Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003507.1 Hibiscus syriacus cultivar Beakdansim tig00007414_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: 120670
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:8598 original size:2 final size:2
Alignment explanation
Indices: 8591--8623 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8581 TTTGTATCCA
8591 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
8624 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:8628 original size:2 final size:2
Alignment explanation
Indices: 8623--8659 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8613 TCTCTCTCTC
8623 TA TA 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 TA TA T
8660 GCTTTGAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16972 original size:38 final size:39
Alignment explanation
Indices: 16930--17004 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
16920 ATGTTATCTT
*
16930 TATAACATTTTCAGTTG-AATTAAAAATATTACAAAGAA
1 TATAACATTTTCAGTTGCAATCAAAAATATTACAAAGAA
* *
16968 TATAATATTTTCAGTTGTCAATCGAAAATATTACAAA
1 TATAACATTTTCAGTTG-CAATCAAAAATATTACAAA
17005 AAAGGGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 16 0.50
40 16 0.50
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (39 bp):
TATAACATTTTCAGTTGCAATCAAAAATATTACAAAGAA
Found at i:22076 original size:115 final size:116
Alignment explanation
Indices: 21885--22122 Score: 295
Period size: 115 Copynumber: 2.1 Consensus size: 116
21875 AATGTTCCTA
* ** * *
21885 ATTTTTTATATTTATAATTAGGATCTTTTATTTTATAATTTTATAAAATTTTTAGTTTTTGATCA
1 ATTTTTTATATTTATAATTAGGACCCCTTATTTTATAATTTCATAAAATGTTTAGTTTTTGATCA
* *
21950 TCTTTTTCATTTATCTTATTAATTCATTCAGTTTTGAATTAAATATAA-TT
66 TCTTTTTCATTTATCTTATTAACTCATTCAGTTTTAAATTAAATATAACTT
* * *
22000 ATTTTTTATATTTATTATTA-GACCCCTTATTTTTATAATTTCATTATATGTTTAG-TTTTGACT
1 ATTTTTTATATTTATAATTAGGACCCCTTA-TTTTATAATTTCATAAAATGTTTAGTTTTTGA-T
* * *
22063 C-TCTTTTTCCATTTCTCTTATTTACTCATTCAGTTTTAAATTAAATTTAATCTT
64 CATCTTTTT-CATTTATCTTATTAACTCATTCAGTTTTAAATTAAATATAA-CTT
22117 ATTTTT
1 ATTTTT
22123 CTCCTTTTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
114 19 0.18
115 78 0.74
117 8 0.08
ACGTcount: A:0.27, C:0.10, G:0.05, T:0.58
Consensus pattern (116 bp):
ATTTTTTATATTTATAATTAGGACCCCTTATTTTATAATTTCATAAAATGTTTAGTTTTTGATCA
TCTTTTTCATTTATCTTATTAACTCATTCAGTTTTAAATTAAATATAACTT
Found at i:22756 original size:20 final size:20
Alignment explanation
Indices: 22727--22768 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
22717 GCACTTTTTT
*
22727 TTTATTCTTTTCCAATATAA
1 TTTATCCTTTTCCAATATAA
**
22747 TTTATCCTTTTTTAATATAA
1 TTTATCCTTTTCCAATATAA
22767 TT
1 TT
22769 GAGTCCTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATCCTTTTCCAATATAA
Found at i:23538 original size:20 final size:20
Alignment explanation
Indices: 23491--23758 Score: 260
Period size: 20 Copynumber: 13.2 Consensus size: 20
23481 AATGACCAAC
23491 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
23510 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
23530 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* *
23550 AAGATCGCAACACGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
23572 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
23592 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
23614 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
23634 AAAATCGCAACACGATTCAG
1 AAAATCGCAACGCGATTCAG
*
23654 AAAATCGCAACGCGGTTCAG
1 AAAATCGCAACGCGATTCAG
*
23674 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
23694 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
23714 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
23734 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
23754 AAAAT
1 AAAAT
23759 GAGTAAATTC
Statistics
Matches: 206, Mismatches: 29, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
18 1 0.00
19 23 0.11
20 149 0.72
21 3 0.01
22 27 0.13
23 3 0.01
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:23865 original size:6 final size:6
Alignment explanation
Indices: 23854--23973 Score: 219
Period size: 6 Copynumber: 20.5 Consensus size: 6
23844 GACACGTATT
23854 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
23902 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
23950 ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
23974 CGAGACGAGA
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.13
6 99 0.87
ACGTcount: A:0.32, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:24478 original size:6 final size:6
Alignment explanation
Indices: 24462--24571 Score: 213
Period size: 6 Copynumber: 18.5 Consensus size: 6
24452 CGCCGTCTCG
24462 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
24509 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
24557 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
24572 AATACGTGTC
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.05
