Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003652.1 Hibiscus syriacus cultivar Beakdansim tig00007759_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: 54650
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:11346 original size:15 final size:15
Alignment explanation
Indices: 11326--11409 Score: 59
Period size: 15 Copynumber: 5.7 Consensus size: 15
11316 TTGCTTGAAA
*
11326 AAATAATGAAAAATG
1 AAATAAAGAAAAATG
* *
11341 AAATAAAAAAAAAAG
1 AAATAAAGAAAAATG
*
11356 AAAAAAAGAAAAAAATG
1 AAATAAAG--AAAAATG
11373 -AA-AAAGAAAAATG
1 AAATAAAGAAAAATG
*
11386 -AATGAAA-AAAAAGG
1 AAAT-AAAGAAAAATG
*
11400 AAAAAAAGAA
1 AAATAAAGAA
11410 GGGTTCAAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
13 9 0.16
14 9 0.16
15 29 0.53
16 2 0.04
17 6 0.11
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (15 bp):
AAATAAAGAAAAATG
Found at i:12475 original size:55 final size:55
Alignment explanation
Indices: 12330--12620 Score: 237
Period size: 53 Copynumber: 5.4 Consensus size: 55
12320 ATTTCCCAAT
* *
12330 AATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGC
1 AATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACAC
* * * *
12385 AATTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGATATATGGG-GCAGACAC
1 AATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATA-GGGAGCAGACAC
* * *
12438 AATCGTTGAAGATCGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCATACAC
1 AATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACAC
* * * * * *
12493 GATTGTTGAAGA-TATTCGAGT-TC-TATTCTCCTTAAAGAAAGAAGGAGC-GA-AC
1 AATTGTTGAAGATTGTTCGAGTCTCATACTCT-C-TGAAGAAATAGGGAGCAGACAC
*** * * *
12545 CCGT-TTGAAGAGATG-TCTAAGT-TCCATACTCCCTGAAGAAATAGGGAGCAGACAC
1 AATTGTTGAAGA-TTGTTC-GAGTCT-CATACTCTCTGAAGAAATAGGGAGCAGACAC
* *
12600 GATTGTTGAAGA-TATTCGAGT
1 AATTGTTGAAGATTGTTCGAGT
12621 TCTATTCTCC
Statistics
Matches: 184, Mismatches: 37, Indels: 31
0.73 0.15 0.12
Matches are distributed among these distances:
51 7 0.04
52 10 0.05
53 63 0.34
54 36 0.20
55 61 0.33
56 7 0.04
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (55 bp):
AATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACAC
Found at i:12648 original size:107 final size:107
Alignment explanation
Indices: 12463--12911 Score: 534
Period size: 107 Copynumber: 4.2 Consensus size: 107
12453 TTCGAGTCTC
* * *
12463 ATACTCTCTGAAGAAATAGGGAGCATACACGATTGTTGAAGATATTCGAGTTCTATTCTCCTTAA
1 ATACTCCCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATATTCGAGTTCTATACTCCTTAA
*
12528 AGAAAGAAGGAGCGAACCCGTTTGAAGAGATG-TCTAAGTTCC
66 AGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTC-AAGTTCT
*
12570 ATACTCCCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATATTCGAGTTCTATTCTCCTTAA
1 ATACTCCCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATATTCGAGTTCTATACTCCTTAA
** *
12635 AGAAAGAAGGAGCGAATTCGTTTG-A-AGATGTTCGAGTTCT
66 AGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTCAAGTTCT
* * * * * * *
12675 ATACTCCTTAAAGAAAGAAGGAGC-GAACCCG--T-TTGAAGATGTTCGAGTTTTATACTCCTTA
1 ATACTCCCTGAAGAAATAGGGAGCAG-ACACGATTGTTGAAGATATTCGAGTTCTATACTCCTTA
*
12736 AAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTCGAGTTCT
65 AAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTCAAGTTCT
* * * * * * * * *
12779 ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTTTTAAAAGATTTTCAAGTTCTATACTCCCTG
1 ATACTCCCTGAAGAAATAGGGAGCAGACACGATTGTT-GAAGATATTCGAGTTCTATACTCCTTA
* * * *
12844 AAGAAAGAGGGAGAGAACCCGTTTGCAGAAGATTTTCAAGTTCT
65 AAGAAAGAAGGAGCGAACCCGTTTGAAG-AGATGTTCAAGTTCT
* *
12888 ATACTCCCTGAAGGAAGAGGGAGC
1 ATACTCCCTGAAGAAATAGGGAGC
12912 GAACCCGTAG
Statistics
Matches: 296, Mismatches: 36, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
102 49 0.17
103 2 0.01
104 38 0.13
105 35 0.12
106 4 0.01
107 87 0.29
108 46 0.16
109 35 0.12
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (107 bp):
ATACTCCCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATATTCGAGTTCTATACTCCTTAA
AGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTCAAGTTCT
Found at i:12663 original size:51 final size:51
Alignment explanation
