Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002358.1 Hibiscus syriacus cultivar Beakdansim tig00004812_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: 72794
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:4535 original size:132 final size:131
Alignment explanation
Indices: 4298--4535 Score: 291
Period size: 132 Copynumber: 1.8 Consensus size: 131
4288 TTTTTCGCCA
* * * *
4298 TGAAGTTGAGTCGATCTTGGATGACTTGAGCTTGATATCCTTCATCGTGAAGTTGAAATCTAGCT
1 TGAAGTCGAGTCAATCTTGGATGACTTGAGCATGATATCCTTCATCGTGAAGTAGAAATCTAGCT
* * * * *
4363 CGAAATCTAAGCTGAAAATAACTCCTTGTTGTTGAGTTAAGCTAAATTATGGTTGGCTTCTTCAT
66 CAAAATATAAGC-GAAAATAACTCATCGTTGTTGACTTAAGCTAAATTATGGTTGGCTTCTTCAT
4428 CG
130 CG
* **
4430 TGAAGTCGAGTCAATCTTGGATGACTTGAGCATGATGTCCTTTGTCGTGAAGTAGAAAT-TAGCT
1 TGAAGTCGAGTCAATCTTGGATGACTTGAGCATGATATCCTTCATCGTGAAGTAGAAATCTAGCT
* * *
4494 CAAAATATGGAATG-GGAAATAGCTCATCGTTTTTGACTTAAG
66 CAAAATAT--AA-GCGAAAATAACTCATCGTTGTTGACTTAAG
4536 GTAGATCGTA
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
131 11 0.12
132 74 0.84
133 2 0.02
134 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (131 bp):
TGAAGTCGAGTCAATCTTGGATGACTTGAGCATGATATCCTTCATCGTGAAGTAGAAATCTAGCT
CAAAATATAAGCGAAAATAACTCATCGTTGTTGACTTAAGCTAAATTATGGTTGGCTTCTTCATC
G
Found at i:10207 original size:8 final size:10
Alignment explanation
Indices: 10179--10212 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
10169 TTTTTCTTTA
*
10179 TTTTACTCTC
1 TTTTCCTCTC
10189 TTTTCCTCTC
1 TTTTCCTCTC
10199 TTTTCCTCT-
1 TTTTCCTCTC
10208 TTTTC
1 TTTTC
10213 TCATTGTACC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTCCTCTC
Found at i:15773 original size:21 final size:21
Alignment explanation
Indices: 15743--15790 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
15733 TAATTTTCAA
*
15743 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
15764 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
15785 ACATTG
1 ACATTG
15791 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:20415 original size:21 final size:22
Alignment explanation
Indices: 20380--20430 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 22
20370 TTTACCCATT
20380 TAATTTTCAAACATTATTGCACC
1 TAATTTT-AAACATTATTGCACC
*
20403 TAATTTT-AACATTGTTGCACC
1 TAATTTTAAACATTATTGCACC
20424 TAATTTT
1 TAATTTT
20431 GATATTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 20 0.74
23 7 0.26
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (22 bp):
TAATTTTAAACATTATTGCACC
Found at i:21424 original size:37 final size:37
Alignment explanation
Indices: 21348--21424 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
21338 TTTTTATATT
*
21348 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
21385 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
21422 TTT
1 TTT
21425 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:22261 original size:22 final size:21
Alignment explanation
Indices: 22236--22297 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 21
22226 TAATTTGATT
*
22236 ATTTAAATTTTTTAAATATTTG
1 ATTTAAATTATTTAAA-ATTTG
* *
22258 ATTTTAATTATTTAAAATTTA
1 ATTTAAATTATTTAAAATTTG
**
22279 AAATAAA-TATTTAAAATTT
1 ATTTAAATTATTTAAAATTT
22298 TGAATTTAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 12 0.35
21 8 0.24
22 14 0.41
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTAAATTATTTAAAATTTG
Found at i:28950 original size:8 final size:8
Alignment explanation
Indices: 28937--28961 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28927 CCAGTAGTCT
28937 TGTGGACA
1 TGTGGACA
28945 TGTGGACA
1 TGTGGACA
28953 TGTGGACA
1 TGTGGACA
28961 T
1 T
28962 TCAACCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.28
Consensus pattern (8 bp):
TGTGGACA
Found at i:40942 original size:13 final size:14
Alignment explanation
Indices: 40914--40945 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40904 CATATAAAAT
40914 AAAA-AAAATAATG
1 AAAATAAAATAATG
40927 AAAATAAAATAA-G
1 AAAATAAAATAATG
40940 AAAATA
1 AAAATA
40946 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (14 bp):
AAAATAAAATAATG
Found at i:41181 original size:8 final size:8
Alignment explanation
Indices: 41168--41217 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
41158 ACAAAATGTG
41168 TACATATA
1 TACATATA
41176 TACATATA
1 TACATATA
*
41184 TATATATA
1 TACATATA
*
41192 TATATATA
1 TACATATA
*
41200 TATATAATA
1 TACAT-ATA
41209 TAACATATA
1 T-ACATATA
41218 AGTGAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 28 0.74
9 7 0.18
10 3 0.08
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (8 bp):
TACATATA
Found at i:41184 original size:2 final size:2
Alignment explanation
Indices: 41171--41210 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
41161 AAATGTGTAC
*
41171 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41211 ACATATAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:41218 original size:12 final size:12
Alignment explanation
Indices: 41171--41217 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
41161 AAATGTGTAC
41171 ATATATACATAT
1 ATATATACATAT
*
41183 ATATATATATAT
1 ATATATACATAT
*
41195 ATATATATATA-
1 ATATATACATAT
41206 ATATA-ACATAT
1 ATATATACATAT
41217 A
1 A
