Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000271.1 Hibiscus syriacus cultivar Beakdansim tig00000499_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: 42089
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3960 original size:24 final size:25
Alignment explanation
Indices: 3918--3964 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3908 TCTAGTTTAT
*
3918 AAAGTTCTTTATTTCTTTATTTTTC
1 AAAGTTCTTCATTTCTTTATTTTTC
*
3943 AAAGTT-TTCATTTTTTTATTTT
1 AAAGTTCTTCATTTCTTTATTTT
3965 AAGTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.21, C:0.09, G:0.04, T:0.66
Consensus pattern (25 bp):
AAAGTTCTTCATTTCTTTATTTTTC
Found at i:6865 original size:20 final size:21
Alignment explanation
Indices: 6840--6891 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
6830 GGGGTGATAA
* *
6840 AGTGCATCCTTGTACC-CTAC
1 AGTGCATCCATGCACCTCTAC
*
6860 AGTGCATCCATGCACCTCTGC
1 AGTGCATCCATGCACCTCTAC
6881 AGTGCATCCAT
1 AGTGCATCCAT
6892 ACACATGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.21, C:0.35, G:0.17, T:0.27
Consensus pattern (21 bp):
AGTGCATCCATGCACCTCTAC
Found at i:8989 original size:9 final size:10
Alignment explanation
Indices: 8964--8988 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
8954 AATACTTTGA
8964 TTTTTTAATT
1 TTTTTTAATT
8974 TTTTTTAATT
1 TTTTTTAATT
8984 TTTTT
1 TTTTT
8989 ACCTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:9444 original size:18 final size:18
Alignment explanation
Indices: 9423--9470 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
9413 TAACATTTTC
9423 ATATATTTTAAACAATTG
1 ATATATTTTAAACAATTG
*
9441 ATATCATTTTGTTAACAATTG
1 ATAT-A-TTT-TAAACAATTG
*
9462 ATATCTTTT
1 ATATATTTT
9471 TCATTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 5 0.20
19 4 0.16
20 3 0.12
21 13 0.52
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.50
Consensus pattern (18 bp):
ATATATTTTAAACAATTG
Found at i:9758 original size:20 final size:19
Alignment explanation
Indices: 9691--9761 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 19
9681 AGGGTGTCAA
*
9691 AGTGCATCCATGCACCCTGC
1 AGTGCATCCATGCA-CCTGT
9711 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTG----T
*
9734 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACC-TGT
9754 AGTGCATC
1 AGTGCATC
9762 TGTGCACCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
19 4 0.09
20 23 0.52
23 15 0.34
24 2 0.05
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.23
Consensus pattern (19 bp):
AGTGCATCCATGCACCTGT
Found at i:14748 original size:21 final size:21
Alignment explanation
Indices: 14722--14766 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
14712 TTGAGGATGT
14722 TTTTACCA-TATTCATTTTCAA
1 TTTTA-CATTATTCATTTTCAA
* *
14743 TTTTACATTCTTTATTTTCAA
1 TTTTACATTATTCATTTTCAA
14764 TTT
1 TTT
14767 AAATAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTACATTATTCATTTTCAA
Found at i:14776 original size:21 final size:21
Alignment explanation
Indices: 14735--14776 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
14725 TACCATATTC
* *
14735 ATTTTCAATTTTACATTCTTT
1 ATTTTCAATTTTAAATACTTT
14756 ATTTTCAA-TTTAAATAACTTT
1 ATTTTCAATTTTAAAT-ACTTT
14777 TTTATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTCAATTTTAAATACTTT
Found at i:23799 original size:21 final size:21
Alignment explanation
Indices: 23682--23820 Score: 77
Period size: 21 Copynumber: 6.7 Consensus size: 21
23672 ACGCGAAATA
**
23682 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
23702 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
23722 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
23743 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* * **
23764 AAATTTGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * **
23785 AAAATCGCAACGCGAATATGA
1 AAAATCGCAACGCGATTTTCC
23806 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
23821 ACACATAAAT
Statistics
Matches: 87, Mismatches: 28, Indels: 7
0.71 0.23 0.06
Matches are distributed among these distances:
19 1 0.01
20 24 0.28
21 60 0.69
22 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:23821 original size:21 final size:20
Alignment explanation
Indices: 23785--23839 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
23775 GCGATTTTCC
* *
23785 AAAATCGCAACGCGAATATGA
1 AAAATCGCAACGCGAACA-CA
23806 AAAATCGCAACGCGAACACA
1 AAAATCGCAACGCGAACACA
*
23826 TAAATCGCAACGCG
1 AAAATCGCAACGCG
23840 TATCCGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAACACA
Found at i:23832 original size:20 final size:20
Alignment explanation
Indices: 23807--23980 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
23797 CGAATATGAA
* *
23807 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
23827 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
23847 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
23867 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
23887 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
23907 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
23927 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
23947 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
23968 AAATCGCAACGCG
1 AAATCGCAACGCG
23981 ATATTTAAAG
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 113 0.86
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:23877 original size:60 final size:60
Alignment explanation
Indices: 23807--23980 Score: 249
Period size: 60 Copynumber: 2.9 Consensus size: 60
23797 CGAATATGAA
* *
23807 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
* *** * *
23867 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
