Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008433.1 Hibiscus syriacus cultivar Beakdansim tig00111231_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: 451884
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 3
Found at i:5123 original size:105 final size:104
Alignment explanation
Indices: 4940--5604 Score: 1079
Period size: 105 Copynumber: 6.4 Consensus size: 104
4930 AGGTTTTACC
4940 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
5005 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATT
* *
5045 TAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
5110 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAA-TT
*
5150 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
5215 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATT
*
5255 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
5320 ACGAAGGGACCGCTGGTTTTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAA-TT
*
5360 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
5425 ACGAAGGGACCGCTGCTTGTCAAC-AACGACTTCCCAATCT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAT-T
*
5465 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
5530 ACGAAGGGACCGCTGCTTGTCAACAAA-A-TT-TC-ATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
** * *
5565 CAGATTCAATTTCAACTTCACAACGAAGGACATCGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
5605 GAAACAACAC
Statistics
Matches: 533, Mismatches: 21, Indels: 17
0.93 0.04 0.03
Matches are distributed among these distances:
100 37 0.07
101 2 0.00
102 1 0.00
103 2 0.00
104 9 0.02
105 478 0.90
106 4 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (104 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:5928 original size:3 final size:3
Alignment explanation
Indices: 5920--5948 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5910 AATTTATTTG
5920 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5949 TTTTTTCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:7298 original size:21 final size:21
Alignment explanation
Indices: 7261--7304 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
7251 CATTCAATAA
*
7261 TTATTTATTCCATTTTTA-TT
1 TTATTTATTCCACTTTTACTT
*
7281 TTATTTATTTCCCCTTTTACTT
1 TTATTTA-TTCCACTTTTACTT
7303 TT
1 TT
7305 TACTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTATTCCACTTTTACTT
Found at i:7357 original size:20 final size:19
Alignment explanation
Indices: 7310--7361 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
7300 CTTTTTACTA
7310 TTATTATTAT-TTATTTAT
1 TTATTATTATATTATTTAT
*
7328 TTATGCTATTATATTATTATTT
1 TTAT--TATTATATTATT-TAT
7350 TTATTATTATAT
1 TTATTATTATAT
7362 ACGTATATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 4 0.14
20 14 0.48
21 5 0.17
22 6 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTATTATATTATTTAT
Found at i:8289 original size:112 final size:112
Alignment explanation
Indices: 8087--8341 Score: 404
Period size: 112 Copynumber: 2.3 Consensus size: 112
8077 GGTGGCGACA
* * *
8087 GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTG
1 GGATAGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTG
*
8152 TCATTTATAGACCGATTTTGTCATTTTTTTACCTGTTATATTGTTAT
66 TCATTTATAGACCGATTTTATCATTTTTTTACCTGTTATATTGTTAT
* * *
8199 GGATAGATACATTTTTATAAAGTATAGACACTTTCAATATATCCGATAGTGCTTTACTTGTTTTG
1 GGATAGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTG
* *
8264 TCATTTATAGACCGGTTTTATCATTTTTTTACTTGTTATATTGTTAT
66 TCATTTATAGACCGATTTTATCATTTTTTTACCTGTTATATTGTTAT
*
8311 GGATCA-ATATATTTTTATAAAGTATCGACAC
1 GGAT-AGATACATTTTTATAAAGTATCGACAC
8342 AAACCGACAA
Statistics
Matches: 131, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
112 130 0.99
113 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (112 bp):
GGATAGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTG
TCATTTATAGACCGATTTTATCATTTTTTTACCTGTTATATTGTTAT
Found at i:8841 original size:25 final size:25
Alignment explanation
Indices: 8813--8894 Score: 92
Period size: 25 Copynumber: 3.1 Consensus size: 25
8803 TTTTTTAAGT
8813 TTATAATTTTGAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
* *
8838 TTATAAGTTTGGGAATATTTTTTATTTAA
1 TTATAA-TTT-TGAA-A-TTTTAATTTAA
* *
8867 ATATAATTTTAAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
8892 TTA
1 TTA
8895 ATTTTATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
25 18 0.39
26 4 0.09
27 5 0.11
28 4 0.09
29 15 0.33
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (25 bp):
TTATAATTTTGAAATTTTAATTTAA
Found at i:9864 original size:16 final size:15
Alignment explanation
Indices: 9843--9884 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
9833 TTTATATTCA
9843 ATTATAATTTGATC-TT
1 ATTAT-ATTT-ATCATT
9859 ATTATATTTATCATT
1 ATTATATTTATCATT
9874 ATTATTATTTA
1 ATTA-TATTTA
9885 GTTTAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 10 0.42
16 11 0.46
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (15 bp):
ATTATATTTATCATT
Found at i:11054 original size:41 final size:41
Alignment explanation
Indices: 11006--11087 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
10996 TGTAATTCAC
11006 GATGCAATCATTTGAATCAGTCAATTTGCAAGAGACCGTCA
1 GATGCAATCATTTGAATCAGTCAATTTGCAAGAGACCGTCA
11047 GATGCAATCATTTGAATCAGTCAATTTGCAAGAGACCGTCA
1 GATGCAATCATTTGAATCAGTCAATTTGCAAGAGACCGTCA
11088 ATGTGCGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (41 bp):
GATGCAATCATTTGAATCAGTCAATTTGCAAGAGACCGTCA
Found at i:13754 original size:74 final size:73
Alignment explanation
Indices: 13611--13754 Score: 180
Period size: 74 Copynumber: 2.0 Consensus size: 73
13601 TACAAACGAC
* * *
13611 CAACAGGTTCGCCATATAGCGACTTTTTTGGCACAAACACCGCAATAGATTTGATATTTATAGGC
1 CAACAGGTTCGCCATATAGCGACTTTTTAGGCACAAACACCGCAACAGATTTGATATTTAGAGGC
13676 GTTTCCCG
66 GTTTCCCG
* * * * ** *
13684 CAACATGTTCGCTATTTAGCGACATTTTTAGTCACAAATGCCGCAACAGATTTGATATTTAGCGG
1 CAACAGGTTCGCCATATAGCGAC-TTTTTAGGCACAAACACCGCAACAGATTTGATATTTAGAGG
*
13749 TGTTTC
65 CGTTTC
13755 GGGCACAAAC
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
73 20 0.34
74 39 0.66
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (73 bp):
CAACAGGTTCGCCATATAGCGACTTTTTAGGCACAAACACCGCAACAGATTTGATATTTAGAGGC
GTTTCCCG
Found at i:14180 original size:12 final size:11
Alignment explanation
Indices: 14165--14227 Score: 62
Period size: 12 Copynumber: 5.8 Consensus size: 11
14155 TACTTCTCTA
14165 TGCTTCTCTCGC
1 TGCTTCTCTC-C
*
14177 TGC-TCTAT-C
1 TGCTTCTCTCC
14186 TGCTTCTCTCCC
1 TGCTTCTCT-CC
14198 TGCTTCTCTCGC
1 TGCTTCTCTC-C
14210 TGC-TCTC-CC
1 TGCTTCTCTCC
14219 TGCTTCTCT
1 TGCTTCTCT
14228 TGCTTCAGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
9 8 0.19
10 9 0.21
11 9 0.21
12 17 0.40
ACGTcount: A:0.02, C:0.43, G:0.13, T:0.43
Consensus pattern (11 bp):
TGCTTCTCTCC
Found at i:14204 original size:33 final size:33
Alignment explanation
Indices: 14165--14227 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
14155 TACTTCTCTA
*
14165 TGCTTCTCTCGCTGCTCTATCTGCTTCTCTCCC
1 TGCTTCTCTCGCTGCTCTACCTGCTTCTCTCCC
*
14198 TGCTTCTCTCGCTGCTCTCCCTGCTTCTCT
1 TGCTTCTCTCGCTGCTCTACCTGCTTCTCT
14228 TGCTTCAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.02, C:0.43, G:0.13, T:0.43
Consensus pattern (33 bp):
TGCTTCTCTCGCTGCTCTACCTGCTTCTCTCCC
Found at i:28392 original size:40 final size:41
Alignment explanation
Indices: 28296--28404 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 41
28286 GCTCTATAGC
* * *
28296 GGCGTTTTAGTGACAAACACCACTAAGGTTCACCTCTATTGT
1 GGCGTTTTAGTAACAAACGCCACTAA-GTTCACCTCTATTAT
*
28338 GGCGTTTTAGTAACAAACGCCACTAAGTT-GCCTCTATTAT
1 GGCGTTTTAGTAACAAACGCCACTAAGTTCACCTCTATTAT
* *
28378 GGCATTTTTA-TAACAAATGCCACTAAG
1 GGC-GTTTTAGTAACAAACGCCACTAAG
28405 GTACGGATCT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
40 28 0.47
41 8 0.13
42 24 0.40
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (41 bp):
GGCGTTTTAGTAACAAACGCCACTAAGTTCACCTCTATTAT
Found at i:29346 original size:22 final size:21
Alignment explanation
Indices: 29311--29354 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
29301 CACCGGAAAA
29311 CTAAGGGAGAAAAAAATATTTT
1 CTAAGGGAGAAAAAAAT-TTTT
*
29333 CTAA-GGAGAGAAAATATTTTT
1 CTAAGGGAGA-AAAAAATTTTT
29354 C
1 C
29355 AAGACAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (21 bp):
CTAAGGGAGAAAAAAATTTTT
Found at i:29599 original size:83 final size:83
Alignment explanation
Indices: 29430--29754 Score: 466
Period size: 83 Copynumber: 4.0 Consensus size: 83
29420 GGAATTTCGA
* *
29430 GAGAGTTTTACTCCAACTAAAACTCTTTTAATATCTAAA---AATAGATA--ATAATATCTTTTA
1 GAGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAA-ACATATTATAATATCTTTTA
* *
29490 AATTTAAAATATTAAATAT
65 AATTTATAATATTAAATCT
*
29509 GAGAGTTTTACTCTAACCAAAACTCTTTTAATATCTAAATTTAAACATATTATAATATCTTTTAA
1 GAGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACATATTATAATATCTTTTAA
*
29574 ATTTATAATATTAAACCT
66 ATTTATAATATTAAATCT
* *
29592 GGGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACATGTTATAATATCTTTTAA
1 GAGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACATATTATAATATCTTTTAA
29657 ATTTATAATATTAAATCT
66 ATTTATAATATTAAATCT
* * * * *
29675 CAGAGTTTCACTCCAACCTAAACTCTTTTAATATCTAAATTTAAATATATAATAATAT-TGTTTA
1 GAGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACATATTATAATATCT-TTTA
29739 AATTTA-AATATTAAAT
65 AATTTATAATATTAAAT
29755 ATATATTTCC
Statistics
