Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000370.1 Hibiscus syriacus cultivar Beakdansim tig00000671_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: 127574
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:856 original size:15 final size:16
Alignment explanation
Indices: 836--866 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
826 AATGGGCAGT
836 AATCCCTGC-AAAAAA
1 AATCCCTGCGAAAAAA
851 AATCCCTGCGAAAAAA
1 AATCCCTGCGAAAAAA
867 TCTCTGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.13
Consensus pattern (16 bp):
AATCCCTGCGAAAAAA
Found at i:2579 original size:25 final size:26
Alignment explanation
Indices: 2516--2580 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 26
2506 ACATATCGAT
*
2516 AAACTATTAAATATTTGAAAACAATAC
1 AAACAATT-AATATTTGAAAACAATAC
*
2543 AAACAGTT-ATATTT-AAAAC-ATAC
1 AAACAATTAATATTTGAAAACAATAC
*
2566 AAAATAATTAATATT
1 -AAACAATTAATATT
2581 GACCATGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 4 0.12
24 11 0.34
25 11 0.34
27 6 0.19
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.32
Consensus pattern (26 bp):
AAACAATTAATATTTGAAAACAATAC
Found at i:3323 original size:43 final size:42
Alignment explanation
Indices: 3263--3597 Score: 409
Period size: 43 Copynumber: 7.8 Consensus size: 42
3253 CCATAGTTCA
3263 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* ** * * * *
3305 GATATCTATAGCAACGTTTTTAGAACAAACACTGCAAAAAGTC
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* * *
3348 AAGATCTATAGCGGCGTTTATGGAATAAACGCCACAAAAGGTC
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
*
3391 GAGATCTATAGCGGCGTTTTTTGAACAAACGCCGCAAAAGGTC
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
3434 AAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTC
1 -AGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTC
* * * *
3478 AGATCTATAGCGGCATTTTTAGAACAAACGCCGTAAAAGGCC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* * **
3520 AGATCTATAGCGGCGTTTCTGAACACAAACGCCGCAAAATATC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTC
* * *
3563 ATATCTATAGCAGTGTTTTTGGATACAAACGCCGC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGC
3598 TAATTACCAT
Statistics
Matches: 247, Mismatches: 43, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
42 36 0.15
43 192 0.78
44 19 0.08
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (42 bp):
AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
Found at i:6995 original size:41 final size:41
Alignment explanation
Indices: 6922--7388 Score: 358
Period size: 41 Copynumber: 11.3 Consensus size: 41
6912 TTTGTAACAC
* * * * * *
6922 AAACGCCATTAAAATACGAGTTTTTTGTGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
6963 AAACGCCATTAAAGTACAAGTCTATAACGGCGTTTGTAAACAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT--ATAA
* * *
7006 AAACGCCACGAAAGAACGAGTCTTTAGCGGCGTTTGTA-AA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
7046 AAATGCCACTAAAGTACAAGTCTATAGCAGCGTTTATAAACAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT--ATAA
* *
7089 AAACTCCACTAAAGTACGAGTCTATAGCGGCGTTTGAATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
7130 AAACGCCACTAAAGTATGAGT-TATAGCAGCATTTTTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* ** * *
7170 AAACGCCACTACAA-TACGAGT-TATAACAACGATTTATAAAAA
1 AAACGCCACTA-AAGTACGAGTCTATAGCGGCG-TTTGT-ATAA
* *
7212 AAATGCCACTAAAGTACGAGTCT-TA-CAGGTGTTTGTATAAA
1 AAACGCCACTAAAGTACGAGTCTATAGC-GGCGTTTGTAT-AA
* * *
7253 AAACGCTCA-TAAAGTATGATTCTATAGCGGCGTTTGTGTAA
1 AAACGC-CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
7294 AAATGCCACTATAGTACTAGTCTTTAGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
7335 AAATGCCACTAAAGTAAGA-TCTTTTGCGGCGTTTGT-TCAAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAT--AA
*
7376 AAACGCCGCTAAA
1 AAACGCCACTAAA
7389 AATGCCGCTA
Statistics
Matches: 340, Mismatches: 68, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
39 1 0.00
40 89 0.26
41 145 0.43
42 36 0.11
43 69 0.20
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:7013 original size:84 final size:84
Alignment explanation
Indices: 6907--7388 Score: 346
Period size: 83 Copynumber: 5.8 Consensus size: 84
6897 TTTAAATTTG
* * * * * *
6907 CGGCATTTGT-AACACAAACGCCATTAAAATACGAGTTTTTTGTGGCGTTTGTATAAAAACGCCA
1 CGGCGTTTGTAAACAAAAACGCCACTAAAATACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCA
*
6971 TTAAAGTACAAGTCTATAA
66 CTAAAGTACAAGTCTATAA
* *
6990 CGGCGTTTGTAAACAAAAACGCCACGAAAGA-ACGAGTCTTTAGCGGCGTTTGTA-AAAAATGCC
1 CGGCGTTTGTAAACAAAAACGCCACTAAA-ATACGAGTCTTTAGCGGCGTTTGTATAAAAACGCC
*
7053 ACTAAAGTACAAGTCTATAG
65 ACTAAAGTACAAGTCTATAA
* * * * * *
7073 CAGCGTTTATAAACAAAAACTCCACTAAAGTACGAGTCTATAGCGGCGTTTGAATAAAAACGCCA
1 CGGCGTTTGTAAACAAAAACGCCACTAAAATACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCA
** *
7138 CTAAAGTATGAGT-TATAG
66 CTAAAGTACAAGTCTATAA
* * * * * * * ** * * *
7156 CAGCATTTTTATAC--AAACGCCACTACAATACGAGT-TATAACAACGATTTATAAAAAAAATGC
1 CGGCGTTTGTAAACAAAAACGCCACTAAAATACGAGTCTTTAGCGGCG-TTTGT-ATAAAAACGC
*
7218 CACTAAAGTACGAGTCT-T-A
64 CACTAAAGTACAAGTCTATAA
* * * * * * * *
7237 CAGGTGTTTGTATA-AAAAACGCTCA-TAAAGTATGATTCTATAGCGGCGTTTGTGTAAAAATGC
1 C-GGCGTTTGTAAACAAAAACGC-CACTAAAATACGAGTCTTTAGCGGCGTTTGTATAAAAACGC
* * * *
7300 CACTATAGTACTAGTCTTTAG
64 CACTAAAGTACAAGTCTATAA
* * * * *
7321 CGGCGTTTGTATAC--AAATGCCACTAAAGTAAGA-TCTTTTGCGGCGTTTGT-TCAAAAAACGC
1 CGGCGTTTGTAAACAAAAACGCCACTAAAATACGAGTCTTTAGCGGCGTTTGTAT--AAAAACGC
*
7382 CGCTAAA
64 CACTAAA
7389 AATGCCGCTA
Statistics
Matches: 321, Mismatches: 60, Indels: 37
0.77 0.14 0.09
Matches are distributed among these distances:
80 8 0.02
81 39 0.12
82 80 0.25
83 128 0.40
84 65 0.20
85 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (84 bp):
CGGCGTTTGTAAACAAAAACGCCACTAAAATACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCA
CTAAAGTACAAGTCTATAA
Found at i:12458 original size:29 final size:29
Alignment explanation
Indices: 12414--12567 Score: 177
Period size: 29 Copynumber: 5.3 Consensus size: 29
12404 ATTTTATATC
*
12414 TTAACATTAAAAATATATTTTATTTTTATA
1 TTAAC-TTAAAAATATATTTTATTCTTATA
* * *
12444 TTAA-TT-TAAATATATTTTATTCTTGTC
1 TTAACTTAAAAATATATTTTATTCTTATA
* * *
12471 TTACCCTAAAAATATATTTTATTCTTATT
1 TTAACTTAAAAATATATTTTATTCTTATA
* *
12500 TTAACTTAAAAATATATTTTAATCTTTATC
1 TTAACTTAAAAATATATTTTATTC-TTATA
*
12530 TTAATTTAAAAAATATATTTTATTCTTATA
1 TTAACTT-AAAAATATATTTTATTCTTATA
12560 TTAACTTA
1 TTAACTTA
12568 TTACATAAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
27 20 0.19
28 3 0.03
29 40 0.39
30 24 0.23
31 16 0.16
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTCTTATA
Found at i:12481 original size:56 final size:59
Alignment explanation
Indices: 12401--12567 Score: 196
Period size: 60 Copynumber: 2.8 Consensus size: 59
12391 ACATATCAAA
* * * *
12401 TTAATTTTATATCTTAACATTAAAAATATATTTTATTTTTATATTAA-TT-TAAATATATT
1 TTAATCTT-TATCTTAAC-CTAAAAATATATTTTATTCTTATATTAACTTAAAAATATATT
* * * *
12460 TTATTC-TTGTCTTACCCTAAAAATATATTTTATTCTTATTTTAACTTAAAAATATATT
1 TTAATCTTTATCTTAACCTAAAAATATATTTTATTCTTATATTAACTTAAAAATATATT
**
12518 TTAATCTTTATCTTAATTTAAAAAATATATTTTATTCTTATATTAACTTA
1 TTAATCTTTATCTTAACCT-AAAAATATATTTTATTCTTATATTAACTTA
12568 TTACATAAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
56 25 0.28
57 9 0.10
58 15 0.17
59 12 0.13
60 29 0.32
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.54
Consensus pattern (59 bp):
TTAATCTTTATCTTAACCTAAAAATATATTTTATTCTTATATTAACTTAAAAATATATT
Found at i:26739 original size:2 final size:2
Alignment explanation
Indices: 26728--26764 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
26718 CAGGGTCGTT
26728 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26765 GGGATAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27167 original size:20 final size:20
Alignment explanation
Indices: 27142--27192 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
27132 CTCTTTACCT
27142 GTTTTGTCATAATGAAACTA
1 GTTTTGTCATAATGAAACTA
*
27162 GTTTTGTCATAATGAAACTG
1 GTTTTGTCATAATGAAACTA
27182 GTTTTGTCATA
1 GTTTTGTCATA
27193 TTTTTACATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (20 bp):
GTTTTGTCATAATGAAACTA
Found at i:27533 original size:74 final size:74
Alignment explanation
Indices: 27330--28192 Score: 961
Period size: 74 Copynumber: 11.8 Consensus size: 74
27320 CAACATATCT
* ** *
27330 GGTAGGTACTTTAATGTAATAGGCAGCGCCTATTTTTTTTTTACCGTTTACATTATTAGCAACC-
1 GGTAGGTATTTTAATGTAATAGATAGCGCCTA--TTTTTTTTACCGTTTACATTATTAACAACCT
*
27394 TCAAAAAAACC
64 TCAAAAAAATC
* * * * *
27405 GGTAGGTATTTTAAAGTAATA-AGTAGCGCATA-ATCTTTTACCGTTTACATTATTAACAGCCTT
1 GGTAGGTATTTTAATGTAATAGA-TAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTT
27468 CAAAAAAATC
65 CAAAAAAATC
* * * *
27478 AGTAGGTATTTTAATGTAATAGTTAGCACCTATTTTTTTTACCGTTTACATTATTAATAACCTTC
1 GGTAGGTATTTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
27543 AAAAAAAATC
66 -AAAAAAATC
* * *
27553 GGTAGGTATTTTAATGTAATAGGTAGTGCCTATTTTTTTTACTGTTTACATTATTAACAACCTTC
1 GGTAGGTATTTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
*
27618 AAAAAAACC
66 AAAAAAATC
* * * *
27627 GGTAGGTATTTTAATGTAATAGGTAAG-GCCTGTTTTTTTTTACCATTTATATTATTAACAACCT
1 GGTAGGTATTTTAATGTAATAGAT-AGCGCCT-ATTTTTTTTACCGTTTACATTATTAACAACCT
*
27691 T-AAAAAAACC
64 TCAAAAAAATC
* * *
27701 GATAGGTATTTTAATGAAATA-AGTAGCGCCTATTTTTTTTACCATTTACATTATTAACAACCTT
1 GGTAGGTATTTTAATGTAATAGA-TAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTT
27765 CAAAAAAATC
65 CAAAAAAATC
* * *
27775 GATAGATATTTTAATGTAATAGATAGCACCTATTTTTTTTACCGTTTACATTATTAACAACCTT-
1 GGTAGGTATTTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
