Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006126.1 Hibiscus syriacus cultivar Beakdansim tig00014528_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: 72053
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:12887 original size:23 final size:23
Alignment explanation
Indices: 12850--12913 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
12840 CATCTCATAT
*
12850 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAA
* * *
12873 AATTGCACCGTAGTGCCGCGTAA
1 AAATGCACCGAAGTGCCACGTAA
12896 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
12914 TATAAGATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAA
Found at i:13761 original size:2 final size:2
Alignment explanation
Indices: 13754--13780 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13744 GTATTCATAC
13754 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
13781 ATCTATTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17424 original size:2 final size:2
Alignment explanation
Indices: 17417--17456 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
17407 AAAAAGAGTG
17417 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
17457 TAATATTGCT
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:24313 original size:14 final size:15
Alignment explanation
Indices: 24275--24315 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
24265 GTTTTTTCGG
24275 TTCGGTTCGGGTTTT
1 TTCGGTTCGGGTTTT
24290 TTAACGGTTCGGG-TTT
1 TT--CGGTTCGGGTTTT
24306 TTCGGTTCGG
1 TTCGGTTCGG
24316 TTCGGTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.33
15 2 0.08
16 5 0.21
17 9 0.38
ACGTcount: A:0.05, C:0.15, G:0.34, T:0.46
Consensus pattern (15 bp):
TTCGGTTCGGGTTTT
Found at i:24485 original size:26 final size:27
Alignment explanation
Indices: 24433--24487 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
24423 ACCCGAACCG
*
24433 AACCGAATCAAAAAAATGAAGCCTTTA
1 AACCGAATCAAAAAAACGAAGCCTTTA
*
24460 AACCGAA-CAAAAAACCGAA-CCGTTTA
1 AACCGAATCAAAAAAACGAAGCC-TTTA
24486 AA
1 AA
24488 GCCAAACCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 16 0.64
27 7 0.28
ACGTcount: A:0.53, C:0.22, G:0.11, T:0.15
Consensus pattern (27 bp):
AACCGAATCAAAAAAACGAAGCCTTTA
Found at i:35971 original size:17 final size:17
Alignment explanation
Indices: 35951--35986 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
35941 TATTTATTTT
35951 ATATTTTTATTGTTAAA
1 ATATTTTTATTGTTAAA
*
35968 ATATTTTTATTTTTAAA
1 ATATTTTTATTGTTAAA
35985 AT
1 AT
35987 TTTATAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
ATATTTTTATTGTTAAA
Found at i:42082 original size:30 final size:30
Alignment explanation
Indices: 42047--42106 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
42037 GGGTGCTTTT
42047 TATCCATGATACATAATTAGTGGGGCGGCC
1 TATCCATGATACATAATTAGTGGGGCGGCC
*
42077 TATCCATGATACATCATTAGTGGGGCGGCC
1 TATCCATGATACATAATTAGTGGGGCGGCC
42107 AGCAACTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (30 bp):
TATCCATGATACATAATTAGTGGGGCGGCC
Found at i:42863 original size:75 final size:75
Alignment explanation
Indices: 42688--42870 Score: 235
Period size: 75 Copynumber: 2.4 Consensus size: 75
42678 CTTAACCGGT
* *
42688 TAAAATAAAATA-AGTGTTACCTATTATGTTAAACTACATACCGCTTTGTTTGAAGGTCACTAAT
1 TAAAATAAAATAGA-TGTTACCTATTATGTTAAAATACATACCGCTTTGTTTAAAGGTCACTAAT
42752 AATGTAAACGG
65 AATGTAAACGG
* * * * * *
42763 TAAAATAAAATAGGTGTTACATATTACGTTAAAATATC-TACCGGTTTGTTTAAAGGTTAGTAAT
1 TAAAATAAAATAGATGTTACCTATTATGTTAAAATA-CATACCGCTTTGTTTAAAGGTCACTAAT
*
42827 AATGTGAACGG
65 AATGTAAACGG
* *
42838 TAAAATAAAATAGACGTTGCCTATTATGTTAAA
1 TAAAATAAAATAGATGTTACCTATTATGTTAAA
42871 TAGGCGATAC
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
75 91 0.99
