Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006441.1 Hibiscus syriacus cultivar Beakdansim tig00015559_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: 57094
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:2415 original size:18 final size:19
Alignment explanation
Indices: 2384--2422 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
2374 TTATATTATA
2384 ATGATTGTTGTTAAATATT
1 ATGATTGTTGTTAAATATT
2403 ATGATTG-TGTTAAATATT
1 ATGATTGTTGTTAAATATT
2421 AT
1 AT
2423 TTATAGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (19 bp):
ATGATTGTTGTTAAATATT
Found at i:3764 original size:161 final size:161
Alignment explanation
Indices: 3496--3818 Score: 596
Period size: 161 Copynumber: 2.0 Consensus size: 161
3486 GAAAACAATG
3496 AGGGCAAAGACAACTTTGGGTGTAATCATCGACAACGACGATCACTGGTGATTGGTGACGGAAAC
1 AGGGCAAAGACAACTTTGGGTGTAATCATCGACAACGACGATCACTGGTGATTGGTGACGGAAAC
3561 TAAAGATGACTAGCGAGTGTGATAAGTGACGGTCGATGATAGGAATTTTAACTGAATTCATGGAT
66 TAAAGATGACTAGCGAGTGTGATAAGTGACGGTCGATGATAGGAATTTTAACTGAATTCA-GGAT
*
3626 TAAATTGATATTTTATCTAAAATTTAAGGGTTA
130 T-AATTGATATTTTATCTAAAATTTAAGAGTTA
3659 AGGGCAAAGACAACTTT-GGTGTAATCATCGACAACGACGATCACTGGTGATTGGTGACGG-AAC
1 AGGGCAAAGACAACTTTGGGTGTAATCATCGACAACGACGATCACTGGTGATTGGTGACGGAAAC
*
3722 TAAAGATGACTAGTGAGTGTGATAAGTGACGGTCGATGATAGGAATTTTAACTGAATTCAGGATT
66 TAAAGATGACTAGCGAGTGTGATAAGTGACGGTCGATGATAGGAATTTTAACTGAATTCAGGATT
3787 AATTGATATTTTATCTAAAATTTAAGAGTTA
131 AATTGATATTTTATCTAAAATTTAAGAGTTA
3818 A
1 A
3819 ATTAATATTT
Statistics
Matches: 158, Mismatches: 2, Indels: 4
0.96 0.01 0.02
Matches are distributed among these distances:
159 31 0.20
160 5 0.03
161 62 0.39
162 43 0.27
163 17 0.11
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (161 bp):
AGGGCAAAGACAACTTTGGGTGTAATCATCGACAACGACGATCACTGGTGATTGGTGACGGAAAC
TAAAGATGACTAGCGAGTGTGATAAGTGACGGTCGATGATAGGAATTTTAACTGAATTCAGGATT
AATTGATATTTTATCTAAAATTTAAGAGTTA
Found at i:6463 original size:15 final size:15
Alignment explanation
Indices: 6443--6480 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6433 TAATTTTCAG
6443 TTAAATTTAAC-AATT
1 TTAAATTT-ACGAATT
6458 TTAAATTTACGAATT
1 TTAAATTTACGAATT
6473 TTCAAATT
1 TT-AAATT
6481 GAATTTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 14 0.67
16 5 0.24
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAAATTTACGAATT
Found at i:12464 original size:18 final size:18
Alignment explanation
Indices: 12441--12487 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
12431 ATGGAAACGT
12441 TAAATACAAACGGAAAAA
1 TAAATACAAACGGAAAAA
12459 TAAATACAAACGGAAAAA
1 TAAATACAAACGGAAAAA
*
12477 TAAATGCAAAC
1 TAAATACAAAC
12488 AATTGAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.64, C:0.13, G:0.11, T:0.13
Consensus pattern (18 bp):
TAAATACAAACGGAAAAA
Found at i:16295 original size:18 final size:18
Alignment explanation
Indices: 16274--16308 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16264 AAATAATTAT
16274 TATTTTATTT-TTCAAACA
1 TATTTT-TTTGTTCAAACA
16292 TATTTTTTTGTTCAAAC
1 TATTTTTTTGTTCAAAC
16309 GACCATACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (18 bp):
