCCAGTACCACAAAGACACAAGGGAAAGGGAAAGAT
*
188053 CTAAGCCGCAACAGCTGATCCAGTACC-ACGAAGACAC-AAGGGAAAGATCTAAG-CTG-TAATG
66 CTAAGCCGCAACAGCGGATCCAGTACCTACGAAGACACAAAGGGAAAGATCTAAGTC-GCT-ATG
188114 ACGAACCT-TATACCTCAGAGACATA
129 ACGAACCTAT-TACCTCAGAGACATA
* * * *
188139 AAGGGAAAGATTTAAGTCGCAGCGGTGAATCCAGTACCACAAAGA
1 AAGGGAAAGATCTAAGCCGCAACAGTGAATCCAGTACCACAAAGA
188184 TTTGAAGGGA
Statistics
Matches: 162, Mismatches: 25, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
148 43 0.27
150 3 0.02
151 74 0.46
153 9 0.06
154 33 0.20
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.16
Consensus pattern (153 bp):
AAGGGAAAGATCTAAGCCGCAACAGTGAATCCAGTACCACAAAGACACAAGGGAAAGGGAAAGAT
CTAAGCCGCAACAGCGGATCCAGTACCTACGAAGACACAAAGGGAAAGATCTAAGTCGCTATGAC
GAACCTATTACCTCAGAGACATA
Found at i:188648 original size:39 final size:39
Alignment explanation
Indices: 188605--188747 Score: 128
Period size: 39 Copynumber: 3.7 Consensus size: 39
188595 CAGCCATTTG
*
188605 ATCTTTTACCTAGAGCTTGGGGCAGATCATCGTCAACCA
1 ATCTTTTACCTCGAGCTTGGGGCAGATCATCGTCAACCA
* * * * ***
188644 ATC-TTTACCTCGAGCCTGGGGCAGATTGA-AGCCATTTA
1 ATCTTTTACCTCGAGCTTGGGGCAGA-TCATCGTCAACCA
* * *
188682 ATCTTTTACCCCGAGCTTGGGGTAGATCATCATCAACCA
1 ATCTTTTACCTCGAGCTTGGGGCAGATCATCGTCAACCA
* * **
188721 ATCTCTTACCCCGAGCCAGGGGCAGAT
1 ATCTTTTACCTCGAGCTTGGGGCAGAT
188748 TACAGCCATT
Statistics
Matches: 79, Mismatches: 22, Indels: 6
0.74 0.21 0.06
Matches are distributed among these distances:
38 29 0.37
39 50 0.63
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (39 bp):
ATCTTTTACCTCGAGCTTGGGGCAGATCATCGTCAACCA
Found at i:188769 original size:78 final size:78
Alignment explanation
Indices: 188554--188826 Score: 327
Period size: 78 Copynumber: 3.5 Consensus size: 78
188544 AGTGAAGTTA
* * * * *
188554 CATCATCAACCAATCTCTTACCCTGAGCCTGGTGCAAAATGCAGCCATTTGATCTTTTACCTAGA
1 CATCATCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATTTGATCTTTTACCTAGA
*
188619 GCTTGGGGCAGAT
66 GCTTGGGGTAGAT
* * * **
188632 CATCGTCAACCAATCT-TTACCTCGAGCCTGGGGCAGATTGA-AGCCATTTAATCTTTTACCCCG
1 CATCATCAACCAATCTCTTACCCCGAGCCTGGGGCAGATT-ACAGCCATTTGATCTTTTACCTAG
188695 AGCTTGGGGTAGAT
65 AGCTTGGGGTAGAT
* * *
188709 CATCATCAACCAATCTCTTACCCCGAGCCAGGGGCAGATTACAGCCATTCGAT-TTCTTACCTTG
1 CATCATCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATTTGATCTT-TTACCTAG
*
188773 AGCTTGAGGTAGAT
65 AGCTTGGGGTAGAT
* * * * *
188787 CACCATCAACTAATCTCCTACCCCGAGTCTGAGGCAGATT
1 CATCATCAACCAATCTCTTACCCCGAGCCTGGGGCAGATT
188827 GTAGTTTTCC
Statistics
Matches: 166, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
77 68 0.41
78 98 0.59
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (78 bp):
CATCATCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATTTGATCTTTTACCTAGA
GCTTGGGGTAGAT
Found at i:189290 original size:6 final size:6
Alignment explanation
Indices: 189279--189351 Score: 50
