Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004195.1 Hibiscus syriacus cultivar Beakdansim tig00009174_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: 66384
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2901 original size:20 final size:21
Alignment explanation
Indices: 2855--2902 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
2845 CAGAAGGGCA
*
2855 TATCGATACCATAGTATAGTAG
1 TATCGATACCATAGTAAAG-AG
*
2877 TATCGATACCATGGTAAAG-G
1 TATCGATACCATAGTAAAGAG
2897 TATCGA
1 TATCGA
2903 CACCGGGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
22 17 0.71
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (21 bp):
TATCGATACCATAGTAAAGAG
Found at i:2995 original size:20 final size:22
Alignment explanation
Indices: 2949--3000 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
2939 CTGGAAGGGG
*
2949 GTATCGATACCATATTAGGGTA
1 GTATCGATACCATAGTAGGGTA
*
2971 GTATCGATACCATGGT-GGG-A
1 GTATCGATACCATAGTAGGGTA
2991 GTATCGATAC
1 GTATCGATAC
3001 TGAAGAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.39
21 3 0.11
22 14 0.50
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:3543 original size:59 final size:59
Alignment explanation
Indices: 3329--3658 Score: 487
Period size: 59 Copynumber: 5.7 Consensus size: 59
3319 ATGACACTAA
*
3329 GTGTGCTAAAATGTTAAG-AATTCATACTAAGTGTATGAA--T---TATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
* * *
3382 GTGTGCTAAAATGCTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGAACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
**
3441 GTGTAAT-AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
* * *
3499 GTGAGCTAAAATGTTAAGAAATTCATACTAAGTGTATGATTTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
* *
3558 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACCTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
* *
3617 ATGTGCT-AAATGATAAGAAATTCATACTAAGTGTATGAATTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTT
3659 ATGTATGGGA
Statistics
Matches: 250, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
53 17 0.07
54 21 0.08
56 1 0.00
58 86 0.34
59 125 0.50
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
Found at i:3548 original size:117 final size:117
Alignment explanation
Indices: 3335--3654 Score: 467
Period size: 117 Copynumber: 2.8 Consensus size: 117
3325 CTAAGTGTGC
*
3335 TAAAATGTTAAG-AATTCATACTAAGTGTATGAA--T---TATAGGGCACTTCGTGTGCTAAAAT
1 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTTGTGTGCTAAAAT
* *
3394 GCTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGAACTTTGTGTAA
66 GATAAGAAATTCATACTAAGTGTATG-ATTTTCGTATAGGGAACTTCGTGTAA
*
3447 T-AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTTGTGAGCTAAAAT
1 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTTGTGTGCTAAAAT
* * **
3511 GTTAAGAAATTCATACTAAGTGTATGATTTTCCGTATAGGGCACTTCGTGTGC
66 GATAAGAAATTCATACTAAGTGTATGATTTT-CGTATAGGGAACTTCGTGTAA
* * *
3564 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACCTTATGTGCT-AAAT
1 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTTGTGTGCTAAAAT
3628 GATAAGAAATTCATACTAAGTGTATGA
66 GATAAGAAATTCATACTAAGTGTATGA
3655 ATTTATGTAT
Statistics
Matches: 188, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
111 10 0.05
112 22 0.12
114 1 0.01
116 5 0.03
117 96 0.51
118 54 0.29
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (117 bp):
TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTTGTGTGCTAAAAT
GATAAGAAATTCATACTAAGTGTATGATTTTCGTATAGGGAACTTCGTGTAA
Found at i:3636 original size:176 final size:170
Alignment explanation
Indices: 3333--3658 Score: 508
Period size: 176 Copynumber: 1.9 Consensus size: 170
3323 CACTAAGTGT
3333 GCTAAAATGTTAAGAATTCATACTAAGTGTATGAATTATAGGGCACTTCGTGTGCTAAAATGCTA
1 GCTAAAATGTTAAGAATTCATACTAAGTGTATGAATTATAGGGCACTTCGTGTGCTAAAATGCTA
* * * *
3398 AGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGAACTTTGTGTAATAAATGTTAAGAAATT
66 AGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGAACCTTATGTAATAAATGATAAGAAATT
3463 CATACTAAGTGTATGAATTTCCGTATAGGGCACTTTGTGA
131 CATACTAAGTGTATGAATTTCCGTATAGGGCACTTTGTGA
*
3503 GCTAAAATGTTAAGAAATTCATACTAAGTGTATGATTTTCCGTATAGGGCACTTCGTGTGCTAAA
1 GCTAAAATGTTAAG-AATTCATACTAAGTGTATGA--AT---TATAGGGCACTTCGTGTGCTAAA
* * * **
3568 ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACCTTATGTGCTAAATGATAA
60 ATGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGAACCTTATGTAATAAATGATAA
3633 GAAATTCATACTAAGTGTATGAATTT
125 GAAATTCATACTAAGTGTATGAATTT
3659 ATGTATGGGA
Statistics
Matches: 140, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
170 14 0.10
171 20 0.14
173 1 0.01
176 105 0.75
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (170 bp):
GCTAAAATGTTAAGAATTCATACTAAGTGTATGAATTATAGGGCACTTCGTGTGCTAAAATGCTA
AGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGAACCTTATGTAATAAATGATAAGAAATT
CATACTAAGTGTATGAATTTCCGTATAGGGCACTTTGTGA
Found at i:5083 original size:19 final size:20
Alignment explanation
Indices: 5055--5094 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5045 AGATGAAGTT
5055 AAAAAGATATAATAA-AATA
1 AAAAAGATATAATAATAATA
*
5074 AAAAATATATAATAATAATA
1 AAAAAGATATAATAATAATA
5094 A
1 A
5095 TAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAAAGATATAATAATAATA
Found at i:5131 original size:43 final size:41
Alignment explanation
Indices: 5068--5147 Score: 115
Period size: 43 Copynumber: 1.9 Consensus size: 41
5058 AAGATATAAT
* *
5068 AAAATAAAAAATATATAATAATAATAATAATAAATAAATGGG
1 AAAATAAAAAATAAAAAATAATAATAATAA-AAATAAATGGG
*
5110 AAAATAATAAAATAAAAAATAATAGTAATAAAAATAAA
1 AAAATAA-AAAATAAAAAATAATAATAATAAAAATAAA
5148 AAGTGGGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 14 0.41
43 20 0.59
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (41 bp):
AAAATAAAAAATAAAAAATAATAATAATAAAAATAAATGGG
Found at i:5146 original size:15 final size:15
Alignment explanation
Indices: 5063--5143 Score: 65
Period size: 16 Copynumber: 5.0 Consensus size: 15
5053 TTAAAAAGAT
5063 ATAATAAAATAAAAA
1 ATAATAAAATAAAAA
5078 ATATATAATAATAATAATA
1 ATA-ATAA-AATAA-AA-A
**
5097 ATAA-ATAAATGGGAAA
1 ATAATA-AAAT-AAAAA
5113 ATAATAAAATAAAAA
1 ATAATAAAATAAAAA
*
5128 ATAATAGTAATAAAAA
1 ATAATA-AAATAAAAA
5144 TAAAAAGTGG
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
15 12 0.23
16 21 0.40
17 12 0.23
18 4 0.08
19 4 0.08
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (15 bp):
ATAATAAAATAAAAA
Found at i:5195 original size:19 final size:19
Alignment explanation
Indices: 5171--5217 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
5161 AAAGTTGTTT
*
5171 TTAAAATAAAAGATAAGAA
1 TTAAAATAAAAGAAAAGAA
*
5190 TTAAAATAAAAGAAAATAA
1 TTAAAATAAAAGAAAAGAA
5209 TT-AAATAAA
1 TTAAAATAAA
5218 TAATTTAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (19 bp):
TTAAAATAAAAGAAAAGAA
Found at i:5730 original size:12 final size:12
Alignment explanation
Indices: 5709--5738 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5699 GGAAATATGC
5709 GAAAAATAGAGA
1 GAAAAATAGAGA
*
5721 GAAAACTAGAGA
1 GAAAAATAGAGA
5733 GAAAAA
1 GAAAAA
5739 GAACATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:7350 original size:37 final size:37
Alignment explanation
Indices: 7309--7382 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
7299 ATCCGATGAA
7309 GGCCTCTTTGTACAAGATTCTCAACATTAGGATACGG
1 GGCCTCTTTGTACAAGATTCTCAACATTAGGATACGG
7346 GGCCTCTTTGTACAAGATTCTCAACATTAGGATACGG
1 GGCCTCTTTGTACAAGATTCTCAACATTAGGATACGG
7383 AGGTATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (37 bp):
GGCCTCTTTGTACAAGATTCTCAACATTAGGATACGG
Found at i:9021 original size:41 final size:42
Alignment explanation
Indices: 8969--9052 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 42
8959 TCACTGAGTC
* *
8969 TTAATATGATATTATCCCAAATTTTATTTATCAATCTAGTTT
1 TTAATATGATATTATCCCAAATTTTATTTACCAATCCAGTTT
*
9011 TTAA-ATGATATTATCTCAAATTTTATTTACCAATCCAGTTT
1 TTAATATGATATTATCCCAAATTTTATTTACCAATCCAGTTT
9052 T
1 T
9053 AAAGGATGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 35 0.90
42 4 0.10
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (42 bp):
TTAATATGATATTATCCCAAATTTTATTTACCAATCCAGTTT
Found at i:9229 original size:3 final size:3
Alignment explanation
Indices: 9169--9213 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
9159 GTTTTTTTAA
9169 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
9214 ATACAAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:13233 original size:39 final size:39
Alignment explanation
Indices: 13179--13257 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 39
13169 CCTGTACACC
*
13179 CAGTAACGGCTTACCCTGTGCACAAAG-CAGAGGAGCCTA
1 CAGTAACGGCTTACCCTGAGCACAAAGCCA-AGGAGCCTA
*
