Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005635.1 Hibiscus syriacus cultivar Beakdansim tig00013138_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: 63624
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:4010 original size:52 final size:52
Alignment explanation
Indices: 3946--4044 Score: 153
Period size: 52 Copynumber: 1.9 Consensus size: 52
3936 ACTGAAATAG
* *
3946 ATATTATTTCTTTAAACAAATTCATTTAAATGTTATTCTCTATTTTTCATAA
1 ATATTATATCTTTAAACAAATTCATTTAAATGTTATTATCTATTTTTCATAA
* * *
3998 ATATTATATCTTTATATAAATTCATTTAAATGTTATTATTTATTTTT
1 ATATTATATCTTTAAACAAATTCATTTAAATGTTATTATCTATTTTT
4045 GAGAACAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (52 bp):
ATATTATATCTTTAAACAAATTCATTTAAATGTTATTATCTATTTTTCATAA
Found at i:5823 original size:2 final size:2
Alignment explanation
Indices: 5816--5843 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5806 CAGCTACAAC
5816 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
5844 TCGGTTGTTC
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):
AT
Found at i:6511 original size:7 final size:7
Alignment explanation
Indices: 6494--6539 Score: 83
Period size: 7 Copynumber: 6.4 Consensus size: 7
6484 ACCATTTACC
6494 ATTTCCTT
1 ATTTCC-T
6502 ATTTCCT
1 ATTTCCT
6509 ATTTCCT
1 ATTTCCT
6516 ATTTCCT
1 ATTTCCT
6523 ATTTCCT
1 ATTTCCT
6530 ATTTCCT
1 ATTTCCT
6537 ATT
1 ATT
6540 AAATTACCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 32 0.84
8 6 0.16
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTCCT
Found at i:14925 original size:17 final size:17
Alignment explanation
Indices: 14890--14925 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
14880 TAAGATATAT
*
14890 ATATTAAACTAAACCTA
1 ATATTAAACTAAACATA
*
14907 ATATTAAACTAATCATA
1 ATATTAAACTAAACATA
14924 AT
1 AT
14926 CTACATCACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATTAAACTAAACATA
Found at i:14987 original size:28 final size:27
Alignment explanation
Indices: 14947--15005 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
14937 AGGAACCCAA
*
14947 CCTCACGCTTTACTCTTTACTTTCTCT
1 CCTCACACTTTACTCTTTACTTTCTCT
*
14974 GCCTCACACTTTACTCTTTATTTTCTCT
1 -CCTCACACTTTACTCTTTACTTTCTCT
15002 CCTC
1 CCTC
15006 CTTTCTTGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.12, C:0.37, G:0.03, T:0.47
Consensus pattern (27 bp):
CCTCACACTTTACTCTTTACTTTCTCT
Found at i:16544 original size:55 final size:55
Alignment explanation
Indices: 16472--17059 Score: 520
Period size: 55 Copynumber: 10.8 Consensus size: 55
16462 AAAAATATTC
* * *
16472 AAAAACGGGTCTGCTCCCTATTCTTTCA-AGAAGTATATG-ACTTGAACAATCTTCG
1 AAAAACGGGTCCGCTCCCTATTCTTTCAGAG-AGTATA-GAACTCGAACAATCTTCA
** * * * *
16527 GCAAACGGGTCCACTCCCTATTCTTT-AAAGGAGTATAGAACTCGATCAATCTTCT
1 AAAAACGGGTCCGCTCCCTATTCTTTCAGA-GAGTATAGAACTCGAACAATCTTCA
* * * * *
16582 GAAAACGGGT----TCGC--TTCTTT-AAAGGAGTATAGAACTCGAACAATCCTCT
1 AAAAACGGGTCCGCTCCCTATTCTTTCAGA-GAGTATAGAACTCGAACAATCTTCA
* ** * * * * * *
16631 GAAAACATGTTCGCTCCTTATTCGTTCAGGGAGTATAGAACTTGAACAATCTTCT
1 AAAAACGGGTCCGCTCCCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCA
* * * ** * * *
16686 GAAAATGGGTTCAATCCCTATTCGTTCAGGGAGTATAGACCTCGAACAATCTTCA
1 AAAAACGGGTCCGCTCCCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCA
* * * * * * *