Matches: 223, Mismatches: 17, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
79 37 0.17
81 4 0.02
82 13 0.06
83 169 0.76
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (83 bp):
GAGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACATATTATAATATCTTTTAA
ATTTATAATATTAAATCT
Found at i:36524 original size:26 final size:26
Alignment explanation
Indices: 36477--36527 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
36467 TTAAAATGGA
**
36477 AACATTGAAGTTTGTGTAATTAAAAG
1 AACATTGAAGGATGTGTAATTAAAAG
36503 AACATTGAAGGATGT-TATATTAAAA
1 AACATTGAAGGATGTGTA-ATTAAAA
36528 CTGACAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (26 bp):
AACATTGAAGGATGTGTAATTAAAAG
Found at i:50215 original size:47 final size:47
Alignment explanation
Indices: 50146--50240 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
50136 ATTTTAGTAC
50146 GGAGATGGTAGAATTCAAACCTCTAATCTATGTGATGCAATCAAATT
1 GGAGATGGTAGAATTCAAACCTCTAATCTATGTGATGCAATCAAATT
50193 GGAGATGGTAGAATTCAAACCTCTAATCTATGTGATGCAATCAAATT
1 GGAGATGGTAGAATTCAAACCTCTAATCTATGTGATGCAATCAAATT
50240 G
1 G
50241 TAATTAGTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (47 bp):
GGAGATGGTAGAATTCAAACCTCTAATCTATGTGATGCAATCAAATT
Found at i:52794 original size:16 final size:17
Alignment explanation
Indices: 52757--52794 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
52747 TGCAGATCAT
52757 TTTTTGTCTTAAAAATA
1 TTTTTGTCTTAAAAATA
* *
52774 ATTTT-TCTTAAAATTA
1 TTTTTGTCTTAAAAATA
52790 TTTTT
1 TTTTT
52795 AAAAAACGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTTGTCTTAAAAATA
Found at i:53392 original size:21 final size:21
Alignment explanation
Indices: 53353--53392 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53343 GCCATCGAGA
* *
53353 ATGCTATTGCGGTCTTCGCAG
1 ATGCTATTGCGGCCGTCGCAG
53374 ATGCTATTGCGGCCGTCGC
1 ATGCTATTGCGGCCGTCGC
53393 GGGTAACTCG
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:0.12, C:0.28, G:0.30, T:0.30
Consensus pattern (21 bp):
ATGCTATTGCGGCCGTCGCAG
Found at i:55987 original size:24 final size:23
Alignment explanation
Indices: 55942--55987 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
55932 TTTATTTAAG
*
55942 ATATTATATTATAAAATTTAAAT
1 ATATTATATTATAAAATATAAAT
* *
55965 ATATTAATGTTATAATATATAAA
1 ATATT-ATATTATAAAATATAAA
55988 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATTATATTATAAAATATAAAT
Found at i:56369 original size:3 final size:3
Alignment explanation
Indices: 56363--56422 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
56353 TCTTCTTCTT
* * * *
56363 CTC CTC CTC CTC CTC CTC TTC CTC TTC TTC CTC TTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
*
56411 CTTC TTC CTC CT
1 C-TC CTC CTC CT
56423 ATCATCTAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 46 0.96
4 2 0.04
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (3 bp):
CTC
Found at i:58655 original size:19 final size:19
Alignment explanation
Indices: 58631--58668 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
58621 CTTTGTATTT
*
58631 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
58650 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
58669 GATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:58671 original size:75 final size:76
Alignment explanation
Indices: 58588--58730 Score: 193
Period size: 76 Copynumber: 1.9 Consensus size: 76
58578 TAAACTCAAA
* *
58588 TTTTAGGATAATA-TTTTAAACATTATATTT-TATCTT-TGTATTTTATTTTAAATAGGTTTTAG
1 TTTTAGGATAATATTTTTAAACATTATATTTGT-T-TTAGGTATTTTAGTTTAAATAGGTTTTAG
58650 TATTTTAATTAAG
64 TATTTTAATTAAG
* * **
58663 TTTTAGGATATTATTTTTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
1 TTTTAGGATAATATTTTTAAACATTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
58728 TTT
66 TTT
58731 GTATTAGGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
75 14 0.24
76 44 0.75
77 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.11, T:0.59
Consensus pattern (76 bp):
TTTTAGGATAATATTTTTAAACATTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
TTTTAATTAAG
Found at i:58686 original size:32 final size:32
Alignment explanation
Indices: 58644--58705 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
58634 TTTAAATAGG
58644 TTTTAGTATTTTA-ATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTATATT-AGTTTTAGG-TATTAT
*
58677 TTTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTTAGTATTTTATATTAGTTTTAGGTATT
58706 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTAGTATTTTATATTAGTTTTAGGTATTAT
Found at i:58835 original size:64 final size:64
Alignment explanation
Indices: 58686--58807 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 64
58676 TTTTTATATT
*
58686 TTATATT-TGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTGTATTAGGATTTAGAATA
1 TTATATTATTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTGTATTAGGATTTAGAATA
*
58749 TTATATTATTTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTT-TAATTAGGATTTA
1 TTATATTATTTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTGT-ATTAGGATTTA
58808 AGATGTTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
63 13 0.24
64 41 0.76
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.56
Consensus pattern (64 bp):
TTATATTATTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTGTATTAGGATTTAGAATA
Found at i:59775 original size:20 final size:19
Alignment explanation
Indices: 59746--59783 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
59736 TATGCTCGGA
59746 GGGAACCGATTCCCCCCAG
1 GGGAACCGATTCCCCCCAG
59765 GGGATACCGATTCCCCCCA
1 GGGA-ACCGATTCCCCCCA
59784 CTGTTCAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.21, C:0.42, G:0.24, T:0.13
Consensus pattern (19 bp):
GGGAACCGATTCCCCCCAG
Found at i:65592 original size:19 final size:20
Alignment explanation
Indices: 65549--65604 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
65539 TTTGGTGCAA
65549 AGGGAATCGATACCCCCATG
1 AGGGAATCGATACCCCCATG
*
65569 AGGGAATCGATTCCCCC-T-
1 AGGGAATCGATACCCCCATG
65587 AGGGGAATCGATACCCCC
1 A-GGGAATCGATACCCCC
65605 CTGGGGTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 1 0.03
19 16 0.48
20 16 0.48
ACGTcount: A:0.27, C:0.32, G:0.25, T:0.16
Consensus pattern (20 bp):
AGGGAATCGATACCCCCATG
Found at i:69124 original size:22 final size:21
Alignment explanation
Indices: 69060--69125 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
69050 AAAAATCCCC
* *
69060 TTTTATATTTATTACTATTATTA
1 TTTTTTATTTATT-TTATT-TTA
* *
69083 TTTATTA-TTATATTAGTTTTCA
1 TTTTTTATTTATTTTA-TTTT-A
69105 TTTTTTATTTATTTTATTTTA
1 TTTTTTATTTATTTTATTTTA
69126 ATATATCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
21 5 0.15
22 17 0.50
23 12 0.35
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTTATTTATTTTATTTTA
Found at i:71642 original size:95 final size:95
Alignment explanation
Indices: 71526--71714 Score: 369
Period size: 95 Copynumber: 2.0 Consensus size: 95
71516 CACCGCTTGC
*
71526 GGTGGTTGGGAACCATAAAATCTATCCCAAATAAACCCAGAGCCTCCAATTCGACTCCCTAAAGC
1 GGTGGTCGGGAACCATAAAATCTATCCCAAATAAACCCAGAGCCTCCAATTCGACTCCCTAAAGC
71591 TAAATTTGAAACTAAAACCACCATGCAAGT
66 TAAATTTGAAACTAAAACCACCATGCAAGT
71621 GGTGGTCGGGAACCATAAAATCTATCCCAAATAAACCCAGAGCCTCCAATTCGACTCCCTAAAGC
1 GGTGGTCGGGAACCATAAAATCTATCCCAAATAAACCCAGAGCCTCCAATTCGACTCCCTAAAGC
71686 TAAATTTGAAACTAAAACCACCATGCAAG
66 TAAATTTGAAACTAAAACCACCATGCAAG
71715 CTCTTCAAGT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (95 bp):
GGTGGTCGGGAACCATAAAATCTATCCCAAATAAACCCAGAGCCTCCAATTCGACTCCCTAAAGC
TAAATTTGAAACTAAAACCACCATGCAAGT
Found at i:77475 original size:537 final size:537
Alignment explanation
Indices: 74794--77473 Score: 4917
Period size: 537 Copynumber: 5.0 Consensus size: 537
74784 TGCTTAATTG
*
74794 ATCGAACACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAA---G--
1 ATCGAGCACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAAGGGGTA
* * *
74854 AAATTCAACGGATAAGTCTCAGTTTTGCTTACTTTTTGCTCATTAAATATCGTAATGTTGCATGG
66 AAATTCAACGGATAAGTCTCGGCTTCGCTTACTTTTTGCTCATTAAATATCGTAATGTTGCATGG
*
74919 TCAGAATAAACAACAATATTAGTTCCCAGCAAATATGATCTAAATTTTTTCAAAGCAAATATTAT
131 TCAGAATAAACAACAATATTAGTTCCCAGCAAATATGATCTAAATTTTTCCAAAGCAAATATTAT
*
74984 AGTAAAAAATTCTTTTTCGGTTATAGAGTAATTTTTCTGCTCTGAATCTAAGGTGTGTGATGCAT
196 AGTAAAAAATTCTTTTTCGGTTATAGAGTAATTTTTCTGCTCTAAATCTAAGGTGTGTGATGCAT
* * *
75049 AGGCAATGACATGCGGTATTTTGTTGACTTTTTAACTTAGAACTACTCCAACACTAGTGTCTGAC
261 AGGCAATGACATGCGGTATTTTGCTGACTTTTTAACTGAGAACTACTCCAACACTAGTGTCTGAG
*
75114 GAATCATACATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTTATATTA-
326 GAATCATACATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTGATATTAG
* *
75178 TTTTTCCCTT-AAAATGACGAACAATTCCTTGCATTTTTTGTTGAAATCAAAGACTTTATCTTTT
391 TTTTT-CCTTCAAAATGACGAACAATTCCTTGCATTCTTGGTTGAAATCAAAGACTTTATCTTTT
* *
75242 TGAAGTAGATTACACAATGATTGTGTTATCTTTGAGAAGTATTTGATGAACCTGAGGTAAAATCT
455 TGAAGTAGATTACACAACGATTGTGTTATCTTTGAGAAGTCTTTGATGAACCTGAGGTAAAATCT
75307 TGCATGGCCAAGAAAAAA
520 TGCATGGCCAAGAAAAAA
75325 ATCGAGCACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAAGGGGTA
1 ATCGAGCACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAAGGGGTA
*
75390 AAATTCAAAGGGATAAGTCTCGGCTTCGCTTACTTTTTGCTCATTAAATATCGTAATGTTGCATG
66 AAATTC-AACGGATAAGTCTCGGCTTCGCTTACTTTTTGCTCATTAAATATCGTAATGTTGCATG
75455 GTCAGAATAAACAACAATATTAGTTCCCAGCAAATATGATCTAAATTTTTCCAAAGCAAATATTA
130 GTCAGAATAAACAACAATATTAGTTCCCAGCAAATATGATCTAAATTTTTCCAAAGCAAATATTA