**
23927 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCG
23981 ATATTTAAAG
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 66 0.68
61 31 0.32
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:24428 original size:33 final size:33
Alignment explanation
Indices: 24362--24432 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
24352 TTCACTTAGA
* * * *
24362 TTTCATTTCGCGTTACGATTCTGTCTTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTCCGAT
* *
24395 TTTCATTTCGCGTTGCTATTATCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTCCGAT
24428 TTTCA
1 TTTCA
24433 AGTTAGTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.13, C:0.23, G:0.15, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTATCTCGTTCCGAT
Found at i:24538 original size:21 final size:21
Alignment explanation
Indices: 24512--24584 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
24502 TGCAGAAGAG
24512 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGATAAATGAAAA
* ***
24533 TCGCAACGAGA-GAATGACTG
1 TCGCAACGAGATAAATGAAAA
24553 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGATAAATGAAAA
*
24574 GCGCAACGAGA
1 TCGCAACGAGA
24585 GAATCGCAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGATAAATGAAAA
Found at i:24568 original size:41 final size:38
Alignment explanation
Indices: 24505--24621 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
24495 TTCAATTTGC
*
24505 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGATAAATGAAAATCGCAACGAG
*
24543 AGAATGACTGTCGCAACGAGATAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGATAAATGAAAATCGCAACGAG
*
24584 AG-A-A-TCGCAACGCG--AAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGATAAATGAAAATCGCAACGAG
24617 AGAAT
1 AGAAT
24622 CGCAACGCGA
Statistics
Matches: 70, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
33 20 0.29
34 1 0.01
35 9 0.13
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.47
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGATAAATGAAAATCGCAACGAG
Found at i:24594 original size:14 final size:14
Alignment explanation
Indices: 24575--24628 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
24565 AAATGAAAAG
24575 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
24589 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
24608 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
24622 CGCAACG
1 CGCAACG
24629 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:24605 original size:33 final size:33
Alignment explanation
Indices: 24565--24633 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
24555 GCAACGAGAT
24565 AAATGAAAAGCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAAGCGCAACGAGAGAATCGCAACGCG
*
24598 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAAGCGCAACGAGAGAATCGCAACGCG
24631 AAA
1 AAA
24634 CCAAATCGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.20, G:0.25, T:0.07
Consensus pattern (33 bp):
AAATGAAAAGCGCAACGAGAGAATCGCAACGCG
Found at i:24666 original size:19 final size:19
Alignment explanation
Indices: 24639--24722 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
24629 CGAAACCAAA
*
24639 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
24658 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
24677 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
24691 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
24710 TCGCGTTGCGATT
1 TCGCGTTGCGATT
24723 CTCTCGTTGC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 41 0.73
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:24699 original size:14 final size:14
Alignment explanation
Indices: 24680--24736 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
24670 TTTCATTTCG
24680 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
24694 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
24711 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
24727 CGTTGCGATT
1 CGTTGCGATT
24737 TTCATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
15 1 0.03
16 5 0.13
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.09, C:0.26, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:24703 original size:33 final size:33
Alignment explanation
Indices: 24661--24744 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
24651 TTTCATTTCG
24661 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
24694 CGTTGCGATTGTCATCTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
24727 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
24745 AACCAAAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:26596 original size:93 final size:93
Alignment explanation
Indices: 26437--26908 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
26427 TAGATTGCTT
*
26437 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26502 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
26530 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26595 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
26623 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTT-ACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26686 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
26714 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26779 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
26807 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26872 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
26900 AGTAAATTT
1 AGTAAATTT
26909 ATCCATTCAA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 76 0.20
92 29 0.08
93 269 0.72
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:26748 original size:184 final size:186
Alignment explanation
