Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2139
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: 24508
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:597 original size:1 final size:1
Alignment explanation
Indices: 591--675 Score: 80
Period size: 1 Copynumber: 85.0 Consensus size: 1
581 CGTCCTCCAC
* * * ** * * *
591 AAAAAAAAAAAACAAAAAAAAACAAAACAAAAAAAAGCAAAAACAAAAAAAAAACAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
656 CAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
676 GGTCCGGATG
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:609 original size:10 final size:10
Alignment explanation
Indices: 594--675 Score: 103
Period size: 10 Copynumber: 7.8 Consensus size: 10
584 CCTCCACAAA
594 AAAAAAAAAC
1 AAAAAAAAAC
604 AAAAAAAAAC
1 AAAAAAAAAC
614 AAAACAAAAA-
1 AAAA-AAAAAC
*
624 AAAGCAAAAAC
1 AAA-AAAAAAC
635 AAAAAAAAAAC
1 -AAAAAAAAAC
646 AAAAACAAAAC
1 AAAAA-AAAAC
657 AAAAAAAAAAC
1 -AAAAAAAAAC
668 AAAAAAAA
1 AAAAAAAA
676 GGTCCGGATG
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
10 35 0.55
11 21 0.33
12 8 0.12
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:609 original size:11 final size:11
Alignment explanation
Indices: 593--675 Score: 116
Period size: 11 Copynumber: 7.7 Consensus size: 11
583 TCCTCCACAA
593 AAAAAAAAAAC
1 AAAAAAAAAAC
604 -AAAAAAAAAC
1 AAAAAAAAAAC
*
614 AAAACAAAAA-
1 AAAAAAAAAAC
**
624 AAAGCAAAAAC
1 AAAAAAAAAAC
635 AAAAAAAAAAC
1 AAAAAAAAAAC
*
646 AAAAACAAAAC
1 AAAAAAAAAAC
657 AAAAAAAAAAC
1 AAAAAAAAAAC
668 AAAAAAAA
1 AAAAAAAA
676 GGTCCGGATG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
10 19 0.30
11 45 0.70
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:632 original size:38 final size:38
Alignment explanation
Indices: 589--675 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 38
579 GGCGTCCTCC
589 ACAAAAAAAAAAAACAAAAAAAAACAAAAC-AAAAAAAA
1 ACAAAAAAAAAAAA-AAAAAAAAACAAAACAAAAAAAAA
* *
627 GCAAAAACAAAAAAAAAACAAAAACAAAACAAAAAAAAA
1 ACAAAAA-AAAAAAAAAAAAAAAACAAAACAAAAAAAAA
666 ACAAAAAAAA
1 ACAAAAAAAA
676 GGTCCGGATG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 23 0.52
39 21 0.48
ACGTcount: A:0.87, C:0.11, G:0.01, T:0.00
Consensus pattern (38 bp):
ACAAAAAAAAAAAAAAAAAAAAACAAAACAAAAAAAAA
Found at i:2110 original size:29 final size:29
Alignment explanation
Indices: 2055--2589 Score: 260
Period size: 30 Copynumber: 17.6 Consensus size: 29
2045 TCACCCTTCA
* *
2055 AAAGTCCACAAGTCAGTGACATC-TTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
2083 AAAGCCCACAAGTCAGTGGCATTTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA--TCTTTTTC
* *
2114 AAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2142 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * * *
2172 GAAGCCCACAAGCCGGTAGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2201 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
2231 TTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTTCTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCA-TC----T-TTTTC
* * *
2271 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
2300 AAAGCGCACAAGTCAGTGACATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
2329 AAAGCCCACAAGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* *
2359 AAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2387 AAAGCCCACAAATCAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
2416 TGAAGCCCCCAAGTCGGTGGCATCTTTTCC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2446 AAAGTCCACAACTCTGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
2476 TTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCA-TCTTTTTC
* * * *
2511 TTTTTAAGCCCACAAGTTAGTGGCACCATTTTC
1 ----AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2544 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
2573 AAAGCCCACAAGTCAGT
1 AAAGCCCACAAGTCAGT
2590 AGCAACCTTC
Statistics
Matches: 392, Mismatches: 81, Indels: 68
0.72 0.15 0.13
Matches are distributed among these distances:
27 41 0.10
28 63 0.16
29 69 0.18
30 82 0.21
31 26 0.07
32 21 0.05
33 7 0.02
34 18 0.05
35 44 0.11
36 15 0.04
39 1 0.00
40 5 0.01
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:2150 original size:27 final size:28
Alignment explanation
Indices: 2049--2167 Score: 107
Period size: 27 Copynumber: 4.1 Consensus size: 28
2039 CATTCCTCAC
* *
2049 CCTTCAAAAGTCCACAAGTCAGTGACAT
1 CCTTCAAAAGCCCACAAGTCAGTGGCAT
*
2077 CTTTTC-AAAGCCCACAAGTCAGTGGCATTTTT
1 C-CTTCAAAAGCCCACAAGTCAGTGGCA----T
** *
2109 TTTTCAAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAT
* *
2137 CCTTC-AAAGCCCACAAATCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAT
2164 CCTT
1 CCTT
2168 TTCCGAAGCC
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
27 24 0.32
28 23 0.30
29 3 0.04
31 4 0.05
32 22 0.29
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.24
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAT
Found at i:2382 original size:88 final size:88
Alignment explanation
Indices: 2261--2443 Score: 251
Period size: 88 Copynumber: 2.1 Consensus size: 88
2251 ATAGCACTCT
* * * *
2261 TTTTCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCGCACAAGTCAGTGACATCTTT
1 TTTT-TTTTCAAAAGCCCACAAGTCAGTGGCAACC-TTAAAAGCCCACAAATCAGTGACACCCTT
2326 TTC-AAAGCCCACAAGTCAGTGGCA
64 TTCTAAAGCCCACAAGTCAGTGGCA
* *
2350 TTTTTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTT
1 TTTTTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTAAAAGCCCACAAATCAGTGACACCCTTTT
* * *
2415 CTGAAGCCCCCAAGTCGGTGGCA
66 CTAAAGCCCACAAGTCAGTGGCA
*
2438 TCTTTT
1 TTTTTT
2444 CCAAAGTCCA
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
87 26 0.31
88 53 0.64
89 4 0.05
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (88 bp):
TTTTTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTAAAAGCCCACAAATCAGTGACACCCTTTT
CTAAAGCCCACAAGTCAGTGGCA
Found at i:2402 original size:27 final size:27
Alignment explanation
Indices: 2272--2412 Score: 129
Period size: 27 Copynumber: 5.0 Consensus size: 27
2262 TTTCTTTTCA
*
2272 AAAGCCCACAAGTCAGTGGCAACCTTTA
1 AAAGCCCACAAGTCAGTGGCAACC-TTC
* * * *
2300 AAAGCGCACAAGTCAGTGACATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAAC--CTTC
***
2329 AAAGCCCACAAGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA---ACCTTC
2359 AAAAGCCCACAAGTCAGTGGCAACCTTC
1 -AAAGCCCACAAGTCAGTGGCAACCTTC
* *
2387 AAAGCCCACAAATCAGTGGCACCCTT
1 AAAGCCCACAAGTCAGTGGCAACCTT
2413 TTCTGAAGCC
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
27 24 0.26
28 23 0.24
29 21 0.22
30 4 0.04
31 21 0.22
32 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (27 bp):
AAAGCCCACAAGTCAGTGGCAACCTTC
Found at i:2491 original size:245 final size:244
Alignment explanation
Indices: 2051--2589 Score: 895
Period size: 245 Copynumber: 2.2 Consensus size: 244
2041 TTCCTCACCC
*
2051 TTCAAAAGTCCACAAGTCAGTGACATCTTTTCAAAGCCCACAAGTCAGTGGCATTTTTTTTTCAA
1 TTCAAAAGCCCACAAGTCAGTGACATCTTTTCAAAGCCCACAAGTCAGTGGCATTTTTTTTTCAA
2116 AAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCAC
66 AAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCAC
2181 AAGCCGGTAGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCTCACA
131 AAGCCGGTAGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCTCACA
2246 ACTCTATAGCACTCTTTTTCTTTTCAAAAGCCCACAAGTCAGTGGCAACC-T
196 ACTCTATAGCACTCTTTTTCTTTT--AAAGCCCACAAGTCAGTGGC-ACCAT
*
2297 TT-AAAAGCGCACAAGTCAGTGACATCTTTTTCAAAGCCCACAAGTCAGTGGCA-TTTTTTTTCA
1 TTCAAAAGCCCACAAGTCAGTGACATC-TTTTCAAAGCCCACAAGTCAGTGGCATTTTTTTTTCA
* *
2360 AAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCTGAAGCCCC
65 AAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCA
* * *
2425 CAAGTCGGTGGCATCTTTTCCAAAGTCCACAACTCTGTGGCACTCTTTTTCTTTTGTAAGCTCAC
130 CAAGCCGGTAGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCTCAC
* *
2490 AACTCTATAGCACTCTTTTTCTTTTTAAGCCCACAAGTTAGTGGCACCATT
195 AACTCTATAGCACTCTTTTTCTTTTAAAGCCCACAAGTCAGTGGCACCA-T
* * * *
