Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 18 of 322
Found at i:5091498 original size:43 final size:42
Alignment explanation
Indices: 5091298--5091501 Score: 214
Period size: 43 Copynumber: 4.7 Consensus size: 42
5091288 GACCTATCGT
* * * * *
5091298 GGCGTTTGTGGAAAAAGC-TCCACTAAAGCTCCAGAGCTCTAGC
1 GGCGTTTGT-GAAAAAGCGT-CGCTAAAGGTCCTGATCTATAGC
* *
5091341 GGTGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
1 GGCGTTTGT-GAAAAAGCGTCGCTAAAGGTCCTGATCTATAGC
* * * * *
5091384 GGCGTTTATGGGAAAAA-CGCCACTAAAGGTCTTGGTCTATAGC
1 GGCG-TT-TGTGAAAAAGCGTCGCTAAAGGTCCTGATCTATAGC
*
5091427 AGCGTTTGTGAAGAAAGCGTCGCTAAAGGTCCTGATCTATAGC
1 GGCGTTTGTGAA-AAAGCGTCGCTAAAGGTCCTGATCTATAGC
5091470 GGCGTTTGTGAAGAAAGCGTCGCTAAAGGTCC
1 GGCGTTTGTGAA-AAAGCGTCGCTAAAGGTCC
5091502 CAATTTCACA
Statistics
Matches: 137, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
41 5 0.04
42 5 0.04
43 117 0.85
44 8 0.06
45 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (42 bp):
GGCGTTTGTGAAAAAGCGTCGCTAAAGGTCCTGATCTATAGC
Found at i:5091611 original size:112 final size:113
Alignment explanation
Indices: 5091406--5091613 Score: 267
Period size: 112 Copynumber: 1.8 Consensus size: 113
5091396 AAAAACGCCA
* * * *
5091406 CTAAAGGTCTTGGTCTATAGCAGCGTTTGTGAAGAAAGCGTCGCTAAAGGTCCTGATCTATAGCG
1 CTAAAGGTCTTGATCTATAGCAGCGTTTCTGAAGAAAGCGCCACTAAAGGTCCTGATCTATAGCG
* * *
5091471 GCGTTTGTGAAGAAAGCGTCGCTAAAGGTCCCAATTTCACAAACGTCG
66 GCATTTGTGAAGAAAACGCCGCTAAAGGTCCCAATTTCACAAACGTCG
* * *
5091519 CTAAAGGTCTTGATCTATAGC-GACGTTTCTG-AGGAAGTGCCACTAAAGGTCCTGATCTATAGT
1 CTAAAGGTCTTGATCTATAGCAG-CGTTTCTGAAGAAAGCGCCACTAAAGGTCCTGATCTATAGC
* ** *
5091582 GGCATTTTTGGGGAAAATGCCGCTAAAGGTCC
65 GGCATTTGTGAAGAAAACGCCGCTAAAGGTCC
5091614 TGATCTTTAG
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
112 53 0.66
113 27 0.34
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (113 bp):
CTAAAGGTCTTGATCTATAGCAGCGTTTCTGAAGAAAGCGCCACTAAAGGTCCTGATCTATAGCG
GCATTTGTGAAGAAAACGCCGCTAAAGGTCCCAATTTCACAAACGTCG
Found at i:5091613 original size:43 final size:42
Alignment explanation
Indices: 5091517--5091626 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
5091507 TCACAAACGT
* * * * *
5091517 CGCTAAAGGTCTTGATCTATAGCGACGTTTCTGAGGAAGTGC
1 CGCTAAAGGTCCTGATCTATAGTGGCATTTCTGAGGAAATGC
* * *
5091559 CACTAAAGGTCCTGATCTATAGTGGCATTTTTGGGGAAAATGC
1 CGCTAAAGGTCCTGATCTATAGTGGCATTTCTGAGG-AAATGC
*
5091602 CGCTAAAGGTCCTGATCTTTAGTGG
1 CGCTAAAGGTCCTGATCTATAGTGG
5091627 TGCTTGTAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 29 0.51
43 28 0.49
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
CGCTAAAGGTCCTGATCTATAGTGGCATTTCTGAGGAAATGC
Found at i:5092613 original size:24 final size:26
Alignment explanation
Indices: 5092576--5092624 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
5092566 AATTCAATTG
*
5092576 AATTTCTTCTCCTAATTAAACTCTGC
1 AATTTCTTCTCCTAATCAAACTCTGC
5092602 AATTT-TT-TCCTAATCAAACTCTG
1 AATTTCTTCTCCTAATCAAACTCTG
5092625 ATTAGTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.68
25 2 0.09
26 5 0.23
ACGTcount: A:0.29, C:0.24, G:0.04, T:0.43
Consensus pattern (26 bp):
AATTTCTTCTCCTAATCAAACTCTGC
Found at i:5093409 original size:27 final size:27
Alignment explanation
Indices: 5093372--5093447 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 27
5093362 AGCAGGCCAG
*
5093372 AAAAAAGAAAGGAGAAAAAAGGA-AAA
1 AAAAAAAAAAGGAGAAAAAAGGAGAAA
5093398 AAGAAAAAAAAGG-GAAAAAAAGGAGAAA
1 AA-AAAAAAAAGGAG-AAAAAAGGAGAAA
5093426 AAATAAAAAAAGGAAGAAAAAA
1 AAA-AAAAAAAGG-AGAAAAAA
5093448 AAGCCCAAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
26 3 0.07
27 19 0.44
28 14 0.33
29 6 0.14
30 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (27 bp):
AAAAAAAAAAGGAGAAAAAAGGAGAAA
Found at i:5093424 original size:37 final size:40
Alignment explanation
Indices: 5093374--5093447 Score: 109
Period size: 37 Copynumber: 1.9 Consensus size: 40
5093364 CAGGCCAGAA
*
5093374 AAAAGAAAGGAGAAAAAAGGAAAAAA-GAA-AAAAAAGGG
1 AAAAGAAAGGAGAAAAAAGAAAAAAAGGAAGAAAAAAGGG
*
5093412 AAAA-AAAGGAGAAAAAATAAAAAAAGGAAGAAAAAA
1 AAAAGAAAGGAGAAAAAAGAAAAAAAGGAAGAAAAAA
5093448 AAGCCCAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 19 0.59
38 7 0.22
39 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (40 bp):
AAAAGAAAGGAGAAAAAAGAAAAAAAGGAAGAAAAAAGGG
Found at i:5093426 original size:18 final size:18
Alignment explanation
Indices: 5093374--5093446 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
5093364 CAGGCCAGAA
5093374 AAAAGAAAGGAGAAAAAAGG
1 AAAA-AAAGGAG-AAAAAGG
* *
5093394 -AAAAAAGAAAAAAAAGGG
1 AAAAAAAGGAGAAAAA-GG
**
5093412 AAAAAAAGGAGAAAAAAT
1 AAAAAAAGGAGAAAAAGG
5093430 AAAAAAAGGAAGAAAAA
1 AAAAAAAGG-AGAAAAA
5093447 AAAGCCCAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
17 5 0.11
18 16 0.36
19 23 0.52
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (18 bp):
AAAAAAAGGAGAAAAAGG
Found at i:5094009 original size:17 final size:17
Alignment explanation
Indices: 5093989--5094035 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
5093979 ACGATACTTC
5093989 TTTAAAAAAAATTCGTG
1 TTTAAAAAAAATTCGTG
**
5094006 TTTAAAAAATTTTCGTG
1 TTTAAAAAAAATTCGTG
**
5094023 TTTTCAAAAAATT
1 TTTAAAAAAAATT
5094036 TTCATGTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (17 bp):
TTTAAAAAAAATTCGTG
Found at i:5094058 original size:54 final size:54
Alignment explanation
Indices: 5094000--5094116 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 54
5093990 TTAAAAAAAA
* ** *
5094000 TTCGTGTTTAAAAAATTTTCGTGTTTTCAAAAAATTTTCATGT-TTTCAAAAATT
1 TTCGTGTTTAAAAAATTTTCGAG-TTTCAAAAAAAATTCATGTGTCTCAAAAATT
* * *
5094054 TTCGTGTTTCAAAAGTTTTCGAGTTTCAAAAAAAATTCTTGTGTCTCAAAAATT
1 TTCGTGTTTAAAAAATTTTCGAGTTTCAAAAAAAATTCATGTGTCTCAAAAATT
5094108 TTCGTGTTT
1 TTCGTGTTT
5094117 TCAAAAAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 16 0.29
54 39 0.71
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (54 bp):
TTCGTGTTTAAAAAATTTTCGAGTTTCAAAAAAAATTCATGTGTCTCAAAAATT
Found at i:5094074 original size:17 final size:17
Alignment explanation
Indices: 5094000--5094123 Score: 124
Period size: 17 Copynumber: 6.9 Consensus size: 17
5093990 TTAAAAAAAA
*
5094000 TTCGTGTTTAAAAAATT
1 TTCGTGTTTCAAAAATT
5094017 TTCGTGTTTTCAAAAAATT
1 TTCGTG-TTTC-AAAAATT
*
5094036 TTCATGTTTTCAAAAATT
1 TTCGTG-TTTCAAAAATT
*
5094054 TTCGTGTTTCAAAAGTT
1 TTCGTGTTTCAAAAATT
*
5094071 TTCGAGTTTCAAAAAAAATT
1 TTCGTGTTTC---AAAAATT
*
5094091 CTT-GTGTCTCAAAAATT
1 -TTCGTGTTTCAAAAATT
5094108 TTCGTGTTTTCAAAAA
1 TTCGTG-TTTCAAAAA
5094124 AAATATTGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
16 2 0.02
17 35 0.39
18 23 0.26
19 17 0.19
20 11 0.12
21 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (17 bp):
TTCGTGTTTCAAAAATT
Found at i:5094140 original size:37 final size:37
Alignment explanation
Indices: 5094009--5094141 Score: 121
Period size: 37 Copynumber: 3.6 Consensus size: 37
5093999 ATTCGTGTTT
* *
5094009 AAAAAATTTTCGTGTTTTCAAAAAATTTTCATGTTTTC--
1 AAAAAATATT-GTG-TTTC-AAAAATTTTCGTGTTTTCAA
* * *
5094047 -AAAAATTTTCGTGTTTCAAAAGTTTTCGAG-TTTCAA
1 AAAAAATATT-GTGTTTCAAAAATTTTCGTGTTTTCAA
* *
5094083 AAAAAATTCTTGTGTCTCAAAAATTTTCGTGTTTTCAA
1 AAAAAA-TATTGTGTTTCAAAAATTTTCGTGTTTTCAA
*
5094121 AAAAAATATTGTATTTCAAAA
1 AAAAAATATTGTGTTTCAAAA
5094142 TTCTCATATT
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
34 4 0.05
35 10 0.12
36 4 0.05
37 47 0.59
38 15 0.19
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.42
Consensus pattern (37 bp):
AAAAAATATTGTGTTTCAAAAATTTTCGTGTTTTCAA
Found at i:5095362 original size:28 final size:28
Alignment explanation
Indices: 5095324--5095382 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
5095314 CAACTAGATA
5095324 AAAACAGATTCAAGATAGCAATGTGAAT
1 AAAACAGATTCAAGATAGCAATGTGAAT
5095352 AAAACAGATTCAAGATAGCAATGTGAAT
1 AAAACAGATTCAAGATAGCAATGTGAAT
5095380 AAA
1 AAA
5095383 TTATAGAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (28 bp):
AAAACAGATTCAAGATAGCAATGTGAAT
Found at i:5095558 original size:5 final size:5
Alignment explanation
Indices: 5095550--5095585 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
5095540 ATGTAATGTA
5095550 TAATT TAATT TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT T
5095586 TCAAGTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TAATT
Found at i:5104435 original size:27 final size:27
Alignment explanation
Indices: 5104405--5104460 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5104395 CATAAACTTT
5104405 GTCTCCACAATCAGATGATGAGATTGA
1 GTCTCCACAATCAGATGATGAGATTGA
5104432 GTCTCCACAATCAGATGATGAGATTGA
1 GTCTCCACAATCAGATGATGAGATTGA
5104459 GT
1 GT
5104461 ACATGTCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (27 bp):
GTCTCCACAATCAGATGATGAGATTGA
Found at i:5107538 original size:23 final size:22
Alignment explanation
Indices: 5107496--5107540 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
5107486 ACTTGAGGAA
*
5107496 TTTTATATATCTTTTGTTTTTC
1 TTTTATATATCTTTTATTTTTC
5107518 TTTTA-ATATCTTACTTATTTTTC
1 TTTTATATATCTT--TTATTTTTC
5107541 ATAGTTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTATATATCTTTTATTTTTC
Found at i:5116986 original size:8 final size:8
Alignment explanation
Indices: 5116973--5117008 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
5116963 AGTGAAATAT
5116973 TATTTTTA
1 TATTTTTA
*
5116981 TATTTTAA
1 TATTTTTA
5116989 TTATTTTTA
1 -TATTTTTA
5116998 TATTTTTA
1 TATTTTTA
5117006 TAT
1 TAT
5117009 AACTTTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TATTTTTA
Found at i:5116991 original size:17 final size:17
Alignment explanation
Indices: 5116971--5117003 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5116961 TTAGTGAAAT
5116971 ATTATTTTTATATTTTA
1 ATTATTTTTATATTTTA
5116988 ATTATTTTTATATTTT
1 ATTATTTTTATATTTT
5117004 TATATAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTATTTTTATATTTTA
Found at i:5120701 original size:2 final size:2
Alignment explanation
Indices: 5120696--5120732 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5120686 TCACTTGTTT
5120696 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5120733 CTCGTTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5121403 original size:27 final size:27
Alignment explanation
Indices: 5121352--5121403 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5121342 ATCACTATCG
*
5121352 TTTTAGATCATTTCTAATTTGCTCACT
1 TTTTAGATCATTTCTAATTTACTCACT
* * *
5121379 TTTTAGATCGTTTTTATTTTACTCA
1 TTTTAGATCATTTCTAATTTACTCA
5121404 ATCTTCGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (27 bp):
TTTTAGATCATTTCTAATTTACTCACT
Found at i:5125492 original size:27 final size:27
Alignment explanation
Indices: 5125431--5125595 Score: 179
Period size: 27 Copynumber: 6.1 Consensus size: 27
5125421 TTACACTGTT
* * * *
5125431 ATGACCGAAATA-CCCTATAAGATAAA
1 ATGACCAAAATACCCCCATAGGGTAAA
*
5125457 ATGACCAAAATACCCCCATATGGTAAA
1 ATGACCAAAATACCCCCATAGGGTAAA
* *
5125484 ATGATCAAAATACCCCTATAGGGTAAA
1 ATGACCAAAATACCCCCATAGGGTAAA
* **
5125511 ATAACCAAAATACCCTGATAGGGTAAA
1 ATGACCAAAATACCCCCATAGGGTAAA
* * * *
5125538 ATTATCAAAATACCCCCACAAGGTAAA
1 ATGACCAAAATACCCCCATAGGGTAAA
* *
5125565 ATAACCTAAATACCCCCATAGGGTAAA
1 ATGACCAAAATACCCCCATAGGGTAAA
5125592 ATGA
1 ATGA
5125596 TTGTTATACC
Statistics
Matches: 115, Mismatches: 23, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
26 11 0.10
27 104 0.90
ACGTcount: A:0.47, C:0.22, G:0.12, T:0.19
Consensus pattern (27 bp):
ATGACCAAAATACCCCCATAGGGTAAA
Found at i:5125512 original size:54 final size:54