Period size: 6 Copynumber: 13.2 Consensus size: 6
189269 TTCTAAATTT
* * * *
189279 ATTTAA ATTTAA ATTT-G TTTTAA ATTTAA ATTT-- AGTTAA ATTT-G
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
189323 TTTTAA ATTTAA ATTT-- AGTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
189352 ATGGTTTTAA
Statistics
Matches: 49, Mismatches: 12, Indels: 12
0.67 0.16 0.16
Matches are distributed among these distances:
4 6 0.12
5 6 0.12
6 37 0.76
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:189293 original size:16 final size:16
Alignment explanation
Indices: 189272--189351 Score: 80
Period size: 16 Copynumber: 5.2 Consensus size: 16
189262 GAATTGATTC
189272 TAAATTTATTTAAATT
1 TAAATTTATTTAAATT
*
189288 TAAATTTGTTTTAAATT
1 TAAATTT-ATTTAAATT
*
189305 TAAATTTAGTTAAA-T
1 TAAATTTATTTAAATT
*
189320 T---TGT-TTTAAATT
1 TAAATTTATTTAAATT
*
189332 TAAATTTAGTTAAATT
1 TAAATTTATTTAAATT
189348 TAAA
1 TAAA
189352 ATGGTTTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
11 5 0.10
12 4 0.08
15 4 0.08
16 23 0.45
17 15 0.29
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
TAAATTTATTTAAATT
Found at i:189293 original size:27 final size:29
Alignment explanation
Indices: 189235--189333 Score: 100
Period size: 27 Copynumber: 3.6 Consensus size: 29
189225 GATCAAACTT
* *
189235 TTTGATTTTCAAATTTATATTAAGTTTGAA
1 TTTGATTTT-AAATTTATATTAAATTTAAA
*
189265 -TTGATTCTAAATTTAT-TTAAATTTAAA
1 TTTGATTTTAAATTTATATTAAATTTAAA
* * *
189292 TTTG-TTTTAAATTTAAATT-TAGTTAAA
1 TTTGATTTTAAATTTATATTAAATTTAAA
189319 TTTG-TTTTAAATTTA
1 TTTGATTTTAAATTTA
189334 AATTTAGTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 40 0.67
28 13 0.22
29 7 0.12
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTGATTTTAAATTTATATTAAATTTAAA
Found at i:189302 original size:17 final size:17
Alignment explanation
Indices: 189280--189362 Score: 67
Period size: 17 Copynumber: 5.4 Consensus size: 17
189270 TCTAAATTTA
189280 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGT
189297 TTTAAATTTAAA-----
1 TTTAAATTTAAATTTGT
*
189309 TTT--AGTTAAATTTGT
1 TTTAAATTTAAATTTGT
189324 TTTAAATTTAAATTTAG-
1 TTTAAATTTAAATTT-GT
* *
189341 -TTAAATTTAAAATGGT
1 TTTAAATTTAAATTTGT
189357 TTTAAA
1 TTTAAA
189363 CTTGAAATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 20
0.68 0.05 0.26
Matches are distributed among these distances:
10 6 0.12
12 3 0.06
15 4 0.08
16 12 0.23
17 26 0.50
18 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAAATTTGT
Found at i:189309 original size:33 final size:33
Alignment explanation
Indices: 189272--189380 Score: 104
Period size: 27 Copynumber: 3.4 Consensus size: 33
189262 GAATTGATTC
189272 TAAATTTATTTAAATTTAAATTTGTTTTAAATT
1 TAAATTTATTTAAATTTAAATTTGTTTTAAATT
*
189305 T-AA---ATTT--AGTTAAATTTGTTTTAAATT
1 TAAATTTATTTAAATTTAAATTTGTTTTAAATT
* * *
189332 TAAATTTAGTTAAATTTAAAATGGTTTTAAACTT
1 TAAATTTATTTAAATTTAAATTTGTTTTAAA-TT
* *
189366 GAAATTAAATTTAAA