75520 TAGTAAAAAATTCTTTTTCGGTTATAGAGTAATTTTTCTGCTCTAAATCTAAGGTGTGTGATGCA
195 TAGTAAAAAATTCTTTTTCGGTTATAGAGTAATTTTTCTGCTCTAAATCTAAGGTGTGTGATGCA
* *
75585 TAGGCAATGACATGCGGTATTTTGCCGACTTTTTAACTGAGAACTACTTCAACACTAGTGTCTGA
260 TAGGCAATGACATGCGGTATTTTGCTGACTTTTTAACTGAGAACTACTCCAACACTAGTGTCTGA
75650 GGAATCATACATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTGATATTA
325 GGAATCATACATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTGATATTA
75715 GTTTTTCCTTCAAAATGACGAACAATTCCTTGCATTCTTGGTTGAAATCAAAGACTTTATCTTTT
390 GTTTTTCCTTCAAAATGACGAACAATTCCTTGCATTCTTGGTTGAAATCAAAGACTTTATCTTTT
*
75780 TGAAGTAGATTACACAACGATTGTGTTATCTTTGAGAAGTCTTTAATGAACCTGAGGTAAAATCT
455 TGAAGTAGATTACACAACGATTGTGTTATCTTTGAGAAGTCTTTGATGAACCTGAGGTAAAATCT
75845 TGCATGGCCAAGAAAAAA
520 TGCATGGCCAAGAAAAAA
75863 ATCGAGCACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAAGGGGTA
1 ATCGAGCACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAAGGGGTA
*
75928 AAATTCAACGGATAAGTCTCGGCTTCTCTTACTTTTTGCTCATTAAATATCGTAATGTTGCATGG
66 AAATTCAACGGATAAGTCTCGGCTTCGCTTACTTTTTGCTCATTAAATATCGTAATGTTGCATGG
*
75993 TCAGAATAAACAACAATATTAGTTCCCAACAAATATGATCTAAATTTTTCCAAAGCAAATATTAT
131 TCAGAATAAACAACAATATTAGTTCCCAGCAAATATGATCTAAATTTTTCCAAAGCAAATATTAT
* *
76058 AGTAAAAAATTCTTTTTCGGTTATAGAGTAATTTTTCTGCTCTAAATCTAAGGTGTATGATCCAT
196 AGTAAAAAATTCTTTTTCGGTTATAGAGTAATTTTTCTGCTCTAAATCTAAGGTGTGTGATGCAT
*
76123 AGGCAATGACATGCGGTATTTTGCTGACTTTTTAACTGAGAACTACTTCAACACTAGTGTCTGAG
261 AGGCAATGACATGCGGTATTTTGCTGACTTTTTAACTGAGAACTACTCCAACACTAGTGTCTGAG
76188 GAATCATACATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTGATATTAG
326 GAATCATACATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTGATATTAG
76253 TTTTTCCTTCAAAATGACGAACAATTCCTTGCATTCTTGGTTGAAATCAAAGACTTTATCTTTTT
391 TTTTTCCTTCAAAATGACGAACAATTCCTTGCATTCTTGGTTGAAATCAAAGACTTTATCTTTTT
* *
76318 GAAGTAGATTACACAACGATTGTGTTATCTTTGAGAAGTATTTGATGAACCTAAGGTAAAATCTT
456 GAAGTAGATTACACAACGATTGTGTTATCTTTGAGAAGTCTTTGATGAACCTGAGGTAAAATCTT
76383 GCATGGCCAAGAAAAAA
521 GCATGGCCAAGAAAAAA
76400 ATCGAGCACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAAGGGGTA
1 ATCGAGCACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAAGGGGTA
*
76465 AAATTCAACGGATAAGTCTCGGCTTCACTTACTTTTTGCTCATTAAATATCGTAATGTTGCATGG
66 AAATTCAACGGATAAGTCTCGGCTTCGCTTACTTTTTGCTCATTAAATATCGTAATGTTGCATGG
* *
76530 TCAGAATAAACAACAATATTAGTTCCAAGAAAATATGATCTAAATTTTTCCAAAGCAAATATTAT
131 TCAGAATAAACAACAATATTAGTTCCCAGCAAATATGATCTAAATTTTTCCAAAGCAAATATTAT
*
76595 AGTAAAAAATTCTTTTTCGGTTATAGAGTAATTTTTCTGCTCTAAATCTAAGGTGTGTGATTCAT
196 AGTAAAAAATTCTTTTTCGGTTATAGAGTAATTTTTCTGCTCTAAATCTAAGGTGTGTGATGCAT
76660 AGGCAATGACATGCGGTATTTTGCTGACTTTTTAACTGAGAACTACTCCAACACTAGTGTCTGAG
261 AGGCAATGACATGCGGTATTTTGCTGACTTTTTAACTGAGAACTACTCCAACACTAGTGTCTGAG
76725 GAATCATACATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTGATATTAG
326 GAATCATACATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTGATATTAG
* *
76790 TTTTTCCTTCAAAAGGACGAACAATTCCTTGTATTCTTGGTTGAAATCAAAGACTTTATCTTTTT
391 TTTTTCCTTCAAAATGACGAACAATTCCTTGCATTCTTGGTTGAAATCAAAGACTTTATCTTTTT
*
76855 GAAGTAGATTACACAACGATTGTGTTATCTTTGAGAAGTCTTTGATGAACCTAAGGTAAAATCTT
456 GAAGTAGATTACACAACGATTGTGTTATCTTTGAGAAGTCTTTGATGAACCTGAGGTAAAATCTT
76920 GCATGGCCAAGAAAAAA
521 GCATGGCCAAGAAAAAA
76937 ATCGAGCACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAAGGGGTA
1 ATCGAGCACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAAGGGGTA
* *
77002 AAATTCAACGAATAAGTCTCGGCTTCGTTTACTTTTTGCTCATTAAATATCGTAATGTTGCATGG
66 AAATTCAACGGATAAGTCTCGGCTTCGCTTACTTTTTGCTCATTAAATATCGTAATGTTGCATGG
77067 TCAGAATAAACAACAATATTAGTTCCCAGCAAATATGATCTAAATTTTTCCAAAGCAAATATTAT
131 TCAGAATAAACAACAATATTAGTTCCCAGCAAATATGATCTAAATTTTTCCAAAGCAAATATTAT
* * *
77132 AGTAAAAAATTCTTTTTCGGTTATAAAGTAA-TTTTCTGCTTTGAATCTAAGGTGTGTGATGCAT
196 AGTAAAAAATTCTTTTTCGGTTATAGAGTAATTTTTCTGCTCTAAATCTAAGGTGTGTGATGCAT
*
77196 AGGCAATGACATGCGTTATTTTGCTGACTTTTTAACTGAGAACTACTCCAACACTAGTGTCTGAG
261 AGGCAATGACATGCGGTATTTTGCTGACTTTTTAACTGAGAACTACTCCAACACTAGTGTCTGAG
*
77261 GAATCATAAATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTGATATTAG
326 GAATCATACATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTGATATTAG
77326 TTTTTCCTTCAAAATGACGAACAATTCCTTGCATTCTTGGTTGAAATCAAAGACTTTATCTTTTT
391 TTTTTCCTTCAAAATGACGAACAATTCCTTGCATTCTTGGTTGAAATCAAAGACTTTATCTTTTT
* *
77391 GAAGTAGATTACACAACGATTGTGTTATCTTTAAGAAGTCTTTGATGAACCTGAGGTAAAATATT
456 GAAGTAGATTACACAACGATTGTGTTATCTTTGAGAAGTCTTTGATGAACCTGAGGTAAAATCTT
77456 GCATGGCCAAGAAAAAA
521 GCATGGCCAAGAAAAAA
77473 A
1 A
77474 ATTTATTTTT
Statistics
Matches: 2088, Mismatches: 53, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
531 58 0.03
534 1 0.00
536 307 0.15
537 1514 0.73
538 208 0.10
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (537 bp):
ATCGAGCACCAAATTCTCACATCCTTTCTTATCCTTGATTTTTAAATTAAATTCTTGAAGGGGTA
AAATTCAACGGATAAGTCTCGGCTTCGCTTACTTTTTGCTCATTAAATATCGTAATGTTGCATGG
TCAGAATAAACAACAATATTAGTTCCCAGCAAATATGATCTAAATTTTTCCAAAGCAAATATTAT
AGTAAAAAATTCTTTTTCGGTTATAGAGTAATTTTTCTGCTCTAAATCTAAGGTGTGTGATGCAT
AGGCAATGACATGCGGTATTTTGCTGACTTTTTAACTGAGAACTACTCCAACACTAGTGTCTGAG
GAATCATACATGATCTCGAAAGGATAATCCCAATTTGGCATTTGTACAATCGGAGCTGATATTAG
TTTTTCCTTCAAAATGACGAACAATTCCTTGCATTCTTGGTTGAAATCAAAGACTTTATCTTTTT
GAAGTAGATTACACAACGATTGTGTTATCTTTGAGAAGTCTTTGATGAACCTGAGGTAAAATCTT
GCATGGCCAAGAAAAAA
Found at i:79323 original size:18 final size:18
Alignment explanation
Indices: 79300--79339 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
79290 TGAGGGGAAA
79300 GGAGGTGGAGCATCATAG
1 GGAGGTGGAGCATCATAG
79318 GGAGGTGGAGCATCATAG
1 GGAGGTGGAGCATCATAG
79336 GGAG
1 GGAG
79340 ATGGCACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.10, G:0.47, T:0.15
Consensus pattern (18 bp):
GGAGGTGGAGCATCATAG
Found at i:80666 original size:49 final size:49
Alignment explanation
Indices: 80593--80710 Score: 173
Period size: 49 Copynumber: 2.4 Consensus size: 49
80583 TGTTTTTAGT
* * * *
80593 TGATTCAATCCCATTTTTAGAATAGACCATATGGAAAGTAGGAAGAATA
1 TGATTCAAACCCATTTTTAGAATAGACCACATAGAAAGTAGGAAGAAGA
* * *
80642 TGATTCAACCCCGTTTTTATAATAGACCACATAGAAAGTAGGAAGAAGA
1 TGATTCAAACCCATTTTTAGAATAGACCACATAGAAAGTAGGAAGAAGA
80691 TGATTCAAACCCATTTTTAG
1 TGATTCAAACCCATTTTTAG
80711 TTGAAACAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (49 bp):
TGATTCAAACCCATTTTTAGAATAGACCACATAGAAAGTAGGAAGAAGA
Found at i:82962 original size:17 final size:17
Alignment explanation
Indices: 82907--82986 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
82897 TATTAATATG
*
82907 TATCTGATAATTGTAAAA
1 TATCTGATAACTGT-AAA
* * ** *
82925 TATATTATATTTGTAAT
1 TATCTGATAACTGTAAA
82942 TATCTGATAACTGTAAA
1 TATCTGATAACTGTAAA
*
82959 TATCTGATAACTGAAAA
1 TATCTGATAACTGTAAA
*
82976 TCATTTGATAA
1 T-ATCTGATAA
82987 TTTTAAACAT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
17 31 0.62
18 19 0.38
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (17 bp):
TATCTGATAACTGTAAA
Found at i:83200 original size:3 final size:3
Alignment explanation
Indices: 83192--83236 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
83182 CTTTAACACT
83192 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
83237 CAAATCAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:89175 original size:29 final size:28
Alignment explanation
Indices: 89111--89175 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
89101 TATATATAGC
*
89111 AAAAACAGAAACTTAAGTGACTAAAATA
1 AAAAACAGAAACTAAAGTGACTAAAATA
*
89139 AAATAACAGAAACTAAAGTGTC-AAAATCA
1 AAA-AACAGAAACTAAAGTGACTAAAAT-A
89168 AGAAAACA
1 A-AAAACA
89176 TATATATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 8 0.25
29 22 0.69
30 2 0.06
ACGTcount: A:0.62, C:0.12, G:0.11, T:0.15
Consensus pattern (28 bp):
AAAAACAGAAACTAAAGTGACTAAAATA
Found at i:89941 original size:3 final size:3
Alignment explanation
Indices: 89933--89999 Score: 91
Period size: 3 Copynumber: 21.7 Consensus size: 3
89923 TTAGGTATGG
*
89933 TAA TAA TAA TTAT TAA TAA TAA TAA TAAA TACA -AA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TA-A TAA TAA TAA TAA TAA
89980 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
90000 TTTTTTAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 1 0.02
3 51 0.88
4 6 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:92243 original size:3 final size:3
Alignment explanation
Indices: 92235--92260 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
92225 CTCCAGGGGT
92235 TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
92261 TTTTTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.35, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:105824 original size:60 final size:59
Alignment explanation
Indices: 105725--105901 Score: 196
Period size: 60 Copynumber: 3.0 Consensus size: 59
105715 CCATATGTTT
* * * *
105725 TCAAACTATGGCTCTCA-TCTATATTAGT-TTCTAAACTTTTGAATATTCTAATTTCATCC
1 TCAAACTAT-GATCTCATTCTAAATTAGTCTT-TAAACTTTTGAATATTCCAATTTCATCA
**
105784 TCAAACTATGATACTCATTCTAAATTAGTCTTTAAACTTTTGAGCATTCCAATTTCATCA
1 TCAAACTATGAT-CTCATTCTAAATTAGTCTTTAAACTTTTGAATATTCCAATTTCATCA
* *** * *
105844 TCAAACTATGACTCGCATTCTAAATTAGTCCCCAAACTTTTAAATCTTCCAATTTCAT
1 TCAAACTATGA-TCTCATTCTAAATTAGTCTTTAAACTTTTGAATATTCCAATTTCAT
105902 TCCCCAAATC
Statistics
Matches: 100, Mismatches: 14, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
58 2 0.02