27839 AAAAAAA-C
66 AAAAAAATC
* * * * *
27847 --T-GGTA-GTT-ATGTAATAGGTAGCGTCTATTTTTTTTACCATTTAAATTATTAACAACCTTC
1 GGTAGGTATTTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
27907 AAAAAAATC
66 AAAAAAATC
* * *
27916 GGTAGGTATTTTAATGTAATAGATAACCCCTA-TTTTTTTATCGTTTACATTATTAACAACCTT-
1 GGTAGGTATTTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
27979 AAAAAAA-C
66 AAAAAAATC
* * * * *
27987 GGTAGATATTTTAATGTAATAGATAGCACCTATTTTATTTTATCGTTTACATTATTAGCAATCTT
1 GGTAGGTATTTTAATGTAATAGATAGCGCCTATTTT-TTTTACCGTTTACATTATTAACAACCTT
* * *
28052 TAAACAAATT
65 CAAAAAAATC
* * * * *
28062 GGTAGGTATTTTAATGTAATATG-TATCACCTATTTTTTTTATCGTTTATATTATTAACAATCTT
1 GGTAGGTATTTTAATGTAATA-GATAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTT
**
28126 CCTAAAAATC
65 CAAAAAAATC
* ** * * * ** * *
28136 GATATATAATTTAATATAATAAATAGCGTTTA-TATTTTTACCGTTTATATTATTAAC
1 GGTAGGTATTTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTAAC
28193 TATTTTTAAT
Statistics
Matches: 681, Mismatches: 83, Indels: 50
0.84 0.10 0.06
Matches are distributed among these distances:
67 46 0.07
68 9 0.01
69 4 0.01
70 1 0.00
71 31 0.05
72 40 0.06
73 155 0.23
74 236 0.35
75 158 0.23
76 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (74 bp):
GGTAGGTATTTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
AAAAAAATC
Found at i:34179 original size:24 final size:24
Alignment explanation
Indices: 34162--34262 Score: 125
Period size: 24 Copynumber: 4.2 Consensus size: 24
34152 ATCAAAACAC
34162 AATTCAGGTCAAGTATCATATCAG
1 AATTCAGGTCAAGTATCATATCAG
* *
34186 AATCCAGGTCATGTATCATATCAG
1 AATTCAGGTCAAGTATCATATCAG
* * *
34210 AATCCATGTC-AGTATCAGATCAG
1 AATTCAGGTCAAGTATCATATCAG
*
34233 AATTCAGGTCATA-TATCATAACAG
1 AATTCAGGTCA-AGTATCATATCAG
34257 AATTCA
1 AATTCA
34263 AATCGAAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 19 0.29
24 46 0.70
25 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (24 bp):
AATTCAGGTCAAGTATCATATCAG
Found at i:39339 original size:17 final size:18
Alignment explanation
Indices: 39317--39354 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39307 ACGTTGTATG
39317 ATTAAAAAT-GTTTAGAT
1 ATTAAAAATAGTTTAGAT
*
39334 ATTAAATATCAGTTTAGAT
1 ATTAAAAAT-AGTTTAGAT
39353 AT
1 AT
39355 AACACGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (18 bp):
ATTAAAAATAGTTTAGAT
Found at i:49133 original size:18 final size:19
Alignment explanation
Indices: 49100--49145 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
49090 TTAGTATTTT
49100 TATTTTAAAAATTATAATA
1 TATTTTAAAAATTATAATA
49119 TATTTTAAAAA-TATAATA
1 TATTTTAAAAATTATAATA
*
49137 CATTTTAAA
1 TATTTTAAA
49146 TTTTTCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTTAAAAATTATAATA
Found at i:49381 original size:21 final size:21
Alignment explanation
Indices: 49331--49381 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
49321 TATCATCATC
*
49331 CATAGTAGATTATCATGTAAA
1 CATAGTAGATTATCACGTAAA
* *
49352 TATCA-TAGATTATCACGTAAG
1 CAT-AGTAGATTATCACGTAAA
49373 CATAGTAGA
1 CATAGTAGA
49382 CCATCAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (21 bp):
CATAGTAGATTATCACGTAAA
Found at i:50047 original size:5 final size:5
Alignment explanation
Indices: 50039--50063 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
50029 AAATAAAGTC
50039 GAATT GAATT GAATT GAATT GAATT
1 GAATT GAATT GAATT GAATT GAATT
50064 TTCAAGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
GAATT
Found at i:50846 original size:35 final size:36
Alignment explanation
Indices: 50762--50858 Score: 117
Period size: 35 Copynumber: 2.7 Consensus size: 36
50752 AATGGATTAT
* * * *
50762 GAATTTGGGGTTGAGCATGTAATTGAAGTGTTTTTG
1 GAATTTTGGGTTTAGAATGTAATTGAAGTGATTTTG
*
50798 GAA-TTTGAAGTTTAGAATGTAATTGAAGT-ATTTTG
1 GAATTTTG-GGTTTAGAATGTAATTGAAGTGATTTTG
*
50833 GAATTTTGGGTTTATAATGTAATTGA
1 GAATTTTGGGTTTAGAATGTAATTGA
50859 TGAAGGTGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
35 27 0.52
36 25 0.48
ACGTcount: A:0.29, C:0.01, G:0.27, T:0.43
Consensus pattern (36 bp):
GAATTTTGGGTTTAGAATGTAATTGAAGTGATTTTG
Found at i:55594 original size:31 final size:31
Alignment explanation
Indices: 55569--55649 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
55559 TCCATAGATT
* *
55569 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
55600 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
55631 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
55650 CCTCGACCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:58249 original size:18 final size:18
Alignment explanation
Indices: 58211--58249 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
58201 TCCCTTCTGA
*
58211 CTTAACTCCATATTCATT
1 CTTAACTCCATATTCAAT
* *
58229 CTTAACTCCTTATTTAAT
1 CTTAACTCCATATTCAAT
58247 CTT
1 CTT
58250 CCAGTACCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (18 bp):