Alignment explanation
Indices: 5125438--5125596 Score: 221
Period size: 54 Copynumber: 3.0 Consensus size: 54
5125428 GTTATGACCG
* * *
5125438 AAATA-CCCTATAAGATAAAATGACCAAAATACCCCCATATGGTAAAATGATCA
1 AAATACCCCTATAAGGTAAAATAACCAAAATACCCCCATAGGGTAAAATGATCA
* ** *
5125491 AAATACCCCTATAGGGTAAAATAACCAAAATACCCTGATAGGGTAAAATTATCA
1 AAATACCCCTATAAGGTAAAATAACCAAAATACCCCCATAGGGTAAAATGATCA
* * *
5125545 AAATACCCCCACAAGGTAAAATAACCTAAATACCCCCATAGGGTAAAATGAT
1 AAATACCCCTATAAGGTAAAATAACCAAAATACCCCCATAGGGTAAAATGAT
5125597 TGTTATACCC
Statistics
Matches: 91, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
53 5 0.05
54 86 0.95
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.20
Consensus pattern (54 bp):
AAATACCCCTATAAGGTAAAATAACCAAAATACCCCCATAGGGTAAAATGATCA
Found at i:5125606 original size:81 final size:80
Alignment explanation
Indices: 5125438--5125593 Score: 213
Period size: 81 Copynumber: 1.9 Consensus size: 80
5125428 GTTATGACCG
* * * * *
5125438 AAATACCCTATAAGATAAAATGACCAAAATACCCCCATATGGTAAAATGATCAAAATACCCCTAT
1 AAATACCCTATAAGATAAAATGACCAAAATACCCCCACAAGGTAAAATAACCAAAATACCCCCAT
5125503 AGGGTAAAATAACCA
66 AGGGTAAAATAACCA
* * * * *
5125518 AAATACCCTGATAGGGTAAAATTATCAAAATACCCCCACAAGGTAAAATAACCTAAATACCCCCA
1 AAATACCCT-ATAAGATAAAATGACCAAAATACCCCCACAAGGTAAAATAACCAAAATACCCCCA
5125583 TAGGGTAAAAT
65 TAGGGTAAAAT
5125594 GATTGTTATA
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 9 0.14
81 56 0.86
ACGTcount: A:0.47, C:0.22, G:0.11, T:0.20
Consensus pattern (80 bp):
AAATACCCTATAAGATAAAATGACCAAAATACCCCCACAAGGTAAAATAACCAAAATACCCCCAT
AGGGTAAAATAACCA
Found at i:5134946 original size:9 final size:9
Alignment explanation
Indices: 5134914--5135388 Score: 313
Period size: 9 Copynumber: 56.2 Consensus size: 9
5134904 TATAAATGAC
5134914 TTATGTAAG
1 TTATGTAAG
*
5134923 TTACGTAAG
1 TTATGTAAG
5134932 TTATGTAAG
1 TTATGTAAG
*
5134941 TAATGT-A-
1 TTATGTAAG
5134948 TTATGTAAG
1 TTATGTAAG
* *
5134957 TTGTGTATAATA
1 TTATG--TAA-G
*
5134969 TTATTTAAG
1 TTATGTAAG
5134978 TTATGTAAG
1 TTATGTAAG
*
5134987 TTGTGT-A-
1 TTATGTAAG
5134994 TTATGTAAG
1 TTATGTAAG
*
5135003 TTACGTAAG
1 TTATGTAAG
*
5135012 TTATGTAGG
1 TTATGTAAG
* *
5135021 CTATGT--T
1 TTATGTAAG
5135028 TTATGTAAG
1 TTATGTAAG
*
5135037 TTACGTAAG
1 TTATGTAAG
*
5135046 TTATGTAGG
1 TTATGTAAG
* **
5135055 CTA--TATT
1 TTATGTAAG
5135062 TTATGTAAG
1 TTATGTAAG
*
5135071 TTATTTAAG
1 TTATGTAAG
5135080 TTATGTAAG
1 TTATGTAAG
*
5135089 CTATGT-A-
1 TTATGTAAG
*
5135096 TTATGCAAG
1 TTATGTAAG
5135105 TTATGTAAG
1 TTATGTAAG
5135114 -TAGTGT-A-
1 TTA-TGTAAG
*
5135121 TTATGAAAG
1 TTATGTAAG
5135130 TTATGTAAG
1 TTATGTAAG
*
5135139 TTGTGT-A-
1 TTATGTAAG
5135146 TTATGTAAG
1 TTATGTAAG
*
5135155 TTACGTAAG
1 TTATGTAAG
*
5135164 TTATGTAGG
1 TTATGTAAG
*
5135173 CTATGT-A-
1 TTATGTAAG
5135180 TTATGTAAG
1 TTATGTAAG
*
5135189 TTATTTAAG
1 TTATGTAAG
5135198 TTATGTAAG
1 TTATGTAAG
5135207 TTATGTAAG
1 TTATGTAAG
5135216 -TAGTGT-A-
1 TTA-TGTAAG
*
5135223 TTATGAAAG
1 TTATGTAAG
5135232 TTATGTAAG
1 TTATGTAAG
5135241 -TAGTGT-A-
1 TTA-TGTAAG
*
5135248 TTATATAAG
1 TTATGTAAG
*
5135257 TTATAT-A-
1 TTATGTAAG
*
5135264 TTATGAAAG
1 TTATGTAAG
5135273 TTATGTAAG
1 TTATGTAAG
* *
5135282 CTGTGT-A-
1 TTATGTAAG
5135289 TTATGT-A-
1 TTATGTAAG
5135296 TTATGTAAG
1 TTATGTAAG
*
5135305 GTATGTAAG
1 TTATGTAAG
*
5135314 TTGTGT-A-
1 TTATGTAAG
5135321 TTATGT-A-
1 TTATGTAAG
5135328 TTATGTAAG
1 TTATGTAAG
*
5135337 GTATGTAAG
1 TTATGTAAG
*
5135346 TTGTGT-A-
1 TTATGTAAG
5135353 TTATGT-A-
1 TTATGTAAG
5135360 TTATGTAAG
1 TTATGTAAG
*
5135369 TTATGTGAG
1 TTATGTAAG
*
5135378 TTGTGTAAG
1 TTATGTAAG
5135387 TT
1 TT
5135389 GAGTTATGAT
Statistics
Matches: 362, Mismatches: 67, Indels: 74
0.72 0.13 0.15
Matches are distributed among these distances:
7 78 0.22
8 35 0.10
9 240 0.66
10 3 0.01
11 3 0.01
12 3 0.01
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5134954 original size:34 final size:34
Alignment explanation
Indices: 5134914--5135388 Score: 295
Period size: 34 Copynumber: 13.9 Consensus size: 34
5134904 TATAAATGAC
* *
5134914 TTATGTAAGTTACGTAAGTTATGTAAGTAATGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* * *
5134948 TTATGTAAGTTGTGTATAATATTATTTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATG--TAA-GTTATGTAAG---T-T-A--T--GTA
* * * *
5134994 TTATGTAAGTTACGTAAGTTATGTAGGCTATGTT
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* * * * *
5135028 TTATGTAAGTTACGTAAGTTATGTAGGCTATATT
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* *
5135062 TTATGTAAGTTATTTAAGTTATGTAAGCTATGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* *
5135096 TTATGCAAGTTATGTAAG-TAGTGT-A-TTATGAAA
1 TTATGTAAGTTATGTAAGTTA-TGTAAGTTATG-TA
* *
5135129 GTTATGTAAGTTGTGT-A-TTATGTAAGTTACGTAA
1 -TTATGTAAGTTATGTAAGTTATGTAAGTTATGT-A
* * *
5135163 GTTATGTAGGCTATGT-A-TTATGTAAGTTATTTAA
1 -TTATGTAAGTTATGTAAGTTATGTAAGTTATGT-A
*
5135197 GTTATGTAAGTTATGTAAG-TAGTGT-A-TTATGAAA
1 -TTATGTAAGTTATGTAAGTTA-TGTAAGTTATG-TA
* *
5135231 GTTATGTAAG-TAGTGT-A-TTATATAAGTTATATA
1 -TTATGTAAGTTA-TGTAAGTTATGTAAGTTATGTA
* * *
5135264 TTATGAAAGTTATGTAAGCTGTGT-A-TTATGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* *
5135296 TTATGTAAGGTATGTAAGTTGTGT-A-TTATGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* *
5135328 TTATGTAAGGTATGTAAGTTGTGT-A-TTATGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* *
5135360 TTATGTAAGTTATGTGAGTTGTGTAAGTT
1 TTATGTAAGTTATGTAAGTTATGTAAGTT
5135389 GAGTTATGAT
Statistics
Matches: 361, Mismatches: 48, Indels: 64
0.76 0.10 0.14
Matches are distributed among these distances:
32 109 0.30
33 20 0.06
34 183 0.51
35 4 0.01
36 7 0.02
37 8 0.02
38 1 0.00
39 1 0.00
40 1 0.00
42 1 0.00
43 7 0.02
44 4 0.01
46 15 0.04
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
Found at i:5134956 original size:25 final size:25
Alignment explanation
Indices: 5134927--5135343 Score: 296
Period size: 25 Copynumber: 16.8 Consensus size: 25
5134917 TGTAAGTTAC
*
5134927 GTAAGTTATGTAAGTAATGTATTAT
1 GTAAGTTATGTAAGTTATGTATTAT
* *
5134952 GTAAGTTGTGT-A--TA-ATATTAT
1 GTAAGTTATGTAAGTTATGTATTAT
* *
5134973 TTAAGTTATGTAAGTTGTGTATTAT
1 GTAAGTTATGTAAGTTATGTATTAT
* *
5134998 GTAAGTTACGTAAGTTATGTAGGCTAT
1 GTAAGTTATGTAAGTTATGTA--TTAT
* *
5135025 GT--TTTATGTAAGTTACGTAAGTTAT
1 GTAAGTTATGTAAGTTATGT-A-TTAT
* * **
5135050 GTAGGCTA--TATTTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGT-A-TTAT
* *
5135075 TTAAGTTATGTAAGCTATGTATTAT
1 GTAAGTTATGTAAGTTATGTATTAT
*
5135100 GCAAGTTATGTAAG-TAGTGTATTAT
1 GTAAGTTATGTAAGTTA-TGTATTAT
* *
5135125 GAAAGTTATGTAAGTTGTGTATTAT
1 GTAAGTTATGTAAGTTATGTATTAT
* *
5135150 GTAAGTTACGTAAGTTATGTAGGCTAT
1 GTAAGTTATGTAAGTTATGTA--TTAT
*
5135177 GT-A-TTATGTAAGTTATTTAAGTTAT
1 GTAAGTTATGTAAGTTATGT-A-TTAT
5135202 GTAAGTTATGTAAG-TAGTGTATTAT
1 GTAAGTTATGTAAGTTA-TGTATTAT
*
5135227 GAAAGTTATGTAAG-TAGTGTATTAT
1 GTAAGTTATGTAAGTTA-TGTATTAT
* * *
5135252 ATAAGTTATAT-A-TTATGAAAGTTAT
1 GTAAGTTATGTAAGTTATG-TA-TTAT
* *
5135277 GTAAGCTGTGT-A-TTATGTATTAT
1 GTAAGTTATGTAAGTTATGTATTAT
* *
5135300 GTAAGGTATGTAAGTTGTGTATTAT
1 GTAAGTTATGTAAGTTATGTATTAT
*
5135325 GT-A-TTATGTAAGGTATGTA
1 GTAAGTTATGTAAGTTATGTA
5135344 AGTTGTGTAT
Statistics
Matches: 314, Mismatches: 54, Indels: 50
0.75 0.13 0.12
Matches are distributed among these distances:
21 15 0.05
22 2 0.01
23 28 0.09
24 11 0.04
25 219 0.70
26 9 0.03
27 30 0.10
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.45
Consensus pattern (25 bp):
GTAAGTTATGTAAGTTATGTATTAT
Found at i:5135297 original size:7 final size:7
Alignment explanation
Indices: 5135285--5135366 Score: 56
Period size: 7 Copynumber: 10.6 Consensus size: 7
5135275 ATGTAAGCTG
5135285 TGTATTA
1 TGTATTA
5135292 TGTATTA
1 TGTATTA
*
5135299 TGTAAGGTA
1 TGT-A-TTA
*
5135308 TGTAAGTTG
1 TGT-A-TTA
5135317 TGTATTA
1 TGTATTA
5135324 TGTATTA
1 TGTATTA
*
5135331 TGTAAGGTA
1 TGT-A-TTA
*
5135340 TGTAAGTTG
1 TGT-A-TTA
5135349 TGTATTA
1 TGTATTA
5135356 TGTATTA
1 TGTATTA
5135363 TGTA
1 TGTA
5135367 AGTTATGTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
7 35 0.56
8 4 0.06
9 24 0.38
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (7 bp):
TGTATTA
Found at i:5135396 original size:32 final size:32
Alignment explanation
Indices: 5135117--5135384 Score: 230
Period size: 32 Copynumber: 7.9 Consensus size: 32
5135107 ATGTAAGTAG
* *
5135117 TGTATTATGAAAGTTATGTAAGTTGTGTATTA
1 TGTATTATGTAAGGTATGTAAGTTGTGTATTA
* * * * *
5135149 TGTAAGTTACGTAAGTTATGTAGGCTATGTATTA
1 TGT-A-TTATGTAAGGTATGTAAGTTGTGTATTA
* * * *
5135183 TGTAAGTTATTTAAGTTATGTAAGTTATGTAAGTA
1 TGT-A-TTATGTAAGGTATGTAAGTTGTGT-ATTA
* * *
5135218 GTGTATTATGAAAGTTATGTAAGTAGTGTATTATA
1 -TGTATTATGTAAGGTATGTAAGTTGTGTA-T-TA
* * *
5135253 TAAGTTATATATTATGAAAGTTATGTAAGCTGTGTATTA
1 T--G-----TATTATGTAAGGTATGTAAGTTGTGTATTA
5135292 TGTATTATGTAAGGTATGTAAGTTGTGTATTA
1 TGTATTATGTAAGGTATGTAAGTTGTGTATTA
5135324 TGTATTATGTAAGGTATGTAAGTTGTGTATTA
1 TGTATTATGTAAGGTATGTAAGTTGTGTATTA
* *
5135356 TGTATTATGTAAGTTATGTGAGTTGTGTA
1 TGTATTATGTAAGGTATGTAAGTTGTGTA
5135385 AGTTGAGTTA
Statistics
Matches: 201, Mismatches: 22, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
32 89 0.44
33 2 0.01
34 70 0.35
35 6 0.03
36 4 0.02
37 1 0.00
39 3 0.01
40 1 0.00
41 25 0.12
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.45
Consensus pattern (32 bp):
TGTATTATGTAAGGTATGTAAGTTGTGTATTA
Found at i:5135679 original size:121 final size:121
Alignment explanation
Indices: 5135541--5136035 Score: 660
Period size: 121 Copynumber: 4.1 Consensus size: 121
5135531 TACACATAAA
* *
5135541 ATAGGTAATATAT-CCATACTAATATAGGTGATATATTAAAAATATAGATTT-TA-ATATTTAAA
1 ATAGGTTATAT-TCCCATACTAATATAGGTGATATATTAAAAATATAG-TTTAAACATATTT-AA
* * *
5135603 AATATAAAATAAATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTGAAAT
63 AATATAAAATAAATAAATATGTTTAAAATTTAAAAAGTAATTAGTAATGAATCTGAAAT
* *
5135662 ATAGGTTATATTCCCATACTAATATAGGTGATAGATTAAAAATATAGGTTT-TA-ATATTTAAAA
1 ATAGGTTATATTCCCATACTAATATAGGTGATATATTAAAAATATA-GTTTAAACATATTT-AAA
* ** *
5135725 ATATAAAATAAATAATTATGTTTAAAATTTAAAAAGTTGTTAGTAATGAATTTGAAAT
64 ATATAAAATAAATAAATATGTTTAAAATTTAAAAAGTAATTAGTAATGAATCTGAAAT
* * *
5135783 ATAGGTTATATTCCCATACTAATATAGGTTATATATTAACAATAAAGTTTAAACATATTTAAAAT
1 ATAGGTTATATTCCCATACTAATATAGGTGATATATTAAAAATATAGTTTAAACATATTTAAAAT
* ** * *
5135848 ATAATATTTATAAATATTTTTAAAATTTAAAAAATAATTAGTAATGAATCTGAAAT
66 ATAAAATAAATAAATATGTTTAAAATTTAAAAAGTAATTAGTAATGAATCTGAAAT
* *
5135904 ATAGGTTATATTCCCATACTAATATAGGTTATATATTAACAATATAGTTTAAACATATTTAAAAT
1 ATAGGTTATATTCCCATACTAATATAGGTGATATATTAAAAATATAGTTTAAACATATTTAAAAT
* * * * *
5135969 ATACTAGT-TATAAATATTTTTAAAAATTAAAAAGTAATTAGTAATGAATCTGAAAT
66 ATA-AAATAAATAAATATGTTTAAAATTTAAAAAGTAATTAGTAATGAATCTGAAAT
5136025 ATAGGTTATAT
1 ATAGGTTATAT
5136036 ATTTGATTAA
Statistics
Matches: 346, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
120 5 0.01
121 333 0.96
122 8 0.02
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.39
Consensus pattern (121 bp):
ATAGGTTATATTCCCATACTAATATAGGTGATATATTAAAAATATAGTTTAAACATATTTAAAAT
ATAAAATAAATAAATATGTTTAAAATTTAAAAAGTAATTAGTAATGAATCTGAAAT
Found at i:5135851 original size:24 final size:25
Alignment explanation
Indices: 5135824--5135878 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
5135814 TATATTAACA
5135824 ATAAAGTT-TAAACATATTTAAAAT
1 ATAAAGTTATAAACATATTTAAAAT
* * *
5135848 ATAATATTTATAAATATTTTTAAAAT
1 ATAA-AGTTATAAACATATTTAAAAT
*
5135874 TTAAA
1 ATAAA
5135879 AAATAATTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 4 0.16
25 4 0.16
