Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001889.1 Hibiscus syriacus cultivar Beakdansim tig00003833_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: 88606
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:4473 original size:28 final size:28
Alignment explanation
Indices: 4433--4489 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
4423 GTATCGTCGT
* *
4433 TCTTTCAAGCACTAGCTCGACGATATAA
1 TCTTTCAAGCACTAGCTCAACAATATAA
*
4461 TCTTTCAAGCACTAGGTCAACAATATAA
1 TCTTTCAAGCACTAGCTCAACAATATAA
4489 T
1 T
4490 GTAAACAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (28 bp):
TCTTTCAAGCACTAGCTCAACAATATAA
Found at i:5283 original size:67 final size:68
Alignment explanation
Indices: 5199--5337 Score: 244
Period size: 68 Copynumber: 2.1 Consensus size: 68
5189 AAATACTTAG
5199 GTAAAACGACTTCATTATTATCATGATTTG-CTTGATTATGCTAAACTTTTATTATTTTTAATAT
1 GTAAAACGACTTCATTATTATCATGATTTGACTTGATTATGCTAAACTTTTATTATTTTTAATAT
5263 ATA
66 ATA
* * *
5266 GTAAAATGACTTCATTATTATCATGATTTGATTTTATTATGCTAAACTTTTATTATTTTTAATAT
1 GTAAAACGACTTCATTATTATCATGATTTGACTTGATTATGCTAAACTTTTATTATTTTTAATAT
5331 ATA
66 ATA
5334 GTAA
1 GTAA
5338 TTATTTGAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
67 29 0.43
68 39 0.57
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (68 bp):
GTAAAACGACTTCATTATTATCATGATTTGACTTGATTATGCTAAACTTTTATTATTTTTAATAT
ATA
Found at i:5951 original size:25 final size:25
Alignment explanation
Indices: 5923--5970 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
5913 TAATTATGCG
5923 TTTAATT-TAAGTT-TATAATTAAATT
1 TTTAATTGTAA-TTCTA-AATTAAATT
5948 TTTAATTGTAATTCTAAATTAAA
1 TTTAATTGTAATTCTAAATTAAA
5971 AACTAACTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTAATTGTAATTCTAAATTAAATT
Found at i:10447 original size:15 final size:17
Alignment explanation
Indices: 10427--10468 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
10417 GATAAAATAA
10427 AATGATT-AAGCG-CTG
1 AATGATTCAAGCGCCTG
*
10442 AATGATTCAATCGCCTG
1 AATGATTCAAGCGCCTG
10459 AATGATTCAA
1 AATGATTCAA
10469 AGGCTCTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 7 0.29
16 4 0.17
17 13 0.54
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (17 bp):
AATGATTCAAGCGCCTG
Found at i:10708 original size:23 final size:23
Alignment explanation
Indices: 10678--10730 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
10668 TAATGCTGAA
*
10678 TCATTCAACAGTGTTTTGTTGTT
1 TCATTCAACAGTGTTTTGATGTT
10701 TCATTCAACAGTGTTTTGATGTT
1 TCATTCAACAGTGTTTTGATGTT
10724 TCATTCA
1 TCATTCA
10731 GCATAGTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (23 bp):
TCATTCAACAGTGTTTTGATGTT
Found at i:13707 original size:39 final size:39
Alignment explanation
Indices: 13660--13808 Score: 228
Period size: 39 Copynumber: 3.8 Consensus size: 39
13650 GTCTAAATCT
13660 GAGAGGTTAATGTTGCAATC-GATTCTTCAAAATCTGAGG
1 GAGAGGTTAATGTTGCAA-CAGATTCTTCAAAATCTGAGG
13699 GAGAGGTTAATGTTGCAACAGATTCTTCAAAATCTGAGG
1 GAGAGGTTAATGTTGCAACAGATTCTTCAAAATCTGAGG
* * *
13738 GAGAGGTTAATGTTGTAACCGATTCTTCAAAATTTGAGG
1 GAGAGGTTAATGTTGCAACAGATTCTTCAAAATCTGAGG
* **
13777 AAGAGGTTAATGTTGCAACTTATTCTTCAAAA
1 GAGAGGTTAATGTTGCAACAGATTCTTCAAAA
13809 GCTGCTGTTG
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
38 1 0.01
39 101 0.99
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (39 bp):
GAGAGGTTAATGTTGCAACAGATTCTTCAAAATCTGAGG
Found at i:16759 original size:16 final size:17
Alignment explanation
Indices: 16723--16760 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
16713 CAGTTTACTA
16723 ATTTTTGTCTTCTAATC
1 ATTTTTGTCTTCTAATC
16740 ATTTTCTGTCTT-TAAT-
1 ATTTT-TGTCTTCTAATC
