Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007234.1 Hibiscus syriacus cultivar Beakdansim tig00019147_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: 58922
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:520 original size:13 final size:13
Alignment explanation
Indices: 502--531 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
492 TTATTATTAT
*
502 TATATATCATAAA
1 TATATATAATAAA
515 TATATATAATAAA
1 TATATATAATAAA
528 TATA
1 TATA
532 ATTTATATAT
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:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATAATAAA
Found at i:571 original size:25 final size:25
Alignment explanation
Indices: 521--566 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
511 TAAATATATA
521 TAATAAATATAATTTATATATTTTT
1 TAATAAATATAATTTATATATTTTT
*
546 TAATAAAT-TATTTTA-ATATTT
1 TAATAAATATAATTTATATATTT
567 ATTTTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TAATAAATATAATTTATATATTTTT
Found at i:11782 original size:4 final size:4
Alignment explanation
Indices: 11773--11822 Score: 61
Period size: 4 Copynumber: 13.0 Consensus size: 4
11763 TTGAAGAGAA
*
11773 AAAG AAAG AAAG AAAA AAATG AAA- AAA- AAAG AAAG AAAG AAAG AAA-
1 AAAG AAAG AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAAG
11819 AAAG
1 AAAG
11823 GGAGTTCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 9 0.22
4 29 0.71
5 3 0.07
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:11798 original size:9 final size:8
Alignment explanation
Indices: 11766--11821 Score: 53
Period size: 8 Copynumber: 7.1 Consensus size: 8
11756 ATTATGCTTG
*
11766 AAGAGAAA
1 AAGAAAAA
*
11774 AAGAAAGA
1 AAGAAAAA
11782 AAGAAAAA
1 AAGAAAAA
11790 AATG-AAAA
1 AA-GAAAAA
*
11798 AA-AAAGA
1 AAGAAAAA
*
11805 AAGAAAGA
1 AAGAAAAA
11813 AAGAAAAA
1 AAGAAAAA
11821 A
1 A
11822 GGGAGTTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
7 5 0.12
8 34 0.85
9 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:11798 original size:23 final size:22
Alignment explanation
Indices: 11769--11821 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
11759 ATGCTTGAAG
*
11769 AGAAAAAGAAAGAAAGAAAAAA
1 AGAAAAAAAAAGAAAGAAAAAA
*
11791 ATGAAAAAAAAAGAAAGAAAGAA
1 A-GAAAAAAAAAGAAAGAAAAAA
11814 AGAAAAAA
1 AGAAAAAA
11822 GGGAGTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (22 bp):
AGAAAAAAAAAGAAAGAAAAAA
Found at i:11805 original size:19 final size:19
Alignment explanation
Indices: 11773--11822 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
11763 TTGAAGAGAA
11773 AAAGAAAGAAAGAAAAAAATG
1 AAAGAAA-AAAGAAAAAAA-G
*
11794 AAA-AAAAAAGAAAGAAAG
1 AAAGAAAAAAGAAAAAAAG
11812 AAAGAAAAAAG
1 AAAGAAAAAAG
11823 GGAGTTCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 4 0.15
19 17 0.63
20 3 0.11
21 3 0.11
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAAGAAAAAAAG
Found at i:14243 original size:113 final size:113
Alignment explanation
Indices: 14045--14933 Score: 1394
Period size: 113 Copynumber: 8.0 Consensus size: 113
14035 GCAAAGATTT
* *
14045 AAATCTATCACTTGATGGATTATCTTTTCCATTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
14110 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
14158 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
14223 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
14271 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
14336 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAATCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
14384 AAATCCATCACTTGATGGA-TATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
14448 AAGGAAGAAGAAGTTCATAAT--GAAGAATTTATTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
14494 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
14559 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* ** * * *
14607 AAATCCATCACTTGATGGATTAGCTTTTCCAG-AAGAAGTTCATAATAAGAAGAACTCATTTAAA
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