26 17 0.68
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
ATAAAGTTATAAACATATTTAAAAT
Found at i:5139017 original size:14 final size:14
Alignment explanation
Indices: 5138994--5139043 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
5138984 ACCCCCAACA
*
5138994 CCTAAACCTTAAAC
1 CCTAACCCTTAAAC
5139008 CCTAACCCTTAAAC
1 CCTAACCCTTAAAC
* * *
5139022 CATAATCCTAAAAC
1 CCTAACCCTTAAAC
5139036 CCTTAACC
1 CC-TAACC
5139044 TATATTCGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
14 25 0.86
15 4 0.14
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTAACCCTTAAAC
Found at i:5139020 original size:21 final size:20
Alignment explanation
Indices: 5138972--5139022 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
5138962 AACCTTAAAC
* * *
5138972 CCCTAACCCTTAACCCCCAA
1 CCCTAAACCTTAAACCCTAA
5138992 CACCTAAACCTTAAACCCTAA
1 C-CCTAAACCTTAAACCCTAA
5139013 CCCTTAAACC
1 CCC-TAAACC
5139023 ATAATCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (20 bp):
CCCTAAACCTTAAACCCTAA
Found at i:5139439 original size:113 final size:111
Alignment explanation
Indices: 5139238--5139962 Score: 528
Period size: 114 Copynumber: 6.5 Consensus size: 111
5139228 TGGTGTTTTC
* * * * * * *
5139238 AAAAATCGCCGCTAATGCTTGACTTTTACGGCGCTTTTTGTAAAA-CGCCGCTAATGACTGT-AA
1 AAAAAGCGCCGCTAATGCTTGACTTCTGCGGCG-TTTTTATAAAAGCGCCACTAATGTCTCTAAA
* * * * *
5139301 CGCTCAACAAAAAATGAAGCCGTTTGCTTAAAATTTTTGCAGCGCTTCTA
65 C-CTCAACAAAAAA--ACGTCGTTTGCTTAAAACTTTTGCGGCGCTTCTG
* *
5139351 AAAAAGCGCCGCTAATACTTGACTTCTGCGGCGTTTTTATAAAAGCGCCACTAATGTCTGTAAAC
1 AAAAAGCGCCGCTAATGCTTGACTTCTGCGGCGTTTTTATAAAAGCGCCACTAATGTCTCTAAAC
* * * *
5139416 CTCAACAAAAAACATTGTTGTTTGCTTATAAACTTTTGCGGTGCTACTG
66 CTCAACAAAAAA-A-CGTCGTTTGCTTA-AAACTTTTGCGGCGCTTCTG
** * * * * * ** *
5139465 TGAAAGCGCGGCTAATTCCTGACTTTTGCGGTGTTTTTAGGAAAGCGCCACTAATGTCTCTAAAA
1 AAAAAGCGCCGCTAATGCTTGACTTCTGCGGCGTTTTTATAAAAGCGCCACTAATGTCTCTAAAC
* * * * * * *
5139530 CTGAAAAAACAAACGACGTCGTTTGCTTGAAACTTATGTGGGGCTTTTG
66 CTCAACAAA-AAA--ACGTCGTTTGCTTAAAACTTTTGCGGCGCTTCTG
* * * *
5139579 AAAAAGTGCTGCTAATGAC-TGACTTCTGCGGCGTTTTTCA-AAAAGCGCCACTACTGTCTGTAA
1 AAAAAGCGCCGCTAATG-CTTGACTTCTGCGGCGTTTTT-ATAAAAGCGCCACTAATGTCTCTAA
* * * * **
5139642 AGCTCAACAAAAATGACGTCGTTTGCTTAGAAACTTTTGTGGCACTAATG
64 ACCTCAACAAAAA-AACGTCGTTTGCTTA-AAACTTTTGCGGCGCTTCTG
* * * * * *
5139692 AGAAGGCACCGCTAATGCTTGACTTCTGCGGCGTTTTT-TGGAAAGCCCCACTAATGTGTCTAAA
1 AAAAAGCGCCGCTAATGCTTGACTTCTGCGGCGTTTTTAT-AAAAGCGCCACTAATGTCTCTAAA
* * * **
5139756 CCTCAACAAAAAAAATGACATTGTTTG-TTAAAACCTTT---GCG-AAC--
65 CCTCAAC--AAAAAA--ACGTCGTTTGCTTAAAACTTTTGCGGCGCTTCTG
* * * * *
5139800 -AAAAGTGTCGCTAATGCTTGACTTCTGCGGCATTTTT-TGGAAAGCGCCACTAATGTGTCTAAA
1 AAAAAGCGCCGCTAATGCTTGACTTCTGCGGCGTTTTTAT-AAAAGCGCCACTAATGTCTCTAAA
* * *
5139863 CCTCAACAAAAAAACGTCGTTTG-TTAAAACCTTTGCAGCGCTTTTG
65 CCTCAACAAAAAAACGTCGTTTGCTTAAAACTTTTGCGGCGCTTCTG
* * * * *
5139909 AGAAAGCGTCGCTAATGCTTGACTTTTGCGGC-TTTTATTTAGAAGCGCCACTAA
1 AAAAAGCGCCGCTAATGCTTGACTTCTGCGGCGTTTT-TATAAAAGCGCCACTAA
5139963 GGTATTTGAG
Statistics
Matches: 493, Mismatches: 93, Indels: 55
0.77 0.15 0.09
Matches are distributed among these distances:
103 19 0.04
105 6 0.01
106 3 0.01
107 63 0.13
109 4 0.01
110 42 0.09
111 3 0.01
112 25 0.05
113 138 0.28
114 158 0.32
115 23 0.05
116 9 0.02
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (111 bp):
AAAAAGCGCCGCTAATGCTTGACTTCTGCGGCGTTTTTATAAAAGCGCCACTAATGTCTCTAAAC
CTCAACAAAAAAACGTCGTTTGCTTAAAACTTTTGCGGCGCTTCTG
Found at i:5144870 original size:9 final size:9
Alignment explanation
Indices: 5144841--5144877 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5144831 TGAGTTTTTG
5144841 AATTCGAAT
1 AATTCGAAT
*
5144850 AACTCGAAT
1 AATTCGAAT
5144859 AATTCGAAT
1 AATTCGAAT
*
5144868 AATTTGAAT
1 AATTCGAAT
5144877 A
1 A
5144878 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5145124 original size:30 final size:31
Alignment explanation
Indices: 5145090--5145149 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
5145080 AAACATTTTA
*
5145090 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAAATTTTACTCCCTTCCCAC
* *
5145120 TTTTCCCCTAAAAATTTTATTCCCTTCCCA
1 TTTTCCCCCAAAAATTTTACTCCCTTCCCA
5145150 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAAATTTTACTCCCTTCCCAC
Found at i:5145806 original size:5 final size:5
Alignment explanation
Indices: 5145796--5145821 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5145786 GAACAAATAT
5145796 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
5145822 ATTCTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:5149149 original size:110 final size:107
Alignment explanation
Indices: 5148893--5149212 Score: 399
Period size: 110 Copynumber: 2.9 Consensus size: 107
5148883 ATTCAAGAGG
* * *
5148893 ATATTTGGCAATTTGGTTAAACGAGAAATCAAAACCCAGTACCTTAGGGCACGTTCCTCGAATTT
1 ATATTTAGCAATTTGGTTGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTT
* *
5148958 CCAAACGCAAAACATTGCCTTATTTTGTAATTTTTGAAAAGG
66 CCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAAAAGA
* * * *
5149000 ATATTAAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCGAAT
1 ATATTTAGCAATTTGGTTGAACGAG--AAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAAT
5149065 TTCCAAACCGCAAAACATTGCCTTATTTTTGAAAAGTTTTT-AAAAGA
64 TTCCAAA-CGCAAAACATTGCCTTA-TTTTG-AAA-TTTTTGAAAAGA
* * * * *
5149112 ATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACATTAGGGCATGTTTTCTCGAATT
1 ATATTTAGCAATTTGGTTGAACGAGAAATCGAAACCCAGTACCTTAGGGCACG-TTCCTCGAATT
* * * * *
5149177 TCCAAAGGCTAAATATTGCCTCATTTAGAAATTTTT
65 TCCAAACGCAAAACATTGCCTTATTTTGAAATTTTT
5149213 TTGCTTTTTT
Statistics
Matches: 184, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
107 26 0.14
108 3 0.02
109 46 0.25
110 54 0.29
111 21 0.11
112 29 0.16
113 5 0.03
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (107 bp):
ATATTTAGCAATTTGGTTGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTT
CCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAAAAGA
Found at i:5149359 original size:26 final size:26
Alignment explanation
Indices: 5149308--5149363 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5149298 TATATGTATG
* *
5149308 TATATAAAATTATGAAAATGTGAAAA
1 TATATAAAATTATGAAAATATAAAAA
*
5149334 TATATATAAATTAT-AAGATATAAAAA
1 TATATA-AAATTATGAAAATATAAAAA
5149360 TATA
1 TATA
5149364 AGTATGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (26 bp):
TATATAAAATTATGAAAATATAAAAA
Found at i:5151908 original size:132 final size:132
Alignment explanation
Indices: 5151459--5151854 Score: 693
Period size: 132 Copynumber: 3.0 Consensus size: 132
5151449 CTTCTGTCTG
*
5151459 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGA
** * * * *
5151524 TAAGATTCACCATCTTCAATCTACTCCACTACTGCTTAGGGTAACAGAATCTACAATCTTCAACC
66 TAAGATTCACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
5151589 TA
131 TA
*
5151591 CTCCAATACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGA
* * *
5151656 TAAGATTCACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACGGAATCTGCGATCTTCGACC
66 TAAGATTCACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
5151721 TA
131 TA
5151723 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGA
5151788 TAAGATTCACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
66 TAAGATTCACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
5151853 TA
131 TA
5151855 TTTCACTGCC
Statistics
Matches: 249, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 249 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (132 bp):
CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGA
TAAGATTCACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
TA
Found at i:5153054 original size:21 final size:21
Alignment explanation
Indices: 5153028--5153074 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5153018 GGTATAGCAA
5153028 GATCACCACATGCCCCAATC-T
1 GATCACCACATGCCCC-ATCTT
**
5153049 GATCACTTCATGCCCCATCTT
1 GATCACCACATGCCCCATCTT
5153070 GATCA
1 GATCA
5153075 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.26, C:0.38, G:0.11, T:0.26
Consensus pattern (21 bp):
GATCACCACATGCCCCATCTT
Found at i:5153922 original size:6 final size:6
Alignment explanation
Indices: 5153911--5153954 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
5153901 TTGACCTCTC
* *
5153911 CTTTTT CTTTTT CTTTTT ATTTCT -TTTTT CTTTTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT CTTTTT CT
5153955 CCTATTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.12
6 23 0.70
7 6 0.18
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:5153928 original size:7 final size:7
Alignment explanation
Indices: 5153912--5153952 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
5153902 TGACCTCTCC
5153912 TTTTTCT
1 TTTTTCT
*
5153919 TTTTCTTT
1 TTTT-TCT
5153927 TTATTTCT
1 TT-TTTCT
5153935 TTTTTCT
1 TTTTTCT
5153942 TTTTTCT
1 TTTTTCT
5153949 TTTT
1 TTTT
5153953 CTCCTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 20 0.67
8 8 0.27
9 2 0.07
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:5153962 original size:23 final size:21
Alignment explanation
Indices: 5153907--5153962 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
5153897 CGCCTTGACC
5153907 TCTCCTTTTTCTTTTTCTTTTT
1 TCTCCTTTTTCTTTTTC-TTTT
* *
5153929 ATTTCTTTTTTCTTTTTTCTTTT
1 -TCTCCTTTTTC-TTTTTCTTTT
5153952 TCTCCTATTTT
1 TCTCCT-TTTT
5153963 TGACTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 4 0.15
23 17 0.63
24 6 0.22
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.77
Consensus pattern (21 bp):
TCTCCTTTTTCTTTTTCTTTT
Found at i:5153962 original size:24 final size:23
Alignment explanation
Indices: 5153908--5153963 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
5153898 GCCTTGACCT
5153908 CTCC-TTTTTCTTTTTCTTTTTA
1 CTCCTTTTTTCTTTTTCTTTTTA
* *
5153930 TTTCTTTTTTCTTTTTTCTTTTT-
1 CTCCTTTTTTC-TTTTTCTTTTTA
5153953 CTCCTATTTTT
1 CTCCT-TTTTT
5153964 GACTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 9 0.33
24 16 0.59
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.77
Consensus pattern (23 bp):
CTCCTTTTTTCTTTTTCTTTTTA
Found at i:5153998 original size:36 final size:35
Alignment explanation
Indices: 5153959--5154028 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 35
5153949 TTTTCTCCTA
5153959 TTTTTGACTTTTATT-TTTTGATTGATTTTTTTTTGAT
1 TTTTTGA-TTTT-TTATTTT-ATTGATTTTTTTTTGAT
*
5153996 TTTTTGATTTTTTGATTTTTTTGATTTTTTTTT
1 TTTTTGATTTTTT-ATTTTATTGATTTTTTTTT
5154029 AGTCTGAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
35 2 0.07
36 17 0.57
37 11 0.37
ACGTcount: A:0.11, C:0.01, G:0.10, T:0.77
Consensus pattern (35 bp):
TTTTTGATTTTTTATTTTATTGATTTTTTTTTGAT
Found at i:5154000 original size:8 final size:8
Alignment explanation
Indices: 5153967--5154025 Score: 70
Period size: 8 Copynumber: 7.5 Consensus size: 8
5153957 TATTTTTGAC
5153967 TTTT-ATT
1 TTTTGATT
5153974 TTTTGATT
1 TTTTGATT
*
5153982 GATTT--TT
1 -TTTTGATT
5153989 TTTTGATT
1 TTTTGATT
5153997 TTTTGATT
1 TTTTGATT
5154005 TTTTGATTT
1 TTTTGA-TT
5154014 TTTTGATT
1 TTTTGATT
5154022 TTTT
1 TTTT
5154026 TTTAGTCTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
6 3 0.07
7 6 0.13
8 25 0.56
9 11 0.24
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (8 bp):
TTTTGATT
Found at i:5154023 original size:16 final size:16
Alignment explanation
Indices: 5153967--5154025 Score: 70
Period size: 17 Copynumber: 3.8 Consensus size: 16
5153957 TATTTTTGAC
5153967 TTTT-ATTTTTTGATT
1 TTTTGATTTTTTGATT
*
5153982 GATTT--TTTTTTGATT
