Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012163.1 Kokia drynarioides strain JFW-HI SEQ_127164, 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: 27830
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:133 original size:6 final size:6
Alignment explanation
Indices: 124--190 Score: 70
Period size: 6 Copynumber: 11.7 Consensus size: 6
114 AATTTATCTC
* * *
124 AAATTT AAATTT AAATCT -ATTTT AAATTT AAATTT -ACTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
170 AAATTT -AA-TT AAATTT GAAAT
1 AAATTT AAATTT AAATTT -AAAT
191 GGTTTTAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
4 2 0.04
5 11 0.22
6 33 0.66
7 4 0.08
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:139 original size:23 final size:23
Alignment explanation
Indices: 110--159 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
100 TTAAATTGGT
*
110 TTTAAATTTATCTCAAATTTAAA
1 TTTAAATCTATCTCAAATTTAAA
* *
133 TTTAAATCTATTTTAAATTTAAA
1 TTTAAATCTATCTCAAATTTAAA
156 TTTA
1 TTTA
160 CTTTAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAATCTATCTCAAATTTAAA
Found at i:174 original size:17 final size:16
Alignment explanation
Indices: 126--190 Score: 85
Period size: 17 Copynumber: 3.9 Consensus size: 16
116 TTTATCTCAA
*
126 ATTTAAATTTAAATCT
1 ATTTAAATTTAAATTT
142 ATTTTAAATTTAAATTT
1 A-TTTAAATTTAAATTT
159 ACTTTAAATTTAAATTT
1 A-TTTAAATTTAAATTT
*
176 AATTAAATTTGAAAT
1 ATTTAAATTT-AAAT
191 GGTTTTAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.20
17 35 0.80
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTAAATTTAAATTT
Found at i:179 original size:11 final size:11
Alignment explanation
Indices: 88--185 Score: 60
Period size: 11 Copynumber: 8.8 Consensus size: 11
78 AACTTTTGAT
88 TTTAAA-TTAA
1 TTTAAATTTAA
***
98 GTTTAAATTGGT
1 -TTTAAATTTAA
110 TTTAAATTT-A
1 TTTAAATTTAA
*
120 TCTCAAATTTAAA
1 T-TTAAATTT-AA
* *
133 TTTAAATCTAT
1 TTTAAATTTAA
144 TTTAAATTTAAA
1 TTTAAATTT-AA
*
156 TTT-ACTTTAAA
1 TTTAAATTT-AA
167 TTTAAATTTAA
1 TTTAAATTTAA
178 -TTAAATTT
1 TTTAAATTT
186 GAAATGGTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
10 9 0.13
11 42 0.62
12 15 0.22
13 2 0.03
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:1295 original size:84 final size:83
Alignment explanation
Indices: 1196--1362 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 83
1186 CAAACTTCAG
*
1196 TTTTTCAAAAAAGATCGAGGCTCGATCTTGTCAGATCTGAGCCCGATCAAAGTTTTTTAAAAAAA
1 TTTTTCAAAAAAGATCGAGGCTCGATCATGTCAGATCTGAGCCCGATCAAAGTTTTTTAAAAAAA
1261 TAAAAAGAAAAATGAAAA
66 TAAAAAGAAAAATGAAAA
1279 NTTTTTCAAAAAAGATCGAGGCTCGATCATGTCAGATCTGAGCCCGATCAAAGTTTTTTAAAAAA
1 -TTTTTCAAAAAAGATCGAGGCTCGATCATGTCAGATCTGAGCCCGATCAAAGTTTTTTAAAAAA
1344 ATAAAAAGAAAAATGAAAA
65 ATAAAAAGAAAAATGAAAA
1363 AGTGAATAAG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (83 bp):
TTTTTCAAAAAAGATCGAGGCTCGATCATGTCAGATCTGAGCCCGATCAAAGTTTTTTAAAAAAA
