Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001899.1 Hibiscus syriacus cultivar Beakdansim tig00003848_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: 183856
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1302 original size:32 final size:33
Alignment explanation
Indices: 1260--1326 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
1250 ATACAATCTG
*
1260 TCCATCACCATATCA-CGCCAATAACATCATCCT
1 TCCATCACCATATCATCACCAATAA-ATCATCCT
* *
1293 TCCAT-ACCATTTCATCACCATTAAATCATCCT
1 TCCATCACCATATCATCACCAATAAATCATCCT
1325 TC
1 TC
1327 ATTCATCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.31, C:0.37, G:0.01, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCATCACCAATAAATCATCCT
Found at i:7589 original size:11 final size:11
Alignment explanation
Indices: 7575--7635 Score: 52
Period size: 13 Copynumber: 5.1 Consensus size: 11
7565 TCTTTTTGAA
7575 TTCTTTTTCTT
1 TTCTTTTTCTT
7586 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
7599 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
7612 TGTCTTTTTC-T
1 T-TCTTTTTCTT
7623 TTCTTTTTGCTT
1 TTCTTTTT-CTT
7635 T
1 T
7636 GTACGCCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
10 7 0.17
11 6 0.15
12 9 0.22
13 15 0.37
14 4 0.10
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:7599 original size:19 final size:18
Alignment explanation
Indices: 7575--7635 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
7565 TCTTTTTGAA
7575 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
7593 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
7612 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
*
7630 TGCTTT
1 TTCTTT
7636 GTACGCCAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 4 0.11
18 16 0.42
19 13 0.34
20 5 0.13
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:10604 original size:19 final size:20
Alignment explanation
Indices: 10564--10613 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
10554 GAAACCCCTT
**
10564 TGAAAA-ACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
10583 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
10602 TGAAGATACATG
1 TGAAAATACATG
10614 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:16404 original size:18 final size:19
Alignment explanation
Indices: 16369--16415 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
16359 CGGCCAAGAG
*
16369 CATGTATCTTCAT-TAAAAT
1 CATGTAT-TTCATCAAAAAT
16388 CATGTATTTCATCAAAAAT
1 CATGTATTTCATCAAAAAT
16407 CATGTATTT
1 CATGTATTT
16416 TCAAAGGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (19 bp):
CATGTATTTCATCAAAAAT
Found at i:38641 original size:14 final size:14
Alignment explanation
Indices: 38622--38649 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38612 ATCTAATACT
38622 AATAGAATAGAAAA
1 AATAGAATAGAAAA
38636 AATAGAATAGAAAA
1 AATAGAATAGAAAA
38650 GACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:38669 original size:17 final size:17
Alignment explanation
Indices: 38619--38685 Score: 86
Period size: 17 Copynumber: 4.1 Consensus size: 17
38609 CCAATCTAAT
38619 ACTAATAGAATAGAAA-
1 ACTAATAGAATAGAAAG
38635 A--AATAGAATAGAAAAG
1 ACTAATAGAATAG-AAAG
*
38651 ACTAATATAATAGAAAG
1 ACTAATAGAATAGAAAG
*
38668 ACTAATATAATAGAAAG
1 ACTAATAGAATAGAAAG
38685 A
1 A
38686 AAAGAACTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.22
15 3 0.07
16 2 0.04
17 22 0.48
18 9 0.20
ACGTcount: A:0.63, C:0.04, G:0.13, T:0.19
Consensus pattern (17 bp):
ACTAATAGAATAGAAAG
Found at i:43807 original size:21 final size:24
Alignment explanation
Indices: 43781--43835 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
