Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013908.1 Kokia drynarioides strain JFW-HI SEQ_128937, 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: 142081
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:4874 original size:69 final size:70
Alignment explanation
Indices: 4800--4971 Score: 204
Period size: 69 Copynumber: 2.5 Consensus size: 70
4790 GTTCTGGGCA
*
4800 ACAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAATCAAAGAGCACACAAAGTA
1 ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAATCAAAGAGCACACAAAGTA
4865 CTAAT
66 CTAAT
* ** * * * * *
4870 -CAGAGAGCACACAAAGTGCTAATTAGAGAGCACACAAAGTGCTAATTAGAGAGCACACACAGTG
1 ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAATCAAAGAGCACACAAAGTA
4934 CTAAT
66 CTAAT
* * *
4939 AACAGAGTGCACGAGAC-GTGCTAAACGGAGAGC
1 -ACAGAGAGCAC-ACACAGTGCTAAACAGAGAGC
4972 GCGCTAGTGT
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
69 60 0.71
71 22 0.26
72 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (70 bp):
ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAATCAAAGAGCACACAAAGTA
CTAAT
Found at i:4938 original size:23 final size:23
Alignment explanation
Indices: 4801--4938 Score: 195
Period size: 23 Copynumber: 6.0 Consensus size: 23
4791 TTCTGGGCAA
* *
4801 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAT
* *
4824 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
4847 CAAAGAGCACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
4870 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
4893 TAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
4916 TAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
4939 AACAGAGTGC
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 105 1.00
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.14
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:9756 original size:26 final size:24
Alignment explanation
Indices: 9716--9764 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
9706 TTATCAATCA
9716 TCACCATTCATTATTCATATTTCCAT
1 TCACCATTCATTATTC-T-TTTCCAT
9742 TCACCATTTCA-TATTCTTTTCCA
1 TCACCA-TTCATTATTCTTTTCCA
9765 CATTTCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
25 1 0.05
26 11 0.50
27 4 0.18
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (24 bp):
TCACCATTCATTATTCTTTTCCAT
Found at i:18325 original size:151 final size:151
Alignment explanation
Indices: 18160--18460 Score: 584
Period size: 151 Copynumber: 2.0 Consensus size: 151
18150 ACTTTAATAA
*
18160 TTTTTTTTTACTAAAATAAATGTTATTTATCAAGATTATATGAGTCCTAAATTATTTATTAAAAT
1 TTTTTTTTTACTAAAATAAATGTTATTTATCAAGATGATATGAGTCCTAAATTATTTATTAAAAT
18225 AATATATTTTGAACCGTAACTTGAAATTTTTAATTTTTTATCAGTTATTAGAAATTTCAAGGTGA
66 AATATATTTTGAACCGTAACTTGAAATTTTTAATTTTTTATCAGTTATTAGAAATTTCAAGGTGA
18290 TAGAGATTTTTTATCTTGTTT
131 TAGAGATTTTTTATCTTGTTT
18311 TTTTTTTTTACTAAAATAAATGTTATTTATCAAGATGATATGAGTCCTAAATTATTTATTAAAAT
1 TTTTTTTTTACTAAAATAAATGTTATTTATCAAGATGATATGAGTCCTAAATTATTTATTAAAAT
*
18376 AATATATTTTGAACCGTAACTTGAAATTTTTAATTTTTTATCAGTTATTAGAAATTTCAAGGTGG
66 AATATATTTTGAACCGTAACTTGAAATTTTTAATTTTTTATCAGTTATTAGAAATTTCAAGGTGA
18441 TAGAGATTTTTTATCTTGTT
131 TAGAGATTTTTTATCTTGTT
18461 GGACTGATGT
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 148 1.00
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.49
Consensus pattern (151 bp):
TTTTTTTTTACTAAAATAAATGTTATTTATCAAGATGATATGAGTCCTAAATTATTTATTAAAAT
AATATATTTTGAACCGTAACTTGAAATTTTTAATTTTTTATCAGTTATTAGAAATTTCAAGGTGA
TAGAGATTTTTTATCTTGTTT
Found at i:26444 original size:22 final size:21
Alignment explanation
Indices: 26410--26451 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
26400 TACTGCATGT
26410 TTTATTTAGGTTAGTTTATTA
1 TTTATTTAGGTTAGTTTATTA
* *
26431 TTTATGTTGGGTTATTTTATT
1 TTTAT-TTAGGTTAGTTTATT
26452 TATACAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (21 bp):
TTTATTTAGGTTAGTTTATTA
Found at i:28757 original size:25 final size:26
Alignment explanation
Indices: 28699--28777 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 26
28689 CTAGACAGAG
* *
28699 TACGCTCTTAAGAGCCAGAATCAGAAT
1 TACGCTCTTACGAGCCA-AATCAAAAT
28726 TACGCTCTTACGAGCCAAA-CAAAAT
1 TACGCTCTTACGAGCCAAATCAAAAT
28751 TACGCTCTTACGAGCCAAAATCAAAAT
1 TACGCTCTTACGAGCC-AAATCAAAAT
28778 ATCTTCGTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
25 21 0.44
26 5 0.10
27 22 0.46
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.22
Consensus pattern (26 bp):
TACGCTCTTACGAGCCAAATCAAAAT
Found at i:32360 original size:15 final size:17
Alignment explanation
Indices: 32328--32360 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
32318 TTAAAAATAA
32328 ATAATCTAATGAGAATT
1 ATAATCTAATGAGAATT
32345 ATAAT-TAATG-GAATT
1 ATAATCTAATGAGAATT
32360 A
1 A
