Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004828.1 Hibiscus syriacus cultivar Beakdansim tig00010874_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: 74271
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5814 original size:37 final size:38
Alignment explanation
Indices: 5756--6073 Score: 358
Period size: 38 Copynumber: 8.7 Consensus size: 38
5746 AAACTATATA
*
5756 ATAT-ATTTTTT--AAAATAATTTTGAAAACGTATAAT
1 ATATAATTTTTTAAAAAATATTTTTGAAAACGTATAAT
*
5791 ATATAATTTTTTAAAAAATATTTTTGAAAATGTATAAT
1 ATATAATTTTTTAAAAAATATTTTTGAAAACGTATAAT
* * *
5829 ATATAGTTTTTT--AAAATAGTTTTGAAAAAGTATAAT
1 ATATAATTTTTTAAAAAATATTTTTGAAAACGTATAAT
* * * *
5865 ATAT-AGTTTTT-AAAAATTTATTTTGGAAACATATAAT
1 ATATAATTTTTTAAAAAATAT-TTTTGAAAACGTATAAT
* **
5902 ATA-GA---TTTAAAAAA-A-AATTGAAAACGTATAAT
1 ATATAATTTTTTAAAAAATATTTTTGAAAACGTATAAT
*
5934 ATATAGTTTTTT-AAAAATATTTTTGAAAACGTATAAT
1 ATATAATTTTTTAAAAAATATTTTTGAAAACGTATAAT
* *
5971 ATATAGTTTTTTTAAAAAAATATTTTTGAAAACATATAAT
1 ATATA-ATTTTTT-AAAAAATATTTTTGAAAACGTATAAT
*
6011 ATATAGTTTTTTAAAAAATATTTTTGAAAACGTATAAT
1 ATATAATTTTTTAAAAAATATTTTTGAAAACGTATAAT
*
6049 ATATAGTTTTTTAAAAAATATTTTT
1 ATATAATTTTTTAAAAAATATTTTT
6074 TTGTTATTAT
Statistics
Matches: 242, Mismatches: 25, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
32 16 0.07
34 3 0.01
35 19 0.08
36 42 0.17
37 38 0.16
38 89 0.37
39 6 0.02
40 29 0.12
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (38 bp):
ATATAATTTTTTAAAAAATATTTTTGAAAACGTATAAT
Found at i:6107 original size:17 final size:17
Alignment explanation
Indices: 6093--6146 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
6083 TTGTTATTAT
6093 ATTATTTATTATATTTA
1 ATTATTTATTATATTTA
6110 ATTATTTATTATGTATTTA
1 ATTATTTATTA--TATTTA
*
6129 TTATATTTATT-TATTTA
1 AT-TATTTATTATATTTA
6146 A
1 A
6147 CCATTTCAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 17 0.53
19 7 0.22
20 8 0.25
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTATTTATTATATTTA
Found at i:6118 original size:4 final size:4
Alignment explanation
Indices: 6089--6145 Score: 62
Period size: 4 Copynumber: 13.8 Consensus size: 4
6079 ATTATTGTTA
* *
6089 TTAT ATTAT TTAT TATAT TTAA TTAT TTA- TTAT GTAT TTAT TATAT TTAT
1 TTAT -TTAT TTAT T-TAT TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT
6139 TTAT TTA
1 TTAT TTA
6146 ACCATTTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
3 3 0.07
4 30 0.67
5 12 0.27
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:6126 original size:28 final size:29
Alignment explanation
Indices: 6086--6145 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
6076 GTTATTATTG
*
6086 TTATTATATTATTTATTATATTTAATTAT
1 TTATTATAGTATTTATTATATTTAATTAT
*
6115 TTATTAT-GTATTTATTATATTTATTTAT
1 TTATTATAGTATTTATTATATTTAATTAT
6143 TTA
1 TTA
6146 ACCATTTCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (29 bp):
TTATTATAGTATTTATTATATTTAATTAT
Found at i:6218 original size:17 final size:18
Alignment explanation
Indices: 6179--6219 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6169 GCCGGGTCCA
* *
6179 GGTCCAATAGTCCAACTG
1 GGTCCAACAGTCCAACGG
6197 GGTCCAACAGTCCAA-GG
1 GGTCCAACAGTCCAACGG
6214 GGTCCA
1 GGTCCA
6220 TCAAGGAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (18 bp):
GGTCCAACAGTCCAACGG
