Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009597.1 Hibiscus syriacus cultivar Beakdansim tig00116976_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1557931
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 7
Found at i:184 original size:21 final size:21
Alignment explanation
Indices: 158--214 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
148 TTTAACCTTG
* *
158 ATGCATCGGTGCACTATGGAT
1 ATGCATCGATGCACTATGAAT
179 ATGCATCGATGCACTATGAAT
1 ATGCATCGATGCACTATGAAT
200 ATGCATCGATGCACT
1 ATGCATCGATGCACT
215 CTACCCAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
ATGCATCGATGCACTATGAAT
Found at i:7497 original size:15 final size:15
Alignment explanation
Indices: 7477--7509 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
7467 CGTAGGACCC
7477 CTACATCCCGAAAGA
1 CTACATCCCGAAAGA
*
7492 CTACATCCCGAAGGA
1 CTACATCCCGAAAGA
7507 CTA
1 CTA
7510 TTATCCCTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.15, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAAGA
Found at i:7657 original size:23 final size:26
Alignment explanation
Indices: 7620--7688 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
7610 TTCTCTTGTG
7620 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
7644 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
7669 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
7689 AATATATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:7670 original size:12 final size:12
Alignment explanation
Indices: 7653--7688 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
7643 TATCATGTTC
7653 TCATATCACATG
1 TCATATCACATG
*
7665 TCATATCACATA
1 TCATATCACATG
7677 TCATATCACATG
1 TCATATCACATG
7689 AATATATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:8101 original size:63 final size:64
Alignment explanation
Indices: 7994--8213 Score: 232
Period size: 64 Copynumber: 3.5 Consensus size: 64
7984 TAATGAAAGT
* * ** * **
7994 ATGCATCGATGCACTACTAATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTA-TGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCATTATTAATGGG
* * **
8057 ATGTATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGGG
* * **
8121 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATG-TTTCATTATTAATGGG
**
8184 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
8214 ACACCTTCAA
Statistics
Matches: 133, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
62 2 0.02
63 46 0.35
64 79 0.59
65 6 0.05
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:23466 original size:31 final size:31
Alignment explanation
Indices: 23431--23507 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
23421 AGTTACATCG
*
23431 GGGACTATATTGTAAACAGACTAAATGTTGA
1 GGGACTATATTGCAAACAGACTAAATGTTGA
* * *
23462 GGGACCATATTGCAAACGGACTAAATGTTGG
1 GGGACTATATTGCAAACAGACTAAATGTTGA
*
23493 GGGATTATATTGCAA
1 GGGACTATATTGCAA
23508 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (31 bp):
GGGACTATATTGCAAACAGACTAAATGTTGA
Found at i:23765 original size:16 final size:18
Alignment explanation
Indices: 23737--23771 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
23727 TTCTAAATTA
23737 TGATTTAAATTA-TAAAT
1 TGATTTAAATTATTAAAT
23754 TGATTT-AATTATTAAAT
1 TGATTTAAATTATTAAAT
23771 T
1 T
23772 TTATGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TGATTTAAATTATTAAAT
Found at i:25183 original size:29 final size:29
Alignment explanation
Indices: 25140--25222 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
25130 CTCACCTAAC
25140 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
25170 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
25199 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
25223 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:29949 original size:29 final size:29
Alignment explanation
Indices: 29906--29988 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
29896 CTCACCTAAC
29906 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
29936 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
29965 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
29989 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:34715 original size:24 final size:24
Alignment explanation
Indices: 34686--34743 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
34676 AAAAATTTAA
34686 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAACTCGAGACTC
34710 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAACTCGAGACTC
34734 GAGCTCGATT
1 GAGCTCGATT
34744 GAAGCTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (24 bp):
GAGCTCGATTAAAACTCGAGACTC
Found at i:34763 original size:12 final size:12
Alignment explanation
Indices: 34746--34790 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
34736 GCTCGATTGA
34746 AGCTCAATTCTG
1 AGCTCAATTCTG
*
34758 AGCTCAATTC-A
1 AGCTCAATTCTG
*
34769 AGCTCGATTCTG
1 AGCTCAATTCTG
34781 AGCTCAATTC
1 AGCTCAATTC
34791 AAGCTCGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (12 bp):
AGCTCAATTCTG
Found at i:34771 original size:23 final size:23
Alignment explanation
Indices: 34734--34801 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
34724 CTCGAGACTC
* * *
34734 GAGCTCGATTGAAGCTCAATTCT
1 GAGCTCAATTCAAGCTCGATTCT
34757 GAGCTCAATTCAAGCTCGATTCT
1 GAGCTCAATTCAAGCTCGATTCT
34780 GAGCTCAATTCAAGCTCGATTC
1 GAGCTCAATTCAAGCTCGATTC
34802 AAGCTCGACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (23 bp):
GAGCTCAATTCAAGCTCGATTCT
Found at i:34778 original size:11 final size:11
Alignment explanation
Indices: 34735--34809 Score: 78
Period size: 11 Copynumber: 6.6 Consensus size: 11
34725 TCGAGACTCG
*
34735 AGCTCGATTGA
1 AGCTCGATTCA
* *
34746 AGCTCAATTCTG
1 AGCTCGATTC-A
*
34758 AGCTCAATTCA
1 AGCTCGATTCA
*
34769 AGCTCGATTCTG
1 AGCTCGATTC-A
*
34781 AGCTCAATTCA
1 AGCTCGATTCA
34792 AGCTCGATTCA
1 AGCTCGATTCA
34803 AGCTCGA
1 AGCTCGA
34810 CATTGCCCCA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
11 34 0.64
12 19 0.36
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:35347 original size:14 final size:14
Alignment explanation
Indices: 35330--35372 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
35320 GAACATAAAT
*
35330 GAACATAACCGAAC
1 GAACATAAACGAAC
35344 GAACATAAACGAAC
1 GAACATAAACGAAC
*
35358 GAACATAATCGAAC
1 GAACATAAACGAAC
35372 G
1 G
35373 TTCACGAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.09
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:50630 original size:178 final size:176
Alignment explanation
Indices: 50277--50785 Score: 511
Period size: 180 Copynumber: 2.8 Consensus size: 176
50267 TCCCTTTTTT
* * ** *
50277 ACACTAAAAGGGGCAGTTCACCGGAGAGCTCTACAAATAAAGCTCTCTGAATTCAA-AACAAAAG
1 ACACTAAAAGAGGCAGTTCAGCGGAGAATTCTACAAATAAAGCTCTCTGAATT-AAGAATAAAAG
** *
50341 AAATAATAACAAAGAAATTGGGAAAAGATTCATCTTTTACTTCATAAGCTACAAAATTACACTAA
65 AAATAATAA-AAA-AAAGAGGGAAAAGATTCA----TT--TTC-TAA-CTTCAAAATTACAC-AA
* * * * * ** **
50406 ATCCATCATTAGATTCACCACAAAGTTCCAAGACAGATGTGTCTTTCATCCTTTTTTCC
119 ACCCATCACTAAATTCACCACAAAGTACCAAAACAGATAAGTCTTTCATCCTACTTT-C
* ** *
50465 ATACTAAAAGAGGCAGTTCAGCAAAGAATTCTACAAATAAAGCTCTCTTAATTAAGAATAAAAGA
1 ACACTAAAAGAGGCAGTTCAGCGGAGAATTCTACAAATAAAGCTCTCTGAATTAAGAATAAAAGA
* * *
50530 AATAGTAAAAAAAAGGGGGAAAAGATTCATTTTCTAACTTCAAAATTTCAGCAAACCCATCACTA
66 AATAATAAAAAAAAGAGGGAAAAGATTCATTTTCTAACTTCAAAATTACA-CAAACCCATCACTA
50595 AATTCACCACAAAGTACCAAAACAGATAAGTCTTTCATCCTACTTTC
130 AATTCACCACAAAGTACCAAAACAGATAAGTCTTTCATCCTACTTTC
* * * * * * *
50642 ACACTAAAACATGCAATCCAGCGGAGAATTCTACGAATAAAG-TCCTCTGAATTCAGAATAAAGG
1 ACACTAAAAGAGGCAGTTCAGCGGAGAATTCTACAAATAAAGCT-CTCTGAATTAAGAATAAAAG
* *
50706 AAATAATAACAAAAAAAAGAGGGAAAAGATAT-ATTTTTTTACTTCAAAATTACAACAAACCCAT
65 AAATAAT---AAAAAAAAGAGGGAAAAGAT-TCATTTTCTAACTTCAAAATTAC-ACAAACCCAT
*
50770 CACTGAATTCACCACA
125 CACTAAATTCACCACA
50786 GAGTTTCAAT
Statistics
Matches: 273, Mismatches: 40, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
176 1 0.00
177 58 0.21
178 61 0.22
179 4 0.01
180 64 0.23
181 2 0.01
182 2 0.01
186 16 0.06
187 5 0.02
188 60 0.22
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (176 bp):
ACACTAAAAGAGGCAGTTCAGCGGAGAATTCTACAAATAAAGCTCTCTGAATTAAGAATAAAAGA
AATAATAAAAAAAAGAGGGAAAAGATTCATTTTCTAACTTCAAAATTACACAAACCCATCACTAA
ATTCACCACAAAGTACCAAAACAGATAAGTCTTTCATCCTACTTTC
Found at i:51027 original size:219 final size:210
Alignment explanation