13218 CAGTAA-GGACTTACCCTGAGTACAAAGCCAAGGAGCCTA
1 CAGTAACGG-CTTACCCTGAGCACAAAGCCAAGGAGCCTA
13257 C
1 C
13258 GGAAAGTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 2 0.06
39 32 0.89
40 2 0.06
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (39 bp):
CAGTAACGGCTTACCCTGAGCACAAAGCCAAGGAGCCTA
Found at i:13322 original size:44 final size:44
Alignment explanation
Indices: 13266--13576 Score: 424
Period size: 44 Copynumber: 7.1 Consensus size: 44
13256 ACGGAAAGTA
* * *
13266 GTAAGGTCTTACCCTTGTACATAGTAGAGGAGCCTGCAGAAACG
1 GTAAGGTCTTACCCTTGCACTTAGCAGAGGAGCCTGCAGAAACG
* * * *
13310 GTAAGGTCTTACCCTTGCACGTAGAAGAGGAGCCTACAGAAATG
1 GTAAGGTCTTACCCTTGCACTTAGCAGAGGAGCCTGCAGAAACG
* * *
13354 GTAAGGTCTTACCCTTGCACTTAGCATAGGAGCTTGCATAAACG
1 GTAAGGTCTTACCCTTGCACTTAGCAGAGGAGCCTGCAGAAACG
* * * *
13398 GTAAGGTCTTACCCTTGCACATAGGAGAAGAGCCTGCAGAAATG
1 GTAAGGTCTTACCCTTGCACTTAGCAGAGGAGCCTGCAGAAACG
* * * * *
13442 ATAAGTTCTTACCCTTGCACTTAGCAAAGGAGCCTGCAAAAATG
1 GTAAGGTCTTACCCTTGCACTTAGCAGAGGAGCCTGCAGAAACG
*
13486 GTAAGGTCTTACCCTTGCACTTAGTAGAGGAGCCTGCAGAAACG
1 GTAAGGTCTTACCCTTGCACTTAGCAGAGGAGCCTGCAGAAACG
* *
13530 GTAATGTCTTACCCTTACACTTAGCAGAGGAGCCTGCAGAAACG
1 GTAAGGTCTTACCCTTGCACTTAGCAGAGGAGCCTGCAGAAACG
13574 GTA
1 GTA
13577 CAGGCCTGAA
Statistics
Matches: 232, Mismatches: 35, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 232 1.00
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (44 bp):
GTAAGGTCTTACCCTTGCACTTAGCAGAGGAGCCTGCAGAAACG
Found at i:19833 original size:23 final size:22
Alignment explanation
Indices: 19798--19842 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
19788 ATAAAAGATT
*
19798 CATATGATAAAAATATATGTATA
1 CATATGATAAAAAAAT-TGTATA
19821 CATATG-TAAAAAAAATTGTATA
1 CATATGAT-AAAAAAATTGTATA
19843 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (22 bp):
CATATGATAAAAAAATTGTATA
Found at i:19840 original size:22 final size:23
Alignment explanation
Indices: 19798--19842 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
19788 ATAAAAGATT
*
19798 CATATGATAAAAATATATGTATA
1 CATATGATAAAAAAATATGTATA
19821 CATATG-TAAAAAAA-ATTGTATA
1 CATATGATAAAAAAATA-TGTATA
19843 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 13 0.65
23 6 0.30
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (23 bp):
CATATGATAAAAAAATATGTATA
Found at i:20269 original size:44 final size:44
Alignment explanation
Indices: 20205--20477 Score: 278
Period size: 44 Copynumber: 6.1 Consensus size: 44
20195 CTAGTAGGGG
* * * *
20205 CTTACCCTGTGCACAAAGCAGAGGAGCCTACATAAATGGTAAGGT
1 CTTACCCT-TGCACATAGCAGAGGAGCCTGCAGAAACGGTAAGGT
* * * *
20250 CTTACCCTTGCACTTAGCAGAGGAGCTTGCAGAAATGATAATTAGGT
1 CTTACCCTTGCACATAGCAGAGGAGCCTGCAGAAACGGT-A--AGGT
* *
20297 CTTACCCTTGCACATAGCAGAGAAGTCTGCAGAAACGGTAAGGT
1 CTTACCCTTGCACATAGCAGAGGAGCCTGCAGAAACGGTAAGGT
* * * * *
20341 CTTACCCTTTCAGATAGTAGAGGAGCTTGCAGAAATGGTAAGGT
1 CTTACCCTTGCACATAGCAGAGGAGCCTGCAGAAACGGTAAGGT
* * * * * **
20385 CGTACCCTTGTACTTAGCAGAAGAGGCTATAGAAACGGTAAGGT
1 CTTACCCTTGCACATAGCAGAGGAGCCTGCAGAAACGGTAAGGT
* *
20429 CTTACCCTTGCAC-TAAGCAGAGGATCCTGCAGAAACAGTAAGGT
1 CTTACCCTTGCACAT-AGCAGAGGAGCCTGCAGAAACGGTAAGGT
20473 CTTAC
1 CTTAC
20478 AAGTCATAGA
Statistics
Matches: 185, Mismatches: 39, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
43 1 0.01
44 137 0.74
45 9 0.05
46 1 0.01
47 37 0.20
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (44 bp):
CTTACCCTTGCACATAGCAGAGGAGCCTGCAGAAACGGTAAGGT
Found at i:36140 original size:3 final size:3
Alignment explanation
Indices: 36130--36168 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
36120 AAAGTATTAT
36130 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TGAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
36169 AACCCAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:36499 original size:104 final size:102
Alignment explanation
Indices: 36391--36695 Score: 281
Period size: 104 Copynumber: 2.9 Consensus size: 102
36381 CAATCCAGAT
* * * *
36391 ATAATATAGTGTTGAAGACGGTGCTTCCCATCCATGTTGAAGAGTTGTGGTCATTTTTAGATGAC
1 ATAATTTAGTGTTGAAGACGATGCTT-CCATCCATGTTGAAGAGTTCTGG-CATTTTCAGATGAC
36456 ATTGTTCCTTCTTATTGAGGAAGTCGAGTCAAGATAGAG
64 ATTGTTCCTTCTTATTGAGGAAGTCGAGTCAAGATAGAG
* ** * * ** *
36495 ATAATTTAGTGTTGAAGATGACACTGGCCATCCATGTTGAAGAGTTCTAGCCGCTTTCAGATGAT
1 ATAATTTAGTGTTGAAGACGATGCT-TCCATCCATGTTGAAGAGTTCT-GGCATTTTCAGATGAC
