Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006011.1 Hibiscus syriacus cultivar Beakdansim tig00014179_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: 58414
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4970 original size:2 final size:2
Alignment explanation
Indices: 4963--5020 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
4953 ATCATAAGTG
*
4963 CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
5005 CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA
5021 TATATATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:9590 original size:6 final size:6
Alignment explanation
Indices: 9555--9612 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
9545 CCTCATCTGC
* ** * * *
9555 ATCATC ATCATT ATCATT ATCAAC ATCATT ATCATT GTCACT ATTATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
9603 ATCATT ATCA
1 ATCATT ATCA
9613 CAGTTCATTA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (6 bp):
ATCATT
Found at i:9613 original size:18 final size:17
Alignment explanation
Indices: 9555--9614 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
9545 CCTCATCTGC
9555 ATCATCATCATTATCATT
1 ATCA-CATCATTATCATT
9573 ATCAACATCATTATCATT
1 ATC-ACATCATTATCATT
* *
9591 GTCACTATTATTATCATT
1 ATCAC-ATCATTATCATT
9609 ATCACA
1 ATCACA
9615 GTTCATTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.08
18 33 0.89
19 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.42
Consensus pattern (17 bp):
ATCACATCATTATCATT
Found at i:9767 original size:23 final size:23
Alignment explanation
Indices: 9737--9830 Score: 89
Period size: 23 Copynumber: 4.1 Consensus size: 23
9727 CACTGATATG
*
9737 CCACATAGAAATGTCCTGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* * *
9760 CCATATAGTACTGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* * *
9783 CCGCGTAGAAATGTCCCGAATGA
1 CCACATAGAAATGTCCCGAAGGA
* * * *
9806 CCACGTAGAATTGTTCCAAAGGA
1 CCACATAGAAATGTCCCGAAGGA
9829 CC
1 CC
9831 GCGTAGAACC
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAGGA
Found at i:9794 original size:46 final size:46
Alignment explanation
Indices: 9742--9838 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
9732 ATATGCCACA
* * * *
9742 TAGAAATGTCCTGAAGGACCATATAGTACTGTCCCGAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCACATAGAACTGTCCCAAAGGACCGCG
* * * *
9788 TAGAAATGTCCCGAATGACCACGTAGAATTGTTCCAAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCACATAGAACTGTCCCAAAGGACCGCG
9834 TAGAA
1 TAGAA
9839 CCCTTGACTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (46 bp):
TAGAAATGTCCCGAAGGACCACATAGAACTGTCCCAAAGGACCGCG
Found at i:9835 original size:23 final size:23
Alignment explanation
Indices: 9771--9838 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
9761 CATATAGTAC
*
9771 TGTCCCGAAGGACCGCGTAGAAA
1 TGTCCCAAAGGACCGCGTAGAAA
* * * *
9794 TGTCCCGAATGACCACGTAGAAT
1 TGTCCCAAAGGACCGCGTAGAAA
*
9817 TGTTCCAAAGGACCGCGTAGAA
1 TGTCCCAAAGGACCGCGTAGAA
9839 CCCTTGACTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (23 bp):
TGTCCCAAAGGACCGCGTAGAAA
Found at i:12209 original size:15 final size:15
Alignment explanation
Indices: 12189--12217 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12179 TTCATTTTAA
12189 TTAATATATTATTTT
1 TTAATATATTATTTT
12204 TTAATATATTATTT
1 TTAATATATTATTT
12218 AAAATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTAATATATTATTTT
