Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 1 of 168
Found at i:2573 original size:5 final size:5
Alignment explanation
Indices: 2559--2593 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
2549 AAAAAATATT
*
2559 AATAA CATAA AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA
2594 TTAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:7641 original size:51 final size:51
Alignment explanation
Indices: 7565--7668 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
7555 ATATTTAACC
7565 AAATATGTGCGGATTCTTCGATACTAGGATCTGCATCTGTATTAGGTGCTA
1 AAATATGTGCGGATTCTTCGATACTAGGATCTGCATCTGTATTAGGTGCTA
7616 AAATATGTGCGGATTCTTCGATACTAGGATCTGCATCTGTATTAGGTGCTA
1 AAATATGTGCGGATTCTTCGATACTAGGATCTGCATCTGTATTAGGTGCTA
7667 AA
1 AA
7669 GAATCAGGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (51 bp):
AAATATGTGCGGATTCTTCGATACTAGGATCTGCATCTGTATTAGGTGCTA
Found at i:8653 original size:5 final size:5
Alignment explanation
Indices: 8639--8673 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
8629 AAAAAATATT
*
8639 AATAA CATAA AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA
8674 TTAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:17406 original size:22 final size:21
Alignment explanation
Indices: 17376--17433 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
17366 GAATGGTATC
17376 TACAAATCAAATCTCTAAGAT
1 TACAAATCAAATCTCTAAGAT
* * *
17397 TACAAAATCATATCTTCTACGGT
1 TAC-AAATCAAATC-TCTAAGAT
*
17420 TACATATCAAATCT
1 TACAAATCAAATCT
17434 ACGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (21 bp):
TACAAATCAAATCTCTAAGAT
Found at i:22608 original size:139 final size:139
Alignment explanation
Indices: 22335--22661 Score: 525
Period size: 139 Copynumber: 2.4 Consensus size: 139
22325 TAGAAAAAAA
* *
22335 AATTATATTCTTTTC-AAA-AAAGTATTAATTTCCATGTCTTTTATATTTTGACCGAAATCAATT
1 AATTATATTCTTTCCAAAAGAAAATATTAATTTCCATGTCTTTTATA-TTTGACCGAAATCAATT
* * *
22398 AATATAATTATTTATATTCATAAATTTAGTAAAATATATAAAATTAATATTTTGTATGAATCAAA
65 AATATAACTATTTATATTAATAAATTGAGTAAAATATATAAAATTAATATTTTGTATGAATCAAA
22463 TTCATATATT
130 TTCATATATT
** *
22473 AATTATATTCTTTCCAAAAGAAAATATTAATTTCCATGTCTTTTATATTTGATTGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAAAATATTAATTTCCATGTCTTTTATATTTGACCGAAATCAATTA
*
22538 ATATAACTATTTATATTAATAAATTCGA-TAAAATATATACAATTAATATTTTGTATGAATCAAA
66 ATATAACTATTTATATTAATAAATT-GAGTAAAATATATAAAATTAATATTTTGTATGAATCAAA
22602 TTCATATATT
130 TTCATATATT
*
22612 AATTATATTCTTTCCAAAAGAAAATATTAATTTTCATGTCTTTTATATTT
1 AATTATATTCTTTCCAAAAGAAAATATTAATTTCCATGTCTTTTATATTT
22662 TCGGCAAAAT
Statistics
Matches: 176, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
138 14 0.08
139 135 0.77
140 27 0.15
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (139 bp):
AATTATATTCTTTCCAAAAGAAAATATTAATTTCCATGTCTTTTATATTTGACCGAAATCAATTA
ATATAACTATTTATATTAATAAATTGAGTAAAATATATAAAATTAATATTTTGTATGAATCAAAT
TCATATATT
Found at i:25628 original size:20 final size:20
Alignment explanation
Indices: 25603--25686 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
25593 TACAGGATTG
25603 GCACTTCGGTGCTCCTGTTT
1 GCACTTCGGTGCTCCTGTTT
** * *
25623 GCACTTCTTTGCCCCTGTAT
1 GCACTTCGGTGCTCCTGTTT
* * *
25643 ACACTTTGGTG-TCCTTGTTC
1 GCACTTCGGTGCTCC-TGTTT
*
25663 GCACTACGGTGCTCCTGTTT
1 GCACTTCGGTGCTCCTGTTT
25683 GCAC
1 GCAC
25687 ATTTGTACCC
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
19 2 0.04
20 42 0.89
21 3 0.06
ACGTcount: A:0.10, C:0.31, G:0.21, T:0.38
Consensus pattern (20 bp):
GCACTTCGGTGCTCCTGTTT
Found at i:25714 original size:40 final size:40
Alignment explanation
Indices: 25670--25766 Score: 176
Period size: 40 Copynumber: 2.4 Consensus size: 40
25660 TTCGCACTAC
*
25670 GGTGCTCCTGTTTGCACATTTGTACCCTTATTTACACTTT
1 GGTGCCCCTGTTTGCACATTTGTACCCTTATTTACACTTT
25710 GGTGCCCCTGTTTGCACATTTGTACCCTTATTTACACTTT
1 GGTGCCCCTGTTTGCACATTTGTACCCTTATTTACACTTT
25750 GGTGCCCCTGTTATGCA
1 GGTGCCCCTGTT-TGCA
25767 TCTATGGTGC
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 51 0.93
41 4 0.07
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (40 bp):
GGTGCCCCTGTTTGCACATTTGTACCCTTATTTACACTTT
Found at i:25718 original size:21 final size:21
Alignment explanation
Indices: 25694--25758 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 21
25684 CACATTTGTA
25694 CCCTTATTTACACTTTGGTGC
1 CCCTTATTTACACTTTGGTGC
* * *
25715 CCC-TGTTTGCACATTT-GT-A
1 CCCTTATTTACAC-TTTGGTGC
25734 CCCTTATTTACACTTTGGTGC
1 CCCTTATTTACACTTTGGTGC
25755 CCCT
1 CCCT
25759 GTTATGCATC
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 6 0.18
20 18 0.53
21 10 0.29
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.42
Consensus pattern (21 bp):
CCCTTATTTACACTTTGGTGC
Found at i:27304 original size:9 final size:9
Alignment explanation
Indices: 27290--27319 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
27280 GAATAATAAA
27290 TTTTTTTAT
1 TTTTTTTAT
27299 TTTTTTTAT
1 TTTTTTTAT
*
27308 TTTTTTAAT
1 TTTTTTTAT
27317 TTT
1 TTT
27320 AAAATACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:27330 original size:11 final size:11
Alignment explanation
Indices: 27316--27341 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27306 ATTTTTTTAA
27316 TTTTAAAATAC
1 TTTTAAAATAC
27327 TTTTAAAATAC
1 TTTTAAAATAC
27338 TTTT
1 TTTT
27342 TTTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:27363 original size:11 final size:11
Alignment explanation
Indices: 27349--27379 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
27339 TTTTTTTTAA
27349 TTTTAAAATTT
1 TTTTAAAATTT
27360 TTTTAAAATTT
1 TTTTAAAATTT
27371 TTTTAAAAT
1 TTTTAAAAT
27380 ACATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:27446 original size:21 final size:21
Alignment explanation
Indices: 27408--27447 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27398 ATTTTAAAAT
**
27408 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
27429 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
27448 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:27454 original size:22 final size:20
Alignment explanation
Indices: 27407--27454 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
27397 AATTTTAAAA
* *
27407 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
27427 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
27450 TATTT
1 TATTT
27455 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 11 0.48
22 10 0.43
23 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:29002 original size:42 final size:41
Alignment explanation
Indices: 28953--29184 Score: 259
Period size: 42 Copynumber: 5.5 Consensus size: 41
28943 ATAAGTTAAA
* * *
28953 TGCTATGTGCTGATTCCCCTTATCATTGAATATAAATGTGGT
1 TGCTATGTGCTGATTCCCCGTATCATTGATTATAAA-GGGGT
* * *
28995 TGCTATGTGCTGATTCCACCGTATCCTTGACTGTGAAAGGGGT
1 TGCTATGTGCTGATTCC-CCGTATCATTGATTAT-AAAGGGGT
29038 TGCTATGTGCTGATTCCCCGTATCATTGATTAT-AAGGCGGT
1 TGCTATGTGCTGATTCCCCGTATCATTGATTATAAAGG-GGT
* * * *
29079 TGCTAAGTGCTGATTTCACCGTATCCTTGATTGTGAAAGGGGT
1 TGCTATGTGCTGA-TTCCCCGTATCATTGATTAT-AAAGGGGT
* * *
29122 TGCTATGTGCTGATTCCCCGTATCATTTATTATAATGTGGT
1 TGCTATGTGCTGATTCCCCGTATCATTGATTATAAAGGGGT
* *
29163 TGCTAAGTGTTGATTCCACCGT
1 TGCTATGTGCTGATTCC-CCGT
29185 GTAACGGTTA
Statistics
Matches: 162, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
40 4 0.02
41 36 0.22
42 67 0.41
43 48 0.30
44 7 0.04
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
TGCTATGTGCTGATTCCCCGTATCATTGATTATAAAGGGGT
Found at i:29114 original size:84 final size:84
Alignment explanation
Indices: 28953--29184 Score: 374
Period size: 84 Copynumber: 2.8 Consensus size: 84
28943 ATAAGTTAAA
* * *
28953 TGCTATGTGCTGATTCCCCTTATCATTGAATATAAATGTGGTTGCTATGTGCTGATTCCACCGTA
1 TGCTATGTGCTGATTCCCCGTATCATTGATTAT-AATGTGGTTGCTAAGTGCTGATTCCACCGTA
29018 TCCTTGACTGTGAAAGGGGT
65 TCCTTGACTGTGAAAGGGGT
* * *
29038 TGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGCGGTTGCTAAGTGCTGATTTCACCGTAT
1 TGCTATGTGCTGATTCCCCGTATCATTGATTATAATGTGGTTGCTAAGTGCTGATTCCACCGTAT
*
29103 CCTTGATTGTGAAAGGGGT
66 CCTTGACTGTGAAAGGGGT
* *
29122 TGCTATGTGCTGATTCCCCGTATCATTTATTATAATGTGGTTGCTAAGTGTTGATTCCACCGT
1 TGCTATGTGCTGATTCCCCGTATCATTGATTATAATGTGGTTGCTAAGTGCTGATTCCACCGT
29185 GTAACGGTTA
Statistics
Matches: 135, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 104 0.77
85 31 0.23
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (84 bp):
TGCTATGTGCTGATTCCCCGTATCATTGATTATAATGTGGTTGCTAAGTGCTGATTCCACCGTAT
CCTTGACTGTGAAAGGGGT
Found at i:31804 original size:5 final size:5
Alignment explanation
Indices: 31755--31792 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
31745 GTTCTTGCAT
* *
31755 TTTTA TTTTA TTTTA TTTTA -TATA TTTTA TTTTC TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
31793 GCGTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
4 3 0.10
5 26 0.90
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:35232 original size:15 final size:15
Alignment explanation
Indices: 35212--35249 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
35202 TACTGGTATT
35212 GAGGCAGTATAGATC
1 GAGGCAGTATAGATC
35227 GAGGCAGTATAGATC
1 GAGGCAGTATAGATC
35242 GAGGCAGT
1 GAGGCAGT
35250 TCATACCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.37, T:0.18
Consensus pattern (15 bp):
GAGGCAGTATAGATC
Found at i:36291 original size:20 final size:20
Alignment explanation
Indices: 36262--36301 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
36252 TTCACCTCAT
*
36262 GCATCGCATCATATGCATTA
1 GCATCACATCATATGCATTA
36282 GCATCACATCATATGCATTA
1 GCATCACATCATATGCATTA
36302 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
GCATCACATCATATGCATTA
Found at i:44444 original size:50 final size:50
Alignment explanation
Indices: 44385--44858 Score: 298
Period size: 50 Copynumber: 9.5 Consensus size: 50
44375 AAAAATTAAA
* *
44385 AGATTGAAGCCATAACGGCGGATCTTACTTCCTTAGCAGTGCAGCAGAAC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTAGAAC
* * * *** * * * *
44435 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCT-GATATTGCAATTA-AA-
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGC-AGTAGAAC
*
44484 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAAC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTAGAAC
* * * *** * * * * ** *
44534 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCT-GATATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGCAGTAGAAC
* * *
44584 AGATTGAAGCCACAATGGCGGATCTTACTTCCTTAGCAGTACAGTGGAAC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTAGAAC
* * * *** * * * * *
44634 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCT-GATATTGCAATTA-AAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGC-AGTAGAAC
* * *
44684 AGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGTGGAAC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTAGAAC
* * * *** * * * * *
44734 AGATTGAAGCTACGACAGCGGATCTGGTTTCCCT-GATATTGCAATTAAAAC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGC-AGTAGAAC