Indices: 50638--51047 Score: 527
Period size: 219 Copynumber: 1.9 Consensus size: 210
50628 TTCATCCTAC
* * * *
50638 TTTCACACTAAAACATGCAATCCAGCGGAGAATTCTACGAATAAAGTCCTCTGAATTCAGAATAA
1 TTTCACAATAAAACAGGCAATCCAGCAGAGAATTCTACAAATAAAGTCCTCTGAATTCAGAATAA
50703 AGGAAATAATAACAAAAAAAAGAGGGAAAAGATATATTTTTTTACTTCAAAATTACAACAAACCC
66 AGGAAATAATAACAAAAAAAAGAGGGAAAAGATATATTTTTTTACTTCAAAATTACAACAAACCC
* * * *
50768 ATCACTGAATTCACCACAGAGTTTCAATATAAAGCTCTATAAACAGCATAACAATAAAAAATATT
131 ATCACTAAATTCACCAAAAAGTTTCAATATAAACCTCTATAAACAGCATAACAATAAAAAATATT
50833 TTTCTTTCATCAATT
196 TTTCTTTCATCAATT
* * *
50848 TTTCACAATATAACAGGCAATTCAGCAGAG-ATTCTACAAATAAAG-CTCTCTGAATTCGGAATA
1 TTTCACAATAAAACAGGCAATCCAGCAGAGAATTCTACAAATAAAGTC-CTCTGAATTCAGAATA
* * * * *
50911 AAGGAAGTAGTAACAAGAAAAAGAGGGAAAAGATCCAATTTTTTTACTCCACTAACTTCAAATTT
65 AAGGAAATAATAACAAAAAAAAGAGGGAAAAGAT---ATATTTTT--T----T-ACTTCAAAATT
* * * *
50976 TCAACAAACCCATCACTAAATTCACCAAAAAGTTTCAATATAATCCTCTATAAACATCATATCAA
120 ACAACAAACCCATCACTAAATTCACCAAAAAGTTTCAATATAAACCTCTATAAACAGCATAACAA
51041 TAAAAAA
185 TAAAAAA
51048 GACGACCCTT
Statistics
Matches: 169, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
208 1 0.01
209 60 0.36
210 25 0.15
212 7 0.04
214 1 0.01
218 1 0.01
219 74 0.44
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (210 bp):
TTTCACAATAAAACAGGCAATCCAGCAGAGAATTCTACAAATAAAGTCCTCTGAATTCAGAATAA
AGGAAATAATAACAAAAAAAAGAGGGAAAAGATATATTTTTTTACTTCAAAATTACAACAAACCC
ATCACTAAATTCACCAAAAAGTTTCAATATAAACCTCTATAAACAGCATAACAATAAAAAATATT
TTTCTTTCATCAATT
Found at i:61451 original size:47 final size:47
Alignment explanation
Indices: 61400--61497 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
61390 ACCTATTGAG
61400 TTGAGTGTATAAGTGGTAAAAGTGAATGTTATTTTCTTTATAGGACT
1 TTGAGTGTATAAGTGGTAAAAGTGAATGTTATTTTCTTTATAGGACT
61447 TTGAGTGTATAAGTGGTAAAAGTGAATGTTATTTTCTTTATAGGACT
1 TTGAGTGTATAAGTGGTAAAAGTGAATGTTATTTTCTTTATAGGACT
61494 TTGA
1 TTGA
61498 TTCAAATAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.43
Consensus pattern (47 bp):
TTGAGTGTATAAGTGGTAAAAGTGAATGTTATTTTCTTTATAGGACT
Found at i:63329 original size:24 final size:23
Alignment explanation
Indices: 63302--63347 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
63292 GTGCTTACTT
63302 AACAAAATATAAT-TAATATAAAAA
1 AACAAAAT-TAATATAAT-TAAAAA
63326 AACAAAATTAATATAATTAAAA
1 AACAAAATTAATATAATTAAAA
63348 TACATACTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (23 bp):
AACAAAATTAATATAATTAAAAA
Found at i:69481 original size:16 final size:16
Alignment explanation
Indices: 69457--69489 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
69447 TATCGCCGAC
*
69457 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
69473 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
69489 C
1 C
69490 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:72343 original size:10 final size:10
Alignment explanation
Indices: 72328--72384 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
72318 CACTTTTTAA
72328 AAAAATCAAT
1 AAAAATCAAT
72338 AAAAATGCAAT
1 AAAAAT-CAAT
**
72349 AAAAAGGAATT
1 AAAAATCAA-T
* *
72360 AAAAGTGAAT
1 AAAAATCAAT
*
72370 AAAATTCAAT
1 AAAAATCAAT
72380 AAAAA
1 AAAAA
72385 CGTCAACTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 21 0.55
11 17 0.45
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (10 bp):
AAAAATCAAT
Found at i:72348 original size:11 final size:11
Alignment explanation
Indices: 72328--72384 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
72318 CACTTTTTAA
72328 AAAAAT-CAAT
1 AAAAATGCAAT
72338 AAAAATGCAAT
1 AAAAATGCAAT
*
72349 AAAAA-GGAATT
1 AAAAATGCAA-T
*
72360 AAAAGTG-AAT
1 AAAAATGCAAT
*
72370 -AAAATTCAAT
1 AAAAATGCAAT
72380 AAAAA
1 AAAAA
72385 CGTCAACTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
9 4 0.11
10 13 0.34
11 20 0.53
12 1 0.03
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (11 bp):
AAAAATGCAAT
Found at i:72353 original size:21 final size:20
Alignment explanation
Indices: 72328--72384 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
72318 CACTTTTTAA
72328 AAAAATCAATAAAAATGCAAT
1 AAAAATCAATAAAAATG-AAT
** *
72349 AAAAAGGAATTAAAAGTGAAT
1 AAAAATCAA-TAAAAATGAAT
*
72370 AAAATTCAATAAAAA
1 AAAAATCAATAAAAA
72385 CGTCAACTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 5 0.18
21 16 0.57
22 7 0.25
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (20 bp):
AAAAATCAATAAAAATGAAT
Found at i:72564 original size:21 final size:21
Alignment explanation
Indices: 72538--72596 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
72528 TTCATTTTTT
*
72538 TAAAAATCAATAAAAATTCAA
1 TAAAAATCAATAAAAAGTCAA
** * *
72559 TAAAAAAGAATTAAAAGTGAA
1 TAAAAATCAATAAAAAGTCAA
*
72580 TAAAATTCAATACAAAA
1 TAAAAATCAATA-AAAA
72597 AACATATAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (21 bp):
TAAAAATCAATAAAAAGTCAA
Found at i:78233 original size:2 final size:2
Alignment explanation
Indices: 78226--78257 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
78216 GGAGAGGCAC
78226 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
78258 CGACAACTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:79409 original size:93 final size:93
Alignment explanation
Indices: 79250--79435 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
79240 AAATGAGCTT
79250 GGTTTTGATATTAATGATTCATTCATATTCTTACATCCATGCTTGTCTCTATCTTTCAGGTGATC
1 GGTTTTGATATTAATGATTCATTCATATTCTTACATCCATGCTTGTCTCTATCTTTCAGGTGATC
79315 ATTTAGTTGGTGCAAAGAGTTAACTATC
66 ATTTAGTTGGTGCAAAGAGTTAACTATC
79343 GGTTTTGATATTAATGATTCATTCATATTCTTACATCCATGCTTGTCTCTATCTTTCAGGTGATC
1 GGTTTTGATATTAATGATTCATTCATATTCTTACATCCATGCTTGTCTCTATCTTTCAGGTGATC
79408 ATTTAGTTGGTGCAAAGAGTTAACTATC
66 ATTTAGTTGGTGCAAAGAGTTAACTATC
79436 TAATGTGTTT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (93 bp):
GGTTTTGATATTAATGATTCATTCATATTCTTACATCCATGCTTGTCTCTATCTTTCAGGTGATC
ATTTAGTTGGTGCAAAGAGTTAACTATC
Found at i:81445 original size:141 final size:141
Alignment explanation
Indices: 81191--81475 Score: 552
Period size: 141 Copynumber: 2.0 Consensus size: 141
81181 ATCAAGTATA
81191 TCCTTACGCTTTGCTTGGTGCATGCTTGCTAGGAAAGATATAAATGGGCAATGTCAGAAAAGTGT
1 TCCTTACGCTTTGCTTGGTGCATGCTTGCTAGGAAAGATATAAATGGGCAATGTCAGAAAAGTGT
*
81256 TTAATCCAACAGTTAAGCTACATGTTTGAAAGTGGTTACGAAACCTAATTATTAGATTAAAGTTT
66 TTAATCAAACAGTTAAGCTACATGTTTGAAAGTGGTTACGAAACCTAATTATTAGATTAAAGTTT
81321 CCTTTCTTCAT
131 CCTTTCTTCAT
*
81332 TCCTTAGGCTTTGCTTGGTGCATGCTTGCTAGGAAAGATATAAATGGGCAATGTCAGAAAAGTGT
1 TCCTTACGCTTTGCTTGGTGCATGCTTGCTAGGAAAGATATAAATGGGCAATGTCAGAAAAGTGT
81397 TTAATCAAACAGTTAAGCTACATGTTTGAAAGTGGTTACGAAACCTAATTATTAGATTAAAGTTT
66 TTAATCAAACAGTTAAGCTACATGTTTGAAAGTGGTTACGAAACCTAATTATTAGATTAAAGTTT
81462 CCTTTCTTCAT
131 CCTTTCTTCAT
81473 TCC
1 TCC
81476 ACTATATCTT
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 142 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (141 bp):
TCCTTACGCTTTGCTTGGTGCATGCTTGCTAGGAAAGATATAAATGGGCAATGTCAGAAAAGTGT
TTAATCAAACAGTTAAGCTACATGTTTGAAAGTGGTTACGAAACCTAATTATTAGATTAAAGTTT
CCTTTCTTCAT
Found at i:86285 original size:16 final size:16
Alignment explanation
Indices: 86264--86299 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
86254 ATGATGTCTA
86264 AAAATAGA-TATAATTT
1 AAAATAGATTAT-ATTT
86280 AAAATAGATTATATTT
1 AAAATAGATTATATTT
86296 AAAA
1 AAAA
86300 AATTAACGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
AAAATAGATTATATTT
Found at i:93413 original size:14 final size:15
Alignment explanation
Indices: 93378--93421 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
93368 GTTTTTTTAG
93378 ATTTTTATAATTAAAT
1 ATTTTTAT-ATTAAAT
93394 ATTTTTATATTAAA-
1 ATTTTTATATTAAAT
93408 ATTTTTAT-TTAAAT
1 ATTTTTATATTAAAT
93422 TCGACCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 8 0.30
15 6 0.22
16 8 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTATATTAAAT
Found at i:96037 original size:17 final size:17
Alignment explanation
Indices: 96015--96049 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
96005 AAAAACGGTG
96015 CCATGTGTACCGAAAGC
1 CCATGTGTACCGAAAGC
96032 CCATGTGTACCGAAAGC
1 CCATGTGTACCGAAAGC
96049 C
1 C
96050 TGCATTAAAT
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:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (17 bp):
CCATGTGTACCGAAAGC
Found at i:99818 original size:24 final size:25
Alignment explanation