16741 ACAAATGTGTGCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCA
1 AAAAACGGGTCCGCTCCCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCA
* * * * *
16796 ACAAACGTGTCCGCTCTCTATT-TCTTCAGAGAGTATAGGACTCAAACAATCTTCA
1 AAAAACGGGTCCGCTCCCTATTCT-TTCAGAGAGTATAGAACTCGAACAATCTTCA
* * *
16851 TAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA
1 AAAAACGGGTCCGCTCCCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCA
* * * *
16906 TAAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA
1 AAAAACGGGTCCGCTCCCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCA
* * *
16961 ACAAACGGGTCCGCTCCCTATTCTATCAGAGAGTATAGGACTCGAACAATCTTCA
1 AAAAACGGGTCCGCTCCCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCA
* *
17016 ACAAAC-GGTCTGCTCCCTATT-TTATCAGAGAGTATA-AGACTCGA
1 AAAAACGGGTCCGCTCCCTATTCTT-TCAGAGAGTATAGA-ACTCGA
17060 TCTTCATAAA
Statistics
Matches: 456, Mismatches: 63, Indels: 29
0.83 0.11 0.05
Matches are distributed among these distances:
49 41 0.09
51 3 0.01
53 3 0.01
54 34 0.07
55 373 0.82
56 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (55 bp):
AAAAACGGGTCCGCTCCCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCA
Found at i:16619 original size:49 final size:49
Alignment explanation
Indices: 16547--16645 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
16537 CCACTCCCTA
* * *
16547 TTCTTTAAAGGAGTATAGAACTCGATCAATCTTCTGAAAACGGGTTCGC
1 TTCTTTAAAGGAGTATAGAACTCGAACAATCCTCTGAAAACAGGTTCGC
*
16596 TTCTTTAAAGGAGTATAGAACTCGAACAATCCTCTGAAAACATGTTCGC
1 TTCTTTAAAGGAGTATAGAACTCGAACAATCCTCTGAAAACAGGTTCGC
16645 T
1 T
16646 CCTTATTCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (49 bp):
TTCTTTAAAGGAGTATAGAACTCGAACAATCCTCTGAAAACAGGTTCGC
Found at i:17125 original size:37 final size:38
Alignment explanation
Indices: 17070--17141 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 38
17060 TCTTCATAAA
*
17070 ATGAGTTTGCTTCACTACTCTTCCGTGGAGGCTTATAT
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAT
17108 ATGA-TTTGCTTCACTACTCTTCCGTGAAGGCTTA
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTA
17142 AGATTAGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (38 bp):
ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAT
Found at i:18447 original size:5 final size:6
Alignment explanation
Indices: 18428--18523 Score: 52
Period size: 6 Copynumber: 15.0 Consensus size: 6
18418 CCCTTTTTTA
* * * *
18428 TTTCTT TTTCTT TTTCTT TTT-TC ATTATT TTTCATTT TTTCAT TTTCTTAT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC--TT TTTCTT TTTC-T-T
* *
18479 TTTCTT ATT-TT TTTCATTT TTTCATT TTTCAT TTTCTCT TTTCTT
1 TTTCTT TTTCTT TTTC--TT TTTC-TT TTTCTT TTTCT-T TTTCTT
18524 CATTTTTCAT
Statistics
Matches: 69, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
5 7 0.10
6 32 0.46
7 13 0.19
8 17 0.25
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:18458 original size:23 final size:21
Alignment explanation
Indices: 18422--18554 Score: 63
Period size: 23 Copynumber: 6.0 Consensus size: 21
18412 TGAACCCCCT
* *
18422 TTTTTATTTCTTTTTCTTTTTC
1 TTTTTCTTT-TTTTTATTTTTC
*
18444 TTTTTTCATTATTTTTCATTTTTTC
1 -TTTTTC-TT-TTTTTTA-TTTTTC
* * * *
18469 ATTTTC-TTATTTTCTTATT-
1 TTTTTCTTTTTTTTATTTTTC
* *
18488 TTTTTCATTTTTTCATTTTTC
1 TTTTTCTTTTTTTTATTTTTC
* *
18509 ATTTTCTCTTTTCTTCATTTTTC
