Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005931.1 Hibiscus syriacus cultivar Beakdansim tig00013921_pilon, 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: 50828
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3106 original size:17 final size:16
Alignment explanation
Indices: 3084--3115 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
3074 TTATACTTGA
3084 AAAAAAAGGGAAAAAAG
1 AAAAAAA-GGAAAAAAG
3101 AAAAAAAGGAAAAAA
1 AAAAAAAGGAAAAAA
3116 TTGAACCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAAAGGAAAAAAG
Found at i:3614 original size:32 final size:32
Alignment explanation
Indices: 3578--3639 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
3568 TCTGGAAACA
* *
3578 AGAAGTA-CCTCTACGATATGAACATAACAACG
1 AGAAGTATCC-CTACAAAATGAACATAACAACG
*
3610 AGAAGTATCCCTACAAAATGAGCATAACAA
1 AGAAGTATCCCTACAAAATGAACATAACAA
3640 TCATTTCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.18
Consensus pattern (32 bp):
AGAAGTATCCCTACAAAATGAACATAACAACG
Found at i:8388 original size:45 final size:45
Alignment explanation
Indices: 8329--8477 Score: 226
Period size: 45 Copynumber: 3.3 Consensus size: 45
8319 GGGAGCTTTT
*
8329 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
8374 TGATGTTTTTAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* ** *
8419 TGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
8464 GGATGTTGTCAAAA
1 TGATGTTTTCAAAA
8478 AACCCTTCGG
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 94 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:8510 original size:122 final size:123
Alignment explanation
Indices: 8374--8845 Score: 684
Period size: 122 Copynumber: 3.9 Consensus size: 123
8364 CTTCAGTGCA
* *
8374 TGATGTTTTTAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTC-AAAACCTTC
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAAACCTTC
* *
8438 GGGTCATCCATAAGACCTTCAGTGCAGGATGTTGTCAAAAAACCCTTCGGGAGCTTTT
66 GGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAAACCTTCGGGAGCTTTT
* *
8496 TGATATTTTCAAAACCTTCGGTTCATCTGTTAGCCCTTCAGTGCATGATGCTTTC-AAAACCTTC
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAAACCTTC
* * * *
8560 TGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAAGCCTTTGGGAGCTTTT
66 GGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAAACCTTCGGGAGCTTTT
8618 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTATCAAAAACCTT
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTT-TCAAAAACCTT
** * * *
8682 CGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAAACCTTCGAGAGCTTTT
65 CGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAAACCTTCGGGAGCTTTT
** * * *
8741 TGATA-TTT-AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAAA-CCTT
* * *
8804 TGTGTCATCCATAAGACCTTCAGTGCAGTATGTTTTCAAAAA
65 CGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAA
8846 GCCTTCAGGT
Statistics
Matches: 316, Mismatches: 30, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
121 45 0.14
122 207 0.66
123 64 0.20
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (123 bp):
TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAAACCTTC
GGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAAACCTTCGGGAGCTTTT
Found at i:8512 original size:167 final size:167
Alignment explanation
Indices: 8230--8599 Score: 614
Period size: 167 Copynumber: 2.2 Consensus size: 167
8220 CTATTTCCCA
8230 CATCTATAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