41218 AGTGAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 4 0.12
11 6 0.19
12 22 0.69
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATACATAT
Found at i:43364 original size:105 final size:105
Alignment explanation
Indices: 43111--43837 Score: 1255
Period size: 105 Copynumber: 6.9 Consensus size: 105
43101 CTGGGACTGG
* * * *** *
43111 GAAATTGTTTGTCGGCAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCC
1 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
43176 AATATCCTTCGTTGTGAAGTTGAAATTGG----GAAATTGT
65 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
* *
43213 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
43278 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
65 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
43319 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
43384 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
* *
43424 GAAATGTTTGTTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAATCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
43489 ATATCCTTCGTTGCGAAGTTGAAATTGGCTCTGAATTTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
43529 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
43594 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
*
43634 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
43699 ATTATCATTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
66 A-TATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
43740 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
43805 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
43838 GGTAAAACCT
Statistics
Matches: 596, Mismatches: 23, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
102 84 0.14
105 400 0.67
106 112 0.19
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
Found at i:44691 original size:14 final size:14
Alignment explanation
Indices: 44674--44702 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44664 TTTTCTTTCC
44674 TTTTTTTTTCAACT
1 TTTTTTTTTCAACT
44688 TTTTTTTTTCAACT
1 TTTTTTTTTCAACT
44702 T
1 T
44703 AGGACGCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTTTTCAACT
Found at i:55279 original size:13 final size:14
Alignment explanation
Indices: 55251--55282 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
55241 CATATAAAAT
55251 AAAA-AAAATAATG
1 AAAATAAAATAATG
55264 AAAATAAAATAA-G
1 AAAATAAAATAATG
55277 AAAATA
1 AAAATA
55283 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (14 bp):
AAAATAAAATAATG
Found at i:55520 original size:8 final size:8
Alignment explanation
Indices: 55507--55550 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
55497 ACAAAATGTG
55507 TACATATA
1 TACATATA
55515 TACATATA
1 TACATATA
55523 T--ATATA
1 TACATATA
*
55529 TATATATA
1 TACATATA
55537 TA-ATATA
1 TACATATA
55544 -ACATATA
1 TACATATA
55551 AGTGAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
6 7 0.21
7 10 0.30
8 16 0.48
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (8 bp):
TACATATA
Found at i:55523 original size:2 final size:2
Alignment explanation
Indices: 55510--55543 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
55500 AAATGTGTAC
*
55510 AT AT AT AC AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55544 ACATATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:55525 original size:10 final size:10
Alignment explanation
Indices: 55510--55550 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
55500 AAATGTGTAC
55510 ATATATACAT
1 ATATATACAT
*
55520 ATATATATAT
1 ATATATACAT
*
55530 ATATATATA-
1 ATATATACAT
55539 ATATA-ACAT
1 ATATATACAT
55548 ATA
1 ATA
55551 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 2 0.07
9 8 0.29
10 18 0.64
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATACAT
Found at i:57690 original size:193 final size:188
Alignment explanation
Indices: 57173--57756 Score: 584
Period size: 192 Copynumber: 3.0 Consensus size: 188
57163 ACTCAAAAGA
* * * * *
57173 AAATATTTAGGTTATCACTTTATTAAAAGGTAACATCG-CTAAAAAAATACTAAGTGGATAGAAT
1 AAATA-TTATGTTATCACTTTATTAAAAGGTAATAT-GATTAATAAAATATTAAGTGGATA-AAT
* * * * * * * *
57237 TAAATTTCGTATTCTGATTCAAGAGGAAAATTTATTTAGATA-TCAGTTTGAGATAAAGTACATA
63 TAAATTTCATATTCTAATTTAAGAGAAAAATTTCTTTAGATATTAACTTT-A-AAAAAGTACATA
* * * * * *
57301 ATTCATCTATCAACATAAAAGTAAAAAATATTTAAATTCCAACTCAAAAGAAAATATTTAATTA
126 ATTCATATATCAACTTAAAAAT-AAAAATATTTAAATTCCAACTTAAAAGAAAATATTTAGTTC
* * * * ** *
57365 AAATATTATGTTATTACGTTATTAAAAGATAATATCATTAATAAAAATATTAAGCAGATAAAATC
1 AAATATTATGTTATCACTTTATTAAAAGGTAATATGATTAAT-AAAATATTAAGTGGAT-AAATT
* * * * *
57430 AAATTTCAAATTCTAATTTAGGAGAAAAAATTCTTTAGATGTAAAC-TTAAGAGAAAGTACATAA
64 AAATTTCATATTCTAATTTAAGAGAAAAATTTCTTTAGATATTAACTTTAA-A-AAAGTACATAA
* *
57494 TTCATGTATCAACTTAAAAATAAAAATTATTTAAATACCAACTTAAAAGAAAATATTTTAGTTC
127 TTCATATATCAACTTAAAAATAAAAA-TATTTAAATTCCAACTTAAAAGAAAATA-TTTAGTTC
57558 AAATATTATGTTATCACTTTA-TACAAAGGTAATATGATTAATAAAATGCATTAAGTGGATGAAA
1 AAATATTATGTTATCACTTTATTA-AAAGGTAATATGATTAATAAAAT--ATTAAGTGGAT-AAA
* * *
57622 TTAAATTTTATATTCTAATTTAAAAGCAAAATTTCTTTAGATATTAACTTTAAAAAAGTAGC-TA
62 TTAAATTTCATATTCTAATTTAAGAGAAAAATTTCTTTAGATATTAACTTTAAAAAAGTA-CATA
* * * * * *
57686 ATTCATATATCAATTTGAAAATAAAAAAATTTTAAATTTCAACATAAAAGAAAGTATTTAGTTC
