Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001446.1 Hibiscus syriacus cultivar Beakdansim tig00002796_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: 69252
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3513 original size:14 final size:14
Alignment explanation
Indices: 3494--3525 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3484 GTAGCAGATC
*
3494 GAAATCCAGAACGG
1 GAAATCAAGAACGG
3508 GAAATCAAGAACGG
1 GAAATCAAGAACGG
3522 GAAA
1 GAAA
3526 GAAAGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.28, T:0.06
Consensus pattern (14 bp):
GAAATCAAGAACGG
Found at i:6554 original size:31 final size:31
Alignment explanation
Indices: 6516--6733 Score: 174
Period size: 31 Copynumber: 7.0 Consensus size: 31
6506 GTCGAAGAAT
**
6516 TACCTATGTCTTTCGGGACATATTAACAGTA
1 TACCTATGTCTTTCGGGACATATGGACAGTA
* * *
6547 TACCTATGT-TCTACGGAACATATGGACAGAA
1 TACCTATGTCT-TTCGGGACATATGGACAGTA
6578 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 -TACCTATGTCTTTCGGGACATATGGACAGTA
* * * **
6610 TACCTATGT-TCTACGGAACACATGGACAAAA
1 TACCTATGTCT-TTCGGGACATATGGACAGTA
**
6641 TTACCTATGTCTTTCGGGACATATGTTCAGTA
1 -TACCTATGTCTTTCGGGACATATGGACAGTA
*** * * *
6673 TACCTATGT-TCTAAAGAACATATGGACAATT
1 TACCTATGTCT-TTCGGGACATATGGACAGTA
* *
6704 TACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATGTCT-TTCGGGACATATGGACAGT
6734 TGTCGAGGTT
Statistics
Matches: 145, Mismatches: 35, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
30 3 0.02
31 92 0.63
32 48 0.33
33 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTCTTTCGGGACATATGGACAGTA
Found at i:6589 original size:63 final size:62
Alignment explanation
Indices: 6511--6722 Score: 302
Period size: 63 Copynumber: 3.4 Consensus size: 62
6501 CAAGAGTCGA
6511 AGAATTACCTATGTCTTTCGGGACATATTAACAGTATACCTATGTTCTACGGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATT-ACAGTATACCTATGTTCTACGGAACATATGGAC
* *
6574 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACACATGGAC
1 AGAATTACCTATGTCTTTCGGGACATAT-TACAGTATACCTATGTTCTACGGAACATATGGAC
* * **
6637 AAAATTACCTATGTCTTTCGGGACATATGTTCAGTATACCTATGTTCTAAAGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATAT-TACAGTATACCTATGTTCTACGGAACATATGGAC
* *
6700 A-ATTTACCTAGGT-TCTTCGGGAC
1 AGAATTACCTATGTCT-TTCGGGAC
6723 CTATGGACAG
Statistics
Matches: 137, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
61 1 0.01
62 18 0.13
63 118 0.86
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (62 bp):
AGAATTACCTATGTCTTTCGGGACATATTACAGTATACCTATGTTCTACGGAACATATGGAC
Found at i:7053 original size:30 final size:32
Alignment explanation
Indices: 6990--7054 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
6980 ATATGAGTAC
* *
6990 TGATAAGTATTGTAATGGTATATGCTTTTATA
1 TGATAAGTATTGTAATGGTATATGCATTAATA
* *
7022 TGAT-AGTATT-TAATTGTTTATGCATTAATA
1 TGATAAGTATTGTAATGGTATATGCATTAATA
7052 TGA
1 TGA
7055 GTAGAGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 19 0.66
31 6 0.21
32 4 0.14
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (32 bp):
TGATAAGTATTGTAATGGTATATGCATTAATA
Found at i:7477 original size:21 final size:21
Alignment explanation
Indices: 7451--7509 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
7441 GAATTTTTGG
7451 TGCATCGATGCACTGTAACAA
1 TGCATCGATGCACTGTAACAA
*
