Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009126.1 Hibiscus syriacus cultivar Beakdansim tig00112622_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: 86541
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:1607 original size:29 final size:29
Alignment explanation
Indices: 1573--1634 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 29
1563 TGGACTAATT
1573 ATTTAAT-AATAAGGAAATAATTTGAGCAG
1 ATTTAATAAAT-AGGAAATAATTTGAGCAG
1602 ATTTAATAAATAGGAAATAATTTGAGCAG
1 ATTTAATAAATAGGAAATAATTTGAGCAG
1631 ATTT
1 ATTT
1635 TCTATGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (29 bp):
ATTTAATAAATAGGAAATAATTTGAGCAG
Found at i:2614 original size:30 final size:29
Alignment explanation
Indices: 2546--2625 Score: 92
Period size: 27 Copynumber: 2.8 Consensus size: 29
2536 GTCGACGAGC
* * *
2546 CTGCGTCCGGAGCAGCCGGTGTCAACGAA
1 CTGCGTTCGGAGCTGCCAGTGTCAACGAA
*
2575 C--CTTTCGGAGCTGCCAGTGTCAACGAA
1 CTGCGTTCGGAGCTGCCAGTGTCAACGAA
*
2602 CGTGCGTTCGGAGCTGCCTGTGTC
1 C-TGCGTTCGGAGCTGCCAGTGTC
2626 GATGGACCAG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 23 0.55
29 1 0.02
30 18 0.43
ACGTcount: A:0.16, C:0.30, G:0.33, T:0.21
Consensus pattern (29 bp):
CTGCGTTCGGAGCTGCCAGTGTCAACGAA
Found at i:9880 original size:26 final size:26
Alignment explanation
Indices: 9851--9912 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
9841 CCTAAGAATG
9851 AAGAATTGTAAATCTTTCTTAATTTA
1 AAGAATTGTAAATCTTTCTTAATTTA
9877 AAGAATTGTAAATCTTTCTTAATTTA
1 AAGAATTGTAAATCTTTCTTAATTTA
9903 AAGAATTGTA
1 AAGAATTGTA
9913 TAGCTCAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (26 bp):
AAGAATTGTAAATCTTTCTTAATTTA
Found at i:20479 original size:27 final size:27
Alignment explanation
Indices: 20427--20479 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
20417 AATTGAATAT
* *
20427 ATTTTATTAATTTATAATTGTGTTTTG
1 ATTTTATTAATATATAATTCTGTTTTG
*
20454 ATTTTATTTATATAT-ATTCTGATTTT
1 ATTTTATTAATATATAATTCTG-TTTT
20480 TTGTTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (27 bp):
ATTTTATTAATATATAATTCTGTTTTG
Found at i:20528 original size:16 final size:18
Alignment explanation
Indices: 20502--20546 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
20492 TACTTTGCCG
*
20502 TTGCAAATTATGTTT-TT
1 TTGCTAATTATGTTTCTT
20519 TT-CTAATTAT-TTTCTT
1 TTGCTAATTATGTTTCTT
*
20535 TTGTTAATTATG
1 TTGCTAATTATG
20547 AAACGTAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 3 0.13
16 11 0.48
17 9 0.39
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.62
Consensus pattern (18 bp):
TTGCTAATTATGTTTCTT
Found at i:21910 original size:30 final size:30
Alignment explanation
Indices: 21874--21942 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
21864 GGTGTAGGTA
*
21874 GTGGAGGTGGTGGCGGATTCGGAGGTGGTG
1 GTGGAGGTGGTGGCGGATTCGGAGGTAGTG
*
21904 GTGGAGGTGGTGGCGGATTCGGTGGTAGTG
1 GTGGAGGTGGTGGCGGATTCGGAGGTAGTG
21934 GTGGAGGTG
1 GTGGAGGTG
21943 CCAGCGGTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.10, C:0.06, G:0.59, T:0.25
Consensus pattern (30 bp):
