Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004411.1 Hibiscus syriacus cultivar Beakdansim tig00009666_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: 52053
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3506 original size:22 final size:22
Alignment explanation
Indices: 3473--3540 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 22
3463 TTCTTCATTT
3473 TTATT-TA-AATATTATTTATA
1 TTATTATATAATATTATTTATA
3493 TTATTATATAATATTA-TTAT-
1 TTATTATATAATATTATTTATA
* * *
3513 TTA-TATTTTATATTATTAATA
1 TTATTATATAATATTATTTATA
3534 TTATTAT
1 TTATTAT
3541 TACAAACAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 10 0.25
20 11 0.28
21 9 0.22
22 10 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTATATAATATTATTTATA
Found at i:3515 original size:25 final size:28
Alignment explanation
Indices: 3482--3541 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 28
3472 TTTATTTAAA
3482 TATTATTTATATTAT-TA-TA-TAATAT
1 TATTATTTATATTATATATTATTAATAT
*
3507 TATTATTTATATTTTATATTATTAATAT
1 TATTATTTATATTATATATTATTAATAT
3535 TATTATT
1 TATTATT
3542 ACAAACAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 14 0.45
26 2 0.06
27 2 0.06
28 13 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TATTATTTATATTATATATTATTAATAT
Found at i:3541 original size:22 final size:21
Alignment explanation
Indices: 3473--3541 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 21
3463 TTCTTCATTT
3473 TTATTTAAATATTATTTATATTA
1 TTATTT-AATATTA-TTATATTA
*
3496 TTATATAATATTATTAT-TTA
1 TTATTTAATATTATTATATTA
*
3516 -TATTTTATATTATTAATATTA
1 TTATTTAATATTATT-ATATTA
3537 TTATT
1 TTATT
3542 ACAAACAGGC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 12 0.30
20 5 0.12
21 7 0.17
22 11 0.28
23 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTTAATATTATTATATTA
Found at i:16332 original size:14 final size:15
Alignment explanation
Indices: 16307--16336 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
16297 AAATAAGGGA
16307 AAAAGAAAGAAAAAG
1 AAAAGAAAGAAAAAG
16322 AAAAG-AAGAAAAAG
1 AAAAGAAAGAAAAAG
16336 A
1 A
16337 GAGGGTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAAG
Found at i:18113 original size:114 final size:114
Alignment explanation
Indices: 17912--18251 Score: 522
Period size: 114 Copynumber: 3.0 Consensus size: 114
17902 AAGTGCCATG
*
17912 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
17977 TGATTTGATATGAACCCCAAAATCAATCATTAGATTTTAAAGATGAATT
66 TGATTTGATATGAACCCCAAAATCAATCATTAGATTTGAAAGATGAATT
*
18026 TGCTCATAGTAGAAATAAGAATACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
18091 TGATTT-AGTATGAACCCTAAAATCAATCATTGGATTTGAAAGATGAATT
66 TGATTTGA-TATGAACCCCAAAATCAATCATTAGATTTGAAAGATGAATT
* *
18140 TGCTCATAGTAGAAAGAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * *
18205 TGGTTCGGTAAGAACCACAAAACCAATCATT-GAAATTGAAAGATGAA
66 TGATTTGATATGAACCCCAAAATCAATCATTAG-ATTTGAAAGATGAA
18252 CTGCATGATC
Statistics
Matches: 207, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
113 2 0.01
114 205 0.99
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTTGATATGAACCCCAAAATCAATCATTAGATTTGAAAGATGAATT
Found at i:19142 original size:113 final size:113
Alignment explanation
Indices: 18954--19224 Score: 400
Period size: 113 Copynumber: 2.4 Consensus size: 113
18944 CATCATTCGG
* * ** * *
18954 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAATAAGTT
1 TGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
19019 CATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
66 CATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
* * *
19067 TGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 TGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * **
19131 TCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCGTTTGA
65 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
*
19180 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATC
1 TGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATC
19225 ATCTGAAGAA
Statistics
Matches: 141, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
112 1 0.01
113 140 0.99
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (113 bp):
TGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
Found at i:19302 original size:95 final size:95
Alignment explanation
Indices: 19139--19319 Score: 245
Period size: 95 Copynumber: 1.9 Consensus size: 95
19129 GTTCATAATG
* * * ** * *
19139 AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCGTTTGATGGATCAACATTGCCAGGTAGAGT
1 AGAAGAAATTGTTCAACCTTTTGCTTAAATTCATCACTCGATGAATCAACATTGCCAGGTAGAGT