59 13 0.13
60 82 0.82
61 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (59 bp):
TCAAACTATGATCTCATTCTAAATTAGTCTTTAAACTTTTGAATATTCCAATTTCATCA
Found at i:106931 original size:18 final size:19
Alignment explanation
Indices: 106908--106949 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
106898 TTGTAATCTT
106908 ATTCC-CTAATAATCTTAC
1 ATTCCACTAATAATCTTAC
*
106926 ATTCCCACTGATAATCTTAC
1 ATT-CCACTAATAATCTTAC
106946 ATTC
1 ATTC
106950 TGTGAACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 3 0.14
20 15 0.71
ACGTcount: A:0.31, C:0.29, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTCCACTAATAATCTTAC
Found at i:109045 original size:2 final size:2
Alignment explanation
Indices: 109038--109070 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
109028 TGAGGTTTAT
109038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
109071 TTGATCTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:113264 original size:20 final size:20
Alignment explanation
Indices: 113235--113272 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
113225 ATTTATGTTT
* *
113235 GTGTTTGTTTGTTTTTTTAG
1 GTGTTCGTTTATTTTTTTAG
113255 GTGTTCGTTTATTTTTTT
1 GTGTTCGTTTATTTTTTT
113273 TAAAGGCGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.03, G:0.21, T:0.71
Consensus pattern (20 bp):
GTGTTCGTTTATTTTTTTAG
Found at i:115946 original size:276 final size:278
Alignment explanation
Indices: 115402--115958 Score: 1075
Period size: 276 Copynumber: 2.0 Consensus size: 278
115392 TGTGGCGTTT
115402 TTCCAATAAATGCCACTGTAGACTTGTACAGTAATGGCGTTTTTAAAGAAATGCCGTTATAGAAT
1 TTCCAATAAATGCCACTGTAGACTTGTACAGTAATGGCGTTTTTAAAGAAATGCCGTTATAGAAT
115467 CGGACAATCGTGGTGTTTTTAAAGAAACGTCACAAGAGACTTGGACTATAGTGGCGTTTGTTGTG
66 CGGACAATCGTGGTGTTTTTAAAGAAACGTCACAAGAGACTTGGACTATAGTGGCG-TTGTTGTG
115532 AAAATGCCGCCAAAACGCCCACATTAGTGATGGTTTACTGGAAAAACGCCGCAAAAGGGTAACAT
130 AAAATGCCGCCAAAACGCCCACATTAGTGATGGTTTACTGGAAAAACGCCGCAAAAGGGTAACAT
115597 ATGCCTCCCCCTGCCCGATCCCTAAAATTTATTTCAACCTCTTCTTTAAAAAACTTCTTCTTCCT
195 ATGCCTCCCCCTGCCCGATCCCTAAAATTTATTTCAACCTCTTCTTTAAAAAACTTCTTCTTCCT
115662 CACTCTGGTATACAACATC
260 CACTCTGGTATACAACATC
115681 TTCCAATAAATGCCACTGTAGACTTGTACAGTAATGGCGTTTTTAAAGAAATGCCGTTATAGAAT
1 TTCCAATAAATGCCACTGTAGACTTGTACAGTAATGGCGTTTTTAAAGAAATGCCGTTATAGAAT
115746 CGGACAATCGTGGTGTTTTTAAAGAAACGTCACAAGAGACTTGGACTATAGTGGCG-T-TTGTGA
66 CGGACAATCGTGGTGTTTTTAAAGAAACGTCACAAGAGACTTGGACTATAGTGGCGTTGTTGTGA
115809 AAATGCCGCCAAAACGCCCACATTAGTGATGGTTTACTGGAAAAAACGCCGCAAAA-GGTAACAT
131 AAATGCCGCCAAAACGCCCACATTAGTGATGGTTTACTGG-AAAAACGCCGCAAAAGGGTAACAT
115873 ATGCCTCCCCCTGCCCGATCCCTAAAATTTATTTCAACCTCTTCTTTAAAAAACTTCTTCTTCCT
195 ATGCCTCCCCCTGCCCGATCCCTAAAATTTATTTCAACCTCTTCTTTAAAAAACTTCTTCTTCCT
115938 CACTCTGGTATACAACATC
260 CACTCTGGTATACAACATC
115957 TT
1 TT
115959 TAGCCCACAT
Statistics
Matches: 277, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
276 140 0.51
277 16 0.06
279 121 0.44
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (278 bp):
TTCCAATAAATGCCACTGTAGACTTGTACAGTAATGGCGTTTTTAAAGAAATGCCGTTATAGAAT
CGGACAATCGTGGTGTTTTTAAAGAAACGTCACAAGAGACTTGGACTATAGTGGCGTTGTTGTGA
AAATGCCGCCAAAACGCCCACATTAGTGATGGTTTACTGGAAAAACGCCGCAAAAGGGTAACATA
TGCCTCCCCCTGCCCGATCCCTAAAATTTATTTCAACCTCTTCTTTAAAAAACTTCTTCTTCCTC
ACTCTGGTATACAACATC
Found at i:117084 original size:43 final size:43
Alignment explanation
Indices: 116977--117086 Score: 166
Period size: 43 Copynumber: 2.6 Consensus size: 43
116967 TCTGCCGGAC
* *
116977 ACGCCGCTACATATCAAATCAATTGCGGCGTTTGTGACTACAA
1 ACGCCGCTACATATCAAATCTATTGCGACGTTTGTGACTACAA
*
117020 ACGCCGCTACATATCAAATCTATTGCGATGTTTGTGACTACAA
1 ACGCCGCTACATATCAAATCTATTGCGACGTTTGTGACTACAA
* **
117063 ACGCCGCTAAATATCGGATCTATT
1 ACGCCGCTACATATCAAATCTATT
117087 TCAAGAAAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (43 bp):
ACGCCGCTACATATCAAATCTATTGCGACGTTTGTGACTACAA
Found at i:117842 original size:28 final size:28
Alignment explanation
Indices: 117810--117866 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
117800 CCATTTTCTT
117810 ATTATTTTATTTGGTTTTTTTAATAACA
1 ATTATTTTATTTGGTTTTTTTAATAACA
117838 ATTATTTTATTTGGTTTTTTTAATAACA
1 ATTATTTTATTTGGTTTTTTTAATAACA
117866 A
1 A
117867 ATAATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.60
Consensus pattern (28 bp):
ATTATTTTATTTGGTTTTTTTAATAACA
Found at i:117881 original size:31 final size:30
Alignment explanation
Indices: 117810--117882 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 30
117800 CCATTTTCTT
*
117810 ATTATTTTATTTGGTTTTTTTAATAACAATT
1 ATTA-TTTATTTGGTTTTTTTAATAACAATA
117841 A-T-TTTATTTGGTTTTTTTAATAACAAATA
1 ATTATTTATTTGGTTTTTTTAATAAC-AATA
117870 ATTATTTATTTGG
1 ATTATTTATTTGG
117883 AAAATTATCA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 22 0.58
29 4 0.11
30 2 0.05
31 10 0.26
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (30 bp):
ATTATTTATTTGGTTTTTTTAATAACAATA
Found at i:119034 original size:10 final size:11
Alignment explanation
Indices: 119009--119038 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
118999 GGCCATCATG
119009 TTAACAAATCA
1 TTAACAAATCA
119020 TTAACAAAT-A
1 TTAACAAATCA
119030 TTAACAAAT
1 TTAACAAAT
119039 TGTCAACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (11 bp):
TTAACAAATCA
Found at i:125209 original size:30 final size:32
Alignment explanation
Indices: 125141--125217 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 32
125131 TTCAAAATAC
125141 ATAAGATATGGTCACTTACGTTTTCTATTTAA
1 ATAAGATATGGTCACTTACGTTTTCTATTTAA
* * **
125173 ACAAGATTTGGT-ACTTTTGTTTT-TATTTAA
1 ATAAGATATGGTCACTTACGTTTTCTATTTAA
* *
125203 TTAAGATGTGGTCAC
1 ATAAGATATGGTCAC
125218 CCCGCCGAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 16 0.43
31 11 0.30
32 10 0.27
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (32 bp):
ATAAGATATGGTCACTTACGTTTTCTATTTAA
Found at i:125838 original size:25 final size:23
Alignment explanation
Indices: 125809--125879 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 23
125799 ATATATATAT
125809 AATATAATTATATATATTAACTTAA
1 AATAT-ATT-TATATATTAACTTAA
125834 AATAT-TTT-TATATTAACTTATTA
1 AATATATTTATATATTAACTTA--A
125857 AATATATTT-TATATTTAACTTAA
1 AATATATTTATATA-TTAACTTAA
125880 TTTAAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
21 12 0.29
22 1 0.02
23 9 0.21
24 7 0.17
25 13 0.31
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATATTTATATATTAACTTAA
Found at i:125845 original size:21 final size:22
Alignment explanation
Indices: 125821--125879 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 22
125811 TATAATTATA
125821 TATATTAACTTAAAATAT-TTT
1 TATATTAACTTAAAATATATTT
125842 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
125866 TATATTTAACTTAA
1 TATA-TTAACTTAA
125880 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.35
23 7 0.21
24 7 0.21
25 8 0.24
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:125891 original size:27 final size:26
Alignment explanation
Indices: 125832--125918 Score: 88
Period size: 28 Copynumber: 3.3 Consensus size: 26
125822 ATATTAACTT
125832 AAAATATTTT-TATATTAACTTA-TTA
1 AAAATATTTTATAT-TTAACTTATTTA
*
125857 AATATATTTTATATTTAACTTAATTTA
1 AAAATATTTTATATTTAACTT-ATTTA
* **
125884 AAAATATTTTATTTTTTATTTTCATTTA
1 AAAATATTTTA-TATTTAACTT-ATTTA
125912 AAAATAT
1 AAAATAT
125919 ATAATTTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
25 16 0.31
26 4 0.08
27 13 0.25
28 19 0.37
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (26 bp):
AAAATATTTTATATTTAACTTATTTA
Found at i:125896 original size:25 final size:24
Alignment explanation
Indices: 125832--125897 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 24
125822 ATATTAACTT
125832 AAAATATTTTTATATTAACTTATTA
1 AAAATATTTTTAT-TTAACTTATTA
*
125857 AATATATTTTATATTTAACTTAATTTA
1 AAAATATTTT-TATTTAACTT-A-TTA
125884 AAAATA-TTTTATTT
1 AAAATATTTTTATTT
125898 TTTATTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 21 0.58
26 7 0.19
27 8 0.22
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
AAAATATTTTTATTTAACTTATTA
Found at i:138582 original size:21 final size:21
Alignment explanation
Indices: 138531--138583 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
138521 ATTATGACTA
*
138531 TCGCAATGCGATTTTCTAATT
1 TCGCAATGCGATTTTCCAATT
**
138552 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
138573 TCGCAATGCGA
1 TCGCAATGCGA
138584 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:138598 original size:20 final size:21
Alignment explanation
Indices: 138573--138624 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
138563 TTTTCCCAAT
*
138573 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
138593 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
138614 TCGCAATGCGA
1 TCGCAATGCGA
138625 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:138637 original size:41 final size:41
Alignment explanation
Indices: 138610--138707 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
138600 GCGAATTGGG
*
138610 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
138651 AAAATCGCAACGCGATATTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
138692 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
138708 TTTCAAAGCG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:138680 original size:20 final size:20
Alignment explanation
Indices: 138613--138707 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
