Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011989.1 Kokia drynarioides strain JFW-HI SEQ_126987, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 186767
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 70 characters in sequence are not A, C, G, or T
Found at i:281 original size:17 final size:17
Alignment explanation
Indices: 259--292 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
249 TTTTGGATGA
*
259 ATTTGGGCTTGTTGGGT
1 ATTTGGGCCTGTTGGGT
276 ATTTGGGCCTGTTGGGT
1 ATTTGGGCCTGTTGGGT
293 TAGGGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.41, T:0.44
Consensus pattern (17 bp):
ATTTGGGCCTGTTGGGT
Found at i:2420 original size:16 final size:16
Alignment explanation
Indices: 2399--2430 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2389 ATCGTGTCAC
2399 ACGGTCATGTGGCTCA
1 ACGGTCATGTGGCTCA
*
2415 ACGGTCGTGTGGCTCA
1 ACGGTCATGTGGCTCA
2431 CACAGTCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.25, G:0.34, T:0.25
Consensus pattern (16 bp):
ACGGTCATGTGGCTCA
Found at i:5554 original size:29 final size:28
Alignment explanation
Indices: 5522--5624 Score: 77
Period size: 30 Copynumber: 3.5 Consensus size: 28
5512 CATTCGGGGG
*
5522 TAAAAGGGTAATTTTGAGAGTTTTGAGGT
1 TAAAATGG-AATTTTGAGAGTTTTGAGGT
*
5551 TAAAAATGGAAATTTTG-GAAG-TTCGAGGGT
1 T-AAAATGG-AATTTTGAG-AGTTTTGA-GGT
*
5581 AAAAATGGAATTTTTCGA-AGTTTTGAGGT
1 TAAAATGGAA-TTTT-GAGAGTTTTGAGGT
*
5610 TAAAAATGGGATTTT
1 T-AAAATGGAATTTT
5625 TGGAAGTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
28 2 0.03
29 26 0.44
30 31 0.53
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (28 bp):
TAAAATGGAATTTTGAGAGTTTTGAGGT
Found at i:5565 original size:30 final size:30
Alignment explanation
Indices: 5531--5618 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
5521 GTAAAAGGGT
5531 AATTTTGAGAGTTTTGAGGTTAAAAATGGA
1 AATTTTGAGAGTTTTGAGGTTAAAAATGGA
* *
5561 AATTTTG-GAAG-TTCGAGGGTAAAAATGGA
1 AATTTTGAG-AGTTTTGAGGTTAAAAATGGA
*
5590 ATTTTTCGA-AGTTTTGAGGTTAAAAATGG
1 AATTTT-GAGAGTTTTGAGGTTAAAAATGG
5619 GATTTTTGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 24 0.49
30 25 0.51
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.35
Consensus pattern (30 bp):
AATTTTGAGAGTTTTGAGGTTAAAAATGGA
Found at i:5612 original size:59 final size:58
Alignment explanation
Indices: 5485--5957 Score: 474
Period size: 59 Copynumber: 8.0 Consensus size: 58
5475 TTGGGAAAAA
* * * *
5485 TTGGGGTTTAAAAATGGTATTTTTAGACA-TTCGGGGGT-AAAAGGGTAA-TTTT-GAGAGTT
1 TTGGGG-TTAAAAATGGGATTTTTGGA-AGTT-GAGGGTAAAAATGG-AATTTTTGGA-AGTT
* * * *
5544 TTGAGGTTAAAAATGGAAATTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTCGAAGTT
1 TTGGGGTTAAAAATGGGATTTTTGGAAGTT-GAGGGTAAAAATGGAATTTTTGGAAGTT
* * * * * *
5603 TTGAGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATTAGAAGTTTTAGAAGTT
1 TTGGGGTTAAAAATGGGATTTTTGGAAGTTGA-GGGTAAAAATGGAATTTTTGGAAGTT
* * *
5662 TTGGGGTCT-AAAATGGGTTTTTTGGAAGTTTAGGGGTAAAAAT-GAATTTTTTGAAAGTT
1 TTGGGGT-TAAAAATGGGATTTTTGGAAGTTGA-GGGTAAAAATGGAA-TTTTTGGAAGTT
* * * * *
5721 TTGGGGTCAAAAATAGGTTTTTTGGAAGTTGGGGAGTAAAAATGAAATTTTTGGAAGTT
1 TTGGGGTTAAAAATGGGATTTTTGGAAGTTGAGG-GTAAAAATGGAATTTTTGGAAGTT
* *
5780 TAGGGGTTAAAAAT-GGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGAAGTT
1 TTGGGGTTAAAAATGGGATTTTTGGAAGTT-GAGGGTAAAAATGGAATTTTTGGAAGTT
* * * *
5838 TTGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTGGGAGTT
1 TTGGGGTTAAAAATGGGATTTTTGGAAGTTGA-GGGTAAAAATGGAATTTTTGGAAGTT
* * * *
5897 TTGGGTTTAAAAAAGGGTTTTTTGGAAATTCGAGGGTAAAAATGGAATTTTTGGATAGTT
1 TTGGGGTTAAAAATGGGATTTTTGGAAGTT-GAGGGTAAAAATGGAATTTTTGGA-AGTT
5957 T
1 T
5958 AGGGATCTCT
Statistics
Matches: 356, Mismatches: 43, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
57 1 0.00
58 84 0.24
59 260 0.73
60 11 0.03
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (58 bp):
TTGGGGTTAAAAATGGGATTTTTGGAAGTTGAGGGTAAAAATGGAATTTTTGGAAGTT
Found at i:5642 original size:29 final size:29
Alignment explanation
Indices: 5551--5961 Score: 368
Period size: 29 Copynumber: 14.0 Consensus size: 29
5541 GTTTTGAGGT
* *
5551 TAAAAATGGAAATTTTGGAAG-TTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTTAG-GGG
* * *
5580 TAAAAATGGAATTTTTCGAAGTTTTGAGGT
1 TAAAAATGGAATTTTTGGAAGTTTAG-GGG
*
5610 TAAAAATGGGATTTTTGGAAGTTTAGGGG
1 TAAAAATGGAATTTTTGGAAGTTTAGGGG
* * * * *
5639 TAAAATTAGAAGTTTTAGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTAGGGG
* **
5668 TCTAAAATGGGTTTTTTGGAAGTTTAGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTAGGGG
* *
5698 TAAAAAT-GAATTTTTTGAAAGTTTTGGGG
1 TAAAAATGGAA-TTTTTGGAAGTTTAGGGG
* *
5727 TCAAAAATAGG-TTTTTTGGAAG-TTGGGGAG
1 T-AAAAAT-GGAATTTTTGGAAGTTTAGGG-G
*
5757 TAAAAATGAAATTTTTGGAAGTTTAGGGG
1 TAAAAATGGAATTTTTGGAAGTTTAGGGG
*
5786 TTAAAAATGG-ATTTTTGGAAG-TTCGAGGG
1 -TAAAAATGGAATTTTTGGAAGTTTAG-GGG
* *
5815 TAAAAATGAAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTAGGGG
*
5844 TCAAAAATGGGATTTTTGGAAGTTTAGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTAGGGG
* * * *
5874 TAAAAATAGAATTTTTGGGAGTTTTGGGTT
1 TAAAAATGGAATTTTTGGAAGTTTAGGG-G
* ** * *
5904 TAAAAAAGGGTTTTTTGGAA-ATTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTTAG-GGG
5933 TAAAAATGGAATTTTTGGATAGTTTAGGG
1 TAAAAATGGAATTTTTGGA-AGTTTAGGG
5962 ATCTCTAGGG
Statistics
Matches: 306, Mismatches: 58, Indels: 35
0.77 0.15 0.09
Matches are distributed among these distances:
28 13 0.04
29 160 0.52
30 129 0.42
31 3 0.01
32 1 0.00
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTAGGGG
Found at i:5677 original size:118 final size:118
Alignment explanation
Indices: 5540--5957 Score: 542
Period size: 118 Copynumber: 3.5 Consensus size: 118
5530 TAATTTTGAG
* * * *
5540 AGTTTTGAGGTTAAAAATGGAAATTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTCGAAGTTTT
1 AGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTT
* * * * *
5605 GAGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATTAGAAGTTTTAGA
66 GGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTGGA
* * *
5658 AGTTTTGGGGTCT-AAAATGGGTTTTTTGGAAGTT-TAGGGGTAAAAAT-GAATTTTTTGAAAGT
1 AGTTTTGGGGT-TAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAAATGGAA-TTTTTGGAAGT
* * *
5720 TTTGGGGTCAAAAATAGGTTTTTTGGAAG-TTGGGGAGTAAAAAT-GAAATTTTTGGA
63 TTTGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGG-GTAAAAATAG-AATTTTTGGA
* *
5776 AGTTTAGGGGTTAAAAAT-GGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGAAGTTTT
1 AGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTT
*
5840 GGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTGGG
66 GGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTGGA
* * * *
5893 AGTTTTGGGTTTAAAAAAGGGTTTTTTGGAAATTCGAGGGTAAAAATGGAATTTTTGGATAGTTT
1 AGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGA-AGTTT
5958 AGGGATCTCT
Statistics
Matches: 258, Mismatches: 30, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
117 104 0.40
118 148 0.57
119 6 0.02
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (118 bp):
AGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTT
GGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTGGA
Found at i:17093 original size:59 final size:59
Alignment explanation
Indices: 17030--17450 Score: 376
Period size: 59 Copynumber: 7.1 Consensus size: 59
17020 TAATTTTGAG
** * *
17030 AGTTTTCAGGTCGAAAATGGAGA-TTTTGGAAGTTCGAGGGAAAAAACGAAATTTTTGGA
1 AGTTTTCAGGTTAAAAATGGAGATTTTTGGAAGTT-GAGGGTAAAAATGAAATTTTTGGA
* * * *
17089 AG-TTTCGGGGATCAAAAAT-GAGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTTC-AGG-TTAAAAATGGAGATTTTTGGAAG-TTGAGGGTAAAAATGAAATTTTTGGA
* * * *
17149 AGTTTTGAGGTAAAAAATGG-GATTTTTGGAAGTTTAGAGGTAAAAATGGAATTTTTGGA
1 AGTTTTCAGGTTAAAAATGGAGATTTTTGGAAGTTGAG-GGTAAAAATGAAATTTTTGGA
** * *
17208 AGTTTTGGGGTTAAAAATGG-GATTTTTGGAAGTTTAGGGGTAAAAATGAAATTTTTTGA
1 AGTTTTCAGGTTAAAAATGGAGATTTTTGGAAGTTGA-GGGTAAAAATGAAATTTTTGGA
* * *
17267 AG-TTTCGAGGTTAAAAATAG-GATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTGTGGA
1 AGTTTTC-AGGTTAAAAATGGAGATTTTTGGAAG-TTGAGGGTAAAAATGAAATTTTTGGA
** * * *
17326 AGTTTTGGGGTTAAAAATGGA-ATTTTTGGAAGTTCAAGGGTAAAAACGAAATTTTTTGGG
1 AGTTTTCAGGTTAAAAATGGAGATTTTTGGAAGTT-GAGGGTAAAAATGAAA-TTTTTGGA
* * * * * * *
17386 AG-TTTAAGGGTCAAAAACGG-GATTTTTAGAAATGTGAGGGTGAAAATGGAATTTTTGGA
1 AGTTTTCA-GGTTAAAAATGGAGATTTTTGGAAGT-TGAGGGTAAAAATGAAATTTTTGGA
17445 TAGTTT
1 -AGTTT
17451 AGGGACCTTC
Statistics
Matches: 302, Mismatches: 41, Indels: 36
0.80 0.11 0.09
Matches are distributed among these distances:
58 12 0.04
59 193 0.64
60 89 0.29
61 8 0.03
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
AGTTTTCAGGTTAAAAATGGAGATTTTTGGAAGTTGAGGGTAAAAATGAAATTTTTGGA
Found at i:17132 original size:118 final size:115
Alignment explanation
Indices: 16962--17450 Score: 402
Period size: 118 Copynumber: 4.1 Consensus size: 115
16952 GCAAAATGGT
* * * * * * *
16962 AATTTTGGGAAATTTTAGGGTTTAAAAATGGTTTTTTAGACA-TTCGGGGGTAAAAGGGTAA-TT
1 AATTTTTGGAAGTTTT-GGGGTTAAAAATGGATTTTTGGA-AGTTTGGGGGTAAAAAGG-AATTT
** * *
17025 TTGAGAGTTTTCAGGTCGAAAATGGAGATTTTGGAAGTTCGAGGGAAAAAACGA
63 TTGAGAGTTTTCAGGTAAAAAATGGAGATTTTGGAAGTT-GAGGGTAAAAATGA
* *
17079 AATTTTTGGAAGTTTCGGGGATCAAAAATGAGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTT
1 AATTTTTGGAAGTTTTGGGG-TTAAAAATG-GATTTTTGGAAGTTTGGGGGTAAAAA-GGAATTT
* * *
17144 TTG-GAAGTTTTGAGGTAAAAAATGG-GATTTTTGGAAGTTTAGAGGTAAAAATGG
63 TTGAG-AGTTTTCAGGTAAAAAATGGAGA-TTTTGGAAGTTGAG-GGTAAAAATGA
* *
17198 AATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGAAATTTT
1 AATTTTTGGAAGTTTTGGGGTTAAAAAT-GGATTTTTGGAAGTTTGGGGGTAAAAA-GGAA-TTT
* * *
17263 TTGA-AG-TTTCGAGGTTAAAAATAGGA-TTTTTGGAAGTTTGGGGGTAAAAATGA
63 TTGAGAGTTTTC-AGGTAAAAAAT-GGAGATTTTGGAAG-TTGAGGGTAAAAATGA
* *** *
17316 AATTTGTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAACGAAATTTT
1 AATTTTTGGAAGTTTTGGGGTTAAAAATGG-ATTTTTGGAAGTTTGGGGGTAAAAA-GGAA-TTT
* * * * * * * *
17381 TTGGGAG-TTTAAGGGTCAAAAACGG-GATTTTTAGAAATGTGAGGGTGAAAATGG
63 TTGAGAGTTTTCA-GGTAAAAAATGGAGA-TTTTGGAAGT-TGAGGGTAAAAATGA
17435 AATTTTTGGATAGTTT
1 AATTTTTGGA-AGTTT
17451 AGGGACCTTC
Statistics
Matches: 309, Mismatches: 41, Indels: 41
0.79 0.10 0.10
Matches are distributed among these distances:
116 3 0.01
117 27 0.09
118 159 0.51
119 115 0.37
120 5 0.02
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (115 bp):
AATTTTTGGAAGTTTTGGGGTTAAAAATGGATTTTTGGAAGTTTGGGGGTAAAAAGGAATTTTTG
AGAGTTTTCAGGTAAAAAATGGAGATTTTGGAAGTTGAGGGTAAAAATGA
Found at i:17167 original size:30 final size:29
Alignment explanation
Indices: 17043--17450 Score: 360
Period size: 29 Copynumber: 13.8 Consensus size: 29
17033 TTTCAGGTCG
*
17043 AAAATGGAGA-TTTTGGAAG-TTCGAGGGAA
1 AAAATGGA-ATTTTTGGAAGTTTCG-GGGTA
* *
17072 AAAACGAAATTTTTGGAAGTTTCGGGGATCA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-T-A
*
17103 AAAAT-GAGATTTTTGGAAGTTTGGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTCGGGGTA
* *
17132 AAAATGGAATTTTTGGAAGTTTTGAGGTAA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
* * *
17162 AAAATGGGATTTTTGGAAGTTTAGAGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
*
17191 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
* *
17221 AAAATGGGATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* * *
17250 AAAATGAAATTTTTTGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
*
17280 AAAATAGG-ATTTTTGGAAGTTTGGGGGTA
1 AAAAT-GGAATTTTTGGAAGTTTCGGGGTA
* * *
17309 AAAATGAAATTTGTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
*
17339 AAAATGGAATTTTTGGAAG-TTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
* * * **
17368 AAAACGAAATTTTTTGGGAGTTTAAGGGTCA
1 AAAATGGAA-TTTTTGGAAGTTTCGGGGT-A
* * * * * *
17399 AAAACGGGATTTTTAGAAATGT-GAGGGTG
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
17428 AAAATGGAATTTTTGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
17451 AGGGACCTTC
Statistics
Matches: 313, Mismatches: 48, Indels: 35
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 140 0.45
30 137 0.44
31 34 0.11
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:17412 original size:31 final size:30
Alignment explanation
Indices: 17053--17404 Score: 120
Period size: 30 Copynumber: 11.8 Consensus size: 30
17043 AAAATGGAGA
* *
17053 TTTTGGAAGTTCGAGGGAAAAAACGAAA-T
1 TTTTGGAAGTTCAAGGGTAAAAACGAAATT
* * *
17082 TTTTGGAAGTTTC-GGGGATCAAAAATGAGA-T
1 TTTTGGAAG-TTCAAGGG-T-AAAAACGAAATT
*** * *
17113 TTTTGGAAGTTTGGGGGTAAAAATGGAA-T
1 TTTTGGAAGTTCAAGGGTAAAAACGAAATT
** * **
17142 TTTTGGAAGTT-TTGAGGTAAAAAATGGGA-T
1 TTTTGGAAGTTCAAG-GGT-AAAAACGAAATT
* * *
17172 TTTTGGAAGTT-TAGAGGTAAAAATGGAA-T
1 TTTTGGAAGTTCAAG-GGTAAAAACGAAATT
*** * **
17201 TTTTGGAAGTTTTGGGGTTAAAAATGGGA-T
1 TTTTGGAAGTTCAAGGG-TAAAAACGAAATT
* * *
17231 TTTTGGAAGTTTAGGGGTAAAAATGAAATT
1 TTTTGGAAGTTCAAGGGTAAAAACGAAATT
* * * *
17261 TTTT-GAAGTTTCGAGGTTAAAAA-TAGGA-T
1 TTTTGGAAG-TTCAAGGGTAAAAACGA-AATT
*** *
17290 TTTTGGAAGTTTGGGGGTAAAAATGAAA-T
1 TTTTGGAAGTTCAAGGGTAAAAACGAAATT
* *** * *
17319 TTGTGGAAGTTTTGGGGTTAAAAATGGAA-T
1 TTTTGGAAGTTCAAGGG-TAAAAACGAAATT
17349 TTTTGGAAGTTCAAGGGTAAAAACGAAATT
1 TTTTGGAAGTTCAAGGGTAAAAACGAAATT
* *
17379 TTTTGGGAGTTTAAGGGTCAAAAACG
1 TTTTGGAAGTTCAAGGGT-AAAAACG
17405 GGATTTTTAG
Statistics
Matches: 268, Mismatches: 39, Indels: 30
0.80 0.12 0.09
Matches are distributed among these distances:
28 1 0.00
29 114 0.43
30 124 0.46
31 29 0.11
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (30 bp):
TTTTGGAAGTTCAAGGGTAAAAACGAAATT
Found at i:19196 original size:23 final size:23
Alignment explanation
Indices: 19170--19214 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
19160 ATTGGACATT
19170 ATTTA-AATAAATTTTAAATTTAA
1 ATTTATAATAAA-TTTAAATTTAA
19193 ATTTATAATAAATTTAAATTTA
1 ATTTATAATAAATTTAAATTTA
19215 TTGGGCCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTATAATAAATTTAAATTTAA
Found at i:22285 original size:31 final size:31
Alignment explanation
Indices: 22223--22285 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
22213 AAATTAATTT
* * *
22223 TTGAACTTGATAAATATTTCCATATTGAAGC
1 TTGAACTTGATAAATACTACCACATTGAAGC
* *
22254 TTGAACTTGATAAATACTAGCACATTTAAGC
1 TTGAACTTGATAAATACTACCACATTGAAGC
22285 T
1 T
22286 CTATTTTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (31 bp):
TTGAACTTGATAAATACTACCACATTGAAGC
Found at i:25717 original size:13 final size:14
Alignment explanation
Indices: 25699--25727 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
25689 GAATTCACAA
25699 AAAAAGAAA-AAAG
1 AAAAAGAAAGAAAG
25712 AAAAAGAAAGAAAG
1 AAAAAGAAAGAAAG
25726 AA
1 AA
25728 GAATATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAG
Found at i:25723 original size:17 final size:16
Alignment explanation
Indices: 25697--25730 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
25687 AAGAATTCAC
25697 AAAAAAAGAAAAAAGA
1 AAAAAAAGAAAAAAGA
*
25713 AAAAGAAAGAAAGAAGA
1 AAAA-AAAGAAAAAAGA
25730 A
1 A
25731 TATTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAGA
Found at i:27704 original size:18 final size:16
Alignment explanation
Indices: 27662--27712 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
27652 ATTAAAAAGT
* *
27662 TTAAGAAAATACAAAAA
1 TTAA-AAAATATAATAA
27679 TTAAAAAATATATATAA
1 TTAAAAAATATA-ATAA
27696 TTCAAAAAATATAATAA
1 TT-AAAAAATATAATAA
27713 ATTGAGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 7 0.23
17 13 0.43
18 10 0.33
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (16 bp):
TTAAAAAATATAATAA
Found at i:27715 original size:18 final size:17
Alignment explanation
Indices: 27662--27715 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
27652 ATTAAAAAGT
*
27662 TTAAGAAAATACAA-AAA
1 TTAA-AAAATATAATAAA
27679 TTAAAAAATAT-ATATAA
1 TTAAAAAATATAATA-AA
27696 TTCAAAAAATATAATAAA
1 TT-AAAAAATATAATAAA
27714 TT
1 TT
27716 GAGAATACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 1 0.03
16 7 0.22
17 8 0.25
18 13 0.41
19 3 0.09
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (17 bp):
TTAAAAAATATAATAAA
Found at i:32798 original size:13 final size:14
Alignment explanation
Indices: 32780--32809 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
32770 AGGATTTTTA
32780 TTTAATTTTTG-GT
1 TTTAATTTTTGTGT
32793 TTTAATTTTTGTGT
1 TTTAATTTTTGTGT
32807 TTT
1 TTT
32810 TTTCTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (14 bp):
TTTAATTTTTGTGT
Found at i:33284 original size:42 final size:40
Alignment explanation
Indices: 33216--33640 Score: 402
Period size: 42 Copynumber: 10.5 Consensus size: 40
33206 TGTTTTTGGA
* * *
33216 TTAGGGTTAAAAGATTGGATAG-CTTCAATTTACCCTATGG
1 TTAGGG-TAAAAGATTGGATGGTCTTCAATCTGCCCTATGG
* *
33256 TTAGGGTAAGAGATTGGATGATGTCTTCAA-CTTGCCCTCTGG
1 TTAGGGTAAAAGATTGGATG--GTCTTCAATC-TGCCCTATGG
33298 TTAGGGTAAAAGATTGGATGG-CTTCAATCTG-CCTCATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCT-ATGG
* * * *
33337 TCAGGGTAAGAA-ATTGGATGGTGTCTTCAATTTTCCCTCTGG
1 TTAGGGTAA-AAGATTGGAT-G-GTCTTCAATCTGCCCTATGG
*
33379 TTAGGGTACAAA-ATTGAATGGT-TTCAATCTG-CCTCATGG
1 TTAGGGTA-AAAGATTGGATGGTCTTCAATCTGCCCT-ATGG
* * * * * * *
33418 -TCGAGGTAAGAGGTTAGATGGTGTCTTTAATCTGCCCTCTAG
1 TTAG-GGTAAAAGATTGGAT-G-GTCTTCAATCTGCCCTATGG
* *
33460 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGA
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTATGG
* * *
33500 TTAGGGTAAAAGATTGGATGG-ATTCAATCTACCCCATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTATGG
* * * *
33539 TTAGGGTAAGAGATTGGGTGGTATCTTTAATCTGCCCTTTGG
1 TTAGGGTAAAAGATTGGATGG--TCTTCAATCTGCCCTATGG
*
33581 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTATGG
33621 TTAGGGTAAAAGATTGGATG
1 TTAGGGTAAAAGATTGGATG
33641 TGGTGATATA
Statistics
Matches: 315, Mismatches: 47, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
38 10 0.03
39 90 0.29
40 87 0.28
41 6 0.02
42 113 0.36
43 9 0.03
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (40 bp):
TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTATGG
Found at i:33315 original size:81 final size:79
Alignment explanation
Indices: 33216--33640 Score: 423
Period size: 81 Copynumber: 5.3 Consensus size: 79
33206 TGTTTTTGGA
* *
33216 TTAGGGTTAAAAGATTGGATAGCTTCAATTTACCCTATGGTTAGGGTAAGAGATTGGATGATGTC
1 TTAGGG-TAAAAGATTGGATGGCTTCAATCT-CCCTATGGTTAGGGTAAGAGATTGGATG-TGTC
33281 TTCAA-CTTGCCCTCTGG
63 TTCAATC-TGCCCTCTGG
* * *
33298 TTAGGGTAAAAGATTGGATGGCTTCAATCTGCCTCATGGTCAGGGTAAGAAATTGGATGGTGTCT
1 TTAGGGTAAAAGATTGGATGGCTTCAATCTCCCT-ATGGTTAGGGTAAGAGATTGGAT-GTGTCT
* *
33363 TCAATTTTCCCTCTGG