*
19204 TCATAATGAGAAGAACTCATCATCTGAAGA
66 TCATAATAAGAAGAACTCATCATCTGAAGA
* * * * *
19234 AGAAGAAATTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGAATCAACATTTCCAGTTCGAGT
1 AGAAGAAATTGTTCAACCTTTTGCTTAAATTCATCACTCGATGAATCAACATTGCCAGGTAGAGT
19299 TCATAATAAGAAGAACTCATC
66 TCATAATAAGAAGAACTCATC
19320 TGAAGAAAGA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 73 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (95 bp):
AGAAGAAATTGTTCAACCTTTTGCTTAAATTCATCACTCGATGAATCAACATTGCCAGGTAGAGT
TCATAATAAGAAGAACTCATCATCTGAAGA
Found at i:19359 original size:113 final size:109
Alignment explanation
Indices: 19234--19533 Score: 358
Period size: 104 Copynumber: 2.7 Consensus size: 109
19224 CATCTGAAGA
*
19234 AGAAGAAATTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGAATCAACATTTCCAGTTCGAGT
1 AGAAGAAATTGTTCAACTTTTTGCTTAAATTCATCA-T--GTG-ATCAACATTACCAGTTCGAGT
19299 TCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
62 TCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
* * * ** *
19347 AGAAGAACTTGTTCAACTTTTGGCTTGAA-T--TCA--TGATCAGTATTACCAGTTCGAGTTTAT
1 AGAAGAAATTGTTCAACTTTTTGCTTAAATTCATCATGTGATCAACATTACCAGTTCGAGTTCAT
*
19407 AATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 AATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
* * * * * *
19451 AGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGT
1 AGAAGAAATTGTTCAACTTTTTGCTTAAATTCATCA--TG-T-GATCAACATTACCAGTTCGAGT
*
19516 TCATAATGAGAAGAACTC
62 TCATAATAAGAAGAACTC
19534 GTCATCTGGA
Statistics
Matches: 158, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
104 88 0.56
105 3 0.02
107 3 0.02
110 3 0.02
112 2 0.01
113 59 0.37
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (109 bp):
AGAAGAAATTGTTCAACTTTTTGCTTAAATTCATCATGTGATCAACATTACCAGTTCGAGTTCAT
AATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
Found at i:19531 original size:312 final size:315
Alignment explanation
Indices: 18939--19690 Score: 966
Period size: 312 Copynumber: 2.4 Consensus size: 315
18929 GCAAAGATTA
* * * * *
18939 AAATCCATCATTCGGTGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAT
1 AAATTCATCACTCGGTGAATCAACATTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
* * *
19004 AAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTCGAATTCATCACTTGAT
66 AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGCTCGAATT-AT-AC-T-AT
* *
19068 GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
127 GGATCAGCTTTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
* *
19133 ATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCGTTTGATGGATCAACATTGCCAGG
192 ATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGG
* *
19198 TAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGAAGAAATTGTTCAACTTTTTGCTT
257 TAGAGTTCATAATGAGAAGAACTCATCATCTG--G-AGAAGAAATTATTCAACTTTTTGCAT
19260 AAATTCATCACTCGGTGAATCAACATTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATTCATCACTCGGTGAATCAACATTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
*
19325 AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGGCTTGAA-T-T-C-AT-GAT
66 AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGCTCGAATTATACTATGGAT
**** *
19384 CAG-TATTACCAGTTCGAGTTTATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
131 CAGCT-TTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
19448 ATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAG
195 ATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAG
* *
19513 AGTTCATAATGAGAAGAACTCGTCATCTGGAGAAGAATTTATTCAACTTTTTGCAT
260 AGTTCATAATGAGAAGAACTCATCATCTGGAGAAGAAATTATTCAACTTTTTGCAT
** * ****
19569 -AATTCTATCACAAAAGGAGATAGATCAGCATCAACCTTTCCAGAGAAAGTTCATAATAAGAAGA
1 AAATTC-ATCAC---TCG-G-T-G---A--ATCAACATTTCCAGTTCGAGTTCATAATAAGAAGA
* *
19633 ACTCATCTGAAG-AAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGG
54 ACTCATCTGAAGAAAG-AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGG
19691 ATGACTCTAT
Statistics
Matches: 384, Mismatches: 31, Indels: 32
0.86 0.07 0.07
Matches are distributed among these distances:
308 5 0.01
309 28 0.07
310 1 0.00
311 1 0.00
312 150 0.39
313 3 0.01
314 1 0.00
315 1 0.00
316 1 0.00
318 2 0.01
319 3 0.01
320 80 0.21
321 108 0.28
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (315 bp):
AAATTCATCACTCGGTGAATCAACATTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGCTCGAATTATACTATGGAT
CAGCTTTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
TGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
GTTCATAATGAGAAGAACTCATCATCTGGAGAAGAAATTATTCAACTTTTTGCAT