Indices: 99758--99818 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
99748 TTGGGCTGGG
99758 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
99781 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
99805 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
99819 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:99878 original size:13 final size:12
Alignment explanation
Indices: 99847--99880 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
99837 TTTTAATATT
*
99847 TATCGGGTCGGG
1 TATCGGGGCGGG
99859 TATCGGGGCGGG
1 TATCGGGGCGGG
99871 TAATCGGGGC
1 T-ATCGGGGC
99881 AGGGATTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.12, C:0.18, G:0.50, T:0.21
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:111182 original size:2 final size:2
Alignment explanation
Indices: 111175--111212 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
111165 TCGTTGTGGC
111175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
111213 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:121703 original size:14 final size:15
Alignment explanation
Indices: 121669--121737 Score: 50
Period size: 16 Copynumber: 4.3 Consensus size: 15
121659 ATAGTTATTA
121669 TATTTTATATTAATAT
1 TATTTTATA-TAATAT
*
121685 AATTTTATA-AATAT
1 TATTTTATATAATAT
* *
121699 TATTTTTTTATTAAAAT
1 TA-TTTTATA-TAATAT
*
121716 AATATTTATATAATTAT
1 TAT-TTTATATAA-TAT
121733 TATTT
1 TATTT
121738 ATTTAAATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
14 6 0.15
15 6 0.15
16 14 0.35
17 14 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTATATAATAT
Found at i:121718 original size:31 final size:34
Alignment explanation
Indices: 121663--121742 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 34
121653 TTTAAAATAG
* *
121663 TTATTATATTTTATATTAATATAAT-TTTATA-AA
1 TTATTAT-TTTTTTATTAAAATAATATTTATATAA
121696 -TATTATTTTTTTATTAAAATAATATTTATATAA
1 TTATTATTTTTTTATTAAAATAATATTTATATAA
*
121729 TTATTATTTATTTA
1 TTATTATTTTTTTA
121743 AATTTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 15 0.37
32 12 0.29
33 2 0.05
34 12 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TTATTATTTTTTTATTAAAATAATATTTATATAA
Found at i:121924 original size:17 final size:16
Alignment explanation
Indices: 121903--121941 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
121893 TTGTTATGTT
*
121903 TAATTTAAATTTATTA
1 TAATTTAAATTAATTA
*
121919 TGAATTTATATTAATTA
1 T-AATTTAAATTAATTA
121936 TAATTT
1 TAATTT
121942 TTTATAATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TAATTTAAATTAATTA
Found at i:123489 original size:42 final size:42
Alignment explanation
Indices: 123392--123494 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 42
123382 GCCACAGTGG
* * *
123392 TACATGCCCAA-CCCTCCACTTCAGATGTCATATCCTCAGGGA
1 TACATG-CCAAGCCCACCAGTTCAGATGTCATATCCGCAGGGA
* * * *
123434 TATATGCCAAGCCCACCAGTTCATATGTCATCTCCGCAGGGT
1 TACATGCCAAGCCCACCAGTTCAGATGTCATATCCGCAGGGA
* * *
123476 TACATTCCTAGCCCGCCAG
1 TACATGCCAAGCCCACCAG
123495 GTTACATGCC
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (42 bp):
TACATGCCAAGCCCACCAGTTCAGATGTCATATCCGCAGGGA
Found at i:123518 original size:21 final size:21
Alignment explanation
Indices: 123467--123518 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
123457 TATGTCATCT
*
123467 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
123488 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
123509 CCGCAGGGTT
1 CCGCAGGGTT
123519 TTATACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:124082 original size:34 final size:34
Alignment explanation
Indices: 124039--124145 Score: 178
Period size: 34 Copynumber: 3.1 Consensus size: 34
124029 ATAAATGTTT
124039 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* *
124073 TTAAAATACAAATAATATTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* *
124107 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
124141 TTAAA
1 TTAAA
124146 TTCAACTTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 67 1.00
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:124993 original size:127 final size:126
Alignment explanation
Indices: 124568--125072 Score: 818
Period size: 127 Copynumber: 4.0 Consensus size: 126
124558 GCGCTTTAAA
* ** * *
124568 GTCCCCTAAGAAATAGTAGGTATTGACATGAATAGTTATCGGGGGATATAAGTGACATAACAGGG
1 GTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
*
124633 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAATGTGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC-CCCCCGGGAACGTGCCTTCACG
* *
124695 G-CCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATATG
1 GTCCCC-TAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGG
* *
124759 ACAATGATAACATATTCTCTGACAAAATAATGGAAGGCG-CCCCCGGGAACGCGCCTTCACG
65 GCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGTGCCTTCACG
* *
124820 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGAGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
124885 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCCGGGAACGTGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCG-CCCCCCGGGAACGTGCCTTCACG
*
124947 GTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTAACATAATAGGG
1 GTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* *
125012 TAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCCCCGGGAAC-TCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGT-GCCTTCACG
125073 CGAATAGTAC
Statistics
Matches: 354, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
125 116 0.33
126 29 0.08
127 209 0.59
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (126 bp):
GTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGTGCCTTCACG
Found at i:125019 original size:252 final size:253
Alignment explanation
Indices: 124568--125072 Score: 843
Period size: 252 Copynumber: 2.0 Consensus size: 253
124558 GCGCTTTAAA
* * * *
124568 GTCCCCTAAGAAATAGTAGGTATTGACATGAATAGTTATCGGGGGATATAAGTGACATAACAGGG
1 GTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTACCGAGGGACATAAGTGACATAACAGGG
* *
124633 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAATGTGCCTTCACGGCC
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCCGGGAACGTGCCTTCACGGCC
* * *
124698 CCTTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATATGACAA
131 CCTTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTAACATAATAGGACAA
124763 TGATAACATATTCTCTGACAAAATAATGGAAGGCG-CCCCCGGGAACGCGCCTTCACG
196 TGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCACG
* * *
124820 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGAGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTACCGAGGGACATAAGTGACATAACAGGG
124885 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCCGGGAACGTGCCTTCACGGTC
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCCGGGAACGTGCCTTCACGG-C
**
124950 CCC-TAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTAACATAATAGGGTA
130 CCCTTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTAACATAATAGGACA
* *
125014 ATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCCCCGGGAACTCGCCTTCACG
195 ATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCACG
125073 CGAATAGTAC
Statistics
Matches: 235, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
252 210 0.89
253 25 0.11
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (253 bp):
GTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTACCGAGGGACATAAGTGACATAACAGGG
CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCCGGGAACGTGCCTTCACGGCC
CCTTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTAACATAATAGGACAA
TGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCACG
Found at i:128524 original size:24 final size:23
Alignment explanation
Indices: 128497--128542 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
128487 ATATATTACT
128497 AATTTATAATAATAATAAAAATAA
1 AATTTATAATAATAA-AAAAATAA
* * *
128521 AATTTTTATTATTAAAAAAATA
1 AATTTATAATAATAAAAAAATA
128543 TCATCGTGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AATTTATAATAATAAAAAAATAA
Found at i:132169 original size:29 final size:29
Alignment explanation
Indices: 132136--132194 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
132126 AGCATCCACA
132136 TTATTAAAAAGAGTATCTCTTATGATGAT
1 TTATTAAAAAGAGTATCTCTTATGATGAT
* *
132165 TTATTAAATAGAGTATCTCTTATGCTGAT
1 TTATTAAAAAGAGTATCTCTTATGATGAT
132194 T
1 T
132195 ATCATACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (29 bp):
