Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003230.1 Hibiscus syriacus cultivar Beakdansim tig00006800_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: 217729
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:202313 original size:29 final size:29
Alignment explanation
Indices: 202251--202346 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 29
202241 CTATATAATA
*
202251 TATATATGTTTTCAAAATGTTTTTAAAAAC
1 TATATATATTTTCAAAATG-TTTTAAAAAC
202281 TATATATATTTTCAAAATGTTTTAAAAAC
1 TATATATATTTTCAAAATGTTTTAAAAAC
* * *
202310 TATATA-A-TAT-ATAAATGTTTTCAAAAT
1 TATATATATTTTCA-AAATGTTTTAAAAAC
202337 TATATATATT
1 TATATATATT
202347 ATATATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.02
27 21 0.36
28 2 0.03
29 17 0.29
30 18 0.31
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (29 bp):
TATATATATTTTCAAAATGTTTTAAAAAC
Found at i:202325 original size:27 final size:27
Alignment explanation
Indices: 202265--202351 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 27
202255 TATGTTTTCA
*
202265 AAATGTTTTTAAAAACTATAT-ATATTTT
1 AAATG-TTTTAAAAACTATATAATA-TAT
202293 CAAAATGTTTTAAAAACTATATAATATAT
1 --AAATGTTTTAAAAACTATATAATATAT
* *
202322 AAATGTTTTCAAAATTATATATATTATAT
1 AAATGTTTTAAAAACTATATA-A-TATAT
202351 A
1 A
202352 TATATATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 19 0.37
28 1 0.02
29 23 0.45
30 8 0.16
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (27 bp):
AAATGTTTTAAAAACTATATAATATAT
Found at i:202369 original size:42 final size:44
Alignment explanation
Indices: 202310--202404 Score: 126
Period size: 42 Copynumber: 2.2 Consensus size: 44
202300 TTTTAAAAAC
* * *
202310 TATATA-ATA-TATAAATGTTTTCAAAAT-TATATATA-TTATA
1 TATATATATATTAAAAATGTTTTCAAAATATATATATACATACA
*
202350 TATATATATATTAAAAATGTTTTCAAACTATATATATACATACA
1 TATATATATATTAAAAATGTTTTCAAAATATATATATACATACA
202394 TATATATATAT
1 TATATATATAT
202405 GTGTGTGTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 6 0.13
41 3 0.06
42 16 0.34
43 8 0.17
44 14 0.30
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (44 bp):
TATATATATATTAAAAATGTTTTCAAAATATATATATACATACA
Found at i:202378 original size:68 final size:67
Alignment explanation
Indices: 202226--202387 Score: 186
Period size: 68 Copynumber: 2.4 Consensus size: 67
202216 ATATGCTTTC
* * * *
202226 AAAATGATTTCAAAACTATATAATATATATATGTTTTCAAAATGTTTTTAAAAACTATATATATT
1 AAAATGTTTTC-AAACTATATAATATATAAATGTTTTCAAAATGTTTATAAAAACTATATATATA
*
202291 TTC
65 TTA
* * *
202294 AAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAAT-TATATATATTATA-TATATAT
1 AAAATGTTTT-CAAACTATATAATATATAAATGTTTTCAAAATGT-T-TATA-AAAACTATATAT
202357 ATATTA
62 ATATTA
202363 AAAATGTTTTCAAACTATAT-ATATA
1 AAAATGTTTTCAAACTATATAATATA
202388 CATACATATA
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
67 6 0.07
68 49 0.60
69 24 0.30
70 2 0.02
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (67 bp):
AAAATGTTTTCAAACTATATAATATATAAATGTTTTCAAAATGTTTATAAAAACTATATATATAT
TA
Found at i:204302 original size:41 final size:39
Alignment explanation
Indices: 204194--204369 Score: 129
Period size: 41 Copynumber: 4.4 Consensus size: 39
204184 AATGACCAAC
* * ****
204194 AAAATCGCAACGCGAAATAAAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATATCAAAATCGCAACGCGATTTTG
* ** *
204233 AGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGA-TAT-CAAAATCGCAACGCGATT-TTG
* * ** *
204274 AAAATCGCAATGCGATAGTCAAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATA-TCAAAATCGCAACGCGATTTT-G
* * *
204315 AAAATCGCAACGCGAATATGAAAATCGCAACGCGAATATG
1 AAAATCGCAACGCG-ATATCAAAATCGCAACGCGATTTTG
204355 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
204370 ACACATAAAT
Statistics
Matches: 104, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
38 1 0.01
39 12 0.12
40 32 0.31
41 54 0.52
42 5 0.05
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (39 bp):
AAAATCGCAACGCGATATCAAAATCGCAACGCGATTTTG
Found at i:204403 original size:60 final size:60
Alignment explanation
Indices: 204336--204530 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
204326 GCGAATATGA
** * *
204336 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * * ***
204396 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * * ** *
204456 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
204517 AAATCGCAACGCGA
1 AAATCGCAACGCGA
204531 TATTTAAAGC
Statistics
Matches: 112, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:204431 original size:20 final size:20
Alignment explanation
Indices: 204316--204529 Score: 207
Period size: 20 Copynumber: 10.7 Consensus size: 20
204306 CGATTTTCCA
* ** *
204316 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* ** *
204336 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
204356 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
