Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000312.1 Hibiscus syriacus cultivar Beakdansim tig00000588_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: 40113
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:970 original size:23 final size:22
Alignment explanation
Indices: 926--970 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
916 TTTTATCTTT
*
926 TTAAAAATACTTTTAAATTAAA
1 TTAAAAATACTTTTAAACTAAA
* *
948 TTAAATAATATTTTTAACCTAAA
1 TTAAA-AATACTTTTAAACTAAA
971 ATGTATAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAAATACTTTTAAACTAAA
Found at i:1508 original size:20 final size:20
Alignment explanation
Indices: 1483--1542 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
1473 TAATTACTAA
*
1483 ATATTTAA-AATATATTTATT
1 ATATTTAATAATATA-ATATT
1503 ATATTTCTAATAATATAATATT
1 ATA-TT-TAATAATATAATATT
* *
1525 ATATTTTATATTATAATA
1 ATATTTAATAATATAATA
1543 AAATAATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.41
21 4 0.12
22 10 0.29
23 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTTAATAATATAATATT
Found at i:1527 original size:22 final size:20
Alignment explanation
Indices: 1499--1542 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1489 AAAATATATT
1499 TATTATATTTCTAATAATATAA
1 TATTATATTT-T-ATAATATAA
*
1521 TATTATATTTTATATTATAA
1 TATTATATTTTATAATATAA
1541 TA
1 TA
1543 AAATAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
22 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTATATTTTATAATATAA
Found at i:1541 original size:28 final size:28
Alignment explanation
Indices: 1501--1603 Score: 92
Period size: 23 Copynumber: 3.8 Consensus size: 28
1491 AATATATTTA
*
1501 TTATATTTCTAATAATATAATATTATATT
1 TTATA-TTATAATAATATAATATTATATT
* *
1530 TTATATTATAATAAAAT-A-ATCA-A--
1 TTATATTATAATAATATAATATTATATT
1553 TTATATTATAATAATATAAGATATTATATT
1 TTATATTATAATAATAT-A-ATATTATATT
*
1583 TTATTTTTATAAT-ATATAATA
1 TTA-TATTATAATAATATAATA
1604 AATTATAATA
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
23 16 0.27
25 1 0.02
26 4 0.07
27 4 0.07
28 14 0.23
29 6 0.10
30 7 0.12
31 8 0.13
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (28 bp):
TTATATTATAATAATATAATATTATATT
Found at i:1861 original size:19 final size:20
Alignment explanation
Indices: 1837--1880 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1827 AATATTTTTA
*
1837 TTAATAAATTATAAAATA-T
1 TTAATAAATAATAAAATATT
*
1856 TTAAT-AATAATAAATTATT
1 TTAATAAATAATAAAATATT
1875 TTAATA
1 TTAATA
1881 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATAAATAATAAAATATT
Found at i:2735 original size:29 final size:28
Alignment explanation
Indices: 2670--2851 Score: 129
Period size: 29 Copynumber: 6.4 Consensus size: 28
2660 ACTTTCAAAG
* * *
2670 ATATATTTTATT-TTGTCTTAACTTATAA
1 ATATATTTTATTCTTATTTTAA-TTAAAA
* *
2698 ATCTATTTTATTCTAATTTTAATATAAAA
1 ATATATTTTATTCTTATTTTAAT-TAAAA
* * * *
2727 ATATTTTTTATT-ATA-TTCACTTAAAA
1 ATATATTTTATTCTTATTTTAATTAAAA
* * *
2753 CTATATTTTATTCTTATTTAAAGTTGAAA
1 ATATATTTTATTCTTATTTTAA-TTAAAA
* * *
2782 ATATATTTTATT-TTGTCTTAACTTATAA
1 ATATATTTTATTCTTATTTTAA-TTAAAA
*
2810 ATCTATTTTATTCTTATTTTAATATAAAA
1 ATATATTTTATTCTTATTTTAAT-TAAAA
*
2839 ATATTTTATTATT
1 ATATATT-TTATT
2852 ATCTTCACTA
Statistics
Matches: 116, Mismatches: 30, Indels: 14
0.73 0.19 0.09
Matches are distributed among these distances:
26 15 0.13
27 6 0.05
28 38 0.33
29 52 0.45
30 5 0.04
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (28 bp):
ATATATTTTATTCTTATTTTAATTAAAA
Found at i:2749 original size:55 final size:56
Alignment explanation
Indices: 2672--2874 Score: 236
Period size: 57 Copynumber: 3.6 Consensus size: 56
2662 TTTCAAAGAT
* * * *
2672 ATATTTTATT-TTGTCTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAA
1 ATATTTTATTATTATCTTCACTTATAAATATATTTTATTCTTATTTTAATATAAAA
* *
2727 ATATTTT-TTATTATATTCACTTA-AAACTATATTTTATTCTTATTTAAAGT-TGAAAA
1 ATATTTTATTATTATCTTCACTTATAAA-TATATTTTATTCTTATTTTAA-TAT-AAAA
* * *
2783 TATATTTTATT-TTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATATAAAA
1 -ATATTTTATTATTATCTTCACTTATAAATATATTTTATTCTTATTTTAATATAAAA
*
2839 ATATTTTATTATTATCTTCACTAAATAAATATATTT
1 ATATTTTATTATTATCTTCACT-TATAAATATATTT
2875 ATAAGTTAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 18
0.79 0.10 0.12
Matches are distributed among these distances:
54 5 0.04
55 46 0.37
56 19 0.15
57 48 0.39
58 5 0.04
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.54
Consensus pattern (56 bp):
ATATTTTATTATTATCTTCACTTATAAATATATTTTATTCTTATTTTAATATAAAA
Found at i:2795 original size:112 final size:114
Alignment explanation
Indices: 2670--2874 Score: 360
Period size: 112 Copynumber: 1.8 Consensus size: 114
2660 ACTTTCAAAG
2670 ATATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAATATTTT-
1 ATATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAATATTTTA
* *
2734 TTATTATATTCACTTAA-AACTATATTTTATTCTTATTTAAAGTTGAAA
66 TTATTATATTCACTAAATAAATATATTTTATTCTTATTTAAAGTTGAAA
*
2782 ATATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATATAAAAATATTTTA
1 ATATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAATATTTTA
*
2847 TTATTATCTTCACTAAATAAATATATTT
