Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000005.1 Hibiscus syriacus cultivar Beakdansim tig00000011_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: 90555
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2448 original size:19 final size:19
Alignment explanation
Indices: 2424--2476 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
2414 CCATGTCATA
2424 GCATTTAGTTTCATTAGAG
1 GCATTTAGTTTCATTAGAG
*
2443 GCATTTAGTTTCATTTATAG
1 GCATTTAGTTTCA-TTAGAG
*
2463 TCATTTAGTTTCAT
1 GCATTTAGTTTCAT
2477 GTTGTAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (19 bp):
GCATTTAGTTTCATTAGAG
Found at i:5856 original size:24 final size:22
Alignment explanation
Indices: 5821--5880 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
5811 ACTTCAATGA
5821 ATCAGTTG-TAAGGAAGATTAGTAT
1 ATCAG-TGCTAAGGAA-ATTA-TAT
* *
5845 ATCAGTGCTAAGGTAATTATGT
1 ATCAGTGCTAAGGAAATTATAT
5867 A-CAGTGCTAAGGAA
1 ATCAGTGCTAAGGAA
5881 CTTCAGATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 12 0.38
22 3 0.09
23 6 0.19
24 11 0.34
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (22 bp):
ATCAGTGCTAAGGAAATTATAT
Found at i:14183 original size:23 final size:23
Alignment explanation
Indices: 14156--14201 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
14146 TGGGTGAGGA
14156 ACGATGGTCTAGCTAGCCCAAGG
1 ACGATGGTCTAGCTAGCCCAAGG
14179 ACGATGGTCTAGCTAGCCCAAGG
1 ACGATGGTCTAGCTAGCCCAAGG
14202 GGGCGACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.17
Consensus pattern (23 bp):
ACGATGGTCTAGCTAGCCCAAGG
Found at i:17675 original size:21 final size:20
Alignment explanation
Indices: 17633--17673 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
17623 AATTATAAGA
17633 TAGATAAAAATATATTGAAAT
1 TAGATAAAAATATATT-AAAT
17654 TAGATAAATAATTATATTAA
1 TAGATAAA-AA-TATATTAA
17674 TTTTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
TAGATAAAAATATATTAAAT
Found at i:20832 original size:31 final size:31
Alignment explanation
Indices: 20794--20866 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
20784 ATAATTTTTA
* * *
20794 AAATTTGTGATGGAATATGTGGACCCATTAC
1 AAATTTGTGACGGAATACGTGGACCCATCAC
* *
20825 AAATTTGTGACGGAATACGTGGATCCGTCAC
1 AAATTTGTGACGGAATACGTGGACCCATCAC
*
20856 AAATTTCTGAC
1 AAATTTGTGAC
20867 AGATTCACCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (31 bp):
AAATTTGTGACGGAATACGTGGACCCATCAC
Found at i:20891 original size:31 final size:31
Alignment explanation
Indices: 20851--20920 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
20841 ACGTGGATCC
* *
20851 GTCACAAATTTCTGACAGATTCACCTATTCT
1 GTCACAAATTTCTGACAGATCCACATATTCT
* * *
20882 GTCAGAAATTTCTGACGGGTCCACATATTCT
1 GTCACAAATTTCTGACAGATCCACATATTCT
20913 GTCACAAA
1 GTCACAAA
20921 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (31 bp):
GTCACAAATTTCTGACAGATCCACATATTCT
Found at i:21545 original size:17 final size:17
Alignment explanation
Indices: 21490--21547 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
21480 GACTTGTTAG
*
21490 TATTATTATT-ATTATCT
1 TATTATT-TTAATTATAT
*
21507 AATT-TTTTAATTA-AT
1 TATTATTTTAATTATAT
21522 GTAATTATTTTAATTATAT
1 -T-ATTATTTTAATTATAT
21541 TATTATT
1 TATTATT
21548 AATTTTTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
15 3 0.09
16 6 0.18
17 12 0.36
18 10 0.30
19 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TATTATTTTAATTATAT
Found at i:23140 original size:2 final size:2
Alignment explanation
Indices: 23133--23162 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23123 CATAGCAGTA
23133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23163 TTGGAATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27248 original size:13 final size:13
Alignment explanation
Indices: 27230--27254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27220 ATTTCACATT
27230 TACACTTTGAAAA
1 TACACTTTGAAAA
27243 TACACTTTGAAA
1 TACACTTTGAAA
27255 CACTCATCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TACACTTTGAAAA