Found at i:19777 original size:124 final size:122
Alignment explanation
Indices: 19542--19777 Score: 296
Period size: 124 Copynumber: 1.9 Consensus size: 122
19532 TCGTCATCTG
* * * * *
19542 GAGAAGAATTTATTCAACTTTTTGCATAATTCTATCACAAAAGGAGATAGATCAGCATCAACCTT
1 GAGAAGAACTTATTCAACCTTTTGCATAACTCTATCACAAAAGGAAATAGATCAACATCAACC--
19607 TCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAAT
64 TCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAAT
* * * * * *
19666 GAGAAGAGCTTATTCAACCTTTTGGATGACTCTATCACATAAGGAAATAGGTCAACATCATCC-C
1 GAGAAGAACTTATTCAACCTTTTGCATAACTCTATCACAAAAGGAAATAGATCAACATCAACCTC
* * * *
19730 CAGCGGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAA-AGAGAAGAA
66 CAG-AGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAAGAAGAA
19778 TTTATTAAAC
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
121 12 0.12
122 32 0.33
124 52 0.54
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.24
Consensus pattern (122 bp):
GAGAAGAACTTATTCAACCTTTTGCATAACTCTATCACAAAAGGAAATAGATCAACATCAACCTC
CAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAAT
Found at i:19929 original size:9 final size:9
Alignment explanation
Indices: 19915--19976 Score: 65
Period size: 9 Copynumber: 6.9 Consensus size: 9
19905 TTTCATTTAA
19915 ATATTATTT
1 ATATTATTT
19924 ATATTA-TT
1 ATATTATTT
**
19932 AT-TATAAAT
1 ATAT-TATTT
19941 ATTATTATTT
1 A-TATTATTT
19951 ATATTATTT
1 ATATTATTT
*
19960 ATATTATTA
1 ATATTATTT
19969 ATATTATT
1 ATATTATT
19977 ATTACAAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
7 1 0.02
8 6 0.13
9 32 0.71
10 5 0.11
11 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
ATATTATTT
Found at i:19936 original size:15 final size:15
Alignment explanation
Indices: 19916--19980 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 15
19906 TTCATTTAAA
*
19916 TATTATTTATATTAT
1 TATTATTAATATTAT
*
19931 TATTATAAATATTAT
1 TATTATTAATATTAT
*
19946 TATT-TATATTATT-T
1 TATTAT-TAATATTAT
19960 ATATTATTAATATTAT
1 -TATTATTAATATTAT
19976 TATTA
1 TATTA
19981 CAAACATGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 2 0.05
15 37 0.90
16 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTAATATTAT
Found at i:19944 original size:24 final size:24
Alignment explanation
Indices: 19912--19980 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
19902 TTTTTTCATT
19912 TAAATATTATTTATATTATTATTA
1 TAAATATTATTTATATTATTATTA
19936 TAAATATTA-TTAT-TTA-TATTA
1 TAAATATTATTTATATTATTATTA
** *
19957 TTTATATTATTAATATTATTATTA
1 TAAATATTATTTATATTATTATTA
19981 CAAACATGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
21 12 0.31
22 6 0.15
23 7 0.18
24 14 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TAAATATTATTTATATTATTATTA
Found at i:19968 original size:12 final size:12
Alignment explanation
Indices: 19916--19958 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
19906 TTCATTTAAA
19916 TATTATTTATAT
1 TATTATTTATAT
19928 TATTATTATAAATAT
1 TATTATT-T--ATAT
19943 TATTATTTATAT
1 TATTATTTATAT
19955 TATT
1 TATT
19959 TATATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 15 0.54
13 1 0.04
14 1 0.04
15 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTATTTATAT
Found at i:19976 original size:12 final size:12
Alignment explanation
Indices: 19914--19980 Score: 58
Period size: 12 Copynumber: 6.1 Consensus size: 12
19904 TTTTCATTTA
19914 AATATTATT-TAT
1 AATATTATTAT-T
* *
19926 ATTATTATTATA
1 AATATTATTATT
19938 AATATTATTATT
1 AATATTATTATT
19950 --TA-TATTATT
1 AATATTATTATT
19959 --TA-TATTATT
1 AATATTATTATT
19968 AATATTATTATT
1 AATATTATTATT
19980 A
1 A
19981 CAAACATGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
9 16 0.34
10 2 0.04
11 2 0.04
12 26 0.55
13 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
AATATTATTATT
Found at i:26202 original size:194 final size:197
Alignment explanation
Indices: 25990--26367 Score: 584
Period size: 194 Copynumber: 1.9 Consensus size: 197
25980 CACATTGATG
* *
25990 AGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTAATAAACTAT
1 AGGGATCAAATCGAAATAATTTTAAATTGTAAGGTTGAAATTAATACAAAAAAGTAATAAACTAT
* *
26055 ACCCATTTAAAAATTTATGGGCCAATTTAA-AAATAAAAATAAGTAATGAGTATGGGTCAATTT-
66 ACCCATTTAAAAAGTTATGGGCCAA-TTAACAAATAAAAATAAGTAATAAGTATGGGTCAATTTA
*
26118 CA-G-AAATAAAATTTGGAGGACTAAAATGAACAAATATGAAATTACAAATAAATTAAAAAACAC
130 CATGCAAATAAAATGTGGAGGACTAAAATGAACAAATATGAAATTACAAATAAATTAAAAAACAC
26181 AAA
195 AAA
* * * *
26184 AGGGATCAAATCGAAATAATTTTAAATTTTAAGGTTGAAATTAATACAAAAATGTACTAAATTAT
1 AGGGATCAAATCGAAATAATTTTAAATTGTAAGGTTGAAATTAATACAAAAAAGTAATAAACTAT