66 TTATTATATTCACTAAATAAATATATTT
2875 ATAAGTTAAA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
112 63 0.72
113 15 0.17
114 9 0.10
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (114 bp):
ATATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAATATTTTA
TTATTATATTCACTAAATAAATATATTTTATTCTTATTTAAAGTTGAAA
Found at i:2818 original size:57 final size:55
Alignment explanation
Indices: 2672--2848 Score: 234
Period size: 55 Copynumber: 3.2 Consensus size: 55
2662 TTTCAAAGAT
*
2672 ATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAA
1 ATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATATAAAA
* * * * *
2727 ATATTTT-TTATTATATTCACTTA-AAACTATATTTTATTCTTATTTAAAGT-TGAAAA
1 ATATTTTATT-TTGTCTTAACTTATAAA-TCTATTTTATTCTTATTTTAA-TAT-AAAA
2783 TATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATATAAAA
1 -ATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATATAAAA
2839 ATATTTTATT
1 ATATTTTATT
2849 ATTATCTTCA
Statistics
Matches: 103, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
54 5 0.05
55 46 0.45
56 10 0.10
57 37 0.36
58 5 0.05
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (55 bp):
ATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATATAAAA
Found at i:2898 original size:112 final size:110
Alignment explanation
Indices: 2670--2897 Score: 325
Period size: 112 Copynumber: 2.1 Consensus size: 110
2660 ACTTTCAAAG
2670 ATATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAATATTTTT
1 ATATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAATATTTTT
* * * * * **
2735 TATTATATTCACTTAAAACTATATTTTATTCTTATTTAAAGTTGAAA
66 TATTATATTCACTAAAAAATATATTTTA-T-TAAGTTAAAATAAAAA
*
2782 ATATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATATAAAAATATTTTA
1 ATATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAATATTTT-
*
2847 TTATTATCTTCACTAAATAAATATA-TTTA-TAAGTTAAAATAAAAA
65 TTATTATATTCACTAAA-AAATATATTTTATTAAGTTAAAATAAAAA
2892 ATATAT
1 ATATAT
2898 ACTTTTAAGA
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
110 17 0.16
112 63 0.60
113 19 0.18
114 6 0.06
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (110 bp):
ATATATTTTATTTTGTCTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAATATTTTT
TATTATATTCACTAAAAAATATATTTTATTAAGTTAAAATAAAAA
Found at i:3202 original size:47 final size:47
Alignment explanation
Indices: 3114--3206 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
3104 ATTCGCCAAT
* * *
3114 TTCGCAACTCAATTACCGATATAGGTAACATGGTTAAAAAAATCCGG
1 TTCGCAACTCAATTACCGATATAAGTAACATCGATAAAAAAATCCGG
*
3161 TTCGCAACTCAATTACCGATATAAGTAAACA-CGATAGAAAAATCCG
1 TTCGCAACTCAATTACCGATATAAGT-AACATCGATAAAAAAATCCG
3207 ATAAAAAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 37 0.90
48 4 0.10
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (47 bp):
TTCGCAACTCAATTACCGATATAAGTAACATCGATAAAAAAATCCGG
Found at i:3505 original size:20 final size:21
Alignment explanation
Indices: 3480--3520 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3470 ACGAATTTGC
3480 CAAATTCG-CAATTCAGTTTT
1 CAAATTCGTCAATTCAGTTTT
* *
3500 CAAATTGGTGAATTCAGTTTT
1 CAAATTCGTCAATTCAGTTTT
3521 TTTACCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (21 bp):
CAAATTCGTCAATTCAGTTTT
Found at i:4506 original size:42 final size:42
Alignment explanation
Indices: 4440--4520 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
4430 CTGAAATTCC
* * * *
4440 GTGTTTGTTTCATGTAATTTGTTTTCTGAAAAATGTTTTTAT
1 GTGTTTGTTTCACGGAATTCGTTTTCCGAAAAATGTTTTTAT
*
4482 GTGTTTGTTTCACGGAATTCGTTTTCCGGAAAATGTTTT
1 GTGTTTGTTTCACGGAATTCGTTTTCCGAAAAATGTTTT
4521 CCAGTGTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.52
Consensus pattern (42 bp):
GTGTTTGTTTCACGGAATTCGTTTTCCGAAAAATGTTTTTAT
Found at i:4528 original size:42 final size:42
Alignment explanation
Indices: 4436--4530 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
4426 TTCCCTGAAA
* * * *
4436 TTCC-GTGTTTGTTTCATGTAATTTGTTTTCTGAAAAATGTT
1 TTCCAGTGTTTGTTTCACGGAATTCGTTTTCCGAAAAATGTT
* *
4477 TT-TATGTGTTTGTTTCACGGAATTCGTTTTCCGGAAAATGTT
1 TTCCA-GTGTTTGTTTCACGGAATTCGTTTTCCGAAAAATGTT
4519 TTCCAGTGTTTG
1 TTCCAGTGTTTG
4531 GTTTGAGGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 2 0.05
42 41 0.93
43 1 0.02
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.51
Consensus pattern (42 bp):
TTCCAGTGTTTGTTTCACGGAATTCGTTTTCCGAAAAATGTT
Found at i:4793 original size:27 final size:27
Alignment explanation
Indices: 4753--4809 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
4743 AAATATTTAA
*
4753 AATATATTTATTAATA-TCTAATAATAT
1 AATATATTTATTAATATTATAATAA-AT
4780 AATATTATTT-TTAATATTATAATAAAT
1 AATA-TATTTATTAATATTATAATAAAT
4807 AAT
1 AAT
4810 CAATTATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
AATATATTTATTAATATTATAATAAAT
Found at i:4989 original size:21 final size:21
Alignment explanation
Indices: 4964--5005 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4954 TTTGTAAAAT
*
4964 ATAATATAAT-TACTTTAATAA
1 ATAAT-TAATATAATTTAATAA
4985 ATAATTAATATAATTTAATAA
1 ATAATTAATATAATTTAATAA
5006 TATTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATTAATATAATTTAATAA
Found at i:8174 original size:81 final size:82
Alignment explanation
Indices: 8085--8337 Score: 224
Period size: 83 Copynumber: 3.1 Consensus size: 82
8075 GCGTTTTTGA
8085 ACAAACACCAC-AAAATACTA-TAATTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGA-ATCGT
1 ACAAACACCACTAAAA-ACTAGTAATTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGACA-CGT
*
8147 AATGTAGTGGCATTTTTAT
64 AATGTAGTGGCATTTTAAT
* * * * * * *
8166 ACAAACACCGCTATAAACTAGTATTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTAC
1 ACAAACACCACTAAAAACTAGTAATTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGACACGTAA
* *
8231 TTTTGTGGCATTTTAAT
66 TGTAGTGGCATTTTAAT
* * * * * * * * * * *
8248 ACCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTA
1 A-CAAACACCACTAAAAACTAGTAATTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGACACGTA
* * * *
8313 CTTTTGTGGCGTTTTAAT
65 ATGTAGTGGCATTTTAAT
8331 ACCAAAC
1 A-CAAAC
8338 GCCGCTATAG
Statistics
Matches: 151, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
81 14 0.09
82 55 0.36
83 82 0.54
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (82 bp):
ACAAACACCACTAAAAACTAGTAATTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGACACGTAA
TGTAGTGGCATTTTAAT
Found at i:8213 original size:82 final size:83
Alignment explanation
Indices: 8108--8508 Score: 424
Period size: 82 Copynumber: 4.8 Consensus size: 83
8098 AATACTATAA
* * * * * * *
8108 TTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGAATCGTAATGTAGTGGCATTTTTATACAAACA
1 TTTAGTGGCGTTTTTATACAAACGCCGCTATAGAATCGTACTTTAGTGGCATTTTAATACAAACG
*
8173 CCGCTATAAACTA-GTA-T
66 CCGCTATAGAC-ACGTACT
*
8190 TTTAGTGGCGTTTTTATACAAACGCCGCTATAGACA-CGTACTTTTGTGGCATTTTAATACCAAA
1 TTTAGTGGCGTTTTTATACAAACGCCGCTATAGA-ATCGTACTTTAGTGGCATTTTAATA-CAAA
*
8254 CGCCGCTATAGACTCGTAC-
64 CGCCGCTATAGACACGTACT
* * * *
8273 TTTAGTGGCATTTTTACACAAACGCCGCTATAGACA-CGTACTTTTGTGGCGTTTTAATACCAAA
1 TTTAGTGGCGTTTTTATACAAACGCCGCTATAGA-ATCGTACTTTAGTGGCATTTTAATA-CAAA
8337 CGCCGCTATAGACACGTACT
64 CGCCGCTATAGACACGTACT
* * * * *
8357 TTT-GTGGCGTTTTAATGCCAAACACCGCTATAGATTCGTACTTTAGTGGCGTTTTACAT--AAA
1 TTTAGTGGCGTTTTTAT-ACAAACGCCGCTATAGAATCGTACTTTAGTGGCATTTTA-ATACAAA
* *
8419 CGCCACTATAGACATGTACT
64 CGCCGCTATAGACACGTACT
* * * * *
8439 TTT-GTGGCGTTTTAATACCAAATGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATACCAAT
1 TTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGAATCGTACTTTAGTGGCATTTTAATA-CAAA
8503 CGCCGC
64 CGCCGC
8509 AATTGTCATA
Statistics
Matches: 278, Mismatches: 29, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
81 2 0.01
82 122 0.44
83 108 0.39
84 44 0.16
85 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (83 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTATAGAATCGTACTTTAGTGGCATTTTAATACAAACG
CCGCTATAGACACGTACT
Found at i:8262 original size:42 final size:42
Alignment explanation
Indices: 8127--8508 Score: 433
Period size: 42 Copynumber: 9.2 Consensus size: 42
8117 GTTTGTATAA
* * * * * *
8127 AAACGCCGCTAAAGA-ATCGTAATGTAGTGGCATTTTTATA-C
1 AAACGCCGCTATAGACA-CGTACTTTTGTGGCGTTTTAATACC
* * *
8168 AAACACCGCTATAAACTA-GTA-TTTTAGTGGCGTTTTTATA-C
1 AAACGCCGCTATAGAC-ACGTACTTTT-GTGGCGTTTTAATACC
*
8209 AAACGCCGCTATAGACACGTACTTTTGTGGCATTTTAATACC
1 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
* * *
8251 AAACGCCGCTATAGACTCGTACTTTAGTGGCATTTT--TACAC
1 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATAC-C
8292 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
1 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
*
8334 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATGCC
1 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
* ** *
8376 AAACACCGCTATAGATTCGTACTTTAGTGGCGTTTTACAT---
1 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTA-ATACC
* *
8416 AAACGCCACTATAGACATGTACTTTTGTGGCGTTTTAATACC
1 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
* * *
8458 AAATGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATACC
1 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
*
8500 AATCGCCGC
1 AAACGCCGC
8509 AATTGTCATA
Statistics
Matches: 295, Mismatches: 33, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.01
40 37 0.13
41 92 0.31
42 158 0.54
43 6 0.02
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (42 bp):
AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
Found at i:8279 original size:124 final size:125
Alignment explanation
Indices: 8127--8508 Score: 538
Period size: 124 Copynumber: 3.1 Consensus size: 125
8117 GTTTGTATAA
* * * * * *
8127 AAACGCCGCTAAAGAATCGTAATGTAGTGGCATTTTTATACAAACACCGCTATAAACTA-GTA-T
1 AAACGCCGCTATAGAATCGTACTTTAGTGGCATTTTTACACAAACGCCGCTATAGAC-ACGTACT
* *
8190 TTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGACACGTACTTTTGTGGCATTTTAATACC
65 TTT-GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
*
8251 AAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTT
1 AAACGCCGCTATAGAATCGTACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTT
*
8316 TTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATGCC
66 TTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
* * * * * *