GTGGAGGTGGTGGCGGATTCGGAGGTAGTG
Found at i:21937 original size:36 final size:36
Alignment explanation
Indices: 21874--21975 Score: 101
Period size: 36 Copynumber: 3.0 Consensus size: 36
21864 GGTGTAGGTA
*
21874 GTGGAGGTGGTGGCGGATTC---GG-A--GGTGGTG
1 GTGGAGGTGGTGGCGGATTCGGTGGTAGTGGTGGAG
21904 GTGGAGGTGGTGGCGGATTCGGTGGTAGTGGTGGAG
1 GTGGAGGTGGTGGCGGATTCGGTGGTAGTGGTGGAG
* * * *
21940 GTGCCA-GCGGTGGTGGGTTCGGTGGTAGTGGTGGAG
1 GTG-GAGGTGGTGGCGGATTCGGTGGTAGTGGTGGAG
21976 CGGGTGGAGG
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
30 20 0.33
33 2 0.03
34 1 0.02
36 36 0.60
37 1 0.02
ACGTcount: A:0.10, C:0.08, G:0.58, T:0.25
Consensus pattern (36 bp):
GTGGAGGTGGTGGCGGATTCGGTGGTAGTGGTGGAG
Found at i:21988 original size:36 final size:39
Alignment explanation
Indices: 21900--21988 Score: 105
Period size: 36 Copynumber: 2.4 Consensus size: 39
21890 ATTCGGAGGT
21900 GGTGGTGGAGGTGGTGGCGGATTCGGTGGTAGTGGTGGA
1 GGTGGTGGAGGTGGTGGCGGATTCGGTGGTAGTGGTGGA
*** *
21939 GGTGCCAGCGGTGGT-G-GG-TTCGGTGGTAGTGGTGGA
1 GGTGGTGGAGGTGGTGGCGGATTCGGTGGTAGTGGTGGA
21975 GCG-GGTGGAGGTGG
1 G-GTGGTGGAGGTGG
21989 AGGTGCTAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
36 26 0.63
37 3 0.07
38 1 0.02
39 11 0.27
ACGTcount: A:0.09, C:0.08, G:0.60, T:0.24
Consensus pattern (39 bp):
GGTGGTGGAGGTGGTGGCGGATTCGGTGGTAGTGGTGGA
Found at i:22020 original size:18 final size:18
Alignment explanation
Indices: 21984--22022 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21974 AGCGGGTGGA
*
21984 GGTGGAGGTGCTAGCGGT
1 GGTGGAGGTGCTAGAGGT
* *
22002 GGTGTAGGTGCTGGAGGT
1 GGTGGAGGTGCTAGAGGT
22020 GGT
1 GGT
22023 ATTGGAGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.10, C:0.08, G:0.56, T:0.26
Consensus pattern (18 bp):
GGTGGAGGTGCTAGAGGT
Found at i:22108 original size:30 final size:30
Alignment explanation
Indices: 22074--22131 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
22064 TGGTGGTGTA
* *
22074 GGTGTAGGAGGAGGTGCAGGTGCTGGAGGT
1 GGTGTAGGAGCAGGTGCAGGAGCTGGAGGT
* * *
22104 GGTGTTGGTGCAGGTGGAGGAGCTGGAG
1 GGTGTAGGAGCAGGTGCAGGAGCTGGAG
22132 TTGGAGTTGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.16, C:0.07, G:0.57, T:0.21
Consensus pattern (30 bp):
GGTGTAGGAGCAGGTGCAGGAGCTGGAGGT
Found at i:22125 original size:24 final size:24
Alignment explanation
Indices: 22086--22135 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
22076 TGTAGGAGGA
* * *
22086 GGTGCAGGTGCTGGAGGTGGTGTT
1 GGTGCAGGTGCAGGAGCTGGAGTT
*
22110 GGTGCAGGTGGAGGAGCTGGAGTT
1 GGTGCAGGTGCAGGAGCTGGAGTT
22134 GG
1 GG
22136 AGTTGGAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.08, G:0.56, T:0.24
Consensus pattern (24 bp):
GGTGCAGGTGCAGGAGCTGGAGTT
Found at i:22137 original size:36 final size:36
Alignment explanation
Indices: 22065--22149 Score: 89
Period size: 36 Copynumber: 2.4 Consensus size: 36
22055 TGGCGGAGGT
* * * *
22065 GGTGGTGTAGGTGTAGGAGGAGGTGCAGGTGCTGGA
1 GGTGGTGTTGGTGCAGGAGGAGGAGCAGGAGCTGGA
* * *
22101 GGTGGTGTTGGTGCAGGTGGAGGAGCTGGAGTTGGA
1 GGTGGTGTTGGTGCAGGAGGAGGAGCAGGAGCTGGA
* *