* *
44785 -GATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTGCAGTGGAAC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTAGAAC
* * *
44834 AGACTGAAGCTACGACGGCGGATCT
1 AGATTGAAGCCACAACGGCGGATCT
44859 GGTTTCCCCG
Statistics
Matches: 303, Mismatches: 106, Indels: 30
0.69 0.24 0.07
Matches are distributed among these distances:
48 2 0.01
49 44 0.15
50 245 0.81
51 12 0.04
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTAGAAC
Found at i:44891 original size:100 final size:99
Alignment explanation
Indices: 44378--44866 Score: 843
Period size: 100 Copynumber: 4.9 Consensus size: 99
44368 CGGGTTGAAA
* **
44378 AATTAAAAGATTGAAGCCATAACGGCGGATCTTACTTCCTTAGCAGTGCAGCAGAACAGATTGAA
1 AATTAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAA
44443 GCTACGACGGCAGATCTGGTTTCCCTGATATTGC
66 GCTACGACGGCAGATCTGGTTTCCCTGATATTGC
44477 AATTAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAA
1 AATTAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAA
44542 GCTACGACGGCAGATCTGGTTTCCCTGATATTGC
66 GCTACGACGGCAGATCTGGTTTCCCTGATATTGC
* *
44576 AATTTAAAAGATTGAAGCCACAATGGCGGATCTTACTTCCTTAGCAGTACAGTGGAACAGATTGA
1 AA-TTAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGA
44641 AGCTACGACGGCAGATCTGGTTTCCCTGATATTGC
65 AGCTACGACGGCAGATCTGGTTTCCCTGATATTGC
* *
44676 AATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGTGGAACAGATTGA
1 AATT-AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGA
* *
44741 AGCTACGACAGCGGATCTGGTTTCCCTGATATTGC
65 AGCTACGACGGCAGATCTGGTTTCCCTGATATTGC
* *
44776 AATTAAAACGATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGACTGA
1 AATTAAAA-GATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGA
*
44841 AGCTACGACGGCGGATCTGGTTTCCC
65 AGCTACGACGGCAGATCTGGTTTCCC
44867 CGACATTACA
Statistics
Matches: 373, Mismatches: 14, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
99 104 0.28
100 269 0.72
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (99 bp):
AATTAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAA
GCTACGACGGCAGATCTGGTTTCCCTGATATTGC
Found at i:49251 original size:7 final size:6
Alignment explanation
Indices: 49225--49249 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
49215 AATAAATATA
49225 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
49250 TAATTTCAAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:51673 original size:38 final size:38
Alignment explanation
Indices: 51625--51701 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
51615 TCTTGACAAA
51625 TATAGCATGCATGAGAAACGG-AAACTACTCAAACTTTG
1 TATAGCATGCATGAGAAA-GGCAAACTACTCAAACTTTG
* *
51663 TATAGGATGCATGAGAAAGGCAAACTACTCAACCTTTG
1 TATAGCATGCATGAGAAAGGCAAACTACTCAAACTTTG
51701 T
1 T
51702 GCTGCTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (38 bp):
TATAGCATGCATGAGAAAGGCAAACTACTCAAACTTTG
Found at i:58449 original size:19 final size:20
Alignment explanation
Indices: 58408--58458 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
58398 GTAGTTATTA
58408 GAGA-ATATTGTTATTTAGT
1 GAGATATATTGTTATTTAGT
* *
58427 GAGATATATTTTTATTTTG-
1 GAGATATATTGTTATTTAGT
*
58446 GAGATATTTTGTT
1 GAGATATATTGTT
58459 TTCTATCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (20 bp):
GAGATATATTGTTATTTAGT
Found at i:60315 original size:20 final size:20
Alignment explanation
Indices: 60226--60321 Score: 72
Period size: 20 Copynumber: 4.8 Consensus size: 20
60216 TGTTCGCATA
*
60226 TATGTGTCTCTATTTGCACAT
1 TATGTGCCTCTATTTGCAC-T
*
60247 T-CGTGCCT-TGATTTGCACT
1 TATGTGCCTCT-ATTTGCACT
* *
60266 TAAGTGCCTCCATTTGCACT
1 TATGTGCCTCTATTTGCACT
** *
60286 TCGGTACCTCTATTTGCACAT
1 TATGTGCCTCTATTTGCAC-T
*
60307 T-TGTGCCTCTGTTTG
1 TATGTGCCTCTATTTG
60322 TGTCACATCC
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.05
20 54 0.90
21 3 0.05
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.43
Consensus pattern (20 bp):
TATGTGCCTCTATTTGCACT
Found at i:60481 original size:7 final size:7
Alignment explanation
Indices: 60469--60493 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
60459 TTTATCATAG
60469 AGGTCTT
1 AGGTCTT
60476 AGGTCTT
1 AGGTCTT
60483 AGGTCTT
1 AGGTCTT
60490 AGGT
1 AGGT
60494 TCAAGTCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (7 bp):
AGGTCTT
Found at i:65864 original size:22 final size:22
Alignment explanation
Indices: 65785--65864 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
65775 TTTTTGATTT
* *
65785 TTTTTAAAAAAAGAAAGTTTAGA
1 TTTTTAAAATAA-AAAGTTTAAA
* *
65808 TTTTTAGAAATAAAAA-TCT-AT
1 TTTTTA-AAATAAAAAGTTTAAA
**
65829 TTTTTAAAGGAAAAAGTTTAAA
1 TTTTTAAAATAAAAAGTTTAAA
*
65851 ATTTTAAAATAAAA
1 TTTTTAAAATAAAA
65865 TTTTGATTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 7
0.70 0.18 0.11
Matches are distributed among these distances:
20 7 0.16
21 8 0.19
22 14 0.33
23 9 0.21
24 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTTTAAAATAAAAAGTTTAAA
Found at i:68601 original size:13 final size:13
Alignment explanation
Indices: 68583--68616 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
68573 GGAGCACGCA
*
68583 TAAAACATATCTT
1 TAAAACATAGCTT
68596 TAAAACATAGCTT
1 TAAAACATAGCTT
*
68609 TAGAACAT
1 TAAAACAT
68617 GACTTGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (13 bp):
TAAAACATAGCTT
Found at i:82441 original size:12 final size:13
Alignment explanation
Indices: 82424--82452 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
82414 CTCATACATG
82424 AATAAATAAA-GC
1 AATAAATAAATGC
82436 AATAAATAAATGC
1 AATAAATAAATGC
82449 AATA
1 AATA
82453 GTTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:85591 original size:19 final size:19
Alignment explanation
Indices: 85567--85603 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
85557 TCAATATTTG
*
85567 GCTAGCTTATTTCTAAGTA
1 GCTAGCATATTTCTAAGTA
85586 GCTAGCATATTTCTAAGT
1 GCTAGCATATTTCTAAGT
85604 GCATGGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (19 bp):
GCTAGCATATTTCTAAGTA
Found at i:86372 original size:25 final size:25
Alignment explanation
Indices: 86334--86411 Score: 111
Period size: 25 Copynumber: 3.1 Consensus size: 25
86324 TCATTAGGGT
*
86334 TACCGATTTATAGCTTGTAAGAGCA
1 TACCGATTTATAGCTCGTAAGAGCA
*
86359 TACTGATTTATAGCTCGTAAGAGCA
1 TACCGATTTATAGCTCGTAAGAGCA
* * *
86384 TACCAATTCATAGCTCATAAGAGCA
1 TACCGATTTATAGCTCGTAAGAGCA
86409 TAC
1 TAC
86412 AACTCGTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (25 bp):
TACCGATTTATAGCTCGTAAGAGCA
Found at i:102654 original size:14 final size:15
Alignment explanation
Indices: 102632--102708 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
102622 CAATCAAACA
102632 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
102646 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
102661 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
102681 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
102695 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
102709 ACTGGCTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:102673 original size:20 final size:20
Alignment explanation
Indices: 102648--102687 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
102638 AATATTTTCC
*
102648 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
102668 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
102688 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:102693 original size:34 final size:35
Alignment explanation
Indices: 102636--102702 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
102626 CAAACACCAG
*
102636 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
102671 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
102703 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:102709 original size:14 final size:14
Alignment explanation
Indices: 102671--102710 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
102661 ACAGAAAAGT
*
102671 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
102685 AAATCATTTTACGG
1 AAAACATTTTACAG
102699 AAAACATTTTAC
1 AAAACATTTTAC
102711 TGGCTATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:103214 original size:20 final size:20
Alignment explanation
Indices: 103189--103230 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
103179 ATTCAAATTA
103189 GCTCAGAAGTATCAATACTT
1 GCTCAGAAGTATCAATACTT
103209 GCTCAGAAGTATCAATACTT
1 GCTCAGAAGTATCAATACTT
103229 GC
1 GC
103231 GCCCAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (20 bp):
GCTCAGAAGTATCAATACTT
Found at i:103241 original size:20 final size:20
Alignment explanation
Indices: 103195--103246 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
103185 ATTAGCTCAG
* *
103195 AAGTATCAATACTTGCTCAG
1 AAGTATCAATACTTGCGCAC
*
103215 AAGTATCAATACTTGCGCCC
1 AAGTATCAATACTTGCGCAC
*
103235 AATTATCAATAC
1 AAGTATCAATAC
103247 CTCTGTACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.29
Consensus pattern (20 bp):
AAGTATCAATACTTGCGCAC
Found at i:104424 original size:5 final size:5
Alignment explanation
Indices: 104414--104444 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
104404 AAAATAATAA
104414 GCCCG GCCCG GCCCG GCCCG GCCCG GCCCG G
1 GCCCG GCCCG GCCCG GCCCG GCCCG GCCCG G
104445 TTTTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.58, G:0.42, T:0.00
Consensus pattern (5 bp):
GCCCG
Found at i:104472 original size:21 final size:19
Alignment explanation
Indices: 104446--104484 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
104436 CCGGCCCGGT
104446 TTTTAATAAAAACAAAAAATA
1 TTTTAA-AAAAA-AAAAAATA
*
104467 TTTTAAAAATAAAAAAAT
1 TTTTAAAAAAAAAAAAAT
104485 TTAAGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
TTTTAAAAAAAAAAAAATA
Found at i:104475 original size:18 final size:17
Alignment explanation
Indices: 104452--104486 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
104442 CGGTTTTTAA
104452 TAAAAACAAAAAATATTT
1 TAAAAACAAAAAA-ATTT
*
104470 TAAAAATAAAAAAATTT
1 TAAAAACAAAAAAATTT
104487 AAGTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAACAAAAAAATTT
Found at i:104521 original size:25 final size:23
Alignment explanation
Indices: 104450--104521 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
104440 CCCGGTTTTT
*
104450 AATAAAAACAA-AAAATATTTTAAA
1 AATAAAAA-AATATAATATTTT-AA
*
104474 AATAAAAAAATTTAAGTATTTTAA
1 AATAAAAAAATATAA-TATTTTAA
104498 AATAAAAAAATATATATATATTTA
1 AATAAAAAAATATA-ATAT-TTTA
104522 TTATATTCGG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 2 0.05
24 28 0.68
25 11 0.27
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (23 bp):
AATAAAAAAATATAATATTTTAA
Found at i:106576 original size:27 final size:27
Alignment explanation
Indices: 106517--106603 Score: 149
Period size: 27 Copynumber: 3.3 Consensus size: 27
106507 AGAGGTATAA
*
106517 CAGTCATTTTACCCTAT-AGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
106543 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
*
106570 CAATCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
106597 CAGTCAT
1 CAGTCAT
