Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002908.1 Hibiscus syriacus cultivar Beakdansim tig00006008_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: 54097
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Found at i:5670 original size:30 final size:30
Alignment explanation
Indices: 5634--5694 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
5624 TTTAAGGTCG
5634 GTAGCTTCTGTTGTCCTCGAATACAAACCA
1 GTAGCTTCTGTTGTCCTCGAATACAAACCA
*
5664 GTAGCTTCTTTTGTCCTCGAATACAAACCA
1 GTAGCTTCTGTTGTCCTCGAATACAAACCA
5694 G
1 G
5695 GAAAAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (30 bp):
GTAGCTTCTGTTGTCCTCGAATACAAACCA
Found at i:7170 original size:26 final size:26
Alignment explanation
Indices: 7121--7182 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
7111 TGTATGTATG
* *
7121 TATGTATGTAAATGACTACCTATATC
1 TATGTATGTAAATGACTAACTATATA
* *
7147 TATGTATGTAAATGGCTAATTATATA
1 TATGTATGTAAATGACTAACTATATA
*
7173 TATGGATGTA
1 TATGTATGTA
7183 TGTAGGAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.40
Consensus pattern (26 bp):
TATGTATGTAAATGACTAACTATATA
Found at i:16532 original size:15 final size:15
Alignment explanation
Indices: 16512--16584 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 15
16502 ATTATCGATG
16512 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
16527 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
* *
16542 -A--TAT-TATCAAT
1 AATTTTTATATAAAT
16553 GAATTTTTATATAAAT
1 -AATTTTTATATAAAT
*
16569 AATTTTTATCTAAAT
1 AATTTTTATATAAAT
16584 A
1 A
16585 TTAGAATTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 5 0.11
12 2 0.04
13 1 0.02
14 1 0.02
15 31 0.67
16 6 0.13
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:16543 original size:42 final size:42
Alignment explanation
Indices: 16497--16585 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
16487 ATAATAATGT
* *
16497 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCAATGAATTTTTATATAAATAATTTTTATCTA
16539 AATATATTATCAATGAATTTTTATATAAATAATTTTTATCTA
1 AATATATTATCAATGAATTTTTATATAAATAATTTTTATCTA
16581 AATAT
1 AATAT
16586 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (42 bp):
AATATATTATCAATGAATTTTTATATAAATAATTTTTATCTA
Found at i:17975 original size:21 final size:21
Alignment explanation
Indices: 17919--17976 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
17909 TCCAAGTTAC
*
17919 CCGCGACGGTCGCAATAGCGT
1 CCGCGACGGCCGCAATAGCGT
* *
17940 CCGCGACGACTGCAATAGCG-
1 CCGCGACGGCCGCAATAGCGT
*
17960 CCTGCTACGGCCGCAAT
1 CC-GCGACGGCCGCAAT
17977 CACGGTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.21, C:0.36, G:0.29, T:0.14
Consensus pattern (21 bp):
CCGCGACGGCCGCAATAGCGT
Found at i:18764 original size:18 final size:19
Alignment explanation
Indices: 18729--18765 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
18719 CACGGAATGT
18729 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
18749 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
18766 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:22747 original size:21 final size:21
Alignment explanation
Indices: 22721--22779 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
22711 ATTTACCGTG
*
22721 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGAGCT
* *
22742 ATTGCGGTCGTCGCGGAAGCT
1 ATTGCGGCCGTCGCGGGAGCT
*
22763 ATTGCAGCCGTCGCGGG
1 ATTGCGGCCGTCGCGGG