22137 GTTGGAGTTGGTG
1 GGTGGTGTTGGTG
22150 TCAGTGGTGG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.14, C:0.05, G:0.55, T:0.26
Consensus pattern (36 bp):
GGTGGTGTTGGTGCAGGAGGAGGAGCAGGAGCTGGA
Found at i:22141 original size:30 final size:30
Alignment explanation
Indices: 22085--22141 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
22075 GTGTAGGAGG
* *
22085 AGGTGCAGGTGCTGGAGGTGGTGTTGGTGC
1 AGGTGCAGGAGCTGGAGGTGGAGTTGGTGC
* *
22115 AGGTGGAGGAGCTGGAGTTGGAGTTGG
1 AGGTGCAGGAGCTGGAGGTGGAGTTGG
22142 AGTTGGTGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.14, C:0.07, G:0.54, T:0.25
Consensus pattern (30 bp):
AGGTGCAGGAGCTGGAGGTGGAGTTGGTGC
Found at i:22317 original size:15 final size:15
Alignment explanation
Indices: 22287--22353 Score: 62
Period size: 15 Copynumber: 4.5 Consensus size: 15
22277 TGTAGGTGCT
**
22287 GGAGGTGGTGCTGGA
1 GGAGGTGGTGGAGGA
*
22302 GCAGGTGGTGGAGGA
1 GGAGGTGGTGGAGGA
* * *
22317 GGGGGAGGAGGAGGA
1 GGAGGTGGTGGAGGA
*
22332 GGAGGTGGTGGTGGA
1 GGAGGTGGTGGAGGA
*
22347 GGTGGTG
1 GGAGGTG
22354 TTGGTGCAGT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.16, C:0.03, G:0.66, T:0.15
Consensus pattern (15 bp):
GGAGGTGGTGGAGGA
Found at i:22347 original size:12 final size:12
Alignment explanation
Indices: 22281--22507 Score: 58
Period size: 12 Copynumber: 19.5 Consensus size: 12
22271 TGGTGGTGTA
*
22281 GGTGCTGGAGGT
1 GGTGGTGGAGGT
* **
22293 GGTGCTGGAGCA
1 GGTGGTGGAGGT
22305 GGTGGTGGAGG-
1 GGTGGTGGAGGT
* *
22316 AG-GG-GGAGGA
1 GGTGGTGGAGGT
* *
22326 GGAGGAGGAGGT
1 GGTGGTGGAGGT
22338 GGTGGTGGAGGT
1 GGTGGTGGAGGT
* * *
22350 GGTGTTGG-TGC
1 GGTGGTGGAGGT
* * *
22361 AGTGGAGGAGGA
1 GGTGGTGGAGGT
* * *
22373 GGAGCTGGAGTT
1 GGTGGTGGAGGT
*
22385 GGT-GTCGGCGGT
1 GGTGGT-GGAGGT
22397 GGT-GT--AGGT
1 GGTGGTGGAGGT
* * *
22406 GCTGGAGGTGGT
1 GGTGGTGGAGGT
* * *
22418 GTTGGAGCAGGT
1 GGTGGTGGAGGT
* * *
22430 GGAGGAGGAGGA
1 GGTGGTGGAGGT
*
22442 CGTGGTGGAGGT
1 GGTGGTGGAGGT
* * *
22454 GGAGTTGGAGTT
1 GGTGGTGGAGGT
*
22466 GGTGGTGG-TGT
1 GGTGGTGGAGGT
*
22477 AGGTGTTGGAGGT
1 -GGTGGTGGAGGT
* *
22490 GGTGTTGGAGCT
1 GGTGGTGGAGGT
22502 GGTGGT
1 GGTGGT
22508 AGCGGTGGAG
Statistics
Matches: 151, Mismatches: 54, Indels: 20
0.67 0.24 0.09
Matches are distributed among these distances:
9 10 0.07
10 4 0.03
11 11 0.07
12 124 0.82
13 2 0.01
ACGTcount: A:0.14, C:0.05, G:0.59, T:0.23
Consensus pattern (12 bp):
GGTGGTGGAGGT
Found at i:22415 original size:18 final size:18
Alignment explanation
Indices: 22394--22494 Score: 58
Period size: 18 Copynumber: 5.4 Consensus size: 18
22384 TGGTGTCGGC
22394 GGTGGTGTAGGTGCTGGA
1 GGTGGTGTAGGTGCTGGA
* *
22412 GGTGGTGTTGGAGCAGGTGGA
1 GGTGGTGTAGGTGC---TGGA
* * * * *
22433 GGAGGAGGACGTGGTGGA
1 GGTGGTGTAGGTGCTGGA
* * * * *
22451 GGTGGAGTTGGAGTTGGT
1 GGTGGTGTAGGTGCTGGA
*
22469 GGTGGTGTAGGTGTTGGA
1 GGTGGTGTAGGTGCTGGA
22487 GGTGGTGT
1 GGTGGTGT
22495 TGGAGCTGGT
Statistics
Matches: 60, Mismatches: 20, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
18 49 0.82
21 11 0.18
ACGTcount: A:0.13, C:0.03, G:0.57, T:0.27