Found at i:18976 original size:24 final size:24
Alignment explanation
Indices: 18949--18998 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
18939 ATAAAGAACC
18949 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
18973 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
18997 AA
1 AA
18999 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:24551 original size:24 final size:24
Alignment explanation
Indices: 24523--24572 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
24513 ATAAAGAACC
24523 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
24547 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
24571 AA
1 AA
24573 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:26711 original size:39 final size:37
Alignment explanation
Indices: 26645--27007 Score: 347
Period size: 39 Copynumber: 9.8 Consensus size: 37
26635 TATATAACTA
* *
26645 TATAATGTATAG-TTTTT-AAAATAATTTTGAAAACG
1 TATAATATATAGTTTTTTAAAAATATTTTTGAAAACG
26680 TATAATATATAGCCTTTCTTTAAAAATATTTTTGAAAACG
1 TATAATATATAG--TTT-TTTAAAAATATTTTTGAAAACG
* * **
26720 TATAATATATAATTTTTT-AAAATAGTTTTGAAAATA
1 TATAATATATAGTTTTTTAAAAATATTTTTGAAAACG
26756 TATAATATATAGTTTTTTAAAAAAATATTTTTGAAAACG
1 TATAATATATAGTTTTTT--AAAAATATTTTTGAAAACG
* **
26795 TATAATATATAG-TTTTT--AAATTTGTTTTGAAAAAA
1 TATAATATATAGTTTTTTAAAAATAT-TTTTGAAAACG
* *
26830 TATAATATATAATTTTTTAAAAATATTTTTAAAAACG
1 TATAATATATAGTTTTTTAAAAATATTTTTGAAAACG
* *
26867 AATAATATATAGTTTTTTTTTAAAAAAATATTTTTGAAAACA
1 TATAATATATAG---TTTTTT--AAAAATATTTTTGAAAACG
* *
26909 TATAATATATATTTTTTTAAAAATATATTTTTAAAAACG
1 TATAATATATAGTTTTTT-AAAA-ATATTTTTGAAAACG
*
26948 TATAATATATA-TTTTTT-----TA-ATTTGAAAACG
1 TATAATATATAGTTTTTTAAAAATATTTTTGAAAACG
* * *
26978 TATAGTATATAATTTTTAAAAAATATTTTT
1 TATAATATATAGTTTTTTAAAAATATTTTT
27008 TTCATTATTA
Statistics
Matches: 272, Mismatches: 31, Indels: 48
0.77 0.09 0.14
Matches are distributed among these distances:
30 19 0.07
31 7 0.03
34 5 0.02
35 31 0.11
36 39 0.14
37 24 0.09
38 26 0.10
39 60 0.22
40 34 0.12
42 27 0.10
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (37 bp):
TATAATATATAGTTTTTTAAAAATATTTTTGAAAACG
Found at i:26925 original size:79 final size:80
Alignment explanation
Indices: 26662--26965 Score: 289
Period size: 74 Copynumber: 3.9 Consensus size: 80
26652 TATAGTTTTT
* ** * * *
26662 AAAATAATTTTGAAAACGTATAATATATAGCCTTTCTTT-AAAA-ATATTTTTGAAAACGTATAA
1 AAAATATTTTTGAAAAAATATAATATATA--ATTT-TTTAAAAATATATTTTTAAAAACGAATAA
*
26725 TATATA--ATTTTTT---
63 TATATATTTTTTTTTAAA
* * * * * *
26738 AAAATAGTTTTGAAAATATATAATATATAGTTTTTTAAAAAAATATTTTTGAAAACGTATAATAT
1 AAAATATTTTTGAAAAAATATAATATATAATTTTTTAAAAATATATTTTTAAAAACGAATAATAT
*
26803 ATA---GTTTTT---
66 ATATTTTTTTTTAAA
*
26812 -AAATTTGTTTTGAAAAAATATAATATATAATTTTTT-AAAA-ATATTTTTAAAAACGAATAATA
1 AAAATAT-TTTTGAAAAAATATAATATATAATTTTTTAAAAATATATTTTTAAAAACGAATAATA
26874 TATAGTTTTTTTTTAAA
65 TATA-TTTTTTTTTAAA
* * *
26891 AAAATATTTTTGAAAACATATAATATATATTTTTTTAAAAATATATTTTTAAAAACGTATAATAT
1 AAAATATTTTTGAAAAAATATAATATATAATTTTTTAAAAATATATTTTTAAAAACGAATAATAT
26956 ATATTTTTTT
66 ATATTTTTTT
26966 AATTTGAAAA
Statistics
Matches: 199, Mismatches: 16, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
72 24 0.12
73 11 0.06
74 39 0.20
75 26 0.13
76 31 0.16
79 27 0.14
80 16 0.08
81 25 0.13