6 99 0.95
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:24723 original size:20 final size:19
Alignment explanation
Indices: 24670--25023 Score: 204
Period size: 20 Copynumber: 17.2 Consensus size: 19
24660 TTTACTCATT
24670 TTCTGAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
24688 TTCTTGGAAGATCGCGTTGCGAA
1 TTC-T-G-A-ATCGCGTTGCGAA
*
24711 TTACTGAATCGCGTTGCGATT
1 TT-CTGAATCGCGTTGCGA-A
*
24732 TTCTTAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
*
24750 TTCTTGGAAGATCGCGTTGCGATT
1 TTC-T-G-A-ATCGCGTTGCGA-A
* *
24774 TTCTTATTCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
24792 TTCTTGGAAGATCGCGTTGCG-A
1 TTC-T-G-A-ATCGCGTTGCGAA
*
24814 TTCTTGGAATCGCGTTGCGATT
1 TTC-T-GAATCGCGTTGCGA-A
24836 TTCTGAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
*
24854 TTCTTGGAATCGCGTTGCGATT
1 TTC-T-GAATCGCGTTGCGA-A
*
24876 TTCTTAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
24894 TTCTTGGAAGATCGCGTTGCG-A
1 TTC-T-G-A-ATCGCGTTGCGAA
*
24916 TTCTTGGAAGATCGCGTTGCGATT
1 TTC-T-G-A-ATCGCGTTGCGA-A
*
24940 TTCTGAATCGCGTTGCGATT
1 TTCTGAATCGCGTTGCGA-A
24960 TTCTGAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
*
24978 TTCTTGGAAGATCGCGTTGCGATT
1 TTC-T-G-A-ATCGCGTTGCGA-A
* *
25002 TTATGAATCGCATTGCG-A
1 TTCTGAATCGCGTTGCGAA
25020 TTCT
1 TTCT
25024 TGGAAGATCG
Statistics
Matches: 278, Mismatches: 23, Indels: 70
0.75 0.06 0.19
Matches are distributed among these distances:
18 21 0.08
19 6 0.02
20 128 0.46
21 14 0.05
22 93 0.33
23 7 0.03
24 9 0.03
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (19 bp):
TTCTGAATCGCGTTGCGAA
Found at i:24743 original size:62 final size:60
Alignment explanation
Indices: 24667--25047 Score: 344
Period size: 62 Copynumber: 6.1 Consensus size: 60
24657 GAATTTACTC
* * *
24667 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAATTACTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCG
* * *
24729 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTATTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCG
**
24791 ATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
** *
24853 ATTCTT-GGAATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTCTT-GGAAGATCGCGTTGC
1 ATT-TTCTAAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGC
24914 G
60 G
** *
24915 ATTCTTGGAAGATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
** * * *
24977 ATTCTTGGAAGATCGCGTTGCGATT-TTATGAATCGCATTGCGATTCTT-GGAAGATCGCGTTGC
1 ATT-TTCTAA-ATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGC
25040 G
60 G
*
25041 ATCTTCT
1 ATTTTCT
25048 TTTCAACGTT
Statistics
Matches: 283, Mismatches: 20, Indels: 31
0.85 0.06 0.09
Matches are distributed among these distances:
60 28 0.10
61 7 0.02
62 174 0.61
63 14 0.05
64 60 0.21
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (60 bp):
ATTTTCTAAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
Found at i:24847 original size:104 final size:104
Alignment explanation
Indices: 24667--25047 Score: 530
Period size: 104 Copynumber: 3.7 Consensus size: 104
24657 GAATTTACTC
*
24667 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAATTAC-T-G-A-ATCGCGTTGC
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG-ATT-CTTGGAAGATCGCGTTGC
*
24728 GATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
64 GATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
24771 ATTTTCTTATTCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGA
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGA
24834 TTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
66 TTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
24873 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGA
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGA
*
24938 TTTTCTGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
66 TTTTCTGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*** * *
24977 ATTCTTGGAAGATCGCGTTGCGATT-TT--ATGAATCGCATTGCGATTCTTGGAAGATCGCGTTG
1 ATT-TTCTTA-ATCGCGTTGCGATTCTTGGAAG-ATCGCGTTGCGATTCTTGGAAGATCGCGTTG
*
25039 CGATCTTCT
63 CGATTTTCT
25048 TTTCAACGTT
Statistics
Matches: 258, Mismatches: 11, Indels: 16
0.91 0.04 0.06
Matches are distributed among these distances:
102 61 0.24
103 10 0.04
104 168 0.65
105 5 0.02
106 14 0.05
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (104 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGA
TTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:25042 original size:42 final size:41
Alignment explanation
Indices: 24667--25102 Score: 421
Period size: 42 Copynumber: 10.6 Consensus size: 41
24657 GAATTTACTC
24667 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG
* * ***
24709 AATTACTGAATCGCGTTGCGATT-TTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCG
* *** *
24749 ATTCTT-GGAAGATCGCGTTGCGATT-TTCTTATTCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTTGGAAATCGCGTTGCG
*
24791 ATTCTT-GGAAGATCGCGTTGCGATTCTTGG-AATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTTGGAAATCGCGTTGCG
24833 ATTTTCTGAATCGCGTTGCGATTCTTGG-AATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCG
*
24873 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG
* *
24915 ATTCTT-GGAAGATCGCGTTGCGATT-TTCTG-AATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTT-GGAAATCGCGTTGCG
24957 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG
* *
24999 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG
* ** * * **
25041 ATCTTCT-TTTCAACGTTGCGCTT-TTCTAAATCGCGTTGCG
1 ATTTTCTGAATC-GCGTTGCGATTCTTGGAAATCGCGTTGCG
*
25081 -GTTT-TGATATCGCGTTGCGATT
1 ATTTTCTGA-ATCGCGTTGCGATT
25103 TTGTTGGTCA
Statistics
Matches: 340, Mismatches: 36, Indels: 39
0.82 0.09 0.09
Matches are distributed among these distances:
38 1 0.00
39 11 0.03
40 100 0.29
41 21 0.06
42 184 0.54
43 8 0.02
44 15 0.04
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (41 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCG
Found at i:25058 original size:104 final size:101
Alignment explanation
Indices: 24673--25105 Score: 474
Period size: 104 Copynumber: 4.2 Consensus size: 101
24663 ACTCATTTTC
24673 TGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAATTAC-T-G-A-ATCGCGTTGCGATTTT
1 TGAATCGCGTTGCGATT-TTGGAAGATCGCGTTGCG-ATT-CTTGGAAGATCGCGTTGCGATTTT
* *
24734 CTTAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTTT
63 CTGAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGA-TTT
* *
24776 CTTATTCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTC
1 -TGAATCGCGTTGCGATT-TTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTC
*
24839 TGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTT
64 TGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCGA-TTT
*
24878 CTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTC
1 -TGAATCGCGTTGCGATT-TTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTC
24943 TGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCT
64 TGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-T
* * *
24982 TGGAAGATCGCGTTGCGATTTT--ATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCT
1 T-G-A-ATCGCGTTGCGATTTTGGAAG-ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTT
** * * * *
25045 TCT-TTTCAACGTTGCGCTTTTCTAAATCGCGTTGCGGTTT
62 TCTGAATC-GCGTTGCGATTTTCTGAATCGCGTTGCGATTT
25085 TGATATCGCGTTGCGATTTTG
1 TGA-ATCGCGTTGCGATTTTG
25106 TTGGTCATTT
Statistics
Matches: 301, Mismatches: 16, Indels: 26
0.88 0.05 0.08
Matches are distributed among these distances:
101 17 0.06
102 62 0.21
103 17 0.06
104 188 0.62
105 3 0.01
106 14 0.05
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (101 bp):
TGAATCGCGTTGCGATTTTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTG
AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTT
Found at i:37249 original size:22 final size:21
Alignment explanation
Indices: 37211--37251 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
37201 GGGGTGGGGG
* *
37211 AATGATGTATGCGTTGGAATA
1 AATGATGAATGCATTGGAATA
37232 AATGATGGAATGCATTGGAA
1 AATGAT-GAATGCATTGGAA
37252 CATATAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (21 bp):
AATGATGAATGCATTGGAATA
Found at i:41770 original size:36 final size:36
Alignment explanation
Indices: 41723--41863 Score: 255
Period size: 36 Copynumber: 3.9 Consensus size: 36
41713 TCCTGTTTAG
41723 CAATTCTTCACCCTTCATCTCCTCGCCATGGATTAC
1 CAATTCTTCACCCTTCATCTCCTCGCCATGGATTAC
*
41759 CAATTCTTCACCCTTCATCTCCTCGCCATGGACTAC
1 CAATTCTTCACCCTTCATCTCCTCGCCATGGATTAC
*
41795 CAATTCTTCACCCTTCATCTCCTCACCATGGATTAC
1 CAATTCTTCACCCTTCATCTCCTCGCCATGGATTAC
*
41831 CAATTCTTCACCCTTCATCTCCTCGCCAAGGAT
1 CAATTCTTCACCCTTCATCTCCTCGCCATGGAT
41864 AGAGAGCCCG
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.21, C:0.40, G:0.08, T:0.32
Consensus pattern (36 bp):
CAATTCTTCACCCTTCATCTCCTCGCCATGGATTAC
Found at i:43686 original size:65 final size:65
Alignment explanation
Indices: 43604--43728 Score: 205
Period size: 65 Copynumber: 1.9 Consensus size: 65
43594 AATTCTTCAC
*
43604 CCTTCATCGGGAAACTGTTGCAAATAGCAAAGGGACGAACTGTCATTTATCGTTGCTAGGTGCCA
1 CCTTCATCGGGAAACTGTTGCAAATAGCAAAGGGACGAACTGTCACTTATCGTTGCTAGGTGCCA
* * * *
43669 CCTTCCTCGGGAAACTGTTGCAAGTTGCAAAGGGACGAGCTGTCACTTATCGTTGCTAGG
1 CCTTCATCGGGAAACTGTTGCAAATAGCAAAGGGACGAACTGTCACTTATCGTTGCTAGG
43729 CAAGCGTCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (65 bp):
CCTTCATCGGGAAACTGTTGCAAATAGCAAAGGGACGAACTGTCACTTATCGTTGCTAGGTGCCA
Found at i:49190 original size:18 final size:19
Alignment explanation
Indices: 49167--49218 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 19
49157 TTATTTAAAT
49167 TAATTTAAATAAAAT-TGA
1 TAATTTAAATAAAATATGA
* *
49185 TAATTT-ATTAAAATATTA
1 TAATTTAAATAAAATATGA
49203 T-ATTTATAATAAAATA
1 TAATTTA-AATAAAATA
49219 ATATAAAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 11 0.39