7472 TGCATCGATGTACTGTAACAA
1 TGCATCGATGCACTGTAACAA
*
7493 TGCATCGATGCATTGTA
1 TGCATCGATGCACTGTA
7510 TCACTGTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACTGTAACAA
Found at i:11784 original size:60 final size:60
Alignment explanation
Indices: 11706--11818 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
11696 AAATGGTTCT
*
11706 CGACTATAGGATGATGCTTTGTTGAGT-CTCTCAACTATTAAAAGTTACAAAATTATCTCA
1 CGACTATAGGATGATGCTTTGTTGAATCCTC-CAACTATTAAAAGTTACAAAATTATCTCA
11766 CGACTATAGGAT-ATTGCTTTGTTGAATCCTCCAACTATTAAAAGTTACAAAAT
1 CGACTATAGGATGA-TGCTTTGTTGAATCCTCCAACTATTAAAAGTTACAAAAT
11819 AGTCACCTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
59 1 0.02
60 46 0.92
61 3 0.06
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (60 bp):
CGACTATAGGATGATGCTTTGTTGAATCCTCCAACTATTAAAAGTTACAAAATTATCTCA
Found at i:11999 original size:28 final size:28
Alignment explanation
Indices: 11953--12008 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
11943 ACCACCGTTG
* **
11953 CTTTCAAGCAGTAAATTGATTGTATAAT
1 CTTTCAAGCACTAAATTGAAAGTATAAT
* *
11981 CTTTCAAGCACTGACTTGAAAGTATAAT
1 CTTTCAAGCACTAAATTGAAAGTATAAT
12009 GTAAACGGAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (28 bp):
CTTTCAAGCACTAAATTGAAAGTATAAT
Found at i:12276 original size:60 final size:59
Alignment explanation
Indices: 12149--12264 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 59
12139 AATAGTCGGT
* *
12149 AACCATTTTGTACCTTTTAATAGTTGGAAGACTCAACAAAGTAGCATCCTGTAGTCAAAG
1 AACCATTTTGTAACTTTTAATAGTTGGAAGACTCAACAAAGTAG-ATCCTATAGTCAAAG
* *
12209 AATCATTTTGTAACTTTTAATA-TTCGGATGACTCAACAAAGTAG-TGCCTATAGTCA
1 AACCATTTTGTAACTTTTAATAGTT-GGAAGACTCAACAAAGTAGAT-CCTATAGTCA
12265 GGGGACCCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
58 1 0.02
59 11 0.22
60 38 0.76
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (59 bp):
AACCATTTTGTAACTTTTAATAGTTGGAAGACTCAACAAAGTAGATCCTATAGTCAAAG
Found at i:15626 original size:32 final size:33
Alignment explanation
Indices: 15584--15645 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
15574 GAGTAGTTGT
* *
15584 TTCATGGACAAGAGA-ATCAAGAAAGATATACA
1 TTCATAGACAAGAAAGATCAAGAAAGATATACA
*
15616 TTCATAGACAAGAAAGATCAAGTAAGATAT
1 TTCATAGACAAGAAAGATCAAGAAAGATAT
15646 TATGGCATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (33 bp):
TTCATAGACAAGAAAGATCAAGAAAGATATACA
Found at i:17418 original size:2 final size:2
Alignment explanation
Indices: 17411--17461 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
17401 TGATATTACC
* **
17411 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA GG TA -A 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
17452 TA TA TA TA TA
1 TA TA TA TA TA
17462 CTTTTATTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:17744 original size:4 final size:4
Alignment explanation
Indices: 17730--17831 Score: 52
Period size: 4 Copynumber: 26.0 Consensus size: 4
17720 ATTTTTTCCC
* * *
17730 TTAT CTTAT TTAT TTAG TTAT CTAT TTAT TTA- TT-T TTCT TTA- TT-T
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * **
17775 TTCT TTAT CT-T TGAT TTAT TTACT CATAT TTGT TTAT TTAT TTAT CCAT
1 TTAT TTAT TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT
17824 TTAT TTAT
1 TTAT TTAT
17832 GTATATTGTC
Statistics