22780 TAACTCGGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.10, C:0.29, G:0.41, T:0.20
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGAGCT
Found at i:23674 original size:7 final size:7
Alignment explanation
Indices: 23662--23697 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
23652 AGCTTGTTTT
23662 TTTGTAA
1 TTTGTAA
23669 TTTGTAA
1 TTTGTAA
23676 TTTGTAA
1 TTTGTAA
23683 TTTGTAA
1 TTTGTAA
23690 TTTGTAA
1 TTTGTAA
23697 T
1 T
23698 CTATATACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (7 bp):
TTTGTAA
Found at i:24572 original size:19 final size:19
Alignment explanation
Indices: 24530--24572 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
24520 TAAGATAATA
24530 TTATTACTAAATTTACTTT
1 TTATTACTAAATTTACTTT
* *
24549 ATATTACTAAATTTAGTTT
1 TTATTACTAAATTTACTTT
24568 TTATT
1 TTATT
24573 TATTTTGACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATTACTAAATTTACTTT
Found at i:26818 original size:54 final size:54
Alignment explanation
Indices: 26753--26862 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
26743 TGCATGGAAG
26753 AGGAGAAATAGCATGCAAACCATCTCTAAGTCTTTTAACCATTTTATAATTTGT
1 AGGAGAAATAGCATGCAAACCATCTCTAAGTCTTTTAACCATTTTATAATTTGT
*
26807 AGGAGAAATAGCATGCAAATCATCTCTAAGTCTTTTAACCATTTTATAATTTGT
1 AGGAGAAATAGCATGCAAACCATCTCTAAGTCTTTTAACCATTTTATAATTTGT
26861 AG
1 AG
26863 AAGCATTGCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (54 bp):
AGGAGAAATAGCATGCAAACCATCTCTAAGTCTTTTAACCATTTTATAATTTGT
Found at i:27632 original size:13 final size:13
Alignment explanation
Indices: 27614--27650 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
27604 CATTTGTTAG
*
27614 AATAAAAAATAAA
1 AATAAAAAACAAA
*
27627 AATAAAAAACAAC
1 AATAAAAAACAAA
27640 AATAAAAAACA
1 AATAAAAAACA
27651 GCAATGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (13 bp):
AATAAAAAACAAA
Found at i:27655 original size:13 final size:13
Alignment explanation
Indices: 27627--27672 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
27617 AAAAAATAAA
*
27627 AATAAAAAACAAC
1 AATAAAAAACAGC
27640 AATAAAAAACAGC
1 AATAAAAAACAGC
* *
27653 AAT-GAAATCAG-
1 AATAAAAAACAGC
27664 AATAAAAAA
1 AATAAAAAA
27673 ACCAAATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
11 3 0.11
12 9 0.33
13 15 0.56
ACGTcount: A:0.72, C:0.11, G:0.07, T:0.11
Consensus pattern (13 bp):
AATAAAAAACAGC
Found at i:27692 original size:20 final size:20
Alignment explanation
Indices: 27667--27707 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
27657 AAATCAGAAT
27667 AAAAAAACCA-AATATAAAAC
1 AAAAAAA-CATAATATAAAAC
27687 AAAAAAACATAATATAAAAC
1 AAAAAAACATAATATAAAAC
27707 A
1 A
27708 TAAACATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAAAAACATAATATAAAAC
Found at i:27713 original size:26 final size:24
Alignment explanation
Indices: 27683--27742 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
27673 ACCAAATATA
*
27683 AAACAAAAAAACATAATATAAAACAT
1 AAACAAAAAAACAGAA-AT-AAACAT
* *
27709 AAACATAAAAACAGAAATCAACAT
1 AAACAAAAAAACAGAAATAAACAT
27733 AATACAAAAA
1 AA-ACAAAAA
27743 TAAGAGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.24
25 8 0.28
26 14 0.48
ACGTcount: A:0.72, C:0.13, G:0.02, T:0.13
Consensus pattern (24 bp):
AAACAAAAAAACAGAAATAAACAT
Found at i:27714 original size:18 final size:19
Alignment explanation
Indices: 27668--27716 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