1 TAAATT-TATTTAAA
189381 ATGTACAAGC
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
27 20 0.33
28 2 0.03
29 4 0.07
31 3 0.05
32 2 0.03
33 16 0.27
34 7 0.12
35 6 0.10
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.50
Consensus pattern (33 bp):
TAAATTTATTTAAATTTAAATTTGTTTTAAATT
Found at i:189334 original size:27 final size:27
Alignment explanation
Indices: 189287--189348 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
189277 TTATTTAAAT
189287 TTAAATTTGTTTTAAATTTAAATTTAG
1 TTAAATTTGTTTTAAATTTAAATTTAG
189314 TTAAATTTGTTTTAAATTTAAATTTAG
1 TTAAATTTGTTTTAAATTTAAATTTAG
189341 TTAAATTT
1 TTAAATTT
189349 AAAATGGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.56
Consensus pattern (27 bp):
TTAAATTTGTTTTAAATTTAAATTTAG
Found at i:191563 original size:29 final size:29
Alignment explanation
Indices: 191516--191703 Score: 134
Period size: 29 Copynumber: 6.3 Consensus size: 29
191506 AACTTTACAT
* *
191516 AATTCCATTTTGA-CCTCGATTTTCCAAA
1 AATTACATTTTTACCCTCGATTTTCCAAA
*
191544 AATTACATTTTTACCCTCGAACTTTCC-AA
1 AATTACATTTTTACCCTCG-ATTTTCCAAA
* **
191573 AATTCCATTTTTGA-CCTTAATTTTTTTTCC-AA
1 AATTACATTTTT-ACCCTCGA----TTTTCCAAA
* * *
191605 AATTACCA-TTTTACCCTTGAATCTCCAAA
1 AATTA-CATTTTTACCCTCGATTTTCCAAA
**
191634 AATTACATTTTTACCCTCGAACTTCCAAA
1 AATTACATTTTTACCCTCGATTTTCCAAA
* *
191663 AATTCCATTTTTAACCTCGATTTTTCCAAA
1 AATTACATTTTTACCCTCGA-TTTTCCAAA
*
191693 AACTACCATTT
1 AATTA-CATTT
191704 GACCCCTAGA
Statistics
Matches: 127, Mismatches: 20, Indels: 23
0.75 0.12 0.14
Matches are distributed among these distances:
28 18 0.14
29 64 0.50
30 17 0.13
31 6 0.05
32 20 0.16
33 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (29 bp):
AATTACATTTTTACCCTCGATTTTCCAAA
Found at i:191572 original size:30 final size:30
Alignment explanation
Indices: 191386--191703 Score: 149
Period size: 30 Copynumber: 10.7 Consensus size: 30
191376 AAGGTCCCTT
* * * *
191386 AACTGTCCAAAAATCACATTTTAACCCTCA
1 AACTTTCCAAAAATTACATTTTTACCCTCG
* * * * *
191416 AACTTTTCTAAAATTATATTTTAACCC-CTA
1 AACTTTCCAAAAATTACATTTTTACCCTC-G
* * ** *
191446 AAATTCTCC-AAAATTATATTTCGACCCCCG
1 AACTT-TCCAAAAATTACATTTTTACCCTCG
**** *
191476 AACTTTTTGGAAATTACATTTTTACCC-CTA
1 AACTTTCCAAAAATTACATTTTTACCCTC-G
* * * *
191506 AACTTTAC-ATAATTCCATTTTGA-CCTCG
1 AACTTTCCAAAAATTACATTTTTACCCTCG
*
191534 -ATTTTCCAAAAATTACATTTTTACCCTCG
1 AACTTTCCAAAAATTACATTTTTACCCTCG
* *
191563 AACTTTCC-AAAATTCCATTTTTGA-CCT-T
1 AACTTTCCAAAAATTACATTTTT-ACCCTCG
* *
191591 AATTTTTTTTCC-AAAATTACCA-TTTTACCCTTG
1 AA----CTTTCCAAAAATTA-CATTTTTACCCTCG
*
191624 AA-TCTCCAAAAATTACATTTTTACCCTCG
1 AACTTTCCAAAAATTACATTTTTACCCTCG
* *
191653 AAC-TTCCAAAAATTCCATTTTTAACCTCG
1 AACTTTCCAAAAATTACATTTTTACCCTCG
** *
191682 ATTTTTCCAAAAACTACCATTT
1 AACTTTCCAAAAATTA-CATTT
191704 GACCCCTAGA
Statistics
Matches: 221, Mismatches: 45, Indels: 43
0.72 0.15 0.14
