Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009030.1 Hibiscus syriacus cultivar Beakdansim tig00112430_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: 53432
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4923 original size:76 final size:79
Alignment explanation
Indices: 4791--4944 Score: 208
Period size: 76 Copynumber: 2.0 Consensus size: 79
4781 ATATAGTAAG
4791 TAAACATTAAATGAATGTAATTCTAATTACAACACTTTTAATGTATATTTAATTTGAACTAATTA
1 TAAACATTAAATGAATGTAATTCTAATTACAACACTTTTAATGTATATTTAATTTGAACTAATTA
*
4856 AGTAAGAGTTTAAA
66 AATAAGAGTTTAAA
* * ** *
4870 TAAACATTAAAT-ATTGTAATTC-AGATTATAAGTC-TTTAATG-ATATTTTATTTGAACTAATT
1 TAAACATTAAATGAATGTAATTCTA-ATTACAACACTTTTAATGTATATTTAATTTGAACTAATT
*
4931 AAATAAGATTTTAA
65 AAATAAGAGTTTAA
4945 TTAATTTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
76 31 0.46
77 8 0.12
78 16 0.24
79 12 0.18
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (79 bp):
TAAACATTAAATGAATGTAATTCTAATTACAACACTTTTAATGTATATTTAATTTGAACTAATTA
AATAAGAGTTTAAA
Found at i:5806 original size:2 final size:2
Alignment explanation
Indices: 5801--5851 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5791 TGTGTGTATG
5801 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5843 TA TA TA TA T
1 TA TA TA TA T
5852 GATTTGCACT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15609 original size:31 final size:31
Alignment explanation
Indices: 15531--15609 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
15521 TCAAAAAACA
* *
15531 TAAGTTTTGGTCACTTACGTTATTGTTTTAT
1 TAAGTTTTGGTCACTTGCGTTATTATTTTAT
*
15562 TAAGTTTTGGTCACTTGTGTT-TTCATTTTAT
1 TAAGTTTTGGTCACTTGCGTTATT-ATTTTAT
15593 TAAGTTTTGGTCACTTG
1 TAAGTTTTGGTCACTTG
15610 GACATTGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 2 0.05
31 42 0.95
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.54
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTGCGTTATTATTTTAT
Found at i:16262 original size:20 final size:20
Alignment explanation
Indices: 16237--16276 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16227 TTCTTAAAGC
16237 ACATTTAGG-TACATATAGTT
1 ACATTTAGGAT-CATATAGTT
16257 ACATTTAGGATCATATAGTT
1 ACATTTAGGATCATATAGTT
16277 TTATGTGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
ACATTTAGGATCATATAGTT
Found at i:18559 original size:31 final size:31
Alignment explanation
Indices: 18524--18598 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
18514 AACATCCAAT
*
18524 TGACCAAAACTTAATAAAACGATAATATAAG
1 TGACCAAAACTTAATAAAACGATAACATAAG
* * *
18555 TGACCAAAACATAATAAAATGATAACGTAAG
1 TGACCAAAACTTAATAAAACGATAACATAAG
18586 TGACCAAAACTTA
1 TGACCAAAACTTA
18599 TATTTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (31 bp):
TGACCAAAACTTAATAAAACGATAACATAAG
Found at i:19242 original size:31 final size:31
Alignment explanation
Indices: 19173--19245 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
19163 TAAGGAAAAG
*
19173 CGATTTTGATCTTTTACATTATCAATCATTT
1 CGATTTTGATCCTTTACATTATCAATCATTT
**
19204 -GATTTTGATCCTTTACATTATCGGT-ATGTT
1 CGATTTTGATCCTTTACATTATCAATCAT-TT
19234 CGATTTTGATCC
1 CGATTTTGATCC
19246 CTCAGCCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 2 0.05
30 24 0.65
31 11 0.30
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.49
Consensus pattern (31 bp):
CGATTTTGATCCTTTACATTATCAATCATTT
Found at i:24608 original size:16 final size:16
Alignment explanation
Indices: 24565--24609 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
24555 ACAGAGCCTC
* *
24565 TGAATCATTTAACATT
1 TGAATCATTCAGCATT
24581 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
24597 TGAATCATTCAGC
1 TGAATCATTCAGC
24610 GCTTAATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:24619 original size:15 final size:16
Alignment explanation
Indices: 24565--24620 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
24555 ACAGAGCCTC
* * *
24565 TGAATCATTTAACATT
1 TGAATCATTCAGCACT
*
24581 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
24597 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
24613 T-AATCATT
1 TGAATCATT
24621 TTGAAGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 7 0.19
16 29 0.81
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:26756 original size:7 final size:7
Alignment explanation
Indices: 26744--26771 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
26734 TGAGGATGAA
26744 TTTGATG
1 TTTGATG
26751 TTTGATG
1 TTTGATG
26758 TTTGATG
1 TTTGATG
26765 TTTGATG
1 TTTGATG
26772 ATGATTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (7 bp):
TTTGATG
Found at i:29861 original size:20 final size:20