138603 AATTGGGAAA
* *
138613 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATGACT
*
138633 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
*
138654 ATCGCAACGCGATATTGACT
1 ATCGCAACGCGATAATGACT
* *
138674 TTCGCAACGAGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
138694 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
138708 TTTCAAAGCG
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.07
20 28 0.47
21 25 0.42
22 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:138898 original size:22 final size:22
Alignment explanation
Indices: 138873--138923 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
138863 CTACGGCAAC
138873 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
138895 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
*
138917 ATTCGTC
1 ATCCGTC
138924 TATCTCCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:139239 original size:20 final size:20
Alignment explanation
Indices: 139200--139258 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
139190 GCGATTCTCT
**
139200 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
139220 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * **
139240 TGTTGTGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
139259 AGAAATTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:139449 original size:25 final size:24
Alignment explanation
Indices: 139395--139449 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
139385 TGTTTATTAT
* *
139395 TGTTTTTGGTATATCTTTACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
139419 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
139445 TGTTT
1 TGTTT
139450 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:141232 original size:19 final size:20
Alignment explanation
Indices: 141177--141244 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
141167 GAAACTTAAA
* *
141177 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
141197 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* **
141217 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGACT
141236 ATCGCAACG
1 ATCGCAACG
141245 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:141242 original size:39 final size:35
Alignment explanation
Indices: 141197--141300 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 35
141187 GAAAATGACT
141197 ATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAA
1 ATCGCAACGC-GAAAT-G--ATCGCAATGCGAAATGAAA
141236 ATCGCAACGAC-AAA--ATCGCAATGCGAAATGAAA
1 ATCGCAACG-CGAAATGATCGCAATGCGAAATGAAA
*
141269 ATCGCAACGAGAAAATGAAAATCGCAATGCGA
1 ATCGCAACGCG-AAATG---ATCGCAATGCGA
141301 TTTGTGTTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
33 28 0.50
34 3 0.05
38 3 0.05
39 21 0.38
40 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (35 bp):
ATCGCAACGCGAAATGATCGCAATGCGAAATGAAA
Found at i:141259 original size:33 final size:33
Alignment explanation
Indices: 141217--141284 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
141207 GGAAATGGCT
141217 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
141250 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
141283 AT
1 AT
141285 GAAAATCGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:141284 original size:14 final size:14
Alignment explanation
Indices: 141232--141284 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
141222 AATGCGAAAT
141232 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
141246 CAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
141264 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
141279 GAAAAT
1 GAAAAT
141285 GAAAATCGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 16 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.31
ACGTcount: A:0.51, C:0.19, G:0.19, T:0.11
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:141286 original size:20 final size:19
Alignment explanation
Indices: 141247--141295 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
141237 TCGCAACGAC
* *
141247 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGAGAAATG
141266 AAAATCGCAACGAGAAAATG
1 AAAATCGCAACGAG-AAATG
141286 AAAATCGCAA
1 AAAATCGCAA
141296 TGCGATTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGAGAAATG
Found at i:141329 original size:14 final size:14
Alignment explanation
Indices: 141307--141370 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
141297 GCGATTTGTG
141307 TTTTG-CGTTGCGA
1 TTTTGTCGTTGCGA
*
141320 TTTTGTCGTTGTGA
1 TTTTGTCGTTGCGA
*
141334 TTTTCATTTCGCATTGCGA
1 -TTT--TGTCG--TTGCGA
141353 TTTTGTCGTTGCGA
1 TTTTGTCGTTGCGA
141367 TTTT
1 TTTT
141371 CATTTCGCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
13 5 0.12
14 17 0.41
15 3 0.07
16 4 0.10
17 4 0.10
18 3 0.07
19 5 0.12
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.53
Consensus pattern (14 bp):
TTTTGTCGTTGCGA
Found at i:141351 original size:33 final size:33
Alignment explanation
Indices: 141314--141382 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
141304 GTGTTTTGCG
*
141314 TTGCGATTTTGTCGTTGTGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
141347 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
141380 TTG
1 TTG
141383 TGATAGCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.51
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
Found at i:141398 original size:20 final size:20
Alignment explanation
Indices: 141373--141426 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
141363 GCGATTTTCA
*
141373 TTTCGCATTGTGATAGCCAT
1 TTTCGCATTGCGATAGCCAT
* *
141393 TTTCGCGTTGCGATAGTCAT
1 TTTCGCATTGCGATAGCCAT
*
141413 TTTCGCGTTGCGAT
1 TTTCGCATTGCGAT
141427 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
TTTCGCATTGCGATAGCCAT
Found at i:141436 original size:20 final size:20
Alignment explanation
Indices: 141393--141451 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
141383 TGATAGCCAT
* *
141393 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTAAG
**
141413 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATAGTAAG
* *
141433 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGATAGTAA
141452 ACTATTCTTC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTAAG
Found at i:141844 original size:21 final size:20
Alignment explanation
Indices: 141792--141852 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
141782 GACTCACTTG
141792 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
141812 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
141833 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
141853 CCCCCACCGT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:141881 original size:43 final size:42
Alignment explanation
Indices: 141790--141881 Score: 130
Period size: 43 Copynumber: 2.2 Consensus size: 42
141780 CCGACTCACT
* * *
141790 TGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCC
1 TGTCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCAC
* *
141832 TATCATCCCTCAAGAGTCCCCCCCCCACCGTTCAAGAGGCCAC
1 TGTCATCCCTCAAGAGT-CCCCCCCAACCGTTCAAGAGGCCAC
141875 TGTCATC
1 TGTCATC
141882 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 16 0.37
43 27 0.63
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
TGTCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCAC
Found at i:143323 original size:14 final size:14
Alignment explanation
Indices: 143289--143327 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
143279 TTGATTGTTT
143289 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
143303 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
143317 TGTTGATTTGT
1 AATTGATTTGT
143328 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:143473 original size:14 final size:14
Alignment explanation
Indices: 143454--143507 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
143444 GAAACTGACT
*
143454 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
143468 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
143487 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
143501 ATCGCAA
1 ATCGCAA
143508 TGTGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:143548 original size:19 final size:19
Alignment explanation
Indices: 143511--143572 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
143501 ATCGCAATGT
*
143511 GATTTTCATTTTCGTATTGC
1 GATTTTCA-TTTCGCATTGC
143531 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
***
143550 GATAGCCATTTCCGCATTGC
1 GATTTTCATTT-CGCATTGC
143570 GAT
1 GAT
143573 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 18 0.49
20 19 0.51
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:143573 original size:20 final size:20
Alignment explanation
Indices: 143537--143616 Score: 144
Period size: 20 Copynumber: 4.0 Consensus size: 20
143527 TTGCGATTTT
143537 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
143556 CATTTCCGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
143576 CATTTCCACATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
143596 CATTTCCGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
143616 C
1 C
143617 CCGTTGCGAT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
19 5 0.09
20 53 0.91
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:147011 original size:41 final size:41
Alignment explanation
Indices: 146948--147025 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
146938 CGAAAATTGG
* *