1 CATCTATAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
* *
8295 CAGGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTA
66 CAGGATGTTGTCAAAAAACCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTA
* *
8360 AGCCCTTCAGTGCATGATGTTTTTAAAACCTTCGGGT
131 AGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* *
8397 CATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTG
1 CATCTATAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
* *
8462 CAGGATGTTGTCAAAAAACCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGTTCATCTGTT
66 CAGGATGTTGTCAAAAAACCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTA
*
8527 AGCCCTTCAGTGCATGATGCTTTCAAAACCTTCTGGT
131 AGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* * * * *
8564 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAA
1 CATCTATAAGCCCTTCAGTGCATGATGCTTTCAAAA
8600 AAGCCTTTGG
Statistics
Matches: 188, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
167 188 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (167 bp):
CATCTATAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
CAGGATGTTGTCAAAAAACCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTA
AGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
Found at i:8552 original size:45 final size:45
Alignment explanation
Indices: 8502--8599 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
8492 TTTTTGATAT
** * * * *
8502 TTTCAAAACCTTC-GGTTCATCTGTTAGCCCTTCAGTGCATGATGC
1 TTTCAAAACCTTCTGG-TCATCCATAAGACCTGCAGTGCAGGATGC
*
8547 TTTCAAAACCTTCTGGTCATCCATAAGACCTGCAGTGCAGGATGT
1 TTTCAAAACCTTCTGGTCATCCATAAGACCTGCAGTGCAGGATGC
8592 TTTCAAAA
1 TTTCAAAA
8600 AAGCCTTTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (45 bp):
TTTCAAAACCTTCTGGTCATCCATAAGACCTGCAGTGCAGGATGC
Found at i:8679 original size:46 final size:46
Alignment explanation
Indices: 8628--8723 Score: 165
Period size: 46 Copynumber: 2.1 Consensus size: 46
8618 TGATATTTTC
* *
8628 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCA
1 AAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTATCA
*
8674 AAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCA
1 AAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTATCA
8720 AAAA
1 AAAA
8724 AACCTTCGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (46 bp):
AAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTATCA
Found at i:8813 original size:47 final size:47
Alignment explanation
Indices: 8749--8889 Score: 223
Period size: 47 Copynumber: 3.0 Consensus size: 47
8739 TTTGATATTT
*
8749 AAAA-CCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCA
1 AAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCA
* *
8795 AAAAGCCTT-TGTGTCATCCATAAGACCTTCAGTGCAGTATGTTTTCA
1 AAAAGCCTTCAG-GTCATCCATAAGACCTTCAGTGCAGGATGTTTTCA
*
8842 AAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCATGATGTTTTCA
1 AAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCA
8889 A
1 A
8890 CATTTCCGTT
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
46 5 0.06
47 81 0.93
48 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (47 bp):
AAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCA
Found at i:8813 original size:245 final size:243
Alignment explanation
Indices: 8374--8850 Score: 710
Period size: 245 Copynumber: 2.0 Consensus size: 243
8364 CTTCAGTGCA
* *
8374 TGATGTTTTTAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
* * *
8439 GGTCATCCATAAGACCTTCAGTGCAGGATGTTGTCAAAAAACCCTTCGGGAGCTTTTTGATATTT
66 GGTCATCCATAAGACCTACAGTGCAGGATGTTGTCAAAAAAACCTTCGAGAGCTTTTTGATATTT