Found at i:13204 original size:14 final size:13
Alignment explanation
Indices: 13185--13215 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
13175 TTCATCCCAC
13185 TATTATTATTATAT
1 TATTATTATTAT-T
13199 TATTATTATTATT
1 TATTATTATTATT
13212 TATT
1 TATT
13216 TTACATCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:17422 original size:3 final size:3
Alignment explanation
Indices: 17409--17497 Score: 128
Period size: 3 Copynumber: 30.0 Consensus size: 3
17399 TTTCATGCAT
* *
17409 TTA TT- TTA TTA TTA TTA TATA TTA TTA TTA TTA ATA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
*
17454 TTA TTA TTA ATA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17498 ATAAATAAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
2 4 0.05
3 71 0.91
4 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:17902 original size:23 final size:23
Alignment explanation
Indices: 17872--17921 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
17862 CTGGTCCGAG
17872 GCCATCACCATGGTGGCTATAAA
1 GCCATCACCATGGTGGCTATAAA
17895 GCCATCACCATGGTGGCTATAAA
1 GCCATCACCATGGTGGCTATAAA
17918 GCCA
1 GCCA
17922 CCAAACCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (23 bp):
GCCATCACCATGGTGGCTATAAA
Found at i:18894 original size:15 final size:16
Alignment explanation
Indices: 18861--18897 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
18851 ACATTTTTCA
18861 TTTAATATATTTGCAT
1 TTTAATATATTTGCAT
18877 TTTAATAT-TATTGC-T
1 TTTAATATAT-TTGCAT
18892 TTTAAT
1 TTTAAT
18898 TTCTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTAATATATTTGCAT
Found at i:18976 original size:12 final size:11
Alignment explanation
Indices: 18903--18989 Score: 63
Period size: 12 Copynumber: 7.4 Consensus size: 11
18893 TTAATTTCTT
18903 TTATTTTGATTA
1 TTATTTT-ATTA
18915 TTATTATTATT-
1 TTATT-TTATTA
*
18926 TGT-TTGTTTTTA
1 T-TATT-TTATTA
18938 TTATTTT-TTA
1 TTATTTTATTA
18948 TATATGTTTAAATTA
1 T-TAT-TTT--ATTA
18963 TTATTTTCATTA
1 TTATTTT-ATTA
18975 TTATTTTATTA
1 TTATTTTATTA
18986 TTAT
1 TTAT
18990 CTTAAGTCGT
Statistics
Matches: 63, Mismatches: 3, Indels: 19
0.74 0.04 0.22
Matches are distributed among these distances:
10 4 0.06
11 21 0.33
12 26 0.41
13 5 0.08
14 3 0.05
15 4 0.06
ACGTcount: A:0.25, C:0.01, G:0.05, T:0.69
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:18982 original size:25 final size:23
Alignment explanation
Indices: 18912--18989 Score: 67
Period size: 25 Copynumber: 3.4 Consensus size: 23
18902 TTTATTTTGA
* *
18912 TTATTATTATTATTTGT-T-TGT
1 TTATTATTATTTTTTATATATGT
18933 TT-TTATTATTTTTTATATATGT
1 TTATTATTATTTTTTATATATGT
18955 TTAAATTATTATTTTCATTAT-TAT-T
1 TT--ATTATTATTTT--TTATATATGT
18980 TTATTATTAT
1 TTATTATTAT
18990 CTTAAGTCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
20 12 0.25
21 3 0.06
22 5 0.10
23 8 0.17
25 13 0.27
26 3 0.06
27 4 0.08
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (23 bp):
TTATTATTATTTTTTATATATGT
Found at i:19191 original size:23 final size:23
Alignment explanation
Indices: 19159--19202 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
19149 CATTTTCTGA
*
19159 TATTTTTAAATA-AATAAATATTT
1 TATTTATAAATATAA-AAATATTT
19182 TATTTATAAATATAAAAATAT
1 TATTTATAAATATAAAAATAT
19203 ATTAATCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTTATAAATATAAAAATATTT
Found at i:21302 original size:6 final size:7
Alignment explanation
Indices: 21261--21301 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
21251 TTTTCATACA
21261 TGCA-TT
1 TGCATTT
21267 TGCATTT
1 TGCATTT
21274 TGCATCTT
1 TGCAT-TT
21282 TGCATTT
1 TGCATTT
21289 T-CATTT
1 TGCATTT
21295 TGCATTT
1 TGCATTT
21302 GTTGTTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.31
7 15 0.47
8 7 0.22
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:24453 original size:9 final size:9
Alignment explanation
Indices: 24441--24476 Score: 58
Period size: 8 Copynumber: 4.2 Consensus size: 9
24431 GAAAAAAAAT
24441 AAAAAGGAA
1 AAAAAGGAA
24450 AAAAAGG-A
1 AAAAAGGAA
24458 AAAAAGGAA
1 AAAAAGGAA
24467 AAAAA-GAA
1 AAAAAGGAA
24475 AA
1 AA
24477 TATGAGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 13 0.50
9 13 0.50
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAGGAA
Found at i:24454 original size:17 final size:17
Alignment explanation
Indices: 24431--24476 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
24421 TCATTCATCA
*
24431 GAAAAAAA-ATAAAAAG
1 GAAAAAAAGAAAAAAAG
*
24447 GAAAAAAAGGAAAAAAG
1 GAAAAAAAGAAAAAAAG
24464 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
24477 TATGAGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
GAAAAAAAGAAAAAAAG
Found at i:29250 original size:22 final size:22
Alignment explanation
Indices: 29222--29275 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
29212 TCTACATTCC
29222 TCAAAGATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTCT
*
29244 TCAAAGATGATAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTCT
29266 TCAAAGATGA
1 TCAAAGATGA
29276 AAGCTTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTCT
Found at i:34146 original size:10 final size:10
Alignment explanation
Indices: 34133--34183 Score: 63
Period size: 10 Copynumber: 5.4 Consensus size: 10
34123 TTTTTTGAAA
34133 TTTTGGCTTT
1 TTTTGGCTTT
34143 TTTTGGCTTT
1 TTTTGGCTTT
34153 TTTT-G-TTT
1 TTTTGGCTTT
*
34161 TTTTGCCTTT
1 TTTTGGCTTT
*
34171 TTTTTG-TTT
1 TTTTGGCTTT
34180 TTTT
1 TTTT
34184 TTAAAAATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
8 7 0.19
9 8 0.22
10 21 0.58
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:34154 original size:18 final size:18
Alignment explanation
Indices: 34133--34183 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
34123 TTTTTTGAAA
*
34133 TTTTGGCTTTTTTTGGCTT
1 TTTTGG-TTTTTTTGCCTT
*
34152 TTTTTGTTTTTTTGCCTTT
1 TTTTGGTTTTTTTGCC-TT
*
34171 TTTTTGTTTTTTT
1 TTTTGGTTTTTTT
34184 TTAAAAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (18 bp):
TTTTGGTTTTTTTGCCTT
Found at i:34174 original size:19 final size:18
Alignment explanation
Indices: 34140--34183 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
34130 AAATTTTGGC
*
34140 TTTTTTTGGCTTTTTTTG
1 TTTTTTTGCCTTTTTTTG
34158 TTTTTTTGCCTTTTTTTTG
1 TTTTTTTGCC-TTTTTTTG
34177 TTTTTTT
1 TTTTTTT
34184 TTAAAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (18 bp):
TTTTTTTGCCTTTTTTTG
Found at i:34534 original size:11 final size:11
Alignment explanation
Indices: 34510--34554 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
34500 TATGTGCTGG
34510 AAACAAGATAA
1 AAACAAGATAA
* *
34521 AAATAAGATTA
1 AAACAAGATAA
34532 AAACAAGATAA
1 AAACAAGATAA
34543 AGAA-AAGATAA
1 A-AACAAGATAA
34554 A
1 A