* *
26249 ACTCATTTAAAAAGTTATGGGCCAATTAACAAATAGAAATAAGTAATAAGTATGGGTCAATTTAA
66 ACCCATTTAAAAAGTTATGGGCCAATTAACAAATAAAAATAAGTAATAAGTATGGGTCAATTT-A
* * *
26314 GATGCAAATAAAATGTGGAGGACTAAATTGAACAAATATGAAATTATAAATAAA
130 CATGCAAATAAAATGTGGAGGACTAAAATGAACAAATATGAAATTACAAATAAA
26368 ATTTTAAATA
Statistics
Matches: 165, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
193 4 0.02
194 113 0.68
196 1 0.01
197 1 0.01
198 46 0.28
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (197 bp):
AGGGATCAAATCGAAATAATTTTAAATTGTAAGGTTGAAATTAATACAAAAAAGTAATAAACTAT
ACCCATTTAAAAAGTTATGGGCCAATTAACAAATAAAAATAAGTAATAAGTATGGGTCAATTTAC
ATGCAAATAAAATGTGGAGGACTAAAATGAACAAATATGAAATTACAAATAAATTAAAAAACACA
AA
Found at i:26480 original size:2 final size:2
Alignment explanation
Indices: 26475--26796 Score: 70
Period size: 2 Copynumber: 161.0 Consensus size: 2
26465 AAAACAACTA
* * *
26475 AT AT AT AT AT AT AT AA ACT AT AT AGT TT AT AT AT AA AGT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A-T AT AT
* * * *
26518 GT AT -T AT AT AT AT AA ACT AT TT AGT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT
* * * * *
26561 AT AT -T AT GT AT AA ACT AT AT AT ACC AT GT AT AA AT -T AT A- AT
1 AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * *
26602 ACT AT AT AGT TT AT AT AT -T A- ACT GT -T GA- AT -T AT AT AG AA
1 A-T AT AT A-T AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT
* * *
26641 ACT AC AT AGT TT AT AT AT AA AT -T AT AT AGT A- AT -T AT AT AT
1 A-T AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * * *
26681 AA AT -T AT ACG AT TT AT AT TT AT GT AT A- AT -T AT AA AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
26721 AT -T GT AT AA AT -T AT AT AGT TT AT -T A- AT AT AA ACT AT AT AGT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T
*
26762 TT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
26797 GGTTTGGGGT
Statistics
Matches: 225, Mismatches: 57, Indels: 76
0.63 0.16 0.21
Matches are distributed among these distances:
1 19 0.08
2 186 0.83
3 20 0.09
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:26505 original size:20 final size:20
Alignment explanation
Indices: 26482--26788 Score: 132
Period size: 20 Copynumber: 14.4 Consensus size: 20
26472 CTAATATATA
26482 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
*
26502 TATATATAAAGTATAT-GTATT
1 TATATATAAACTATATAG--TT
*
26523 ATATATATAAACTATTTAGTT
1 -TATATATAAACTATATAGTT
26544 TATATATATATA-TATATA-TAT
1 TATATATA-A-ACTATATAGT-T
*
26565 TATGTATAAACTATATA-TACCAT
1 TATATATAAACTATATAGT----T
26588 GTATAAATTATAATACTATATAGTT
1 -TAT--A-TATAA-ACTATATAGTT
* * *
26613 TATATATTAACTGT-T-GAAT
1 TATATATAAACTATATAG-TT
* *
26632 TATATAGAAACTACATAGTT
1 TATATATAAACTATATAGTT
*
26652 TATATATAAATTATATAGTAAT
1 TATATATAAACTATATAGT--T
26674 TATATATAAA-T-TATACGATT
1 TATATATAAACTATATA-G-TT
* *
26694 TATATTTATGTATAATTATAAATA-TA
1 TATA--TA--TA-AACTAT--ATAGTT
* *
26720 TATTGTATAAATTATATAGTT
1 TA-TATATAAACTATATAGTT
26741 TATTAATATAAACTATATAGTT
1 TA-T-ATATAAACTATATAGTT
* *
26763 TATATATATA-TATATA-TA
1 TATATATAAACTATATAGTT
26781 TATATATA
1 TATATATA
26789 GTATATATGG
Statistics
Matches: 227, Mismatches: 24, Indels: 74
0.70 0.07 0.23
Matches are distributed among these distances:
18 10 0.04
19 20 0.09
20 72 0.32
21 31 0.14
22 53 0.23
23 5 0.02
24 8 0.04
25 5 0.02
26 4 0.02
27 7 0.03
28 8 0.04
29 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (20 bp):
TATATATAAACTATATAGTT
Found at i:26508 original size:22 final size:22
Alignment explanation
Indices: 26480--26793 Score: 110
Period size: 22 Copynumber: 14.5 Consensus size: 22
26470 AACTAATATA
26480 TATATATATAAACTATATAG-T
1 TATATATATAAACTATATAGTT
*
26501 T-TATATATAAAGTATAT-GTAT
1 TATATATATAAACTATATAGT-T
*
26522 TATATATATAAACTATTTAGTT
1 TATATATATAAACTATATAGTT
* *
26544 TATATATATATA-TATATA-TA
1 TATATATATAAACTATATAGTT
*
26564 T-TATGTATAAACTATATA---
1 TATATATATAAACTATATAGTT
* * * * *
26582 TACCATGTATAAATTATAATACTA
1 TA-TATATATAAACTAT-ATAGTT
* * *
26606 TATAGTTTATATATTA-ACT-GTT
1 TATA-TATATAAACTATA-TAGTT
* * *
26628 GAATTATATAGAAACTACATAG-T
1 -TA-TATATATAAACTATATAGTT
*
26651 T-TATATATAAATTATATAG-T
1 TATATATATAAACTATATAGTT
*
26671 AATTATATATAAA-T-TATACGATT
1 TA-TATATATAAACTATATA-G-TT
* * * *
26694 TATATTTATGTATAATTATA-AATA
1 TATA--TATATA-AACTATATAGTT
* *
26718 TATATTGTATAAATTATATAGTT
1 TATA-TATATAAACTATATAGTT
26741 TAT-TAATATAAACTATATAGTT
1 TATAT-ATATAAACTATATAGTT
* *
26763 TATATATATATA-TATATA-TA
1 TATATATATAAACTATATAGTT
26783 TATATAGTATA
1 TATATA-TATA
26794 TATGGTTTGG
Statistics