1 -TTTT-TCTTTTTTTTATTTTTC
18532 ATTTTTCATTTTTTTTAATTTTT
1 -TTTTTC-TTTTTTTT-ATTTTT
18555 TAATTTTTAA
Statistics
Matches: 84, Mismatches: 17, Indels: 17
0.71 0.14 0.14
Matches are distributed among these distances:
19 5 0.06
20 13 0.15
21 4 0.05
22 7 0.08
23 31 0.37
24 17 0.20
25 7 0.08
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTCTTTTTTTTATTTTTC
Found at i:18466 original size:8 final size:8
Alignment explanation
Indices: 18438--18589 Score: 113
Period size: 8 Copynumber: 18.8 Consensus size: 8
18428 TTTCTTTTTC
18438 TTTTTC-T
1 TTTTTCAT
18445 TTTTTCATT
1 TTTTTCA-T
18454 ATTTTTCAT
1 -TTTTTCAT
18463 TTTTTCAT
1 TTTTTCAT
18471 TTTCTT-AT
1 TTT-TTCAT
18479 TTTCTT-ATT
1 TTT-TTCA-T
18488 TTTTTCAT
1 TTTTTCAT
18496 TTTTTCA-
1 TTTTTCAT
18503 TTTTTCAT
1 TTTTTCAT
*
18511 TTTCTC-T
1 TTTTTCAT
18518 TTTCTTCA-
1 TTT-TTCAT
18526 TTTTTCA-
1 TTTTTCAT
18533 TTTTTCATTT
1 TTTTTCA--T
*
18543 TTTTTAAT
1 TTTTTCAT
*
18551 TTTTT-AA
1 TTTTTCAT
*
18558 TTTTTAAT
1 TTTTTCAT
*
18566 TTTTCTCTCT
1 TTTT-TC-AT
18576 TTTTTCAT
1 TTTTTCAT
18584 TTTTTC
1 TTTTTC
18590 TTCAAGCGAA
Statistics
Matches: 122, Mismatches: 8, Indels: 29
0.77 0.05 0.18
Matches are distributed among these distances:
7 34 0.28
8 58 0.48
9 12 0.10
10 18 0.15
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTCAT
Found at i:18554 original size:25 final size:25
Alignment explanation
Indices: 18526--18587 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
18516 CTTTTCTTCA
* *
18526 TTTTTCATTTTTCATTTTT-TTTAAT
1 TTTTTCATTTTTAATTTTTCTCT-AT
* *
18551 TTTTTAATTTTTAATTTTTCTCTCT
1 TTTTTCATTTTTAATTTTTCTCTAT
18576 TTTTTCATTTTT
1 TTTTTCATTTTT
18588 TCTTCAAGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTTCATTTTTAATTTTTCTCTAT
Found at i:18562 original size:71 final size:70
Alignment explanation
Indices: 18428--18562 Score: 177
Period size: 71 Copynumber: 1.9 Consensus size: 70
18418 CCCTTTTTTA
* * *
18428 TTTCTTTTTCTTTTTCTTTTTTCATTATTTTTCATTTTTTCATTTTCTTATTTTCTTATTTTTTT
1 TTTCTTTTTCATTTTCTCTTTTCATTATTTTTCATTTTTTCATTTTCTTATTTTCTTAATTTTTT
18493 CATTT
66 CATTT
*
18498 TTTCATTTTTCATTTTCTCTTTTC-TTCATTTTTCA-TTTTTCATTTTTTTTAATTTT-TTAATT
1 TTTC-TTTTTCATTTTCTCTTTTCATT-ATTTTTCATTTTTTCA-TTTTCTT-ATTTTCTTAATT
18560 TTT
62 TTT
18563 AATTTTTCTC
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
70 13 0.23
71 39 0.68
72 5 0.09
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.76
Consensus pattern (70 bp):
TTTCTTTTTCATTTTCTCTTTTCATTATTTTTCATTTTTTCATTTTCTTATTTTCTTAATTTTTT
CATTT
Found at i:29613 original size:17 final size:17
Alignment explanation
Indices: 29578--29613 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29568 TAAGATATAT
*
29578 ATATTAAACTAAACCTA
1 ATATTAAACTAAACATA
*
29595 ATATTAAACTAATCATA
1 ATATTAAACTAAACATA
29612 AT
1 AT
29614 CTACTTCACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATTAAACTAAACATA
Found at i:33237 original size:21 final size:21
Alignment explanation
Indices: 33198--33237 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
33188 TATAACTAAT
* *
33198 AAGAGAGTAATATTCTCCATC
1 AAGAGAGTAAAAGTCTCCATC
*
33219 AAGAGAGTAAAAGTGTCCA
1 AAGAGAGTAAAAGTCTCCA
33238 AACTTCAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (21 bp):
AAGAGAGTAAAAGTCTCCATC
Found at i:41368 original size:2 final size:2