Found at i:30102 original size:26 final size:26
Alignment explanation
Indices: 30066--30117 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
30056 TCCTCTAGTT
30066 TATTTTGTTGTTTTGATTTTAAAAAA
1 TATTTTGTTGTTTTGATTTTAAAAAA
30092 TATTTTGTTGTTTTGATTTTAAAAAA
1 TATTTTGTTGTTTTGATTTTAAAAAA
30118 AATATTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TATTTTGTTGTTTTGATTTTAAAAAA
Found at i:30389 original size:15 final size:16
Alignment explanation
Indices: 30353--30391 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
30343 ATAGCCTCTG
30353 AATCATTCAACATTTA
1 AATCATTCAACATTTA
*
30369 AATCATTCAACGTTT-
1 AATCATTCAACATTTA
30384 AATCATTC
1 AATCATTC
30392 TGAAGTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (16 bp):
AATCATTCAACATTTA
Found at i:31147 original size:3 final size:3
Alignment explanation
Indices: 31127--31192 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
31117 TATGTAACAT
* * * *
31127 TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TGTA TTA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* *
31172 TAG TTA TAA TAA T-A TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
31193 TAAATAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 4 0.08
3 44 0.88
4 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:31207 original size:39 final size:36
Alignment explanation
Indices: 31126--31220 Score: 102
Period size: 39 Copynumber: 2.5 Consensus size: 36
31116 ATATGTAACA
* *
31126 TTAATGATAATAGTAATAATAATAATAATAATGTATT
1 TTAAT-ATAATAGTTATAATAATAATAATAATGAATT
*
31163 ATAATATAATAGTTATAATAATATAATAATTAAAT-AATT
1 TTAATATAATAGTTATAAT-A-ATAATAA-T-AATGAATT
*
31202 TTAATATAATATTTATAAT
1 TTAATATAATAGTTATAAT
31221 CCGAACAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
36 13 0.27
37 5 0.10
38 7 0.14
39 21 0.43
40 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (36 bp):
TTAATATAATAGTTATAATAATAATAATAATGAATT
Found at i:41593 original size:38 final size:38
Alignment explanation
Indices: 41542--41619 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
41532 AAAGGCGGAA
41542 TCCCTTCACTCCATGGGTGATTCCCATAAAGAGAGCCT
1 TCCCTTCACTCCATGGGTGATTCCCATAAAGAGAGCCT
41580 TCCCTTCACTCCATGGGTGATTCCCATAAAGAGAGCCT
1 TCCCTTCACTCCATGGGTGATTCCCATAAAGAGAGCCT
41618 TC
1 TC
41620 TTTGCTCTCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (38 bp):
TCCCTTCACTCCATGGGTGATTCCCATAAAGAGAGCCT
Found at i:45562 original size:18 final size:17
Alignment explanation
Indices: 45531--45565 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
45521 ACTTCCATTA
*
45531 CCTTTGGTATCGGTACC
1 CCTTTGGTACCGGTACC
45548 CCTTCTGGTACCGGTACC
1 CCTT-TGGTACCGGTACC
45566 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.11, C:0.34, G:0.23, T:0.31
Consensus pattern (17 bp):
CCTTTGGTACCGGTACC
Found at i:45658 original size:107 final size:106
Alignment explanation
Indices: 45466--45755 Score: 386
Period size: 107 Copynumber: 2.7 Consensus size: 106
45456 AATAATATTT
* * *
45466 TATTCT-AGAATTTGAGCAATGTTGGTACTATCGATACTACATTGTGAGTATCGATACTTCCATT
1 TATTCTGA-AATTTGAGCAATGTTGGTAGTATCGATACTACCTTGTGAGTATCGATACTT-CAAT
* * *
45530 ACCTTTGGTATCGGTACCCCTTCTGG-TACCGGTACCATTTTTG
64 ACCTTTGGTATCAGTACCCCTT-TGGATAACAGTACCATTTTTG
* *
45573 TATTCTGAAATTTGAGTAATGTTGGTAGTATCGATACTACCTTGTGAGTATCGATACTTCTGATA
1 TATTCTGAAATTTGAGCAATGTTGGTAGTATCGATACTACCTTGTGAGTATCGATACTTC-AATA
*
45638 CCTTTGGTATCAGTATCCCTTTGGATAACAGTACCATTTTTG
65 CCTTTGGTATCAGTACCCCTTTGGATAACAGTACCATTTTTG
* * * * *
45680 CATTATGGAATTTGAGCAATGTTGGTAGTATCAATACTATCTTGTGAGTATCGATACTTCCAATA
1 TATTCTGAAATTTGAGCAATGTTGGTAGTATCGATACTACCTTGTGAGTATCGATACTT-CAATA
*
45745 CCTTTAGTATC
65 CCTTTGGTATC
45756 GGTAATATAT
Statistics
Matches: 162, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
106 4 0.02
107 156 0.96
108 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (106 bp):
TATTCTGAAATTTGAGCAATGTTGGTAGTATCGATACTACCTTGTGAGTATCGATACTTCAATAC