146948 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
*
146989 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTT
147026 CCCAATTCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.37
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:147014 original size:20 final size:20
Alignment explanation
Indices: 146888--147022 Score: 119
Period size: 20 Copynumber: 6.7 Consensus size: 20
146878 GATTCTGTAT
*
146888 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
146908 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * **
146928 AATCGCGTTGCGAAAATTGG
1 TATCGCGTTGCGATAGTCAG
*
146948 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
146968 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
146989 TATCGCGTTGCGATAGTAAG
1 TATCGCGTTGCGATAGTCAG
*
147009 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
147023 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
19 3 0.03
20 77 0.80
21 14 0.15
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:147036 original size:41 final size:41
Alignment explanation
Indices: 146948--147043 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
146938 CGAAAATTGG
* * * ** *
146948 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
146989 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
147031 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
147044 TTACTTATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:147104 original size:21 final size:22
Alignment explanation
Indices: 147052--147104 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
147042 ATTTACTTAT
*
147052 TCGCATTGTG-AATTGGAAAAA
1 TCGCATTGCGAAATTGGAAAAA
**
147073 TCGCAACGCGAAATTGG-AAAA
1 TCGCATTGCGAAATTGGAAAAA
147094 TCGCATTGCGA
1 TCGCATTGCGA
147105 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGAAAAA
Found at i:149852 original size:15 final size:15
Alignment explanation
Indices: 149832--149913 Score: 103
Period size: 15 Copynumber: 5.5 Consensus size: 15
149822 TTCAAGAAAA
*
149832 TGAATTATTGGAATT
1 TGAATTACTGGAATT
*
149847 TGAATTACTGTAATT
1 TGAATTACTGGAATT
**
149862 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
149877 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
149892 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
149906 TGAATTAC
1 TGAATTAC
149914 ATTTCTGTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
14 12 0.21
15 45 0.79
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:149911 original size:29 final size:30
Alignment explanation
Indices: 149832--149913 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
149822 TTCAAGAAAA
* ** *
149832 TGAATTATTGGAATTTGAATTACTGTAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
149862 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
149892 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
149914 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 16 0.33
30 32 0.67
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:149919 original size:20 final size:20
Alignment explanation
Indices: 149896--149966 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
149886 GGAATTTGAA
149896 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
149916 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
149936 TTTTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
149956 TTCTGGAAAAT
1 TTCTGGAAAAT
149967 ATCTGGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.38
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:150176 original size:26 final size:25
Alignment explanation
Indices: 150144--150268 Score: 85
Period size: 26 Copynumber: 4.8 Consensus size: 25
150134 TTATTGAAAT
150144 ATATAAATAATATTATTCATTATTAA
1 ATATAAATAATATTATT-ATTATTAA
*
150170 ATATAAA-AAAATTTATTATATATTAAA
1 ATATAAATAATA-TTATTAT-TATT-AA
*
150197 ATAAAAATAATATCTA-TATTATTATA
1 ATATAAATAATAT-TATTATTATTA-A
* *
150223 ATATAATTGATTATT-TTATAATATTAA
1 ATATAAAT-AATATTATTAT--TATTAA
* * *
150250 AAATATATTATATTATTAT
1 ATATAAATAATATTATTAT
150269 AAATATTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
25 6 0.08
26 35 0.45
27 26 0.34
28 10 0.13
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (25 bp):
ATATAAATAATATTATTATTATTAA
Found at i:150266 original size:19 final size:19
Alignment explanation
Indices: 150238--150274 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
150228 ATTGATTATT
150238 TTATAATATTAAAAATATA
1 TTATAATATTAAAAATATA
* *
150257 TTATATTATTATAAATAT
1 TTATAATATTAAAAATAT
150275 TAATAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATAATATTAAAAATATA
Found at i:150293 original size:47 final size:49
Alignment explanation
Indices: 150198--150294 Score: 130
Period size: 47 Copynumber: 2.0 Consensus size: 49
150188 TATATTAAAA
* *
150198 TAAAAATAATATCTATATTATTATAATATAATTGATTATTTTATAATAT
1 TAAAAATAATATCTATATTATTATAATATAATTAAATATTTTATAATAT
150247 TAAAAAT-ATAT-TATATTATTATAAATATTAA-TAAATATTTTA-AATAT
1 TAAAAATAATATCTATATTATTAT-AATA-TAATTAAATATTTTATAATAT
150294 T
1 T
150295 TTAATAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
47 17 0.39
48 17 0.39
49 10 0.23
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (49 bp):
TAAAAATAATATCTATATTATTATAATATAATTAAATATTTTATAATAT
Found at i:150294 original size:28 final size:28
Alignment explanation
Indices: 150203--150307 Score: 83
Period size: 28 Copynumber: 3.7 Consensus size: 28
150193 TAAAATAAAA
*
150203 ATAATATCTATATTATT-ATAATATA-ATT
1 ATAATAT-TATAATATTAATAA-ATATATT
* *
150231 GATTATTTTATAATATTAA-AAATATATT
1 -ATAATATTATAATATTAATAAATATATT
* *
150259 ATATTATTATAAATATTAATAAATATTTT
1 ATAATATTAT-AATATTAATAAATATATT
*
150288 A-AATATTTTAATAATTAATA
1 ATAATATTATAAT-ATTAATA
150308 TTTTGATGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
27 13 0.21
28 34 0.55
29 15 0.24
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
ATAATATTATAATATTAATAAATATATT
Found at i:150542 original size:42 final size:42
Alignment explanation
Indices: 150483--150602 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
150473 ATGAATTACA
*
150483 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
150525 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
150567 TTCTGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
150603 TTCGGGGAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:163453 original size:2 final size:2
Alignment explanation
Indices: 163448--163516 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
163438 GTAAACGAAC
163448 TA TA 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 TA TA
163490 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
163517 GGATCAATTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:164675 original size:17 final size:17
Alignment explanation
Indices: 164643--164676 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
164633 ATATTGTTGA
*
164643 AATTCAAAACAGCCAAC
1 AATTCAAAACAACCAAC
*
164660 AATTCAAAGCAACCAAC
1 AATTCAAAACAACCAAC
164677 GGCTAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.29, G:0.06, T:0.12
Consensus pattern (17 bp):
AATTCAAAACAACCAAC
Found at i:174392 original size:26 final size:25
Alignment explanation
Indices: 174363--174416 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 25
174353 ATTTAAGCTT
174363 TTTCTT-TTTATTTTTCAAAGTTTTTA
1 TTTCTTCTTTATTTTTC-AAG-TTTTA
174389 TTTCTTCTTTATTTTTCAAGTTTTA
1 TTTCTTCTTTATTTTTCAAGTTTTA
174414 TTT
1 TTT
174417 TTATGCTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 8 0.30
26 9 0.33
27 10 0.37
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTCTTCTTTATTTTTCAAGTTTTA
Found at i:180745 original size:26 final size:26
Alignment explanation
Indices: 180716--180765 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
180706 ATTTAAGCTT
180716 TTTCTT-TTTATTTTTCAAAGTTTTTA
1 TTTCTTCTTTATTTTTC-AAGTTTTTA
180742 TTTCTTCTTTATTTTTCAAGTTTT
1 TTTCTTCTTTATTTTTCAAGTTTT
180766 GTTTTTATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.16, C:0.10, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTCTTCTTTATTTTTCAAGTTTTTA
Found at i:180931 original size:18 final size:18
Alignment explanation
Indices: 180908--180957 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
180898 CTGCGTTTAT
180908 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
180926 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
180944 TTTTCAAAATCAAA
1 TTTTCAAAATCAAA
180958 GATTGACTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (18 bp):
TTTTCAAAATCAAAACAG
Found at i:184313 original size:25 final size:28
Alignment explanation
Indices: 184285--184335 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
184275 GAAAACCCAT
*
184285 ATCATCA-AACC-CACAC-AAAAACAGA
1 ATCATCATAACCAAACACGAAAAACAGA
184310 ATCATCATAACCAAACACGAAAAACA
1 ATCATCATAACCAAACACGAAAAACA
184336 CAAGCCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 4 0.18
27 4 0.18
28 7 0.32
ACGTcount: A:0.57, C:0.29, G:0.04, T:0.10
Consensus pattern (28 bp):
ATCATCATAACCAAACACGAAAAACAGA
Found at i:184327 original size:27 final size:27
Alignment explanation
Indices: 184266--184337 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 27
184256 CCACAGTAAG
*
184266 CCAAACACAGAAAACCCATATCATCAAA
1 CCAAACACA-AAAACACATATCATCAAA
* *
184294 CC-CACACAAAAACAGA-ATCATCATAA
1 CCAAACACAAAAACACATATCATCA-AA
184320 CCAAACACGAAAAACACA
1 CCAAACAC-AAAAACACA
184338 AGCCAACAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 7 0.19