32361 CTTTTGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (17 bp):
ATAATCTAATGAGAATT
Found at i:34421 original size:19 final size:20
Alignment explanation
Indices: 34375--34438 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
34365 TTTTATATTT
34375 TTTTTAAAAATATAAATTTTGAAA
1 TTTTTAAAAAT-T--ATTTTG-AA
*
34399 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTGAA
34418 -TTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
34437 TT
1 TT
34439 ATTTTGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 8 0.22
19 11 0.31
20 7 0.19
22 1 0.03
24 9 0.25
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:37008 original size:20 final size:20
Alignment explanation
Indices: 36985--37052 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
36975 ATAATATATC
36985 AAATAAATTTAAAAACATTA
1 AAATAAATTTAAAAACATTA
37005 AAAT-AATCATTAAAAA-A-T-
1 AAATAAAT--TTAAAAACATTA
*
37023 AAACAAATTTAAAAAACATTA
1 AAATAAATTT-AAAAACATTA
37044 AAA-AAATTT
1 AAATAAATTT
37053 TATATTAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
17 2 0.05
18 8 0.20
19 8 0.20
20 12 0.30
21 10 0.25
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAAATTTAAAAACATTA
Found at i:37143 original size:22 final size:22
Alignment explanation
Indices: 37118--37172 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
37108 CTACAATATT
*
37118 AAAATAATATTAAAAA-AGCGTGA
1 AAAATAATATTAAAAACA-CAT-A
*
37141 AAAA-AATAGTAAAAACACATA
1 AAAATAATATTAAAAACACATA
37162 AAAATAATATT
1 AAAATAATATT
37173 CAAACAACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 5 0.19
22 17 0.63
23 5 0.19
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.22
Consensus pattern (22 bp):
AAAATAATATTAAAAACACATA
Found at i:37198 original size:12 final size:12
Alignment explanation
Indices: 37183--37238 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
37173 CAAACAACCT
*
37183 AAATAACAGCAA
1 AAATAACAACAA
37195 AAATAACAACAA
1 AAATAACAACAA
*
37207 AAATAGCAACAA
1 AAATAACAACAA
* * *
37219 AGACAATAACAA
1 AAATAACAACAA
37231 AAATAACA
1 AAATAACA
37239 GCATCAAAAC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.70, C:0.16, G:0.05, T:0.09
Consensus pattern (12 bp):
AAATAACAACAA
Found at i:37210 original size:24 final size:24
Alignment explanation
Indices: 37183--37250 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
37173 CAAACAACCT
*
37183 AAATAACAGCAAAAATAACAACAA
1 AAATAACAGCAAAAACAACAACAA
* * * *
37207 AAATAGCAACAAAGACAATAACAA
1 AAATAACAGCAAAAACAACAACAA
37231 AAATAACAGCATCAAAACAA
1 AAATAACAGCA--AAAACAA
37251 TTAAAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
24 28 0.82
26 6 0.18
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.09
Consensus pattern (24 bp):
AAATAACAGCAAAAACAACAACAA
Found at i:37226 original size:27 final size:26
Alignment explanation
Indices: 37196--37260 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
37186 TAACAGCAAA
*
37196 AATAACAACAAA-AATAGCAACAAAGAC
1 AATAACAA-AAATAACAGCAACAAA-AC
*
37223 AATAACAAAAATAACAGCATCAAAAC
1 AATAACAAAAATAACAGCAACAAAAC
*
37249 AATTAAAAAAAA
1 AA-TAACAAAAA
37261 CCAAAACAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 7 0.21
27 26 0.79
ACGTcount: A:0.69, C:0.15, G:0.05, T:0.11
Consensus pattern (26 bp):
AATAACAAAAATAACAGCAACAAAAC
Found at i:37296 original size:22 final size:22
Alignment explanation
Indices: 37226--37298 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
37216 CAAAGACAAT
* *
37226 AACAAAAATAACAGCATCAAAAC
1 AACAAAAA-AACAACACCAAAAC
**
37249 AA-TTAAAAA-AA-ACCAAAAC
1 AACAAAAAAACAACACCAAAAC
**
37268 AGTAAAAAAACAACACCAAAAC
1 AACAAAAAAACAACACCAAAAC
37290 AACAAAAAA
1 AACAAAAAA
37299 TAGTAACAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
19 8 0.21
20 6 0.16
21 4 0.11
22 18 0.47
23 2 0.05
ACGTcount: A:0.71, C:0.19, G:0.03, T:0.07
Consensus pattern (22 bp):
AACAAAAAAACAACACCAAAAC
Found at i:37861 original size:23 final size:23
Alignment explanation
Indices: 37826--38922 Score: 1103
Period size: 23 Copynumber: 47.3 Consensus size: 23
37816 ATCTTAATTC
*
37826 TTTAAGTACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
37849 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
37872 TTTAAGCATAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
37895 TTTAAACACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * **
37918 TTTAATCAGAAATCGGATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
37941 TCTAAACACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
37964 TTTGAGCACAAATCATATTAATC
1 TTTAAGCACAAATCACATTAATA
37987 TTTGAA-CACAAATCACATTAATA
1 TTT-AAGCACAAATCACATTAATA
38010 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
** *
38033 TTTAAGCGTAAATTACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