16756 ATTTT
1 ATTTT
16761 AATTGTCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 9 0.45
18 6 0.30
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.63
Consensus pattern (17 bp):
ATTTTTGTCTTCTAATC
Found at i:22147 original size:20 final size:21
Alignment explanation
Indices: 22109--22148 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
22099 AAAAATACAT
*
22109 AAAATACATATTTAGAATATA
1 AAAATACATATATAGAATATA
*
22130 AAAATA-ATATATATAATAT
1 AAAATACATATATAGAATAT
22149 CAACTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAATACATATATAGAATATA
Found at i:22272 original size:59 final size:59
Alignment explanation
Indices: 22179--22309 Score: 176
Period size: 59 Copynumber: 2.2 Consensus size: 59
22169 AATTTAGGGT
** *
22179 AAAG-TACACAAATGATCCTCCGACTATAGGGTGTTGC-GTGTTGAGTTTCTCGACTATTA
1 AAAGTTACA-AAATGATCCTCCGACTATAAAGTGTTGCTGTGATGAG-TTCTCGACTATTA
* * *
22238 AAAGTTACAAAATGATCCTCTGACTATAAAGTGTTGCTTTGATGAGTTCTCTACTATTA
1 AAAGTTACAAAATGATCCTCCGACTATAAAGTGTTGCTGTGATGAGTTCTCGACTATTA
22297 AAAGTTACAAAAT
1 AAAGTTACAAAAT
22310 AGTCACCTGG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
59 54 0.84
60 10 0.16
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (59 bp):
AAAGTTACAAAATGATCCTCCGACTATAAAGTGTTGCTGTGATGAGTTCTCGACTATTA
Found at i:23661 original size:23 final size:24
Alignment explanation
Indices: 23635--23695 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
23625 CACCACAACT
*
23635 CGTATAATTGCACCGA-AGTGCCA
1 CGTAGAATTGCACCGAGAGTGCCA
*
23658 CGTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCGAGAGTGCCA
*
23681 CATAGAATTGCACCG
1 CGTAGAATTGCACCG
23696 TAGTACCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.20
Consensus pattern (24 bp):
CGTAGAATTGCACCGAGAGTGCCA
Found at i:25322 original size:21 final size:21
Alignment explanation
Indices: 25297--25340 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
25287 TTCTGGTTCG
* * *
25297 CTTGAGGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
25318 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
25339 CT
1 CT
25341 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:26259 original size:351 final size:351
Alignment explanation
Indices: 25610--26317 Score: 1353
Period size: 351 Copynumber: 2.0 Consensus size: 351
25600 TTGAGTAAAA
* *
25610 AACTCCATTCCAGAATTTCATTCAAAAACTCTTGATCTTTAATCTCTCCTAATTCCATCATCCTT
1 AACTCCATTCCAGAATTTCATTCAAAAACTCTTGATCTTTAATCTCTCATAATTCCACCATCCTT
25675 TGTTTTTAAGATGATTTAAGCTTTCCTAAAGCTTAATTATCATCCAATAATCATAACCAAATCCT
66 TGTTTTTAAGATGATTTAAGCTTTCCTAAAGCTTAATTATCATCCAATAATCATAACCAAATCCT
25740 AAATTCAGCTAAATATCAACTAACAAGAGATCTTACCGTTGCTTATGGCTTCACGGTGGAAAAGA
131 AAATTCAGCTAAATATCAACTAACAAGAGATCTTACCGTTGCTTATGGCTTCACGGTGGAAAAGA
*
25805 AGAGAATGAAGAAGAGAAGTCTGGAACTCTCTCATATTTCCCACATTTTATAATACTCAAAAAAG
196 AGAGAATGAAGAAGAGAAATCTGGAACTCTCTCATATTTCCCACATTTTATAATACTCAAAAAAG
*
25870 GGAAGATAAAAATATTTCCCATGAAAAGACCATTTTGCCCCTTTAGTTCATCCATCTTTGGTATT
261 GGAAGATAAAAATATTTCCCATGAAAAGACCATTTTGCCCCTTTAGTTCATCCATCTTTGCTATT
25935 TAATCCAATATTAAAATTCTTTACTT
326 TAATCCAATATTAAAATTCTTTACTT
*
25961 AACTCTATTCCAGAATTTCATTCAAAAACTCTTGATCTTTAATCTCTCATAATTCCACCATCCTT
1 AACTCCATTCCAGAATTTCATTCAAAAACTCTTGATCTTTAATCTCTCATAATTCCACCATCCTT
26026 TGTTTTTAAGATGATTTAAGCTTTCCTAAAGCTTAATTATCATCCAATAATCATAACCAAATCCT
66 TGTTTTTAAGATGATTTAAGCTTTCCTAAAGCTTAATTATCATCCAATAATCATAACCAAATCCT
26091 AAATTCAGCTAAATATCAACTAACAAGAGATCTTACCGTTGCTTATGGCTTCACGGTGGAAAAGA
131 AAATTCAGCTAAATATCAACTAACAAGAGATCTTACCGTTGCTTATGGCTTCACGGTGGAAAAGA
*
26156 AGAGAATGAAGAAGAGAAATCTGGAACTCTCTCATATTTCCCACGTTTTATAATACTCAAAAAAG
