Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014183.1 Kokia drynarioides strain JFW-HI SEQ_129216, 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: 52496
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:6459 original size:49 final size:49
Alignment explanation
Indices: 6332--6867 Score: 351
Period size: 49 Copynumber: 10.9 Consensus size: 49
6322 TCACTAGAAG
* ** * * *
6332 GATATAGAGGGAAAGGTTTAAGTCGCAACGGTAAACCTTGTACCTCAGAA
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAATCTAGTACCAC-GAA
** * **
6382 G--ATGAGATGGGAAATATTTGAG-CTGCAACAACGAATCTAGTACCACGAA
1 GATATG-GA-GGGAAAGGTTTAAGTC-GCAACGGCGAATCTAGTACCACGAA
* * *
6431 GATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAACCTTA-TACCTCAGAA
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAATC-TAGTACCAC-GAA
* * * ** * * * *
6481 G-CATGAAGGAAAATATTTAAGCCGCAACGACGAATCCAATACCACGAA
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAATCTAGTACCACGAA
* * * * *
6529 GATATGGAGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTACCTC-AA
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAATCTAGTACCACGAA
* * * * *
6577 AAGATGAGATGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACGAA
1 GATATG-GA-GGGAAAGGTTTAAGTCGCAACGGCGAATCTAGTACCACGAA
* * * *
6628 GATATGGAGGGAAAGGTTTAAGTAGCAACGGTGAACCTTGTACCTTA-GAA
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAATCTAGTACC--ACGAA
* * * * *
6678 G-CATGAAGGGAAAGATTTAAG-CAGTAACGGCGAATCCAGTACCACGAA
1 GATATGGAGGGAAAGGTTTAAGTC-GCAACGGCGAATCTAGTACCACGAA
* * * * *
6726 GATATGGGGGGAAAGGTTTAAGTCGCAATGGCG-ACCTTGTACCTCAGAA
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAATCTAGTACCAC-GAA
* * * *
6775 G--ATGAGATAGGAAAGATTTAAG-CAGCAACGGTGAATCTAGTACCACGAT
1 GATATG-GA-GGGAAAGGTTTAAGTC-GCAACGGCGAATCTAGTACCACGAA
* * * *
6824 GATATGGAGGGAAAAGTTTAAGTCACAACGGCGAACCTTGTACC
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAATCTAGTACC
6868 TTAGAAACAT
Statistics
Matches: 365, Mismatches: 94, Indels: 55
0.71 0.18 0.11
Matches are distributed among these distances:
47 4 0.01
48 27 0.07
49 236 0.65
50 85 0.23
51 13 0.04
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.20
Consensus pattern (49 bp):
GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAATCTAGTACCACGAA
Found at i:6542 original size:98 final size:98
Alignment explanation
Indices: 6332--6903 Score: 729
Period size: 98 Copynumber: 5.8 Consensus size: 98
6322 TCACTAGAAG
* ** *
6332 GATATAGAGGGAAAGGTTTAAGTCGCAACGGTAAACCTTGTACCTCAGAAGATGAGATGGGAAAT
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGATGAGA-GGGAAAG
* * **
6397 ATTTGAGCTGCAACAACGAATCTAGTACCACGAA
65 ATTTAAGCCGCAACGGCGAATCTAGTACCACGAA
* * * *
6431 GATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAACCTTATACCTCAGAAGCATGA-AGGAAAAT
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-ATGAGAGGGAAAG
* * *
6495 ATTTAAGCCGCAACGACGAATCCAATACCACGAA
65 ATTTAAGCCGCAACGGCGAATCTAGTACCACGAA
* * *
6529 GATATGGAGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTACCTCAAAAGATGAGATGGGAAAG
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGATGAGA-GGGAAAG
*
6594 ATTTAAGCCGCAACGGTGAATCTAGTACCACGAA
65 ATTTAAGCCGCAACGGCGAATCTAGTACCACGAA
* * *