26 10 0.28
27 9 0.25
28 10 0.28
ACGTcount: A:0.56, C:0.32, G:0.04, T:0.08
Consensus pattern (27 bp):
CCAAACACAAAAACACATATCATCAAA
Found at i:185083 original size:14 final size:15
Alignment explanation
Indices: 185066--185098 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
185056 TTTTTTTATC
185066 TATTTTTATTATT-T
1 TATTTTTATTATTGT
185080 TA-TTTTATTATTGT
1 TATTTTTATTATTGT
185094 TATTT
1 TATTT
185099 CTTTCCCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.59
14 5 0.29
15 2 0.12
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TATTTTTATTATTGT
Found at i:185091 original size:22 final size:23
Alignment explanation
Indices: 185054--185097 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
185044 ACTTTAACCC
* *
185054 TTTTTTTTTATCTATTTTTATTA
1 TTTTATTTTATCTATTGTTATTA
185077 TTTTATTTTAT-TATTGTTATT
1 TTTTATTTTATCTATTGTTATT
185098 TCTTTCCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTATTTTATCTATTGTTATTA
Found at i:185356 original size:30 final size:30
Alignment explanation
Indices: 185305--185365 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
185295 TTTGATTTAT
*
185305 ATTCATTTATTTATTTATTTTTTTCTTCCTA
1 ATTCATTTACTTATTTATTTTTTT-TTCCTA
*
185336 ATTCA-TTACTTATTTGTTTTTTTTTCCTA
1 ATTCATTTACTTATTTATTTTTTTTTCCTA
185365 A
1 A
185366 CATCTTCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.25
30 16 0.57
31 5 0.18
ACGTcount: A:0.20, C:0.13, G:0.02, T:0.66
Consensus pattern (30 bp):
ATTCATTTACTTATTTATTTTTTTTTCCTA
Found at i:190693 original size:165 final size:165
Alignment explanation
Indices: 190421--191139 Score: 1339
Period size: 165 Copynumber: 4.4 Consensus size: 165
190411 TAAACAAACT
* *
190421 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
190486 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
190551 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
190586 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
190651 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
190716 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* *
190751 ATCTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTAGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
190816 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
190881 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
190916 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
190981 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGATAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
*
191046 TTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * **
191081 ATTGGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAAAGACCTTCGAGTTCGATTA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
191140 TATTCAACTT
Statistics
Matches: 540, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
165 540 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (165 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:191821 original size:26 final size:27
Alignment explanation
Indices: 191792--191843 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
191782 GTTTAAAACA
* *
191792 TTTTTGAAAATATGTATAT-TATATAG
1 TTTTTAAAAACATGTATATATATATAG
*
191818 TTTTTAAAAACATTTATATATATATA
1 TTTTTAAAAACATGTATATATATATA
191844 TATATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (27 bp):
TTTTTAAAAACATGTATATATATATAG
Found at i:191824 original size:37 final size:37
Alignment explanation
Indices: 191755--191832 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
191745 TTGCAAATTG
191755 TTTTTGAAAATACATATATAATATATAGTTT-AAAACA
1 TTTTTGAAAATA-ATATATAATATATAGTTTAAAAACA
* *
191792 TTTTTGAAAAT-ATGTATATTATATAGTTTTTAAAAACA
1 TTTTTGAAAATAATATATAATATATAG--TTTAAAAACA
191830 TTT
1 TTT
191833 ATATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
35 13 0.36
37 14 0.39
38 9 0.25
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAATAATATATAATATATAGTTTAAAAACA
Found at i:191848 original size:38 final size:35
Alignment explanation
Indices: 191759--191848 Score: 83
Period size: 38 Copynumber: 2.4 Consensus size: 35
191749 AAATTGTTTT
* *
191759 TGAAAATACATATATAATATATAGTTTAAAACATTTT
1 TGAAAAT--ATATATATTATATAGTTTAAAACATTTA
*
191796 TGAAAATATGTATATTATATAGTTTTTAAAAACATTTA
1 TGAAAATATATATATTATATAG--TTT-AAAACATTTA
*
191834 T-ATATATATATATAT
1 TGA-AAATATATATAT
191849 ATTTTTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
35 13 0.30
37 11 0.25
38 20 0.45
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (35 bp):
TGAAAATATATATATTATATAGTTTAAAACATTTA
Found at i:191850 original size:35 final size:33
Alignment explanation
Indices: 191768--191850 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 33
191758 TTGAAAATAC
*
191768 ATATATA-ATATATAGTTTAAAACATTTTTGAAA
1 ATATATATATATATAGTTTAAAACATTTAT-AAA
* *
191801 ATATGTATATTATATAGTTTTTAAAAACATTTAT-AT
1 ATATATATA-TATATAG--TTT-AAAACATTTATAAA
191837 ATATATATATATAT
1 ATATATATATATAT
191851 TTTTTTATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
33 6 0.15
34 1 0.02
35 12 0.29
36 9 0.22
37 3 0.07
38 10 0.24
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (33 bp):
ATATATATATATATAGTTTAAAACATTTATAAA
Found at i:191865 original size:4 final size:4
Alignment explanation
Indices: 191829--191894 Score: 50
Period size: 4 Copynumber: 17.5 Consensus size: 4
191819 TTTTAAAAAC
* * * * *
191829 ATTT ATAT ATAT ATAT ATAT ATTT TTTT A-TT ATTT A-TT -TTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
*
191874 -TTA ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT AT
191895 CTGTCTCCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
3 9 0.17
4 43 0.83
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:191870 original size:13 final size:13
Alignment explanation
Indices: 191852--191892 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
191842 TATATATATT
191852 TTTTTATTATTTA
1 TTTTTATTATTTA
191865 TTTTTATT-TTTA
1 TTTTTATTATTTA
*
191877 -ATTTATTTATTTA
1 TTTTTA-TTATTTA
191890 TTT
1 TTT
191893 ATCTGTCTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 4 0.17
12 6 0.26
13 12 0.52
14 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTATTATTTA
Found at i:191882 original size:17 final size:15
Alignment explanation
Indices: 191848--191891 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
191838 TATATATATA
191848 TATTTTTTTATTATT
1 TATTTTTTTATTATT
*
191863 TATTTTTATTTTTAATT
1 TATTTTT-TTATT-ATT
*
191880 TATTTATTTATT
1 TATTTTTTTATT
191892 TATCTGTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 9 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTTTTATTATT
Found at i:192296 original size:25 final size:28
Alignment explanation
Indices: 192268--192318 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
192258 GAAAACCCAT
*
192268 ATCATCA-AACC-CACAC-AAAAACAGA
1 ATCATCATAACCAAACACGAAAAACAGA
192293 ATCATCATAACCAAACACGAAAAACA
1 ATCATCATAACCAAACACGAAAAACA
192319 CAAGCCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 4 0.18
27 4 0.18
28 7 0.32
ACGTcount: A:0.57, C:0.29, G:0.04, T:0.10
Consensus pattern (28 bp):
ATCATCATAACCAAACACGAAAAACAGA
Found at i:192310 original size:27 final size:27
Alignment explanation
Indices: 192249--192320 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 27
192239 CCACAGTAAG
*
192249 CCAAACACAGAAAACCCATATCATCAAA
1 CCAAACACA-AAAACACATATCATCAAA
* *
192277 CC-CACACAAAAACAGA-ATCATCATAA
1 CCAAACACAAAAACACATATCATCA-AA
192303 CCAAACACGAAAAACACA
1 CCAAACAC-AAAAACACA
192321 AGCCAACAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 7 0.19
26 10 0.28
27 9 0.25
28 10 0.28
ACGTcount: A:0.56, C:0.32, G:0.04, T:0.08
Consensus pattern (27 bp):
CCAAACACAAAAACACATATCATCAAA
Found at i:194671 original size:15 final size:16
Alignment explanation
Indices: 194651--194684 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
194641 AGCTGGACGG
194651 TAAAATAGATA-TAAA
1 TAAAATAGATATTAAA
*
194666 TAAAATAGTTATTAAA
1 TAAAATAGATATTAAA
194682 TAA
1 TAA
194685 TTAAATTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
TAAAATAGATATTAAA
Found at i:194883 original size:27 final size:27
Alignment explanation
Indices: 194836--194897 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
194826 TTTATAAATG
* *
194836 CACAAAGATATTGTTATGAGTAATAGCA
1 CACAAA-ATACTGTTACGAGTAATAGCA
194864 CACAAAATACTGTTACGAGTAATAGCA
1 CACAAAATACTGTTACGAGTAATAGCA
194891 CACAAAA
1 CACAAAA
194898 GTGTCATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 26 0.81
28 6 0.19
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.23
Consensus pattern (27 bp):
CACAAAATACTGTTACGAGTAATAGCA
Found at i:196874 original size:24 final size:24
Alignment explanation
Indices: 196847--196924 Score: 88
Period size: 23 Copynumber: 3.3 Consensus size: 24
196837 CCGAAGTGTA
* *
196847 ACATAGAAATTGTCTCGAATGACC
1 ACATAGAATTTGTCCCGAATGACC
* *
196871 ACATAG-TTTTGTCCCGAATGACA
1 ACATAGAATTTGTCCCGAATGACC
* *
196894 ACATA-AGTTTGTCCCGAAGGACC
1 ACATAGAATTTGTCCCGAATGACC
196917 ACATAGAA
1 ACATAGAA
196925 CCCTCGACCC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 37 0.84
24 7 0.16
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (24 bp):
ACATAGAATTTGTCCCGAATGACC
Found at i:196888 original size:23 final size:22
Alignment explanation
Indices: 196856--196922 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
196846 AACATAGAAA
*
196856 TTGTCTCGAATGACCACATAGTT
1 TTGTCCCGAATGACCACATAG-T
*
196879 TTGTCCCGAATGACAACATAAGT