38056 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38079 TTTAAGCATAAACCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38102 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
38125 ATTAAGCAAAAATCACATTAATT
1 TTTAAGCACAAATCACATTAATA
* **
38148 TTTTAGCACAAATCGTATTAATA
1 TTTAAGCACAAATCACATTAATA
*
38171 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38194 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38217 TTTAAGCATAAACCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
38240 TTTGAGCACAAATCAAATTTATA
1 TTTAAGCACAAATCACATTAATA
* **
38263 TTTAAGCATAAAAAACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
38286 TTTGAA-CACAAATCATATTAATA
1 TTT-AAGCACAAATCACATTAATA
* * *
38309 TTTAAGCATAAATAATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38332 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38355 TTTAAGCATAAATAACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38378 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
38401 TTTAAGCATAAATAAAATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * * *
38424 ATTGAGCACAAATCATACTAAAA
1 TTTAAGCACAAATCACATTAATA
* *
38447 TTTAAGCATAAATCACATAAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
38470 TTTGAGCACAAATCATACTAAAA
1 TTTAAGCACAAATCACATTAATA
* *
38493 TTTAAGCATAAATCACATAAATA
1 TTTAAGCACAAATCACATTAATA
*
38516 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
38539 TTTGAA-CACAAATCACATTAATA
1 TTT-AAGCACAAATCACATTAATA
* * * *
38562 TTTAAGTATAAATTACATTTATA
1 TTTAAGCACAAATCACATTAATA
* *
38585 TTTGAA-CACAAATCATATTATTA
1 TTT-AAGCACAAATCACATTAATA
*
38608 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38631 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38654 TTTAAGCATAAACCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38677 TTTGAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38700 TTTAAACATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
38723 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
38746 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
38769 TTTGAGCACAAATCAACATCAATAACA
1 TTTAAGCACAAATC-ACAT---TAATA
* * * *
38796 TTAATATTTG-AGCATA-AATCA-TATTAA
1 TT--TA--AGCA-CAAATCA-CATTAAT-A
*
38823 TATTTAAGCATAAATCACATTAATA
1 --TTTAAGCACAAATCACATTAATA
* *
38848 TTTGAA-CACAAATCATATTAAGA
1 TTT-AAGCACAAATCACATTAATA
* *
38871 CTTAAGCACAAATCTCATTAATA
1 TTTAAGCACAAATCACATTAATA
38894 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
38917 TTTAAG
1 TTTAAG
38923 TATAGATATA
Statistics
Matches: 871, Mismatches: 177, Indels: 52
0.79 0.16 0.05
Matches are distributed among these distances:
22 10 0.01
23 816 0.94
24 12 0.01
25 6 0.01
26 7 0.01
27 9 0.01
29 4 0.00
30 3 0.00
31 4 0.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:37877 original size:46 final size:46
Alignment explanation
Indices: 37826--38922 Score: 1214
Period size: 46 Copynumber: 23.6 Consensus size: 46
37816 ATCTTAATTC
* * * *
37826 TTTAAGTACAAATCACATTAATATTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * * *
37872 TTTAAGCATAAATTATATTAATATTTAAACACAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * ** * * *
37918 TTTAATCAGAAATCGGATTAATATCTAAACACAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * *
37964 TTTGAGCACAAATCATATTAATCTTTGAA-CACAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATATTT-AAGCATAAATCACATTAATA
* * *
38010 TTTAAGCACAAATCACATTAATATTTAAGCGTAAATTACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * *
38056 TTTAAGCATAAATCACATTAATATTTAAGCATAAACCACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * * *
38102 TTTGAGCACAAATCATATTAATAATTAAGCAAAAATCACATTAATT
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* *
38148 TTTTAGCACAAATCGTATTAATATTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* *
38194 TTTGAGCACAAATCATATTAATATTTAAGCATAAACCACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * * **
38240 TTTGAGCACAAATCAAATTTATATTTAAGCATAAAAAACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* *
38286 TTTGAA-CACAAATCATATTAATATTTAAGCATAAATAATATTAATA
1 TTT-AAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* *
38332 TTTGAGCACAAATCATATTAATATTTAAGCATAAATAACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * *
38378 TTTGAGCACAAATCATATTAATATTTAAGCATAAATAAAATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * * * *
38424 ATTGAGCACAAATCATACTAAAATTTAAGCATAAATCACATAAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * * *
38470 TTTGAGCACAAATCATACTAAAATTTAAGCATAAATCACATAAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * *
38516 TTTGAGCACAAATCACATTAATATTTGAA-CACAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATATTT-AAGCATAAATCACATTAATA
* * * * * * * *
38562 TTTAAGTATAAATTACATTTATATTTGAA-CACAAATCATATTATTA
1 TTTAAGCACAAATCATATTAATATTT-AAGCATAAATCACATTAATA
* * * * *