Indices: 12498--12919 Score: 366
Period size: 51 Copynumber: 8.0 Consensus size: 51
12488 TACACGATTG
*
12498 TTGAAGATATTCGAGTTCTATTCTCCTTAAAGAAAGAAGGAGCGAACCCGT
1 TTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
* * * * * * * *
12549 TTGAAGAGATGTCTAAGTTCCATACTCCCTGAAGAAATAGGGAGC-AGACACGATT
1 TTGAAGATAT-TC-GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGA-ACCCG--T
* **
12604 GTTGAAGATATTCGAGTTCTATTCTCCTTAAAGAAAGAAGGAGCGAATTCGT
1 -TTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
*
12656 TTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
1 TTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
* *
12707 TTGAAGATGTTCGAGTTTTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
1 TTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
* * * *
12758 TTGAAGAGATGTTCGAGTTCTATACTCTCTGAAGGAATAG--GGAGC-AGACACGTTTT
1 TTG-A-AGATATTCGAGTTCTATACTC-CTTAAAGAA-AGAAGGAGCGA-ACCCG---T
* * * * * * *
12814 TTAAAAGATTTTCAAGTTCTATACTCCCTGAAGAAAGAGGGAGAGAACCCGT
1 TT-GAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
* * * * * *
12866 TTGCAGAAGATTTTCAAGTTCTATACTCCCTGAAGGAAGAGGGAGCGAACCCGT
1 TT---GAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
12920 AGGCAAAAGA
Statistics
Matches: 310, Mismatches: 40, Indels: 39
0.80 0.10 0.10
Matches are distributed among these distances:
51 109 0.35
52 9 0.03
53 59 0.19
54 86 0.28
55 33 0.11
56 14 0.05
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (51 bp):
TTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
Found at i:12747 original size:209 final size:211
Alignment explanation
Indices: 12498--12919 Score: 571
Period size: 209 Copynumber: 2.0 Consensus size: 211
12488 TACACGATTG
*
12498 TTGAAGATATTCGAGTTCTATTCTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATG-TC
1 TTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTC
* *
12562 TAAGTTCCATACTCCCTGAAGAAATAGGGAGCAGACACGATTGTT-GAAGATATTCGAGTTCTAT
66 -AAGTTCCATACTCCCTGAAGAAATAGGGAGCAGACACGATTGTTAAAAGATATTCAAGTTCTAT
* * * ** * *
12626 TCTCCTTAAAGAAAGAAGGAGCGAATTCGTTT-GAAGATGTTCGAGTTCTATACTCCTTAAAGAA
130 ACTCCCTAAAGAAAGAAGGAGAGAACCCGTTTAGAAGATGTTCAAGTTCTATACTCCCTAAAGAA
12690 AGAAGGAGCGAACCCGT
195 AGAAGGAGCGAACCCGT
* *
12707 TTGAAGATGTTCGAGTTTTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTC
1 TTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTC
* * * * * * *
12772 GAGTTCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTTTTAAAAGATTTTCAAGTTCTATA
66 AAGTTCCATACTCCCTGAAGAAATAGGGAGCAGACACGATTGTTAAAAGATATTCAAGTTCTATA
* * * * *
12837 CTCCCTGAAGAAAGAGGGAGAGAACCCGTTTGCAGAAGATTTTCAAGTTCTATACTCCCTGAAGG
131 CTCCCTAAAGAAAGAAGGAGAGAACCCGTTT--AGAAGATGTTCAAGTTCTATACTCCCTAAAGA
*
12902 AAGAGGGAGCGAACCCGT
194 AAGAAGGAGCGAACCCGT
12920 AGGCAAAAGA
Statistics
Matches: 183, Mismatches: 25, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
209 97 0.53
210 43 0.23
213 43 0.23
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (211 bp):
TTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTC
AAGTTCCATACTCCCTGAAGAAATAGGGAGCAGACACGATTGTTAAAAGATATTCAAGTTCTATA
CTCCCTAAAGAAAGAAGGAGAGAACCCGTTTAGAAGATGTTCAAGTTCTATACTCCCTAAAGAAA
GAAGGAGCGAACCCGT
Found at i:12930 original size:54 final size:53
Alignment explanation
Indices: 12446--12970 Score: 386
Period size: 54 Copynumber: 9.8 Consensus size: 53
12436 ACAATCGTTG
* * * * **
12446 AAGATCGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGC-ATACACGATTGTTG
1 AAGAT-GTTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCGA-ACCCGTTTG-AA
* * * * *
12501 AAGATATTCGAGTTCTATTCTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAA
1 AAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
* * * * * * **
12554 GAGATG-TCTAAGTTCCATACTCCCTGAAGAAATAGGGAGC-AGACACGATTGTTG
1 AAGATGTTC-GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGA-ACCCGTTTG-AA
* * * * * **
12608 AAGATATTCGAGTTCTATTCTCCTTAAAGAAAGAAGGAGCGAATTCGTTTG--
1 AAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
* * *
12659 AAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG--