106604 AACAGTGTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 17 0.30
27 40 0.70
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTATTT
Found at i:112845 original size:20 final size:21
Alignment explanation
Indices: 112808--112846 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
112798 CGAATATCCT
*
112808 TTTAAAATCAAAATAATAAGA
1 TTTAAAATCAAAAAAATAAGA
112829 TTTAAAAT-AAAAAAATAA
1 TTTAAAATCAAAAAAATAA
112847 AGGCAAGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
TTTAAAATCAAAAAAATAAGA
Found at i:134110 original size:39 final size:40
Alignment explanation
Indices: 134054--134158 Score: 142
Period size: 39 Copynumber: 2.6 Consensus size: 40
134044 AATTTTTTAA
*
134054 TTTTAAAATACTTTTTTTTTATTTTTTAAAATTTT-AAATTT
1 TTTTAAAATAC--TTTTTTTATTTTTTAAAATTTTAAAATAT
* *
134095 TTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATAT
1 TTTTAAAATACTTTTTTTATTTTTTAAAATTTTAAAATAT
*
134135 TTTTAAAATA-TTTTTTTAATTTTT
1 TTTTAAAATACTTTTTTTATTTTTT
134159 GTTTTAATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
39 32 0.55
40 15 0.26
41 11 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (40 bp):
TTTTAAAATACTTTTTTTATTTTTTAAAATTTTAAAATAT
Found at i:134121 original size:40 final size:40
Alignment explanation
Indices: 134054--134158 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 40
134044 AATTTTTTAA
* * *
134054 TTTTAAAATACTTTTTTTTTATTTTTTAAAATTTT-AAATTT
1 TTTTAAAATAC--TTTTTTAATTTTTTTAAATTTTAAAATAT
134095 TTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATAT
1 TTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATAT
*
134135 TTTTAAAATATTTTTTTAATTTTT
1 TTTTAAAATACTTTTTTAATTTTT
134159 GTTTTAATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
39 20 0.34
40 28 0.47
41 11 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (40 bp):
TTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATAT
Found at i:134158 original size:10 final size:10
Alignment explanation
Indices: 134085--134158 Score: 55
Period size: 11 Copynumber: 7.2 Consensus size: 10
134075 TTTTTTAAAA
134085 TTTTAAATTT
1 TTTTAAATTT
134095 TTTTAAAATACTT
1 TTTT-AAAT--TT
134108 TTTT-AATTT
1 TTTTAAATTT
134117 TTTTAAA--T
1 TTTTAAATTT
*
134125 TTTAAAATATT
1 TTTTAAAT-TT
*
134136 TTTAAAATATT
1 TTTTAAAT-TT
*
134147 TTTTTAATTT
1 TTTTAAATTT
134157 TT
1 TT
134159 GTTTTAATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
8 7 0.13
9 6 0.11
10 10 0.19
11 25 0.46
13 6 0.11
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:150970 original size:39 final size:39
Alignment explanation
Indices: 150923--151164 Score: 274
Period size: 39 Copynumber: 6.2 Consensus size: 39
150913 TAGAAATATA
* * *
150923 GTGATTATTCGAGCTATGTGCTTAGCAAGTTGTGTGCCG
1 GTGATTATTCGAGCTATGTGCCTAGCAGGCTGTGTGCCG
* * *
150962 GTAATTATTTGGGCTATGTGCCTAGCAGGCTGTGTGCCG
1 GTGATTATTCGAGCTATGTGCCTAGCAGGCTGTGTGCCG
*
151001 TTGATTATTCGATGC-ATGTGCCTAGCAGGCTGTGTGCCG
1 GTGATTATTCGA-GCTATGTGCCTAGCAGGCTGTGTGCCG
* *
151040 GTGATTATTC-AGGCTATGTGCCTAGCAAG-TAGTGTGTCG
1 GTGATTATTCGA-GCTATGTGCCTAGCAGGCT-GTGTGCCG
* * * * *
151079 GTAATTATTCGGGCTTTGTGCCTAGCAGGCTCTGTGCTG
1 GTGATTATTCGAGCTATGTGCCTAGCAGGCTGTGTGCCG
* * *
151118 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTATGTCG
1 GTGATTATTCGAGCTATGTGCCTAGCAGGCTGTGTGCCG
151157 GTGTATTA
1 GTG-ATTA
151165 AAAATTTGCA
Statistics
Matches: 170, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
38 4 0.02
39 159 0.94
40 7 0.04
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (39 bp):
GTGATTATTCGAGCTATGTGCCTAGCAGGCTGTGTGCCG
Found at i:151137 original size:117 final size:117
Alignment explanation
Indices: 150923--151164 Score: 344
Period size: 117 Copynumber: 2.1 Consensus size: 117
150913 TAGAAATATA
* * *
150923 GTGATTATTCGAGCTATGTGCTTAGCAAGTTGTGTGCCGGTAATTATTTGGGCTATGTGCCTAGC
1 GTGATTATTCGAGCTATGTGCCTAGCAAGTAGTGTGCCGGTAATTATTCGGGCTATGTGCCTAGC
* * * *
150988 AGGCTGTGTGCCGTTGATTATTCGATGCATGTGCCTAGCAGGCTGTGTGCCG
66 AGGCTCTGTGCCGGTGATTATTCGAGGCATGTGCCTAGCAGGCTGTATGCCG
* *
151040 GTGATTATTC-AGGCTATGTGCCTAGCAAGTAGTGTGTCGGTAATTATTCGGGCTTTGTGCCTAG
1 GTGATTATTCGA-GCTATGTGCCTAGCAAGTAGTGTGCCGGTAATTATTCGGGCTATGTGCCTAG
* *
151104 CAGGCTCTGTGCTGGTGATTATTCG-GGCTATGTGCCTAGCAGGCTGTATGTCG
65 CAGGCTCTGTGCCGGTGATTATTCGAGGC-ATGTGCCTAGCAGGCTGTATGCCG
151157 GTGTATTA
1 GTG-ATTA
151165 AAAATTTGCA
Statistics
Matches: 111, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
116 3 0.03
117 104 0.94
118 4 0.04
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (117 bp):
GTGATTATTCGAGCTATGTGCCTAGCAAGTAGTGTGCCGGTAATTATTCGGGCTATGTGCCTAGC
AGGCTCTGTGCCGGTGATTATTCGAGGCATGTGCCTAGCAGGCTGTATGCCG
Found at i:158134 original size:17 final size:18
Alignment explanation
Indices: 158114--158147 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
158104 ATATTTGGAT
*
158114 AAATTA-TTGATTTGATA
1 AAATTAGTTAATTTGATA
158131 AAATTAGTTAATTTGAT
1 AAATTAGTTAATTTGAT
158148 GAATTTCGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (18 bp):
AAATTAGTTAATTTGATA
Found at i:158524 original size:39 final size:39
Alignment explanation
Indices: 158481--158786 Score: 445
Period size: 39 Copynumber: 7.9 Consensus size: 39
158471 TAGAAATACA
*
158481 GTGATTATTCGGGCTATGTGCCTAACAGGCTGTGTGCCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCG
* * *
158520 GTGATTATTCAGGCTATGTGCCTAGAAGGCTGTGTGTCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCG
*
158559 ATGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCG
* * *
158598 GTGATTATTCAGGCTATGTGCCTAGAAGGCTGTGTGTCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCG
* * *
158637 ATGATTATTCGGGCTATGTGCCTAGCAGGCTGTATGTCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCG
* *
158676 GTGATTATTCAGGTTATGTGCCTAGCAGGCTGTGTGCCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCG
* * *
158715 GTGATTATTCGGGCTATGTGCCTAGCAGGTTTTGTGCCA
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCG
*
158754 GTGATTATTCGGGC-ATGTGTCT-GCAGGCTGTGT
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGT
158787 ACCGTTAATT
Statistics
Matches: 238, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
37 9 0.04
38 7 0.03
39 222 0.93
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (39 bp):
GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCG
Found at i:158921 original size:39 final size:37
Alignment explanation
Indices: 158808--158921 Score: 104
Period size: 39 Copynumber: 2.9 Consensus size: 37
158798 TTAGAGCTTT
** * *
158808 GTGATTATTTGGGCTATGTGCCTAGTAGAAG-GTGTACC
1 GTGATTATTCAGGCTATGTGCCTAGCAG--GTGTGTGCC
* * *
158846 GATGATTATTCAAGATTTGTGCCTAGCAGGTAGTGTGCC
1 G-TGATTATTCAGGCTATGTGCCTAGCAGGT-GTGTGCC
158885 AGTGATTATTCAGGCTATGTGCCTAGCAGGCTGTGTG
1 -GTGATTATTCAGGCTATGTGCCTAGCAGG-TGTGTG
158922 TCGGTGTATT
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
37 1 0.02
38 1 0.02
39 57 0.93
40 2 0.03
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (37 bp):
GTGATTATTCAGGCTATGTGCCTAGCAGGTGTGTGCC
Found at i:161698 original size:40 final size:40
Alignment explanation
Indices: 161654--161781 Score: 175
Period size: 40 Copynumber: 3.2 Consensus size: 40
161644 GATTATATAA
* *
161654 GAATGCTCATACGTGCCCCTGTTTGTACTTGGGTACCCCT
1 GAATGCACATACGTGCCCCTGTTTGTACTTAGGTACCCCT
* * *
161694 GAATGAACATACGTGTCCATGTTTGTACTTAGGTACCCCT
1 GAATGCACATACGTGCCCCTGTTTGTACTTAGGTACCCCT
* * *
161734 GAATGCACATACATGCCCCTGTTTGTACTTCGGTACTCCAT
1 GAATGCACATACGTGCCCCTGTTTGTACTTAGGTAC-CCCT
161775 GAATGCA
1 GAATGCA
161782 TTATAATGTC
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
40 66 0.87
41 10 0.13
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
GAATGCACATACGTGCCCCTGTTTGTACTTAGGTACCCCT
Found at i:164066 original size:5 final size:5
Alignment explanation
Indices: 164056--164081 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
164046 TCAAAAGTTA
164056 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
164082 CTAAAATAAT
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:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:173034 original size:31 final size:30
Alignment explanation
Indices: 172996--173055 Score: 111
Period size: 31 Copynumber: 2.0 Consensus size: 30
172986 AAGTTTGTAT
172996 ATTAAATTGCATACAGGAAATTAAGCAGGAA
1 ATTAAATTGCATACAGGAAATTAA-CAGGAA
173027 ATTAAATTGCATACAGGAAATTAACAGGA
1 ATTAAATTGCATACAGGAAATTAACAGGA
173056 TATGAGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.23
Consensus pattern (30 bp):
ATTAAATTGCATACAGGAAATTAACAGGAA
Found at i:173045 original size:19 final size:19
Alignment explanation
Indices: 172996--173050 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
172986 AAGTTTGTAT
172996 ATTAAATTGCATACAGGAA
1 ATTAAATTGCATACAGGAA
173015 ATT-AA--G----CAGGAA
1 ATTAAATTGCATACAGGAA
173027 ATTAAATTGCATACAGGAA
1 ATTAAATTGCATACAGGAA
173046 ATTAA
1 ATTAA
173051 CAGGATATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
12 9 0.31
13 2 0.07
15 1 0.03
16 1 0.03
18 2 0.07
19 14 0.48
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (19 bp):
ATTAAATTGCATACAGGAA
Found at i:184654 original size:50 final size:50
Alignment explanation
Indices: 184596--184727 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 50
184586 TATTGAGGTT
** *
184596 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* * *
184646 ATGAGAGGTCTCC-TGTAAGACCATGTTTGGGACATGGCATGGGCATCGAT
1 ATGAGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
** ** *
184696 ATGAGAACTCTTATGTAAGACCATATCTGGGA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGA
184728 TATGAAATTT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
50 66 0.97
51 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
Found at i:188345 original size:20 final size:20
Alignment explanation
Indices: 188320--188459 Score: 93
Period size: 20 Copynumber: 7.0 Consensus size: 20
188310 GATGTCCGTT
*
188320 CAGGGGTACCAAAGTACAAC
1 CAGGGGTACCAAAGTACAAA
* ** * * **
188340 CAGGGGCACTTATGTGCATT
1 CAGGGGTACCAAAGTACAAA
**
188360 CAGGGGTACCGGAGTACAAA
1 CAGGGGTACCAAAGTACAAA
* *
188380 CAGGGGCACCGAAGTACAAA
1 CAGGGGTACCAAAGTACAAA
* * * **
188400 CAGGGGCA-CATATGTGCATT
1 CAGGGGTACCA-AAGTACAAA
* *
188420 CAGGGGTATCGAAGTACAAA
1 CAGGGGTACCAAAGTACAAA
188440 CAGGGGTACCAAAGTACAAA
1 CAGGGGTACCAAAGTACAAA
188460 TAGAGGCATG
Statistics
Matches: 88, Mismatches: 30, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
19 1 0.01
20 86 0.98
21 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.29, T:0.15
Consensus pattern (20 bp):
CAGGGGTACCAAAGTACAAA
Found at i:188395 original size:60 final size:60
Alignment explanation
Indices: 188320--188485 Score: 235
Period size: 60 Copynumber: 2.8 Consensus size: 60
188310 GATGTCCGTT
* *
188320 CAGGGGTACCAAAGTACAACCAGGGGCACTTATGTGCATTCAGGGGTACCGGAGTACAAA
1 CAGGGGTACCAAAGTACAAACAGGGGCACTTATGTGCATTCAGGGGTACCGAAGTACAAA
* * * *
188380 CAGGGGCACCGAAGTACAAACAGGGGCACATATGTGCATTCAGGGGTATCGAAGTACAAA
1 CAGGGGTACCAAAGTACAAACAGGGGCACTTATGTGCATTCAGGGGTACCGAAGTACAAA
* * *