Alignment explanation
Indices: 41363--41404 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
41353 AAGATAAGAC
41363 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
41405 TGATAGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45546 original size:20 final size:20
Alignment explanation
Indices: 45521--45561 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
45511 GTCGTTGCCC
45521 CTTTTTCATAGGACTAACAT
1 CTTTTTCATAGGACTAACAT
45541 CTTTTTCATAGGACTAACAT
1 CTTTTTCATAGGACTAACAT
45561 C
1 C
45562 CAAGGTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (20 bp):
CTTTTTCATAGGACTAACAT
Found at i:47757 original size:16 final size:15
Alignment explanation
Indices: 47717--47792 Score: 71
Period size: 17 Copynumber: 4.7 Consensus size: 15
47707 TTTTTTTAAT
*
47717 AATTCAAAAATATTA
1 AATTTAAAAATATTA
47732 ACATTATAAAAATATTA
1 A-ATT-TAAAAATATTA
*
47749 AATATTAAAAGTATTTTA
1 AAT-TTAAAA--ATATTA
47767 AATTTAAAAATATTA
1 AATTTAAAAATATTA
*
47782 ATTGTTAAAAA
1 AAT-TTAAAAA
47793 ATATAAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
15 8 0.16
16 17 0.33
17 18 0.35
18 8 0.16
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (15 bp):
AATTTAAAAATATTA
Found at i:49322 original size:18 final size:18
Alignment explanation
Indices: 49301--49351 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
49291 TGCATTGTAG
49301 CACTTTGGTACATTCTGA
1 CACTTTGGTACATTCTGA
* * *
49319 CACTTTTGTGCA-T-TAA
1 CACTTTGGTACATTCTGA
*
49335 CACTTTGATACATTCTG
1 CACTTTGGTACATTCTG
49352 GGCATTTGTG
Statistics
Matches: 24, Mismatches: 7, Indels: 4
0.69 0.20 0.11
Matches are distributed among these distances:
16 11 0.46
17 2 0.08
18 11 0.46
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.41
Consensus pattern (18 bp):
CACTTTGGTACATTCTGA
Found at i:52347 original size:123 final size:120
Alignment explanation
Indices: 52179--52416 Score: 359
Period size: 123 Copynumber: 2.0 Consensus size: 120
52169 TGAGAATGAC
* * * *
52179 AATGTTGATGTTGATTTATCTCATTCTGTGATAGAATCGATCAAAAGGTTGAATAAGTTCTTCAG
1 AATGTTGAAGTTGATCTATCTCATTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTCAG
* *
52244 ATTATGAACTTCTTCTTTCTCTTTAGATGAATTCTTCTTATTACGAACTCCTTCTAGA
66 ATTATGAACTTCTTCTTCCTCTTCAGATG---TCTTCTTATTACGAACTCCTTCTAGA
* * *
52302 AATGTTGAAGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
1 AATGTTGAAGTTGATCTATCTCATTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTCAG
*
52367 ATTATGAACTTCTTCTTCCTCTTCAGATGTGTTCTTATTACGAACTCCTT
66 ATTATGAACTTCTTCTTCCTCTTCAGATGTCTTCTTATTACGAACTCCTT
52417 TTGGAAATTT
Statistics
Matches: 105, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
120 20 0.19
123 85 0.81
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (120 bp):
AATGTTGAAGTTGATCTATCTCATTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTCAG
ATTATGAACTTCTTCTTCCTCTTCAGATGTCTTCTTATTACGAACTCCTTCTAGA
Found at i:52564 original size:73 final size:73
Alignment explanation
Indices: 52437--52912 Score: 633
Period size: 73 Copynumber: 6.5 Consensus size: 73
52427 TGATCCATCG
* * *
52437 AGTGATGA-AAATTTCTATTTCTAGTGAAACTGTCTCAAGC--AAGATAAATCTTGTTTTAAGAA
1 AGTGA-GATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAAAGA-AAGT-TTGTTTTAAGAA
52499 AAACAATCTCA
63 AAACAATCTCA
* * * *
52510 AGTGAGATAAATTACTGTTTCGAGTGAAACTATCTCAAGCGAAACAAAGTTTGTTTTAAGAAAAA
