Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003727.1 Hibiscus syriacus cultivar Beakdansim tig00007968_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: 105825
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3811 original size:38 final size:38
Alignment explanation
Indices: 3735--3813 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 38
3725 TATATCTAAA
* * *
3735 TTTTAGTTTTTGTTTCATTTTAGTACTCGCCGTTAAAAT
1 TTTTAGCTTTTGTTTCATTTTAGTAC-CGACATTAAAAT
3774 TTTTAGCTTTTGTTTCATTTTAGTGA-C-ACATTCAAAAT
1 TTTTAGCTTTTGTTTCATTTTAGT-ACCGACATT-AAAAT
3812 TT
1 TT
3814 GACGTTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
37 3 0.09
38 8 0.23
39 23 0.66
40 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.53
Consensus pattern (38 bp):
TTTTAGCTTTTGTTTCATTTTAGTACCGACATTAAAAT
Found at i:10628 original size:3 final size:3
Alignment explanation
Indices: 10620--10656 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
10610 CATACTTTTT
10620 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10657 ATGTTTCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:15139 original size:3 final size:3
Alignment explanation
Indices: 15133--15158 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
15123 TTTTGAGTGG
15133 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
15159 TGCTGATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:20605 original size:50 final size:50
Alignment explanation
Indices: 20530--20730 Score: 285
Period size: 50 Copynumber: 4.0 Consensus size: 50
20520 AATTTAATGT
* ** *
20530 TACATGATTGGGAGAAAAGAGTAGAGGGGCTTGTATAAGAGTGTAACATC
1 TACATGATTGGTAGAAAAGAGTAGAGGGATTTGTATAAAAGTGTAACATC
* *
20580 TACATGATTGGTAGAAAAGAGTAGAGGGATTTATATAAAAGTGTAATATC
1 TACATGATTGGTAGAAAAGAGTAGAGGGATTTGTATAAAAGTGTAACATC
* * *
20630 TACATGATTGGTGGAAATGAGTAGAGGGATTTGTATAAAAGTGTAATATC
1 TACATGATTGGTAGAAAAGAGTAGAGGGATTTGTATAAAAGTGTAACATC
* * * *
20680 TACATGATTGGTGGAAATGAGTAGAGGAATTTGTATGAAAGTGTAACATC
1 TACATGATTGGTAGAAAAGAGTAGAGGGATTTGTATAAAAGTGTAACATC
20730 T
1 T
20731 CTACTTAAAT
Statistics
Matches: 139, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 139 1.00
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.29
Consensus pattern (50 bp):
TACATGATTGGTAGAAAAGAGTAGAGGGATTTGTATAAAAGTGTAACATC
Found at i:24986 original size:31 final size:32
Alignment explanation
Indices: 24942--25013 Score: 121
Period size: 31 Copynumber: 2.3 Consensus size: 32
24932 AAAATAAAAT
*
24942 ATTAGTCATTAATATTATCGATTTATAACAAA
1 ATTAGTCACTAATATTATCGATTTATAACAAA
24974 ATTA-TCACTAATATTATCGATTTATAACAAA
1 ATTAGTCACTAATATTATCGATTTATAACAAA
25005 A-TAGTCACT
1 ATTAGTCACT
25014 CTGCCCTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 2 0.05
31 32 0.84
32 4 0.11
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (32 bp):
ATTAGTCACTAATATTATCGATTTATAACAAA
Found at i:31108 original size:2 final size:2
Alignment explanation
Indices: 31103--31130 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31093 TCTCTCTCTC
31103 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
31131 AAGCATACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38482 original size:76 final size:76
Alignment explanation
Indices: 38391--38539 Score: 280
Period size: 76 Copynumber: 2.0 Consensus size: 76
38381 ACTATAAGGT
38391 GTTGTTTTATTAAGTTTATTGATTATCAAAAGTTATAAAATGAGTCCCGACTAAAGGATGTTGTT
