Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004645.1 Hibiscus syriacus cultivar Beakdansim tig00010415_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: 74655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1000 original size:19 final size:19
Alignment explanation
Indices: 978--1036 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
968 GGAAATTACT
978 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
997 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1011 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1030 ATCGCAA
1 ATCGCAA
1037 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1078 original size:33 final size:33
Alignment explanation
Indices: 979--1078 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 33
969 GAAATTACTA
* *
979 TCGCAATGCGAAATGAAAATCGCAACGAGAGA-A
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-ATT
*
1012 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
1045 TCGCAATGCGAAATGAAAATTGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1078 T
1 T
1079 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 1 0.02
33 60 0.98
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:1250 original size:14 final size:14
Alignment explanation
Indices: 1231--1266 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1221 CATCAATTAA
1231 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1245 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1259 ACAAATCA
1 ACAAATCA
1267 TTAAACAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2665 original size:21 final size:21
Alignment explanation
Indices: 2599--2665 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2589 GTGAATCGGG
* *
2599 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGATGGGAGGGGA
* ** * *
2619 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGATGGGAGGGGA
2641 CTCTTGAACGATGGGAGGGGA
1 CTCTTGAACGATGGGAGGGGA
2662 CTCT
1 CTCT
2666 CGAGGAATGA
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGA
Found at i:2684 original size:42 final size:42
Alignment explanation
Indices: 2638--2717 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
2628 CGATGACAGT
* *
2638 GGCCTCTTGAACGATGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * *
2680 GGCCTCTTCAATGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
2718 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:3100 original size:88 final size:89
Alignment explanation
Indices: 2936--3116 Score: 271
Period size: 95 Copynumber: 2.0 Consensus size: 89
2926 ATTTCAAACT
2936 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATACACAGTTTAGC
3001 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGC-ACCGAATAAATTTAC
3029 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATA-A-A-TTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATACACAGTTTAGCA
*
3090 GTATTGGCAGCACCGAATAAATTTAC
64 GAATTGGCAGCACCGAATAAATTTAC
3116 T
1 T
3117 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 1, Indels: 10
0.89 0.01 0.10
Matches are distributed among these distances:
87 16 0.19
88 17 0.20
89 1 0.01
90 1 0.01
91 4 0.05
93 19 0.22
95 27 0.32
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (89 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATACACAGTTTAGCAGA
ATTGGCAGCACCGAATAAATTTAC
Found at i:4830 original size:14 final size:14
Alignment explanation
Indices: 4811--4866 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
4801 GGAAATGACT
4811 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
4825 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
4842 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
4858 ATCGCAACG
1 ATCGCAACG
4867 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:4841 original size:33 final size:33
Alignment explanation
Indices: 4795--4885 Score: 155
Period size: 33 Copynumber: 2.7 Consensus size: 33
4785 TAATGAGAAT
4795 CAACGCGGAAATGACTATCGCAACGAGAGAATCG
1 CAACGC-GAAATGACTATCGCAACGAGAGAATCG
4829 CAACGCGAAATGACTATCGCAACGAGAGAATCG
1 CAACGCGAAATGACTATCGCAACGAGAGAATCG
**
4862 CAACGCGAAATGAAAATCGCAACG
1 CAACGCGAAATGACTATCGCAACG
4886 CGAAATGAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 49 0.89
34 6 0.11
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (33 bp):
CAACGCGAAATGACTATCGCAACGAGAGAATCG
Found at i:4895 original size:19 final size:19
Alignment explanation
Indices: 4764--4907 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
4754 TCTTTTGGTT
*
4764 GAAATGAAAATCGCAACGG
1 GAAATGAAAATCGCAACGC
*
4783 GATAATGAGAAT--CAACGC
1 GA-AATGAAAATCGCAACGC
**
4801 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
4819 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
4835 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
4852 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4868 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
4887 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
4906 GA
1 GA
4908 TTTTGGTTTC
Statistics