* ** * * *
8504 TCAAAACCTTCGGTTCATCTGTTAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCTGGTCATCC
131 TCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGCTTTCAAAACCTTCTGGTCATCC
8569 ATAAGACCTGCAGTGCAGGATGTTTTCAAAAAAGCCTTTGGGAGCTTTT
196 ATAAGACCTGCAGTGCAGGATGTTTTC-AAAAAGCCTTTGGGAGCTTTT
8618 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTATCAAAAACCTT
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTT-TC-AAAACCTT
** * *
8682 CGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAAACCTTCGAGAGCTTTTTGATA-
64 CGGGTCATCCATAAGACCTACAGTGCAGGATGTTGTCAAAAAAACCTTCGAGAGCTTTTTGATAT
*
8746 TTT-AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTT-TGTGT
129 TTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGCTTTC-AAAA-CCTTCTG-GT
* *
8809 CATCCATAAGACCTTCAGTGCAGTATGTTTTCAAAAAGCCTT
191 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
8851 CAGGTCATCC
Statistics
Matches: 210, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
243 40 0.19
244 69 0.33
245 101 0.48
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (243 bp):
TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
GGTCATCCATAAGACCTACAGTGCAGGATGTTGTCAAAAAAACCTTCGAGAGCTTTTTGATATTT
TCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGCTTTCAAAACCTTCTGGTCATCC
ATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTT
Found at i:9427 original size:16 final size:16
Alignment explanation
Indices: 9406--9436 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9396 GTTGCAGCTA
9406 TAAAGGCAGATTTGTC
1 TAAAGGCAGATTTGTC
9422 TAAAGGCAGATTTGT
1 TAAAGGCAGATTTGT
9437 GGTGGCCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (16 bp):
TAAAGGCAGATTTGTC
Found at i:10373 original size:2 final size:2
Alignment explanation
Indices: 10362--10390 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10352 ATTACTTTAA
10362 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10391 TTAGATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:12320 original size:27 final size:27
Alignment explanation
Indices: 12277--12344 Score: 90
Period size: 26 Copynumber: 2.6 Consensus size: 27
12267 TTTAAATTAA
12277 AAATATTAT-ATTATCTTTAAAATTTTAT
1 AAAT-TTATCATT-TCTTTAAAATTTTAT
12305 AAATTTATCATTTC-TTAAAATTTTAT
1 AAATTTATCATTTCTTTAAAATTTTAT
12331 AAATTTA-C-TTTCTT
1 AAATTTATCATTTCTT
12345 AATACACATT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.11
25 2 0.05
26 19 0.50
27 6 0.16
28 7 0.18
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.54
Consensus pattern (27 bp):
AAATTTATCATTTCTTTAAAATTTTAT
Found at i:12851 original size:29 final size:30
Alignment explanation
Indices: 12801--12863 Score: 110
Period size: 29 Copynumber: 2.1 Consensus size: 30
12791 ATGAAATTCC
12801 TTCAATATTTTAAGATTATATTAAAATAGT
1 TTCAATATTTTAAGATTATATTAAAATAGT
*
12831 TTCAATA-TTTAAGATTGTATTAAAATAGT
1 TTCAATATTTTAAGATTATATTAAAATAGT
12860 TTCA
1 TTCA
12864 TTATGCTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (30 bp):
TTCAATATTTTAAGATTATATTAAAATAGT
Found at i:16354 original size:6 final size:6
Alignment explanation
Indices: 16345--16399 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
16335 TTCTGTTGGG
*
16345 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT- TTTAT- TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
16391 TTTTT- TTTT
1 TTTTTA TTTT
16400 ACGTTTGGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
5 12 0.26
6 34 0.74