76 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAGATGTTACCTATTATGTTAAAATACATACCGCTTTGTTTAAAGGTCACTAATA
ATGTAAACGG
Found at i:42883 original size:23 final size:23
Alignment explanation
Indices: 42857--42939 Score: 121
Period size: 23 Copynumber: 3.6 Consensus size: 23
42847 ATAGACGTTG
*
42857 CCTATTATGTTAAATAGGCGATA
1 CCTATTACGTTAAATAGGCGATA
42880 CCTATTACGTTAAATAGGCGATA
1 CCTATTACGTTAAATAGGCGATA
*** *
42903 CCTATTACGTTAAATAAATGTTA
1 CCTATTACGTTAAATAGGCGATA
42926 CCTATTACGTTAAA
1 CCTATTACGTTAAA
42940 CTAGCTATTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (23 bp):
CCTATTACGTTAAATAGGCGATA
Found at i:43666 original size:75 final size:75
Alignment explanation
Indices: 43583--43765 Score: 258
Period size: 75 Copynumber: 2.4 Consensus size: 75
43573 CTTAACCGGT
* * * *
43583 TAAAATAAAATAGGCGATACATATTATGTTAAACTACCTACAGGTTTGTTTGAAGGCTATTAAAA
1 TAAAATAAAATAGGCGATACCTATTATGTTAAAATACCTACAGGTTTGTTTAAAGGCTACTAAAA
*
43648 ATGTAAACGG
66 ATGTAAACAG
* * * * * *
43658 TAAAATAAAATAGGTGTTACCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGGCGATACCTATTATGTTAAAATACCTACAGGTTTGTTTAAAGGCTACTAAAA
43723 ATGTAAACAG
66 ATGTAAACAG
*
43733 TACAATAAAATAGGCGATACCTATTATGTTAAA
1 TAAAATAAAATAGGCGATACCTATTATGTTAAA
43766 TAGATGCTAC
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 93 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (75 bp):
TAAAATAAAATAGGCGATACCTATTATGTTAAAATACCTACAGGTTTGTTTAAAGGCTACTAAAA
ATGTAAACAG
Found at i:43776 original size:23 final size:23
Alignment explanation
Indices: 43750--43812 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
43740 AAATAGGCGA
* * *
43750 TACCTATTATGTTAAATAGATGC
1 TACCTATTACGTTAAATAAACGC
*
43773 TACCTATTACGTTAAATAAACGT
1 TACCTATTACGTTAAATAAACGC
*
43796 TACCTATTACATTAAAT
1 TACCTATTACGTTAAAT
43813 TAGTTATTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (23 bp):
TACCTATTACGTTAAATAAACGC
Found at i:43866 original size:17 final size:19
Alignment explanation
Indices: 43830--43866 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
43820 TGATTTGTTT
*
43830 AAAGGTTAATAATAATATA
1 AAAGGTTAATAATAAAATA
43849 AAAGG-TAA-AATAAAATA
1 AAAGGTTAATAATAAAATA
43866 A
1 A
43867 GCACCATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (19 bp):
AAAGGTTAATAATAAAATA
Found at i:43902 original size:75 final size:75
Alignment explanation
Indices: 43823--44013 Score: 217
Period size: 75 Copynumber: 2.5 Consensus size: 75
43813 TAGTTATTGA
* * *
43823 TTTGTTTAAAGGTTAATAATAATATAAAAGGTAAAATAAAATAAGCACCA-TC-TGTTACGTTAA
1 TTTGTTTAAAGGTTAATAATAATGTAAAAGGTAAAATAAAATAA--ACCAGACTTATTACGTTAA
* *
43886 AATATCTGCCAG
64 AATACCTACCAG
* * * * *
43898 TTTGTTTAAAGATTAAGAATAATGTAAGCA-GAAAAATAAAATAAACGAGACTTATTACGTTAAA
1 TTTGTTTAAAGGTTAATAATAATGTAA-AAGGTAAAATAAAATAAACCAGACTTATTACGTTAAA
43962 ATACCTACCAG
65 ATACCTACCAG
* * *
43973 TTTGTTTAAATGTTACTAATAATGTAAAGGGTAAAATAAAA
1 TTTGTTTAAAGGTTAATAATAATGTAAAAGGTAAAATAAAA
44014 CATGTGTTAC
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
73 3 0.03
74 1 0.01
75 90 0.95
76 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (75 bp):
TTTGTTTAAAGGTTAATAATAATGTAAAAGGTAAAATAAAATAAACCAGACTTATTACGTTAAAA
TACCTACCAG
Found at i:44369 original size:20 final size:17
Alignment explanation
Indices: 44344--44391 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
44334 CTCTAAATGT
44344 TAATAATAATGTATTTA
1 TAATAATAATGTATTTA
44361 TAATAATAATGTATTTA
1 TAATAATAATGTATTTA
44378 TAATAATAATGTAT
1 TAATAATAATGTAT
44392 CCATACTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TAATAATAATGTATTTA
Found at i:44828 original size:108 final size:107
Alignment explanation
Indices: 44601--44868 Score: 306
Period size: 108 Copynumber: 2.5 Consensus size: 107
44591 TGTTAATATT
* * * * *
44601 TATTTATAACAAAATAAGAAATTAACCTATTTTGTTGTCGT-GTGATTTCAAAGGCATATCAGCT