Alignment explanation
Indices: 29838--29889 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
29828 AACGCGATCC
29838 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
29858 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
29878 CCAAAATCGCAA
1 CCAGAATCGCAA
29890 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:29970 original size:20 final size:20
Alignment explanation
Indices: 29945--30138 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
29935 GATTTTCCAT
* *
29945 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
29965 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
29985 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
30005 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
30025 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
30045 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
30065 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
30085 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
30106 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
30126 AATCGCAACGCGA
1 AATCGCAACGCGA
30139 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:29990 original size:40 final size:39
Alignment explanation
Indices: 29941--30138 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
29931 TTGCGATTTT
* ** *
29941 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
29979 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
30020 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
30060 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
30099 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
30139 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:30028 original size:60 final size:60
Alignment explanation
Indices: 29945--30137 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
29935 GATTTTCCAT
* ** * *
29945 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
30005 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
30065 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
30126 AATCGCAACGCG
1 AATCGCAACGCG
30138 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:30556 original size:33 final size:33
Alignment explanation
Indices: 30517--30587 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
30507 TTCGCTTAGA
*
30517 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
30550 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
30583 TTTCA
1 TTTCA
30588 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:30727 original size:14 final size:14
Alignment explanation
Indices: 30708--30762 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
30698 AGAATGACTG
30708 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
30722 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
30741 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
30755 TCGCAACG
1 TCGCAACG
30763 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:30745 original size:33 final size:33
Alignment explanation
Indices: 30708--30778 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
30698 AGAATGACTG
**
30708 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
30741 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
30774 TCGCA
1 TCGCA
30779 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:30815 original size:14 final size:14
Alignment explanation
Indices: 30796--30885 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
30786 TTTCATTTCG
30796 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
30810 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
30829 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
30843 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
*
30860 CGCGTTGTGATTCTCT
1 --CGTTGCGATTCTCT
30876 CGTTGCGATT
1 CGTTGCGATT
30886 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:30821 original size:33 final size:33
Alignment explanation
Indices: 30779--30893 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
30769 CAAAATCGCA
30779 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
30812 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* * *
30845 TTGCGATTGTCATCTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
30878 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
30894 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:30865 original size:19 final size:18
Alignment explanation
Indices: 30774--30886 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
30764 GAAACCAAAA
* *
30774 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
