Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006291.1 Hibiscus syriacus cultivar Beakdansim tig00015027_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: 145327
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:9227 original size:22 final size:22
Alignment explanation
Indices: 9199--9276 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
9189 GTTTATAGTA
9199 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
9221 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
* *
9243 GTTCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
*
9265 ATCCTTCGGGAT
1 GTCCTTCGGGAT
9277 AAATATTTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.14, C:0.23, G:0.31, T:0.32
Consensus pattern (22 bp):
GTCCTTCGGGATGTATCCAGTG
Found at i:13450 original size:20 final size:19
Alignment explanation
Indices: 13413--13450 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
13403 CAAACCTAAC
*
13413 CCTAAAAATTCCTTTTTCT
1 CCTAAAAATTCCTGTTTCT
13432 CCTAAAAATTCCTCGTTTC
1 CCTAAAAATTCCT-GTTTC
13451 ACTCGAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (19 bp):
CCTAAAAATTCCTGTTTCT
Found at i:17074 original size:21 final size:21
Alignment explanation
Indices: 17028--17090 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
17018 ATATGCTCAC
*
17028 TAATTTTTCAAATTGGTCATT
1 TAATTTTTCAAATTGATCATT
* *
17049 AAATTTTTCAAATTGATCTTT
1 TAATTTTTCAAATTGATCATT
*
17070 TAATTCTTT-AACTTGATCATT
1 TAATT-TTTCAAATTGATCATT
17091 CATTATAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 32 0.91
22 3 0.09
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.52
Consensus pattern (21 bp):
TAATTTTTCAAATTGATCATT
Found at i:20048 original size:79 final size:78
Alignment explanation
Indices: 19938--20116 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 78
19928 TTCAATCTTA
* * *
19938 ACTCAACTTCACAATGAAGGAGTCACCCACGATTTCAACTTCACAATGAAGGATATCGTGCCCAA
1 ACTCAACTTCACAAAGAATGAGTCACCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCAA
* *
20003 GACACTCGAAATTG
66 AACACTCGAAA-TC
* * * * *
20017 ACTCAACTTCACGACGAATGAGTCATCCACGATTTCAACTTCACGACGAATGATATCGTGCCCAA
1 ACTCAACTTCACAAAGAATGAGTCACCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCAA
* *
20082 AATACTCGATATC
66 AACACTCGAAATC
20095 AGCTCAACTTCACAAAGAATGA
1 A-CTCAACTTCACAAAGAATGA
20117 TATTGAACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 2 0.02
79 84 0.98
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (78 bp):
ACTCAACTTCACAAAGAATGAGTCACCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCAA
AACACTCGAAATC
Found at i:20814 original size:31 final size:30
Alignment explanation
Indices: 20771--20959 Score: 140
Period size: 31 Copynumber: 6.0 Consensus size: 30
20761 CCCTTTTATG
* * *
20771 TTATATATTATATAGTATAGTATATAGTATA
1 TTATATAATATATATTATATTATATA-TATA
20802 TTATATAATATATAGTGTATTATTATATATAGTA
1 TTATATAATATATA-T-TA-TATTATATATA-TA
*
20836 TATATTATATTATATATTATATTATTATTATAGTA
1 T-TA-TATAATATATATTATATTA-TA-TATA-TA
20871 TTATAT--TATATATTATA-TATATATATA
1 TTATATAATATATATTATATTATATATATA
*
20898 TT-TATTATAT-TATTATA-TATATTATAGTA
1 TTATATAATATATATTATATTATA-TATA-TA
*
20927 TT-TATATTATTATTATATATATTATATATATA
1 TTATATAATA-TA-TAT-TATATTATATATATA
20959 T
1 T
20960 CGTAGTATTT
Statistics
Matches: 135, Mismatches: 6, Indels: 33
0.78 0.03 0.19
Matches are distributed among these distances:
26 3 0.02
27 15 0.11
28 11 0.08
29 11 0.08
30 3 0.02
31 24 0.18
32 6 0.04
33 20 0.15
34 21 0.16
35 11 0.08
36 10 0.07
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (30 bp):
TTATATAATATATATTATATTATATATATA
Found at i:20831 original size:36 final size:36
Alignment explanation
Indices: 20791--20968 Score: 156
Period size: 38 Copynumber: 4.9 Consensus size: 36
20781 TATAGTATAG
*
20791 TATATAGTATATTATATAATATATAGTGTATTATTAT
1 TATATA-TATATTATATAATATATAGTATATTATTAT
*
20828 ATATAGTATATATTATAT--TATATATTATATTATTAT
1 -TATA-TATATATTATATAATATATAGTATATTATTAT
*
20864 TATAGTATTATATTATATATTATATA-TATA-TA-TAT
1 TATA-TA-TATATTATATAATATATAGTATATTATTAT
*
20899 T-TAT-TATATTATTATATATATTATAGTATTTATATTAT
1 TATATATATATTA-TATA-ATA-TATAGTATAT-TATTAT
*
20937 TATTATATATATTATAT-ATATATCGTAGTATT
1 TA-TATATATATTATATAATATATAGTA-TATT
20969 TATATTGTTA
Statistics
Matches: 119, Mismatches: 6, Indels: 31
0.76 0.04 0.20
Matches are distributed among these distances:
31 7 0.06
32 4 0.03
33 3 0.03
34 6 0.05
35 14 0.12
36 28 0.24
37 13 0.11
38 29 0.24
39 2 0.02
40 6 0.05
41 7 0.06
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (36 bp):
TATATATATATTATATAATATATAGTATATTATTAT
Found at i:20872 original size:50 final size:51
Alignment explanation
Indices: 20772--20953 Score: 186
Period size: 50 Copynumber: 3.6 Consensus size: 51
20762 CCTTTTATGT
*
20772 TATATATTATATAGTATAGTATATAGTATATTATA-TAATA-TATAGTGTATTATTA-
1 TATATATTATATA-T-TA-TATATA-TATATTATATTATTATTATA--GTATTA-TAG
* *
20827 TATATAGTATATATTATAT-TATATATTATATTATTATTATAGTATTATAT
1 TATATATTATATATTATATATATATATTATATTATTATTATAGTATTATAG
*
20877 TATATATTATATA-TATATATATTTATTATATTATTA-TATA-TATTATAG
1 TATATATTATATATTATATATATATATTATATTATTATTATAGTATTATAG
*
20925 TATTTA-TAT-TATTAT-TATATATATTATAT
1 TATATATTATATATTATATATATATATTATAT
20954 ATATATCGTA
Statistics
Matches: 115, Mismatches: 7, Indels: 19
0.82 0.05 0.13
Matches are distributed among these distances:
46 15 0.13
47 6 0.05
48 12 0.10
49 11 0.10
50 43 0.37
51 6 0.05
52 7 0.06
53 2 0.02
54 1 0.01
55 12 0.10
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (51 bp):
TATATATTATATATTATATATATATATTATATTATTATTATAGTATTATAG
Found at i:27464 original size:22 final size:22
Alignment explanation
Indices: 27436--27513 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
27426 GTTTATAGTA
*
27436 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
27458 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
*
27480 GTTCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
*
27502 ATCCTTCGGGAT
1 GTCCTTCGGGAT
27514 AAATATTTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.14, C:0.23, G:0.31, T:0.32
Consensus pattern (22 bp):
GTCCTTCGGGATGTATCCAGTG