CTTTGGTATCAGTACCCCTTTGGATAACAGTACCATTTTTG
Found at i:56593 original size:32 final size:31
Alignment explanation
Indices: 56557--56633 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
56547 CGGGGCCGTG
*
56557 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
56589 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
56620 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
56634 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:56616 original size:63 final size:63
Alignment explanation
Indices: 56510--56633 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
56500 CCCTAAGGGA
* * ** *
56510 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
56573 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
56634 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:57534 original size:5 final size:5
Alignment explanation
Indices: 57524--57581 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
57514 AACGGTCAAC
* * *
57524 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTTG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
57573 GGTCG GGTC
1 GGTCG GGTC
57582 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 35 0.81
7 8 0.19
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:57545 original size:22 final size:22
Alignment explanation
Indices: 57517--57581 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
57507 AACGGTCAAC
57517 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
57539 GGTCAACGGTCGGGTTGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
57561 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
57582 AGACCGGTCA
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:0.09, C:0.22, G:0.49, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:57596 original size:9 final size:9
Alignment explanation
Indices: 57578--57705 Score: 121
Period size: 9 Copynumber: 13.3 Consensus size: 9
57568 GGTCGGGTCG
*
57578 GGTCAGACC
1 GGTCAAACC
57587 GGTCAAACC
1 GGTCAAACC
* *
57596 GATTCAGACC
1 G-GTCAAACC
57606 GGTCAAACC
1 GGTCAAACC
*
57615 GGTTCGAACC
1 GG-TCAAACC
*
57625 GGTTGAAACC
1 GG-TCAAACC
57635 GGTCAAACC
1 GGTCAAACC
57644 GGTCAGAACC
1 GGTCA-AACC
*
57654 GGTTGAAACC
1 GG-TCAAACC
57664 GGTCAAACC
1 GGTCAAACC
57673 GGTCAGAACC
1 GGTCA-AACC
*
57683 GGTTGAAAACC
1 GG-T-CAAACC
57694 GGTCAAACC
1 GGTCAAACC
57703 GGT
1 GGT
57706 TTCCAGCAGC
Statistics
Matches: 99, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
9 47 0.47
10 42 0.42
11 9 0.09
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:57602 original size:19 final size:19
Alignment explanation
Indices: 57580--57685 Score: 110
Period size: 19 Copynumber: 5.5 Consensus size: 19
57570 TCGGGTCGGG
*
57580 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
57599 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
57618 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
57637 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
57657 TGAAACCGGTCAAACCGG-
1 TCAGACCGGTCAAACCGGT
57675 TCAGAACCGGT
1 TCAG-ACCGGT
57686 TGAAAACCGG
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
18 5 0.07
19 50 0.68
20 19 0.26
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.15
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:57624 original size:10 final size:9
Alignment explanation
Indices: 57603--57705 Score: 80
Period size: 10 Copynumber: 10.7 Consensus size: 9
57593 ACCGATTCAG
*
57603 ACCGGTCAA
1 ACCGGTCGA
57612 ACCGGTTCGA
1 ACCGG-TCGA
*
57622 ACCGGTTGAA
1 ACCGGTCG-A
*
57632 ACCGGTCAA
1 ACCGGTCGA
57641 ACCGGTCAGA
1 ACCGGTC-GA
*
57651 ACCGGTTGAA
1 ACCGGTCG-A
*
57661 ACCGGTCAA
1 ACCGGTCGA
57670 ACCGGTCAGA
1 ACCGGTC-GA
*
57680 ACCGGTTGAAA
1 ACCGGTCG--A
*
57691 ACCGGTCAA
1 ACCGGTCGA
57700 ACCGGT
1 ACCGGT
57706 TTCCAGCAGC
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
9 32 0.43
10 36 0.48
11 7 0.09
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
ACCGGTCGA