43771 AAAATCCAGC
43781 AAAGAA-AAA-TCAAAGCACTC-A
1 AAAGAAGAAATTCAAAGCACTCGA
* *
43802 AAAGAAGAAATTGAAAGTACTCGA
1 AAAGAAGAAATTCAAAGCACTCGA
43826 AAAGAAGAAA
1 AAAGAAGAAA
43836 AAGAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 3 0.10
23 9 0.31
24 11 0.38
ACGTcount: A:0.62, C:0.11, G:0.16, T:0.11
Consensus pattern (24 bp):
AAAGAAGAAATTCAAAGCACTCGA
Found at i:43811 original size:24 final size:25
Alignment explanation
Indices: 43782--43837 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
43772 AAATCCAGCA
43782 AAGAAAAATCAAAGCACTC-AAAAG
1 AAGAAAAATCAAAGCACTCGAAAAG
* * *
43806 AAG-AAATTGAAAGTACTCGAAAAG
1 AAGAAAAATCAAAGCACTCGAAAAG
43830 AAGAAAAA
1 AAGAAAAA
43838 GAAAGAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 12 0.46
24 11 0.42
25 3 0.12
ACGTcount: A:0.62, C:0.11, G:0.16, T:0.11
Consensus pattern (25 bp):
AAGAAAAATCAAAGCACTCGAAAAG
Found at i:43841 original size:24 final size:23
Alignment explanation
Indices: 43782--43842 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
43772 AAATCCAGCA
*
43782 AAGAAAAATCAAAGCACTCAAAAG
1 AAGAAAAA-GAAAGCACTCAAAAG
** *
43806 AAGAAATTGAAAGTACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
43830 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
43843 AAAGAAAAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 8 0.27
24 22 0.73
ACGTcount: A:0.62, C:0.10, G:0.18, T:0.10
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:56324 original size:22 final size:23
Alignment explanation
Indices: 56281--56325 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
56271 GAGAAAAAGC
**
56281 ACTCAAAAAGAAGAAATTGAAAA
1 ACTCAAAAAGAAGAAAAAGAAAA
56304 ACTC-AAAAGAAGAAAAAGAAAA
1 ACTCAAAAAGAAGAAAAAGAAAA
56326 GAAAAGTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.69, C:0.09, G:0.13, T:0.09
Consensus pattern (23 bp):
ACTCAAAAAGAAGAAAAAGAAAA
Found at i:61681 original size:16 final size:16
Alignment explanation
Indices: 61660--61691 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
61650 TAGTTAGCTC
61660 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
61676 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
61692 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:63084 original size:14 final size:13
Alignment explanation
Indices: 63065--63114 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
63055 AAGCAAAAAG
63065 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
63079 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
63092 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
63103 AAAGAAAAAGAA
1 AAAGAAAAAGAA
63115 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:63111 original size:19 final size:18
Alignment explanation
Indices: 63054--63114 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 18
63044 ATTGGCGTAC
*
63054 AAAGCAAAAAG-AAAGAA
1 AAAGAAAAAAGAAAAGAA
63071 AAAGACAAAAAGAAGAAG-A
1 AAAGA-AAAAAGAA-AAGAA
63090 AAAGAAGAAAAGAAAAGAA
1 AAAGAA-AAAAGAAAAGAA
63109 AAAGAA
1 AAAGAA
63115 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 4 0.11
18 10 0.26
19 21 0.55
20 3 0.08
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAGAAAAGAA
Found at i:65229 original size:16 final size:16
Alignment explanation
Indices: 65208--65239 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
65198 TAGTTAGCTC
65208 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
65224 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
65240 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:69233 original size:16 final size:17
Alignment explanation
