Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000844.1 Hibiscus syriacus cultivar Beakdansim tig00001628_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: 63146
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:14537 original size:27 final size:26
Alignment explanation
Indices: 14502--14554 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
14492 ATAATAAAAA
14502 TATAAAAAATAAAAATAATATATAAT
1 TATAAAAAATAAAAATAATATATAAT
* *
14528 TATAATAAAATAAAAATATTTTATAAT
1 TATAA-AAAATAAAAATAATATATAAT
14555 AACTCACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TATAAAAAATAAAAATAATATATAAT
Found at i:14539 original size:18 final size:19
Alignment explanation
Indices: 14486--14539 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
14476 TGTATCAAAT
14486 TAAATTATAATAAAA-ATA
1 TAAATTATAATAAAATATA
** *
14504 TAAAAAATAAAAATAATATA
1 TAAATTATAATAA-AATATA
14524 T-AATTATAATAAAATA
1 TAAATTATAATAAAATA
14540 AAAATATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
18 14 0.50
19 10 0.36
20 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAATTATAATAAAATATA
Found at i:16758 original size:68 final size:68
Alignment explanation
Indices: 16648--16778 Score: 194
Period size: 68 Copynumber: 1.9 Consensus size: 68
16638 TTAATATTGT
* * *
16648 GTATTAAAGATAAAATAGCAAGCTCATCCTTCATATTCAAAAACCTGGAATCACTTCAAAGAAGA
1 GTATTAAAGATAAAATAGCAAGCTCATCCTTCATATTAAAAAACCTGGAATCAATTAAAAGAAGA
16713 AAG
66 AAG
*
16716 GTATTAAAGATAAACA-AGCAAGTTCATCC-TCATATTAAAAAAACCTGGAATCAATTAAAAGAA
1 GTATTAAAGATAAA-ATAGCAAGCTCATCCTTCATATT-AAAAAACCTGGAATCAATTAAAAGAA
16779 ACAGAATATT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
67 7 0.12
68 49 0.86
69 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (68 bp):
GTATTAAAGATAAAATAGCAAGCTCATCCTTCATATTAAAAAACCTGGAATCAATTAAAAGAAGA
AAG
Found at i:16794 original size:68 final size:68
Alignment explanation
Indices: 16649--16795 Score: 183
Period size: 68 Copynumber: 2.2 Consensus size: 68
16639 TAATATTGTG
* * *
16649 TATTAAAGATAAAATAGCAAGCTCATCCTTCATATTCAAAAACCTGGAATCACTTCAAAGAAGAA
1 TATTAAAGATAAAATAGCAAGCTCATCCTTCATATTAAAAAACCTGGAATCAATTAAAAGAAGAA
*
16714 AGG
66 AGA
*
16717 TATTAAAGATAAACA-AGCAAGTTCATCC-TCATATTAAAAAAACCTGGAATCAATTAAAAGAA-
1 TATTAAAGATAAA-ATAGCAAGCTCATCCTTCATATT-AAAAAACCTGGAATCAATTAAAAGAAG
*
16779 ACAGAA
64 AAAG-A
*
16785 TATTCAAGATA
1 TATTAAAGATA
16796 TCAGTATGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
67 10 0.14
68 58 0.84
69 1 0.01
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.24
Consensus pattern (68 bp):
TATTAAAGATAAAATAGCAAGCTCATCCTTCATATTAAAAAACCTGGAATCAATTAAAAGAAGAA
AGA
Found at i:18474 original size:61 final size:58
Alignment explanation
Indices: 18404--18588 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 58
18394 TTGGATGAAC
* * *
18404 TTGGGGATGACATTGAAAGATTTAAAAGTTTAGGGGACTAATTTAGAATGAGATTTATAGT
1 TTGGGGATGA-ATTGAAAG-TTTAAAAGTTTA-AGGACTAATTTAGAATGAGAGTCATAGT
* * * * *
18465 TTGGGGATGAATTTCAAATGTTCAAAAAGTTTAAAGACTAATTTAGAATGGGAGTCGTAGT
1 TTGGGGATGAA-TTGAAA-GTT-TAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGT
* * *
18526 TTGAGGATGAAATTGGAATGTTTAAAAGTTTAAGGACTAATTT-GAAATGAGAGTCATGGT
1 TTGGGGATG-AATT-GAAAGTTTAAAAGTTTAAGGACTAATTTAG-AATGAGAGTCATAGT
18586 TTG
1 TTG
18589 AGGACATGTG
Statistics
Matches: 102, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
59 1 0.01
60 35 0.34
61 52 0.51
62 14 0.14
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (58 bp):
TTGGGGATGAATTGAAAGTTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGT
Found at i:18580 original size:60 final size:60
Alignment explanation
Indices: 18424--18592 Score: 196
Period size: 61 Copynumber: 2.8 Consensus size: 60
18414 CATTGAAAGA
* * * * *
18424 TTTAAAAGTTTAGGGGACTAATTTAGAATGAGATTTATAGTTTGGGGATGAATTTCAAATG
1 TTTAAAAGTTTA-AGGACTAATTTAGAATGAGAGTCATAGTTTGAGGATGAAATTCAAATG