204376 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
204396 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
204416 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
204436 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
204456 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTATCCGT
* * *
204476 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
204496 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
204517 AAATCGCAACGCG
1 AAATCGCAACGCG
204530 ATATTTAAAG
Statistics
Matches: 162, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
19 2 0.01
20 142 0.88
21 17 0.10
22 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:204952 original size:33 final size:32
Alignment explanation
Indices: 204908--204977 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
204898 TTCACTTAGA
*
204908 TTTCATTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTCGCGTTACGATTCTCTCATTGCGAT
* *
204940 TTTCATTTCGCGTTGCTATTCTCTCATTGCGAT
1 TTTCA-TTCGCGTTACGATTCTCTCATTGCGAT
204973 TTTCA
1 TTTCA
204978 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 5 0.15
33 29 0.85
ACGTcount: A:0.13, C:0.24, G:0.16, T:0.47
Consensus pattern (32 bp):
TTTCATTCGCGTTACGATTCTCTCATTGCGAT
Found at i:205113 original size:19 final size:20
Alignment explanation
Indices: 205056--205130 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
205046 TGCAGAAGAG
* *
205056 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGACAA
**
205077 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
*
205097 TCGCAACGCGA-AATGACAA
1 TCGCAACGAGAGAATGACAA
205116 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
205131 CGCAACGCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 16 0.36
20 18 0.40
21 11 0.24
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:205118 original size:39 final size:35
Alignment explanation
Indices: 205068--205186 Score: 138
Period size: 33 Copynumber: 3.4 Consensus size: 35
205058 GCAACGAGAT
205068 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAAT-A---TCGCAACGCG
*
205107 AAATGACAATCGCAACGAGAG-A-ATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATATCGCAACGCG
*
205140 AAATAAAAATCGCAACGAGAG-A-ATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATATCGCAACGCG
**
205173 AAACCAAAATCGCA
1 AAATGAAAATCGCA
205187 TTGCGATTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
33 53 0.71
36 1 0.01
38 1 0.01
39 20 0.27
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.10
Consensus pattern (35 bp):
AAATGAAAATCGCAACGAGAGAATATCGCAACGCG
Found at i:205133 original size:14 final size:14
Alignment explanation
Indices: 205114--205170 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
205104 GCGAAATGAC
205114 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
205128 AATCGCAACGCGAAATAAA
1 AATCGCAA--CG--A-GAG
205147 AATCGCAACGAGAG
1 AATCGCAACGAGAG
205161 AATCGCAACG
1 AATCGCAACG
205171 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:205139 original size:33 final size:33
Alignment explanation
Indices: 205097--205186 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
205087 AGAATGACTG
* *
205097 TCGCAACGCGAAATGACAATCGCAACGAGAGAA
1 TCGCAACGCGAAATAAAAATCGCAACGAGAGAA
205130 TCGCAACGCGAAATAAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAATAAAAATCGCAACGAGAGAA
**
205163 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAATAAAAATCGCA
205187 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.44, C:0.26, G:0.21, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAATAAAAATCGCAACGAGAGAA
Found at i:205223 original size:14 final size:14
Alignment explanation
Indices: 205204--205260 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
205194 TTTTATTTCG
205204 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
205218 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
205237 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
205251 CGTTGCGATT
1 CGTTGCGATT
205261 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:205242 original size:19 final size:19
Alignment explanation
Indices: 205182--205307 Score: 92
Period size: 19 Copynumber: 7.1 Consensus size: 19
205172 GAAACCAAAA
* *
205182 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
205201 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
205215 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
205234 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
205248 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
***
205267 TCGCGTTGCGACAGTCATT
1 TCGCGTTGCGATTTTCATT
*
205286 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
205306 TC
1 TC
205308 AACCAAAAGA
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
14 20 0.24
16 5 0.06
17 5 0.06
19 38 0.46
20 15 0.18
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:205298 original size:39 final size:33