18 9 0.32
19 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TAATTTAAATAAAATATGA
Found at i:49397 original size:23 final size:22
Alignment explanation
Indices: 49354--49395 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
49344 AACTAAAAAA
*
49354 AATAAAATAATATTAGATTTAT
1 AATAAAATAATATTAAATTTAT
49376 AATAACAATAATA-TAAATTT
1 AATAA-AATAATATTAAATTT
49396 TACTTATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AATAAAATAATATTAAATTTAT
Found at i:49909 original size:32 final size:32
Alignment explanation
Indices: 49827--49909 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 32
49817 AATCAACTAT
* * * *
49827 TCCGATATTGATCTGAACCAAAATGTAACTGA
1 TCCGATATTAATCAGACCCAAAATGTAACCGA
* * * *
49859 TCTGGTATTAACCCGACCCAAAAAT-TAACCGA
1 TCCGATATTAATCAGACCC-AAAATGTAACCGA
49891 TCCGATATTAATCAGACCC
1 TCCGATATTAATCAGACCC
49910 GAATTTGACC
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
32 34 0.87
33 5 0.13
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (32 bp):
TCCGATATTAATCAGACCCAAAATGTAACCGA
Found at i:53784 original size:35 final size:34
Alignment explanation
Indices: 53727--53810 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 34
53717 TAAAATAATA
* * *
53727 TTATTAATTAATAATATTTTATTATTTATTATTTT
1 TTATTAATAAATAATATATTATTATTTA-GATTTT
53762 TTATTAATAAATTAATA-ATTATTATTTAGATTTT
1 TTATTAATAAA-TAATATATTATTATTTAGATTTT
*
53796 TT-TGAATGAAATAAT
1 TTATTAAT-AAATAAT
53811 TTTGAAGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
33 8 0.19
34 10 0.23
35 20 0.47
36 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (34 bp):
TTATTAATAAATAATATATTATTATTTAGATTTT
Found at i:54352 original size:327 final size:325
Alignment explanation
Indices: 53735--54383 Score: 1235
Period size: 327 Copynumber: 2.0 Consensus size: 325
53725 TATTATTAAT
53735 TAATAATATTTTATTATTTATTATTTTTTATTAATAAATTAATAATTATTATTTAGATTTTTTTG
1 TAATAATATTTTATTATTTATTATTTTTTATTAATAAATTAATAATTATTATTTAGATTTTTTTG
*
53800 AATGAAATAATTTTGAAGTAATTAGTAAAAATATATTTTAAAAAATTAACGAGCTGCTCACGAAC
66 AATGAAATAATTTTGAAGTAATTAGTAAAAATATATTTTAAAAAATTAACGAGCCGCTCACGAAC
* *
53865 TTATCGAGTTGAGTTAGACTTTGTTCGACTCAGCTTGTTAAATTCTCGAGTCGAGTTTGATTTTG
131 TTATCAAGTCGAGTTAGACTTTGTTCGACTCAGCTTGTTAAATTCTCGAGTCGAGTTTGATTTTG
*
53930 ATTTGAGCCAACTTAAATCTAGCGTTTACCAAATTTTAATCGAATCAAGTTCAAACTATTCACTA
196 ATTTGAGCCAACTTAAATCTAACGTTTACCAAATTTTAATCGAATCAAGTTCAAACTATTCACTA
53995 ACCGTTAAATTCGTTAATCACACCTAGTTTTTTTTTTTAAATAATACAGGTCTCATTAAAAAATC
261 ACCGTTAAATTCGTTAATCACACCTAG-TTTTTTTTTTAAATAATACAGGTCTCATTAAAAAATC
54060 C
325 C
54061 TAATAATATTTTATTATTTATTATTTTTTTATTAATAAATTAATAATTATTATTTAGATTTTTTT
1 TAATAATATTTTATTATTTATTA-TTTTTTATTAATAAATTAATAATTATTATTTAGATTTTTTT
54126 GAATGAAATAATTTTGAAGTAATTAGTAAAAATATATTTTAAAAAATTAACGAGCCGCTCACGAA
65 GAATGAAATAATTTTGAAGTAATTAGTAAAAATATATTTTAAAAAATTAACGAGCCGCTCACGAA
54191 CTTATCAAGTCGAGTTAGACTTTGTTCGACTCAGCTTGTTAAATTCTCGAGTCGAGTTTGATTTT
130 CTTATCAAGTCGAGTTAGACTTTGTTCGACTCAGCTTGTTAAATTCTCGAGTCGAGTTTGATTTT
54256 GATTTGAGCCAACTTAAATCTAACGTTTACCAAATTTTAATCGAATCAAGTTCAAACTATTCACT
195 GATTTGAGCCAACTTAAATCTAACGTTTACCAAATTTTAATCGAATCAAGTTCAAACTATTCACT
*
54321 AGCCGTTAAATTCGTTAATCACACCTAGTTTTTTTTTTAAATAATACAGGTCTCATTAAAAAA
260 AACCGTTAAATTCGTTAATCACACCTAGTTTTTTTTTTAAATAATACAGGTCTCATTAAAAAA
54384 ACCCTAATCA
Statistics
Matches: 317, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
326 58 0.18
327 259 0.82
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (325 bp):
TAATAATATTTTATTATTTATTATTTTTTATTAATAAATTAATAATTATTATTTAGATTTTTTTG
AATGAAATAATTTTGAAGTAATTAGTAAAAATATATTTTAAAAAATTAACGAGCCGCTCACGAAC
TTATCAAGTCGAGTTAGACTTTGTTCGACTCAGCTTGTTAAATTCTCGAGTCGAGTTTGATTTTG
ATTTGAGCCAACTTAAATCTAACGTTTACCAAATTTTAATCGAATCAAGTTCAAACTATTCACTA
ACCGTTAAATTCGTTAATCACACCTAGTTTTTTTTTTAAATAATACAGGTCTCATTAAAAAATCC
Found at i:60814 original size:55 final size:55
Alignment explanation
Indices: 60755--61255 Score: 249
Period size: 55 Copynumber: 9.1 Consensus size: 55
60745 GTCAGGATAA
* * *
60755 ATAAGACTTGAAAAATCTTCA-AATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGT
1 ATAAGACTTGAACAATCTTCATAA-AACGAGCCTGCTCCCTATTCATTCAGAG-AGT
* * * * *
60810 ATAAGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTATTCATTCAGAGAGT
1 ATAAGACTTGAACAATCTTCATAAAACGAGCCTGCTCCCTATTCATTCAGAGAGT
* * * * * *
60865 ATAATACTTGAACAATCTTAAAAAAAAACGGGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAGACTTGAACAATCTT--CATAAAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * *
60922 AT-AGAACTCAGAA-AATCTTCA-ATAAACAAGTCC-GCTCCCTATTCTTTCAGAGAGT
1 ATAAG-ACT-TGAACAATCTTCATA-AAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * * * *
60977 ATAGGAC-T---CAATCTTTA-ACAAACGTGTCC-ACTCCCTATTCCTTCAGAGAGT
1 ATAAGACTTGAACAATCTTCATA-AAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * * * *
61028 AT-AGAACTCGAGCAATCTTCATAAAACGGGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATAAAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * * * * *
61083 AT-AGAACTCGAACAATCTTCA-ACAAATGTGTCC-GCTCTCTATTCCTTCAAAGAGT
1 ATAAG-ACTTGAACAATCTTCATA-AAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * * * *
61138 AT-AGAACTCGAACAATCTTCATGAAACGGGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATAAAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* ** *
61193 AT-AGAACTAGAACAATCTT--TAACGAACTTGTCC-GCTCCCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATAA--AACGAG-CCTGCTCCCTATTCATTCAGAGAGT
*
61248 ATAGGACT
1 ATAAGACT
61256 CAATCTTCAA
Statistics
Matches: 374, Mismatches: 51, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
50 1 0.00
51 40 0.11
53 2 0.01
54 2 0.01
55 279 0.75
56 7 0.02
57 39 0.10
58 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (55 bp):
ATAAGACTTGAACAATCTTCATAAAACGAGCCTGCTCCCTATTCATTCAGAGAGT
Found at i:61142 original size:110 final size:109
Alignment explanation
Indices: 60788--61256 Score: 585
Period size: 110 Copynumber: 4.3 Consensus size: 109
60778 TGACGAGCCT
* * *
60788 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTA
* * * *
60851 TTCATTCAGAGAGTATA-ATACTTGAACAATCTTAAAAAAAAACGGGTCC
64 TTCCTTCAGAGAGTATAGA-AC-TGAACAATCTT--TAACAAACGTGTCC
* ** *
60900 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAGAA-AATCTTCA-ATAAACAAGTCCGCTCCCTA
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCATA-AAACGGGTCCGCTCTCTA
* *
60963 TTCTTTCAGAGAGTATAGGACT---CAATCTTTAACAAACGTGTCC
64 TTCCTTCAGAGAGTATAGAACTGAACAATCTTTAACAAACGTGTCC
* *
61006 ACTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
* *
61071 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAATGTGTCC
66 CCTTCAGAGAGTATAGAACT-GAACAATCTTTAACAAACGTGTCC
* * *
61116 GCTCTCTATTCCTTCAAAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
* *
61181 CCTTCAGAGAGTATAGAACTAGAACAATCTTTAACGAACTTGTCC
66 CCTTCAGAGAGTATAGAACT-GAACAATCTTTAACAAACGTGTCC
*
61226 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC
61257 AATCTTCAAC
Statistics
Matches: 312, Mismatches: 34, Indels: 24
0.84 0.09 0.06
Matches are distributed among these distances:
105 2 0.01
106 83 0.27
107 1 0.00
108 7 0.02
110 147 0.47
111 2 0.01
112 65 0.21
113 5 0.02
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (109 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTGAACAATCTTTAACAAACGTGTCC
Found at i:61251 original size:165 final size:164
Alignment explanation
Indices: 60788--61257 Score: 546
Period size: 165 Copynumber: 2.9 Consensus size: 164
60778 TGACGAGCCT
* * *
60788 GCTCCCTATTCCTTC-AGGAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAAAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGTGTCCGCTCTCTA
* * *
60851 TTCATTCAGAGAGTATA-ATACTTGAACAATCTTAAAAAAAAACGGGTCCGCTCTCTATTCCTTC
64 TTCCTTCAGAGAGTATAGA-ACTAGAACAATCTT---ATAAAACGGGTCCGCTCTCTATTCCTTC
*
60915 AGAGAGTATAGAACTCAGAAAATCTTCAATAAACAAGTCC
125 AGAGAGTATAGAACTCAGAAAATCTTCAACAAACAAGTCC
* * * * * *
60955 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTTA-ACAAACGTGTCCACTCCCTAT
1 GCTCCCTATTCCTTCAAAGAGTATAGAACTCGAACAATCTTCATA-AAACGTGTCCGCTCTCTAT
* *
61015 TCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAG
65 TCCTTCAGAGAGTATAGAACTAGAACAATCTT-ATAAAACGGGTCCGCTCTCTATTCCTTCAGAG
***
61080 AGTATAGAACTC-GAACAATCTTCAACAAATGTGTCC
129 AGTATAGAACTCAGAA-AATCTTCAACAAACAAGTCC
* * *
61116 GCTCTCTATTCCTTCAAAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAAAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCCGCTCTCTATT
** *
61181 CCTTCAGAGAGTATAGAACTAGAACAATCTT-TAACGAACTTGTCCGCTCCCTATTCCTTCAGAG
66 CCTTCAGAGAGTATAGAACTAGAACAATCTTATAA--AACGGGTCCGCTCTCTATTCCTTCAGAG
*
61245 AGTATAGGACTCA
129 AGTATAGAACTCA
61258 ATCTTCAACA
Statistics
Matches: 257, Mismatches: 33, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
160 3 0.01
161 85 0.33
162 1 0.00
163 53 0.21
164 1 0.00
165 90 0.35
167 23 0.09
168 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (164 bp):
GCTCCCTATTCCTTCAAAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTAGAACAATCTTATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAG
TATAGAACTCAGAAAATCTTCAACAAACAAGTCC
Found at i:61272 original size:55 final size:52
Alignment explanation
Indices: 60821--61271 Score: 417
Period size: 55 Copynumber: 8.3 Consensus size: 52
60811 TAAGACTCGA
* * *
60821 ACAATCTTCATA-AAATGTGTCTGCTCTCTATTCATTCAGAGAGTATA-ATACTT
1 ACAATCTTCA-ACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-AC-T
* * *
60874 GAACAATCTTAAAAAAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 --ACAATCTT--CAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* * ** * * *
60930 CAGAAAATCTTCAATAAACAAGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACT
1 ---ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* * *
60985 -CAATCTTTAACAAACGTGTCCACTCCCTATTCCTTCAGAGAGTATAGAACT
1 ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