Matches: 72, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
3 9 0.12
4 55 0.76
5 6 0.08
6 2 0.03
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:17773 original size:10 final size:10
Alignment explanation
Indices: 17758--17782 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17748 TATCTATTTA
17758 TTTATTTTTC
1 TTTATTTTTC
17768 TTTATTTTTC
1 TTTATTTTTC
17778 TTTAT
1 TTTAT
17783 CTTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:28362 original size:19 final size:21
Alignment explanation
Indices: 28338--28377 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28328 CCTAAATTGA
28338 GAAAAGA-AA-AAAAAAAGAG
1 GAAAAGAGAATAAAAAAAGAG
*
28357 GAAAAGAGAATAAAAGAAGAG
1 GAAAAGAGAATAAAAAAAGAG
28378 CAAATAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (21 bp):
GAAAAGAGAATAAAAAAAGAG
Found at i:29598 original size:106 final size:106
Alignment explanation
Indices: 29130--29862 Score: 1283
Period size: 106 Copynumber: 6.9 Consensus size: 106
29120 AGGTTTTACC
29130 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
29195 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
*
29235 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
29300 ACGAAGGGACCGCTGGTTGTCAGCAAAC-ATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
29340 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
29405 ACGAAGGGACCGCTGGTTGTCAACAAAC-ACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
* * *
29445 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
29510 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
* *
29551 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
29616 ACGAAGGGACCGTTGGTTGTCAACAAACAATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
* *
29657 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
29722 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
*
29763 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
29828 ACGAAGGGACTGCTGGTTGTCAATAAACAACTTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTC
29863 AACTTCACAA
Statistics
Matches: 604, Mismatches: 22, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
105 294 0.49
106 307 0.51
107 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
Found at i:31721 original size:2 final size:2
Alignment explanation
Indices: 31714--31786 Score: 112
Period size: 2 Copynumber: 37.0 Consensus size: 2
31704 TGATATTACC
* **
31714 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA GG TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31755 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31787 CTTTTATTGT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:32068 original size:4 final size:4
Alignment explanation
Indices: 32054--32155 Score: 52
Period size: 4 Copynumber: 26.0 Consensus size: 4
32044 ATTTTTTCCC
* * *
32054 TTAT CTTAT TTAT TTAG TTAT CTAT TTAT TTA- TT-T TTCT TTA- TT-T
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * **
32099 TTCT TTAT CT-T TGAT TTAT TTACT CATAT TTGT TTAT TTAT TTAT CCAT
1 TTAT TTAT TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT
32148 TTAT TTAT
1 TTAT TTAT
32156 GTATATTGTC
Statistics
Matches: 72, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
3 9 0.12
4 55 0.76
5 6 0.08
6 2 0.03
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:32097 original size:10 final size:10