Matches: 99, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
14 18 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 15 0.15
19 46 0.46
20 11 0.11
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:5547 original size:20 final size:20
Alignment explanation
Indices: 5459--5592 Score: 135
Period size: 20 Copynumber: 6.7 Consensus size: 20
5449 CGCTATGTAA
* * *
5459 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* * *
5479 ATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
5499 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
5520 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
*
5540 ATCACATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
5560 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
5580 ATCGCATTGCGAT
1 ATCGCATTGCGAT
5593 TTTCCTAATT
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.03
20 82 0.83
21 12 0.12
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:5611 original size:81 final size:81
Alignment explanation
Indices: 5465--5613 Score: 192
Period size: 81 Copynumber: 1.8 Consensus size: 81
5455 GTAAATCGCG
* * * * * *
5465 TTGCGAAAGTCAGAATCTCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGC
1 TTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCTAATATCGCATTGC
5530 GATAGTAAGTATCACA
66 GATAGTAAGTATCACA
* * * *
5546 TTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCTAAT-TCGCGTTG
1 TTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CTAATATCGCATTG
5610 CGAT
65 CGAT
5614 TTACTTATTC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
81 54 0.95
82 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (81 bp):
TTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCTAATATCGCATTGC
GATAGTAAGTATCACA
Found at i:5625 original size:20 final size:21
Alignment explanation
Indices: 5581--5632 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
5571 ATAGTCAGTA
*
5581 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTACTAAT
* *
5602 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACTAAT
5622 TCGCATTGCGA
1 TCGCATTGCGA
5633 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACTAAT
Found at i:9640 original size:24 final size:26
Alignment explanation
Indices: 9613--9663 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
9603 TCCGTTTTTA
*
9613 TACATTTTT-TTTTCTATTTTT-GGT
1 TACATTTTTGTTATCTATTTTTAGGT
*
9637 TACATTTTTGTTATCTTTTTTTAGGT
1 TACATTTTTGTTATCTATTTTTAGGT
9663 T
1 T
9664 GGATTTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 10 0.43
26 4 0.17
ACGTcount: A:0.14, C:0.08, G:0.10, T:0.69
Consensus pattern (26 bp):
TACATTTTTGTTATCTATTTTTAGGT
Found at i:11091 original size:23 final size:23
Alignment explanation
Indices: 11044--11093 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
11034 AATAACATAT
* **
11044 TAGGTAGTGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
11067 TAGGTAGCGTTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
11090 TAGG
1 TAGG
11094 CATTTAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:14248 original size:18 final size:18
Alignment explanation
Indices: 14221--14272 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
14211 GTGAAGTATG
*
14221 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
14239 AATGGTGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
14257 AATGGTGTTGTCGTGG
1 AATGGTGTTGTCGTGG
14273 TAAGTGTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.15, C:0.12, G:0.40, T:0.33
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:15570 original size:15 final size:15
Alignment explanation
Indices: 15550--15578 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
15540 TATCATTGTC
15550 GTTGAGAAGAGCTTG
1 GTTGAGAAGAGCTTG
15565 GTTGAGAAGAGCTT
1 GTTGAGAAGAGCTT
15579 TGAGAAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.38, T:0.28
Consensus pattern (15 bp):
GTTGAGAAGAGCTTG
Found at i:16358 original size:201 final size:201
Alignment explanation
Indices: 15869--16836 Score: 1345
Period size: 201 Copynumber: 4.8 Consensus size: 201
15859 TGCGAAATTT
* *
15869 AAAAAGGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGAACGCT-TT-TCT-AGTTA
1 AAAAA-GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTTG-AC-CTATTCTCTCA-TAA
* * * * * *
15931 AACCAATGTATTTATACCGATTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGAT
62 AACCAGTATATTTATACCGATTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGAT
* *
15996 GTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCATGCACCTCG-TTGGGCATT
127 GTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATT
16060 CATTCTGGAC
192 CATTCTGGAC
* ** * * *
16070 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
1 AAAAAGTATCGACACAAATTTCAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACC
* * * * * *
16135 GGTATATTTATACAGGTTACATTGAAAAGTTACCTATTACATTATAATTATAGGTTTTGATGTTT
66 AGTATATTTATACCGATTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* *
16200 TTGAGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTAGTTTGGGCATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