34555 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:34538 original size:22 final size:22
Alignment explanation
Indices: 34510--34551 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
34500 TATGTGCTGG
34510 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
34532 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
34552 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:36896 original size:17 final size:17
Alignment explanation
Indices: 36862--36898 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
36852 TCAACTTTTC
* *
36862 TTTCTTTTATTTTTCTT
1 TTTCTTTTATTCTCCTT
36879 TTTCTTTTATTCTCCTT
1 TTTCTTTTATTCTCCTT
36896 TTT
1 TTT
36899 GAGTGCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTTATTCTCCTT
Found at i:36940 original size:24 final size:24
Alignment explanation
Indices: 36888--36940 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
36878 TTTTCTTTTA
* *
36888 TTCTCCTTTTTGAGTGCTTAAATT
1 TTCTTCTTTTGGAGTGCTTAAATT
* *
36912 TTCTTCTTTTGGAGTGCTTGACTT
1 TTCTTCTTTTGGAGTGCTTAAATT
36936 TTCTT
1 TTCTT
36941 TGTTGATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.57
Consensus pattern (24 bp):
TTCTTCTTTTGGAGTGCTTAAATT
Found at i:48154 original size:46 final size:47
Alignment explanation
Indices: 48078--48175 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 47
48068 GAGTCGAGTG
* * * * * *
48078 TTCTACGCAGTCCTTCGGGACAATTCTATGTGGTCA-TTCGG-GAGAA
1 TTCTACACAGTACTTCGGGAAAAATATATGTGG-CACTTCGGTGAAAA
48124 TTCTACACAGTACTTCGGGAAAAATATATGTGGCACTTCGGTGAAAA
1 TTCTACACAGTACTTCGGGAAAAATATATGTGGCACTTCGGTGAAAA
48171 TTCTA
1 TTCTA
48176 TGGGCTGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 2 0.05
46 33 0.75
47 9 0.20
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (47 bp):
TTCTACACAGTACTTCGGGAAAAATATATGTGGCACTTCGGTGAAAA
Found at i:48989 original size:127 final size:123
Alignment explanation
Indices: 48743--48975 Score: 333
Period size: 127 Copynumber: 1.8 Consensus size: 123
48733 CCCTTACAGT
*
48743 GGGTTGTGATGTACAATACTTTATCTCTCTACCCCGGGCATGATTTCATTGTTAGAAAAGGAATA
1 GGGTTGTGATGTACAATACTTTATCTCTCTACCCCGGGCATGATTTCATTGTCAGAAAAGGAATA
**
48808 AGGTTATCCGCTTGAATTATTGACCTTTCGATCGAGTTTGCTGAATGATATATCTTCGG
66 AGGTTATCCGCTTGAATTATTGACCAGTCGATCGAGTTTGCTGAATGA-ATATCTTCGG
* *
48867 GGGTTGT-ATGTACAATACCTTATCTCTACCTCTACCCCGGGCATGATTTCATTGTCAGAGAAGG
1 GGGTTGTGATGTACAATA-CTT-TATCT--CTCTACCCCGGGCATGATTTCATTGTCAGAAAAGG
*
48931 AAATAAGGTTATTCGCTTGAATGTTATTGACCAGTCGATCGAGTT
62 -AATAAGGTTATCCGCTTGAA--TTATTGACCAGTCGATCGAGTT
48976 GTTGACTGAT
Statistics
Matches: 96, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
123 10 0.10
124 10 0.10
125 4 0.04
127 33 0.34
128 19 0.20
130 20 0.21
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (123 bp):
GGGTTGTGATGTACAATACTTTATCTCTCTACCCCGGGCATGATTTCATTGTCAGAAAAGGAATA
AGGTTATCCGCTTGAATTATTGACCAGTCGATCGAGTTTGCTGAATGAATATCTTCGG
Found at i:57987 original size:15 final size:15
Alignment explanation
Indices: 57967--58003 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
57957 AGAGTGCATT
57967 TATTATGTACTTATA
1 TATTATGTACTTATA
57982 TATTATGTACTTATA
1 TATTATGTACTTATA
*
57997 TGTTATG
1 TATTATG
58004 AAAGTCATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (15 bp):
TATTATGTACTTATA
Found at i:58129 original size:54 final size:54
Alignment explanation
Indices: 58043--58414 Score: 443