TAAAAAGAAAAATGAAAA
Found at i:1716 original size:106 final size:106
Alignment explanation
Indices: 1529--1738 Score: 404
Period size: 106 Copynumber: 2.0 Consensus size: 106
1519 GATCTTTAGG
1529 GAGAACCAAGGAGAGACAGAGAGGACAATCTCTTTTTTTTTTTAAATAAAGGAGTAAAAATGATT
1 GAGAACCAAGGAGAGACAGAGAGGACAATCTCTTTTTTTTTTTAAATAAAGGAGTAAAAATGATT
1594 TTTTTTGGGTTAAAATTGGTTTTATAGCAGTTATGAAACGC
66 TTTTTTGGGTTAAAATTGGTTTTATAGCAGTTATGAAACGC
1635 NGAGAACCAAGGAGAGACAGAGAGGACAATCTC-TTTTTTTTTTAAATAAAGGAGTAAAAATGAT
1 -GAGAACCAAGGAGAGACAGAGAGGACAATCTCTTTTTTTTTTTAAATAAAGGAGTAAAAATGAT
1699 TTTTTTTGGGTTAAAATTGGTTTTATAGCAGTTATGAAAC
65 TTTTTTTGGGTTAAAATTGGTTTTATAGCAGTTATGAAAC
1739 ACTACCGTTT
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 71 0.69
107 32 0.31
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.34
Consensus pattern (106 bp):
GAGAACCAAGGAGAGACAGAGAGGACAATCTCTTTTTTTTTTTAAATAAAGGAGTAAAAATGATT
TTTTTTGGGTTAAAATTGGTTTTATAGCAGTTATGAAACGC
Found at i:2306 original size:58 final size:57
Alignment explanation
Indices: 2241--2547 Score: 318
Period size: 58 Copynumber: 5.3 Consensus size: 57
2231 CCCTAAATTT
* * *
2241 TTCCACAATTCCATTTTTGACCTTGATTTTCCCAAAAATTATCATTTTACCCCCGAAC
1 TTCCAAAATTCCATTTTTGACCTAGATTTT-CCAAAAATTACCATTTTACCCCCGAAC
* * *
2299 TTCCACAAATTCCATTTTTAACCTCGATTTTTCCAAAAATTACCA-TTTACCTCCGAAC
1 TTCCA-AAATTCCATTTTTGACCTAGA-TTTTCCAAAAATTACCATTTTACCCCCGAAC
* *
2357 TTCCAAAAATTCCA-TTTTGACCCAGATTTTCCAAAAATTACCATTTTACCCTCGAAC
1 TTCC-AAAATTCCATTTTTGACCTAGATTTTCCAAAAATTACCATTTTACCCCCGAAC
* * * *
2414 TTCCTAAAATTCCA-TTTTGACCTCAAACTTTCCAAAAATTATCATTTTACCTCCGAA-
1 TTCC-AAAATTCCATTTTTGACCT-AGATTTTCCAAAAATTACCATTTTACCCCCGAAC
* * * * * * *
2471 TGTCTAAAATTCCATTTTTGACCTTGAACTTTCCCAAAATTACCATTTTGCCCTCG-AG
1 T-TCCAAAATTCCATTTTTGACCTAG-ATTTTCCAAAAATTACCATTTTACCCCCGAAC
2529 TGTCCAAAATTACCATTTT
1 T-TCCAAAATT-CCATTTT
2548 GCCCCGAGTA
Statistics
Matches: 213, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
56 17 0.08
57 52 0.24
58 102 0.48
59 38 0.18
60 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (57 bp):
TTCCAAAATTCCATTTTTGACCTAGATTTTCCAAAAATTACCATTTTACCCCCGAAC
Found at i:2316 original size:28 final size:28
Alignment explanation
Indices: 2272--2488 Score: 156
Period size: 29 Copynumber: 7.6 Consensus size: 28
2262 CTTGATTTTC
*
2272 CCAAAAATTATCATTTTACCCCCGAACTT
1 CCAAAAATT-CCATTTTACCCCCGAACTT
* * * **
2301 CCACAAATTCCATTTTTAACCTCGATTTTT
1 CCAAAAATTCCA-TTTTACCCCCGA-ACTT
*
2331 CCAAAAATTACCA-TTTACCTCCGAACTT
1 CCAAAAATT-CCATTTTACCCCCGAACTT
* **
2359 CCAAAAATTCCATTTTGA-CCCAGATTTT
1 CCAAAAATTCCATTTT-ACCCCCGAACTT
*
2387 CCAAAAATTACCATTTTACCCTCGAACTT
1 CCAAAAATT-CCATTTTACCCCCGAACTT
* * *
2416 CCTAAAATTCCATTTTGA-CCTCAAACTTT
1 CCAAAAATTCCATTTT-ACCCCCGAAC-TT
* *
2445 CCAAAAATTATCATTTTACCTCCGAA-TGT
1 CCAAAAATT-CCATTTTACCCCCGAACT-T
*
2474 -CTAAAATTCCATTTT
1 CCAAAAATTCCATTTT
2489 TGACCTTGAA