27658 AATCAGAATA
27668 AAAAAACCA-AATATAAAAC
1 AAAAAA-CATAATATAAAAC
27687 AAAAAAACATAATATAAAAC
1 -AAAAAACATAATATAAAAC
*
27707 -ATAAACATAA
1 AAAAAACATAA
27717 AAACAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 9 0.33
19 2 0.07
20 16 0.59
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAAACATAATATAAAAC
Found at i:27941 original size:16 final size:15
Alignment explanation
Indices: 27925--28014 Score: 65
Period size: 16 Copynumber: 5.8 Consensus size: 15
27915 AAACAGAAAT
27925 ATAAAAAAAATAGAA
1 ATAAAAAAAATAGAA
** *
27940 TATAAACCAAATATAA
1 -ATAAAAAAAATAGAA
27956 ATAAATAAAAATAGAA
1 ATAAA-AAAAATAGAA
** *
27972 ATCGAAAAAACAGAA
1 ATAAAAAAAATAGAA
* *
27987 AT-AAAATACTAGAA
1 ATAAAAAAAATAGAA
28001 TATAAAACAAAATA
1 -ATAAAA-AAAATA
28015 TTTAAGAATA
Statistics
Matches: 55, Mismatches: 15, Indels: 7
0.71 0.19 0.09
Matches are distributed among these distances:
14 8 0.15
15 18 0.33
16 25 0.45
17 4 0.07
ACGTcount: A:0.70, C:0.07, G:0.06, T:0.18
Consensus pattern (15 bp):
ATAAAAAAAATAGAA
Found at i:28531 original size:103 final size:103
Alignment explanation
Indices: 28323--28826 Score: 577
Period size: 103 Copynumber: 5.0 Consensus size: 103
28313 AGAAAAGTTT
* * * *
28323 GAATGGTTTATTTAGGGATGAATAGATGAAGAATATGGGTTAGGGTTTGTGTTTTGATCGA-AAA
1 GAATGGGTTATTTAGGGAAGAATAGATGAAGAATAAGAGTTAGGGTTTGTGTTTTGATCGAGAAA
* * *
28387 ACAA-A-AATTGAAGGAAAATTTGTGTTTATTTTGGATT
66 A-AATAGAATCGAAGGAAGATTTGTGTTTATTTTGGATC
*
28424 GAATGGGTTATTTAGGGAATAATAGATGAAGAATAAGAGTTA-GGTTTGTGTTTTGATCGAGAAA
1 GAATGGGTTATTTAGGGAAGAATAGATGAAGAATAAGAGTTAGGGTTTGTGTTTTGATCGAGAAA
* *
28488 AAAAAGAACTCGAAGGAAGATTTGTGTTTGTTTTGGATC
66 AAATAGAA-TCGAAGGAAGATTTGTGTTTATTTTGGATC
* * * *
28527 GAATGAGTTATTTAGGGAAGAATAGATAAAGAAT-AGGGATTAGGGTTTGTGTTTTGATCAAGAA
1 GAATGGGTTATTTAGGGAAGAATAGATGAAGAATAAGAG-TTAGGGTTTGTGTTTTGATCGAGAA
28591 AAACATA-AATCGAAGGAAGATTTGTGTTTATTTTGGATC
65 AAA-ATAGAATCGAAGGAAGATTTGTGTTTATTTTGGATC
* * * * *
28630 GAATGGGTTATTTATGGAAGAATAAATGAAGAATGAGATTTAGGGTTTATGTTTTGATCGAG-AA
1 GAATGGGTTATTTAGGGAAGAATAGATGAAGAATAAGAGTTAGGGTTTGTGTTTTGATCGAGAAA
28694 AAATAGAAATCGAAGGAATG-TTTGTGTTTATTTTGGATC
66 AAATAG-AATCGAAGGAA-GATTTGTGTTTATTTTGGATC
* * *
28733 AAAT-GGTTATTTA--G--G-A-A-A-GAA-CA-AAG-GTTAGTGTTTGTGTTTTGATC--GAAA
1 GAATGGGTTATTTAGGGAAGAATAGATGAAGAATAAGAGTTAGGGTTTGTGTTTTGATCGAGAAA
28784 AAATAGAAATCGAAGGAATG-TTTGTGTTTATTTTGGATC
66 AAATAG-AATCGAAGGAA-GATTTGTGTTTATTTTGGATC
28823 GAAT
1 GAAT
28827 ACTTTTGATG
Statistics
Matches: 360, Mismatches: 31, Indels: 35
0.85 0.07 0.08
Matches are distributed among these distances:
89 1 0.00
90 44 0.12
91 18 0.05
92 2 0.01
93 1 0.00
94 3 0.01
95 1 0.00
96 1 0.00
97 1 0.00
98 1 0.00
100 21 0.06
101 45 0.12
102 18 0.05
103 173 0.48
104 28 0.08
105 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (103 bp):
GAATGGGTTATTTAGGGAAGAATAGATGAAGAATAAGAGTTAGGGTTTGTGTTTTGATCGAGAAA
AAATAGAATCGAAGGAAGATTTGTGTTTATTTTGGATC
Found at i:28709 original size:206 final size:201
Alignment explanation
Indices: 28324--28826 Score: 638
Period size: 206 Copynumber: 2.5 Consensus size: 201
28314 GAAAAGTTTG
28324 AATGGTTTATTTAGGGATGAATAGATGAAGAATATGGGTTAGGGTTTGTGTTTTGATC-GAAAAA
1 AATGG-TTATTTAGGGA-GAATAGAT-AAGAATA-GGGTTAGGGTTTGTGTTTTGATCAGAAAAA
* * * * *
28388 CAAAAATTGAAGGAAAATTTGTGTTTATTTTGGATTGAATGGGTTATTTAGGGAATAATAGATGA