188440 CAGGGGTACCAAAGTACAAATAGAGGCA-TGTACGTGCATTCAGGGG
1 CAGGGGTACCAAAGTACAAACAGGGGCACT-TATGTGCATTCAGGGG
188486 CACAAATGTG
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.33, C:0.20, G:0.31, T:0.16
Consensus pattern (60 bp):
CAGGGGTACCAAAGTACAAACAGGGGCACTTATGTGCATTCAGGGGTACCGAAGTACAAA
Found at i:188404 original size:40 final size:40
Alignment explanation
Indices: 188320--188459 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 40
188310 GATGTCCGTT
* ** * * **
188320 CAGGGGTACCAAAGTACAACCAGGGGCACTTATGTGCATT
1 CAGGGGTACCAAAGTACAAACAGGGGCACCGAAGTACAAA
**
188360 CAGGGGTACCGGAGTACAAACAGGGGCACCGAAGTACAAA
1 CAGGGGTACCAAAGTACAAACAGGGGCACCGAAGTACAAA
* * * ** * *
188400 CAGGGGCA-CATATGTGCATTCAGGGGTATCGAAGTACAAA
1 CAGGGGTACCA-AAGTACAAACAGGGGCACCGAAGTACAAA
188440 CAGGGGTACCAAAGTACAAA
1 CAGGGGTACCAAAGTACAAA
188460 TAGAGGCATG
Statistics
Matches: 75, Mismatches: 23, Indels: 4
0.74 0.23 0.04
Matches are distributed among these distances:
39 1 0.01
40 72 0.96
41 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.29, T:0.15
Consensus pattern (40 bp):
CAGGGGTACCAAAGTACAAACAGGGGCACCGAAGTACAAA
Found at i:196139 original size:15 final size:15
Alignment explanation
Indices: 196119--196151 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
196109 TTCATAAGAT
196119 TTTGCATACTTACCA
1 TTTGCATACTTACCA
196134 TTTGCATACTTACCA
1 TTTGCATACTTACCA
196149 TTT
1 TTT
196152 CATTTCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (15 bp):
TTTGCATACTTACCA
Found at i:202011 original size:17 final size:17
Alignment explanation
Indices: 201991--202025 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
201981 TGACGTCGTC
201991 TTTCACTTATTAAAATA
1 TTTCACTTATTAAAATA
202008 TTTCACTTATTAAAATA
1 TTTCACTTATTAAAATA
202025 T
1 T
202026 GTATAGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTCACTTATTAAAATA
Found at i:206695 original size:50 final size:50
Alignment explanation
Indices: 206620--206720 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
206610 AATTCAATCC
* * *
206620 TAAAACATCATAGTTGTCTATGCCTTAACTTTATCAGTTCTTCCTTTTCT
1 TAAAACACCATAGTTGTCAATGCCTTAACTTTACCAGTTCTTCCTTTTCT
*
206670 TAAAACACCATAGTTGTCAATGCCTTAACTTTACCATTTCTTCCTTTTCT
1 TAAAACACCATAGTTGTCAATGCCTTAACTTTACCAGTTCTTCCTTTTCT
206720 T
1 T
206721 TTTGGACTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.45
Consensus pattern (50 bp):
TAAAACACCATAGTTGTCAATGCCTTAACTTTACCAGTTCTTCCTTTTCT
Found at i:206787 original size:72 final size:72
Alignment explanation
Indices: 206670--206809 Score: 271
Period size: 72 Copynumber: 1.9 Consensus size: 72
206660 TTCCTTTTCT
206670 TAAAACACCATAGTTGTCAATGCCTTAACTTTACCATTTCTTCCTTTTCTTTTTGGACTTAAACT
1 TAAAACACCATAGTTGTCAATGCCTTAACTTTACCATTTCTTCCTTTTCTTTTTGGACTTAAACT
206735 TCAATCC
66 TCAATCC
*
206742 TAAAACATCATAGTTGTCAATGCCTTAACTTTACCATTTCTTCCTTTTCTTTTTGGACTTAAACT
1 TAAAACACCATAGTTGTCAATGCCTTAACTTTACCATTTCTTCCTTTTCTTTTTGGACTTAAACT
206807 TCA
66 TCA
206810 CCATTTCAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (72 bp):
TAAAACACCATAGTTGTCAATGCCTTAACTTTACCATTTCTTCCTTTTCTTTTTGGACTTAAACT
TCAATCC
Found at i:210462 original size:27 final size:27
Alignment explanation
Indices: 210413--210466 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
210403 TTTTGGACGT
210413 ATAAAGTGTATGTAAATGTATATATTTA
1 ATAAAGTGTATGTAAATGTATAT-TTTA
*
210441 ATAAAGGTGTCTG-AAA-GTATATTTTA
1 ATAAA-GTGTATGTAAATGTATATTTTA
210467 TATACGTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 6 0.25
28 8 0.33
29 6 0.25
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.41
Consensus pattern (27 bp):
ATAAAGTGTATGTAAATGTATATTTTA
Found at i:210729 original size:3 final size:3
Alignment explanation
Indices: 210721--210789 Score: 93
Period size: 3 Copynumber: 22.7 Consensus size: 3
210711 AAATAAAGCC
** * *
210721 AAT AAT AATT AAT AAT AGC AGT AAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
210767 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
210790 CACTAAAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:211935 original size:14 final size:15
Alignment explanation
Indices: 211904--211939 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
211894 TTTTATGAAA
*
211904 TTGGGCTTGGGTGTT
1 TTGGGCTTCGGTGTT
211919 TTGGGCTTCGG-GTT
1 TTGGGCTTCGGTGTT
211933 TTGGGCT
1 TTGGGCT
211940 GTATTTGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.11, G:0.44, T:0.44
Consensus pattern (15 bp):
TTGGGCTTCGGTGTT
Found at i:212535 original size:99 final size:97
Alignment explanation
Indices: 212341--213610 Score: 1298
Period size: 96 Copynumber: 13.0 Consensus size: 97
212331 TAAAATGTCA
* * * * * * *
212341 GGGAAGCGAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGTACCTGCTTAGGAA-TAAGATTT
1 GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATC-GCCT-GGAAGTAAGATTC
*
212405 GCCGTTGTGGCCTCAATCTTTT-AATTGCAATGT
64 GCCGTTGTGGCTTCAATCTTTTAAATTGCAATGT
* * * *
212438 CAGGGGAGTGAGATTCGCCATTGTAGCTTCAATCTGTTCCGCTGCATTGCTTGGAAGTAAGA-TC
1 --GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTC
* * * *
212502 TGCCGTCGTGGCCTCAATTTTTTAAATTACAATGT
64 -GCCGTTGTGGCTTCAATCTTTTAAATTGCAATGT
* * * * * * *
212537 CGAGGGAGTGAGATCCGCCATTGTAGCTTCAATTTGTTCCTCTAG-ATCGCTTGGAAGTAAGATC
1 -G-GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCT-GCATCGCCTGGAAGTAAGATT
* * *
212601 CGCCGTCGTGGCCTCAATCTTTTAAATTGTAATGT
63 CGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGT
* * *
212636 CGGGGAAGTGAGATTCGCCGTTGCAGCTTCAATCTGTTTCGCTGCATCG-CTAAGTAAGTAAGAT
1 --GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCT--GGAAGTAAGAT
* * *
212700 CCGCCGTCGTGGCCTCAATCTTTTAAATTGCAATGT
62 TCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGT
* * *
212736 CGGGGAAGTGAGATTCACCGTTGTAGCTTCAATCTGTTTCGCTGCATCGCCTGAAAGTAAGATTC
1 --GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTC
* *
212801 GCCGTTGTGGCTTCGATCTTTTTAATTGCAATGTT
64 GCCGTTGTGGCTTCAATCTTTTAAATTGCAATG-T
* * * * * * *
212836 AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCAAT-GATGTGAGACT
1 -GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCC--TGGAAGTAAGATT
* * * *
212900 CGCTGTTGTAGCTTCAATCTATTT-GACTGCAATGTT
63 CGCCGTTGTGGCTTCAATCT-TTTAAATTGCAATG-T
* * * ** *
212936 GGGGAAGTGAGACTCGCTGTTGTAGCTTCAATCTGTTTCATTGCATTGCCTGGAAGTAAGATTCG
1 -GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCG
** *
213001 TTGTTGTGGCTTCGATCTTTTAAATTGCAATG-
65 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGT
* *
213033 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
1 GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGC
*
213098 CGTTGTGGCTTCGATCTTTTAAATTGCAATG-
66 CGTTGTGGCTTCAATCTTTTAAATTGCAATGT
* * * * * *
213129 GGGAAGTCAGACTCGCTGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCTGGAAGTAAAATTCAC
1 GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGC
*
213194 CGTTGTGGCTTCGATCTTTTAAATTGCAATG-
66 CGTTGTGGCTTCAATCTTTTAAATTGCAATGT
* * * ** *
213225 GGGAAGTGAGACTCGCCATTGTAGCTTCAATCTATTTTGCTGCATCGCCTGAAAGTAAGATTCGC
1 GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGC
* *
213290 TGTTGTGGCTTCGATCTTTTAAATTGCAATG-
66 CGTTGTGGCTTCAATCTTTTAAATTGCAATGT
* * * *** *
213321 GGGAAGTGAGACTCGCCGTCTTTGTCGCTT--GT-TAGTAATGGTGCATCGCCTGGAAGTAAGAT
1 GGGAAGTGAGATTCGCCG---TTGTAGCTTCAATCT-GTTCCGCTGCATCGCCTGGAAGTAAGAT
*
213383 TCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATG-
62 TCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGT
*
213418 GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
1 GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGC
* ***
213483 CGTTGTGGCTTCAATCTGTT-CGCTGC-ATCGCCT
66 CGTTGTGGCTTCAATCTTTTAAATTGCAAT-G--T
* * * * *
213516 -GAAAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCCACTGCATCGCCTGAAAGTAAGATTCG
1 GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTT-CCGCTGCATCGCCTGGAAGTAAGATTCG
* *
213580 CCGTTGTGGCTTCGATCTTTTTAATTGCAAT
65 CCGTTGTGGCTTCAATCTTTTAAATTGCAAT
213611 CTATGGTTAC
Statistics
Matches: 1015, Mismatches: 125, Indels: 61
0.85 0.10 0.05
Matches are distributed among these distances:
94 10 0.01
95 4 0.00
96 327 0.32
97 113 0.11
98 82 0.08
99 298 0.29
100 175 0.17
101 6 0.01
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (97 bp):
GGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGC
CGTTGTGGCTTCAATCTTTTAAATTGCAATGT
Found at i:212668 original size:50 final size:49
Alignment explanation
Indices: 212399--213450 Score: 251
Period size: 49 Copynumber: 21.5 Consensus size: 49
212389 CTTAGGAATA
* * *
212399 AGATTTGCCGTTGTGGCCTCAATCTTTT-AATTGCAATGTCAGGGG-AGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTG-AATGTC-GGGGAAGTG
* * **** * ** *
212448 AGATTCGCCATTGTAGCTTCAATCTGTTCCGCTGCAT-TGCTTGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGAATGT-CGGGGAAGTG
* * * * *
212497 AGA-TCTGCCGTCGTGGCCTCAATTTTTTAAATTACAATGTCGAGGG-AGTG
1 AGATTC-GCCGTTGTAGCTTCAATCTTTTAAATT-GAATGTCG-GGGAAGTG
* * ** ** *
212547 AGATCCGCCATTGTAGCTTCAAT-TTGTT-CCTCT-AGATCG-CTTGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTT-TTAAAT-TGA-AT-GTCGGGGAAGTG
* * * *
212596 AGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGTAATGTCGGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTG-AATGTCGGGGAAGTG
* *** * ** * *
212646 AGATTCGCCGTTGCAGCTTCAATCTGTTT-CGCTGCATCG-CTAAGTAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCT-TTTAAATTGAAT-GTC-GGGGAAGTG
* * * *
212696 AGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAATGTCGGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTG-AATGTCGGGGAAGTG
* *** * ** * *
212746 AGATTCACCGTTGTAGCTTCAATCTGTTT-CGCTGCATCG-CCTGAAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCT-TTTAAATTGAAT-GTCGGGGAAGTG
* * * ** *
212795 AGATTCGCCGTTGTGGCTTCGATCTTTTTAATTGCAATGTTAGGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTG-AATGTCGGGGAAGTG
* * * *** * * *** *
212845 AGATCCGCTGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCAATGATGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGAAT-GTCGGGGAAGTG
* * * * *
212895 AGACTCGCTGTTGTAGCTTCAATCTATTT-GACTGCAATGTTGGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCT-TTTAAATTG-AATGTCGGGGAAGTG
* * * * ** *
212945 AGACTCGCTGTTGTAGCTTCAATCTGTTT-CATTGCAT-TGCCTGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCT-TTTAAATTGAATGT-CGGGGAAGTG
** * *
212994 AGATTCGTTGTTGTGGCTTCGATCTTTTAAATTGCAA--T-GGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTG-AATGTCGGGGAAGTG
* * **** * ** * *
213041 AGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCG-CCTGAAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGAAT-GTCGGGGAAGTG
* * *
213090 AGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAA--T-GGGGAAGTC
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTG-AATGTCGGGGAAGTG
* * * *** * ** *
213137 AGACTCGCTGTTGTAGCTTCAATCTGTTCCGTTGCATCG-CCTGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGAAT-GTCGGGGAAGTG
* * * *