Indices: 69209--69241 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
69199 CTTCACTTGC
69209 ATTTCTCTTTTT-TTGT
1 ATTTCTCTTTTTGTTGT
*
69225 ATTTTTCTTTTTGTTGT
1 ATTTCTCTTTTTGTTGT
69242 TGTTACACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.76
Consensus pattern (17 bp):
ATTTCTCTTTTTGTTGT
Found at i:76305 original size:10 final size:10
Alignment explanation
Indices: 76286--76315 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
76276 ATAACAGCAT
*
76286 ATTCATCTAC
1 ATTCAGCTAC
76296 ATTCAGCTAC
1 ATTCAGCTAC
76306 ATTCAGCTAC
1 ATTCAGCTAC
76316 CTTTGACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (10 bp):
ATTCAGCTAC
Found at i:80122 original size:555 final size:557
Alignment explanation
Indices: 79023--80134 Score: 1797
Period size: 555 Copynumber: 2.0 Consensus size: 557
79013 TCAAGTGAGG
* * *
79023 TTTTGTGAGTTTGCTGGTAAGGTTTTCAATTCATTTTATTTGCACTAACCATGTCTCAAAGCCCT
1 TTTTGTGAGTGTGCTGGTAAGGTTTTAAATTCACTTTATTTGCACTAACCATGTCTCAAAGCCCT
79088 AGAGAAAATGCAAGAACACCAAACTTACAAATGCAGGCACTCATTGGCGAAATGATGAGAATGTT
66 AGAGAAAATGCAAGAACACCAAACTTACAAATGCAGGCACTCATTGGCGAAATGATGAGAATGTT
* * * * *
79153 TCGTGAAGAGTTCGATGCTCTTCATGAAAAGATAGATCAACGCCAGGATCTACCACTAGGCCATA
131 TCGAGAAGAGTTCAATGCTCTTCATGAAAAGATAGATCAACACCAGGATCTACCACCAGACCATA
* * * *
79218 ATAATGGAGTCCCTTGAAGACAACAACCACCACCACCTCCAGAAGAAGATGTTCAAGAAACTTTT
196 ATAATGGAGTCCATAGAAGACAACAACAACCACCACCTCCAGAAGAAGATGTTCAAGAAAATTTT
* *
79283 GACGAGGGAGAAAAAGTAGCATTCCAAGGCCCTAGACGTGCCATTGTTGATGACAATCTGAGTAA
261 GACGAGGGAGAAAAAGAAGCATTCCAAGGCCCTAGACGTGCCATTGTTGATGACAATCTGAGAAA
* * * *
79348 TATCAAGATCAAAATTCCTCAATTTCAAGGAAAAACTGATCCTGAAGCTTATCACGAATGGTAAA
326 CATCAAGATCAAAATTCCTCAATTCCAAGGAAAAACTGATCCTGAAGCCTATCACGAATGGGAAA
79413 GCAAAGTGGAACATGTTTTTAGTTGCCACAACTATTCCGAAATGAAGAAAGTGAGATTGGCAGCC
391 GCAAAGTGGAACATGTTTTTAGTTGCCACAACTATTCCGAAATGAAGAAAGTGAGATTGGCAGCC
*
79478 ATGGAGTTCATAGACTATGCTTTAATATGGTGGGATCAACTTACCTTGAACCGAAGGAGGAATGG
456 ATGGAGTTCATAGACTATGCCTTAATATGGTGGGATCAACTTACCTTGAACCGAAGGAGGAATGG
79543 AGAACGACCGGTCTCAACTTGGCTTGAAATGAAAGGT
521 AGAACGACCGGTCTCAACTTGGCTTGAAATGAAAGGT
*
79580 TTTTGTGAGTGTGCTGGTAAGGTTTTAAATT-ACTTTATTT-CACTAATCATGTCTCAAAGTCCC
1 TTTTGTGAGTGTGCTGGTAAGGTTTTAAATTCACTTTATTTGCACTAACCATGTCTCAAAG-CCC
* * * *
79643 -CGAGGAAATGCAGGAACACCAAACTTACAAATAG-AGGCACTCATTGGTGAAATGATGAGAATG
65 TAGAGAAAATGCAAGAACACCAAACTTACAAAT-GCAGGCACTCATTGGCGAAATGATGAGAATG
*
79706 TTTCGAGAAGAGTTCAATGCTCTTCATGAAAAGATAGATCAACACCATGATCTACCACCA-ACCT
129 TTTCGAGAAGAGTTCAATGCTCTTCATGAAAAGATAGATCAACACCAGGATCTACCACCAGACC-
* *
79770 GTAATAATGGAG-CCAATAGAAGACAACAACAACCACCCCCTCCAGAAGAAGATGTTCAAGAAAA
193 ATAATAATGGAGTCC-ATAGAAGACAACAACAACCACCACCTCCAGAAGAAGATGTTCAAGAAAA
* * *
79834 TTTTGACGAGGGTGAACAAGAAGCATTCCAAGGCCCTAGACGTGCCATTGTTGATGACAATTTGA
257 TTTTGACGAGGGAGAAAAAGAAGCATTCCAAGGCCCTAGACGTGCCATTGTTGATGACAATCTGA
* * * **
79899 GAAACATTAAGATCAAAATTCCTCAATTCCAAGGAAAGAGTGATCCTGAAGCCTATCTTGAATGG
322 GAAACATCAAGATCAAAATTCCTCAATTCCAAGGAAAAACTGATCCTGAAGCCTATCACGAATGG
* *
79964 GAAAGCAAAGTGGAACATGTTTTTAGTTGCCACAACTATTTCGAGATGAAGAAAGTGAGATTGGC
387 GAAAGCAAAGTGGAACATGTTTTTAGTTGCCACAACTATTCCGAAATGAAGAAAGTGAGATTGGC
80029 AGCCATGGAGTTCATAGACTATGCCTTAATATGGTGGGATCAACTTACCCTT-AACCGAAGGAGG
452 AGCCATGGAGTTCATAGACTATGCCTTAATATGGTGGGATCAACTTA-CCTTGAACCGAAGGAGG
80093 AATGGAGAACGACCGGTCTCAACTTGGCTTGAAATGAAAGGT
516 AATGGAGAACGACCGGTCTCAACTTGGCTTGAAATGAAAGGT
80135 ATTATGCGGA
Statistics
Matches: 513, Mismatches: 37, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
554 4 0.01
555 464 0.90
556 16 0.03
557 29 0.06