62 CAAAAATCGAAGGAAGATTTGTGTTTATTTTGGATCGAATGGGTTATTTAGGGAAGAATAAATGA
* *
28453 AGAATAAGAGTTAGGTTTGTGTTTTGATCGAGAAAAAAAAGAACTCGAAGGAA-GATTTGTGTTT
127 AGAATAAGAGTTAGGTTTATGTTTTGATCGAGAAAAAAAAGAAATCGAAGGAATG-TTTGTGTTT
* *
28517 GTTTTGGATCG
191 ATTTTGGATCA
28528 AATGAGTTATTTAGGGAAGAATAGATAAAGAATAGGGATTAGGGTTTGTGTTTTGATCAAGAAAA
1 AATG-GTTATTTAGGG-AGAATAGAT-AAGAATAGGG-TTAGGGTTTGTGTTTTGATC-AGAAAA
* *
28593 ACATAAATCGAAGGAAGATTTGTGTTTATTTTGGATCGAATGGGTTATTTATGGAAGAATAAATG
61 ACAAAAATCGAAGGAAGATTTGTGTTTATTTTGGATCGAATGGGTTATTTAGGGAAGAATAAATG
* * *
28658 AAGAATGAGATTTAGGGTTTATGTTTTGATCGAG-AAAAATAGAAATCGAAGGAATGTTTGTGTT
126 AAGAATAAGAGTTA-GGTTTATGTTTTGATCGAGAAAAAAAAGAAATCGAAGGAATGTTTGTGTT
28722 TATTTTGGATCA
190 TATTTTGGATCA
* *
28734 AATGGTTATTTA--G-GAA-AG--AACAA-A-GGTTAGTGTTTGTGTTTTGATC-GAAAAA-ATA
1 AATGGTTATTTAGGGAGAATAGATAAGAATAGGGTTAGGGTTTGTGTTTTGATCAGAAAAACA-A
28789 GAAATCGAAGGAATG-TTTGTGTTTATTTTGGATCGAAT
65 -AAATCGAAGGAA-GATTTGTGTTTATTTTGGATCGAAT
28827 ACTTTTGATG
Statistics
Matches: 271, Mismatches: 18, Indels: 31
0.85 0.06 0.10
Matches are distributed among these distances:
191 1 0.00
192 6 0.02
193 35 0.13
194 20 0.07
195 2 0.01
196 1 0.00
197 4 0.01
200 2 0.01
201 3 0.01
203 4 0.01
204 49 0.18
205 10 0.04
206 115 0.42
207 19 0.07
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (201 bp):
AATGGTTATTTAGGGAGAATAGATAAGAATAGGGTTAGGGTTTGTGTTTTGATCAGAAAAACAAA
AATCGAAGGAAGATTTGTGTTTATTTTGGATCGAATGGGTTATTTAGGGAAGAATAAATGAAGAA
TAAGAGTTAGGTTTATGTTTTGATCGAGAAAAAAAAGAAATCGAAGGAATGTTTGTGTTTATTTT
GGATCA
Found at i:29400 original size:14 final size:14
Alignment explanation
Indices: 29381--29450 Score: 70
Period size: 14 Copynumber: 4.8 Consensus size: 14
29371 ATTATAGTCT
*
29381 TATAGTTTGTATAA
1 TATAGTTTATATAA
29395 TATAGTTTATAT-A
1 TATAGTTTATATAA
* *
29408 CACAGTTTATAGTATATA
1 TATAG-TT-TA-TATA-A
29426 TATAGTTTATATAA
1 TATAGTTTATATAA
29440 TATAGTTTATA
1 TATAGTTTATA
29451 GTTTATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
13 4 0.09
14 25 0.54
15 6 0.13
16 5 0.11
17 2 0.04
18 4 0.09
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.49
Consensus pattern (14 bp):
TATAGTTTATATAA
Found at i:29452 original size:32 final size:31
Alignment explanation
Indices: 29389--29460 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
29379 CTTATAGTTT
29389 GTATA-ATATAGTTTATATACACAGTTTATA
1 GTATATATATAGTTTATATACACAGTTTATA
* *
29419 GTATATATATAGTTTATATAATATAGTTTATA
1 GTATATATATAGTTTATAT-ACACAGTTTATA
*
29451 GTTTATATAT
1 GTATATATAT
29461 GTAAGCACCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 5 0.14
31 13 0.35
32 19 0.51
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.49
Consensus pattern (31 bp):
GTATATATATAGTTTATATACACAGTTTATA
Found at i:29460 original size:18 final size:18
Alignment explanation
Indices: 29395--29460 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
29385 GTTTGTATAA
*
29395 TATAGTTTATATACACAGTT
1 TATAGTTTATAT--ATAGTT
*
29415 TATAGTATATATATAGTT
1 TATAGTTTATATATAGTT
29433 TATA---TA-ATATAGTT
1 TATAGTTTATATATAGTT
29447 TATAGTTTATATAT
1 TATAGTTTATATAT
29461 GTAAGCACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 12 0.30
15 2 0.05
17 2 0.05
18 13 0.32
20 11 0.28
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (18 bp):
TATAGTTTATATATAGTT
Found at i:31584 original size:7 final size:7
Alignment explanation
Indices: 31574--31756 Score: 81