16265 CTGGAC
196 CTGGAC
* * * *
16271 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGATCTATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTCAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACC
* *
16336 AGTATATTTATACTGATTACATTAAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
66 AGTATATTTATACCGATTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * *
16401 TTGGGATCGATACTTTGTATAAATGTATCGAAACTTTATGCGTGCAGCTAGTTTGGGCATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
16466 CTGGAC
196 CTGGAC
* * * * * * *
16472 AAAACGTATCAACACAAATTTCAAAAGTGTCAATACATTATATTGACATATTCTCACATAAAATC
1 AAAAAGTATCGACACAAATTTCAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACC
* *
16537 GGTATATTTATACCGGTTACATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
66 AGTATATTTATACCGATTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
* * *** *
16601 TTTGGGATCGAGACTTTTTATAAATGTATCGACACTTTATGCGTGTACCGCTTTTGAGCATTCAT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCAT
16666 TCTGGAC
195 TCTGGAC
* * *
16673 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTCAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACC
*
16738 AGTATATTTATACCTG-TTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTTGATGTT
66 AGTATATTTATACC-GATTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
* * *
16802 TTTGGGATTGATGCTTTGTATAAATGTATCGACAC
130 TTTGGGATCGATACTTTTTATAAATGTATCGACAC
16837 ATCTGTTTAC
Statistics
Matches: 684, Mismatches: 76, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
198 1 0.00
199 4 0.01
200 153 0.22
201 524 0.77
202 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (201 bp):
AAAAAGTATCGACACAAATTTCAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACC
AGTATATTTATACCGATTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
CTGGAC
Found at i:17324 original size:19 final size:19
Alignment explanation
Indices: 17285--17332 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
17275 TTATATTCAC
*
17285 ATACAAAATT-TAAATCGT
1 ATACAAAATTATAAACCGT
*
17303 ATACAAAATTATAAACCTT
1 ATACAAAATTATAAACCGT
17322 ATACAAAATTA
1 ATACAAAATTA
17333 ACCCTACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAACCGT
Found at i:18842 original size:18 final size:18
Alignment explanation
Indices: 18819--18857 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
18809 TCCTCCTCAT
18819 TTCCTCCATCTTTTATTC
1 TTCCTCCATCTTTTATTC
*
18837 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTATTC
18855 TTC
1 TTC
18858 ATATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATCTTTTATTC
Found at i:21779 original size:182 final size:182
Alignment explanation
Indices: 21287--21764 Score: 762
Period size: 182 Copynumber: 2.6 Consensus size: 182
21277 TACGCGTACT
* *
21287 TATTAAAGTATCGACACTTTCAACATATCCAGTAGCGCTTTACCGGTTTTTTCATTTTGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGAGACCG
* * *
21352 GTTTTGTCATATTTTTATCTGTTATATT-ATTATGGATCGATACATTTGTATAAAGTATCGACAC
66 ATTTTGTCATATTTTTACCTGTTATATTGA-TATGGATCGATACATTTTTATAAAGTATCGACAC
*
21416 TTTATAGGAGCTATTACTACTTGTCTTTTAAATTCTAAAAGTGTCGATACTTA
130 TTTATAGGAGCTATTACTACTTGTCTTTTAAATTCCAAAAGTGTCGATACTTA
* **
21469 TAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTATCATCGTG-GTACC
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGAG-ACC
* *
21533 GATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
65 GATTTTGTCATATTTTTACCTGTTATATTGATATGGATCGATACATTTTTATAAAGTATCGACAC
* * *
21598 TTTATAGGTGCTATTACTGCTTGTCTTTTAAATTCCAAAGGTGTCGATACTTA
130 TTTATAGGAGCTATTACTACTTGTCTTTTAAATTCCAAAAGTGTCGATACTTA
* **
21651 TATTAAAGTATTGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTGGTCATTTTGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGAGACCG
*
21716 ATTTTGTCATATTTTTACCTGTTATATTGATATGGATCTATACATTTTT
66 ATTTTGTCATATTTTTACCTGTTATATTGATATGGATCGATACATTTTT
21765 TATTTGTATC
Statistics
Matches: 270, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
181 1 0.00
182 268 0.99
183 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGAGACCG
ATTTTGTCATATTTTTACCTGTTATATTGATATGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGAGCTATTACTACTTGTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:23682 original size:26 final size:26
Alignment explanation
Indices: 23625--23674 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
23615 CTTATAATTT
*
23625 ATTATATATATTTATTATTTTTAAAA
1 ATTATATATATTTACTATTTTTAAAA
23651 ATTATA-ATATTATACTATTTTTAA
1 ATTATATATATT-TACTATTTTTAA
23675 TATGTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTATATATATTTACTATTTTTAAAA
Found at i:23712 original size:22 final size:22
Alignment explanation
Indices: 23680--23768 Score: 67
Period size: 23 Copynumber: 4.0 Consensus size: 22
23670 TTTAATATGT
*
23680 ATATTCAATTTTTTAGTAATTTA
1 ATATTTAATTTTTTAGT-ATTTA
* *
23703 AT-TTTTA-TTTTTAGTATTTT
1 ATATTTAATTTTTTAGTATTTA
*
23723 ATATTTAATTTTTTTAATATTTGA
1 ATATTTAA-TTTTTTAGTATTT-A
*