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (557 bp):
TTTTGTGAGTGTGCTGGTAAGGTTTTAAATTCACTTTATTTGCACTAACCATGTCTCAAAGCCCT
AGAGAAAATGCAAGAACACCAAACTTACAAATGCAGGCACTCATTGGCGAAATGATGAGAATGTT
TCGAGAAGAGTTCAATGCTCTTCATGAAAAGATAGATCAACACCAGGATCTACCACCAGACCATA
ATAATGGAGTCCATAGAAGACAACAACAACCACCACCTCCAGAAGAAGATGTTCAAGAAAATTTT
GACGAGGGAGAAAAAGAAGCATTCCAAGGCCCTAGACGTGCCATTGTTGATGACAATCTGAGAAA
CATCAAGATCAAAATTCCTCAATTCCAAGGAAAAACTGATCCTGAAGCCTATCACGAATGGGAAA
GCAAAGTGGAACATGTTTTTAGTTGCCACAACTATTCCGAAATGAAGAAAGTGAGATTGGCAGCC
ATGGAGTTCATAGACTATGCCTTAATATGGTGGGATCAACTTACCTTGAACCGAAGGAGGAATGG
AGAACGACCGGTCTCAACTTGGCTTGAAATGAAAGGT
Found at i:84900 original size:8 final size:8
Alignment explanation
Indices: 84887--84948 Score: 65
Period size: 8 Copynumber: 7.8 Consensus size: 8
84877 TTTTTTTTTC
84887 AAAAAACA
1 AAAAAACA
84895 AAAAAA-A
1 AAAAAACA
*
84902 AAAAAAAA
1 AAAAAACA
*
84910 AAAAAAAA
1 AAAAAACA
84918 AAAAAACA
1 AAAAAACA
84926 AAAAAGA-A
1 AAAAA-ACA
*
84934 AAAAAGCCA
1 AAAAA-ACA
84943 AAAAAA
1 AAAAAA
84949 AAATTGCAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
7 7 0.15
8 34 0.71
9 7 0.15
ACGTcount: A:0.90, C:0.06, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:84909 original size:17 final size:17
Alignment explanation
Indices: 84894--84951 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
84884 TTCAAAAAAC
84894 AAAAAAAAAAAAAA-AA
1 AAAAAAAAAAAAAACAA
84910 AAAAAAAAAAAAAACAA
1 AAAAAAAAAAAAAACAA
* **
84927 AAAAGAAAAAAAGCCAA
1 AAAAAAAAAAAAAACAA
84944 AAAAAAAA
1 AAAAAAAA
84952 TTGCAAACGA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 14 0.38
17 23 0.62
ACGTcount: A:0.91, C:0.05, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAACAA
Found at i:84951 original size:1 final size:1
Alignment explanation
Indices: 84887--84938 Score: 77
Period size: 1 Copynumber: 52.0 Consensus size: 1
84877 TTTTTTTTTC
* * *
84887 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
84939 GCCAAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.94, C:0.04, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:101063 original size:34 final size:34
Alignment explanation
Indices: 100984--101086 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
100974 ATACAATCTG
*
100984 TCCATCACCATTATCACGCC-ATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T-T
*
101019 TCTATCACCATATCACGCCAATAACATCATCCTT
1 TCCATCACCATATCACGCCAATAACATCATCCTT
* * * *
101053 TCCATTACCATTTCATCACCATTAA-ATCATCCTT
1 TCCATCACCATATCA-CGCCAATAACATCATCCTT
101087 CATTCATCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
34 31 0.53
35 25 0.43
36 2 0.03
ACGTcount: A:0.31, C:0.35, G:0.02, T:0.32
Consensus pattern (34 bp):
TCCATCACCATATCACGCCAATAACATCATCCTT
Found at i:105519 original size:34 final size:34
Alignment explanation
Indices: 105465--105567 Score: 104
Period size: 34 Copynumber: 3.0 Consensus size: 34
105455 ATACAATCTG
*
105465 TCCATCACCATTATCACGCC-ATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T-T
105500 TCCATCACCATATCACGCCAATAACATCATCCTT
1 TCCATCACCATATCACGCCAATAACATCATCCTT
* * * *
105534 TCCATTACCATTTCATCACCATTAA-ATCATCCTT
1 TCCATCACCATATCA-CGCCAATAACATCATCCTT
105568 CATTCATCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
34 32 0.53
35 26 0.43
36 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (34 bp):
TCCATCACCATATCACGCCAATAACATCATCCTT
Found at i:115198 original size:35 final size:35
Alignment explanation
Indices: 115157--115227 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
115147 TCAAATAAGC
115157 ATAGGATGGAAATAATAATATGATAATTTATACTA