8376 AAACACCGCTATAGATTCGTACTTTAGTGGC-GTTTTACATAAACGCCACTATAGACATGTACTT
1 AAACGCCGCTATAGAATCGTACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTT
* * *
8440 TTGTGGCGTTTTAATACCAAATGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATACC
66 TTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
*
8500 AATCGCCGC
1 AAACGCCGC
8509 AATTGTCATA
Statistics
Matches: 233, Mismatches: 22, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
123 1 0.00
124 158 0.68
125 74 0.32
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (125 bp):
AAACGCCGCTATAGAATCGTACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTT
TTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
Found at i:12536 original size:43 final size:43
Alignment explanation
Indices: 12475--12756 Score: 260
Period size: 43 Copynumber: 6.6 Consensus size: 43
12465 AAGGTAATTA
* * *
12475 GCGGCGTTTGTATCCAAAAACGCCGCTATAAGTCTGACTTTTT
1 GCGGCGTTTGTGTTCAAAAACGCCGCTATAAGTCTGACATTTT
* *
12518 GCGGCGTTTGTGTTCAAAAACGCCGTTATAGGTCTGACATTTT
1 GCGGCGTTTGTGTTCAAAAACGCCGCTATAAGTCTGACATTTT
* * * *
12561 GCAGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTT
1 GCGGCGTTTGTGTTCAAAAACGCCGCTATAAGTCTGACATTTT
* *
12604 GCGGCG-TT-TGTTCTAAAAACGCCAG-TATAGGTCTG-CTCTTTT
1 GCGGCGTTTGTGTTC-AAAAACGCC-GCTATAAGTCTGAC-ATTTT
*
12646 GCGGCGTTTGT-ATCAAGAAACGCCGCTAT-AGATCTGACATTTT
1 GCGGCGTTTGTGTTCAA-AAACGCCGCTATAAG-TCTGACATTTT
* * * *
12689 GCGGCGTTT-TTTTCTAGAAACGCCGCTAT-AGATATCGACCTTTT
1 GCGGCGTTTGTGTTC-AAAAACGCCGCTATAAG-TCT-GACATTTT
*
12733 CCGGCG-TT-TGTTCAAAAAACGCCG
1 GCGGCGTTTGTGTTC-AAAAACGCCG
12757 TAATTGATAT
Statistics
Matches: 205, Mismatches: 22, Indels: 24
0.82 0.09 0.10
Matches are distributed among these distances:
41 5 0.02
42 37 0.18
43 148 0.72
44 15 0.07
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTGTGTTCAAAAACGCCGCTATAAGTCTGACATTTT
Found at i:12718 original size:128 final size:129
Alignment explanation
Indices: 12475--12756 Score: 374
Period size: 128 Copynumber: 2.2 Consensus size: 129
12465 AAGGTAATTA
* *
12475 GCGGCGTTTGTATCCAAAAACGCCGCTATAAGTCTGACTTTTTGCGGCGTTTGTGTTCAAAAACG
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAAGTCTGACTTTTTGCGGCGTTTGTGATCAAAAACG
* * * *
12540 CCGTTATAGGTCTGACATTTTGCAGCGTTTGTGTCCAAAAACGCCGCTATAGGTCT-GACCTTTT
65 CCGCTATAGATCTGACATTTTGCAGCGTTTGTGTCCAAAAACGCCGCTATAGATATCGACCTTTT
* *
12604 GCGGCGTTTGTTCTAAAAACGCCAG-TATAGGTCTG-CTCTTTTGCGGCGTTTGT-ATCAAGAAA
1 GCGGCGTTTGTTCAAAAAACGCC-GCTATAAGTCTGACT-TTTTGCGGCGTTTGTGATCAA-AAA
* * * * *
12666 CGCCGCTATAGATCTGACATTTTGCGGCGTTTTTTTCTAGAAACGCCGCTATAGATATCGACCTT
63 CGCCGCTATAGATCTGACATTTTGCAGCGTTTGTGTCCAAAAACGCCGCTATAGATATCGACCTT
12731 TT
128 TT
*
12733 CCGGCGTTTGTTCAAAAAACGCCG
1 GCGGCGTTTGTTCAAAAAACGCCG
12757 TAATTGATAT
Statistics
Matches: 135, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
127 6 0.04
128 88 0.65
129 41 0.30
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (129 bp):
GCGGCGTTTGTTCAAAAAACGCCGCTATAAGTCTGACTTTTTGCGGCGTTTGTGATCAAAAACGC
CGCTATAGATCTGACATTTTGCAGCGTTTGTGTCCAAAAACGCCGCTATAGATATCGACCTTTT
Found at i:18566 original size:4 final size:4
Alignment explanation
Indices: 18557--18582 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
18547 ATTGATTCAA
18557 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
18583 TATACTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:19771 original size:43 final size:42
Alignment explanation
Indices: 19706--20088 Score: 333
Period size: 43 Copynumber: 8.9 Consensus size: 42
19696 CGTTAAAAAT
* * *
19706 TAGGTATTGATATTTAGCGGCGTTTGTGTGAAAAACGTCGCAA
1 TAGGTGTTGATATTTAGCGGCGTTTGT-TTAAAAACGCCGCAA
*
19749 TAGGTGTTGATATTTAGTGGCGTTTGTTATAAAAACGCCGCAA
1 TAGGTGTTGATATTTAGCGGCGTTTGTT-TAAAAACGCCGCAA
* * *
19792 TAGGTGTTAATATTTAGCGGCGTTTGTCATAAAAATGCCGCAA
1 TAGGTGTTGATATTTAGCGGCGTTTGT-TTAAAAACGCCGCAA
* * * *
19835 TATGTGTTAATATTTAGCAGTGTTT-TTTAACAAACGCCG-ACA
1 TAGGTGTTGATATTTAGCGGCGTTTGTTTAA-AAACGCCGCA-A
* * *
19877 TAGGTGTTGATATTTAGTGGCATTTTTTATAAAAACGCCGCAA
1 TAGGTGTTGATATTTAGCGGCGTTTGTT-TAAAAACGCCGCAA
* * * *
19920 AAGGTGTTGATATTTAGCGACGTTTGTCATAAAAACGCCGTAA
1 TAGGTGTTGATATTTAGCGGCGTTTGT-TTAAAAACGCCGCAA
* * * * *
19963 TAGGTGTTAATATTTAGCAGCGTTT-CTCAGACAAACGCCGTAA
1 TAGGTGTTGATATTTAGCGGCGTTTGTTTA-A-AAACGCCGCAA
* * * * * *
20006 TATGT-TATGATGTTTAGCGGCATTTTTTGTTAAAACGCCGCAG
1 TAGGTGT-TGATATTTAGCGGCGTTTGTT-TAAAAACGCCGCAA
* * * *
20049 TAGGTGTTGATGTTTTGCGGCGTTTCTGCTAAAAACGCCG
1 TAGGTGTTGATATTTAGCGGCGTTTGT-TTAAAAACGCCG
20089 GTACATGTCT
Statistics
Matches: 276, Mismatches: 49, Indels: 30
0.78 0.14 0.08
Matches are distributed among these distances:
41 5 0.02
42 31 0.11
43 233 0.84
44 7 0.03
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (42 bp):
TAGGTGTTGATATTTAGCGGCGTTTGTTTAAAAACGCCGCAA
Found at i:19884 original size:128 final size:129
Alignment explanation
Indices: 19706--20088 Score: 450
Period size: 128 Copynumber: 3.0 Consensus size: 129
19696 CGTTAAAAAT
* * * * ** * * * *
19706 TAGGTATTGATATTTAGCGGCGTTTGTGTGAAAAACGTCGCAATAGGTGTTGATATTTAGTGGCG
1 TAGGTGTTAATATTTAGCAGCGTTTCTCAGACAAACGCCGTAATAGGTGTTGATATTTAGTGGCA
* * *