1 AAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
* * * *
12710 AAGATGTTCGAGTTTTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAA
1 AAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
* * * * * *
12763 GAGATGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGC-AGACACGTTTTTTAA
1 AAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGA-ACCCG--TTTGAA
* * * *
12818 AAGATTTTCAAGTTCTATACTCCCTGAAGAAAGAGGGAGAGAACCCGTTTGCAG
1 AAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG-AA
* * * **
12872 AAGATTTTCAAGTTCTATACTCCCTGAAGGAAGAGGGAGCGAACCCGTAGGCAA
1 AAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG-AA
* * * * *
12926 AAGATTGTACGAGTT-TCTACTCCATGAAGGAATAGGGAGCGAACC
1 AAGA-TGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACC
12971 TGTTGTCTGA
Statistics
Matches: 383, Mismatches: 72, Indels: 31
0.79 0.15 0.06
Matches are distributed among these distances:
51 97 0.25
52 4 0.01
53 74 0.19
54 146 0.38
55 61 0.16
56 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (53 bp):
AAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
Found at i:16559 original size:63 final size:62
Alignment explanation
Indices: 16491--16615 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 62
16481 AGGTATTACC
* * *
16491 TATTTAATTTTGAATATTA-AAGAT-AATTATATCTTTTTGAATATTTCAAATTAAAATAATATT
1 TATTTAAGTTTAAATAGTACAAGATGAATT-TATC-TTTTGAATATTTCAAATTAAAAT-ATATT
* * *
16554 TATTTAAGTTTAAATAGTACAAGGTGACTTTATCTTTTGAATATTTCAGATTAAAATATATT
1 TATTTAAGTTTAAATAGTACAAGATGAATTTATCTTTTGAATATTTCAAATTAAAATATATT
16616 ATTATTTGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
62 5 0.09
63 38 0.70
64 8 0.15
65 3 0.06
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (62 bp):
TATTTAAGTTTAAATAGTACAAGATGAATTTATCTTTTGAATATTTCAAATTAAAATATATT
Found at i:17675 original size:2 final size:2
Alignment explanation
Indices: 17668--17709 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
17658 CCGCCCCTAT
17668 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17709 T
1 T
17710 TTTATATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20925 original size:22 final size:22
Alignment explanation
Indices: 20873--20932 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
20863 TCTTATACCA
* *
20873 AAACCTTAAAACCCTAAATTCT
1 AAACCTTTAAACCATAAATTCT
*
20895 AAACC-TTAAACCATAACTTC-
1 AAACCTTTAAACCATAAATTCT
20915 ATAACCTTTAAA-CATAAA
1 A-AACCTTTAAACCATAAA
20933 CCCTAACATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 21 0.66
22 10 0.31
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (22 bp):
AAACCTTTAAACCATAAATTCT
Found at i:20944 original size:20 final size:20
Alignment explanation
Indices: 20916--20959 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
20906 CATAACTTCA
*
20916 TAACCTTTAAACATAAACCC
1 TAACATTTAAACATAAACCC
20936 TAACATTTAAACATAAACCC
1 TAACATTTAAACATAAACCC
20956 TAAC
1 TAAC
20960 TTACAACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (20 bp):
TAACATTTAAACATAAACCC
Found at i:28493 original size:35 final size:34
Alignment explanation
Indices: 28449--28561 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
28439 AAAACAATTC
*
28449 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
28484 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * * *
28519 TCAATTACATTCTAAAACTCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
*
28554 TTAATTTC
1 TCAATTTC
28562 TGTCTTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.91
36 5 0.07
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:29636 original size:35 final size:34
Alignment explanation
Indices: 29588--29699 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
29578 ATTTCTCCTT
*
29588 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTT-GAATTTGGGGTTTAGAATG
* *
29623 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTT-GAATTTGGGGTTTAGAATG
* * *
29658 AAATTGAATTACTTTGAAATTTGGGATTTATAATG
1 AAATTGAATTATTTTG-AATTTGGGGTTTAGAATG
29693 AAATTGA
1 AAATTGA
29700 GGAATGTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
34 1 0.01
35 66 0.99
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGAATTTGGGGTTTAGAATG
Found at i:30888 original size:16 final size:16
Alignment explanation
Indices: 30867--30898 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
30857 AAGCCAGTGC
30867 ACTAACAGCTTAGTAA
1 ACTAACAGCTTAGTAA
30883 ACTAACAGCTTAGTAA
1 ACTAACAGCTTAGTAA
30899 GCGAACACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
ACTAACAGCTTAGTAA
Found at i:30905 original size:16 final size:16
Alignment explanation
Indices: 30870--30905 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30860 CCAGTGCACT
*
30870 AACAGCTTAGTAAACT
1 AACAGCTTAGTAAACG
*
30886 AACAGCTTAGTAAGCG
1 AACAGCTTAGTAAACG
30902 AACA
1 AACA
30906 CAAGGGGGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (16 bp):
AACAGCTTAGTAAACG
Found at i:35877 original size:80 final size:80
Alignment explanation
Indices: 35744--35904 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
35734 AGATTTACAT
35744 TTTAGGTCACTTAATGTAGCATCAATTTTCATTTAGTTCACGAAATCCCAATTTTGACTCTGTTC
1 TTTAGGTCACTTAATGTAGCATCAATTTTCATTTAGTTCACGAAATCCCAATTTTGACTCTGTTC
35809 AGAAAGTATGTCACA
66 AGAAAGTATGTCACA
35824 TTTAGGTCACTTAATGTAGCATCAATTTTCATTTAGTTCACGAAATCCCAATTTTGACTCTGTTC
1 TTTAGGTCACTTAATGTAGCATCAATTTTCATTTAGTTCACGAAATCCCAATTTTGACTCTGTTC
35889 AGAAAGTATGTCACA
66 AGAAAGTATGTCACA
35904 T
1 T
35905 ATGCATGCTA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (80 bp):
TTTAGGTCACTTAATGTAGCATCAATTTTCATTTAGTTCACGAAATCCCAATTTTGACTCTGTTC
AGAAAGTATGTCACA
Found at i:37065 original size:2 final size:2
Alignment explanation
Indices: 37060--37113 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
37050 GCGCACACAC
37060 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
37102 AT AT AT AT AT AT
1 AT AT AT AT AT AT
37114 GGTCCCTCGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38599 original size:16 final size:16
Alignment explanation
Indices: 38554--38599 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
38544 AATACCAAAA
38554 AAATA-AAATATT-AT
1 AAATATAAATATTAAT
38568 ACAATAT-AATATTTAAT
1 A-AATATAAATA-TTAAT
38585 AAATATAAATATTAA
1 AAATATAAATATTAA
38600 ATTAATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.04
15 8 0.30
16 11 0.41
17 7 0.26
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATATAAATATTAAT
Found at i:42564 original size:39 final size:38
Alignment explanation
Indices: 42467--42582 Score: 112
Period size: 39 Copynumber: 3.1 Consensus size: 38
42457 TATTATATTT
* * * *
42467 TAATTTTCAAT-TCTCAAATTATTTAACTCTAACATCC
1 TAATTTTTAATATCTTAAATTATTTTACTCTAACATTC
*
42504 TAAATTTTTAATATCTTAAATTATTTTACTATAACATTC
1 T-AATTTTTAATATCTTAAATTATTTTACTCTAACATTC
* * *
42543 TAATTTCTTGAT-TTTTAAAATTATTTT-TTCTAACATTC
1 TAATTT-TTAATATCTT-AAATTATTTTACTCTAACATTC
42581 TA
1 TA
42583 TGTTATTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
37 1 0.02
38 28 0.42
39 37 0.56
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.51
Consensus pattern (38 bp):
TAATTTTTAATATCTTAAATTATTTTACTCTAACATTC
Found at i:43949 original size:13 final size:13
Alignment explanation
Indices: 43931--43960 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
43921 CAAGTATACA
*
43931 TTTTTATAATCAC
1 TTTTTAAAATCAC
43944 TTTTTAAAATCAC
1 TTTTTAAAATCAC
43957 TTTT
1 TTTT
43961 GAGATGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAAATCAC
Found at i:45128 original size:17 final size:18
Alignment explanation
Indices: 45095--45138 Score: 81
Period size: 17 Copynumber: 2.5 Consensus size: 18
45085 AAATGGGTAC
45095 CGATACCCTACCCAGTAT
1 CGATACCCTACCCAGTAT
45113 CGATACCCTA-CCAGTAT
1 CGATACCCTACCCAGTAT
45130 CGATACCCT
1 CGATACCCT
45139 TACATATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.27, C:0.39, G:0.11, T:0.23
Consensus pattern (18 bp):
CGATACCCTACCCAGTAT
Found at i:49376 original size:23 final size:21
Alignment explanation
Indices: 49351--49390 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49341 TAAAATGTTA
*
49351 AAAAATATTAATATTTTATGT
1 AAAAATAATAATATTTTATGT
49372 AAAAATAATAATATTTTAT
1 AAAAATAATAATATTTTAT
49391 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
AAAAATAATAATATTTTATGT
Done.