Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009106.1 Hibiscus syriacus cultivar Beakdansim tig00112571_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: 61895
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:937 original size:12 final size:12
Alignment explanation
Indices: 922--954 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
912 AACATTTTTT
922 ATCACCTTTAGA
1 ATCACCTTTAGA
*
934 ATCACCTTTAGG
1 ATCACCTTTAGA
946 ATCACCTTT
1 ATCACCTTT
955 TCCACTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (12 bp):
ATCACCTTTAGA
Found at i:14880 original size:153 final size:153
Alignment explanation
Indices: 14594--14952 Score: 522
Period size: 153 Copynumber: 2.3 Consensus size: 153
14584 ATTGGCTTCA
* * * * * *
14594 TGACATTCATGGGTGCTTAAGCTCCTTTCTTCTTCATCTCCGTATTCGTCGCGGTCATCTTCTTG
1 TGACATTCATGGCTGCTTAAGATCCTTTCTTCTTCGTCTTCGTCTTC-T-TC-GTCATCTTCTTG
* * *
14659 TTCTTCTTCACCCTGATCACCTTCTGGATGCAAATTTGTCTGCTGGCAACACATCGGTTGGAGGG
63 TTCTTCTTCACCCTGATCACCTTCTGGATGCAAATTTGTATGCAGGCAACACATCGGTTGGAGAG
14724 TTTCTTCCTTACCCTCAAACTCTTGC
128 TTTCTTCCTTACCCTCAAACTCTTGC
* * * *
14750 TGACATTCATGGCTGCTTAA-ACTCCTTTCTTTTTCTTTTTCTTCTTCTTCGTCATCTTCTTGTT
1 TGACATTCATGGCTGCTTAAGA-TCCTTTCTTCTTCGTCTTCGTCTTCTTCGTCATCTTCTTGTT
* * *
14814 CTTCTTCACCCTGATCACCTTCTGGATGCAAATTTGTATGGAGGCAACACATGGGTTGGATAGTT
65 CTTCTTCACCCTGATCACCTTCTGGATGCAAATTTGTATGCAGGCAACACATCGGTTGGAGAGTT
*
14879 TCTTCCTTACCCTCAACCTCTTGC
130 TCTTCCTTACCCTCAAACTCTTGC
14903 TGACATTCATGGCTGCTTAAGATCCTTTCTTCTTCGTCTTCGTCTTCTTC
1 TGACATTCATGGCTGCTTAAGATCCTTTCTTCTTCGTCTTCGTCTTCTTC
14953 TTCTTGTTCG
Statistics
Matches: 181, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
153 140 0.77
154 2 0.01
155 1 0.01
156 38 0.21
ACGTcount: A:0.15, C:0.28, G:0.16, T:0.41
Consensus pattern (153 bp):
TGACATTCATGGCTGCTTAAGATCCTTTCTTCTTCGTCTTCGTCTTCTTCGTCATCTTCTTGTTC
TTCTTCACCCTGATCACCTTCTGGATGCAAATTTGTATGCAGGCAACACATCGGTTGGAGAGTTT
CTTCCTTACCCTCAAACTCTTGC
Found at i:15754 original size:78 final size:78
Alignment explanation
Indices: 15645--15989 Score: 465
Period size: 78 Copynumber: 4.4 Consensus size: 78
15635 GATGCTGCCG
* * * *
15645 CATCGCCCTCTTCTTCACCAATCTCATTCTCTACAGTAACTTGAGACTGAGAGTCTAGCCTGAGA
1 CATCACCCTCTTCTTCACCAATCTCATTCTCTACAGTATCTTGAGACTGAGACTCTAGCCCGAGA
15710 TGCTGATGATGAT
66 TGCTGATGATGAT
* ** * * *
15723 CATCACCTTCTTCTTCACCAATCTCATTCTCTATGGTATTTTGAGACTGAGAATATAGCCCGAGA
1 CATCACCCTCTTCTTCACCAATCTCATTCTCTACAGTATCTTGAGACTGAGACTCTAGCCCGAGA
15788 TGCTGATGATGAT
66 TGCTGATGATGAT
* * *
15801 CATCACCCTCTTCTTCATCAATCTCATTCTCTACGGTATCATGAGACTGAGACTCTAGCCCGAGA
1 CATCACCCTCTTCTTCACCAATCTCATTCTCTACAGTATCTTGAGACTGAGACTCTAGCCCGAGA
* *
15866 TGCTGATGAAGAC
66 TGCTGATGATGAT
** * * * *
15879 CATTGCCCTCTTCTTCACTAATCTCATTCTCTACATTATCCTGAAACTGAGACTCTAGCCCGAGA
1 CATCACCCTCTTCTTCACCAATCTCATTCTCTACAGTATCTTGAGACTGAGACTCTAGCCCGAGA
15944 TGCTGATGATGAT
66 TGCTGATGATGAT
* * **
15957 CATCGCCCTCTTCTTCACCTATCTTGTTCTCTA
1 CATCACCCTCTTCTTCACCAATCTCATTCTCTA
15990 TGCTAAAATT
Statistics
Matches: 234, Mismatches: 33, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 234 1.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (78 bp):
CATCACCCTCTTCTTCACCAATCTCATTCTCTACAGTATCTTGAGACTGAGACTCTAGCCCGAGA
TGCTGATGATGAT
Found at i:16361 original size:204 final size:202
Alignment explanation
Indices: 16104--16698 Score: 901