Found at i:31709 original size:20 final size:19
Alignment explanation
Indices: 31672--31709 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
31662 CAAACCTAAC
*
31672 CCTAAAAATTCCTTTTTCT
1 CCTAAAAATTCCTGTTTCT
31691 CCTAAAAATTCCTCGTTTC
1 CCTAAAAATTCCT-GTTTC
31710 ACTCGAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (19 bp):
CCTAAAAATTCCTGTTTCT
Found at i:35453 original size:21 final size:21
Alignment explanation
Indices: 35407--35469 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
35397 ATATGCTCAC
*
35407 TAATTTTTCAAATTGGTCATT
1 TAATTTTTCAAATTGATCATT
* *
35428 AAATTTTTCAAATTGATCTTT
1 TAATTTTTCAAATTGATCATT
*
35449 TAATTCTTT-AACTTGATCATT
1 TAATT-TTTCAAATTGATCATT
35470 CATTATAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 32 0.91
22 3 0.09
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.52
Consensus pattern (21 bp):
TAATTTTTCAAATTGATCATT
Found at i:38419 original size:79 final size:78
Alignment explanation
Indices: 38309--38487 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 78
38299 TTCAATCTTA
* * *
38309 ACTCAACTTCACAATGAAGGAGTCACCCACGATTTCAACTTCACAATGAAGGATATCGTGCCCAA
1 ACTCAACTTCACAAAGAATGAGTCACCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCAA
* *
38374 GACACTCGAAATTG
66 AACACTCGAAA-TC
* * * * *
38388 ACTCAACTTCACGACGAATGAGTCATCCACGATTTCAACTTCACGACGAATGATATCGTGCCCAA
1 ACTCAACTTCACAAAGAATGAGTCACCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCAA
* *
38453 AATACTCGATATC
66 AACACTCGAAATC
38466 AGCTCAACTTCACAAAGAATGA
1 A-CTCAACTTCACAAAGAATGA
38488 TATTGAACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 2 0.02
79 84 0.98
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (78 bp):
ACTCAACTTCACAAAGAATGAGTCACCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCAA
AACACTCGAAATC
Found at i:39163 original size:2 final size:2
Alignment explanation
Indices: 39151--39354 Score: 173
Period size: 2 Copynumber: 109.5 Consensus size: 2
39141 CCTTTTATGT
*
39151 TA TA TA T- TA TA TA GTA TA GTA TA TA GTA TA T- TA TA TA TA GTG
1 TA TA TA TA TA TA TA -TA TA -TA TA TA -TA TA TA TA TA TA TA -TA
39193 TA T- TA T- TA TA TA GTA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39233 TA GTA TA TA T- TA TA T- TA TA T- TA TA T- TA T- TA T- TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39270 T- TA TA TA TA T- TA TA TA TA TA TA T- TA T- TA TA TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
39306 TA TA TA TA T- TA TA GTA TT TA TA T- TA T- TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39345 T- TA TA TA TA T
1 TA TA TA TA TA T
39355 CGTAGTATTT
Statistics
Matches: 169, Mismatches: 4, Indels: 58
0.73 0.02 0.25
Matches are distributed among these distances:
1 22 0.13
2 134 0.79
3 13 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (2 bp):
TA
Found at i:39286 original size:71 final size:70
Alignment explanation
Indices: 39151--39354 Score: 248
Period size: 71 Copynumber: 3.0 Consensus size: 70
39141 CCTTTTATGT
* * *
39151 TATATAT-TATATAGTATAGTATATAGTATATTATA-TATAGT-GTATTAT-TATATAGTATAT-
1 TATATATATATATAGTATAGTATATATTATATTATATTATATTATTATTATATATATA-TATATA
39211 TATATA
65 TATATA
39217 TATATATATATATA-TATAGTATATATTATATTATATTATATTATTATTATATAT-TATATATAT
1 TATATATATATATAGTATAGTATATATTATATTATATTATATTATTATTATATATATATATATA-
39280 TATATA
65 TATATA
* *
39286 TATATATTATTATATATTATTA-TATATATTATAGTAT-TTATATTATTATTATATATATAT-TA
1 TATATA-TA-TATATAGTA-TAGTATATATTATATTATATTATATTATTATTATATATATATATA
39348 TATATAT
63 TATATAT
39355 CGTAGTATTT
Statistics
Matches: 123, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
66 27 0.22
67 16 0.13
68 8 0.07
69 15 0.12
70 7 0.06
71 29 0.24
72 19 0.15
73 2 0.02
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (70 bp):
TATATATATATATAGTATAGTATATATTATATTATATTATATTATTATTATATATATATATATAT
ATATA
Found at i:39375 original size:124 final size:122
Alignment explanation
Indices: 39151--39369 Score: 297
Period size: 121 Copynumber: 1.8 Consensus size: 122
39141 CCTTTTATGT
* * *
39151 TATATATTATATAGTATAGTATATAGTATATTATATATAGTGTATTATTATATAGTATATTATAT
1 TATATATTATATAATATAGTATATAGTATATTATATATAGTATAGTATTATATAGTATATTATAT
39216 ATATATATATATATATATAGTATATATTATATTATATTATATTATTATTATATATTA
66 ATATATATATATATATATAGTATATATTATATTATATTATATTATTATTATATATTA
* *
39273 TATATATTATATATATATATTATTATA-TATTATTATATATATTATAGTATT-TATA-T-TATTA
1 TATATATTATATA-ATATAGTA-TATAGTA-TATTATATATAGTATAGTATTATATAGTATATTA
*
39334 T-TATATATATATTATATATATCGTAGTAT-TTATATT
63 TATATATATATA-TATATATATAGTA-TATATTATATT
39370 GTTATAGAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
120 10 0.12
121 25 0.29
122 17 0.20
123 12 0.14
124 22 0.26
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (122 bp):
TATATATTATATAATATAGTATATAGTATATTATATATAGTATAGTATTATATAGTATATTATAT
ATATATATATATATATATAGTATATATTATATTATATTATATTATTATTATATATTA
Found at i:45918 original size:22 final size:22
Alignment explanation
Indices: 45890--45967 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
45880 GTTTATAGTA
45890 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
45912 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
* * *
45934 GTTCTTCGAGACGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
*
45956 ATCCTTCGGGAT
1 GTCCTTCGGGAT
45968 AAATATTTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.32
Consensus pattern (22 bp):
GTCCTTCGGGATGTATCCAGTG
Found at i:50159 original size:20 final size:19
Alignment explanation
Indices: 50122--50159 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
50112 CAAACCTAAC
*
50122 CCTAAAAATTCCTTTTTCT
1 CCTAAAAATTCCTATTTCT
50141 CCTAAAAATTCCTCATTTC
1 CCTAAAAATTCCT-ATTTC
50160 ACTCGAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (19 bp):
CCTAAAAATTCCTATTTCT
Found at i:53898 original size:21 final size:21
Alignment explanation
Indices: 53852--53914 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
53842 ATATGCTCAC
*
53852 TAATTTTTCAAATTGGTCATT
1 TAATTTTTCAAATTGATCATT
* *
53873 AAATTTTTCAAATTGATCTTT
1 TAATTTTTCAAATTGATCATT
*
53894 TAATTCTTT-AACTTGATCATT
1 TAATT-TTTCAAATTGATCATT