TTATTAAAAAGAGTATCTCTTATGATGAT
Found at i:133814 original size:22 final size:22
Alignment explanation
Indices: 133773--133853 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
133763 CTCGTATAAA
133773 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
133796 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
133818 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
133840 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
133854 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:133849 original size:13 final size:13
Alignment explanation
Indices: 133787--133849 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
133777 CCGAAGTGCC
133787 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
133800 CC---GAAGTGC-
1 CCGTAGAATTGCA
133809 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
133822 CC---GAAGTGC-
1 CCGTAGAATTGCA
133831 CCGTAGAATTGCA
1 CCGTAGAATTGCA
133844 CCGTAG
1 CCGTAG
133850 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:134099 original size:30 final size:30
Alignment explanation
Indices: 134064--134140 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
134054 CCGTAGTTCA
* * *
134064 TATCACGTAGTCATATTATTTCCATACCTT
1 TATCACATAGTCATATCATTTACATACCTT
134094 TATCACATAGTCATATCATTTACATACCTT
1 TATCACATAGTCATATCATTTACATACCTT
134124 TATCACATAGCTCATAT
1 TATCACATAG-TCATAT
134141 AACTTTTCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.40
Consensus pattern (30 bp):
TATCACATAGTCATATCATTTACATACCTT
Found at i:134224 original size:29 final size:29
Alignment explanation
Indices: 134154--134225 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
134144 TTTTCTGCAT
* * *
134154 ATTCATGTCATGCAATACATATCATATGA
1 ATTCATGTCATGTAATACATATAATATAA
*
134183 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACATATAATATAA
134212 ATTCATGTCATGTA
1 ATTCATGTCATGTA
134226 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATAA
Found at i:134678 original size:67 final size:68
Alignment explanation
Indices: 134529--134679 Score: 232
Period size: 68 Copynumber: 2.2 Consensus size: 68
134519 TTTTCTCATG
* *
134529 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGAT
*
134594 GAG
66 GAA
* * *
134597 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGAT
134661 GAA
66 GAA
*
134664 GGGGTATCGATTCCCC
1 GGGGTATCGGTTCCCC
134680 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
67 26 0.34
68 50 0.66
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (68 bp):
GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGAT
GAA
Found at i:134683 original size:21 final size:21
Alignment explanation
Indices: 134659--134701 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
134649 ATCATATTCG
*
134659 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
134680 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
134701 T
1 T
134702 AGCCCGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:140785 original size:22 final size:22
Alignment explanation
Indices: 140744--140824 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
140734 CTCGTATAAA
140744 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
140767 TGCACCGAAATGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
140789 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
140811 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
140825 ATATAATGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 44 0.80
23 11 0.20
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:140820 original size:13 final size:13
Alignment explanation
Indices: 140758--140820 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
140748 CCGAAGTGCC
140758 CCGTAGAATTGCA
1 CCGTAGAATTGCA
140771 CCG-A-AA-TGC-
1 CCGTAGAATTGCA
140780 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
140793 CC---GAAGTGC-
1 CCGTAGAATTGCA
140802 CCGTAGAATTGCA
1 CCGTAGAATTGCA
140815 CCGTAG
1 CCGTAG
140821 TGCCATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 5 0.12
10 10 0.25
11 4 0.10
12 10 0.25
13 11 0.28
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:141070 original size:30 final size:30
Alignment explanation
Indices: 141035--141111 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
141025 CCGTAGTTCA
* * *
141035 TATCACGTAGTCATATTATTTCCATACCTT
1 TATCACATAGTCATATCATTTACATACCTT
141065 TATCACATAGTCATATCATTTACATACCTT
1 TATCACATAGTCATATCATTTACATACCTT
141095 TATCACATAGCTCATAT
1 TATCACATAG-TCATAT
141112 AACTTTTCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.40
Consensus pattern (30 bp):
TATCACATAGTCATATCATTTACATACCTT
Found at i:141195 original size:29 final size:29
Alignment explanation
Indices: 141125--141196 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
141115 TTTTCTGCAT
* * *
141125 ATTCATGTCATGCAATACATATCATATGA
1 ATTCATGTCATGTAATACATATAATATAA
*
141154 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACATATAATATAA
141183 ATTCATGTCATGTA
1 ATTCATGTCATGTA
141197 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATAA
Found at i:141620 original size:67 final size:68
Alignment explanation
Indices: 141475--141625 Score: 241
Period size: 68 Copynumber: 2.2 Consensus size: 68
141465 TTTTCTCATG
* *
141475 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGAT
*
141540 GAG
66 GAA
* * *
141543 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGAT
141607 GAA
66 GAA
141610 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
141626 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 27 0.35
68 50 0.65
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (68 bp):
GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGAT
GAA
Found at i:141635 original size:21 final size:21
Alignment explanation
Indices: 141605--141647 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
141595 ATCATATTCG
* *
141605 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
141626 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
141647 T
1 T
141648 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:143525 original size:33 final size:33
Alignment explanation
Indices: 143488--143550 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
143478 CGCAGAGGAT
143488 GCATCCACCGCATCTGATGCAGCAGACCTTGGA
1 GCATCCACCGCATCTGATGCAGCAGACCTTGGA
** *
143521 GCATCCACCGGGTCTGTTGCAGCAGACCTT
1 GCATCCACCGCATCTGATGCAGCAGACCTT
143551 CGATGTCGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.21, C:0.33, G:0.25, T:0.21
Consensus pattern (33 bp):
GCATCCACCGCATCTGATGCAGCAGACCTTGGA
Found at i:143876 original size:20 final size:19
Alignment explanation
Indices: 143851--143888 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
143841 GGAGTAAGGT
143851 GGCGGACGACTGACGGAGGC
1 GGCGGACGAC-GACGGAGGC
*
143871 GGCGGATGACGACGGAGG
1 GGCGGACGACGACGGAGG
143889 ACAATGGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.21, C:0.21, G:0.53, T:0.05
Consensus pattern (19 bp):
GGCGGACGACGACGGAGGC
Found at i:149367 original size:2 final size:2
Alignment explanation
Indices: 149360--149387 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
149350 ACAAATACAA
149360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
149388 GCATCAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:150660 original size:2 final size:2
Alignment explanation
Indices: 150653--150707 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
150643 ACGCATAATG
150653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
150695 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
150708 ATTGAACTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:153498 original size:49 final size:48
Alignment explanation
Indices: 153445--153566 Score: 138
Period size: 49 Copynumber: 2.5 Consensus size: 48
153435 AGATACTCAG
* * *
153445 GTATAACGCGGATCAGGGGCGCACTATACCTACGTGGCGCCAGATCACC
1 GTATAACGCGGATCAGGGGCGCACTATACCCACATGGCGCCAAATCA-C
* **
153494 GTATATCGCGGGGCAGGGG-GCACCTATACCCACATGGCGCCAAATCAC
1 GTATAACGCGGATCAGGGGCGCA-CTATACCCACATGGCGCCAAATCAC
* * *
153542 GTATAACGCAGTTCAAGGGCGCACT
1 GTATAACGCGGATCAGGGGCGCACT
153567 TTACTGCTAC
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
48 20 0.33
49 40 0.67
ACGTcount: A:0.25, C:0.30, G:0.29, T:0.16
Consensus pattern (48 bp):
GTATAACGCGGATCAGGGGCGCACTATACCCACATGGCGCCAAATCAC
Found at i:155692 original size:16 final size:16
Alignment explanation