* * * * **
18485 TTCAAAAAGTTTAAAGACTAATTTAGAATGGGAGTCGTAGTTTGAGGATGAAATTGGAATG
1 TT-TAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGAGGATGAAATTCAAATG
*
18546 TTTAAAAGTTTAAGGACTAATTT-GAAATGAGAGTCATGGTTTGAGGA
1 TTTAAAAGTTTAAGGACTAATTTAG-AATGAGAGTCATAGTTTGAGGA
18593 CATGTGATGC
Statistics
Matches: 90, Mismatches: 16, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 1 0.01
60 38 0.42
61 42 0.47
62 9 0.10
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.34
Consensus pattern (60 bp):
TTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGAGGATGAAATTCAAATG
Found at i:18844 original size:2 final size:2
Alignment explanation
Indices: 18837--18876 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
18827 ACCATATACA
18837 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
18877 TTCTTCATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19324 original size:13 final size:13
Alignment explanation
Indices: 19306--19372 Score: 70
Period size: 13 Copynumber: 5.4 Consensus size: 13
19296 AATTAAATTT
19306 ATTTAATAATATA
1 ATTTAATAATATA
19319 ATTTAAT-A-AT-
1 ATTTAATAATATA
19329 A-TTAATAATATA
1 ATTTAATAATATA
* *
19341 ATTTTATAAATATT
1 ATTTAAT-AATATA
*
19355 ATTTAATAATTTA
1 ATTTAATAATATA
19368 ATTTA
1 ATTTA
19373 TAAAAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
9 5 0.11
10 2 0.05
11 4 0.09
12 2 0.05
13 20 0.45
14 11 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTTAATAATATA
Found at i:19333 original size:22 final size:23
Alignment explanation
Indices: 19308--19369 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
19298 TTAAATTTAT
19308 TTAATAATATAATTTAAT-AATA
1 TTAATAATATAATTTAATAAATA
*
19330 TTAATAATATAATTTTATAAATA
1 TTAATAATATAATTTAATAAATA
* *
19353 TTATTTA-ATAATTTAAT
1 TTAATAATATAATTTAAT
19370 TTATAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 26 0.74
23 9 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATAATATAATTTAATAAATA
Found at i:21954 original size:16 final size:16
Alignment explanation
Indices: 21935--21968 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21925 CAATATACGA
21935 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
21951 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
21967 AT
1 AT
21969 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:22040 original size:16 final size:18
Alignment explanation
Indices: 22008--22041 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
21998 ACATTATGTA
22008 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
22026 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
22042 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:23185 original size:35 final size:35
Alignment explanation
Indices: 23138--23210 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
23128 TGAATTTAAA
* *
23138 TGAATTATTTTGGAATTTAGGGTTTATAATGAAAT
1 TGAATTACTTTGGAAATTAGGGTTTATAATGAAAT
*
23173 TGAATTACTTTGGAAATTGGGGTTTATAATGAAAT
1 TGAATTACTTTGGAAATTAGGGTTTATAATGAAAT
23208 TGA
1 TGA
23211 GGATTGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.01, G:0.22, T:0.42
Consensus pattern (35 bp):
TGAATTACTTTGGAAATTAGGGTTTATAATGAAAT
Found at i:25278 original size:211 final size:210
Alignment explanation
Indices: 24800--25510 Score: 1134
Period size: 211 Copynumber: 3.4 Consensus size: 210
24790 ATTTTATGAA
* * * * *
24800 AAATATAAATTTAAGAATTAAATTGAACAAATATGAAATTACAAATAAAAATTTATATAAATTAA
1 AAATAAAAATTGAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* *
24865 ACAACACACATTGATGAGGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
66 ACAACACA-A---A--AGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAA
* * * *
24930 AAAAGTACTAAAGTATACCCATTTAAAAATTTATGGGCCAATTTAAAAATAGAATTAAGTAAAAA
125 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAA
*
24995 GTATGGATCAATTTCAGATGC