* * * * * * *
36560 TTTGTTCCTTCTTGTTGAGGAAGTTGACTTAAGCTGGAG
64 ATTGTTCCTTCTTATTGAGGAAGTCGAGTCAAGATAGAG
* * * * * *
36599 ATAATTTGGTGTTGAAGATGACAATG-TT-CATCCATATTGAAGAGTTCTGGCCTCTTCCATATG
1 ATAATTTAGTGTTG-A-A-GACGATGCTTCCATCCATGTTGAAGAGTTCTGGCAT-TTTCAGATG
* *
36662 ACATTGTTCCTTCTCATTGAGGAAGTCGGGTCAA
62 ACATTGTTCCTTCTTATTGAGGAAGTCGAGTCAA
36696 TCTAGATAAT
Statistics
Matches: 156, Mismatches: 39, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
103 2 0.01
104 147 0.94
105 2 0.01
106 2 0.01
107 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (102 bp):
ATAATTTAGTGTTGAAGACGATGCTTCCATCCATGTTGAAGAGTTCTGGCATTTTCAGATGACAT
TGTTCCTTCTTATTGAGGAAGTCGAGTCAAGATAGAG
Found at i:37356 original size:102 final size:100
Alignment explanation
Indices: 37242--37553 Score: 367
Period size: 102 Copynumber: 3.1 Consensus size: 100
37232 AAAATTTCCG
* * * *
37242 AGTGAAACAATTTCAAAATATGTGTTTGAAGGTAAAATTATCTCAAGTGAGATGAAATTTGTTTT
1 AGTGAAAGAATTTCAAAATTTGTGTTTAAAGG-AAAATTATCTCAAGTGAAAT-AAATTTGTTTT
* * * * * *
37307 TAGGAAAACAATATCAAATTATATCAAATTAGTTTCA
64 TAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCA
* *
37344 AGTGAAAGAATTTCAAAATTTGTGTTTCAAGGAAAAATTATCTCAAGCGAAACTAAATTTGTTTT
1 AGTGAAAGAATTTCAAAATTTGTGTTTAAAGG-AAAATTATCTCAAGTGAAA-TAAATTTGTTTT
*
37409 TAGGAAAACAATCTCAAGCGAGATCAATTTTG-TTCA
64 TAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCA
* * * * * *
37445 AGTGAAAGAATTCCAAAATTTGAGTTTCAAACGAAAACTGTCTCAAGCATGACA-AAATTTGTTT
1 AGTGAAAGAATTTCAAAATTTGTGTTT-AAAGGAAAATTATCTCAAG--TGAAATAAATTTGTTT
37509 TTAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCA
63 TTAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCA
*
37547 ATTGAAA
1 AGTGAAA
37554 CTCTCAAATG
Statistics
Matches: 182, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
101 83 0.46
102 95 0.52
103 4 0.02
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (100 bp):
AGTGAAAGAATTTCAAAATTTGTGTTTAAAGGAAAATTATCTCAAGTGAAATAAATTTGTTTTTA
GGAAAACAATCTCAAGTGAGATCAATTTTGTTTCA
Found at i:37492 original size:101 final size:102
Alignment explanation
Indices: 37296--37553 Score: 342
Period size: 101 Copynumber: 2.5 Consensus size: 102
37286 AAGTGAGATG
* * * * * * *
37296 AAATTTGTTTTTAGGAAAACAATATCAAATTATATCAAATTAGTTTCAAGTGAAAGAATTTCAAA
1 AAATTTGTTTTTAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAAGAATTCCAAA
* * * *
37361 ATTTGTGTTTCAAGGAAAAATTATCTCAAGCGA-AACT
66 ATTTGAGTTTCAACGAAAAACTATCTCAAGC-ATAACA
*
37398 AAATTTGTTTTTAGGAAAACAATCTCAAGCGAGATCAATTTTG-TTCAAGTGAAAGAATTCCAAA
1 AAATTTGTTTTTAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAAGAATTCCAAA
* *
37462 ATTTGAGTTTCAAACG-AAAACTGTCTCAAGCATGACA
66 ATTTGAGTTTC-AACGAAAAACTATCTCAAGCATAACA
*
37499 AAATTTGTTTTTAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCAATTGAAA
1 AAATTTGTTTTTAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAA
37554 CTCTCAAATG
Statistics
Matches: 137, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
100 1 0.01
101 87 0.64
102 49 0.36
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (102 bp):
AAATTTGTTTTTAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAAGAATTCCAAA
ATTTGAGTTTCAACGAAAAACTATCTCAAGCATAACA
Found at i:39172 original size:4 final size:4
Alignment explanation
Indices: 39163--39204 Score: 59
Period size: 4 Copynumber: 10.5 Consensus size: 4
39153 TGAATACAAC
*
39163 ATAA ATAA ATAA A-AA TATTA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA AT
39205 TACTATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 2 0.06
4 31 0.91
5 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:40584 original size:3 final size:3
Alignment explanation
Indices: 40578--40654 Score: 102
Period size: 3 Copynumber: 25.7 Consensus size: 3
40568 ATTATTTTTT
** *
40578 TAA TAA TAA TAA TAA -AA TAA TTT TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
40625 TAA TAA TAAA TAA AAA TAA TAA TAA TAA TA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA
40655 TAAATAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 59 0.92
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:40660 original size:9 final size:8
Alignment explanation
Indices: 40578--40665 Score: 61
Period size: 9 Copynumber: 10.0 Consensus size: 8
40568 ATTATTTTTT
40578 TAATAATAA
1 TAATAA-AA
40587 TAATAAAA
1 TAATAAAA
**
40595 TAATTTTAA