64 TCAATCTGCCCTCTGG
* * * * * *
33379 TTAGGGTACAAA-ATTGAATGGTTTCAATCTGCCTCATGG-TCGAGGTAAGAGGTTAGATGGTGT
1 TTAGGGTA-AAAGATTGGATGGCTTCAATCTCCCT-ATGGTTAG-GGTAAGAGATTGGAT-GTGT
* *
33442 CTTTAATCTGCCCTCTAG
62 CTTCAATCTGCCCTCTGG
* * * *
33460 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGATG-G-AT
1 TTAGGGTAAAAGATTGGATGG-CTTCAATCT-CCCTATGGTTAGGGTAAGAGATTGGATGTGTCT
*
33523 TCAATCTACCC-CATGG
64 TCAATCTGCCCTC-TGG
* * * * *
33539 TTAGGGTAAGAGATTGGGTGGTATCTTTAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATG-GT
1 TTAGGGTAAAAGATTGGATGG---CTTCAATCT-CCCTATGGTTAGGGTAAGAGATTGGATGTGT
33603 CTTCAATCTGCCCTCTGG
62 CTTCAATCTGCCCTCTGG
33621 TTAGGGTAAAAGATTGGATG
1 TTAGGGTAAAAGATTGGATG
33641 TGGTGATATA
Statistics
Matches: 288, Mismatches: 41, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
78 1 0.00
79 31 0.11
80 8 0.03
81 178 0.62
82 65 0.23
83 5 0.02
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (79 bp):
TTAGGGTAAAAGATTGGATGGCTTCAATCTCCCTATGGTTAGGGTAAGAGATTGGATGTGTCTTC
AATCTGCCCTCTGG
Found at i:33529 original size:121 final size:121
Alignment explanation
Indices: 33216--33640 Score: 413
Period size: 121 Copynumber: 3.5 Consensus size: 121
33206 TGTTTTTGGA
* * * * *
33216 TTAGGGTTAAAAGATTGGATAG-CTTCAATTTACCCTATGGTTAGGGTAAGAGATTGGATGATGT
1 TTAGGG-TAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATG--G-
* * * * * * *
33280 CTTCAA-CTTGCCCTC-TGGTTAGGGTAAAAGATTGGATGG---CTTCAATCTG-CCTCATGG
62 ATTCAATC-TACCC-CATGGTGAGGGTAAGAGATTAGATGGTATCTTTAATCTGCCCTC-TAG
* * * *
33337 TCAGGGTAAGAA-ATTGGATGGTGTCTTCAATTTTCCCTCTGGTTAGGGTACAAA-ATTGAATGG
1 TTAGGGTAA-AAGATTGGAT-G-GTCTTCAATCTGCCCTCTGGTTAGGGTA-AAAGATTGGATGG
* * * * *
33400 TTTCAATCTGCCTCATGGTCGA-GGTAAGAGGTTAGATGGTGTCTTTAATCTGCCCTCTAG
62 ATTCAATCTACCCCATGGT-GAGGGTAAGAGATTAGATGGTATCTTTAATCTGCCCTCTAG
*
33460 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCC-CATGATTAGGGTAAAAGATTGGATGGATT
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTGGATGGATT
* * * * *
33524 CAATCTACCCCATGGTTAGGGTAAGAGATTGGGTGGTATCTTTAATCTGCCCTTTGG
65 CAATCTACCCCATGGTGAGGGTAAGAGATTAGATGGTATCTTTAATCTGCCCTCTAG
33581 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATG
33641 TGGTGATATA
Statistics
Matches: 257, Mismatches: 30, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
119 1 0.00
120 42 0.16
121 146 0.57
122 5 0.02
123 57 0.22
124 6 0.02
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (121 bp):
TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGATTC
AATCTACCCCATGGTGAGGGTAAGAGATTAGATGGTATCTTTAATCTGCCCTCTAG
Found at i:33837 original size:93 final size:94
Alignment explanation
Indices: 33660--34167 Score: 373
Period size: 93 Copynumber: 5.3 Consensus size: 94
33650 AACTTTACTT
* * * *
33660 CATTCTATTGTAACCTCAGGGATATTGAGATCCG-TTACTCATTTTAATCTGATCCACTAAAACT
1 CATTCCATTGTAACCTCAGGGATATTGAGATCTGCTTACTCATTTTAATCCGATCCACTACAACT
33724 TCAAGGATATAGGATCTGATGCCTCACTC
66 TCAAGGATATAGGATCTGATGCCTCACTC
* ** * * **
33753 CATTCCATTGTAACCTTAGGGATATTGAGATCTGCTT-CATTGTTTTAATCCAAACCACTGTAAC
1 CATTCCATTGTAACCTCAGGGATATTGAGATCTGCTTAC-TCATTTTAATCCGATCCACTACAAC
* * * * ** *
33817 -TCAGGGGTATGGGATTTGATGTTGTAATTTCTC
65 TTCAAGGATATAGGATCTGATG-CCTCA---CTC
* * *
33850 TCAATTCCATTGTAACCTCAGGGATATTGAGATCT-ATTACTCATTTTGATCTGATCCACTACAA
1 -C-ATTCCATTGTAACCTCAGGGATATTGAGATCTGCTTACTCATTTTAATCCGATCCACTACAA
* *
33914 CTTCAAGGATATAGGATCTGGTGCTTCACTC
64 CTTCAAGGATATAGGATCTGATGCCTCACTC
* * * * ** * *
33945 CATTCCACTATAACCTTAGGGACATTGAGATCTGCTT-CGTTGTTTTAATCCGACCCACTGCAAC
1 CATTCCATTGTAACCTCAGGGATATTGAGATCTGCTTAC-TCATTTTAATCCGATCCACTACAAC
* * * * * * *
34009 -TCAGGGGTATGGGGTTTGATGTTGTAACTTCTCTC
65 TTCAAGGATATAGGATCTGA---TG---CCTCACTC
* * * * * * *
34044 CATTCCACTATAACCTCAGGGACATTGAGATCCG-TTACTCATTTTGATCTGATCCACTGCAACT
1 CATTCCATTGTAACCTCAGGGATATTGAGATCTGCTTACTCATTTTAATCCGATCCACTACAACT
* * *
34108 TTAAGGATATAGGATCTGGTGCTTCACTC
66 TCAAGGATATAGGATCTGATGCCTCACTC
* * * *
34137 CATTCCACTGTAACCTTAGAGACATTGAGAT
1 CATTCCATTGTAACCTCAGGGATATTGAGAT
34168 TAGTTTAATC
Statistics
Matches: 324, Mismatches: 71, Indels: 40
0.74 0.16 0.09
Matches are distributed among these distances:
93 126 0.39
94 44 0.14
95 3 0.01
96 4 0.01
97 3 0.01
98 44 0.14
99 100 0.31
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (94 bp):
CATTCCATTGTAACCTCAGGGATATTGAGATCTGCTTACTCATTTTAATCCGATCCACTACAACT
TCAAGGATATAGGATCTGATGCCTCACTC
Found at i:33873 original size:99 final size:99
Alignment explanation
Indices: 33750--34276 Score: 357
Period size: 99 Copynumber: 5.5 Consensus size: 99
33740 TGATGCCTCA
* * * * * *
33750 CTCCATTCCATTGTAACCTTAGGGATATTGAGATCTGCTTCATTGTTTTAATCCAAACCACTGTA
1 CTCCATTCCACTATAACCTCAGGGACATTGAGATCTGCTTCATTGTTTTAATCCGAACCACTGCA
*
33815 ACTCAGGGGTATGGGATTTGATGTTGTAATTTCT
66 ACTCAGGGGTATGGGATTTGATGTTGTAACTTCT
* * * * * ** * * * *
33849 CTCAATTCCATTGTAACCTCAGGGATATTGAGATCT-ATT-ACTCATTTTGATCTGATCCACTAC
1 CTCCATTCCACTATAACCTCAGGGACATTGAGATCTGCTTCA-TTGTTTTAATCCGAACCACTGC
* * * * *
33912 AACTTCAAGGATATAGGATCTG--G-TG---CTTCA
65 AAC-TCAGGGGTATGGGATTTGATGTTGTAACTTCT
* * *
33942 CTCCATTCCACTATAACCTTAGGGACATTGAGATCTGCTTCGTTGTTTTAATCCGACCCACTGCA
1 CTCCATTCCACTATAACCTCAGGGACATTGAGATCTGCTTCATTGTTTTAATCCGAACCACTGCA
*
34007 ACTCAGGGGTATGGGGTTTGATGTTGTAACTTCT
66 ACTCAGGGGTATGGGATTTGATGTTGTAACTTCT
* ** * * *
34041 CTCCATTCCACTATAACCTCAGGGACATTGAGATCCG-TT-ACTCATTTTGATCTGATCCACTGC
1 CTCCATTCCACTATAACCTCAGGGACATTGAGATCTGCTTCA-TTGTTTTAATCCGAACCACTGC
* * * * * *
34104 AACTTTAAGGATATAGGATCTG--G-TG---CTTCA
65 AAC-TCAGGGGTATGGGATTTGATGTTGTAACTTCT
* * * * * * *
34134 CTCCATTCCACTGTAACCTTAGAGACATTGAGA-----TT-A--G-TTTAATCTGACCCATTACA
1 CTCCATTCCACTATAACCTCAGGGACATTGAGATCTGCTTCATTGTTTTAATCCGAACCACTGCA
* * *
34190 AATCAGGGATATGAGATTTGATGTTGTAACTTCT
66 ACTCAGGGGTATGGGATTTGATGTTGTAACTTCT
* * * * *
34224 CTCCATTCCATTGTAACCTTAAGGACATTGAGATCTGCTTCGTTGTTTTAATC
1 CTCCATTCCACTATAACCTCAGGGACATTGAGATCTGCTTCATTGTTTTAATC
34277 TGCTTCACTG
Statistics
Matches: 331, Mismatches: 70, Indels: 54
0.73 0.15 0.12
Matches are distributed among these distances:
84 13 0.04
85 16 0.05
86 1 0.00
87 2 0.01
89 3 0.01
90 34 0.10
93 81 0.24
94 21 0.06
95 3 0.01
96 6 0.02
97 3 0.01
98 42 0.13
99 106 0.32
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (99 bp):
CTCCATTCCACTATAACCTCAGGGACATTGAGATCTGCTTCATTGTTTTAATCCGAACCACTGCA
ACTCAGGGGTATGGGATTTGATGTTGTAACTTCT
Found at i:33993 original size:192 final size:192
Alignment explanation
Indices: 33661--34258 Score: 818
Period size: 192 Copynumber: 3.2 Consensus size: 192
33651 ACTTTACTTC
* * *
33661 ATTCTATTGTAACCTCAGGGATATTGAGATCCGTTACTCATTTTAATCTGATCCACTAAAACTTC
1 ATTCCATTGTAACCTCAGGGATATTGAGATCCGTTACTCATTTTGATCTGATCCACTACAACTTC
* * * *
33726 AAGGATATAGGATCTGATGCCTCACTCCATTCCATTGTAACCTTAGGGATATTGAGATCTGCTTC
66 AAGGATATAGGATCTGGTGCTTCACTCCATTCCACTGTAACCTTAGGGACATTGAGATCTGCTTC
* *
33791 ATTGTTTTAATCCAAACCACTGTAACTCAGGGGTATGGGATTTGATGTTGTAATTTCTCTCA
131 ATTGTTTTAATCCAAACCACTGCAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCA
**
33853 ATTCCATTGTAACCTCAGGGATATTGAGATCTATTACTCATTTTGATCTGATCCACTACAACTTC
1 ATTCCATTGTAACCTCAGGGATATTGAGATCCGTTACTCATTTTGATCTGATCCACTACAACTTC
*
33918 AAGGATATAGGATCTGGTGCTTCACTCCATTCCACTATAACCTTAGGGACATTGAGATCTGCTTC
66 AAGGATATAGGATCTGGTGCTTCACTCCATTCCACTGTAACCTTAGGGACATTGAGATCTGCTTC
* * * * *
33983 GTTGTTTTAATCCGACCCACTGCAACTCAGGGGTATGGGGTTTGATGTTGTAACTTCTCTCC
131 ATTGTTTTAATCCAAACCACTGCAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCA
* * * * *
34045 ATTCCACTATAACCTCAGGGACATTGAGATCCGTTACTCATTTTGATCTGATCCACTGCAACTTT
1 ATTCCATTGTAACCTCAGGGATATTGAGATCCGTTACTCATTTTGATCTGATCCACTACAACTTC
*
34110 AAGGATATAGGATCTGGTGCTTCACTCCATTCCACTGTAACCTTAGAGACATTGAGA-----TT-
66 AAGGATATAGGATCTGGTGCTTCACTCCATTCCACTGTAACCTTAGGGACATTGAGATCTGCTTC
** * * * * * * *
34169 A--G-TTTAATCTGACCCATTACAAATCAGGGATATGAGATTTGATGTTGTAACTTCTCTCC
131 ATTGTTTTAATCCAAACCACTGCAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCA
* * *
34228 ATTCCATTGTAACCTTAAGGACATTGAGATC
1 ATTCCATTGTAACCTCAGGGATATTGAGATC
34259 TGCTTCGTTG
Statistics
Matches: 368, Mismatches: 38, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
183 77 0.21
184 1 0.00
187 2 0.01
192 288 0.78
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (192 bp):
ATTCCATTGTAACCTCAGGGATATTGAGATCCGTTACTCATTTTGATCTGATCCACTACAACTTC
AAGGATATAGGATCTGGTGCTTCACTCCATTCCACTGTAACCTTAGGGACATTGAGATCTGCTTC
ATTGTTTTAATCCAAACCACTGCAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCA
Found at i:34598 original size:49 final size:49
Alignment explanation
Indices: 34478--34686 Score: 172
Period size: 49 Copynumber: 4.3 Consensus size: 49
34468 TCTCATCTTC
* * * *
34478 AGGGTATAAGATTCACCGTTGC-AGTTTCAATCTTTCCGT-TCACATCTCT
1 AGGGTATAAGATTCACCATTGCGA-CTTCAACCTTTCCCTCT-ACATCTCT
** * *** *
34527 AATGTATAAGGTTTGTCATTGCGACTTCAACCTTTCCCTCAACATCTCT
1 AGGGTATAAGATTCACCATTGCGACTTCAACCTTTCCCTCTACATCTCT
* * * ** *
34576 AGGGTATAAGGTTCACCGTTGCGGCTTTGACCTTTCCCTCTATATCTCT
1 AGGGTATAAGATTCACCATTGCGACTTCAACCTTTCCCTCTACATCTCT
* ** * * *
34625 AGGGTACAAGATTCGTCATTGCGACTTCAATCTCTCTCTCTACATCTCT
1 AGGGTATAAGATTCACCATTGCGACTTCAACCTTTCCCTCTACATCTCT
34674 A-GGTATAAGATTC
1 AGGGTATAAGATTC
34687 GTTGTTGTGG