6628 GATATGGAGGGAAAGGTTTAAGTAGCAACGGTGAACCTTGTACCTTAGAAGCATGA-AGGGAAAG
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-ATGAGAGGGAAAG
* * *
6692 ATTTAAGCAGTAACGGCGAATCCAGTACCACGAA
65 ATTTAAGCCGCAACGGCGAATCTAGTACCACGAA
* * *
6726 GATATGGGGGGAAAGGTTTAAGTCGCAATGGCG-ACCTTGTACCTCAGAAGATGAGATAGGAAAG
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGATGAGA-GGGAAAG
* * *
6790 ATTTAAGCAGCAACGGTGAATCTAGTACCACGAT
65 ATTTAAGCCGCAACGGCGAATCTAGTACCACGAA
* * * *
6824 GATATGGAGGGAAAAGTTTAAGTCACAACGGCGAACCTTGTACCTTAGAAACATGA-AGGGAAAG
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAG-AAGATGAGAGGGAAAG
* *
6888 ATTGAAGCCACAACGG
65 ATTTAAGCCGCAACGG
6904 TGAGTTAGAT
Statistics
Matches: 415, Mismatches: 50, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
96 4 0.01
97 21 0.05
98 232 0.56
99 144 0.35
100 14 0.03
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.20
Consensus pattern (98 bp):
GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGATGAGAGGGAAAGA
TTTAAGCCGCAACGGCGAATCTAGTACCACGAA
Found at i:6680 original size:197 final size:197
Alignment explanation
Indices: 6332--6902 Score: 849
Period size: 197 Copynumber: 2.9 Consensus size: 197
6322 TCACTAGAAG
* * *
6332 GATATAGAGGGAAAGGTTTAAGTCGCAACGGTAAACCTTGTACCTCAGAAGATGAGATGGGAAAT
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCAAACCTTGTACCTCAGAAGATGAGATGGGAAAG
* * *** *
6397 ATTTGAGCTGCAACAACGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGG
66 ATTTAAGCAGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTAGCAACGG
* * * *
6462 TGAACCTTATACCTCAGAAGCATGAAGGAAAATATTTAAGCCGCAACGACGAATCCAATACCACG
131 TGAACCTTGTACCTTAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAATACCACG
6527 AA
196 AA
* *
6529 GATATGGAGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTACCTCAAAAGATGAGATGGGAAAG
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCAAACCTTGTACCTCAGAAGATGAGATGGGAAAG
*
6594 ATTTAAGCCGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTAGCAACGG
66 ATTTAAGCAGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTAGCAACGG
* * * *
6659 TGAACCTTGTACCTTAGAAGCATGAAGGGAAAGATTTAAGCAGTAACGGCGAATCCAGTACCACG
131 TGAACCTTGTACCTTAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAATACCACG
6724 AA
196 AA
* * * *
6726 GATATGGGGGGAAAGGTTTAAGTCGCAATGGC-GACCTTGTACCTCAGAAGATGAGATAGGAAAG
1 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCAAACCTTGTACCTCAGAAGATGAGATGGGAAAG
* *
6790 ATTTAAGCAGCAACGGTGAATCTAGTACCACGATGATATGGAGGGAAAAGTTTAAGTCA-CAACG
66 ATTTAAGCAGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGT-AGCAACG
* * * *
6854 GCGAACCTTGTACCTTAGAAACATGAAGGGAAAGATTGAAGCCACAACG
130 GTGAACCTTGTACCTTAGAAGCATGAAGGGAAAGATTTAAGCCGCAACG
6903 GTGAGTTAGA
Statistics
Matches: 339, Mismatches: 34, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
196 131 0.39
197 208 0.61
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.20
Consensus pattern (197 bp):
GATATGGAGGGAAAGGTTTAAGTCGCAACGGCAAACCTTGTACCTCAGAAGATGAGATGGGAAAG
ATTTAAGCAGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTAGCAACGG
TGAACCTTGTACCTTAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAATACCACG
AA
Found at i:7006 original size:49 final size:49
Alignment explanation