53915 CATTATAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 32 0.91
22 3 0.09
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.52
Consensus pattern (21 bp):
TAATTTTTCAAATTGATCATT
Found at i:56864 original size:79 final size:78
Alignment explanation
Indices: 56754--56932 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 78
56744 TTCAATCTTA
* * *
56754 ACTCAACTTCACAATGAAGGAGTCACCCACGATTTC-AACTTCACAATGAAGGATATCGTGCCCA
1 ACTCAACTTCACAAAGAATGAGTCACCCACGATTTCAAAC-TCACAACGAAGGATATCGTGCCCA
* *
56818 AGACACTCGAAATTG
65 AAACACTCGAAA-TC
* * * * *
56833 ACTCAACTTCACGACGAATGAGTCATCCACGATTTCAAACTCACGACGAATGATATCGTGCCCAA
1 ACTCAACTTCACAAAGAATGAGTCACCCACGATTTCAAACTCACAACGAAGGATATCGTGCCCAA
* *
56898 AATACTCGATATC
66 AACACTCGAAATC
56911 AGCTCAACTTCACAAAGAATGA
1 A-CTCAACTTCACAAAGAATGA
56933 TATTGAACTA
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
78 2 0.02
79 80 0.94
80 3 0.04
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (78 bp):
ACTCAACTTCACAAAGAATGAGTCACCCACGATTTCAAACTCACAACGAAGGATATCGTGCCCAA
AACACTCGAAATC
Found at i:57600 original size:7 final size:7
Alignment explanation
Indices: 57588--57881 Score: 201
Period size: 7 Copynumber: 39.6 Consensus size: 7
57578 CCCTTTTATG
57588 TTATATA
1 TTATATA
57595 TTATATA
1 TTATATA
57602 GTATAGTATA
1 -T-TA-TATA
57612 TTATATA
1 TTATATA
*
57619 ATATATA
1 TTATATA
57626 GTGTAT-TA
1 -T-TATATA
57634 TTATATA
1 TTATATA
57641 -TAGTATA
1 TTA-TATA
57648 TTATATA
1 TTATATA
*
57655 GTATATA
1 TTATATA
*
57662 GTATATA
1 TTATATA
*
57669 TCATATA
1 TTATATA
57676 -TATAGTA
1 TTATA-TA
57683 TATATTATA
1 T-TA-TATA
57692 TTATATA
1 TTATATA
57699 TTATATTA
1 TTATA-TA
57707 TTATTATA
1 TTA-TATA
*
57715 GTATTATA
1 TTA-TATA
57723 TTATATA
1 TTATATA
57730 TTATATA
1 TTATATA
57737 TTATATA
1 TTATATA
57744 -TATATA
1 TTATATA
57750 TTTATATA
1 -TTATATA
57758 TTATATATA
1 -T-TATATA
57767 TTATAGTA
1 TTATA-TA
57775 TT-TATA
1 TTATATA
57781 TTAT-TA
1 TTATATA
57787 TTATATA
1 TTATATA
57794 TATATATA
1 T-TATATA
57802 TCGTAGTAT-
1 T--TA-TATA
*
57811 TTATATTG
1 TTATA-TA
*
57819 TTATAGA
1 TTATATA
*
57826 GTATACTA
1 TTATA-TA
*
57834 TTATAGTTG
1 TTATA--TA
57843 TTATATA
1 TTATATA
*
57850 TTAGA-A
1 TTATATA
57856 TTATATTA
1 TTATA-TA
57864 TATATATA
1 T-TATATA
57872 TTATAT-
1 TTATATA
57878 TTAT
1 TTAT
57882 TACGTTATAT
Statistics
Matches: 238, Mismatches: 19, Indels: 61
0.75 0.06 0.19
Matches are distributed among these distances:
6 35 0.15
7 102 0.43
8 60 0.25
9 32 0.13
10 9 0.04
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (7 bp):
TTATATA
Found at i:57601 original size:2 final size:2
Alignment explanation
Indices: 57589--57802 Score: 164
Period size: 2 Copynumber: 112.5 Consensus size: 2
57579 CCTTTTATGT
*
57589 TA TA TA T- TA TA TA GTA TA GTA TA T- TA TA TA -A TA TA TA GTG
1 TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA -TA
57629 TA T- TA T- TA TA TA TA GTA TA T- TA TA TA GTA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA
57669 TCA TA TA TA TA GTA TA TA T- TA TA T- TA TA TA T- TA TA T- TA T-
1 T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57708 TA T- TA TA GTA T- TA TA T- TA TA TA T- TA TA TA T- TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
57746 TA TA TT TA TA TA T- TA TA TA TA T- TA TA GTA TT TA TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
57785 TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
57803 CGTAGTATTT
Statistics
Matches: 175, Mismatches: 6, Indels: 62
0.72 0.02 0.26
Matches are distributed among these distances:
1 21 0.12
2 135 0.77
3 19 0.11
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (2 bp):
TA
Found at i:57780 original size:89 final size:88
Alignment explanation
Indices: 57590--57875 Score: 152
Period size: 94 Copynumber: 3.2 Consensus size: 88
57580 CTTTTATGTT
* * * *
57590 ATATATTATAT-AGTA-TAGTATATTATATAATATA-TAGTGTATTATTATATATAGTATATTAT
1 ATATATTATATTATTATTA-TATATTATATTATATATTA-TATATTA-TATATATA-TATAATAT
* * *
57652 ATAGTATA-TAGTATATATCATATA-T
62 ATATTATATTATTATATATAATATATT
*
57677 ATAGTA-TATATTA-TATTATATATTATATTAT-TATTATAGTATTATAT-TATATATTATATAT
1 ATA-TATTATATTATTATTATATATTATATTATATATTATA-TATTATATATATATATAATATA-
57738 TATATATATATATTTATATATTATATATATT
63 TAT-TATAT-TA-TTATATA-TA-ATATATT
** *
57769 ATAGTATTTATATTATTATTATATA-TATA-TATATCGTAGTAT-TTATAT-TGT-TATAGAGTA
1 ATA-TA-TTATATTATTATTATATATTATATTATATATTA-TATATTATATATATATATA-A-TA
*
57829 TACTATTATAGTTGTTATATATTAGAATTATATT
61 TA-TATTATA-TTATTATATA-T--AA-TATATT
57863 ATATA-TATATTAT
1 ATATATTATATTAT
57876 ATTTATTACG
Statistics
Matches: 162, Mismatches: 13, Indels: 44
0.74 0.06 0.20
Matches are distributed among these distances:
84 7 0.04
85 6 0.04
86 10 0.06
87 29 0.18
88 7 0.04
89 6 0.04
90 1 0.01
91 13 0.08
92 19 0.12
93 20 0.12
94 33 0.20
95 11 0.07
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.52
Consensus pattern (88 bp):
ATATATTATATTATTATTATATATTATATTATATATTATATATTATATATATATATAATATATAT
TATATTATTATATATAATATATT
Found at i:57817 original size:35 final size:34
Alignment explanation
Indices: 57588--57802 Score: 159
Period size: 37 Copynumber: 6.3 Consensus size: 34
57578 CCCTTTTATG
*
57588 TTATATATTATATAGTATAGTATATTATATAATATATA
1 TTATATA-TATATA-TAT-GTATATT-TATATTATATA
*
57626 GTGTAT-TAT-TATATATAGTATATTATATAGTATATA
1 -T-TATATATATATATAT-GTATATT-TATATTATATA
*
57662 GTATATATCATATATATAGTATATATTATATTATATA
1 TTATATAT-ATATATAT-GTATAT-TTATATTATATA
*
57699 TTATAT-TAT-TAT-TATAGTA-TTATATTATATA
1 TTATATATATATATATGTA-TATTTATATTATATA
*
57730 TTATATAT-TATATATATATATTTATA-TAT-TA
1 TTATATATATATATATGTATATTTATATTATATA
*
57761 -TATATAT-TATAGTATTTATA-TTATTATTATATA
1 TTATATATATATA-TATGTATATTTA-TATTATATA
57794 -TATATATAT
1 TTATATATAT
57803 CGTAGTATTT
Statistics
Matches: 155, Mismatches: 6, Indels: 35
0.79 0.03 0.18
Matches are distributed among these distances:
30 14 0.09
31 30 0.19
32 14 0.09
33 21 0.14
34 7 0.05
35 5 0.03
36 23 0.15
37 33 0.21
38 2 0.01
39 3 0.02
40 3 0.02
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (34 bp):
TTATATATATATATATGTATATTTATATTATATA
Found at i:57889 original size:67 final size:65
Alignment explanation