Period size: 7 Copynumber: 27.6 Consensus size: 7
31564 TATAGTTTAT
31574 TATAGTA
1 TATAGTA
31581 TATAGTA
1 TATAGTA
*
31588 TATATTA
1 TATAGTA
* **
31595 TTTAGGG
1 TATAGTA
*
31602 TTTAGTA
1 TATAGTA
31609 TATA--A
1 TATAGTA
*
31614 TTTA-TA
1 TATAGTA
31620 TATAGTA
1 TATAGTA
31627 TATAGT-
1 TATAGTA
31633 T-TA-TA
1 TATAGTA
*
31638 TATATTA
1 TATAGTA
*
31645 TATAAATA
1 TAT-AGTA
*
31653 AACTA-TA
1 TA-TAGTA
31660 TATAGT-
1 TATAGTA
31666 T-TA-TA
1 TATAGTA
31671 TATAGTA
1 TATAGTA
*
31678 TAAAGTA
1 TATAGTA
*
31685 TATAGTT
1 TATAGTA
31692 TATA-TA
1 TATAGTA
*
31698 TATAGTT
1 TATAGTA
31705 TATATGTA
1 TATA-GTA
31713 -A-AGTA
1 TATAGTA
31718 TATAGAATA
1 TATAG--TA
* *
31727 TAAAGTT
1 TATAGTA
*
31734 TAT-CTA
1 TATAGTA
31740 TATAGTA
1 TATAGTA
31747 TATA-TA
1 TATAGTA
31753 TATA
1 TATA
31757 AAGTTTATAT
Statistics
Matches: 133, Mismatches: 25, Indels: 37
0.68 0.13 0.19
Matches are distributed among these distances:
4 2 0.02
5 13 0.10
6 29 0.22
7 75 0.56
8 7 0.05
9 7 0.05
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (7 bp):
TATAGTA
Found at i:31708 original size:11 final size:11
Alignment explanation
Indices: 31540--31916 Score: 112
Period size: 11 Copynumber: 35.4 Consensus size: 11
31530 GATTATGGCA
*
31540 ATATAGATTAT
1 ATATAGTTTAT
*
31551 ATATAGTATAAT
1 ATATAGT-TTAT
*
31563 TTATAGTTTAT
1 ATATAGTTTAT
*
31574 -TATAGTATAT
1 ATATAGTTTAT
31584 AGTATA-TATTAT
1 A-TATAGT-TTAT
* **
31596 TTAGGGTTTAGT
1 ATATAGTTTA-T
*
31608 ATATAATTTAT
1 ATATAGTTTAT
31619 ATATAG----T
1 ATATAGTTTAT
31626 ATATAGTTTAT
1 ATATAGTTTAT
31637 ATATA-TTATAT
1 ATATAGTT-TAT
* ***
31648 AAATAAACTAT
1 ATATAGTTTAT
31659 ATATAGTTTAT
1 ATATAGTTTAT
*
31670 ATATAGTATAAAGT
1 ATATAGT-T-TA-T
31684 ATATAGTTTAT
1 ATATAGTTTAT
31695 ATATA-TAGTT-T
1 ATATAGT--TTAT
**
31706 ATAT-GTAAAGT
1 ATATAGTTTA-T
*
31717 ATATAG--AAT
1 ATATAGTTTAT
*
31726 ATAAAGTTTATCT
1 ATATAGTTTA--T
31739 ATATAGTATATAT
1 ATATAGT-T-TAT
31752 ATATAAAGTTTAT
1 ATAT--AGTTTAT
31765 ATA-A-TTTAT
1 ATATAGTTTAT
**
31774 -TA-A-TAAAT
1 ATATAGTTTAT
31782 ATATAGTTTAT
1 ATATAGTTTAT
*
31793 ATATA-TAGT-T
1 ATATAGT-TTAT
*
31803 ATATGGTTTAT
1 ATATAGTTTAT
31814 ATATA---TAT
1 ATATAGTTTAT
*
31822 ATAT--TTCAT
1 ATATAGTTTAT
*
31831 ATATAGTTCAT
1 ATATAGTTTAT
* *
31842 ACATAGTATAT
1 ATATAGTTTAT
* **
31853 AAATA-TAAAT
1 ATATAGTTTAT
31863 ATATAGTTTAT
1 ATATAGTTTAT
31874 ATATA---TAT
1 ATATAGTTTAT
*
31882 ATATA-TAT-T
1 ATATAGTTTAT
31891 ATATAGTTTAT
1 ATATAGTTTAT
*
31902 ATATAGTTCAT
1 ATATAGTTTAT
31913 ATAT
1 ATAT
31917 TATATACTGT
Statistics
Matches: 275, Mismatches: 47, Indels: 88
0.67 0.11 0.21
Matches are distributed among these distances:
7 7 0.03
8 21 0.08
9 25 0.09
10 34 0.12
11 124 0.45
12 29 0.11
13 20 0.07
14 10 0.04
15 5 0.02
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (11 bp):
ATATAGTTTAT
Found at i:31859 original size:60 final size:60
Alignment explanation
Indices: 31784--31908 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
31774 TAATAAATAT
* * ** * *
31784 ATAGTTTATATATATAGTTATATGGTTTATATATATATATATTTCA-TATATAGTTCATAC
1 ATAGTATATAAATATAAATATATAGTTTATATATATATATATAT-ATTATATAGTTCATAC
* *
31844 ATAGTATATAAATATAAATATATAGTTTATATATATATATATATATTATATAGTTTATAT
1 ATAGTATATAAATATAAATATATAGTTTATATATATATATATATATTATATAGTTCATAC
31904 ATAGT
1 ATAGT
31909 TCATATATTA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (60 bp):
