Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012421.1 Kokia drynarioides strain JFW-HI SEQ_127425, 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: 107265
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 230 characters in sequence are not A, C, G, or T
Found at i:2386 original size:19 final size:19
Alignment explanation
Indices: 2346--2414 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
2336 AAATTTTAAT
*
2346 AAAAAATATTAAAAAT-TCA
1 AAAAAATATAAAAAATAT-A
2365 AAAAAATATAAAAAATATA
1 AAAAAATATAAAAAATATA
***
2384 AAATTTTAT-AAAAATCAT-
1 AAAAAATATAAAAAAT-ATA
2402 AAAAAATATAAAA
1 AAAAAATATAAAA
2415 TGCATTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
18 12 0.30
19 27 0.68
20 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAAATATAAAAAATATA
Found at i:2415 original size:28 final size:27
Alignment explanation
Indices: 2344--2415 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 27
2334 TTAAATTTTA
*
2344 ATAAAAAATATTAAAAATTCAAAAAAAT
1 ATAAAAAATA-TAAAATTTCAAAAAAAT
* *
2372 ATAAAAAATATAAAATTTTATAAAAAT
1 ATAAAAAATATAAAATTTCAAAAAAAT
2399 CATAAAAAATATAAAAT
1 -ATAAAAAATATAAAAT
2416 GCATTAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 14 0.35
28 26 0.65
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (27 bp):
ATAAAAAATATAAAATTTCAAAAAAAT
Found at i:2553 original size:16 final size:17
Alignment explanation
Indices: 2532--2564 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2522 ACATGTGACA
2532 AAAAATGATA-AAAAAT
1 AAAAATGATAGAAAAAT
*
2548 AAAAATTATAGAAAAAT
1 AAAAATGATAGAAAAAT
2565 TATAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAAATGATAGAAAAAT
Found at i:2728 original size:19 final size:19
Alignment explanation
Indices: 2675--2728 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
2665 TCTCTTTTAT
*
2675 ATTTTTATATTTTTTTACG
1 ATTTTTATAATTTTTTACG
* **
2694 ATTTATATAAAATTTTAC-
1 ATTTTTATAATTTTTTACG
2712 ACTTTTTATAATTTTTT
1 A-TTTTTATAATTTTTT
2729 TTATATTTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 1 0.04
19 26 0.96
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTTATAATTTTTTACG
Found at i:4383 original size:31 final size:31
Alignment explanation
Indices: 4348--4411 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
4338 GTAAAAAACT
*
4348 TATAAAT-TTATT-AAATATTAAAATAATAAAA
1 TATAAATATTATTAAAAAATTAAAA-AA-AAAA
*
4379 TATAAATATTTTTAAAAAATTAAAAAAAAAA
1 TATAAATATTATTAAAAAATTAAAAAAAAAA
4410 TA
1 TA
4412 GTATAGCGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 13 0.45
32 6 0.21
33 10 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
TATAAATATTATTAAAAAATTAAAAAAAAAA
Found at i:8159 original size:162 final size:161
Alignment explanation
Indices: 7870--8194 Score: 420
Period size: 162 Copynumber: 2.0 Consensus size: 161
7860 GACCTTTTGG
* * ** * *
7870 ATACAGTGAGTGACGTTGCGACATCAGGCCCTTCACATCGCAATTAGGAATCGATAGTGGGTTGC
1 ATACAGTGAGTGACGTCGCGACATCAGACCCTTCACATCGCAACGAAGAATCGATAGTGAGTTGC
* *
7935 GTCATGACATGAAACCCCCGAAGTCATGATGTCAAACCGATAAATTGAAATCTTTTCATTTTAGT
66 GTCATGACATGAAACCCCCAAAGTCATGATGTCAAACCGATAAATTAAAATCTTTTCATTTTAGT
**
8000 CCTTATTCGATCTTGAGTTATTAAAAAGAGTT
131 CCTTATTCGATCCCGAGTTATTAAAAA-AGTT
* * * *
8032 ATACAGTGAGTGACGTCGTGACGTCAGACCCTTCACGTCGCGACGAAGAATCGATAGTGAGTTGC
1 ATACAGTGAGTGACGTCGCGACATCAGACCCTTCACATCGCAACGAAGAATCGATAGTGAGTTGC
* * * * **
8097 GTCATGACCTGAAACCCCCAAAGTCGTGATGT-TAACTTGATAGTTTAAAAT-TTTTGCATTTTA
66 GTCATGACATGAAACCCCCAAAGTCATGATGTCAAAC-CGATAAATTAAAATCTTTT-CATTTTA
*
8160 GTCCTTATTCGATCCCGAGTTATTAACAAAGTT