Indices: 155671--155703 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
155661 ACAGAATAAT
155671 CTGGTCCAACCCAGAC
1 CTGGTCCAACCCAGAC
155687 CTGGTCCAACCCAGAC
1 CTGGTCCAACCCAGAC
155703 C
1 C
155704 CAAAGCACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.12
Consensus pattern (16 bp):
CTGGTCCAACCCAGAC
Found at i:157716 original size:19 final size:19
Alignment explanation
Indices: 157692--157733 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
157682 TTTCGATCCT
157692 TATTGCTTACTTTTGATTA
1 TATTGCTTACTTTTGATTA
157711 TATTGCTTACTTTTGATTA
1 TATTGCTTACTTTTGATTA
157730 TATT
1 TATT
157734 TTCGAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.60
Consensus pattern (19 bp):
TATTGCTTACTTTTGATTA
Found at i:159670 original size:11 final size:11
Alignment explanation
Indices: 159653--159683 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
159643 AAGAAAAAAG
159653 AGAAAAAACAAA
1 AGAAAAAAC-AA
159665 AGAAAAAACAA
1 AGAAAAAACAA
159676 AGAAAAAA
1 AGAAAAAA
159684 TAAAAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (11 bp):
AGAAAAAACAA
Found at i:159670 original size:12 final size:12
Alignment explanation
Indices: 159653--159688 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
159643 AAGAAAAAAG
159653 AGAAAAAACAAA
1 AGAAAAAACAAA
159665 AGAAAAAAC-AA
1 AGAAAAAACAAA
*
159676 AGAAAAAATAAA
1 AGAAAAAACAAA
159688 A
1 A
159689 AGAGAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.83, C:0.06, G:0.08, T:0.03
Consensus pattern (12 bp):
AGAAAAAACAAA
Found at i:159681 original size:21 final size:21
Alignment explanation
Indices: 159641--159688 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
159631 AATCAGAACA
*
159641 AAAAGAAAAAAGAGAAAAAAC
1 AAAAGAAAAAACAGAAAAAAC
*
159662 AAAAGAAAAAACAAAGAAAAAAT
1 AAAAGAAAAAAC--AGAAAAAAC
159685 AAAA
1 AAAA
159689 AGAGAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
23 12 0.52
ACGTcount: A:0.83, C:0.04, G:0.10, T:0.02
Consensus pattern (21 bp):
AAAAGAAAAAACAGAAAAAAC
Found at i:159689 original size:29 final size:29
Alignment explanation
Indices: 159656--159712 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
159646 AAAAAAGAGA
159656 AAAAACA-AAAGAAAAAACAAAGAAAAAAT
1 AAAAACAGAAA-AAAAAACAAAGAAAAAAT
* * *
159685 AAAAAGAGAAACAAAAACAAAGGAAAAA
1 AAAAACAGAAAAAAAAACAAAGAAAAAA
159713 GTGAAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.02
Consensus pattern (29 bp):
AAAAACAGAAAAAAAAACAAAGAAAAAAT
Found at i:159701 original size:30 final size:32
Alignment explanation
Indices: 159667--159729 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
159657 AAAACAAAAG
159667 AAAAAACAAA-GAAAAAAT-AAAAAGAGAA-AC
1 AAAAAACAAAGGAAAAAATGAAAAA-AGAAGAC
*
159697 -AAAAACAAAGGAAAAAGTGAAAAAAGAAGAC
1 AAAAAACAAAGGAAAAAATGAAAAAAGAAGAC
159728 AA
1 AA
159730 GACGCATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
29 9 0.32
30 11 0.39
31 7 0.25
32 1 0.04
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.03
Consensus pattern (32 bp):
AAAAAACAAAGGAAAAAATGAAAAAAGAAGAC
Found at i:161576 original size:23 final size:23
Alignment explanation
Indices: 161517--161580 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
161507 AGCTCGTATA
*
161517 AAATGCA-TCGAAGTACCACGTAG
1 AAATGCACT-GAAGTGCCACGTAG
* *
161540 AATTGCACCT-AAGTGCCGCGTAG
1 AAATGCA-CTGAAGTGCCACGTAG
161563 AAATGCACTGAAGTGCCA
1 AAATGCACTGAAGTGCCA
161581 TATAAGATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 2 0.06
23 30 0.91
25 1 0.03
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (23 bp):
AAATGCACTGAAGTGCCACGTAG
Found at i:163269 original size:64 final size:64
Alignment explanation
Indices: 163160--163281 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
163150 ACATTCTACA
* *
163160 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
** * **
163224 GTGCATCGATGCACT-CTTTATGCATCGATACACTAATTGCATTCGATGTTTCCATTTT
1 GTGCATCGATGCACTAC-CCATGCATCGATACACAAATCACATTCGATGTTTCCATTTT
163282 TTAATGGGTG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 1 0.02
64 49 0.98
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
Found at i:164757 original size:110 final size:110
Alignment explanation
Indices: 164564--164960 Score: 679
Period size: 110 Copynumber: 3.6 Consensus size: 110
164554 GTCGAGAAAA
* *
164564 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACATCGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
* *
164629 ATTGGACTCAAGGCAACACAAGCTCAACTTCACAGCGAAGGGGCG
66 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCG
* * *
164674 ACTGACTGTCAACAAACAACTTTTTAATTTCATTCAGAGTCAATTTCAACTGCACAGCGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
*
164739 ATTGGACTCGAGACAACACAAACTCAACTTCACAGCGAAGGGGCG
66 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCG
* *
164784 ATTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCAAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
164849 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCG
66 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCG
* *
164894 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCATAGTCAATTTCAACTTCACA-CGAAAGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
164958 ATT
66 ATT
164961 AAACTCGAAG
Statistics
Matches: 269, Mismatches: 18, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
109 9 0.03
110 260 0.97
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (110 bp):
ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCG
Found at i:167245 original size:2 final size:2
Alignment explanation
Indices: 167238--167271 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
167228 ATTTTATCAT
*
167238 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
167272 CTATTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:168731 original size:43 final size:43
Alignment explanation
Indices: 168683--168769 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
168673 CCTAAACACG
* *
168683 TCAAGTAATCCAATAATAGAAAAGAATGTTGTTATTTATAGGA
1 TCAAGTAATCCAATAATAAAAAAGAATGTTATTATTTATAGGA
* * *
168726 TCAAGTAATCTAGTAATAAAAAAGAATGTTATTATTTTTAGGA
1 TCAAGTAATCCAATAATAAAAAAGAATGTTATTATTTATAGGA
168769 T
1 T
168770 GATGTTACCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.36
Consensus pattern (43 bp):
TCAAGTAATCCAATAATAAAAAAGAATGTTATTATTTATAGGA
Found at i:170528 original size:3 final size:3
Alignment explanation
Indices: 170511--170543 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
170501 AACACAAAAA
*
170511 AAG AAA AAG AA- AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
170544 GAAATCTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:171101 original size:21 final size:21
Alignment explanation
Indices: 171024--171101 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
171014 CCCAGGTTCC
*
171024 AAATTCGCAACGCGAAAGTCG
1 AAATTCGCAACGCGATAGTCG
**
171045 AAATTCGCAACGCGAT--TTT
1 AAATTCGCAACGCGATAGTCG
* * *
171064 AAGATTCAC-ATGTGATAGTCG
1 AA-ATTCGCAACGCGATAGTCG
171085 AAATTCGCAACGCGATA
1 AAATTCGCAACGCGATA
171102 CTCCAAAATC
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
19 8 0.19
20 10 0.24
21 24 0.57
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (21 bp):
AAATTCGCAACGCGATAGTCG
Found at i:171716 original size:7 final size:7
Alignment explanation
Indices: 171706--171733 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
171696 TCCAACTTCC
171706 AAATGTT
1 AAATGTT
171713 AAATGTT
1 AAATGTT
171720 AAATGTT
1 AAATGTT
171727 AAATGTT
1 AAATGTT
171734 TCAACTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
AAATGTT
Found at i:172263 original size:2 final size:2
Alignment explanation
Indices: 172256--172282 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
172246 GATTTGGTAC
172256 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
172283 ATTTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:175128 original size:16 final size:16
Alignment explanation
Indices: 175087--175128 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
175077 TTAAATGCTC
* *
175087 TAAGGATAAAGAAATT
1 TAAGGACAATGAAATT
175103 TAAGGACAATGAAATT
1 TAAGGACAATGAAATT
175119 TAAGGACAAT
1 TAAGGACAAT
175129 TTTGAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (16 bp):
TAAGGACAATGAAATT
Found at i:176738 original size:27 final size:29
Alignment explanation
Indices: 176681--176738 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