Found at i:63971 original size:32 final size:31
Alignment explanation
Indices: 63935--64011 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
63925 CGGGGCCATG
*
63935 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
63967 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
63998 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
64012 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:64894 original size:7 final size:7
Alignment explanation
Indices: 64882--64933 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
64872 GTCAAAGAAA
64882 GTCAACG
1 GTCAACG
*
64889 GTCAACA
1 GTCAACG
64896 GTCAACG
1 GTCAACG
64903 GTCAACG
1 GTCAACG
64910 GTCAACG
1 GTCAACG
64917 GTCAACG
1 GTCAACG
*
64924 GCCAACG
1 GTCAACG
64931 GTC
1 GTC
64934 GGGTCGGGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (7 bp):
GTCAACG
Found at i:65009 original size:19 final size:19
Alignment explanation
Indices: 64968--65031 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
64958 GTCGGGTCAG
*
64968 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
64986 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
*
65006 ACCGGTTGAAACCGG-TCAGA
1 ACCGG-TCAAACCGGTTC-GA
65026 ACCGGT
1 ACCGGT
65032 TGAAAACCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:65019 original size:20 final size:20
Alignment explanation
Indices: 64994--65052 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
64984 CAGACCGGTC
64994 AAACCGGTTCGAACCGGTTG-
1 AAACCGG-TCGAACCGGTTGA
65014 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTC-GAACCGGTTGA
*
65035 AAACCGGTCAAACCGGTT
1 AAACCGGTCGAACCGGTT
65053 TCCAGCAGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 2 0.06
20 25 0.69
21 9 0.25
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (20 bp):
AAACCGGTCGAACCGGTTGA
Found at i:72040 original size:22 final size:22
Alignment explanation
Indices: 72012--72054 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
72002 TTCATGTGAG
72012 AAAGCTAAAGTCCTATTAATTA
1 AAAGCTAAAGTCCTATTAATTA
72034 AAAGCTAAAGTCCTATTAATT
1 AAAGCTAAAGTCCTATTAATT
72055 TAATCCAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (22 bp):
AAAGCTAAAGTCCTATTAATTA
Found at i:75704 original size:183 final size:182
Alignment explanation
Indices: 75362--75955 Score: 917
Period size: 183 Copynumber: 3.3 Consensus size: 182
75352 CATATAAAAA
* * * *
75362 TATGACAAAACCGGTAAAGCGCTACTGGATATGTTGAAAGTATCGATTA-GATTGAAATTAGTAT
1 TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGA-TACCATTGAAATAAGTAT
* * * * *
75426 --ATA-TTTATGGAATTTAAAATAGAAGCAGTAATAGTGCCAATAAAGTGTCGATACAAATAAAA
65 CGACACTTT-TGGAATTTAAAAGAGAAGTAGTAATAGCGCCTATAAAGTGTCGATACAAATAAAA
* *
75488 ATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACATGTTTCAT
129 ATGTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCAT
* * *
75542 TATGACAAAACCGGTAAATCGCTACCGGATATTTTGAATGTGTCGATACCATTGAAATAAGTATC
1 TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTATC
* **
75607 GACACTTTTGGAATTTAAAAGGGAAGTAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAA
66 GACACTTTTGGAATTTAAAAGAGAAGTAGTAATAGCGCCTATAAAGTGTCGATAC-AAATAAAAA
* *
75672 TGTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACACGTATCAT
130 TGTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCAT
* * *
75725 TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTCTTGATTCCATTGAAATAAGTATC
1 TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTATC
*
75790 GACACTTTTGGAATTTAAAAGAGAAGTAATAATAGCGCCTATAAAGTGTCGATACAAATAAAAAT
66 GACACTTTTGGAATTTAAAAGAGAAGTAGTAATAGCGCCTATAAAGTGTCGATACAAATAAAAAT
75855 GTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCAT
131 GTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCAT
*
75907 TATGACAAAACCGATAAAGCGCTACCGGATATGTTGAAAGTGTCGATAC
1 TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAC
75956 TTTAATAATT
Statistics
Matches: 374, Mismatches: 35, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