Matches are distributed among these distances:
27 5 0.02
28 22 0.10
29 79 0.36
30 84 0.38
31 9 0.04
32 18 0.08
33 4 0.02
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (30 bp):
AACTTTCCAAAAATTACATTTTTACCCTCG
Found at i:197311 original size:24 final size:22
Alignment explanation
Indices: 197283--197327 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
197273 AAGATTTATA
197283 ATTTTTAGTAATAAATTTAGTACT
1 ATTTTTAGT--TAAATTTAGTACT
*
197307 ATTTTTAGTTTAATTTAGTAC
1 ATTTTTAGTTAAATTTAGTAC
197328 ATTAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (22 bp):
ATTTTTAGTTAAATTTAGTACT
Found at i:198370 original size:18 final size:20
Alignment explanation
Indices: 198347--198390 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
198337 AAAATGTAGC
* *
198347 AGAAAAA-TAACAAAATAA-
1 AGAAAAACTAAAAAAAAAAT
198365 AGAAAAACTAAAAAAAAAAT
1 AGAAAAACTAAAAAAAAAAT
198385 AGAAAA
1 AGAAAA
198391 CGAAACATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 9 0.41
20 6 0.27
ACGTcount: A:0.80, C:0.05, G:0.07, T:0.09
Consensus pattern (20 bp):
AGAAAAACTAAAAAAAAAAT
Found at i:200363 original size:6 final size:6
Alignment explanation
Indices: 200352--200378 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
200342 TGATGGGCTA
200352 TTGCTT TTGCTT TTGCTT TTGCTT TTG
1 TTGCTT TTGCTT TTGCTT TTGCTT TTG
200379 AGAGGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.19, T:0.67
Consensus pattern (6 bp):
TTGCTT
Found at i:201392 original size:34 final size:34
Alignment explanation
Indices: 201354--201430 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
201344 TCTACATTGC
* *
201354 CAAGGCTTTCAATTTAGTCCCTGATTGGCACATG
1 CAAGGCTCTCAATTTAATCCCTGATTGGCACATG
201388 CAAGGCTCTCAATTTAATCCCTGATTGGCACATG
1 CAAGGCTCTCAATTTAATCCCTGATTGGCACATG
201422 CAAGGCTCT
1 CAAGGCTCT
201431 ATACGACGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (34 bp):
CAAGGCTCTCAATTTAATCCCTGATTGGCACATG
Found at i:203455 original size:13 final size:13
Alignment explanation
Indices: 203439--203466 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
203429 AAACTCAATT
203439 TTTAGGATTAATA
1 TTTAGGATTAATA
203452 TTTAGGATTAATA
1 TTTAGGATTAATA
203465 TT
1 TT
203467 ATTATATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TTTAGGATTAATA
Found at i:210859 original size:36 final size:36
Alignment explanation
Indices: 210808--210906 Score: 126
Period size: 36 Copynumber: 2.7 Consensus size: 36
210798 AACAGGCATT
* * *
210808 ACCTTTAGGTTAACAGGGAGAAAAATGAGCATAATG
1 ACCTTTAGGTCAACAGGGAGTAAAACGAGCATAATG
* *
210844 ACCTTTAGGTCAACAGAGAGTAAAACGAGCATCATG
1 ACCTTTAGGTCAACAGGGAGTAAAACGAGCATAATG
* *
210880 ACCTTCGAGGTCAACAAGGAGTAAAAC
1 ACCTT-TAGGTCAACAGGGAGTAAAAC
210907 AAATAACAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
36 36 0.67
37 18 0.33
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (36 bp):
ACCTTTAGGTCAACAGGGAGTAAAACGAGCATAATG