38608 TTTAAGCATAAATCACATTAATATTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * * * * *
38654 TTTAAGCATAAACCACATTAATATTTGAGAACAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * * * *
38700 TTTAAACATAAATCACATTAATATTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * *
38746 TTTAAGCATAAATCACATTAATATTTGAGCACAAATCAACATCAATAACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAG--C--AT-AA-ATC----ACATTAATA
* *
38802 TTTGAGCATAAATCATATTAATATTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
* * * *
38848 TTTGAA-CACAAATCATATTAAGACTTAAGCACAAATCTCATTAATA
1 TTT-AAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
*
38894 TTTAAGCACAAATCACATTAATATTTAAG
1 TTTAAGCACAAATCATATTAATATTTAAG
38923 TATAGATATA
Statistics
Matches: 932, Mismatches: 101, Indels: 36
0.87 0.09 0.03
Matches are distributed among these distances:
45 6 0.01
46 870 0.93
47 6 0.01
48 1 0.00
50 4 0.00
51 4 0.00
52 5 0.01
54 1 0.00
56 35 0.04
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (46 bp):
TTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATA
Found at i:38823 original size:56 final size:55
Alignment explanation
Indices: 38737--38847 Score: 168
Period size: 56 Copynumber: 2.0 Consensus size: 55
38727 AGCACAAATC
*
38737 ACATTAATATTTAAGCATAAATCACATTAATATTTGAGCACAAATCAACATCAATA
1 ACATTAATATTTAAGCATAAATCACATTAATATTTAAGCACAAATC-ACATCAATA
* * * *
38793 ACATTAATATTTGAGCATAAATCATATTAATATTTAAGCATAAATCACATTAATA
1 ACATTAATATTTAAGCATAAATCACATTAATATTTAAGCACAAATCACATCAATA
38848 TTTGAACACA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 8 0.16
56 42 0.84
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (55 bp):
ACATTAATATTTAAGCATAAATCACATTAATATTTAAGCACAAATCACATCAATA
Found at i:38835 original size:79 final size:79
Alignment explanation
Indices: 38704--38862 Score: 273
Period size: 79 Copynumber: 2.0 Consensus size: 79
38694 TTAATATTTA
*
38704 AACATAAATCACATTAATATTTGAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
1 AACATAAATAACATTAATATTTGAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
*
38769 TTTGAGCACAAATC
66 TTTGAACACAAATC
* * *
38783 AACATCAATAACATTAATATTTGAGCATAAATCATATTAATATTTAAGCATAAATCACATTAATA
1 AACATAAATAACATTAATATTTGAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
38848 TTTGAACACAAATC
66 TTTGAACACAAATC
38862 A
1 A
38863 TATTAAGACT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (79 bp):
AACATAAATAACATTAATATTTGAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
TTTGAACACAAATC
Found at i:38868 original size:102 final size:102
Alignment explanation
Indices: 38691--38884 Score: 282
Period size: 102 Copynumber: 1.9 Consensus size: 102
38681 AGAACAAATC
* *
38691 ACATTAATATTTAAACATAAATCACATTAATATTTGAGCACAAATCACATTAATATTTAAGCATA
1 ACATTAATATTTAAACATAAATCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCACA
* * *
38756 AATCACATTAATATTTGAGCACAAATCAACATCAATA
66 AATCACATTAAGACTTAAGCACAAATCAACATCAATA
* * * *
38793 ACATTAATATTTGAGCATAAATCATATTAATATTTAAGCATAAATCACATTAATATTTGAA-CAC
1 ACATTAATATTTAAACATAAATCACATTAATATTTAAGCACAAATCACATTAATATTT-AAGCAC
*
38857 AAATCATATTAAGACTTAAGCACAAATC
65 AAATCACATTAAGACTTAAGCACAAATC
38885 TCATTAATAT
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
102 79 0.98
103 2 0.02
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (102 bp):
ACATTAATATTTAAACATAAATCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCACA
AATCACATTAAGACTTAAGCACAAATCAACATCAATA
Found at i:38890 original size:125 final size:124
Alignment explanation
Indices: 38668--38916 Score: 381
Period size: 125 Copynumber: 2.0 Consensus size: 124
38658 AGCATAAACC
*
38668 ACATTAATATTTGAGAACAAATCACATTAATATTTAAACATAAATCACATTAATATTTGAGCACA
1 ACATTAATATTTGAGAACAAATCACATTAATATTTAAACATAAATCACATTAATATTTGAACACA
* * * *
38733 AATCACATTAATATTTAAGCATAAATCACATTAATATTTGAGCACAAATCAACATCAATA
66 AATCACATTAAGACTTAAGCACAAATCACATTAATATTTAAGCACAAATC-ACATCAATA
* * * *
38793 ACATTAATATTTGAGCATAAATCATATTAATATTTAAGCATAAATCACATTAATATTTGAACACA
1 ACATTAATATTTGAGAACAAATCACATTAATATTTAAACATAAATCACATTAATATTTGAACACA
* * *
38858 AATCATATTAAGACTTAAGCACAAATCTCATTAATATTTAAGCACAAATCACATTAATA
66 AATCACATTAAGACTTAAGCACAAATCACATTAATATTTAAGCACAAATCACATCAATA
38917 TTTAAGTATA
Statistics
Matches: 112, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
124 8 0.07
125 104 0.93
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (124 bp):
ACATTAATATTTGAGAACAAATCACATTAATATTTAAACATAAATCACATTAATATTTGAACACA
AATCACATTAAGACTTAAGCACAAATCACATTAATATTTAAGCACAAATCACATCAATA
Found at i:38915 original size:148 final size:148
Alignment explanation
Indices: 38647--38919 Score: 420
Period size: 148 Copynumber: 1.8 Consensus size: 148
38637 CACAAATCAT
* *
38647 ATTAATATTTAAGCATAAACCACATTAATATTTGAGAACAAATCACATTAATATTTAAACATAAA