213186 AAATTCACCGTTGTGGCTTCGATCTTTTAAATTGCAA--T-GGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTG-AATGTCGGGGAAGTG
* * *** * ** * *
213233 AGACTCGCCATTGTAGCTTCAATCTATTT-TGCTGCATCG-CCTGAAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCT-TTTAAATTGAAT-GTCGGGGAAGTG
* * *
213282 AGATTCGCTGTTGTGGCTTCGATCTTTTAAATTGCAA--T-GGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTG-AATGTCGGGGAAGTG
* * * * ** *
213329 AGACTCGCCGTCT-TTG--TC--GCTTGTTAGTAATGGTGCATCG-CCTGGAAGTA
1 AGATTCGCCGT-TGTAGCTTCAATCTT-TTA--AAT--TGAAT-GTCGGGGAAGTG
* *
213379 AGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAA--T-GGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTG-AATGTCGGGGAAGTG
213426 AGATTCGCCGTTGTAGCTTCAATCT
1 AGATTCGCCGTTGTAGCTTCAATCT
213451 GTTCCGCTGC
Statistics
Matches: 692, Mismatches: 239, Indels: 146
0.64 0.22 0.14
Matches are distributed among these distances:
43 3 0.00
44 3 0.00
45 2 0.00
46 6 0.01
47 134 0.19
48 24 0.03
49 247 0.36
50 244 0.35
51 21 0.03
52 2 0.00
53 3 0.00
54 3 0.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (49 bp):
AGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGAATGTCGGGGAAGTG
Found at i:212762 original size:199 final size:195
Alignment explanation
Indices: 212334--213610 Score: 1315
Period size: 199 Copynumber: 6.5 Consensus size: 195
212324 ATCTGTTTAA
* * * * * * * *
212334 AATGTCAGGGAAGCGAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGTACCTGCTTAGGAA-T
1 AATGTCGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCTCTGCATC-GCCT-GGAAGT
* * * * *
212398 AAGATTTGCCGTTGTGGCCTCAATCTTTT-AATTGCAATGTCAGGGGAGTGAGATTCGCCATTGT
64 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATG---GGGAAGTGAGATTCGCCGTTGT
* * * * * * *
212462 AGCTTCAATCTGTTCCGCTGCATTGCTTGGAAGTAAGATCTGCCGTCGTGGCCTCAATTTTTTAA
126 AGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAA
*
212527 ATTAC
191 ATTGC
* * *
212532 AATGTCGAGGG-AGTGAGA-TCCGCCATTGTAGCTTCAATTTGTTCCTCTAG-ATCGCTTGGAAG
1 AATGTCG-GGGAAGTGAGACT-CGCCGTTGTAGCTTCAATCTGTTCCTCT-GCATCGCCTGGAAG
* * * * *
212594 TAAGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGTAATGTCGGGGAAGTGAGATTCGCCGTTG
63 TAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAA--T-GGGGAAGTGAGATTCGCCGTTG
* * * * *
212659 CAGCTTCAATCTGTTTCGCTGCATCG-CTAAGTAAGTAAGATCCGCCGTCGTGGCCTCAATCTTT
125 TAGCTTCAATCTGTTCCGCTGCATCGCCT--GAAAGTAAGATCCGCCGTTGTGGCTTCAATCTTT
212723 TAAATTGC
188 TAAATTGC
* * * * *
212731 AATGTCGGGGAAGTGAGATTCACCGTTGTAGCTTCAATCTGTTTCGCTGCATCGCCTGAAAGTAA
1 AATGTCGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCTCTGCATCGCCTGGAAGTAA
* * * *
212796 GATTCGCCGTTGTGGCTTCGATCTTTTTAATTGCAATGTTAGGGAAGTAAGATCCGCTGTTGTAG
66 GATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATG---GGGAAGTGAGATTCGCCGTTGTAG
* * * * *
212861 CTTCAATCTGTTCCGTTGCATCGCCAATG-ATGTGAGA-CTCGCTGTTGTAGCTTCAATCTATTT
128 CTTCAATCTGTTCCGCTGCATCGCC--TGAAAGTAAGATC-CGCCGTTGTGGCTTCAATCT-TTT
* *
212924 -GACTGC
189 AAATTGC
* * * *
212930 AATGTTGGGGAAGTGAGACTCGCTGTTGTAGCTTCAATCTGTTTCAT-TGCATTGCCTGGAAGTA
1 AATGTCGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTG-TTCCTCTGCATCGCCTGGAAGTA
** *
212994 AGATTCGTTGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCT
65 AGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGATTCGCCGTTGTAGCT
* *
213059 TCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTG
130 TCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAATTG
213124 C
195 C
* *
213125 AA--T-GGGGAAGTCAGACTCGCTGTTGTAGCTTCAATCTGTTCCGT-TGCATCGCCTGGAAGTA
1 AATGTCGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCC-TCTGCATCGCCTGGAAGTA
* * * *
213186 AAATTCACCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCATTGTAGCT
65 AGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGATTCGCCGTTGTAGCT
* ** * * *
213251 TCAATCTATTTTGCTGCATCGCCTGAAAGTAAGATTCGCTGTTGTGGCTTCGATCTTTTAAATTG
130 TCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAATTG
213316 C
195 C
* * ** *
213317 AA--T-GGGGAAGTGAGACTCGCCGTCTTTGTCGCTT--GT-TAG-TAATGGTGCATCGCCTGGA
1 AATGTCGGGGAAGTGAGACTCGCCG---TTGTAGCTTCAATCT-GTTCCT-CTGCATCGCCTGGA
213375 AGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGATTCGCCGTTGT
61 AGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGATTCGCCGTTGT
* * *
213440 AGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTGTT-C
126 AGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAA
**
213504 GCTGC
191 ATTGC
** * * * * * *
213509 -ATCG-CCTGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCCACTGCATCGCCTGAAAGT
1 AAT-GTCGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTT-CCTCTGCATCGCCTGGAAGT
*
213572 AAGATTCGCCGTTGTGGCTTCGATCTTTTTAATTGCAAT
64 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
213611 CTATGGTTAC
Statistics
Matches: 923, Mismatches: 115, Indels: 86
0.82 0.10 0.08
Matches are distributed among these distances:
191 13 0.01
192 198 0.21
193 136 0.15
194 74 0.08
195 37 0.04
196 49 0.05
197 34 0.04
198 94 0.10
199 277 0.30
200 9 0.01
201 1 0.00
202 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (195 bp):
AATGTCGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCTCTGCATCGCCTGGAAGTAA
GATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGATTCGCCGTTGTAGCTT
CAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGC
Found at i:213038 original size:47 final size:47
Alignment explanation
Indices: 212691--213610 Score: 312
Period size: 49 Copynumber: 18.9 Consensus size: 47
212681 ATCGCTAAGT
* * * *
212691 AAGTAAGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAATGTCGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAA--T-GGGG
* * * * *** * *
212741 AAGTGAGATTCACCGTTGTAGCTTCAATCTGTTT-CGCTGC-ATCGCCTGA
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCT-TTTAAATTGCAAT-G--GGG
*
212790 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTTAATTGCAATGTTAGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATG---GGG
* * * * * *** **
212840 AAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCGTTGC-ATCGCCAATG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G---GGG
* * * * * * * *
212890 ATGTGAGACTCGCTGTTGTAGCTTCAATCTATTT-GACTGCAATGTTGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCT-TTTAAATTGCAA---TGGGG
* * * * * * * *
212940 AAGTGAGACTCGCTGTTGTAGCTTCAATCTGTTT-CATTGCATTGCCTGG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCT-TTTAAATTGCAATG--GGG
**
212989 AAGTAAGATTCGTTGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
* * * * * **** * *
213036 AAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTGA
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGG
213085 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
* * * * * * *** *
213132 AAGTCAGACTCGCTGTTGTAGCTTCAATCTGTTCCGTTGC-ATCGCCTGG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGG
* *
213181 AAGTAAAATTCACCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
* * * * * *** * *
213228 AAGTGAGACTCGCCATTGTAGCTTCAATCTATTT-TGCTGC-ATCGCCTGA
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCT-TTTAAATTGCAAT-G--GGG
*
213277 AAGTAAGATTCGCTGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
* * * *
213324 AAGTGAGACTCGCCGTCT-TTG--TCG--CTTGTTAGTAATGGTGC-ATCGCCTGG
1 AAGTAAGATTCGCCGT-TGTGGCTTCGATCTT-TTA--AAT--TGCAAT-G--GGG
213374 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
* * * * **** * *
213421 AAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTGA
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGG
* * *** * *
213470 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTT-CGCTGC-ATCGCCTGA
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGG
* *** * * *
213518 AAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCCACTGC-ATCGCCTGA
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCT-TTTAAATTGCAAT-G--GGG
*
213568 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTTAATTGCAAT
1 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
213611 CTATGGTTAC
Statistics
Matches: 664, Mismatches: 156, Indels: 100
0.72 0.17 0.11
Matches are distributed among these distances:
43 3 0.00
44 3 0.00
45 3 0.00
46 11 0.02
47 152 0.23
48 62 0.09
49 207 0.31
50 203 0.31
51 9 0.01
52 3 0.00
53 4 0.01
54 4 0.01
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (47 bp):
AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGG
Found at i:213580 original size:50 final size:49
Alignment explanation
Indices: 212349--213597 Score: 520
Period size: 50 Copynumber: 25.5 Consensus size: 49
212339 CAGGGAAGCG
* * * * * * *
212349 AGATTCGCCATTGTAGCTTCAATCTGTTCCACTGTACCTGCTTAGGAA-TA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATC-GCCT-GGAAGTA
* * * ** * *
212399 AGATTTGCCGTTGTGGCCTCAATCTTTTA-ATTGCAAT-GTCAGGGGAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGC-ATCG-CCTGGAAGTA
* * * ** * *
212448 AGATTCGCCATTGTAGCTTCAATCTGTTCCGCTGCATTGCTTGGAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCCTGGAAGTA
* * * * * * ** * *
212497 AGA-TCTGCCGTCGTGGCCTCAATTTTTTAAATTACAAT-GTCGAGGGAGTG
1 AGATTC-GCCGTTGTGGCTTCAATCTGTTACATTGC-ATCG-CCTGGAAGTA
* * * * * *
212547 AGATCCGCCATTGTAGCTTCAATTTGTT-CCTCTAG-ATCGCTTGGAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACAT-T-GCATCGCCTGGAAGTA
* * * * * * ** *
212596 AGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGTAAT-GTCGGGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTG-CATCG-CCTGGAAGTA
** * ** *
212646 AGATTCGCCGTTGCAGCTTCAATCTGTTTCGCTGCATCG-CTAAGTAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCCT--GGAAGTA
* * * * * ** *
212696 AGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAAT-GTCGGGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGC-ATCG-CCTGGAAGTA
* * * ** *
212746 AGATTCACCGTTGTAGCTTCAATCTGTTTCGCTGCATCGCCTGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCCTGGAAGTA
* * *
212795 AGATTCGCCGTTGTGGCTTCGATCTTTTTA-ATTGCAAT-G-TTAGGGAAGTA
1 AGATTCGCCGTTGTGGCTTCAATC-TGTTACATTGC-ATCGCCT--GGAAGTA
* * * * * * *
212845 AGATCCGCTGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCAAT-GATGTG
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCC--TGGAAGTA
* * * * ** * * *
212895 AGACTCGCTGTTGTAGCTTCAATCTATTTGACTGCAAT-G-TTGGGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGC-ATCGCCT--GGAAGTA
* * * * *
212945 AGACTCGCTGTTGTAGCTTCAATCTGTTTCATTGCATTGCCTGGAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCCTGGAAGTA
** * * * * *
212994 AGATTCGTTGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGC-ATCGCCTGGAAGTA
* * * ** *
213041 AGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCCTGGAAGTA
* * * * *
213090 AGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGGAAGTC
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGC-ATCGCCTGGAAGTA
* * * * *
213137 AGACTCGCTGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCTGGAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCCTGGAAGTA
* * * * * * *
213186 AAATTCACCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGC-ATCGCCTGGAAGTA