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (80 bp):
AAAATATTTTTGAAAAAATATAATATATAATTTTTTAAAAATATATTTTTAAAAACGAATAATAT
ATATTTTTTTTTAAA
Found at i:27043 original size:4 final size:4
Alignment explanation
Indices: 27027--27065 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
27017 ATTGTTACGA
*
27027 TTAT TTAT ATTAT TTAT TTA- TTAT GTAT TTAT TTAT TTA
1 TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
27066 ACCATTTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.77
5 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:27057 original size:15 final size:14
Alignment explanation
Indices: 27027--27063 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
27017 ATTGTTACGA
27027 TTATTTA-TATTAT
1 TTATTTATTATTAT
27040 TTATTTATTATGTAT
1 TTATTTATTAT-TAT
27055 TTATTTATT
1 TTATTTATT
27064 TAACCATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 7 0.32
14 3 0.14
15 12 0.55
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TTATTTATTATTAT
Found at i:28685 original size:20 final size:20
Alignment explanation
Indices: 28660--28716 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
28650 GAATGAGGTA
28660 GTATCGATATCATGGTAAGG
1 GTATCGATATCATGGTAAGG
28680 GTATCGATA-CAATGGTAAGG
1 GTATCGATATC-ATGGTAAGG
**
28700 GTATTAATATCA-GGTAA
1 GTATCGATATCATGGTAA
28717 CATCGATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 6 0.18
20 26 0.79
21 1 0.03
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (20 bp):
GTATCGATATCATGGTAAGG
Found at i:28727 original size:16 final size:16
Alignment explanation
Indices: 28706--28738 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28696 AAGGGTATTA
28706 ATATCAGGTAACATCG
1 ATATCAGGTAACATCG
28722 ATATCAGGTAACATCG
1 ATATCAGGTAACATCG
28738 A
1 A
28739 ACCTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (16 bp):
ATATCAGGTAACATCG
Found at i:29314 original size:59 final size:59
Alignment explanation
Indices: 29238--29758 Score: 670
Period size: 59 Copynumber: 8.8 Consensus size: 59
29228 GATTACCAGA
* * * * *
29238 AGGGCACTTCGTGTGCTAACATGAGAATGATTTCATGCTAAATGTATGAATTTTCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * *
29297 AGGGCAGTTCATATGCTAACATGAGAAGGAATTCATACTAGGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* *
29356 AGGGCACTTTGTGTGCTAACATGAGAATGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
29415 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* *
29474 AGAGCACTTTGTGTGCTAACATGAGAAGGAATTCATACTATA-TGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTA-AGTGTATGAATTTCCATAT
* * * **
29533 AGGGCATTTCGTGTTCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCTGTAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * * ** *
29592 AGGGCGCTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTAGGAATTTCTGTAG
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * *
29651 AGGGTC-CTTCGTTTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1 AGGG-CACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * *
29710 TGGGCACCTT-GTGTGCCAAAATGATAAGAAATTCATACTAAGTGTATGA
1 AGGGCA-CTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGA
29759 TTATATGGGA
Statistics
Matches: 417, Mismatches: 40, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
58 2 0.00
59 410 0.98
60 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