1 TTGTCCCGAATGACCACAT-AGT
*
196902 TTGTCCCGAAGGACCACATAG
1 TTGTCCCGAATGACCACATAG
196923 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
22 2 0.05
23 35 0.90
24 2 0.05
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (22 bp):
TTGTCCCGAATGACCACATAGT
Found at i:197128 original size:16 final size:15
Alignment explanation
Indices: 197098--197131 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
197088 TATATTATTT
197098 TCATATAGAACATAA
1 TCATATAGAACATAA
*
197113 TCATATATATACATAA
1 TCATATAGA-ACATAA
197129 TCA
1 TCA
197132 AAACAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (15 bp):
TCATATAGAACATAA
Found at i:205373 original size:16 final size:16
Alignment explanation
Indices: 205330--205366 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
205320 AAGTTAAACA
205330 CTTTCCCTCTTCACAT
1 CTTTCCCTCTTCACAT
205346 CTTTCCCTCTTCACAT
1 CTTTCCCTCTTCACAT
205362 CTTTC
1 CTTTC
205367 TTCCTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.11, C:0.43, G:0.00, T:0.46
Consensus pattern (16 bp):
CTTTCCCTCTTCACAT
Found at i:207839 original size:18 final size:18
Alignment explanation
Indices: 207818--207873 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
207808 AATAATAAAT
*
207818 TAATTTAAATAAAATTGA
1 TAATTTAAATAAAATTAA
* *
207836 TAATTT-ATTAAAAATAA
1 TAATTTAAATAAAATTAA
207853 TAGATTTATAATAAAA-TAA
1 TA-ATTTA-AATAAAATTAA
207872 TA
1 TA
207874 GAAAGTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 10 0.32
18 10 0.32
19 5 0.16
20 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (18 bp):
TAATTTAAATAAAATTAA
Found at i:207870 original size:19 final size:19
Alignment explanation
Indices: 207820--207875 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
207810 TAATAAATTA
*
207820 ATTTA-AATAAAATTGATA-
1 ATTTATAATAAAA-TAATAG
*
207838 ATTTATTA-AAAATAATAG
1 ATTTATAATAAAATAATAG
207856 ATTTATAATAAAATAATAG
1 ATTTATAATAAAATAATAG
207875 A
1 A
207876 AAGTTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.12
18 16 0.50
19 12 0.38
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
ATTTATAATAAAATAATAG
Found at i:208464 original size:32 final size:32
Alignment explanation
Indices: 208430--208599 Score: 92
Period size: 32 Copynumber: 5.2 Consensus size: 32
208420 TAACCTATCG
208430 AAAATCAACTGATCCAATATTGACCCAACCC-
1 AAAATCAACTGATCCAATATTGACCCAACCCA
* * *** * *
208461 GAAATCTAACTAATCTGGTATTAACCCGACCCA
1 AAAATC-AACTGATCCAATATTGACCCAACCCA
* * * *
208494 AAAAGCAACCGATCCGATATTGACCCTACCTGATCCA
1 AAAATCAACTGATCCAATATTGACCC-A----ACCCA
* ** *
208531 AAAATCAACTGATCCAATGTTGATCTGAACCGA
1 AAAATCAACTGATCCAATATTGA-CCCAACCCA
* * * *
208564 AAAA-CAACCGATCCAATAATCACCCGACCCA
1 AAAATCAACTGATCCAATATTGACCCAACCCA
208595 AAAAT
1 AAAAT
208600 TGACCCAACC
Statistics
Matches: 98, Mismatches: 32, Indels: 17
0.67 0.22 0.12
Matches are distributed among these distances:
31 14 0.14
32 48 0.49
33 11 0.11
37 24 0.24
38 1 0.01
ACGTcount: A:0.41, C:0.29, G:0.11, T:0.19
Consensus pattern (32 bp):
AAAATCAACTGATCCAATATTGACCCAACCCA
Found at i:210658 original size:23 final size:24
Alignment explanation
Indices: 210606--210668 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
210596 TTAATAATTT
* *
210606 TGTCTTTATGAAAC-GTATTCTTC
1 TGTCTTTATGACACATTATTCTTC
**
210629 TACCTTTATGACACATTATTC-TC
1 TGTCTTTATGACACATTATTCTTC
210652 TGTCTTTATGACACATT
1 TGTCTTTATGACACATT
210669 TTTAGTCGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 28 0.85
24 5 0.15
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.46
Consensus pattern (24 bp):
TGTCTTTATGACACATTATTCTTC
Found at i:213684 original size:21 final size:21
Alignment explanation
Indices: 213637--213684 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
213627 TAAATTTCAA
*
213637 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
*
213658 ACATTGTTGTACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
213679 ACATTG
1 ACATTG
213685 CAATATTAGG
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:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:223805 original size:29 final size:30
Alignment explanation
Indices: 223751--223808 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
223741 AACAATTATA
* *
223751 GAGTTTAATATTTTTGAACTGCTCAAATAC
1 GAGTTTAATATTTTTGAAATGATCAAATAC
*
223781 GAGTTTAAT-TTTTTTAAATGATCAAATA
1 GAGTTTAATATTTTTGAAATGATCAAATA
223809 AAATATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (30 bp):
GAGTTTAATATTTTTGAAATGATCAAATAC
Found at i:224848 original size:24 final size:23
Alignment explanation
Indices: 224816--224891 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 23
224806 TCATTTATTG
* *
224816 TGTTTGTTTACGTTCGTTCGTTTG
1 TGTTCGTTTAC-TTCGTTCGTTTA
224840 TGTTCGTTTAC-T--TTCGTTTA
1 TGTTCGTTTACTTCGTTCGTTTA
* *
224860 TGTTCGCTTACATCCGTTCGTTTA
1 TGTTCGTTTAC-TTCGTTCGTTTA
224884 TGTTCGTT
1 TGTTCGTT
224892 CATTTGTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 17 0.40
22 1 0.02
24 25 0.58
ACGTcount: A:0.08, C:0.17, G:0.20, T:0.55
Consensus pattern (23 bp):
TGTTCGTTTACTTCGTTCGTTTA
Found at i:224855 original size:20 final size:20
Alignment explanation
Indices: 224832--224889 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
224822 TTTACGTTCG
* *
224832 TTCGTTTGTGTTCGTTTACT
1 TTCGTTTATGTTCGCTTACT
224852 TTCGTTTATGTTCGCTTACAT
1 TTCGTTTATGTTCGCTTAC-T
224873 CCGTTCGTTTATGTTCG
1 ---TTCGTTTATGTTCG
224890 TTCATTTGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
21 1 0.03
24 14 0.44
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGTTTATGTTCGCTTACT
Found at i:224865 original size:10 final size:10
Alignment explanation
Indices: 224831--224891 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 10
224821 GTTTACGTTC
*
224831 GTTCGTTTGT
1 GTTCGTTTAT
224841 GTTCGTTTACT
1 GTTCGTTTA-T
224852 -TTCGTTTAT
1 GTTCGTTTAT
*
224861 GTTCGCTTACAT
1 GTTCG-TT-TAT
224873 CCGTTCGTTTAT
1 --GTTCGTTTAT
224885 GTTCGTT
1 GTTCGTT
224892 CATTTGTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
9 1 0.02
10 27 0.64
11 3 0.07
12 4 0.10
13 2 0.05
14 5 0.12
ACGTcount: A:0.08, C:0.18, G:0.20, T:0.54
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:226193 original size:30 final size:30
Alignment explanation
Indices: 226149--227037 Score: 789
Period size: 30 Copynumber: 29.7 Consensus size: 30
226139 ACAATTATGC
* *
226149 GTCACCTCCACCTCCTCCATATGTTTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * *
226179 ATCACCAT-CGCCTCCGCCATATGAGTACAA
1 GTCACC-TCCTCCTCCTCCATATGTGTACAA
* * * * * * *
226209 GTCTCCACCACCTCCTCCGTACGTTTA-TA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * *
226238 GCTCTCCGCCTCCGCCTCCATATGAGTACAA
1 G-TCACCTCCTCCTCCTCCATATGTGTACAA
* * * * *
226269 GTCTCCACCACCTCCTCCGTACGTGTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * * * * * *
226299 CTCTCCACCACCACCTCCATACGAGTATAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * *
226329 GTCACCACCTCCTCCTCCTTATGTTTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * **
226359 ATCACCTCCTCCACCTCCATATAAGTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * *
226389 GTCACCTCCACCTCCTCCGTATGTTTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * *
226419 ATCACCTCCTCCCCCTCCATACGTCTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * *
226449 GTCTCCTCCTCCACCTCCATATGAGTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* *
226479 GTCACCTCCTCCTCCTCCTTATGTTTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * *
226509 ATCACCTCCTCCCCCTCCATATGAGTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* *
226539 GTCACCTCCTCCTCCTCCTTATGTCTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * *
226569 ATCACCTCCTCCCCCTCCATATGAGTATAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * *
226599 GTCACCACCACCTCCTCCATACGTCTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
*
226629 GTCACCTCCTCCTCCTCCATATGTTTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
*
226659 GTCACCTCCTCCTCCTCCATATGTCTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * *
226689 GTCACCTCCACCTCCTCCTTATGTTTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * *
226719 ATCACCTCCTCCCCCTCCATATGAGTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* *
226749 GTCACCTCCTCCTCCTCCTTATGTCTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * *
226779 ATCTCCTCCTCCCCCTCCATATGAGTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * * *
226809 GTCACCACCACCTCCTCCATACGTCTACGA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
*
226839 GTCACCTCCTCCTCCTCCATATGTTTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
*
226869 GT---CTCCTCCTCCTCCATATGTCTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * **
226896 GTCACCTCCACCTCCTCCATATGTTTATGA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* ** *
226926 GTCACCACCTCCTCCTCCATACATGTATAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * *
226956 GTCTCCTCCTCCACCTCCATATGTTTACAC
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * **
226986 GTCACCGCCACCACCTCCATACATGTACAA
1 GTCACCTCCTCCTCCTCCATATGTGTACAA
* * * *
227016 TTCACCACCACCTCCCCCATAT
1 GTCACCTCCTCCTCCTCCATAT
227038 TACAAGTAAA
Statistics
Matches: 684, Mismatches: 168, Indels: 14
0.79 0.19 0.02
Matches are distributed among these distances:
27 26 0.04
29 2 0.00
30 653 0.95
31 3 0.00
ACGTcount: A:0.23, C:0.42, G:0.08, T:0.27
Consensus pattern (30 bp):
GTCACCTCCTCCTCCTCCATATGTGTACAA
Done.