Matches: 225, Mismatches: 37, Indels: 62
0.69 0.11 0.19
Matches are distributed among these distances:
18 1 0.00
19 9 0.04
20 62 0.28
21 24 0.11
22 71 0.32
23 27 0.12
24 25 0.11
25 2 0.01
26 2 0.01
27 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (22 bp):
TATATATATAAACTATATAGTT
Found at i:26665 original size:11 final size:11
Alignment explanation
Indices: 26651--26688 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
26641 ACTACATAGT
26651 TTATATATAAA
1 TTATATATAAA
26662 TTATATAGT-AA
1 TTATATA-TAAA
26673 TTATATATAAA
1 TTATATATAAA
26684 TTATA
1 TTATA
26689 CGATTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.04
11 23 0.92
12 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TTATATATAAA
Found at i:26756 original size:150 final size:149
Alignment explanation
Indices: 26482--26769 Score: 347
Period size: 150 Copynumber: 1.9 Consensus size: 149
26472 CTAATATATA
* * * *
26482 TATATATAAACTATATAGTTTATATATAAAGTATATGTATTATATATATAAACTATTTAGTTTAT
1 TATATAGAAACTACATAGTTTATATATAAAGTATATGTATTATATATATAAACGATTTAATTTAT
*
26547 ATATATATATATATATATTATGTATAAACTATATATACCATGTATAAATTATAATACTATATAGT
66 ATATATATAAATATATATTATGTATAAACTATATATA-CATGTATAAATTATAATACTATATAGT
26612 TTATATATTAACTGTTGAAT
130 TTATATATTAACTGTTGAAT
* *
26632 TATATAGAAACTACATAGTTTATATATAAATTATATAGTAATTATATATAAATTATACGATTTAT
1 TATATAGAAACTACATAGTTTATATATAAAGTATAT-GT-ATTATATAT--A-TAAACGATTTA-
* * * *
26697 ATTTATGTATAATTATAAATATATA-T-TGTATAAA-T-TATATA-GTTTATTAA-TATAA-ACT
60 ATTTATATAT-A-TATAAATATATATTATGTATAAACTATATATACATGTATAAATTATAATACT
26755 ATATAGTTTATATAT
123 ATATAGTTTATATAT
26770 ATATATATAT
Statistics
Matches: 119, Mismatches: 11, Indels: 16
0.82 0.08 0.11
Matches are distributed among these distances:
150 51 0.43
151 7 0.06
152 15 0.13
154 7 0.06
155 10 0.08
156 16 0.13
157 2 0.02
158 11 0.09
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (149 bp):
TATATAGAAACTACATAGTTTATATATAAAGTATATGTATTATATATATAAACGATTTAATTTAT
ATATATATAAATATATATTATGTATAAACTATATATACATGTATAAATTATAATACTATATAGTT
TATATATTAACTGTTGAAT
Found at i:26767 original size:69 final size:67
Alignment explanation
Indices: 26656--26788 Score: 164
Period size: 69 Copynumber: 2.0 Consensus size: 67
26646 ATAGTTTATA
* *
26656 TATAAATTATATAGTAATTATATATAAATTATACGATTTATATTTATGTATAATTATAAATATAT
1 TATAAATTATATAGTAATTATATATAAATTATACGATTTATATATATATAT-A-TATAAATATAT
26721 ATTG
64 ATTG
* *
26725 TATAAATTATATAGTTTATTA-ATATAAACTATATA-G-TTTATATATATATATATATATATATA
1 TATAAATTATATAG-TAATTATATATAAA-T-TATACGATTTATATATATATATATATAAATATA
26787 TA
63 TA
26789 GTATATATGG
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
67 11 0.19
68 1 0.02
69 34 0.60
70 7 0.12
71 4 0.07
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (67 bp):
TATAAATTATATAGTAATTATATATAAATTATACGATTTATATATATATATATATAAATATATAT
TG
Found at i:27636 original size:13 final size:13
Alignment explanation
Indices: 27608--27643 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
27598 TATGTTTATG
*
27608 TTATGTTTAT-AT
1 TTATATTTATAAT
27620 TTATATTTATAAT
1 TTATATTTATAAT
27633 TTATATTTATA
1 TTATATTTATA
27644 TACTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
TTATATTTATAAT
Found at i:27644 original size:6 final size:6
Alignment explanation
Indices: 26847--27629 Score: 1460
Period size: 6 Copynumber: 132.0 Consensus size: 6
26837 AAGGATTACG
*
26847 GTTTATT GTTTAT ATTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTA-T GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
26896 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
26944 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
26992 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27040 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27088 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27136 GTTTAT GTTTAT G-TT-T GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27182 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27230 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27278 GTTTAT GTTTAT G-TT-T GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27324 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT G-TT-T
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27370 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27418 G-TTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT G-TT-T GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27463 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27511 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
27559 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