*
61036 CGAGCAATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 --A-CAATCTTCA-ACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* *
61091 CGAACAATCTTCAACAAATGTGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACT
1 ---ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
** *
61146 CGAACAATCTTCATGAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 ---ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* * * * *
61201 AGAACAATCTTTAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
1 ---ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
61256 -CAATCTTCAACAAACG
1 ACAATCTTCAACAAACG
61272 AGTTTGCTTC
Statistics
Matches: 335, Mismatches: 49, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
51 56 0.17
54 1 0.00
55 232 0.69
56 4 0.01
57 41 0.12
58 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (52 bp):
ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
Found at i:62648 original size:17 final size:18
Alignment explanation
Indices: 62626--62725 Score: 63
Period size: 18 Copynumber: 5.8 Consensus size: 18
62616 CCTCCTTTTA
62626 TTTCTCTTTTT-TTCATT
1 TTTCTCTTTTTCTTCATT
* *
62643 TTTCTCTTTTTGTT-TTT
1 TTTCTCTTTTTCTTCATT
62660 CTTTCAT-TTTTTCTTCATT
1 -TTTC-TCTTTTTCTTCATT
*
62679 TTTCT-TTTATC-TCATT
1 TTTCTCTTTTTCTTCATT
* *
62695 TCT-TC-ATTTCTTCA-T
1 TTTCTCTTTTTCTTCATT
*
62710 TTTCTTTTTCTTCTTC
1 TTTCTCTTT-TTCTTC
62726 TCATTTTTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
15 7 0.11
16 11 0.17
17 20 0.31
18 23 0.36
19 3 0.05
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.72
Consensus pattern (18 bp):
TTTCTCTTTTTCTTCATT
Found at i:62697 original size:36 final size:34
Alignment explanation
Indices: 62632--62753 Score: 90
Period size: 36 Copynumber: 3.4 Consensus size: 34
62622 TTTATTTCTC
**
62632 TTTTTTTCATTTTTCTCTTTT-TGTTTTTCTTTCAT
1 TTTTTTTCATTTTTCT-TTTTCT-CATTTCTTTCAT
62667 TTTTTCTTCATTTTTCTTTTATCTCATTTC-TTCATT
1 TTTTT-TTCATTTTTCTTTT-TCTCATTTCTTTCA-T
* *
62703 TCTTCATTTTC-TTTTTCTTCTTCTCATTT-TTATTAT
1 T-TT--TTTTCATTTTTCTTTTTCTCATTTCTT-TCAT
62739 TATTTTTTCATTTTT
1 T-TTTTTTCATTTTT
62754 TTCTTCTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
34 5 0.07
35 17 0.24
36 31 0.43
37 14 0.19
38 3 0.04
39 2 0.03
ACGTcount: A:0.10, C:0.16, G:0.01, T:0.73
Consensus pattern (34 bp):
TTTTTTTCATTTTTCTTTTTCTCATTTCTTTCAT
Found at i:62767 original size:23 final size:23
Alignment explanation
Indices: 62731--62784 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
62721 TCTTCTCATT
* *
62731 TTTATTATTATTTTTTC-ATTTT-
1 TTTATTCTT-TTTTTTCTCTTTTA
*
62753 TTTCTTCTTTTTTTTCTCTTTTA
1 TTTATTCTTTTTTTTCTCTTTTA
62776 TTTATTCTT
1 TTTATTCTT
62785 CAAGCAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.27
22 11 0.42
23 8 0.31
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTATTCTTTTTTTTCTCTTTTA
Found at i:72481 original size:45 final size:47
Alignment explanation
Indices: 72413--72501 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
72403 TGCTTTGTTA
72413 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
*
72460 TTCA-AAAAATAAAT-CTAACCGCATGATATCTAGTTCGCATGC
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
72502 ATTTATTCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 27 0.66
46 10 0.24
47 4 0.10
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.29
Consensus pattern (47 bp):
TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
Found at i:79296 original size:60 final size:60
Alignment explanation
Indices: 79203--79323 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
79193 TCCCTGCCAC
* * *
79203 ATAGCCGATAAGAACTTTAGATACACTGTACACGCACATAGGCCATGTGCAAATGAAAGA
1 ATAGCCGATAAGAACTTTAGATACACCGTACACGCACATAGGCCAAGTACAAATGAAAGA
*
79263 ATAGCTGATAAGAACTTTAGATACACCGTACACGCACATAGGCCAAGTACAAATGAAAGA
1 ATAGCCGATAAGAACTTTAGATACACCGTACACGCACATAGGCCAAGTACAAATGAAAGA
79323 A
1 A
79324 CTTCCGATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (60 bp):
ATAGCCGATAAGAACTTTAGATACACCGTACACGCACATAGGCCAAGTACAAATGAAAGA
Found at i:84522 original size:59 final size:59
Alignment explanation
Indices: 84450--84587 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 59
84440 AAAATAGAGT
84450 AAAGTATACAAATGATCATTTGACTAT-AGACATTACTTTATTAAGTCCCAT-AACTATTA
1 AAAGT-TACAAATGATCATTTGACTATAAGACATTACTTTATTAAGT-CCATCAACTATTA
* * * * *
84509 AAAGTTACAAAATGGTCCA-TTGACTATAAGACATTACTTTGTTGAGTCCTTCGACTATTA
1 AAAGTTAC-AAATGAT-CATTTGACTATAAGACATTACTTTATTAAGTCCATCAACTATTA
*
84569 AAAGTTATGAAATGATCAT
1 AAAGTTA-CAAATGATCAT
84588 CCAACTATTC
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
58 3 0.05
59 24 0.36
60 39 0.59
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.35
Consensus pattern (59 bp):
AAAGTTACAAATGATCATTTGACTATAAGACATTACTTTATTAAGTCCATCAACTATTA
Found at i:90397 original size:16 final size:17
Alignment explanation
Indices: 90378--90410 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