126 ATTCATATATCAACTTAAAAATAAAAATA-TTTAAATTCCAACTTAAAAGAAAATATTTAGTTC
*
57750 AGATATT
1 AAATATT
57757 TTTTTGAGAG
Statistics
Matches: 321, Mismatches: 57, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
190 1 0.00
191 34 0.11
192 132 0.41
193 97 0.30
194 53 0.17
195 4 0.01
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.35
Consensus pattern (188 bp):
AAATATTATGTTATCACTTTATTAAAAGGTAATATGATTAATAAAATATTAAGTGGATAAATTAA
ATTTCATATTCTAATTTAAGAGAAAAATTTCTTTAGATATTAACTTTAAAAAAGTACATAATTCA
TATATCAACTTAAAAATAAAAATATTTAAATTCCAACTTAAAAGAAAATATTTAGTTC
Found at i:64441 original size:20 final size:19
Alignment explanation
Indices: 64418--64464 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
64408 CGATATAACA
64418 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
64438 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
64458 GGTAAAA
1 GGTAAAA
64465 CGCTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:64466 original size:181 final size:183
Alignment explanation
Indices: 64024--64497 Score: 763
Period size: 181 Copynumber: 2.6 Consensus size: 183
64014 GATCCAAATT
* * * **
64024 AAAAATGTATCGATCCACAACGATATAACATATAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * ** * *
64089 AAACCGGTAAAGCGGTACATGATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
64154 GTTAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTAAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTAAA
*
64207 AAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATG
1 AAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
64272 AAACCGATAAAACGCTACCGGATGTATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
64336 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCTTATAAAGTGTCGATACTTT-AA
131 GTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTAAA
*
64388 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
64453 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT
64498 CGTAAGTACG
Statistics
Matches: 269, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
181 108 0.40
182 65 0.24
183 96 0.36
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (183 bp):
AAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTAAA
Found at i:66730 original size:21 final size:21
Alignment explanation
Indices: 66704--66768 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
66694 AAGACAATCA
*
66704 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
66725 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
66746 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
66767 AG
1 AG
66769 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:66844 original size:33 final size:33
Alignment explanation
Indices: 66802--66867 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
66792 AAATAGATGG
*
66802 AGTGATGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
66835 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
66868 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:67135 original size:36 final size:33
Alignment explanation
Indices: 67055--67127 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
67045 AAAATATGAA
*
67055 GAAGAAAAGAGGGAGGATGAAGAAGAAGAGACG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGACG
* *
67088 GAAGAAAAGAGGGATGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGACG
67121 GAAGAAA
1 GAAGAAA
67128 TGAAGAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.53, C:0.01, G:0.41, T:0.04
Consensus pattern (33 bp):
GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGACG
Found at i:68713 original size:19 final size:19
Alignment explanation
Indices: 68689--68737 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
68679 AATGTAGGGT
68689 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
68708 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
68727 TAATTTTGTAT
1 TAATTTTGTAT
68738 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:69319 original size:200 final size:200
Alignment explanation
Indices: 68964--70345 Score: 2323
Period size: 200 Copynumber: 6.9 Consensus size: 200
68954 AATTTACAAT
*
68964 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
69029 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* *
69094 ATGAGAGAATAGGTGCA-AT-ATATGTATCGATACTTTTTAATTTTGTGTCGATACTATTAGTCC
131 ATGAGAGAATAGGT--ATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCC
69157 AGAATGA
194 AGAATGA
*
69164 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
69229 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTTAATCTAACCGGTATAAGTATACCGTTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
69294 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
69359 AATGA
196 AATGA
*
69364 ATGGCAAACAGGGTGCAACCATAAAGTTTCGATCCATATATAAAAGGTGTCGAT-CCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
69428 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * *
69493 ATGAGAGATTAGGTATATAATATATATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAT
131 ATGAGAGAATAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
69558 AATGA
196 AATGA
* * *
69563 ATGCCAAACAGGGTGCAACCATAAAGTGTTGATCCATATATAAAATGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
69628 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCAGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* *