1 -TTTTGATTTTTTGATT
5153997 TTTTGATTTTTTGATTT
1 TTTTGATTTTTTGA-TT
5154014 TTTTGATTTTTT
1 TTTTGATTTTTT
5154026 TTTAGTCTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
14 3 0.08
15 10 0.26
16 11 0.29
17 14 0.37
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (16 bp):
TTTTGATTTTTTGATT
Found at i:5155304 original size:19 final size:20
Alignment explanation
Indices: 5155275--5155323 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5155265 CACTTCGTGA
* *
5155275 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
5155294 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
5155314 AAATG-AATGC
1 AAATGTAATGC
5155324 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:5155832 original size:19 final size:20
Alignment explanation
Indices: 5155803--5155851 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5155793 CACTTCGTGA
* *
5155803 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
5155822 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
5155842 AAATG-AATGC
1 AAATGTAATGC
5155852 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:5155984 original size:528 final size:528
Alignment explanation
Indices: 5154988--5156044 Score: 2114
Period size: 528 Copynumber: 2.0 Consensus size: 528
5154978 TAATTATTTA
5154988 GAACACTCCCGAGTTTATAAGGGCGGATATCTAACAAGGTCCCTTTTCAGTTGTCTTCATGTATG
1 GAACACTCCCGAGTTTATAAGGGCGGATATCTAACAAGGTCCCTTTTCAGTTGTCTTCATGTATG
5155053 ACATTGATATGAACATTTTTTGACCTCTTCACAAAACTCTATCTTGCTGGACCTTAGGTTACCGC
66 ACATTGATATGAACATTTTTTGACCTCTTCACAAAACTCTATCTTGCTGGACCTTAGGTTACCGC
5155118 TCTTATATTTGCAGTTGTAGTTGGTCTTGCCTCCCCCTTTGGAATCGTTCAAGTTTTTTAATCTT
131 TCTTATATTTGCAGTTGTAGTTGGTCTTGCCTCCCCCTTTGGAATCGTTCAAGTTTTTTAATCTT
5155183 TGGTCCATGTTTTTTTTTATTCGGGTACCGCAAAAATGTTGGTTTTCCAGACTTTTCTGAAATAA
196 TGGTCCATGTTTTTTTTTATTCGGGTACCGCAAAAATGTTGGTTTTCCAGACTTTTCTGAAATAA
5155248 TTTTACCTAATTAAGGTCACTTCGTGAAAATCTAATGCATATGATGCAATGTAATGCAAATGCAT
261 TTTTACCTAATTAAGGTCACTTCGTGAAAATCTAATGCATATGATGCAATGTAATGCAAATGCAT
5155313 GAAATGAATGCCTAAAGAGACGTTGATTCTGATTCAATTACATTTAGGAAGCTTTTCTAGAAAGT
326 GAAATGAATGCCTAAAGAGACGTTGATTCTGATTCAATTACATTTAGGAAGCTTTTCTAGAAAGT
5155378 AAATTCCCTTACACAAAACGGATACATGTACGACCTCACCCACATATTCCAAGAAACATCGGTCT
391 AAATTCCCTTACACAAAACGGATACATGTACGACCTCACCCACATATTCCAAGAAACATCGGTCT
5155443 TTTTCTTCATCTGCATGCTTGAGGTAATCTCGCCAATAGATGCCATTGCTAGCTCATTTTCTTGA
456 TTTTCTTCATCTGCATGCTTGAGGTAATCTCGCCAATAGATGCCATTGCTAGCTCATTTTCTTGA
5155508 TCTTGGTC
521 TCTTGGTC
5155516 GAACACTCCCGAGTTTATAAGGGCGGATATCTAACAAGGTCCCTTTTCAGTTGTCTTCATGTATG
1 GAACACTCCCGAGTTTATAAGGGCGGATATCTAACAAGGTCCCTTTTCAGTTGTCTTCATGTATG
5155581 ACATTGATATGAACATTTTTTGACCTCTTCACAAAACTCTATCTTGCTGGACCTTAGGTTACCGC
66 ACATTGATATGAACATTTTTTGACCTCTTCACAAAACTCTATCTTGCTGGACCTTAGGTTACCGC
5155646 TCTTATATTTGCAGTTGTAGTTGGTCTTGCCTCCCCCTTTGGAATCGTTCAAGTTTTTTAATCTT
131 TCTTATATTTGCAGTTGTAGTTGGTCTTGCCTCCCCCTTTGGAATCGTTCAAGTTTTTTAATCTT
5155711 TGGTCCATGTTTTTTTTTATTCGGGTACCGCAAAAATGTTGGTTTTCCAGACTTTTCTGAAATAA
196 TGGTCCATGTTTTTTTTTATTCGGGTACCGCAAAAATGTTGGTTTTCCAGACTTTTCTGAAATAA
5155776 TTTTACCTAATTAAGGTCACTTCGTGAAAATCTAATGCATATGATGCAATGTAATGCAAATGCAT
261 TTTTACCTAATTAAGGTCACTTCGTGAAAATCTAATGCATATGATGCAATGTAATGCAAATGCAT
5155841 GAAATGAATGCCTAAAGAGACGTTGATTCTGATTCAATTACATTTAGGAAGCTTTTCTAGAAAGT
326 GAAATGAATGCCTAAAGAGACGTTGATTCTGATTCAATTACATTTAGGAAGCTTTTCTAGAAAGT
5155906 AAATTCCCTTACACAAAACGGATACATGTACGACCTCACCCACATATTCCAAGAAACATCGGTCT
391 AAATTCCCTTACACAAAACGGATACATGTACGACCTCACCCACATATTCCAAGAAACATCGGTCT
5155971 TTTTCTTCATCTGCATGCTTGAGGTAATCTCGCCAATAGATGCCATTGCTAGCTCATTTTCTTGA
456 TTTTCTTCATCTGCATGCTTGAGGTAATCTCGCCAATAGATGCCATTGCTAGCTCATTTTCTTGA
5156036 TCTTGGTC
521 TCTTGGTC
5156044 G
1 G
5156045 CGATCCATCA
Statistics
Matches: 529, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
528 529 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (528 bp):
GAACACTCCCGAGTTTATAAGGGCGGATATCTAACAAGGTCCCTTTTCAGTTGTCTTCATGTATG
ACATTGATATGAACATTTTTTGACCTCTTCACAAAACTCTATCTTGCTGGACCTTAGGTTACCGC
TCTTATATTTGCAGTTGTAGTTGGTCTTGCCTCCCCCTTTGGAATCGTTCAAGTTTTTTAATCTT
TGGTCCATGTTTTTTTTTATTCGGGTACCGCAAAAATGTTGGTTTTCCAGACTTTTCTGAAATAA
TTTTACCTAATTAAGGTCACTTCGTGAAAATCTAATGCATATGATGCAATGTAATGCAAATGCAT
GAAATGAATGCCTAAAGAGACGTTGATTCTGATTCAATTACATTTAGGAAGCTTTTCTAGAAAGT
AAATTCCCTTACACAAAACGGATACATGTACGACCTCACCCACATATTCCAAGAAACATCGGTCT
TTTTCTTCATCTGCATGCTTGAGGTAATCTCGCCAATAGATGCCATTGCTAGCTCATTTTCTTGA
TCTTGGTC
Found at i:5157187 original size:102 final size:103
Alignment explanation
Indices: 5156876--5157194 Score: 500
Period size: 102 Copynumber: 3.0 Consensus size: 103
5156866 TTTTTTTTTG
*
5156876 TAATTTTTGAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGG
1 TAATTTTTGAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCAACACCCAGCACCTTAGG
* *
5156941 GCACG-TTCCTCGAATTTCCAAACGCAGAACATTGCCTTATTT
66 GCATGTTTTCTCGAATTTCCAAACGCAGAACATTGCC-----T
5156983 TGAAATTTTTGAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCAACACCCAGCACCTTA
1 T--AATTTTTGAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCAACACCCAGCACCTTA
5157048 GGGCATGTTTTCTCGAATTTCCAAACGCAGAACATTGCCT
64 GGGCATGTTTTCTCGAATTTCCAAACGCAGAACATTGCCT
5157088 T-ATTTTTGAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCAACACCCAGCACCTTAGG
1 TAATTTTTGAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCAACACCCAGCACCTTAGG
*
5157152 GCATGTTTTCTCGAATTTCCAAACGCCA-AATATTGCCT
66 GCATGTTTTCTCGAATTTCCAAACG-CAGAACATTGCCT
*
5157190 CAATT
1 TAATT
5157195 AGAAATATTT
Statistics
Matches: 202, Mismatches: 5, Indels: 14
0.91 0.02 0.06
Matches are distributed among these distances:
102 97 0.48
103 5 0.02
105 2 0.01
107 1 0.00
109 67 0.33
110 30 0.15
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (103 bp):
TAATTTTTGAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCAACACCCAGCACCTTAGG
GCATGTTTTCTCGAATTTCCAAACGCAGAACATTGCCT
Found at i:5157270 original size:21 final size:20
Alignment explanation
Indices: 5157238--5157279 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5157228 ATTTATATGC
*
5157238 ATGATGGAATAATAAACATG
1 ATGATGGAATAAAAAACATG
*
5157258 ATGATGTGAATAAAAAATATG
1 ATGATG-GAATAAAAAACATG
5157279 A
1 A
5157280 ACAAAAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.52, C:0.02, G:0.19, T:0.26
Consensus pattern (20 bp):
ATGATGGAATAAAAAACATG
Found at i:5170058 original size:25 final size:25
Alignment explanation
Indices: 5170022--5170069 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5170012 ATAAAAATGT
*
5170022 TACAGATCACAGTGTT-TCAGAATA
1 TACAGATCACAGAGTTCTCAGAATA
5170046 TACAGAATCACAGAGTTCTCAGAA
1 TACAG-ATCACAGAGTTCTCAGAA
5170070 CGTATATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 10 0.48
26 6 0.29
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (25 bp):
TACAGATCACAGAGTTCTCAGAATA
Found at i:5170238 original size:22 final size:22
Alignment explanation
Indices: 5170212--5170256 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5170202 AATAGTAAAT
5170212 ATTTGCAGATAAACTACCAGTA
1 ATTTGCAGATAAACTACCAGTA
* * *
5170234 ATTTGCGGTTAAACTGCCAGTA
1 ATTTGCAGATAAACTACCAGTA
5170256 A
1 A
5170257 AAAGTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (22 bp):
ATTTGCAGATAAACTACCAGTA
Found at i:5170381 original size:29 final size:29
Alignment explanation
Indices: 5170315--5170383 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
5170305 CGGCTATACT
* * **
5170315 GCCAGAACTCCGATATTTGCAGATTGACC
1 GCCAAAACTCCCATATTTGCAGATAAACC
* *
5170344 ACCAAAACTCCCATATTTGTAGATAAACC
1 GCCAAAACTCCCATATTTGCAGATAAACC
*
5170373 GCCATAACTCC
1 GCCAAAACTCC
5170384 ACAGAACTCC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.23
Consensus pattern (29 bp):
GCCAAAACTCCCATATTTGCAGATAAACC
Found at i:5176206 original size:40 final size:38
Alignment explanation
Indices: 5176142--5176216 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 38
5176132 GATTGATTGA
* *
5176142 TATTGTTTATTGTTTGCTGTAAAAGCATGTCACTGTTT
1 TATTGTTTATTGGTTGCTGTAAAAGCATGACACTGTTT
5176180 TATTGTATATATTGGTTGCATG-AAAAGCATGACACTG
1 TATTGT-T-TATTGGTTGC-TGTAAAAGCATGACACTG
5176217 ATATTGATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 6 0.19
39 1 0.03
40 23 0.72
41 2 0.06
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.43
Consensus pattern (38 bp):
TATTGTTTATTGGTTGCTGTAAAAGCATGACACTGTTT
Found at i:5176222 original size:38 final size:36
Alignment explanation
Indices: 5176139--5176222 Score: 89
Period size: 40 Copynumber: 2.2 Consensus size: 36
5176129 ATTGATTGAT
* *
5176139 TGATATTGTTTATTGTTTGCTGTAAAAGCATGTCAC
1 TGATATTGTTTATTGGTTGCTGTAAAAGCATGACAC
*
5176175 TGTTTTATTGTATATATTGGTTGCATG-AAAAGCATGACAC
1 TG--ATATTGT-T-TATTGGTTGC-TGTAAAAGCATGACAC
5176215 TGATATTG
1 TGATATTG
5176223 ATAAACTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
36 2 0.05
38 11 0.28
39 1 0.03
40 23 0.59
41 2 0.05
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (36 bp):
TGATATTGTTTATTGGTTGCTGTAAAAGCATGACAC
Found at i:5178507 original size:5 final size:5
Alignment explanation
Indices: 5178497--5178522 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5178487 TTTCTTTAGG
5178497 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
5178523 TCCGGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:5178878 original size:61 final size:61
Alignment explanation
Indices: 5178776--5178892 Score: 198
Period size: 61 Copynumber: 1.9 Consensus size: 61
5178766 CAAGTAGGAG
* *
5178776 AGAAGTTTGAAAAACTAGATCGACTACGATCAAAGGTACGTCAATGATTAAAATCTCTTTT
1 AGAAGTTTGAAAAACTAGATCGACAACGATCAAAGGCACGTCAATGATTAAAATCTCTTTT
* *
5178837 AGAAGTTTGAAAAACTAGATCGACAACGATCAGAGGCACGTCAATGATTAGAATCT
1 AGAAGTTTGAAAAACTAGATCGACAACGATCAAAGGCACGTCAATGATTAAAATCT
5178893 ATTTCAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (61 bp):
AGAAGTTTGAAAAACTAGATCGACAACGATCAAAGGCACGTCAATGATTAAAATCTCTTTT
Found at i:5178912 original size:52 final size:52
Alignment explanation
Indices: 5178842--5179052 Score: 255
Period size: 52 Copynumber: 4.1 Consensus size: 52
5178832 CTTTTAGAAG
* *
5178842 TTTGAAAAACTAGATCGACAACGATCAGAGGCACGTCAATGATTAGAATCTA
1 TTTGAAAAACTAGATCGACAACGATCAGAAGCACGCCAATGATTAGAATCTA
* * * * **
5178894 TTTCAAAAACTAGGTCGACAACGATCAAAAGTACGTTAAT-AGTTAGAATCTA
1 TTTGAAAAACTAGATCGACAACGATCAGAAGCACGCCAATGA-TTAGAATCTA
*
5178946 TTTGAAAAACTAGATCGACAATGATCAGAAGCACGCCAATGATTAGAATCTA
1 TTTGAAAAACTAGATCGACAACGATCAGAAGCACGCCAATGATTAGAATCTA
* * * * * *
5178998 TTTGGAAAACTAGATCGACGATC-ACCAGAGGTATGCCAATGATTAGAATCTA
1 TTTGAAAAACTAGATCGAC-AACGATCAGAAGCACGCCAATGATTAGAATCTA
5179050 TTT
1 TTT
5179053 ACCAAGTTTG
Statistics
Matches: 136, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
51 1 0.01
52 133 0.98
53 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (52 bp):
TTTGAAAAACTAGATCGACAACGATCAGAAGCACGCCAATGATTAGAATCTA
Found at i:5186907 original size:26 final size:26
Alignment explanation
Indices: 5186877--5186936 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
5186867 AATCAAATCT
5186877 AAATTTAAAACCACAAACCAAAA-CCC
1 AAATTTAAAACC-CAAACCAAAATCCC
* * **
5186903 TAATTTGAAACCCAAGTCAAAATCCC
1 AAATTTAAAACCCAAACCAAAATCCC
5186929 AAATTTAA
1 AAATTTAA
5186937 GGCTTTCAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.52, C:0.25, G:0.03, T:0.20
Consensus pattern (26 bp):
AAATTTAAAACCCAAACCAAAATCCC
Found at i:5192038 original size:28 final size:28
Alignment explanation
Indices: 5191998--5192059 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
5191988 GCTTCTATAA
* *
5191998 ATGGTCAGCTCTGTCGCCTGAATGATAT