1 TAA-TAAAA
*
40604 TAATATTAA
1 TAATA-AAA
40613 TAATAATAA
1 TAATAA-AA
40622 TAATAATAA
1 TAATAA-AA
40631 TAAATAAAAA
1 T-AAT-AAAA
40641 TAATAATAA
1 TAATAA-AA
40650 TAATATAAA
1 TAATA-AAA
40659 TAA-AAAA
1 TAATAAAA
40666 CAAATGGATG
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
7 3 0.04
8 9 0.13
9 47 0.69
10 7 0.10
11 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAATAAAA
Found at i:41203 original size:139 final size:138
Alignment explanation
Indices: 40894--41236 Score: 403
Period size: 139 Copynumber: 2.5 Consensus size: 138
40884 CTAGCAAAAT
* * * *
40894 GTTGAACAAGTTCTTTTCATTATGAAATTCTTCTTCATCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
** * *
40959 C-TCCTTCTGGGAATGATGATCCTCAAAAGTGGTGTCATTGATTCAACTTCATATGTGATGAAAT
66 CTTCCTTCTGAAAATGATGATCCTCAAAAGAGGTGTCATTGATTCAACTCCATATGTGATGAAAT
41023 AAGGCAAG
131 AAGGCAAG
* *
41031 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* ** * * *
41096 CTTCCTT-TGAAAAT-ATTGATTCTCAAGTGAGGTTCTTCTTTTATTCAACTCCATA-GATGATG
66 CTTCCTTCTGAAAATGA-TGATCCTCAAAAGAGG-T-GTCATTGATTCAACTCCATATG-TGATG
41158 -AATCAA-GCTAA-
127 AAAT-AAGGC-AAG
* * *
41169 GTTCGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTCAGACGAGTTCTCCTCATTATGA
1 GTT-GAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGA
41234 ACT
65 ACT
41237 CTACCTGGCA
Statistics
Matches: 179, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
136 1 0.01
137 79 0.44
138 15 0.08
139 84 0.47
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (138 bp):
GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTTCCTTCTGAAAATGATGATCCTCAAAAGAGGTGTCATTGATTCAACTCCATATGTGATGAAAT
AAGGCAAG
Found at i:41254 original size:139 final size:136
Alignment explanation
Indices: 40894--41623 Score: 395
Period size: 123 Copynumber: 5.6 Consensus size: 136
40884 CTAGCAAAAT
* * * *
40894 GTTGAACAAGTTCTTTTCATTATGAAATTCTTCTTCATCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
40959 CTCCTTCTGGGAATGATGATCCTCAAAAGTGGTGTCATTGATTCAACTTCATATGTGATGAAATA
66 CT-CTCCTGGAAATGTTGATCCTCAAAAGAGGTGTCATTGATTCAACTCCATATGTGATGAAATA
41024 AGGCAAG
130 AGGCAAG
* *
41031 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * ** * * *
41096 CT-TCCTTTGAAAATATTGATTCTCAAGTGAGGTTCTTCTTTTATTCAACTCCATA-GATGATG-
66 CTCTCC--TGGAAATGTTGATCCTCAAAAGAGG-T-GTCATTGATTCAACTCCATATG-TGATGA
41158 AATCAA-GCTAA-
126 AAT-AAGGC-AAG
* * *
41169 GTTCGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTCAGACGAGTTCTCCTCATTATGA
1 GTT-GAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGA
* ** ** * **
41234 ACTCTACCTGGCAATGTTGA---T--ATTGA----TC--T-A-T---CTCTTTCTGTGATAGAGT
65 ACTCT-CCTGGAAATGTTGATCCTCAAAAGAGGTGTCATTGATTCAACTCCATATGTGAT-GAAA
** **
41283 CGAGCAAAAG
128 TAAG-GCAAG
* *
41293 GTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
41358 CTCTACCTGGAAATATTGAT-GT----TGA----T-A-T-A-TCTACT---TCTGTGATAG-AAT
66 CTCT-CCTGGAAATGTTGATCCTCAAAAGAGGTGTCATTGATTCAACTCCATATGTGAT-GAAAT
**
41406 CGGGCAAAAG
129 AAGGC--AAG
*
41416 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
41481 CTTTACCTGGAAATGTTGATGCT-----GA----TC--T-A-T---CTCCTTCTGTGATAG-AAT
66 CTCT-CCTGGAAATGTTGATCCTCAAAAGAGGTGTCATTGATTCAACTCCATATGTGAT-GAAAT
41529 CAA-GCAAAAAG
129 -AAGGC---AAG
* *
41540 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTAT-AA
1 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
*
41604 CTCTTTCTGGAAATGTTGAT
66 CTC-TCCTGGAAATGTTGAT
41624 ACATCGAGTT
Statistics
Matches: 502, Mismatches: 59, Indels: 78
0.79 0.09 0.12
Matches are distributed among these distances:
120 2 0.00
121 8 0.02
122 4 0.01
123 216 0.43
124 72 0.14
125 2 0.00
126 3 0.01
128 2 0.00
134 4 0.01
135 2 0.00
136 1 0.00
137 80 0.16
138 10 0.02
139 93 0.19
140 1 0.00
141 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (136 bp):
GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTCTCCTGGAAATGTTGATCCTCAAAAGAGGTGTCATTGATTCAACTCCATATGTGATGAAATAA
GGCAAG
Found at i:41396 original size:123 final size:122
Alignment explanation
Indices: 41177--41623 Score: 698
Period size: 123 Copynumber: 3.6 Consensus size: 122
41167 AAGTTCGAAA
* * *
41177 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTCAGACGAGTTCTCCTCATTATGAACTCTACC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
* * * *
41242 TGGCAATGTTGATATTGATCTATCTCTTTCTGTGATAGAGTCGAGCAAAAGGTTGAAT