Alignment explanation
Indices: 205187--205307 Score: 170
Period size: 33 Copynumber: 3.5 Consensus size: 33
205177 CAAAATCGCA
*
205187 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
205220 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
205253 TTGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCG
205292 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
205308 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
33 52 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 24 0.30
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:207205 original size:93 final size:93
Alignment explanation
Indices: 206992--207458 Score: 870
Period size: 93 Copynumber: 5.1 Consensus size: 93
206982 TAGATTGCTT
* *
206992 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
207057 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
207084 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
207149 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
207177 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
207242 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
207270 AGTAAA-TTGTTCGGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
207334 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
207363 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTTTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
207428 TTTGTCTTTGTTTTGTCTTTTGG-TG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
207454 AGTAA
1 AGTAA
207459 TGCAATCCAT
Statistics
Matches: 369, Mismatches: 3, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
91 6 0.02
92 73 0.20
93 282 0.76
94 8 0.02
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:207546 original size:19 final size:18
Alignment explanation
Indices: 207506--207633 Score: 83
Period size: 19 Copynumber: 7.3 Consensus size: 18
207496 TAGTTTACTT
*
207506 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC--AAAA
207526 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
* *
207545 TCACAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
207564 TCGCAA--CG--ACAGAA
1 TCGCAACGCGAAACAAAA
* **
207578 TCGCAATGCGAAATGAAA
1 TCGCAACGCGAAACAAAA
*
207596 TCGCAA--CG-AA-AGAA
1 TCGCAACGCGAAACAAAA
207610 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
207629 TCGCA
1 TCGCA
207634 CTGCGATTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
14 17 0.20
15 3 0.04
16 6 0.07
17 4 0.05
18 9 0.11
19 33 0.39
20 12 0.14
21 1 0.01
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.10
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:207581 original size:14 final size:14
Alignment explanation
Indices: 207562--207617 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
207552 GCGAAATGAA
*
207562 AATCGCAACGACAG
1 AATCGCAACGAAAG
207576 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
207593 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
207608 AATCGCAACG
1 AATCGCAACG
207618 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 1 0.03
16 9 0.24
17 1 0.03
18 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:207602 original size:32 final size:33
Alignment explanation
Indices: 207543--207633 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 33
207533 GCGAAACCAA
* *
207543 AATCACAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
207576 AATCGCAATGCGAAATG-AAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
207608 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
207634 CTGCGATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 28 0.55
33 23 0.45
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:207651 original size:19 final size:19
Alignment explanation
Indices: 207635--207763 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
207625 AAAATCGCAC
207635 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
207654 TGCGA--TTC-TTT--CGT
1 TGCGATTTTCATTTCGCGT
*
207668 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
*
207687 TGCGA--TTC-TGT--CGT
1 TGCGATTTTCATTTCGCGT
207701 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
207720 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
207739 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
207759 TGCGA
1 TGCGA
207764 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.17
16 11 0.12
17 11 0.12
19 41 0.46
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:207670 original size:14 final size:14
Alignment explanation
Indices: 207651--207707 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
207641 TTTCATTTCG
207651 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
207665 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
207682 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
207698 CGTTGCGATT
1 CGTTGCGATT