1 AGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAAAGAAAGTTTGTTTTAAGAAAAA
52575 CAATCTCA
66 CAATCTCA
*
52583 AGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAGAGAAAGTTTGTTTTAAGAAAAA
1 AGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAAAGAAAGTTTGTTTTAAGAAAAA
*
52648 CAATATCA
66 CAATCTCA
* * * *
52656 AGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGTG--AGAAAGTTGGTTTTAAGAAAAG
1 AGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAAAGAAAGTTTGTTTTAAGAAAA-
*
52719 AAAATCTCA
65 ACAATCTCA
* * * *
52728 AGTGAGATAATTTAATATTTCAAGTGAAACTTTCTCAAGC-AAGAAAAAGTTTGTTTTAAGAAAA
1 AGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAA-AGAAAGTTTGTTTTAAGAAAA
*
52792 ACAATCTTA
65 ACAATCTCA
* * *
52801 AGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCGAGAA-AAAGTTTGTTTTAAGAAAA
1 AGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGA-AAGAAAGTTTGTTTTAAGAAAA
52865 ACAATCTCA
65 ACAATCTCA
* *
52874 AGTGAGATAAATTGCTATTTCGAGTGAAACTGTCTCAAG
1 AGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAG
52913 TGAGATGTCG
Statistics
Matches: 362, Mismatches: 32, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
71 20 0.06
72 45 0.12
73 269 0.74
74 24 0.07
75 4 0.01
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (73 bp):
AGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAAAGAAAGTTTGTTTTAAGAAAAA
CAATCTCA
Found at i:52756 original size:218 final size:219
Alignment explanation
Indices: 52437--52918 Score: 720
Period size: 218 Copynumber: 2.2 Consensus size: 219
52427 TGATCCATCG
* * ** *
52437 AGTGATGA-AAATTTCTATTTCTAGTGAAACTGTCTCAAGCAAGATAAATCTTGTTTTAAGAAAA
1 AGTGA-GATAAATTGCTATTTCAAGTGAAACTGTCTCAAGTGAGATAAATCTGGTTTTAAGAAAA
* * * * *
52501 ACAATCTCAAGTGAGATAAATTACTGTTTCGAGTGAAACTATCTCAAGCGAA-ACAAAGTTTGTT
65 AAAATCTCAAGTGAGATAAATTAATATTTCAAGTGAAACTATCTCAAGC-AAGAAAAAGTTTGTT
*
52565 TTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAGAGAA
129 TTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAGAAAA
52630 AGTTTGTTTTAAGAAAAACAATATCA
194 AGTTTGTTTTAAGAAAAACAATATCA
* *
52656 AGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGTGAGA-AAGT-TGGTTTTAAGAAAAG
1 AGTGAGATAAATTGCTATTTCAAGTGAAACTGTCTCAAGTGAGATAAATCTGGTTTTAAGAAAA-
* *
52719 AAAATCTCAAGTGAGATAATTTAATATTTCAAGTGAAACTTTCTCAAGCAAGAAAAAGTTTGTTT
65 AAAATCTCAAGTGAGATAAATTAATATTTCAAGTGAAACTATCTCAAGCAAGAAAAAGTTTGTTT
* * * *
52784 TAAGAAAAACAATCTTAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCGAGAAAAA
130 TAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAGAAAAA
*
52849 GTTTGTTTTAAGAAAAACAATCTCA
195 GTTTGTTTTAAGAAAAACAATATCA
*
52874 AGTGAGATAAATTGCTATTTCGAGTGAAACTGTCTCAAGTGAGAT
1 AGTGAGATAAATTGCTATTTCAAGTGAAACTGTCTCAAGTGAGAT
52919 GTCGCTGATT
Statistics
Matches: 237, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
217 15 0.06
218 186 0.78
219 36 0.15
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (219 bp):
AGTGAGATAAATTGCTATTTCAAGTGAAACTGTCTCAAGTGAGATAAATCTGGTTTTAAGAAAAA
AAATCTCAAGTGAGATAAATTAATATTTCAAGTGAAACTATCTCAAGCAAGAAAAAGTTTGTTTT
AAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTGTCTCAAGCGAGAAAAAG
TTTGTTTTAAGAAAAACAATATCA
Found at i:53041 original size:42 final size:42
Alignment explanation