CTTAACTCCATATTCAAT
Found at i:60463 original size:31 final size:31
Alignment explanation
Indices: 60425--60549 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
60415 CCCGAAGGAC
* * *
60425 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
60456 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
60487 CAGTCCATATGTCCCGAAGAATATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
60518 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
60549 C
1 C
60550 CCTCGATCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:69934 original size:149 final size:148
Alignment explanation
Indices: 69658--70611 Score: 921
Period size: 149 Copynumber: 6.6 Consensus size: 148
69648 TAAATCATTT
* * *
69658 TATTTCACCCGGCCTACTCCATACGTTA-AGGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACT
1 TATTTCACCCGACCTACTCCACACGTTAGA-GCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* *
69722 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACGTTGAGGCGCTCGA
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTACACGTTGAAGCGCTCGA
* *
69787 CCTGATATTAAAGCGCATTC
130 CGTGATATTAAAGCACA-TC
* *
69807 TATTTCACCCGACCTACTCTACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
1 TATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * *
69872 CCCTCTAGAAGCGCTCGGCATGAACTCTGTCTACCCTGCTTACCCTACACGTTG-AGATGCTCGG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTACACGTTGAAG-CGCTCGA
**
69936 CGTGA-ATCT---G-GGA-C
130 CGTGATAT-TAAAGCACATC
* * *
69950 -A---C-CCTG-CCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTC
1 TATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * * *
70009 CCCTTTGGAAGCGCTCGGCATGCACTCTGTCT-CCTCTGCCTACTCTAAACGTTGAAGCGCTCGG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACC-CTGCCTACCCTACACGTTGAAGCGCTCGA
* *
70073 CGTGACATTAAGGCACATC
130 CGTGATATTAAAGCACATC
*
70092 TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
1 -TATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* * * *
70157 CCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCT-CAACGTTGAAGTGCTCG
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTAC-ACGTTGAAGCGCTCG
*
70221 ACGTGATATTATAGCACATC
129 ACGTGATATTAAAGCACATC
*
70241 TTGTTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
1 -TATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* * * * *
70306 CCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCT-CAACATTGAAGTGCTCG
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTAC-ACGTTGAAGCGCTCG
* *
70370 GCGTGATATT--A-TA-A-C
129 ACGTGATATTAAAGCACATC
* * * * * * *
70385 -A---C-CCTG-CCTACTCCACAAGTTAGAGCGCCCGACGTAAGATCAAGTCATCCTGCCTATTC
1 TATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * * * * *
70444 CCCACCGGAAGCGCTCGGCATGAACTTTGTC-CCCCTTCCAACTCTTA-ACAG-TGAAGCGCTCG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTAC-CCTACAC-GTTGAAGCGCTCG
* *
70506 GCGTGA-A--AATAGGA-A--
129 ACGTGATATTAA-AGCACATC
* * * * * * * * *
70521 TA---C-CCTG-CCTACCCCATACATTAGAGCGCCCGTCGTAAGATCAGGTCATCCGGCCTATTC
1 TATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
*
70581 CCCACTGGAAGCGCTCGGCATGAACTCTGTC
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTC
70612 CCCCTTCTAA
Statistics
Matches: 706, Mismatches: 71, Indels: 68
0.84 0.08 0.08
Matches are distributed among these distances:
135 1 0.00
136 30 0.04
137 264 0.37
138 10 0.01
139 2 0.00
140 1 0.00
141 1 0.00
142 2 0.00
143 1 0.00
144 2 0.00
145 3 0.00
146 2 0.00
147 2 0.00
148 6 0.01
149 377 0.53
150 2 0.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (148 bp):
TATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTACACGTTGAAGCGCTCGAC
GTGATATTAAAGCACATC
Found at i:69980 original size:46 final size:46
Alignment explanation
Indices: 69811--70077 Score: 148
Period size: 46 Copynumber: 5.8 Consensus size: 46
69801 GCATTCTATT
* * * *
69811 TCACCC-GACCTACTCTACACGTTAGGGCGCTCGGCGTAAGAC-CAGG
1 TCACCCTG-CCTACTCCACACGTTAGAGCGCTCGGCGTGA-ACTCTGG
* *
69857 TCATCCTGCCTACTCC-C-C-TCTAGAAGCGCTCGGCATGAACTCT-G
1 TCACCCTGCCTACTCCACACGT-TAG-AGCGCTCGGCGTGAACTCTGG
* *
69901 TCTACCCTGCTTAC-CCTACACGTT-GAGATGCTCGGCGTGAA-TCTGGG
1 TC-ACCCTGCCTACTCC-ACACGTTAGAG-CGCTCGGCGTGAACTCT-GG
* * * *
69948 ACACCCTGCCTACTCCACACGTTAGAGCGCTCGACGT-AAGATCAGG
1 TCACCCTGCCTACTCCACACGTTAGAGCGCTCGGCGTGAA-CTCTGG
* * * * *
69994 TCATCCTGCCTACTCC-C-CTTTGGAAGCGCTCGGCATGCACTCT-G
1 TCACCCTGCCTACTCCACACGTTAG-AGCGCTCGGCGTGAACTCTGG
* * *
70038 TCTCCTCTGCCTACTCTAAACGTT-GAAGCGCTCGGCGTGA
1 TCACC-CTGCCTACTCCACACGTTAG-AGCGCTCGGCGTGA
70078 CATTAAGGCA
Statistics
Matches: 169, Mismatches: 31, Indels: 42
0.70 0.13 0.17
Matches are distributed among these distances:
43 1 0.01
44 19 0.11
45 52 0.31
46 81 0.48
47 15 0.09
48 1 0.01
ACGTcount: A:0.19, C:0.35, G:0.22, T:0.24
Consensus pattern (46 bp):