23747 ATAATTTTATATTTTTA-TATTT
1 AT-ATTTAAT-TTTTTAGTATTT
23769 TTTTTAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
20 6 0.11
21 12 0.23
22 3 0.06
23 13 0.25
24 8 0.15
25 11 0.21
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.65
Consensus pattern (22 bp):
ATATTTAATTTTTTAGTATTTA
Found at i:23721 original size:20 final size:22
Alignment explanation
Indices: 23680--23735 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
23670 TTTAATATGT
*
23680 ATATTCAATTTTTTAGTAATTTA
1 ATATTTAA-TTTTTAGTAATTTA
* *
23703 AT-TTTTATTTTTAGT-ATTTT
1 ATATTTAATTTTTAGTAATTTA
23723 ATATTTAATTTTT
1 ATATTTAATTTTT
23736 TTAATATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.21
21 17 0.61
22 3 0.11
23 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (22 bp):
ATATTTAATTTTTAGTAATTTA
Found at i:23762 original size:8 final size:8
Alignment explanation
Indices: 23704--23770 Score: 50
Period size: 8 Copynumber: 8.5 Consensus size: 8
23694 AGTAATTTAA
23704 TTTT-TAT
1 TTTTATAT
23711 TTTTAGTA-
1 TTTTA-TAT
23719 TTTTATA-
1 TTTTATAT
* *
23726 TTTAATTT
1 TTTTATAT
23734 TTTTAATAT
1 TTTT-ATAT
** *
23743 TTGAATAA
1 TTTTATAT
23751 TTTTATAT
1 TTTTATAT
23759 TTTTATAT
1 TTTTATAT
23767 TTTT
1 TTTT
23771 TTTAAAATTA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
7 11 0.24
8 28 0.61
9 7 0.15
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (8 bp):
TTTTATAT
Found at i:24959 original size:9 final size:9
Alignment explanation
Indices: 24945--24969 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
24935 TCGAGCTATG
24945 CTCTTCTTT
1 CTCTTCTTT
24954 CTCTTCTTT
1 CTCTTCTTT
24963 CTCTTCT
1 CTCTTCT
24970 GCATTTACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (9 bp):
CTCTTCTTT
Found at i:27264 original size:21 final size:21
Alignment explanation
Indices: 27234--27427 Score: 170
Period size: 21 Copynumber: 9.2 Consensus size: 21
27224 GAATTACATA
*
27234 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
27255 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
27278 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
27297 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
27320 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
27339 TTCACGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
27362 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
27381 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
27404 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
27423 TTCGC
1 TTCGC
27428 AACGACGGTA
Statistics
Matches: 140, Mismatches: 17, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
19 36 0.26
21 68 0.49
23 36 0.26
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:27287 original size:42 final size:42
Alignment explanation
Indices: 27240--27427 Score: 331
Period size: 42 Copynumber: 4.5 Consensus size: 42
27230 CATATTCGCA
*
27240 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
27282 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
27324 TTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
27366 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
27408 TTGCGATAGTCCAAGTTCGC
1 TTGCGATAGTCCAAGTTCGC
27428 AACGACGGTA
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 141 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:27528 original size:12 final size:12
Alignment explanation
Indices: 27507--27562 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 12
27497 GACACGTATT
27507 ACCACAACCACG
1 ACCACAACCACG
*
27519 ACCACGACCACG
1 ACCACAACCACG
27531 A-CACAA-CACG
1 ACCACAACCACG
27541 A-CACAA-CACG
1 ACCACAACCACG
27551 A-CACAA-CACG
1 ACCACAACCACG
27561 AC
1 AC
27563 ACGACCCGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
10 25 0.61
11 4 0.10
12 12 0.29
ACGTcount: A:0.45, C:0.45, G:0.11, T:0.00
Consensus pattern (12 bp):
ACCACAACCACG
Found at i:27542 original size:10 final size:10
Alignment explanation
Indices: 27527--27564 Score: 76
Period size: 10 Copynumber: 3.8 Consensus size: 10
27517 CGACCACGAC
27527 CACGACACAA
1 CACGACACAA
27537 CACGACACAA
1 CACGACACAA
27547 CACGACACAA
1 CACGACACAA
27557 CACGACAC
1 CACGACAC
27565 GACCCGAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.47, C:0.42, G:0.11, T:0.00
Consensus pattern (10 bp):
CACGACACAA
Found at i:27544 original size:5 final size:5
Alignment explanation
Indices: 27515--27567 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
27505 TTACCACAAC
* * *
27515 CACGA CCACGA CCACGA CACAA CACGA CACAA CACGA CACAA CACGA CACGA
1 CACGA -CACGA -CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA
27567 C
1 C
27568 CCGAGACGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
5 30 0.73
6 11 0.27
ACGTcount: A:0.43, C:0.43, G:0.13, T:0.00
Consensus pattern (5 bp):
CACGA
Found at i:28222 original size:21 final size:21
Alignment explanation
Indices: 28198--28326 Score: 174
Period size: 21 Copynumber: 6.2 Consensus size: 21
28188 TTTGGAATAA
*
28198 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