19771 TTTGTTATAAAAACGCCGCAATAGGTGTTAATATTTAGCGGCGTTTGTCATAAAAATGCCGCAA
66 TTTTTTATAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACGCCGCAA
* * * *
19835 TATGTGTTAATATTTAGCAGTGTTTTTTA-ACAAACGCCG-ACATAGGTGTTGATATTTAGTGGC
1 TAGGTGTTAATATTTAGCAGCGTTTCTCAGACAAACGCCGTA-ATAGGTGTTGATATTTAGTGGC
* * *
19898 ATTTTTTATAAAAACGCCGCAAAAGGTGTTGATATTTAGCGACGTTTGTCATAAAAACGCCGTAA
65 ATTTTTTATAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACGCCGCAA
* * *
19963 TAGGTGTTAATATTTAGCAGCGTTTCTCAGACAAACGCCGTAATATGT-TATGATGTTTAGCGGC
1 TAGGTGTTAATATTTAGCAGCGTTTCTCAGACAAACGCCGTAATAGGTGT-TGATATTTAGTGGC
* * * * * *
20027 ATTTTTTGTTAAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTCTGC-TAAAAACGCCG
65 ATTTTTTATAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT-CATAAAAACGCCG
20089 GTACATGTCT
Statistics
Matches: 217, Mismatches: 32, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
127 1 0.00
128 114 0.53
129 100 0.46
130 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (129 bp):
TAGGTGTTAATATTTAGCAGCGTTTCTCAGACAAACGCCGTAATAGGTGTTGATATTTAGTGGCA
TTTTTTATAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACGCCGCAA
Found at i:20566 original size:21 final size:21
Alignment explanation
Indices: 20517--20569 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
20507 GCAACTTCTT
20517 TCTCTGCTTCCGCTGCTGCTC
1 TCTCTGCTTCCGCTGCTGCTC
* *
20538 TGGT-TGCTTCTGCTGCTGCTC
1 T-CTCTGCTTCCGCTGCTGCTC
20559 TCTCTGCTTCC
1 TCTCTGCTTCC
20570 CTTGCTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.00, C:0.38, G:0.21, T:0.42
Consensus pattern (21 bp):
TCTCTGCTTCCGCTGCTGCTC
Found at i:28707 original size:42 final size:41
Alignment explanation
Indices: 28661--28988 Score: 338
Period size: 41 Copynumber: 7.9 Consensus size: 41
28651 GGCATTTATC
* * *
28661 TAAAAACACCACTAAGGGTACGAGTCTATAGCAGCGTTTGTA
1 TAAAAACGCCACTAA-AGTACGAGTCTATAGCGGCGTTTGTA
* * * *
28703 TAAAAACGCCACTAAAGTACTAGTCTATAGCGACATTTATA
1 TAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA
** *
28744 TAAAAACGCTTCTAAAGTACGAGTCTTTAGCGGCGTTT-TCA
1 TAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT-A
* * *
28785 TTCAAAACGCCACTAAAGTACGAGTTTATAGCAGCGTTTAG-A
1 -TAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-GTA
* * *
28827 TTCAAAACGCCACTAAAGTATGAGTATATAGCGGCGTTTGTA
1 -TAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA
* * * * *
28869 TAGAAACACCACTAAAGTACTAGTATATAGCGGCATTTGTA
1 TAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA
* * * *
28910 TAAAAATGCCACTAACGTACTATTCTATAGCGGCGTTTGTA
1 TAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA
* *
28951 TAAAAACGCCACTAAAGTACGTA-TCTTTAGCGCCGTTT
1 TAAAAACGCCACTAAAGTACG-AGTCTATAGCGGCGTTT
28989 CTAGATACAA
Statistics
Matches: 240, Mismatches: 40, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
40 1 0.00
41 154 0.64
42 85 0.35
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (41 bp):
TAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA
Found at i:28883 original size:166 final size:166
Alignment explanation
Indices: 28663--28971 Score: 424
Period size: 166 Copynumber: 1.9 Consensus size: 166
28653 CATTTATCTA
* * * *
28663 AAAACACCACTAAGGGTACGAGTCTATAGCAGCGTTTGTATAAAAACGCCACTAAAGTACTAGTC
1 AAAACACCACTAAGAGTACGAGTATATAGCAGCGTTTGTATAAAAACACCACTAAAGTACTAGTA
** * *
28728 TATAGCGACATTTATATAAAAACGCTTCTAAAGTACGAGTCTTTAGCGGCGTTT-TCATTCAAAA
66 TATAGCGACATTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT-A-TAAAAA
28792 CGCCACTAAAGTACGAGTTTATAGCAGCGTTTAGATTC
129 CGCCACTAAAGTACGAGTTTATAGCAGCGTTTAGATTC
* * * *
28830 AAAACGCCACTAA-AGTATGAGTATATAGCGGCGTTTGTATAGAAACACCACTAAAGTACTAGTA
1 AAAACACCACTAAGAGTACGAGTATATAGCAGCGTTTGTATAAAAACACCACTAAAGTACTAGTA
* * * * * *
28894 TATAGCGGCATTTGTATAAAAATGCCACTAACGTACTATTCTATAGCGGCGTTTGTATAAAAACG
66 TATAGCGACATTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACG
28959 CCACTAAAGTACG
131 CCACTAAAGTACG
28972 TATCTTTAGC
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
165 20 0.16
166 90 0.73
167 13 0.11
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (166 bp):
AAAACACCACTAAGAGTACGAGTATATAGCAGCGTTTGTATAAAAACACCACTAAAGTACTAGTA
TATAGCGACATTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACG
CCACTAAAGTACGAGTTTATAGCAGCGTTTAGATTC
Found at i:30310 original size:41 final size:42
Alignment explanation
Indices: 30244--30417 Score: 203
Period size: 41 Copynumber: 4.2 Consensus size: 42
30234 TAACATTTTT
* *
30244 CGGCGTTTATACAAAAAAACGCCACTATTGATT-ACACTATTG
1 CGGCGTTTAT-TAAAAAAATGCCACTATTGATTAACACTATTG
* * *
30286 TGGCGTTTGTTAAAAAAATGCCACTATTGATTAAAACTATTG
1 CGGCGTTTATTAAAAAAATGCCACTATTGATTAACACTATTG
* *
30328 CGGCGTTTTTCTAAAAACA--CCACTATTGATTAACACTATTG
1 CGGCGTTTAT-TAAAAAAATGCCACTATTGATTAACACTATTG
* * * *
30369 CGGCGTTTATT-TAAAAATGCCATTATTTATTATCACTATTG
1 CGGCGTTTATTAAAAAAATGCCACTATTGATTAACACTATTG
30410 CGGCGTTT
1 CGGCGTTT
30418 TAAGAATAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
39 4 0.04
40 1 0.01
41 77 0.68
42 24 0.21
43 7 0.06
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (42 bp):
CGGCGTTTATTAAAAAAATGCCACTATTGATTAACACTATTG
Found at i:30358 original size:82 final size:82