179 2 0.01
180 54 0.14
182 147 0.39
183 171 0.46
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTATC
GACACTTTTGGAATTTAAAAGAGAAGTAGTAATAGCGCCTATAAAGTGTCGATACAAATAAAAAT
GTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCAT
Found at i:77965 original size:21 final size:24
Alignment explanation
Indices: 77922--77972 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
77912 TTTTGTTTTT
77922 TTATATAAAATGATAGTATATTT-A
1 TTATATAAAATGATAG-ATATTTAA
77946 TTATATAAAATGATA-A-ATTTAA
1 TTATATAAAATGATAGATATTTAA
77968 TTATA
1 TTATA
77973 AATGCAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
24 15 0.58
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TTATATAAAATGATAGATATTTAA
Found at i:78262 original size:18 final size:18
Alignment explanation
Indices: 78241--78280 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
78231 GTGGATGTAC
78241 TGGAGGCAG-AGGAGGTAG
1 TGGAGGCAGTA-GAGGTAG
*
78259 TGGATGCAGTAGAGGTAG
1 TGGAGGCAGTAGAGGTAG
78277 TGGA
1 TGGA
78281 AGCAATGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.28, C:0.05, G:0.50, T:0.17
Consensus pattern (18 bp):
TGGAGGCAGTAGAGGTAG
Found at i:78293 original size:45 final size:45
Alignment explanation
Indices: 78208--78296 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
78198 ATTGGTAAGA
* * * * *
78208 AGGTAGAGGATGCAGTGGAAGAAGTGGATGTACTGGAGGCAGAGG
1 AGGTAGAGGATGCAGTAGAAGAAGTGGAAGCAATGAAGGCAGAGG
* * *
78253 AGGTAGTGGATGCAGTAGAGGTAGTGGAAGCAATGAAGGCAGAG
1 AGGTAGAGGATGCAGTAGAAGAAGTGGAAGCAATGAAGGCAGAG
78297 AAGAAGGAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.33, C:0.07, G:0.45, T:0.16
Consensus pattern (45 bp):
AGGTAGAGGATGCAGTAGAAGAAGTGGAAGCAATGAAGGCAGAGG
Found at i:78342 original size:15 final size:15
Alignment explanation
Indices: 78322--78352 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
78312 ATGGTCGTAT
78322 GGGATGAAGGTGAGG
1 GGGATGAAGGTGAGG
78337 GGGATGAAGGTGAGG
1 GGGATGAAGGTGAGG
78352 G
1 G
78353 AATACAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.61, T:0.13
Consensus pattern (15 bp):
GGGATGAAGGTGAGG
Found at i:78645 original size:14 final size:16
Alignment explanation
Indices: 78626--78658 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
78616 AAAAAGTTGG
78626 ATGAAGGG-GAAA-AA
1 ATGAAGGGTGAAATAA
78640 ATGAAGGGTGAAATAA
1 ATGAAGGGTGAAATAA
78656 ATG
1 ATG
78659 CGATGAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (16 bp):
ATGAAGGGTGAAATAA
Found at i:83939 original size:199 final size:198
Alignment explanation
Indices: 83585--84725 Score: 1497
Period size: 199 Copynumber: 5.7 Consensus size: 198
83575 ATAATTAAAA
* **
83585 GTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACAATGTAAGAG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * * *
83650 GTATAAATATATCAGTTTAATTAAAAAATAGATCAACATAATGTATCGATACATTTTAAATTTGT
66 GTAGAAATATA-CCGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
* * * * *
83715 GTCGATATTTTTTGTCCATAATGAATGCCCAACGAGATGCACACATAAAGTGTCGATACATTTAA
130 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAA
83780 AATT
195 AATT
* * *
83784 GTATCGATCCTAAAAACATCGCAATCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* ** * *
83849 ATTA-AAATATACCAGTTTTGTGAGAAAATAGGTCAATATAATGTATCGACACTTTTTAAATTTG
66 -GTAGAAATATACC-GTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTG
* * * *
83913 TGTCAATACTTTTGGTCCAGAATGAATGCCTAAACAAGGTGCACACATAAAGTGTCGATACATTT
129 TGTCGATACTTTTGGTCCAGAATGAATGCC-CAACGAGGTGCACGCATAAAGTGTCGATACA---
83978 TTTTAAAA--
190 -TTTAAAATT
* * *
83986 GTATCGACCCCAAAAACATCGAAACCGATCATTATAATGTAATAGGTAAATTTACAATGTAATCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * *
84051 GTAGAAATATACCGATTAATTAGAAAATAGGTAAACATAATGTATGGACACTTTTTAAATTTGTG
66 GTAGAAATATACCGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGTG
* *
84116 TCGATACTTGTT-GTCCATAATGAATCCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTA
131 TCGATACTT-TTGGTCCAGAATGAATGCCC-AACGAGGTGCACGCATAAAGTGTCGATACATTTA
*
84180 TTAAA-A
194 --AAATT
* **
84186 GTATCGATCCCAAAAACATCAAAACATATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* *
84251 GTAGAAATATACCGATTTAATTAGAAAATAGGT-AATCACAATGTATAGACAC--TTTAAATTTG
66 GTAGAAATATACCG-TTTAATTAGAAAATAGGTCAA-CATAATGTATCGACACTTTTTAAATTTG
* * * * *
84313 TTTCGATACTTTTTGTCCTGAATGAATGCCCAAACGAGGTGCACGTATAAAGTATCGATACATTT
129 TGTCGATACTTTTGGTCCAGAATGAATGCCC-AACGAGGTGCACGCATAAAGTGTCGATACATTT
84378 AAAATT
193 AAAATT
*
84384 GTATCGATCCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATATAACC
1 GTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACC
** * *
84449 GGTAGAAATATATTGGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTGTTAAGTTTG
65 GGTAGAAATATA-CCGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTG
* * *
84514 TGTCGATACTTTTGGTCCAAAATGAATGACCAACGAGGTGCACGCATAAAGTGTCGATATATTTA
129 TGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA
84579 AAATT
194 AAATT
* * * * *
84584 GTATCGATCCCAAAAACATCAAAACCGATAATTATAATATAATAAGTAAATTAACAATGTAACCA
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * *
84649 GTAGAAATATATCGGTTTAATAAAAAAATAGGTCAACATAATGTATCGACACTTGTTAAATTTGT
66 GTAGAAATATA-CCGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
*
84714 GTTGATACTTTT
130 GTCGATACTTTT
84726 TTTAAATTAC
Statistics
Matches: 832, Mismatches: 88, Indels: 44
0.86 0.09 0.05
Matches are distributed among these distances:
197 7 0.01
198 14 0.02
199 417 0.50
200 155 0.19
201 162 0.19
202 70 0.08
204 7 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (198 bp):
GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
GTAGAAATATACCGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGTG
TCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAAA
ATT
Found at i:87035 original size:23 final size:24
Alignment explanation
Indices: 87004--87049 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
86994 ATCAGCTTTA
*
87004 ATAATGCGCAACCTATTATGTTAC
1 ATAATGCGCAACCTAATATGTTAC
* *
87028 ATAA-GCGCTACTTAATATGTTA
1 ATAATGCGCAACCTAATATGTTA
87050 TTATGCTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (24 bp):
ATAATGCGCAACCTAATATGTTAC
Found at i:87310 original size:23 final size:23
Alignment explanation
Indices: 87284--87333 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
87274 TAAGTAATTA
**
87284 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
87307 ACCTATTACGTTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
87330 ACCT
1 ACCT
87334 GATATGTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:87320 original size:135 final size:135
Alignment explanation
Indices: 87013--87320 Score: 472
Period size: 135 Copynumber: 2.3 Consensus size: 135
87003 AATAATGCGC
* * * * * **
87013 AACCTATTATGTTACATAAGCGCTACTTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTA
1 AACCTATTTTATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATATTAACAGTAATTA
* *
87078 ACCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
66 ACCGGTTATGTTATCATTGGTAACATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAG
87143 TAAAT
131 TAAAT
* * *
87148 AACCTATTTTATTATATAAGCGCTACCTAAAATGTTATTGTGCTTGATAATATTAACGGTAATTA
1 AACCTATTTTATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATATTAACAGTAATTA
*
87213 ACCGGTTATGTTATCATTGGTAACATTTTATGCATTTACCTAATATGTTGTAATAACAAATTAAG
66 ACCGGTTATGTTATCATTGGTAACATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAG
*
87278 TAATT
131 TAAAT
* *
87283 AACCTATTTTATTATATAAGCGCTACCTATTACGTTAT
1 AACCTATTTTATTATATAAGCGCTACCTAATATGTTAT
87321 ATAAGCGCTA
Statistics
Matches: 156, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
135 156 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (135 bp):
AACCTATTTTATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATATTAACAGTAATTA
ACCGGTTATGTTATCATTGGTAACATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAG
TAAAT
Done.