66 TGGAAATGTTGATGTTGATCTATCTC-TTCTGTGATAGAATCGAGCAAAAGGTTGAAC
*
41300 AAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
* * *
41365 TGGAAATATTGATGTTGATATATCTACTTCTGTGATAGAATCGGGCAAAAGGTTGAAC
66 TGGAAATGTTGATGTTGATCTATCT-CTTCTGTGATAGAATCGAGCAAAAGGTTGAAC
*
41423 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTACC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
* *
41488 TGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAAGGTTGAAC
66 TGGAAATGTTGATGTTGATCTATCT-CTTCTGTGATAGAATCGAGC-AAAAGGTTGAAC
* **
41547 AAGTTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTAT-AACTCTTTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
41611 TGGAAATGTTGAT
66 TGGAAATGTTGAT
41624 ACATCGAGTT
Statistics
Matches: 299, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
123 232 0.78
124 67 0.22
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (122 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
TGGAAATGTTGATGTTGATCTATCTCTTCTGTGATAGAATCGAGCAAAAGGTTGAAC
Found at i:47696 original size:43 final size:43
Alignment explanation
Indices: 47606--47730 Score: 198
Period size: 43 Copynumber: 2.9 Consensus size: 43
47596 TCGGTACATC
* * * *
47606 AAACAAAACTTTATATATAAGGG-TAGCTTTCACTTCTAACTT
1 AAACAAAACTTTACATATAGGGGATAACTTTCACTCCTAACTT
*
47648 CAACAAAACTTTACATATAGGGGATAACTTTCACTCCTAACTT
1 AAACAAAACTTTACATATAGGGGATAACTTTCACTCCTAACTT
47691 AAACAAAACTTTACATATAGGGGATAACTTTCACTCCTAA
1 AAACAAAACTTTACATATAGGGGATAACTTTCACTCCTAA
47731 TTTCTCTACA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 20 0.26
43 56 0.74
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (43 bp):
AAACAAAACTTTACATATAGGGGATAACTTTCACTCCTAACTT
Found at i:48600 original size:19 final size:19
Alignment explanation
Indices: 48578--48615 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
48568 CAAAAGAAAT
48578 CAATATAAACAAATTAGAG
1 CAATATAAACAAATTAGAG
48597 CAATATAAACAAATTAGAG
1 CAATATAAACAAATTAGAG
48616 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.21
Consensus pattern (19 bp):
CAATATAAACAAATTAGAG
Found at i:48623 original size:19 final size:19
Alignment explanation
Indices: 48582--48624 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
48572 AGAAATCAAT
* *
48582 ATAAACAAATTAGAGCAAT
1 ATAAACAAATTAGAGAAAA
48601 ATAAACAAATTAGAGAAAA
1 ATAAACAAATTAGAGAAAA
48620 ATAAA
1 ATAAA
48625 ATGTATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.65, C:0.07, G:0.09, T:0.19
Consensus pattern (19 bp):
ATAAACAAATTAGAGAAAA
Found at i:50146 original size:4 final size:4
Alignment explanation
Indices: 50137--50176 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
50127 TGAATAAAAC
50137 ATAA ATAA ATAA A-AA ATTAA ATAA A-AA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA A-TAA ATAA ATAA ATAA ATAA ATAA A
50177 ATATTATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 6 0.18
4 24 0.73
5 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:50149 original size:15 final size:14
Alignment explanation
Indices: 50129--50177 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
50119 AATATTAGTG
50129 AATAAAACATAAATA
1 AATAAAA-ATAAATA
*
50144 AAT-AAAA-AATTA
1 AATAAAAATAAATA
50156 AATAAAAAATAAATA
1 AAT-AAAAATAAATA
50171 AATAAAA
1 AATAAAA
50178 TATTATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 7 0.24
13 1 0.03
14 11 0.38
15 10 0.34
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
AATAAAAATAAATA
Found at i:50159 original size:12 final size:11
Alignment explanation
Indices: 50139--50172 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
50129 AATAAAACAT
50139 AAATAAATAAA
1 AAATAAATAAA
50150 AAATTAAATAAA
1 AAA-TAAATAAA
50162 AAATAAATAAA
1 AAATAAATAAA
50173 TAAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:50161 original size:27 final size:27
Alignment explanation
Indices: 50129--50182 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
50119 AATATTAGTG
*
50129 AATAAAACATAAATAAATAAAAAATTA
1 AATAAAAAATAAATAAATAAAAAATTA
*
50156 AATAAAAAATAAATAAATAAAATATTA
1 AATAAAAAATAAATAAATAAAAAATTA
50183 TATTTAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (27 bp):
AATAAAAAATAAATAAATAAAAAATTA
Found at i:51540 original size:3 final size:3
Alignment explanation
Indices: 51534--51623 Score: 134
Period size: 3 Copynumber: 31.0 Consensus size: 3
51524 ATTTATTATT
51534 TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