1 ATAGGATGGAAATAATAATATGATAATTTATACTA
115192 ATAGGATGGAAATAATAATATGATAATTTATACTA
1 ATAGGATGGAAATAATAATATGATAATTTATACTA
115227 A
1 A
115228 CATGTGAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (35 bp):
ATAGGATGGAAATAATAATATGATAATTTATACTA
Found at i:127891 original size:14 final size:15
Alignment explanation
Indices: 127862--127893 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
127852 GCAAGATATG
127862 TATTATAATAACATA
1 TATTATAATAACATA
127877 TATTATAAT-ACATA
1 TATTATAATAACATA
127891 TAT
1 TAT
127894 AAAGTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTATAATAACATA
Found at i:131173 original size:36 final size:36
Alignment explanation
Indices: 131121--131269 Score: 237
Period size: 36 Copynumber: 4.2 Consensus size: 36
131111 GATACTATTT
* *
131121 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
131157 TCATCACCATAGTCCATCACCATTATCACGTCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
131193 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
* *
131229 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
131264 ACATCA
1 TCATCA
131270 TCCTTCCATT
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 17 0.16
36 89 0.84
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:131176 original size:13 final size:11
Alignment explanation
Indices: 131121--131255 Score: 80
Period size: 13 Copynumber: 11.3 Consensus size: 11
131111 GATACTATTT
131121 TCATCACCATAA
1 TCATCACCAT-A
*
131133 TCCATCTCCATTA
1 T-CATCACCA-TA
*
131146 TCA-CGCCTATA
1 TCATCACC-ATA
131157 TCATCACCATA
1 TCATCACCATA
131168 GTCCATCACCAT-
1 -T-CATCACCATA
131180 T-ATCACGTCTATA
1 TCATCAC--C-ATA
131193 TCATCACCATA
1 TCATCACCATA
131204 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
131218 TCA-CGCCTATA
1 TCATCACC-ATA
131229 TCATCACCATA
1 TCATCACCATA
131240 TTCCATCACCATA
1 -T-CATCACCATA
131253 TCA
1 TCA
131256 CGCCAATAAC
Statistics
Matches: 100, Mismatches: 5, Indels: 37
0.70 0.04 0.26
Matches are distributed among these distances:
9 5 0.05
11 29 0.29
12 20 0.20
13 38 0.38
14 8 0.08
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:131284 original size:33 final size:33
Alignment explanation
Indices: 131133--131308 Score: 99
Period size: 36 Copynumber: 5.1 Consensus size: 33
131123 ATCACCATAA
* * *
131133 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* * *
131167 AGTCCATCACCATTATCACGTCTATATCATCA-CCAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
131203 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
131241 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
131274 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
131307 TC
1 TC
131309 ATTCATCAAC
Statistics
Matches: 127, Mismatches: 9, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
33 24 0.19
34 7 0.06
35 17 0.13
36 77 0.61
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:131743 original size:13 final size:14
Alignment explanation
Indices: 131727--131759 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
131717 TTTGGAGTGC
131727 AAAAGAAAGAAAA-A
1 AAAAG-AAGAAAAGA
131741 AAAAGAAGAAAAGA
1 AAAAGAAGAAAAGA
131755 AAAAG
1 AAAAG
131760 CAAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAGA
Found at i:131766 original size:17 final size:17
Alignment explanation
Indices: 131725--131770 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
131715 AATTTGGAGT
131725 GCAAAAG-AAAGAAAAA
1 GCAAAAGAAAAGAAAAA
**
131741 AAAAGAAGAAAAGAAAAA
1 GCAA-AAGAAAAGAAAAA
131759 GCAAAAGAAAAG
1 GCAAAAGAAAAG
131771 TGAAGCAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.08
17 11 0.46
18 11 0.46