190 GTATGGGTCAATTTCAGATGC
* *
25016 AAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATAAAAATTGAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* *
25081 ACGACACAAAAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTTAAATTAATACAAAAAAGT
66 ACAACACAAAAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGT
*
25146 ACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAAATAGAAATAAGTAATAAGTATG
131 ACTAAATTATACCCATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATG
25211 GGTCAATTTCAGATGC
195 GGTCAATTTCAGATGC
* *
25227 AAATAAAAATTGAAGGACTAAATTGAATAAATATGAAATTAAAAATAAAAATTTAAATAAATTAA
1 AAATAAAAATTGAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* *
25292 ACAAGACTAAAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGT
66 ACAACACAAAAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGT
*
25357 ACTAAATTATACTCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGG
131 ACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGG
25422 GTCAATTTCAGATGC
196 GTCAATTTCAGATGC
* * *
25437 AAATAAAGATTGGAGGACTAAATTAAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATAAAAATTGAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
25502 ACAACACAA
66 ACAACACAA
25511 GGGATATTTA
Statistics
Matches: 460, Mismatches: 34, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
210 196 0.43
211 197 0.43
212 1 0.00
215 1 0.00
216 65 0.14
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (210 bp):
AAATAAAAATTGAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACACAAAAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGT
ACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGG
GTCAATTTCAGATGC
Found at i:25532 original size:7 final size:7
Alignment explanation
Indices: 25517--25573 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
25507 ACAAGGGATA
*
25517 TTTATGG
1 TTTAGGG
25524 TTTAGGG
1 TTTAGGG
25531 TTTA-GG
1 TTTAGGG
*
25537 TATTATGG
1 T-TTAGGG
*
25545 TTTAAGG
1 TTTAGGG
*
25552 TTTAAGG
1 TTTAGGG
*
25559 TTTAGGA
1 TTTAGGG
25566 TTTAGGG
1 TTTAGGG
25573 T
1 T
25574 GTTATTTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
6 3 0.07
7 37 0.86
8 3 0.07
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:25542 original size:21 final size:21
Alignment explanation
Indices: 25517--25573 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
25507 ACAAGGGATA
25517 TTTATGGTTTAGGGTTT-AGG
1 TTTATGGTTTAGGGTTTAAGG
*
25537 TATTATGGTTTAAGGTTTAAGG
1 T-TTATGGTTTAGGGTTTAAGG
25559 TTTA-GGATTTAGGGT
1 TTTATGG-TTTAGGGT
25574 GTTATTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 3 0.09
21 25 0.78
22 4 0.12
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (21 bp):
TTTATGGTTTAGGGTTTAAGG
Found at i:25587 original size:6 final size:6
Alignment explanation
Indices: 25576--25614 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
25566 TTTAGGGTGT
*
25576 TATTTA TATTTA TATTTA TATTTA TGTTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TAT
25615 AAACTACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:25666 original size:24 final size:26
Alignment explanation
Indices: 25635--25683 Score: 75
Period size: 24 Copynumber: 1.9 Consensus size: 26
25625 CTATAATTTA
25635 TATTTATAT-ACTATA-TTTATATAC
1 TATTTATATAACTATAGTTTATATAC
25659 TATTTATATAAACTATAGTTTATAT
1 TATTTATAT-AACTATAGTTTATAT
25684 TTATATACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
26 6 0.27
27 7 0.32
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (26 bp):
TATTTATATAACTATAGTTTATATAC
Found at i:25683 original size:33 final size:33
Alignment explanation
Indices: 25646--25739 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
25636 ATTTATATAC
*
25646 TATATTTATATACTATTTATATAAACTATAGTT
1 TATATTTATATACTATATATATAAACTATAGTT
*
25679 TATATTTATATACTATATATATGAACTATAGTT
1 TATATTTATATACTATATATATAAACTATAGTT
*
25712 TACA--TATGA-ACTATATATATAAACTATA