* * * * **** *
213233 AGACTCGCCATTGTAGCTTCAATCTATTTTGCTGCATCGCCTGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCCTGGAAGTA
* * * * * *
213282 AGATTCGCTGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGC-ATCGCCTGGAAGTA
* * *
213329 AGACTCGCCGTCTTTGTCGCTT--GT-TAG-TA-ATGGTGCATCGCCTGGAAGTA
1 AGATTCGCCG---TTGTGGCTTCAATCT-GTTACAT--TGCATCGCCTGGAAGTA
* * * * *
213379 AGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGC-ATCGCCTGGAAGTA
* * ** *
213426 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCCTGGAAGTA
** *
213475 AGATTCGCCGTTGTGGCTTCAATCTGTT-CGCTGCATCGCCTGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCCTGGAAGTA
* * *
213523 AGATTCGCCGTTGTGGCTTCAATCTGTTCCCACTGCATCGCCTGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTGTT-ACATTGCATCGCCTGGAAGTA
*
213573 AGATTCGCCGTTGTGGCTTCGATCT
1 AGATTCGCCGTTGTGGCTTCAATCT
213598 TTTTAATTGC
Statistics
Matches: 880, Mismatches: 248, Indels: 142
0.69 0.20 0.11
Matches are distributed among these distances:
46 10 0.01
47 158 0.18
48 61 0.07
49 301 0.34
50 341 0.39
51 8 0.01
53 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (49 bp):
AGATTCGCCGTTGTGGCTTCAATCTGTTACATTGCATCGCCTGGAAGTA
Found at i:227524 original size:14 final size:15
Alignment explanation
Indices: 227493--227528 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
227483 TTTTATGAAA
*
227493 TTGGGCTTGGGTGTT
1 TTGGGCTTCGGTGTT
227508 TTGGGCTTCGG-GTT
1 TTGGGCTTCGGTGTT
227522 TTGGGCT
1 TTGGGCT
227529 GTATTTGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.11, G:0.44, T:0.44
Consensus pattern (15 bp):
TTGGGCTTCGGTGTT
Found at i:227590 original size:82 final size:82
Alignment explanation
Indices: 227462--227622 Score: 322
Period size: 82 Copynumber: 2.0 Consensus size: 82
227452 GTTTCAGTCT
227462 CTGAAACCCTAGGCAGATTTTTTTTATGAAATTGGGCTTGGGTGTTTTGGGCTTCGGGTTTTGGG
1 CTGAAACCCTAGGCAGATTTTTTTTATGAAATTGGGCTTGGGTGTTTTGGGCTTCGGGTTTTGGG
227527 CTGTATTTGGGTTAAGA
66 CTGTATTTGGGTTAAGA
227544 CTGAAACCCTAGGCAGATTTTTTTTATGAAATTGGGCTTGGGTGTTTTGGGCTTCGGGTTTTGGG
1 CTGAAACCCTAGGCAGATTTTTTTTATGAAATTGGGCTTGGGTGTTTTGGGCTTCGGGTTTTGGG
227609 CTGTATTTGGGTTA
66 CTGTATTTGGGTTA
227623 GTTTTAGGTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.41
Consensus pattern (82 bp):
CTGAAACCCTAGGCAGATTTTTTTTATGAAATTGGGCTTGGGTGTTTTGGGCTTCGGGTTTTGGG
CTGTATTTGGGTTAAGA
Found at i:227606 original size:14 final size:15
Alignment explanation
Indices: 227575--227610 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
227565 TTTTATGAAA
*
227575 TTGGGCTTGGGTGTT
1 TTGGGCTTCGGTGTT
227590 TTGGGCTTCGG-GTT
1 TTGGGCTTCGGTGTT
227604 TTGGGCT
1 TTGGGCT
227611 GTATTTGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.11, G:0.44, T:0.44
Consensus pattern (15 bp):
TTGGGCTTCGGTGTT
Found at i:227968 original size:6 final size:6
Alignment explanation
Indices: 227957--227983 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
227947 GGGGCGTCGC
227957 CGGTGG CGGTGG CGGTGG CGGTGG CGG
1 CGGTGG CGGTGG CGGTGG CGGTGG CGG
227984 CTGAAACCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.67, T:0.15
Consensus pattern (6 bp):
CGGTGG
Found at i:234007 original size:30 final size:30
Alignment explanation
Indices: 233971--234029 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
233961 AATCAAGCAT
* * *
233971 TGAAAATTCCAATCTGTAATTTTGCTTCAG
1 TGAAAATCCCAATATCTAATTTTGCTTCAG
234001 TGAAAATCCCAATATCTAATTTTGCTTCA
1 TGAAAATCCCAATATCTAATTTTGCTTCA
234030 AACTATCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (30 bp):
TGAAAATCCCAATATCTAATTTTGCTTCAG
Found at i:234262 original size:18 final size:18
Alignment explanation
Indices: 234235--234271 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
234225 CGAAGAAACA
234235 TCATCATCGTCATCGTCC
1 TCATCATCGTCATCGTCC
*
234253 TCATCGTCGTCATCGTCC
1 TCATCATCGTCATCGTCC
234271 T
1 T
234272 TTTTGCAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.38, G:0.14, T:0.35
Consensus pattern (18 bp):
TCATCATCGTCATCGTCC
Found at i:236676 original size:14 final size:12
Alignment explanation
Indices: 236657--236765 Score: 64
Period size: 13 Copynumber: 8.8 Consensus size: 12
236647 CAAATTAAAT
236657 GTATATTTATAACA
1 GTATA-TTA-AACA
236671 GTATATTAAA-A
1 GTATATTAAACA
236682 GT-TA--AAACA
1 GTATATTAAACA
*
236691 TTATATTAAAACA
1 GTATATT-AAACA
236704 GTATATTTATAACA
1 GTATA-TTA-AACA
*
236718 ATATATTAAAACA
1 GTATATT-AAACA
* *
236731 ATATATTAAAAA
1 GTATATTAAACA
* *
236743 ATATATTTATAATA
1 GTATA-TTA-AACA
236757 GTATATTAA
1 GTATATTAA
236766 TTGTTAAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
8 3 0.04
9 2 0.03
10 4 0.05
11 3 0.04
12 12 0.15
13 32 0.41
14 23 0.29
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (12 bp):
GTATATTAAACA
Found at i:236701 original size:13 final size:13
Alignment explanation
Indices: 236683--236749 Score: 91
Period size: 13 Copynumber: 5.2 Consensus size: 13
236673 ATATTAAAAG
*
236683 TTAAAACATTATA
1 TTAAAACAATATA
*
236696 TTAAAACAGTATA
1 TTAAAACAATATA
*
236709 TTTATAACAATATA
1 -TTAAAACAATATA
236723 TTAAAACAATATA
1 TTAAAACAATATA
236736 TTAAAA-AATATA
1 TTAAAACAATATA
236748 TT
1 TT
236750 TATAATAGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
12 8 0.16
13 30 0.61
14 11 0.22
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.37
Consensus pattern (13 bp):
TTAAAACAATATA
Found at i:236711 original size:47 final size:45
Alignment explanation
Indices: 236657--236784 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 45
236647 CAAATTAAAT
*
236657 GTATATTTATAACAGTATATTAAAAGTTAAAACATTATATTAAAACA
1 GTATATTTATAACAGTATATT-AAAGTTAAAACAATATATTAAAA-A
236704 GTATATTTATAACA--ATA-T--A-TTAAAACAATATATTAAAAA
1 GTATATTTATAACAGTATATTAAAGTTAAAACAATATATTAAAAA
* * * * *
236743 ATATATTTATAATAGTATATTAATTGTTAAAATAGTATATTA
1 GTATATTTATAACAGTATATTAA-AGTTAAAACAATATATTA
236785 CAAATTTTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
39 13 0.19
40 18 0.26
41 4 0.06
42 1 0.01
44 1 0.01
45 3 0.04
46 14 0.21
47 14 0.21
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (45 bp):
GTATATTTATAACAGTATATTAAAGTTAAAACAATATATTAAAAA
Found at i:236722 original size:27 final size:26
Alignment explanation
Indices: 236686--236763 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 26
236676 TTAAAAGTTA
*
236686 AAACATTATATTAAAACAGTATATTT
1 AAACAATATATTAAAACAGTATATTT
*
236712 ATAACAATATATTAAAACAATATA-TT
1 A-AACAATATATTAAAACAGTATATTT
* * *
236738 AAAAAATATATTTATAATAGTATATT
1 AAACAATATA-TTAAAACAGTATATT
236764 AATTGTTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 8 0.19
26 14 0.33
27 21 0.49
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (26 bp):
AAACAATATATTAAAACAGTATATTT
Found at i:236762 original size:39 final size:40
Alignment explanation
Indices: 236683--236765 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 40
236673 ATATTAAAAG
* *
236683 TTAAAACATTATATTAAAACAGTATATTTATAACAATATA
1 TTAAAACAATATATTAAAACAATATATTTATAACAATATA
* *
236723 TTAAAACAATATATTAAAA-AATATATTTATAATAGTATA
1 TTAAAACAATATATTAAAACAATATATTTATAACAATATA
236762 TTAA
1 TTAA
236766 TTGTTAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 21 0.54
40 18 0.46
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (40 bp):
TTAAAACAATATATTAAAACAATATATTTATAACAATATA
Found at i:237692 original size:2 final size:2
Alignment explanation
Indices: 237687--237716 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
237677 TCGAACCTTG
237687 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
237717 ACCTTTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:242016 original size:22 final size:23
Alignment explanation
Indices: 241988--242032 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
241978 ATGCAATTTT
241988 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
242010 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
242033 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:242274 original size:79 final size:79
Alignment explanation
Indices: 242143--242293 Score: 275
Period size: 79 Copynumber: 1.9 Consensus size: 79
242133 ATTGTAAAAT
**
242143 ACTTGAGTTTGGAGCAACAATAATTCTTAAGAGCATTCACTCAAATTTCTCCCTCTCTTGTGTTC
1 ACTTGAGTTTGGAGCAACAATAATTCTTAAGAGCATTCACTCAAATTTCTCCCTCTCTTGCATTC
242208 TTATTTTTCGTGAC
66 TTATTTTTCGTGAC
*
242222 ACTTGAGTTTGGAGCAATAATAATTCTTAAGAGCATTCACTCAAATTTCTCCCTCTCTTGCATTC
1 ACTTGAGTTTGGAGCAACAATAATTCTTAAGAGCATTCACTCAAATTTCTCCCTCTCTTGCATTC
242287 TTATTTT
66 TTATTTT
242294 CTGTGGCTTG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (79 bp):
ACTTGAGTTTGGAGCAACAATAATTCTTAAGAGCATTCACTCAAATTTCTCCCTCTCTTGCATTC
TTATTTTTCGTGAC
Found at i:244713 original size:19 final size:19
Alignment explanation
Indices: 244689--244732 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
244679 TCTTTCTTTT
*
244689 TGCATT-CATTCCATGCATC
1 TGCATTACATTCCAT-CATA
*
244708 TGCATTACATTGCATCATA
1 TGCATTACATTCCATCATA
244727 TGCATT
1 TGCATT
244733 TGATTTTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (19 bp):
TGCATTACATTCCATCATA
Found at i:248942 original size:24 final size:24
Alignment explanation
Indices: 248906--248961 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
248896 GTCCCAAAAG
* *
248906 TACAGTGGATTGAACCTTGAAGAT
1 TACAGTGGATTGAACCATGAAGAC
*
248930 TACAGTGGTTTGAACCATGAAGAC
1 TACAGTGGATTGAACCATGAAGAC
248954 TACAGTGG
1 TACAGTGG
248962 GGGAAATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (24 bp):
TACAGTGGATTGAACCATGAAGAC
Found at i:249293 original size:44 final size:44
Alignment explanation
Indices: 249238--249692 Score: 394
Period size: 44 Copynumber: 10.2 Consensus size: 44
249228 TAGTGAAACC
* * * *
249238 ACAAATCTTATCTCTCTGAGGTTGCAATGGAGCGGATTAAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT
* * * * * * **
249282 ACAAGTCTTATCTCTCTGAAGTTACAGTGGAGTAGACTGAAGAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT
* * * * * *
249326 AGCAAGTCTTAT-TCCCCTGAAGTTGTAGTGGGGTAGACTAAAGATG
1 A-CAAATCTTATCT-CCCTGAAGTTGCAGTGGAGCAGATTAAAG-TT
* * * **
249372 GCAAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTAAAGCC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT
* * * *
249416 A-ATAATCCTATCTCCCTAAAGTTGCAATGGAGCGGATTAAAGTT
1 ACA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT
* * * * **
249460 ACAAGTCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT
* * * * * ** *
249504 AGCAAGTTTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGCAGATG
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TT
* * *
249550 GCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGTC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT
*
249594 A-ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT
1 ACA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT
* *
249638 ACAAATCCTATCTCCCTGAAGTTGCAGTGGACCAGATTAAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT
*
249682 ACAAGTCTTAT
1 ACAAATCTTAT
249693 TGAAGAAAGC
Statistics
Matches: 331, Mismatches: 70, Indels: 20
0.79 0.17 0.05