Alignment explanation
Indices: 30258--30418 Score: 234
Period size: 82 Copynumber: 2.0 Consensus size: 82
30248 GTTTATACAA
* * *
30258 AAAAACGCCACTATTGATT-ACACTATTGTGGCGTTTGTTAAAAAAATGCCACTATTGATTAAAA
1 AAAAACACCACTATTGATTAACACTATTGCGGCGTTTATT-AAAAAATGCCACTATTGATTAAAA
30322 CTATTGCGGCGTTTTTCT
65 CTATTGCGGCGTTTTTCT
* * * **
30340 AAAAACACCACTATTGATTAACACTATTGCGGCGTTTATTTAAAAATGCCATTATTTATTATCAC
1 AAAAACACCACTATTGATTAACACTATTGCGGCGTTTATTAAAAAATGCCACTATTGATTAAAAC
30405 TATTGCGGCGTTTT
66 TATTGCGGCGTTTT
30419 AAGAATAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
82 52 0.74
83 18 0.26
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (82 bp):
AAAAACACCACTATTGATTAACACTATTGCGGCGTTTATTAAAAAATGCCACTATTGATTAAAAC
TATTGCGGCGTTTTTCT
Found at i:30490 original size:42 final size:41
Alignment explanation
Indices: 30444--30602 Score: 107
Period size: 42 Copynumber: 3.9 Consensus size: 41
30434 TATATCTGTA
30444 ATCTATTGCGACGTTTGTGGTATAAACGCCACTAATTTACC
1 ATCTATTGCGACGTTTGTGGTATAAACGCCACTAATTTACC
* *
30485 GATCTATTGC-AGCGTTT-TAGCTA-AAACGCCACTATATGTTAAACT
1 -ATCTATTGCGA-CGTTTGT-GGTATAAACGCCACTA-AT-TT--ACC
* *
30530 AT-TATT--G-CGTTTGTGGTATAAACTCCGCTAATTTACC
1 ATCTATTGCGACGTTTGTGGTATAAACGCCACTAATTTACC
* * * * * *
30567 ACCCTATTACGACATTTTTTGTAAAAACGCCACTAA
1 A-TCTATTGCGACGTTTGTGGTATAAACGCCACTAA
30603 ATGTTAAATA
Statistics
Matches: 90, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
37 3 0.03
39 6 0.07
40 10 0.11
41 24 0.27
42 37 0.41
43 6 0.07
44 2 0.02
45 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (41 bp):
ATCTATTGCGACGTTTGTGGTATAAACGCCACTAATTTACC
Found at i:30592 original size:82 final size:81
Alignment explanation
Indices: 30455--30618 Score: 192
Period size: 82 Copynumber: 2.0 Consensus size: 81
30445 TCTATTGCGA
* *
30455 CGTTTGTGGTATAAACGCCACTAATTTACCGATCTATTGCAGCGTTTTAGCT-AAAACGCCACTA
1 CGTTTGTGGTATAAACGCCACTAATTTACCGACCTATTACAGCGTTTTAGCTAAAAACGCCACTA
*
30519 TATGTTAAACTATTATTG
66 AATGTTAAA-TA-TATTG
* * * *
30537 CGTTTGTGGTATAAACTCCGCTAATTTACC-ACCCTATTAC-GACATTTTTTG-TAAAAACGCCA
1 CGTTTGTGGTATAAACGCCACTAATTTACCGA-CCTATTACAG-C-GTTTTAGCTAAAAACGCCA
30599 CTAAATGTTAAATATATTG
63 CTAAATGTTAAATATATTG
30618 C
1 C
30619 AACGTTTTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
81 8 0.11
82 38 0.54
83 25 0.35
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (81 bp):
CGTTTGTGGTATAAACGCCACTAATTTACCGACCTATTACAGCGTTTTAGCTAAAAACGCCACTA
AATGTTAAATATATTG
Found at i:30802 original size:8 final size:8
Alignment explanation
Indices: 30789--32813 Score: 3134
Period size: 8 Copynumber: 254.4 Consensus size: 8
30779 TAAACACATA
30789 TATGTATG
1 TATGTATG
30797 TATGTATG
1 TATGTATG
30805 TATGTATG
1 TATGTATG
*
30813 CATGTATG
1 TATGTATG
30821 TATGTATG
1 TATGTATG
*
30829 CATGTATG
1 TATGTATG
*
30837 CATGTATG
1 TATGTATG
*
30845 CATGTATG
1 TATGTATG
*
30853 CATGTATG
1 TATGTATG
*
30861 CATGTATG
1 TATGTATG
*
30869 CATGTATG
1 TATGTATG
*
30877 CATGTATG
1 TATGTATG
*
30885 CATGTATG
1 TATGTATG
*
30893 CATGTATG
1 TATGTATG
*
30901 CATGTATG
1 TATGTATG
*
30909 CATGTATG
1 TATGTATG
*
30917 CATGTATG
1 TATGTATG
*
30925 CATGTATG
1 TATGTATG
*
30933 CATGTATG
1 TATGTATG
*
30941 CATGTATG
1 TATGTATG
*
30949 CATGTATG
1 TATGTATG
*
30957 CATGTATG
1 TATGTATG
*
30965 CATGTATG
1 TATGTATG
*
30973 CATGTATG
1 TATGTATG
*
30981 CATGTATG
1 TATGTATG
*
30989 CATGTATG
1 TATGTATG
*
30997 CATGTATG
1 TATGTATG
*
31005 CATGTATG
1 TATGTATG
*
31013 CATGTATG
1 TATGTATG
*
31021 CATGTATG
1 TATGTATG
*
31029 CATGTATG
1 TATGTATG
31037 TATGTATG
1 TATGTATG
31045 TATGTATG
1 TATGTATG
*
31053 TATGCATG
1 TATGTATG
*
31061 TATGCATG
1 TATGTATG
*
31069 TATGCATG
1 TATGTATG
*
31077 TATGCATG
1 TATGTATG
*
31085 TATGCATG
1 TATGTATG
*
31093 TATGCATG
1 TATGTATG
*
31101 TATGCATG
1 TATGTATG
31109 TATGTATG
1 TATGTATG
*
31117 TATGCATG
1 TATGTATG
*
31125 TATGCATG
1 TATGTATG
*
31133 TATGCATG
1 TATGTATG
*
31141 TATGCATG
1 TATGTATG
31149 TATGTATG
1 TATGTATG
31157 TATGTATG
1 TATGTATG
*
31165 CATGTATG
1 TATGTATG
*
31173 CATGTATG
1 TATGTATG
* *
31181 CATGCATG
1 TATGTATG
*
31189 CATGTATG
1 TATGTATG
* *
31197 CATGCATG
1 TATGTATG
*
31205 CATGTATG
1 TATGTATG
*
31213 TATGCATG
1 TATGTATG
*
31221 TATGCATG
1 TATGTATG
*
31229 TATGCATG
1 TATGTATG
* *
31237 TATGCATA
1 TATGTATG
* * *
31245 CATGCATA
1 TATGTATG
* *
31253 CATGCATG
1 TATGTATG
*
31261 TATGCATG
1 TATGTATG
* *
31269 TGTGCATG
1 TATGTATG
*
31277 TATGCATG
1 TATGTATG
* *
31285 TGTGCATG
1 TATGTATG
*
31293 TATGTGTG
1 TATGTATG
* * *
31301 TGTGTGTA
1 TATGTATG
* *
31309 TGTGTGTG
1 TATGTATG
* *
31317 TGTGTGTG
1 TATGTATG
* *
31325 TGTGTGTG
1 TATGTATG
* *
31333 TGTGTGTG
1 TATGTATG
* *
31341 TGTGTGTG
1 TATGTATG
* *
31349 TGTGTGTG
1 TATGTATG
*
31357 TGTGTATG
1 TATGTATG
* *
31365 TGTGTGTG
1 TATGTATG
* *
31373 TGTGTGTG
1 TATGTATG
* *
31381 TGTGTGTG
1 TATGTATG
*
31389 TATGTGTG
1 TATGTATG
* *
31397 TGTGTGTG
1 TATGTATG
*
31405 TGTGTATG
1 TATGTATG
31413 TATGTATG
1 TATGTATG
31421 TA--TATG
1 TATGTATG
31427 TATGTATG
1 TATGTATG
31435 TATGTATG
1 TATGTATG
31443 TATGTATG
1 TATGTATG
31451 TATGTATG
1 TATGTATG
31459 TATGTATG
1 TATGTATG
31467 TATGTATG
1 TATGTATG
