Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001099.1 Hibiscus syriacus cultivar Beakdansim tig00002180_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: 81086
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:982 original size:18 final size:18
Alignment explanation
Indices: 961--995 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
951 AAAATAAATC
961 ATAAAAATAAAATTGAAA
1 ATAAAAATAAAATTGAAA
979 ATAAAAATAAAATTGAA
1 ATAAAAATAAAATTGAA
996 CAAACGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (18 bp):
ATAAAAATAAAATTGAAA
Found at i:5508 original size:23 final size:24
Alignment explanation
Indices: 5472--5518 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
5462 GGTTGCCCTG
5472 TTCTGCCCCCACGTCAGGGATATT
1 TTCTGCCCCCACGTCAGGGATATT
5496 TTCTG-CCCCACGTCAGGGATATT
1 TTCTGCCCCCACGTCAGGGATATT
5519 CCTCCATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.17, C:0.32, G:0.21, T:0.30
Consensus pattern (24 bp):
TTCTGCCCCCACGTCAGGGATATT
Found at i:7888 original size:3 final size:3
Alignment explanation
Indices: 7873--7925 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
7863 TTCATTTAAA
* *
7873 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
7918 TAT TAT TA
1 TAT TAT TA
7926 AAAAAATAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 44 0.96
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:7933 original size:24 final size:24
Alignment explanation
Indices: 7886--7937 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
7876 TATTTATATT
** *
7886 ATTATTATTATTATTATTATAATA
1 ATTATTATTATTATTAAAAAAATA
7910 ATTATTATTATTATTAAAAAAATA
1 ATTATTATTATTATTAAAAAAATA
7934 ATTA
1 ATTA
7938 CAGGCCCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTATTATTATTATTAAAAAAATA
Found at i:7937 original size:21 final size:21
Alignment explanation
Indices: 7892--7937 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
7882 TATTATTATT
* * *
7892 ATTATTATTATTATAATAATT
1 ATTATTATTATTAAAAAAATA
7913 ATTATTATTATTAAAAAAATA
1 ATTATTATTATTAAAAAAATA
7934 ATTA
1 ATTA
7938 CAGGCCCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTATTATTAAAAAAATA
Found at i:20830 original size:7 final size:7
Alignment explanation
Indices: 20818--20877 Score: 72
Period size: 7 Copynumber: 8.9 Consensus size: 7
20808 ATGCTTGAAG
20818 AAAAAGA
1 AAAAAGA
20825 AAAAAGA
1 AAAAAGA
20832 AAAAA-A
1 AAAAAGA
*
20838 AAGAAGA
1 AAAAAGA
20845 AAGAAA-A
1 AA-AAAGA
20852 AAAAA-A
1 AAAAAGA
*
20858 GAAAAGA
1 AAAAAGA
20865 AAAAAGA
1 AAAAAGA
20872 AAAAAG
1 AAAAAG
20878 GGTGTCAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
6 13 0.28
7 31 0.67
8 2 0.04
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:20838 original size:17 final size:17
Alignment explanation
Indices: 20818--20869 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
20808 ATGCTTGAAG
20818 AAAAAGAAAAAAGAAAA
1 AAAAAGAAAAAAGAAAA
*
20835 AAAAAGAAGAAAGAAAA
1 AAAAAGAAAAAAGAAAA
*
20852 AAAAA-AGAAAAGAAAA
1 AAAAAGAAAAAAGAAAA
20868 AA
1 AA
20870 GAAAAAAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 11 0.34
17 21 0.66
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAGAAAA
Found at i:20841 original size:23 final size:23
Alignment explanation
Indices: 20815--20877 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
20805 ATTATGCTTG
20815 AAGAAAAAGAAAAAAGAAAAAAA
1 AAGAAAAAGAAAAAAGAAAAAAA
*
20838 AAGAAGAAAGAAAAAA-AAAAGAA
1 AAGAA-AAAGAAAAAAGAAAAAAA
20861 AAGAAAAAAGAAAAAAG
1 AAG-AAAAAGAAAAAAG
20878 GGTGTCAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 24 0.67
24 12 0.33
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAAAAGAAAAAAA
Found at i:22022 original size:94 final size:94
Alignment explanation
Indices: 21861--22240 Score: 565
Period size: 94 Copynumber: 4.1 Consensus size: 94
21851 GTGCCGTGTG
* *
21861 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTATGAACCCCAAAAAA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAAAA
21926 CCAATCATTGAATTTGAAAGATGAATGTA
66 CCAATCATTGAATTTGAAAGATGAATGTA
21955 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAAAA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAAAA
*
22020 CCAATCATTGAATTTGAAAGATGAATGTG
66 CCAATCATTGAATTTGAAAGATGAATGTA
* * *
22049 CTCATAGCATCTTCTGGAAGCGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCCTG-AAAA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAAAA
* * *
22113 CCAATCATTGGATTTG-AA-AT-AAAGAGA
66 CCAATCATTGAATTTGAAAGATGAATG-TA
* * *
22140 CTCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAA-ACC-ACAG
1 CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA-AA
* *
22203 AACCAATCATTGGATTTGAAAGATGAATGTG
64 AACCAATCATTGAATTTGAAAGATGAATGTA