Indices: 26437--26908 Score: 912
Period size: 184 Copynumber: 2.5 Consensus size: 186
26427 TAGATTGCTT
*
26437 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26502 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
26567 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
26623 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTT-ACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26686 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
26751 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
26807 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26872 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
26909 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
184 168 0.60
185 30 0.11
186 84 0.30
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:26991 original size:19 final size:19
Alignment explanation
Indices: 26951--27079 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
26941 TAGTTTACTT
* *
26951 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
26971 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
26990 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
27009 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
27023 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
27042 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
27056 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
27075 TCGCA
1 TCGCA
27080 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:27030 original size:33 final size:32
Alignment explanation
Indices: 26987--27079 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
26977 CGCGAAACCA
**
26987 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
27019 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
27052 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
27080 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:27077 original size:52 final size:52
Alignment explanation
Indices: 26951--27079 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
26941 TAGTTTACTT
**
26951 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
27003 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
27056 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
27080 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:27097 original size:19 final size:19
Alignment explanation
Indices: 27075--27209 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
27065 GAAACCAAAA
*
27075 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27094 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
27110 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
27127 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
27143 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
27160 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
27179 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
27199 TCGTGTTGCGA
1 TCGCGTTGCGA
27210 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:27116 original size:14 final size:14
Alignment explanation
Indices: 27097--27153 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
27087 TTTCATTTCG
27097 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
27111 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
27128 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
27144 CGTTGCGATT
1 CGTTGCGATT
27154 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:27122 original size:33 final size:33
Alignment explanation
Indices: 27080--27172 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
27070 CAAAATCGCA
*
27080 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
27113 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
27146 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
27173 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:29148 original size:14 final size:14
Alignment explanation
Indices: 29129--29164 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
29119 ATTGTTTAAT
29129 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
29143 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
29157 TGATTTGT
1 TGATTTGT
29165 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:29294 original size:19 final size:19
Alignment explanation
Indices: 29270--29369 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
29260 AAAATTGACT
29270 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
29289 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
29308 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
29322 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
29341 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
29361 ATCGCAATG
1 ATCGCAATG
29370 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:29399 original size:53 final size:53
Alignment explanation
Indices: 29270--29386 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
29260 AAAATTGACT
29270 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
29322 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
29375 ATCGCAATGCGA
1 ATCGCAATGCGA
29387 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:29404 original size:19 final size:19
Alignment explanation
Indices: 29376--29524 Score: 148
Period size: 19 Copynumber: 8.6 Consensus size: 19
29366 AATGGGAGAA
* *
29376 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
29395 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
29411 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29428 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29447 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