90368 TCATTTCTAT
90378 TCATT-GTTTTGGATTA
1 TCATTAGTTTTGGATTA
*
90394 TCATTAGTTTTTGATTA
1 TCATTAGTTTTGGATTA
90411 ACGTGATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.21, C:0.06, G:0.15, T:0.58
Consensus pattern (17 bp):
TCATTAGTTTTGGATTA
Found at i:94330 original size:16 final size:16
Alignment explanation
Indices: 94309--94342 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
94299 CGATGTTCGG
*
94309 ATTATGTTTACCTATC
1 ATTATGTTTAACTATC
94325 ATTATGTTTAACTATC
1 ATTATGTTTAACTATC
94341 AT
1 AT
94343 GTTTTTGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTATGTTTAACTATC
Found at i:95226 original size:15 final size:15
Alignment explanation
Indices: 95206--95236 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
95196 CATGCAATAG
95206 GTGCTTACATTACTT
1 GTGCTTACATTACTT
*
95221 GTGCTTATATTACTT
1 GTGCTTACATTACTT
95236 G
1 G
95237 CACTCGGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (15 bp):
GTGCTTACATTACTT
Found at i:103224 original size:55 final size:55
Alignment explanation
Indices: 103146--103258 Score: 208
Period size: 55 Copynumber: 2.1 Consensus size: 55
103136 ATATTCAGCT
*
103146 TCTCAACTTACTCTCAACATTCAGAATTTACTCTCCAAGTATTTTCTAAATATTC
1 TCTCAACTTACTCTCAACATTCAGAATTCACTCTCCAAGTATTTTCTAAATATTC
*
103201 TCTCAACTTACTCTCAACATTCAGAATTCACTCTCCAAGTGTTTTCTAAATATTC
1 TCTCAACTTACTCTCAACATTCAGAATTCACTCTCCAAGTATTTTCTAAATATTC
103256 TCT
1 TCT
103259 TTGTGTTCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40
Consensus pattern (55 bp):
TCTCAACTTACTCTCAACATTCAGAATTCACTCTCCAAGTATTTTCTAAATATTC
Found at i:112193 original size:24 final size:24
Alignment explanation
Indices: 112166--112221 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
112156 AACAGACTCG
*
112166 TTTATGAGCTCGTCTATAAG-TCCA
1 TTTATGAGCTCATCTATAAGCT-CA
*
112190 TTTATGAGCTCATTTATAAGCTCA
1 TTTATGAGCTCATCTATAAGCTCA
112214 TTTATGAG
1 TTTATGAG
112222 ATTGTTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (24 bp):
TTTATGAGCTCATCTATAAGCTCA
Found at i:112205 original size:12 final size:12
Alignment explanation
Indices: 112166--112221 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
112156 AACAGACTCG
*
112166 TTTATGAGCTCG
1 TTTATGAGCTCA
* *
112178 TCTATAAG-TCCA
1 TTTATGAGCT-CA
112190 TTTATGAGCTCA
1 TTTATGAGCTCA
*
112202 TTTATAAGCTCA
1 TTTATGAGCTCA
112214 TTTATGAG
1 TTTATGAG
112222 ATTGTTTGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
11 1 0.03
12 33 0.94
13 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (12 bp):
TTTATGAGCTCA
Found at i:112519 original size:24 final size:24
Alignment explanation
Indices: 112459--112583 Score: 101
Period size: 24 Copynumber: 5.2 Consensus size: 24
112449 TCACTGAACA
* *
112459 AACATGTTCGTGAACA-CTAAATG
1 AACATGTTCGTGAACATATAAACG
* **
112482 AACACGTTTATGAACATATAAACG
1 AACATGTTCGTGAACATATAAACG
* * *
112506 AATATGTTCGTGAACATATAGATG
1 AACATGTTCGTGAACATATAAACG
* ** *
112530 AGCATGTTCACGAACAT-TAAGCG
1 AACATGTTCGTGAACATATAAACG
112553 AACATGTTCGTGAACAATAAATAAACG
1 AACATGTTCGTGAAC-AT--ATAAACG
112580 AACA
1 AACA
112584 CGATACTAAA
Statistics
Matches: 75, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
23 28 0.37
24 38 0.51
27 9 0.12
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (24 bp):
AACATGTTCGTGAACATATAAACG
Found at i:112560 original size:47 final size:47
Alignment explanation
Indices: 112459--112574 Score: 137
Period size: 47 Copynumber: 2.5 Consensus size: 47
112449 TCACTGAACA
* *
112459 AACATGTTCGTGAACACTAAATGAACACGTTTATGAACATATAAACG
1 AACATGTTCGTGAACACTAAATGAACACGTTCACGAACATATAAACG
* * * *
112506 AATATGTTCGTGAACA-TATAGATGAGCATGTTCACGAACAT-TAAGCG
1 AACATGTTCGTGAACACTA-A-ATGAACACGTTCACGAACATATAAACG
*
112553 AACATGTTCGTGAACAATAAAT
1 AACATGTTCGTGAACACTAAAT
112575 AAACGAACAC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
46 4 0.07
47 37 0.63
48 18 0.31
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.27
Consensus pattern (47 bp):
AACATGTTCGTGAACACTAAATGAACACGTTCACGAACATATAAACG
Found at i:115906 original size:12 final size:12
Alignment explanation
Indices: 115889--115913 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
115879 CTAAATCATA
115889 AAACTTTTGTTC
1 AAACTTTTGTTC
115901 AAACTTTTGTTC
1 AAACTTTTGTTC
115913 A
1 A
115914 TATTCATTTT
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (12 bp):
AAACTTTTGTTC
Found at i:117209 original size:213 final size:215
Alignment explanation
Indices: 116841--118897 Score: 2575
Period size: 214 Copynumber: 9.7 Consensus size: 215
116831 CAACACATGT
* * * * * * * * *
116841 CCATATCCAACACAATCAAGTCTGAGTAGCATA-ATCACCAGCATGACAAATA-GCGTAAAACCA
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAA-AGGTGTAAAGCCA
* * *
116904 TGATGTTTATAGGAAAGT--AACTAGTACTCGTTTCCATTTCAGAGAGTTTGAGCTAAGCTCTAC
65 TGATGTTTATACGAAGGTAAAAC-AGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTAC
* *
