Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006959.1 Hibiscus syriacus cultivar Beakdansim tig00017897_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: 95383
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1281 original size:14 final size:15
Alignment explanation
Indices: 1256--1285 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1246 GTAAAAGTTT
1256 ATTTTATAAAACATG
1 ATTTTATAAAACATG
1271 ATTTT-TAAAACATG
1 ATTTTATAAAACATG
1285 A
1 A
1286 ACACTACCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTTTATAAAACATG
Found at i:7328 original size:17 final size:16
Alignment explanation
Indices: 7302--7335 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7292 TAGGGTTGTG
7302 AAAAGAAAGAAAGAAAT
1 AAAAGAAAG-AAGAAAT
*
7319 AAAAGGAAGAAGAAAT
1 AAAAGAAAGAAGAAAT
7335 A
1 A
7336 TGAAGTGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (16 bp):
AAAAGAAAGAAGAAAT
Found at i:12391 original size:5 final size:5
Alignment explanation
Indices: 12381--12406 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12371 TATGCCTTAA
12381 AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG A
12407 GGAGGCTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:13307 original size:95 final size:95
Alignment explanation
Indices: 13016--13304 Score: 443
Period size: 95 Copynumber: 3.0 Consensus size: 95
13006 TTGCATGTTT
* **
13016 TATTGTTAAATCTTGCTGCATGTTGCTTGAAGTACGAAATGAAGATTTAGTTCCTTGCATTTACG
1 TATTGTTAAATCTTGCTGCATGTCGCTTGAAGTATAAAATGAAGATTTAGTTCCTTGCATTTACG
*
13081 TGCTGCTGCCCTTTTCTTCTTATCAGACTA
66 TGCTGCTGCCCTTTTCTGCTTATCAGACTA
* * *
13111 TATTGTTAAATCTTGCTGCATGTCGCTTGAAGTATAATATGAAGTTTTAGTTCCTTGCATTTATG
1 TATTGTTAAATCTTGCTGCATGTCGCTTGAAGTATAAAATGAAGATTTAGTTCCTTGCATTTACG
13176 TGCTGCTGCCCTTTTCTGCTTATCAGACTA
66 TGCTGCTGCCCTTTTCTGCTTATCAGACTA
* * * *
13206 TATTTTTAAATCGTGCTGCTTGTCGTTTGAAGTATAAAATGAAGATTTAGTTCCTTGCATTTACG
1 TATTGTTAAATCTTGCTGCATGTCGCTTGAAGTATAAAATGAAGATTTAGTTCCTTGCATTTACG
* * * *
13271 TGCTGCTGCACTCTTCTGCGTATCAGACTC
66 TGCTGCTGCCCTTTTCTGCTTATCAGACTA
13301 TATT
1 TATT
13305 TTTTTATTTG
Statistics
Matches: 176, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 176 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (95 bp):
TATTGTTAAATCTTGCTGCATGTCGCTTGAAGTATAAAATGAAGATTTAGTTCCTTGCATTTACG
TGCTGCTGCCCTTTTCTGCTTATCAGACTA
Found at i:14494 original size:39 final size:39
Alignment explanation
Indices: 14440--14518 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
14430 TTTCTATCGG
14440 TGATTCGACCGCGTTTGTGTTGTATGGATTTTAATACAT
1 TGATTCGACCGCGTTTGTGTTGTATGGATTTTAATACAT
14479 TGATTCGACCGCGTTTGTGTTGTATGGATTTTAATACAT
1 TGATTCGACCGCGTTTGTGTTGTATGGATTTTAATACAT
14518 T
1 T
14519 CATATATGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (39 bp):
TGATTCGACCGCGTTTGTGTTGTATGGATTTTAATACAT
Found at i:18515 original size:11 final size:11
Alignment explanation
Indices: 18499--18524 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18489 CGAGTATAAT
18499 ATTTTATTTAA
1 ATTTTATTTAA
18510 ATTTTATTTAA
1 ATTTTATTTAA
18521 ATTT
1 ATTT
18525 ATGAAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTATTTAA
Found at i:18962 original size:11 final size:11
Alignment explanation
Indices: 18948--18974 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
18938 TTCAAATTTG
18948 ATAAAAATAAA
1 ATAAAAATAAA
18959 ATAAAAATAAA
1 ATAAAAATAAA
18970 ATAAA
1 ATAAA
18975 TAAAAAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:18970 original size:16 final size:17
Alignment explanation
Indices: 18951--18993 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
18941 AAATTTGATA
18951 AAAATAAAATAAAAA-T
1 AAAATAAAATAAAAAGT
18967 AAAAT-AAATAAAAAGT
1 AAAATAAAATAAAAAGT
*
18983 ATAATAAAATA
1 AAAATAAAATA
18994 TCTTCAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 10 0.42
17 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAATAAAATAAAAAGT
Found at i:29469 original size:20 final size:20
Alignment explanation
Indices: 29432--29485 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
29422 AAAATGTATC
29432 ATAAAAAT-AG-AT-TAAAA
1 ATAAAAATAAGAATATAAAA
29449 ATAAAAATAAGAATATAAAA
1 ATAAAAATAAGAATATAAAA
*
29469 A-AATAATAAGAAATATA
1 ATAAAAATAAG-AATATA
29486 TACAATAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 8 0.25
18 2 0.06
19 10 0.31
20 12 0.38
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (20 bp):
ATAAAAATAAGAATATAAAA
Found at i:31933 original size:18 final size:17
Alignment explanation
Indices: 31892--31935 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
31882 ATCGTTTTCC
*
31892 TATAAATTTAAAATTAT
1 TATATATTTAAAATTAT
* *
31909 CATATATTTAAAATTTT
1 TATATATTTAAAATTAT
31926 GTATATATTT
1 -TATATATTT
31936 TATTAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TATATATTTAAAATTAT
Found at i:34298 original size:16 final size:16
Alignment explanation
Indices: 34277--34310 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
34267 GGAGTTGGAT
34277 TGGAAGAAGAAGCTAA
1 TGGAAGAAGAAGCTAA
34293 TGGAAGAAGAAGCTAA
1 TGGAAGAAGAAGCTAA
34309 TG
1 TG
34311 TTGCGGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.32, T:0.15
Consensus pattern (16 bp):
TGGAAGAAGAAGCTAA
Found at i:39698 original size:21 final size:20
Alignment explanation
Indices: 39671--39734 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
39661 TTTTTCAAAG
39671 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
39691 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
39706 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
39726 AAATCATTT
1 AAA-CATTT
39735 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:39708 original size:35 final size:35
Alignment explanation
Indices: 39633--39735 Score: 143
Period size: 35 Copynumber: 2.9 Consensus size: 35
39623 ATTTCTCAAC
* * *
39633 AAACATCTACCAAAATTTGAAAAACTATTTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCA--TTTTCAAAG
39671 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
*
39706 AAACATTTACCAAACTTTGAAAATCATTTT
1 AAACATTTACCAAACTTTGAAAACCATTTT
39736 TTCAAAGTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 38 0.62
37 6 0.10
38 17 0.28
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (35 bp):
AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
Found at i:44232 original size:48 final size:48
Alignment explanation
Indices: 44178--44274 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
44168 GCCCTTAGCC
44178 ATCAATCCCTTCTATTGCCAAGCCTTTTCTCGACAATAATATCGGAAG
1 ATCAATCCCTTCTATTGCCAAGCCTTTTCTCGACAATAATATCGGAAG
44226 ATCAATCCCTTCTATTGCCAAGCCTTTTCTCGACAATAATATCGGAAG
1 ATCAATCCCTTCTATTGCCAAGCCTTTTCTCGACAATAATATCGGAAG
44274 A
1 A
44275 ACAGTTGGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (48 bp):
ATCAATCCCTTCTATTGCCAAGCCTTTTCTCGACAATAATATCGGAAG
Found at i:50924 original size:24 final size:24
Alignment explanation
Indices: 50889--50937 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
50879 AGTGTTAGAA
50889 AAGTCAAAAAGAGGGCCTAAGGGG
1 AAGTCAAAAAGAGGGCCTAAGGGG
* *
50913 AAGTCAATAAGAGGGGCTAAGGGG
1 AAGTCAAAAAGAGGGCCTAAGGGG
50937 A
1 A
50938 CACCGAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.39, T:0.10
Consensus pattern (24 bp):
AAGTCAAAAAGAGGGCCTAAGGGG
Found at i:52485 original size:14 final size:11
Alignment explanation
Indices: 52451--52476 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52441 TTATCTTCAT
52451 TCATATTATTA
1 TCATATTATTA
52462 TCATATTATTA
1 TCATATTATTA
52473 TCAT
1 TCAT
52477 TAATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.54
Consensus pattern (11 bp):
TCATATTATTA
Found at i:60251 original size:23 final size:21
Alignment explanation
Indices: 60202--60264 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
60192 TTTTGGTGCA
* *