Period size: 198 Copynumber: 2.9 Consensus size: 202
16094 ACGGTTTCTG
* * *
16104 CAGTTTCTTGTGAGCCAAGGAAGAGATATTGTTGGCTGTTGGACCCCTGCTTTATGGCCACCTCA
1 CAGTTTCTTGTGAGCCAAGGAAGAGATATTGCTGGCTGTTGGACCCTTGCTTTACGG-CA-CTCA
* * * * * *
16169 TTTTTCGATTGACGCTTCAAGGGTGTACTTGGCTTTGCAATTTTTGATGATTCACAGCATCTCGC
64 TTCTTCGATTTACCCTTCAAGGGTGTCCTTGGCTTTGCAATTTTTGGTGATTCACAGCATCTTGC
* * *
16234 TTCAAGCCTTGTTTTCAGTTGCACGGAATCTGAAAATGGCTTGGCCTGTTCATGAATATCTTTAT
129 TTCAAGCCTTGTTTTCAGTTGTATGGAATCTGAAAATGGCTTGGCCTGTTCATGAATATCTTCAT
16299 TTCGAGTTA
194 TTCGAGTTA
* *
16308 CAGTTTCTTGTGAGACAAGGAAGAGATTTTGCTGGCTGTTGGACCCTTGCTTTACGG----CATT
1 CAGTTTCTTGTGAGCCAAGGAAGAGATATTGCTGGCTGTTGGACCCTTGCTTTACGGCACTCATT
*
16369 CTTCGATTTACCCTTCAAGCGTGTCCTTGGCTTTGCAATTTTTGGTGATTCACAGCATCTTGCTT
66 CTTCGATTTACCCTTCAAGGGTGTCCTTGGCTTTGCAATTTTTGGTGATTCACAGCATCTTGCTT
*
16434 CAAGCCTTGTTTTCAGTTGTATGGAATCTGAAAATGGTTTGGCCTGTTCATGAATATCTTCATTT
131 CAAGCCTTGTTTTCAGTTGTATGGAATCTGAAAATGGCTTGGCCTGTTCATGAATATCTTCATTT
*
16499 TGAGTTA
196 CGAGTTA
* * *
16506 CAGTTTCTTGTGAGCCAAGGAAGAGATGTTGCCGGCTGTTGGACCCTTTCTTTACGGACAACTCA
1 CAGTTTCTTGTGAGCCAAGGAAGAGATATTGCTGGCTGTTGGACCCTTGCTTTACGG-C-ACTCA
* * *
16571 TTCTTCGATTTACCCTTCAAGGGTGTCCTTGGCTTTGCGATTTTTGGTGAATCACAGCATCTTGT
64 TTCTTCGATTTACCCTTCAAGGGTGTCCTTGGCTTTGCAATTTTTGGTGATTCACAGCATCTTGC
* *
16636 TTCAAGGCTTGTTTTCTGTTGTATGGAATCTGAAAATGGCTTGGCCTGTTCATGAATATCTTC
129 TTCAAGCCTTGTTTTCAGTTGTATGGAATCTGAAAATGGCTTGGCCTGTTCATGAATATCTTC
16699 GTTTTTATTC
Statistics
Matches: 357, Mismatches: 28, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
198 182 0.51
204 175 0.49
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (202 bp):
CAGTTTCTTGTGAGCCAAGGAAGAGATATTGCTGGCTGTTGGACCCTTGCTTTACGGCACTCATT
CTTCGATTTACCCTTCAAGGGTGTCCTTGGCTTTGCAATTTTTGGTGATTCACAGCATCTTGCTT
CAAGCCTTGTTTTCAGTTGTATGGAATCTGAAAATGGCTTGGCCTGTTCATGAATATCTTCATTT
CGAGTTA
Found at i:23297 original size:14 final size:15
Alignment explanation
Indices: 23270--23298 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23260 ATATCATATA
23270 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
23285 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
23299 ATCATGTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:25696 original size:31 final size:31
Alignment explanation
Indices: 25658--25763 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
25648 TAAGGCGACC
25658 CTTGGGTAGGCTCCGAGGCCCCGAGATATTT
1 CTTGGGTAGGCTCCGAGGCCCCGAGATATTT
* * * **
25689 CTTGGGTAGGC-CTTGGGGCCTCGAGATCCTT
1 CTTGGGTAGGCTC-CGAGGCCCCGAGATATTT
* **
25720 CTTGGGTAGGCCCCTTGGCCCCGAGCA-ACTTT
1 CTTGGGTAGGCTCCGAGGCCCCGAG-ATA-TTT
25752 CTTGGGTAGGCT
1 CTTGGGTAGGCT
25764 TTCAGGCCTC
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
30 1 0.02
31 43 0.73
32 15 0.25
ACGTcount: A:0.12, C:0.27, G:0.33, T:0.27
Consensus pattern (31 bp):
CTTGGGTAGGCTCCGAGGCCCCGAGATATTT
Found at i:26704 original size:46 final size:46
Alignment explanation
Indices: 26627--26714 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
26617 TAAGAGCTAT
* * * *
26627 GCTTAGGAGCAAACCACTAACAGTTTGGAAGAAGATGAAGAATATA
1 GCTTAGCAGCAAACCACTAACAGTTTAGAAGAAAAAGAAGAATATA
*
26673 GCTTAGCAGCAAACCACTAACGGTTTAGAAGAAAAAGAAGAA
1 GCTTAGCAGCAAACCACTAACAGTTTAGAAGAAAAAGAAGAA
26715 GAGTCAAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (46 bp):
GCTTAGCAGCAAACCACTAACAGTTTAGAAGAAAAAGAAGAATATA