Statistics
Matches: 147, Mismatches: 29, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
27 9 0.06
28 54 0.37
29 61 0.41
30 20 0.14
31 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (28 bp):
CCAAAAATTCCATTTTACCCCCGAACTT
Found at i:2446 original size:29 final size:30
Alignment explanation
Indices: 2247--2548 Score: 212
Period size: 28 Copynumber: 10.4 Consensus size: 30
2237 ATTTTTCCAC
* *
2247 AATT-CCATTTTTGACCTTG-ATTTTCCCAAA
1 AATTACCA-TTTTGACCTCGAACTTT-CCAAA
* * *
2277 AATTATCATTTT-ACCCCCGAAC-TTCCACA
1 AATTACCATTTTGA-CCTCGAACTTTCCAAA
* **
2306 AATT-CCATTTTTAACCTCGATTTTTCCAAA
1 AATTACCA-TTTTGACCTCGAACTTTCCAAA
2336 AATTACCA-TTT-ACCTCCGAAC-TTCCAAA
1 AATTACCATTTTGACCT-CGAACTTTCCAAA
*
2364 AATT-CCATTTTGACC-C-AGATTTTCCAAA
1 AATTACCATTTTGACCTCGA-ACTTTCCAAA
*
2392 AATTACCATTTT-ACCCTCGAAC-TTCCTAA
1 AATTACCATTTTGA-CCTCGAACTTTCCAAA
*
2421 AATT-CCATTTTGACCTCAAACTTTCCAAA
1 AATTACCATTTTGACCTCGAACTTTCCAAA
* * *
2450 AATTATCATTTT-ACCTCCGAA-TGT-CTAA
1 AATTACCATTTTGACCT-CGAACTTTCCAAA
* *
2478 AATT-CCATTTTTGACCTTGAACTTTCCCAA
1 AATTACCA-TTTTGACCTCGAACTTTCCAAA
* * *
2508 AATTACCATTTTGCCCTCG-AGTGTCC-AA
1 AATTACCATTTTGACCTCGAACTTTCCAAA
2536 AATTACCATTTTG
1 AATTACCATTTTG
2549 CCCCGAGTAT
Statistics
Matches: 218, Mismatches: 29, Indels: 52
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.00
27 7 0.03
28 75 0.34
29 74 0.34
30 51 0.23
31 10 0.05
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (30 bp):
AATTACCATTTTGACCTCGAACTTTCCAAA
Found at i:2463 original size:115 final size:113
Alignment explanation
Indices: 2247--2548 Score: 367
Period size: 115 Copynumber: 2.6 Consensus size: 113
2237 ATTTTTCCAC
* *
2247 AATTCCATTTTTGACCTTGATTTTCCCAAAAATTATCATTTTACCCCCGAACTTCCACAAATTCC
1 AATTCCATTTTTGACCTTGATTTT-CCAAAAATTACCATTTTACCCTCGAACTTCCA-AAATTCC
* * **
2312 ATTTTTAACCTCGATTTTTCCAAAAATTACCATTTACCTCCGAACT-TCCAAA
64 A-TTTTGACCTCAAACTTTCCAAAAATTACCATTTACCTCCGAA-TGT-CAAA
**
2364 AATTCCA-TTTTGACCCAGATTTTCCAAAAATTACCATTTTACCCTCGAACTTCCTAAAATTCCA
1 AATTCCATTTTTGACCTTGATTTTCCAAAAATTACCATTTTACCCTCGAACTTCC-AAAATTCCA
* *
2428 TTTTGACCTCAAACTTTCCAAAAATTATCATTTTACCTCCGAATGTCTAA
65 TTTTGACCTCAAACTTTCCAAAAATTACCA-TTTACCTCCGAATGTCAAA
* * * *
2478 AATTCCATTTTTGACCTTGAACTTTCCCAAAATTACCATTTTGCCCTCG-AGTGTCCAAAATTAC
1 AATTCCATTTTTGACCTTG-ATTTTCCAAAAATTACCATTTTACCCTCGAACT-TCCAAAATT-C
2542 CATTTTG
63 CATTTTG
2549 CCCCGAGTAT
Statistics
Matches: 162, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
114 36 0.22
115 67 0.41
116 52 0.32
117 7 0.04
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (113 bp):
AATTCCATTTTTGACCTTGATTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAATTCCAT
TTTGACCTCAAACTTTCCAAAAATTACCATTTACCTCCGAATGTCAAA
Found at i:2563 original size:27 final size:28
Alignment explanation
Indices: 2504--2564 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
2494 TTGAACTTTC