1 ATGGTCAGCTCTGCCGCCTGAATAATAT
5192026 ATGGTCAGCTCTGCCGCCTGAATAATAT
1 ATGGTCAGCTCTGCCGCCTGAATAATAT
5192054 ATGGTC
1 ATGGTC
5192060 GGCCCTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (28 bp):
ATGGTCAGCTCTGCCGCCTGAATAATAT
Found at i:5192071 original size:28 final size:28
Alignment explanation
Indices: 5191998--5192072 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
5191988 GCTTCTATAA
* * *
5191998 ATGGTCAGCTCTGTCGCCTGAATGATAT
1 ATGGTCAGCCCTATCGCCTGAATAATAT
* **
5192026 ATGGTCAGCTCTGCCGCCTGAATAATAT
1 ATGGTCAGCCCTATCGCCTGAATAATAT
*
5192054 ATGGTCGGCCCTATCGCCT
1 ATGGTCAGCCCTATCGCCT
5192073 TTGTATTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (28 bp):
ATGGTCAGCCCTATCGCCTGAATAATAT
Found at i:5192895 original size:14 final size:14
Alignment explanation
Indices: 5192859--5192894 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
5192849 TGAAAAAATA
5192859 TTTTACAAAAGTGC
1 TTTTACAAAAGTGC
5192873 -TTTACAAAAGTGC
1 TTTTACAAAAGTGC
5192886 TTTTA-AAAA
1 TTTTACAAAA
5192895 ATTTGATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (14 bp):
TTTTACAAAAGTGC
Found at i:5193588 original size:6 final size:7
Alignment explanation
Indices: 5193562--5193587 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5193552 AAATATATAC
5193562 TTTTTTA
1 TTTTTTA
5193569 TTTTTTA
1 TTTTTTA
5193576 TTTTTTA
1 TTTTTTA
5193583 TTTTT
1 TTTTT
5193588 AAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:5193598 original size:12 final size:12
Alignment explanation
Indices: 5193582--5193610 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
5193572 TTTATTTTTT
5193582 ATTTTTAAAAT-
1 ATTTTTAAAATA
5193593 ATTTTTAAAATA
1 ATTTTTAAAATA
5193605 ATTTTT
1 ATTTTT
5193611 TGGTGTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTTAAAATA
Found at i:5193969 original size:28 final size:28
Alignment explanation
Indices: 5193937--5193993 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5193927 TTTAATTACT
5193937 CAATTTAAGTCTCCAATCTAACTTTTAA
1 CAATTTAAGTCTCCAATCTAACTTTTAA
5193965 CAATTTAAGTCTCCAATCTAACTTTTAA
1 CAATTTAAGTCTCCAATCTAACTTTTAA
5193993 C
1 C
5193994 CTTTGTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (28 bp):
CAATTTAAGTCTCCAATCTAACTTTTAA
Found at i:5194532 original size:15 final size:15
Alignment explanation
Indices: 5194512--5194543 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5194502 TAATGTCTCA
5194512 TGTCATTCTTGAACT
1 TGTCATTCTTGAACT
5194527 TGTCATTCTTGAACT
1 TGTCATTCTTGAACT
5194542 TG
1 TG
5194544 CCCTTCTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (15 bp):
TGTCATTCTTGAACT
Found at i:5194550 original size:15 final size:15
Alignment explanation
Indices: 5194515--5194552 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5194505 TGTCTCATGT
*
5194515 CATTCTTGAACTTGT
1 CATTCTTGAACTTGC
5194530 CATTCTTGAACTTGC
1 CATTCTTGAACTTGC
*
5194545 CCTTCTTG
1 CATTCTTG
5194553 CATCTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.26, G:0.13, T:0.45
Consensus pattern (15 bp):
CATTCTTGAACTTGC
Found at i:5195279 original size:22 final size:22
Alignment explanation
Indices: 5195230--5195271 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
5195220 TATATTTTAG
5195230 TTAATATTTTATATATTTTATAA
1 TTAA-ATTTTATATATTTTATAA
*
5195253 TTAAATTTTAT-TTTTTTAT
1 TTAAATTTTATATATTTTAT
5195272 TATTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTAAATTTTATATATTTTATAA
Found at i:5199074 original size:44 final size:44
Alignment explanation
Indices: 5199025--5199112 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
5199015 TTGAAAGCCC
5199025 CTGGGAGAGATGGTTTTTATGCCTTATTTTTCCAAAGTCAATGG
1 CTGGGAGAGATGGTTTTTATGCCTTATTTTTCCAAAGTCAATGG
5199069 CTGGGAGAGATGGTTTTTATGCCTTATTTTTCCAAAGTCAATGG
1 CTGGGAGAGATGGTTTTTATGCCTTATTTTTCCAAAGTCAATGG
5199113 GATCATGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.39
Consensus pattern (44 bp):
CTGGGAGAGATGGTTTTTATGCCTTATTTTTCCAAAGTCAATGG
Found at i:5210754 original size:14 final size:14
Alignment explanation
Indices: 5210735--5210776 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
5210725 AGTTGAACTA
5210735 TATTAAGCAGTTAG
1 TATTAAGCAGTTAG
*
5210749 TATTAAGTAGTTAG
1 TATTAAGCAGTTAG
5210763 TATTAAGCAGTTAG
1 TATTAAGCAGTTAG
5210777 AAAGTTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (14 bp):
TATTAAGCAGTTAG
Found at i:5212084 original size:78 final size:78
Alignment explanation
Indices: 5211955--5212109 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 78
5211945 TTTTTATGGC
*
5211955 CAAGGGAACTATGCTAGTCAAAATAGGCATGTTGATGGTCAAAATTGGTGTGCTGGCGTGCAAAA
1 CAAGGGAACTATGCTAGTCAAAATAGGCATGTTGATGGTCAAAATTGGTGTGCTGGCATGCAAAA
*
5212020 TGATCATTTGGTA
66 TGATAATTTGGTA
*
5212033 CAAGGGAACTATGCTAGTCAAAATAGGCATGTTGATGGTCAAAATTGGTGTGCTGGCATGTAAAA
1 CAAGGGAACTATGCTAGTCAAAATAGGCATGTTGATGGTCAAAATTGGTGTGCTGGCATGCAAAA
5212098 TGATAATTTGGT
66 TGATAATTTGGT
5212110 GCGTGTGCCA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.29
Consensus pattern (78 bp):
CAAGGGAACTATGCTAGTCAAAATAGGCATGTTGATGGTCAAAATTGGTGTGCTGGCATGCAAAA
TGATAATTTGGTA
Found at i:5215901 original size:14 final size:14
Alignment explanation
Indices: 5215882--5215909 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5215872 GATGGATGAA
5215882 TATTAAGCAGTTAG
1 TATTAAGCAGTTAG
5215896 TATTAAGCAGTTAG
1 TATTAAGCAGTTAG
5215910 AAAGTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
TATTAAGCAGTTAG
Found at i:5219466 original size:21 final size:21
Alignment explanation
Indices: 5219440--5219480 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5219430 CCTATGAGCT
5219440 GGACCGGGTTTGGGTTGGGCC
1 GGACCGGGTTTGGGTTGGGCC
5219461 GGACCGGGTTTGGGTTGGGC
1 GGACCGGGTTTGGGTTGGGC
5219481 TAGGCTAAAA
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:0.05, C:0.17, G:0.54, T:0.24
Consensus pattern (21 bp):
GGACCGGGTTTGGGTTGGGCC
Found at i:5228095 original size:86 final size:86
Alignment explanation
Indices: 5227946--5228293 Score: 480
Period size: 86 Copynumber: 4.0 Consensus size: 86
5227936 AGTAAAAATT
* * * *
5227946 GAAGATAAACCTTACCTCTCTCGGTCGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGACTTCCT
1 GAAGACAAACCTTGCCTCTCTCGGTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
*
5228011 GCATTGATAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* *
5228032 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATTGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCTCTCTCGGTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
*
5228097 ACATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* * * * *
5228118 GAAGCCAAACCTTGCCTCTCTCGGTTATAGCAAAGCTGGTTGAAGATAACAGATCTTGCCTTCAT
1 GAAGACAAACCTTGCCTCTCTCGGTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
5228183 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* * * * * * * *
5228204 AAAGAAAAAACTTGCCTCTCTCGTTTGTAGCAGAGCTGGCTAAAGATAGCAGATATTCCCTTCCT
1 GAAGACAAACCTTGCCTCTCTCGGTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
* *
5228269 GTATTTGGCAGCGAAGCAGATC
66 GCA-TTGACAGCGAAGCAGATC
5228291 GAA
1 GAA
5228294 AATGGCAGAT
Statistics
Matches: 229, Mismatches: 32, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
86 210 0.92
87 19 0.08
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (86 bp):
GAAGACAAACCTTGCCTCTCTCGGTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
GCATTGACAGCGAAGCAGATC
Found at i:5228506 original size:134 final size:134
Alignment explanation
Indices: 5228253--5228658 Score: 452
Period size: 134 Copynumber: 3.1 Consensus size: 134
5228243 CTAAAGATAG
* *
5228253 CAGATATTCCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAAATGGCAGATTTTACCTCCCTGTG
1 CAGATCTTCCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTG
* *** *
5228318 ACTACAGTGGAGTACATTGAAGCCAATAACTCTATCT-CCTTGGTTGGCAATGGAATAGATTGAA
66 ACTACAGTGGAGTACATTGAAGCCAATAACTCTATCTCCCTAGG-CAACAGTGGAATAGATTGAA
*
5228382 TATTA
130 GATTA
*
5228387 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTG
1 CAGATCTTCCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTG
* *
5228452 ACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTAGGCAACAGTGGAATAGATCGAAG
66 ACTACAGTGGAGTACATTGAAGCCAATAACTCTATCTCCCTAGGCAACAGTGGAATAGATTGAAG
5228517 ATTA
131 ATTA
* * * * * * *
5228521 AAGATCTTATCCC--CCTAAGCA-ATAG-TG-GAA-CAGGTCGAAGATGGCGGATTTTACCT--C
1 CAGATC-T-TCCCTTCCT--GTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCC
* * * * * ** * * *
5228578 TCTGATTACGGTAGAGTACATTAAAGCCAATAGTTCTATCTCCTTGGGCAACAGTGGAATAGAGT
62 TGTGACTACAGTGGAGTACATTGAAGCCAATAACTCTATCTCCCTAGGCAACAGTGGAATAGATT
5228643 GAAGATTA
127 GAAGATTA
5228651 CAGATCTT
1 CAGATCTT
5228659 ATCTCCCTAA
Statistics
Matches: 235, Mismatches: 32, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
128 1 0.00
129 1 0.00
130 67 0.29
132 24 0.10
133 3 0.01
134 126 0.54
135 8 0.03
136 5 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (134 bp):
CAGATCTTCCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTG
ACTACAGTGGAGTACATTGAAGCCAATAACTCTATCTCCCTAGGCAACAGTGGAATAGATTGAAG
ATTA
Found at i:5228757 original size:82 final size:82
Alignment explanation
Indices: 5228655--5229342 Score: 1099
Period size: 82 Copynumber: 8.4 Consensus size: 82
5228645 AGATTACAGA
* **
5228655 TCTTATCTCCCTAAGCAATAGCGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAACAGTG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
* *
5228720 GAGTAGATTGCATCAAG
66 GAGCAGATCGCATCAAG
* *
5228737 TCTTATCTCCCTAAGAAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
*
5228802 GAGCAGATCACATCAAG
66 GAGCAGATCGCATCAAG
* *
5228819 TCTTATCTCCTTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
5228884 GAGCAGATCGCATCAAG
66 GAGCAGATCGCATCAAG
* * *
5228901 TCTTATCTCCCTAAGCAATAGTGGAGCAGACGGAACTATAGATCTTATCTCCCTAAGCAGTAGTG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
5228966 GAGCAGATCGCATCAAG
66 GAGCAGATCGCATCAAG
* * *
5228983 TCTTATCTCCCTAAGCAATAGTGGAGCAGACGGAACTATAGATCTTATCTCCCTAAGCAGTAGTG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
5229048 GAGCAGATCGCATCAAG
66 GAGCAGATCGCATCAAG
* * *
5229065 TCTTATCTCCCTAAGCAATAGTGGAGCAGACGGAACTATAGATCTTATCTCCCTAAGCAGTAGTG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
5229130 GAGCAGATCGCATCAAG
66 GAGCAGATCGCATCAAG
* * *
5229147 TCTTATCTCCCTAAGCAATAGTGGAGCAGACGGAACTATAGATCTTATCTCCCTAAGCAGTAGTG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
5229212 GAGCAGATCGCATCAAG
66 GAGCAGATCGCATCAAG
5229229 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTAT-TCCCCTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTATCT-CCCTAAGCAGTAGT
* * *
5229293 GGAGTAGATCACATCCAG
65 GGAGCAGATCGCATCAAG
* * * *
5229311 TTTTAACTGCCTAAGCAGTAGTGGAGCAGACA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGACA
5229343 AAAAAAACCA
Statistics
Matches: 577, Mismatches: 28, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
81 1 0.00
82 576 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (82 bp):
TCTTATCTCCCTAAGCAATAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGCATCAAG
Found at i:5230061 original size:15 final size:15
Alignment explanation
Indices: 5230041--5230095 Score: 67
Period size: 15 Copynumber: 3.5 Consensus size: 15
5230031 TGATATTTCG
*
5230041 TTTTTTAGTATGT-GT
1 TTTTTTA-TATCTAGT
5230056 TTTTTTATATCTAGTTT
1 TTTTTTATATCTAG--T
5230073 TTTTTTATATCTAGT
1 TTTTTTATATCTAGT
5230088 TTTTTTAT
1 TTTTTTAT
5230096 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 4 0.11
15 17 0.47
17 15 0.42