1 TATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTCG-GATTTCTAAGGCATATCAGCT
* * ** *
44665 TAAATTTTGGTAACATTTTTTGCTCTACCTAATATGTTGATAA
65 TAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAA
* * * * *
44708 AATTAATAACAAAATAAGTAATTAACTTAATTTGTTATCATCGGATTTCTAAGGCCCCT-TCAGC
1 TATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTCGGATTTCTAAGG--CATATCAGC
* *
44772 TTAAACTTTGATAATATTTTAGGCGCTACTTAATATGTTGATAA
64 TTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAA
* * *
44816 TATTGATAACAAAATTAAGTAATTAACATGTTTTGTTATCGTCAGATTTCTAA
1 TATTAATAACAAAA-TAAGTAATTAACATATTTTGTTATCGTCGGATTTCTAA
44869 AGCTCCATCA
Statistics
Matches: 134, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
107 44 0.33
108 55 0.41
109 35 0.26
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (107 bp):
TATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTCGGATTTCTAAGGCATATCAGCTT
AAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAA
Found at i:45566 original size:57 final size:57
Alignment explanation
Indices: 45504--45617 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
45494 GTTTCCAAAT
* *
45504 TCGCAACGCGAACATCGACTATCGCAATGCGGTTTTTCAAATTCGTTGCGATAGTCC
1 TCGCAACGCGAACATCGACTATCGCAATGCGATTTTCCAAATTCGTTGCGATAGTCC
*
45561 TCGCAACGCGAACTTCGACTATCGCAATGCGATTTTCCAAATTCGTTGCGATAGTCC
1 TCGCAACGCGAACATCGACTATCGCAATGCGATTTTCCAAATTCGTTGCGATAGTCC
45618 AAATTCGCGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (57 bp):
TCGCAACGCGAACATCGACTATCGCAATGCGATTTTCCAAATTCGTTGCGATAGTCC
Found at i:45612 original size:19 final size:19
Alignment explanation
Indices: 45588--45654 Score: 80
Period size: 21 Copynumber: 3.3 Consensus size: 19
45578 ACTATCGCAA
45588 TGCGATTTTCCAAATTCGT
1 TGCGATTTTCCAAATTCGT
**
45607 TGCGATAGTCCAAATTCGCGT
1 TGCGATTTTCCAAATT--CGT
45628 TGCGATTTATTCCAAATTCGT
1 TGCGA-TT-TTCCAAATTCGT
45649 TGCGAT
1 TGCGAT
45655 AGTCCAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 14 0.35
20 1 0.03
21 16 0.40
22 1 0.03
23 8 0.20
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (19 bp):
TGCGATTTTCCAAATTCGT
Found at i:45645 original size:42 final size:40
Alignment explanation
Indices: 45588--45667 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 40
45578 ACTATCGCAA
*
45588 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAATTCGCGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAAATCGCGT
45628 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAATCGC
1 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAAATCGC
45668 AACGACTGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 5 0.14
41 2 0.05
42 30 0.81
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (40 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAAATCGCGT
Found at i:45662 original size:19 final size:19
Alignment explanation
Indices: 45596--45662 Score: 89
Period size: 19 Copynumber: 3.3 Consensus size: 19
45586 AATGCGATTT
45596 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
*
45615 TCCAAATTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
45638 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
45657 TCCAAA
1 TCCAAA
45663 ATCGCAACGA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
19 16 0.38
21 16 0.38
23 10 0.24
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:45761 original size:6 final size:6
Alignment explanation
Indices: 45750--45776 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
45740 AGACACGTAT
45750 GACCAC GACCAC GACCAC GACCAC GAC
1 GACCAC GACCAC GACCAC GACCAC GAC
45777 GAGACGAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.48, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:46653 original size:21 final size:21
Alignment explanation