*
2504 CCAAAATTACCATTTTGCCCTCGAGTGT
1 CCAAAATTACCATTTTGCCCTCGAGTAT
2532 CCAAAATTACCATTTTGCCC-CGAGTAT
1 CCAAAATTACCATTTTGCCCTCGAGTAT
2559 CCAAAA
1 CCAAAA
2565 ATCTCATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 12 0.38
28 20 0.62
ACGTcount: A:0.31, C:0.30, G:0.11, T:0.28
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCTCGAGTAT
Found at i:2572 original size:27 final size:28
Alignment explanation
Indices: 2504--2574 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
2494 TTGAACTTTC
* *
2504 CCAAAATTACCATTTTGCCCTCGAGTGT
1 CCAAAAATACCATTTTGCCCTCGAGTAT
*
2532 CCAAAATTACCATTTTGCCC-CGAGTAT
1 CCAAAAATACCATTTTGCCCTCGAGTAT
2559 CCAAAAAT-CTCATTTT
1 CCAAAAATAC-CATTTT
2575 CAACTCCGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.47
28 20 0.50
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (28 bp):
CCAAAAATACCATTTTGCCCTCGAGTAT
Found at i:5834 original size:19 final size:20
Alignment explanation
Indices: 5805--5851 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5795 TTTCAATGGA
5805 TAATATT-TTTTAATTATGT
1 TAATATTATTTTAATTATGT
* *
5824 TAAT-TTATTTTATTTATTT
1 TAATATTATTTTAATTATGT
5843 TAATATTAT
1 TAATATTAT
5852 GTTATCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 18 0.75
20 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TAATATTATTTTAATTATGT
Found at i:6081 original size:16 final size:16
Alignment explanation
Indices: 6052--6092 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
6042 CTTAAAATAC
6052 TTAA-TTTTTCAACAA
1 TTAATTTTTTCAACAA
*
6067 TT-ATTTTTTCTAACAC
1 TTAATTTTTTC-AACAA
6083 TTAATTTTTT
1 TTAATTTTTT
6093 TAGTTTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 8 0.36
16 6 0.27
17 7 0.32
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATTTTTTCAACAA
Found at i:7080 original size:33 final size:33
Alignment explanation
Indices: 7038--7106 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
7028 ATTTAGGGGG
*
7038 ATTGGTAGGGGCTCCGACCCTCTTAAAATAGAA
1 ATTGGTAGGGGCTCCGACCCTCCTAAAATAGAA
7071 ATTGGTAGGGGCTCCGACCCTCCTAAAATAGAA
1 ATTGGTAGGGGCTCCGACCCTCCTAAAATAGAA
7104 ATT
1 ATT
7107 TTATCATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (33 bp):
ATTGGTAGGGGCTCCGACCCTCCTAAAATAGAA
Found at i:8901 original size:58 final size:58
Alignment explanation
Indices: 8839--8958 Score: 186
Period size: 58 Copynumber: 2.1 Consensus size: 58
8829 ACTCATCAAC
* *
8839 AAACTAAACCCAAATATTTTTAAACTCAAATACAATTTCATTCTTAAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATACAATTTCATTCCTAAAAAACACTCAT
* * * *
8897 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATACAATTTCATTCCTAAAAAACACTCAT
8955 AAAC
1 AAAC
8959 AACTCCATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATACAATTTCATTCCTAAAAAACACTCAT
Found at i:9194 original size:21 final size:22
Alignment explanation
Indices: 9165--9215 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