Alignment explanation
Indices: 32082--32106 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
32072 TATCTATTTA
32082 TTTATTTTTC
1 TTTATTTTTC
32092 TTTATTTTTC
1 TTTATTTTTC
32102 TTTAT
1 TTTAT
32107 CTTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:35915 original size:38 final size:38
Alignment explanation
Indices: 35873--35948 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
35863 GGGAAACATA
35873 AGACCTGAAATATTTTATTATCTATTTTCCAAACAAAT
1 AGACCTGAAATATTTTATTATCTATTTTCCAAACAAAT
*
35911 AGACCTGGAATATTTTATTATCTATTTTCCAAACAAAT
1 AGACCTGAAATATTTTATTATCTATTTTCCAAACAAAT
35949 CATCATTTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (38 bp):
AGACCTGAAATATTTTATTATCTATTTTCCAAACAAAT
Found at i:39812 original size:30 final size:31
Alignment explanation
Indices: 39777--39847 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
39767 TTAAAATTCT
*
39777 CAAAAAAATCTTAAA-TTCCAGAAAATCTCAA
1 CAAAAAAATCCTAAACTTCCA-AAAATCTCAA
* *
39808 -AAAAAACTCCTAAACTTCTAAAAATCTCAA
1 CAAAAAAATCCTAAACTTCCAAAAATCTCAA
39838 CAACAAAAAT
1 CAA-AAAAAT
39848 AAACTCTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
30 22 0.67
31 6 0.18
32 5 0.15
ACGTcount: A:0.56, C:0.21, G:0.01, T:0.21
Consensus pattern (31 bp):
CAAAAAAATCCTAAACTTCCAAAAATCTCAA
Found at i:43262 original size:127 final size:127
Alignment explanation
Indices: 43113--43566 Score: 533
Period size: 127 Copynumber: 3.6 Consensus size: 127
43103 GGATTGACTT
* *
43113 GGCTCCTACATGATGAGGAGATCTGGTCGGTTGATGACACTGCTCATACT-ATGATAAGTCTTGG
1 GGCTCCTACATGATGAGGAGATCTGGTCGGGTGATGACACTGCTCAT-CTGATCATAAGTCTTGG
* * * * *
43177 CCATCTAAGGGTGATAACACGATTCCTACGTGATGAGGATGGA-TGGTTATCAAAGGTTGACAC
65 CCATCTAAGGGTGATAACACGGTTCCTAAGTGATAAGGA-CGACTGGTTATCAGAGGTTGACAC
* * *
43240 GGCTCCTACGTGATGAGGAGATCAT-GTCGGGTGATGAAACTGCTCATACT-ATGATAAGTCTTG
1 GGCTCCTACATGATGAGGAGATC-TGGTCGGGTGATGACACTGCTCAT-CTGATCATAAGTCTTG
* * * *
43303 GCCATCAAATGGTGATAACACGGTTCCTAAGTGATAAGGACGACTGGTTATCAGGGGTTGACAT
64 GCCATCTAAGGGTGATAACACGGTTCCTAAGTGATAAGGACGACTGGTTATCAGAGGTTGACAC
* * * * * *
43367 GGCTCCTACATGATGAGGATATCAGGTCGGGTGATGACACTACTCATCTGTTCATGAGTCTTGGT
1 GGCTCCTACATGATGAGGAGATCTGGTCGGGTGATGACACTGCTCATCTGATCATAAGTCTTGGC
* * * * *
43432 CATATAAGGGTGATAACATGGTTCCTATGTGATAAGGACAACTGGTTATCTGA-GTT-ACAC
66 CATCTAAGGGTGATAACACGGTTCCTAAGTGATAAGGACGACTGGTTATCAGAGGTTGACAC
** * * * * * *
43492 AACTCCTACATAATGAGGAGATCTGGTCAGGTGATGACATTGCTCATCTGTTCATGAGTTTTGGC
1 GGCTCCTACATGATGAGGAGATCTGGTCGGGTGATGACACTGCTCATCTGATCATAAGTCTTGGC
43557 CATCTAAGGG
66 CATCTAAGGG
43567 ATTTTGATTT
Statistics
Matches: 282, Mismatches: 41, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
125 67 0.24
126 7 0.02
127 207 0.73
128 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (127 bp):
GGCTCCTACATGATGAGGAGATCTGGTCGGGTGATGACACTGCTCATCTGATCATAAGTCTTGGC
CATCTAAGGGTGATAACACGGTTCCTAAGTGATAAGGACGACTGGTTATCAGAGGTTGACAC
Found at i:48729 original size:13 final size:13
Alignment explanation
Indices: 48711--48749 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
48701 GTCATGAATC
*
48711 TATGACGCACATT
1 TATGACGCGCATT
48724 TATGACGCGCATT
1 TATGACGCGCATT
48737 TATGACGCGCATT
1 TATGACGCGCATT
48750 GCGCGTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:48943 original size:85 final size:85