30793 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
*
30809 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
30826 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
30842 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
*
30859 TCGCGTTGTGA-TTC-TC
1 TCGCGTTGCGATTTCATC
30875 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
30887 TCATTTCAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 26
0.71 0.06 0.24
Matches are distributed among these distances:
14 23 0.30
15 3 0.04
16 12 0.16
17 13 0.17
18 1 0.01
19 25 0.32
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:32619 original size:92 final size:93
Alignment explanation
Indices: 32376--32837 Score: 806
Period size: 92 Copynumber: 5.1 Consensus size: 93
32366 TAGATTGCTT
*
32376 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32441 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
32468 AGTAAATTTGTTCGGTTGCTGCC-ATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32531 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32559 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32624 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32651 AGTAAA-TT-TTCGGTTGCTGCCAATTCCTGCTAAACTGTGTATTC-TTAACACTGTGAAATA-T
1 AGTAAATTTGTTCGGTTGCTGCCAATT-CTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
32712 A-TTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
32740 AGTAAATTTGTTCGGTTGCTGCC-ATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32804 TTTGTCTTTGTTTTG--TTTT-GTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32829 AGTAAATTT
1 AGTAAATTT
32838 ATCCATTCAA
Statistics
Matches: 358, Mismatches: 3, Indels: 21
0.94 0.01 0.05
Matches are distributed among these distances:
89 68 0.19
90 77 0.22
91 105 0.29
92 106 0.30
93 2 0.01
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:32684 original size:183 final size:180
Alignment explanation
Indices: 32376--32837 Score: 810
Period size: 183 Copynumber: 2.6 Consensus size: 180
32366 TAGATTGCTT
*
32376 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32441 TTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCATTCTGCTAAACTG
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAA-TT-TTCGGTTGCTGCCATTCTGCTAAACTG
32505 TATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
129 TATATTC-TTAACACTGTGAAATATA-TTGTCTTTGTTTTGTCTTTTGGTTGAA
32559 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32624 -TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTTCGGTTGCTGCCAATTCCTGCTAAACTG
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTTCGGTTGCTGCC-ATT-CTGCTAAACTG
*
32688 TGTATTCTTAACACTGTGAAATATATTGTCTTTGTTTTGTCTTTTGGTTGAA
129 TATATTCTTAACACTGTGAAATATATTGTCTTTGTTTTGTCTTTTGGTTGAA
32740 AGTAAATTTGTTCGGTTGCTGCC-ATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32804 TTTGTCTTTGTTTTG--TTTT-GTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
32838 ATCCATTCAA
Statistics
Matches: 273, Mismatches: 2, Indels: 13
0.95 0.01 0.05
Matches are distributed among these distances:
178 15 0.05
179 4 0.01
180 41 0.15
181 77 0.28
182 39 0.14
183 97 0.36
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (180 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTTCGGTTGCTGCCATTCTGCTAAACTGTA
TATTCTTAACACTGTGAAATATATTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:32920 original size:19 final size:19
Alignment explanation
Indices: 32880--33006 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
32870 TAGTTTACTT
* *
32880 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
32900 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
32919 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
32938 TCGCAA--CG--A-C-AAA
1 TCGCAACGCGAAACCAAAA
32951 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
32970 TCGCAA--CG--A-C-AGA
1 TCGCAACGCGAAACCAAAA
32983 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
33002 TCGCA
1 TCGCA
33007 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 25
0.73 0.06 0.21
Matches are distributed among these distances:
13 17 0.19
14 1 0.01
15 6 0.07
17 6 0.07
18 2 0.02
19 43 0.49
20 13 0.15
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:32957 original size:32 final size:32
Alignment explanation
Indices: 32916--33006 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
32906 CGCGAAACCA
**
32916 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
32948 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
32980 AGATCGCAACGCGAAACCAAAATCGCA
1 AAATCGCAACGCGAAACCAAAATCGCA
33007 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:33003 original size:51 final size:51