Statistics
Matches: 123, Mismatches: 35, Indels: 5
0.75 0.21 0.03
Matches are distributed among these distances:
48 11 0.09
49 111 0.90
50 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.36
Consensus pattern (49 bp):
AGGGTATAAGATTCACCATTGCGACTTCAACCTTTCCCTCTACATCTCT
Found at i:34725 original size:97 final size:98
Alignment explanation
Indices: 34478--34735 Score: 270
Period size: 98 Copynumber: 2.6 Consensus size: 98
34468 TCTCATCTTC
* * * * * * ** * * *
34478 AGGGTATAAGATTCACCGTTGCAG-TTTCAATCTTTCCGTTCACATCTCTAATGTATAAGGTTTG
1 AGGGTATAAGATTCACCGTTGCGGCTTT-GACCTTTCCCTCCATATCTCTAGGGTACAAGATTCG
*
34542 TCATTGCGACTTCAACCTTTCCCTCAACATCTCT
65 TCATTGCGACTTCAACCTCTCCCTCAACATCTCT
* *
34576 AGGGTATAAGGTTCACCGTTGCGGCTTTGACCTTTCCCTCTATATCTCTAGGGTACAAGATTCGT
1 AGGGTATAAGATTCACCGTTGCGGCTTTGACCTTTCCCTCCATATCTCTAGGGTACAAGATTCGT
* * *
34641 CATTGCGACTTCAATCTCTCTCTCTACATCTCT
66 CATTGCGACTTCAACCTCTCCCTCAACATCTCT
*** * * *
34674 A-GGTATAAGATTCGTTGTTGTGGCTTT-AGTCTTTCCCTCCATATCTTTAGGGTACAAGATTC
1 AGGGTATAAGATTCACCGTTGCGGCTTTGA-CCTTTCCCTCCATATCTCTAGGGTACAAGATTC
34736 TCCATTATGG
Statistics
Matches: 133, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
96 1 0.01
97 51 0.38
98 78 0.59
99 3 0.02
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.37
Consensus pattern (98 bp):
AGGGTATAAGATTCACCGTTGCGGCTTTGACCTTTCCCTCCATATCTCTAGGGTACAAGATTCGT
CATTGCGACTTCAACCTCTCCCTCAACATCTCT
Found at i:34756 original size:49 final size:49
Alignment explanation
Indices: 34503--34777 Score: 176
Period size: 49 Copynumber: 5.6 Consensus size: 49
34493 CCGTTGCAGT
* * * ** * * * * *
34503 TTCAATCTTTCCGTTCACATCTCTAATGTATAAGGTTTGTCATTGCGAC
1 TTCAATCTTTCCCTCCATATCTCTAGGGTACAAGATTCGTCATTGTGGC
* * * * * ** * *
34552 TTCAACCTTTCCCTCAACATCTCTAGGGTATAAGGTTCACCGTTGCGGC
1 TTCAATCTTTCCCTCCATATCTCTAGGGTACAAGATTCGTCATTGTGGC
** * * * *
34601 TTTGACCTTTCCCTCTATATCTCTAGGGTACAAGATTCGTCATTGCGAC
1 TTCAATCTTTCCCTCCATATCTCTAGGGTACAAGATTCGTCATTGTGGC
* * * * * **
34650 TTCAATCTCTCTCTCTACATCTCTA-GGTATAAGATTCGTTGTTGTGGC
1 TTCAATCTTTCCCTCCATATCTCTAGGGTACAAGATTCGTCATTGTGGC
* * * *
34698 TTTAGTCTTTCCCTCCATATCTTTAGGGTACAAGATTC-TCCATTATGGC
1 TTCAATCTTTCCCTCCATATCTCTAGGGTACAAGATTCGT-CATTGTGGC
* *
34747 TTCAATCTTTCCCTTCATGTCTTCTAGGGTA
1 TTCAATCTTTCCCTCCATATC-TCTAGGGTA
34778 TATGATTCAA
Statistics
Matches: 175, Mismatches: 48, Indels: 5
0.77 0.21 0.02
Matches are distributed among these distances:
48 37 0.21
49 130 0.74
50 8 0.05
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (49 bp):
TTCAATCTTTCCCTCCATATCTCTAGGGTACAAGATTCGTCATTGTGGC
Found at i:35420 original size:112 final size:112
Alignment explanation
Indices: 35219--35431 Score: 282
Period size: 112 Copynumber: 1.9 Consensus size: 112
35209 GTTAGACCAG
* * * ** *
35219 TAACCGCTATTTCAATGCAAAAATGCTTCAACAGGATTGTAAGGTGGATAAATTTGAATTTTATT
1 TAACCGCTATTTCAACGCAAAAATGCTTCAACAGGATCGCAAGGCAGATAAAATTGAATTTTATT
*
35284 AGAGGTAAAACTCGCATGAATGAAAAGATTAAAAATTATTGGTCCAC
66 AGAGGCAAAACTCGCATGAATGAAAAGATTAAAAATTATTGGTCCAC
* * * * *
35331 TAACCGTTATTTCAACGTAAAAATGTTTGAACAGGGTCGCAAGGCAGATAAAATTGAATTTTATT
1 TAACCGCTATTTCAACGCAAAAATGCTTCAACAGGATCGCAAGGCAGATAAAATTGAATTTTATT
* ***
35396 AGAGGCAAAGCTCGCATTTCTGAAAAGATTAAAAAT
66 AGAGGCAAAACTCGCATGAATGAAAAGATTAAAAAT
35432 GACCCATATT
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
112 85 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (112 bp):
TAACCGCTATTTCAACGCAAAAATGCTTCAACAGGATCGCAAGGCAGATAAAATTGAATTTTATT
AGAGGCAAAACTCGCATGAATGAAAAGATTAAAAATTATTGGTCCAC
Found at i:35760 original size:18 final size:18
Alignment explanation
Indices: 35738--35788 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
35728 TCATCTCGAC
*
35738 CTCTTTTTTTTTCTTGTTT
1 CTCTTTTTTTTT-TTCTTT
35757 -TCTTGTTTTCTTTTTCTTT
1 CTCTT-TTTT-TTTTTCTTT
35776 CTCTTTTATTTTT
1 CTCTTTT-TTTTT
35789 GGGTGAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 4 0.15
19 14 0.52
20 9 0.33
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (18 bp):
CTCTTTTTTTTTTTCTTT
Found at i:35986 original size:31 final size:31
Alignment explanation
Indices: 35948--36010 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
35938 TTTGTAGACA
35948 GGATCATTTTCAAAACCAGAGCTCCTTTATG
1 GGATCATTTTCAAAACCAGAGCTCCTTTATG
35979 GGATCATTTTCAAAACCAGAGCTCCTTTATG
1 GGATCATTTTCAAAACCAGAGCTCCTTTATG
36010 G
1 G
36011 AATTCTCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (31 bp):
GGATCATTTTCAAAACCAGAGCTCCTTTATG
Found at i:40302 original size:22 final size:24
Alignment explanation
Indices: 40268--40327 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
40258 TATTTTTTTT
40268 AAAA-AAAATAAAAGGATT-A-AA
1 AAAATAAAATAAAAGGATTAATAA
*
40289 AAAATAAAACAAAAGGATTGAATAA
1 AAAATAAAATAAAAGGATT-AATAA
40314 AAAATAAAATAAAA
1 AAAATAAAATAAAA
40328 TAAAAAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 1 0.03
25 15 0.45
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (24 bp):
AAAATAAAATAAAAGGATTAATAA
Found at i:41244 original size:7 final size:6
Alignment explanation
Indices: 41235--41259 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41225 AAAGAAAAGA
41235 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
41260 TGTATCTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:41700 original size:13 final size:14
Alignment explanation
Indices: 41682--41710 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41672 AATATTTTTA
41682 TTTAATTTTTG-GT
1 TTTAATTTTTGTGT
41695 TTTAATTTTTGTGT
1 TTTAATTTTTGTGT
41709 TT
1 TT
41711 AGTTTTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (14 bp):
TTTAATTTTTGTGT
Found at i:42445 original size:15 final size:15
Alignment explanation
Indices: 42425--42466 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
42415 TAGTTGTGGC
42425 CTTAAATTGTGAAAG
1 CTTAAATTGTGAAAG
42440 CTTAAATTGT---AG
1 CTTAAATTGTGAAAG
42452 CTTCAAATTGTGAAA
1 CTT-AAATTGTGAAA
42467 TTAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 5 0.22
13 7 0.30
15 10 0.43
16 1 0.04
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (15 bp):
CTTAAATTGTGAAAG
Found at i:43562 original size:25 final size:25
Alignment explanation
Indices: 43528--43576 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
43518 GGAGCTCATC
43528 TCAAAAGATCAATGCTGAAAGAAGG
1 TCAAAAGATCAATGCTGAAAGAAGG
43553 TCAAAAGATCAATGCTGAAAGAAG
1 TCAAAAGATCAATGCTGAAAGAAG
43577 AATGCAGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.12, G:0.22, T:0.16
Consensus pattern (25 bp):
TCAAAAGATCAATGCTGAAAGAAGG
Found at i:48954 original size:20 final size:20
Alignment explanation
Indices: 48929--48969 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
48919 TTGACAAGTT
48929 TCGTTCATATGTTATTGGCA
1 TCGTTCATATGTTATTGGCA
48949 TCGTTCATATGTTATTGGCA
1 TCGTTCATATGTTATTGGCA
48969 T
1 T
48970 AAAACTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (20 bp):
TCGTTCATATGTTATTGGCA
Found at i:62412 original size:259 final size:259
Alignment explanation
Indices: 61953--62659 Score: 1279
Period size: 259 Copynumber: 2.7 Consensus size: 259
61943 TTCTCAGCTC
*
61953 TTCCAAGTTTTTCCATGTATTTGGAGGATCCTTATATGGGAGTACTCTAGGAAAAATGAAGAGTC
1 TTCCAAGTTTTTCCATGTATTTGGAGGATCCTTATATGGGAGTACTCTAAGAAAAATGAAGAGTC
* *
62018 GGAGCAACTTAAAACCTGACTATTCCACCCTTCCCTCTTTCTCCAACTCTTCATTCATTTTCATC
66 GGAGCAACATAAATCCTGACTATTCCACCCTTCCCTCTTTCTCCAACTCTTCATTCATTTTCATC
*
62083 TGTCCCTACTCGATTCTCTTCATGAGAACCCAGCCAAGTAAAAACAAATACACAGATGATATTCC
131 TGTCCCTACTCGATTCTCTTCATGAGAACCCAGCCAAGTAAAAACAAATACACAGATGACATTCC
* * *
62148 CAAACATCATAAACCGGTCCTAAGCACGTGGCCTATATTCTCAAACTCGGGGTCCATTCAATTT
196 CAAACATCATAAACCAGTCCTAAGCACGCGGCCTATATTCTCAAACTCGAGGTCCATTCAATTT
*
62212 TTCCAAGTTTTTCCATGTATTTGGAGGATCCTTATATGGGAGTACTCTAAGAAAAATGAAGGGTC
1 TTCCAAGTTTTTCCATGTATTTGGAGGATCCTTATATGGGAGTACTCTAAGAAAAATGAAGAGTC
*
62277 GGAGCAACATAAATCCTGACTATTCCACCCTTTCCTCTTTCTCCAACTCTTCATTCATTTTCATC
66 GGAGCAACATAAATCCTGACTATTCCACCCTTCCCTCTTTCTCCAACTCTTCATTCATTTTCATC
*
62342 TGTCCCTACTCGGTTCTCTTCATGAGAACCCAGCCAAGTAAAAACAAATACACAGATGACATTCC
131 TGTCCCTACTCGATTCTCTTCATGAGAACCCAGCCAAGTAAAAACAAATACACAGATGACATTCC
* *
62407 CAAACATCATAAACCAGTCCTAAGCACGCGGCCTATATTCTGAGACTCGAGGTCCATTCAATTT
196 CAAACATCATAAACCAGTCCTAAGCACGCGGCCTATATTCTCAAACTCGAGGTCCATTCAATTT
*
62471 TTCCAAGTTTTTCCATGTATTTGGAGGATCCTTATATGGGAGTACTCTAAGAAAAATGAAGACTC
1 TTCCAAGTTTTTCCATGTATTTGGAGGATCCTTATATGGGAGTACTCTAAGAAAAATGAAGAGTC
* *
62536 AGAGCAACATAAATCCTGACTATTCCGCCCTTCCCTCTTTCTCCAACTCTTCATTCATTTTCATC
66 GGAGCAACATAAATCCTGACTATTCCACCCTTCCCTCTTTCTCCAACTCTTCATTCATTTTCATC
62601 TGTCCCTACTCGATTCTCTTCATGAGAACCCAGCCAAGTAAAAACAAATACACAGATGA
131 TGTCCCTACTCGATTCTCTTCATGAGAACCCAGCCAAGTAAAAACAAATACACAGATGA
62660 ATGTATATCA
Statistics
Matches: 430, Mismatches: 18, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
259 430 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (259 bp):
TTCCAAGTTTTTCCATGTATTTGGAGGATCCTTATATGGGAGTACTCTAAGAAAAATGAAGAGTC
GGAGCAACATAAATCCTGACTATTCCACCCTTCCCTCTTTCTCCAACTCTTCATTCATTTTCATC
TGTCCCTACTCGATTCTCTTCATGAGAACCCAGCCAAGTAAAAACAAATACACAGATGACATTCC
CAAACATCATAAACCAGTCCTAAGCACGCGGCCTATATTCTCAAACTCGAGGTCCATTCAATTT
Found at i:65152 original size:3 final size:3