196 AGAGAATGAAGAAGAGAAATCTGGAACTCTCTCATATTTCCCACATTTTATAATACTCAAAAAAG
*
26221 GGAAGATAAAAATCTTTCCCATGAAAAGACCATTTTGCCCCTTTAGTTCATCCATCTTTGCTATT
261 GGAAGATAAAAATATTTCCCATGAAAAGACCATTTTGCCCCTTTAGTTCATCCATCTTTGCTATT
26286 TAATCCAATATTAAAATTCTTTACTT
326 TAATCCAATATTAAAATTCTTTACTT
26312 AACTCC
1 AACTCC
26318 CGAGACTTTT
Statistics
Matches: 349, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
351 349 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.34
Consensus pattern (351 bp):
AACTCCATTCCAGAATTTCATTCAAAAACTCTTGATCTTTAATCTCTCATAATTCCACCATCCTT
TGTTTTTAAGATGATTTAAGCTTTCCTAAAGCTTAATTATCATCCAATAATCATAACCAAATCCT
AAATTCAGCTAAATATCAACTAACAAGAGATCTTACCGTTGCTTATGGCTTCACGGTGGAAAAGA
AGAGAATGAAGAAGAGAAATCTGGAACTCTCTCATATTTCCCACATTTTATAATACTCAAAAAAG
GGAAGATAAAAATATTTCCCATGAAAAGACCATTTTGCCCCTTTAGTTCATCCATCTTTGCTATT
TAATCCAATATTAAAATTCTTTACTT
Found at i:29275 original size:23 final size:23
Alignment explanation
Indices: 29249--29317 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
29239 CACCACAGCT
*
29249 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
29272 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
29295 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
29318 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:33479 original size:18 final size:18
Alignment explanation
Indices: 33447--33484 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
33437 TTTCTTCTAA
33447 TATTTAATAAAAATAATTT
1 TATTTAATAAAAAT-ATTT
*
33466 TATTT-ATAATAATATTT
1 TATTTAATAAAAATATTT
33483 TA
1 TA
33485 AGTGAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTAATAAAAATATTT
Found at i:36531 original size:3 final size:3
Alignment explanation
Indices: 36523--36548 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36513 AAATGAACAC
36523 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
36549 TGGGCGGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40235 original size:3 final size:3
Alignment explanation
Indices: 40227--40308 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
40217 ACCACAAATG
40227 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40275 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40309 GGACCAATAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41203 original size:23 final size:23
Alignment explanation
Indices: 41177--41236 Score: 54
Period size: 23 Copynumber: 2.6 Consensus size: 23
41167 AATAATTATT
41177 TTATGTTTAATTTTA-TCTAATAA
1 TTATGTTTAATTTTATTC-AATAA
* *
41200 TTATCGATTAA-ATTATTCAATAA
1 TTAT-GTTTAATTTTATTCAATAA
41223 TTAT-TTATAATTTT
1 TTATGTT-TAATTTT
41237 TTATTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
21 1 0.03
22 3 0.10
23 18 0.62
24 7 0.24
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (23 bp):
TTATGTTTAATTTTATTCAATAA
Found at i:42235 original size:9 final size:9
Alignment explanation
Indices: 42223--42256 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
42213 TAATATTATG
42223 TATTTAATT
1 TATTTAATT
*
42232 TATTT-AGT
1 TATTTAATT
42240 TATTTAATT
1 TATTTAATT
42249 TATTTAAT
1 TATTTAAT
42257 ATTTTACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (9 bp):
TATTTAATT
Found at i:42262 original size:17 final size:17
Alignment explanation
Indices: 42223--42260 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
42213 TAATATTATG
*
42223 TATTTAATTTATTTAGT
1 TATTTAATTTATTTAAT
42240 TATTTAATTTATTTAA-
1 TATTTAATTTATTTAAT
42256 TATTT
1 TATTT
42261 TACTAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TATTTAATTTATTTAAT
Found at i:43938 original size:18 final size:18
Alignment explanation