ATAGTATATAAATATAAATATATAGTTTATATATATATATATATATTATATAGTTCATAC
Found at i:31897 original size:49 final size:50
Alignment explanation
Indices: 31607--31902 Score: 125
Period size: 51 Copynumber: 5.8 Consensus size: 50
31597 TAGGGTTTAG
* * *
31607 TATATAATTTATATATAGTATATAGTTTA--TATATATTATATAAATA-AACTA
1 TATATAGTTTATATATA-TATATA-TATAGTTATATAGTATATAAATATAA--A
* * *
31658 TATATAGTTTATATATAGTATAAAGTATATAGTT-TATA-TATAT-AGTTTATA
1 TATATAGTTTATATATA-TAT--A-TATATAGTTATATAGTATATAAATATAAA
* * * * * * *
31709 TGTAAAGTATATAGA-ATATAAAGTTTA-TCTATATAGTATATATATATAAA
1 TATATAGTTTATATATATATATA-TATAGT-TATATAGTATATAAATATAAA
* * ** **
31759 GTTTATATAATTTAT-TA-ATAAATATATAGTT-TATA-TATATAGTTATATGG
1 ---TATATAGTTTATATATATATATATATAGTTATATAGTATATAAATATA-AA
* * *
31809 TTTATA-TATATATATATTTCATATATAGTTCATACATAGTATATAAATATAAA
1 TATATAGTTTATATATATAT-ATATATAGTT-AT--ATAGTATATAAATATAAA
*
31862 TATATAGTTTATATATATATATATATA-TTATATAGTTTATA
1 TATATAGTTTATATATATATATATATAGTTATATAGTATATA
31903 TATAGTTCAT
Statistics
Matches: 181, Mismatches: 39, Indels: 52
0.67 0.14 0.19
Matches are distributed among these distances:
46 6 0.03
47 12 0.07
48 6 0.03
49 37 0.20
50 9 0.05
51 39 0.22
52 11 0.06
53 33 0.18
54 27 0.15
55 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (50 bp):
TATATAGTTTATATATATATATATATAGTTATATAGTATATAAATATAAA
Found at i:31922 original size:2 final size:2
Alignment explanation
Indices: 31607--31906 Score: 105
Period size: 2 Copynumber: 144.0 Consensus size: 2
31597 TAGGGTTTAG
* *
31607 TA TA TA -A TT TA TA TA TA GTA TA TA GTT TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
31649 AA TA AA CTA TA TA TA GTT TA TA TA TA GTA TA AA GTA TA TA GTT TA
1 TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA -TA TA
* * * * * *
31694 TA TA TA TA GTT TA TA TG TA AA GTA TA TA GA -A TA TA AA GTT TA
1 TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* * * *
31736 TC TA TA TA GTA TA TA TA TA TA AA GTT TA TA TA -A TT TA T- TA -A
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
31777 TA AA TA TA TA GTT TA TA TA TA TA GT- TA TA TGG TT TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA T-A TA TA TA TA TA
* * * *
31819 TA TA TA TT TCA TA TA TA GT- TCA TA CA TA GTA TA TA AA TA TA AA
1 TA TA TA TA T-A TA TA TA -TA T-A TA TA TA -TA TA TA TA TA TA TA
* *
31862 TA TA TA GTT TA TA TA TA TA TA TA TA TA T- TA TA TA GTT TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
31905 TA
1 TA
31907 GTTCATATAT
Statistics
Matches: 216, Mismatches: 52, Indels: 60
0.66 0.16 0.18
Matches are distributed among these distances:
1 9 0.04
2 184 0.85
3 23 0.11
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (2 bp):
TA
Found at i:32252 original size:65 final size:65
Alignment explanation
Indices: 32134--32255 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 65
32124 ATGCACAACT
* * *
32134 ATGCATCGATGCACTCTTGAATTTATTAAAACATCGAATGCATTTTATGTACCGATGAACAGGCC
1 ATGCATCGATGCACTCATGAATTTATTAAAACATCGAATGCATATTATATACCGATGAACAGGCC
** * *
32199 ATGCATCGATGCACTCATGGCTCTT-TTGAAACATCGAATGTA-ATTAGTATACCGATG
1 ATGCATCGATGCACTCATGAAT-TTATTAAAACATCGAATGCATATTA-TATACCGATG
32256 CACTAAGTCT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
64 3 0.06
65 43 0.90
66 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (65 bp):
ATGCATCGATGCACTCATGAATTTATTAAAACATCGAATGCATATTATATACCGATGAACAGGCC