Found at i:212245 original size:25 final size:23
Alignment explanation
Indices: 212202--212373 Score: 130
Period size: 23 Copynumber: 7.7 Consensus size: 23
212192 CACTAGCGCA
*
212202 CTCTCTGATTAACA-TTGTGTGTG
1 CTCTCTGATTAGCACTT-TGTGTG
*
212225 CTCTCTGATTAGCACTGTGTGTG
1 CTCTCTGATTAGCACTTTGTGTG
* *
212248 CTCTCTGTTTAGCACGTTT-CGTG
1 CTCTCTGATTAGCAC-TTTGTGTG
*
212271 CTCTCTGTTATTAGCACTTCGTGTG
1 CTCTCTG--ATTAGCACTTTGTGTG
*
212296 CTCTTTGATTAGCACTTT-TGTG
1 CTCTCTGATTAGCACTTTGTGTG
* *
212318 --CTC-----AGTACTTTGTGTA
1 CTCTCTGATTAGCACTTTGTGTG
* *
212334 CTCTCTGTTTAGCACTTTATGTG
1 CTCTCTGATTAGCACTTTGTGTG
* *
212357 CTCTCTGTTTAGTACTT
1 CTCTCTGATTAGCACTT
212374 CGGTACTCTC
Statistics
Matches: 119, Mismatches: 17, Indels: 26
0.73 0.10 0.16
Matches are distributed among these distances:
15 7 0.06
16 3 0.03
18 3 0.03
20 2 0.02
22 4 0.03
23 79 0.66
24 5 0.04
25 16 0.13
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (23 bp):
CTCTCTGATTAGCACTTTGTGTG
Found at i:212298 original size:48 final size:45
Alignment explanation
Indices: 212222--212320 Score: 128
Period size: 48 Copynumber: 2.1 Consensus size: 45
212212 AACATTGTGT
*
212222 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTTTC
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCAC-TTTC
* *
212268 GTGCTCTCTGTTATTAGCACT-TCGTGTGCTCTTTGATTAGCACTTTT
1 GTGCTCTCTG--ATTAGCACTGT-GTGTGCTCTCTGATTAGCACTTTC
212315 GTGCTC
1 GTGCTC
212321 AGTACTTTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
46 10 0.21
47 10 0.21
48 27 0.57
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.43
Consensus pattern (45 bp):
GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTC
Found at i:212388 original size:22 final size:22
Alignment explanation
Indices: 212321--212388 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
212311 TTTTGTGCTC
*
212321 AGTACTTTGTGTACTCTCTGTTT
1 AGTACTTAG-GTACTCTCTGTTT
* * *
212344 AGCACTTTATGTGCTCTCTGTTT
1 AGTAC-TTAGGTACTCTCTGTTT
* *
212367 AGTACTTCGGTACTCTCCGTTT
1 AGTACTTAGGTACTCTCTGTTT
212389 GTTCTGTTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
22 13 0.37
23 20 0.57
24 2 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (22 bp):
AGTACTTAGGTACTCTCTGTTT
Found at i:216710 original size:116 final size:114
Alignment explanation
Indices: 216530--216788 Score: 338
Period size: 116 Copynumber: 2.2 Consensus size: 114
216520 AGAACTCATG
** * * *
216530 CTTGTATCGGTAGAAGCACAGGGTAGCAGAGGTTATTCTTTGACTTGAGTTGTTTCCATAGTTGT
1 CTTGTATCGGTAGAAGTTCAGGGTAGGAGAGGTTATTCTCTAACTTGAGTTGTTTCCATAGTTGT
*
216595 ATAACAGGTATCGGTAGTTCTATACATTTAGGTATCAGTAGTTTAAATA
66 ATAACAGGTATCGGTAGTTCTATACATTGAGGTATCAGTAGTTTAAATA
* * ** *
216644 CTTGTATCAGTAGAAGTTCAGGGTAGGAGAAAGGTTGTTCTCTAACTTGAGTTGTTTCGGTTGTT
1 CTTGTATCGGTAGAAGTTCAGGGTAGGAG--AGGTTATTCTCTAACTTGAGTTGTTTCCATAGTT
* * * *
216709 GTATAATAGGTATCGGTAGTTCTGTACATTGAGGTTTTAGTAGTTTAAATA