TATTTTTTTGTTCAAACA
Found at i:21755 original size:14 final size:14
Alignment explanation
Indices: 21736--21844 Score: 64
Period size: 14 Copynumber: 7.9 Consensus size: 14
21726 TATTATACCA
21736 TAAACCCTAAA-TC
1 TAAACCCTAAACTC
21749 TTAAACCCTAAACTC
1 -TAAACCCTAAACTC
* * *
21764 TAAACCATAAAATA
1 TAAACCCTAAACTC
* *
21778 TAAACACTGAACAT-
1 TAAACCCTAAAC-TC
* *
21792 TAAACCTTAAACCC
1 TAAACCCTAAACTC
*
21806 TAAA-CTTAAAC-C
1 TAAACCCTAAACTC
**
21818 TTAAATACTAAACTC
1 -TAAACCCTAAACTC
*
21833 TAAGCCCTAAAC
1 TAAACCCTAAAC
21845 CCTGAGCCCT
Statistics
Matches: 73, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
12 1 0.01
13 11 0.15
14 57 0.78
15 4 0.05
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACTC
Found at i:21760 original size:7 final size:7
Alignment explanation
Indices: 21736--21847 Score: 55
Period size: 7 Copynumber: 16.1 Consensus size: 7
21726 TATTATACCA
21736 TAAACCC
1 TAAACCC
* *
21743 TAAATCT
1 TAAACCC
21750 TAAACCC
1 TAAACCC
*
21757 TAAACTC
1 TAAACCC
*
21764 TAAACCA
1 TAAACCC
***
21771 TAAAATA
1 TAAACCC
*
21778 TAAACAC
1 TAAACCC
* **
21785 TGAACAT
1 TAAACCC
*
21792 TAAACCT
1 TAAACCC
21799 TAAACCC
1 TAAACCC
*
21806 TAAA-CT
1 TAAACCC
*
21812 TAAACCT
1 TAAACCC
**
21819 TAAATAC
1 TAAACCC
*
21826 TAAACTC
1 TAAACCC
*
21833 TAAGCCC
1 TAAACCC
21840 TAAACCC
1 TAAACCC
21847 T
1 T
21848 GAGCCCTTAA
Statistics
Matches: 78, Mismatches: 26, Indels: 2
0.74 0.25 0.02
Matches are distributed among these distances:
6 5 0.06
7 73 0.94
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.24
Consensus pattern (7 bp):
TAAACCC
Found at i:21766 original size:21 final size:20
Alignment explanation
Indices: 21736--21847 Score: 80
Period size: 21 Copynumber: 5.4 Consensus size: 20
21726 TATTATACCA
21736 TAAACCCTAAATCTTAAACCC
1 TAAACCCTAAA-CTTAAACCC
* * ***
21757 TAAACTCTAAACCATAAAATA
1 TAAACCCTAAA-CTTAAACCC
* * *
21778 TAAACACTGAACATTAAACCT
1 TAAACCCTAAAC-TTAAACCC
*
21799 TAAACCCTAAACTTAAACCT
1 TAAACCCTAAACTTAAACCC
** *
21819 TAAATACTAAACTCTAAGCCC
1 TAAACCCTAAACT-TAAACCC
21840 TAAACCCT
1 TAAACCCT
21848 GAGCCCTTAA
Statistics
Matches: 69, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 20 0.29
21 49 0.71
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.24
Consensus pattern (20 bp):
TAAACCCTAAACTTAAACCC
Found at i:25701 original size:23 final size:23
Alignment explanation
Indices: 25671--25718 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
25661 TTTTCTTTAC
25671 AATACAAATATATCTTATTCCAA
1 AATACAAATATATCTTATTCCAA
25694 AATACAAATATATCTTATTCCAA
1 AATACAAATATATCTTATTCCAA
25717 AA
1 AA
25719 ATTAATCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (23 bp):
AATACAAATATATCTTATTCCAA
Found at i:26128 original size:43 final size:42
Alignment explanation
Indices: 26063--26316 Score: 127
Period size: 43 Copynumber: 5.8 Consensus size: 42
26053 TATTTTTCTT
* *
26063 TATAATTGATACTTCTACTTTTTGTAATCTCACTTTTTACCTC
1 TATAATTGATACTTCTAATTTTT-TAATCCCACTTTTTACCTC
* * * * ** *
26106 TATAGTTGATGCTTTTAATTTTTTTATCCCACTTTTTATATTTATA
1 TATAATTGATACTTCTAATTTTTTAATCCCAC-TTTT-TA--CCTC