Alignment explanation
Indices: 65144--65175 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
65134 CTTCAACTAA
65144 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
65176 ACCATCCCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:66383 original size:17 final size:17
Alignment explanation
Indices: 66349--66390 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
66339 TCCCTTGACT
*
66349 TTTAACTTTCCATCTTC
1 TTTAACTTTCCATATTC
66366 TTTAAC-TTCTCATATTC
1 TTTAACTTTC-CATATTC
66383 TTATAACT
1 TT-TAACT
66391 ATTTTTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 14 0.67
18 4 0.19
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAACTTTCCATATTC
Found at i:66508 original size:8 final size:8
Alignment explanation
Indices: 66495--66522 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
66485 CGCAATTTAA
66495 ATTCTCAT
1 ATTCTCAT
66503 ATTCTCAT
1 ATTCTCAT
66511 ATTCTCAT
1 ATTCTCAT
66519 ATTC
1 ATTC
66523 ATCCTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTCTCAT
Found at i:71762 original size:33 final size:33
Alignment explanation
Indices: 71725--71790 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
71715 ATTTGAATTA
71725 TTTGAAAATTTGAATAAGAAAAGACAAAACTAT
1 TTTGAAAATTTGAATAAGAAAAGACAAAACTAT
71758 TTTGAAAATTTGAATAAGAAAAGACAAAACTAT
1 TTTGAAAATTTGAATAAGAAAAGACAAAACTAT
71791 GTAGTTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (33 bp):
TTTGAAAATTTGAATAAGAAAAGACAAAACTAT
Found at i:72600 original size:16 final size:16
Alignment explanation
Indices: 72557--72600 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
72547 AAATCATAAT
72557 ATAAATTAAAATTTAA
1 ATAAATTAAAATTTAA
* * *
72573 AAAAATCAAAAATTAA
1 ATAAATTAAAATTTAA
72589 ATTAAATTAAAA
1 A-TAAATTAAAA
72601 GTACCAAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAATTAAAATTTAA
Found at i:72976 original size:21 final size:21
Alignment explanation
Indices: 72951--72992 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
72941 GTCAATTACT
72951 ATTT-ATAAAAAATAATATTTA
1 ATTTAATAAAAAAT-ATATTTA
*
72972 ATTTAATATAAAATATATTTA
1 ATTTAATAAAAAATATATTTA
72993 TTTTCTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTAATAAAAAATATATTTA
Found at i:73186 original size:17 final size:19
Alignment explanation
Indices: 73164--73208 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
73154 TAATCATTAC
73164 CATATTTA-AAAT-AAAAT
1 CATATTTATAAATAAAAAT
*
73181 CATATTTATATATAAAAAT
1 CATATTTATAAATAAAAAT
*
73200 TATATTTAT
1 CATATTTAT
73209 TTAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 3 0.12
19 13 0.54
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
CATATTTATAAATAAAAAT
Found at i:73386 original size:17 final size:17
Alignment explanation
Indices: 73364--73416 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
73354 AGACCCATTC
73364 AAAATAAACAAAATTAA
1 AAAATAAACAAAATTAA
* *
73381 AAAATAGAC-AAATGAA
1 AAAATAAACAAAATTAA
73397 TAAAAT-AA-AAAA-TAA
1 -AAAATAAACAAAATTAA
73412 AAAAT
1 AAAAT
73417 TAAATTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
14 5 0.17
15 2 0.07
16 10 0.33
17 13 0.43
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (17 bp):
AAAATAAACAAAATTAA
Found at i:73635 original size:23 final size:24
Alignment explanation
Indices: 73605--73671 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
73595 TAGCTCATGG
73605 CTACATCAGCAC-T-ACGTCAGCAA
1 CTACATCAG-ACGTCACGTCAGCAA
73628 CTACATCA-ACGTCACGTCAGCAA
1 CTACATCAGACGTCACGTCAGCAA
* *
73651 CTACGTCAG-TGTCACGTCAGC
1 CTACATCAGACGTCACGTCAGC
73672 GCCATGTCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.05
22 1 0.03
23 36 0.92
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.19
Consensus pattern (24 bp):
CTACATCAGACGTCACGTCAGCAA
Found at i:73658 original size:12 final size:12
Alignment explanation
Indices: 73605--73659 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
73595 TAGCTCATGG
*
73605 CTACATCAGC-A
1 CTACGTCAGCAA
73616 CTACGTCAGCAA
1 CTACGTCAGCAA
* * **
73628 CTACATCAACGT
1 CTACGTCAGCAA
73640 C-ACGTCAGCAA
1 CTACGTCAGCAA
73651 CTACGTCAG
1 CTACGTCAG
73660 TGTCACGTCA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
11 16 0.48
12 17 0.52
ACGTcount: A:0.33, C:0.35, G:0.15, T:0.18
Consensus pattern (12 bp):
CTACGTCAGCAA
Found at i:74731 original size:17 final size:17
Alignment explanation
Indices: 74709--74778 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
74699 GACCCAACAG
74709 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
74726 ATTTAAGTTTATATTAA
1 ATTTAAATTTATTTTAA
** **
74743 ATTTAAATCCATTTGGA
1 ATTTAAATTTATTTTAA
*
74760 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
74777 AT
1 AT
74779 ATAAGTTTAA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:75423 original size:3 final size:3
Alignment explanation
Indices: 75400--75451 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
75390 AAATGAACAT
* * *
75400 TAA TAT TAA TTAA TAAA TAA TAA TAA TAA TAA TAA TAA -CA TAA AAA
1 TAA TAA TAA -TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
75446 TAA TAA
1 TAA TAA
75452 CATAAAATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 1 0.03
3 33 0.82
4 6 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:75450 original size:14 final size:14
Alignment explanation
Indices: 75414--75458 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
75404 ATTAATTAAT
*
75414 AAATAATAATAATAA
1 AAATAATAA-CATAA
*
75429 TAATAATAACATAA
1 AAATAATAACATAA
75443 AAATAATAACATAA
1 AAATAATAACATAA
75457 AA
1 AA
75459 TAGAAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAATAACATAA
Found at i:76636 original size:30 final size:29
Alignment explanation
Indices: 76602--76667 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
76592 TGAAGGTCCC
*
76602 TAAACTGTCCAAAAATCATATTTTGACCCT
1 TAAACTGTCC-AAAATCATATTTTGAACCT
* * *
76632 TAAACTTTTCCAAAATTATATTTTTAACCT
1 TAAAC-TGTCCAAAATCATATTTTGAACCT
76662 TAAACT
1 TAAACT
76668 TTTTGAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 26 0.84
31 4 0.13
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (29 bp):
TAAACTGTCCAAAATCATATTTTGAACCT
Found at i:76668 original size:30 final size:30
Alignment explanation
Indices: 76613--76737 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 30
76603 AAACTGTCCA
* * *
76613 AAAATCATATTTTGACCCTTAAACTTTTCC
1 AAAATTATATTTTTAACCTTAAACTTTTCC
**
76643 AAAATTATATTTTTAACCTTAAACTTTTTG
1 AAAATTATATTTTTAACCTTAAACTTTTCC
* * ** *
76673 AAAATTACATTTTTACCCCCAAACTTTT-T
1 AAAATTATATTTTTAACCTTAAACTTTTCC
* * *
76702 AAAATT-TCATTTTTGA-CTTCAATTTTTCC
1 AAAATTAT-ATTTTTAACCTTAAACTTTTCC
76731 AAAATTA
1 AAAATTA
76738 CCATTTACCC
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
28 7 0.09
29 18 0.24
30 49 0.66
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (30 bp):
AAAATTATATTTTTAACCTTAAACTTTTCC
Found at i:76793 original size:116 final size:117
Alignment explanation
Indices: 76673--76924 Score: 275
Period size: 117 Copynumber: 2.2 Consensus size: 117
76663 AAACTTTTTG
*** * * *
76673 AAAATTA-CATTTTTACCCCCAAACTTTTTAAAATTTCATTTTTGA-CTTCAATTTTTCCAAA-A
1 AAAATTACCA-TTTTACCCCCAAACTTCCAAAAATTCCATTTTTAATC-CCAATTTTTCCAAAGA
*
76735 TTACCATTTACCC-CTAAACT-TCCAAAAATTCTATTTTGACCTCGATTTTTCCAA
64 TTACCAGTTACCCTC-AAA-TGTCCAAAAATTCTATTTTGACCTCGATTTTTCCAA
* *
76789 AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAATCCCGATTTTTCCAAAGATT
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTAATCCCAATTTTTCCAAAGATT
* * * **
76854 ACCAGTTACCCTCAAATGTCTAAAAATTCTATTTTTAACCCCGAATCCTTCC--
66 ACCAGTTACCCTCAAATGTCCAAAAATTCTA-TTTTGACCTCG-ATTTTTCCAA
76906 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
76925 TGGATATCTA
Statistics
Matches: 115, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
116 49 0.43
117 50 0.43
118 10 0.09
119 6 0.05
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTAATCCCAATTTTTCCAAAGATT
ACCAGTTACCCTCAAATGTCCAAAAATTCTATTTTGACCTCGATTTTTCCAA
Found at i:76820 original size:59 final size:59
Alignment explanation
Indices: 76673--77046 Score: 288
Period size: 59 Copynumber: 6.4 Consensus size: 59
76663 AAACTTTTTG
* * * * * *
76673 AAAATTA-CATTTTTACCCCCAAACTTTTTAAAATT-TCATTTTTGACTTCAATTTTTCC-
1 AAAATTACCA-TTTTACCCCCGAACTTCTAAAAATTCT-ATTTTTAACCTCGATTTTTCCA
** * *
76731 AAAATTACCA-TTTACCCCTAAACTTCCAAAAATTCTA-TTTTGACCTCGATTTTTCCAA
1 AAAATTACCATTTTACCCCCGAACTTCTAAAAATTCTATTTTTAACCTCGATTTTTCC-A
* *
76789 AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAATCC-CGATTTTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCTAAAAATTCTATTTTTAA-CCTCGATTTTTCCA
* * * * * **
76848 AAGATTACCA-GTTACCCTC-AAATGTCTAAAAATTCTATTTTTAACCCCGAATCCTTCC-
1 AAAATTACCATTTTACCCCCGAACT-TCTAAAAATTCTATTTTTAACCTCG-ATTTTTCCA
* * * ***
76906 AAAATTACCATTTTACCCCTGGA-TATCTAAAAAATCTATTTTTAACCTCGAACCTTCCA
1 AAAATTACCATTTTACCCCCGAACT-TCTAAAAATTCTATTTTTAACCTCGATTTTTCCA
* * * **
76965 AAAATTACCATTTTACCCTCGAA-TGTCTAAAAAGTCCATTTTTAACCTCGAACCTTT-C-
1 AAAATTACCATTTTACCCCCGAACT-TCTAAAAATTCTATTTTTAACCTCG-ATTTTTCCA
*
77023 AAAATTACCATTTTGTCCCCCGAA
1 AAAATTACCATTTT-ACCCCCGAA
77047 TATCCAAAAT
Statistics
Matches: 264, Mismatches: 37, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
56 17 0.06
57 26 0.10
58 75 0.28