28219 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
28240 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
28260 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
28281 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
28302 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
28323 ATCG
1 ATCG
28327 TTGCGATAGT
Statistics
Matches: 96, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
20 17 0.18
21 79 0.82
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:28281 original size:62 final size:64
Alignment explanation
Indices: 28170--28314 Score: 208
Period size: 62 Copynumber: 2.3 Consensus size: 64
28160 CGTTGCGATT
* *
28170 TTGGACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAATATGG-ATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
* *
28233 TTGGACTATCGCAATGCGAATAT-G-TAAATCGCAATGCGAACTTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAATGCGAATATGGATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
*
28295 TTCGACTATCGCAATGCGAA
1 TTGGACTATCGCAATGCGAA
28315 CTTCGACTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
62 54 0.72
63 14 0.19
64 1 0.01
65 6 0.08
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (64 bp):
TTGGACTATCGCAATGCGAATATGGATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
Found at i:28353 original size:21 final size:21
Alignment explanation
Indices: 28327--28374 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
28317 TCGACTATCG
28327 TTGCGATAGTCCAAGTTCGCA
1 TTGCGATAGTCCAAGTTCGCA
*
28348 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCA
28369 TTGCGA
1 TTGCGA
28375 ATCTGGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCA
Found at i:35533 original size:25 final size:25
Alignment explanation
Indices: 35499--35557 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
35489 GTAACAGTTC
35499 ATAAAGTGTTTGATGCACATCCAGA
1 ATAAAGTGTTTGATGCACATCCAGA
35524 ATAAAGTGTTTGATGCACATCCAGA
1 ATAAAGTGTTTGATGCACATCCAGA
35549 ATAAAGTGT
1 ATAAAGTGT
35558 CGTTCAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (25 bp):
ATAAAGTGTTTGATGCACATCCAGA
Found at i:38421 original size:25 final size:25
Alignment explanation
Indices: 38372--38421 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
38362 TATATATATA
**
38372 TATATATATATTTAAAAAATTAAAC
1 TATATATATATTTAAAAAAGAAAAC
*
38397 TATATATATTTTTAAAAAAGAAAAC
1 TATATATATATTTAAAAAAGAAAAC
38422 ATAAATTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
TATATATATATTTAAAAAAGAAAAC
Found at i:40917 original size:23 final size:22
Alignment explanation
Indices: 40886--40953 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
40876 TTCAAATTAA
*
40886 ATATTCAAACCATTCAAACAAAT
1 ATATCCAAA-CATTCAAACAAAT
* * *
40909 ATATCCAAACATCCAAAACACAC
1 ATATCCAAACATTC-AAACAAAT
*
40932 AAATCCAAAACATTCAAA-AAAT
1 ATATCC-AAACATTCAAACAAAT
40954 GTTTTAACAA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
22 6 0.17
23 22 0.63
24 7 0.20
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (22 bp):
ATATCCAAACATTCAAACAAAT
Found at i:42323 original size:12 final size:13
Alignment explanation
Indices: 42306--42338 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
42296 ATGGGCAAAA
*
42306 TTTGAAAACTAT-
1 TTTGAAAACAATG
42318 TTTGAAAACAATG
1 TTTGAAAACAATG
42331 TTTGAAAA
1 TTTGAAAA
42339 ATCATAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:42847 original size:23 final size:21
Alignment explanation
Indices: 42819--42876 Score: 55
Period size: 23 Copynumber: 2.7 Consensus size: 21
42809 TACAATTGTG
42819 AGTGTATCGATACACATTCA-
1 AGTGTATCGATACACATTCAT
* * *
42839 AGGAATGTAACGGTACATATTCAT
1 A-G--TGTATCGATACACATTCAT
42863 AGTGTATCGATACA
1 AGTGTATCGATACA
42877 TAGCAAGGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
23 16 0.55
24 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (21 bp):
AGTGTATCGATACACATTCAT
Found at i:47255 original size:18 final size:18
Alignment explanation
Indices: 47215--47256 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
47205 ACTCGAACGC
*
47215 TATTCTTTTTCTCCGTCT
1 TATTCTTTGTCTCCGTCT
*
47233 CATTCTTTGTCT-CGTCCT
1 TATTCTTTGTCTCCGT-CT
47251 TATTCT
1 TATTCT
47257 CGAGGTCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.07, C:0.29, G:0.07, T:0.57
Consensus pattern (18 bp):
TATTCTTTGTCTCCGTCT
Found at i:50699 original size:50 final size:50
Alignment explanation
Indices: 50611--50709 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
50601 TTGAAACCAC
* *
50611 TGCTGTTGAAACCACTAATCCAACCGATTTACAAGATTTTACTGATAAAT
1 TGCTATTGAAACCACTAATCCAACCGACTTACAAGATTTTACTGATAAAT
* * **
50661 TGCTATTGAAACCACTAATCCAATCGACTTGCTGGATTTTACTGATAAA
1 TGCTATTGAAACCACTAATCCAACCGACTTACAAGATTTTACTGATAAA
50710 GATATATTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.32
Consensus pattern (50 bp):
TGCTATTGAAACCACTAATCCAACCGACTTACAAGATTTTACTGATAAAT
Found at i:52091 original size:21 final size:20
Alignment explanation
Indices: 52065--52113 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