Consensus pattern (18 bp):
GGTGGTGTAGGTGCTGGA
Found at i:22505 original size:24 final size:24
Alignment explanation
Indices: 22443--22580 Score: 69
Period size: 24 Copynumber: 6.0 Consensus size: 24
22433 GGAGGAGGAC
* * *
22443 GTGGTGGAGGTGGAGTTGGAGTTG
1 GTGGTGGAGCTGGTGTTGGAGGTG
*
22467 GTGGTGGTG-TAGGTGTTGGAGGTG
1 GTGGTGGAGCT-GGTGTTGGAGGTG
* * *
22491 GTGTTGGAGCTGGTG--GTA-GCG
1 GTGGTGGAGCTGGTGTTGGAGGTG
* * *
22512 GTGGAGGA---GGTGTTGGTGGCG
1 GTGGTGGAGCTGGTGTTGGAGGTG
* *
22533 GTGTTGGAGCTGGTGTTGG-TGTCG
1 GTGGTGGAGCTGGTGTTGGAGGT-G
*
22557 GTGGTGGTG-TAGGTGTTGGAGGTG
1 GTGGTGGAGCT-GGTGTTGGAGGTG
22581 ATGCTGGCGC
Statistics
Matches: 85, Mismatches: 18, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
18 4 0.05
20 1 0.01
21 17 0.20
22 2 0.02
23 3 0.04
24 55 0.65
25 3 0.04
ACGTcount: A:0.09, C:0.04, G:0.57, T:0.31
Consensus pattern (24 bp):
GTGGTGGAGCTGGTGTTGGAGGTG
Found at i:22537 original size:12 final size:12
Alignment explanation
Indices: 22520--22575 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
22510 CGGTGGAGGA
22520 GGTGTTGGTGGC
1 GGTGTTGGTGGC
*
22532 GGTGTTGG-AGC
1 GGTGTTGGTGGC
*
22543 TGGTGTTGGTGTC
1 -GGTGTTGGTGGC
* **
22556 GGTGGTGGTGTA
1 GGTGTTGGTGGC
22568 GGTGTTGG
1 GGTGTTGG
22576 AGGTGATGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 2 0.06
12 33 0.92
13 1 0.03
ACGTcount: A:0.04, C:0.05, G:0.55, T:0.36
Consensus pattern (12 bp):
GGTGTTGGTGGC
Found at i:22580 original size:18 final size:18
Alignment explanation
Indices: 22447--22580 Score: 79
Period size: 18 Copynumber: 7.4 Consensus size: 18
22437 GAGGACGTGG
* *
22447 TGGAGGTGGAGTTGGAGT
1 TGGAGGTGGTGTTGGTGT
* *
22465 TGGTGGTGGTGTAGGTGT
1 TGGAGGTGGTGTTGGTGT
* *
22483 TGGAGGTGGTGTTGGAGC
1 TGGAGGTGGTGTTGGTGT
* * * * * *
22501 TGGTGGTAGCGGTGGAGG
1 TGGAGGTGGTGTTGGTGT
* * * **
22519 AGGTGTTGGTGGCGGTGT
1 TGGAGGTGGTGTTGGTGT
*
22537 TGGAGCTGGTGTTGGTGT
1 TGGAGGTGGTGTTGGTGT
* * *
22555 CGGTGGTGGTGTAGGTGT
1 TGGAGGTGGTGTTGGTGT
22573 TGGAGGTG
1 TGGAGGTG
22581 ATGCTGGCGC
Statistics
Matches: 85, Mismatches: 31, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 85 1.00
ACGTcount: A:0.09, C:0.04, G:0.56, T:0.31
Consensus pattern (18 bp):
TGGAGGTGGTGTTGGTGT
Found at i:22674 original size:30 final size:30
Alignment explanation
Indices: 22597--22661 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
22587 GCGCCAGAGT
* * * *
22597 TGGTTTAGGAGGACGTGGTGGAGGTGGTGC
1 TGGTGTAGGAGGAGGAGCTGGAGGTGGTGC
*
22627 TGGTGTAGGAGGAGGAGCTGGAGGTGGTGT
1 TGGTGTAGGAGGAGGAGCTGGAGGTGGTGC
22657 TGGTG
1 TGGTG
22662 CTGGCGGTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.14, C:0.05, G:0.55, T:0.26
Consensus pattern (30 bp):
TGGTGTAGGAGGAGGAGCTGGAGGTGGTGC
Found at i:22689 original size:42 final size:42
Alignment explanation
Indices: 22643--22743 Score: 184
Period size: 42 Copynumber: 2.4 Consensus size: 42
22633 AGGAGGAGGA
22643 GCTGGAGGTGGTGTTGGTGCTGGCGGTGGAGCAGGTGCAGAG
1 GCTGGAGGTGGTGTTGGTGCTGGCGGTGGAGCAGGTGCAGAG
*
22685 GCTGGAAGTGGTGTTGGTGCTGGCGGTGGAGCAGGTGCAGAG