ACGTcount: A:0.16, C:0.04, G:0.09, T:0.71
Consensus pattern (15 bp):
TTTTTTATATCTAGT
Found at i:5230075 original size:17 final size:17
Alignment explanation
Indices: 5230055--5230093 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
5230045 TTAGTATGTG
5230055 TTTTTTTATATCTAGTT
1 TTTTTTTATATCTAGTT
5230072 TTTTTTTATATCTAGTT
1 TTTTTTTATATCTAGTT
5230089 TTTTT
1 TTTTT
5230094 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTTTTATATCTAGTT
Found at i:5235666 original size:12 final size:11
Alignment explanation
Indices: 5235649--5235704 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
5235639 GTTTATAAAG
*
5235649 ATATATATGCAT
1 ATATATAT-AAT
5235661 ATATATAATAAT
1 ATATAT-ATAAT
5235673 ATATATATAAT
1 ATATATATAAT
* *
5235684 A-AGATATAAAG
1 ATATATAT-AAT
5235695 ATATATATAA
1 ATATATATAA
5235705 GTAGTTACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
10 5 0.14
11 11 0.30
12 19 0.51
13 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (11 bp):
ATATATATAAT
Found at i:5235676 original size:14 final size:14
Alignment explanation
Indices: 5235659--5235691 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5235649 ATATATATGC
*
5235659 ATATATATAATAAT
1 ATATATATAATAAG
5235673 ATATATATAATAAG
1 ATATATATAATAAG
5235687 ATATA
1 ATATA
5235692 AAGATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
ATATATATAATAAG
Found at i:5235698 original size:22 final size:21
Alignment explanation
Indices: 5235642--5235704 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
5235632 AAAAAACGTT
* *
5235642 TATAAAGATATATATGCATATA
1 TATAAAGATATATAT-AATAGA
*
5235664 TATAATAATATATATATAATAAGA
1 TAT-A-AAGATATATATAAT-AGA
5235688 TATAAAGATATATATAA
1 TATAAAGATATATATAA
5235705 GTAGTTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 15 0.44
23 4 0.12
24 15 0.44
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (21 bp):
TATAAAGATATATATAATAGA
Found at i:5235788 original size:17 final size:17
Alignment explanation
Indices: 5235766--5235812 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
5235756 TAAATATGAA
5235766 ATAATAATATAACAATG
1 ATAATAATATAACAATG
*
5235783 ATAAT-ATAAAACTAATG
1 ATAATAATATAAC-AATG
5235800 AT-ATAATATAACA
1 ATAATAATATAACA
5235813 GTAGTAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (17 bp):
ATAATAATATAACAATG
Found at i:5236840 original size:12 final size:12
Alignment explanation
Indices: 5236825--5236857 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
5236815 AGTTGTATAG
5236825 TGTAATTAGCAA
1 TGTAATTAGCAA
5236837 TGTAATTAGCAA
1 TGTAATTAGCAA
5236849 TGTAATTAG
1 TGTAATTAG
5236858 TTACACCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (12 bp):
TGTAATTAGCAA
Found at i:5241453 original size:12 final size:12
Alignment explanation
Indices: 5241438--5241470 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
5241428 AGTTGTATAG
5241438 TGTAATTAGCAA
1 TGTAATTAGCAA
5241450 TGTAATTAGCAA
1 TGTAATTAGCAA
5241462 TGTAATTAG
1 TGTAATTAG
5241471 TTACACCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (12 bp):
TGTAATTAGCAA
Found at i:5248232 original size:15 final size:16
Alignment explanation
Indices: 5248205--5248234 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5248195 GAAAACATAG
5248205 TAATTTAAATATAATT
1 TAATTTAAATATAATT
5248221 TAATTT-AATATAAT
1 TAATTTAAATATAAT
5248235 ACATAACCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTTAAATATAATT
Found at i:5248650 original size:17 final size:18
Alignment explanation
Indices: 5248619--5248652 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5248609 GAGAACATTG
*
5248619 ATAAGATGTTTTTTTAAC
1 ATAAGATGTTCTTTTAAC
5248637 ATAA-ATGTTCTTTTAA
1 ATAAGATGTTCTTTTAA
5248653 TAGTTCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (18 bp):
ATAAGATGTTCTTTTAAC
Found at i:5251457 original size:21 final size:20
Alignment explanation
Indices: 5251418--5251457 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5251408 CTTCGATAAA
**
5251418 ATTTAAAATTTAATTATTAT
1 ATTTAAAATTTAAAAATTAT
5251438 ATTTAAAAATTTAAAAATTA
1 ATTT-AAAATTTAAAAATTA
5251458 AGTACTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAAAATTTAAAAATTAT
Found at i:5260987 original size:600 final size:600
Alignment explanation
Indices: 5259847--5261045 Score: 2272
Period size: 600 Copynumber: 2.0 Consensus size: 600
5259837 GTGACCGTTG
5259847 CGTACTACACAGAGATATCAAAGCGAGCAACATTATGTTAGATTCTAGTTTCAATGCTAAACTTG
1 CGTACTACACAGAGATATCAAAGCGAGCAACATTATGTTAGATTCTAGTTTCAATGCTAAACTTG
5259912 GGGATTTCGGGCTTGCTAGGCTAGTGGATCATGAAAAAGCGTCACAAACCACCCATTTAGCTGGG
66 GGGATTTCGGGCTTGCTAGGCTAGTGGATCATGAAAAAGCGTCACAAACCACCCATTTAGCTGGG
5259977 ACTATGGGCTATTTGGCACCTGAATGTGTTTCATCGGGAAAAGCTAGTAAGGAATCGGATGTCTA
131 ACTATGGGCTATTTGGCACCTGAATGTGTTTCATCGGGAAAAGCTAGTAAGGAATCGGATGTCTA
5260042 CAGCTTTGGAGTTGTGGCATTGGAGATTGCATGCGGTAGAAGATCAATAGAGTCCAAATATGAAG
196 CAGCTTTGGAGTTGTGGCATTGGAGATTGCATGCGGTAGAAGATCAATAGAGTCCAAATATGAAG
* *
5260107 AATCTCAAGTTCCATTGGTAGCTTGGGTGTGGGATTCATATGGAAGCCAACGGTTGCTTGATGTG
261 AATCTCAAGTTCCATTGGTAGATTGGGTGTGGGATTCATATGGAAGCCAACGGTTGCTTGATGTA
*
5260172 GCTGACCCAAAATTAAGTATGAACTTTGATGCGAAACAAATGGAATGCTTGTTAATGATTGGATT
326 GCTGACCCAAAATTAAGTATGAACTTTAATGCGAAACAAATGGAATGCTTGTTAATGATTGGATT
*
5260237 GTGGTGCGTCCATCCAGACCAGCATTTTAGACCGTCGATAAGGCAAACAATTCAGGTTCTTAATT
391 GTGGTGCGTCCATCCAGACCAGCATTTAAGACCGTCGATAAGGCAAACAATTCAGGTTCTTAATT
* *
5260302 TTGAAGCACCATGGCTGAAGCTTCCAAGTACGAGGCCAACTGCTACATATAATGCACAAATCACT
456 TTGAAGCACCATGGCCGAAGCTTCCAAGTACGAGGCCAACTGCCACATATAATGCACAAATCACT
* *
5260367 TCAGAAATTCAAACAAGTGAGCCATGTTTTTCTGATATGAGTATTATGGTCCCGCGTTAGATATA
521 TCAGAAATTCAAACAAGTGAGCCATGTTTTTCTGATATGAGTATTACGGTCCCACGTTAGATATA
5260432 CATAATATTCAAATT
586 CATAATATTCAAATT
5260447 CGTACTACACAGAGATATCAAAGCGAGCAACATTATGTTAGATTCTAGTTTCAATGCTAAACTTG
1 CGTACTACACAGAGATATCAAAGCGAGCAACATTATGTTAGATTCTAGTTTCAATGCTAAACTTG
5260512 GGGATTTCGGGCTTGCTAGGCTAGTGGATCATGAAAAAGCGTCACAAACCACCCATTTAGCTGGG
66 GGGATTTCGGGCTTGCTAGGCTAGTGGATCATGAAAAAGCGTCACAAACCACCCATTTAGCTGGG
*
5260577 ACTTTGGGCTATTTGGCACCTGAATGTGTTTCATCGGGAAAAGCTAGTAAGGAATCGGATGTCTA
131 ACTATGGGCTATTTGGCACCTGAATGTGTTTCATCGGGAAAAGCTAGTAAGGAATCGGATGTCTA
5260642 CAGCTTTGGAGTTGTGGCATTGGAGATTGCATGCGGTAGAAGATCAATAGAGTCCAAATATGAAG
196 CAGCTTTGGAGTTGTGGCATTGGAGATTGCATGCGGTAGAAGATCAATAGAGTCCAAATATGAAG
* *
5260707 AATCTCAAGTTTCATTGGTGGATTGGGTGTGGGATTCATATGGAAGCCAACGGTTGCTTGATGTA
261 AATCTCAAGTTCCATTGGTAGATTGGGTGTGGGATTCATATGGAAGCCAACGGTTGCTTGATGTA
*
5260772 GCTGACCCAAAATTAAGTATGAACTTTAATGCTAAACAAATGGAATGCTTGTTAATGATTGGATT
326 GCTGACCCAAAATTAAGTATGAACTTTAATGCGAAACAAATGGAATGCTTGTTAATGATTGGATT
5260837 GTGGTGCGTCCATCCAGACCAGCATTTAAGACCGTCGATAAGGCAAACAATTCAGGTTCTTAATT
391 GTGGTGCGTCCATCCAGACCAGCATTTAAGACCGTCGATAAGGCAAACAATTCAGGTTCTTAATT
* *
5260902 TTGAAGCACCATTGCCGAAGCTTCCAAGTACGAGGCCAACTGCCACATATAATGCAGAAATCACT
456 TTGAAGCACCATGGCCGAAGCTTCCAAGTACGAGGCCAACTGCCACATATAATGCACAAATCACT
5260967 TCAGAAATTCAAACAAGTGAGCCATGTTTTTCTGATATGAGTATTACGGTCCCACGTTAGATATA
521 TCAGAAATTCAAACAAGTGAGCCATGTTTTTCTGATATGAGTATTACGGTCCCACGTTAGATATA
5261032 CATAATATTCAAAT
586 CATAATATTCAAAT
5261046 CGATAAAAGA
Statistics
Matches: 585, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
600 585 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (600 bp):
CGTACTACACAGAGATATCAAAGCGAGCAACATTATGTTAGATTCTAGTTTCAATGCTAAACTTG
GGGATTTCGGGCTTGCTAGGCTAGTGGATCATGAAAAAGCGTCACAAACCACCCATTTAGCTGGG
ACTATGGGCTATTTGGCACCTGAATGTGTTTCATCGGGAAAAGCTAGTAAGGAATCGGATGTCTA
CAGCTTTGGAGTTGTGGCATTGGAGATTGCATGCGGTAGAAGATCAATAGAGTCCAAATATGAAG
AATCTCAAGTTCCATTGGTAGATTGGGTGTGGGATTCATATGGAAGCCAACGGTTGCTTGATGTA
GCTGACCCAAAATTAAGTATGAACTTTAATGCGAAACAAATGGAATGCTTGTTAATGATTGGATT
GTGGTGCGTCCATCCAGACCAGCATTTAAGACCGTCGATAAGGCAAACAATTCAGGTTCTTAATT
TTGAAGCACCATGGCCGAAGCTTCCAAGTACGAGGCCAACTGCCACATATAATGCACAAATCACT
TCAGAAATTCAAACAAGTGAGCCATGTTTTTCTGATATGAGTATTACGGTCCCACGTTAGATATA
CATAATATTCAAATT
Found at i:5271461 original size:15 final size:16
Alignment explanation
Indices: 5271433--5271462 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5271423 AAGAATATTG
5271433 AATTAAAAATTAGAGA
1 AATTAAAAATTAGAGA
5271449 AATTAAAAA-TAGAG
1 AATTAAAAATTAGAG
5271463 TTAAGAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (16 bp):
AATTAAAAATTAGAGA
Found at i:5289979 original size:26 final size:25
Alignment explanation
Indices: 5289949--5289997 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5289939 TCTATGATTA
*
5289949 TATAAAAAAAATCAATTAACATAATT
1 TATAAAAAAAATAAATTAA-ATAATT
* *
5289975 TATAAATATAATAAATTAAATAA
1 TATAAAAAAAATAAATTAAATAA
5289998 ATAACTCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
TATAAAAAAAATAAATTAAATAATT
Found at i:5293581 original size:147 final size:148
Alignment explanation
Indices: 5293391--5293686 Score: 567
Period size: 147 Copynumber: 2.0 Consensus size: 148
5293381 CTGTAACATA
* *
5293391 AATGGGTGTGTTTTTTTTCTCTTTTTTTGTCCTCTTTTCATTTTCCCTTTTTGCAATAGACGAAC
1 AATGGGTGTGTTTTTTTTCTCTTTTCTTGTCCTCTTTTCATTTTCCCTTTTTACAATAGACGAAC
5293456 TTTGAGAGAAATAAAAATAGAAAACCAATTTAAAAGGGGA-TTTTTTTATTTCATTTTGGGTTCG
66 TTTGAGAGAAATAAAAATAGAAAACCAATTTAAAAGGGGATTTTTTTTATTTCATTTTGGGTTCG
5293520 ATTCTTTTATTGGATTTT
131 ATTCTTTTATTGGATTTT
5293538 AATGGGTGTGTTTTTTTTCTCTTTTCTTGTCCTCTTTTCATTTTCCCTTTTTACAATAGACGAAC
1 AATGGGTGTGTTTTTTTTCTCTTTTCTTGTCCTCTTTTCATTTTCCCTTTTTACAATAGACGAAC
5293603 TTTGAGAGAAATAAAAATAGAAAACCAATTTAAAAGGGGATTTTTTTTATTTCATTTTGGGTTCG
66 TTTGAGAGAAATAAAAATAGAAAACCAATTTAAAAGGGGATTTTTTTTATTTCATTTTGGGTTCG
5293668 ATTCTTTTATTGGATTTT
131 ATTCTTTTATTGGATTTT
5293686 A
1 A
5293687 TTGTTCTTTT
Statistics
Matches: 146, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
147 103 0.71
148 43 0.29
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (148 bp):
AATGGGTGTGTTTTTTTTCTCTTTTCTTGTCCTCTTTTCATTTTCCCTTTTTACAATAGACGAAC
TTTGAGAGAAATAAAAATAGAAAACCAATTTAAAAGGGGATTTTTTTTATTTCATTTTGGGTTCG
ATTCTTTTATTGGATTTT
Found at i:5294624 original size:3 final size:3
Alignment explanation
Indices: 5294616--5294649 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5294606 TTTAATCTTG
5294616 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5294650 TACTCATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5295441 original size:71 final size:73
Alignment explanation
Indices: 5295317--5295453 Score: 197
Period size: 71 Copynumber: 1.9 Consensus size: 73
5295307 AACCTAAGTT
* * * *
5295317 TTTTAAACGATATCAGGAATTAAAGAAGAGATTGTGTCCTAACTTATTGGGCATGAT-CCTTTTT
1 TTTTAAACGATATCAGGAATTAAAGAAAAGATCGTGTCCTAACTTACTCGGCATGATCCCTTTTT
5295381 TCCTCAAG
66 TCCTCAAG
* **
5295389 TTTTAAACGATCTTGGGAATT-AAGAAAAGATCGTGTCCTAACTTACTCGGCATGATCCCTTTTT
1 TTTTAAACGATATCAGGAATTAAAGAAAAGATCGTGTCCTAACTTACTCGGCATGATCCCTTTTT
5295453 T
66 T
5295454 AATCTGAGAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 31 0.54
72 26 0.46
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (73 bp):
TTTTAAACGATATCAGGAATTAAAGAAAAGATCGTGTCCTAACTTACTCGGCATGATCCCTTTTT
TCCTCAAG
Found at i:5301177 original size:89 final size:89
Alignment explanation
Indices: 5301026--5301200 Score: 260
Period size: 89 Copynumber: 2.0 Consensus size: 89
5301016 AACAGATCAG
* * *
5301026 TAAAGATAGCAGATCTTACCTTCCTATACTGACAGTGAAGCTGATCGAAGACACCAGCCTTGCCT
1 TAAAGATAGCAGATCTTACCTTCATATACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
5301091 TCCTATACTGACAGCGGAGCATAC
66 TCCTATACTGACAGCGAAGCATAC
* * * * *
5301115 TAAAGATAGTAGATGTTGCCTTCATGTACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