* * * *
26152 TATAATTGAGA-TCCCTAATTTTTTCAATCTCACTATTTACCTC
1 TATAATTGATACT-TCTAATTTTTT-AATCCCACTTTTTACCTC
* * * * * * *
26195 TATAACTGAGGAC-CCTAATTTTTTCAATCTCACTTTATAGCTT
1 TATAATTGA-TACTTCTAATTTTTT-AATCCCACTTTTTACCTC
* * * * *
26238 TATAATTGA-AGCTCCTAATTTTTTCAATCTCACTTTAATAGCTT
1 TATAATTGATA-CTTCTAATTTTTT-AATCCCACTTT-TTACCTC
* * *
26282 TATAATTGAAACTTCTGATTTTTTAATCTCACTTT
1 TATAATTGATACTTCTAATTTTTTAATCCCACTTT
26317 ATATTTTTAT
Statistics
Matches: 171, Mismatches: 28, Indels: 24
0.77 0.13 0.11
Matches are distributed among these distances:
41 1 0.01
42 8 0.05
43 100 0.58
44 31 0.18
45 4 0.02
46 21 0.12
47 6 0.04
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (42 bp):
TATAATTGATACTTCTAATTTTTTAATCCCACTTTTTACCTC
Found at i:26271 original size:86 final size:83
Alignment explanation
Indices: 26152--26639 Score: 375
Period size: 86 Copynumber: 5.7 Consensus size: 83
26142 TATATTTATA
* * * *
26152 TATAATTG-AGATCCCTAATTTTTTCAATCTCACTATTTACCTCTATAACTGAGGACCCTAATTT
1 TATAATTGAAGCT-CCTAATTTTTTCAATCTCACT-TTTACATTTATAATTGAGGACCCTAATTT
26216 TTTCAATCTCACTTTATAGCTT
64 TTT-AATCTCACTTTATA-CTT
* * *
26238 TATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTAATAGC-TTTATAATTGA-AACTTCTGAT
1 TATAATTGAAGCTCCTAATTTTTTCAATCTCACTTT--TA-CATTTATAATTGAGGAC-CCTAAT
*
26301 TTTTTAATCTCACTTTATATTTT
62 TTTTTAATCTCACTTTATA-CTT
* * *
26324 TATAATTGAAGCCCCTATTTTTTTTTTCAATCTTACCTTTTACATTTATAATTGAGG-CCCTAAT
1 TATAATTGAAGCTCCTA---ATTTTTTCAATCTCA-CTTTTACATTTATAATTGAGGACCCTAAT
*
26388 TTTTGTAATCTCACTTTTTAACTT
62 TTTT-TAATCTCACTTTAT-ACTT
* * * * * *
26412 TACAATTG-AGACAT-TTAATTTTTTCAATCCCACCTTTTACATTTATAATTAAAGCCCCTGAAT
1 TATAATTGAAG-C-TCCTAATTTTTTCAATCTCA-CTTTTACATTTATAATTGAGGACCCT-AAT
*
26475 TTTTTAATCTAACTTCT-TACATT
62 TTTTTAATCTCACTT-TATAC-TT
* * **
26498 TATAATTGAAGC-CCTTGATTTTTTTCAATCTCACTTTTTACTTTTATAATTGAGGTGCCTAATT
1 TATAATTGAAGCTCC-T-AATTTTTTCAATCTCAC-TTTTACATTTATAATTGAGGACCCTAATT
*
26562 TTTTAATCTCACTTTTTACCTT
63 TTTTAATCTCACTTTATA-CTT
* * * * * * *
26584 TATGAA-TGAGACCT-TTAATTTTTCCAATTTAACTTTTTACTTTTATAATTTAGGAC
1 TAT-AATTGA-AGCTCCTAATTTTTTCAATCTCAC-TTTTACATTTATAATTGAGGAC
26640 TATAATTTAA
Statistics
Matches: 329, Mismatches: 44, Indels: 59
0.76 0.10 0.14
Matches are distributed among these distances:
85 70 0.21
86 118 0.36
87 83 0.25
88 40 0.12
89 14 0.04
90 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.48
Consensus pattern (83 bp):
TATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTTACATTTATAATTGAGGACCCTAATTTTT
TAATCTCACTTTATACTT
Found at i:26347 original size:43 final size:42
Alignment explanation
Indices: 26164--26586 Score: 345
Period size: 43 Copynumber: 9.8 Consensus size: 42
26154 TAATTGAGAT
* * * *
26164 CCCTAATTTTTTCAATCTCACTATTTACCTCTATAACTGAGGA
1 CCCTAATTTTTTCAATCTCACT-TTTACCTTTATAATTGAAGC
*
26207 CCCTAATTTTTTCAATCTCACTTTATAGCTTTATAATTGAAGC
1 CCCTAATTTTTTCAATCTCACTTT-TACCTTTATAATTGAAGC
* * *
26250 TCCTAATTTTTTCAATCTCACTTTAATAGCTTTATAATTGAAAC
1 CCCTAATTTTTTCAATCTCACTTT--TACCTTTATAATTGAAGC
** * **
26294 TTCTGATTTTTT-AATCTCACTTTATATTTTTATAATTGAAGC