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:16382 original size:22 final size:21
Alignment explanation
Indices: 16351--16398 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 21
16341 TGGGTTTTTA
16351 TTTTTATTTTTATTTTTATTT
1 TTTTTATTTTTATTTTTATTT
16372 TTTTTATTTTTTATTTTTATTT
1 TTTTTA-TTTTTATTTTTATTT
16394 TTTTT
1 TTTTT
16399 TACGTTTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (21 bp):
TTTTTATTTTTATTTTTATTT
Found at i:16385 original size:28 final size:26
Alignment explanation
Indices: 16345--16399 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 26
16335 TTCTGTTGGG
16345 TTTTTATTTTTATTTTTATTTTTATTT
1 TTTTTATTTTTATTTTTATTTTT-TTT
16372 TTTTTATTTTTTATTTTTATTTTTTTT
1 TTTTTA-TTTTTATTTTTATTTTTTTT
16399 T
1 T
16400 ACGTTTGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (26 bp):
TTTTTATTTTTATTTTTATTTTTTTT
Found at i:25174 original size:30 final size:30
Alignment explanation
Indices: 25140--25207 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
25130 AATTAATCCA
25140 GGGACGGGGAAAAA-TCGTTTATGCTAAACG
1 GGGACGGGGAAAAACT-GTTTATGCTAAACG
* *
25170 GGGACGGGGAAAAACTGTTTATGTTAAATG
1 GGGACGGGGAAAAACTGTTTATGCTAAACG
25200 GGGACGGG
1 GGGACGGG
25208 TTTAGTAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.38, T:0.21
Consensus pattern (30 bp):
GGGACGGGGAAAAACTGTTTATGCTAAACG
Found at i:25294 original size:6 final size:7
Alignment explanation
Indices: 25265--25362 Score: 50
Period size: 6 Copynumber: 14.4 Consensus size: 7
25255 AATATTAAAA
25265 ATAAT-T
1 ATAATAT
25271 ATAATAT
1 ATAATAT
25278 AT-ATAT
1 ATAATAT
25284 ATAATAT
1 ATAATAT
25291 -TAATAAAT
1 ATAAT--AT
*
25299 TTAA-AT
1 ATAATAT
25305 -TAA-AT
1 ATAATAT
*
25310 -TAAAAT
1 ATAATAT
25316 ATATATAT
1 ATA-ATAT
25324 ATATATAT
1 ATA-ATAT
25332 ATAATAT
1 ATAATAT
*
25339 TTATATAT
1 ATA-ATAT
* *
25347 TTAATTT
1 ATAATAT
25354 A-AATAT
1 ATAATAT
25360 ATA
1 ATA
25363 TACCCTGCCC
Statistics
Matches: 77, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
5 8 0.10
6 24 0.31
7 19 0.25
8 23 0.30
9 3 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
ATAATAT
Found at i:25321 original size:2 final size:2
Alignment explanation
Indices: 25314--25364 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
25304 TTAAATTAAA
* * *
25314 AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
25354 AA AT AT AT AT A
1 AT AT AT AT AT A
25365 CCCTGCCCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:26090 original size:19 final size:19
Alignment explanation
Indices: 26066--26107 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
26056 TTTTTCAAAT
*
26066 ACTTAAAAATAACGTTTAA
1 ACTTAAAAATAACGATTAA
26085 ACTTAAAAATAACGATTAA
1 ACTTAAAAATAACGATTAA
26104 ACTT
1 ACTT
26108 GTATAGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (19 bp):
ACTTAAAAATAACGATTAA
Found at i:27071 original size:20 final size:21
Alignment explanation
Indices: 27046--27086 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
27036 TATGAAATTG
27046 AAAAAAT-ATATTAA-AATAAA
1 AAAAAATAATA-TAAGAATAAA
27066 AAAAAATAATATAAGAATAAA
1 AAAAAATAATATAAGAATAAA
27087 TATTAATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAAAATAATATAAGAATAAA
Found at i:27184 original size:19 final size:18
Alignment explanation
Indices: 27142--27185 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
27132 AAAATAAAAA
*
27142 AAATAAAAAATAAGAATC
1 AAATAAAAAAAAAGAATC
* *
27160 AAATAAAAGAAAAATAATT
1 AAATAAAA-AAAAAGAATC
27179 AAATAAA
1 AAATAAA