31475 TATGTATG
1 TATGTATG
31483 TATGTATG
1 TATGTATG
31491 TATGTATG
1 TATGTATG
31499 TATGTATG
1 TATGTATG
31507 TA--TATG
1 TATGTATG
31513 TATGTATG
1 TATGTATG
*
31521 TATGTATA
1 TATGTATG
* *
31529 AATTTATG
1 TATGTATG
31537 TATGTATG
1 TATGTATG
31545 TATGTATG
1 TATGTATG
31553 TATGTATG
1 TATGTATG
31561 TATGTATG
1 TATGTATG
31569 TATGTATG
1 TATGTATG
31577 TATGTATG
1 TATGTATG
31585 TATGTATG
1 TATGTATG
31593 TATGTATG
1 TATGTATG
31601 TATGTATG
1 TATGTATG
31609 TATGTATG
1 TATGTATG
31617 TATGTATG
1 TATGTATG
31625 TATGTATG
1 TATGTATG
31633 TATGTATG
1 TATGTATG
31641 TATGTATG
1 TATGTATG
31649 TATGTATG
1 TATGTATG
31657 TATGTATG
1 TATGTATG
31665 TATGTATG
1 TATGTATG
31673 TATGTATG
1 TATGTATG
31681 TATGTATG
1 TATGTATG
31689 TATGTATG
1 TATGTATG
31697 TATGTATG
1 TATGTATG
31705 TATGTATG
1 TATGTATG
31713 TATGTATG
1 TATGTATG
31721 TATGTATG
1 TATGTATG
31729 TATGTATG
1 TATGTATG
31737 TATGTATG
1 TATGTATG
31745 TATGTATG
1 TATGTATG
31753 TATGTATG
1 TATGTATG
31761 TATGTATG
1 TATGTATG
31769 TATGTATG
1 TATGTATG
31777 TATGTATG
1 TATGTATG
31785 TATGTATG
1 TATGTATG
31793 TATGTATG
1 TATGTATG
31801 TATGTATG
1 TATGTATG
31809 TATGTATG
1 TATGTATG
31817 TATGTATG
1 TATGTATG
31825 TATGTATG
1 TATGTATG
31833 TATGTA--
1 TATGTATG
31839 TATGTATG
1 TATGTATG
31847 TATGTATG
1 TATGTATG
31855 TATGTA--
1 TATGTATG
31861 TATGTATG
1 TATGTATG
31869 TATGTATG
1 TATGTATG
31877 TATGTATG
1 TATGTATG
31885 TATGTATG
1 TATGTATG
31893 TATGTATG
1 TATGTATG
31901 TATGTATG
1 TATGTATG
31909 TATGTATG
1 TATGTATG
31917 TATGTATG
1 TATGTATG
31925 TATGTATG
1 TATGTATG
31933 TATGTATG
1 TATGTATG
31941 TATGTATG
1 TATGTATG
31949 TATGTATG
1 TATGTATG
31957 TATGTATG
1 TATGTATG
31965 TATGTATG
1 TATGTATG
31973 TATGTATG
1 TATGTATG
31981 TATGTATG
1 TATGTATG
31989 TATGTATG
1 TATGTATG
31997 TATGTATG
1 TATGTATG
32005 TATGTATG
1 TATGTATG
32013 TATGTATG
1 TATGTATG
32021 TATGTATG
1 TATGTATG
32029 TATGTATG
1 TATGTATG
32037 TATGTATG
1 TATGTATG
32045 TATGTATG
1 TATGTATG
32053 TATGTATG
1 TATGTATG
32061 TATGTATG
1 TATGTATG
32069 TATGTATG
1 TATGTATG
32077 TATGTATG
1 TATGTATG
32085 TATGTATG
1 TATGTATG
32093 TATGTATG
1 TATGTATG
32101 TATGTATG
1 TATGTATG
32109 TATGTATG
1 TATGTATG
32117 TATGTATG
1 TATGTATG
32125 TATGTATG
1 TATGTATG
32133 TATGTATG
1 TATGTATG
32141 TATGTATG
1 TATGTATG
32149 TATGTATG
1 TATGTATG
32157 TATGTATG
1 TATGTATG
32165 TA--TATG
1 TATGTATG
32171 TATGTATG
1 TATGTATG
32179 TATGTATG
1 TATGTATG
32187 TATGTATG
1 TATGTATG
32195 TATGTATG
1 TATGTATG
32203 TATGTATG
1 TATGTATG
32211 TATGTATG
1 TATGTATG
32219 TATGTATG
1 TATGTATG
32227 TATGTATG
1 TATGTATG
32235 TATGTATG
1 TATGTATG
32243 TATGTATG
1 TATGTATG
32251 TATGTATG
1 TATGTATG
32259 TATGTATG
1 TATGTATG
32267 TATGTATG
1 TATGTATG
32275 TATGTATG
1 TATGTATG
32283 TATGTATG
1 TATGTATG
32291 TATGTATG
1 TATGTATG
32299 TATGTATG
1 TATGTATG
32307 TATGTATG
1 TATGTATG
32315 TATGTATG
1 TATGTATG
32323 TATGTATG
1 TATGTATG
32331 TATGTATG
1 TATGTATG
32339 TATGTATG
1 TATGTATG
32347 TATGTATG
1 TATGTATG
32355 TATGTATG
1 TATGTATG
32363 TATGTATG
1 TATGTATG
32371 TATGTATG
1 TATGTATG
32379 TATGTATG
1 TATGTATG
32387 TATGTATG
1 TATGTATG
32395 TATGTATG
1 TATGTATG
32403 TATGTATG
1 TATGTATG
32411 TATGTATG
1 TATGTATG
32419 TATGTATG
1 TATGTATG
32427 TATGTATG
1 TATGTATG
32435 TATGTATG
1 TATGTATG
32443 TATGTATG
1 TATGTATG
32451 TATGTATG
1 TATGTATG
32459 TATGTATG
1 TATGTATG
32467 TATGTATG
1 TATGTATG
32475 TATGTATG
1 TATGTATG
32483 TATGTATG
1 TATGTATG
32491 TATGTATG
1 TATGTATG
32499 TATGTATG
1 TATGTATG
32507 TATGTATG
1 TATGTATG
32515 TATGTATG
1 TATGTATG
32523 TATGTATG
1 TATGTATG
32531 TATGTATG
1 TATGTATG
32539 TATGTATG
1 TATGTATG
32547 TATGTATG
1 TATGTATG
32555 TATGTATG
1 TATGTATG
32563 TATGTATG
1 TATGTATG
32571 TATGTATG
1 TATGTATG
32579 TATGTATG
1 TATGTATG
32587 TATGTATG
1 TATGTATG
32595 TATGTATG
1 TATGTATG
32603 TATGTATG
1 TATGTATG
32611 TATGTATG
1 TATGTATG
32619 TATGTATG
1 TATGTATG
32627 TATGTATG
1 TATGTATG
32635 TATGTATG
1 TATGTATG
32643 TATGTATG
1 TATGTATG
32651 TATGTATG
1 TATGTATG
32659 TATGTATG
1 TATGTATG
32667 TATGTATG
1 TATGTATG
32675 TATGTATG
1 TATGTATG
32683 TATGTATG
1 TATGTATG
32691 TATGTATG
1 TATGTATG
32699 TATGTATG
1 TATGTATG
32707 TATGTATG
1 TATGTATG
32715 TATGTATG
1 TATGTATG
32723 TATGTATG
1 TATGTATG
32731 TATGTATG
1 TATGTATG
32739 TATGTATG
1 TATGTATG
32747 TATGTATG
1 TATGTATG
32755 TATGTATG
1 TATGTATG
32763 TATGTATG
1 TATGTATG
32771 TATGTATG
1 TATGTATG
*
32779 TATATATG
1 TATGTATG
*
32787 TATGTATA
1 TATGTATG
32795 TATGTATG
1 TATGTATG
32803 TATGTATG
1 TATGTATG
32811 TAT
1 TAT
32814 ACAATAATTT
Statistics
Matches: 1963, Mismatches: 44, Indels: 20
0.97 0.02 0.01
Matches are distributed among these distances:
6 30 0.02
8 1933 0.98
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (8 bp):
TATGTATG
Found at i:31300 original size:2 final size:2
Alignment explanation
Indices: 31295--31409 Score: 203
Period size: 2 Copynumber: 57.5 Consensus size: 2
31285 TGTGCATGTA
*
31295 TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
31337 TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
31379 TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
31410 ATGTATGTAT