Indices: 57761--57890 Score: 149
Period size: 67 Copynumber: 2.0 Consensus size: 65
57751 TTATATATTA
** *
57761 TATATATTATAGTATTTATATTATTATTATATATATATATATCGTAGTATTTATATTGTTATAGA
1 TATATATTATAGTATTTATATTAGAATTATATATATATATATC-TAGTATTTATATCGTTATAGA
57826 G
65 G
*
57827 TATACTATTATAGTTGTTATATATTAGAATTATATTATATATATAT-TA-TATTTAT-TACGTTA
1 TATA-TATTATAG-TATT-TATATTAGAATTATA-TATATATATATCTAGTATTTATAT-CGTTA
57889 TA
61 TA
57891 TTTATTAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
66 5 0.09
67 21 0.38
68 5 0.09
69 13 0.24
70 11 0.20
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (65 bp):
TATATATTATAGTATTTATATTAGAATTATATATATATATATCTAGTATTTATATCGTTATAGAG
Found at i:58219 original size:6 final size:6
Alignment explanation
Indices: 58200--58242 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
58190 TGTTAAACGA
* *
58200 GGACGG GGATGG GGACGG GGACGG GGACGG GGACGA GGACGG G
1 GGACGG GGACGG GGACGG GGACGG GGACGG GGACGG GGACGG G
58243 TTTGGTAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.19, C:0.14, G:0.65, T:0.02
Consensus pattern (6 bp):
GGACGG
Found at i:58223 original size:18 final size:18
Alignment explanation
Indices: 58196--58242 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
58186 TTTATGTTAA
*
58196 ACGAGGACGGGGATGGGG
1 ACGAGGACGGGGACGGGG
*
58214 ACGGGGACGGGGACGGGG
1 ACGAGGACGGGGACGGGG
58232 ACGAGGACGGG
1 ACGAGGACGGG
58243 TTTGGTAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.21, C:0.15, G:0.62, T:0.02
Consensus pattern (18 bp):
ACGAGGACGGGGACGGGG
Found at i:65559 original size:11 final size:12
Alignment explanation
Indices: 65536--65561 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
65526 ATTTTTCTGA
65536 TTTTTGTATTTT
1 TTTTTGTATTTT
65548 TTTTTGTATTTT
1 TTTTTGTATTTT
65560 TT
1 TT
65562 ATATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTTGTATTTT
Found at i:65577 original size:19 final size:19
Alignment explanation
Indices: 65527--65578 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
65517 TGTTTTGTAA
*
65527 TTTTTCTGATTTTTGTATT
1 TTTTTATGATTTTTGTATT
*
65546 TTTTTTTGTATTTTT-TATAT
1 TTTTTATG-ATTTTTGTAT-T
65566 TTTTTATGATTTT
1 TTTTTATGATTTT
65579 ATTCAAGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.13, C:0.02, G:0.08, T:0.77
Consensus pattern (19 bp):
TTTTTATGATTTTTGTATT
Found at i:66512 original size:12 final size:12
Alignment explanation
Indices: 66497--66538 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
66487 AAAATAAATG
66497 TTTAAATAATAC
1 TTTAAATAATAC
* *
66509 TTTAAAT-TTAG
1 TTTAAATAATAC
66520 TTTAAATAATAC
1 TTTAAATAATAC
66532 TTTAAAT
1 TTTAAAT
66539 TTATTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (12 bp):
TTTAAATAATAC
Found at i:66522 original size:23 final size:23
Alignment explanation
Indices: 66496--66550 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
66486 AAAAATAAAT
66496 GTTTAAATAATACTTTAAATTTA
1 GTTTAAATAATACTTTAAATTTA
66519 GTTTAAATAATACTTTAAATTTA
1 GTTTAAATAATACTTTAAATTTA
*
66542 TTTTAAATA
1 GTTTAAATA
66551 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
GTTTAAATAATACTTTAAATTTA
Found at i:66557 original size:10 final size:11
Alignment explanation
Indices: 66497--66558 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
66487 AAAATAAATG
*
66497 TTTAAATAATAC
1 TTTAAAT-ATAT
* *
66509 TTTAAATTTAG
1 TTTAAATATAT
*
66520 TTTAAATAATAC
1 TTTAAAT-ATAT
*
66532 TTTAAATTTAT
1 TTTAAATATAT
66543 TTTAAATAT-T
1 TTTAAATATAT
66553 TTTAAA
1 TTTAAA
66559 AAAATTCCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
10 7 0.17
11 19 0.45
12 16 0.38
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (11 bp):
TTTAAATATAT
Found at i:67171 original size:254 final size:256
Alignment explanation
Indices: 66722--67239 Score: 862
Period size: 254 Copynumber: 2.0 Consensus size: 256
66712 TTTTAAAAAG
66722 ACCTATATTTCTTTAAATCATAAAAAAACTCAAAATCTTAAAATTTTTAATTTTAACTCTCGTCA
1 ACCTATATTTCTTTAAATCATAAAAAAACTCAAAATCTTAAAATTTTTAATTTTAACTCTCGTCA
* *
66787 GTCATCTTTCATCATCACTTTTATCATCCAATAATCGCCCACATATCACCGTCTGCCCACTAACT
66 GTCATCTTTCATCATCACTTTTATCATCCAATAATCACCCACATATCACCGTCTGCCCACTAACC
66852 GACACTGCCCTTATCATATCCTTAAATTTATAAATCCTTAAACCCTAAATTCATAAATATTTCAA
131 GACACTGCCCTTATCATATCCTTAAATTTATAAATCCTTAAACCCTAAATTCATAAATATTTCAA
*
66917 CAAATTAA-CGG-T-GATAACTTAGGTGATGTTTGGTTCATTGGGAATTAAGAGGAATTGA
196 CAAATTAAGCGGTTCGATAACTTAGGTGACGTTTGGTTCATTGGGAATTAAGAGGAATTGA
66975 ACCTATATTTCTTTAAATCATAAAAAAAACTCAAAATCTTAAAATTTTTAATTTTAACTCTCGTC
1 ACCTATATTTCTTTAAATCAT-AAAAAAACTCAAAATCTTAAAATTTTTAATTTTAACTCTCGTC
*
67040 GGTCATCTTTCATCATCACTTTTATCATCCAATAATCACCCACATATCACCGTCTGCCCACTAAC
65 AGTCATCTTTCATCATCACTTTTATCATCCAATAATCACCCACATATCACCGTCTGCCCACTAAC
* * *
67105 CGACACTGCCCTTATCATATCCTTAAATTTATAAATCTTTAAACTCTAAATTCATAAATGTTTCA
130 CGACACTGCCCTTATCATATCCTTAAATTTATAAATCCTTAAACCCTAAATTCATAAATATTTCA
* *
67170 ACAAATTAATGGTGGTGGGGTTCGATAACTTAGGTGACGTTTGGTTCGTTGGGAATTAAGAGGAA
195 ACAAATTAA-------GCGGTTCGATAACTTAGGTGACGTTTGGTTCATTGGGAATTAAGAGGAA
67235 TTGA
253 TTGA
67239 A
1 A
67240 ATCCAATTTC
Statistics
Matches: 245, Mismatches: 9, Indels: 11
0.92 0.03 0.04
Matches are distributed among these distances:
253 21 0.09
254 176 0.72
262 2 0.01
263 1 0.00
264 45 0.18
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.35
Consensus pattern (256 bp):
ACCTATATTTCTTTAAATCATAAAAAAACTCAAAATCTTAAAATTTTTAATTTTAACTCTCGTCA
GTCATCTTTCATCATCACTTTTATCATCCAATAATCACCCACATATCACCGTCTGCCCACTAACC
GACACTGCCCTTATCATATCCTTAAATTTATAAATCCTTAAACCCTAAATTCATAAATATTTCAA
CAAATTAAGCGGTTCGATAACTTAGGTGACGTTTGGTTCATTGGGAATTAAGAGGAATTGA
Found at i:70849 original size:60 final size:61
Alignment explanation
Indices: 70678--70851 Score: 174
Period size: 60 Copynumber: 2.9 Consensus size: 61
70668 AATATGATAC
* * * *
70678 TACTTTGTTGAGTCTATCGACTATTAAAAGTTATAAAATAATCTCTCAATA-ATAGAGAGT
1 TACTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATAATCACTGACTATATAGAGAGT
* * * * * ***
70738 TATTTTTGTTGAGTCCTTCAACTATTAAAAGATACAAAATGGCCACTTGACTATA-AG-GAGT
1 TA-CTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATAATCAC-TGACTATATAGAGAGT