1 GTTGTTTTATTAAGTTTATTGATTATCAAAAGTTATAAAATGAGTCCCGACTAAAGGATGTTGTT
38456 TTATTGAACCC
66 TTATTGAACCC
*
38467 GTTGTTTTATTAAGTTTATTGATTATCAAAAGTTATAAAATGGGTCCCGACTAAAGGATGTTGTT
1 GTTGTTTTATTAAGTTTATTGATTATCAAAAGTTATAAAATGAGTCCCGACTAAAGGATGTTGTT
*
38532 TTGTTGAA
66 TTATTGAA
38540 TCCCTCGACT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.42
Consensus pattern (76 bp):
GTTGTTTTATTAAGTTTATTGATTATCAAAAGTTATAAAATGAGTCCCGACTAAAGGATGTTGTT
TTATTGAACCC
Found at i:38633 original size:22 final size:22
Alignment explanation
Indices: 38608--38670 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
38598 TATTCTAAAT
38608 ACTCTCAATCATTTGACAAAAA
1 ACTCTCAATCATTTGACAAAAA
* *
38630 ACTCTCAATCATTTGATAATAA
1 ACTCTCAATCATTTGACAAAAA
* *
38652 ACTCTTAGTCATTTGACAA
1 ACTCTCAATCATTTGACAA
38671 TTGACGCTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (22 bp):
ACTCTCAATCATTTGACAAAAA
Found at i:41591 original size:28 final size:27
Alignment explanation
Indices: 41558--41616 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
41548 CGGTTTTTTT
* *
41558 ACCGGATTAAAAACCGGTTTTTTTTCAA
1 ACCGGATAAAAAACC-GTTTTTTTGCAA
41586 ACCGGATAAAAAACCGTTTTTTTGCAA
1 ACCGGATAAAAAACCGTTTTTTTGCAA
41613 ACCG
1 ACCG
41617 AAACCGGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (27 bp):
ACCGGATAAAAAACCGTTTTTTTGCAA
Found at i:50514 original size:20 final size:20
Alignment explanation
Indices: 50478--50515 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50468 ATCCTATTCC
**
50478 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
50498 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
50516 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:50855 original size:38 final size:38
Alignment explanation
Indices: 50769--50855 Score: 86
Period size: 38 Copynumber: 2.3 Consensus size: 38
50759 ATTTTCGGTC
* ** * *
50769 AACCCGACCCGAAAATTATATATTCTTCACCCGATCTG
1 AACCCGACCCGAAAATTATACACCCTCCACCAGATCTG
* **
50807 AATCTAACCCGAAAATTATACACCCTCCACCAGA-CTCG
1 AACCCGACCCGAAAATTATACACCCTCCACCAGATCT-G
50845 AACCCGACCCG
1 AACCCGACCCG
50856 TCCTTTTAAG
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
37 2 0.05
38 35 0.95
ACGTcount: A:0.33, C:0.37, G:0.10, T:0.20
Consensus pattern (38 bp):
AACCCGACCCGAAAATTATACACCCTCCACCAGATCTG
Found at i:57668 original size:17 final size:17
Alignment explanation
Indices: 57645--57693 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
57635 TGAACGAACC
57645 AATTATCACCACTATAT
1 AATTATCACCACTATAT
* * *
57662 TATTATCAGCC-CTTTGT
1 AATTATCA-CCACTATAT
57679 AATTATCACCACTAT
1 AATTATCACCACTAT
57694 TGAGTTCAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 2 0.08
17 21 0.84
18 2 0.08
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (17 bp):
AATTATCACCACTATAT
Found at i:62853 original size:177 final size:177
Alignment explanation
Indices: 62506--62863 Score: 646
Period size: 178 Copynumber: 2.0 Consensus size: 177
62496 TATTTTAGAT
* * * *
62506 AAATGGATTTAATATTTATTAAAATATTAATCATTGTATGATAAAACTGACTTGGATTAATGATT
1 AAATAGATCTAATATTTATTAAAATATTAATCATTGTATGATAAAACTGACTTAGATTAATGAAT
* *
62571 AAAACACGTAATTAAATTATCATAAGCTTTGAATACTTAACGAATTATACCTTAATATTTTCTTT
66 AAAACACGTAATTAAAATATCAAAAGCTTTGAATACTTAACGAATTATACCTTAATATTTTCTTT
62636 TAAAAATTATGAAATGACCCTCAAAGCTTTGAGTTTTTTTATTTCTC
131 TAAAAATTATGAAATGACCCTCAAAGCTTTGAGTTTTTTTATTTCTC