Alignment explanation
Indices: 48721--48934 Score: 277
Period size: 85 Copynumber: 2.5 Consensus size: 85
48711 TATGACGCAC
* * ***
48721 ATTTATGACGCGCATTTATGACGCGCATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATTA
1 ATTTATGACACGCATATATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATTA
*
48786 CACATATTTGTGTGACATAA
66 CACACATTTGTGTGACATAA
* * ** * *
48806 ATTTATGACATGCATGTATGACTTACATTAAGCGTCATTGAAGCCCCCGTCATAAA-TATGCTTG
1 ATTTATGACACGCATATATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATT-
* *
48870 ACATACATTTGTGTGCCATAA
65 ACACACATTTGTGTGACATAA
*
48891 ATTTATGACACGCATATATGACTTACATTGCGTGTCATTGAAGC
1 ATTTATGACACGCATATATGACTTACATTGCGCGTCATTGAAGC
48935 ACATGTCATT
Statistics
Matches: 110, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
84 5 0.05
85 105 0.95
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (85 bp):
ATTTATGACACGCATATATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATTA
CACACATTTGTGTGACATAA
Found at i:57425 original size:20 final size:21
Alignment explanation
Indices: 57395--57439 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
57385 CCCTTATAAA
57395 ATTTCCTTAACTTATTATTAT
1 ATTTCCTTAACTTATTATTAT
57416 ATTT-CTTAACTTATTATTAT
1 ATTTCCTTAACTTATTATTAT
57436 ATTT
1 ATTT
57440 TTATCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTCCTTAACTTATTATTAT
Found at i:59704 original size:29 final size:27
Alignment explanation
Indices: 59671--59735 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
59661 TTTGTGCAAT
* *
59671 AAAATAACATGTTAGTGATAACAATAAGA
1 AAAATAA-AAGTTAGT-ACAACAATAAGA
*
59700 AAAATGAAAAGTTAGTACAATAATAAGA
1 AAAAT-AAAAGTTAGTACAACAATAAGA
*
59728 CAAATAAA
1 AAAATAAA
59736 TAAAAGTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 3 0.10
28 14 0.45
29 12 0.39
30 2 0.06
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.22
Consensus pattern (27 bp):
AAAATAAAAGTTAGTACAACAATAAGA
Found at i:62222 original size:56 final size:56
Alignment explanation
Indices: 62162--62272 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
62152 TGACAAAATT
*
62162 GAAGAAATTTAAAATTACAAATAAAATCTTAAAATATAAATTAAACAACACACATG
1 GAAGAAATGTAAAATTACAAATAAAATCTTAAAATATAAATTAAACAACACACATG
62218 GAAGAAATGTAAAATTACAAATAAAATCTTAAAATATAAATTAAACAACACACAT
1 GAAGAAATGTAAAATTACAAATAAAATCTTAAAATATAAATTAAACAACACACAT
62273 AGGTAAGGGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.24
Consensus pattern (56 bp):
GAAGAAATGTAAAATTACAAATAAAATCTTAAAATATAAATTAAACAACACACATG
Found at i:62747 original size:2 final size:2
Alignment explanation
Indices: 62563--62731 Score: 193
Period size: 2 Copynumber: 84.5 Consensus size: 2
62553 AAAATTGAAA
62563 AT AT AT AT AT AT 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 AT AT AT AT AT AT
62605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
62645 AGT TT AT AT AT AA ACT AT AT TT AT AT -T AT AT AT -T AT AT AT AT
1 A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
62687 AT AT AT GT TT AT GT AA ACT AT AT AT AT AA ACT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT
62731 A
1 A
62732 AATTTATAAT
Statistics
Matches: 142, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
1 4 0.03
2 135 0.95
3 3 0.02
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Done.