116967 ACATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGTAGGGGATATGGCTGTTCGAAGATCT
129 ACATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCT
117032 CCCAAACCCACATTGGACAC-C
194 CCCAAACCCACATTGGACACAC
* * *
117053 CCATATCCAAGACACTCAAGTCGGAGTAACATACACCATCGGCGTGAGAAAAGGTGTAAAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
117118 GATGTTTGTAGGAAGGTAAAACGGTACTCGTTTCCCTTTTAGAGAGTTTGAGCTAAGCTTTACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
* *
117183 -TGCTTGAAAGACAGAACTTTATGACCAAAACTCGTGCAGGGGATATGACCGTTCGAAGATCTCC
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
117247 CAAACCCACATTGGACACACAC
196 CAAACCCACATTGG--ACACAC
* * *
117269 CCATATCCGACACACTCAAGTCAGAGTAACATAGACGATCGGCATGAGAAAAGGTGTAAAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
117334 GATGTTTATACGAAGGTAAAAC-GTTACTCGTTTCCATCTCCGAGAGCTTGAGCTAAGCTATACA
66 GATGTTTATACGAAGGTAAAACAG-TACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACA
** *
117398 CATGCAAG-AAG--AGAACTTCATGACCAAAACTCCTGCAGGGGATATGACTGTTCGAAGATC-C
130 CATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTC
117459 CCAAACCCACATTGGACACGCAC
195 CCAAACCCACATTGGACA--CAC
** * * **
117482 CCATATCTGACACACTCAAGTCGGAGTAACATAGACCATTGGCGTGAGAAAAGGTGTAAAGATAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
117547 GATGTTTGTAGGAAGGTAAAACGGTACTCGTTTCCCTTTCAAAGTGTTTGAGCTAAGCTCTACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
117612 ATGCTTGAAAGAC--AACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
*
117675 CAAACCCAAATTGGACACAC
196 CAAACCCACATTGGACACAC
* * *
117695 ACCATATCCGACACACTCAAGTCAGAGTAGCATAGACCATCGGCATGAGAAAAGGTGTAAAGCCA
1 -CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCA
* * * * *
117760 TGATGTTTATACGAAGGTAAAACATTACTCGTTTCCCTCTCCGAGAGCTTGAGCTAAGCTATACA
65 TGATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACA
** * * *
117825 CATGCAGGAAAGAGAGAACTTCATGACCAAAACTCTTGCAGGGGATATGA-TCGTTCAAAGATCT
130 CATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACT-GTTCGAAGATCT
117889 -CCAAACCCACATTGGACACA-
194 CCCAAACCCACATTGGACACAC
* *
117909 -C--A--C--C-CA-TCAAGTCGGAGTAACATAGACTATCGAC-T--------GTGTAAAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
117956 GTATGTTTATACGAAGGTAAAACCGTACTTGTTT--CTTTCAGAGTGTATGAGGTAAGCTCTACA
66 G-ATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACA
* * * *
118019 CATGCTTG-AAGACAGAACTTCATGACCAAAACTCGGGCAGGAGA-ATGACCG-TCGAAGATCTT
130 CATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTC
118081 CCAAA-CCACATTGGACAAGCAC
195 CCAAACCCACATTGGAC-A-CAC
* **
118103 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCGTGAGAAAAGGTGTAAAGATAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
118168 GATGTTTGTAGGAAGGTAAAACGGTACTTGTTTCCCTTTCAAAGAGTTTGAGCTAAGCTCTACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
*
118233 ATGCTTGAAAGAC--AACTTCATGACCAAAACTCGTGCAGGGGATATGACCGTTCGAAGATCTCC
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
118296 CAAACCCACATTGGACACACAC
196 CAAACCCACATTGG--ACACAC
* *
118318 CCATATCAAACACACTCAAGTCAGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
118383 GATGTTTATACGAAGGTAAAACATTACTCGTTTCCCTCTCTGAGAGCTTGAGCTAAGCTATACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
* * * *
118448 ATGCTGGAAAG--AGAACTTCATGGCCAAAACTCCTGC-GGGGATATGA-TCGTTCAAAGATCT-
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACT-GTTCGAAGATCTC
118508 CCAAA--C-CATTGGACACACAC
195 CCAAACCCACATTGG--ACACAC
118528 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAG-AAAGGTGT-AAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * *
118591 GATGTTTATACGAAGGTTAAACCGTACTCGTTTCCCTTTCAGAGAGTATGAGGTAAGCTCTACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
* * *
118656 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGGGCAGGAGATATGACAGTTCGAAGATCTCC
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
118721 CAAACCC-CATTGGACACACAC
196 CAAACCCACATTGG--ACACAC
* ** *
118742 CCATAT-CGACACACTCAAGTTAGAGTAACCATAGACCATCGGCATGAGAAAAGGTGTAAAGTCA
1 CCATATCCAACACACTCAAGTCGGAGTAA-CATAGACCATCGGCATGAGAAAAGGTGTAAAGCCA
* * *
118806 TGATGTTTATACAAAGGTAAAACAGTACTCGTTTCCCCTTTCCGAGAGCTTGAGCTAAGCTCTAC
65 TGATGTTTATACGAAGGTAAAACAGTACTCGTTT-CCCTTTCAGAGAGTTTGAGCTAAGCTCTAC
* * *
118871 ACATGCATGAAAGAGAGAACTTAATGA
129 ACATGCTTGAAAGACAGAACTTCATGA
118898 AATAAACAAA
Statistics
Matches: 1608, Mismatches: 171, Indels: 127
0.84 0.09 0.07
Matches are distributed among these distances:
191 20 0.01
192 11 0.01
193 34 0.02
194 28 0.02
195 14 0.01
196 29 0.02
197 1 0.00
199 1 0.00
201 1 0.00
202 2 0.00
203 27 0.02
204 25 0.02
205 2 0.00
206 1 0.00
208 74 0.05
209 8 0.00
210 83 0.05
211 53 0.03
212 74 0.05
213 314 0.20
214 339 0.21
215 212 0.13
216 199 0.12
217 56 0.03
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (215 bp):
CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
CAAACCCACATTGGACACAC
Done.