176671 AAATGTTCAC
* *
176681 AAAAAAAGTACCAAGAATCAGTGGCTCAAA
1 AAAAAAAGTACCAAGAATCAGTAGC-AAAA
176711 AAAAAAAGTACCAAGAATCA-TAG-AAAA
1 AAAAAAAGTACCAAGAATCAGTAGCAAAA
176738 A
1 A
176739 CTAAGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.15
29 2 0.08
30 20 0.77
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.12
Consensus pattern (29 bp):
AAAAAAAGTACCAAGAATCAGTAGCAAAA
Found at i:187981 original size:164 final size:166
Alignment explanation
Indices: 187710--188039 Score: 646
Period size: 164 Copynumber: 2.0 Consensus size: 166
187700 GGAGAAGAAA
187710 ACTTTTTTTCTTCAAACTTTTTCCTTAAATGTCGGTCAAAAGTTTTGGGAGTCAAACATATAACA
1 ACTTTTTTTCTTCAAACTTTTTCCTTAAATGTCGGTCAAAAGTTTTGGGAGTCAAACATATAACA
187775 AAATAGTACTAGGTTAACGGTTTAACGTGTCACATCAGTATCCTGTCATCCCA-TAATAGTCATT
66 AAATAGTACTAGGTTAACGGTTTAACGTGTCACATCAGTATCCTGTCATCCCAGTAATAGTCATT
187839 AAC-GCAAGTGATTGATTTGTTGTAAATCTATAACG
131 AACGGCAAGTGATTGATTTGTTGTAAATCTATAACG
187874 ACTTTTTTTCTTCAAACTTTTTCCTTAAATGTCGGTCAAAAGTTTTGGGAGTCAAACATATAACA
1 ACTTTTTTTCTTCAAACTTTTTCCTTAAATGTCGGTCAAAAGTTTTGGGAGTCAAACATATAACA
187939 AAATAGTACTAGGTTAACGGTTTAACGTGTCACATCAGTATCCTGTCATCCCAGTAATAGTCATT
66 AAATAGTACTAGGTTAACGGTTTAACGTGTCACATCAGTATCCTGTCATCCCAGTAATAGTCATT
188004 AACGGCAAGTGATTGATTTGTTGTAAATCTATAACG
131 AACGGCAAGTGATTGATTTGTTGTAAATCTATAACG
188040 TTAGTGACAA
Statistics
Matches: 164, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
164 118 0.72
165 14 0.09
166 32 0.20
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (166 bp):
ACTTTTTTTCTTCAAACTTTTTCCTTAAATGTCGGTCAAAAGTTTTGGGAGTCAAACATATAACA
AAATAGTACTAGGTTAACGGTTTAACGTGTCACATCAGTATCCTGTCATCCCAGTAATAGTCATT
AACGGCAAGTGATTGATTTGTTGTAAATCTATAACG
Found at i:194567 original size:6 final size:6
Alignment explanation
Indices: 194556--194584 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
194546 GATAAAAGGA
194556 ATATGG ATATGG ATATGG ATATGG ATATG
1 ATATGG ATATGG ATATGG ATATGG ATATG
194585 AATAATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (6 bp):
ATATGG
Found at i:200276 original size:124 final size:126
Alignment explanation
Indices: 200122--200373 Score: 465
Period size: 128 Copynumber: 2.0 Consensus size: 126
200112 CAACCTCCCA
200122 CCCGAGGCACACCAACTCCGGCCCCCATTTATAT-ACACCCATTTGCCT-CCCCGTAATCACCAT
1 CCCGAGGCACACCAACTCCGGCCCCCATTTATATAACACCCATTTGCCTCCCCCGTAATCACCAT
200185 CTGAACTTGTTTTTAAA-CCATTGCTCGGCCTCTTGTTCCGATGAATTTTGGTCGGAAAGTG
66 CTGAACTTGTTTTTAAACCCATTGCTCGGCCTCTTGTTCCGATGAATTTTGGTCGG-AAGTG
200246 CCCGAGGCACACCAACTCCGGCCCCCATTTATATAACACCCATTTGCCTCCCCCGTAATCACCAT
1 CCCGAGGCACACCAACTCCGGCCCCCATTTATATAACACCCATTTGCCTCCCCCGTAATCACCAT
200311 CTGAACTTGTTTTTAAACCCCATTGCTCGGCCTCTTGTTCCGATGAATTTTGGTCGGAAGTG
66 CTGAACTTGTTTTTAAA-CCCATTGCTCGGCCTCTTGTTCCGATGAATTTTGGTCGGAAGTG
200373 C
1 C
200374 AGCAGGCATT
Statistics
Matches: 124, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
124 34 0.27
125 14 0.11
126 32 0.26
127 6 0.05
128 38 0.31
ACGTcount: A:0.21, C:0.33, G:0.17, T:0.29
Consensus pattern (126 bp):
CCCGAGGCACACCAACTCCGGCCCCCATTTATATAACACCCATTTGCCTCCCCCGTAATCACCAT
CTGAACTTGTTTTTAAACCCATTGCTCGGCCTCTTGTTCCGATGAATTTTGGTCGGAAGTG
Found at i:202050 original size:48 final size:45
Alignment explanation
Indices: 201979--202072 Score: 161
Period size: 48 Copynumber: 2.0 Consensus size: 45
201969 CTGGTACTTG
201979 ACAGTGGTGCAAGCAATCACATGTGTGGAAGGAAAGACATGTTTGTGA
1 ACAGTGGTGCAAGCAATCACATGTGTGG-A--AAAGACATGTTTGTGA
202027 ACAGTGGTGCAAGCAATCACATGTGTGGAAAAGACATGTTTGTGA
1 ACAGTGGTGCAAGCAATCACATGTGTGGAAAAGACATGTTTGTGA
202072 A
1 A
202073 GCTAGACGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
45 17 0.37
47 1 0.02
48 28 0.61
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (45 bp):
ACAGTGGTGCAAGCAATCACATGTGTGGAAAAGACATGTTTGTGA
Found at i:205147 original size:29 final size:29
Alignment explanation
Indices: 205112--205193 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
205102 AAACTAAATT
*
205112 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
205141 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
205170 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
205194 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:210299 original size:37 final size:37
Alignment explanation
Indices: 210249--210319 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
210239 GTCTTTAGGA
*
210249 TATAAATGGTTTAAACATTTATTTTATTAAAATATGT
1 TATAAATAGTTTAAACATTTATTTTATTAAAATATGT
*
210286 TATAAATAGTTTAAGCATTTATTTTATTAAAATA
1 TATAAATAGTTTAAACATTTATTTTATTAAAATA
210320 AAACAAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (37 bp):
TATAAATAGTTTAAACATTTATTTTATTAAAATATGT
Found at i:216718 original size:19 final size:19
Alignment explanation
Indices: 216694--216732 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
216684 CTATTATGAG
216694 TAAAATTCTTCTCCTCCTC
1 TAAAATTCTTCTCCTCCTC
216713 TAAAATTCTTCTCCTCCTC
1 TAAAATTCTTCTCCTCCTC
216732 T
1 T
216733 CCTAGGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATTCTTCTCCTCCTC
Found at i:217576 original size:21 final size:21
Alignment explanation
Indices: 217550--217598 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
217540 ACCTAATATT
217550 ACAATGTCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
217571 ACAATGTCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
*
217592 ATAATGT
1 ACAATGT
217599 TTGAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (21 bp):
ACAATGTCAAAATTAGGTGCA
Found at i:222269 original size:77 final size:77
Alignment explanation
Indices: 222165--222374 Score: 264
Period size: 75 Copynumber: 2.8 Consensus size: 77
222155 GACCGTTGAA
* * * * *
222165 CAGGGGGGAATCGGTACCCCCTTTGGGGGGGAATCGGTTCCCTCCGAGCGTACTGGAATTCTCGG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
**
222230 AACAAAAATGTT
66 AACAAAAACATT
* **
222242 TAGGGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCCGAGCATTTTGGAAATCTCGG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
* * *
222305 AGCCAAACCATT
66 AACAAAAACATT
*
222317 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAA
222375 TTTTTGGCTT
Statistics
Matches: 113, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
75 65 0.58
77 48 0.42
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (77 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
AACAAAAACATT
Found at i:222842 original size:132 final size:132
Alignment explanation
Indices: 222605--222865 Score: 522
Period size: 132 Copynumber: 2.0 Consensus size: 132
222595 TGTTTCAACA
222605 ATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAAGATTTTTGAAATCAAGTTTTGA
1 ATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAAGATTTTTGAAATCAAGTTTTGA
222670 AATTACTCCCCCTTACTTTAACACTTCTTCAATTTATCATGTAAAACATTTAACACTTATTCTTA
66 AATTACTCCCCCTTACTTTAACACTTCTTCAATTTATCATGTAAAACATTTAACACTTATTCTTA
222735 TT
131 TT
222737 ATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAAGATTTTTGAAATCAAGTTTTGA
1 ATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAAGATTTTTGAAATCAAGTTTTGA
222802 AATTACTCCCCCTTACTTTAACACTTCTTCAATTTATCATGTAAAACATTTAACACTTATTCTT
66 AATTACTCCCCCTTACTTTAACACTTCTTCAATTTATCATGTAAAACATTTAACACTTATTCTT
222866 CTCCCCTTTT
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 129 1.00
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (132 bp):
ATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAAGATTTTTGAAATCAAGTTTTGA
AATTACTCCCCCTTACTTTAACACTTCTTCAATTTATCATGTAAAACATTTAACACTTATTCTTA
TT
Found at i:225177 original size:21 final size:21
Alignment explanation
Indices: 225092--225174 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
225082 TTTAACAGAA
*
225092 CCCT-AGGGGGGTATCGATTC
1 CCCTCAGGGGGGAATCGATTC
** *
225112 CCCTGTGGGGGGAATCGGTTC
1 CCCTCAGGGGGGAATCGATTC
* *
225133 CCCTTCAAAGGGGGAATCGGTT-
1 CCC-TC-AGGGGGGAATCGATTC
*
225155 CCCTCAGGGGGGGATCGATT
1 CCCTCAGGGGGGAATCGATT
225175 TCCTCTACAC
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 16 0.31
21 18 0.35
22 4 0.08
23 13 0.25
ACGTcount: A:0.16, C:0.24, G:0.37, T:0.23
Consensus pattern (21 bp):
CCCTCAGGGGGGAATCGATTC
Found at i:225179 original size:20 final size:20
Alignment explanation
Indices: 225092--225179 Score: 61
Period size: 20 Copynumber: 4.2 Consensus size: 20
225082 TTTAACAGAA
*
225092 CCCT-AGGGGGGTATCGATT
1 CCCTCAGGGGGGAATCGATT
** *
225111 CCCCTGTGGGGGGAATCGGTT