59 124 0.47
60 20 0.08
61 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAACTTCTAAAAATTCTATTTTTAACCTCGATTTTTCCA
Found at i:76912 original size:117 final size:116
Alignment explanation
Indices: 76702--77065 Score: 366
Period size: 117 Copynumber: 3.1 Consensus size: 116
76692 CAAACTTTTT
* * * * *
76702 AAAATTTCATTTTTGACTTCAATTTTTCCAAAATTACCATTTACCC-CTAAACT-TCCAAAAATT
1 AAAATTCCATTTTTAACCTCGATTTTTCCAAAATTACCATTTACCCTC-AAA-TGTCTAAAAATT
* **
76765 CTA-TTTTGACCTCG-ATTTTTCCAAAAAATTACCATTTTACCCCCGAACT-TCCA
64 CTATTTTTAACCTCGAATCCTTCC--AAAATTACCATTTTACCCCCGAA-TATCCA
*
76818 AAAATTCCATTTTTAATCC-CGATTTTTCCAAAGATTACCAGTTACCCTCAAATGTCTAAAAATT
1 AAAATTCCATTTTTAA-CCTCGATTTTTCCAAA-ATTACCATTTACCCTCAAATGTCTAAAAATT
* * * *
76882 CTATTTTTAACCCCGAATCCTTCCAAAATTACCATTTTACCCCTGGATATCTA
64 CTATTTTTAACCTCGAATCCTTCCAAAATTACCATTTTACCCCCGAATATCCA
* * *** * *
76935 AAAAATCTATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCTAAAAAGT
1 AAAATTCCATTTTTAACCTCGATTTTTCC-AAAATTACCA-TTTACCCTCAAATGTCTAAAAATT
* * *
77000 CCATTTTTAACCTCGAA-CCTTTCAAAATTACCATTTTGTCCCCCGAATATCC-
64 CTATTTTTAACCTCGAATCCTTCCAAAATTACCATTTT-ACCCCCGAATATCCA
77052 AAAATTACCATTTT
1 AAAATT-CCATTTT
77066 ACTCTCGGGC
Statistics
Matches: 206, Mismatches: 30, Indels: 22
0.80 0.12 0.09
Matches are distributed among these distances:
116 30 0.15
117 105 0.51
118 65 0.32
119 6 0.03
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (116 bp):
AAAATTCCATTTTTAACCTCGATTTTTCCAAAATTACCATTTACCCTCAAATGTCTAAAAATTCT
ATTTTTAACCTCGAATCCTTCCAAAATTACCATTTTACCCCCGAATATCCA
Found at i:76920 original size:30 final size:29
Alignment explanation
Indices: 76727--77066 Score: 120
Period size: 29 Copynumber: 11.7 Consensus size: 29
76717 ACTTCAATTT
* *
76727 TTCCAAAATTACCA-TTT-ACCCCTAAAC
1 TTCCAAAATTACCATTTTAACCCCGAATC
* * * * *
76754 TTCCAAAAATT-CTATTTTGACCTCGATTT
1 TTCC-AAAATTACCATTTTAACCCCGAATC
*
76783 TTCCAAAAAATTACCATTTTACCCCCGAA-C
1 TTCC--AAAATTACCATTTTAACCCCGAATC
* * *
76813 TTCCAAAAATT-CCATTTTTAATCCCGATTT
1 TTCC-AAAATTACCA-TTTTAACCCCGAATC
* *
76843 TTCCAAAGATTACCA-GTT-ACCCTCAAAT-
1 TTCCAAA-ATTACCATTTTAACCC-CGAATC
* * *
76871 GTCTAAAAATT-CTATTTTTAACCCCGAATCC
1 TTC-CAAAATTACCA-TTTTAACCCCGAAT-C
76902 TTCCAAAATTACCATTTT-ACCCCTGGATATC
1 TTCCAAAATTACCATTTTAACCCC--GA-ATC
** * * *
76933 -TAAAAAATCTA--TTTTTAACCTCGAACC
1 TTCCAAAAT-TACCATTTTAACCCCGAATC
76960 TTCCAAAAATTACCATTTT-ACCCTCGAAT-
1 TTCC-AAAATTACCATTTTAACCC-CGAATC
* * * * *
76989 GTCTAAAAAGT-CCATTTTTAACCTCGAACC
1 TTC-CAAAATTACCA-TTTTAACCCCGAATC
* **
77019 TTTCAAAATTACCATTTTGTCCCCCGAAT-
1 TTCCAAAATTACCATTTT-AACCCCGAATC
*
77048 ATCCAAAATTACCATTTTA
1 TTCCAAAATTACCATTTTA
77067 CTCTCGGGCA
Statistics
Matches: 226, Mismatches: 54, Indels: 65
0.66 0.16 0.19
Matches are distributed among these distances:
27 10 0.04
28 28 0.12
29 100 0.44
30 63 0.28
31 23 0.10
32 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (29 bp):
TTCCAAAATTACCATTTTAACCCCGAATC
Found at i:80975 original size:18 final size:19
Alignment explanation
Indices: 80943--80980 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
80933 CGCCTTCTCT
80943 TGCATTGCACACATT-GCA
1 TGCATTGCACACATTCGCA
**
80961 TGCATTGCATTCATTCGCA
1 TGCATTGCACACATTCGCA
80980 T
1 T
80981 TACATTCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (19 bp):
TGCATTGCACACATTCGCA
Found at i:88993 original size:49 final size:48
Alignment explanation
Indices: 88940--89682 Score: 423
Period size: 49 Copynumber: 15.2 Consensus size: 48
88930 TTAAGTTGCG
*
88940 ACGGTGAACTGTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCA
1 ACGGCGAACT-TGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCA
* ** * * * * * *
88989 ACGGTGAATCCAGTACCAC-GAAGAGACGAAGGGAAAGGTTTAAGTCGTA
1 ACGGCGAA-CTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCA
* * *
89038 ATGGCGAACCTTGTAGCTCAGAAGCATGAAGGGAAAGATTTAAGCTGCA
1 ACGGCGAA-CTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCA
* * * * *
89087 ACGGCGAGTCTAGTACCAC-GAAGACATGAAGGGAAAGGTTTAAGTCGCA
1 ACGGCGA-ACTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCA
* *
89136 AAGGCGAACCTTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCA
1 ACGGCGAA-CTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCA
** * ** * * * * * *
89185 ACAACAAATCCAGTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTCACA
1 ACGGCGAA-CTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCA
*
89234 ACGGTGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCA
1 ACGGCGAA-CTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCA
* ** ** * * * *
89283 ATGGTAAATCCAGTACCACA-AAGATATGGAGGGAAAGATTTAAGTCGCA
1 ACGGCGAA-CTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCA
*
89332 ACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGTA
1 ACGGCGAA-CTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCA
** * * * * **
89381 ATAGCTAATCTAGTA-C-CATGAAGATATGGAA-GGAAAGGTTTAAGTTGCA
1 ACGGCGAA-CTTGTACCTCA-GAAG-CAT-GAAGGGAAAGATTTAAGCCGCA
* * * * * *
89430 ACGGCAAACCTTGTAGCTCAGAAGCATGACGGGAAATATTTAAGCTGCC
1 ACGGCGAA-CTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCA
* ** * * * *
89479 ATGGCGAATCCAGTACCAC-GAAG-ATACGGAGGGAAAGGTTTAAGTCGCA
1 ACGGCGAA-CTTGTACCTCAGAAGCAT--GAAGGGAAAGATTTAAGCCGCA
* * * *
89528 ATGACGAACTTAATACCTCAG-AG-ACTCGAAGAGAAAGATTTAAGCCGCA
1 ACGGCGAACTT-GTACCTCAGAAGCA-T-GAAGGGAAAGATTTAAGCCGCA
* ** * * * *
89577 ATGGCGAATCCAGTACCGC-GAAGACATAAAAGGGAAAGGTTTAAGTCGCA
1 ACGGCGAA-CTTGTACCTCAGAAG-CAT-GAAGGGAAAGATTTAAGCCGCA
* ** * *
89627 ATGGCGAACCTTACACCTCAGAAGCATGAAAGGAAA-ATTTAAGCCGTA
1 ACGGCGAA-CTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCA
*
89675 ATGGCGAA
1 ACGGCGAA
89683 TTTAGTACTA
Statistics
Matches: 519, Mismatches: 148, Indels: 55
0.72 0.20 0.08
Matches are distributed among these distances:
47 4 0.01
48 44 0.08
49 403 0.78
50 61 0.12
51 7 0.01
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (48 bp):
ACGGCGAACTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCA
Found at i:89690 original size:98 final size:98
Alignment explanation
Indices: 88919--89683 Score: 930
Period size: 98 Copynumber: 7.8 Consensus size: 98
88909 CGATGCATAG
* * *
88919 AGGGAAAAGGTTTAAGTTGCGACGGTGAA-CTGTGTACCTCAGAAGCATGAAGGGAAAGATTTAA
1 AGGG-AAAGGTTTAAGTCGCAACGGCGAACCT-TGTACCTCAGAAGCATGAAGGGAAAGATTTAA
* * * *
88983 GCCGCAACGGTGAATCCAGTACCACGAAGAGACGA
64 GCCGCAATGGCGAATCCAGTACCACGAAGATATGA
* * *
89018 AGGGAAAGGTTTAAGTCGTAATGGCGAACCTTGTAGCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * * *
89083 TGCAACGGCGAGTCTAGTACCACGAAGACATGA
66 CGCAATGGCGAATCCAGTACCACGAAGATATGA
* *
89116 AGGGAAAGGTTTAAGTCGCAAAGGCGAACCTTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
*** * *
89181 CGCAACAACAAATCCAGTACCACGAAGATATGG
66 CGCAATGGCGAATCCAGTACCACGAAGATATGA
* *
89214 AGGGAAAGGTTTAAGTCACAACGGTGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
** * *
89279 CGCAATGGTAAATCCAGTACCACAAAGATATGG
66 CGCAATGGCGAATCCAGTACCACGAAGATATGA
*
89312 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * * *
89377 CGTAATAGCTAATCTAGTACCATGAAGATATGGA
66 CGCAATGGCGAATCCAGTACCACGAAGATAT-GA
* * * * *
89411 A-GGAAAGGTTTAAGTTGCAACGGCAAACCTTGTAGCTCAGAAGCATGACGGGAAATATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * *
89475 TGCCATGGCGAATCCAGTACCACGAAGATACGG
66 CGCAATGGCGAATCCAGTACCACGAAGATATGA
* * * *
89508 AGGGAAAGGTTTAAGTCGCAATGACGAA-CTTAATACCTCAG-AG-ACTCGAAGAGAAAGATTTA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTT-GTACCTCAGAAGCA-T-GAAGGGAAAGATTTA
* * *
89570 AGCCGCAATGGCGAATCCAGTACCGCGAAGACATAAA
63 AGCCGCAATGGCGAATCCAGTACCACGAAGATAT-GA
* ** *
89607 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTACACCTCAGAAGCATGAAAGGAAA-ATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
*
89671 CGTAATGGCGAAT
66 CGCAATGGCGAAT
89684 TTAGTACTAT
Statistics
Matches: 576, Mismatches: 80, Indels: 21
0.85 0.12 0.03
Matches are distributed among these distances:
96 1 0.00
97 8 0.01
98 510 0.89
99 50 0.09
100 6 0.01
101 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.19
Consensus pattern (98 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
CGCAATGGCGAATCCAGTACCACGAAGATATGA
Found at i:90109 original size:17 final size:17
Alignment explanation
Indices: 90087--90156 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
90077 GGCCCAACAG
90087 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
90104 ATTTAAGTTTATATTAA
1 ATTTAAATTTATTTTAA
** **
90121 ATTTAAATCCATTTGGA
1 ATTTAAATTTATTTTAA
*
90138 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
90155 AT
1 AT
90157 ATAAGTTTAA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:92051 original size:29 final size:29
Alignment explanation
Indices: 92003--92324 Score: 169
Period size: 29 Copynumber: 11.0 Consensus size: 29
91993 ACCCCTAAAC
92003 TTTTCC-AAAATTCCATTTTTAACCTC-AA
1 TTTTCCAAAAATTCCA-TTTTAACCTCGAA
* *
92031 TTTTTCC-AAGATTACCATTTTACCCTCGAA
1 -TTTTCCAAAAATT-CCATTTTAACCTCGAA
* * * *
92061 -CTTCCAAAAATTCCATTTTTGACCTTGAT
1 TTTTCCAAAAATTCCA-TTTTAACCTCGAA
*
92090 TTTTCCAAAAATTACCATTTTACCCTCGAA
1 TTTTCCAAAAATT-CCATTTTAACCTCGAA
* *
92120 CTTT-CAAAAATTCCATTTGTAACC-CTAAA
1 TTTTCCAAAAATTCCATTT-TAACCTC-GAA
* * *
92149 TTTTCCAAAGATTACCATTTTACCCAC-AA