Indices: 6917--7014 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
6907 GTTAGATACA
* * * *
6917 ATGAAGATTTTAAGGGAAAGTTTATGACCGCGATGACGAACCCGGTACC
1 ATGAAGATTTAAAGGGAAAGGTTATGACCGCGAAGACGAACCCAGTACC
*
6966 ATGAAGATTTAAAGGGAAAGGTTATGATCGCGACAG-CGAACCCAGTACC
1 ATGAAGATTTAAAGGGAAAGGTTATGACCGCGA-AGACGAACCCAGTACC
7015 TTAGAAACAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 42 0.98
50 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (49 bp):
ATGAAGATTTAAAGGGAAAGGTTATGACCGCGAAGACGAACCCAGTACC
Found at i:7219 original size:97 final size:97
Alignment explanation
Indices: 7095--7464 Score: 408
Period size: 97 Copynumber: 3.8 Consensus size: 97
7085 TCAAATCTAC
* * * * *
7095 AATAGCAAGTCTTTATCTGTCTGAAGTTGCAGTAAGAGCAAGATGAAACTTCAATGTTAAATTCT
1 AATAGCAAGTCTTTATCTATCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
*
7160 ATCCTCTTGAAGTTGTAGTAAAGTTGGATTAA
66 ATCCTCTTGAAGTTGCAGTAAAGTTGGATTAA
*
7192 AATAGCAAGTCTTTATCTATCTTAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
1 AATAGCAAGTCTTTATCTATCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
* *
7257 ATCCTCTTAAAGTTGCAATAAAGTTGGATTAAAAACA
66 ATCCTCTTGAAGTTGCAGTAAAGTTGGATT----A-A
* * *
7294 AATAGCAAGTATTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCT
1 AATAGCAAGTCTTTATCTATCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
* * * *
7359 ATCTTCCTGAAGTTGCAGTGAAGTTGAATTAA
66 ATCCTCTTGAAGTTGCAGTAAAGTTGGATTAA
*** ** * * * * *
7391 AA-A-CAA--AAATA-AAAACTGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAACATTAAACCCT
1 AATAGCAAGTCTTTATCTATCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
* *
7451 ATCTTCCTGAAGTT
66 ATCCTCTTGAAGTT
7465 ACGATGAAGT
Statistics
Matches: 240, Mismatches: 28, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
92 56 0.23
93 3 0.01
95 3 0.01
96 1 0.00
97 89 0.37
98 1 0.00
101 1 0.00
102 86 0.36
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (97 bp):
AATAGCAAGTCTTTATCTATCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
ATCCTCTTGAAGTTGCAGTAAAGTTGGATTAA
Found at i:7336 original size:102 final size:102
Alignment explanation
Indices: 7095--7397 Score: 427
Period size: 102 Copynumber: 3.0 Consensus size: 102
7085 TCAAATCTAC
* * * * *
7095 AATAGCAAGTCTTTATCTGTCTGAAGTTGCAGTAAGAGCAAGATGAAACTTCAATGTTAAATTCT
1 AATAGCAAGTCTTTATCTATCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
*
7160 ATCCTCTTGAAGTTGTAGTAAAGTTGGATT----A-A
66 ATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAACA
*
7192 AATAGCAAGTCTTTATCTATCTTAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
1 AATAGCAAGTCTTTATCTATCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
* *
7257 ATCCTCTTAAAGTTGCAATAAAGTTGGATTAAAAACA
66 ATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAACA
* * *
7294 AATAGCAAGTATTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCT
1 AATAGCAAGTCTTTATCTATCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
* * * *
7359 ATCTTCCTGAAGTTGCAGTGAAGTTGAATTAAAAACA
66 ATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAACA
7396 AA
1 AA
7398 AATAAAAACT
Statistics
Matches: 182, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
97 86 0.47
101 1 0.01
102 95 0.52
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (102 bp):
AATAGCAAGTCTTTATCTATCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCT
ATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAACA
Found at i:7369 original size:51 final size:50
Alignment explanation
Indices: 7215--7377 Score: 127
Period size: 51 Copynumber: 3.2 Consensus size: 50
7205 TATCTATCTT
* * *
7215 AAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTA
1 AAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTAT-CTCCTG
* *** * *** *
7266 AAGTTGCAATAA-AGTTGGATTAA-AAACAA-ATAGCAAGTAT-TTATCTCTCTG
1 AAGTTGCAGTAAGAGCAAGATGAAGCTTCAACAT--CAA--ATCCTATCTC-CTG
7317 AAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTATCTTCCTG
1 AAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTATC-TCCTG
7368 AAGTTGCAGT
1 AAGTTGCAGT
7378 GAAGTTGAAT
Statistics
Matches: 81, Mismatches: 21, Indels: 20
0.66 0.17 0.16
Matches are distributed among these distances:
48 1 0.01
49 3 0.04
50 15 0.19
51 43 0.53
52 14 0.17
53 3 0.04
54 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (50 bp):
AAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTATCTCCTG
Found at i:15552 original size:7 final size:7
Alignment explanation
Indices: 15532--15564 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
15522 ACTAACTTTT
15532 AATTCAA
1 AATTCAA
15539 TAA-TCAA
1 -AATTCAA
15546 AATTCAA
1 AATTCAA
15553 AATTCAA
1 AATTCAA
15560 AATTC
1 AATTC
15565 CATATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 2 0.08
7 20 0.83
8 2 0.08
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (7 bp):
AATTCAA
Found at i:17822 original size:52 final size:52
Alignment explanation
Indices: 17739--17925 Score: 243
Period size: 52 Copynumber: 3.6 Consensus size: 52
17729 ATTTCAATTA
* * *
17739 ATACTCATGATGACATATAGTCATC-GAACCTCATAATCTGTAAAAGATCCAT
1 ATACTCACGATGACACATAGTCATCAG-ACCTCATAATCTGTAAAGGATCCAT
* *
17791 ATACTCACGATGACACATAGTCATTAGACCTCATAATTTGTAAAGGA-CTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCTGTAAAGGATC-CAT
* * * ** *
17843 ATACTCACGATGACACATAGTTATCGGACCTCATTATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCTGTAAAGGATCCAT
17895 ATACTCACGATGACACATAGTCATCAGACCT
1 ATACTCACGATGACACATAGTCATCAGACCT
17926 TTTACATTTA
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
51 1 0.01
52 115 0.98
53 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCTGTAAAGGATCCAT
Found at i:23009 original size:85 final size:85
Alignment explanation
Indices: 22863--23032 Score: 286
Period size: 85 Copynumber: 2.0 Consensus size: 85
22853 TCGTTGTACA
*
22863 AATTATATTACAACCTGACCTGTATACTTGCAGAATTCGAAAACACATACCGAATGAGAGTACGT
1 AATTATATTACAACCTGACCTGTATACTTGAAGAATTCGAAAACACATACCGAATGAGAGTACGT
*
22928 TCGAAGGCGATCAAATTGTT
66 TCGAAGGCAATCAAATTGTT
* * *
22948 AATTATATTACAACCTGGCCTGTATACTTGAAGAATTTGAAAACACATACCGAATGGGAGTACGT
1 AATTATATTACAACCTGACCTGTATACTTGAAGAATTCGAAAACACATACCGAATGAGAGTACGT
*
23013 TCGGAGGCAATCAAATTGTT
66 TCGAAGGCAATCAAATTGTT
23033 GGTGTCGTTG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (85 bp):
AATTATATTACAACCTGACCTGTATACTTGAAGAATTCGAAAACACATACCGAATGAGAGTACGT
TCGAAGGCAATCAAATTGTT
Found at i:23167 original size:18 final size:18
Alignment explanation