Alignment explanation
Indices: 32880--33006 Score: 143
Period size: 51 Copynumber: 2.5 Consensus size: 51
32870 TAGTTTACTT
*
32880 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAAC-CAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * * *
32932 T-G-AAAATCGCAACGACAAATCGCAACGCGAAACCAAAATCGCAACGAC-AGA
1 TCGCAACA-CGAAACCA-AAATCGCAACGCGAAACCAAAATCGCAACG-CGAAA
*
32983 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACACGAAACCAAAATCGCA
33007 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
50 4 0.06
51 47 0.76
52 9 0.15
53 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (51 bp):
TCGCAACACGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:33024 original size:19 final size:19
Alignment explanation
Indices: 33002--33136 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
32992 GAAACCAAAA
*
33002 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
33021 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
33037 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
33054 TCGC-ATGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
33069 TCG-TTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
33087 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
33106 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
33126 TCGTGTTGCGA
1 TCGCGTTGCGA
33137 AAAGTAAACT
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 8 0.09
15 9 0.10
16 9 0.10
17 9 0.10
18 9 0.10
19 38 0.40
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:33043 original size:14 final size:15
Alignment explanation
Indices: 33019--33099 Score: 56
Period size: 16 Copynumber: 4.9 Consensus size: 15
33009 GCGATTTTCA
33019 TTTCGCGTTGCGATTC
1 TTTCGC-TTGCGATTC
33035 TTTCG-TTGCGATTTTC
1 TTTCGCTTGCGA--TTC
*
33051 ATTTCGCATGCGATTC
1 -TTTCGCTTGCGATTC
* *
33067 TGTCGTTTGCGATTTTC
1 TTTCGCTTGCGA--TTC
33084 ATTTCGCGTTGCGATT
1 -TTTCGC-TTGCGATT
33100 TTGGTTTCGC
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
14 6 0.12
15 9 0.18
16 11 0.22
17 10 0.20
18 9 0.18
19 6 0.12
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (15 bp):
TTTCGCTTGCGATTC
Found at i:33073 original size:32 final size:34
Alignment explanation
Indices: 33007--33099 Score: 154
Period size: 33 Copynumber: 2.8 Consensus size: 34
32997 CAAAATCGCA
*
33007 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG-
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
33040 TTGCGATTTTCATTTCGC-ATGCGATTCTGTCGT
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
33073 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
33100 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 12 0.22
33 36 0.65
34 7 0.13
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:35170 original size:19 final size:19
Alignment explanation
Indices: 35154--35255 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
35144 AAAAATGACT
35154 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35173 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
35192 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
35206 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35225 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
35245 ATCGCAATGCG
1 ATCGCAATGCG
35256 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:35308 original size:19 final size:19
Alignment explanation
Indices: 35284--35574 Score: 374
Period size: 19 Copynumber: 16.4 Consensus size: 19
35274 GATTATCTCG
35284 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35303 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35322 TTGCGA--TTC--TTCG--
1 TTGCGATTTTCATTTCGCA
35335 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35354 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35373 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35392 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35411 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
35430 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
35449 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
35463 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35482 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
*
35500 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
35514 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
35534 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
35548 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
35567 TTGCGATT
1 TTGCGATT
35575 GTATTTTCCG
Statistics
Matches: 241, Mismatches: 8, Indels: 46
0.82 0.03 0.16
Matches are distributed among these distances:
13 6 0.02
14 23 0.10
15 7 0.03
16 18 0.07
17 16 0.07
18 15 0.06
19 144 0.60
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:35352 original size:51 final size:50
Alignment explanation
Indices: 35262--35574 Score: 319
Period size: 51 Copynumber: 5.9 Consensus size: 50
35252 TGCGTTTATA
35262 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGATTTTC
35314 ATTTCGCATTGCGATTCTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-TTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
35365 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA---T--TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
** * * *
35422 ATTTCGCATTGCGATTTTAATTTCGCA-TTGCGA-TTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTTC-ATTTC-G-CATTGCGATTTTC
* * * *
35474 ATTTCGCATTGCGATTTTCATT-CGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* *
35525 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTTC--GTTGCGATTTTCATTTCGCATTGCGATT
35575 GTATTTTCCG
Statistics
Matches: 231, Mismatches: 12, Indels: 35
0.83 0.04 0.13
Matches are distributed among these distances:
50 10 0.04
51 77 0.33
52 69 0.30
53 14 0.06
54 8 0.03
55 8 0.03
56 1 0.00
57 44 0.19
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (50 bp):
ATTTCGCATTGCGATTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:37842 original size:12 final size:12
Alignment explanation
Indices: 37825--37849 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37815 TCTTCGGGGA
37825 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37837 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37849 C
1 C
37850 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:38056 original size:23 final size:23
Alignment explanation
Indices: 38023--38067 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
38013 CTGAAACATC
38023 ATCAAAATCCGTG-TATTGACCAT
1 ATCAAAATCCG-GATATTGACCAT
*
38046 ATCAAAGTCCGGATATTGACCA
1 ATCAAAATCCGGATATTGACCA
38068 AGACCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (23 bp):
ATCAAAATCCGGATATTGACCAT
Found at i:38648 original size:20 final size:21
Alignment explanation
Indices: 38619--38657 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
38609 ACCTGTTGCC
*
38619 GGATTGGGAA-GGATGTCGTT
1 GGATTAGGAACGGATGTCGTT
38639 GGATTAGGAACGGATGTCG
1 GGATTAGGAACGGATGTCG
38658 CCGGAGAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.08, G:0.44, T:0.26
Consensus pattern (21 bp):
GGATTAGGAACGGATGTCGTT
Found at i:38773 original size:20 final size:20
Alignment explanation
Indices: 38745--39107 Score: 406
Period size: 20 Copynumber: 18.4 Consensus size: 20
38735 AAAATTTAGT
* * * *
38745 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
38765 GTTGCGATTTATGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
38785 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
38805 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
38825 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
38845 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
38865 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
38885 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
38905 ATTGCGA-TTACGGATA--C
1 GTTGCGATTTACGGATACGC
38922 GTTGCGATTTACGGATA--C
1 GTTGCGATTTACGGATACGC
38940 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
38960 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
38980 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
39000 ATTGCGATTTAC-CATACGC
1 GTTGCGATTTACGGATACGC
*
39019 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
39039 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
39059 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
39079 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
39099 GTTGCGATT
1 GTTGCGATT
39108 ATGGAAAATC
Statistics
Matches: 301, Mismatches: 28, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.03
18 25 0.08
19 31 0.10
20 231 0.77
21 6 0.02
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:38967 original size:115 final size:116
Alignment explanation
Indices: 38786--39106 Score: 391
Period size: 115 Copynumber: 2.7 Consensus size: 116
38776 TGGATTATCG
* **
38786 TTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCG
1 TTGCGATTTACGGA-TAACGTTGCGATTTACGGA-TA-CGTTGCGATTTACGGATACGCGTTGCG
* * * *
38851 ATTTACGGATTA-TCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCA
63 ATTTACGGA-TACGCGTTGCGATATACGGATACGCATTGCGATTTAC-CATACGCA
38906 TTGCGA-TTACGGAT-ACGTTGCGATTTACGGATACGTTGC-AGTTTACGGATACGCGTTGCGAT
1 TTGCGATTTACGGATAACGTTGCGATTTACGGATACGTTGCGA-TTTACGGATACGCGTTGCGAT