1 GCTGGAGGTGGTGTTGGTGCTGGCGGTGGAGCAGGTGCAGAG
*
22727 GTTGGAGGTGGTGTTGG
1 GCTGGAGGTGGTGTTGG
22744 AGTTGGTGTC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.12, C:0.10, G:0.54, T:0.24
Consensus pattern (42 bp):
GCTGGAGGTGGTGTTGGTGCTGGCGGTGGAGCAGGTGCAGAG
Found at i:26825 original size:51 final size:51
Alignment explanation
Indices: 26694--26825 Score: 137
Period size: 51 Copynumber: 2.6 Consensus size: 51
26684 CTTCAAGTCG
* *
26694 AAGTGACGAATTTTAATAAAAAATATT-TTTTATTCAAACTTTTTACCTCG
1 AAGTGACGAATTTTAATAAAAAATATTATTTTATTCAAACTTTTCACCTCA
* ** *
26744 ATGTGATAAATTTTAATCAAAAAT-TATATTTTATT-AGAA-TTTATCACCTCA
1 AAGTGACGAATTTTAATAAAAAATAT-TATTTTATTCA-AACTTT-TCACCTCA
* *
26795 AAGTGACGAGTTTAAATAAAAAATATTATTT
1 AAGTGACGAATTTTAATAAAAAATATTATTT
26826 GTTAGAACTC
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
49 1 0.02
50 25 0.38
51 38 0.58
52 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (51 bp):
AAGTGACGAATTTTAATAAAAAATATTATTTTATTCAAACTTTTCACCTCA
Found at i:33205 original size:24 final size:24
Alignment explanation
Indices: 33177--33234 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
33167 GGTATTAAAT
33177 CAGCCCAAGCCATGGTCTATAGGG
1 CAGCCCAAGCCATGGTCTATAGGG
33201 CAGCCCAAGCCATGGTCTATAGGG
1 CAGCCCAAGCCATGGTCTATAGGG
33225 CAGCCCAAGC
1 CAGCCCAAGC
33235 AATATGCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.26, C:0.33, G:0.28, T:0.14
Consensus pattern (24 bp):
CAGCCCAAGCCATGGTCTATAGGG
Found at i:33617 original size:32 final size:32
Alignment explanation
Indices: 33526--33620 Score: 93
Period size: 32 Copynumber: 3.0 Consensus size: 32
33516 TGATTAGATA
* * *
33526 ATATCACATC-TTCACTTTGAATAACGTGACAC
1 ATATCACATCATT-ATTTTAAATAATGTGACAC
* *** *
33558 ATATCATATCATTATTTTGGGTAATGTGATAC
1 ATATCACATCATTATTTTAAATAATGTGACAC
*
33590 ATATCACATCATTATTTTAAATGATGTGACA
1 ATATCACATCATTATTTTAAATAATGTGACA
33621 TGTACGCTGG
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 48 0.96
33 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (32 bp):
ATATCACATCATTATTTTAAATAATGTGACAC
Found at i:36019 original size:15 final size:16
Alignment explanation
Indices: 35999--36031 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35989 TAATTTAATG
*
35999 ATTATAT-ATAAATAA
1 ATTATATAAAAAATAA
36014 ATTATATAAAAAATAA
1 ATTATATAAAAAATAA
36030 AT
1 AT
36032 ATAATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTATATAAAAAATAA
Found at i:36487 original size:14 final size:15
Alignment explanation
Indices: 36454--36497 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
36444 TTGTTGGAAA
*
36454 TAAAATAAAATAAAT
1 TAAAATTAAATAAAT
36469 T-AAATTAAAT-AAT
1 TAAAATTAAATAAAT
36482 TAAAATT-AATAAAT
1 TAAAATTAAATAAAT
36496 TA
1 TA
36498 TCTTCTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 7 0.27
14 18 0.69
15 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATTAAATAAAT
Found at i:48085 original size:21 final size:22
Alignment explanation
Indices: 48056--48097 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
48046 CCTGTTTCCT
48056 CCTTCTTCTTGACCTTGTAAGG
