Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004896.1 Hibiscus syriacus cultivar Beakdansim tig00011019_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: 50536
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:810 original size:15 final size:15
Alignment explanation
Indices: 784--827 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
774 TGGAGAGGAA
784 ATGGAGGATGAGCATG
1 ATGGA-GATGAGCATG
800 ATGGAGATGAGCATG
1 ATGGAGATGAGCATG
* *
815 AAGCAGATGAGCA
1 ATGGAGATGAGCA
828 CATAGATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.36, C:0.09, G:0.39, T:0.16
Consensus pattern (15 bp):
ATGGAGATGAGCATG
Found at i:2596 original size:18 final size:18
Alignment explanation
Indices: 2573--2628 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
2563 ATATATATAC
2573 CCCTACTGAGTACTAATA
1 CCCTACTGAGTACTAATA
* *
2591 CCCTACTCAGTACTGATA
1 CCCTACTGAGTACTAATA
*
2609 TCCCCA-TGAGTACTCAATA
1 -CCCTACTGAGTACT-AATA
2628 C
1 C
2629 TATCTATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 24 0.77
19 7 0.23
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (18 bp):
CCCTACTGAGTACTAATA
Found at i:10645 original size:16 final size:15
Alignment explanation
Indices: 10620--10673 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
10610 TTTCAAATTG
10620 AAAT-TAATAACAAAT
1 AAATATAATAA-AAAT
10635 AAATATAAT--AAAT
1 AAATATAATAAAAAT
*
10648 AAATATAATAATAAT
1 AAATATAATAAAAAT
10663 -AATAATAATAA
1 AAAT-ATAATAA
10674 TTATTATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 13 0.38
14 3 0.09
15 14 0.41
16 4 0.12
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATAATAAAAAT
Found at i:10646 original size:9 final size:9
Alignment explanation
Indices: 10632--10704 Score: 64
Period size: 9 Copynumber: 8.1 Consensus size: 9
10622 ATTAATAACA
10632 AATAAATAT
1 AATAAATAT
10641 AATAAATA-
1 AATAAATAT
10649 AATATAATAAT
1 AATA-AAT-AT
10660 AAT-AATAAT
1 AATAAAT-AT
*
10669 AATAATTATT
1 AATAAATA-T
*
10679 ATTAAATAT
1 AATAAATAT
10688 AAT-AATAT
1 AATAAATAT
10696 -ATAAATAT
1 AATAAATAT
10704 A
1 A
10705 GTAATTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
7 2 0.04
8 14 0.26
9 24 0.45
10 10 0.19
11 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AATAAATAT
Found at i:10700 original size:16 final size:15
Alignment explanation
Indices: 10632--10709 Score: 72
Period size: 16 Copynumber: 5.0 Consensus size: 15
10622 ATTAATAACA
10632 AATAAATATAAT-A-
1 AATAAATATAATAAT
10645 AATAAATATAATAAT
1 AATAAATATAATAAT
10660 AAT-AATAATAATAATT
1 AATAAAT-ATAATAA-T
10676 ATTATTAAATATAATAAT
1 A--A-TAAATATAATAAT
*
10694 ATATAAATATAGTAAT
1 A-ATAAATATAATAAT
10710 TAAAATAGAT
Statistics
Matches: 56, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
13 12 0.21
14 4 0.07
15 10 0.18
16 14 0.25
17 2 0.04
18 3 0.05
19 8 0.14
20 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (15 bp):
AATAAATATAATAAT
Found at i:10711 original size:29 final size:28
Alignment explanation
Indices: 10639--10745 Score: 77
Period size: 29 Copynumber: 4.0 Consensus size: 28
10629 ACAAATAAAT
*
10639 ATAATAAATAAAT-ATAA-T-AATAATA-
1 ATAATATATAAATAATAATTAAAT-ATAG
* *
10664 ATAATA-AT-AATTATTATTAAATATA-
1 ATAATATATAAATAATAATTAAATATAG
10689 ATAATATATAAATATAGTAATTAAA-ATAG
1 ATAATATATAAATA-A-TAATTAAATATAG
* *
10718 ATATTTTATAAATAATAATTATAATATA
1 ATAATATATAAATAATAATTA-AATATA
10746 TTTTGAAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
23 3 0.04
24 5 0.07
25 16 0.24
26 5 0.07
27 9 0.13
28 7 0.10
29 22 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
ATAATATATAAATAATAATTAAATATAG
Found at i:10743 original size:9 final size:9
Alignment explanation
Indices: 10632--10743 Score: 52
Period size: 9 Copynumber: 12.4 Consensus size: 9
10622 ATTAATAACA
*
10632 AATAAATAT
1 AATAATTAT
* *
10641 AATAAATAA
1 AATAATTAT
*
10650 ATATAATAAT
1 A-ATAATTAT
*
10660 AATAATAAT
1 AATAATTAT
10669 AATAATTATT
1 AATAATTA-T
* *
10679 ATTAAATAT
1 AATAATTAT
10688 AATAA-TAT
1 AATAATTAT
*
10696 -ATAAATAT
1 AATAATTAT
* *
10704 AGTAATTAA
1 AATAATTAT
*
10713 AATAGATATTT
1 AATA-AT-TAT
*
10724 TATAA--AT
1 AATAATTAT
10731 AATAATTAT
1 AATAATTAT
10740 AATA
1 AATA
10744 TATTTTGAAA
Statistics
Matches: 78, Mismatches: 17, Indels: 16
0.70 0.15 0.14