* *
70799 TACTTTGTTGAGTCCCTCGACTATTAAAATTTATAAAATAATCACATGACTAT
1 TACTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATAATCAC-TGACTAT
70852 TTATTATATT
Statistics
Matches: 89, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
60 43 0.48
61 39 0.44
62 6 0.07
63 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (61 bp):
TACTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATAATCACTGACTATATAGAGAGT
Found at i:71403 original size:28 final size:29
Alignment explanation
Indices: 71339--71410 Score: 103
Period size: 28 Copynumber: 2.5 Consensus size: 29
71329 AACCTTGATT
71339 AAATATTTGATAATTTTAATTTCCCAAAA
1 AAATATTTGATAATTTTAATTTCCCAAAA
* *
71368 AAGTATTTGATAATTTT-ATTAT-TCAAAA
1 AAATATTTGATAATTTTAATT-TCCCAAAA
71396 AAATATTTGATAATT
1 AAATATTTGATAATT
71411 CTATATAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 22 0.56
29 17 0.44
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (29 bp):
AAATATTTGATAATTTTAATTTCCCAAAA
Found at i:75726 original size:20 final size:21
Alignment explanation
Indices: 75686--75725 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
75676 AGAATGTGCA
75686 GGGGGGTACAGATTCCCCCCT
1 GGGGGGTACAGATTCCCCCCT
75707 GGGGGGTATC-GATTCCCCC
1 GGGGGGTA-CAGATTCCCCC
75726 TAAATGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.12, C:0.33, G:0.35, T:0.20
Consensus pattern (21 bp):
GGGGGGTACAGATTCCCCCCT
Found at i:76266 original size:22 final size:22
Alignment explanation
Indices: 76238--76315 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
76228 GTTTATAGTA
76238 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
*
76260 GTCCTTCGGGATGTATCCAGGG
1 GTCCTTCGGGATGTATCCAGTG
* *
76282 GTTCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
*
76304 ATCCTTCGGGAT
1 GTCCTTCGGGAT
76316 AAATATTTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.14, C:0.23, G:0.32, T:0.31
Consensus pattern (22 bp):
GTCCTTCGGGATGTATCCAGTG
Found at i:80515 original size:20 final size:19
Alignment explanation
Indices: 80478--80515 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
80468 CAAACCTAAC
*
80478 CCTAAAAATTCCTTTTTCT
1 CCTAAAAATTCCTATTTCT
80497 CCTAAAAATTCCTCATTTC
1 CCTAAAAATTCCT-ATTTC
80516 ACTCGAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (19 bp):
CCTAAAAATTCCTATTTCT
Found at i:84259 original size:21 final size:21
Alignment explanation
Indices: 84213--84275 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
84203 ATATGCTCAC
*
84213 TAATTTTTCAAATTGGTCATT
1 TAATTTTTCAAATTGATCATT
*
84234 AAATTTTTCAAATTGAT-ATTT
1 TAATTTTTCAAATTGATCA-TT
*
84255 TAATTCTTT-AACTTGATCATT
1 TAATT-TTTCAAATTGATCATT
84276 CATTATAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 1 0.03
21 30 0.86
22 4 0.11
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (21 bp):
TAATTTTTCAAATTGATCATT
Found at i:87300 original size:79 final size:79
Alignment explanation
Indices: 87123--87301 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 79
87113 TTCAATCTTA
* * * * *
87123 ACTCAACTTCACAATGAAGGAGTCACCCACGATTTCAACTTCACAATGAAGGATATTGTGCCCAA
1 ACTCAACTTCACAAAGAATGAGTCACCCACGACTTCAACTTCACAACGAAGGATATCGTGCCCAA
* *
87188 GACACTCGAAATTG
66 AACACTCGAAATAG
** * * * *
87202 ACTCAACTTCATGACGAATGAGTCATCCACGACTTCAACTTCACGACGAATGATATCGTGCCCAA
1 ACTCAACTTCACAAAGAATGAGTCACCCACGACTTCAACTTCACAACGAAGGATATCGTGCCCAA
* *
87267 AATACTCGATATCAG
66 AACACTCGAAAT-AG
87282 -CTCAACTTCACAAAGAATGA
1 ACTCAACTTCACAAAGAATGA
87302 TATTGAACTA
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
79 81 0.99
80 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (79 bp):
ACTCAACTTCACAAAGAATGAGTCACCCACGACTTCAACTTCACAACGAAGGATATCGTGCCCAA
AACACTCGAAATAG
Found at i:87965 original size:2 final size:2
Alignment explanation
Indices: 87958--88183 Score: 160
Period size: 2 Copynumber: 120.5 Consensus size: 2
87948 CCTTTTATGT
*
87958 TA TA TA TA TA GTA TA GTA TA TA GTA TA T- TA TA TA -A TA TA GTG
1 TA TA TA TA TA -TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA
88000 TA T- TA T- TA TA TA TA GTA TA T- TA TA TA T- TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
88040 TCA TA TA TA TA GTA TA TA T- TA TA T- TA TA T- TA TA TA T- TA T-
1 T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88079 TA T- TA T- TA T- TA TA GTA T- TA TA T- TA TA TA T- TA TA TA T-
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
88115 TA TA -A TA TA TA TA TA TA TT TA T- TA TA TA TA TA T- TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
88155 TT TA TA T- TA T- TA T- TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
88184 CGTAGTATTT
Statistics
Matches: 183, Mismatches: 6, Indels: 70
0.71 0.02 0.27
Matches are distributed among these distances:
1 25 0.14
2 139 0.76
3 19 0.10
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (2 bp):
TA
Found at i:87979 original size:7 final size:6
Alignment explanation
Indices: 87958--88183 Score: 160
Period size: 5 Copynumber: 40.2 Consensus size: 6
87948 CCTTTTATGT
*
87958 TATATA TATAGTA TAGTATA TAGTATA T-TATA TA-ATA TAGTGTA T-TAT-
1 TATATA TATA-TA TA-TATA TA-TATA TATATA TATATA TA-TATA TATATA
88006 TATATA TAGTATA T-TATA TAT-TA TATAGTA TATATCA TATATA TAGTATA
1 TATATA TA-TATA TATATA TATATA TATA-TA TATAT-A TATATA TA-TATA
88056 TAT-TA TAT-TA TAT-TA TATAT- TAT-TA T-TAT- TAT-TA TAGTAT-
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TA-TATA
*
88096 TATAT- TATATA T-TATA TAT-TA TA-ATA TATATA TATATT TAT-TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
88139 TATATA TAT-TA TAGTATT TATAT- TAT-TA T-TATA TAT-TA TATATA
1 TATATA TATATA TA-TATA TATATA TATATA TATATA TATATA TATATA
88183 T
1 T
88184 CGTAGTATTT
Statistics
Matches: 184, Mismatches: 5, Indels: 62
0.73 0.02 0.25
Matches are distributed among these distances:
4 7 0.04
5 89 0.48
6 42 0.23
7 44 0.24
8 2 0.01
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
TATATA
Found at i:88204 original size:33 final size:32
Alignment explanation
Indices: 87981--88261 Score: 111
Period size: 30 Copynumber: 8.9 Consensus size: 32
87971 TAGTATATAG
* *
87981 TATATTATATA-AT-ATAGTGTATTATTATATATA