1 CCTTCTTCTTGACCTTGTAAGG
48078 CCTT-TTCTTGACCTTGTAAG
1 CCTTCTTCTTGACCTTGTAAG
48098 ACCCCAGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (22 bp):
CCTTCTTCTTGACCTTGTAAGG
Found at i:49307 original size:20 final size:20
Alignment explanation
Indices: 49279--49332 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
49269 TTGTTTCACA
*
49279 GAATATAAGATTATTAGTGG
1 GAATGTAAGATTATTAGTGG
49299 GAATGTAAGATTATTAGTGG
1 GAATGTAAGATTATTAGTGG
*
49319 GAGTGTAAGATTAT
1 GAATGTAAGATTAT
49333 CAGGGAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35
Consensus pattern (20 bp):
GAATGTAAGATTATTAGTGG
Found at i:49567 original size:37 final size:37
Alignment explanation
Indices: 49494--49568 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
49484 GTTGAAAAAT
* *
49494 ATTTATATATTTTATTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAAATTAAAAATCATAAA
* *
49531 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTATTTAAAAAATTAAAAATCATAAA
49568 A
1 A
49569 ATGTTTAATG
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:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTATTTAAAAAATTAAAAATCATAAA
Found at i:51283 original size:37 final size:36
Alignment explanation
Indices: 51208--51283 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
51198 TTTTTATATT
*
51208 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
51244 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
51281 TTT
1 TTT
51284 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:52189 original size:32 final size:29
Alignment explanation
Indices: 52122--52189 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
52112 TATATATTTT
52122 AAATGATGATGTGGCATATCACATGTAAA
1 AAATGATGATGTGGCATATCACATGTAAA
* *
52151 AAATGATGATGTGGTATATCACATGTCAA
1 AAATGATGATGTGGCATATCACATGTAAA
52180 AAATGATGAT
1 AAATGATGAT
52190 ATTATACATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (29 bp):
AAATGATGATGTGGCATATCACATGTAAA
Found at i:57286 original size:15 final size:14
Alignment explanation
Indices: 57254--57299 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
57244 ATATTTAGTA
57254 TTTAAATTATT-AAT
1 TTTAAATT-TTAAAT
*
57268 TTTAATTTTTAATAT
1 TTTAAATTTTAA-AT
57283 TTTAAATTTTAAAT
1 TTTAAATTTTAAAT
57297 TTT
1 TTT
57300 GTTAAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.07
14 13 0.46
15 13 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAAATTTTAAAT
Found at i:60037 original size:190 final size:189
Alignment explanation
Indices: 59676--60046 Score: 559
Period size: 190 Copynumber: 2.0 Consensus size: 189
59666 ATTTTAAATA
* * *
59676 TATTATATATAACATATGGGCTCAACCCAAACCATTTAATATCCAATTAATAATTTAAGATCCAA
1 TATTATATATAACATATAGGCTCAACCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAA
* *
59741 TAATTTTTAAACCTAAATCAATATTAAATAATTAAAAAAAATTATATAAAATTATTATTTTATAA
66 TAACTTTTAAACCTAAATCAATATTAAATAATTAAAAAAAATTATATAAAATTATTAATTTATAA
* *
59806 TTATATATTATTTAAATTAATTGTAAAGTTTTTTCTGAATTAAAAAAATATTAAATATAT
131 TTATATATTATTTAAATTAATTATAAAGTTTGTTCTGAATT-AAAAAATATTAAATATAT