2541 TTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGT
1 TTCAAAAGCCCACAAGTCAGTGACATCTTTTCAAAGCCCACAAGTCAGT
2590 AGCAACCTTC
Statistics
Matches: 275, Mismatches: 14, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
242 3 0.01
243 18 0.07
244 23 0.08
245 203 0.74
246 28 0.10
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (244 bp):
TTCAAAAGCCCACAAGTCAGTGACATCTTTTCAAAGCCCACAAGTCAGTGGCATTTTTTTTTCAA
AAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCAC
AAGCCGGTAGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCTCACA
ACTCTATAGCACTCTTTTTCTTTTAAAGCCCACAAGTCAGTGGCACCAT
Found at i:2525 original size:34 final size:35
Alignment explanation
Indices: 2451--2525 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
2441 TTTCCAAAGT
* *
2451 CCACAACTCTGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCTATAGCACTCTTTTTCTTTTGTAAGC
*
2486 TCACAACTCTATAGCACTCTTTTTCTTTT-TAAGC
1 CCACAACTCTATAGCACTCTTTTTCTTTTGTAAGC
2520 CCACAA
1 CCACAA
2526 GTTAGTGGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.39
Consensus pattern (35 bp):
CCACAACTCTATAGCACTCTTTTTCTTTTGTAAGC
Found at i:2550 original size:30 final size:29
Alignment explanation
Indices: 2516--2639 Score: 132
Period size: 28 Copynumber: 4.3 Consensus size: 29
2506 TTTTCTTTTT
*
2516 AAGCCCACAAGTTAGTGGC-ACCATTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC--TTTCAA
2546 AAGCCCACAAGTCAGTGGCAACCTTT-AA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
2574 AAGCCCACAAGTCAGTAGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* * *
2602 AAGCACACAAGT-TGAT-GCAAACCTCTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTTCAA
2631 AAGCCCACA
1 AAGCCCACA
2640 CAAGTTGGTG
Statistics
Matches: 83, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.06
28 42 0.51
29 15 0.18
30 18 0.22
31 3 0.04
ACGTcount: A:0.38, C:0.30, G:0.15, T:0.17
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:2785 original size:49 final size:48
Alignment explanation
Indices: 2659--2888 Score: 245
Period size: 48 Copynumber: 4.8 Consensus size: 48
2649 GGCGTCTCCT
* *
2659 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCC
* * **
2707 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTCATA
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC-CC
* * * *
2756 TTTAAGTCCAATGTAGTTGACCTTGAATCAGCACATTGGCA-----CC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCC
* *
2799 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--CTTCC--C
* * *
2851 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
2889 ACATCCTTTT
Statistics
Matches: 149, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
43 36 0.24
48 42 0.28
49 35 0.23
50 1 0.01
52 35 0.23
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (48 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCC
Found at i:2823 original size:43 final size:43
Alignment explanation
Indices: 2756--2840 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
2746 CACCTTCATA
* * *
2756 TTTAAGTCCAATGTAGTTGACCTTGAATCAGCACATTGGCACC
1 TTTAAGCCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
* *
2799 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 TTTAAGCCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
2841 ATTTTCCATC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
TTTAAGCCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
Found at i:2834 original size:92 final size:95
Alignment explanation
Indices: 2659--2897 Score: 286
Period size: 92 Copynumber: 2.5 Consensus size: 95
2649 GGCGTCTCCT
* * * * * * *
2659 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGTCCAATATCGC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATT-G-A-CAT-CCTTTAAGCCCAATATAGC
2724 TGGCCTTAAATCAGCATATTGGCAC-CTT-CATA
62 TGGCCTTAAATCAGCATATTGGCACACTTCCATA
* *
2756 TTTAAGTCCAATGTAGTTGACCTTGAATCAGCACATTGGCA-CCTTTAAGCCCAATATAGCTGGC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTTAAGCCCAATATAGCTGGC
* * *
2820 CTTGAATCAGCATATTGGCACATTTTCCATC