Indices: 52994--53110 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
52984 TATCATCTTA
* *
52994 CTCGAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATG
1 CTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATG
53036 CTCGAAAGACTTACTA-ATGACCCGAAGGATTTAAACATCATG
1 CTCGAAAGACTTAC-AGATGACCCGAAGGATTTAAACATCATG
* * **
53078 CTCGTAAGACTTACTGAAAACCCGAAGGATTTA
1 CTCGAAAGACTTACAGATGACCCGAAGGATTTA
53111 CAAATTCGGG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 66 0.99
43 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (42 bp):
CTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATG
Found at i:56124 original size:2 final size:2
Alignment explanation
Indices: 56117--56149 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
56107 CCTCATTACC
56117 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56150 GCTTATAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56495 original size:18 final size:18
Alignment explanation
Indices: 56474--56520 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
56464 CCCAAAGGAC
56474 CACTATGTCCCGAATGAT
1 CACTATGTCCCGAATGAT
56492 CACTATGTCCCGAATGAT
1 CACTATGTCCCGAATGAT
56510 CACTATGTCCC
1 CACTATGTCCC
56521 AAAGGACCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.28
Consensus pattern (18 bp):
CACTATGTCCCGAATGAT
Found at i:56853 original size:22 final size:23
Alignment explanation
Indices: 56825--56880 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
56815 TCATGGAATT
56825 TCATATCTCATTATCATAT-ATC
1 TCATATCTCATTATCATATGATC
56847 TCATATCAT-ATTATCATATGATC
1 TCATATC-TCATTATCATATGATC
* *
56870 ACATAACTCAT
1 TCATATCTCAT
56881 GTCACTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.41
Consensus pattern (23 bp):
TCATATCTCATTATCATATGATC
Found at i:56861 original size:15 final size:15
Alignment explanation
Indices: 56827--56857 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
56817 ATGGAATTTC
56827 ATATCTCATTATCAT
1 ATATCTCATTATCAT
56842 ATATCTCA-TATCAT
1 ATATCTCATTATCAT
56856 AT
1 AT
56858 TATCATATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATCTCATTATCAT
Found at i:58329 original size:18 final size:18
Alignment explanation
Indices: 58306--58344 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
58296 ATTTGGGATA
58306 TTACAAATCTCCATCCTT
1 TTACAAATCTCCATCCTT
58324 TTACAAATCTCCATCCTT
1 TTACAAATCTCCATCCTT
58342 TTA
1 TTA
58345 AGAAAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (18 bp):
TTACAAATCTCCATCCTT
Found at i:61310 original size:18 final size:18
Alignment explanation
Indices: 61285--61351 Score: 89
Period size: 18 Copynumber: 3.7 Consensus size: 18
61275 ACTTAGAATT
61285 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * *
61303 TCTCCCGAATGATCACTA
1 TGTCCCGAAGGACCACTA
*
61321 TGTCCCGAAGGATCACTA
1 TGTCCCGAAGGACCACTA
*
61339 TGTCCCAAAGGAC
1 TGTCCCGAAGGAC
61352 AACATATCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:61674 original size:22 final size:23
Alignment explanation
Indices: 61648--61697 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
61638 TCATGAAATT
*
61648 TCATATCTTATTATCATAT-ATC
1 TCATATCATATTATCATATGATC
61670 TCATATCATATTATCATATGATC
1 TCATATCATATTATCATATGATC
*
61693 ACATA
1 TCATA
61698 ACTCATGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (23 bp):
TCATATCATATTATCATATGATC
Done.