27186 CAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (18 bp):
AAATAAAAAAAAAGAATC
Found at i:27869 original size:64 final size:65
Alignment explanation
Indices: 27768--27894 Score: 197
Period size: 64 Copynumber: 2.0 Consensus size: 65
27758 AAAAACATCT
*
27768 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACC-AAAA-AAATGATATAATATT
1 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAT-ATAAAATATT
27831 A
65 A
*
27832 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATAT
1 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAATATAAAATAT
27895 AAAAATAATA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
63 5 0.09
64 37 0.64
65 12 0.21
66 4 0.07
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (65 bp):
TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAATATAAAATATTA
Found at i:27890 original size:25 final size:24
Alignment explanation
Indices: 27843--27890 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
27833 AAATCCTAAT
** *
27843 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
27867 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
27891 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:27911 original size:32 final size:32
Alignment explanation
Indices: 27870--27931 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
27860 TTTAAACTAA
27870 AATACCTAAAAC-AAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
27901 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
27932 CTTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:27995 original size:16 final size:18
Alignment explanation
Indices: 27960--27995 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27950 TAAAGATAAA
27960 ATATAATGTTTAAAATAT
1 ATATAATGTTTAAAATAT
27978 ATATAATGTTTAAAATAT
1 ATATAATGTTTAAAATAT
27996 TATCCTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATAATGTTTAAAATAT
Found at i:33477 original size:279 final size:280
Alignment explanation
Indices: 32954--33510 Score: 657
Period size: 279 Copynumber: 2.0 Consensus size: 280
32944 CTAAATTTAA
* * * *
32954 AAAGAATGTTCTTAAAAACATAAATTAGATAAAGATTAATTTTGAAAAACATAATAATAAATTTT
1 AAAGAATATTCTTAAAAACAT--AGTAGATAAAGATTAATTATGAAAAACATAATAATAAATTTA
* * * * *
33019 ATGAAAAAATCAAAGTACACTAGGGGAGACGCATTGTAGTCATGGAGTCTGCCCACATTTCAATC
64 AAGAAAAAATCAAAGTACACTAGGGGAAACACATTGCAATCATGGAGTCTGCCCACATTTCAATC
** * * * **
33084 GAAGACGCACTGAAATCCTTATGTCACACCTTGATTATGTAGTAAATGTATTATTCGAGTAAATA
129 GAAGACGCACCAAAATCCTTACGTCACACCTCGATTATGTAGCAAATGTATTATTCGAACAAATA
* * * *
33149 ATTATGGTTCACCATTATTCTAGTAATTTTTTTCCAGACAATTATCGTAAAAAATTTGCCTATCA
194 ATTATGGTTCACCATTATTCAAGTAATTTTTTTCCAGACAATGATCGT-AAAAATTTACCCATCA
33214 T-G-GACTAAATAAAAAATCTGG
258 TAGAGACTAAATAAAAAATCTGG
*
33235 AAAGAATATTCTTAAAAACAT-GTAGATAAAGATTAATTATGAAAAACCTAATAATAAAATTTAA
1 AAAGAATATTCTTAAAAACATAGTAGATAAAGATTAATTATGAAAAACATAATAAT-AAATTT-A
* *
33299 AAGAAAAAA-CTGAAGTACACTA-GGGAAACACATTGCAATCCT-GACGTCT-CCACACATTTCA
64 AAGAAAAAATC-AAAGTACACTAGGGGAAACACATTGCAATCATGGA-GTCTGCC-CACATTTCA
* * * *
33360 TTCGAAGACGCACCAAAATCCTTGCGTCACATCGTCG-TTCTGTAGCAAAT-TCATTATTCGAAC
126 ATCGAAGACGCACCAAAATCCTTACGTCACA-CCTCGATTATGTAGCAAATGT-ATTATTCGAAC
* * * **
33423 AAATAATTTTGGTTCACCATTATTCAAGT-ATTTTTTTCCCATACCATGATCGTAAATTTTTACC
189 AAATAATTATGGTTCACCATTATTCAAGTAATTTTTTT-CCAGACAATGATCGTAAAAATTTACC
33487 CATCATAGAGACTAAATAAAAAAT
253 CATCATAGAGACTAAATAAAAAAT
33511 AAAATCATAT
Statistics
Matches: 234, Mismatches: 32, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