66 CTTAAATCAGCATATTGGCACA-CTTCCATA
* *
2851 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTT
2898 TTCTCATCTT
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
92 41 0.34
94 3 0.02
95 40 0.33
96 6 0.05
97 32 0.26
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (95 bp):
TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTTAAGCCCAATATAGCTGGC
CTTAAATCAGCATATTGGCACACTTCCATA
Found at i:2868 original size:52 final size:54
Alignment explanation
Indices: 2798--2944 Score: 181
Period size: 52 Copynumber: 2.7 Consensus size: 54
2788 ACATTGGCAC
2798 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CATTTTC-CAT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
** * * * *
2850 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * *
2905 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGG
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGG
2945 TATCTTTATC
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
52 37 0.48
54 6 0.08
55 34 0.44
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (54 bp):
CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
Found at i:3786 original size:13 final size:13
Alignment explanation
Indices: 3768--3792 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3758 CATAAAGTAT
3768 TGTATCGATACAA
1 TGTATCGATACAA
3781 TGTATCGATACA
1 TGTATCGATACA
3793 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3786 original size:33 final size:33
Alignment explanation
Indices: 3748--3814 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3738 TTCAACAATT
3748 TGTATCGATACATAAAGTATTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAA
*** *
3781 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAA
3814 T
1 T
3815 TCAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTATTGTATCGATACAA
Found at i:4706 original size:13 final size:13
Alignment explanation
Indices: 4688--4713 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4678 CAATTTTTTG
4688 TGTATCGATACAT
1 TGTATCGATACAT
4701 TGTATCGATACAT
1 TGTATCGATACAT
4714 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7070 original size:21 final size:21
Alignment explanation
Indices: 7046--7092 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
7036 TTTAATGCTG
7046 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
7066 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
7087 ATTTTG
1 ATTTTG
7093 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:7231 original size:13 final size:13
Alignment explanation
Indices: 7213--7251 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
7203 ATAATCACCC
*
7213 TGTATCGATACAG
1 TGTATCGATACAA
7226 TGTATCGATACAA
1 TGTATCGATACAA
7239 TGTATCGATACAA
1 TGTATCGATACAA
7252 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:7262 original size:20 final size:20
Alignment explanation
Indices: 7237--7313 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
7227 GTATCGATAC
7237 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
7257 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
7282 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
7302 CATGTATCGATA
1 AATGTATCGATA
7314 TATTTTGGAC
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:9332 original size:15 final size:15
Alignment explanation
Indices: 9312--9342 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9302 ATTTCGTTTG
*
9312 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
9327 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
9342 G
1 G
9343 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:11175 original size:21 final size:21
Alignment explanation
Indices: 11146--11190 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
11136 AAGTTTTCAT
*
11146 TTTTCTTAGCTAA-TTCATTA
1 TTTTCTTAGCCAACTTCATTA
*
11166 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
11188 TTT
1 TTT
11191 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:13426 original size:13 final size:13