1 -CCCTCAGGGGGGAATCGATT
* *
225132 CCCCTTCAAAGGGGGAATCGGTT
1 -CCC-TC-AGGGGGGAATCGATT
*
225155 CCCTCAGGGGGGGATCGATT
1 CCCTCAGGGGGGAATCGATT
*
225175 TCCTC
1 CCCTC
225180 TACACCAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
20 20 0.36
21 18 0.33
22 4 0.07
23 13 0.24
ACGTcount: A:0.15, C:0.26, G:0.35, T:0.24
Consensus pattern (20 bp):
CCCTCAGGGGGGAATCGATT
Found at i:231057 original size:75 final size:76
Alignment explanation
Indices: 230929--231136 Score: 283
Period size: 75 Copynumber: 2.7 Consensus size: 76
230919 CCGTTGAACA
* * * *
230929 GGGGGAATCGGTACCCCCTTTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAAC
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAAC
** *
230994 AAAAATGTTTAG
65 AAAAACATTCAG
* * *
231006 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACA
*
231070 AAACCATTCAG
66 AAAACATTCAG
* *
231081 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAATT
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
231137 TTTGGCTTTG
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
75 67 0.58
76 31 0.27
77 18 0.16
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACA
AAAACATTCAG
Found at i:232103 original size:21 final size:21
Alignment explanation
Indices: 232078--232125 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
232068 CCTAATATTG
232078 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
232099 CAATGTCAGAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
232120 TAATGT
1 CAATGT
232126 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:232951 original size:4 final size:4
Alignment explanation
Indices: 232942--232974 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
232932 CAACGCTGAT
232942 ATAA ATAA ATAA ATAA ATAA AT-A ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
232975 GACACATGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:232959 original size:12 final size:11
Alignment explanation
Indices: 232942--232974 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
232932 CAACGCTGAT
232942 ATAAATAAATAA
1 ATAAATAAAT-A
232954 ATAAATAAATA
1 ATAAATAAATA
232965 ATAAATAAAT
1 ATAAATAAAT
232975 GACACATGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAATAAATA
Found at i:233050 original size:23 final size:26
Alignment explanation
Indices: 233004--233054 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 26
232994 TGAAACTCCT
233004 TTTGTCCTTTCGATTTAACCCACAAC
1 TTTGTCCTTTCGATTTAACCCACAAC
*
233030 TTTGT-CTTTC-A-TTATCCCACAAC
1 TTTGTCCTTTCGATTTAACCCACAAC
233053 TT
1 TT
233055 CTGCTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 13 0.54
24 1 0.04
25 5 0.21
26 5 0.21
ACGTcount: A:0.22, C:0.29, G:0.06, T:0.43
Consensus pattern (26 bp):
TTTGTCCTTTCGATTTAACCCACAAC
Found at i:234070 original size:26 final size:27
Alignment explanation
Indices: 234043--234107 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
234033 ATTAAAATTA
*
234043 TTATATATTTTAAATATTTTTTTATATT
1 TTATA-ATTTTAAATATGTTTTTATATT
* *
234071 TTATAATGTT-AATATGTTTTTATCTT
1 TTATAATTTTAAATATGTTTTTATATT
234097 TTATAATTTTA
1 TTATAATTTTA
234108 TAAGTTTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 23 0.72
27 4 0.12
28 5 0.16
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (27 bp):
TTATAATTTTAAATATGTTTTTATATT
Found at i:234072 original size:9 final size:9
Alignment explanation
Indices: 234043--234109 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
234033 ATTAAAATTA
234043 TTATATATT
1 TTATATATT
*
234052 TTAAATATTT
1 TTATATA-TT
*
234062 TTTTATATT
1 TTATATATT
*
234071 TTATA-ATG
1 TTATATATT
234079 TTA-ATATGT
1 TTATATAT-T
* *
234088 TTTTATCTT
1 TTATATATT
234097 TTATA-ATT
1 TTATATATT
234105 TTATA
1 TTATA
234110 AGTTTGTTCT
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
7 1 0.02
8 14 0.32
9 19 0.43
10 10 0.23
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (9 bp):
TTATATATT
Found at i:244551 original size:169 final size:168
Alignment explanation
Indices: 244248--244551 Score: 398
Period size: 168 Copynumber: 1.8 Consensus size: 168
244238 GAGCATTGTA
* * * * * *
244248 AGATGGATATGACTATCTGTTAGCTTTGTACTTGGGGGTTGGGGAAAGTAAAAAAATGATAAAAA
1 AGATGGATATGACTAACTGCTAGCCTTGTACTTGGAGGTTGGAGAAAGAAAAAAAATGATAAAAA
* * * * *
244313 GCAAGCTCGTATATGGTGATGTGTGAGTTTTCTACCTTAAAATTTTGATAAGCACGCTTTTAGAG
66 GCAAGCTCGTATATAGTGATATGTGAGTTGTCTACCTAAAAATTTTGACAAGCACGCTTTTAGAG
244378 GACATTGAAGTGCTTGCTTGTTAAGAATAACCACTGAG
131 GACATTGAAGTGCTTGCTTGTTAAGAATAACCACTGAG
244416 AGATGGATATGACTAACTGCTA-CCTTGTACTTGGAGGTTGGAGAAAGAAAAAATAATGATGAAA
1 AGATGGATATGACTAACTGCTAGCCTTGTACTTGGAGGTTGGAGAAAGAAAAAA-AATGAT-AAA
* * * ** *
244480 AA-CTAGCTTGTCT-TCAGTGATATGTGAGTTGTCTACCCTAAAAATTTTGACAAGCTTGTTTTT
64 AAGCAAGCTCGTATAT-AGTGATATGTGAGTTGTCTA-CCTAAAAATTTTGACAAGCACGCTTTT
244543 AGAGGACAT
127 AGAGGACAT
244552 GTTCATTCAA
Statistics
Matches: 115, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
167 28 0.24
168 51 0.44
169 36 0.31
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (168 bp):
AGATGGATATGACTAACTGCTAGCCTTGTACTTGGAGGTTGGAGAAAGAAAAAAAATGATAAAAA
GCAAGCTCGTATATAGTGATATGTGAGTTGTCTACCTAAAAATTTTGACAAGCACGCTTTTAGAG
GACATTGAAGTGCTTGCTTGTTAAGAATAACCACTGAG
Found at i:248294 original size:20 final size:21
Alignment explanation
Indices: 248269--248320 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
248259 TTTTCCCAAT
*
248269 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
248289 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
248310 TCGCAATGCGA
1 TCGCAATGCGA
248321 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:248334 original size:20 final size:20
Alignment explanation
Indices: 248309--248422 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
248299 AATTGGGAAA
*
248309 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
248329 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
248349 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
248370 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
248390 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
248410 TTCGCAACGCGAT
1 ATCGCAACGCGAT
248423 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:248354 original size:61 final size:61
Alignment explanation
Indices: 248306--248422 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
248296 GCGAATTGGG
* * * *
248306 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATAC
* * * *
248367 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGAT
248423 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATAC
Found at i:248976 original size:19 final size:19
Alignment explanation
Indices: 248938--249004 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
248928 TTCGAGAATG
248938 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
248958 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
248977 AAAAACGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
248996 AAAATCGCA
1 AAAATCGCA
249005 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.49, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:249022 original size:19 final size:19
Alignment explanation
Indices: 249000--249150 Score: 150
Period size: 19 Copynumber: 8.1 Consensus size: 19
248990 GAAACCAAAA
*
249000 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
249019 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
249038 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
249057 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
249071 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
249090 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
249109 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
249129 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
249149 TC
1 TC
249151 AACCAAAAGA
Statistics
Matches: 111, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.07
16 2 0.02
17 3 0.03
19 65 0.59
20 32 0.29
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:251308 original size:42 final size:42
Alignment explanation
Indices: 251232--251434 Score: 201
Period size: 42 Copynumber: 4.8 Consensus size: 42
251222 GACTCGCCTG
* * *
251232 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * ** *
251274 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCATTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
251316 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