TCACCCTGCCTACTCCACACGTTAGAGCGCTCGGCGTGAACTCTGG
Found at i:70061 original size:137 final size:137
Alignment explanation
Indices: 69819--70616 Score: 843
Period size: 137 Copynumber: 5.7 Consensus size: 137
69809 TTTCACCCGA
* * *
69819 CCTACTCTACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTAGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * *
69884 GCTCGGCATGAACTCTGTCTACCCTGCTTACCCTACACGTTG-AGATGCTCGGCGTGA-ATCTGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAG-TGCTCGGCGTGATAT-TGG
*
69947 GACACCCTG
129 AACACCCTG
* * *
69956 CCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTTTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * *
70021 GCTCGGCATGCACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGACATTAAGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGATATT--GG
*
70086 CACATCTTATTTCACCCGG
129 ---A----A---CACCCTG
70105 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * *
70170 GCTCGGCATGTACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGTGCTCGACGTGATATTATAG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGATA-T-T-G
*
70235 CACATCTTGTTTCACCC-G
128 GA-A--------CACCCTG
70253 ACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAG
1 -CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAG
* * * **
70318 CGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCTCAACATTGAAGTGCTCGGCGTGATATTATA
65 CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGATATTGGA
70383 ACACCCTG
130 ACACCCTG
* * * * * * * *
70391 CCTACTCCACAAGTTAGAGCGCCCGACGTAAGATCAAGTCATCCTGCCTATTCCCCACCGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * * * *
70456 GCTCGGCATGAACTTTGTC-CCCCTTCCAACTCTTAACAG-TGAAGCGCTCGGCGTGAAAATAGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAAC-GTTGAAGTGCTCGGCGTG-ATATTGG
*
70519 AATACCCTG
129 AACACCCTG
* * * * * * * * *
70528 CCTACCCCATACATTAGAGCGCCCGTCGTAAGATCAGGTCATCCGGCCTATTCCCCACTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
70593 GCTCGGCATGAACTCTGTC-CCCCT
66 GCTCGGCATGAACTCTGTCTCCCCT
70617 TCTAACTCTT
Statistics
Matches: 577, Mismatches: 59, Indels: 50
0.84 0.09 0.07
Matches are distributed among these distances:
136 30 0.05
137 277 0.48
138 5 0.01
139 2 0.00
144 1 0.00
145 1 0.00
146 2 0.00
147 2 0.00
148 2 0.00
149 251 0.44
150 3 0.01
151 1 0.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (137 bp):
CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGATATTGGAA
CACCCTG
Found at i:70187 original size:286 final size:281
Alignment explanation
Indices: 69663--70642 Score: 1038
Period size: 286 Copynumber: 3.4 Consensus size: 281
69653 CATTTTATTT
* *
69663 CACCCGGCCTACTCCATACGTTA-AGGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCT
1 CACCCTGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCT
* * * * * *
69727 CTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACGTTGAGGCGCTCGACCTGA
65 CTGGAAGCGCTCGGCATGAACTCTGTCT-CCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGA
* * *
69792 TATTAAAGCGCATTCTATTTCACCCGACCTACTCTACACGTTAGGGCGCTCGGCGTAAGACCAGG
129 -ATT-AAGC-CATT-TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGG
* * *
69857 TCATCCTGCCTACTCCCCTCTAGAAGCGCTCGGCATGAACTCTGTCTACCCTGCTTACCCTACAC
190 TCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACCCTACAC
* *
69922 GTTG-AGATGCTCGGCGTGAATCTGGGA
255 GTTGAAG-TGCTCGGCGTGAATATGGAA
* *
69949 CACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTT
1 CACCCTGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
*
70014 TGGAAGCGCTCGGCATGCACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAC
66 TGGAAGCGCTCGGCATGAACTCTGTCTCC-CTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGA-
70079 ATTAAGGCACATCTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGT
129 ATTAA-GC-CAT-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGT
* *
70144 CATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCT-CAAC
191 CATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACCCTAC-AC
* *
70208 GTTGAAGTGCTCGACGTGATATTATAGCACA
255 GTTGAAGTGCTCGGCGTGA-A-TAT-GGA-A
*
70239 TCTTGTTTCACCC-GACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCT
1 --------CACCCTG-CCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCT
* * * *
70303 ACTCCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCTCAACATTGAAGTGCT
57 ACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCT-CCCTGCCTACTCTAAACGTTGAAGCGCT
** * * * * *
70368 CGGCGTG-A-T-----A-TTATAACACCCTGCCTACTCCACAAGTTAGAGCGCCCGACGTAAGAT
121 CGGCGTGAATTAAGCCATTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGAC
* * * * * * * *
70425 CAAGTCATCCTGCCTATTCCCCACCGGAAGCGCTCGGCATGAACTTTGTC-CCCCTTCCAACTCT
186 CAGGTCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTAC-CC
* *
70489 TA-ACAG-TGAAGCGCTCGGCGTGAAAATAGGAA
250 TACAC-GTTGAAGTGCTCGGCGTGAATAT-GGAA