*
38968 TTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACCATACGCG
65 TTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACCATACGCA
* *
39020 TTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCGCGTTGC
1 TTGCGATTTACGGATA-ACGTTGCGATTTACGGATA--CGTTGCGATTTACG-GATACGCGTTGC
* ** *
39084 GATTTTCATATTCGCGTTGCGAT
62 GATTTACGGATACGCGTTGCGAT
39107 TATGGAAAAT
Statistics
Matches: 179, Mismatches: 13, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
114 15 0.08
115 73 0.41
116 2 0.01
117 35 0.20
118 1 0.01
119 45 0.25
120 8 0.04
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (116 bp):
TTGCGATTTACGGATAACGTTGCGATTTACGGATACGTTGCGATTTACGGATACGCGTTGCGATT
TACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACCATACGCA
Found at i:43191 original size:16 final size:16
Alignment explanation
Indices: 43170--43209 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
43160 ACAGTTCGGG
*
43170 TTCAGTTCGGGTTAAT
1 TTCAGTTCGGATTAAT
43186 TTCAGTTCGGATTAAT
1 TTCAGTTCGGATTAAT
*
43202 TTTAGTTC
1 TTCAGTTC
43210 AGGTAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (16 bp):
TTCAGTTCGGATTAAT
Found at i:46006 original size:2 final size:2
Alignment explanation
Indices: 45981--46166 Score: 94
Period size: 2 Copynumber: 95.5 Consensus size: 2
45971 AAACTTGTGC
*
45981 AT AT A- AT AT AA AT AT AT ACT -T AT AT A- AGT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT
* * *
46020 AT -T AT AC AT -T AT ACT -T AT A- AT AT AT GT AC AT A- AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
46058 ACT -T AT TT AT AT AT AT AA AT AA AGT AT A- AT AT TT AT AA ACT
1 A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T
* *
46099 AT AA AGT AT A- AGT AT AT AA AT -T AT AT AGT AT AT AT AT AT AT
1 AT AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
46140 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
46167 ACTATCAAGC
Statistics
Matches: 139, Mismatches: 22, Indels: 46
0.67 0.11 0.22
Matches are distributed among these distances:
1 14 0.10
2 115 0.83
3 10 0.07
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:46012 original size:8 final size:7
Alignment explanation
Indices: 45981--46167 Score: 71
Period size: 7 Copynumber: 26.9 Consensus size: 7
45971 AAACTTGTGC
45981 ATATAAT
1 ATATAAT
45988 ATA-AAT
1 ATATAAT
*
45994 ATATACTT
1 ATATA-AT
46002 ATATAAGT
1 ATATAA-T
46010 ATAT-A-
1 ATATAAT
46015 ATATAAT
1 ATATAAT
46022 -TATACAT
1 ATATA-AT
*
46029 -TATACT
1 ATATAAT
46035 -TATAAT
1 ATATAAT
*
46041 ATAT-GT
1 ATATAAT
*
46047 ACATAAT
1 ATATAAT
*
46054 ATATACTT
1 ATATA-AT
*
46062 ATTTATAT
1 ATATA-AT
46070 ATATAA-
1 ATATAAT
46076 ATA-AAGT
1 ATATAA-T
46083 ATA-ATAT
1 ATATA-AT
*
46090 TTATAA-
1 ATATAAT
46096 ACTATAA-
1 A-TATAAT
46103 AGTATAAGT
1 A-TATAA-T
46112 ATATAAATT
1 ATAT-AA-T
*
46121 ATATAGT
1 ATATAAT
46128 ATAT-AT
1 ATATAAT
46134 ATAT-AT
1 ATATAAT
46140 ATAT-AT
1 ATATAAT
46146 ATATATAT
1 ATATA-AT
46154 ATATATAT
1 ATATA-AT
46162 ATATAA
1 ATATAA
46168 CTATCAAGCA
Statistics
Matches: 142, Mismatches: 19, Indels: 38
0.71 0.10 0.19
Matches are distributed among these distances:
5 6 0.04
6 41 0.29
7 45 0.32
8 42 0.30
9 8 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:46292 original size:32 final size:33
Alignment explanation
Indices: 46256--46351 Score: 133
Period size: 32 Copynumber: 2.9 Consensus size: 33
46246 ATATATATAT
* *
46256 ATATATTATATAGTTTTGCAAATGA-TTTTGAA
1 ATATATTATATAGTTTTGAAAACGATTTTTGAA
46288 ATATATAATATATAGTTTTGAAAACGATTTTTGAA
1 ATATAT--TATATAGTTTTGAAAACGATTTTTGAA
*
46323 ATATA-TATATAGTTTTGAAAACAATTTTT
1 ATATATTATATAGTTTTGAAAACGATTTTT
46352 AAAAATGTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
32 29 0.50
34 17 0.29
35 12 0.21
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (33 bp):
ATATATTATATAGTTTTGAAAACGATTTTTGAA
Found at i:46292 original size:34 final size:35
Alignment explanation
Indices: 46254--46392 Score: 146
Period size: 34 Copynumber: 4.0 Consensus size: 35
46244 ATATATATAT
* *
46254 ATATATATTATATAGTTTTGCAAATGA-TTTTGAA
1 ATATATATTATATAGTTTTGAAAACGATTTTTGAA
*
46288 ATATATAATATATAGTTTTGAAAACGATTTTTG-A
1 ATATATATTATATAGTTTTGAAAACGATTTTTGAA
* *
46322 A-ATATA-TATATAGTTTTGAAAACAATTTTTAAAA
1 ATATATATTATATAGTTTTGAAAACGATTTTT-GAA
*
46356 ATGTATATATTATATAGCTTTTAAAAAC-A-TTTTGAA
1 A--TATATATTATATAG-TTTTGAAAACGATTTTTGAA
46392 A
1 A
46393 GCATATATAT
Statistics
Matches: 90, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
32 23 0.26
33 5 0.06
34 28 0.31
35 5 0.06
36 3 0.03
37 9 0.10
38 8 0.09
39 9 0.10
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (35 bp):