1 TATATTATATATATAATAGTAT-TTA-TAT-TTTA
**
88014 GTATATTATATAT-TATATAGTA--TATATCATA
1 -TATATTATATATATA-ATAGTATTTATATTTTA
* * *
88045 TATA-TAGTATATATTATATTATATTATATATTA
1 TATATTA-TATATATAATAGTAT-TTATATTTTA
88078 T-TATTAT-TAT-T-ATAGTA-TTATA--TTA
1 TATATTATATATATAATAGTATTTATATTTTA
*
88103 TATATTATATATTATAATA-TATATATATATTTA
1 TATATTATATA-TATAATAGTATTTATAT-TTTA
*
88136 T-TA-TATATATATTATAGTATTTATATTATTATTA
1 TATATTATATATATAATAGTA-TT-TA-TATT-TTA
**
88170 TATATTATATATATCGTAGTATTTATATTGTTA
1 TATATTATATATATAATAGTATTTATATT-TTA
* * *
88203 TAGAGTATACTAT-T-ATAGT-TGTTATATATTA
1 TATATTATA-TATATAATAGTAT-TTATATTTTA
* *
88234 GA-ATTATAT-TAT-ATATTATATTATATTT
1 TATATTATATATATAATAGTAT-TTATATTT
88262 ATTACGTTAT
Statistics
Matches: 196, Mismatches: 22, Indels: 62
0.70 0.08 0.22
Matches are distributed among these distances:
25 4 0.02
26 6 0.03
27 7 0.04
28 2 0.01
29 16 0.08
30 41 0.21
31 20 0.10
32 19 0.10
33 34 0.17
34 24 0.12
35 4 0.02
36 19 0.10
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (32 bp):
TATATTATATATATAATAGTATTTATATTTTA
Found at i:94111 original size:20 final size:21
Alignment explanation
Indices: 94069--94109 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
94059 CCAGAATGTG
94069 TAGGGGGTACAGATTCCCCCC
1 TAGGGGGTACAGATTCCCCCC
94090 TAGGGGGTATC-GATTCCCCC
1 TAGGGGGTA-CAGATTCCCCC
94110 TAAATGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.32, G:0.29, T:0.22
Consensus pattern (21 bp):
TAGGGGGTACAGATTCCCCCC
Found at i:94695 original size:23 final size:22
Alignment explanation
Indices: 94622--94700 Score: 113
Period size: 22 Copynumber: 3.5 Consensus size: 22
94612 GTTTATAGTA
94622 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
94644 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGATGTATCCAGTG
* * *
94666 GTTCTTCGGGACGTATTTCAGTG
1 GTCCTTCGGGATGTA-TCCAGTG
*
94689 ATCCTTCGGGAT
1 GTCCTTCGGGAT
94701 AAATATTTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
22 35 0.70
23 15 0.30
ACGTcount: A:0.14, C:0.22, G:0.30, T:0.34
Consensus pattern (22 bp):
GTCCTTCGGGATGTATCCAGTG
Found at i:102618 original size:21 final size:21
Alignment explanation
Indices: 102594--102646 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
102584 TATGCTCACT
*
102594 AATTTTTCAAATTGGTCATTA
1 AATTTTTCAAATTGATCATTA
* *
102615 AATTTTTCAAATTGATCTTTT
1 AATTTTTCAAATTGATCATTA
102636 AATTCTTTCAA
1 AATT-TTTCAA
102647 TATTTTGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (21 bp):
AATTTTTCAAATTGATCATTA
Found at i:105574 original size:79 final size:78
Alignment explanation
Indices: 105464--105642 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 78
105454 TTCAATCTTA
* * * *
105464 ACTCAACTTCACAATGAAGGAGTCACCCACGATTTCAACTTCACAATGAAGGATATCGTGCCCAA
1 ACTCAACTTCACAAAGAATGAGTCACCCACGACTTCAACTTCACAACGAAGGATATCGTGCCCAA
* *
105529 GACACTCGAAATTG
66 AACACTCGAAA-TC
* * * * *
105543 ACTCAACTTCACGACGAATGAGTCATCCACGACTTCAACTTCACGACGAATGATATCGTGCCCAA
1 ACTCAACTTCACAAAGAATGAGTCACCCACGACTTCAACTTCACAACGAAGGATATCGTGCCCAA
* *
105608 AATACTCGATATC
66 AACACTCGAAATC
105621 AGCTCAACTTCACAAAGAATGA
1 A-CTCAACTTCACAAAGAATGA
105643 TATTGAACTA
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 2 0.02
79 83 0.98
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (78 bp):
ACTCAACTTCACAAAGAATGAGTCACCCACGACTTCAACTTCACAACGAAGGATATCGTGCCCAA
AACACTCGAAATC
Found at i:106311 original size:2 final size:2
Alignment explanation
Indices: 106299--106510 Score: 192
Period size: 2 Copynumber: 111.5 Consensus size: 2
106289 CCTTTTATGT
106299 TA TA TA T- TA TA TA GTA TA GTA TA TA GTA TA T- TA TA TA -A TA
1 TA TA TA TA TA TA TA -TA TA -TA TA TA -TA TA TA TA TA TA TA TA
*
106339 TA TA GTG TA T- TA T- TA TA TA TA GTA TA T- TA TA TA TA TA TA GTA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA
106381 TA TA TA TA TA TA TA TA TA T- TA TA T- TA T- TA T- TA TA GTA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
106419 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA T- TA TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
106458 TA TA TA TA T- TA TA GTA TT TA TA T- TA T- TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
106497 TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA T
106511 CGTAGTATTT
Statistics
Matches: 177, Mismatches: 6, Indels: 54
0.75 0.03 0.23
Matches are distributed among these distances:
1 19 0.11
2 143 0.81
3 15 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:106316 original size:12 final size:11
Alignment explanation
Indices: 106299--106586 Score: 187
Period size: 12 Copynumber: 26.1 Consensus size: 11
106289 CCTTTTATGT
106299 TATATATTATA
1 TATATATTATA
*
106310 TAGTATAGTATA
1 TA-TATATTATA
106322 TAGTATATTATA
1 TA-TATATTATA
106334 TA-ATA-TATA
1 TATATATTATA
* *
106343 -GTGTATTAT-
1 TATATATTATA
106352 TATATA-TAGTA
1 TATATATTA-TA
106363 TAT-TA-TATA
1 TATATATTATA
*
106372 TATATAGTATA
1 TATATATTATA
106383 TATATA-TATA
1 TATATATTATA
106393 TATATATTATA
1 TATATATTATA
106404 T-TATTATTATA
1 TATA-TATTATA
106415 GTAT-TATATATA
1 -TATATAT-TATA
106427 TATATATATATA
1 TATATAT-TATA
106439 TATATATT-TA
1 TATATATTATA
106449 T-TATATTATTA
1 TATATATTA-TA
106460 TATATATTATA
1 TATATATTATA
106471 GTATTTATATTAT-
1 -TA--TATATTATA
106484 TAT-TATATATA
1 TATATAT-TATA
106495 TATATATTATA
1 TATATATTATA
**
106506 TATATCGTAGTA
1 TATATATTA-TA
* *
106518 TTTATATTGT-
1 TATATATTATA
* *
106528 TATAGAGTATA
1 TATATATTATA
*
106539 CTATTATAGTTGT-
1 -TA-TATA-TTATA
*
106552 TATATATTAGA
1 TATATATTATA
106563 -ATTATATTATA
1 TA-TATATTATA
106574 TATTATATTATA
1 TA-TATATTATA
106586 T
1 T
106587 TTATTACGTT
Statistics
Matches: 224, Mismatches: 22, Indels: 61
0.73 0.07 0.20
Matches are distributed among these distances:
9 22 0.10
10 44 0.20
11 66 0.29
12 78 0.35
13 4 0.02
14 10 0.04
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.53
Consensus pattern (11 bp):
TATATATTATA
Found at i:106495 original size:106 final size:105
Alignment explanation
Indices: 106293--106510 Score: 273
Period size: 106 Copynumber: 2.1 Consensus size: 105
106283 CGGGACCCTT
* *