129 GTCCTTATTCGATCCCGAGTTATTAAAAAAGTT
8193 AT
1 AT
8195 CTTAAGCTCG
Statistics
Matches: 140, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
161 13 0.09
162 127 0.91
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (161 bp):
ATACAGTGAGTGACGTCGCGACATCAGACCCTTCACATCGCAACGAAGAATCGATAGTGAGTTGC
GTCATGACATGAAACCCCCAAAGTCATGATGTCAAACCGATAAATTAAAATCTTTTCATTTTAGT
CCTTATTCGATCCCGAGTTATTAAAAAAGTT
Found at i:8460 original size:55 final size:55
Alignment explanation
Indices: 8381--8489 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
8371 ATATATCATG
*
8381 ATCAGGTTTATAGTAATAAAGTAAAAATTCTAAACCAAAAAACTTGATATCTTTA
1 ATCAGGTTAATAGTAATAAAGTAAAAATTCTAAACCAAAAAACTTGATATCTTTA
* *
8436 ATCATGTTAATAGTAATAATGTAAAAATTCTAAACCAAAAAACTTGATATCTTT
1 ATCAGGTTAATAGTAATAAAGTAAAAATTCTAAACCAAAAAACTTGATATCTTT
8490 GCGTGTCGAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (55 bp):
ATCAGGTTAATAGTAATAAAGTAAAAATTCTAAACCAAAAAACTTGATATCTTTA
Found at i:17052 original size:15 final size:12
Alignment explanation
Indices: 17004--17050 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
16994 TAAGTGAGCC
*
17004 TATGTTTTAAGA
1 TATGTTTTAAAA
17016 TATGTTTTAAAA
1 TATGTTTTAAAA
17028 TATGATTTTATAAA
1 TATG-TTTTA-AAA
17042 TTATGTTTT
1 -TATGTTTT
17051 TACATGTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 15 0.48
13 5 0.16
14 7 0.23
15 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (12 bp):
TATGTTTTAAAA
Found at i:17338 original size:20 final size:21
Alignment explanation
Indices: 17302--17351 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
17292 ATTGACATGG
*
17302 TTTATATTAAGTGTAAATA-GA
1 TTTA-ATTAAGTGTAAAAATGA
17323 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
17344 -TTAATTAA
1 TTTAATTAA
17352 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Found at i:33257 original size:15 final size:17
Alignment explanation
Indices: 33237--33277 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
33227 TCTTTTAATA
33237 TAATTTTAAA-ATTT-T
1 TAATTTTAAACATTTAT
33252 TAATTTTTAAACATTTCAT
1 TAA-TTTTAAACATTT-AT
33271 TAATTTT
1 TAATTTT
33278 TAAGAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 7 0.32
17 4 0.18
18 4 0.18
19 4 0.18
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTTTAAACATTTAT
Found at i:41408 original size:91 final size:91
Alignment explanation
Indices: 41253--41436 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 91
41243 ATACAATGGT
41253 AAGAGTTTACAAAGATATGGAAAGAATCAAAAGGAAATATTCTTGATTATGTGCCACTTGTCATA
1 AAGAGTTTACAAAGATATGGAAAGAATCAAAAGGAAATATTCTTGATTATGTGCCACTTGTCATA
41318 TCTGCTTTGAAAGGCTCTTCAATCCC
66 TCTGCTTTGAAAGGCTCTTCAATCCC
*
41344 AAGAGTTTACAAAGATATGGAAATAATCAAAAGGAAATATTCTTGATTATGTGCCACTTGTCATA
1 AAGAGTTTACAAAGATATGGAAAGAATCAAAAGGAAATATTCTTGATTATGTGCCACTTGTCATA
41409 TCTGCTTTGAAAGGCTCTTCAATCCC
66 TCTGCTTTGAAAGGCTCTTCAATCCC
41435 AA
1 AA
41437 ATGTTGGGCT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (91 bp):
AAGAGTTTACAAAGATATGGAAAGAATCAAAAGGAAATATTCTTGATTATGTGCCACTTGTCATA
TCTGCTTTGAAAGGCTCTTCAATCCC
Found at i:43561 original size:97 final size:97
Alignment explanation
Indices: 43371--43560 Score: 215
Period size: 98 Copynumber: 1.9 Consensus size: 97
43361 TAAGTAATTT
** * * * *
43371 TAATTAAATAAAAAATTTTAATGTTCGTGATAATAAAGTAATTAATATTTTCTTTTATTAAAAAA
1 TAATTAAATAAAAAATTTTAATGTTAATGATAATAAAATAATTAAGATTTTCTTTGAATAAAAAA
*
43436 GTAAGATACATAATTATTGTTCAAAAAATTAAA
66 GTAAGATAAATAATTATTGTT-AAAAAATTAAA
* * *
43469 TAATT-AATAAATATTTTTAATGTTAATGATAATAAAAATAATTAAGATTTTCTTTGAATAGGAA