1 CCCTAATTTTTTCAATCTCACTTT-TACCTTTATAATTGAAGC
* * * *
26336 CCCTATTTTTTTTTTCAATCTTACCTTTTACATTTATAATTG-AGG
1 CCCTA---ATTTTTTCAATCTCA-CTTTTACCTTTATAATTGAAGC
* *
26381 CCCTAATTTTTGT-AATCTCACTTTTTAACTTTACAATTG-AGAC
1 CCCTAATTTTT-TCAATCTCAC-TTTTACCTTTATAATTGAAG-C
*** * * *
26424 ATTTAATTTTTTCAATCCCACCTTTTACATTTATAATTAAAGC
1 CCCTAATTTTTTCAATCTCA-CTTTTACCTTTATAATTGAAGC
* *
26467 CCCTGAATTTTTT-AATCTAACTTCTTACATTTATAATTGAAGC
1 CCCT-AATTTTTTCAATCTCACTT-TTACCTTTATAATTGAAGC
* * * * *
26510 CCTTGATTTTTTTCAATCTCACTTTTTACTTTTATAATTGAGGT
1 CCCT-AATTTTTTCAATCTCAC-TTTTACCTTTATAATTGAAGC
*
26554 GCCTAATTTTTT-AATCTCACTTTTTACCTTTAT
1 CCCTAATTTTTTCAATCTCAC-TTTTACCTTTAT
26587 GAATGAGACC
Statistics
Matches: 313, Mismatches: 50, Indels: 35
0.79 0.13 0.09
Matches are distributed among these distances:
41 1 0.00
42 71 0.23
43 140 0.45
44 64 0.20
45 15 0.05
46 18 0.06
47 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (42 bp):
CCCTAATTTTTTCAATCTCACTTTTACCTTTATAATTGAAGC
Found at i:26646 original size:43 final size:42
Alignment explanation
Indices: 26171--26647 Score: 157
Period size: 43 Copynumber: 11.1 Consensus size: 42
26161 GATCCCTAAT
* * * * * **
26171 TTTTTCAATCTCACTATTTACCTCTATAACTGAGGACCCTAA
1 TTTTTCAATCTAACTTTTTACTTTTATAATTGAGGACTATAA
* * * *
26213 TTTTTTCAATCTCACTTTATAGC-TTTATAATTGAAG-CTCCTAA
1 -TTTTTCAATCTAACTTTTTA-CTTTTATAATTGAGGACT-ATAA
* * * * *
26256 TTTTTTCAATCTCACTTTAATAGC-TTTATAATTGA-AACTTCTGA
1 -TTTTTCAATCTAACTTT-TTA-CTTTTATAATTGAGGAC-TATAA
* * * * ** **
26300 TTTTTTAATCTCACTTTATATTTTTATAATTGAAGCCCCTATTTTT
1 TTTTTCAATCTAACTTTTTACTTTTATAATTG-AG-GACTA--TAA
* * * **
26346 TTTTTCAATCTTACCTTTTACATTTATAATTGAGG-CCCTAA
1 TTTTTCAATCTAACTTTTTACTTTTATAATTGAGGACTATAA
* * * *
26387 TTTTTGTAATCTCACTTTTTAAC-TTTACAATTGA-GACATTTAA
1 TTTTT-CAATCTAACTTTTT-ACTTTTATAATTGAGGAC-TATAA
** * * * * * **
26430 TTTTTTCAATCCCACCTTTTACATTTATAATTAAAGCCCCTGAA
1 -TTTTTCAATCTAACTTTTTACTTTTATAATTGAGGACTAT-AA
* * * ** *
26474 TTTTTTAATCTAACTTCTTACATTTATAATTGAAGCCCT-TGATT
1 TTTTTCAATCTAACTTTTTACTTTTATAATTG-AGGACTAT-A-A
* * *
26518 TTTTTCAATCTCACTTTTTACTTTTATAATTGAGGTGC-CTAA
1 TTTTTCAATCTAACTTTTTACTTTTATAATTGAGG-ACTATAA
* * * *
26560 TTTTTTAATCTCACTTTTTACCTTTATGAA-TGA-GACCTTTAA
1 TTTTTCAATCTAACTTTTTACTTTTAT-AATTGAGGA-CTATAA
* *
26602 TTTTTCCAATTTAACTTTTTACTTTTATAATTTAGGACTATAA
1 TTTTT-CAATCTAACTTTTTACTTTTATAATTGAGGACTATAA
26645 TTT
1 TTT
26648 AATCAATTTT
Statistics
Matches: 338, Mismatches: 67, Indels: 58
0.73 0.14 0.13
Matches are distributed among these distances:
41 9 0.03
42 76 0.22
43 156 0.46
44 66 0.20
45 4 0.01
46 27 0.08
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.48
Consensus pattern (42 bp):
TTTTTCAATCTAACTTTTTACTTTTATAATTGAGGACTATAA
Found at i:28188 original size:9 final size:9
Alignment explanation
Indices: 28156--28215 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
28146 CTGCTGGAAA
28156 ACCGGTTTG
1 ACCGGTTTG
*
28165 ACCAGTTTTG
1 ACC-GGTTTG
28175 AACCGGTTTG
1 -ACCGGTTTG
*
28185 ACCGGTTCG
1 ACCGGTTTG
28194 AACCGGTTTG
1 -ACCGGTTTG
*
28204 ACCGGTCTG
1 ACCGGTTTG
28213 ACC
1 ACC