1 TAAAGATAGCAGATCTTACCTTCATATACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
5301180 TCCTGTACTGACAGCGAAGCA
66 TCCTATACTGACAGCGAAGCA
5301201 GATCGAAGAC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 76 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (89 bp):
TAAAGATAGCAGATCTTACCTTCATATACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
TCCTATACTGACAGCGAAGCATAC
Found at i:5301266 original size:89 final size:89
Alignment explanation
Indices: 5301130--5301570 Score: 516
Period size: 89 Copynumber: 5.0 Consensus size: 89
5301120 ATAGTAGATG
* * *
5301130 TTGCCTTCATGTACTGACAGC-GAAGCAGA-TCGAAGACA-CTAG-CCTTGCCTTCCTGTACTGA
1 TTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAGC-AGATCTTGCCTTCCTGTACTGA
*
5301191 CAGCGAAGCAGATCGAAGACACTAGCC
63 CAGCGAAGCAGATCGAAGACACCAGCC
* *** * *
5301218 TTGCCTTCCTGTACTGACAGTGGAGTGGACTGAAGATAGCAGATCTTGCCTTCCTATACTGATAG
1 TTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAG
5301283 CGAAGCAGATCGAAGACACCAGCC
66 CGAAGCAGATCGAAGACACCAGCC
* * ** *
5301307 TTGCCTTCCTATACTGATAGTAGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAG
1 TTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAG
5301372 CGAAGCAGATCGAAGACACCAGCC
66 CGAAGCAGATCGAAGACACCAGCC
* * ** * * *
5301396 TTGCCTTCCTGTTCTGACAGCGAAACAGACTGAAGATAATAGATCTCGCCTTCCCGTACTTACAG
1 TTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAG
* * *
5301461 CGAAGCAGATCGATGACACTAGTC
66 CGAAGCAGATCGAAGACACCAGCC
* * * * * *
5301485 TTACCTCCCTGGGT-TTG-CAGCGGAATAGACTGAAGATAGCAAATCTTGTCTTCCTGTACTGAC
1 TTGCCTTCCT--GTACTGACAGCGGAACAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
5301548 AGCGAAGCAGATCGAAGACACCA
64 AGCGAAGCAGATCGAAGACACCA
5301571 TAGTTTGCAG
Statistics
Matches: 301, Mismatches: 46, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
88 29 0.10
89 268 0.89
90 2 0.01
91 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (89 bp):
TTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAG
CGAAGCAGATCGAAGACACCAGCC
Found at i:5301285 original size:133 final size:133
Alignment explanation
Indices: 5301044--5301568 Score: 535
Period size: 133 Copynumber: 3.9 Consensus size: 133
5301034 GCAGATCTTA
* * * *
5301044 CCTTCCTATACTGACAGTGAAGCTGATCGAAGACACCAGCCTTGCCTTCCTATACTGACAGCGGA
1 CCTTCCTATACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTGACAGCGGA
* * * * *
5301109 GCATACTAAAGATAGTAGATGTTGCCTTCATGTACTGACAGCGAAGCAGATCGAAGACACTAGCC
66 GCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGCC
5301174 TTG
131 TTG
* *
5301177 CCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTGACAGTGGA
1 CCTTCCTATACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTGACAGCGGA
** * * *
5301242 GTGGACTGAAGATAGCAGATCTTGCCTTCCTATACTGATAGCGAAGCAGATCGAAGACACCAGCC
66 GCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGCC
5301307 TTG
131 TTG
* * * *
5301310 CCTTCCTATACTGATAG-TAGAGCAGA-CTGAAGATAGC-AGATCTTGCCTTCCTGTACTGACAG
1 CCTTCCTATACTGACAGCGA-AGCAGATC-GAAGACA-CTAG-CCTTGCCTTCCTGTACTGACAG
* * * * * * *
5301372 CGAAGCAGA-TCGAAGACACCAG-CCTTGCCTTCCTGTTCTGACAGCGAAACAGA-CTGAAGATA
62 CGGAGCAGACT-GAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACA
* * *
5301434 ATAGATCTCG
125 CTAG-CCTTG
** * * * * * *
5301444 CCTTCCCGTACTTACAGCGAAGCAGATCGATGACACTAGTCTTACCTCCCTGGGT-TTG-CAGCG
1 CCTTCCTATACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCT--GTACTGACAGCG
** * *
5301507 GAATAGACTGAAGATAGCAAATCTTGTCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAC
64 GAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAC
5301569 CATAGTTTGC
Statistics
Matches: 318, Mismatches: 59, Indels: 29
0.78 0.15 0.07
Matches are distributed among these distances:
132 3 0.01
133 209 0.66
134 101 0.32
135 5 0.02
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (133 bp):
CCTTCCTATACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTGACAGCGGA
GCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGCC
TTG
Found at i:5301650 original size:50 final size:49
Alignment explanation
Indices: 5301598--5301843 Score: 179
Period size: 50 Copynumber: 4.9 Consensus size: 49
5301588 AATTAAAGAT
* * * *
5301598 AGCGAATCTTACTTCTCTAGCGGTGTAGTGGAACAGATTAAAGCTACAAT
1 AGCGAATCTTACTTC-CTAGCGGTGCAGTGGAAAAGATTGAAGCTACAAC
* ** ** **
5301648 AGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTGAAGCTACAAC
1 AGCGAATCTTACTTCCTAG-CGGTGCAGTGGAAAAGATTGAAGCTACAAC
* ** *
5301698 AGTGAATCTTACTTCCCTAAAGGTGCAGTGGAATAGATTGAAGCTACAAC
1 AGCGAATCTTACTT-CCTAGCGGTGCAGTGGAAAAGATTGAAGCTACAAC
** ** *
5301748 AGCGAATCTTACTTCCCCGACATTGCAGT-TAAATAGATTGAAGCTACAAC
1 AGCGAATCTTACTTCCTAG-CGGTGCAGTGGAAA-AGATTGAAGCTACAAC
* * * * * * * *
5301798 AACAAATCTTATTTCCCTGGCGTTACAGTGGAATAGATTAAAGCTA
1 AGCGAATCTTACTT-CCTAGCGGTGCAGTGGAAAAGATTGAAGCTA
5301844 AAGCAGAGTA
Statistics
Matches: 149, Mismatches: 41, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
49 6 0.04
50 136 0.91
51 7 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (49 bp):
AGCGAATCTTACTTCCTAGCGGTGCAGTGGAAAAGATTGAAGCTACAAC
Found at i:5301742 original size:100 final size:100
Alignment explanation
Indices: 5301600--5301843 Score: 344
Period size: 100 Copynumber: 2.4 Consensus size: 100
5301590 TTAAAGATAG
* * * * *
5301600 CGAATCTTACTTCTCTAGCGGTGTAGTGGAACAGATTAAAGCTACAATAGCGAATCTTGCTTCCC
1 CGAATCTTACTTCCCTAGCGGTGCAGTGGAATAGATTAAAGCTACAACAGCGAATCTTACTTCCC
*
5301665 CGACATTGCAGTTAAAAAGATTGAAGCTACAACAG
66 CGACATTGCAGTTAAAAAGATTGAAGCTACAACAA
* ** *
5301700 TGAATCTTACTTCCCTAAAGGTGCAGTGGAATAGATTGAAGCTACAACAGCGAATCTTACTTCCC
1 CGAATCTTACTTCCCTAGCGGTGCAGTGGAATAGATTAAAGCTACAACAGCGAATCTTACTTCCC
*
5301765 CGACATTGCAGTTAAATAGATTGAAGCTACAACAA
66 CGACATTGCAGTTAAAAAGATTGAAGCTACAACAA
* * * * *
5301800 CAAATCTTATTTCCCTGGCGTTACAGTGGAATAGATTAAAGCTA
1 CGAATCTTACTTCCCTAGCGGTGCAGTGGAATAGATTAAAGCTA
5301844 AAGCAGAGTA
Statistics
Matches: 124, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 124 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (100 bp):
CGAATCTTACTTCCCTAGCGGTGCAGTGGAATAGATTAAAGCTACAACAGCGAATCTTACTTCCC
CGACATTGCAGTTAAAAAGATTGAAGCTACAACAA
Found at i:5302253 original size:44 final size:44
Alignment explanation
Indices: 5302200--5302295 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
5302190 CTTATCTTCT
5302200 TGAAGTTGCAGTAGAGCAGGTTGAAGTA-GCAAACCTTATCCCCC
1 TGAAGTTGCAGTAGAGCAGGTTGAA-TATGCAAACCTTATCCCCC
* * ** *
5302244 TGAAGTTGCAGTGGGGCAGGTTGAATATGCAAGTCTTATCTCCC
1 TGAAGTTGCAGTAGAGCAGGTTGAATATGCAAACCTTATCCCCC
5302288 TGAAGTTG
1 TGAAGTTG
5302296 TAGTGAAGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 2 0.04
44 44 0.96
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (44 bp):
TGAAGTTGCAGTAGAGCAGGTTGAATATGCAAACCTTATCCCCC
Found at i:5302846 original size:43 final size:43
Alignment explanation
Indices: 5302745--5303098 Score: 412
Period size: 43 Copynumber: 8.3 Consensus size: 43
5302735 TTTAAAAAAT
* * * *
5302745 AAACGCAGCTATAGACCATGACCTTTAGCGGTGCTTTTCC-AC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCTAC
* *
5302787 AAACGCCGCTATAGATCAAGACCTATAGCGGTGCTTTTCCTAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCTAC
* *
5302830 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCAAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCTAC
* * * * *
5302873 AAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTT-CTAAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCT-AC
*
5302916 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-ATCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCT-AC
* * *
5302959 AAACGCTGCTATAGACCAAGACCTTTAGCGACGCTTTT-CTCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCT-AC
* * *
5303002 AAACTCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCAAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCTAC
* * ***
5303045 AAACGCCGCTATA-ACTCAAGACTTTTAGCGACGCTTTAATTAC
1 AAACGCCGCTATAGA-TCAAGACCTTTAGCGGCGCTTTTCCTAC
5303088 AAACGCCGCTA
1 AAACGCCGCTA
5303099 AAAATTTCGT
Statistics
Matches: 272, Mismatches: 36, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
42 38 0.14
43 233 0.86
44 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCTAC
Found at i:5302953 original size:129 final size:128
Alignment explanation
Indices: 5302742--5303098 Score: 459
Period size: 129 Copynumber: 2.8 Consensus size: 128
5302732 CGTTTTAAAA
* * *
5302742 AATAAACGCAGCTATAGACCATGACCTTTAGCGGTGCTTTTCCACAAACGCCGCTATAGATCAAG
1 AATAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCAACAAACGCCGCTATAGATCAAG
* * * * *
5302807 ACCTATAGCGGTGCTTTTCCTACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTC-C
66 ACCTTTAGCGGCGCTTTT-ATACAAACGCCGCTATAGACCAAGACCTTTAGCGACGCTTTTCTC
* * *
5302870 AATAAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTCTAACAAACGCCGCTATAGATCAA
1 AATAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTC-AACAAACGCCGCTATAGATCAA
*
5302935 GACCTTTAGCGGCGCTTTTATCACAAACGCTGCTATAGACCAAGACCTTTAGCGACGCTTTTCTC
65 GACCTTTAGCGGCGCTTTTAT-ACAAACGCCGCTATAGACCAAGACCTTTAGCGACGCTTTTCTC
* * * * *
5303000 -ACAAACTCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCAACAAACGCCGCTATA-ACTCA
1 AATAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTT-CAACAAACGCCGCTATAGA-TCA
* * *
5303063 AGACTTTTAGCGACGCTTTAATTACAAACGCCGCTA
64 AGACCTTTAGCGGCGCTTTTA-TACAAACGCCGCTA
5303099 AAAATTTCGT
Statistics
Matches: 199, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
128 39 0.20
129 157 0.79
130 3 0.02
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (128 bp):
AATAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCAACAAACGCCGCTATAGATCAAG
ACCTTTAGCGGCGCTTTTATACAAACGCCGCTATAGACCAAGACCTTTAGCGACGCTTTTCTC
Found at i:5303191 original size:16 final size:16
Alignment explanation
Indices: 5303172--5303205 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5303162 AAATATTAAA
*
5303172 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
5303188 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
5303204 TA
1 TA
5303206 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:5307616 original size:22 final size:22
Alignment explanation
Indices: 5307590--5307666 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
5307580 ATCTAAACAC
* * * *
5307590 TAAACCCTTAATCCCTATCCTT
1 TAAACCCTTAAACCCAAACCCT
*
5307612 TAAACCC-TAAACCCCAACCCCT
1 TAAACCCTTAAA-CCCAAACCCT
*
5307634 TAAA-CCTTAAACCCCAACCCT
1 TAAACCCTTAAACCCAAACCCT
5307655 TAAACCCTTAAA
1 TAAACCCTTAAA
5307667 ACCTAAATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
21 17 0.37
22 29 0.63
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.23
Consensus pattern (22 bp):
TAAACCCTTAAACCCAAACCCT
Found at i:5308170 original size:41 final size:40
Alignment explanation
Indices: 5308125--5308463 Score: 356
Period size: 41 Copynumber: 8.3 Consensus size: 40
5308115 AATACATTGT
* * *
5308125 GCGGCGCTTTTCGAAAAACGCCGCAAAAGATCAGAGCATTA
1 GCGGCGCTTTTC-AAAAACGCCGCTATAGACCAGAGCATTA
*
5308166 GCGGCGCTTATTCAAAAACGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTT-TTCAAAAACGCCGCTATAGACCAGAGCATTA
* * *
5308207 GCGGCGCTTTCCCAAAAGCGCCGCTATAGACTAGAGCATTA
1 GCGGCGCTTT-TCAAAAACGCCGCTATAGACCAGAGCATTA
* **
5308248 GCGGCGCTTCAT-AAAAAGCGCTTCTATAGACCAGAGCATTA
1 GCGGCGCTT-TTCAAAAA-CGCCGCTATAGACCAGAGCATTA
* * * *
5308289 GTGTCGCTTCATCATAAACGCCGCTATAGACCAGAGCATTA
1 GCGGCGCTT-TTCAAAAACGCCGCTATAGACCAGAGCATTA
* * *
5308330 GCGGCGCTTTCCCAAAAGCGCCGCTATAGACCACAGCATTA
1 GCGGCGCTTT-TCAAAAACGCCGCTATAGACCAGAGCATTA
* *
5308371 GCGGCGCTTCATCAAAAACGCCGCTATAGACCAAAGCATTA