1 ATTAATATTTAAGCATAAACCACATTAATATTTAAGAACAAATCACATTAATATTTAAACACAAA
* * * *
38712 TCACATTAATATTTGAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATATTTGAGCA
66 TCACATTAAGACTTAAGCACAAATCACATTAATATTTAAGCACAAATCACATTAATATTTGAGCA
38777 CAAATCAACATCAATAAC
131 CAAATCAACATCAATAAC
* * * * * *
38795 ATTAATATTTGAGCATAAATCATATTAATATTTAAGCATAAATCACATTAATATTTGAACACAAA
1 ATTAATATTTAAGCATAAACCACATTAATATTTAAGAACAAATCACATTAATATTTAAACACAAA
* *
38860 TCATATTAAGACTTAAGCACAAATCTCATTAATATTTAAGCACAAATCACATTAATATTT
66 TCACATTAAGACTTAAGCACAAATCACATTAATATTTAAGCACAAATCACATTAATATTT
38920 AAGTATAGAT
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
148 111 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (148 bp):
ATTAATATTTAAGCATAAACCACATTAATATTTAAGAACAAATCACATTAATATTTAAACACAAA
TCACATTAAGACTTAAGCACAAATCACATTAATATTTAAGCACAAATCACATTAATATTTGAGCA
CAAATCAACATCAATAAC
Found at i:57348 original size:15 final size:15
Alignment explanation
Indices: 57325--57359 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
57315 AGATTAAAAT
* *
57325 TTAATATTATAATGG
1 TTAAAATTATAATGA
57340 TTAAAATTATAATGA
1 TTAAAATTATAATGA
57355 TTAAA
1 TTAAA
57360 TTTGAAAAGA
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:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TTAAAATTATAATGA
Found at i:59099 original size:52 final size:52
Alignment explanation
Indices: 58974--59257 Score: 372
Period size: 52 Copynumber: 5.4 Consensus size: 52
58964 TTCATTTAAA
* * * ** *
58974 ACTCACGAAGACA-TATAGTCAACGGACCTCTTTTTCCGTAAAGGAATTCATGT
1 ACTCACGATGACACT-TAGTCATCGGACCTCATAATCCGTAAAGG-ATTCATAT
* * *
59027 ACTCACGATGACACTCAGTCATCGGACCTTACAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
* *
59079 ACTCACGATGACACTTAGTCATCGAACCTCATAATCCATAAAGGATTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
* * *
59131 ACTCACGATAACACTTAGTCATTGGACCTCATAATCCGTAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
* * * *
59183 ACTCACGATGACACTTAGTCATAGGACCTTATAATCAGTAAAGTATTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
*
59235 ACTCACGATGACACTTAATCATC
1 ACTCACGATGACACTTAGTCATC
59258 ACACCCTTTT
Statistics
Matches: 203, Mismatches: 27, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
52 168 0.83
53 34 0.17
54 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (52 bp):
ACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
Found at i:60178 original size:24 final size:20
Alignment explanation
Indices: 60126--60167 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
60116 GCTTTTATAA
60126 TTAACC-TAATTAATCCACT
1 TTAACCTTAATTAATCCACT
60145 TTAACCTTAATTAATCTCACT
1 TTAACCTTAATTAATC-CACT
60166 TT
1 TT
60168 TAAGCACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
20 9 0.43
21 6 0.29
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAACCTTAATTAATCCACT
Found at i:66100 original size:4 final size:4
Alignment explanation
Indices: 66091--66125 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
66081 ATGCTATAGT
66091 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
66126 ATGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:66138 original size:14 final size:14
Alignment explanation
Indices: 66095--66129 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
66085 TATAGTTATG
66095 TATGTATGTATGTA
1 TATGTATGTATGTA
66109 TGTATGTATGTATGTA
1 --TATGTATGTATGTA
66125 TATGT
1 TATGT
66130 GTGTGTGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
16 14 0.74
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (14 bp):
TATGTATGTATGTA
Found at i:68680 original size:26 final size:26
Alignment explanation
Indices: 68631--68701 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
68621 GTTACACCTT
* * *
68631 GAGCCGGTGACT-AATAGTAGGCTTC
1 GAGCCGGTGATTAAATAGCAAGCTTC
68656 GAGCCGGTGATTAAATAGCAAGCTTC
1 GAGCCGGTGATTAAATAGCAAGCTTC
* *
68682 GAGTCGATGATTAAATAGCA
1 GAGCCGGTGATTAAATAGCA
68702 GGCCATGAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 11 0.28
26 29 0.73
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (26 bp):
GAGCCGGTGATTAAATAGCAAGCTTC
Found at i:73555 original size:34 final size:34
Alignment explanation
Indices: 73512--73576 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
73502 TGAAACAAGG
73512 AGTGAATTTATAACCGCCACCTCTAAGTATAGGT
1 AGTGAATTTATAACCGCCACCTCTAAGTATAGGT
* *
73546 AGTGAATTTATAACCTCTACCTCTAAGTATA
1 AGTGAATTTATAACCGCCACCTCTAAGTATA
73577 AGTAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (34 bp):
AGTGAATTTATAACCGCCACCTCTAAGTATAGGT
Found at i:75449 original size:51 final size:51
Alignment explanation
Indices: 75343--75617 Score: 365
Period size: 51 Copynumber: 5.3 Consensus size: 51
75333 TAATACTCTT
** * *
75343 GATGACA-TATAGTCATCGGACCCCTTTGTTCCGTATAGGAATTCATATACTCAC