278 57 0.24
279 121 0.52
280 36 0.15
281 20 0.09
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (280 bp):
AAAGAATATTCTTAAAAACATAGTAGATAAAGATTAATTATGAAAAACATAATAATAAATTTAAA
GAAAAAATCAAAGTACACTAGGGGAAACACATTGCAATCATGGAGTCTGCCCACATTTCAATCGA
AGACGCACCAAAATCCTTACGTCACACCTCGATTATGTAGCAAATGTATTATTCGAACAAATAAT
TATGGTTCACCATTATTCAAGTAATTTTTTTCCAGACAATGATCGTAAAAATTTACCCATCATAG
AGACTAAATAAAAAATCTGG
Found at i:36487 original size:36 final size:36
Alignment explanation
Indices: 36447--36539 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
36437 TGAGGAGGAG
*
36447 GTTGAAACTGCTGCAAATCAAATGCAACAACACACA
1 GTTGAAACTGCTGCAGATCAAATGCAACAACACACA
* *
36483 GTTGAAACTGCTGCAGATCAAATGCAGCAACATACA
1 GTTGAAACTGCTGCAGATCAAATGCAACAACACACA
* *
36519 GTTGTAACTACTGCAGATCAA
1 GTTGAAACTGCTGCAGATCAA
36540 GTTTAACAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (36 bp):
GTTGAAACTGCTGCAGATCAAATGCAACAACACACA
Found at i:38949 original size:28 final size:28
Alignment explanation
Indices: 38909--38978 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
38899 TGAGATGGGG
* *
38909 TAGGTCTCCATGCACGCCCATCGACCTA
1 TAGGTCGCCATGCACGCCCAGCGACCTA
38937 TAGGTCGCCATGCACGCCCAGCGACCTA
1 TAGGTCGCCATGCACGCCCAGCGACCTA
38965 TAGGTCGCCATGCA
1 TAGGTCGCCATGCA
38979 ATCATGGCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.19
Consensus pattern (28 bp):
TAGGTCGCCATGCACGCCCAGCGACCTA
Found at i:39174 original size:24 final size:25
Alignment explanation
Indices: 39147--39217 Score: 99
Period size: 24 Copynumber: 2.9 Consensus size: 25
39137 CTGCTGCATT
*
39147 ATTACAGCGTTCAACGCTCAAA-TA
1 ATTACAGCCTTCAACGCTCAAATTA
*
39171 ATTACAGCCTTCAACGCTCAAATTT
1 ATTACAGCCTTCAACGCTCAAATTA
**
39196 ATTGTAGCCTTCAACGCTCAAA
1 ATTACAGCCTTCAACGCTCAAA
39218 GTGAGTTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (25 bp):
ATTACAGCCTTCAACGCTCAAATTA
Found at i:39287 original size:19 final size:19
Alignment explanation
Indices: 39263--39308 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
39253 GAAGCATAAG
39263 AAAGAAAGAAATTTTGTCA
1 AAAGAAAGAAATTTTGTCA
* * *
39282 AAAGAAATAAATTTTTTCG
1 AAAGAAAGAAATTTTGTCA
39301 AAAGAAAG
1 AAAGAAAG
39309 GAAAGGAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.26
Consensus pattern (19 bp):
AAAGAAAGAAATTTTGTCA
Found at i:39398 original size:18 final size:17
Alignment explanation
Indices: 39365--39398 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39355 GAGGTAATTT
*
39365 TTTATTATTTAAATTAG
1 TTTATTATTGAAATTAG
39382 TTTATTATATGAAATTA
1 TTTATTAT-TGAAATTA
39399 TTAGTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTATTATTGAAATTAG
Found at i:39468 original size:21 final size:21
Alignment explanation
Indices: 39443--39486 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
39433 AATTTAGTTA
39443 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
39464 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
39485 AT
1 AT
39487 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:39559 original size:44 final size:48
Alignment explanation
Indices: 39464--39571 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 48
39454 AGTATAAATT
39464 ATTAGTTTGTTAGTTTAAGTTATATATTATATTATATAAAAAATTAGTTA
1 ATTAGTTTGTTAGTTTAAG-T-TATATTATATTATATAAAAAATTAGTTA
* * *
39514 ATTAGTTTATTAGTTTAAG-T-TATTATA-TGTA-AAAAAATTATTTA
1 ATTAGTTTGTTAGTTTAAGTTATATTATATTATATAAAAAATTAGTTA
*
39558 ATTAATTTGTTAGT
1 ATTAGTTTGTTAGT