* * *
14671 GAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * ****
14720 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
14785 AA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTC-AGCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
14829 AAATCCATCACTTGATGGGTCAGT-TTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATC---
1 AAATCCATCACTTGATGGATTA-TCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGA
* ** *
14888 AGGA-GAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
14934 AATGACTCTA
Statistics
Matches: 731, Mismatches: 35, Indels: 25
0.92 0.04 0.03
Matches are distributed among these distances:
105 4 0.01
107 28 0.04
108 31 0.04
109 36 0.05
110 72 0.10
111 66 0.09
112 68 0.09
113 425 0.58
114 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:14681 original size:336 final size:337
Alignment explanation
Indices: 14045--14933 Score: 1383
Period size: 336 Copynumber: 2.7 Consensus size: 337
14035 GCAAAGATTT
* *
14045 AAATCTATCACTTGATGGATTATCTTTTCCATTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGA-TATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
14110 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
65 AAGGAAGAAGAAGTTCATAAT-AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
14175 GATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
129 GATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
14240 TAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTATCTTTTCCAGTT
194 TAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAGTA
* * * *
14305 CGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
259 AGAGTTCATAATAAGAAGAACTCATCTAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
*
14370 TCA-ATCTTTTGCTC
324 TCAGCT-TTTTGCTC
14384 AAATCCATCACTTGATGGATATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AAATCCATCACTTGATGGATATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
14449 AGGAAGAAGAAGTTCATAAT-GAAGAATTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGA
66 AGGAAGAAGAAGTTCATAATAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGA
14513 TTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
131 TTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
14578 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAG-AAG
196 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAGTAAG
*
14642 AAGTTCATAATAAGAAGAACTCATTTAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
261 -AGTTCATAATAAGAAGAACTCATCTAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
14707 CAGCTTTTTGCTC
325 CAGCTTTTTGCTC
* * ****
14720 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGAT-ATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
14785 AA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTC-AGCTTTTGCTCAAATCCATCACTTGATG
65 AAGGAAGAAGAAGTTCATAAT-AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
* * * *
14846 GGTCAGT-TTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATC---AGGA-GAAGAAGAAGTT
129 GATTA-TCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
** *
14904 CATAATGAGAAGAGCTTATTCAACCTTTTG
192 CATAATGAGAAGAATTTGTTCAACCTTTTG
14934 AATGACTCTA
Statistics
Matches: 517, Mismatches: 26, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
330 39 0.08
331 3 0.01
333 1 0.00
334 39 0.08
335 39 0.08
336 272 0.53
337 41 0.08
338 65 0.13
339 18 0.03
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (337 bp):
AAATCCATCACTTGATGGATATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGA
TTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAGTAAG
AGTTCATAATAAGAAGAACTCATCTAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AGCTTTTTGCTC
Found at i:14916 original size:17 final size:17
Alignment explanation
Indices: 14861--14916 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
14851 GTTTTTCCAG
14861 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
*