1 TTTTCCAAAAATT-CCATTTTAACCTCGAA
*** * *
92178 ACATCTAAAAATTCCATTTTAAACCTCAAA
1 TTTTCCAAAAATTCCATTTT-AACCTCGAA
* * *
92208 TCCTT-CTAAAATTACCATTTTACCCTCGAA
1 T-TTTCCAAAAATT-CCATTTTAACCTCGAA
* * * * *
92238 -TATCTAAAAATTCTATTTTTAACCCCAAA
1 TTTTCCAAAAATTCCA-TTTTAACCTCGAA
** *
92267 CCTTCCAAAAATTACCATTTTACCCTCGAA
1 TTTTCCAAAAATT-CCATTTTAACCTCGAA
* * *
92297 -TGTCTAAAAATTCCTTTTTTAACCTCGA
1 TTTTCCAAAAATTCC-ATTTTAACCTCGA
92325 CCATTCCAAA
Statistics
Matches: 221, Mismatches: 52, Indels: 40
0.71 0.17 0.13
Matches are distributed among these distances:
28 26 0.12
29 101 0.46
30 73 0.33
31 21 0.10
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTTCCAAAAATTCCATTTTAACCTCGAA
Found at i:92113 original size:59 final size:59
Alignment explanation
Indices: 92005--92345 Score: 354
Period size: 59 Copynumber: 5.8 Consensus size: 59
91995 CCCTAAACTT
* *
92005 TTCC-AAAATTCCATTTTTAACCTCAATTTTTCC-AAGATTACCATTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTAACCTCAATCTTTCCAAAAATTACCATTTTACCCTCGAAC
* ** *
92062 TTCCAAAAATTCCATTTTTGACCTTGATTTTTCCAAAAATTACCATTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTAACCTCAATCTTTCCAAAAATTACCATTTTACCCTCGAAC
* * * * * *
92121 TTTCAAAAATTCCATTTGTAACCCTAAAT-TTTCCAAAGATTACCATTTTACCCACAAAC
1 TTCCAAAAATTCCATTTTTAA-CCTCAATCTTTCCAAAAATTACCATTTTACCCTCGAAC
* * * * *
92180 ATCTAAAAATTCCATTTTAAACCTCAAATCCTT-CTAAAATTACCATTTTACCCTCGAA-
1 TTCCAAAAATTCCATTTTTAACCTC-AATCTTTCCAAAAATTACCATTTTACCCTCGAAC
* * * * *
92238 TATCTAAAAATTCTATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAA-
1 T-TCCAAAAATTCCATTTTTAACCTCAATCTTTCCAAAAATTACCATTTTACCCTCGAAC
* * * * *
92297 TGTCTAAAAATTCCTTTTTTAACCTCGACCATTCC-AAAATTACCATTTT
1 T-TCCAAAAATTCCATTTTTAACCTCAATCTTTCCAAAAATTACCATTTT
92346 GCCCCTCTGA
Statistics
Matches: 241, Mismatches: 36, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
57 4 0.02
58 49 0.20
59 181 0.75
60 7 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (59 bp):
TTCCAAAAATTCCATTTTTAACCTCAATCTTTCCAAAAATTACCATTTTACCCTCGAAC
Found at i:92188 original size:118 final size:116
Alignment explanation
Indices: 92004--92345 Score: 391
Period size: 118 Copynumber: 2.9 Consensus size: 116
91994 CCCCTAAACT
* * * *
92004 TTTCCAAAATTCCATTTTTAA-CCTCAATTTTTCC-AAGATTACCATTTTACCCTCGAACTTCCA
1 TTTCAAAAATTCCATTTTTAACCCT-AAATTTTCCAAAGATTACCATTTTACCCTCGAACATCTA
* * **
92067 AAAATTCCATTTTTGACCTTGATTTTTCCAAAAATTACCATTTTACCCTCGAA
65 AAAATTCCATTTTTAACCTAGATCATTCC-AAAATTACCATTTTACCCTCGAA
* * *
92120 CTTTCAAAAATTCCATTTGTAACCCTAAATTTTCCAAAGATTACCATTTTACCCACAAACATCTA
1 -TTTCAAAAATTCCATTTTTAACCCTAAATTTTCCAAAGATTACCATTTTACCCTCGAACATCTA
* * * *
92185 AAAATTCCATTTTAAACCTCAAATCCTTCTAAAATTACCATTTTACCCTCGAA
65 AAAATTCCATTTTTAACCT-AGATCATTCCAAAATTACCATTTTACCCTCGAA
* * * ** * **
92238 TATCTAAAAATTCTATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCTA
1 TTTC-AAAAATTCCATTTTTAACCCTAAATTTTCCAAAGATTACCATTTTACCCTCGAACATCTA
* * *
92303 AAAATTCCTTTTTTAACCTCGACCATTCCAAAATTACCATTTT
65 AAAATTCCATTTTTAACCTAGATCATTCCAAAATTACCATTTT
92346 GCCCCTCTGA
Statistics
Matches: 189, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
117 49 0.26
118 135 0.71
119 5 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (116 bp):
TTTCAAAAATTCCATTTTTAACCCTAAATTTTCCAAAGATTACCATTTTACCCTCGAACATCTAA
AAATTCCATTTTTAACCTAGATCATTCCAAAATTACCATTTTACCCTCGAA
Found at i:92288 original size:30 final size:30
Alignment explanation
Indices: 92041--92345 Score: 176
Period size: 29 Copynumber: 10.4 Consensus size: 30
92031 TTTTTCCAAG
*
92041 ATTACCATTTT-ACCCTCGAACTTCCAAAA
1 ATTACCATTTTAACCCTCAAACTTCCAAAA
* * * ***
92070 ATT-CCATTTTTGACCTTGATTTTTCCAAAA
1 ATTACCA-TTTTAACCCTCAAACTTCCAAAA
* *
92100 ATTACCATTTT-ACCCTCGAACTTTCAAAA
1 ATTACCATTTTAACCCTCAAACTTCCAAAA
* *
92129 ATT-CCATTTGTAACCCT-AAATTTTCCAAAG
1 ATTACCATTT-TAACCCTCAAA-CTTCCAAAA
* * *
92159 ATTACCATTTT-ACCCACAAACATCTAAAA
1 ATTACCATTTTAACCCTCAAACTTCCAAAA
* *
92188 ATT-CCATTTTAAACCTCAAATCCTT-CTAAA
1 ATTACCATTTTAACCCTCAAA--CTTCCAAAA
* *
92218 ATTACCATTTT-ACCCTCGAA-TATCTAAAA
1 ATTACCATTTTAACCCTCAAACT-TCCAAAA
*
92247 ATT-CTATTTTTAACCC-CAAACCTTCCAAAA
1 ATTACCA-TTTTAACCCTCAAA-CTTCCAAAA
* *
92277 ATTACCATTTT-ACCCTCGAA-TGTCTAAAA
1 ATTACCATTTTAACCCTCAAACT-TCCAAAA
* * *
92306 ATT-CCTTTTTTAA-CCTCGACCATTCC-AAA
1 ATTACC-ATTTTAACCCTCAAAC-TTCCAAAA
92335 ATTACCATTTT
1 ATTACCATTTT
92346 GCCCCTCTGA
Statistics
Matches: 209, Mismatches: 41, Indels: 52
0.69 0.14 0.17
Matches are distributed among these distances:
27 1 0.00
28 22 0.11
29 89 0.43
30 75 0.36
31 22 0.11
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (30 bp):
ATTACCATTTTAACCCTCAAACTTCCAAAA
Found at i:92334 original size:177 final size:174
Alignment explanation
Indices: 92009--92345 Score: 419
Period size: 177 Copynumber: 1.9 Consensus size: 174
91999 AAACTTTTCC
* ** *
92009 AAAATTCCATTTTTAACCTCAATTTTTCCAAGATTACCATTTTACCCTCGAACTTCCAAAAATTC
1 AAAATTCCATTTTAAACCTCAATCCTTCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATTC
* *** *** *
92074 CATTTTTGACCTTGATTTTTCCAAAAATTACCATTTTACCCTCGAACTTTCAAAAATTCCATTTG
66 CATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAACTGTCAAAAATTCCATTTG
*
92139 TAACCCTAAATTTTCCAAAGATTACCATTTTACCCACAAACATCTA
131 TAACCCGAAA-TTTCCAAA-ATTACCATTTTACCCACAAACATCTA
* *
92185 AAAATTCCATTTTAAACCTCAAATCCTTCTAAAATTACCATTTTACCCTCGAA-TATCTAAAAAT
1 AAAATTCCATTTTAAACCTC-AATCCTTCCAAAATTACCATTTTACCCTCGAACT-TCCAAAAAT
* *
92249 TCTATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAA-TGTCTAAAAATTCCTT
64 TCCATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAACTGTC-AAAAATTCCAT
* *
92313 TTTTAACCTCGACCA-TTCCAAAATTACCATTTT
128 TTGTAACC-CGA-AATTTCCAAAATTACCATTTT
92346 GCCCCTCTGA
Statistics
Matches: 137, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
176 34 0.25
177 100 0.73
178 2 0.01
179 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (174 bp):
AAAATTCCATTTTAAACCTCAATCCTTCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATTC
CATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAACTGTCAAAAATTCCATTTG
TAACCCGAAATTTCCAAAATTACCATTTTACCCACAAACATCTA
Found at i:92494 original size:20 final size:20
Alignment explanation
Indices: 92471--92508 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
92461 ATTAATTGTT
92471 CATTCGTATTTAAAATTACA
1 CATTCGTATTTAAAATTACA
* *
92491 CATTTGTTTTTAAAATTA
1 CATTCGTATTTAAAATTA
92509 TTTTAAAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (20 bp):
CATTCGTATTTAAAATTACA
Found at i:126445 original size:23 final size:24
Alignment explanation
Indices: 126418--126504 Score: 92
Period size: 23 Copynumber: 3.8 Consensus size: 24
126408 AGAAACGTTT
126418 CACAAGGCA-AAGAAAAAGCGTGC
1 CACAAGGCAGAAGAAAAAGCGTGC
126441 CACAAGGCAGAAGAAAAA-CGTGC
1 CACAAGGCAGAAGAAAAAGCGTGC
* * * *
126464 TATAAGGAAGAAG-AAAAGCGTGT
1 CACAAGGCAGAAGAAAAAGCGTGC
*
126487 CACAAAGGCA-AATAAAAA
1 CAC-AAGGCAGAAGAAAAA
126505 CTAGAAGAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
22 4 0.08
23 31 0.60
24 17 0.33
ACGTcount: A:0.52, C:0.16, G:0.24, T:0.08
Consensus pattern (24 bp):
CACAAGGCAGAAGAAAAAGCGTGC
Found at i:130260 original size:73 final size:73
Alignment explanation
Indices: 130179--130323 Score: 290
Period size: 73 Copynumber: 2.0 Consensus size: 73
130169 ATGTTATTTA
130179 ATTTGATTCAATGGGTAATTAAGGCTTAAAAAAGTGGGTAAATATATGAAATATTATATGATCAT
1 ATTTGATTCAATGGGTAATTAAGGCTTAAAAAAGTGGGTAAATATATGAAATATTATATGATCAT
130244 GAAAGCTG
66 GAAAGCTG
130252 ATTTGATTCAATGGGTAATTAAGGCTTAAAAAAGTGGGTAAATATATGAAATATTATATGATCAT
1 ATTTGATTCAATGGGTAATTAAGGCTTAAAAAAGTGGGTAAATATATGAAATATTATATGATCAT
130317 GAAAGCT
66 GAAAGCT
130324 ATAATGGAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (73 bp):
ATTTGATTCAATGGGTAATTAAGGCTTAAAAAAGTGGGTAAATATATGAAATATTATATGATCAT
GAAAGCTG
Found at i:136502 original size:22 final size:22
Alignment explanation
Indices: 136476--136519 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
136466 ATTATGTTTA
136476 ATAAATAAGAATTATATTGATG
1 ATAAATAAGAATTATATTGATG
136498 ATAAATAAGAATTATATTGATG
1 ATAAATAAGAATTATATTGATG
136520 TTTGCTCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (22 bp):
ATAAATAAGAATTATATTGATG
Found at i:136848 original size:41 final size:41
Alignment explanation
Indices: 136785--137000 Score: 258
Period size: 41 Copynumber: 5.2 Consensus size: 41
136775 ACTTGATGTA
*
136785 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGACTCGAGATGAGCATGAGATTATAT
** *
136827 TAAAGGAAGACTTGTGACTCGAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATAT
* * * *
136868 TAAAGGAAGACTCATGTCTCGGGGTGAGCATGAGATTTTAT
1 TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATAT
* *
136909 TAAAGGAAGACTCGTGACTCGGGATGAGCATGAGATTATATT
1 TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATA-T
* * *
136951 TAAAGGAAGACTTATGACTCG-G-TAGAGCATAAGATTGT-T
1 TAAAGGAAGACTCATGACTCGAGAT-GAGCATGAGATTATAT
136990 TAAAAGGAAGA
1 T-AAAGGAAGA
137001 TCTACAACTC
Statistics
Matches: 152, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.01
40 10 0.07
41 116 0.76
42 24 0.16
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (41 bp):
TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATAT
Found at i:136927 original size:82 final size:83
Alignment explanation
Indices: 136785--137000 Score: 294
Period size: 82 Copynumber: 2.6 Consensus size: 83
136775 ACTTGATGTA
* *
136785 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATTAAAGGAAGACTTGTGACTCGAA
1 TAAA-GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGAAGACTCGTGACTCGAA
136850 ATGAGCATGAGATTATA-T
65 ATGAGCATGAGATTATATT
* * **
136868 TAAAGGAAGACTCATGTCTCGGGGTGAGCATGAGATTTTATTAAAGGAAGACTCGTGACTCGGGA
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGAAGACTCGTGACTCGAAA
136933 TGAGCATGAGATTATATT
66 TGAGCATGAGATTATATT
* * * * *
136951 TAAAGGAAGACTTATGACTCGGTA-GAGCATAAGATTGT-TTAAAAGGAAGA
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATT-AAAGGAAGA
137001 TCTACAACTC
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
81 2 0.02
82 92 0.77
83 25 0.21
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (83 bp):
TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGAAGACTCGTGACTCGAAA
TGAGCATGAGATTATATT
Found at i:137677 original size:21 final size:21
Alignment explanation
Indices: 137639--137679 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
137629 GTTATTAGAA
*
137639 TCGATAGAAGCATGACTTGTT
1 TCGATAGAAGCATCACTTGTT
137660 TCGATAGAAGTCA-CACTTGT
1 TCGATAGAAG-CATCACTTGT
137680 ATCGGTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (21 bp):
TCGATAGAAGCATCACTTGTT
Found at i:166707 original size:37 final size:37
Alignment explanation
Indices: 166669--166916 Score: 331
Period size: 37 Copynumber: 6.7 Consensus size: 37
166659 CAATGGTACG
*
166669 AAGCCTGCTAGGCACTA-AGCCTGAATACACCGGCACG
1 AAGCCTGCTAGGCAC-ACAGCCTGAATACACCGGCACA
* *
166706 AAGCCTACTAGGCACAAAG-CTCGAATACACCGGCACA
1 AAGCCTGCTAGGCACACAGCCT-GAATACACCGGCACA
* * *
166743 AAACCTGCTAGGCACATAGCCCGAATACACCGGCACA
1 AAGCCTGCTAGGCACACAGCCTGAATACACCGGCACA
* *
166780 AAGCCTGCTAGGCACATAGCCTGAATACACTGGCACA
1 AAGCCTGCTAGGCACACAGCCTGAATACACCGGCACA
* *
166817 AAGCCTACTAGGCACACAGCCTGAATACACCGGTACA
1 AAGCCTGCTAGGCACACAGCCTGAATACACCGGCACA
* * *
166854 AAGCCTGCTAGGCACACAATCC-GAATACACCAGCACG
1 AAGCCTGCTAGGCACAC-AGCCTGAATACACCGGCACA
166891 AAGCCTGCTAGGCACACAGCCTGAAT
1 AAGCCTGCTAGGCACACAGCCTGAAT
166917 TTGTAGATGC
Statistics
Matches: 187, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
36 6 0.03
37 177 0.95
38 4 0.02
ACGTcount: A:0.34, C:0.33, G:0.21, T:0.13
Consensus pattern (37 bp):
AAGCCTGCTAGGCACACAGCCTGAATACACCGGCACA
Found at i:166795 original size:16 final size:16
Alignment explanation
Indices: 166774--166839 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
166764 CGAATACACC
166774 GGCACAAAGCCTGCTA
1 GGCACAAAGCCTGCTA
* *
166790 GGCACATAGCCTGAATACA
1 GGCACAAAGCCTG-CT--A
*
166809 CTGGCACAAAGCCTACTA
1 --GGCACAAAGCCTGCTA
*
166827 GGCACACAGCCTG
1 GGCACAAAGCCTG
166840 AATACACCGG
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
16 23 0.61
17 1 0.03
18 1 0.03
19 1 0.03
20 1 0.03
21 11 0.29
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.14
Consensus pattern (16 bp):
GGCACAAAGCCTGCTA
Found at i:166816 original size:21 final size:20
Alignment explanation
Indices: 166679--166860 Score: 83
Period size: 21 Copynumber: 9.7 Consensus size: 20
166669 AAGCCTGCTA
*
166679 GGCACTAAGCCTGAATACACC
1 GGCACAAAGCCTGAATACA-C
* *
166700 GGCACGAAGCCT-ACT--A-
1 GGCACAAAGCCTGAATACAC
166716 GGCACAAAG-CTCGAATACACC
1 GGCACAAAGCCT-GAATACA-C
* *
166737 GGCACAAAACCTG-CT--A-
1 GGCACAAAGCCTGAATACAC
* *
166753 GGCACATAGCCCGAATACACC
1 GGCACAAAGCCTGAATACA-C
*
166774 GGCACAAAGCCTG-CT--A-
1 GGCACAAAGCCTGAATACAC
*
166790 GGCACATAGCCTGAATACAC
1 GGCACAAAGCCTGAATACAC
*
166810 TGGCACAAAGCCT-ACT--A-
1 -GGCACAAAGCCTGAATACAC
*
166827 GGCACACAGCCTGAATACACC
1 GGCACAAAGCCTGAATACA-C
*
166848 GGTACAAAGCCTG
1 GGCACAAAGCCTG
166861 CTAGGCACAC
Statistics
Matches: 118, Mismatches: 21, Indels: 44
0.64 0.11 0.24
Matches are distributed among these distances:
15 2 0.02
16 41 0.35
17 6 0.05
18 4 0.03
19 4 0.03
20 6 0.05
21 53 0.45
22 2 0.02
ACGTcount: A:0.34, C:0.32, G:0.21, T:0.13
Consensus pattern (20 bp):
GGCACAAAGCCTGAATACAC
Found at i:166855 original size:111 final size:111
Alignment explanation
Indices: 166669--166916 Score: 365
Period size: 111 Copynumber: 2.2 Consensus size: 111
166659 CAATGGTACG
*
166669 AAGCCTGCTAGGCAC-TAAGCCTGAATACACCGGCACGAAGCCTACTAGGCACAAAGCTCGAATA
1 AAGCCTGCTAGGCACAT-AGCCTGAATACACCGGCACAAAGCCTACTAGGCACAAAGCTCGAATA
* * *
166733 CACCGGCACAAAACCTGCTAGGCACATAGCCCGAATACACCGGCACA
65 CACCGGCACAAAACCTGCTAGGCACACAACCCGAATACACCAGCACA
* *
166780 AAGCCTGCTAGGCACATAGCCTGAATACACTGGCACAAAGCCTACTAGGCACACAGC-CTGAATA
1 AAGCCTGCTAGGCACATAGCCTGAATACACCGGCACAAAGCCTACTAGGCACAAAGCTC-GAATA
* * * *
166844 CACCGGTACAAAGCCTGCTAGGCACACAATCCGAATACACCAGCACG
65 CACCGGCACAAAACCTGCTAGGCACACAACCCGAATACACCAGCACA
*
166891 AAGCCTGCTAGGCACACAGCCTGAAT
1 AAGCCTGCTAGGCACATAGCCTGAAT
166917 TTGTAGATGC
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
110 1 0.01
111 122 0.98
112 1 0.01
ACGTcount: A:0.34, C:0.33, G:0.21, T:0.13
Consensus pattern (111 bp):
AAGCCTGCTAGGCACATAGCCTGAATACACCGGCACAAAGCCTACTAGGCACAAAGCTCGAATAC
ACCGGCACAAAACCTGCTAGGCACACAACCCGAATACACCAGCACA
Found at i:172398 original size:10 final size:10
Alignment explanation
Indices: 172379--172413 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
172369 GAATTAACTT
172379 AAATGCAATA
1 AAATGCAATA
*
172389 AAATGAAATA
1 AAATGCAATA
*
172399 AAATGCAATG
1 AAATGCAATA
172409 AAATG
1 AAATG
172414 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (10 bp):
AAATGCAATA
Found at i:177757 original size:41 final size:41
Alignment explanation
Indices: 177712--177795 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 41
177702 TCATTTTGAC
*
177712 TTTT-GATTTTATTTATTTATTTAAAAAGTTTCATGATAAGG
1 TTTTGGATTTAATTTATTTA-TTAAAAAGTTTCATGATAAGG
* *
177753 TTTTGGGTTTAATTTATTTATTACAAAGTTTCATGATAAGG
1 TTTTGGATTTAATTTATTTATTAAAAAGTTTCATGATAAGG
177794 TT
1 TT
177796 GACAGGCACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 26 0.67
42 13 0.33
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (41 bp):
TTTTGGATTTAATTTATTTATTAAAAAGTTTCATGATAAGG
Found at i:182993 original size:21 final size:21
Alignment explanation
Indices: 182926--183073 Score: 109
Period size: 23 Copynumber: 6.5 Consensus size: 21
182916 ACACTAGCGA
* *
182926 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTG-TTAGCACTTGT-GT
182949 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTG-TTAGCAC-TTGTGT
*
182972 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTG-TTAGCAC-TTGTGT
*
182995 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTG-TTAGCACT-TGTGT
*
183018 GCTCTCTGTTGCCCAGCACTTATGT
1 GCTCTCTGTT----AGCACTTGTGT
*
183043 GCTCTCTGTTAGTACTT-TGAT
1 GCTCTCTGTTAGCACTTGTG-T
*
183064 ACTCTCTGTT
1 GCTCTCTGTT
183074 CGTTTCGTAT
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
20 2 0.02
21 16 0.15
22 3 0.03
23 64 0.60
24 2 0.02
25 14 0.13
26 6 0.06
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (21 bp):
GCTCTCTGTTAGCACTTGTGT
Found at i:183067 original size:69 final size:69
Alignment explanation
Indices: 182927--183073 Score: 187
Period size: 69 Copynumber: 2.1 Consensus size: 69
182917 CACTAGCGAG
*
182927 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTG
1 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
*
182992 TGTA
66 TATA
*
182996 CTCTCTGTTTAGCACTGTGT-GTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTA
1 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGATT----AGCACTTTATGTGCTCTCTGATTAGTA
183057 CTTTG-ATA
61 CTTTGTATA
183065 CTCTCTGTT
1 CTCTCTGTT
183074 CGTTTCGTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 36 0.51
70 14 0.20
71 13 0.19
72 5 0.07
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (69 bp):
CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
TATA
Found at i:185680 original size:23 final size:23
Alignment explanation
Indices: 185654--185778 Score: 91
Period size: 23 Copynumber: 5.5 Consensus size: 23
185644 AGTGCTGGGC
185654 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
185677 AACAGAGAGTACACAAAGTAC-A
1 AACAGAGAGCACACACAGTGCTA
* *
185699 AATCAGAGAGTACACAAAGTGCTA
1 AA-CAGAGAGCACACACAGTGCTA
* *
185723 ATCAGATAG----CACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
185743 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
*
185767 AACAAAGAGCAC
1 AACAGAGAGCAC
185779 GCTAGTGTTC
Statistics
Matches: 82, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
19 8 0.10
20 1 0.01
21 7 0.09
22 3 0.04
23 53 0.65
24 3 0.04
25 5 0.06
26 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:186690 original size:34 final size:34
Alignment explanation
Indices: 186650--186740 Score: 166
Period size: 34 Copynumber: 2.7 Consensus size: 34
186640 TCTTTGTTCT
186650 TCTCTTTTCCTTTCTCTTCAATTTGATCCTTGCC
1 TCTCTTTTCCTTTCTCTTCAATTTGATCCTTGCC
186684 TCTCTTTTCCTTTCTCTTCAATTTGATCCTTGCC
1 TCTCTTTTCCTTTCTCTTCAATTTGATCCTTGCC
*
186718 TCTCTTCT-CTTTCTCTTCAATTT
1 TCTCTTTTCCTTTCTCTTCAATTT
186741 CACATAAACA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
33 15 0.27
34 41 0.73
ACGTcount: A:0.09, C:0.32, G:0.04, T:0.55
Consensus pattern (34 bp):
TCTCTTTTCCTTTCTCTTCAATTTGATCCTTGCC
Done.