Indices: 43915--43949 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43905 CAGCAGCCAC
*
43915 CGCAGCCATTTATGATGT
1 CGCAGCCATATATGATGT
43933 CGCAGCCATATATGATG
1 CGCAGCCATATATGATG
43950 CCGCCATCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (18 bp):
CGCAGCCATATATGATGT
Found at i:44520 original size:24 final size:25
Alignment explanation
Indices: 44488--44534 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44478 TTTAATACTT
*
44488 ACTTTATTT-TGTTAAATTTGTTGG
1 ACTTTATTTCAGTTAAATTTGTTGG
*
44512 ACTTTATTTCAGTTAATTTTGTT
1 ACTTTATTTCAGTTAAATTTGTT
44535 TATTACCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (25 bp):
ACTTTATTTCAGTTAAATTTGTTGG
Found at i:44557 original size:20 final size:21
Alignment explanation
Indices: 44534--44573 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
44524 TTAATTTTGT
*
44534 TTATTACCATTTAA-TATCAG
1 TTATTACAATTTAATTATCAG
*
44554 TTATTATAATTTAATTATCA
1 TTATTACAATTTAATTATCA
44574 TTTAATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (21 bp):
TTATTACAATTTAATTATCAG
Found at i:45033 original size:44 final size:44
Alignment explanation
Indices: 44970--45062 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
44960 TTGTCATTAC
44970 TTATGGGGGAAACTCAAATTTGTATACCTTAAAAACTTCATATA
1 TTATGGGGGAAACTCAAATTTGTATACCTTAAAAACTTCATATA
45014 TTATGGGGGAAACTCAAATTTGTATACCTTAAAAACTTCATATA
1 TTATGGGGGAAACTCAAATTTGTATACCTTAAAAACTTCATATA
*
45058 GTATG
1 TTATG
45063 TATACGGGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (44 bp):
TTATGGGGGAAACTCAAATTTGTATACCTTAAAAACTTCATATA
Found at i:50019 original size:43 final size:43
Alignment explanation
Indices: 49958--50044 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
49948 ATAATGGATG
*
49958 TGTGAAAGGATAAGATGAATAGAGCGTAAAGAGTGCAATGTTT
1 TGTGAAAGGATAAGATGAATAGAGAGTAAAGAGTGCAATGTTT
50001 TGTGAAAGGATAAGATGAATAGAGAGTAAAGAGTGCAATGTTT
1 TGTGAAAGGATAAGATGAATAGAGAGTAAAGAGTGCAATGTTT
50044 T
1 T
50045 TTTTAATAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.03, G:0.30, T:0.26
Consensus pattern (43 bp):
TGTGAAAGGATAAGATGAATAGAGAGTAAAGAGTGCAATGTTT
Found at i:51859 original size:82 final size:82
Alignment explanation
Indices: 51696--51866 Score: 193
Period size: 82 Copynumber: 2.1 Consensus size: 82
51686 CTGATGAAAT
* * * * *
51696 AACTTATAGCTCTGAATTTAGATTGTGACAATATATATTCCCATAAAATTATTGATTTTAAAGAT
1 AACTTATAACTCTGAATTTAGAATGTGACAATATATATTCACATAAAATTATTAATTATAAAGAT
* * **
51761 TTATTGATTAAAACTAA
66 ATATAGAACAAAACTAA
* *
51778 AACTTCTAACTCTGAATTTGGAATGTGACAATATATATTCACATAAAATTATTAAATTAT-AAG-
1 AACTTATAACTCTGAATTTAGAATGTGACAATATATATTCACATAAAATTATT-AATTATAAAGA
*
51841 TAATATAGAACAACACTAA
65 T-ATATAGAACAAAACTAA
*
51860 AAGTTAT
1 AACTTAT
51867 GACGACAAAG
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
81 1 0.01
82 68 0.93
83 4 0.05
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (82 bp):
AACTTATAACTCTGAATTTAGAATGTGACAATATATATTCACATAAAATTATTAATTATAAAGAT
ATATAGAACAAAACTAA
Found at i:52039 original size:32 final size:32
Alignment explanation
Indices: 51949--52057 Score: 125
Period size: 31 Copynumber: 3.5 Consensus size: 32
51939 AACCTAATGG
*
51949 TTGACCCGAA-CCG-AAACCAACCGATTCGATA
1 TTGACCC-AACCCGAAAACCAACCGATCCGATA
* * *
51980 TTGACCCGACTC-AAAGCCAACCGATCCGATA
1 TTGACCCAACCCGAAAACCAACCGATCCGATA
* *
52011 TTGACCCAACCCGAAAACCAACCAATCCGACA
1 TTGACCCAACCCGAAAACCAACCGATCCGATA
*
52043 TTGACCCGACCCGAA
1 TTGACCCAACCCGAA
52058 CTGAATTGTC
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
30 1 0.02
31 34 0.52
32 30 0.46
ACGTcount: A:0.35, C:0.37, G:0.15, T:0.14
Consensus pattern (32 bp):
TTGACCCAACCCGAAAACCAACCGATCCGATA