ATATATATTATATAGTTTTGAAAACGATTTTTGAA
Found at i:46414 original size:63 final size:62
Alignment explanation
Indices: 46347--46483 Score: 134
Period size: 63 Copynumber: 2.2 Consensus size: 62
46337 TTGAAAACAA
* * ** *
46347 TTTTTAAAAATGTATATATTATATAGCTTTT-AAAAACATTTTGAAAGCATATAT-ATAATATGG
1 TTTTTAAAAAT-T-TATATAATAT-GCTTTTAAAAAAAAAATTGAAAACATATATAAT-ATATGG
46410 T
62 T
* * *
46411 TTTTTGAAACATTTTTATAATATGGTTTTAAAAAAAAAATTGAAAACATATATAATATATGGT
1 TTTTT-AAAAATTTATATAATATGCTTTTAAAAAAAAAATTGAAAACATATATAATATATGGT
*
46474 TTTTAAAAAA
1 TTTTTAAAAA
46484 ATATCATTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
62 9 0.15
63 38 0.63
64 8 0.13
65 5 0.08
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (62 bp):
TTTTTAAAAATTTATATAATATGCTTTTAAAAAAAAAATTGAAAACATATATAATATATGGT
Found at i:46429 original size:26 final size:27
Alignment explanation
Indices: 46385--46439 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
46375 TTTAAAAACA
46385 TTTTGAAAGCATATATATAATATGGTT
1 TTTTGAAAGCATATATATAATATGGTT
* *
46412 TTTTGAAA-CATTTTTATAATATGGTT
1 TTTTGAAAGCATATATATAATATGGTT
46438 TT
1 TT
46440 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.51
Consensus pattern (27 bp):
TTTTGAAAGCATATATATAATATGGTT
Found at i:46485 original size:35 final size:36
Alignment explanation
Indices: 46450--46730 Score: 180
Period size: 36 Copynumber: 7.6 Consensus size: 36
46440 AAAAAAAAAA
*
46450 TTGAAAACATATATAATATATGGTTTTTAAAAAAATATCATT
1 TTGAAAACATATATAATATATAGTTTTT---AAAA-A--ATT
* *
46492 TTGAAAAAATATATAATATATAGTTTTTGAAAATATT
1 TTGAAAACATATATAATATATAGTTTTT-AAAAAATT
* * * * * **
46529 TTAAAAACTTATATAATATATAATATTGAAATCATT
1 TTGAAAACATATATAATATATAGTTTTTAAAAAATT
* * *
46565 TTGAAAACTTATATAATATATTG-TTTTAAAACATTT
1 TTGAAAACATATATAATATATAGTTTTTAAAA-AATT
* * *
46601 TTGAAAACATTTATAATATAT-G-GTATAAAAACATT
1 TTGAAAACATATATAATATATAGTTTTTAAAAA-ATT
* **
46636 TTG-AAA-ATCATATAATATATAGTTTTGAAAACTTTT
1 TTGAAAACAT-ATATAATATATAGTTTTTAAAA-AATT
* * *
46672 TTAAAAAAATATGTATAATATATAG-TTTTAAAATATT
1 TTGAAAACATA--TATAATATATAGTTTTTAAAAAATT
*
46709 TT-AAAAAATATATATATATATA
1 TTGAAAACATATATA-ATATATA
46731 TATATATATA
Statistics
Matches: 194, Mismatches: 34, Indels: 29
0.75 0.13 0.11
Matches are distributed among these distances:
33 2 0.01
34 18 0.09
35 25 0.13
36 64 0.33
37 34 0.18
38 9 0.05
39 12 0.06
40 4 0.02
42 26 0.13
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (36 bp):
TTGAAAACATATATAATATATAGTTTTTAAAAAATT
Found at i:46582 original size:73 final size:71
Alignment explanation
Indices: 46486--46732 Score: 250
Period size: 73 Copynumber: 3.4 Consensus size: 71
46476 TTAAAAAAAT
*
46486 ATCATTTTGAAAAAATATATAATATATAGTTTTTGAAAATATTTTAAAAACTTATATAATATATA
1 ATCATTTTGAAAAATTATATAATATATAG-TTTTGAAAATATTTTAAAAACTT-TATAATATATA
* *
46551 ATATTGAA
64 GTATTAAA
* * * * *
46559 ATCATTTTGAAAACTTATATAATATATTGTTTT-AAAACATTTTTGAAAACATTTATAATATATG
1 ATCATTTTGAAAAATTATATAATATATAGTTTTGAAAATA-TTTTAAAAAC-TTTATAATATATA
46623 GTA-TAAA
64 GTATTAAA
* * * *
46630 AACATTTTG-AAAATCATATAATATATAGTTTTGAAAACTTTTTTAAAAAAATATGTATAATATA
1 ATCATTTTGAAAAATTATATAATATATAGTTTTGAAAA-TATTTT-AAAAACT-T-TATAATATA
*
46694 TAGTTTTAAA
62 TAGTATTAAA
*
46704 AT-ATTTTAAAAAATATATATATATATATA
1 ATCATTTTGAAAAAT-TATATA-ATATATA
46733 TATATATATA
Statistics
Matches: 142, Mismatches: 21, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
70 20 0.14
71 25 0.18
72 30 0.21
73 45 0.32
74 10 0.07
75 5 0.04
76 7 0.05
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (71 bp):
ATCATTTTGAAAAATTATATAATATATAGTTTTGAAAATATTTTAAAAACTTTATAATATATAGT
ATTAAA
Found at i:46721 original size:2 final size:2
Alignment explanation
Indices: 46716--46743 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46706 ATTTTAAAAA
46716 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
46744 TATTTATTTT
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:46802 original size:14 final size:14
Alignment explanation
Indices: 46751--46802 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
46741 TATTATTTAT
*
46751 TTTTA-TTTATCTTA
1 TTTTATTTTAT-TAA
46765 TTTTATTTTATTAA
1 TTTTATTTTATTAA
* *
46779 TTTCATTTTTTTAA
1 TTTTATTTTATTAA
46793 TTTTTATTTT
1 -TTTTATTTT
46803 GGTCCAGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTATTAA
Found at i:47864 original size:19 final size:19
Alignment explanation
Indices: 47849--47891 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
47839 CTTTTTTTTC
47849 TTTA-TTTTTTCCTTTTAT
1 TTTATTTTTTTCCTTTTAT
*
47867 TTTATTTTTTTCCTTTGA-
1 TTTATTTTTTTCCTTTTAT
47885 TTTATTT