Indices: 46517--46681 Score: 144
Period size: 21 Copynumber: 8.0 Consensus size: 21
46507 CGTTGCAATT
*
46517 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
46536 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
46559 TTGGACTATCGCAA--CAAAT
1 TTGGACTATCGCAACGCGAAC
*
46578 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
46601 TTGGACTATCGCAA--TGAAT
1 TTGGACTATCGCAACGCGAAC
**
46620 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
46641 TTCGACTATCGCAACACGAAC
1 TTGGACTATCGCAACGCGAAC
*
46662 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
46682 TATGTAAATC
Statistics
Matches: 114, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
19 30 0.26
21 65 0.57
23 19 0.17
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:46666 original size:42 final size:42
Alignment explanation
Indices: 46517--46655 Score: 237
Period size: 42 Copynumber: 3.4 Consensus size: 42
46507 CGTTGCAATT
46517 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
46559 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
46601 TTGGACTATCGCAATGAATTTGG-A-AAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
46641 TTCGACTATCGCAAC
1 TTGGACTATCGCAAC
46656 ACGAACTTGG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 29 0.32
41 1 0.01
42 62 0.67
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:46681 original size:42 final size:41
Alignment explanation
Indices: 46517--46681 Score: 226
Period size: 42 Copynumber: 4.0 Consensus size: 41
46507 CGTTGCAATT
46517 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAAT-AATCGCAACGCGAAC
*
46559 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAAT-AATCGCAACGCGAAC
*
46601 TTGGACTATCGCAATGAATTTGGAA-AATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAATCGCAACGCGAAC
* * * *
46641 TTCGACTATCGCAACACGAACTTGGACT-ATCGCAATGCGAA
1 TTGGACTATCGC-A-ACGAATTTGGAATAATCGCAACGCGAA
46682 TATGTAAATC
Statistics
Matches: 112, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
40 26 0.23
41 1 0.01
42 85 0.76
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (41 bp):
TTGGACTATCGCAACGAATTTGGAATAATCGCAACGCGAAC
Found at i:51724 original size:8 final size:8
Alignment explanation
Indices: 51711--51736 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
51701 ATTTAAGCTA
51711 GCAAAAGG
1 GCAAAAGG
51719 GCAAAAGG
1 GCAAAAGG
51727 GCAAAAGG
1 GCAAAAGG
51735 GC
1 GC
51737 CCATATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.15, G:0.38, T:0.00
Consensus pattern (8 bp):
GCAAAAGG
Found at i:52600 original size:17 final size:18
Alignment explanation
Indices: 52580--52613 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
52570 TTTATAAAGT
52580 ATATTTTGTTA-TATTTA
1 ATATTTTGTTAGTATTTA
52597 ATATTTTGTTAGTATTT
1 ATATTTTGTTAGTATTT
52614 TATTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
ATATTTTGTTAGTATTTA
Found at i:52626 original size:8 final size:8
Alignment explanation
Indices: 52613--52650 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
52603 TGTTAGTATT
52613 TTATTTAA
1 TTATTTAA
52621 TTATTTAA
1 TTATTTAA
52629 TTATTTAA
1 TTATTTAA
52637 TTATTTAA
1 TTATTTAA
52645 TTATTT
1 TTATTT
52651 TATTTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTATTTAA
Found at i:56469 original size:21 final size:21
Alignment explanation
Indices: 56437--56493 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
56427 TTTGTTCATA
*
56437 GAAA-GTATAATTATTTTACC
1 GAAATGTAAAATTATTTTACC
*
56457 GAAATGTAAAATTATTTTATC
1 GAAATGTAAAATTATTTTACC
* *
56478 GAAATATAATATTATT
1 GAAATGTAAAATTATT
56494 ATGATAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (21 bp):
GAAATGTAAAATTATTTTACC
Found at i:57515 original size:37 final size:37
Alignment explanation
Indices: 57442--57516 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