1 TATATTTAT-ATACTATATATATAAACTATA
25740 TAAACTATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
31 21 0.38
32 1 0.02
33 34 0.61
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (33 bp):
TATATTTATATACTATATATATAAACTATAGTT
Found at i:25696 original size:13 final size:13
Alignment explanation
Indices: 25633--25683 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
25623 TACTATAATT
25633 TATATTTATATAC
1 TATATTTATATAC
25646 TATATTTATATAC
1 TATATTTATATAC
*
25659 TAT-TTATATAAAC
1 TATATT-TATATAC
25672 TATAGTTTATAT
1 TATA-TTTATAT
25684 TTATATACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 2 0.06
13 25 0.76
14 4 0.12
15 2 0.06
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:25706 original size:13 final size:13
Alignment explanation
Indices: 25690--25741 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
25680 ATATTTATAT
25690 ACTATATATATGA
1 ACTATATATATGA
25703 ACTATAGTTTACATATGA
1 ACTATA---T--ATATGA
*
25721 ACTATATATATAA
1 ACTATATATATGA
25734 ACTATATA
1 ACTATATA
25742 AACTATATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
13 19 0.58
15 1 0.03
16 1 0.03
18 12 0.36
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (13 bp):
ACTATATATATGA
Found at i:25718 original size:18 final size:18
Alignment explanation
Indices: 25697--25934 Score: 122
Period size: 18 Copynumber: 12.7 Consensus size: 18
25687 TATACTATAT
25697 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
25715 ATATGAACTATA-TATATAAAC
1 ATATGAACTATAGT-T-T--AC
*
25736 TATATAAACTATATAGTTTAC
1 -ATATGAAC--TATAGTTTAC
25757 ATATGAACTATA-TATATAC
1 ATATGAACTATAGT-T-TAC
* *
25776 -TA--AAGTTGATA-TTTAT
1 ATATGAA-CT-ATAGTTTAC
25792 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
25810 ATATAAACTATATGGTTTAT
1 ATATGAACTATA--GTTTAC
25830 ATACT-AACTATAGTTTAC
1 ATA-TGAACTATAGTTTAC
* *
25848 ATATAAAATATAGTTGATATTTAC
1 ATATGAACTATA---G---TTTAC
25872 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
25890 ATATGAACTATA---TAC
1 ATATGAACTATAGTTTAC
25905 ATA--AACTATATAGTTTAC
1 ATATGAAC--TATAGTTTAC
*
25923 ATATGACCTATA
1 ATATGAACTATA
25935 TATATATATA
Statistics
Matches: 174, Mismatches: 13, Indels: 66
0.69 0.05 0.26
Matches are distributed among these distances:
13 3 0.02
15 10 0.06
16 4 0.02
17 10 0.06
18 81 0.47
19 6 0.03
20 24 0.14
21 7 0.04
22 7 0.04
23 1 0.01
24 20 0.11
25 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:25730 original size:22 final size:22
Alignment explanation
Indices: 25705--25772 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
25695 ATATATGAAC
25705 TATAGTTTACATATGAACTATA
1 TATAGTTTACATATGAACTATA
** *
25727 TATA-TAAACTATATAAAC--TA
1 TATAGTTTAC-ATATGAACTATA
25747 TATAGTTTACATATGAACTATA
1 TATAGTTTACATATGAACTATA
25769 TATA
1 TATA
25773 TACTAAAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
20 13 0.36
21 6 0.17
22 17 0.47
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (22 bp):
TATAGTTTACATATGAACTATA
Found at i:25731 original size:42 final size:43
Alignment explanation
Indices: 25685--25778 Score: 133
Period size: 42 Copynumber: 2.2 Consensus size: 43
25675 AGTTTATATT
*
25685 TATATACTATA-TATATGAAC-TATAGTTTACATATGAACTATA
1 TATATACTA-ACTATATAAACATATAGTTTACATATGAACTATA
25727 TATATA--AACTATATAAACTATATAGTTTACATATGAACTATA
1 TATATACTAACTATATAAAC-ATATAGTTTACATATGAACTATA
25769 TATATACTAA
1 TATATACTAA
25779 AGTTGATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
39 1 0.02
40 9 0.20
42 34 0.74
44 2 0.04
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (43 bp):
TATATACTAACTATATAAACATATAGTTTACATATGAACTATA
Found at i:25839 original size:38 final size:39
Alignment explanation
Indices: 25786--25902 Score: 148
Period size: 38 Copynumber: 2.9 Consensus size: 39
25776 TAAAGTTGAT
25786 ATTTATATATGAACTATAGTTTACATATAAACTATATG-
1 ATTTATATATGAACTATAGTTTACATATAAACTATATGA