106293 TTATGTTATATATTATATAGTATAGTATATAGTATATTATATAATATATAGTGTATTATTATATA
1 TTATATTATATATTATATAGTATAGTATATAGTATATTATATAATATATAGTATATTATTATATA
*
106358 TAGTATATTATATATATATAGTATATATATATATATATATA
66 TAGTATAGTATATATATATAGTATATATATATATATAT-TA
* * *
106399 TTATATTAT-TATTATAGTATTATA-TATATA-TATATATATATATATATTTATTATATTATTAT
1 TTATATTATATATTATA-TAGTATAGTATATAGTATAT-TATATA-ATATATAGTATATTATTAT
* * *
106461 ATATATTATAGTATTTATAT-TATTATTATATATATATATATTA
63 ATATAGTATAGTATATATATATAGTA-TATATATATATATATTA
106504 TATATAT
1 T-TATAT
106511 CGTAGTATTT
Statistics
Matches: 98, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
104 5 0.05
105 26 0.27
106 67 0.68
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (105 bp):
TTATATTATATATTATATAGTATAGTATATAGTATATTATATAATATATAGTATATTATTATATA
TAGTATAGTATATATATATAGTATATATATATATATATTA
Found at i:106510 original size:56 final size:55
Alignment explanation
Indices: 106318--106510 Score: 213
Period size: 56 Copynumber: 3.4 Consensus size: 55
106308 TATAGTATAG
*
106318 TATATAGTATATTATATAATATATAGTGTATTAT-TATA-TATAGTATATTATATA-TA-
1 TATATA-TATA-TATATTATATATA-T-TATTATATATATTATAGTAT-TTATATATTAT
106374 TATAGTATATATATA-TATATATA-TATTATATTATTATTATAGTA-TTATATATATAT
1 TATA-TATATATATATTATATATATTATTATA-TA-TATTATAGTATTTATATAT-TAT
106430 ATATATATATATATATT-TATTATATTATTATATATATTATAGTATTTATATTATTAT
1 -TATATATATATATATTATA-TATATTATTATATATATTATAGTATTTATA-TATTAT
106487 TATATATATATATATTATATATAT
1 TATATATATATATATTATATATAT
106511 CGTAGTATTT
Statistics
Matches: 121, Mismatches: 1, Indels: 30
0.80 0.01 0.20
Matches are distributed among these distances:
51 6 0.05
53 9 0.07
54 9 0.07
55 13 0.11
56 51 0.42
57 23 0.19
58 10 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (55 bp):
TATATATATATATATTATATATATTATTATATATATTATAGTATTTATATATTAT
Found at i:106962 original size:13 final size:13
Alignment explanation
Indices: 106944--106971 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
106934 CCCCACCCCA
106944 ATTACCCGACCCG
1 ATTACCCGACCCG
106957 ATTACCCGACCCG
1 ATTACCCGACCCG
106970 AT
1 AT
106972 AAATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.43, G:0.14, T:0.18
Consensus pattern (13 bp):
ATTACCCGACCCG
Found at i:114181 original size:18 final size:18
Alignment explanation
Indices: 114153--114212 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
114143 ATACTAATTG
*
114153 TTTTGTAATTTTTCTGATT
1 TTTTGT-ATTTTTATGATT
*
114172 TTTTGTATTTTTTTG-TAT
1 TTTTGTATTTTTATGAT-T
*
114190 TTTTATATTTTTTATGATT
1 TTTTGTA-TTTTTATGATT
114209 TTTT
1 TTTT
114213 TTAAATTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 1 0.03
18 15 0.43
19 18 0.51
20 1 0.03
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (18 bp):
TTTTGTATTTTTATGATT
Found at i:114183 original size:10 final size:10
Alignment explanation
Indices: 114153--114213 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
114143 ATACTAATTG
114153 TTTTGTAATTT
1 TTTTGT-ATTT
*
114164 TTCTG-A-TT
1 TTTTGTATTT
114172 TTTTGTATTT
1 TTTTGTATTT
114182 TTTTGTA--T
1 TTTTGTATTT
*
114190 TTTTATATTT
1 TTTTGTATTT
114200 TTTATG-ATTT
1 TTT-TGTATTT
114210 TTTT
1 TTTT
114214 TAAATTCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
8 13 0.32
9 3 0.07
10 20 0.49
11 5 0.12
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (10 bp):
TTTTGTATTT
Found at i:115149 original size:12 final size:12
Alignment explanation
Indices: 115132--115173 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
115122 AAAAAAAATG
115132 TTTAAATAATAC
1 TTTAAATAATAC
* *
115144 TTTAAAT-TTAG
1 TTTAAATAATAC
115155 TTTAAATAATAC
1 TTTAAATAATAC
115167 TTTAAAT
1 TTTAAAT
115174 TTATTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (12 bp):
TTTAAATAATAC
Found at i:115158 original size:23 final size:23
Alignment explanation
Indices: 115131--115185 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
115121 TAAAAAAAAT
115131 GTTTAAATAATACTTTAAATTTA
1 GTTTAAATAATACTTTAAATTTA
115154 GTTTAAATAATACTTTAAATTTA
1 GTTTAAATAATACTTTAAATTTA
*
115177 TTTTAAATA
1 GTTTAAATA
115186 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
GTTTAAATAATACTTTAAATTTA
Found at i:115160 original size:11 final size:11
Alignment explanation
Indices: 115141--115184 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
115131 GTTTAAATAA
115141 TACTTTAAATT
1 TACTTTAAATT
* *
115152 TAGTTTAAATAA
1 TACTTTAAAT-T
115164 TACTTTAAATT
1 TACTTTAAATT
*
115175 TATTTTAAAT
1 TACTTTAAAT
115185 ATTTTAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (11 bp):
TACTTTAAATT
Found at i:115807 original size:253 final size:256
Alignment explanation
Indices: 115359--115875 Score: 896
Period size: 253 Copynumber: 2.0 Consensus size: 256
115349 TTTTAAAAAG
* *
115359 ACCTATATTTCTTTAAATTATAAAAAAACTTAAAATCTTAAAATTTTTAATTTTAACTCTCGTCA
1 ACCTATATTTCTTTAAATCATAAAAAAACTCAAAATCTTAAAATTTTTAATTTTAACTCTCGTCA
*
115424 GTCATCTTTCATCATCACTTTTATCATCCAATAATCGCCCACATATCACCGTCTGCCCACTAACC
66 GTCATCTTTCATCATCACTTTTATCATCCAATAATCACCCACATATCACCGTCTGCCCACTAACC
115489 GACACTGCCCTTATCATATCCTTAAATTTATAAATCCTTAAACCCTAAATTCATAAATATTTCAA
131 GACACTGCCCTTATCATATCCTTAAATTTATAAATCCTTAAACCCTAAATTCATAAATATTTCAA
115554 CAAATTAAC-GG-T-GATAACTTAGGTGATGTTTGGTTCGTTGGGAATTAAGAGGAATTGA
196 CAAATTAACGGGTTCGATAACTTAGGTGATGTTTGGTTCGTTGGGAATTAAGAGGAATTGA
*
115612 ACCTATATTTCTTTAAATCATAAAAAAACTCAAAATCTTAAAATTTTTAATTTTAACTCTCGTCG
1 ACCTATATTTCTTTAAATCATAAAAAAACTCAAAATCTTAAAATTTTTAATTTTAACTCTCGTCA
115677 GTCATCTTTCATCATCACTTTTATCATCCAATAATCACCCACATATCACCGTCTGCCCACTAACC
66 GTCATCTTTCATCATCACTTTTATCATCCAATAATCACCCACATATCACCGTCTGCCCACTAACC
* *
115742 GACACTGCCCTTATCATATCCTTAAATTTATAAATCTTTAAACCCTAAATTCATAAATGTTTCAA
131 GACACTGCCCTTATCATATCCTTAAATTTATAAATCCTTAAACCCTAAATTCATAAATATTTCAA
115807 CAAATTAACGGTGGTGGGGTTCGATAACTTAGGTGATGTTTGGTTCGTTGGGAATTAAGAGGAAT
196 CAAATTAAC-------GGGTTCGATAACTTAGGTGATGTTTGGTTCGTTGGGAATTAAGAGGAAT
115872 TGA
254 TGA
115875 A
1 A
115876 ATCAAATTTC
Statistics
Matches: 248, Mismatches: 6, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
253 198 0.80
261 2 0.01
262 1 0.00
263 47 0.19