Alignment explanation
Indices: 13408--13433 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13398 CAATTTTTTG
13408 TGTATCGATACAT
1 TGTATCGATACAT
13421 TGTATCGATACAT
1 TGTATCGATACAT
13434 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13876 original size:52 final size:52
Alignment explanation
Indices: 13798--13933 Score: 245
Period size: 52 Copynumber: 2.6 Consensus size: 52
13788 TCCTAACAAT
13798 TATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACAC
1 TATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACAC
*
13850 TATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACAC
1 TATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACAC
**
13902 TATTCAATGTATCGATACATGCAGGCAAATTT
1 TATAAAATGTATCGATACATGCAGGCAAATTT
13934 TCATATTTCG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (52 bp):
TATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACAC
Found at i:19000 original size:32 final size:32
Alignment explanation
Indices: 18899--19616 Score: 816
Period size: 32 Copynumber: 23.1 Consensus size: 32
18889 AAAATGGTGA
* * * * *
18899 TTTGAAAAGGGTTACCACTGACTTGCGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * * ** *
18931 TTTTAAAAGGGTTTCCACAGA-AAGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
18962 TTTTGAAA-GAGGTTCCCATCAACTTGTGTGGGC
1 -TTTGAAATG-GGTTGCCACCGACTTGTGTGGGC
*
18995 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
19027 TTTGAAATGGATTGCCACCGACTTGTGTGGGA
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
19059 TTTGAAATGGGTTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
19091 TTTGAAATGGGTTGCCATCGACTTGTGTAGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* **
19123 TTTGAAAAGGGTTGCCACTTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
19155 TTTGAAATGGGTTTCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
19187 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
19219 TTTGAAATGGGTTGCCACCAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
19251 TTTGAAAT-AG-TGCCACCGACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
19281 TTTGAAAAGGGTTGCCACCGACTTCTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
19313 TTTGAAATGGGTTGCCACCAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
19345 TTTGAAATGGGTTGCCACC-ACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
19376 TTTGAAAT-AG-TGCCATCAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
19406 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
19438 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
19470 TTTGAAAT-AG-TGCCATCGACTTTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
19500 TTTGACAT-GG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* **
19528 TTTGAAAT-GG-TGCTACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* **
19556 TTTGAAA--GGATGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
19584 TTTGAAA--GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
19614 TTT
1 TTT
19617 TAAAAGATCC
Statistics
Matches: 605, Mismatches: 69, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
27 2 0.00
28 75 0.12
29 8 0.01
30 88 0.15
31 30 0.05
32 394 0.65
33 8 0.01
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:19805 original size:27 final size:27
Alignment explanation
Indices: 19674--20503 Score: 1194
Period size: 27 Copynumber: 30.2 Consensus size: 27
19664 GTGGGCTTTG
** *
19674 AAAAGGGTGCCACTAACTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* * **
19702 AGAAGGGAATGCCACTGCCTTGTGGACTT
1 AAAAGGG--TGCCACGGAGTTGTGGACTT
*
19731 AAAAAGGGTGCCACGGAGTTGTGAACTT
1 -AAAAGGGTGCCACGGAGTTGTGGACTT
* *
19759 AAAAGGGATGCCAGGGAGTTGTGGACAT
1 AAAAGGG-TGCCACGGAGTTGTGGACTT
19787 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
19814 AAAAGGGATGCCACGGAGTTGTGGACTT
1 AAAAGGG-TGCCACGGAGTTGTGGACTT
*
19842 AAAAGGGTGCCATGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
19869 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
19896 AAAAGGGTGCCACGAAGTTTTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
19923 AAAAGAGTGCCATGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
19950 AAAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
19978 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
20005 AAAAAAGGTGCCACGGAGTTGTGGACTT
1 -AAAAGGGTGCCACGGAGTTGTGGACTT
20033 AAAAAGGGTGCCACGGAGTTGTGGACTTT
1 -AAAAGGGTGCCACGGAGTTGTGGAC-TT
*
20062 AAAAGGGTGCCACGGAGTTGTGAACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
*
20090 AAAAGGGTGCCATGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
20117 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * **
20144 TAAAGGGTGTCATAGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
20172 AAAAGGGTGTCACGGAATTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
20199 AAAAGGATGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
20226 AAAAGGATGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
20253 AAAAGGGTGCCACGGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
20280 AAAAGGGTGCGACGGAGTGGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
20307 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
20334 AAAAGGGTGCCAGGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
20362 AAAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
20390 AAAA-GGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
** *
20416 AAAAGAATGCAACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
*
20444 AAAAGGATGCCACGGAGTTGTGGACTCT
1 AAAAGGGTGCCACGGAGTTGTGGACT-T
20472 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
20499 TAAAG
1 AAAAG
20504 AGGTCACAGT
Statistics
Matches: 733, Mismatches: 56, Indels: 27
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.01
27 393 0.54
28 308 0.42
29 4 0.01
30 22 0.03
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:19873 original size:82 final size:81
Alignment explanation
Indices: 19674--20503 Score: 1194
Period size: 82 Copynumber: 10.1 Consensus size: 81
19664 GTGGGCTTTG
** * * * **
19674 AAAAGGGTGCCACTAACTTGTGGACTTTAGAAGGGAATGCCACTGCCTTGTGGACTTAAAAAGGG
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGG--TGCCACGGAGTTGTGGACTT-AAAAGGG
*
19739 TGCCACGGAGTTGTGAACTT
62 TGCCACGGAGTTGTGGACTT
* *
19759 AAAAGGGATGCCAGGGAGTTGTGGACATAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATG
1 AAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TG
19824 CCACGGAGTTGTGGACTT
64 CCACGGAGTTGTGGACTT
*
19842 AAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* *
19907 ACGAAGTTTTGGACTT
66 ACGGAGTTGTGGACTT
* *
19923 AAAAGAGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGC
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
19988 CACGGAGTTGTGGACTT
65 CACGGAGTTGTGGACTT
*
20005 AAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGT
1 -AAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGT
*
20070 GCCACGGAGTTGTGAACTTT
63 GCCACGGAGTTGTGGAC-TT
* * *
20090 AAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGTC
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
**
20155 ATAGAGTTGTGGACTTT
66 ACGGAGTTGTGGAC-TT
* * * *
20172 AAAAGGGTGTCACGGAATTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCC
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
20237 ACGGAGTTGTGGACTT
66 ACGGAGTTGTGGACTT
* * *
20253 AAAAGGGTGCCACGGAGTTATGGACTTAAAAGGGTGCGACGGAGTGGTGGACTTAAAAGGGTGCC
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
20318 ACGGAGTTGTGGACTT
66 ACGGAGTTGTGGACTT
*
20334 AAAAGGGTGCCAGGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GGTG
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTG
20398 CCACGGAGTTGTGGACTT
64 CCACGGAGTTGTGGACTT
** * *
20416 AAAAGAATGCAACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTCTAAAAGGGTG
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACT-TAAAAGGGTG
20481 CCACGGAGTTGTGGACTT
64 CCACGGAGTTGTGGACTT
*
20499 TAAAG
1 AAAAG
20504 AGGTCACAGT
Statistics
Matches: 681, Mismatches: 54, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