* *
27607 G-TTAT GTTTAT ATTTAT ATTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT
27630 AATTTATATT
Statistics
Matches: 763, Mismatches: 3, Indels: 21
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.01
5 26 0.03
6 724 0.95
7 5 0.01
ACGTcount: A:0.17, C:0.00, G:0.16, T:0.67
Consensus pattern (6 bp):
GTTTAT
Found at i:27688 original size:44 final size:43
Alignment explanation
Indices: 27651--27736 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 43
27641 ATATACTATA
*
27651 TATATGAAC-TATAGTTTACATATGAACTATATATATATAAAC
1 TATATAAACTTATAGTTTACATATGAACTATATATATATAAAC
27693 TATATAAACTTTATAGTTTACATATGAACTATATATATACTAAA
1 TATATAAAC-TTATAGTTTACATATGAACTATATATATA-TAAA
27737 GTTGATATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 8 0.20
44 28 0.70
45 4 0.10
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (43 bp):
TATATAAACTTATAGTTTACATATGAACTATATATATATAAAC
Found at i:27754 original size:35 final size:35
Alignment explanation
Indices: 27709--27817 Score: 118
Period size: 33 Copynumber: 3.1 Consensus size: 35
27699 AACTTTATAG
27709 TTTACATATGAACTATATATATACTAAAGTTGATA
1 TTTACATATGAACTATATATATACTAAAGTTGATA
* *
27744 TTTATATATGAAC--TATATATA-TAAACTAT-ATA
1 TTTACATATGAACTATATATATACTAAAGT-TGATA
* *
27776 GTTTACATATGACCTATATATATATACTATAGTTGATA
1 -TTTACATATGAAC--TATATATATACTAAAGTTGATA
27814 TTTA
1 TTTA
27818 TATACTATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
32 8 0.13
33 20 0.33
35 12 0.20
37 13 0.22
38 7 0.12
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.43
Consensus pattern (35 bp):
TTTACATATGAACTATATATATACTAAAGTTGATA
Found at i:27764 original size:13 final size:13
Alignment explanation
Indices: 27746--27775 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27736 AGTTGATATT
*
27746 TATATATGAACTA
1 TATATATAAACTA
27759 TATATATAAACTA
1 TATATATAAACTA
27772 TATA
1 TATA
27776 GTTTACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:27776 original size:68 final size:69
Alignment explanation
Indices: 27693--27821 Score: 215
Period size: 70 Copynumber: 1.9 Consensus size: 69
27683 ATATATAAAC
*
27693 TATATAAACTTTATAGTTTACATATGAAC-TATATATATACTAAAGTTGATATTTATATATGAAC
1 TATATAAACTATATAGTTTACATATGAACATATATATATACTAAAGTTGATATTTATATATGAAC
27757 TATA
66 TATA
* *
27761 TATATAAACTATATAGTTTACATATGACCTATATATATATACTATAGTTGATATTTATATA
1 TATATAAACTATATAGTTTACATATGAAC-ATATATATATACTAAAGTTGATATTTATATA
27822 CTATATAGTT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 27 0.48
70 29 0.52
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (69 bp):
TATATAAACTATATAGTTTACATATGAACATATATATATACTAAAGTTGATATTTATATATGAAC
TATA
Found at i:27798 original size:33 final size:33
Alignment explanation
Indices: 27693--27806 Score: 124
Period size: 33 Copynumber: 3.4 Consensus size: 33
27683 ATATATAAAC
* *
27693 TATATAAACTTTATAGTTTACATATGAACTATATA
1 TATATAAACTATATAGTTTACATATG-AC-CTATA
* * *
27728 TATACTAAAGT-TGATA-TTTATATATGAACTATA
1 TATA-TAAACTAT-ATAGTTTACATATGACCTATA
27761 TATATAAACTATATAGTTTACATATGACCTATA
1 TATATAAACTATATAGTTTACATATGACCTATA
*
27794 TATATATACTATA
1 TATATAAACTATA
27807 GTTGATATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
32 8 0.12
33 36 0.54
34 1 0.01
35 14 0.21
36 8 0.12
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (33 bp):
TATATAAACTATATAGTTTACATATGACCTATA
Found at i:27826 original size:33 final size:35
Alignment explanation
Indices: 27722--27828 Score: 116
Period size: 33 Copynumber: 3.1 Consensus size: 35
27712 ACATATGAAC
*
27722 TATATATATACTAAAGTTGATATTTATATATGAACTA
1 TATATATATACTATAGTTGATA-TTATATATG-ACTA
* * *
27759 TATATATAAACTATA-TAG-T-TTACATATGACCTA
1 TATATATATACTATAGTTGATATTATATATGA-CTA
27792 TATATATATACTATAGTTGATATT-TATAT-ACTA
1 TATATATATACTATAGTTGATATTATATATGACTA
27825 TATA
1 TATA
27829 GTTTACATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
32 1 0.02
33 32 0.54
34 3 0.05
35 6 0.10
36 4 0.07
37 13 0.22
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (35 bp):
TATATATATACTATAGTTGATATTATATATGACTA
Found at i:27827 original size:53 final size:53
Alignment explanation
Indices: 27758--27880 Score: 210
Period size: 53 Copynumber: 2.3 Consensus size: 53
27748 TATATGAACT
* * *
27758 ATATATATAAACTATATAGTTTACATATGACCTATATATATATACTATAGTTG
1 ATATTTATATACTATATAGTTTACATATGAACTATATATATATACTATAGTTG
*
27811 ATATTTATATACTATATAGTTTACATATGAACTATATATATATACTATAGTTT
1 ATATTTATATACTATATAGTTTACATATGAACTATATATATATACTATAGTTG
27864 ATATTTATATACTATAT
1 ATATTTATATACTATAT
27881 GTAGACACCC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 66 1.00