60202 GAGGGAATCGATCCCCCCCTT
1 GAGGGAAACGATTCCCCCCTT
*
60223 GAGGGAAACGATTCCCCCTTT
1 GAGGGAAACGATTCCCCCCTT
* *
60244 GAAGGGGAACCGATTTCCCCC
1 G-A-GGGAAACGATTCCCCCC
60265 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 19 0.56
22 1 0.03
23 14 0.41
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.19
Consensus pattern (21 bp):
GAGGGAAACGATTCCCCCCTT
Found at i:60284 original size:21 final size:21
Alignment explanation
Indices: 60246--60285 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
60236 CCCCCTTTGA
**
60246 AGGGGAACCGATTTCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
60267 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
60286 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:67091 original size:11 final size:11
Alignment explanation
Indices: 67075--67100 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
67065 TTATCTTCAT
67075 TCATATTATTA
1 TCATATTATTA
67086 TCATATTATTA
1 TCATATTATTA
67097 TCAT
1 TCAT
67101 TAATTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.54
Consensus pattern (11 bp):
TCATATTATTA
Found at i:67154 original size:18 final size:20
Alignment explanation
Indices: 67131--67168 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
67121 ATCCTATACT
67131 TATCAT-TCA-AACACATCA
1 TATCATATCATAACACATCA
*
67149 TATCATATCATAACATATCA
1 TATCATATCATAACACATCA
67169 CCAAACAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.32
Consensus pattern (20 bp):
TATCATATCATAACACATCA
Found at i:71277 original size:23 final size:21
Alignment explanation
Indices: 71228--71309 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
71218 ACAGAACCCC
* **
71228 AGGGGGGTATCGATTCCCCTGT
1 AGGGGGG-ATCGGTTCCCCTCA
*
71250 GGGGGGGATCGGTTCCCCTTCAA
1 AGGGGGGATCGGTTCCCC-TC-A
*
71273 AGGGGGAATCGGTT-CCCTCA
1 AGGGGGGATCGGTTCCCCTCA
* *
71293 TGGGGGGATCGATTCCC
1 AGGGGGGATCGGTTCCC
71310 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
20 12 0.25
21 14 0.29
22 10 0.21
23 12 0.25
ACGTcount: A:0.15, C:0.24, G:0.38, T:0.23
Consensus pattern (21 bp):
AGGGGGGATCGGTTCCCCTCA
Found at i:71303 original size:20 final size:21
Alignment explanation
Indices: 71251--71311 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
71241 TTCCCCTGTG
71251 GGGGGGATCGGTTCCCCTTCAAA
1 GGGGGGATCGGTT-CCC-TCAAA
* *
71274 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
71294 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
71312 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 12 0.35
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:81052 original size:25 final size:24
Alignment explanation
Indices: 81004--81051 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
80994 ATTGTTAGAA
*
81004 AAGTCAAAAAGGGGGGCTAAGGGG
1 AAGTCAAAAAGAGGGGCTAAGGGG
81028 AAGTCAAAAAGAGGGGCTAAGGGG
1 AAGTCAAAAAGAGGGGCTAAGGGG
81052 GCATCGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.44, T:0.08
Consensus pattern (24 bp):
AAGTCAAAAAGAGGGGCTAAGGGG
Found at i:83752 original size:24 final size:24
Alignment explanation
Indices: 83725--83773 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
83715 CTCCCTAATC
83725 GTAGGCTTAAGATCTATCATTCAT
1 GTAGGCTTAAGATCTATCATTCAT
*
83749 GTAGGGTTAAGATCTATCATTCAT
1 GTAGGCTTAAGATCTATCATTCAT
83773 G
1 G
83774 CATGAGTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (24 bp):
GTAGGCTTAAGATCTATCATTCAT
Found at i:84027 original size:5 final size:5
Alignment explanation
Indices: 84008--84046 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
83998 GTCCGTCCGT
* * *
84008 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
84047 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.03, C:0.41, G:0.33, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:84055 original size:6 final size:6
Alignment explanation
Indices: 84044--84140 Score: 176
Period size: 6 Copynumber: 16.2 Consensus size: 6
84034 TCGGCTCGGC