Found at i:55786 original size:16 final size:16
Alignment explanation
Indices: 55757--55797 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
55747 CGTTTATTTA
55757 ATAAAT-AA-ATGAAC
1 ATAAATGAACATGAAC
55771 ATAAATGAACATGAAC
1 ATAAATGAACATGAAC
*
55787 ATAAACGAACA
1 ATAAATGAACA
55798 AATTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.25
15 2 0.08
16 16 0.67
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (16 bp):
ATAAATGAACATGAAC
Found at i:55906 original size:16 final size:16
Alignment explanation
Indices: 55867--55927 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
55857 TAATAAATAA
*
55867 ACGAACATAAAC-ACGC
1 ACGAACATAAACGA-AC
*
55883 ATGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
55899 ACGGACATAAATGAAC
1 ACGAACATAAACGAAC
55915 ACGAACATAAACG
1 ACGAACATAAACG
55928 TTAGAGACCC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
16 36 0.97
17 1 0.03
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:57043 original size:14 final size:14
Alignment explanation
Indices: 57026--57057 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
57016 AATGAACATA
57026 AACGAACATAACCG
1 AACGAACATAACCG
57040 AACGAACATAACCG
1 AACGAACATAACCG
57054 AACG
1 AACG
57058 TTCACGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:61554 original size:15 final size:15
Alignment explanation
Indices: 61534--61563 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61524 TACAATTTTC
*
61534 AAACAAATATTTCAT
1 AAACAAACATTTCAT
61549 AAACAAACATTTCAT
1 AAACAAACATTTCAT
61564 TTCCCAAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (15 bp):
AAACAAACATTTCAT
Found at i:71206 original size:2 final size:2
Alignment explanation
Indices: 71160--71188 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
71150 ATTTTTTCTA
71160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71189 ATCTAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74331 original size:27 final size:26
Alignment explanation
Indices: 74301--74353 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
74291 AGATAAACAA
*
74301 ATAATTATTAAATAATTAAATTAAAAT
1 ATAATTATGAAA-AATTAAATTAAAAT
* *
74328 ATAATTATGAAAACTTGAATTAAAAT
1 ATAATTATGAAAAATTAAATTAAAAT
74354 TTTTGTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (26 bp):
ATAATTATGAAAAATTAAATTAAAAT
Found at i:77181 original size:34 final size:35
Alignment explanation
Indices: 77138--77205 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
77128 GGAAGAGGAT
77138 CCACCGAGGGTTG-CGAAGGATAGGGACGAGTGCA
1 CCACCGAGGGTTGACGAAGGATAGGGACGAGTGCA
77172 CCACCGAGGGTTGACGAAGGATAGGGACGAGTGC
1 CCACCGAGGGTTGACGAAGGATAGGGACGAGTGC
77206 TGCAATCGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 13 0.39
35 20 0.61
ACGTcount: A:0.26, C:0.21, G:0.41, T:0.12
Consensus pattern (35 bp):
CCACCGAGGGTTGACGAAGGATAGGGACGAGTGCA
Found at i:84732 original size:22 final size:23
Alignment explanation
Indices: 84692--84740 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
84682 GGACCGATTG
84692 GTTT-GGTTCAAGTCAACCATTT
1 GTTTCGGTTCAAGTCAACCATTT
84714 GTTTCGGTTCAAGTC-ACCATTT
1 GTTTCGGTTCAAGTCAACCATTT
84736 GTTTC
1 GTTTC
84741 TTGGGTAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (23 bp):
GTTTCGGTTCAAGTCAACCATTT
Found at i:85400 original size:2 final size:2
Alignment explanation
Indices: 85393--85448 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
85383 TTGCTAGGTC
85393 TA TA TA TA TA TA TA TA T- TA 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
85434 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
85449 TCTTTTTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.