Indices: 23124--23167 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
23114 AGATATGATT
*
23124 TTTTTTATTTTATTTTGC
1 TTTTTTATATTATTTTGC
*
23142 TTGTTTATATTATTTT-C
1 TTTTTTATATTATTTTGC
23159 TTTTCTTAT
1 TTTT-TTAT
23168 TTGTTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTTTATATTATTTTGC
Found at i:34517 original size:275 final size:274
Alignment explanation
Indices: 34017--34565 Score: 895
Period size: 275 Copynumber: 2.0 Consensus size: 274
34007 TTTTCCATTG
*
34017 ATGAATGAGCTTGTCTTTGAATATTTATGAAAGATTTGAAAGCTTGAAGATTGGGTTTAACATGT
1 ATGAATGAGCTTGTCTTTGAATATTTATGAAAGATTTGAAAGCTTAAAGATTGGGTTTAACATGT
* *
34082 TTGAAAAGTGATTTTTGATGAATTTAAGGTTTAAGGACTAGATTGTGAAAATGGTAAAATTACAT
66 TTGAAAAGTGATTTTTGATGAATTTAAGGTTTAAGGACTAGATTATGAAAATGGTAAAAGTACAT
* *
34147 GCTTTGATGTGAAATAAGTGTATGAATGAGTTGATATTTTTGCCCTAGAATATTCGATTGGCAAT
131 GCTTTGATGTGAAATAAATGTATGAATGAGTTGAGATTTTTGCCCTAGAATATTCGATTGGCAAT
* * *
34212 AGGTAAATTTAGAAATGGTTATTTTACATGTTTTGGCTCTAAGGACTAAATTGAATAGAAATGTA
196 AGGCAAATTTAGAAATGATTATTTTACATGTTTTGGCTCTAAGGACTAAATTGAATAGAAATGCA
*
34277 AAGTTTAGGGGTAA
261 AAGTTTAAGGGTAA
* * * *
34291 ATGAGTGAGTTTGTCTTTGAATATTTATGGAATATTTGAAAGCTTAAAGATTGGGTTTAACATGT
1 ATGAATGAGCTTGTCTTTGAATATTTATGAAAGATTTGAAAGCTTAAAGATTGGGTTTAACATGT
*
34356 TTGAAAAGTGAATTTTTGATGAATTTAGGGTTTAAGGACTAGATTATGAAAATGGTAAAAGTACA
66 TTGAAAAGTG-ATTTTTGATGAATTTAAGGTTTAAGGACTAGATTATGAAAATGGTAAAAGTACA
*
34421 TGCTTTGATGTGAAATAAATGTATGAATGAGTTGAGATTTTT-TCCTGAGAATATTC-AGTTGGC
130 TGCTTTGATGTGAAATAAATGTATGAATGAGTTGAGATTTTTGCCCT-AGAATATTCGA-TTGGC
* * *
34484 GATGGGCAAATTTAGAAATGATTATTTTACATGTTTTGGCTCTAAGGATTAAATTGAATAGAAAT
193 AATAGGCAAATTTAGAAATGATTATTTTACATGTTTTGGCTCTAAGGACTAAATTGAATAGAAAT
34549 GCAAAGTTTAAGGGTAA
258 GCAAAGTTTAAGGGTAA
34566 TTTTGTAATT
Statistics
Matches: 254, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
274 74 0.29
275 180 0.71
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (274 bp):
ATGAATGAGCTTGTCTTTGAATATTTATGAAAGATTTGAAAGCTTAAAGATTGGGTTTAACATGT
TTGAAAAGTGATTTTTGATGAATTTAAGGTTTAAGGACTAGATTATGAAAATGGTAAAAGTACAT
GCTTTGATGTGAAATAAATGTATGAATGAGTTGAGATTTTTGCCCTAGAATATTCGATTGGCAAT
AGGCAAATTTAGAAATGATTATTTTACATGTTTTGGCTCTAAGGACTAAATTGAATAGAAATGCA
AAGTTTAAGGGTAA
Found at i:34853 original size:41 final size:41
Alignment explanation
Indices: 34808--34914 Score: 187
Period size: 41 Copynumber: 2.6 Consensus size: 41
34798 AGAAACTCGA
34808 CATATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAT
1 CATATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAT
* *
34849 CATATTAAAGGAAGACTCGTGTCTAGGGATGAGAATGAGAT
1 CATATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAT
*
34890 TATATTAAAGGAAGACTCATGTCTC
1 CATATTAAAGGAAGACTCATGTCTC
34915 AAAATGAGTG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (41 bp):
CATATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAT
Found at i:39442 original size:34 final size:34
Alignment explanation
Indices: 39404--39535 Score: 106
Period size: 34 Copynumber: 3.9 Consensus size: 34
39394 TTTTGATCTG
39404 ATATGACATTCTGATATGATATATGTTTATGAAA
1 ATATGACATTCTGATATGATATATGTTTATGAAA
* * * * *
39438 ATATGACATTTTGATCTAATATATGATTT-TGGAT
1 ATATGACATTCTGATATGATATATG-TTTATGAAA
** * * **
39472 ATATGATGTTCTGATCTGATATAT-TTTCTGTTA