51580 TAA TAA -AA TAA -AA TAA TAA TAA TAA TATT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
51624 ATATAAATAT
Statistics
Matches: 80, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
2 8 0.10
3 70 0.88
4 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:51626 original size:32 final size:30
Alignment explanation
Indices: 51534--51626 Score: 127
Period size: 29 Copynumber: 3.1 Consensus size: 30
51524 ATTTATTATT
*
51534 TAATAATAATAAAATAATAATAATAAT-AA
1 TAATAATAATAATATAATAATAATAATAAA
*
51563 TAATAATAATAATAAAATAATAA-AATAAAA
1 TAATAATAATAATATAATAATAATAAT-AAA
51593 TAATAATAATAATATTTAATAATAATAATAAA
1 TAATAATAATAATA--TAATAATAATAATAAA
51625 TA
1 TA
51627 TAAATATAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
28 3 0.05
29 21 0.38
30 16 0.29
32 13 0.23
33 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATAATAATAATATAATAATAATAATAAA
Found at i:53791 original size:10 final size:10
Alignment explanation
Indices: 53778--53828 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
53768 TTTCTTCTTC
53778 TTTTTTTCCT
1 TTTTTTTCCT
53788 TTTTTTTCC-
1 TTTTTTTCCT
*
53797 TTTTATT-C-
1 TTTTTTTCCT
*
53805 TTTTTCTCCT
1 TTTTTTTCCT
*
53815 TTTTTTTACT
1 TTTTTTTCCT
53825 TTTT
1 TTTT
53829 ATTTTTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
8 6 0.18
9 7 0.21
10 21 0.62
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTTCCT
Found at i:53805 original size:27 final size:27
Alignment explanation
Indices: 53775--53827 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
53765 CTCTTTCTTC
* *
53775 TTCTTTTTTTCCTTTTTTTTCCTTTTA
1 TTCTTTTTCTCCTTTTTTTTACTTTTA
53802 TTCTTTTTCTCCTTTTTTTTACTTTT
1 TTCTTTTTCTCCTTTTTTTTACTTTT
53828 TATTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (27 bp):
TTCTTTTTCTCCTTTTTTTTACTTTTA
Found at i:53828 original size:9 final size:9
Alignment explanation
Indices: 53777--53820 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
53767 CTTTCTTCTT
53777 CTTTTTTTC
1 CTTTTTTTC
53786 CTTTTTTTTC
1 C-TTTTTTTC
*
53796 CTTTTATT-
1 CTTTTTTTC
*
53804 CTTTTTCTC
1 CTTTTTTTC
53813 CTTTTTTT
1 CTTTTTTT
53821 TACTTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 6 0.21
9 14 0.48
10 9 0.31
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (9 bp):
CTTTTTTTC
Found at i:56214 original size:45 final size:45
Alignment explanation
Indices: 56186--56462 Score: 367
Period size: 45 Copynumber: 6.2 Consensus size: 45
56176 AATGCACAAT
* *
56186 TATGCATTTCAATAATGGCATCCTTTCATGCCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCATTTCATGCCGATAATGCACCCA
*
56231 TATGCATTTAAATTA-GGCATCATTTCATGCCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCATTTCATGCCGATAATGCACCCA
* ** *
56275 TATGCATTTCAATTATGACATCATTTCATGATGATAATGCATCCA
1 TATGCATTTCAATTATGGCATCATTTCATGCCGATAATGCACCCA
** * *
56320 TATGCATTTCAATTATGAAATCTTTTCATGCCAATAATGCACCCA
1 TATGCATTTCAATTATGGCATCATTTCATGCCGATAATGCACCCA
* * * * *
56365 TATTCTTTTCAATTATGGCATCCTTTCTTGTCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCATTTCATGCCGATAATGCACCCA
* ** *
56410 TATGCATTTTAATTATGAAATCTTTTCATGCCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCATTTCATGCCGATAATGCACCCA
56455 TATGCATT
1 TATGCATT
56463 ATTTTTTTCT
Statistics
Matches: 201, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
44 42 0.21
45 159 0.79
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (45 bp):
TATGCATTTCAATTATGGCATCATTTCATGCCGATAATGCACCCA
Found at i:56994 original size:20 final size:20
Alignment explanation
Indices: 56969--57021 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
56959 CTATTTTGAA
56969 TGGTATTGATACATT-CCCTT
1 TGGTATTGATAC-TTCCCCTT
56989 TGGTATCT-ATACTTCCCCTT
1 TGGTAT-TGATACTTCCCCTT
* *
57009 CGGTATCGATACT
1 TGGTATTGATACT
57022 GATACAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 2 0.07
20 25 0.89
21 1 0.04
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.42
Consensus pattern (20 bp):
TGGTATTGATACTTCCCCTT
Found at i:63120 original size:45 final size:45
Alignment explanation
Indices: 63071--63368 Score: 300
Period size: 45 Copynumber: 6.6 Consensus size: 45
63061 ATAGCATCTA
* **
63071 TTCATGCTTATAATG-AACCATTACACATTTCAATTATGACATCCT
1 TTCATGCTGATAATGCAACCA-TATGCATTTCAATTATGACATCCT
* *** * *
63116 TTCATG-TCGATAATGCACCCATACATATTTTAATTATGGCATCCT