* * * * * * * * *
70521 TACCCTGCCTACCCCATACATTAGAGCGCCCGTCGTAAGATCAGGTCATCCGGCCTATTCCCCAC
1 CACCCTGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
* * * **
70586 TGGAAGCGCTCGGCATGAACTCTGTCCCCCT-TCTAACTCTTAATATTGAAGCGCTCG
66 TGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCT-ACTCTAAACGTTGAAGCGCTCG
70643 CGAAATTCCT
Statistics
Matches: 600, Mismatches: 69, Indels: 63
0.82 0.09 0.09
Matches are distributed among these distances:
272 2 0.00
273 23 0.04
274 78 0.13
275 1 0.00
282 1 0.00
283 5 0.01
284 1 0.00
285 31 0.05
286 327 0.55
287 5 0.01
288 3 0.00
289 1 0.00
290 1 0.00
295 1 0.00
296 1 0.00
297 1 0.00
298 116 0.19
299 2 0.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (281 bp):
CACCCTGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
TGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAAT
TAAGCCATTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCC
TGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACCCTACACGTTGAA
GTGCTCGGCGTGAATATGGAA
Found at i:71655 original size:52 final size:52
Alignment explanation
Indices: 71561--71677 Score: 139
Period size: 52 Copynumber: 2.2 Consensus size: 52
71551 ATGATAAATA
* * * *
71561 AATTTTAGGATGGACATCATCAATAAAATAATTTACAATCGAAG-AAATTTC
1 AATTTCAGGGTGGACATCATCAATAAAATAAATGACAATCGAAGAAAATTTC
** *
71612 AGATTTCAGGGTGGACA-CTATCAATAAAATAAATGACTTTCGAAGAAAATTTG
1 A-ATTTCAGGGTGGACATC-ATCAATAAAATAAATGACAATCGAAGAAAATTTC
71665 AATTTCAGGGTGG
1 AATTTCAGGGTGG
71678 GCACGTACCC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
51 2 0.04
52 47 0.84
53 7 0.12
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (52 bp):
AATTTCAGGGTGGACATCATCAATAAAATAAATGACAATCGAAGAAAATTTC
Found at i:72111 original size:17 final size:18
Alignment explanation
Indices: 72086--72130 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
72076 ACTATTTCAA
*
72086 AATTTAAAAATCAACTTA-
1 AATTTAAAAA-CAAATTAT
72104 AA-TTAAAAACAAATTAT
1 AATTTAAAAACAAATTAT
72121 AATTTAAAAA
1 AATTTAAAAA
72131 GTATCCCGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
18 9 0.38
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (18 bp):
AATTTAAAAACAAATTAT
Found at i:72127 original size:18 final size:18
Alignment explanation
Indices: 72085--72130 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
72075 AACTATTTCA
*
72085 AAATTTAAAAATCAACTT
1 AAATTTAAAAATCAAATT
72103 AAA-TTAAAAA-CAAATT
1 AAATTTAAAAATCAAATT
72119 ATAATTTAAAAA
1 A-AATTTAAAAA
72131 GTATCCCGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 6 0.24
17 9 0.36
18 10 0.40
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATTTAAAAATCAAATT
Found at i:75303 original size:15 final size:16
Alignment explanation
Indices: 75267--75305 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
75257 AGAGCCTCTA
75267 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
*
75283 AATCATTCAGCGTTT-
1 AATCATTCAGCATTTG
75298 AATCATTC
1 AATCATTC
75306 TGAAGTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (16 bp):
AATCATTCAGCATTTG
Found at i:76855 original size:23 final size:24
Alignment explanation
Indices: 76828--76882 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
76818 TTTGTTCGGT
76828 TTCATTTA-ACATTTG-TGAACATG
1 TTCATTTATACATTTGCT-AACATG
* *
76851 TTCATTCATATATTTGCTAACATG
1 TTCATTTATACATTTGCTAACATG
*
76875 TCCATTTA
1 TTCATTTA
76883 GTATTTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 7 0.27
24 18 0.69
25 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.45
Consensus pattern (24 bp):
TTCATTTATACATTTGCTAACATG
Found at i:78684 original size:20 final size:19
Alignment explanation
Indices: 78647--78689 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
78637 TTAAGTATTT
*
78647 ATTTATATTTGTTATTAATA
1 ATTTATATTTCTTATTAA-A
* *
78667 ATTTATTTTTCTTTTTAAA
1 ATTTATATTTCTTATTAAA
78686 ATTT
1 ATTT
78690 TATAAGTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTATATTTCTTATTAAA
Found at i:81615 original size:197 final size:197
Alignment explanation
Indices: 81281--81678 Score: 771
Period size: 197 Copynumber: 2.0 Consensus size: 197
81271 AGCCGAAACA
81281 AGTAACACCAAAATTCAATCTCCTATAATTTAATCGTTACGGAAAGGAGCGCGCATGATGTCAAT
1 AGTAACACCAAAATTCAATCTCCTATAATTTAATCGTTACGGAAAGGAGCGCGCATGATGTCAAT
*
81346 TTCAGGAACTTCCATGGCATTGCAGACCCATTCAGGGACATCTCCTTTAGGAAACTACAAGATAG
66 TTCAGCAACTTCCATGGCATTGCAGACCCATTCAGGGACATCTCCTTTAGGAAACTACAAGATAG
81411 TGCAAAGTTTCATAAGGTTCGAGGGCGACATAGTACA-TTATAAGACTAATTTGCTCTTAAGCCT
131 TGCAAAGTTTCATAAGGTTCGAGGGCGACATAGTACATTTATAAGACTAATTTGCTCTTAAGCCT
81475 AT
196 AT
81477 AGTAACACCAAAATTCAATCTCCTATAATTTAATCGTTACGGAAAGGAGCGCAGCATGATGTCAA
1 AGTAACACCAAAATTCAATCTCCTATAATTTAATCGTTACGGAAAGGAGCGC-GCATGATGTCAA
81542 TTTCAGCAACTTCCATGGCATTGCAGACCCATTCAGGGACATCTCCTTTAGGAAACTACAAGATA