1 GATGACACT-TAGTCATCGGA--CCTTTAATCCGTAAAGG-ATTCATTTACTCAC
* * * * *
75397 GATGACACTGAGTCATCGAACCTTTAATTCGTCATGGATTCATTTACTCAC
1 GATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCAC
*
75448 GATGACACTTAGTCATCGGACCTTTAATCCGTAAATGATTCATTTACTCAC
1 GATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCAC
*
75499 GATGACACTTAGTCATCGGACCTTTAATCCTTAAAGGATTCATTTACAT-AC
1 GATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTAC-TCAC
* * *
75550 GATGACACTTATTCATCGGACCTTTAATCCTTAAAGGATTCATTTACTCAT
1 GATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCAC
75601 GATGACACTTAGTCATC
1 GATGACACTTAGTCATC
75618 AGGCTCTTTC
Statistics
Matches: 198, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
50 1 0.01
51 168 0.85
52 12 0.06
54 16 0.08
55 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
GATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCAC
Found at i:79621 original size:94 final size:94
Alignment explanation
Indices: 79447--79954 Score: 648
Period size: 94 Copynumber: 5.4 Consensus size: 94
79437 TTTTCATATT
* * * * *
79447 CTCGTCAGCTTAGTCTGAGCAGCATCGT-TA--GGGAATAGTTATATGCACAGATACCGTATTGA
1 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGCACAGATTCCGTATCGA
*
79509 TGGCTAAGGTACCACATATGTTGCGAGTC
66 TGGCTAAGGTACCGCATATGTTGCGAGTC
* * *
79538 CTCGTTAGCTTAGTCTGAGCAGCATCGTATACTGGTAACAGTTATATGCATAGATTCCGTATCGA
1 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGCACAGATTCCGTATCGA
* * *
79603 TAGCTAAGCTACCGCATATGTTACGAGTC
66 TGGCTAAGGTACCGCATATGTTGCGAGTC
* * * * * *
79632 CTCGTCAGCTTAGTGGGAGCAGTATTGTATACTGGTAAGAATTATATGCATAGATAT-CGTATCG
1 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGCACAGAT-TCCGTATCG
* * *
79696 ATGGTTGAGGTACCGCATATGTTGCAAGTC
65 ATGGCTAAGGTACCGCATATGTTGCGAGTC
*
79726 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGCACAGATACCGTATCGA
1 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGCACAGATTCCGTATCGA
*
79791 TGGCTGAGGTACCGCATATGTTGCGAGTC
66 TGGCTAAGGTACCGCATATGTTGCGAGTC
* * * * *
79820 GTCGTCAGCTTAGTATGAGCAGCATTGTATACTGGTAACAGTTATATGTACAAATAT-CGTATCG
1 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGCACAGAT-TCCGTATCG
* * *
79884 ATGGCTGAGGCACCGCATATGTTGTGAGTC
65 ATGGCTAAGGTACCGCATATGTTGCGAGTC
* * * *
79914 CTTGTCAGCTTAGTGTGAGTAGCATCATATACCGGTAACAG
1 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAG
79955 AAATGACATT
Statistics
Matches: 364, Mismatches: 47, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
91 27 0.07
92 2 0.01
94 334 0.92
95 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (94 bp):
CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGCACAGATTCCGTATCGA
TGGCTAAGGTACCGCATATGTTGCGAGTC
Found at i:99653 original size:93 final size:93
Alignment explanation
Indices: 99494--99869 Score: 644
Period size: 93 Copynumber: 4.0 Consensus size: 93
99484 CAATCGAGAG
*
99494 CTTACACAAAACGAGCTCCAATCCGAAGATCCCACCGAGGCTTCTCTGTCACCCAAGACTGAAAC
1 CTTACACAAAACGAGCTCCAATCCGAAGATCCCGCCGAGGCTTCTCTGTCACCCAAGACTGAAAC
99559 TGTTGAGGTCTCTGATATGGACATACAC
66 TGTTGAGGTCTCTGATATGGACATACAC
*
99587 CTTACACAAAACGAGCTCCAATCCGAAGATCCCGCCGAGGCTTCTCTGTCACCCAAGACTCAAAC
1 CTTACACAAAACGAGCTCCAATCCGAAGATCCCGCCGAGGCTTCTCTGTCACCCAAGACTGAAAC
*
99652 TGTTGAGGTCTCTGACATGGACATACAC
66 TGTTGAGGTCTCTGATATGGACATACAC
* * * * *
99680 CTTACACAAAATGAGCTCCCATCTGAAGATCCCGCCGAGGCTTCTTTGTCACCCAAGACTAAAAC
1 CTTACACAAAACGAGCTCCAATCCGAAGATCCCGCCGAGGCTTCTCTGTCACCCAAGACTGAAAC
*
99745 TGTTGAGGTCTCTGATATGGACATGCAC
66 TGTTGAGGTCTCTGATATGGACATACAC
*
99773 CTTACACAAAACGAGCTCCAATCCGAAGATCCTGCCGAGGCTTCTCTGTCACCCAAGACTGAAAC
1 CTTACACAAAACGAGCTCCAATCCGAAGATCCCGCCGAGGCTTCTCTGTCACCCAAGACTGAAAC
* *
99838 TGTCGAGGTCTCCGATATGGACATACAC
66 TGTTGAGGTCTCTGATATGGACATACAC
99866 CTTA
1 CTTA
99870 AAGAAACAAA
Statistics
Matches: 264, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 264 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (93 bp):
CTTACACAAAACGAGCTCCAATCCGAAGATCCCGCCGAGGCTTCTCTGTCACCCAAGACTGAAAC
TGTTGAGGTCTCTGATATGGACATACAC
Found at i:100568 original size:27 final size:27
Alignment explanation
Indices: 100505--100569 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
100495 TTATCTTTTA
100505 AAATTATAAATATAGTTTTAAATTATT
1 AAATTATAAATATAGTTTTAAATTATT
*
100532 AAATTAATAAAT-T-GTTTTTCAATTATT
1 AAATT-ATAAATATAG-TTTTAAATTATT
*
100559 ATCATTATAAA
1 A-AATTATAAA
100570 CAATTAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 1 0.03
27 23 0.70
28 9 0.27
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (27 bp):
AAATTATAAATATAGTTTTAAATTATT
Found at i:108007 original size:20 final size:20
Alignment explanation
Indices: 107968--108007 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
107958 CGATCCAAGA
*
107968 GTCTCTTACCAGCCAGAAGG