1 GCGGCGCTT-TTCAAAAACGCCGCTATAGACCAGAGCATTA
** * * * *
5308412 GCGGCGCTTCAACAAAAACGCCTCTAAAGGCTAGAGCATTA
1 GCGGCGCTT-TTCAAAAACGCCGCTATAGACCAGAGCATTA
*
5308453 ACGGCGCTTTT
1 GCGGCGCTTTT
5308464 TGAGAAACGC
Statistics
Matches: 254, Mismatches: 37, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
40 5 0.02
41 242 0.95
42 7 0.03
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (40 bp):
GCGGCGCTTTTCAAAAACGCCGCTATAGACCAGAGCATTA
Found at i:5308344 original size:123 final size:123
Alignment explanation
Indices: 5308125--5308462 Score: 466
Period size: 123 Copynumber: 2.7 Consensus size: 123
5308115 AATACATTGT
* * * *
5308125 GCGGCGCTT-TTCGAAAAACGCCGCAAAAGATCAGAGCATTAGCGGCGCTT-ATTCAAAAACGCC
1 GCGGCGCTTCATC-AAAAACGCCGCTATAGACCAGAGCATTAGCGGCGCTTCA-TCAAAAACGCC
* *
5308188 GCTAAAGACCAGAGCATTAGCGGCGCTTTCCCAAAAGCGCCGCTATAGACTAGAGCATTA
64 GCTAAAGACCAGAGCATTAGCGGCGCTTTCCCAAAAGCGCCGCTATAGACCACAGCATTA
** * * *
5308248 GCGGCGCTTCAT-AAAAAGCGCTTCTATAGACCAGAGCATTAGTGTCGCTTCATCATAAACGCCG
1 GCGGCGCTTCATCAAAAA-CGCCGCTATAGACCAGAGCATTAGCGGCGCTTCATCAAAAACGCCG
*
5308312 CTATAGACCAGAGCATTAGCGGCGCTTTCCCAAAAGCGCCGCTATAGACCACAGCATTA
65 CTAAAGACCAGAGCATTAGCGGCGCTTTCCCAAAAGCGCCGCTATAGACCACAGCATTA
* * *
5308371 GCGGCGCTTCATCAAAAACGCCGCTATAGACCAAAGCATTAGCGGCGCTTCAACAAAAACGCCTC
1 GCGGCGCTTCATCAAAAACGCCGCTATAGACCAGAGCATTAGCGGCGCTTCATCAAAAACGCCGC
* * *
5308436 TAAAGGCTAGAGCATTAACGGCGCTTT
66 TAAAGACCAGAGCATTAGCGGCGCTTT
5308463 TTGAGAAACG
Statistics
Matches: 187, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
122 5 0.03
123 175 0.94
124 7 0.04
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (123 bp):
GCGGCGCTTCATCAAAAACGCCGCTATAGACCAGAGCATTAGCGGCGCTTCATCAAAAACGCCGC
TAAAGACCAGAGCATTAGCGGCGCTTTCCCAAAAGCGCCGCTATAGACCACAGCATTA
Found at i:5308620 original size:40 final size:40
Alignment explanation
Indices: 5308576--5308654 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
5308566 GCGATTTCCA
5308576 AAAAGCGCCACTAATACTTAATCTTTAGCGGCGTTTTTTT
1 AAAAGCGCCACTAATACTTAATCTTTAGCGGCGTTTTTTT
** * * *
5308616 AAAAGCGCCGGTAATGCTTGATTTTTAGCGGCGTTTTTT
1 AAAAGCGCCACTAATACTTAATCTTTAGCGGCGTTTTTT
5308655 ATACAAAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (40 bp):
AAAAGCGCCACTAATACTTAATCTTTAGCGGCGTTTTTTT
Found at i:5310179 original size:23 final size:22
Alignment explanation
Indices: 5310134--5310179 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
5310124 TATATTATTA
*
5310134 TATTATGTTATTAGTTTTGTAT
1 TATTATGTTATTAGTTTTCTAT
5310156 TATTATAGTTATT-GTATTTCTAT
1 TATTAT-GTTATTAGT-TTTCTAT
5310179 T
1 T
5310180 TAATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.63
Consensus pattern (22 bp):
TATTATGTTATTAGTTTTCTAT
Found at i:5311034 original size:71 final size:73
Alignment explanation
Indices: 5310907--5311046 Score: 221
Period size: 71 Copynumber: 1.9 Consensus size: 73
5310897 TTTCAAACCT
* *
5310907 AAGTTTTAAACGATCTCGGGAATTAAAGAAGAGATTGTGTCATAACTTACTGGGCATGAT-CCTT
1 AAGTTTTAAACGATCTCGGGAATTAAAGAAAAGATTGTGTCATAACTTACTAGGCATGATCCCTT
5310971 TTTTCCTC
66 TTTTCCTC
* * *
5310979 AAGTTTTAAACGATCTTGGGAATT-AAGAAAAGATTGTGTCCTAACTTATTAGGCATGATCCCTT
1 AAGTTTTAAACGATCTCGGGAATTAAAGAAAAGATTGTGTCATAACTTACTAGGCATGATCCCTT
5311043 TTTT
66 TTTT
5311047 AATTTGAGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 31 0.50
72 31 0.50
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (73 bp):
AAGTTTTAAACGATCTCGGGAATTAAAGAAAAGATTGTGTCATAACTTACTAGGCATGATCCCTT
TTTTCCTC
Found at i:5311212 original size:14 final size:14
Alignment explanation
Indices: 5311193--5311220 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5311183 GTCGTATTTT
5311193 AAATCTCTTTAAAG
1 AAATCTCTTTAAAG
5311207 AAATCTCTTTAAAG
1 AAATCTCTTTAAAG
5311221 TTTTCAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
AAATCTCTTTAAAG
Found at i:5314852 original size:25 final size:26
Alignment explanation
Indices: 5314806--5314867 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
5314796 TAAACATATG
5314806 AATTATAAAACATGAAAATATA-AAT
1 AATTATAAAACATGAAAATATATAAT
* **
5314831 AATTATAAAATATGAATGTATATAAT
1 AATTATAAAACATGAAAATATATAAT
5314857 ATATATATAAA
1 A-AT-TATAAA
5314868 CTATATACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.61
26 4 0.13
27 2 0.06
28 6 0.19
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.34
Consensus pattern (26 bp):
AATTATAAAACATGAAAATATATAAT
Found at i:5314894 original size:3 final size:3
Alignment explanation
Indices: 5314888--5314914 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5314878 AAAAAATTTG
5314888 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
5314915 AACGTACTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5316479 original size:44 final size:44
Alignment explanation
Indices: 5316395--5317023 Score: 223
Period size: 44 Copynumber: 14.3 Consensus size: 44
5316385 GAATTACTGG
* * *
5316395 CTTCAATGTACTCCACTGTAA--CCTGAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCAC--TAATGCCT-AGGGAGATAAAATCTGCAAT
* ** *
5316440 CTTCGATCTACTCCACTAATGCCTAGGGAGATAGGATCTGTAAT
1 CTTCAATCTACTCCACTAATGCCTAGGGAGATAAAATCTGCAAT
* ** * * * ***
5316484 CTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTAATGCCTAGGGAGATAAAATCTGCAAT
* * * *
5316527 CTTCAATGTACTCCACTGTAA--CCTCAGGGAGGTAAAATTTGCCAT
1 CTTCAATCTACTCCAC--TAATGCCT-AGGGAGATAAAATCTGCAAT
* * * *
5316572 CTTCGATCTACTCCACTAATGCCTAAGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTAATGCCTAGGGAGATAAAATCTGCAAT
* * ** * * ***
5316616 CTTCAATCTATTCCAATGCTG-CTCAGGGA-AGTAGAAT-TACTGG
1 CTTCAATCTACTCCACTAATGCCT-AGGGAGA-TAAAATCTGCAAT
* * *
5316659 CTTCAATGTACTCCACTGTAA--CC-ACGGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCAC--TAATGCCTA--GGGAGATAAAATCTGCAAT
* * * * *
5316704 CTTCGATCTGCTCTACTAATGCCTAGGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTAATGCCTAGGGAGATAAAATCTGCAAT
* * ** * * * ***
5316748 TTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTAATGCCTAGGGAGATAAAATCTGCAAT
* * * * *
5316791 CTTCAATGTACTCCATTGTAA--CCTCAGGGAGGTAAAATCTTCCAT
1 CTTCAATCTACTCCA--CTAATGCCT-AGGGAGATAAAATCTGCAAT
* * * *
5316836 CTTCGATCTACTCCACTAATGCCTAGAGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTAATGCCTAGGGAGATAAAATCTGCAAT
* ** * * * ***
5316880 CTTCAATCTATTCCACTGCTGCCCAGGGA-AGTAGAAT-TCCTGG
1 CTTCAATCTACTCCACTAATGCCTAGGGAGA-TAAAATCTGCAAT
* * * *
5316923 CTTCAATGTACTCCACTGTAA--CCACAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCAC--TAATGCC-TAGGGAGATAAAATCTGCAAT
** * * * * * * *
5316968 CTTTGATCTGCCCCACTACTGCTTAGGGAGACAAGATCTGAAAT
1 CTTCAATCTACTCCACTAATGCCTAGGGAGATAAAATCTGCAAT
5317012 CTTCAATCTACT
1 CTTCAATCTACT
5317024 TCTCTGTTAA
Statistics
Matches: 404, Mismatches: 146, Indels: 69
0.65 0.24 0.11
Matches are distributed among these distances:
42 1 0.00
43 81 0.20
44 233 0.58
45 88 0.22
46 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (44 bp):
CTTCAATCTACTCCACTAATGCCTAGGGAGATAAAATCTGCAAT
Found at i:5316536 original size:132 final size:132
Alignment explanation
Indices: 5316350--5317021 Score: 1044
Period size: 132 Copynumber: 5.1 Consensus size: 132
5316340 GCCGTCATGA
* * *
5316350 CTTCAATCTATTCCACTACACT-ACCAGAGAAGTAAGAATTACTGGCTTCAATGTACTCCACTGT
1 CTTCAATCTATTCCACT--GCTGCCCAGGGAAGT-AGAATTACTGGCTTCAATGTACTCCACTGT
* *
5316414 AACCTGAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAGGATCT
63 AACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCT
*
5316479 GTAAT
128 GAAAT
5316484 CTTCAATCTATTCCACTGCTGCCCAGGG-AGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 CTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAA
* *
5316548 CCTCAGGGAGGTAAAATTTGCCATCTTCGATCTACTCCACTAATGCCTAAGGAGATAAGATCTGA
65 CCTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGA
5316613 AAT
130 AAT
* *
5316616 CTTCAATCTATTCCAATGCTGCTCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAAC
1 CTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAAC
* * * *
5316681 CACGGGGAGGTAAAATCTGCCATCTTCGATCTGCTCTACTAATGCCTAGGGAGATAAGATCTGAA
66 CTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGAA
5316746 AT
131 AT
* *
5316748 TTTCAATCTATTCCACTGCTGCCCAGGG-AGATAGAATTACTGGCTTCAATGTACTCCATTGTAA
1 CTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAA
* *
5316812 CCTCAGGGAGGTAAAATCTTCCATCTTCGATCTACTCCACTAATGCCTAGAGAGATAAGATCTGA
65 CCTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGA
5316877 AAT
130 AAT
*
5316880 CTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTCCTGGCTTCAATGTACTCCACTGTAAC
1 CTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAAC
* * * * * * *
5316945 CACAGGGAGGTAAAATCTGCCATCTTTGATCTGCCCCACTACTGCTTAGGGAGACAAGATCTGAA
66 CTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGAA
5317010 AT
131 AT
5317012 CTTCAATCTA
1 CTTCAATCTA
5317022 CTTCTCTGTT
Statistics
Matches: 495, Mismatches: 38, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
131 2 0.00
132 466 0.94
133 10 0.02
134 17 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (132 bp):
CTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAAC
CTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGAA
AT
Found at i:5318988 original size:16 final size:16
Alignment explanation
Indices: 5318966--5319004 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5318956 CCAGTGGAAG
5318966 TTTTTTGT-TTCTTTT
1 TTTTTTGTGTTCTTTT
*
5318981 TGTTTTTGTGTTGTTTT
1 T-TTTTTGTGTTCTTTT
5318998 TTTTTTG
1 TTTTTTG
5319005 AATTGAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 13 0.62
17 7 0.33
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (16 bp):
TTTTTTGTGTTCTTTT
Found at i:5322705 original size:14 final size:14
Alignment explanation
Indices: 5322683--5322712 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5322673 CATGATTGCC
5322683 AAATATTTAAAAAA
1 AAATATTTAAAAAA
*
5322697 AAATTTTTAAAAAA
1 AAATATTTAAAAAA
5322711 AA
1 AA
5322713 TGATGATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATATTTAAAAAA
Found at i:5323167 original size:25 final size:26
Alignment explanation
Indices: 5323121--5323172 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
5323111 TAAACATATG
5323121 AATTATAAAACATGAAAATATA-AAT
1 AATTATAAAACATGAAAATATATAAT
* **
5323146 AATTATAAAATATGAATGTATATAAT
1 AATTATAAAACATGAAAATATATAAT
5323172 A
1 A
5323173 TATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (26 bp):
AATTATAAAACATGAAAATATATAAT
Found at i:5323210 original size:3 final size:3
Alignment explanation
Indices: 5323204--5323239 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5323194 AAAAAATTTG
5323204 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5323240 AACGTACTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5323321 original size:8 final size:8
Alignment explanation
Indices: 5323310--5323348 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
5323300 CATACATACA
5323310 ATAATAAT
1 ATAATAAT
5323318 ATAATAAT
1 ATAATAAT
*
5323326 AATAGTAAT
1 -ATAATAAT
5323335 AT-ATAAT
1 ATAATAAT
5323342 ATAATAA
1 ATAATAA
5323349 CAAAGATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.22
8 14 0.52
9 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (8 bp):
ATAATAAT
Found at i:5329663 original size:17 final size:18
Alignment explanation
Indices: 5329632--5329665 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5329622 GAGAACATTG
*
5329632 ATAAGATGTTTTTTTAAC
1 ATAAGATGTTCTTTTAAC
5329650 ATAA-ATGTTCTTTTAA
1 ATAAGATGTTCTTTTAA
5329666 TAGTTCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (18 bp):
ATAAGATGTTCTTTTAAC
Done.