Found at i:32430 original size:13 final size:13
Alignment explanation
Indices: 32408--32455 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
32398 TATTTCAAAT
*
32408 TAAATTATAAAAA
1 TAAATGATAAAAA
*
32421 TAAATGATAAATA
1 TAAATGATAAAAA
*
32434 TAAATAATAAAATTA
1 TAAATGATAAAA--A
32449 TAAATGA
1 TAAATGA
32456 ATTTAGAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 21 0.75
15 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (13 bp):
TAAATGATAAAAA
Found at i:32690 original size:16 final size:17
Alignment explanation
Indices: 32661--32702 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
32651 TAAACCTGAA
32661 TTTTAGACCAAAAATGT
1 TTTTAGACCAAAAATGT
32678 TTTTAGACCAAAAATGT
1 TTTTAGACCAAAAATGT
32695 TTTTAGAC
1 TTTTAGAC
32703 AGAGGTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAGACCAAAAATGT
Found at i:34105 original size:27 final size:27
Alignment explanation
Indices: 34074--34204 Score: 136
Period size: 27 Copynumber: 4.4 Consensus size: 27
34064 TTTGTTCGGG
34074 TCGGGTCGGGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
*
34101 TCGGGTCGAGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
* *
34128 TCGGGTCGAGTCGGGTTTTTTAATTGTAATAT
1 TC--G--G-GTCGGGTTTTTTAAGTGTGATAT
34160 TCGGGTTGGGTCGGGTTTTTTTAAGTGTGATAT
1 TC-----GGGTCGGG-TTTTTTAAGTGTGATAT
34193 TCGGGTCGGGTT
1 TCGGGTCGGGTT
34205 CAGGTTTAGG
Statistics
Matches: 87, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
27 30 0.34
28 8 0.09
29 1 0.01
31 1 0.01
32 28 0.32
33 18 0.21
35 1 0.01
ACGTcount: A:0.15, C:0.08, G:0.34, T:0.44
Consensus pattern (27 bp):
TCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:34141 original size:59 final size:61
Alignment explanation
Indices: 34068--34200 Score: 180
Period size: 59 Copynumber: 2.1 Consensus size: 61
34058 CTTTATTTTG
* *
34068 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTC-GGGTCGAG-TTTTTTAAGTGTGATA
1 TTCGGGTCGAGTCGGGTTTTTTAAGTGTAATATTCGGGGTCGAGTTTTTTTAAGTGTGATA
* *
34127 TTCGGGTCGAGTCGGGTTTTTTAATTGTAATATTCGGGTTGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGAGTCGGGTTTTTTAAGTGTAATATTC--G--GGGTCGAGTTTTTTTAAGTGTGATA
34192 TTCGGGTCG
1 TTCGGGTCG
34201 GGTTCAGGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
59 32 0.50
64 7 0.11
65 25 0.39
ACGTcount: A:0.14, C:0.09, G:0.34, T:0.43
Consensus pattern (61 bp):
TTCGGGTCGAGTCGGGTTTTTTAAGTGTAATATTCGGGGTCGAGTTTTTTTAAGTGTGATA
Found at i:34160 original size:32 final size:32
Alignment explanation
Indices: 34068--34200 Score: 177
Period size: 32 Copynumber: 4.3 Consensus size: 32
34058 CTTTATTTTG
*
34068 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGAGTCGGGTTTTTTAAGTGTGATA
34100 TTCGGGTCGA-----GTTTTTTAAGTGTGATA
1 TTCGGGTCGAGTCGGGTTTTTTAAGTGTGATA
* *
34127 TTCGGGTCGAGTCGGGTTTTTTAATTGTAATA
1 TTCGGGTCGAGTCGGGTTTTTTAAGTGTGATA
* *
34159 TTCGGGTTGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGAGTCGGG-TTTTTTAAGTGTGATA
34192 TTCGGGTCG
1 TTCGGGTCG
34201 GGTTCAGGTT
Statistics
Matches: 87, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
27 27 0.31
32 38 0.44
33 22 0.25
ACGTcount: A:0.14, C:0.09, G:0.34, T:0.43
Consensus pattern (32 bp):
TTCGGGTCGAGTCGGGTTTTTTAAGTGTGATA
Found at i:35010 original size:2 final size:2
Alignment explanation
Indices: 35003--35028 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34993 AATATCAATA