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 107 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:33177 original size:39 final size:39
Alignment explanation
Indices: 33092--33182 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 39
33082 TGTTGTGCAC
*
33092 TTTTGGAGTCTTCTCTATTTGCCTGAAGACGCCATACAA
1 TTTTGGAGTCTTCTCTATTTACCTGAAGACGCCATACAA
** ** * *
33131 TCGTGGAGTCTTCT-TCATTTATTTGAAGACGCTATACAG
1 TTTTGGAGTCTTCTCT-ATTTACCTGAAGACGCCATACAA
*
33170 TTTTGGAGACTTC
1 TTTTGGAGTCTTC
33183 ATACTTAGCT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
38 1 0.02
39 40 0.98
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (39 bp):
TTTTGGAGTCTTCTCTATTTACCTGAAGACGCCATACAA
Found at i:33512 original size:20 final size:20
Alignment explanation
Indices: 33489--33542 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
33479 CAACGCGAAC
*
33489 TCCAATTTCGCAACACAATT
1 TCCAAATTCGCAACACAATT
* *
33509 TCCAAATTCGCAACGCGATT
1 TCCAAATTCGCAACACAATT
33529 TCCAAATTCGCAAC
1 TCCAAATTCGCAAC
33543 TAGATTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.31, G:0.09, T:0.26
Consensus pattern (20 bp):
TCCAAATTCGCAACACAATT
Found at i:33548 original size:20 final size:20
Alignment explanation
Indices: 33506--33549 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
33496 TCGCAACACA
*
33506 ATTTCCAAATTCGCAACGCG
1 ATTTCCAAATTCGCAACGAG
*
33526 ATTTCCAAATTCGCAACTAG
1 ATTTCCAAATTCGCAACGAG
33546 ATTT
1 ATTT
33550 TTGAATTCGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (20 bp):
ATTTCCAAATTCGCAACGAG
Found at i:33622 original size:40 final size:39
Alignment explanation
Indices: 33492--33622 Score: 109
Period size: 40 Copynumber: 3.3 Consensus size: 39
33482 CGCGAACTCC
* * * * *
33492 AATTTCGCAACACAATTTCCAAATTCGCAACGCGATTTCC
1 AATTTCGCAACTCGATTTTCGAATTCGCAACGCGATTT-T
* * * * *
33532 AAATTCGCAACTAGATTTTTGAATTCGCAATGCAAATTTT
1 AATTTCGCAACTCGATTTTCGAATTCGCAACGC-GATTTT
** * *
33572 GTTTTTGCAACTCGATTTTCGAATTCGCAACACGTATTTT
1 AATTTCGCAACTCGATTTTCGAATTCGCAACGCG-ATTTT
33612 AATTTCGCAAC
1 AATTTCGCAAC
33623 ATGTTTTATT
Statistics
Matches: 67, Mismatches: 22, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
40 63 0.94
41 4 0.06
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (39 bp):
AATTTCGCAACTCGATTTTCGAATTCGCAACGCGATTTT
Found at i:33798 original size:14 final size:15
Alignment explanation
Indices: 33779--33816 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
33769 TCCCCATCTC
33779 TAATTTTTTT-TATA
1 TAATTTTTTTCTATA
33793 TAATTTTATTTCTATA
1 TAATTTT-TTTCTATA
33809 TAATTTTT
1 TAATTTTT
33817 CAATGATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 4 0.18
16 11 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTTTTTTCTATA
Found at i:34609 original size:24 final size:24
Alignment explanation
Indices: 34558--34611 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
34548 GTATTCGAAA
*
34558 TTTGATCTTGGTCAATATCCGGAC
1 TTTGATCTTGGTCAATATCCAGAC
*
34582 TTTGATCTTGGTCAATA-CTCAGAT
1 TTTGATCTTGGTCAATATC-CAGAC
34606 TTTGAT
1 TTTGAT
34612 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATATCCAGAC
Found at i:34794 original size:3 final size:3
Alignment explanation
Indices: 34786--34819 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
34776 ATATAACCAT
34786 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
34820 TCCCCAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:37793 original size:182 final size:182
Alignment explanation
Indices: 37484--37958 Score: 661
Period size: 182 Copynumber: 2.6 Consensus size: 182
37474 CGATCCAAAT
* * * * * *
37484 TAAAAATGTATCGATCTATATCAATATAACAGGTAAAAATATCGATAAAACCGATCA-CGAAAAG
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATAT-GATAAAACCGGT-ATCGAAATG
* * * * *
37548 ACAATACCGGTAAA-TCCTTACTGGATATATTGAACGTGTCGATACTTTAATATAAGGATCGACA
64 ATAAAACCGGTAAAGACC-TACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACA
37612 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
128 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
* * *
37667 TAAAAATGTATCGATCCACAACGCTATAACAGGTAAAAATATGACAAAACCGGTATTGAAATGAT
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATGAT
* * * * *
37732 AAAACCGGTAAAGAGCTACCGGATATATTTAAAGTGTCGGTATTTTAATATAAGTATCGACACTT
66 AAAACCGGTAAAGACCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
**
37797 TGTGAATTTAAAAGAGAAGCAGTTTTGGCGCCTATAAAGTGTCGATACTTTA
131 TGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
* * * *
37849 TAAAAATATATCGATCCACAATGATATAACATG-AAAAATATGATAAAACCGGTATCAAAATGAT
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATGAT
37913 AAAACCGGTAAAG-CTCTACCGGATATATTGAAAGTGTCGATACTTT
66 AAAACCGGTAAAGAC-CTACCGGATATATTGAAAGTGTCGATACTTT
37959 CATAAGTACG
Statistics
Matches: 257, Mismatches: 32, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
181 70 0.27
182 149 0.58
183 38 0.15
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (182 bp):
TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATGAT
AAAACCGGTAAAGACCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
TGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
Done.