62683 AAATAGATCTAATATTTATTAAAATATTAATCATTGTATGATAAAACTGACTTAGATTAATGAAT
1 AAATAGATCTAATATTTATTAAAATATTAATCATTGTATGATAAAACTGACTTAGATTAATGAAT
62748 AAAACAACGTAATTAAAATATCAAAAGCTTTGAATACTTAACGAATTATACCTTAATATTTTCTT
66 AAAAC-ACGTAATTAAAATATCAAAAGCTTTGAATACTTAACGAATTATACCTTAATATTTTCTT
62813 TTAAAAATTATGAAATGACCCTCAAAGCTTTGAG-TTTTTTATTTCTC
130 TTAAAAATTATGAAATGACCCTCAAAGCTTTGAGTTTTTTTATTTCTC
62860 AAAT
1 AAAT
62864 GATAAAGCAT
Statistics
Matches: 174, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
177 83 0.48
178 91 0.52
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.40
Consensus pattern (177 bp):
AAATAGATCTAATATTTATTAAAATATTAATCATTGTATGATAAAACTGACTTAGATTAATGAAT
AAAACACGTAATTAAAATATCAAAAGCTTTGAATACTTAACGAATTATACCTTAATATTTTCTTT
TAAAAATTATGAAATGACCCTCAAAGCTTTGAGTTTTTTTATTTCTC
Found at i:64338 original size:20 final size:20
Alignment explanation
Indices: 64315--64353 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
64305 TCCAATTTTA
64315 CAACACAGTTTCCAAATTCG
1 CAACACAGTTTCCAAATTCG
* *
64335 CAACTCAGTTTTCAAATTC
1 CAACACAGTTTCCAAATTC
64354 ACAATTCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (20 bp):
CAACACAGTTTCCAAATTCG
Found at i:64446 original size:22 final size:22
Alignment explanation
Indices: 64418--64471 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
64408 AAAAAATCCA
*
64418 CAACTCGAATTCACCAATTTCG
1 CAACTCGAATTCACCAATTTAG
*
64440 CAACTCGAATTCGCCAATTTAG
1 CAACTCGAATTCACCAATTTAG
64462 CAACTC-AATT
1 CAACTCGAATT
64472 ACTGATATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.33, C:0.30, G:0.09, T:0.28
Consensus pattern (22 bp):
CAACTCGAATTCACCAATTTAG
Found at i:64618 original size:22 final size:21
Alignment explanation
Indices: 64593--64664 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 21
64583 TGAAAACTGA
64593 GTTGCGAATTTAGGAAATTCTT
1 GTTGCGAATTT-GGAAATTCTT
64615 GTTGCGAATTTGGAAA--CTGT
1 GTTGCGAATTTGGAAATTCT-T
* * *
64635 GTTGCGAAATTGG-AGTTCGT
1 GTTGCGAATTTGGAAATTCTT
64655 GTTGCGAATT
1 GTTGCGAATT
64665 CGTTGGTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.07
20 23 0.53
21 6 0.14
22 11 0.26
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.38
Consensus pattern (21 bp):
GTTGCGAATTTGGAAATTCTT
Found at i:64625 original size:42 final size:40
Alignment explanation
Indices: 64574--64664 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 40
64564 TGAATTCAGA
* *
64574 TTGCGAATTTGAAAACTGAGTTGCGAATTTAGGAAATTCTTG
1 TTGCGAATTTGAAAACTGAGTTGCGAAATT-GG-AATTCGTG
* * *
64616 TTGCGAATTTGGAAACTGTGTTGCGAAATTGGAGTTCGTG
1 TTGCGAATTTGAAAACTGAGTTGCGAAATTGGAATTCGTG
64656 TTGCGAATT
1 TTGCGAATT
64665 CGTTGGTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 15 0.34
41 2 0.05
42 27 0.61
ACGTcount: A:0.26, C:0.10, G:0.27, T:0.36
Consensus pattern (40 bp):
TTGCGAATTTGAAAACTGAGTTGCGAAATTGGAATTCGTG
Found at i:64647 original size:20 final size:20
Alignment explanation
Indices: 64574--64648 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 20
64564 TGAATTCAGA
* *
64574 TTGCGAATTTGAAAACTGAG
1 TTGCGAATTTGGAAACTGTG
64594 TTGCGAATTTAGGAAATTCT-TG
1 TTGCGAATTT-GGAAA--CTGTG
64616 TTGCGAATTTGGAAACTGTG
1 TTGCGAATTTGGAAACTGTG
*
64636 TTGCGAAATTGGA
1 TTGCGAATTTGGA
64649 GTTCGTGTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.04
20 24 0.50
21 9 0.19
22 11 0.23
23 2 0.04
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.35