35003 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
35029 TAAATATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37670 original size:17 final size:18
Alignment explanation
Indices: 37637--37670 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
37627 CCGCTACTAG
37637 TGAACCGGTTAGAACCGT
1 TGAACCGGTTAGAACCGT
*
37655 TGAACC-GTTCGAACCG
1 TGAACCGGTTAGAACCG
37671 GATCGGCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (18 bp):
TGAACCGGTTAGAACCGT
Found at i:44590 original size:38 final size:38
Alignment explanation
Indices: 44548--44632 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
44538 ATAGGTCCTA
* * *
44548 CGGGACACATATTACATCCTTCAGGATGACAGGTCTTT
1 CGGGACACAGATGACATCCTTCAGGATGACAGGTCATT
* *
44586 CGGGACACAGATGACATCCTTCGGGATGATAGGTCATT
1 CGGGACACAGATGACATCCTTCAGGATGACAGGTCATT
44624 CGGGACACA
1 CGGGACACA
44633 ATTTATACGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.24
Consensus pattern (38 bp):
CGGGACACAGATGACATCCTTCAGGATGACAGGTCATT
Found at i:46620 original size:3 final size:3
Alignment explanation
Indices: 46612--46643 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
46602 TCATTGGAAT
46612 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
46644 TTGATTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:48026 original size:12 final size:12
Alignment explanation
Indices: 48009--48033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47999 GATAATTTCC
48009 AGATGACATCTA
1 AGATGACATCTA
48021 AGATGACATCTA
1 AGATGACATCTA
48033 A
1 A
48034 TTGACAGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (12 bp):
AGATGACATCTA
Found at i:50870 original size:38 final size:36
Alignment explanation
Indices: 50787--50883 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 36
50777 TATAAGACAT
*
50787 ATGATAGGTCCTACGGGACACAAATACATCCTTCGG
1 ATGATAGGTCCTTCGGGACACAAATACATCCTTCGG
* * * *
50823 ATGACAGGTCTTTCGAGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAAAT-ACATCCTTC-GG
50861 ATGATAGGTCCTTCGGGACACAA
1 ATGATAGGTCCTTCGGGACACAA
50884 TTTATACGAG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 20 0.40
37 9 0.18
38 21 0.42
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (36 bp):
ATGATAGGTCCTTCGGGACACAAATACATCCTTCGG
Found at i:52608 original size:22 final size:22
Alignment explanation
Indices: 52582--52662 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 22
52572 ACCTGGATAG
52582 GGTATCAGTACCCTAAATTAGA
1 GGTATCAGTACCCTAAATTAGA
**
52604 GGTATC-GATACCCT-AA-GGGTA
1 GGTATCAG-TACCCTAAATTAG-A
*
52625 -GTACTCAGTACCCTAACTTAGA
1 GGTA-TCAGTACCCTAAATTAGA
* *
52647 GGTATCGGTGCCCTAA
1 GGTATCAGTACCCTAA
52663 GGGTAGTACC
Statistics
Matches: 45, Mismatches: 7, Indels: 14
0.68 0.11 0.21
Matches are distributed among these distances:
20 4 0.09
21 12 0.27
22 25 0.56
23 4 0.09
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
GGTATCAGTACCCTAAATTAGA
Found at i:52639 original size:43 final size:43
Alignment explanation
Indices: 52586--52671 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
52576 GGATAGGGTA
52586 TCAGTACCCTAAATTAGAGGTATCGATACCCTAAGGGTAGTAC
1 TCAGTACCCTAAATTAGAGGTATCGATACCCTAAGGGTAGTAC
* * *
52629 TCAGTACCCTAACTTAGAGGTATCGGTGCCCTAAGGGTAGTAC
1 TCAGTACCCTAAATTAGAGGTATCGATACCCTAAGGGTAGTAC
52672 CGATACTACT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (43 bp):
TCAGTACCCTAAATTAGAGGTATCGATACCCTAAGGGTAGTAC
Done.