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (17 bp):
GCAAAAGAAAAGAAAAA
Found at i:135294 original size:36 final size:36
Alignment explanation
Indices: 135242--135390 Score: 237
Period size: 36 Copynumber: 4.2 Consensus size: 36
135232 GATACTATTT
* *
135242 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
135278 TCATCACCATAGTCCATCACCATTATCACGTCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
135314 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
* *
135350 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
135385 ACATCA
1 TCATCA
135391 TCCTTCCATT
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 17 0.16
36 89 0.84
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:135297 original size:13 final size:11
Alignment explanation
Indices: 135242--135376 Score: 80
Period size: 13 Copynumber: 11.3 Consensus size: 11
135232 GATACTATTT
135242 TCATCACCATAA
1 TCATCACCAT-A
*
135254 TCCATCTCCATTA
1 T-CATCACCA-TA
*
135267 TCA-CGCCTATA
1 TCATCACC-ATA
135278 TCATCACCATA
1 TCATCACCATA
135289 GTCCATCACCAT-
1 -T-CATCACCATA
135301 T-ATCACGTCTATA
1 TCATCAC--C-ATA
135314 TCATCACCATA
1 TCATCACCATA
135325 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
135339 TCA-CGCCTATA
1 TCATCACC-ATA
135350 TCATCACCATA
1 TCATCACCATA
135361 TTCCATCACCATA
1 -T-CATCACCATA
135374 TCA
1 TCA
135377 CGCCAATAAC
Statistics
Matches: 100, Mismatches: 5, Indels: 37
0.70 0.04 0.26
Matches are distributed among these distances:
9 5 0.05
11 29 0.29
12 20 0.20
13 38 0.38
14 8 0.08
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:135405 original size:33 final size:33
Alignment explanation
Indices: 135254--135429 Score: 99
Period size: 36 Copynumber: 5.1 Consensus size: 33
135244 ATCACCATAA
* * *
135254 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* * *
135288 AGTCCATCACCATTATCACGTCTATATCATCA-CCAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
135324 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
135362 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
135395 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
135428 TC
1 TC
135430 ATTCATCAAC
Statistics
Matches: 127, Mismatches: 9, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
33 24 0.19
34 7 0.06
35 17 0.13
36 77 0.61
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:136229 original size:12 final size:12
Alignment explanation
Indices: 136215--136244 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
136205 AAGCAACAAG
136215 AAAGAAGAAAAGA
1 AAAG-AGAAAAGA
136228 AAAGAGAAAAGA
1 AAAGAGAAAAGA
136240 AAAGA
1 AAAGA
136245 CTCCTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAAGA
Found at i:141128 original size:12 final size:12
Alignment explanation
Indices: 141114--141143 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
141104 AAGCAACAAG
141114 AAAGAAGAAAAGA
1 AAAG-AGAAAAGA
141127 AAAGAGAAAAGA
1 AAAGAGAAAAGA
141139 AAAGA
1 AAAGA
141144 CTCCTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAAGA
Found at i:171482 original size:33 final size:33
Alignment explanation
Indices: 171439--171506 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
171429 ATACAATCTG
*
171439 TCCATCACCATATCA-CGCCAATAACATCATCCT
1 TCCATCACCATATCATCACCAATAA-ATCATCCT
* * *
171472 TCCATTACCATTTCATCACCATTAAATCATCCT
1 TCCATCACCATATCATCACCAATAAATCATCCT
171505 TC
1 TC
171507 ATTCATCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.37, G:0.01, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCATCACCAATAAATCATCCT
Found at i:174613 original size:17 final size:17
Alignment explanation