57432 GTTGAAAAAT
* *
57442 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
57479 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
57516 A
1 A
57517 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:66971 original size:30 final size:29
Alignment explanation
Indices: 66922--67035 Score: 130
Period size: 30 Copynumber: 4.0 Consensus size: 29
66912 GATTTTTTTG
* * * *
66922 GAAAATAATTTATGTAAAATGGATTACTT
1 GAAAATATTTTACGTAAAATGAATTACAT
66951 GAAAATTATTTTACGTAAAATGAATTACAT
1 GAAAA-TATTTTACGTAAAATGAATTACAT
*
66981 GAAAACTA--TTACGTAAAATGAATTACCT
1 GAAAA-TATTTTACGTAAAATGAATTACAT
67009 --AAAT-TTTTACGTAAAATGAATTACAT
1 GAAAATATTTTACGTAAAATGAATTACAT
67035 G
1 G
67036 TTCTGGAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.01
26 22 0.30
28 19 0.26
29 5 0.07
30 27 0.36
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (29 bp):
GAAAATATTTTACGTAAAATGAATTACAT
Found at i:67005 original size:14 final size:14
Alignment explanation
Indices: 66961--67032 Score: 62
Period size: 14 Copynumber: 5.3 Consensus size: 14
66951 GAAAATTATT
66961 TTACGTAAAATGAA
1 TTACGTAAAATGAA
*
66975 TTACATGAAAACT--A
1 TTACGT-AAAA-TGAA
66989 TTACGTAAAATGAA
1 TTACGTAAAATGAA
* **
67003 TTACCT-AAAT-TT
1 TTACGTAAAATGAA
67015 TTACGTAAAATGAA
1 TTACGTAAAATGAA
67029 TTAC
1 TTAC
67033 ATGTTCTGGA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
12 6 0.14
13 12 0.27
14 21 0.48
15 4 0.09
16 1 0.02
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (14 bp):
TTACGTAAAATGAA
Found at i:67025 original size:26 final size:27
Alignment explanation
Indices: 66959--67034 Score: 109
Period size: 26 Copynumber: 2.8 Consensus size: 27
66949 TTGAAAATTA
66959 TTTTACGTAAAATGAATTACATGAAAAC
1 TTTTACGTAAAATGAATTACAT-AAAAC
* * *
66987 TATTACGTAAAATGAATTACCT-AAAT
1 TTTTACGTAAAATGAATTACATAAAAC
67013 TTTTACGTAAAATGAATTACAT
1 TTTTACGTAAAATGAATTACAT
67035 GTTCTGGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.53
28 20 0.47
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (27 bp):
TTTTACGTAAAATGAATTACATAAAAC
Found at i:69749 original size:55 final size:58
Alignment explanation
Indices: 69688--69840 Score: 172
Period size: 60 Copynumber: 2.7 Consensus size: 58
69678 AACTCTCAAT
* *
69688 TAAATTAATCCTTAAACTTTTAAATATCTAATTTTATC-CCAAA-AT-TATCTCATTC
1 TAAATTAATCCTTAAACTTTTAAATATCTAATTTTATCTCCAAACATGAATATCATTC
* *
69743 TAAATTAATCCTTAAACTTTTTAACAT-TCCAATTTCATCTCCAAACTATGAATATCATTC
1 TAAATTAATCCTTAAAC-TTTTAA-ATATCTAATTTTATCTCCAAAC-ATGAATATCATTC
* **
69803 TAAATTAATCCCTAAACTTTTGCATAT-TCAATTTTATC
1 TAAATTAATCCTTAAACTTTTAAATATCT-AATTTTATC
69841 ACCATAGTCA
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
55 17 0.21
56 16 0.20
57 7 0.09
58 2 0.02
59 15 0.19
60 24 0.30
ACGTcount: A:0.37, C:0.20, G:0.01, T:0.42
Consensus pattern (58 bp):
TAAATTAATCCTTAAACTTTTAAATATCTAATTTTATCTCCAAACATGAATATCATTC
Found at i:69820 original size:31 final size:29
Alignment explanation
Indices: 69688--69821 Score: 73
Period size: 31 Copynumber: 4.7 Consensus size: 29
69678 AACTCTCAAT
*
69688 TAAATTAATCCTTAAACTTTTAA-AT-A-TC
1 TAAATTAATCCCTAAAC--TTAATATCATTC
* * * *
69716 TAATTTTATCCC-AAAATT-ATCTCATTC
1 TAAATTAATCCCTAAACTTAATATCATTC
* ** *
69743 TAAATTAATCCTTAAACTTTTTAACATTC
1 TAAATTAATCCCTAAACTTAATATCATTC
* * *
69772 CAATTTCATCTCC-AAACTATGAATATCATTC
1 TAAATTAATC-CCTAAACT-T-AATATCATTC
69803 TAAATTAATCCCTAAACTT
1 TAAATTAATCCCTAAACTT
69822 TTGCATATTC
Statistics
Matches: 75, Mismatches: 22, Indels: 16
0.66 0.19 0.14
Matches are distributed among these distances:
24 1 0.01
25 3 0.04
26 1 0.01
27 14 0.19
28 14 0.19
29 18 0.24
30 5 0.07
31 19 0.25
ACGTcount: A:0.38, C:0.20, G:0.01, T:0.41
Consensus pattern (29 bp):
TAAATTAATCCCTAAACTTAATATCATTC
Done.