1 GTCTCTTACCAGCCAAAAGG
* *
107988 GTCTCTTGCCAGCTAAAAGG
1 GTCTCTTACCAGCCAAAAGG
108008 ACTTTTGGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.23
Consensus pattern (20 bp):
GTCTCTTACCAGCCAAAAGG
Found at i:115128 original size:28 final size:28
Alignment explanation
Indices: 115095--115155 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
115085 AAAATGAGAC
* * *
115095 TTTGGATGCCCGAGGGTAAAATGGTAAT
1 TTTGGATGCCCGAGGGCAAAACGGGAAT
* *
115123 TTTGGATTCTCGAGGGCAAAACGGGAAT
1 TTTGGATGCCCGAGGGCAAAACGGGAAT
115151 TTTGG
1 TTTGG
115156 GAAAATTTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.33, T:0.30
Consensus pattern (28 bp):
TTTGGATGCCCGAGGGCAAAACGGGAAT
Found at i:115350 original size:29 final size:30
Alignment explanation
Indices: 115287--115450 Score: 160
Period size: 30 Copynumber: 5.5 Consensus size: 30
115277 TTTTGGGGTT
* * *
115287 AAAAATGGAAATTTTGG-AGATTC-AGGGTAA
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGT-C
115317 AAAAATGGAATTTTTGGAAGTTTCGA-GTC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
* *
115346 GAAAATTGAATTTTTGGAAGTTTCG-GGTTC
1 AAAAATGGAATTTTTGGAAGTTTCGAGG-TC
115376 AAAAATGGAATTTTTGGAAG-TTCGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGTC
* * *
115405 AAAAATGAAACTTTTGGAAGTTTTGAGGTC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
* *
115435 AAAAATGAAAATTTTG
1 AAAAATGGAATTTTTG
115451 AACGTTTAGG
Statistics
Matches: 115, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
29 49 0.43
30 58 0.50
31 7 0.06
32 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGTC
Found at i:115410 original size:59 final size:58
Alignment explanation
Indices: 115286--115450 Score: 167
Period size: 59 Copynumber: 2.8 Consensus size: 58
115276 TTTTTGGGGT
* * **
115286 TAAAAATGGAAATTTTGG-AGATTCAGGGTAAAAAAATGGAATTTTTGGAAGTTTCGAG
1 TAAAAATTGAAATTTTGGAAGTTTC-GGGTTCAAAAATGGAATTTTTGGAAGTTTCGAG
* *
115344 TCGAAAATTGAATTTTTGGAAGTTTCGGGTTCAAAAATGGAATTTTTGGAAG-TTCGAGGG
1 T-AAAAATTGAAATTTTGGAAGTTTCGGGTTCAAAAATGGAATTTTTGGAAGTTTCGA--G
* * *
115404 TAAAAA-TGAAACTTTTGGAAGTTTTGAGG-TCAAAAATGAAAATTTTG
1 TAAAAATTGAAA-TTTTGGAAGTTTCG-GGTTCAAAAATGGAATTTTTG
115451 AACGTTTAGG
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
58 10 0.11
59 71 0.79
60 9 0.10
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (58 bp):
TAAAAATTGAAATTTTGGAAGTTTCGGGTTCAAAAATGGAATTTTTGGAAGTTTCGAG
Found at i:115464 original size:59 final size:59
Alignment explanation
Indices: 115357--115470 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 59
115347 AAAATTGAAT
* * *
115357 TTTTGGAAGTTTCGGGTTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGAAAC
1 TTTTGGAAGTTTCGGGTTCAAAAATGAAAATTTTGGAAGTTAGAGGGTAAAAATGAAAC
*
115416 TTTTGGAAGTTTTGAGG-TCAAAAATGAAAATTTT-GAACGTTTAG-GGGTAAAAATG
1 TTTTGGAAGTTTCG-GGTTCAAAAATGAAAATTTTGGAA-G-TTAGAGGGTAAAAATG
115471 TGATTTTTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
58 3 0.06
59 40 0.83
60 5 0.10
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.33
Consensus pattern (59 bp):
TTTTGGAAGTTTCGGGTTCAAAAATGAAAATTTTGGAAGTTAGAGGGTAAAAATGAAAC
Found at i:117430 original size:17 final size:17
Alignment explanation
Indices: 117410--117463 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
117400 TTATTTCAAC
117410 TTTAAACCAAATTTAAA
1 TTTAAACCAAATTTAAA
117427 TTT-AACCAAATTTAAA
1 TTTAAACCAAATTTAAA
***
117443 TTTAAAATGAATTTAAA
1 TTTAAACCAAATTTAAA
117460 TTTA
1 TTTA
117464 GAAATAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 16 0.48
17 17 0.52
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTAAACCAAATTTAAA
Found at i:117435 original size:16 final size:16
Alignment explanation
Indices: 117414--117447 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
117404 TTCAACTTTA
117414 AACCAAATTTAAATTT
1 AACCAAATTTAAATTT
117430 AACCAAATTTAAATTT
1 AACCAAATTTAAATTT
117446 AA
1 AA
117448 AATGAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (16 bp):
AACCAAATTTAAATTT
Found at i:117477 original size:18 final size:17
Alignment explanation
Indices: 117387--117483 Score: 72
Period size: 17 Copynumber: 5.6 Consensus size: 17
117377 ATTTTAAAGT
* *
117387 TTTAAGTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
* **
117403 TTTCAACTTTAAACCAAA
1 TTT-AAATTTAAAATAAA
**
117421 TTTAAATTT-AACCAAA
1 TTTAAATTTAAAATAAA
*
117437 TTTAAATTTAAAATGAA
1 TTTAAATTTAAAATAAA
117454 TTTAAATTTAGAAATAAA
1 TTTAAATTTA-AAATAAA
*
117472 TCTAAAATTTAA
1 T-TTAAATTTAA
117484 TCTAAACTCA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
16 19 0.29
17 27 0.41
18 12 0.18
19 8 0.12
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:117599 original size:22 final size:23
Alignment explanation
Indices: 117574--117621 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