28216 CGACCCGACC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 22 0.51
10 18 0.42
11 3 0.07
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:28198 original size:19 final size:19
Alignment explanation
Indices: 28155--28209 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
28145 GCTGCTGGAA
* *
28155 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
28175 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
28194 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
28210 CTGACCCGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:28239 original size:17 final size:17
Alignment explanation
Indices: 28217--28254 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
28207 GGTCTGACCC
28217 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
28234 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
28251 GACC
1 GACC
28255 GTTGACCGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:28254 original size:24 final size:23
Alignment explanation
Indices: 28201--28261 Score: 79
Period size: 22 Copynumber: 2.6 Consensus size: 23
28191 TCGAACCGGT
28201 TTGACCGGTCTGACCCGACCCGACC
1 TTGACC-GT-TGACCCGACCCGACC
*
28226 -CGACCGTTGACCCGACCCGACC
1 TTGACCGTTGACCCGACCCGACC
28248 GTTGACCGTTGACC
1 -TTGACCGTTGACC
28262 GCTGACTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 15 0.47
23 2 0.06
24 15 0.47
ACGTcount: A:0.16, C:0.43, G:0.25, T:0.16
Consensus pattern (23 bp):
TTGACCGTTGACCCGACCCGACC
Found at i:35469 original size:9 final size:9
Alignment explanation
Indices: 35437--35496 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
35427 CTGCTGGAAA
35437 ACCGGTTTG
1 ACCGGTTTG
*
35446 ACCAGTTTTG
1 ACC-GGTTTG
35456 AACCGGTTTG
1 -ACCGGTTTG
*
35466 ACCGGTCTG
1 ACCGGTTTG
35475 AACCGGTTTG
1 -ACCGGTTTG
*
35485 ACCGGTCTG
1 ACCGGTTTG
35494 ACC
1 ACC
35497 CGACCCGACC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 22 0.51
10 18 0.42
11 3 0.07
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:35478 original size:19 final size:19
Alignment explanation
Indices: 35436--35494 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
35426 GCTGCTGGAA
* *
35436 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
35456 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
35475 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
35494 A
1 A
35495 CCCGACCCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
19 24 0.65
20 13 0.35
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:35519 original size:22 final size:22
Alignment explanation
Indices: 35493--35557 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
35483 TGACCGGTCT
35493 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
35515 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
* *
35537 GACCCGTCCCGATCGTTGACC
1 GACCCGACCCGACCGTTGACC
35558 GTTGACTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:42012 original size:2 final size:2
Alignment explanation
Indices: 41990--42061 Score: 119
Period size: 2 Copynumber: 36.5 Consensus size: 2
41980 ATGAAATAAA
* *
41990 AT AT AA AT AT AT AA AT A- 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