9155 ATATTATTAC
9165 TGTTCGTTTTTTA-CTTTTGTTG
1 TGTT-GTTTTTTATCTTTTGTTG
* *
9187 TGTTG-TTTTTATTTTTTGTTT
1 TGTTGTTTTTTATCTTTTGTTG
9208 TGTTGTTT
1 TGTTGTTT
9216 GGCATGGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.24
21 13 0.52
22 6 0.24
ACGTcount: A:0.04, C:0.04, G:0.18, T:0.75
Consensus pattern (22 bp):
TGTTGTTTTTTATCTTTTGTTG
Found at i:11193 original size:59 final size:59
Alignment explanation
Indices: 11116--11229 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
11106 TCCGCTTTTT
*
11116 TTGGTGAATTATAATAATAGGGTAAAGTTCAAACAACAAACGCGACTAGCGCGATGTTG
1 TTGGCGAATTATAATAATAGGGTAAAGTTCAAACAACAAACGCGACTAGCGCGATGTTG
* *
11175 TTGGCGAATTATAATAATAGGGTAAAGTTCGAACAACAAATGCGACTAGCGCGAT
1 TTGGCGAATTATAATAATAGGGTAAAGTTCAAACAACAAACGCGACTAGCGCGAT
11230 TCGAACCCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (59 bp):
TTGGCGAATTATAATAATAGGGTAAAGTTCAAACAACAAACGCGACTAGCGCGATGTTG
Found at i:12533 original size:21 final size:22
Alignment explanation
Indices: 12509--12557 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
12499 TTTTTACTTT
*
12509 TAAAAAAT-ATATAATATGAAA
1 TAAAAAATAATATAAAATGAAA
*
12530 T-AAAAATAATTTAAAATGAAA
1 TAAAAAATAATATAAAATGAAA
12551 -AAAAAAT
1 TAAAAAAT
12558 CCATTGCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (22 bp):
TAAAAAATAATATAAAATGAAA
Found at i:15392 original size:31 final size:30
Alignment explanation
Indices: 15325--15393 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
15315 AAAATTTCAA
* *
15325 AAAAAAATATTTTTTAAATTATTTAAAAAT
1 AAAAAAATACTTTTAAAATTATTTAAAAAT
* * **
15355 ATAAAAATACTTTTAAACATTTTTTAAATTT
1 AAAAAAATACTTTTAAA-ATTATTTAAAAAT
15386 AAAAAAAT
1 AAAAAAAT
15394 TAATTCAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
AAAAAAATACTTTTAAAATTATTTAAAAAT
Found at i:18422 original size:21 final size:21
Alignment explanation
Indices: 18389--18446 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
18379 TAGTACAGAT
* *
18389 TTCTACCAGTACATGTACT-AG
1 TTCTATCAATACATGTA-TAAG
* *
18410 TTCTATCAATACAAGTATAAT
1 TTCTATCAATACATGTATAAG
*
18431 TTCTATCGATACATGT
1 TTCTATCAATACATGT
18447 TATGCATCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (21 bp):
TTCTATCAATACATGTATAAG
Found at i:19294 original size:51 final size:52
Alignment explanation
Indices: 19239--19348 Score: 123
Period size: 51 Copynumber: 2.1 Consensus size: 52
19229 GTTATTGAAT
* *
19239 CTTTAGTCCATCATGAATTCATTTACTCACAATGACACTTAGTCATCAGA-C
1 CTTTAGTCCATAAAGAATTCATTTACTCACAATGACACTTAGTCATCAGACC
* *** * ** *
19290 CTTTAATTTGTAAAGGATTCATTTACTCATGATGACACTTAGTCATCGGACC
1 CTTTAGTCCATAAAGAATTCATTTACTCACAATGACACTTAGTCATCAGACC
19342 CTTTAGT
1 CTTTAGT
19349 TTATAGCTTG
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
51 40 0.85
52 7 0.15
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (52 bp):
CTTTAGTCCATAAAGAATTCATTTACTCACAATGACACTTAGTCATCAGACC
Done.