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (53 bp):
ATATTTATATACTATATAGTTTACATATGAACTATATATATATACTATAGTTG
Found at i:28146 original size:12 final size:13
Alignment explanation
Indices: 28116--28146 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
28106 CCAACCGAGT
28116 GCCCCCACGTGAA
1 GCCCCCACGTGAA
28129 GCCCCCACGTGAA
1 GCCCCCACGTGAA
28142 GCCCC
1 GCCCC
28147 TTGGGGCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.52, G:0.23, T:0.06
Consensus pattern (13 bp):
GCCCCCACGTGAA
Found at i:29286 original size:34 final size:34
Alignment explanation
Indices: 29243--29339 Score: 128
Period size: 34 Copynumber: 2.9 Consensus size: 34
29233 CTTTGTATAT
29243 ATATATATATATATATACTGGTTTATTGTTGTTG
1 ATATATATATATATATACTGGTTTATTGTTGTTG
* *
29277 ATATATATATATATATATTGGTTTATTGCTGTTG
1 ATATATATATATATATACTGGTTTATTGTTGTTG
* * *
29311 GTGTA-A-AT-GATATACTGGTTTATTGTTGT
1 ATATATATATATATATACTGGTTTATTGTTGT
29340 AATGTAAACT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
31 18 0.32
32 2 0.04
33 1 0.02
34 35 0.62
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.52
Consensus pattern (34 bp):
ATATATATATATATATACTGGTTTATTGTTGTTG
Found at i:30799 original size:68 final size:68
Alignment explanation
Indices: 30719--30849 Score: 160
Period size: 68 Copynumber: 1.9 Consensus size: 68
30709 CAAAAAAGTA
* *
30719 ATCATATTAATTTGA-TTATCATAATAATTTATGATAAAATTTTAAA-AA-ATAATCATATTAAT
1 ATCATAATAATTTGATTTATCAT-A-AATTTATGAT-AAATTTAAAATAACATAATCATATTAAT
30781 TTAATC
63 TTAATC
* * * *
30787 ATCATAATAATTTTATTTATCATAAGTTTATTATAAATTTAAAATAACATAATTATATTAATT
1 ATCATAATAATTTGATTTATCATAAATTTATGATAAATTTAAAATAACATAATCATATTAATT
30850 GTAACTTCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
66 9 0.17
67 10 0.19
68 28 0.52
69 7 0.13
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (68 bp):
ATCATAATAATTTGATTTATCATAAATTTATGATAAATTTAAAATAACATAATCATATTAATTTA
ATC
Found at i:32576 original size:11 final size:11
Alignment explanation
Indices: 32549--32595 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
32539 ATGAGATATT
32549 TTAAATATTTTA
1 TTAAATA-TTTA
*
32561 GTAAATATTTA
1 TTAAATATTTA
32572 TTAAATATTTA
1 TTAAATATTTA
32583 --AAATATTCTA
1 TTAAATATT-TA
32593 TTA
1 TTA
32596 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 7 0.23
10 2 0.07
11 14 0.47
12 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
TTAAATATTTA
Found at i:32602 original size:21 final size:20
Alignment explanation
Indices: 32549--32595 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 20
32539 ATGAGATATT
32549 TTAAATATTTTAGTAAATATTTA
1 TTAAATA-TTTA--AAATATTTA
32572 TTAAATATTTAAAATATTCTA
1 TTAAATATTTAAAATATT-TA
32593 TTA
1 TTA
32596 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
21 5 0.22
22 4 0.17
23 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAAATATTTAAAATATTTA
Found at i:32871 original size:18 final size:19
Alignment explanation
Indices: 32829--32879 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
32819 TTTGGTTCAC
32829 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAG-G
*
32849 GGAATGTAAGATTATCA-G
1 GGAATGTAAGATTACCAGG
32867 GGAA--TAAGATTAC
1 GGAATGTAAGATTAC
32880 TGTGAATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 8 0.28
18 5 0.17
20 16 0.55
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.25
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:41982 original size:16 final size:16
Alignment explanation
Indices: 41961--41993 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41951 CAATAATCTC
41961 CCCCTTTTTGATATAA
1 CCCCTTTTTGATATAA
41977 CCCCTTTTTGATATAA
1 CCCCTTTTTGATATAA
41993 C
1 C
41994 AAAACATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (16 bp):
CCCCTTTTTGATATAA
Found at i:46411 original size:11 final size:11
Alignment explanation
Indices: 46395--46421 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
46385 TAAATTTTGA
46395 ATTAAATATTT
1 ATTAAATATTT
46406 ATTAAATATTT
1 ATTAAATATTT
46417 ATTAA
1 ATTAA
46422 TTTTAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTAAATATTT
Found at i:49873 original size:818 final size:820
Alignment explanation
Indices: 48289--49918 Score: 2980
Period size: 818 Copynumber: 2.0 Consensus size: 820
48279 TGATTACTGA
*
48289 GGAAATTGATACTTCCACAGTTGAATTTTTGCCTATAGACTCAGATCAGTCTCCACAAACAGAAG
1 GGAAATTGATACTTACACAGTTGAATTTTTGCCTATAGACTCAGATCAGTCTCCACAAACAGAAG
48354 AAGAAACCCTAGAAATCTCTATGAATGCTATTACTGGCTCTATTGGTCATACTACATTGATAATC
66 AAGAAACCCTAGAAATCTCTATGAATGCTATTACTGGCTCTATTGGTCATACTACATTGATAATC