39572 GTGTTTAAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
44 24 0.45
45 3 0.06
46 7 0.13
47 1 0.02
50 18 0.34
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (48 bp):
ATTAGTTTGTTAGTTTAAGTTATATTATATTATATAAAAAATTAGTTA
Found at i:39927 original size:4 final size:4
Alignment explanation
Indices: 39918--39943 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
39908 TATGTGTAAA
39918 TTAG TTAG TTAG TTAG TTAG TTAG TT
1 TTAG TTAG TTAG TTAG TTAG TTAG TT
39944 TATATTTAGA
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:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (4 bp):
TTAG
Found at i:40042 original size:17 final size:17
Alignment explanation
Indices: 39986--40046 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
39976 ATTTATTCCC
*
39986 GTTTAAAAAAAATATTAT
1 GTTT-AAAAAAATATTTT
*
40004 GTTTAAAAATATTTATTGTT
1 GTTTAAAAA-A-ATATT-TT
40024 GTTTAAAAAAATATTTT
1 GTTTAAAAAAATATTTT
40041 GTTTAA
1 GTTTAA
40047 TTTATATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 13 0.35
18 9 0.24
19 5 0.14
20 10 0.27
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (17 bp):
GTTTAAAAAAATATTTT
Found at i:40042 original size:20 final size:20
Alignment explanation
Indices: 39986--40043 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
39976 ATTTATTCCC
* *
39986 GTTTAAAAAAA-ATATT-AT
1 GTTTAAAAAAATATTTTGTT
*
40004 GTTTAAAAATAT-TTATTGTT
1 GTTTAAAAAAATATT-TTGTT
40024 GTTTAAAAAAATATTTTGTT
1 GTTTAAAAAAATATTTTGTT
40044 TAATTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.34
19 2 0.06
20 17 0.53
21 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (20 bp):
GTTTAAAAAAATATTTTGTT
Found at i:40301 original size:26 final size:28
Alignment explanation
Indices: 40238--40316 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
40228 TATTTATAAT
40238 AAATAATTATTAATAATCATTACTAAATC
1 AAATAATTATTAATAATCATTAC-AAATC
* *
40267 ATATTATTATT-A-AATCATTA-AATATC
1 AAATAATTATTAATAATCATTACAA-ATC
*
40293 AAATAATTAGATTAATAATAATTA
1 AAATAATT--ATTAATAATCATTA
40317 TTAAATCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
25 2 0.05
26 9 0.22
27 8 0.20
28 4 0.10
29 10 0.25
30 7 0.17
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (28 bp):
AAATAATTATTAATAATCATTACAAATC
Found at i:42055 original size:22 final size:22
Alignment explanation
Indices: 42027--42087 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
42017 GGGTCTATGC
**
42027 GGTCCTTCGGGACGTATACAGA
1 GGTCCTTCGGGACAAATACAGA
* *
42049 GGTCCTTCGGAACAAATACATA
1 GGTCCTTCGGGACAAATACAGA
*
42071 GGTCATTCGGGACAAAT
1 GGTCCTTCGGGACAAAT
42088 TTCACATGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (22 bp):
GGTCCTTCGGGACAAATACAGA
Found at i:42647 original size:21 final size:21
Alignment explanation
Indices: 42606--42647 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42596 TACGGAAGTA
**
42606 CTGTAGCAGGGTATCGGTACC
1 CTGTAGCAGGGTATCAATACC
*
42627 CTGTAGCATGGTATCAATACC
1 CTGTAGCAGGGTATCAATACC
42648 ATAGCAGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (21 bp):
CTGTAGCAGGGTATCAATACC
Found at i:46114 original size:40 final size:39
Alignment explanation
Indices: 46065--46168 Score: 135
Period size: 36 Copynumber: 2.7 Consensus size: 39
46055 ATTACTTAAA
46065 AACACAAACTAATTAAATATTTTTATATATAACTAACTAAC
1 AACACAAACTAATTAAATATTTTTATATAT-A-TAACTAAC
* *
46106 AACA-AAACTAATTAATTATTTTT-TA-ATATAACTATC
1 AACACAAACTAATTAAATATTTTTATATATATAACTAAC
*
46142 AA-ACAAACTAATTAAATAATTTTATAT
1 AACACAAACTAATTAAATATTTTTATAT