207708 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:207677 original size:33 final size:33
Alignment explanation
Indices: 207635--207726 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
207625 AAAATCGCAC
*
207635 TGCGATTTTCATTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
207668 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
207701 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
207727 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:209697 original size:14 final size:14
Alignment explanation
Indices: 209678--209713 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
209668 ATTGTTTAAT
209678 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
209692 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
209706 TGATTTGT
1 TGATTTGT
209714 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:209906 original size:20 final size:19
Alignment explanation
Indices: 209820--209920 Score: 133
Period size: 19 Copynumber: 5.6 Consensus size: 19
209810 AAAAATGACT
209820 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
209838 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
209857 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
209871 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
209890 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
*
209910 ATCGCATTGCG
1 ATCGCAATGCG
209921 TTTATAATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 17 0.23
19 23 0.32
20 18 0.25
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:209954 original size:14 final size:14
Alignment explanation
Indices: 209935--209989 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
209925 TAATTTCGCA
*
209935 TTGCGATTCTCTCG
1 TTGCGATTCTTTCG
209949 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
209966 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
209982 TTGCGATT
1 TTGCGATT
209990 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 14 0.40
16 8 0.23
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:209964 original size:33 final size:33
Alignment explanation
Indices: 209927--210116 Score: 192
Period size: 33 Copynumber: 5.5 Consensus size: 33
209917 TGCGTTTATA
*
209927 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
209960 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
209993 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTC
210031 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTC
* *
210067 -TGTCG--TTGCGATTTTCATTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCTTTCG--TTGCGATTTTC
210101 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
210117 TTCATTTCGC
Statistics
Matches: 143, Mismatches: 4, Indels: 18
0.87 0.02 0.11
Matches are distributed among these distances:
32 12 0.08
33 57 0.40
34 3 0.02
35 13 0.09
36 8 0.06
37 6 0.04
38 44 0.31
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
Found at i:209973 original size:19 final size:19
Alignment explanation
Indices: 209911--210202 Score: 323
Period size: 19 Copynumber: 16.7 Consensus size: 19
209901 GAAATGAAAA
*
209911 TCGCATTGCG-TTTATAATT
1 TCGCATTGCGATTT-TCATT
*
209930 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
209946 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
209963 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
209979 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
209996 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
210015 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
210034 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
210053 TCGCATTGCGA--TTC-TG
1 TCGCATTGCGATTTTCATT
210069 TCG--TTGCGATTTTCA-T
1 TCGCATTGCGATTTTCATT
210085 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
210104 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
210123 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
210139 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
210156 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
210174 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
210190 TCGCGTTGCGATT
1 TCGCATTGCGATT
210203 GTAATTTCCG
Statistics
Matches: 236, Mismatches: 9, Indels: 56
0.78 0.03 0.19
Matches are distributed among these distances:
14 35 0.15
16 34 0.14
17 22 0.09
18 16 0.07
19 117 0.50
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:210117 original size:70 final size:71
Alignment explanation
Indices: 209949--210202 Score: 341
Period size: 70 Copynumber: 3.6 Consensus size: 71
209939 GATTCTCTCG
*
209949 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT
210009 TTCATTTCGCA
61 TTCATTTCGCA
*
210020 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTTCA-
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
210084 TTCGCA
66 TTCGCA
210090 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
210155 TTCCGCA
66 TT-CGCA