* *
59866 TATTATATATAACATATAGGCTCAGCCCAAACCATTTAAAACCCAATTAATAATTTAAGATTCAA
1 TATTATATATAACATATAGGCTCAACCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAA
* **
59931 TAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAACTTTATATAAAAATT-TTAATTTATA
66 TAACTTTTAAACCTAAATCAATATTAAATAATTAAAAAAAATTATAT-AAAATTATTAATTTATA
* *
59994 ATTATATATTATTTAATTTAATTATAAACTGTTTGTT-TGAATTATAAAATATT
130 ATTATATATTATTTAAATTAATTATAAA--GTTTGTTCTGAATTAAAAAATATT
60047 TAATTTTTAT
Statistics
Matches: 164, Mismatches: 14, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
189 55 0.34
190 103 0.63
191 6 0.04
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (189 bp):
TATTATATATAACATATAGGCTCAACCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAA
TAACTTTTAAACCTAAATCAATATTAAATAATTAAAAAAAATTATATAAAATTATTAATTTATAA
TTATATATTATTTAAATTAATTATAAAGTTTGTTCTGAATTAAAAAATATTAAATATAT
Found at i:63168 original size:2 final size:2
Alignment explanation
Indices: 63161--63208 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
63151 AATATTAAAA
63161 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
63203 AT AT AT
1 AT AT AT
63209 GACTATTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64124 original size:23 final size:23
Alignment explanation
Indices: 64081--64126 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
64071 TACAACATTC
* *
64081 ATATAATTATGAATATTAATTTA
1 ATATAATTATGAAAATAAATTTA
64104 ATATAATTAT-ATAAATAAATTTA
1 ATATAATTATGA-AAATAAATTTA
64127 TATTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATAATTATGAAAATAAATTTA
Found at i:76177 original size:90 final size:89
Alignment explanation
Indices: 76001--76182 Score: 256
Period size: 90 Copynumber: 2.0 Consensus size: 89
75991 CAAATCTCTA
** *
76001 TGATGGTGGATATTCAGAACCACTCGCTTCTGATTTTCCTCCAGTTTCTACTGTGCAAAGGCACA
1 TGATGGTGGATACCCAAAACCACTCGCTTCTGATTTTCCTCCAGTTTCTACTGTGCAAAGGCACA
* **
76066 AACAATACTCGAGCAGTCAGGTGC
66 AACAATACTCAAGCAACCAGGTGC
* * *
76090 TGATGAGTGGATACCCAAAACCACTCGCTTCTGATTTTCCTCCGGTTTCTGCTGTGCAATGGCAC
1 TGATG-GTGGATACCCAAAACCACTCGCTTCTGATTTTCCTCCAGTTTCTACTGTGCAAAGGCAC
* *
76155 AAGCAATCCTCAAGCAACCAGGTGC
65 AAACAATACTCAAGCAACCAGGTGC
76180 TGA
1 TGA
76183 CGAATGTGGA
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
89 5 0.06
90 76 0.94
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (89 bp):
TGATGGTGGATACCCAAAACCACTCGCTTCTGATTTTCCTCCAGTTTCTACTGTGCAAAGGCACA
AACAATACTCAAGCAACCAGGTGC
Found at i:77535 original size:35 final size:35
Alignment explanation
Indices: 77427--77523 Score: 185
Period size: 35 Copynumber: 2.8 Consensus size: 35
77417 TCTTCGAAAA
77427 GTTCCGAGGCCGAATCGATTAGAGTAACCGTCTCG
1 GTTCCGAGGCCGAATCGATTAGAGTAACCGTCTCG
77462 GTTCCGAGGCCGAATCGATTAGAGTAACCGTCTCG
1 GTTCCGAGGCCGAATCGATTAGAGTAACCGTCTCG
*
77497 GTTCCGAGGCCGAATCGATTAGTGTAA
1 GTTCCGAGGCCGAATCGATTAGAGTAA
77524 TTGCGTTGGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 61 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (35 bp):
GTTCCGAGGCCGAATCGATTAGAGTAACCGTCTCG
Done.