Period size: 54 Copynumber: 7.0 Consensus size: 54
58033 TATGTTATAT
* * *
58043 TTACCGTATTGACACTAT-TCTGCAACCCACGTAATTCATAATGAGTTTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* * * *
58096 TTACCGTACCGCCACTAAGTGTGCAACCCACGTAATTCATAAGGAGTTTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* * * *
58150 TTACCATATTGGCACTA-GTGTGTAACCCACATAATTCATAATGAGTTTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* *
58203 TTACCGTATTGGCACTATGTGTGCATCCCACGTAATTCATAATGA-TTTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
** *
58256 TTACCGTATCAACAATATGTGTGC--CCCACGTAATTCATAATGAG-TTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
** * * * * *
58307 -TACCGTATCGATACTATGTGTGCAACCTAAGTAATTCATAATTACTTTGCGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* * * * *
58360 TTACCGCATCGGTACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTATGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
58414 T
1 T
Statistics
Matches: 277, Mismatches: 35, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
50 20 0.07
51 26 0.09
52 16 0.06
53 97 0.35
54 118 0.43
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (54 bp):
TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
Found at i:58233 original size:107 final size:106
Alignment explanation
Indices: 58043--58414 Score: 412
Period size: 107 Copynumber: 3.5 Consensus size: 106
58033 TATGTTATAT
* * * * * *
58043 TTACCGTATTGACACTATTCTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTACCGC
1 TTACCGTATCGACACTAGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGA
* *
58108 CACTAAGTGTGCAACCCACGTAATTCATAAGGAGTTTGTGAA
66 CACTATGTGTGCAACCCACGTAATTCATAATGA-TTTGTGAA
* * * * * *
58150 TTACCATATTGGCACTAGTGTGTAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATTGG
1 TTACCGTATCGACACTAGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGA
*
58215 CACTATGTGTGCATCCCACGTAATTCATAATGATTTGTGAA
66 CACTATGTGTGCAACCCACGTAATTCATAATGATTTGTGAA
* * *
58256 TTACCGTATCAACAATATGTGTGC--CCCACGTAATTCATAATGAG-TTGTGAA-TACCGTATCG
1 TTACCGTATCGACACTA-GTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * * *
58317 ATACTATGTGTGCAACCTAAGTAATTCATAATTACTTTGCGAA
65 ACACTATGTGTGCAACCCACGTAATTCATAATGA-TTTGTGAA
* ** * *
58360 TTACCGCATCGGTACTATGTGTGCAACCTA-AGTAATTCATAATGAGTTTATGAAT
1 TTACCGTATCGACACTA-GTGTGCAACCCACA-TAATTCATAATGAGTTTGTGAAT
Statistics
Matches: 223, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
103 37 0.17
104 33 0.15
105 19 0.09
106 37 0.17
107 97 0.43
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (106 bp):
TTACCGTATCGACACTAGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGA
CACTATGTGTGCAACCCACGTAATTCATAATGATTTGTGAA
Found at i:58263 original size:27 final size:27
Alignment explanation
Indices: 58181--58263 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 27
58171 GTAACCCACA
58181 TAATTCATAATGAGTTTGTGAATTACCG
1 TAATTCATAATGA-TTTGTGAATTACCG
*** * * * **
58209 T-ATTGGCACT-ATGTGTGCATCCCACG
1 TAATTCATAATGATTTGTGAATTAC-CG
58235 TAATTCATAATGATTTGTGAATTACCG
1 TAATTCATAATGATTTGTGAATTACCG
58262 TA
1 TA
58264 TCAACAATAT
Statistics
Matches: 36, Mismatches: 16, Indels: 7
0.61 0.27 0.12
Matches are distributed among these distances:
25 8 0.22
26 4 0.11
27 14 0.39
28 10 0.28
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (27 bp):
TAATTCATAATGATTTGTGAATTACCG
Done.