48419 TAGGGCTATATACAAGGAAAATCATTAAATATCCTAATTGATAGTGGCAATACACACAGTTTCTT
131 TAGGGCTATATACAAGGAAAATCATTAAATATCCTAATTGATAGTGGCAATA-ACACAGTTTCTT
48484 GGCTCCTAATGGGCTGATGCTGACATTCAGATTACTACCCCTTATCATTTGGCCATCACTGTGGC
195 GGCTCCTAATGGGCTGATGCTGACATTCAGATTACTACCCCTTATCATTTGGCCATCACTGTGGC
48549 TAATGGTCAGCAACTATTCAGTACTGCTAGATGCAACCAAGTACAGTGGCAAATGCAGGGACATA
260 TAATGGTCAGCAACTATTCAGTACTGCTAGATGCAACCAAGTACAGTGGCAAATGCAGGGACATA
*
48614 CATTTTTGTATGATTTTAGATTACTTAAATTGGGTGTGAGTGACATGGTTTTATGATTGGATTGG
325 CATTTTTGCATGATTTTAGATTACTTAAATTGGGTGTGAGTGACATGGTTTTATGATTGGATTGG
48679 ATGAAGTTATTTAGTCCAATATTAATGGACTTCAACAATATGACTTTAAGTTTTGATCATGAAGG
390 ATGAAGTTATTTAGTCCAATATTAATGGACTTCAACAATATGACTTT-AGTTTTGATCATGAAGG
48744 AAAGCATATTTATATTCAAGGACAGCAGCCCTCAACTGAATTGCAACAAATTTCAGGGGTAACAT
454 AAAGCATATTTATATTCAAGGACAGCAGCCCTCAACTGAATTGCAACAAATTTCAGGGGTAACAT
* * *
48809 TATTAAAAATGAGTGCAGGGGATTCTGATATTATGAGATATATTGTCCTATTGACTATGGCAGGA
519 TATTAAAAATAAGTGCAGGGGATTATGATATTATGAGACATATTGTCCTATTGACTATGGCAGGA
* *
48874 AGTTCTTCTTCTATTTCTATGGAACTTCAACATGTATTGGAGAAATACAGCTCAATCTTTGCTGA
584 AGTTCTTCTTCTATTCCTATGGAACTCCAACATGTATTGGAGAAATACAGCTCAATCTTTGCTGA
48939 ACCTAAAGGGCTACCTCCTCAGAGGTCTCATGATCATGCCATTCCACTTAAACCTAATGCTACAC
649 ACCTAAAGGGCTACCTCCTCAGAGGTCTCATGATCATGCCATTCCACTTAAACCTAATGCTACAC
*
49004 CAGTTAATCTGAGGCCTTATAGATTTCCTCATAATCAGAAGGCTAATGTTGAGAAACAGATAACT
714 CAGTTAATCTGAGGCCTTATAGATTTCCTCACAATCAGAAGGCTAATGTTGAGAAACAGATAACT
49069 ACAATGCTTTCTTCTTCTGTCATTTAACCTAGTAATCTCTGT
779 ACAATGCTTTCTTCTTCTGTCATTTAACCTAGTAATCTCTGT
* *
49111 GGAAATTGATACTTACACAGTTGAATTTTTGCCTATAGACTCATATCAGTCTCCACAAATAGAAG
1 GGAAATTGATACTTACACAGTTGAATTTTTGCCTATAGACTCAGATCAGTCTCCACAAACAGAAG
*
49176 AATAAACCCTAGAAATCTCTATGAATGCTATTACTGGCTCTATTGGTCATACTACATTGATAATC
66 AAGAAACCCTAGAAATCTCTATGAATGCTATTACTGGCTCTATTGGTCATACTACATTGATAATC
* * *
49241 TAGGGCTCTATACAAGGAAAATCATTAAATATCCTAATTGATAGTGGTAGT-ACACAGTTTCTTG
131 TAGGGCTATATACAAGGAAAATCATTAAATATCCTAATTGATAGTGGCAATAACACAGTTTCTTG
*
49305 GCTCCTAAATGGGCTGATGCTGCCATTCAGATTACTACCCCTTATCATTTGGCCATCACTGTGGC
196 GCTCCT-AATGGGCTGATGCTGACATTCAGATTACTACCCCTTATCATTTGGCCATCACTGTGGC
49370 TAATGGTCAGCAACTATTCAGTACTGCTAGATGCAACCAAGTACAGTGGCAAATGCAGGGACATA
260 TAATGGTCAGCAACTATTCAGTACTGCTAGATGCAACCAAGTACAGTGGCAAATGCAGGGACATA
*
49435 CATTTTTGCATGATTTTAGATTACTTAAATTGGGTGTGAGTGATATGGTTTTATGATTGGATTGG
325 CATTTTTGCATGATTTTAGATTACTTAAATTGGGTGTGAGTGACATGGTTTTATGATTGGATTGG
*
49500 ATGAAGTTATTTAGTCCAATATTAATGGACTTCAATAATATGAC-TT-GTTTTGATCATGAAGGA
390 ATGAAGTTATTTAGTCCAATATTAATGGACTTCAACAATATGACTTTAGTTTTGATCATGAAGGA
* *
49563 AAGCATATTTATATTCAAGGACAGCAGCCCTTAACTGAATTGCAACAAATTTTAGGGGCT-ACAT
455 AAGCATATTTATATTCAAGGACAGCAGCCCTCAACTGAATTGCAACAAATTTCAGGGG-TAACAT
49627 TATTAAAAATAAGTGCAGGGGATTATGATATTATGAGACATATTGTCCTATTGACTATGGCAGGA
519 TATTAAAAATAAGTGCAGGGGATTATGATATTATGAGACATATTGTCCTATTGACTATGGCAGGA
*
49692 AGTTCTTCTTCTATTCCTATGGAACTCCAACATGTATTGGAGAAATACAGCTCAGTCTTTGCTGA
584 AGTTCTTCTTCTATTCCTATGGAACTCCAACATGTATTGGAGAAATACAGCTCAATCTTTGCTGA
* *
49757 ACCTAAAGGGCTACCTCCTCAGAGGTCTCATGATCATGTCATTCCACTTAAACCTAATGGTACAC
649 ACCTAAAGGGCTACCTCCTCAGAGGTCTCATGATCATGCCATTCCACTTAAACCTAATGCTACAC
* *
49822 CAGTTAATCTGAGGCCTTATAGATTTCCTCACAATCAGAAGGCTGATGTTGAGAAACATATAACT
714 CAGTTAATCTGAGGCCTTATAGATTTCCTCACAATCAGAAGGCTAATGTTGAGAAACAGATAACT
49887 ACAATGCTTTCTTCTTCTGTCATTTAACCTAG
779 ACAATGCTTTCTTCTTCTGTCATTTAACCTAG
49919 AAGAATCCCA
Statistics
Matches: 782, Mismatches: 24, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
818 358 0.46
819 1 0.00
820 21 0.03
821 228 0.29
822 174 0.22
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (820 bp):
GGAAATTGATACTTACACAGTTGAATTTTTGCCTATAGACTCAGATCAGTCTCCACAAACAGAAG
AAGAAACCCTAGAAATCTCTATGAATGCTATTACTGGCTCTATTGGTCATACTACATTGATAATC
TAGGGCTATATACAAGGAAAATCATTAAATATCCTAATTGATAGTGGCAATAACACAGTTTCTTG
GCTCCTAATGGGCTGATGCTGACATTCAGATTACTACCCCTTATCATTTGGCCATCACTGTGGCT
AATGGTCAGCAACTATTCAGTACTGCTAGATGCAACCAAGTACAGTGGCAAATGCAGGGACATAC
ATTTTTGCATGATTTTAGATTACTTAAATTGGGTGTGAGTGACATGGTTTTATGATTGGATTGGA
TGAAGTTATTTAGTCCAATATTAATGGACTTCAACAATATGACTTTAGTTTTGATCATGAAGGAA
AGCATATTTATATTCAAGGACAGCAGCCCTCAACTGAATTGCAACAAATTTCAGGGGTAACATTA
TTAAAAATAAGTGCAGGGGATTATGATATTATGAGACATATTGTCCTATTGACTATGGCAGGAAG
TTCTTCTTCTATTCCTATGGAACTCCAACATGTATTGGAGAAATACAGCTCAATCTTTGCTGAAC
CTAAAGGGCTACCTCCTCAGAGGTCTCATGATCATGCCATTCCACTTAAACCTAATGCTACACCA
GTTAATCTGAGGCCTTATAGATTTCCTCACAATCAGAAGGCTAATGTTGAGAAACAGATAACTAC
AATGCTTTCTTCTTCTGTCATTTAACCTAGTAATCTCTGT
Done.