117564 ATTAAAATAA
117574 TATTTGTGTGTATGTAT-TTATT
1 TATTTGTGTGTATGTATATTATT
* * *
117596 TA-TTGTTTGTTTGTTTATTATT
1 TATTTGTGTGTATGTATATTATT
117618 TATT
1 TATT
117622 AACATTGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.52
22 9 0.43
23 1 0.05
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.69
Consensus pattern (23 bp):
TATTTGTGTGTATGTATATTATT
Found at i:117654 original size:24 final size:23
Alignment explanation
Indices: 117627--117713 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 23
117617 TTATTAACAT
117627 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* * *
117651 TGTTCATGAATATGTTCATTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
117674 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCAATTAA
**
117697 -GTTAAATGAACATGTTC
1 TGTT-CGTGAACATGTTC
117714 GTGACCATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.58
24 19 0.36
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:122500 original size:13 final size:13
Alignment explanation
Indices: 122482--122510 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
122472 AAATAAATAA
122482 AAATCATATTTCT
1 AAATCATATTTCT
122495 AAATCATATTTCT
1 AAATCATATTTCT
122508 AAA
1 AAA
122511 GAAGAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATCATATTTCT
Found at i:125581 original size:16 final size:15
Alignment explanation
Indices: 125560--125589 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
125550 AAAAGCAAAA
125560 AAAATTTATGTGAAAG
1 AAAATTTAT-TGAAAG
125576 AAAATTTATTGAAA
1 AAAATTTATTGAAA
125590 ACACAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (15 bp):
AAAATTTATTGAAAG
Found at i:127356 original size:23 final size:23
Alignment explanation
Indices: 127324--127372 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
127314 AAATTAGGCA
*
127324 AAAAAACATTAATTTCAAGAAAG
1 AAAAAACATTAATTCCAAGAAAG
* *
127347 AAAAAGCATTAATTCCAAGAAGG
1 AAAAAACATTAATTCCAAGAAAG
127370 AAA
1 AAA
127373 TTAGGCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.18
Consensus pattern (23 bp):
AAAAAACATTAATTCCAAGAAAG
Found at i:132894 original size:21 final size:21
Alignment explanation
Indices: 132870--132911 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
132860 GTTGATTGAC
132870 GTTTTCCATTGTAATACGGTT
1 GTTTTCCATTGTAATACGGTT
132891 GTTTTCCATTGTAATACGGTT
1 GTTTTCCATTGTAATACGGTT
132912 AAATTTGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (21 bp):
GTTTTCCATTGTAATACGGTT
Found at i:134044 original size:40 final size:41
Alignment explanation
Indices: 133990--134068 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 41
133980 GAGGGTATTG
*
133990 TGGGAGGTACTCGTGGAAGGTTACCTTTAGGAATCATGCTA
1 TGGGAGGTACTCGTGGAAGGTTACCATTAGGAATCATGCTA
* *
134031 TGGGTGGTA-TCGTGGGAGGTTACCATTAGGAATCATGC
1 TGGGAGGTACTCGTGGAAGGTTACCATTAGGAATCATGC
134069 CGAGGGTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 27 0.77
41 8 0.23
ACGTcount: A:0.23, C:0.14, G:0.34, T:0.29
Consensus pattern (41 bp):
TGGGAGGTACTCGTGGAAGGTTACCATTAGGAATCATGCTA
Found at i:134085 original size:40 final size:40
Alignment explanation
Indices: 134001--134090 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
133991 GGGAGGTACT
* * * * *
134001 CGTGGAAGGTTACCTTTAGGAATCATGCTATGGGTGGTAT
1 CGTGGGAGGTTACCATTAGGAATCATGCGATGGGTGATAC
134041 CGTGGGAGGTTACCATTAGGAATCATGCCGA-GGGTGATAC
1 CGTGGGAGGTTACCATTAGGAATCATG-CGATGGGTGATAC
134081 CGTGGGAGGT
1 CGTGGGAGGT
134091 ACTTGTGGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 42 0.95
41 2 0.05
ACGTcount: A:0.22, C:0.14, G:0.37, T:0.27
Consensus pattern (40 bp):
CGTGGGAGGTTACCATTAGGAATCATGCGATGGGTGATAC
Found at i:141171 original size:137 final size:137
Alignment explanation
Indices: 140923--141198 Score: 498
Period size: 137 Copynumber: 2.0 Consensus size: 137
140913 TTTCAGTTTA
* *
140923 ATTCCTTCCTTCTGTTCATACATGAAGAAAAGTGTTTTGTCTTGAAATTGATTCGTGGATTCTTT
1 ATTCCCTCCTTCTGTTCACACATGAAGAAAAGTGTTTTGTCTTGAAATTGATTCGTGGATTCTTT
*
140988 TCATTTTGAGTCAATCCTCTGTTGATCATTTAGATGCTCATAATGATTGGTCTTTGGGTGTTGGA
66 TCATTTTGAGTCAATCCTCTATTGATCATTTAGATGCTCATAATGATTGGTCTTTGGGTGTTGGA
141053 GGATCAC
131 GGATCAC
141060 ATTCCCTCCTTCTGTTCACACATGAAGAAAAGTGTTTTGTCTTGAAATTGATTCGTGGATTCTTT
1 ATTCCCTCCTTCTGTTCACACATGAAGAAAAGTGTTTTGTCTTGAAATTGATTCGTGGATTCTTT
* * *
141125 TCATTTTGATTCAATCCTCTATTGATCATTTAGATGTTCATCATGATTGGTCTTTGGGTGTTGGA
66 TCATTTTGAGTCAATCCTCTATTGATCATTTAGATGCTCATAATGATTGGTCTTTGGGTGTTGGA
141190 GGATCAC
131 GGATCAC
141197 AT
1 AT
141199 CATATTTTTG
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 133 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (137 bp):
ATTCCCTCCTTCTGTTCACACATGAAGAAAAGTGTTTTGTCTTGAAATTGATTCGTGGATTCTTT
TCATTTTGAGTCAATCCTCTATTGATCATTTAGATGCTCATAATGATTGGTCTTTGGGTGTTGGA
GGATCAC
Done.