22234 CTCATAG
1 CTCATAG
22241 TACAAATAAA
Statistics
Matches: 259, Mismatches: 20, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
90 3 0.01
91 6 0.02
92 70 0.27
93 24 0.09
94 153 0.59
95 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (94 bp):
CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAAAA
CCAATCATTGAATTTGAAAGATGAATGTA
Found at i:22385 original size:115 final size:115
Alignment explanation
Indices: 22129--22347 Score: 343
Period size: 115 Copynumber: 1.9 Consensus size: 115
22119 ATTGGATTTG
* * * *
22129 AAATAAAGAGACTCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG
1 AAATAAAGAGACCCAATAGCAGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTATG
* * *
22194 AAACCACAGAACCAATCATTGGATTTGAAAGATGAATGTGCTCATAGTAC
66 AAACCACAGAACCAATCATTGGAATTAAAAGATGAATCTGCTCATAGTAC
*
22244 AAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTA-G
1 AAATAAAGAGACCCAATAGCAGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTATG
*
22308 GAACCACAGAACCAATCATTGGAATTAAAAGATGAA-CTGC
66 AAACCACAGAACCAATCATTGGAATTAAAAGATGAATCTGC
22348 ATGATCGTCT
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
113 3 0.03
114 34 0.35
115 60 0.62
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (115 bp):
AAATAAAGAGACCCAATAGCAGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTATG
AAACCACAGAACCAATCATTGGAATTAAAAGATGAATCTGCTCATAGTAC
Found at i:23269 original size:113 final size:113
Alignment explanation
Indices: 23071--23581 Score: 688
Period size: 113 Copynumber: 4.5 Consensus size: 113
23061 CCAGAAAAAA
*
23071 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** * *
23136 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGTTCG
66 AACCTTTTGCTTAAATTCATCATTCAATGGATCAACATTACCAGTTCG
* *
23184 AGTTCAAAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
23249 AACTTTTTACTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
66 AACCTTTTGCTTAAATTCATCATTCAATGGATCAACATTACCAGTTCG
* * * *
23297 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** * * * **
23362 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAA
66 AACCTTTTGCTTAAATTCATCATTCAATGGATCAACATTACCAGTTCG
23410 AGTTCATAATGAGAAGAACTCGTCATCTGAAG-A-G--GAAGAAGTTCATAATGAGAAGAACTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
** * *
23471 TTCAAATTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
63 TTCAACCTTTTGCTTAAATTCATCATTCAATGGATCAACATTACCAGTTCG
* * *
23522 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
23582 CATCTGAAGA
Statistics
Matches: 344, Mismatches: 47, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
109 10 0.03
110 2 0.01
111 1 0.00
112 81 0.24
113 237 0.69
114 1 0.00
115 2 0.01
116 10 0.03
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTTAAATTCATCATTCAATGGATCAACATTACCAGTTCG
Found at i:23473 original size:20 final size:20
Alignment explanation
Indices: 23410--23474 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
23400 TGCCAGGTAA
23410 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* * * **
23430 CG-TCAT-CTGAAGAGGAAGA
1 AGTTCATAATG-AGAAGAACT
23449 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
23469 TGTTCA
1 AGTTCA
23475 AATTTTTGCT
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 16 0.52
21 2 0.06
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:23546 original size:225 final size:225
Alignment explanation
Indices: 23071--23581 Score: 857
Period size: 225 Copynumber: 2.3 Consensus size: 225
23061 CCAGAAAAAA
* * * *
23071 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* **
23136 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGTTCGAGTTCAAAATGAGAAGA
66 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAAAGTTCAAAATGAGAAGA
*
23201 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACTTTTTACTTGAATT
131 ACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAAAACTTGTTCAAATTTTTACTTGAATT
23266 CATCATTCAATGGATCAGCATTACCAGTTCG
195 CATCATTCAATGGATCAGCATTACCAGTTCG
*
23297 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAATGAGAAGAACTTGTTC
*
23362 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAAAGTTCATAATGAGAAGA
66 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAAAGTTCAAAATGAGAAGA
* *
23427 ACTCGTCATCTGAAG-A-G-GAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGCTTGAA
131 A--C-TCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAAATTTTTACTTGAA
23489 TTCATCATTCAATGGATCAGCATTACCAGTTCG
193 TTCATCATTCAATGGATCAGCATTACCAGTTCG
23522 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAATGAGAAGAACT
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAATGAGAAGAACT
23582 CATCTGAAGA
Statistics
Matches: 269, Mismatches: 13, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