Found at i:30748 original size:25 final size:25
Alignment explanation
Indices: 30720--30769 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
30710 GAAAAGTTTA
30720 CAGTGCTCTGATCATGAGAAACTGG
1 CAGTGCTCTGATCATGAGAAACTGG
30745 CAGTGCTCTGATCATGAGAAACTGG
1 CAGTGCTCTGATCATGAGAAACTGG
30770 GTGGAGCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (25 bp):
CAGTGCTCTGATCATGAGAAACTGG
Found at i:35782 original size:20 final size:21
Alignment explanation
Indices: 35757--35816 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
35747 GGCTGAATTA
35757 AATGA-GAAGTATCGATACTT
1 AATGAGGAAGTATCGATACTT
* **
35777 AATGAGGTAGTATCGATACCG
1 AATGAGGAAGTATCGATACTT
* *
35798 AATGAGGTAGTATTGATAC
1 AATGAGGAAGTATCGATAC
35817 CGAACGAGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 5 0.14
21 30 0.86
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (21 bp):
AATGAGGAAGTATCGATACTT
Found at i:35788 original size:21 final size:21
Alignment explanation
Indices: 35764--35837 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
35754 TTAAATGAGA
**
35764 AGTATCGATACTTAATGAGGT
1 AGTATCGATACCGAATGAGGT
35785 AGTATCGATACCGAATGAGGT
1 AGTATCGATACCGAATGAGGT
* *
35806 AGTATTGATACCGAACGAGGT
1 AGTATCGATACCGAATGAGGT
*
35827 AGTATTGATAC
1 AGTATCGATAC
35838 TATGGTAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (21 bp):
AGTATCGATACCGAATGAGGT
Found at i:35997 original size:95 final size:94
Alignment explanation
Indices: 35825--36049 Score: 235
Period size: 95 Copynumber: 2.4 Consensus size: 94
35815 ACCGAACGAG
* * ** *
35825 GTAGTATTGATACTATGGTAAGGGTATCGATACCAGGTATCATCGAACCTAATTTTAGTATCGAC
1 GTAGTATTGATACTATGGTATGGGAATCGATACTGGGCATCATCGAACCTAATTTTAGTATCGAC
* *
35890 ACCATATAGGGGTATCGGTACCATAGTATA
66 A-CATATAGGGGTATCGATACCATAGTAGA
* * *
35920 GTAGTATTGATACCATGGTATGGGAATCGATACTGGGCCA-CATCGAATCTAATTTTGGTATCGA
1 GTAGTATTGATACTATGGTATGGGAATCGATACTGGG-CATCATCGAACCTAATTTTAGTATCGA
* *
35984 TA-ATGGA-AGGGGGTATCGATACCATAGTAGG
65 CACAT--ATA-GGGGTATCGATACCATAGTAGA
*
36015 GTAGTATCGATACTAT--TATGGGAGTATCGATACTG
1 GTAGTATTGATACTATGGTATGGGA--ATCGATACTG
36050 AGGAACCATA
Statistics
Matches: 110, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
93 9 0.08
94 1 0.01
95 99 0.90
96 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (94 bp):
GTAGTATTGATACTATGGTATGGGAATCGATACTGGGCATCATCGAACCTAATTTTAGTATCGAC
ACATATAGGGGTATCGATACCATAGTAGA
Found at i:36024 original size:22 final size:21
Alignment explanation
Indices: 35996--36047 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
35986 ATGGAAGGGG
35996 GTATCGATACCATAGTA-GGGTA
1 GTATCGATACC-TAGTATGGG-A
*
36018 GTATCGATA-CTATTATGGGA
1 GTATCGATACCTAGTATGGGA
36038 GTATCGATAC
1 GTATCGATAC
36048 TGAGGAACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 14 0.52
21 4 0.15
22 9 0.33
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (21 bp):
GTATCGATACCTAGTATGGGA
Found at i:36438 original size:59 final size:59
Alignment explanation
Indices: 36363--37010 Score: 935
Period size: 59 Copynumber: 11.0 Consensus size: 59
36353 GATTACCAGA
*
36363 AGGGAACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
36422 AGGGCACTTCGTGTGCTAGCATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
36481 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