52055 GATAGAACAT
*
52065 ATATATATATGGTTTTTGAAA
1 ATATATATATAG-TTTTGAAA
52086 ATATATTATATAGTTTTGAAA
1 ATATA-TATATAGTTTTGAAA
*
52107 ACATATA
1 ATATATA
52114 AAAATATGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.68
22 6 0.24
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (20 bp):
ATATATATATAGTTTTGAAA
Found at i:52112 original size:23 final size:24
Alignment explanation
Indices: 52060--52218 Score: 71
Period size: 22 Copynumber: 7.1 Consensus size: 24
52050 ATAGAGATAG
*
52060 AACATATATATATATGGTTTTTGA
1 AACATATATATATATAGTTTTTGA
52084 AA-ATATAT-TATATAG-TTTTGAA
1 AACATATATATATATAGTTTTTG-A
* * * *
52106 AACATATAAAAATATGGCTTTTGA
1 AACATATATATATATAGTTTTTGA
****
52130 AA-ATA-AT-TA-A-A---AAAAA
1 AACATATATATATATAGTTTTTGA
52146 AACATATATAATATATATAGTTTTTGA
1 AACATATAT---ATATATAGTTTTTGA
*
52173 AA-ACATAT-TATATAGTTTTTGAA
1 AACATATATATATATAGTTTTTG-A
52196 AACATAT-TATATA-A-TTTTTGA
1 AACATATATATATATAGTTTTTGA
52217 AA
1 AA
52219 ATAAAATATA
Statistics
Matches: 100, Mismatches: 17, Indels: 39
0.64 0.11 0.25
Matches are distributed among these distances:
16 3 0.03
17 3 0.03
18 2 0.02
20 1 0.01
21 9 0.09
22 31 0.31
23 20 0.20
24 18 0.18
25 5 0.05
26 5 0.05
27 3 0.03
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (24 bp):
AACATATATATATATAGTTTTTGA
Found at i:52184 original size:22 final size:22
Alignment explanation
Indices: 52159--52219 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
52149 ATATATAATA
52159 TATATAGTTTTTGAAAACATAT
1 TATATAGTTTTTGAAAACATAT
52181 TATATAGTTTTTGAAAACATAT
1 TATATAGTTTTTGAAAACATAT
*
52203 TATATAATTTTTGAAAA
1 TATATAGTTTTTGAAAA
52220 TAAAATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (22 bp):
TATATAGTTTTTGAAAACATAT
Found at i:52228 original size:22 final size:22
Alignment explanation
Indices: 52158--52229 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 22
52148 CATATATAAT
*
52158 ATATATAGTTTTTGAAAACATA
1 ATATATAGTTTTTGAAAACAAA
* *
52180 TTATATAGTTTTTGAAAACATA
1 ATATATAGTTTTTGAAAACAAA
* * *
52202 TTATATAATTTTTGAAAATAAA
1 ATATATAGTTTTTGAAAACAAA
52224 ATATAT
1 ATATAT
52230 GTTATATAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (22 bp):
ATATATAGTTTTTGAAAACAAA
Found at i:52252 original size:27 final size:29
Alignment explanation
Indices: 52202--52256 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
52192 TGAAAACATA
52202 TTATATAATTTTTGAAAATAAAATATATG
1 TTATATAATTTTTGAAAATAAAATATATG
*
52231 TTATATAGTTTTT-AAAAT-AAATATAT
1 TTATATAATTTTTGAAAATAAAATATAT
52257 TGTACATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.32
28 5 0.20
29 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (29 bp):
TTATATAATTTTTGAAAATAAAATATATG
Found at i:52265 original size:29 final size:29
Alignment explanation
Indices: 52204--52270 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
52194 AAAACATATT
*
52204 ATATAATTTTTGAAAATAAAATATATGTT
1 ATATAATTTTTGAAAATAAAATATATGTC
*
52233 ATATAGTTTTT-AAAAT-AAATATATTGTAC
1 ATATAATTTTTGAAAATAAAATATA-TGT-C
*
52262 ATATTATTT
1 ATATAATTT
52271 ATTGTATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 7 0.22
28 8 0.25
29 17 0.53
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (29 bp):
ATATAATTTTTGAAAATAAAATATATGTC
Found at i:52271 original size:27 final size:28
Alignment explanation
Indices: 52210--52264 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
52200 TATTATATAA
*
52210 TTTTTGAAAATAAAATATATGTTATATAG
1 TTTTT-AAAATAAAATATATGTTACATAG
52239 TTTTTAAAAT-AAATATAT-TGTACATA
1 TTTTTAAAATAAAATATATGT-TACATA
52265 TTATTTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.04
27 13 0.54
28 5 0.21
29 5 0.21
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (28 bp):
TTTTTAAAATAAAATATATGTTACATAG
Found at i:52278 original size:12 final size:11
Alignment explanation
Indices: 52265--52325 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 11
52255 ATTGTACATA
*
52265 TTATTTATTGT
1 TTATTTATTAT
*
52276 ATTATATATTAT
1 -TTATTTATTAT
*
52288 TTATAGTATTAT
1 TTAT-TTATTAT
52300 TTATTATATTAT
1 TTATT-TATTAT
52312 ATTATATTATTAT
1 -TTAT-TTATTAT
52325 T
1 T
52326 AATATTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 4 0.10
12 26 0.63
13 10 0.24
14 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:52286 original size:19 final size:19
Alignment explanation
Indices: 52262--52325 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
52252 TATATTGTAC
52262 ATATTATTTATTGTATTAT
1 ATATTATTTATTGTATTAT
*
52281 ATATTATTTATAGTATTAT
1 ATATTATTTATTGTATTAT
* *
52300 TTATTA--TATTATATTAT
1 ATATTATTTATTGTATTAT
52317 ATTATTATT
1 A-TATTATT
52326 AATATTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 9 0.24
18 5 0.14
19 23 0.62
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
ATATTATTTATTGTATTAT
Found at i:52330 original size:12 final size:12
Alignment explanation
Indices: 52275--52334 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
52265 TTATTTATTG
52275 TATTATATATTAT
1 TATTA-ATATTAT
*
52288 T-TATAGTATTATT
1 TAT-TAATATTA-T