225 134 0.50
226 122 0.45
227 1 0.00
228 2 0.01
229 10 0.04
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (225 bp):
AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAAAGTTCAAAATGAGAAGA
ACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAAATTTTTACTTGAATTC
ATCATTCAATGGATCAGCATTACCAGTTCG
Found at i:23787 original size:120 final size:118
Alignment explanation
Indices: 23560--23837 Score: 344
Period size: 120 Copynumber: 2.3 Consensus size: 118
23550 GAAGGCAGAA
* * *
23560 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAATTCACAATGAGAAGAGCTTGTTCAA
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAGTTCACAATGAGAAGAGCTTATTCAA
* * * * * * *
23625 CCTTTTACATAATTTTATCACAAAAGGAGATATATTAGCATCAACCTTTCTAG-AG
66 CCTTTTACATAACTCTATCACAAAAGGAAATAGATCAACATCAACC---CCAGCAG
* *
23680 AAAGTTCATAATGAGAAGAACTCATCTGAAGAATAAGAAGTTCATAATGAGAAGAGCTTATTCAA
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAGTTCACAATGAGAAGAGCTTATTCAA
* * * * *
23745 CCTTTTGA-ATGACTCTATCACAGAAGGAAATAGGTCAACATCATCCCCAGCGG
66 CCTTTT-ACATAACTCTATCACAAAAGGAAATAGATCAACATCAACCCCAGCAG
*
23798 AAAGTTCATAATGAGAAAAACTCATCTGAAGAAAAAGAAG
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAG
23838 AATTTATTCA
Statistics
Matches: 138, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
117 3 0.02
118 39 0.28
120 95 0.69
121 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (118 bp):
AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAGTTCACAATGAGAAGAGCTTATTCAA
CCTTTTACATAACTCTATCACAAAAGGAAATAGATCAACATCAACCCCAGCAG
Found at i:41454 original size:23 final size:23
Alignment explanation
Indices: 41428--41486 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
41418 TTTGGCTAGA
*
41428 GTTGACCGCTAACCGGTCAGATC
1 GTTGACCGTTAACCGGTCAGATC
41451 GTTGACCGTTAACCGGTCAGATC
1 GTTGACCGTTAACCGGTCAGATC
*
41474 GTTGGCCGTTAAC
1 GTTGACCGTTAAC
41487 TTTGACCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GTTGACCGTTAACCGGTCAGATC
Found at i:41770 original size:24 final size:24
Alignment explanation
Indices: 41724--41773 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
41714 ATCGTTTGAT
**
41724 TGTTCGACTCGGTTCCTTTCGATC
1 TGTTCGACTCGGTTCCTCCCGATC
*
41748 TGTTCGACTCGGTTTCTCCCGATC
1 TGTTCGACTCGGTTCCTCCCGATC
41772 TG
1 TG
41774 CTCGTCTACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.30, G:0.22, T:0.40
Consensus pattern (24 bp):
TGTTCGACTCGGTTCCTCCCGATC
Found at i:53205 original size:21 final size:22
Alignment explanation
Indices: 53179--53225 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
53169 CTACTGTATA
* *
53179 ATTTAC-CAGATTTAAAGCCTG
1 ATTTACTCAAATTTAAAGCATG
*
53200 ATTTACTGAAATTTAAAGCATG
1 ATTTACTCAAATTTAAAGCATG
53222 ATTT
1 ATTT
53226 CTTGATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
ATTTACTCAAATTTAAAGCATG
Found at i:70992 original size:22 final size:22
Alignment explanation
Indices: 70945--71000 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
70935 AAGATTATAG
*
70945 ATTACTTAGGATTTTAATTATTT
1 ATTA-TTAGGATTTTAATTATCT
*
70968 ATTATTAGGATTTTAGTT-TACT
1 ATTATTAGGATTTTAATTAT-CT
70990 ATTAATTAGGA
1 ATT-ATTAGGA
71001 ATTAAGTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.03
22 17 0.59
23 11 0.38
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (22 bp):
ATTATTAGGATTTTAATTATCT
Found at i:71778 original size:15 final size:15
Alignment explanation
Indices: 71758--71786 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
71748 TATCTCTCAT
71758 TACAATTAATTTTTA
1 TACAATTAATTTTTA
71773 TACAATTAATTTTT
1 TACAATTAATTTTT
71787 CTTGCTTTTA
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:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TACAATTAATTTTTA
Found at i:75023 original size:3 final size:3
Alignment explanation
Indices: 75015--75046 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
75005 CATTTTTAAA
75015 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
75047 TATTTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:75034 original size:14 final size:14
Alignment explanation
Indices: 75015--75042 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
75005 CATTTTTAAA
75015 ATTATTATTATTAT
1 ATTATTATTATTAT
75029 ATTATTATTATTAT
1 ATTATTATTATTAT
75043 TATTTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATTATTAT
Found at i:75037 original size:17 final size:16
Alignment explanation
Indices: 75015--75050 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
75005 CATTTTTAAA
75015 ATTATTATTATTATATT
1 ATTATTATTATTAT-TT
75032 ATTATTATTATTATTT
1 ATTATTATTATTATTT
75048 ATT
1 ATT
75051 TAATTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTATTATTATTATTT
Done.