* *
25824 GTTTATATACT-AACTATAGTTTACATATAAAATATAGTTGA
1 ATTTATATA-TGAACTATAGTTTACATATAAACTATA--TGA
* *
25865 TATTTACATATGAACTATAGTTTACATATGAACTATAT
1 -ATTTATATATGAACTATAGTTTACATATAAACTATAT
25903 ACATAAACTA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
38 32 0.48
39 1 0.01
40 3 0.04
41 1 0.01
42 30 0.45
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (39 bp):
ATTTATATATGAACTATAGTTTACATATAAACTATATGA
Found at i:25938 original size:2 final size:2
Alignment explanation
Indices: 25931--26061 Score: 72
Period size: 2 Copynumber: 63.0 Consensus size: 2
25921 ACATATGACC
*
25931 TA TA TA TA TA TA TA TA TA TA CTA TA GT- TGA TA TT TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA
* * ** *
25974 TA TA -A TT TA CA TA TGA CC TA TA TA TA TA TA TA -A TA TA GTT TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
26016 TA TT TA TA TA CTG TA TA T- TA TA TA TA AA CTA TA TA TA TA TA GTA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
26060 TA
1 TA
26062 ATTTACATAT
Statistics
Matches: 98, Mismatches: 18, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
1 4 0.04
2 82 0.84
3 12 0.12
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:26003 original size:55 final size:53
Alignment explanation
Indices: 25937--26056 Score: 168
Period size: 55 Copynumber: 2.2 Consensus size: 53
25927 GACCTATATA
* * *
25937 TATATATATATATACTATAGTTGATATTTATATACTATATAATTTACATATGACC
1 TATATATATATATAATATAGTTGATATTTATATACTATAT-A-TTACATATAAAC
* * *
25992 TATATATATATATAATATAGTTTATATTTATATACTGTATATTATATATAAAC
1 TATATATATATATAATATAGTTGATATTTATATACTATATATTACATATAAAC
26045 TATATATATATA
1 TATATATATATA
26057 GTATAATTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 21 0.36
54 1 0.02
55 37 0.63
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (53 bp):
TATATATATATATAATATAGTTGATATTTATATACTATATATTACATATAAAC
Found at i:26010 original size:33 final size:33
Alignment explanation
Indices: 25880--26015 Score: 142
Period size: 33 Copynumber: 4.3 Consensus size: 33
25870 ACATATGAAC
* * *
25880 TATAGTTTACATATGAACTATATACATAAACTA
1 TATAGTTTACATATGACCTATATATATATACTA
25913 TATAGTTTACATATGACCTATATATATATA-TA
1 TATAGTTTACATATGACCTATATATATATACTA
** *
25945 TATA---TAC-TAT-AGTTGATATTTATATACTA
1 TATAGTTTACATATGACCT-ATATATATATACTA
*
25974 TATAATTTACATATGACCTATATATATATA-TAA
1 TATAGTTTACATATGACCTATATATATATACT-A
26007 TATAGTTTA
1 TATAGTTTA
26016 TATTTATATA
Statistics
Matches: 85, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
27 2 0.02
28 13 0.15
29 9 0.11
32 10 0.12
33 49 0.58
34 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (33 bp):
TATAGTTTACATATGACCTATATATATATACTA
Found at i:26052 original size:20 final size:20
Alignment explanation
Indices: 25900--26085 Score: 58
Period size: 20 Copynumber: 9.5 Consensus size: 20
25890 ATATGAACTA
*
25900 TATACATAAACTATATAGT-T
1 TATATATAAACTATATA-TAT
* * *
25920 TACATATGACCTATATATAT
1 TATATATAAACTATATATAT
*
25940 ATATATATATACTATAGTTGATAT
1 -TATATATAAACTATA--T-ATAT
25964 T-TATAT--ACTATATA-ATT
1 TATATATAAACTATATATA-T
* * *
25981 TACATATGACCTATATATA-
1 TATATATAAACTATATATAT
* *
26000 TATATA-ATA-TAGTTTATAT
1 TATATATAAACTA-TATATAT
*
26019 T-TATAT--AC--TGTATAT
1 TATATATAAACTATATATAT
26034 TATATATAAACTATATATA-
1 TATATATAAACTATATATAT
** *
26053 TATAGTATAATTTACATATGAAT
1 TATA-TATAAACTATATAT--AT
26076 TATATATAAA
1 TATATATAAA
26086 ACCATATAAA
Statistics
Matches: 122, Mismatches: 21, Indels: 44
0.65 0.11 0.24
Matches are distributed among these distances:
15 7 0.06
16 6 0.05
17 6 0.05
18 16 0.13
19 11 0.09
20 43 0.35
21 12 0.10
22 11 0.09
23 6 0.05
24 4 0.03
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
TATATATAAACTATATATAT
Found at i:27800 original size:17 final size:17
Alignment explanation
Indices: 27778--27818 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
27768 TCAAAGAGTA