Matches are distributed among these distances:
43 2 0.01
44 193 0.58
45 135 0.41
46 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT
Found at i:249346 original size:45 final size:45
Alignment explanation
Indices: 249283--249668 Score: 201
Period size: 45 Copynumber: 8.7 Consensus size: 45
249273 ATTAAAGTTA
* *
249283 CAAGTCTTATCTCTCTGAAGTTACAGTGGAGTAGACTGAAGAAAG
1 CAAGTCTTATCTCCCTGAAGTTACAGTGGAGTAGACTAAAGAAAG
** * **
249328 CAAGTCTTAT-TCCCCTGAAGTTGTAGTGGGGTAGACTAAAGATGG
1 CAAGTCTTATCT-CCCTGAAGTTACAGTGGAGTAGACTAAAGAAAG
* * * * * * *
249373 CAAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAA-
1 CAAGTCTTATCTCCCTGAAGTTACAGTGGAGTAGACTAAAG-AAAG
* * * * * ** * **
249418 TAA-TCCTATCTCCCTAAAGTTGCAATGGAGCGGATTAAAGTTA-
1 CAAGTCTTATCTCCCTGAAGTTACAGTGGAGTAGACTAAAGAAAG
* * * * * *
249461 CAAGTCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGAAAG
1 CAAGTCTTATCTCCCTGAAGTTACAGTGGAGTAGACTAAAGAAAG
* * * * * ** **
249506 CAAGTTTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGCAGATGG
1 CAAGTCTTATCTCCCTGAAGTTACAGTGGAGTAGACTAAAGAAAG
* * * * * *
249551 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGTCAA-
1 CAAGTCTTATCTCCCTGAAGTTACAGTGGAGTAGACTAAAG-AAAG
* * * * * **
249596 TAA-TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA-
1 CAAGTCTTATCTCCCTGAAGTTACAGTGGAGTAGACTAAAGAAAG
* * *
249639 CAAATCCTATCTCCCTGAAGTTGCAGTGGA
1 CAAGTCTTATCTCCCTGAAGTTACAGTGGA
249669 CCAGATTAAA
Statistics
Matches: 274, Mismatches: 60, Indels: 15
0.79 0.17 0.04
Matches are distributed among these distances:
43 6 0.02
44 126 0.46
45 141 0.51
46 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (45 bp):
CAAGTCTTATCTCCCTGAAGTTACAGTGGAGTAGACTAAAGAAAG
Found at i:249557 original size:178 final size:178
Alignment explanation
Indices: 249258--249692 Score: 633
Period size: 178 Copynumber: 2.4 Consensus size: 178
249248 TCTCTCTGAG
* * *
249258 GTTGCAATGGAGCGGATTAAAGTTACAAGTCTTATC-TCTCTGAAGTTACAGTGGAGTAGACTGA
1 GTTGCAATGGAGCGGATTAAAGTTACAAGTCTTATCTTCT-TGAAGTTGCAGTGGAGCAGATTGA
* * *
249322 AGAAAGCAAGTCTTATTCCCCTGAAGTTGTAGTGGGGTAGACTAAAGATGGCAAATCTTATCT-T
65 AGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTAAAGATGGCAAATCTTATCTCT
249386 CCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAA
130 -CTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAA
249436 GTTGCAATGGAGCGGATTAAAGTTACAAGTCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAA
1 GTTGCAATGGAGCGGATTAAAGTTACAAGTCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAA
* **
249501 GAAAGCAAGTTTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGCAGATGGCAAATCTTATCTCTC
66 GAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTAAAGATGGCAAATCTTATCTCTC
* * *
249566 TGAAGTTGCAGTGGAGCAGATTAAAGTCAATAATCCTATCTCCCTGAA
131 TAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAA
* * * * * * * *
249614 GTTGCAGTGGAGCAGATTAAAGTTACAAATCCTATCTCCCTGAAGTTGCAGTGGACCAGATTAAA
1 GTTGCAATGGAGCGGATTAAAGTTACAAGTCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAA
**
249679 GTTA-CAAGTCTTAT
66 GAAAGCAAGTCTTAT
249693 TGAAGAAAGC
Statistics
Matches: 232, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
177 9 0.04
178 219 0.94
179 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (178 bp):
GTTGCAATGGAGCGGATTAAAGTTACAAGTCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAA
GAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTAAAGATGGCAAATCTTATCTCTC
TAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAA
Found at i:249614 original size:134 final size:133
Alignment explanation
Indices: 249419--249667 Score: 320
Period size: 134 Copynumber: 1.9 Consensus size: 133
249409 TAAAGCCAAT
* * * * * *
249419 AATCCTATCTCCCTAAAGTTGCAATGGAGCGGATTAAAGTTACAAGTCTTATCTTCTTGAAGTTG
1 AATCCTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGTCACAAATCCTATCTCCCTGAAGTTG
* * **
249484 CAGTGGAGCAGATTGAAGAAAGCAAGTTTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGCAGAT
66 CAGTGGAGCAGATTAAAGAAA-CAAATCCTATCCCCCTGAAGTTGCAGTGGGGCAGACTGCAGAT
249549 GGCA
130 GGCA
* * * *
249553 AATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGTCA-ATAATCCTATCTCCCTGAAGTT
1 AATCCTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGTCACA-AATCCTATCTCCCTGAAGTT
** *
249617 GCAGTGGAGCAGATTAAAGTTACAAATCCTATCTCCCTGAAGTTGCAGTGG
65 GCAGTGGAGCAGATTAAAGAAACAAATCCTATCCCCCTGAAGTTGCAGTGG
249668 ACCAGATTAA
Statistics
Matches: 97, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
133 26 0.27
134 71 0.73
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (133 bp):
AATCCTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGTCACAAATCCTATCTCCCTGAAGTTG
CAGTGGAGCAGATTAAAGAAACAAATCCTATCCCCCTGAAGTTGCAGTGGGGCAGACTGCAGATG
GCA
Found at i:250120 original size:224 final size:224
Alignment explanation
Indices: 249779--250184 Score: 509
Period size: 224 Copynumber: 1.8 Consensus size: 224
249769 ACAATAGAAC
* * ** *
249779 AGATTAAAGCTATAAATCATAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCATGTTAAAC
1 AGATCAAAGCTATAAATCATAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAAC
* * * * * *
249844 CTTATCTCTCTGAAGTTGTAGTGGAGTAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAG
66 CTTATCTCTCTAAAGTTGCAGTGGAGAAGATTAAAGACAACAATCCTATCTCCCTAAAGTTGCAG
* * *
249909 TGGAGCGGATTGAAG-TA-AAGTCTTATCT-CTCTGAAGTTGCAGTGGAGCAGCTGAAGATAGCA
131 TGGAGCAGATTGAAGCTATAA-TCCTATCTCCT-TGAAATTGCAGTGGAGCAGCTGAAGATAGCA
249971 AATCTTGTTTCCCTGAAGATTGCAGTGGAAT
194 AATCTTGTTTCCCTGAAGATTGCAGTGGAAT
* *
250002 AGATCAAAGCTATAAATCATAAGATCTTATCTCTCTGAAGTTGCATTGGAGCAGATCACATCAAA
1 AGATCAAAGCTATAAATCATAA-ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAA
* * * * *
250067 CCTTATCTC-CTTAAAGTTGCATTGGAGCAAG-TTGAAA-ATACCAATCTTATCTCCCTAAATTT
65 CCTTATCTCTC-TAAAGTTGCAGTGGAG-AAGATT-AAAGACAACAATCCTATCTCCCTAAAGTT
*
250129 GCAGTGGAGTAGATTGAAGCTATTAATCCTATCTCCTTGAAATTGCAGTGGAGCAG
127 GCAGTGGAGCAGATTGAAGCTA-TAATCCTATCTCCTTGAAATTGCAGTGGAGCAG
250185 ATTAAAATGA
Statistics
Matches: 153, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
223 22 0.14
224 95 0.62
225 7 0.05
226 25 0.16
227 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (224 bp):
AGATCAAAGCTATAAATCATAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAAC
CTTATCTCTCTAAAGTTGCAGTGGAGAAGATTAAAGACAACAATCCTATCTCCCTAAAGTTGCAG
TGGAGCAGATTGAAGCTATAATCCTATCTCCTTGAAATTGCAGTGGAGCAGCTGAAGATAGCAAA
TCTTGTTTCCCTGAAGATTGCAGTGGAAT
Found at i:250201 original size:44 final size:44
Alignment explanation
Indices: 250070--250219 Score: 137
Period size: 44 Copynumber: 3.4 Consensus size: 44
250060 CATCAAACCT
* *
250070 TATCTCCTTAAAGTTGCATTGGAGCA-AGTTGAAAATACCAATCT
1 TATCTCCTTAAAGTTGCAGTGGAGCAGA-TTGAAAATACCAATCC
* * * ** **
250114 TATCTCCCTAAATTTGCAGTGGAGTAGATTGAAGCTATTAATCC
1 TATCTCCTTAAAGTTGCAGTGGAGCAGATTGAAAATACCAATCC
*
250158 TATCTCCTTGAAA-TTGCAGTGGAGCAGATT-AAAATGACGAATCC
1 TATCTCCTT-AAAGTTGCAGTGGAGCAGATTGAAAAT-ACCAATCC
*
250202 TAT-ACCTCTAAAGTTGCA
1 TATCTCCT-TAAAGTTGCA
250220 AATCTTGTCT
Statistics
Matches: 85, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
43 9 0.11
44 72 0.85
45 4 0.05
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (44 bp):
TATCTCCTTAAAGTTGCAGTGGAGCAGATTGAAAATACCAATCC
Found at i:250372 original size:89 final size:89
Alignment explanation
Indices: 250221--250496 Score: 381
Period size: 89 Copynumber: 3.1 Consensus size: 89
250211 AAAGTTGCAA
* *
250221 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTTAC
1 ATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTTGC
*
250286 AGCGGAGCAGATTGAAGATAGTAG
66 AGCGGAGCAGATTGAAAATAGTAG
* * * *
250310 ATCTTGTCTTCTTATATTGGTAGCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTGAGTTTGC
1 ATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTTGC
* *
250375 AGCGGAGCAGACTGAAAATAGCAG
66 AGCGGAGCAGATTGAAAATAGTAG
* ** * *
250399 ATCTTGTCTTCCTGTACTGGCAATGAAGCAGATCGAAAACACCAGCCTTGCCTCTCTGAGTTTGC
1 ATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTTGC
* * * *
250464 AGTGGAGTAGGTTGAAAATTGTAG
66 AGCGGAGCAGATTGAAAATAGTAG
*
250488 ATCCTGTCT
1 ATCTTGTCT
250497 CCCTAAGTAG
Statistics
Matches: 162, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
89 162 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.27
Consensus pattern (89 bp):
ATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTTGC
AGCGGAGCAGATTGAAAATAGTAG
Found at i:251094 original size:22 final size:22
Alignment explanation
Indices: 251034--251091 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
251024 AATCTTCAAG
251034 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
251053 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
251075 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
251092 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:251296 original size:79 final size:79
Alignment explanation
Indices: 251200--251353 Score: 281
Period size: 79 Copynumber: 1.9 Consensus size: 79
251190 TCATTGTAAA
* *
251200 ACACTTGCGTTTGGAGCAATAATAATTCTTAAGAGCATTCACTCAAATTTCTCCCTCTCTTGCGT
1 ACACTTGAGTTTGGAGCAATAATAATTCTTAAGAGCATTCACTCAAATTTCTCCCTCTCTTGCAT
251265 TCTTATTTTCCGTG
66 TCTTATTTTCCGTG
*
251279 ACACTTGAGTTTGGAGCAATAATAATTCTTAAGAGCATTCCCTCAAATTTCTCCCTCTCTTGCAT
1 ACACTTGAGTTTGGAGCAATAATAATTCTTAAGAGCATTCACTCAAATTTCTCCCTCTCTTGCAT
251344 TCTTATTTTC
66 TCTTATTTTC
251354 TGTGGCTTGT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (79 bp):
ACACTTGAGTTTGGAGCAATAATAATTCTTAAGAGCATTCACTCAAATTTCTCCCTCTCTTGCAT
TCTTATTTTCCGTG
Found at i:255539 original size:31 final size:31
Alignment explanation
Indices: 255495--255569 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
255485 GCTATTTTTT
* *
255495 TTTTTTTAAATTTTGAAAGGT-TTATTAAAA
1 TTTTTTAAAATTTTGAAAGGTCTAATTAAAA
255525 TTTTTTAAAGATTTTGAAAGGTCTAATTAAAA
1 TTTTTTAAA-ATTTTGAAAGGTCTAATTAAAA
255557 -TTTTTACAAATTT
1 TTTTTTA-AAATTT
255570 AAAGAGCCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 8 0.20
31 22 0.55
32 10 0.25
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (31 bp):
TTTTTTAAAATTTTGAAAGGTCTAATTAAAA
Found at i:255818 original size:18 final size:18
Alignment explanation
Indices: 255795--255829 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
255785 ATACTATTTG
255795 TAAAATATTT-AATTATTA
1 TAAAAT-TTTAAATTATTA
255813 TAAAATTTTAAATTATT
1 TAAAATTTTAAATTATT
255830 TATATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAAATTTTAAATTATTA
Found at i:256027 original size:29 final size:28
Alignment explanation
Indices: 255995--256063 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
255985 AAAATAATAA
255995 ATTTTATATATTATATGTTA-AATATTTTT
1 ATTTTATATATTATAT-TTAGAATA-TTTT
* *
256024 ATTTTTAAATATTATGTTTAGAATATTTT
1 A-TTTTATATATTATATTTAGAATATTTT
256053 ATTATTATATA
1 ATT-TTATATA
256064 GTTTTATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 2 0.06
29 15 0.44
30 17 0.50
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.59
Consensus pattern (28 bp):