36540 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTAT-CATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATT-TCCATAT
36599 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATAC-AAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
36657 AGGGCACTTCGTGTGCTGACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* *
36716 AGAGCACTTCGTGTGCTGACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * * * **
36775 AGAGCACTTAGTTTGCTAACATGAGAAGAAATT-ATTATTAAGCGTATGAATTTCTGTAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCA-TACTAAGTGTATGAATTTCCATAT
* * * * * **
36834 AGGGCACTTCGTGTGCTAAAATGATAAGAAATTCATATTAAGTGTAGGAATTTCTGTAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * * ** *
36893 AGGGCGCTTCGTGTTCTAAAATGATAAGAAATTCATACTAAGACTATGAATTTCCGTAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * * *
36952 TGGGTACCTT-GTGTGCCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCA-CTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
37011 GGGAATTAAT
Statistics
Matches: 548, Mismatches: 35, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
57 1 0.00
58 56 0.10
59 486 0.89
60 5 0.01
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
Found at i:36897 original size:294 final size:295
Alignment explanation
Indices: 36363--37010 Score: 946
Period size: 294 Copynumber: 2.2 Consensus size: 295
36353 GATTACCAGA
*
36363 AGGGAACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCA
1 AGGGAACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGAGCA
* *
36428 CTTCGTGTGCTAGCATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGT
66 CTTCGTGTGCTAGCATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGAGCACTTAGT
* *
36493 GTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTA
131 GTGCTAACATGAGAAGAAATTCATACTAAGCGTATGAATTTCCATATAGGGCACTTCGTGTGCTA
* * * *
36558 ACATGAGAAGGAATTCATACTAAGTGTATGAATTATCATATAGGGCACTTCGTGTGCTAACATGA
196 AAATGAGAAGAAATTCATACTAAGTGTAGGAATTATCATATAGGGCACTTCGTGTGCTAAAATGA
* **
36623 GAAGGAATTCATAC-AAGTGTATGAATTTCCATAT
261 GAAGAAATTCATACTAAGACTATGAATTTCCATAT
* *
36657 AGGGCACTTCGTGTGCTGACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGAGCA
1 AGGGAACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGAGCA
36722 CTTCGTGTGCT-GACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGAGCACTTAG
66 CTTCGTGTGCTAG-CATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGAGCACTTAG
* * **
36786 TTTGCTAACATGAGAAGAAATT-ATTATTAAGCGTATGAATTTCTGTATAGGGCACTTCGTGTGC
130 TGTGCTAACATGAGAAGAAATTCA-TACTAAGCGTATGAATTTCCATATAGGGCACTTCGTGTGC
* * * * *
36850 TAAAATGATAAGAAATTCATATTAAGTGTAGGAATT-TCTGTATAGGGCGCTTCGTGTTCTAAAA
194 TAAAATGAGAAGAAATTCATACTAAGTGTAGGAATTATC-ATATAGGGCACTTCGTGTGCTAAAA
* *
36914 TGATAAGAAATTCATACTAAGACTATGAATTTCCGTAT
258 TGAGAAGAAATTCATACTAAGACTATGAATTTCCATAT
* * * * * *
36952 TGGGTACCTT-GTGTGCCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGG-AACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
37011 GGGAATTAAT
Statistics
Matches: 316, Mismatches: 33, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
293 4 0.01
294 245 0.78
295 64 0.20
296 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (295 bp):
AGGGAACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGAGCA
CTTCGTGTGCTAGCATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGAGCACTTAGT
GTGCTAACATGAGAAGAAATTCATACTAAGCGTATGAATTTCCATATAGGGCACTTCGTGTGCTA
AAATGAGAAGAAATTCATACTAAGTGTAGGAATTATCATATAGGGCACTTCGTGTGCTAAAATGA
GAAGAAATTCATACTAAGACTATGAATTTCCATAT
Found at i:41044 original size:251 final size:248
Alignment explanation
Indices: 40526--41004 Score: 751
Period size: 251 Copynumber: 1.9 Consensus size: 248
40516 TTGCTGCAGG
*
40526 TTTTAACTTCGTAGAATCGTAGTTATGTTCATTTTCATGTGTTCCTTGCTTGGTAACATAAAACT
1 TTTTAAC-TCATAGAATCGTAGTTATGTTCATTTTCATGTGTTCCTTGCTTGGTAACATAAAACT
40591 GTGGTTGGCGTAGTTTATGCTTTATGTGTACGGTGTACCTTATCTTTTACTATTGCTACTGTCTG
65 GTGGTTGGCGTAGTTTATGCTTTATGTGTACGGTGTACCTTATCTTTTACTATTGCTACTGTCTG
40656 AGGACACTTACATCTGGTTACTTGATAGGCACACTACATGTTGGACTTGCCTTTCTTAAGAAGAA
130 AGGACACTTACATCTGGTTACTTGATAGGCACACTACATGTTGGACTTGCCTTTCTTAAGAAGAA
******* * * *** * * *
40721 AGAATTAGATGAAGGTGCCTCTTTTGTTCAAACTTGCTAAACTTTTTGCTGCAGG
195 AGAATTAGATGAAGGTGCCAAGGAACTACAAAC-AGCTAAACTCCATGATGAAGC
*
40776 TTTTAACTTCGTAGAATCGTAGTTATGTTCATTTTCATGTGTTCCTTGCTTGGTAACATAAAACT
1 TTTTAAC-TCATAGAATCGTAGTTATGTTCATTTTCATGTGTTCCTTGCTTGGTAACATAAAACT
40841 GTGGTTTGGCGTAGTTTATGCTTTATGTGTACGGTGTACCTTATCTTTTACTATTGCTACTGTCT
65 GTGG-TTGGCGTAGTTTATGCTTTATGTGTACGGTGTACCTTATCTTTTACTATTGCTACTGTCT
40906 GAGGACACTTACATCTGGTTACTTGATAGGCACACTACATGTTGGGACTTGCCTTTCTTAAGAAG
129 GAGGACACTTACATCTGGTTACTTGATAGGCACACTACATGTT-GGACTTGCCTTTCTTAAGAAG
*
40971 AAAGAATTAGATGAAGGTGTCAAGGAACTACAAA
193 AAAGAATTAGATGAAGGTGCCAAGGAACTACAAA
41005 AGGTATAGAT
Statistics
Matches: 218, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
250 69 0.32
251 103 0.47
252 46 0.21
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (248 bp):
TTTTAACTCATAGAATCGTAGTTATGTTCATTTTCATGTGTTCCTTGCTTGGTAACATAAAACTG
TGGTTGGCGTAGTTTATGCTTTATGTGTACGGTGTACCTTATCTTTTACTATTGCTACTGTCTGA
GGACACTTACATCTGGTTACTTGATAGGCACACTACATGTTGGACTTGCCTTTCTTAAGAAGAAA
GAATTAGATGAAGGTGCCAAGGAACTACAAACAGCTAAACTCCATGATGAAGC
Found at i:43942 original size:19 final size:17
Alignment explanation
Indices: 43914--43948 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
43904 TCCCTTTGAC
43914 ATTGTTATTTGATTTTTT
1 ATTGTTATTTG-TTTTTT
43932 ATTGATTATTTGTTTTT
1 ATTG-TTATTTGTTTTT
43949 GTTAAGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.71
Consensus pattern (17 bp):
ATTGTTATTTGTTTTTT
Found at i:45531 original size:12 final size:12
Alignment explanation
Indices: 45514--45539 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
45504 TTTCAGATCC
45514 AACAAACGTGGT
1 AACAAACGTGGT
45526 AACAAACGTGGT
1 AACAAACGTGGT
45538 AA
1 AA
45540 GTGGTTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (12 bp):
AACAAACGTGGT
Found at i:55042 original size:21 final size:20
Alignment explanation
Indices: 55000--55043 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
54990 TCAAAAGAAG
*
55000 TTTTGAGATCATCAATTTTC
1 TTTTGAGATCATCAATTATC
55020 TTTTGATGATCATC-ATTGATC
1 TTTTGA-GATCATCAATT-ATC
55041 TTT
1 TTT
55044 GAAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.52
Consensus pattern (20 bp):
TTTTGAGATCATCAATTATC
Found at i:60889 original size:35 final size:35
Alignment explanation
Indices: 60796--60891 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 35
60786 AACACAATCA
* * * *
60796 TCAACTACATTCTAAACCCCAAAATCCAAAATGCT