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (256 bp):
ACCTATATTTCTTTAAATCATAAAAAAACTCAAAATCTTAAAATTTTTAATTTTAACTCTCGTCA
GTCATCTTTCATCATCACTTTTATCATCCAATAATCACCCACATATCACCGTCTGCCCACTAACC
GACACTGCCCTTATCATATCCTTAAATTTATAAATCCTTAAACCCTAAATTCATAAATATTTCAA
CAAATTAACGGGTTCGATAACTTAGGTGATGTTTGGTTCGTTGGGAATTAAGAGGAATTGA
Found at i:119395 original size:61 final size:60
Alignment explanation
Indices: 119311--119476 Score: 174
Period size: 61 Copynumber: 2.8 Consensus size: 60
119301 AATATGATAC
* *
119311 TACTTTGTTGAGT-CTATCGACTATTAAAAGTTATAAAATAATCTCTCAATTAT-AGAGAGT
1 TACTTTGTTGAGTCCT-TCGACTATTAAAAGTTATAAAATAATCACTCAACTATAAG-GAGT
* * * * *** **
119371 TATTTTTGTTGAGTCCTTCAACTATTAAAAGATACAAAATGGCCACTTGACTATAAGGAGT
1 TA-CTTTGTTGAGTCCTTCGACTATTAAAAGTTATAAAATAATCACTCAACTATAAGGAGT
* *
119432 TACTTTGTTGAGTCCCTCGACTATTAAAATTTATAAAATAATCAC
1 TACTTTGTTGAGTCCTTCGACTATTAAAAGTTATAAAATAATCAC
119477 ATGACTATTT
Statistics
Matches: 83, Mismatches: 20, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
60 36 0.43
61 43 0.52
62 4 0.05
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (60 bp):
TACTTTGTTGAGTCCTTCGACTATTAAAAGTTATAAAATAATCACTCAACTATAAGGAGT
Found at i:119482 original size:60 final size:61
Alignment explanation
Indices: 119311--119484 Score: 174
Period size: 60 Copynumber: 2.9 Consensus size: 61
119301 AATATGATAC
* * * *
119311 TACTTTGTTGAGTCTATCGACTATTAAAAGTTATAAAATAATCTCTCAAT-TATAGAGAGT
1 TACTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATAATCACTGACTATATAGAGAGT
* * * * * ***
119371 TATTTTTGTTGAGTCCTTCAACTATTAAAAGATACAAAATGGCCACTTGACTATA-AG-GAGT
1 TA-CTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATAATCAC-TGACTATATAGAGAGT
* *
119432 TACTTTGTTGAGTCCCTCGACTATTAAAATTTATAAAATAATCACATGACTAT
1 TACTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATAATCAC-TGACTAT
119485 TTATTATATT
Statistics
Matches: 89, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
60 43 0.48
61 39 0.44
62 5 0.06
63 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (61 bp):
TACTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATAATCACTGACTATATAGAGAGT
Found at i:120034 original size:28 final size:29
Alignment explanation
Indices: 119970--120041 Score: 103
Period size: 28 Copynumber: 2.5 Consensus size: 29
119960 AACCTTGATT
119970 AAATATTTGATAATTTTAATTTCCCAAAA
1 AAATATTTGATAATTTTAATTTCCCAAAA
* *
119999 AAGTATTTGATAATTTT-ATTAT-TCAAAA
1 AAATATTTGATAATTTTAATT-TCCCAAAA
120027 AAATATTTGATAATT
1 AAATATTTGATAATT
120042 CTATATAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 22 0.56
29 17 0.44
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (29 bp):
AAATATTTGATAATTTTAATTTCCCAAAA
Found at i:121487 original size:81 final size:81
Alignment explanation
Indices: 121352--121524 Score: 303
Period size: 81 Copynumber: 2.1 Consensus size: 81
121342 GAAGTGTGAC
121352 GATGACTAGATGTCCTCAACATGACGGAACAACGTTGTCCACAGATTTGATGTCCTGAAGTGAAG
1 GATGACTAGATGTCCTCAACATGACGGAACAACGTTGTCCACAGATTTGATGTCCTGAAGTGAAG
121417 GATCAAATCTTCTAAA
66 GATCAAATCTTCTAAA
* *
121433 GATGACTAGATGTCCTCAACATGACGGAACAACGTT-TCCCACATATTTGATGTCCTGGAGTGAA
1 GATGACTAGATGTCCTCAACATGACGGAACAACGTTGT-CCACAGATTTGATGTCCTGAAGTGAA
121497 GGATCAAATCTTCTAAA
65 GGATCAAATCTTCTAAA
*
121514 GATGATTAGAT
1 GATGACTAGAT
121525 CTCTTCAATA
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
80 1 0.01
81 87 0.99
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (81 bp):
GATGACTAGATGTCCTCAACATGACGGAACAACGTTGTCCACAGATTTGATGTCCTGAAGTGAAG
GATCAAATCTTCTAAA
Found at i:121488 original size:40 final size:40
Alignment explanation
Indices: 121360--121488 Score: 102
Period size: 40 Copynumber: 3.2 Consensus size: 40
121350 ACGATGACTA
*
121360 GATGTCCTCAACATGACGGAACAACGTTGT-CCACAGATTT
1 GATGTCCTCAACATGACGGAACAACGTT-TCCCACATATTT
* * * * * ** * * *
121400 GATGTCCTGAA-GTGAAGGATCAA-ATCTTCTAAAGATGACTA
1 GATGTCCTCAACATGACGGAACAACGT-TTC-CCACAT-ATTT
121441 GATGTCCTCAACATGACGGAACAACGTTTCCCACATATTT
1 GATGTCCTCAACATGACGGAACAACGTTTCCCACATATTT
121481 GATGTCCT
1 GATGTCCT
121489 GGAGTGAAGG
Statistics
Matches: 62, Mismatches: 21, Indels: 12
0.65 0.22 0.13
Matches are distributed among these distances:
38 2 0.03
39 10 0.16
40 22 0.35
41 15 0.24
42 12 0.19
43 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (40 bp):
GATGTCCTCAACATGACGGAACAACGTTTCCCACATATTT
Found at i:125570 original size:19 final size:19
Alignment explanation
Indices: 125542--125578 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
125532 ACTTATGTTT
125542 ACATATCACA-TTCATATC
1 ACATATCACATTTCATATC
125560 ACATGATCACATTTCATAT
1 ACAT-ATCACATTTCATAT
125579 AACACTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (19 bp):
ACATATCACATTTCATATC
Found at i:126272 original size:21 final size:23
Alignment explanation
Indices: 126248--126298 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
126238 GTTCCCCATA
126248 TATCGATAACCTCCA-CATA-GG
1 TATCGATAACCTCCACCATATGG
*
126269 TATCGAT-ACCTCTACCATATGG
1 TATCGATAACCTCCACCATATGG
126291 TATCGATA
1 TATCGATA
126299 CTATTCATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 11 0.42
22 9 0.35
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (23 bp):
TATCGATAACCTCCACCATATGG
Found at i:129842 original size:21 final size:22
Alignment explanation
Indices: 129802--129853 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
129792 TGTTCCCCAT
*
129802 GTATCGATACCCTCCACATA-A
1 GTATCGATACCCTACACATAGA
*
129823 GTATCGATACCTCTAC-CATAGG
1 GTATCGATACC-CTACACATAGA
129845 GTATCGATA
1 GTATCGATA
129854 ATTTTCATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (22 bp):
GTATCGATACCCTACACATAGA
Found at i:136980 original size:20 final size:22
Alignment explanation
Indices: 136952--136997 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
136942 TCGTTAAATA
*
136952 TTTATCTAAAACATT-AT-TTT
1 TTTAGCTAAAACATTAATGTTT
136972 TTTAGCTAAAACATTAATGTTT
1 TTTAGCTAAAACATTAATGTTT
136994 TTTA
1 TTTA
136998 ATATTTCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.61
21 2 0.09
22 7 0.30
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTAGCTAAAACATTAATGTTT
Done.