65 TTTCAGCAACTTCCATGGCATTGCAGACCCATTCAGGGACATCTCCTTTAGGAAACTACAAGATA
81607 GTGCAAAGTTTCATAAGGTTCGAGGGCGACATAGTACATTTATAAGACTAATTTGCTCTTAAGCC
130 GTGCAAAGTTTCATAAGGTTCGAGGGCGACATAGTACATTTATAAGACTAATTTGCTCTTAAGCC
81672 TAT
195 TAT
81675 AGTA
1 AGTA
81679 CAAGGATCCA
Statistics
Matches: 199, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
196 52 0.26
197 114 0.57
198 33 0.17
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (197 bp):
AGTAACACCAAAATTCAATCTCCTATAATTTAATCGTTACGGAAAGGAGCGCGCATGATGTCAAT
TTCAGCAACTTCCATGGCATTGCAGACCCATTCAGGGACATCTCCTTTAGGAAACTACAAGATAG
TGCAAAGTTTCATAAGGTTCGAGGGCGACATAGTACATTTATAAGACTAATTTGCTCTTAAGCCT
AT
Found at i:86014 original size:17 final size:17
Alignment explanation
Indices: 85992--86029 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
85982 TTAAGTCATT
*
85992 TTTTTTATAATAATTAG
1 TTTTTTATAATAATTAA
86009 TTTTTTATAATAATTAA
1 TTTTTTATAATAATTAA
86026 TTTT
1 TTTT
86030 AGAGGGACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTTTTATAATAATTAA
Found at i:89252 original size:16 final size:18
Alignment explanation
Indices: 89210--89255 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
89200 TTCACAGAAT
89210 GTAAGATTACCAGTGGGAA
1 GTAAGATTACCAG-GGGAA
89229 TGTAAGATTACCA-GGGAA
1 -GTAAGATTACCAGGGGAA
89247 -TAAGATTAC
1 GTAAGATTAC
89256 TGAGAATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.35
18 5 0.19
20 12 0.46
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (18 bp):
GTAAGATTACCAGGGGAA
Found at i:98961 original size:23 final size:23
Alignment explanation
Indices: 98925--98993 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 23
98915 CACCACAACT
*
98925 CATATA-AA-TGCACCGAAGTTC
1 CATATAGAATTGCACCGAAGTGC
*
98946 CATATAGAATTGCACCGTAGTGC
1 CATATAGAATTGCACCGAAGTGC
*** *
98969 CGCGTAGAATTGCACCGTAGTGC
1 CATATAGAATTGCACCGAAGTGC
98992 CA
1 CA
98994 CATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.15
22 2 0.05
23 32 0.80
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (23 bp):
CATATAGAATTGCACCGAAGTGC
Found at i:99180 original size:103 final size:103
Alignment explanation
Indices: 99009--99329 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
98999 TAATGTCCAT
* * *
99009 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
99074 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
99112 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
99177 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
99215 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
99280 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
99318 AAGGACCACATA
1 AAGGACCACATA
99330 GACCCTCGAC
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:105283 original size:17 final size:16
Alignment explanation
Indices: 105263--105304 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
105253 TTTCATATAT
*
105263 TTTTAAAAATTTATTG
1 TTTTAAAAATTAATTG
*
105279 ATTTTTAAAATTAATTG
1 -TTTTAAAAATTAATTG
105296 -TTTAAAAAT
1 TTTTAAAAAT
105305 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 8 0.36
17 14 0.64
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (16 bp):
TTTTAAAAATTAATTG
Found at i:105830 original size:337 final size:334
Alignment explanation
Indices: 105085--106107 Score: 1597
Period size: 334 Copynumber: 3.0 Consensus size: 334
105075 AACTCGATAA
* * * * *
105085 ATTTTAATTTTTACATAAAATTACACAATACGTATAATTTAGTATAGGAAAATTTTGAGGATAAG
1 ATTTTGATTTTT-CATGAAATTACACAATACGTATAATCTAGTATAGGAAAACTTTGAGGGTAAG
* *
105150 TATTTTAAAATATAAATAATTTTATAAAAGTTTTATAACTGATATT-TCTTTTACAAAATGATGA
65 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACAG-TATTCT-TTTTACAAAATGATGA
* *
105214 TGATGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTAAAAATTTATTG
128 TGATGATAATAAATATTTTTTAATTTAGAAAATTATAAATTTCATATATTTTTAAAAATTTATTG
* * *
105279 ATTTTTAAAATTAATTGTTTAAAAATAT-AAAAAATATAAAAATAATCTTTTAATTACAATTGAG
193 AATTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATAAACTTTTAATTACAATTGAG
* *
105343 GGATTAAATGAATTATTATTCATTGATTATT-ATTTTTAACAACAGTTAATAATGTTTATTC-TT
258 GGATCAAATGAATTATTATTCATTAATTATTAATTTTTAACAACAGTTAATAATGTTTATTCATT
105406 TTTAATAAAATT
323 TTTAATAAAATT
*
105418 ATTTTTGATTTTTCTATGAAATTACACAATACGTATAATCTAGTATAGGAAAACTTTTAGGGTAA
1 A-TTTTGATTTTTC-ATGAAATTACACAATACGTATAATCTAGTATAGGAAAACTTTGAGGGTAA
105483 GTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCAGTATTCTTTTTACAAAATGATGA
64 GTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAA-CAGTATTCTTTTTACAAAATGATGA
105548 TGATGATAATAAATATTTTTTAATTTAGAAAATTATAAATTTCATATATTTTTTAAAAATTTATT
128 TGATGATAATAAATATTTTTTAATTTAGAAAATTATAAATTTCATATA-TTTTTAAAAATTTATT
105613 GAATTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATAAACTTTTAATTACAATTGA
192 GAATTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATAAACTTTTAATTACAATTGA
*