ATTTTATATATTATATTTAGAATATTTT
Found at i:256036 original size:30 final size:30
Alignment explanation
Indices: 255996--256052 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
255986 AAATAATAAA
*
255996 TTTTATATATTATATGTTA-AATATTTTTAT
1 TTTTAAATATTATAT-TTAGAATATTTTTAT
*
256026 TTTTAAATATTATGTTTAGAATATTTT
1 TTTTAAATATTATATTTAGAATATTTT
256053 ATTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTAAATATTATATTTAGAATATTTTTAT
Found at i:256054 original size:16 final size:15
Alignment explanation
Indices: 255997--256054 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
255987 AATAATAAAT
* *
255997 TTTATATATTATATG
1 TTTAAATATTTTATG
*
256012 -TTAAATATTTTTATT
1 TTTAAATA-TTTTATG
256027 TTTAAATA--TTATG
1 TTTAAATATTTTATG
256040 TTTAGAATATTTTAT
1 TTTA-AATATTTTAT
256055 TATTATATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
13 8 0.24
14 10 0.29
15 5 0.15
16 11 0.32
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TTTAAATATTTTATG
Found at i:256235 original size:35 final size:33
Alignment explanation
Indices: 256168--256239 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 33
256158 TAAAAATATT
*
256168 ATATTTTATATAATTTATATCATAATTATAAAA
1 ATATTTTATATAATTTATATAATAATTATAAAA
256201 ATATTTTA-ATAAATTATATTATAATAATTATAAAA
1 ATATTTTATAT-AATT-TA-TATAATAATTATAAAA
256236 ATAT
1 ATAT
256240 AATAGGTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
32 2 0.06
33 12 0.34
34 2 0.06
35 19 0.54
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (33 bp):
ATATTTTATATAATTTATATAATAATTATAAAA
Found at i:258432 original size:22 final size:22
Alignment explanation
Indices: 258407--258452 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
258397 TTTGAGCTCG
258407 TATTAGCTTAATCTAGCTAGCC
1 TATTAGCTTAATCTAGCTAGCC
258429 TATTAGCTTAATCTAGCTAGCC
1 TATTAGCTTAATCTAGCTAGCC
258451 TA
1 TA
258453 AGGGAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (22 bp):
TATTAGCTTAATCTAGCTAGCC
Found at i:262856 original size:24 final size:24
Alignment explanation
Indices: 262825--262877 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
262815 TAAGTATGCT
262825 TAAG-GAAGTTAGTCTAAAATGAC
1 TAAGAGAAGTTAGTCTAAAATGAC
262848 TAAGAGAAGTTAGTCTAAAATGAC
1 TAAGAGAAGTTAGTCTAAAATGAC
262872 TAAGAG
1 TAAGAG
262878 GTCTTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.25
Consensus pattern (24 bp):
TAAGAGAAGTTAGTCTAAAATGAC
Found at i:268538 original size:16 final size:17
Alignment explanation
Indices: 268509--268540 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
268499 TTAATAAGAT
268509 TTATATTAAATTTAATC
1 TTATATTAAATTTAATC
268526 TTATATT-AATTTAAT
1 TTATATTAAATTTAAT
268541 ATTAAATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTAAATTTAATC
Found at i:271506 original size:9 final size:9
Alignment explanation
Indices: 271492--271528 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
271482 TATAGTTTGA
271492 TATTCGAAT
1 TATTCGAAT
271501 TATTCGAAT
1 TATTCGAAT
*
271510 TATTCGAGT
1 TATTCGAAT
271519 TATTCGAAT
1 TATTCGAAT
271528 T
1 T
271529 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:272989 original size:14 final size:15
Alignment explanation
Indices: 272967--273010 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
272957 TAAAAAATAA
272967 AGTAAAAA-TAAAAT
1 AGTAAAAATTAAAAT
*
272981 AGTAGAAATTAAAAT
1 AGTAAAAATTAAAAT
*
272996 ATTGAAAAATTAAAA
1 AGT-AAAAATTAAAA
273011 ATATTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 7 0.28
15 8 0.32
16 10 0.40
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (15 bp):
AGTAAAAATTAAAAT
Found at i:278217 original size:29 final size:31
Alignment explanation
Indices: 278152--278220 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
278142 TACAAAAATG
*
278152 GTCACTAAACTATTGACTTTGTTCTATTTCA
1 GTCACTAAACTATTGAATTTGTTCTATTTCA
* *
278183 ATCACTCAACTATT-AATTT-TTCTGATTT-A
1 GTCACTAAACTATTGAATTTGTTCT-ATTTCA
278212 GTCACTAAA
1 GTCACTAAA
278221 TTTTTTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 12 0.38
30 8 0.25
31 12 0.38
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.43
Consensus pattern (31 bp):
GTCACTAAACTATTGAATTTGTTCTATTTCA
Found at i:279898 original size:126 final size:125
Alignment explanation
Indices: 279667--280081 Score: 573
Period size: 126 Copynumber: 3.3 Consensus size: 125
279657 TAATTTAAAA
* * * * *
279667 AAGCTCCCACGTGAACACTCTTTTGCTACAATAGCTCCTGAAAAAATAACTTCGAGAAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCTTGAAAAAATAA-TTCGAGTAGACGTTT
279732 CT-AAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
65 CTGAA-CAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
* * * *
279793 AAGCTCCCATGTGGACCCGCTTTTGCTATAGTAGCTCTTGAAAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCTTGAAAAAATAA-TTCGAGTAGACGTTT
* * *
279858 CTGAACAAATAGTGTCAAAAACGCTTTAAACGGGACGCTTTGTCAGCAAAAGTACTGAAAG
65 CTGAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
* * * * * *
279919 AAGCTCCCACGTGGACGCGGTTTTGCTATAGTAACT-TCTAAAAAAATAATTCTGAGTAGACATT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCT-TGAAAAAATAATTC-GAGTAGACGTT
* * *
279983 TCTGAGCAAATAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGTAAAAGTACTGAAAG
64 TCTGAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
*
280045 AAGCTCCCACGTGGACGCACTTTTGCTACAATAGCTC
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTC
280082 CTGTTTGGCC
Statistics
Matches: 256, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
125 4 0.02
126 250 0.98
127 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (125 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCTTGAAAAAATAATTCGAGTAGACGTTTC
TGAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
Found at i:283474 original size:21 final size:21
Alignment explanation
Indices: 283450--283489 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
283440 TTGTCCAGCT
* * *
283450 TCCGGCGGGGGTTGTGGTTGC
1 TCCGACGGGGATTCTGGTTGC
283471 TCCGACGGGGATTCTGGTT
1 TCCGACGGGGATTCTGGTT
283490 CCACCGGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.20, G:0.45, T:0.30
Consensus pattern (21 bp):
TCCGACGGGGATTCTGGTTGC
Found at i:285640 original size:10 final size:10
Alignment explanation
Indices: 285601--285643 Score: 59
Period size: 10 Copynumber: 4.0 Consensus size: 10
285591 TAAAGCTTTT
285601 TTTGAGAGGAA
1 TTTGAGA-GAA
285612 TTTGAGAGAA
1 TTTGAGAGAA
285622 TATTGGAGAGAA
1 T-TT-GAGAGAA
285634 TTTGAGAGAA
1 TTTGAGAGAA
285644 AGGATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 11 0.37
11 11 0.37
12 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.28
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:286539 original size:16 final size:17
Alignment explanation
Indices: 286518--286552 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
286508 GGAGAAAGCT
286518 ATCACATTGTATT-GTG
1 ATCACATTGTATTGGTG
286534 ATCACATTGTATTGGTG
1 ATCACATTGTATTGGTG
286551 AT
1 AT
286553 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (17 bp):
ATCACATTGTATTGGTG
Found at i:291826 original size:16 final size:17
Alignment explanation
Indices: 291797--291828 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
291787 AAATTGTATT
291797 TATTAAATTAATTTTCC
1 TATTAAATTAATTTTCC
291814 TATTAAA-TAATTTTC
1 TATTAAATTAATTTTC
291829 TCAACCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTAAATTAATTTTCC
Found at i:295567 original size:34 final size:30
Alignment explanation
Indices: 295474--295577 Score: 136
Period size: 30 Copynumber: 3.3 Consensus size: 30
295464 ATCCAATGCT
*
295474 CAAATCAATTCTACAATATATATACATATA
1 CAAATCAATTCAACAATATATATACATATA
* **
295504 CAAATTAATTCGGCAATATATATACATATA
1 CAAATCAATTCAACAATATATATACATATA
295534 CAAATCAATTCAACAATATATATGTATACATATA
1 CAAATCAATTCAAC-A-ATATA--TATACATATA
295568 CAAATCAATT
1 CAAATCAATT
295578 TTAAAACATT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
30 38 0.59
31 1 0.02
32 5 0.08
34 20 0.31
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (30 bp):
CAAATCAATTCAACAATATATATACATATA
Found at i:297722 original size:16 final size:16
Alignment explanation
Indices: 297701--297731 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
297691 TTAATTTAAA
*
297701 TTAATTAATTAATTTC
1 TTAATTAAATAATTTC
297717 TTAATTAAATAATTT
1 TTAATTAAATAATTT
297732 TCTCAACTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATTAAATAATTTC
Found at i:305484 original size:7 final size:7
Alignment explanation
Indices: 305474--305499 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
305464 TAGCATTTTA
305474 TTTTATT
1 TTTTATT
305481 TTTTATT
1 TTTTATT
305488 TTTTATT
1 TTTTATT
305495 TTTTA
1 TTTTA
305500 ACCCACTTTT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:305701 original size:40 final size:38
Alignment explanation
Indices: 305599--305701 Score: 89
Period size: 40 Copynumber: 2.6 Consensus size: 38
305589 AAACATTTAA
* *
305599 TTAATTTTTTAAAATTTTAAAAATTAAAAAAAAATATTT
1 TTAATATTTT-AAATTTTAAAAAGTAAAAAAAAATATTT
* * ** *
305638 TTAAAAATAGAAATTATTAAAAAAGTATAAAAAAATATTTT
1 TTAATATTTTAAATT-TT-AAAAAGTAAAAAAAAATA-TTT
*
305679 TTAATGTTTTAAAGTTTTAAAAA
1 TTAATATTTTAAA-TTTTAAAAA
305702 TTAATTAAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
38 5 0.10
39 7 0.15
40 21 0.44
41 13 0.27
42 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (38 bp):
TTAATATTTTAAATTTTAAAAAGTAAAAAAAAATATTT
Found at i:308749 original size:2 final size:2
Alignment explanation
Indices: 308742--308800 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
308732 CTTAGTAGGA
* *
308742 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CC
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
308784 CT CT CC CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
308801 ATGTTTTGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:316980 original size:3 final size:3
Alignment explanation
Indices: 316960--317027 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
316950 AAATTAGTTA
* *
316960 AAT AAC AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
317008 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
317028 AGGATAGATT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:322922 original size:13 final size:13
Alignment explanation
Indices: 322906--322935 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
322896 TTTTTTTTTG
322906 TTTTTTTTACGGT
1 TTTTTTTTACGGT
*
322919 TTTTTTTTGCGGT
1 TTTTTTTTACGGT
322932 TTTT
1 TTTT
322936 GCTTTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.07, G:0.17, T:0.73
Consensus pattern (13 bp):
TTTTTTTTACGGT
Found at i:324619 original size:26 final size:25
Alignment explanation
Indices: 324568--324621 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
324558 ATTAACCTCT
* * * *
324568 TATAAAATATAAAGTTAGTTATATA
1 TATAAAATACAAAGTTAATCACATA
324593 TATAAATATACAAAGTTAATCACATA
1 TATAAA-ATACAAAGTTAATCACATA
324619 TAT
1 TAT
324622 GATAATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (25 bp):
TATAAAATACAAAGTTAATCACATA
Done.