69693 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTTGATACTATTGGTCCAG
131 ATGAGAGAATAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
69758 AATGA
196 AATGA
*
69763 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCTAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
69828 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACC-GATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* **
69892 AT--GAGAATAGGTGTA-ATATATGTATCGACACTTTTTAATTTTGAATCGATACTATTGGTCCA
131 ATGAGAGAATAGGTATATA-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
*
69954 AAATGA
195 GAATGA
* *
69960 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTTGATCCCAGAAATAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
70025 TGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * **
70090 ATGAGAGAATAGGTGTA-ATATATGTATCGACACATTTTAATTTTGAATCGATACTATTGGTCCA
131 ATGAGAGAATAGGTATATA-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
*
70154 AAATGA
195 GAATGA
* *
70160 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTATCGATCCCAGAAACTT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
70225 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* *
70290 ATGAGATAATAGGTGTA-ATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
131 ATGAGAGAATAGGTATATA-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
70346 ATTTAAATAT
Statistics
Matches: 1128, Mismatches: 47, Indels: 14
0.95 0.04 0.01
Matches are distributed among these distances:
196 1 0.00
197 178 0.16
198 7 0.01
199 199 0.18
200 743 0.66
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
ATGAGAGAATAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:70091 original size:397 final size:398
Alignment explanation
Indices: 68964--70345 Score: 2358
Period size: 399 Copynumber: 3.5 Consensus size: 398
68954 AATTTACAAT
*
68964 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
69029 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * * *
69094 ATGAGAGAATAGGTGCAATATATGTATCGATACTTTTTAATTTTGTGTCGATACTATTAGTCCAG
131 AT--GAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAA
69159 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGA
194 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGA
*
69224 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTTAATCTAACCGGTATAAGTATACCG
259 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCG
*
69289 TTTTTATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
324 GTTTTATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
69354 TCCAGAATGA
389 TCCAGAATGA
*
69364 ATGGCAAACAGGGTGCAACCATAAAGTTTCGATCCATATATAAAAGGTGTCGAT-CCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
69428 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* *
69493 ATGAGAGATTAGGTAT-ATAATATATATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
131 ATGAGA-A-TAGGTGTAAT-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
* * * *
69557 TAATGAATGCCAAACAGGGTGCAACCATAAAGTGTTGATCCATATATAAAATGTGTCGATCCCAG
193 AAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAG
69622 AAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACC
258 AAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACC
* *
69687 AGTTTTATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTTGATACTATTG
323 GGTTTTATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTG
69752 GTCCAGAATGA
388 GTCCAGAATGA
*
69763 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCTAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
69828 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACC-GATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
**
69892 ATGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGAATCGATACTATTGGTCCAAAA
131 ATGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAAAA
* *
69957 TGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTTGATCCCAGAAA
196 TGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAA
* *
70022 TATTGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGT
261 CATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGT
* * * **
70087 TTTATGAGAGAATAGGTGTA-ATATATGTATCGACACATTTTAATTTTGAATCGATACTATTGGT
326 TTTATGAGAGATTAGGTATATA-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGT
*
70151 CCAAAATGA
390 CCAGAATGA
* *
70160 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTATCGATCCCAGAAACTT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
70225 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
70290 ATGAGATAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
131 ATGAG--AATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
70346 ATTTAAATAT
Statistics
Matches: 928, Mismatches: 45, Indels: 18
0.94 0.05 0.02
Matches are distributed among these distances:
396 1 0.00
397 362 0.39
398 15 0.02
399 383 0.41
400 167 0.18
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (398 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
ATGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAAAA
TGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAA
CATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGT
TTTATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTC
CAGAATGA
Done.