1 TAATTAAATAAAAAATTTTAATGTTAATGATAAT-AAAATAATTAAGATTTTCTTTGAATA-AAA
*
43533 AA-TAATATTAAATAATTAATT-TTAAAAA
64 AAGTAAGA-TAAATAATT-ATTGTTAAAAA
43561 TATTTTTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
97 24 0.31
98 36 0.47
99 14 0.18
100 3 0.04
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.41
Consensus pattern (97 bp):
TAATTAAATAAAAAATTTTAATGTTAATGATAATAAAATAATTAAGATTTTCTTTGAATAAAAAA
GTAAGATAAATAATTATTGTTAAAAAATTAAA
Found at i:43877 original size:1 final size:1
Alignment explanation
Indices: 43873--43903 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
43863 NNNNNNNNNN
43873 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43904 AGGCTTGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:53048 original size:3 final size:3
Alignment explanation
Indices: 53040--53090 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
53030 GTGTATTGCA
53040 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53088 AAT
1 AAT
53091 TGTAGAAGAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:57663 original size:6 final size:6
Alignment explanation
Indices: 57642--57675 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
57632 AAAATGAGAG
**
57642 AAAATA AAAACG AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
57676 GAGGTACCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:67105 original size:4 final size:4
Alignment explanation
Indices: 67096--67121 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
67086 AACTCACCTA
67096 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
67122 AACCTTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:67506 original size:18 final size:19
Alignment explanation
Indices: 67478--67521 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
67468 TCTTGTTTAT
*
67478 TTGTTTTATT-AATTTACAA
1 TTGTATTATTAAATTTA-AA
67497 TT-TATTATTAAATTTAAA
1 TTGTATTATTAAATTTAAA
67515 TTGTATT
1 TTGTATT
67522 TATATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (19 bp):
TTGTATTATTAAATTTAAA
Found at i:69645 original size:102 final size:102
Alignment explanation
Indices: 69402--69753 Score: 424
Period size: 102 Copynumber: 3.5 Consensus size: 102
69392 CCGTCAATTC
* * * * * * * *
69402 ATGGCACCCGGTACCTAGCGGATATATCGCGGGATGTGAGCCCAGCTCTAGTTGGATTATCCAAC
1 ATGGCACCCAGTGCCTAGCAGATAAACCGCGAGATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
* * ** *
69467 GATTTGTGCCTAATGCTAGTCGGATAAACTGACGG-T
66 GATTTGCGCCCAGCGCTAGTCAGATAAACTGACGGTT
* * * *
69503 -TGGCACCCAATGCCTAGCAGATAAACAGCGATATGTGAGCCCAACTCTGGTTGGATTAACCAAC
1 ATGGCACCCAGTGCCTAGCAGATAAACCGCGAGATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
* *
69567 GGTTTGCGCCCAGCGCTAGTCAGATAAACTGATGGTT
66 GATTTGCGCCCAGCGCTAGTCAGATAAACTGACGGTT
* * *
69604 ATGGCACCCAGTGCCTAGCAGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGAATCAACCAAC
1 ATGGCACCCAGTGCCTAGCAGATAAACCGCGAGATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
* *
69669 -ATTTTTCACCCAGCGCTAGTCAGATAAACTGACGGTT
66 GA-TTTGCGCCCAGCGCTAGTCAGATAAACTGACGGTT
* * *
69706 ATGGCACCCAGTGCCTAGCGGATAAACTGCGAGA-GTGAGCCCCGCTCT
1 ATGGCACCCAGTGCCTAGCAGATAAACCGCGAGATGTGAGCCCAGCTCT
69754 AGTCAGTTAA
Statistics
Matches: 216, Mismatches: 32, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
100 80 0.37
101 14 0.06
102 122 0.56
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (102 bp):
ATGGCACCCAGTGCCTAGCAGATAAACCGCGAGATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
GATTTGCGCCCAGCGCTAGTCAGATAAACTGACGGTT
Found at i:70390 original size:131 final size:132
Alignment explanation