81 169 0.25
82 281 0.41
83 124 0.18
84 77 0.11
85 16 0.02
86 14 0.02
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (81 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
ACGGAGTTGTGGACTT
Found at i:22020 original size:18 final size:20
Alignment explanation
Indices: 21997--22049 Score: 83
Period size: 18 Copynumber: 2.8 Consensus size: 20
21987 AAAATGCCTG
*
21997 AATGTATCGATACATT-T-T
1 AATGTATCGATACATTGTAA
22015 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGTAA
22035 AATGTATCGATACAT
1 AATGTATCGATACAT
22050 CTGGGTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 16 0.50
19 1 0.03
20 15 0.47
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTGTAA
Found at i:22090 original size:21 final size:21
Alignment explanation
Indices: 22064--22120 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
22054 GTAAACTTCC
22064 TAGATGTATCGATACAAAGAA
1 TAGATGTATCGATACAAAGAA
*
22085 TAGATGTATCGATACACAGAA
1 TAGATGTATCGATACAAAGAA
*
22106 -AAATGTATCGATACA
1 TAGATGTATCGATACA
22121 TTTCCTTGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (21 bp):
TAGATGTATCGATACAAAGAA
Found at i:22176 original size:19 final size:18
Alignment explanation
Indices: 22152--22214 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
22142 AGTGATACAT
22152 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
22171 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
22184 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
22203 TGTATCGATACA
1 TGTATCGATACA
22215 TTTACTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:22186 original size:32 final size:32
Alignment explanation
Indices: 22145--22216 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
22135 GCTTCCTAGT
22145 GATACATTGTATCGATACAAAACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
*
22177 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
22209 GATACATT
1 GATACATT
22217 TACTGAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
GATACATTGTATCGATACAAAACTTATGTATC
Found at i:22189 original size:13 final size:13
Alignment explanation
Indices: 22171--22195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22161 ACAAAACTTA
22171 TGTATCGATACAT
1 TGTATCGATACAT
22184 TGTATCGATACA
1 TGTATCGATACA
22196 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:23101 original size:14 final size:16
Alignment explanation
Indices: 23070--23116 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
23060 AAAAAAAGTC
23070 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCA-AA
23086 AAAATG-AAAAG-AAA
1 AAAATGCAAAAGCAAA
*
23100 AAAGTGCAAAAGCAAA
1 AAAATGCAAAAGCAAA
23116 A
1 A
23117 TAAAAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 13 0.48
17 1 0.04
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAATGCAAAAGCAAA
Found at i:23138 original size:37 final size:37
Alignment explanation
Indices: 23058--23139 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 37
23048 CTTCAAAATG
*
23058 ACAAAAAAAGTCAAAAGCAAAAGCACAAAAAATGAAA
1 ACAAAAAAAGTCAAAAGCAAAAGCACAAAAAAGGAAA
* * *
23095 A-GAAAAAAGTGCAAAAGCAAAA-TA-AAAAAGGGAACA
1 ACAAAAAAAGT-CAAAAGCAAAAGCACAAAAAAGGAA-A
23131 ACAAAAAAA
1 ACAAAAAAA
23140 AACAAGGACA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
35 8 0.22
36 11 0.30
37 18 0.49
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (37 bp):
ACAAAAAAAGTCAAAAGCAAAAGCACAAAAAAGGAAA
Found at i:24464 original size:28 final size:28
Alignment explanation
Indices: 24426--24502 Score: 127
Period size: 28 Copynumber: 2.7 Consensus size: 28
24416 CTGTGACCTC
24426 TTTAAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
24454 TTTAGAGTCCACAACTCCGTGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
24482 TTTAAAGTCCACAACCTCCGT
1 TTTAAAGTCCACAA-CTCCGT
24503 TGCATC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 39 0.87
29 6 0.13
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.27
Consensus pattern (28 bp):
TTTAAAGTCCACAACTCCGTGGCACCCT
Done.