1 ATATGACATTCTGATATGATATATGTTTATGAAA
* * * *
39505 ATATGACATTTTAATATGATATTTGTATATG
1 ATATGACATTCTGATATGATATATGTTTATG
39536 GGTACATCAT
Statistics
Matches: 75, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
32 3 0.04
33 20 0.27
34 49 0.65
35 3 0.04
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (34 bp):
ATATGACATTCTGATATGATATATGTTTATGAAA
Found at i:46165 original size:26 final size:27
Alignment explanation
Indices: 46135--46192 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
46125 AAATACATTC
46135 TAAAATTATT-AAAAATTAAAAAACTA
1 TAAAATTATTAAAAAATTAAAAAACTA
*
46161 TAAAA-TATTAAAAAATTAAAAATCTA
1 TAAAATTATTAAAAAATTAAAAAACTA
*
46187 AAAAAT
1 TAAAAT
46193 AAAATTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (27 bp):
TAAAATTATTAAAAAATTAAAAAACTA
Found at i:46172 original size:8 final size:8
Alignment explanation
Indices: 46145--46196 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
46135 TAAAATTATT
46145 AAAAATTA
1 AAAAATTA
46153 AAAAACTATA
1 AAAAA-T-TA
*
46163 AAATATTA
1 AAAAATTA
46171 AAAAATT-
1 AAAAATTA
46178 AAAAATCTA
1 AAAAAT-TA
46187 AAAAA-TA
1 AAAAATTA
46194 AAA
1 AAA
46197 TTTATGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 11 0.29
8 14 0.37
9 7 0.18
10 6 0.16
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAATTA
Found at i:50499 original size:22 final size:20
Alignment explanation
Indices: 50474--50517 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
50464 TTCACCTAAA
*
50474 CCTAAAACCATAAATTTCGAAC
1 CCTAAAACCA-AAAGTT-GAAC
*
50496 CCTAAACCCAAAAGTTGAAC
1 CCTAAAACCAAAAGTTGAAC
50516 CC
1 CC
50518 CAAACCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.43, C:0.32, G:0.07, T:0.18
Consensus pattern (20 bp):
CCTAAAACCAAAAGTTGAAC
Found at i:50613 original size:20 final size:20
Alignment explanation
Indices: 50588--50647 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
50578 TCAAAAACCC
50588 TTGAACTTTAAACCCAAAAA
1 TTGAACTTTAAACCCAAAAA
* **
50608 TTGAACATTAAAACCCTAAACT
1 TTGAAC-TTTAAACCC-AAAAA
* *
50630 TTAAACGTTAAACCCAAA
1 TTGAACTTTAAACCCAAA
50648 CCCTAAACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 9 0.28
21 15 0.47
22 8 0.25
ACGTcount: A:0.48, C:0.22, G:0.05, T:0.25
Consensus pattern (20 bp):
TTGAACTTTAAACCCAAAAA
Found at i:50673 original size:20 final size:21
Alignment explanation
Indices: 50631--50682 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
50621 CCCTAAACTT
*
50631 TAAACGTTAAA-CCCAAACCC
1 TAAACTTTAAATCCCAAACCC
*
50651 TAAACTTTAAATCCCAAA-TC
1 TAAACTTTAAATCCCAAACCC
*
50671 TAAACTCTAAAT
1 TAAACTTTAAAT
50683 ATTGGGGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.25
Consensus pattern (21 bp):
TAAACTTTAAATCCCAAACCC
Found at i:50714 original size:21 final size:20
Alignment explanation
Indices: 50688--50740 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
50678 TAAATATTGG
50688 GGTTCGGAGTTTAATATTTGA
1 GGTTC-GAGTTTAATATTTGA
50709 GGTTCGAGTTTAA-ATTTTGA
1 GGTTCGAGTTTAATA-TTTGA
*
50729 AGTTCTGAGTTT
1 GGTTC-GAGTTT
50741 TAGTTCAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.03
20 17 0.59
21 11 0.38
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (20 bp):
GGTTCGAGTTTAATATTTGA
Done.