52301 TATT-ATATTA-
1 TATTAATATTAT
52311 TATT-ATATTAT
1 TATTAATATTAT
52322 TATTAATATTAT
1 TATTAATATTAT
52334 T
1 T
52335 TTTTCGGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 10 0.25
11 4 0.10
12 19 0.47
13 6 0.15
14 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (12 bp):
TATTAATATTAT
Found at i:52332 original size:34 final size:31
Alignment explanation
Indices: 52262--52335 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 31
52252 TATATTGTAC
*
52262 ATATTATTTATTGTATTATATATTATTTATA
1 ATATTATTTATTATATTATATATTATTTATA
*
52293 GTATTATTTATTATATTATAT-TATATTATTATTA
1 ATATTATTTATTATATTATATAT-TA-T-TTA-TA
52327 ATATTATTT
1 ATATTATTT
52336 TTTCGGTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 1 0.03
31 21 0.58
32 1 0.03
33 3 0.08
34 10 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (31 bp):
ATATTATTTATTATATTATATATTATTTATA
Found at i:55379 original size:177 final size:177
Alignment explanation
Indices: 55076--55429 Score: 645
Period size: 177 Copynumber: 2.0 Consensus size: 177
55066 AGTTACTATG
*
55076 GTAAGAAGTGACTCATAAAGTGTTATATGATTCTTATGAGTGCATTTTAGTTTATAGGATTATAA
1 GTAAGAAATGACTCATAAAGTGTTATATGATTCTTATGAGTGCATTTTAGTTTATAGGATTATAA
* *
55141 GGAATTGGACTTGTGATAAGTCTATTTCCAATAGTTATAGTGTATAAAGTATTGCTTATAAGGAT
66 GGAATTGGACTTGTGATAAGTCTATTTCCAATAGTTATAGTATATAAAGTATTGATTATAAGGAT
*
55206 GTGAATGACATGAAATGTATGTATACTTGATTATATGAACTGATATA
131 GTGAATGACATGAAATGGATGTATACTTGATTATATGAACTGATATA
*
55253 GTAAGAAATGACTCCTAAAGTGTTATATGATTCTTATGAGTGCATTTTAGTTTATAGGATTATAA
1 GTAAGAAATGACTCATAAAGTGTTATATGATTCTTATGAGTGCATTTTAGTTTATAGGATTATAA
*
55318 GGAATTGGACTTGTGATAAGTCTATTTCCAATAGTTATGGTATATAAAGTATTGATTATAAGGAT
66 GGAATTGGACTTGTGATAAGTCTATTTCCAATAGTTATAGTATATAAAGTATTGATTATAAGGAT
*
55383 GTGAATTACATGAAATGGATGTATACTTGATTATATGAACTGATATA
131 GTGAATGACATGAAATGGATGTATACTTGATTATATGAACTGATATA
55430 TGCTTATATG
Statistics
Matches: 170, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
177 170 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (177 bp):
GTAAGAAATGACTCATAAAGTGTTATATGATTCTTATGAGTGCATTTTAGTTTATAGGATTATAA
GGAATTGGACTTGTGATAAGTCTATTTCCAATAGTTATAGTATATAAAGTATTGATTATAAGGAT
GTGAATGACATGAAATGGATGTATACTTGATTATATGAACTGATATA
Found at i:55538 original size:25 final size:25
Alignment explanation
Indices: 55509--55594 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 25
55499 ATTATATGAG
55509 TATGTGGAAAATATGATTCAAAGTA
1 TATGTGGAAAATATGATTCAAAGTA
*
55534 TATGTGGTATATATATAT-ATAT-ATGAA-CA
1 TATGTGG-A-A-A-ATATGAT-TCA--AAGTA
*
55563 TAGGTGGAAAATATGATTCAAAGTA
1 TATGTGGAAAATATGATTCAAAGTA
55588 TATGTGG
1 TATGTGG
55595 TATATATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 20
0.66 0.06 0.28
Matches are distributed among these distances:
24 2 0.04
25 19 0.40
26 5 0.11
27 2 0.04
28 5 0.11
29 12 0.26
30 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (25 bp):
TATGTGGAAAATATGATTCAAAGTA
Found at i:55634 original size:56 final size:54
Alignment explanation
Indices: 55512--55627 Score: 232
Period size: 54 Copynumber: 2.1 Consensus size: 54
55502 ATATGAGTAT
55512 GTGGAAAATATGATTCAAAGTATATGTGGTATATATATATATATATGAACATAG
1 GTGGAAAATATGATTCAAAGTATATGTGGTATATATATATATATATGAACATAG
55566 GTGGAAAATATGATTCAAAGTATATGTGGTATATATATATATATATGAACATAG
1 GTGGAAAATATGATTCAAAGTATATGTGGTATATATATATATATATGAACATAG
55620 GTGGAAAA
1 GTGGAAAA
55628 GATATGACGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (54 bp):
GTGGAAAATATGATTCAAAGTATATGTGGTATATATATATATATATGAACATAG
Found at i:55916 original size:21 final size:21
Alignment explanation
Indices: 55890--55979 Score: 128
Period size: 21 Copynumber: 4.3 Consensus size: 21
55880 AGGTTCTTGG
*
55890 GGACAATACAGTGGTACTTCA
1 GGACAATACAGTGGTCCTTCA
55911 GGACAATACAGTGGTCCTTCA
1 GGACAATACAGTGGTCCTTCA
* *
55932 AGACAATACAGTGGTCTTTC-
1 GGACAATACAGTGGTCCTTCA
*
55952 GGTACAATACAGTGGTCCTTCT
1 GG-ACAATACAGTGGTCCTTCA
55974 GGACAA
1 GGACAA
55980 ATTTCGTATG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
20 1 0.02
21 59 0.95
22 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (21 bp):
GGACAATACAGTGGTCCTTCA
Found at i:61428 original size:177 final size:177
Alignment explanation
Indices: 61125--61478 Score: 663
Period size: 177 Copynumber: 2.0 Consensus size: 177
61115 AGTTACTATG
61125 GTAAGAAGTGACTCCTAAAGTGTTATATGATTCTTATGAGTGCATTTTAGTTTATAGGATTATAA
1 GTAAGAAGTGACTCCTAAAGTGTTATATGATTCTTATGAGTGCATTTTAGTTTATAGGATTATAA
*
61190 GGAATTGGACTTGTGATAAGTCTATTTCCAATAGTTATAGTGTATAAAGTATTGCTTATAAGGAC
66 GGAATTGGACTTGTGATAAGTCTATTTCCAATAGTTATAGTGTATAAAGTATTGATTATAAGGAC
61255 GTGAATGACATGAAATGTATGTATACTTGATTATATGAACTGATATA
131 GTGAATGACATGAAATGTATGTATACTTGATTATATGAACTGATATA
61302 GTAAGAAGTGACTCCTAAAGTGTTATATGATTCTTATGAGTGCATTTTAGTTTATAGGATTATAA
1 GTAAGAAGTGACTCCTAAAGTGTTATATGATTCTTATGAGTGCATTTTAGTTTATAGGATTATAA
* * *
61367 GGAATTGGACTTGTGATATGTCTATTTCCAATAGTTATAGTGTATAGAGTATTGATTATAAGGAT
66 GGAATTGGACTTGTGATAAGTCTATTTCCAATAGTTATAGTGTATAAAGTATTGATTATAAGGAC
*