* *
210162 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
210203 GTAATTTCCG
Statistics
Matches: 172, Mismatches: 4, Indels: 18
0.89 0.02 0.09
Matches are distributed among these distances:
67 25 0.15
69 1 0.01
70 70 0.41
71 39 0.23
72 16 0.09
73 7 0.04
74 8 0.05
76 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCA
Found at i:212482 original size:12 final size:12
Alignment explanation
Indices: 212465--212489 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
212455 TCTTCGGGGA
212465 CTTTTTCTTCTT
1 CTTTTTCTTCTT
212477 CTTTTTCTTCTT
1 CTTTTTCTTCTT
212489 C
1 C
212490 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:212697 original size:24 final size:24
Alignment explanation
Indices: 212663--212709 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
212653 CTGAAACATC
212663 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
212687 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
212710 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:213570 original size:20 final size:20
Alignment explanation
Indices: 213386--213595 Score: 183
Period size: 20 Copynumber: 10.5 Consensus size: 20
213376 AAATTTCAGT
* * * *
213386 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
213406 GTTGTGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
213426 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
213446 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
*
213466 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
213486 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATACGC
*
213506 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
213526 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
213546 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
213566 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
213586 GTTGCGATTT
1 GTTGCGATTT
213596 TGGAAAATCG
Statistics
Matches: 160, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.02
20 154 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:213589 original size:60 final size:57
Alignment explanation
Indices: 213467--213716 Score: 153
Period size: 60 Copynumber: 4.2 Consensus size: 57
213457 CGGATTATCA
* ** * * * * *
213467 TTGCGATTTACGGATACGCGTTGCGATATACGGAAACGCGTTGCGATTTACGGATACACG
1 TTGCGATTT-CGGATACGCATTGCGAT-TTTGG-ATCGCGTTGCGATTTTCAGATTCGCG
* *
213527 TTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATATTCGCG
1 TTGCGATTT-CGGATACGCATTGCGATTT-TG-GATCGCGTTGCGATTTTCAGATTCGCG
* * * * * * *
213587 TTGCGATTTTGGAAAATCGCAATGCGAATTTGACTATCGCATTGCGATTTTCAAGAATCGCG
1 TTGCGATTTCGG-ATA-CGCATTGCGATTTTG--GATCGCGTTGCGATTTTC-AGATTCGCG
* * * * *
213649 TTGCGATTTTGGACACTG-ATTTGCGATTCTGGGGATCGCGTTGCGATTTTTA-TTTCGCG
1 TTGCGATTTCGGATAC-GCA-TTGCGATT-T-TGGATCGCGTTGCGATTTTCAGATTCGCG
213708 TTGCGATTT
1 TTGCGATTT
213717 TGTTGGTCAT
Statistics
Matches: 151, Mismatches: 29, Indels: 21
0.75 0.14 0.10
Matches are distributed among these distances:
59 17 0.11
60 62 0.41
61 51 0.34
62 20 0.13
63 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (57 bp):
TTGCGATTTCGGATACGCATTGCGATTTTGGATCGCGTTGCGATTTTCAGATTCGCG
Found at i:213612 original size:21 final size:20
Alignment explanation
Indices: 213562--213659 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
213552 ATTTATGTGT
* * * *
213562 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
213582 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
213603 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
213623 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
213644 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
213660 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:213654 original size:41 final size:41
Alignment explanation
Indices: 213562--213718 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
213552 ATTTATGTGT
* * *
213562 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
213603 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
213644 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
213684 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
213719 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:216194 original size:47 final size:45
Alignment explanation
Indices: 216136--216232 Score: 115
Period size: 47 Copynumber: 2.1 Consensus size: 45
216126 ATAAAAAATG
* * * *
216136 ATTTTTTAGGATTT-TTAAAAGATTTTATCAAATGAAAAGATAAATTA
1 ATTTTTGAGGATTTCTCAAAACATCTTA-CAAA-GAAAAGA-AAATTA
*
216183 ATTTTTGAGGATTTCTCAAAACATCTTACAGAGAAAAGAAAATTA
1 ATTTTTGAGGATTTCTCAAAACATCTTACAAAGAAAAGAAAATTA
216228 ATTTT
1 ATTTT
216233 CAAACAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
45 11 0.25
46 7 0.16
47 16 0.36
48 10 0.23
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.39
Consensus pattern (45 bp):
ATTTTTGAGGATTTCTCAAAACATCTTACAAAGAAAAGAAAATTA
Done.