Found at i:30040 original size:13 final size:13
Alignment explanation
Indices: 30022--30058 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
30012 TCCTGCATCA
30022 GGTTTAATTAATT
1 GGTTTAATTAATT
30035 GGTTTAATTAATT
1 GGTTTAATTAATT
*
30048 AGTTTAATTAA
1 GGTTTAATTAA
30059 GGAATAGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (13 bp):
GGTTTAATTAATT
Found at i:33538 original size:36 final size:36
Alignment explanation
Indices: 33496--33571 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
33486 TTATAGCTAA
*
33496 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
33532 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
33568 AAAA
1 AAAA
33572 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:38065 original size:15 final size:15
Alignment explanation
Indices: 38047--38076 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38037 CCACGGTGCT
38047 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
38062 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
38077 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:38541 original size:36 final size:36
Alignment explanation
Indices: 38499--38577 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
38489 TTATAGCTAA
*
38499 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
38535 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
38571 AAAAATC
1 AAAAATC
38578 CCGAAAATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:41170 original size:42 final size:41
Alignment explanation
Indices: 41124--41215 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 41
41114 ATAATAAAAT
41124 AATATATTATCGATAAATTTTTATATAAATAAGTTTTATTTA
1 AATATATTATCGATAAATTTTTATATAAATAA-TTTTATTTA
* *
41166 AATATATTATCTATGAATTTTTATATAAATAATTTTATTTA
1 AATATATTATCGATAAATTTTTATATAAATAATTTTATTTA
41207 AATA-ATTAT
1 AATATATTAT
41216 AATTTCACTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 5 0.10
41 13 0.27
42 30 0.62
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.51
Consensus pattern (41 bp):
AATATATTATCGATAAATTTTTATATAAATAATTTTATTTA
Found at i:41201 original size:14 final size:14
Alignment explanation
Indices: 41142--41213 Score: 67
Period size: 15 Copynumber: 5.1 Consensus size: 14
41132 ATCGATAAAT
41142 TTTTATATAAATAA
1 TTTTATATAAATAA
*
41156 GTTTTATTTAAATATA
1 -TTTTATATAAATA-A
* * *
41172 TTATCTATGAAT--
1 TTTTATATAAATAA
41184 TTTTATATAAATAA
1 TTTTATATAAATAA
*
41198 TTTTATTTAAATAA
1 TTTTATATAAATAA
41212 TT
1 TT
41214 ATAATTTCAC
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
12 9 0.20
14 15 0.33
15 20 0.44
16 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (14 bp):
TTTTATATAAATAA
Found at i:47308 original size:10 final size:10
Alignment explanation
Indices: 47293--47358 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
47283 CGGTTTGACA
47293 GTTTGAACCG
1 GTTTGAACCG
47303 GTTTG-ACCG
1 GTTTGAACCG
*
47312 GTTCGAACCG
1 GTTTGAACCG
47322 GTTTG-ACCG
1 GTTTGAACCG
* *
47331 GTCTGAATCG
1 GTTTGAACCG
47341 GTTGGTGAACCG
1 GTT--TGAACCG
*
47353 GGTTGA
1 GTTTGA
47359 CCCGACTCGA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
9 16 0.36
10 21 0.47
12 8 0.18
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.29
Consensus pattern (10 bp):
GTTTGAACCG
Found at i:47313 original size:9 final size:9
Alignment explanation
Indices: 47283--47332 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