14878 AGAA-CTCATCAGGA-GAAGA
1 AGAAGTTCAT-A--ATG-AGA
14897 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
14914 AGA
1 AGA
14917 GCTTATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 2 0.06
19 9 0.29
20 4 0.13
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Found at i:15171 original size:3 final size:3
Alignment explanation
Indices: 15163--15247 Score: 80
Period size: 3 Copynumber: 27.7 Consensus size: 3
15153 ATGTTATTTA
* * * * *
15163 TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT AAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
15211 AAT TAT TAT TAT TAT TAA TAT ATAT TAGT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TA
15248 CAAGCCCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
3 64 0.91
4 6 0.09
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:15721 original size:11 final size:11
Alignment explanation
Indices: 15707--15741 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
15697 ACAACGCAAC
*
15707 AAAGAAACAGA
1 AAAGAAAAAGA
*
15718 AAAGAAAAAAA
1 AAAGAAAAAGA
15729 AAAGAAAAAGA
1 AAAGAAAAAGA
15740 AA
1 AA
15742 GAAGAGAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:17333 original size:2 final size:2
Alignment explanation
Indices: 17326--17355 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17316 ACATACATTC
17326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17356 GTGTGCGCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17964 original size:232 final size:233
Alignment explanation
Indices: 17551--18011 Score: 789
Period size: 232 Copynumber: 2.0 Consensus size: 233
17541 TGTTCGATTA
* * * * *
17551 GACACTCGTGTTACGACACTCGTAAGATATTTAGACTACAAGAATGACAATGATTTAACTTACTC
1 GACACTAGTGTTACAACACTCGTAAGATACTTAGACTACAAGAACGACAAGGATTTAACTTACTC
17616 GAATGGTCTTATCAGCGGATCCACTTAAAAGGGTCTCTCCTGGTTCAAAGAGTGCAAAACATGTC
66 GAATGGTCTTATCAGCGGATCCACTTAAAAGGGTCTCTCCTGGTTCAAAGAGTGCAAAACATGTC
* *
17681 ACAGAGTCCCTATGCTACTTCACGTCCCATACCAGTGTGGCTGATTGC-TTTTTGATGTCCCATA
131 ACAGAGTCCCTACGCTACTTCACGTCCCATACCAGCGTGGCTGATTGCTTTTTTGATGTCCCATA
*
17745 CCTGTTTAATCAACCGAGTTTCGGAGATTAGGCCTTGG
196 CCTGTTTAATCAACCAAGTTTCGGAGATTAGGCCTTGG
* * *
17783 GACACTAGTGTTACAAGACTCGTAAGATACTTAGACTGCAAGAACGACACGGATTTAACTTACTC
1 GACACTAGTGTTACAACACTCGTAAGATACTTAGACTACAAGAACGACAAGGATTTAACTTACTC
* *
17848 GAATGGTCTTATCAGTGGATCCACTTAAAAGGGTCTCTCCTGGTTCAAAGAGTGCAAAGCATGTC
66 GAATGGTCTTATCAGCGGATCCACTTAAAAGGGTCTCTCCTGGTTCAAAGAGTGCAAAACATGTC
*
17913 ACAGAGTCCCTACGCTCCTTCACGTCCCATACCAGCGTGGCTGATTGCTTTTTTGATGTCCCATA
131 ACAGAGTCCCTACGCTACTTCACGTCCCATACCAGCGTGGCTGATTGCTTTTTTGATGTCCCATA
17978 CCTGTTTAATCAACCAAGTTTCGGAGATTAGGCC
196 CCTGTTTAATCAACCAAGTTTCGGAGATTAGGCC
18012 ATGGAATTAG
Statistics
Matches: 214, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
232 165 0.77
233 49 0.23
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (233 bp):
GACACTAGTGTTACAACACTCGTAAGATACTTAGACTACAAGAACGACAAGGATTTAACTTACTC
GAATGGTCTTATCAGCGGATCCACTTAAAAGGGTCTCTCCTGGTTCAAAGAGTGCAAAACATGTC
ACAGAGTCCCTACGCTACTTCACGTCCCATACCAGCGTGGCTGATTGCTTTTTTGATGTCCCATA
CCTGTTTAATCAACCAAGTTTCGGAGATTAGGCCTTGG
Found at i:37891 original size:102 final size:102
Alignment explanation
Indices: 37715--37924 Score: 314
Period size: 102 Copynumber: 2.1 Consensus size: 102
37705 CTCAGACTCG
37715 GAAAGACCAACCTAAAGGAATCAAAAACGAAAAACCAAAGGAATTTGTCATAAATCCTCATTTTC
1 GAAAGACCAACCTAAAGGAATCAAAAACGAAAAACCAAAGGAATTTGTCATAAATCCTCATTTTC
*
37780 CCACTAGATTCACTAAGTCTAAGAAAGAAGCAGAAGA
66 CCACTAGATTCACTAAGTCCAAGAAAGAAGCAGAAGA
* ** * * *
37817 GAAAGACCAACCTAAAGGACTCAAAAGTGAAAAACCGAATGAATTTTTCATAAATCCTTC-TTTT
1 GAAAGACCAACCTAAAGGAATCAAAAACGAAAAACCAAAGGAATTTGTCATAAATCC-TCATTTT
* * *
37881 CCCGCTAGATTCGCTAAGTCCAATAAAGAAGCAGAAGA
65 CCCACTAGATTCACTAAGTCCAAGAAAGAAGCAGAAGA
37919 GAAAGA
1 GAAAGA
37925 AATTCTTGAG
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 95 0.98
103 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (102 bp):