Matches are distributed among these distances:
7 9 0.12
8 6 0.08
9 43 0.55
10 16 0.21
11 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
AATAATTAT
Found at i:17918 original size:18 final size:20
Alignment explanation
Indices: 17881--17920 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
17871 ATATTTCACC
17881 ATTAGCAGATATTTACAGTT
1 ATTAGCAGATATTTACAGTT
*
17901 ATTAGCCGAT-TTTA-AGTT
1 ATTAGCAGATATTTACAGTT
17919 AT
1 AT
17921 CAAATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 4 0.21
20 9 0.47
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (20 bp):
ATTAGCAGATATTTACAGTT
Found at i:23327 original size:13 final size:12
Alignment explanation
Indices: 23307--23365 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
23297 AATTACTATG
23307 TTTATT-TATTA
1 TTTATTATATTA
*
23318 TTATATTTTAATTA
1 TT-TATTAT-ATTA
23332 TTTATTATACTTA
1 TTTATTATA-TTA
23345 TTTATTATATTTA
1 TTTATTATA-TTA
*
23358 TTTGTTAT
1 TTTATTAT
23366 TAATTTCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 2 0.05
12 5 0.12
13 28 0.68
14 6 0.15
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTATTATATTA
Found at i:23346 original size:30 final size:30
Alignment explanation
Indices: 23285--23356 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
23275 TTATTTAAAA
* *
23285 ATTA-TATATTTTAATTACTATGTTTATTT
1 ATTATTATATTTTAATTACTATGTATACTT
*
23314 ATTATTATATTTTAATTATTTAT-TATACTT
1 ATTATTATATTTTAATTA-CTATGTATACTT
23344 ATTTATTATATTT
1 A-TTATTATATTT
23357 ATTTGTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 4 0.11
30 19 0.51
31 14 0.38
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (30 bp):
ATTATTATATTTTAATTACTATGTATACTT
Found at i:26014 original size:3 final size:3
Alignment explanation
Indices: 26003--26071 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
25993 TTAAATAATA
* *
26003 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAC TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * *
26047 TAT TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
26072 TTTGCAGACT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:30131 original size:41 final size:43
Alignment explanation
Indices: 30086--30174 Score: 128
Period size: 47 Copynumber: 2.0 Consensus size: 43
30076 GCATTCTGTT
30086 TGAAC-TTTTTTTTT-CCACTTTTTCAAGTTTTTGTAAGAACG
1 TGAACTTTTTTTTTTCCCACTTTTTCAAGTTTTTGTAAGAACG
30127 TGAACTTGTTTTTTTTTTCCCCACTTTTTCAAGTTTTTGTAAGAACG
1 TGAAC---TTTTTTTTTT-CCCACTTTTTCAAGTTTTTGTAAGAACG
30174 T
1 T
30175 TTGAATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
41 5 0.12
45 9 0.21
47 28 0.67
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.52
Consensus pattern (43 bp):
TGAACTTTTTTTTTTCCCACTTTTTCAAGTTTTTGTAAGAACG
Found at i:32037 original size:106 final size:106
Alignment explanation
Indices: 31896--33426 Score: 2497
Period size: 106 Copynumber: 14.4 Consensus size: 106
31886 GACAACACAA
*
31896 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
* *
31961 TCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTAT
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* * *
32002 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACGATTTCCCAATATCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
32067 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* * *
32108 GTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
** *
32173 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* *
32214 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTTAATTTCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
*
32279 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAT
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* *
32320 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATATCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
32385 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* *
32426 GTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATATCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
* * *
32491 TCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* *
32532 GTTCAACTTCAAGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
* *
32597 TCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTAT
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* * *
32638 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACGATTTCCCAATATCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
32703 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* * * *
32744 GTTCAACTTCACAACGAAGGGACTGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
* *
32809 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* *
32850 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTTAATTTCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
*
32915 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAT
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* *
32956 GTTCAACTTCACGACGAA-GGACCGCTGGTTGTCAACAAACAATTTCCCAATATCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
33020 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* *
33061 GTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATATCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
* * *
33126 TCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* *
33167 GTTCAACTTCAAGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
* * * *
33232 TCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
* * *
33273 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGTCAATT
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
* * * * * *
33338 TCAACTTCATAGCAAAGGATATTGGACTCAAGACAACGCAA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
*
33379 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTC
1 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTC
33427 AACTTCACGA
Statistics
Matches: 1335, Mismatches: 88, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
105 99 0.07
106 1232 0.92
107 4 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAT
Found at i:32462 original size:318 final size:318
Alignment explanation
Indices: 31880--33426 Score: 2772
Period size: 318 Copynumber: 4.9 Consensus size: 318
31870 ATATCGTGCC
* *
31880 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
31945 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTATGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACT
*
32010 TCACGACGAAGGGACCGCTGGTTGTCAACAAACGATTTCCCAATATCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTC
32075 ACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTG
196 ACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTG
* *
32140 TCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
261 TCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
32198 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
32263 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACT
32328 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTC
32393 ACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTG
196 ACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTG
*
32458 TCAACAAACAATTTCTCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
261 TCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
32516 ACTCTAGACAACGCAAGTTCAACTTCAAGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
32581 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTATGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACT
*
32646 TCACGACGAAGGGACCGCTGGTTGTCAACAAACGATTTCCCAATATCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTC
*
32711 ACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACTGCTGGTTG
196 ACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTG
* *
32776 TCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
261 TCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
32834 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
32899 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACT
32964 TCACGACGAA-GGACCGCTGGTTGTCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTC
33028 ACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTG
196 ACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTG
*
33093 TCAACAAACAATTTCTCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
261 TCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
33151 ACTCTAGACAACGCAAGTTCAACTTCAAGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * *
33216 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACT
* * *
33281 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTC
* * * * * * *
33346 ATAGCAAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
196 ACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTG
*
33411 TCAATAAACAACTTTC
261 TCAACAAACAA-TTTC
33427 AACTTCACGA
Statistics
Matches: 1184, Mismatches: 43, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
317 306 0.26
318 874 0.74
319 4 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (318 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTC
ACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTG
TCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:33613 original size:84 final size:85
Alignment explanation
Indices: 33480--33656 Score: 257
Period size: 84 Copynumber: 2.1 Consensus size: 85
33470 AAAGACCCCC
* * *
33480 GAGTTCGATTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTAT
* * * *
33545 CTTCTAACCAAAGATCT-TT
66 CTGCCAACCAAAGACCTGAT
* * *
33564 GAGTTCGACTACGCTCAGCTCCGAGGCACATCATTTGCAGCATAGCTTAAGTTGAGAAGGGCTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTAT
33629 CTGCCAACCAAAGACCTGAT
66 CTGCCAACCAAAGACCTGAT
33649 GAGTTCGA
1 GAGTTCGA
33657 TTTCATTCAG
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 73 0.89
85 9 0.11
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (85 bp):
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTAT
CTGCCAACCAAAGACCTGAT
Found at i:33896 original size:3 final size:3
Alignment explanation
Indices: 33885--33953 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
33875 TTAAATAATA
* *
33885 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAC TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * *
33929 TAT TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
33954 TTTGCAGACT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:36987 original size:17 final size:18
Alignment explanation
Indices: 36965--36998 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
36955 GTTAATAAAA
36965 TTTTAAATAAA-ATTTAT
1 TTTTAAATAAATATTTAT
*
36982 TTTTAATTAAATATTTA
1 TTTTAAATAAATATTTA
36999 AATTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAATAAATATTTAT
Found at i:38709 original size:36 final size:36
Alignment explanation
Indices: 38669--38822 Score: 202
Period size: 36 Copynumber: 4.2 Consensus size: 36
38659 TAAAATAGTC
* * * *
38669 ATTTCCAATACTAGTGGAAATACCTAATTTGATCAT
1 ATTTCCAATGCTAGTGGAAAAACCTAACTTGAGCAT
38705 ATTTCCAATGCTAGTGGAAAAACCTAACTTGAGCAT
1 ATTTCCAATGCTAGTGGAAAAACCTAACTTGAGCAT
38741 -TTATCCAATGCTAGTGGAAAAACCTAACTTGAGCAT
1 ATT-TCCAATGCTAGTGGAAAAACCTAACTTGAGCAT
* * * *
38777 TTTTCCAGTGCTAGTGGAAATACCTAATTTGAGCATT
1 ATTTCCAATGCTAGTGGAAAAACCTAACTTGAGCA-T
*
38814 TTTTCCAAT
1 ATTTCCAAT
38823 AGTCAATTGA
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
35 2 0.02
36 94 0.88
37 11 0.10
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (36 bp):
ATTTCCAATGCTAGTGGAAAAACCTAACTTGAGCAT
Found at i:44020 original size:36 final size:35
Alignment explanation
Indices: 43969--44107 Score: 155
Period size: 36 Copynumber: 4.0 Consensus size: 35
43959 TAAAATAGTC
*
43969 ATTTCCAATAGTAGTGGAAATACCTAATTTGAGCAT
1 ATTTCCAAT-GTAGTGGAAATACCTAACTTGAGCAT
*
44005 ATTTCCAATGCTAGTGGAAAAACCTAACTTGAGCAT
1 ATTTCCAATG-TAGTGGAAATACCTAACTTGAGCAT
44041 -TTATCCAATGCTAGTGGAAA-ACCCTAACTTGAGCAT
1 ATT-TCCAATG-TAGTGGAAATA-CCTAACTTGAGCAT
* *
44077 TTTTCC-A---AGTGGAAATACCTAATTTGAGCAT
1 ATTTCCAATGTAGTGGAAATACCTAACTTGAGCAT
44108 TTTTTTCCAA
Statistics
Matches: 95, Mismatches: 3, Indels: 15
0.84 0.03 0.13
Matches are distributed among these distances:
31 21 0.22
32 1 0.01
35 5 0.05
36 66 0.69
37 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (35 bp):
ATTTCCAATGTAGTGGAAATACCTAACTTGAGCAT
Found at i:45536 original size:18 final size:19
Alignment explanation
Indices: 45513--45556 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
45503 CCGGTCTGAC
45513 CCGACCTGA-CCGACCCAA-
1 CCGACC-GACCCGACCCAAT
45531 CCGACCGACCCGACCCAAT
1 CCGACCGACCCGACCCAAT
45550 CCGACCG
1 CCGACCG
45557 TTGACCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.08
18 15 0.62
19 7 0.29
ACGTcount: A:0.25, C:0.52, G:0.18, T:0.05
Consensus pattern (19 bp):
CCGACCGACCCGACCCAAT
Done.