47273 GCTGGAAAAT
47283 CGGTTTGA-
1 CGGTTTGAC
*
47291 CAGTTTGAAC
1 CGGTTTG-AC
47301 CGGTTTGAC
1 CGGTTTGAC
*
47310 CGGTTCGAAC
1 CGGTTTG-AC
47320 CGGTTTGAC
1 CGGTTTGAC
47329 CGGT
1 CGGT
47333 CTGAATCGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.17
9 15 0.43
10 14 0.40
ACGTcount: A:0.16, C:0.22, G:0.32, T:0.30
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:47342 original size:19 final size:18
Alignment explanation
Indices: 47283--47343 Score: 77
Period size: 19 Copynumber: 3.3 Consensus size: 18
47273 GCTGGAAAAT
* *
47283 CGGTTTGACAGTTTGAAC
1 CGGTTTGACCGGTTGAAC
47301 CGGTTTGACCGGTTCGAAC
1 CGGTTTGACCGGTT-GAAC
*
47320 CGGTTTGACCGGTCTGAAT
1 CGGTTTGACCGGT-TGAAC
47339 CGGTT
1 CGGTT
47344 GGTGAACCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.32
19 25 0.66
20 1 0.03
ACGTcount: A:0.16, C:0.21, G:0.31, T:0.31
Consensus pattern (18 bp):
CGGTTTGACCGGTTGAAC
Found at i:47376 original size:17 final size:17
Alignment explanation
Indices: 47354--47411 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
47344 GGTGAACCGG
*
47354 GTTGACCCGACTCGACT
1 GTTGACCCGACCCGACT
47371 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
47388 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
47405 GTTGACC
1 GTTGACC
47412 GTTGACCGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.17, C:0.40, G:0.24, T:0.19
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:54505 original size:9 final size:9
Alignment explanation
Indices: 54475--54551 Score: 82
Period size: 9 Copynumber: 8.1 Consensus size: 9
54465 GCTGGAAAAT
54475 CGGTTTGAC
1 CGGTTTGAC
*
54484 CAGTTTTGAAC
1 C-GGTTTG-AC
54495 CGGTTTGAC
1 CGGTTTGAC
*
54504 CGGTTCGAAC
1 CGGTTTG-AC
54514 CGGTTTGAC
1 CGGTTTGAC
54523 CGGTTTGAC
1 CGGTTTGAC
*
54532 CGGTCTGAAC
1 CGGTTTG-AC
*
54542 CGGGTTGAC
1 CGGTTTGAC
54551 C
1 C
54552 CGACCCGACT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
9 29 0.51
10 25 0.44
11 3 0.05
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.29
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:54530 original size:28 final size:28
Alignment explanation
Indices: 54488--54551 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 28
54478 TTTGACCAGT
54488 TTTGAACCGGTTTGACCGGT-TCGAACCGG
1 TTTG-ACCGGTTTGACCGGTCT-GAACCGG
54517 TTTGACCGGTTTGACCGGTCTGAACCGG
1 TTTGACCGGTTTGACCGGTCTGAACCGG
*
54545 GTTGACC
1 TTTGACC
54552 CGACCCGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (28 bp):
TTTGACCGGTTTGACCGGTCTGAACCGG
Found at i:54543 original size:19 final size:19
Alignment explanation
Indices: 54475--54549 Score: 89
Period size: 19 Copynumber: 3.9 Consensus size: 19
54465 GCTGGAAAAT
*
54475 CGGTTTGACCAGTTTTGAAC
1 CGGTTTGACC-GGTTTGAAC
*
54495 CGGTTTGACCGGTTCGAAC
1 CGGTTTGACCGGTTTGAAC
54514 CGGTTTGACCGGTTTG-AC
1 CGGTTTGACCGGTTTGAAC
* *
54532 CGGTCTGAACCGGGTTGA
1 CGGTTTG-ACCGGTTTGA
54550 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 8 0.17
19 30 0.62
20 10 0.21
ACGTcount: A:0.16, C:0.23, G:0.32, T:0.29
Consensus pattern (19 bp):
CGGTTTGACCGGTTTGAAC
Found at i:54567 original size:17 final size:17
Alignment explanation
Indices: 54545--54602 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
54535 TCTGAACCGG
54545 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
54562 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
54579 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