GAAAGACCAACCTAAAGGAATCAAAAACGAAAAACCAAAGGAATTTGTCATAAATCCTCATTTTC
CCACTAGATTCACTAAGTCCAAGAAAGAAGCAGAAGA
Found at i:39200 original size:21 final size:20
Alignment explanation
Indices: 39147--39202 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
39137 TGAGGTAACC
39147 CAATTTTTCATTTTTCATTTTT
1 CAATTTTT-A-TTTTCATTTTT
*
39169 CAATTTCTATTTTCATTCTTT
1 CAATTTTTATTTTCATT-TTT
**
39190 TTATTTTTATTTT
1 CAATTTTTATTTT
39203 TTTCCTTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.28
21 14 0.48
22 7 0.24
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (20 bp):
CAATTTTTATTTTCATTTTT
Found at i:41527 original size:12 final size:12
Alignment explanation
Indices: 41502--41543 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
41492 TAGGGCATGG
* *
41502 GTTTTACATCAA
1 GTTTTTCATTAA
41514 GTTTTTCATTAA
1 GTTTTTCATTAA
*
41526 G-TTTTCTTTAA
1 GTTTTTCATTAA
41537 GTTTTTC
1 GTTTTTC
41544 TTTTTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.57
Consensus pattern (12 bp):
GTTTTTCATTAA
Found at i:41544 original size:12 final size:12
Alignment explanation
Indices: 41512--41546 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
41502 GTTTTACATC
*
41512 AAGTTTTTCATT
1 AAGTTTTTCTTT
41524 AAG-TTTTCTTT
1 AAGTTTTTCTTT
41535 AAGTTTTTCTTT
1 AAGTTTTTCTTT
41547 TTGTGTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (12 bp):
AAGTTTTTCTTT
Found at i:47543 original size:24 final size:23
Alignment explanation
Indices: 47516--47595 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
47506 CACTTAACAG
47516 TGCATCGATGCATCCCTTTGAATA
1 TGCATCGATGCAT-CCTTTGAATA
* *
47540 TGCATCGATTCATCATGTTG---A
1 TGCATCGATGCATCCT-TTGAATA
* *
47561 TGCACCGATGCATGCC-TTGAATG
1 TGCATCGATGCAT-CCTTTGAATA
47584 TGCATCGATGCA
1 TGCATCGATGCA
47596 CATGGTCATG
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
20 3 0.07
21 12 0.27
22 1 0.02
23 13 0.30
24 15 0.34
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (23 bp):
TGCATCGATGCATCCTTTGAATA
Found at i:49727 original size:2 final size:2
Alignment explanation
Indices: 49720--49758 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
49710 TAGCTTAAGC
49720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49759 TTAATCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50351 original size:65 final size:64
Alignment explanation
Indices: 50232--50437 Score: 213
Period size: 65 Copynumber: 3.2 Consensus size: 64
50222 TTTTTCATAG
* * * * **
50232 TGATGCACCGATGCACAAATCCATGCATCGATGCAC-CATGAAATAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACCAA-CCATGCACCGATGCACTCA-G-GATATTTTGAAACATCGAATGCA
50295 TT
63 TT
* *
50297 TCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
50360 TT
63 TT
* * * * *
50362 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
50426 TGATGCATCGAT
1 TGATGCATCGAT
50438 TCACTCTTAG
Statistics
Matches: 119, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 44 0.37
65 65 0.55
66 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:57868 original size:21 final size:21
Alignment explanation
Indices: 57826--57869 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
57816 ACTCCGGGAG
* *
57826 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
57847 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
57868 CT
1 CT
57870 CCTCCAGCTC
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:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:58417 original size:2 final size:2
Alignment explanation
Indices: 58410--58471 Score: 108
Period size: 2 Copynumber: 31.0 Consensus size: 2
58400 GCAGCTTAAT
58410 TA TA TA TA TA TA TA TA TA 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
58452 TA GTA TA T- TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA
58472 ATCAATTGGC
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 55 0.95
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Done.