64 GTATAACAGGTATCGGTAGTTCTATACATTGAGGTATCAGTAGTTTAAATA
* *
216760 CTTGTACCGGTAGAAGTTGTAGGGTAGGA
1 CTTGTATCGGTAGAAGTT-CAGGGTAGGA
216789 CTTTTCAGCG
Statistics
Matches: 124, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
114 25 0.20
116 90 0.73
117 9 0.07
ACGTcount: A:0.26, C:0.10, G:0.27, T:0.37
Consensus pattern (114 bp):
CTTGTATCGGTAGAAGTTCAGGGTAGGAGAGGTTATTCTCTAACTTGAGTTGTTTCCATAGTTGT
ATAACAGGTATCGGTAGTTCTATACATTGAGGTATCAGTAGTTTAAATA
Found at i:218209 original size:34 final size:35
Alignment explanation
Indices: 218138--218210 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
218128 TTTTTGCCTA
* * *
218138 CTTTTCTTCCAGTTTTGCTCTTAAAAGAATTATAG
1 CTTTTCTTCCAGTTTTGCTCCTAAAAGAAATACAG
* *
218173 CTTTT-TTCTAGTTTTGCTCCTAAAATAAATACAG
1 CTTTTCTTCCAGTTTTGCTCCTAAAAGAAATACAG
218207 CTTT
1 CTTT
218211 GTGTTCCATG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 28 0.85
35 5 0.15
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.47
Consensus pattern (35 bp):
CTTTTCTTCCAGTTTTGCTCCTAAAAGAAATACAG
Found at i:221313 original size:67 final size:62
Alignment explanation
Indices: 221217--221361 Score: 202
Period size: 62 Copynumber: 2.3 Consensus size: 62
221207 ATTATACATT
**
221217 TAATTTTACAAT-AAATTTAACCCATTACATTTTTACAATCAAATTCAACCCAATACCCCATGCA
1 TAATTTTACAATCAAATCCAACCCATTACATTTTTACAATCAAATT-----CAATACCCCATGCA
221281 TC
61 TC
* *
221283 TAATTTTACAATCAAATCCAACCCATTACATTTTTACAATCAAATTCAATACCCTATGGATC
1 TAATTTTACAATCAAATCCAACCCATTACATTTTTACAATCAAATTCAATACCCCATGCATC
221345 TAATTTTACAATCAAAT
1 TAATTTTACAATCAAAT
221362 TCAATACCTA
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
62 31 0.42
66 12 0.16
67 31 0.42
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.34
Consensus pattern (62 bp):
TAATTTTACAATCAAATCCAACCCATTACATTTTTACAATCAAATTCAATACCCCATGCATC
Found at i:221356 original size:34 final size:33
Alignment explanation
Indices: 221267--221369 Score: 117
Period size: 34 Copynumber: 3.2 Consensus size: 33
221257 AAATTCAACC
221267 CAATACCCCATGCATCTAATTTTACAATCAAA-T
1 CAATA-CCCATGCATCTAATTTTACAATCAAATT
* * *
221300 CCA-ACCCAT-TA-C-ATTTTTACAATCAAATT
1 CAATACCCATGCATCTAATTTTACAATCAAATT
*
221329 CAATACCCTATGGATCTAATTTTACAATCAAATT
1 CAATACCC-ATGCATCTAATTTTACAATCAAATT
221363 CAATACC
1 CAATACC
221370 TAGAAGGATT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 14 0.24
29 4 0.07
30 5 0.09
31 7 0.12
32 2 0.03
33 3 0.05
34 23 0.40
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (33 bp):
CAATACCCATGCATCTAATTTTACAATCAAATT
Found at i:221649 original size:21 final size:20
Alignment explanation
Indices: 221621--221662 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
221611 CCGGTGTAAT
221621 ATTCATTTCCCCCAACAATG
1 ATTCATTTCCCCCAACAATG
* *
221641 ATTCGATTTCTCCGAACAATG
1 ATTC-ATTTCCCCCAACAATG
221662 A
1 A
221663 ATGAGAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTCATTTCCCCCAACAATG
Done.