29463 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
29480 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
29496 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29513 TCCGCATTGCGA
1 T-CGCATTGCGA
29525 AATGTAATGG
Statistics
Matches: 109, Mismatches: 5, Indels: 31
0.75 0.03 0.21
Matches are distributed among these distances:
14 18 0.17
16 22 0.20
17 20 0.18
18 2 0.02
19 41 0.38
20 6 0.06
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:29439 original size:52 final size:52
Alignment explanation
Indices: 29376--29492 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
29366 AATGGGAGAA
*
29376 TCGCAATGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* * *
29428 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
29480 TCGCATTGCGATT
1 TCGCATTGCGATT
29493 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:29470 original size:33 final size:33
Alignment explanation
Indices: 29433--29524 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
29423 TCATTTCGCA
*
29433 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
29466 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
29499 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
29525 AATGTAATGG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
33 47 0.82
34 10 0.18
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:29471 original size:14 final size:14
Alignment explanation
Indices: 29452--29506 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
29442 TCATTTCGCA
29452 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
29466 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
*
29483 CATTGCGATTCTCTCG
1 --TTGCGATTCTTTCG
29499 TTGCGATT
1 TTGCGATT
29507 TTCATTTCCG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 14 0.40
16 7 0.20
17 8 0.23
19 6 0.17
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:29623 original size:19 final size:19
Alignment explanation
Indices: 29583--29679 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
29573 AAAATTGACT
29583 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
29601 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
29620 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
29634 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
29653 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
29673 ATCGCAA
1 ATCGCAA
29680 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 17 0.24
19 22 0.31
20 16 0.23
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:29711 original size:53 final size:53
Alignment explanation
Indices: 29583--29698 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
29573 AAAATTGACT
29583 ATCGCAATGCGAAATG-AAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
29634 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
29687 ATCGCAATGCGA
1 ATCGCAATGCGA
29699 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 16 0.25
52 12 0.19
53 35 0.56
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:32214 original size:24 final size:24
Alignment explanation
Indices: 32180--32226 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
32170 CTGAAACATC
32180 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
32204 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
32227 GACCAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:33109 original size:20 final size:20
Alignment explanation
Indices: 32908--33137 Score: 252
Period size: 20 Copynumber: 11.6 Consensus size: 20
32898 TTACAATTCT
*
32908 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
* * *
32928 CGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGATACG
*
32948 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
* * *
32968 CGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGATACG
32988 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
33008 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
33028 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
33048 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
33068 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
33088 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
** *
33108 CGTTGCGATTT-CATATTCG
1 CGTTGCGATTTACGGATACG
33127 CGTTGCGATTT
1 CGTTGCGATTT
33138 TGGAAATCGC
Statistics
Matches: 183, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.09
20 164 0.90
21 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:34845 original size:30 final size:30
Alignment explanation
Indices: 34809--34889 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
34799 CATCATTTTT
*
34809 TAATATTTTCGGTCATTTTTTAGCGCCTAG
1 TAATATTTTCGGTCATTTTTTAGCGCCTAA
*
34839 TAATATTTTCGGTCATTTTTTAGCGTCTAA
1 TAATATTTTCGGTCATTTTTTAGCGCCTAA
34869 TAATATTTTCGGTCATTTTTT
1 TAATATTTTCGGTCATTTTTT
34890 CGAAAATCCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (30 bp):
TAATATTTTCGGTCATTTTTTAGCGCCTAA
Found at i:41243 original size:6 final size:6
Alignment explanation
Indices: 41232--41265 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
41222 CGGCTTTGAT
*
41232 AGAGGA AGAGGAA AGAGAA AGAGAA AGAGAA AGA
1 AGAGAA AGA-GAA AGAGAA AGAGAA AGAGAA AGA
41266 TTGGAGAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (6 bp):
AGAGAA
Found at i:41776 original size:16 final size:16
Alignment explanation
Indices: 41749--41795 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
41739 TTGCAAGTTT
*
41749 GTTATCAGCTAGTTCCA
1 GTTAT-AGCTAGTGCCA
41766 GTTATAGCTAGTGCCA
1 GTTATAGCTAGTGCCA
* *
41782 GTTGTAGCTGGTGC
1 GTTATAGCTAGTGC
41796 TAGCTATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (16 bp):
GTTATAGCTAGTGCCA
Done.