Indices: 174593--174628 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
174583 CAGCATCAAA
174593 AATGGACTTGCATCTCC
1 AATGGACTTGCATCTCC
174610 AATGGACTTGCATCTCC
1 AATGGACTTGCATCTCC
174627 AA
1 AA
174629 CCTTTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (17 bp):
AATGGACTTGCATCTCC
Found at i:175926 original size:33 final size:33
Alignment explanation
Indices: 175883--175950 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
175873 ATACAATCTG
*
175883 TCCATCACCATATCA-CGCCAATAACATCATCCT
1 TCCATCACCATATCATCACCAATAA-ATCATCCT
* * *
175916 TCCATTACCATTTCATCACCATTAAATCATCCT
1 TCCATCACCATATCATCACCAATAAATCATCCT
175949 TC
1 TC
175951 ATTCATCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.37, G:0.01, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCATCACCAATAAATCATCCT
Found at i:176944 original size:13 final size:11
Alignment explanation
Indices: 176903--176987 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
176893 ACAATCTGTC
176903 CATCACCATTAT
1 CATCACCA-TAT
*
176915 CATGC-CTATAT
1 CAT-CACCATAT
176926 CATCACCATAGT
1 CATCACCATA-T
176938 CCATCACCATTAT
1 -CATCACCA-TAT
*
176951 CA-CGCCTATAT
1 CATCACC-ATAT
176962 CATCACCATATT
1 CATCACCATA-T
176974 CCATCACCATAT
1 -CATCACCATAT
176986 CA
1 CA
176988 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:176947 original size:36 final size:36
Alignment explanation
Indices: 176900--177004 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
176890 GATACAATCT
*
176900 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
176936 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
176972 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
177005 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:177400 original size:12 final size:12
Alignment explanation
Indices: 177385--177418 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
177375 AAAAAAAGAA
177385 AAAAGAAAAAAG
1 AAAAGAAAAAAG
* *
177397 AAAACAAAAGAG
1 AAAAGAAAAAAG
177409 AAAAGAAAAA
1 AAAAGAAAAA
177419 GACTCCTACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:177405 original size:17 final size:17
Alignment explanation
Indices: 177385--177417 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
177375 AAAAAAAGAA
177385 AAAAGAAAAAAGAAAAC
1 AAAAGAAAAAAGAAAAC
*
177402 AAAAGAGAAAAGAAAA
1 AAAAGAAAAAAGAAAA
177418 AGACTCCTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAC
Found at i:177405 original size:19 final size:18
Alignment explanation
Indices: 177374--177418 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
177364 GTGCTACAAC
*
177374 AAAAAAAAGAAAAAAGAA
1 AAAAAAAACAAAAAAGAA
*
177392 AAAAGAAAACAAAAGAGAA
1 AAAA-AAAACAAAAAAGAA
177411 AAGAAAAA
1 AA-AAAAA
177419 GACTCCTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 17 0.74
20 2 0.09
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAAAACAAAAAAGAA
Found at i:177405 original size:24 final size:23
Alignment explanation
Indices: 177374--177418 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
177364 GTGCTACAAC
177374 AAAAAAAAGAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAGAAAAAAG
*
177397 AAAACAAAAGAGAAAAGAAAAA
1 AAAA-AAAAGAAAAAAGAAAAA
177419 GACTCCTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAAAAAAGAAAAAAGAAAAAAG
Found at i:177414 original size:7 final size:7
Alignment explanation
Indices: 177376--177400 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
177366 GCTACAACAA
177376 AAAAAAG
1 AAAAAAG
177383 AAAAAAG
1 AAAAAAG
177390 AAAAAAG
1 AAAAAAG
177397 AAAA
1 AAAA
177401 CAAAAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Done.