* *
84044 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
84092 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
84140 T
1 T
84141 AATACGTGTC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.02, C:0.16, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:84443 original size:22 final size:22
Alignment explanation
Indices: 84418--84472 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
84408 TCAGGAGTTA
* *
84418 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
84440 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
84462 CGGGAGTTATA
1 CAGGAGTTATA
84473 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:88126 original size:5 final size:5
Alignment explanation
Indices: 88107--88145 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
88097 GTCCGTCCGT
* * *
88107 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
88146 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.03, C:0.41, G:0.33, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:88154 original size:6 final size:6
Alignment explanation
Indices: 88143--88227 Score: 152
Period size: 6 Copynumber: 14.2 Consensus size: 6
88133 TCGGCTCGGC
* *
88143 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
88191 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
88228 AATACGTGTC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.02, C:0.16, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:88530 original size:22 final size:22
Alignment explanation
Indices: 88505--88559 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
88495 TCAGGAGTTA
* *
88505 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
88527 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
88549 CGGGAGTTATA
1 CAGGAGTTATA
88560 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:92032 original size:167 final size:166
Alignment explanation
Indices: 91722--92058 Score: 624
Period size: 167 Copynumber: 2.0 Consensus size: 166
91712 AGTCACTTTC
91722 ATGCAAACTAAAAAAAAAAAAAAAGTTGTGAATCAGACAGATATATACAGCTTAATTACATAAAT
1 ATGCAAACTAAAAAAAAAAAAAAAGTTGTGAATCAGACAGA-ATATACAGCTTAATTACATAAAT
91787 GCCATTGATAATTAATTCTTTTAATGGTGTAGGAACAAATCAAAGCAAGTTGACACTCATGGCAG
65 GCCATTGATAATTAATTCTTTTAATGGTGTAGGAACAAATCAAAGCAAGTTGACACTCATGGCAG
91852 TCGTGTGGTGTGACAGCATTTGAGTGGTTCATATCAT
130 TCGTGTGGTGTGACAGCATTTGAGTGGTTCATATCAT
91889 ATGCAAACTAAAAAAAAAAAAAAAAGTTGTGAATCAAGACAG-ATATACAGCTTAATTACATAAA
1 ATGCAAACT-AAAAAAAAAAAAAAAGTTGTGAATC-AGACAGAATATACAGCTTAATTACATAAA
91953 TGCCATTGATAATTAATTCTTTTTAATGGTGTAGGAACAAATCAAAGCAAGTTGACACTCATGGC
64 TGCCATTGATAATTAATTC-TTTTAATGGTGTAGGAACAAATCAAAGCAAGTTGACACTCATGGC
92018 AGTCGTGT-GTGTGACAGCATTTGAGTGGTTCATATCAT
128 AGTCGTGTGGTGTGACAGCATTTGAGTGGTTCATATCAT
92056 ATG
1 ATG
92059 GGTTTGGAAT
Statistics
Matches: 167, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
167 83 0.50
168 78 0.47
169 6 0.04
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (166 bp):
ATGCAAACTAAAAAAAAAAAAAAAGTTGTGAATCAGACAGAATATACAGCTTAATTACATAAATG
CCATTGATAATTAATTCTTTTAATGGTGTAGGAACAAATCAAAGCAAGTTGACACTCATGGCAGT
CGTGTGGTGTGACAGCATTTGAGTGGTTCATATCAT
Found at i:93063 original size:2 final size:2
Alignment explanation
Indices: 93056--93109 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
93046 TAGTATCTTG
93056 AT AT AT AT AT AT 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 AT AT AT AT AT AT
93098 AT AT AT AT AT AT
1 AT AT AT AT AT AT
93110 GTTGATTTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93752 original size:12 final size:12
Alignment explanation
Indices: 93718--93754 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
93708 TGTTAAATTA
93718 TTAAAAATA-AT
1 TTAAAAATATAT
*
93729 TAAAAAAT-TAT
1 TTAAAAATATAT
93740 TTAAAAATATAT
1 TTAAAAATATAT
93752 TTA
1 TTA
93755 CTTAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTAAAAATATAT
Done.