*
27778 ATCATATTAATTTAATT
1 ATCATAATAATTTAATT
27795 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
27812 ATCATAA
1 ATCATAA
27819 GTTTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
ATCATAATAATTTAATT
Found at i:30384 original size:26 final size:26
Alignment explanation
Indices: 30351--30403 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
30341 TCTCTTTTCA
30351 CACTGATGATAATTGGCATTTCCACT
1 CACTGATGATAATTGGCATTTCCACT
30377 CACTGATGATAATTGGCATTTCCACT
1 CACTGATGATAATTGGCATTTCCACT
30403 C
1 C
30404 TTCAGCTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (26 bp):
CACTGATGATAATTGGCATTTCCACT
Found at i:33016 original size:13 final size:13
Alignment explanation
Indices: 32998--33024 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32988 AAAGTCATCA
32998 AGACTCATGGACC
1 AGACTCATGGACC
33011 AGACTCATGGACC
1 AGACTCATGGACC
33024 A
1 A
33025 AGATGCTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.15
Consensus pattern (13 bp):
AGACTCATGGACC
Found at i:36663 original size:31 final size:31
Alignment explanation
Indices: 36625--36688 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
36615 ACCGTCAAGT
* * *
36625 CCAGTAAGACCCTGAGCACAAATCCGAGGAG
1 CCAGTAAGACCATGAGAACAAAGCCGAGGAG
*
36656 CCAGTAAGGCCATGAGAACAAAGCCGAGGAG
1 CCAGTAAGACCATGAGAACAAAGCCGAGGAG
36687 CC
1 CC
36689 TCCAGGTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.28, G:0.28, T:0.08
Consensus pattern (31 bp):
CCAGTAAGACCATGAGAACAAAGCCGAGGAG
Found at i:47808 original size:46 final size:46
Alignment explanation
Indices: 47758--47934 Score: 228
Period size: 46 Copynumber: 3.8 Consensus size: 46
47748 ATGGTCTTTT
* ** * * * *
47758 TTTCATGCATTAATATATCCGTTCATACATTTTAATCATGACATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGACATCC
* * *
47804 TTTCATGCCCTAACGCATCCTTTCATGCATTTTAGTTATGACATCT
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGACATCC
* * *
47850 TTTCATGCCTTAATGCATCCTTTTATGCATTTTAGTTATGAAATGC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGACATCC
*
47896 TTTCATGCCTTAATGCATCTTTTCATGCATTTTAGTTAT
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
47935 AGATTCAGTT
Statistics
Matches: 113, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 113 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGACATCC
Found at i:47855 original size:26 final size:25
Alignment explanation
Indices: 47818--47934 Score: 78
Period size: 26 Copynumber: 5.0 Consensus size: 25
47808 ATGCCCTAAC
*
47818 GCATCCTTTCATGCATTTTAGTTAT
1 GCATCTTTTCATGCATTTTAGTTAT
*
47843 GACATCTTTTCATGC--CTTA---AT
1 G-CATCTTTTCATGCATTTTAGTTAT
47864 GCATCCTTTT-ATGCATTTTAGTTAT
1 GCAT-CTTTTCATGCATTTTAGTTAT
* *
47889 GAAATGC-TTTCATGC--CTTA---AT
1 G-CAT-CTTTTCATGCATTTTAGTTAT
47910 GCATCTTTTCATGCATTTTAGTTAT
1 GCATCTTTTCATGCATTTTAGTTAT
47935 AGATTCAGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 30
0.64 0.07 0.28
Matches are distributed among these distances:
19 1 0.01
20 17 0.25
21 11 0.16
22 6 0.09
24 6 0.09
25 9 0.13
26 19 0.28
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (25 bp):
GCATCTTTTCATGCATTTTAGTTAT
Found at i:51320 original size:16 final size:17
Alignment explanation
Indices: 51287--51320 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
51277 CATTTTATTT
*
51287 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
51304 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
51320 T
1 T
51321 AATAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:51326 original size:23 final size:23
Alignment explanation
Indices: 51281--51326 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
51271 CGATCACATT
* * **
51281 TTATTTTTATTTTATATTTTAAA
1 TTATTTTTATATTAAATAATAAA
51304 TTATTTTTATATTAAATAATAAA
1 TTATTTTTATATTAAATAATAAA
51327 AATGTCACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATTTTTATATTAAATAATAAA
Done.