1 TTCATGCT-GATAATGCAACCATATGCATTTCAATTATGACATCCT
* * * *
63161 TTCATGCCGATAATACACCCATATGCATTTCAATTATGGCATCCT
1 TTCATGCTGATAATGCAACCATATGCATTTCAATTATGACATCCT
** * *
63206 TTCATGCTGATAATGCATTCATATGCATTTCAATTATGAAATTCT
1 TTCATGCTGATAATGCAACCATATGCATTTCAATTATGACATCCT
* * * * *
63251 TTCATGCTAATACTACACCCATATGCATTTCAATTATGGA-TTCC-
1 TTCATGCTGATAATGCAACCATATGCATTTCAATTAT-GACATCCT
* *
63295 TTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCCT
1 TTCATGCTGATAATGCAACCATATGCATTTCAATTATGACATCCT
*
63340 TTCATG-TCGATAATGCACCCATATGCATT
1 TTCATGCT-GATAATGCAACCATATGCATT
63369 ATTTTTTTCA
Statistics
Matches: 216, Mismatches: 30, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.00
44 39 0.18
45 170 0.79
46 6 0.03
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (45 bp):
TTCATGCTGATAATGCAACCATATGCATTTCAATTATGACATCCT
Found at i:63218 original size:90 final size:90
Alignment explanation
Indices: 63096--63368 Score: 372
Period size: 90 Copynumber: 3.0 Consensus size: 90
63086 AACCATTACA
* *** *
63096 CATTTCAATTATGACATCCTTTCATG-TCGATAATGCACCCATACATATTTTAATTATGGCATCC
1 CATTTCAATTATGGCATCCTTTCATGCT-GATAATGCACCCATATGCATTTCAATTATGGCATCC
63160 TTTCATGCCGATAATACACCCATATG
65 TTTCATGCCGATAATACACCCATATG
** ** *
63186 CATTTCAATTATGGCATCCTTTCATGCTGATAATGCATTCATATGCATTTCAATTATGAAATTCT
1 CATTTCAATTATGGCATCCTTTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCCT
** *
63251 TTCATGCTAATACTACACCCATATG
66 TTCATGCCGATAATACACCCATATG
63276 CATTTCAATTATGG-ATTCC-TTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCC
1 CATTTCAATTATGGCA-TCCTTTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCC
* *
63339 TTTCATGTCGATAATGCACCCATATG
65 TTTCATGCCGATAATACACCCATATG
63365 CATT
1 CATT
63369 ATTTTTTTCA
Statistics
Matches: 158, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
89 65 0.41
90 92 0.58
91 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (90 bp):
CATTTCAATTATGGCATCCTTTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCCT
TTCATGCCGATAATACACCCATATG
Found at i:63352 original size:134 final size:135
Alignment explanation
Indices: 63096--63368 Score: 374
Period size: 134 Copynumber: 2.0 Consensus size: 135
63086 AACCATTACA
* * * * *
63096 CATTTCAATTATGACATCCTTTCATGTCGATAATGCACCCATACATATTTTAATTATGGCATCCT
1 CATTTCAATTATGAAATCCTTTCATGTCAATAATACACCCATACACATTTCAATTATGGCATCCT
**
63161 TTCATGCCGATAATACACCCATATGCATTTCAATTATGGCATCCTTTCATGCTGATAATGCATTC
66 TTCATGCCGATAATACACCCATATGCATTTCAATTATGGCATCCTTTCATGCTGATAATGCACCC
63226 ATATG
131 ATATG
* * **
63231 CATTTCAATTATGAAATTCTTTCATG-CTAATACTACACCCATATGCATTTCAATTATGG-ATTC
1 CATTTCAATTATGAAATCCTTTCATGTC-AATAATACACCCATACACATTTCAATTATGGCA-TC
* *
63294 C-TTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATG-TCGATAATGCA
64 CTTTCATGCCGATAATACACCCATATGCATTTCAATTATGGCATCCTTTCATGCT-GATAATGCA
63357 CCCATATG
128 CCCATATG
63365 CATT
1 CATT
63369 ATTTTTTTCA
Statistics
Matches: 122, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
133 1 0.01
134 70 0.57
135 51 0.42
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (135 bp):
CATTTCAATTATGAAATCCTTTCATGTCAATAATACACCCATACACATTTCAATTATGGCATCCT
TTCATGCCGATAATACACCCATATGCATTTCAATTATGGCATCCTTTCATGCTGATAATGCACCC
ATATG
Found at i:63850 original size:19 final size:19
Alignment explanation
Indices: 63780--63851 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
63770 CTATCTCCTC
* *
63780 GGTATCGATACCCCTATCAT
1 GGTATCGATA-CTCTATTAT
*
63800 GGTATTGATACTACTATATTAT
1 GGTATCGATACT-C--TATTAT
63822 GGTA-CTGATACTCTATTAT
1 GGTATC-GATACTCTATTAT
63841 GGTATCGATAC
1 GGTATCGATAC
63852 CTTTTTTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
19 16 0.37
20 11 0.26
21 1 0.02
22 15 0.35
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (19 bp):
GGTATCGATACTCTATTAT
Found at i:65738 original size:21 final size:21
Alignment explanation
Indices: 65673--65739 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
65663 AAACAAAGAA
65673 ATAAACTTCAATAGATGGATC
1 ATAAACTTCAATAGATGGATC
* *
65694 ATAAGC-T-AACT--ATAGA-C
1 ATAAACTTCAA-TAGATGGATC
*
65711 TTAAACTTCAATAGATGGATC
1 ATAAACTTCAATAGATGGATC
65732 ATAAACTT
1 ATAAACTT
65740 ACAACTTGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
17 5 0.15
18 6 0.18
19 4 0.12
20 6 0.18
21 13 0.38
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (21 bp):
ATAAACTTCAATAGATGGATC
Done.