Indices: 70070--70434 Score: 581
Period size: 131 Copynumber: 2.8 Consensus size: 132
70060 TTCTTGCTCT
* * *
70070 ATATATATAACAATTCAAATCTTTCATTAATCCTTTAAATTTAACTCATTTCAACAATCCAAAAC
1 ATATATATAACAATTCAAATCTTTCATTAATCCTTTATATTCAACTCATTTCAACAATCCAAAAT
* * *
70135 GTTCAATATAATTCACATGGCAAAAA-ATTTTATTTATTTATTTCCAGCCACCAAATATGCATAT
66 GTTCAATATAATTCACATAGCAAAAAGCTTTTATTTATCTATTTCCAGCCACCAAATATGCATAT
70199 CA
131 CA
* * *
70201 ATATATATAACAATTCAAATCTTTCATTAATCATTTGTATTCAATTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATCTTTCATTAATCCTTTATATTCAACTCATTTCAACAATCCAAAAT
*
70266 GTTCAATATAATTCGCATAGCAAAAAGCTTTTATTTATCTATTTCCAGCCACCAAATATGCATAT
66 GTTCAATATAATTCACATAGCAAAAAGCTTTTATTTATCTATTTCCAGCCACCAAATATGCATAT
*
70331 TA
131 CA
*
70333 ATATATATAAAAATTCAAATCTTTCATTAATCCTTTATA-TCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATCTTTCATTAATCCTTTATATTCAACTCATTTCAACAATCCAAAAT
* * *
70397 GTTCAATATAATTTACATAACAAAAAGCATTTATTTAT
66 GTTCAATATAATTCACATAGCAAAAAGCTTTTATTTAT
70435 TTTTGTTAAT
Statistics
Matches: 214, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
131 141 0.66
132 73 0.34
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.38
Consensus pattern (132 bp):
ATATATATAACAATTCAAATCTTTCATTAATCCTTTATATTCAACTCATTTCAACAATCCAAAAT
GTTCAATATAATTCACATAGCAAAAAGCTTTTATTTATCTATTTCCAGCCACCAAATATGCATAT
CA
Found at i:79396 original size:101 final size:105
Alignment explanation
Indices: 79190--79396 Score: 253
Period size: 101 Copynumber: 2.0 Consensus size: 105
79180 GCTAGGATCT
* *
79190 GATGTATAAGGAACCAGTAAAAGGTCCATCTCCCTGTTTTAAAGAATACACAGTTTTAGTTAAAC
1 GATGTATAAGGAACCAGTAAAAGGTCCACCTCCCCGTTTTAAAGAATACACAG--TTA-TTAAAC
* * * *
79255 TGCATGTAGAGTGAAGCATAATAAACTAAATACGTGTTAAACC
63 TGCATATAGAGTAAAACATAATAAACTAAATACGAGTTAAACC
* *
79298 GATGTAT-AGGAACCAGTAGAAGGTCCACCTCCCCG-TTTAAAGAAATACCCAG-T-TT-AACTG
1 GATGTATAAGGAACCAGTAAAAGGTCCACCTCCCCGTTTTAAAG-AATACACAGTTATTAAACTG
* *
79358 CATATAGAGTAAAACATAATAAATTGAATACGAGTTAAA
65 CATATAGAGTAAAACATAATAAACTAAATACGAGTTAAA
79397 ACATCTATGG
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
101 38 0.43
102 2 0.02
104 1 0.01
106 7 0.08
107 33 0.38
108 7 0.08
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (105 bp):
GATGTATAAGGAACCAGTAAAAGGTCCACCTCCCCGTTTTAAAGAATACACAGTTATTAAACTGC
ATATAGAGTAAAACATAATAAACTAAATACGAGTTAAACC
Found at i:90499 original size:11 final size:12
Alignment explanation
Indices: 90476--90505 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
90466 ATTAAAGCAT
90476 ATCATATAGACC
1 ATCATATAGACC
90488 ATCATA-AGACC
1 ATCATATAGACC
90499 ATCATAT
1 ATCATAT
90506 GAATCTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (12 bp):
ATCATATAGACC
Found at i:98257 original size:34 final size:34
Alignment explanation
Indices: 98214--98300 Score: 165
Period size: 34 Copynumber: 2.6 Consensus size: 34
98204 TACTGATATT
98214 AAGAATCAGTAGATGAGTTCAGAAGAAGGAAAAA
1 AAGAATCAGTAGATGAGTTCAGAAGAAGGAAAAA
98248 AAGAATCAGTAGATGAGTTCAGAAGAAGGAAAAA
1 AAGAATCAGTAGATGAGTTCAGAAGAAGGAAAAA
*
98282 AAGAATCAGTAAATGAGTT
1 AAGAATCAGTAGATGAGTT
98301 GTAGATGGAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.52, C:0.06, G:0.25, T:0.17
Consensus pattern (34 bp):
AAGAATCAGTAGATGAGTTCAGAAGAAGGAAAAA
Found at i:99464 original size:5 final size:5
Alignment explanation
Indices: 99454--99478 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
99444 TTGGATAATT
99454 GGAAG GGAAG GGAAG GGAAG GGAAG
1 GGAAG GGAAG GGAAG GGAAG GGAAG
99479 AGCAGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
GGAAG
Done.