42031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42062 AACAATAATT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:46299 original size:30 final size:31
Alignment explanation
Indices: 46265--46328 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 31
46255 AGTATAGGAC
46265 TCTACTTAATATGA-AAGACGTTAAAGACGA
1 TCTACTTAATATGACAAGACGTTAAAGACGA
*
46295 TCTACTTAATATTACTAAGACGTTAAAGACGA
1 TCTACTTAATATGAC-AAGACGTTAAAGACGA
46327 TC
1 TC
46329 GGATTTACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 13 0.42
32 18 0.58
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (31 bp):
TCTACTTAATATGACAAGACGTTAAAGACGA
Found at i:49725 original size:17 final size:17
Alignment explanation
Indices: 49703--49737 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
49693 CCTAACGTTT
49703 GTAACGTTACTATTTTA
1 GTAACGTTACTATTTTA
49720 GTAACGTTACTATTTTA
1 GTAACGTTACTATTTTA
49737 G
1 G
49738 GGTGCATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (17 bp):
GTAACGTTACTATTTTA
Found at i:52468 original size:18 final size:18
Alignment explanation
Indices: 52445--52479 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52435 AATGTAAGAT
*
52445 TACCGTGTTTGGTTAAAA
1 TACCGTGTTTGATTAAAA
52463 TACCGTGTTTGATTAAA
1 TACCGTGTTTGATTAAA
52480 GAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (18 bp):
TACCGTGTTTGATTAAAA
Found at i:52888 original size:41 final size:41
Alignment explanation
Indices: 52842--52926 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
52832 GGTAGACAAT
* * *
52842 TCATAATTATGATTGCCGGAGATCTTCTACGAAAATTGCTC
1 TCATAATTATGACTGCCGGAGATCTTCTAAGAAAACTGCTC
52883 TCATAATTATGACTGCCGGAGATCTTCTAAGAAAACTGCTC
1 TCATAATTATGACTGCCGGAGATCTTCTAAGAAAACTGCTC
52924 TCA
1 TCA
52927 ACCTGACGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (41 bp):
TCATAATTATGACTGCCGGAGATCTTCTAAGAAAACTGCTC
Found at i:54416 original size:3 final size:3
Alignment explanation
Indices: 54408--54452 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
54398 GAGTAGAGTT
54408 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GGAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GA
54453 GGAGGAGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:55285 original size:6 final size:6
Alignment explanation
Indices: 55269--55324 Score: 67
Period size: 6 Copynumber: 9.3 Consensus size: 6
55259 GTTTTAGTAT
* * * *
55269 CGATAC TGATAC CGATAC CGATAT TGATAC CGATAT CGATAC CGATAC
1 CGATAC CGATAC CGATAC CGATAC CGATAC CGATAC CGATAC CGATAC
*
55317 TGATAC CG
1 CGATAC CG
55325 TATAGTATTA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (6 bp):
CGATAC
Found at i:55296 original size:18 final size:18
Alignment explanation
Indices: 55269--55324 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
55259 GTTTTAGTAT
55269 CGATACTGATACCGATAC
1 CGATACTGATACCGATAC
* *
55287 CGATATTGATACCGATAT
1 CGATACTGATACCGATAC
* *
55305 CGATACCGATACTGATAC
1 CGATACTGATACCGATAC
55323 CG
1 CG
55325 TATAGTATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (18 bp):
CGATACTGATACCGATAC
Done.