251358 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
** * *
251400 TCATCGTTGAAGAGGTCCA-TCCCACCATTCAAGAG
1 TCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
251435 CCCGATTCAC
Statistics
Matches: 127, Mismatches: 33, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
42 123 0.97
43 4 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:251407 original size:21 final size:21
Alignment explanation
Indices: 251299--251414 Score: 56
Period size: 21 Copynumber: 5.5 Consensus size: 21
251289 CCCCTCCCAC
*
251299 CGTTCAAGAGGCCATTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
** * *
251320 CCCTCAAGAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTGTC-AT
* * *
251341 CGTTGAAGAGGCCCCTATCATT
1 CGTTCAAGAGGCCACTGTCA-T
* * * * ** *
251363 C-CTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTGTCAT
251383 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
*
251404 CGTTGAAGAGG
1 CGTTCAAGAGG
251415 TCCATCCCAC
Statistics
Matches: 65, Mismatches: 26, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
20 2 0.03
21 60 0.92
22 3 0.05
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTGTCAT
Found at i:251413 original size:84 final size:84
Alignment explanation
Indices: 251229--251404 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
251219 CCCGACTCGC
251229 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
251294 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
251313 TTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
251378 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
251397 CTGTCATC
1 CTGTCATC
251405 GTTGAAGAGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:251434 original size:84 final size:84
Alignment explanation
Indices: 251229--251434 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
251219 CCCGACTCGC
* * * *
251229 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
251294 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * * *
251313 TTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
251378 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
251397 CTGTCATCGTTGAAGAGGTCCA-TCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
251435 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 107 0.96
85 5 0.04
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:252810 original size:14 final size:14
Alignment explanation
Indices: 252791--252826 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
252781 ATTGTTTAAT
252791 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
252805 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
252819 TGATTTGT
1 TGATTTGT
252827 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:253007 original size:19 final size:19
Alignment explanation
Indices: 252985--253135 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
252975 CGAAATTAAA
252985 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
253004 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
253019 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** *
253037 TTCGTATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
253051 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
253070 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
253085 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
253103 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
253122 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
253136 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:253031 original size:33 final size:32
Alignment explanation
Indices: 252989--253115 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
252979 ATTAAATTCG
252989 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
253022 CGTTGCGATTTTCATTTCGTATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
253055 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
253088 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
253116 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:253067 original size:66 final size:66
Alignment explanation
Indices: 252982--253114 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
252972 ACGCGAAATT
* *
252982 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGTATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
253047 G
66 G
*
253048 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
253113 G
66 G
253114 A
1 A
253115 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:255423 original size:12 final size:12
Alignment explanation
Indices: 255406--255430 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
255396 TCTTCGGGGA
255406 CTTTTTCTTCTT
1 CTTTTTCTTCTT
255418 CTTTTTCTTCTT
1 CTTTTTCTTCTT
255430 C
1 C
255431 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:255639 original size:24 final size:24
Alignment explanation
Indices: 255605--255658 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
255595 CTGAAACATC
*
255605 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
255629 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
255653 ATCAAA
1 ATCAAA
255659 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:256420 original size:20 final size:20
Alignment explanation
Indices: 256395--256445 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
256385 TGTATTATCT
256395 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
256415 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
256435 CGTTGCGAAAG
1 CGTTGCGAAAG
256446 GCAATCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:256696 original size:19 final size:20
Alignment explanation
Indices: 256658--256707 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
256648 ATTCATTTGA
*
256658 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
256678 CTATCGCAACGTG-AAATGG
1 CTATCGCAACGCGAAAATGG
256697 CTATCGCAACG
1 CTATCGCAACG
256708 ACAAAATCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:256757 original size:14 final size:14
Alignment explanation
Indices: 256738--256791 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
256728 GAAAATCGCA
256738 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
256752 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
256769 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
256785 TTGCGAT
1 TTGCGAT
256792 AGTCAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:256757 original size:33 final size:33
Alignment explanation
Indices: 256720--256790 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
256710 AAAATCGCAA
*
256720 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
256753 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
256786 TGCGA
1 TGCGA
256791 TAGTCAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:256924 original size:14 final size:14
Alignment explanation
Indices: 256905--256941 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
256895 CATCAATTAA
256905 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
256919 ACAAATCATCTTTT
1 ACAAATCAACATTT
256933 ACAAATCAA
1 ACAAATCAA
256942 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:258834 original size:20 final size:20
Alignment explanation
Indices: 258811--258864 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
258801 GAAACTTAAA
258811 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
258831 ATCGCAACGCTG-AAATGGCT
1 ATCGCAACGC-GAAAATGACT
* *
258851 ATCGTAATGCGAAA
1 ATCGCAACGCGAAA
258865 TAAAAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:258932 original size:19 final size:18
Alignment explanation
Indices: 258882--258932 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
258872 CGCAACGACA
**
258882 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAAAC
*
258900 AAATCGCAACGCGAAACAC
1 AAATCGCAATGCGAAA-AC
*
258919 AAATCGCATTGCGA
1 AAATCGCAATGCGA
258933 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAAAC
Found at i:258963 original size:14 final size:14
Alignment explanation
Indices: 258944--259001 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
258934 TTTCATTTCG
258944 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
258958 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
258974 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
258990 CGTTGCGATTTT
1 CGTTGCGATTTT
259002 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Done.