1 TCAATTACATCCTAAACCCCAAATTCCAAAATACT
* *
60831 TCAATTACATCCTAAACCTCAAATTCTAAAATACT
1 TCAATTACATCCTAAACCCCAAATTCCAAAATACT
* *
60866 TCAATTATATGCC-CAACCCCAAATTC
1 TCAATTACAT-CCTAAACCCCAAATTC
60892 ACAATCCATT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 49 0.96
36 2 0.04
ACGTcount: A:0.41, C:0.30, G:0.02, T:0.27
Consensus pattern (35 bp):
TCAATTACATCCTAAACCCCAAATTCCAAAATACT
Found at i:61318 original size:148 final size:147
Alignment explanation
Indices: 61045--61336 Score: 485
Period size: 148 Copynumber: 2.0 Consensus size: 147
61035 AAATACTCAA
* * ** *
61045 TTCAGTTTATAAAATAGTTGACTCGATTTTTTTTTATTTGAGTTTATGAAATTTAAATCAAGTCG
1 TTCAATTTATAAAATAGTTGACTCGAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTCG
* * *
61110 AATTGAATTGAATTTTCTAGTTTCTATTTAAATTTAATTATAAATATTTATCATATTATAATATT
66 AATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATATT
*
61175 ATTTTATTCTAATTCAG
131 ATTTGATTCTAATTCAG
61192 TTCAATTTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAATTTATAAAATAGTTGACTCG-AATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
*
61257 GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
65 GAATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAT
61322 TATTTGATTCTAATT
130 TATTTGATTCTAATT
61337 TAAATAGTTT
Statistics
Matches: 134, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
147 24 0.18
148 110 0.82
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (147 bp):
TTCAATTTATAAAATAGTTGACTCGAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTCG
AATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATATT
ATTTGATTCTAATTCAG
Found at i:66449 original size:31 final size:31
Alignment explanation
Indices: 66379--66452 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
66369 CTTTTAAAAC
** * *
66379 TTGCAATACAGTCCCCCTACATTTAGTCCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCAT
*
66410 TTGCAATATGGTCCCCCAACATTTAGTCTAT
1 TTGCAATATGGTCCCCCAACATTTAGTCCAT
66441 TTGCAATATGGT
1 TTGCAATATGGT
66453 TCCCGACCGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCCAT
Found at i:68267 original size:18 final size:19
Alignment explanation
Indices: 68237--68272 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
68227 AGAGAAGTGA
68237 AAAAGGAAATTTGAGGTTG
1 AAAAGGAAATTTGAGGTTG
*
68256 AAAAGG-AATTTGGGGTT
1 AAAAGGAAATTTGAGGTT
68273 TAGAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.28
Consensus pattern (19 bp):
AAAAGGAAATTTGAGGTTG
Found at i:68431 original size:31 final size:31
Alignment explanation
Indices: 68396--68463 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
68386 TCAAATGATC
*
68396 GGGGACCATATTGCAAACAG-ACTAAATGTTG
1 GGGGACCATATTGCAAA-AGAACTAAATATTG
*
68427 GGGGACCATATTGCAAATGAACTAAATATTG
1 GGGGACCATATTGCAAAAGAACTAAATATTG
68458 GGGGAC
1 GGGGAC
68464 TGTATTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (31 bp):
GGGGACCATATTGCAAAAGAACTAAATATTG
Found at i:69106 original size:17 final size:17
Alignment explanation
Indices: 69084--69122 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
69074 TGAATCAAAT
69084 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
69101 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
69118 -AATTA
1 TAATTA
69123 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Done.