61432 GTGAATTACATGAAATGTATGTATACTTGATTATATGAACTGATATA
131 GTGAATGACATGAAATGTATGTATACTTGATTATATGAACTGATATA
61479 TGCTTATATG
Statistics
Matches: 172, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
177 172 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (177 bp):
GTAAGAAGTGACTCCTAAAGTGTTATATGATTCTTATGAGTGCATTTTAGTTTATAGGATTATAA
GGAATTGGACTTGTGATAAGTCTATTTCCAATAGTTATAGTGTATAAAGTATTGATTATAAGGAC
GTGAATGACATGAAATGTATGTATACTTGATTATATGAACTGATATA
Found at i:61597 original size:2 final size:2
Alignment explanation
Indices: 61590--61616 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61580 GTATATGTGG
61590 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 T
61617 GAACATAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61918 original size:21 final size:21
Alignment explanation
Indices: 61886--61963 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
61876 GGGTTTCATA
*
61886 GGTCCTTCGGGACAATACAGT
1 GGTCATTCGGGACAATACAGT
* *
61907 GGTCAGTT-GGGATAATATAGT
1 GGTCA-TTCGGGACAATACAGT
*
61928 GGTCATTCGGGACAATACAAT
1 GGTCATTCGGGACAATACAGT
61949 GGTCATTCGGGACAA
1 GGTCATTCGGGACAA
61964 ATTTCATATG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.04
21 45 0.92
22 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (21 bp):
GGTCATTCGGGACAATACAGT
Found at i:65845 original size:21 final size:21
Alignment explanation
Indices: 65816--65858 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
65806 AAAAAAGGAA
*
65816 CAAGCACTGGACACACTTCAT
1 CAAGCACTGGACACACCTCAT
*
65837 CAAGTACTGGACACACCTCAT
1 CAAGCACTGGACACACCTCAT
65858 C
1 C
65859 CTCACAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.35, G:0.14, T:0.19
Consensus pattern (21 bp):
CAAGCACTGGACACACCTCAT
Found at i:67410 original size:10 final size:10
Alignment explanation
Indices: 67394--67443 Score: 73
Period size: 10 Copynumber: 4.8 Consensus size: 10
67384 TTGCATGTAG
67394 CTTTTTTTCTT
1 CTTTTTTTC-T
*
67405 TTTTTTTTCT
1 CTTTTTTTCT
67415 CTTTTTTTTCT
1 C-TTTTTTTCT
67426 CTTTTTTTCT
1 CTTTTTTTCT
67436 CTTTTTTT
1 CTTTTTTT
67444 GGGTTCGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
10 18 0.50
11 18 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
CTTTTTTTCT
Found at i:67411 original size:11 final size:11
Alignment explanation
Indices: 67395--67443 Score: 71
Period size: 11 Copynumber: 4.4 Consensus size: 11
67385 TGCATGTAGC
67395 TTTTTTTCTTT
1 TTTTTTTCTTT
*
67406 TTTTTTTCTCT
1 TTTTTTTCTTT
67417 TTTTTTTCTCTT
1 TTTTTTTCT-TT
*
67429 TTTTTCTCTTT
1 TTTTTTTCTTT
67440 TTTT
1 TTTT
67444 GGGTTCGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
11 25 0.74
12 9 0.26
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:67418 original size:21 final size:21
Alignment explanation
Indices: 67395--67443 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
67385 TGCATGTAGC
*
67395 TTTTTTTCTTTTTTTTTTCTCT
1 TTTTTTTC-TCTTTTTTTCTCT
67417 TTTTTTTCTCTTTTTTTCTCT
1 TTTTTTTCTCTTTTTTTCTCT
67438 TTTTTT
1 TTTTTT
67444 GGGTTCGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTTTTCTCTTTTTTTCTCT
Found at i:67970 original size:3 final size:3
Alignment explanation
Indices: 67962--68000 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
67952 TTTAGCCCTT
67962 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TT
68001 TATTTTTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:68290 original size:10 final size:9
Alignment explanation
Indices: 68271--68323 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
68261 CTTATTTTTA
68271 TTTTTTATT
1 TTTTTTATT
68280 TTTTCTTATT
1 TTTT-TTATT
68290 TTGTTTTATT
1 TT-TTTTATT
* *
68300 TGTTTTGTT
1 TTTTTTATT
68309 TTTTTT-TT
1 TTTTTTATT
68317 TTATTTT
1 TT-TTTT
68324 TCCTTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
8 4 0.11
9 19 0.50
10 13 0.34
11 2 0.05
ACGTcount: A:0.08, C:0.02, G:0.06, T:0.85
Consensus pattern (9 bp):
TTTTTTATT
Found at i:68324 original size:10 final size:10
Alignment explanation
Indices: 68271--68324 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
68261 CTTATTTTTA
68271 TTTTTTATTT
1 TTTTTTATTT
*
68281 TTTCTTATTT
1 TTTTTTATTT
*
68291 TGTTTTATTT
1 TTTTTTATTT
*
68301 GTTTTGTTTTTT
1 -TTTT-TTATTT
68313 TTTTTTATTT
1 TTTTTTATTT
68323 TT
1 TT
68325 CCTTTTTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 24 0.67
11 7 0.19
12 5 0.14
ACGTcount: A:0.07, C:0.02, G:0.06, T:0.85
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:68330 original size:14 final size:13
Alignment explanation
Indices: 68262--68332 Score: 54
Period size: 14 Copynumber: 5.2 Consensus size: 13
68252 GTTTTATTCC
*
68262 TTATTTTTATTTT
1 TTATTTTTCTTTT
68275 TTATTTTTTCTTATT
1 TTA-TTTTTCTT-TT
*
68290 TTGTTTTAT-TTGTT
1 TTATTTT-TCTT-TT
* *
68304 TTGTTTTTTTTTT
1 TTATTTTTCTTTT
68317 TTATTTTTCCTTTT
1 TTATTTTT-CTTTT
68331 TT
1 TT
68333 TGAGATTAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
13 13 0.27
14 30 0.62
15 5 0.10
ACGTcount: A:0.08, C:0.04, G:0.04, T:0.83
Consensus pattern (13 bp):
TTATTTTTCTTTT
Done.