46169 TTATGTATGA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
35 1 0.02
36 26 0.46
37 3 0.05
38 2 0.04
39 2 0.04
40 18 0.32
41 4 0.07
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.38
Consensus pattern (39 bp):
AACACAAACTAATTAAATATTTTTATATATATAACTAAC
Found at i:46231 original size:21 final size:21
Alignment explanation
Indices: 46178--46217 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
46168 TTTATGTATG
46178 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
46199 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
46218 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:46298 original size:17 final size:18
Alignment explanation
Indices: 46269--46302 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
46259 AACAAACTAA
46269 TAATTTAAAATAATAAAC
1 TAATTTAAAATAATAAAC
46287 TAATTT-AAATAATAAA
1 TAATTTAAAATAATAAA
46303 AAATTACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATTTAAAATAATAAAC
Found at i:46358 original size:24 final size:24
Alignment explanation
Indices: 46331--46379 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
46321 GCCTTATCTC
*
46331 CCTTTCT-TCTTCTTCCTTTCATTT
1 CCTTTCTCTCTTCTCCCTTTC-TTT
46355 CCTTTCTCTCTTCTCCCTTTCTTT
1 CCTTTCTCTCTTCTCCCTTTCTTT
46379 C
1 C
46380 TTTTATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (24 bp):
CCTTTCTCTCTTCTCCCTTTCTTT
Found at i:46532 original size:12 final size:12
Alignment explanation
Indices: 46515--46580 Score: 64
Period size: 12 Copynumber: 5.5 Consensus size: 12
46505 AATAATGCAA
46515 CAATAAGTGTTG
1 CAATAAGTGTTG
**
46527 CAATAA-TGCAG
1 CAATAAGTGTTG
46538 CGAATAAGTGTTG
1 C-AATAAGTGTTG
**
46551 CAATAA-TGCAG
1 CAATAAGTGTTG
46562 CGAATAAGTGTTG
1 C-AATAAGTGTTG
46575 CAATAA
1 CAATAA
46581 TGCAGCAGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 8 0.19
12 26 0.62
13 8 0.19
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (12 bp):
CAATAAGTGTTG
Found at i:46548 original size:24 final size:24
Alignment explanation
Indices: 46500--46586 Score: 158
Period size: 24 Copynumber: 3.7 Consensus size: 24
46490 TGCATTGAAG
*
46500 GTTGCAATAATGCAAC-AATAAGT
1 GTTGCAATAATGCAGCGAATAAGT
46523 GTTGCAATAATGCAGCGAATAAGT
1 GTTGCAATAATGCAGCGAATAAGT
46547 GTTGCAATAATGCAGCGAATAAGT
1 GTTGCAATAATGCAGCGAATAAGT
46571 GTTGCAATAATGCAGC
1 GTTGCAATAATGCAGC
46587 AGCTGAATTC
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
23 15 0.24
24 47 0.76
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (24 bp):
GTTGCAATAATGCAGCGAATAAGT
Found at i:46741 original size:28 final size:28
Alignment explanation
Indices: 46672--46746 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
46662 TGGTCGCCGA
* *
46672 GCGTGCATGGCGACCTAGCATGTCGCGGG
1 GCGTGCATGGCGACCTA-CAGGTCACGGG
* * *
46701 GCTTGCATAGCGACCTACAGGTCACTGG
1 GCGTGCATGGCGACCTACAGGTCACGGG
46729 GCGTGCATGGCGACCTAC
1 GCGTGCATGGCGACCTAC
46747 CCCGACGTGC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 24 0.62
29 15 0.38
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.19
Consensus pattern (28 bp):
GCGTGCATGGCGACCTACAGGTCACGGG
Found at i:50576 original size:20 final size:20
Alignment explanation
Indices: 50551--50601 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
50541 TCACAAATGT
*
50551 AAGATTATCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
50571 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
50591 AAGATTACCAG
1 AAGATTACCAG
50602 AGAATAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Done.