54596 GTTGACC
1 GTTGACC
54603 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:54604 original size:7 final size:7
Alignment explanation
Indices: 54592--54629 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
54582 GACCCGACCC
54592 GACCGTT
1 GACCGTT
54599 GACCGTT
1 GACCGTT
54606 GACCGTT
1 GACCGTT
54613 GACCG-T
1 GACCGTT
54619 GACCGTT
1 GACCGTT
54626 GACC
1 GACC
54630 TTCTTTGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:54611 original size:14 final size:13
Alignment explanation
Indices: 54592--54629 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
54582 GACCCGACCC
54592 GACCGTTGACCGTT
1 GACCGTTGACCG-T
54606 GACCGTTGACCGT
1 GACCGTTGACCGT
54619 GACCGTTGACC
1 GACCGTTGACC
54630 TTCTTTGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.24
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:61726 original size:10 final size:10
Alignment explanation
Indices: 61708--61796 Score: 103
Period size: 10 Copynumber: 9.1 Consensus size: 10
61698 GCTGCTGGAA
61708 AACCGGTTTG
1 AACCGGTTTG
*
61718 AACCAGTTTTG
1 AACC-GGTTTG
61729 AACCGGTTTG
1 AACCGGTTTG
*
61739 -ACCGGTTCG
1 AACCGGTTTG
61748 AACCGGTTTG
1 AACCGGTTTG
*
61758 -ACCGGTCTG
1 AACCGGTTTG
61767 AACCGGTTTG
1 AACCGGTTTG
*
61777 -ACCGGTCTG
1 AACCGGTTTG
*
61786 AACCGGGTTG
1 AACCGGTTTG
61796 A
1 A
61797 CCTGACCCGA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
9 24 0.36
10 33 0.50
11 9 0.14
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:61752 original size:19 final size:19
Alignment explanation
Indices: 61708--61798 Score: 121
Period size: 19 Copynumber: 4.7 Consensus size: 19
61698 GCTGCTGGAA
* *
61708 AACCGGTTTGAACCAGTTTTG
1 AACCGGTTTG-ACC-GGTCTG
61729 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
61748 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
61767 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
61786 AACCGGGTTGACC
1 AACCGGTTTGACC
61799 TGACCCGACT
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
18 1 0.02
19 51 0.77
20 4 0.06
21 10 0.15
ACGTcount: A:0.19, C:0.25, G:0.30, T:0.26
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:61814 original size:17 final size:17
Alignment explanation
Indices: 61792--61832 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
61782 TCTGAACCGG
* *
61792 GTTGACCTGACCCGACT
1 GTTGACCCGACCCGACC
61809 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
61826 GTTGACC
1 GTTGACC
61833 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.39, G:0.24, T:0.20
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:61834 original size:7 final size:7
Alignment explanation
Indices: 61822--61866 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
61812 GACCCGACCC
61822 GACCGTT
1 GACCGTT
61829 GACCGTT
1 GACCGTT
61836 GACCGTT
1 GACCGTT
61843 GACCGTT
1 GACCGTT
61850 GACCG-T
1 GACCGTT
61856 GACCGTT
1 GACCGTT
61863 GACC
1 GACC
61867 TTCTTTGACT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.16
7 31 0.84
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:61848 original size:21 final size:20
Alignment explanation
Indices: 61822--61866 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
61812 GACCCGACCC
61822 GACCGTTGACCGTTGACCGTT
1 GACCGTTGACCG-TGACCGTT
61843 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
61863 GACC
1 GACC
61867 TTCTTTGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Done.