105678 GGGATCAAATGAATTATTATTCATTAATT-TTAAATTTTTAACAACAGTTAATAATATTTATTCA
257 GGGATCAAATGAATTATTATTCATTAATTATT-AATTTTTAACAACAGTTAATAATGTTTATTCA
105742 TTTTTAATAAAATT
321 TTTTTAATAAAATT
* *
105756 ATTTTGATTTTTGCATGAAATTATACAATAAGTATAATCTAGTATAGGAAAACTTTGAGGGTAAG
1 ATTTTGATTTTT-CATGAAATTACACAATACGTATAATCTAGTATAGGAAAACTTTGAGGGTAAG
*
105821 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAAACAGTATTCCTTTTACAAAATGATGAT
65 TATTTTAAAATATGAATAATTTTATAAAAGTTTTAT-AACAGTATTCTTTTTAC--AA--A--A-
105886 GGTGATGATGATAATGATAATAAATATTTTTTAATTTAGAAAATTATAAATTTCATATACTTTTT
122 --TGATGATG---ATGATAATAAATATTTTTTAATTTAGAAAATTATAAATTTCATATA-TTTTT
*
105951 AAAAATTTATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAAATATTAAAATAAACTTTT
181 AAAAATTTATTGAATTTTAAAATTAATTGTTTAAAAATAT-AAAAAAATATTAAAATAAACTTTT
*
106016 AATTATAATTGAGGGATCAAATGAATTATTATTCATTAATTATTAATTTTTAACAACAGTTAATA
245 AATTACAATTGAGGGATCAAATGAATTATTATTCATTAATTATTAATTTTTAACAACAGTTAATA
*
106081 ATGTTTATTAATTTTTAATAAAATT
310 ATGTTTATTCATTTTTAATAAAATT
106106 AT
1 AT
106108 AATTTAAAAT
Statistics
Matches: 640, Mismatches: 25, Indels: 33
0.92 0.04 0.05
Matches are distributed among these distances:
333 2 0.00
334 159 0.25
335 49 0.08
336 60 0.09
337 138 0.22
338 18 0.03
339 2 0.00
341 1 0.00
343 1 0.00
346 8 0.01
349 90 0.14
350 110 0.17
351 2 0.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (334 bp):
ATTTTGATTTTTCATGAAATTACACAATACGTATAATCTAGTATAGGAAAACTTTGAGGGTAAGT
ATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACAGTATTCTTTTTACAAAATGATGATGA
TGATAATAAATATTTTTTAATTTAGAAAATTATAAATTTCATATATTTTTAAAAATTTATTGAAT
TTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATAAACTTTTAATTACAATTGAGGGA
TCAAATGAATTATTATTCATTAATTATTAATTTTTAACAACAGTTAATAATGTTTATTCATTTTT
AATAAAATT
Found at i:115740 original size:24 final size:26
Alignment explanation
Indices: 115677--115740 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
115667 AAACTCACAT
*
115677 TAAAATTGACATGTACTAAAATAACAA
1 TAAAATTCACAT-TACTAAAATAACAA
* *
115704 TATAA-TCATATTACT-AAATAA-AA
1 TAAAATTCACATTACTAAAATAACAA
115727 TAAAATTCACATTA
1 TAAAATTCACATTA
115741 GATTTTGTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 6 0.19
24 13 0.42
25 4 0.13
26 4 0.13
27 4 0.13
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (26 bp):
TAAAATTCACATTACTAAAATAACAA
Found at i:115866 original size:15 final size:15
Alignment explanation
Indices: 115825--115873 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
115815 AAAAATTAGC
115825 ATTTCAATTTTT-TAT
1 ATTT-AATTTTTATAT
* * *
115840 TTTTAGTATTTATAT
1 ATTTAATTTTTATAT
115855 ATTTAATTTTTATAT
1 ATTTAATTTTTATAT
115870 ATTT
1 ATTT
115874 GTATAGTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
ATTTAATTTTTATAT
Found at i:115872 original size:23 final size:22
Alignment explanation
Indices: 115838--115896 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 22
115828 TCAATTTTTT
* *
115838 ATTTTTAGTATTTATATATTTA
1 ATTTTTAATATTTATATAGTTA
*
115860 ATTTTTATATATTTGTATAGTTA
1 ATTTTTA-ATATTTATATAGTTA
**
115883 AAATTTAA-ATTTAT
1 ATTTTTAATATTTAT
115897 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 5 0.17
22 8 0.27
23 17 0.57
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
ATTTTTAATATTTATATAGTTA
Found at i:127407 original size:20 final size:20
Alignment explanation
Indices: 127378--127430 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
127368 GCAGCCTTCG
*
127378 TGCATGGATGCACAGCAA-GA
1 TGCATCGATGCACAG-AATGA
127398 TGCATCGATGCACAGAATGA
1 TGCATCGATGCACAGAATGA
*
127418 TACATCGATGCAC
1 TGCATCGATGCAC
127431 TAATTGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGAATGA
Found at i:127463 original size:54 final size:56
Alignment explanation
Indices: 127398--127523 Score: 139
Period size: 59 Copynumber: 2.2 Consensus size: 56
127388 CACAGCAAGA
** *
127398 TGCATCGATGCACAGAATGATACATCGATGCACTA-A-TTGCATTCGGTGTTTGAG
1 TGCATCGATGCACAGAATGATACATCGATAAACTAGACCTGCATTCGGTGTTTGAG
* *** *
127452 TGCATGGATGCACTTCATGATGCATCGATAAACTAGTGCACCTGCATTCGGTGTTTGAG
1 TGCATCGATGCACAGAATGATACATCGATAAACTA--G-ACCTGCATTCGGTGTTTGAG
127511 TGCATCGATGCAC
1 TGCATCGATGCAC
127524 TAGTGCAGGT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
54 28 0.48
58 1 0.02
59 29 0.50
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (56 bp):
TGCATCGATGCACAGAATGATACATCGATAAACTAGACCTGCATTCGGTGTTTGAG
Found at i:127559 original size:21 final size:21
Alignment explanation
Indices: 127533--127573 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
127523 CTAGTGCAGG
127533 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
127554 TGCATGGATGCACTGCAGGG
1 TGCATGGATGCACTGCAGGG
127574 G
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.20, G:0.39, T:0.20
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Done.