1 TTTATTT
47892 AGTATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTATTTTTTTCCTTTTAT
Found at i:47940 original size:8 final size:8
Alignment explanation
Indices: 47927--47975 Score: 62
Period size: 8 Copynumber: 5.8 Consensus size: 8
47917 CTTTGAATTA
47927 TTTTTTAT
1 TTTTTTAT
47935 TTTTTTAT
1 TTTTTTAT
47943 TATTTTTAT
1 T-TTTTTAT
*
47952 GTTTTTAT
1 TTTTTTAT
47960 TTTATTTAT
1 TTT-TTTAT
47969 TATTTTT
1 T-TTTTT
47976 TATCTAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
8 18 0.50
9 16 0.44
10 2 0.06
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTTAT
Found at i:47949 original size:19 final size:18
Alignment explanation
Indices: 47842--47976 Score: 74
Period size: 20 Copynumber: 6.9 Consensus size: 18
47832 AATTTAACTT
**
47842 TTTTTTCTTTATTTTTTCC
1 TTTTTT-TTTATTTTTTTA
* *
47861 TTTTATTTTATTTTTTTCC
1 TTTTTTTTTATTTTTTT-A
47880 TTTGATTTATTTAGTATTTTTTCA
1 TTT--TTT-TTTA-T-TTTTTT-A
* *
47904 TTTTTTTTTCTTTCTTTGAA
1 TTTTTTTTTATTT-TTT-TA
*
47924 TTATTTTTTATTTTTTTA
1 TTTTTTTTTATTTTTTTA
* *
47942 -TTATTTTTATGTTTTTA
1 TTTTTTTTTATTTTTTTA
47959 TTTTATTTATTATTTTTT
1 TTTT-TTT-TTATTTTTT
47977 ATCTAACATT
Statistics
Matches: 91, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
17 14 0.15
18 13 0.14
19 17 0.19
20 24 0.26
21 5 0.05
22 7 0.08
23 1 0.01
24 10 0.11
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTTTTTATTTTTTTA
Found at i:47950 original size:17 final size:17
Alignment explanation
Indices: 47923--47975 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
47913 CTTTCTTTGA
47923 ATTATTTTTTATTTTTTT
1 ATTA-TTTTTATTTTTTT
*
47941 ATTATTTTTATGTTTTT
1 ATTATTTTTATTTTTTT
47958 ATT-TTATTTATTATTTTT
1 ATTATT-TTTATT-TTTTT
47976 TATCTAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 2 0.06
17 20 0.65
18 9 0.29
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (17 bp):
ATTATTTTTATTTTTTT
Found at i:47977 original size:19 final size:18
Alignment explanation
Indices: 47861--47978 Score: 75
Period size: 19 Copynumber: 6.3 Consensus size: 18
47851 TATTTTTTCC
47861 TTTTATTTTATTTTT-TT
1 TTTTATTTTATTTTTATT
* *
47878 CCTTTGA-TTTATTTAGTATT
1 --TTTTATTTTATTT-TTATT
*
47898 TTTTCATTTT-TTTTTCTT
1 TTTT-ATTTTATTTTTATT
*
47916 TCTTTGA-ATTATTTTTTATT
1 T-TTT-ATTTTA-TTTTTATT
*
47936 TTTT-TATTATTTTTATGT
1 TTTTATTTTATTTTTAT-T
47954 TTTTATTTTATTTATTATT
1 TTTTATTTTATTT-TTATT
47973 TTTTAT
1 TTTTAT
47979 CTAACATTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
17 7 0.09
18 25 0.32
19 30 0.38
20 17 0.22
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTATTTTATTTTTATT
Found at i:48531 original size:16 final size:18
Alignment explanation
Indices: 48497--48538 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
48487 AGAACATAAA
48497 ATATATAAATTATATAGT
1 ATATATAAATTATATAGT
*
48515 ATATATATA-TATA-AGT
1 ATATATAAATTATATAGT
*
48531 ACATATAA
1 ATATATAA
48539 GTATATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 4 0.19
18 8 0.38
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (18 bp):
ATATATAAATTATATAGT
Found at i:48871 original size:19 final size:20
Alignment explanation
Indices: 48835--48878 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
48825 TCTCTATTCT
*
48835 CTCTAAATTTTCCAATTTCC
1 CTCTAAATTCTCCAATTTCC
48855 CTCTAAATTCT-CAATTTCC
1 CTCTAAATTCTCCAATTTCC
48874 CTCTA
1 CTCTA
48879 TTATCAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (20 bp):
CTCTAAATTCTCCAATTTCC
Found at i:50796 original size:13 final size:12
Alignment explanation
Indices: 50766--50800 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
50756 AATTTAAAAA
50766 TATTTTAATTAT
1 TATTTTAATTAT
50778 TAATTTTCAATTAT
1 T-ATTTT-AATTAT
50792 TATTTTAAT
1 TATTTTAAT
50801 AACATGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.19
13 10 0.48
14 7 0.33
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:51819 original size:7 final size:7
Alignment explanation
Indices: 51809--51833 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
51799 ATAACTATTA
51809 TAATAAT
1 TAATAAT
51816 TAATAAT
1 TAATAAT
51823 TAATAAT
1 TAATAAT
51830 TAAT
1 TAAT
51834 TTTATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Found at i:51848 original size:29 final size:29
Alignment explanation
Indices: 51806--51865 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
51796 CTAATAACTA
* * *
51806 TTATAATAATTAATAATTAA-TAATTAATT
1 TTATAAAAAATAAT-ATTAATTAAATAATT
*
51835 TTATAAAAAATAATTTTAATTAAATAATT
1 TTATAAAAAATAATATTAATTAAATAATT
51864 TT
1 TT
51866 TATACTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTATAAAAAATAATATTAATTAAATAATT
Done.