Consensus pattern (20 bp):
TTGCGAATTTGGAAACTGTG
Found at i:66281 original size:76 final size:76
Alignment explanation
Indices: 66078--66281 Score: 261
Period size: 75 Copynumber: 2.7 Consensus size: 76
66068 CGTTGAACAA
* * * *
66078 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGC-ATACTGGAATTCTCGGAAC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAAT-CTGGAAATCTCGGAAC
** *
66141 AAAACTGTTTAG
65 AAAACCATTCAG
* * * * *
66153 GGGGGAATCGGTTCCTCCTAT-GGGGGAATTGGTTCCCTCCGAGCATTATGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAACA
66217 AAACCATTCAG
66 AAACCATTCAG
*
66228 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAA
66282 TTTTTGGCTT
Statistics
Matches: 110, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
75 80 0.73
76 30 0.27
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.24
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAACA
AAACCATTCAG
Found at i:66601 original size:21 final size:21
Alignment explanation
Indices: 66575--66617 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
66565 TCAAGTTTTG
* *
66575 AAATTACTCCTCCTTACTTTA
1 AAATTACGCCGCCTTACTTTA
66596 AAATTACGCCGCCTTACTTTA
1 AAATTACGCCGCCTTACTTTA
66617 A
1 A
66618 CACTTCTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (21 bp):
AAATTACGCCGCCTTACTTTA
Found at i:66913 original size:17 final size:17
Alignment explanation
Indices: 66891--66934 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
66881 TTCATAAATC
66891 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
66908 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
66925 -AAATATCCAA
1 CAAA-ATCCAA
66935 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:66926 original size:9 final size:8
Alignment explanation
Indices: 66886--66936 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
66876 TACTATTCAT
66886 AAATCC-A
1 AAATCCAA
66893 AAATCCAA
1 AAATCCAA
*
66901 CAATCCACA
1 AAATCCA-A
66910 AAAT-CAA
1 AAATCCAA
66917 ACAATCCAA
1 A-AATCCAA
66926 AATATCCAA
1 AA-ATCCAA
66935 AA
1 AA
66937 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:68890 original size:21 final size:20
Alignment explanation
Indices: 68866--68924 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
68856 AGAACCCCAG
*
68866 GGGGGTATCGATTCCC-CTGTA
1 GGGGG-ATCGATTCCCTCAG-A
*
68887 GGGGGAATCGGTTCCCTCAGA
1 GGGGG-ATCGATTCCCTCAGA
68908 GGGGGATCGATTCCCTC
1 GGGGGATCGATTCCCTC
68925 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.33
21 20 0.61
22 2 0.06
ACGTcount: A:0.15, C:0.25, G:0.36, T:0.24
Consensus pattern (20 bp):
GGGGGATCGATTCCCTCAGA
Found at i:74781 original size:75 final size:75
Alignment explanation
Indices: 74696--74901 Score: 263
Period size: 75 Copynumber: 2.7 Consensus size: 75
74686 CGTTGAACAA
* *
74696 GGGGGAATCGGTACCCCCT-TAGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
** *
74760 AAACTGTTTAG
65 AAACCATTCAG
* * * * * *
74771 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCCGGAAATCTCGGAGCCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAA
74836 AACCATTCAG
66 AACCATTCAG
*
74846 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 GGGGGAATCGGTTCCTCCTATGGGGGG-ATCGGTTCCCTCCGAGCATA-CTGGAATT
74902 TTTGGCTTTG
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
75 88 0.79
76 24 0.21
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (75 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAA
AACCATTCAG
Found at i:77797 original size:29 final size:30
Alignment explanation
Indices: 77730--77797 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
77720 TAATCATCTG
*
77730 ATGATATAATTGAAGTTAAAATAAAATTTTA
1 ATGATATAATTGAAG-TAAAATAAAAATTTA
* *
77761 AT-ATTATAGTTGAAG-AAATTAAAAATTTA
1 ATGA-TATAATTGAAGTAAAATAAAAATTTA
77790 ATGATATA
1 ATGATATA
77798 TGATCCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 18 0.56
30 2 0.06
31 12 0.38
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (30 bp):
ATGATATAATTGAAGTAAAATAAAAATTTA
Found at i:79224 original size:40 final size:39
Alignment explanation
Indices: 79162--79241 Score: 88
Period size: 40 Copynumber: 2.0 Consensus size: 39
79152 CTTATAAGGT
* * *
79162 TTTTTAATAGGCCTAAATCTGACATATTTAATTAAATAGG
1 TTTTTAAAAGGCCTAAACCTGACAT-TTTAACTAAATAGG
* * * *
79202 TTTTTAAAAGGCCTGAGCCTGACCTTTTTACTAAATAGG
1 TTTTTAAAAGGCCTAAACCTGACATTTTAACTAAATAGG
79241 T
1 T
79242 CAGGTCAGGC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
39 13 0.39
40 20 0.61
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.39
Consensus pattern (39 bp):
TTTTTAAAAGGCCTAAACCTGACATTTTAACTAAATAGG
Found at i:82802 original size:3 final size:3
Alignment explanation
Indices: 82759--82784 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
82749 AAATATTCAC
82759 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
82785 CATTTACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:84142 original size:12 final size:12
Alignment explanation
Indices: 84121--84153 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
84111 CTTATCTTCT
*
84121 AATTGGTGCTTA
1 AATTGATGCTTA
84133 AATTGATGCTTA
1 AATTGATGCTTA
84145 AATTGATGC
1 AATTGATGC
84154 ATAGAATAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (12 bp):
AATTGATGCTTA
Found at i:84327 original size:83 final size:83
Alignment explanation
Indices: 84133--84405 Score: 449
Period size: 83 Copynumber: 3.3 Consensus size: 83
84123 TTGGTGCTTA
* ** * *
84133 AATTGATGCTTAAATTGATGCATAGAATAGCCTAAATGGAAGTGTTAATCTCAAAGGGTCGTTTT
1 AATTGGTGCTTAAATTGATGCATAGCTTAGCCTACATGGAAGTGTTAATCTCAAAGGGTCATTTT
84198 TAGTG-ACCTTATCGTCT
66 TAGTGAACCTTATCGTCT
*
84215 AATTGGTGCTTAAATTTATGCATAGCTTAGCCTACATGGAAGTGTTAATCTCAAAGGGTCATTTT
1 AATTGGTGCTTAAATTGATGCATAGCTTAGCCTACATGGAAGTGTTAATCTCAAAGGGTCATTTT
84280 TAGTGAACCTTATCGTCT
66 TAGTGAACCTTATCGTCT
* *
84298 AATTGGTGCTTAAATTTATGCATAGCTTAGGCTACATGGAAGTGTTAATCTCAAAGGGTCATTTT
1 AATTGGTGCTTAAATTGATGCATAGCTTAGCCTACATGGAAGTGTTAATCTCAAAGGGTCATTTT
*
84363 TAGTGAACCTTATCATCT
66 TAGTGAACCTTATCGTCT
*
84381 AATTGGTGCCTAAATTGATGCATAG
1 AATTGGTGCTTAAATTGATGCATAG
84406 ATGGACCTCA
Statistics
Matches: 180, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 64 0.36
83 116 0.64
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.36
Consensus pattern (83 bp):
AATTGGTGCTTAAATTGATGCATAGCTTAGCCTACATGGAAGTGTTAATCTCAAAGGGTCATTTT
TAGTGAACCTTATCGTCT
Found at i:87021 original size:25 final size:25
Alignment explanation
Indices: 86971--87021 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
86961 TATGACTACG
*
86971 AAAAAATTAAAAATTAAAATATTAA
1 AAAAAATTAAAAATTAAAATACTAA
* * *
86996 AAAAAATTAATAATTTAGATACTAA
1 AAAAAATTAAAAATTAAAATACTAA
87021 A
1 A
87022 TAATACAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAAAATTAAAAATTAAAATACTAA
Done.